Poster Session 3 - RSC - Australian National University

Poster 

Session 3

Poster Session 3 – Tuesday September 16 – 5.30-7.30pm 


PP351 

Regioselectivity in the Heck Reaction 

Carina Bäcktorp, Signe Teuber Henriksen, Per-Ola Norrby 

1 University of Gothenburg, Department of Organic Chemistry, Gothenburg, Sweden, 2 Technical 

University of Denmark, Lyngby, Denmark 

Palladium-catalyzed arylation and vinylation of olefins has been used for more than 30 years in 

organic synthesis. This methodology is known as the Heck reaction and its basic steps are 

schematically depicted below. 

Ar 

Ar 

Ar 

R 

Ar 

R 

R 

Ar 

H 

H 

Pd 

H 

Pd 

HX 

X 

Pd 

R H 

R 

X 

X 

Pd 

X Ar R 

XPd 

Ar 

Pd(0) 

R 

Ar 

R 

H 

Ar 

Ar 

ArX 

Pd 

Pd 

X 

X 

R 

R 

PP352 

Air Oxidation of Ethoxylated Surfactants – Computational Estimations of Energies and 

Reaction Behaviors 

Carina Bäcktorp, Anna Börje, J. Lars G. Nilsson, Ann-Therese Karlberg, Per-Ola Norrby, Gunnar 

Nyman 

1 Department of Chemistry, University of Gothenburg, Gothenburg, Sweden, 2 Göteborg Science Centre 

for Molecular Skin Research, Faculty of Science, University of Gothenburg, Gothenburg, Sweden 

Ethoxylated surfactants are widely used in household and industrial cleaners, in topical 

pharmaceuticals, cosmetics and laundry products. Surfactants are known to be skin irritants. Most 

cases of occupational dermatitis are considered to be irritant contact dermatitis, caused by work with 

water and surfactants. It is also well-known that polyethers, e. g. ethoxylated surfactants are oxidized 

by atmospheric oxygen. 

Our pervious experimental studies have shown that autoxidation of nonionic alcohol ethoxylates 

generates products that are skin allergens. Specific oxidation products, including hydroperoxides, 

have been identified in an autoxidation mixture of the pure ethoxylated alcohol pentaethylene glycol 

mono-n-dodecyl ether (C 12 E 5 ). 

Here we present an investigation where the computational method, DFT (B3LYP), has been used to 

calculate reaction barriers and energies for the pathways for formation of previously observed 

autoxidation products of the ethoxylated surfactant. In addition to the established radical chain 

reaction, several possibilities for intramolecular fragmentation of the intermediate radicals have been 

characterized. The results rationalize the formation of the identified autoxidation products, including 

several, which have been implicated as allergenic. 

H 

PdX 

Much empirical knowledge about the performance for different ligands, substrates, and reaction 

conditions has been built up over the years. However, the complex nature of the reaction still leaves 

many question marks to be answered. Only very recently has it become possible to address this 

complex mechanism computationally without resorting to small model systems. 

We have used DFT methods to investigate the source of selectivities seen in recent experimental 

studies. In the initial carbopalladation step, the effect of ligand on the branching ratio can be well 

reproduced by the calculations. For the next step, β-hydride elimination, the general assumption has 

been that the more reactive hydride is eliminated selectively, but very surprisingly our models instead 

show the selectivity to be determined by a restriction in bond rotation in the alkyl-palladium 

intermediate. In general, the agreement with experimental results is excellent.



PP353 

The Amino Group in Adenine. Is it Co-planar with the Molecular Rings or Not? 

Wiktor Zierkiewicz 1 , Danuta Michalska 1 , Ludwik Komorowski 1 , Jiri Cerny 2 , Pavel Hobza 2 

1 Wroclaw University of Technology, Faculty of Chemistry, Wroclaw, Poland, 2 Academy of Sciences of 

the Czech Republic, Institute of Organic Chemistry and Biochemistry, Prague, Czech Republic 

What is the structure of adenine in the gas phase? Is the amino group in adenine coplanar with the 

molecular rings? These questions seem to be still open, in spite of numerous studies. The planarity of 

the C-NH 2 group is of particularly great importance for investigation of the molecular recognition 

phenomena involving nucleic acids and other systems containing the adenine residues. Ab initio MP2 

and density functional B3LYP methods with various basis sets have been used to calculate the 

optimized structures and the infrared spectra of the N9-H tautomer of adenine. MP2 calculations 

predict the non-planar structure, however, larger basis sets tend to decrease the degree of 

pyramidalization of the C-NH 2 group, while the B3LYP method consistently indicates the planar or 

nearly planar structure. The planarization barrier of adenine calculated with the MP2 complete basis 

set (CBS) limit approach is negligible, 0.015 kcal/mol, which is in agreement with the MP2-predicted 

barrier of 0.020 kcal/mol, reported by S. Wang and H. F. Schaefer III [1]. Thus, it can be concluded 

that the structure of adenine is extremely flexible with a very small degree of non-planarity of the 

amino group, and a low energy barrier to planarization. These results do not support the conclusions 

made by F. Dong and R. E. Miller [2] that the amino group in adenine is tilted about 20° out-of-plane. 

The anharmonic frequencies of adenine have been calculated by the B3LYP method. The theoretical 

results show excellent agreement with the available experimental data. The revised assignment of the 

infrared spectrum of adenine in an Ar matrix has been made. 

PP354 

ChemIME: An Input Method Engine for Chemists 

Haruka Tkeuchi, Xu Yang, Shin-Ya Takane 

Department of Information Systmes Engineering, Osaka Sangyo University, Daito,Osaka, Japan 

In the field of chemistry, which mainly treats various compounds, it is often needed to convert a 

compound name into corresponding molecular equations, 2D or 3D molecular structures. For such 

purpose, there exist some useful commercially available tools to generate the molecular structure or 

rational formula from an IUPAC name, for example, ChemDraw and Chemistry 4D-Draw. These 

software packages, however, are separate applications for each platform and cannot be invoked on 

the spot from other applications. To our knowledge, there is no application that has the function of inline 

conversion for chemical compound names. Our idea is that using an input method mechanism, 

which allows us to input characters other than Roman alphabets with a standard keyboard, it is 

possible to implement such a tool for chemists smoothly and applicably. 

In this paper we present a design and a prototype implementation of the input method engine that can 

convert various compound names (given as an IUPAC name) into corresponding molecular equations 

by using Java and the Java Input Method Framework. We also extend to give various 2D or 3D 

coordinate formats (MDL mol, CML, and Gaussian input file) with the help of CDK (Chemistry 

Development Kit) and some external programs. 

[1] Wang, S.; Schaefer III, H. F. J. Chem. Phys. 2006, 124, 044303. 

[2] Dong, F.; Miller, R. E. Science, 2002, 298, 1227.



PP355 

Ab Initio Calculations of the Zero-Field Splitting Tensors of Organic Open-Shell Molecules 

Kenji Sugisaki, Kazuo Toyota, Kazunobu Sato, Daisuke Shiomi, Takeji Takui 

Departments of Chemistry and Materials Science, Graduate School of Science, Osaka City University, 

3-3-138 Sugimoto, Sumiyoshi-ku, Osaka, Japan 

Zero-field splitting (ZFS) is the separation of multiplet sublevels in the absence of an external 

magnetic field. Its origin is spin-spin (SS) and spin-orbit (SO) couplings. Theoretical calculations of 

ZFS tensor (D tensor) have been the subject of intense interest, because the D tensor contains 

essentially important information on the spatial distributions of unpaired electrons. In ZFS of organic 

open-shell molecules, SS is in general more important than SO, but when (π,π) states and (n,π) states 

are energetically close to each other, strong spin-orbit coupling can be expected from the El-Sayed’s 

rule [1]. In this work, D SS and D SO of organic molecules having (n,n)-, (n,π)-, and (π,π)-types of spin 

configuration are investigated. 

Spin-spin contributions to the D tensor can be calculated as follows [2]. 

D 

SS 

ab 

4 2 

( 2S 

+ 1) 

( d ) ( 2ˆ s sˆ 

− sˆ 

sˆ 

− sˆ 

sˆ 

)Ψ 

= α 

Ψ ∑ 

(1), 

ij ab iz jz ix jx iy jy 

S 

( d ) 

ij ab 

i< j 

r δ 

= 

2 

ij ab 

− 3 

( r ) ( r ) 

ij a ij b 

5 

rij 

In the past decade, calculations of D SS using the CASSCF wavefunction have been reported [3]. To 

investigate D SS of relatively large systems, the SAC-CI method [4] is useful, because computational 

cost of the CASSCF method strongly depends on the size of active space. In this work, we will report 

preliminary results of the D SS calculations based on McWeeny and Mizuno’s equation (eq. 3) [5], which 

is exact when the wavefunction Ψ consists of a single determinant, with the SAC-CI spin density. 

D 

1 

( ) ∑ ρ 

2S 

+ 1 

(2) 

α −β 

α −β 

α −β 

α −β 

* * 

( 

µν 

ρκλ 

− ρ 

µλ 

ρκν 

) ∫ µ ( r1 

) κ ( r2 

)( d12 

) ν ( r1 

) λ( r2 

) 

ab 

dr dr 

SS 

ab 

= 

1 2 

S 

µνκλ 

Spin-orbit contributions to the D tensor in the spherical representation can be calculated in terms of 

the second-order perturbation theory with the sum-over-state formula. 

H 

SO 

D 

SO 

ij 

= 

∑ 

3 

i 

Ψ H 

0 

SO λ 

k λ k 

Ψn 

Ψn 

H 

λ 3 

E − E 

n, λ, 

k 

n 0 

1 ⎡ 

⎢ 

2m 

c ⎢⎣ 

Z e 

r 

A 

= 

2 2 ∑ ∑ 

2 

SO 3 

Ψ 

j 

0 

(4), 

2 

e 

⎤ 

I ˆ 

iA 

⋅ sˆ 

i 

− Iˆ 

ij 

⋅ ( sˆ 

i 

+ 2ˆ s 

j 

) 

3 

⎥ (5) 

i j rij 

⎥⎦ 

i, A iA 

, 

Here, Ψ is the n’th eigenfunction of the non-relativistic Schrödinger equation with λ = 2S+1 and k = M S . 

The calculations of D SO based on eq. 4 at the CASSCF level have been reported [3a,6]. However, 

CASSCF energy difference is not directly comparable to the experimental ∆E. For example, a T 1 state 

of pyrazine is calculated to be ππ* at the CASSCF(10,8)/cc-pVDZ level, rather than nπ*. Incorrect 

energy difference may seriously affect the accuracy of the calculated D SO . To avoid this difficulty, we 

have replaced the CASSCF energy difference to MRMP2 one. 

[1] El-Sayed, M. A. J. Chem. Phys. 1963, 38, 2834–2838. 

[2] Harriman, J. E. Theoretical Foundations of Electron Spin Resonance; Academic Press: New York, 1978. 

[3] (a) Havlas, Z.; Kývala, M.; Michl, J. Mol. Phys. 2005, 103, 407–411., and references therein. (b) Loboda, H., et 

al. Chem. Phys. 2003, 286, 127–137., and reference therein. 

[4] (a) Nakatsuji, H. Chem. Phys. Lett. 1978, 59, 362–364. (b) Nakatsuji, H.; Hirao, K. J. Chem. Phys. 1978, 68, 

2053–2065. (c) Nakatsuji, H. Chem. Phys. Lett. 1979, 67, 329–333. 

[5] McWeeny, R.; Mizuno, Y. Proc. R. Soc. London 1961, 259, 554–571. 

[6] Rubio-Pons, Ò.; Minaev, B.; Loboda, O.; Ågren, H. Theor. Chem. Acc. 2005, 113, 15–27., and references 

therein. 

(3) 

PP356 

A Chemically Reasonable Model of Various Phosphine Ligands: Application of CCSD(T) 

Calculation to Large Transition Metal Complexes 

Yu-ya Ohnishi, Mayu Nakaoka, Yoshihide Nakao, Hirofumi Sato, Shigeyoshi Sakaki 

Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto, 

Kyoto, Japan 

Chemically reasonable models of PR 3 (R = Me, Et, i Pr, t Bu, Cy, or Ph) were constructed to apply the 

CCSD(T) method to large transition metal complexes. We elucidated that the dominant role of PR 3 

listed above is sigma-donation to metal centre with its lone pair orbital. In out new model, R is 

replaced with the one electron pseudo carbon atom including the frontier orbital consistent quantum 

capping potential (FOC-QCP) (eq. 1) [1] which reproduces the frontier orbital energy of PR 3 . The 

steric effect is incorporated well by the new procedure named steric repulsion correction (SRC), which 

was not incorporated in the usual QM/MM methods. 

FOC-QCP 

2 

( −ζ 

) 

U ( r) 

= U ( r) 

− 3 r exp r (1) 

l 

l 

To examine the performance of this FOC-QCP method with the SRC, the activation barriers and 

reaction energies of the reductive elimination reactions of C 2 H 6 and H 2 from M(R 1 ) 2 (PR 2 3) 2 (M = Ni, Pd, 

or Pt; R 1 = Me for R 2 = Me, Et, or i Pr, or R 1 = H for R 2 = t Bu) were evaluated with the DFT[B3PW91], 

MP4(SDQ), and CCSD(T) methods. The FOC-QCP method reproduced very well the DFT[B3PW91]- 

and MP4(SDQ)-calculated energy changes of the real complexes with PMe 3 . For more bulky 

phosphine, the SRC is crucially important to present correct energy change, in which the MP2 method 

presents reliable steric repulsion correction like the CCSD(T) method because the systems calculated 

in the SRC do not include transition metal element. 

Also, the coordination energies of CO, H 2 , N 2 , and C 2 H 4 with a large dinuclear complex [RhCl(P i Pr 3 ) 2 ] 2 

were theoretically calculated by the CCSD(T) method combined with the FOC-QCP and the SRC. The 

CCSD(T)-calculated energies agree well with the experimental ones, as shown in Figure. On the 

other hand, the DFT[B3PW91]-calculated energies of the real complexes considerably deviate from 

the experimental ones. 

We also calculated the reaction energy of CO coordination with CoCl 2 (PR 3 ) 2 (R = Et, Cy, or Ph) (eq. 2) 

and decarbonylation from (PPh 3 ) 2 (Cl)PtC(O)C 6 H 5 (eq. 3) to compare with the experimental results. 

The details of methods and results will be shown in poster session. 

CoCl 2 (PR 3 ) 2 + CO CoCl 2 (CO)(PR 3 ) 2 (2) 

(PPh 3 ) 2 (Cl)PtC(O)C 6 H 5 (PPh 3 ) 2 (Cl)PtC 6 H 5 + CO (3) 

B3PW91 (in vacuo) 

B3PW91 (in toluene) 

B3PW91/FOC-QCP + SRC 

CCSD(T)/FOC-QCP + SRC 

Figure. The error of the coordination energies (kcal/mol) of CO, H 2 , N 2 -end-on, and 

C 2 H 4 to [RhCl(P i Pr 3 ) 2 ] 2 from the experimental values. 

[1] Ohnishi, Y.-y.; Nakao, Y.; Sato, H.; Sakaki, S. J. Phys. Chem. A 2008, 112, 1946-1955.



PP357 

A DFT Study on a Natural Diels-Alder Reaction 

Sadra Kashefolgheta, Mehdi Irani, Mohammad Reza Gholami 

Department of Chemistry-Sharif University of Technology, Tehran, Iran, Islamic Republic of 

Macrophomate synthase (MPS), which promotes the conversion of 2-pyrones to benzoates, has 

garnered considerable attention as a possible natural Diels-Alder reaction [1]. There are two possible 

mechanisms for the MPS-Catalyzed Formation of Macrophomate (i) Michel addition followed by aldol 

condensation and (ii) Diels-Alder reaction [Figure 1]. 

The activation and TS energies of both pathways have been investigated by density functional 

methods in order to find the preference of the mechanisms. The two possible mechanisms, have been 

studied at the B3LYP/6-311++G (d,p) level of theory. In addition, aromatization energy of products has 

been determined consequently in the same method.The catalytic characteristic of MPS has been 

investigated further by changing metal ion and performing calculation with Ca +2 and Ni +2 . The effects 

of different substituents on 2-pyron have been also studied using the DFT method. 

PP358 

Structure and Vibrational Spectra of Hydrogen-Bonded Clusters by the Anharmonic Downward 

Distortion Following Method 

Satoshi Maeda, Yu Watanabe, Yi Luo, Koichi Ohno 

Department of Chemistry, Graduate School of Science, Tohoku University, Sendai, Japan 

Vibrational spectroscopy is a powerful tool to investigate hydrogen-bond (H-bond) clusters. Except for 

very simple cases, calculations are necessary to reveal structures from experimental spectra. At first, 

one needs to explore the potential energy surface (PES) to list up stable isomers. Then, vibrational 

analyses will be made for each structural candidate to find out isomers which correspond to observed 

vibrational spectra. In this study, we show that the anharmonic downward distortion following (ADD- 

Following) method [1] can be a powerful tool for both PES exploration [2] and anharmonic vibrational 

analyses [3], with some examples of applications to H-bond cluster systems [4-6]. 

The ADD-Following [1] is an idea to make uphill walking along reaction routes from a minimum (EQ: 

EQuilibrium structure) to (first-order) saddle points (TS: Transition State structure). Since a real 

(anharmonic) PES distorts downward from a harmonic PES in direction leading to another EQ, the 

ADD can be a symptom of chemical reactions leading to another EQ. ADDs can be found as energy 

minima on an iso-energy hypersurface of harmonic potential centered at a starting EQ, and such 

energy minima can be detected and then traced by the scaled hypersphere search (SHS) method [1]. 

The Full-ADD-Following dealing with all ADDs has been employed in global reaction route mapping on 

PESs of small systems [1]. The Large-ADD-Following (LADD-Following) was proposed for fast 

exploration of low energy parts on PESs by tracing only important large ADDs [2], and it has been 

applied to H-bond clusters such as (H 2 O) 8 [2], H + (H 2 O) n (n = 5-8) [4], and H 2 S(H 2 O) n (n = 5-7) [5]. We 

further developed the SHS based polynomial fitting (SHS-PF) technique for very efficient construction 

of potential energy function (PEF) in the form of sixth-order polynomial [3]. The SHS-PF method can 

dramatically reduce numbers of ab initio data for obtaining a sixth-order-PEF from the sixth power to 

the second power, by selecting sampling points based on ADD data by the SHS method. Anharmonic 

analyses of (H 2 O) n (n = 2-5) were performed by using PEFs constructed by the SHS-PF method, and 

experimental intramolecular-mode frequencies were reproduced with errors of about only 10 cm -1 [6]. 

Figure 1 

[1] Jörg M. Serafimov; Thomas Westfeld; Beat H. Meier; Donald Hilvert. J. Am. Chem. Soc. 2007, 129, 9580. 

[1] Ohno, K.; Maeda, S. Chem. Phys. Lett. 2004, 384, 277. Maeda, S.; Ohno, K. J. Phys. Chem. A 2005, 109, 

5742. Ohno, K.; Maeda, S. J. Phys. Chem. A 2006, 110, 8933. 

[2] Maeda, S.; Ohno, K. J. Phys. Chem. A 2007, 111, 4527. 

[3] Maeda, S.; Watanabe, Y.; Ohno, K. J. Chem. Phys. 2008, 128, 144111. 

[4] Luo, Y.; Maeda, S.; Ohno, K. J. Phys. Chem. A 2007, 111, 10732.; Luo, Y.; Maeda, S.; Ohno, K. (submitted). 

[5] Maeda, S.; Ohno, K. J. Phys. Chem. A 2008, 112, 2962. 

[6] Watanabe, Y.; Maeda, S.; Ohno, K. (submitted).



PP359 

Analysis of an Electronic Spectrum using the Ab Initio Path Integral Molecular Dynamics 

Method 

Masataka Sugimoto 1 , Motoyuki Shiga 2 , Masanori Tachikawa 1 

1 Graduated School of Integaretd Science, Yokohama City University, Yokohama, Japan, 2 Japan 

Atomic Energy Agency, Tokyo, Japan 

In the conventional molecular orbital (MO) calculation, the allowed or forbidden electronic transitions 

are determined by geometrical symmetry of molecules. However, to reproduce the experimental 

electronic spectrum, it is indispensable to take account of “geometrical fluctuation” to molecular 

structure in theoretical study, since the molecules in real system always keep changing its structure 

with vibrational motion due to thermal and quantum effects. Although there are some reports that insist 

importance of these effects on electronic transition by using ab initio path integral simulation [1, 2], 

these reports seem to be not enough because of inconsistency of electronic structure evaluation 

between ground and excited states, and the number of beads on path integral calculation. In the 

present paper, we have analyzed electronic spectrum of ethylene molecule by ab initio path integral 

molecular dynamics (PIMD) calculation with consistent MO level between ground and excited states. 

Figure 1 shows (a) calculated and (b) experimental [3] electronic spectra of ethylene at 300K. 

Geometrical structure of ground state was obtained with MP2 / 6-31+G* level of calculation, and 

electronic structure of excited state was estimated with CIS(D)/6-31+G*. Since the equilibrium 

structure of ethylene has D 2h symmetry, allowed transitions are only B 1u 

(8.14eV, 10.9eV, 11.1eV), B 2u 

(10.6eV), and B 3u (7.76eV, 9.52eV) as shown in vertical lines in Figure 1(a). The electronic spectrum 

of PIMD is broader than that of classical MD, because thermal and quantum effects cause distortion of 

molecular structure and break its symmetry. 

(a) 

(b) 

200 

1 

70 

180 

PIMD 

0.9 

exp. 

Classical 

60 

160 

SP calc. 

0.8 

140 

0.7 

50 

120 

0.6 

40 

100 

0.5 

80 

0.4 

30 

60 

0.3 

20 

40 

0.2 

10 

20 

0.1 

0 

0 

0 

7 8 9 10 11 12 

7 8 9 10 11 12 

Energy / eV 

Energy / eV 

Figure 1. Electronic spectrum of ethylene; (a) our works, (b) experimental data. 

Cross section / Mb 

Oscillator strength 

Cross section / Mb 

PP360 

Computational Study of the Sonogashira Cross-Coupling Reaction in the Gas Phase 

Peeter Burk 1 , Jaana Tammiku-Taul 1 , Lauri Sikk 1 , Andras Kotschy 2 

1 Institute of Chemistry, University of Tartu, Tartu, Estonia, 2 Institute of Chemistry, Eötvös Loránd 

University, Budapest, Hungary 

Many chemical reactions proceed in the presence of catalysts. Cheaper and more effective catalytic 

systems are searched to accelerate the reactions and rise their selectivity. The application of transition 

metals in organic synthesis has become an accepted and valued tool. Cross-coupling reactions are by 

now a widely accepted tool of synthetic chemists. They include a bunch of carbon-carbon bond 

forming reactions [1]. Cross-coupling reactions are usually catalyzed by transition metals and 

distinguished on the basis of the used transmetalating agent. Organocopper reagent is used in case of 

the Sonogashira cross-coupling [2]. 

The aim of current study was to investigate the reaction mechanism of the Sonogashira coupling in the 

gas phase and to find the factors, which influence its kinetics. 

The Sonogashira cross-coupling reaction between bromobenzene and phenylacetylene was modelled 

using density functional theory B3LYP/cc-pVDZ method. In the case of palladium and copper 

Stuttgart-Dresden effective core potential with the accompanying basis sets were used. 

The cross-coupling reaction begins with the oxidative addition of bromobenzene onto the palladium 

catalyst Pd(PH 3 ) 2 , which is followed by the formation of cis-Pd(PH 3 ) 2 BrPh complex. The subsequent 

step is isomerisation leading to trans-Pd(PH 3 ) 2 BrPh complex. The oxidative addition is the reaction 

rate-limiting step. Copper(I) bromide as a co-catalyst reacts with phenylacetylene in the presence of a 

base (trimethylamine) and copper phenylacetylenide is formed, which in a transmetalation step reacts 

with trans-Pd(PH 3 ) 2 BrPh complex. The product of transmetalation step, cis-Pd(PH 3 ) 2 (Ph)C≡CPh, 

decomposes into palladium diphosphine, Pd(PH 3 ) 2 , and diphenylacetylene, Ph-C≡C-Ph, during 

reductive elimination. The regenerated palladium catalyst is ready to enter a next cycle. The complete 

catalytic cycle is exothermic and has a negative Gibbs’ free energy change (∆H = -39.2 kcal/mol, ∆G = 

-38.0 kcal/mol). Our calculated catalytic cycle is in agreement with reaction schemes in literature [2,3]. 

[1]. Kotschy, A.; Timįri, G. Heterocycles from Transition Metal Catalysis, Springer, 2005. 

[2]. Sonogashira, K. J. Organomet. Chem. 2002, 653, 46. 

[3]. Chinchilla, R; Nàjera, C. Chem. Rev. 2007, 107, 874–922. 

[1] Schulte, J; Ramírez, R; Böhm, M. C. Chem. Phys. Let. 2000, 322, 527-535. 

[2] Sala, F. D; Rousseau, R; Görling, A; Marx, D. Phys. Rev. Let. 2004, 92, 183401-1-183401-4. 

[3] Lu, H-C; Chen, H-K; Cheng, B-M. Anal. Chem. Phys. 2004, 76, 5965-5967.



PP361 

Identification of an Aryloxenium Ion by Time Resolved Resonance (TR 3 ) Spectroscopy and 

Density Functional Theory: First Vibrational Spectrum of an Oxenium Ion 

Stephen Glover 1 , Michael Novak 2 , Yue-Ting Wang 2 , David Phillips 3 , Jiadan Xue 3 

1 University of New England, School of Science and Technology, Armidale, New South Wales, 

Australia, 2 Miami University, Department of Chemistry and Biochemistry, Oxford, Ohio, United States, 

3 Hong Kong University, Department of Chemistry, Hong Kong, China 

Aryloxenium ions 2 from solvolysis of 1 have previously been generated and trapped by water and 

azide, and product studies [1-3] as well as DF calculations [4] point to 

their existence in resonance form II rather than I. 

O 

O 

O 

Laser flash photolysis studies on 1 (R=C 6 H 4 Me-4) generated 4'- 

methylbiphenylyloxenium ion 3 with a UV absorption maximum of 460 

nm at pH 7.1 and a lifetime in aqueous solution of 170 ns, similar to 

the150-180 ns established earlier by azide trapping methods [2]. 

Oxenium ion 3 has recently been observed by TR 3 , which with a probe pulse at 460 nm, provides 

resonance enhancement of both IR and Raman vibrational bands. The spectrum (Fig. 1) was 

simulated at the B3LYP/6-31G* level and the spectral lines and intensities correspond to vibrational 

modes of resonance forms 3-II and III. The oxenium ion charge is strongly delocalised into the 4- 

methylphenyl ring and the ion, which better resembles a resonance-delocalised 1-oxo-2,5- 

cyclohexadien-4-yl cation (3-II), possesses a normal cross conjugated carbonyl at 1635 cm -1 . Analysis 

of molecular orbitals indicates that the Raman probe radiation at 460 nm resonates with the carbonyl 

and C=C stretch modes of 3-II and III. 

O 

O 

O 

∗ 

∗ 

Experimental and Theoretical Vibrational Frequencies of 

4'-Methylbiphenylyloxenium ion 

IR1 

R3 

R2 

∗ ∗ 

R1 

R7 

IR4 

R6 

IR3 

R5 

IR2 

AcO 

R4 

1 

R 

R 

I 

Raman Exp. 

IR Calc. 

Raman Calc. 

2 

R 

II 

PP362 

Molecular Dynamic Simulations Can Complement Experiments to Probe Antibiotics Diffusion 

through Bacterial Porins 

Eric Hajjar, Amit Kumar, Enrico Spiga, Francesca Collu, Paolo Ruggerone, Matteo Ceccarelli 

Department of Physics, University of Cagliari., Cagliari, Sardinia., Italy 

The increase in number and complexity of bacterial resistance to antibiotics severely affects the 

treatment of infectious diseases. This calls for a fast development of new antibiotics. As antibiotics 

targets are located inside bacteria, the first step of antibacterial activity is the uptake of antibiotics. The 

process is a severe bottleneck particularly in Gram-negative bacteria since the presence of the outer 

membrane (OM) restricts the entry of any molecule. General diffusion porins, for example outer 

membrane protein F (OmpF) are present in large abundance in the OM and constitute the main 

pathway for different classes of antibiotics, such as beta-lactams and fourth generation of 

floroquinolones. 

Bacteria can resist to antibiotics, either by under expressing porins in the OM or by mutations. The 

understanding of how antibiotics diffuse through porins can provide information on how to design 

novel antibiotics with improved permeation properties, to solve at least partially the problem of 

resistance. One of the ways to tackle the problem of antibiotic resistance is to investigate the 

permeation properties and what governs the translocation process. Recently, experiments combined 

with MD simulations pointed out how the diffusion of antibiotics is a molecular-based process, i.e. 

small differences in the antibiotic structure can affect its flux through porins. 

The high resolution of MD simulations can be particularly useful to the design of antibiotics with 

improved permeation properties. The process of antibiotic diffusion through the porins occurs on 

microsecond time scale. To simulate such process we built a molecular system from the X-ray 

structure of OmpF porin. OmpF was embedded in biological membrane environment. As we want to 

study various antibiotics as well as OmpF porin and its variants, this is not feasible with standard MD 

simulations. Instead we use a recent algorithm, metadynamics, that allows to overcome the timescale 

problem by adding history dependent potential that accelerates the evolution of the system. Each 

antibiotic diffusion process was analysed by (i) constructing the associated free energy map, (ii) 

estimating the free energy barrier, (iii) identifying the binding sites inside the porin, and (iv) 

characterizing the nature of the interactions (h-bonded and hydrophobic) between antibiotics and 

OmpF in the putative binding sites. 

Me 

I 

Me 

II 

3 

Me 

III 

600 800 1000 1200 1400 1600 1800 2000 

Vibrational Frequency (cm-1) 

Figure 1 

Our MD simulation results for different antibiotics were then compared to the experimental data 

available in the literature and provided by our collaborators; this allowed discussing the mechanism of 

antibiotic penetration. For example, in electrophysiology experiments interruptions in ionic current 

(blockage) are related to antibiotic translocation. Our simulation results show good agreement with 

such electrophysiology experiments that report blockage. However, there are cases where we observe 

translocation and electrophysiology do not report blockage. To conclude we discuss the following 

questions: does blockage always imply translocation? Can theory suggest new experiments or help to 

design new measurement strategy? This points out the importance of combining properly theory and 

experiments in order to benefit the design of antibiotics with improved permeation properties. 

[1] Novak, M.; Glover, S. A. J. Am. Chem. Soc. 2004, 126, 7748; 2005, 127, 8090. 

[2] Novak, M.; Poturalski, M. J.; Johnson, W. L.; Jones, M. P.; Wang, Y.; Glover, S. A. J. Org. Chem. 2006, 71, 

3778. 

[3] Novak, M.; Brinster, A. M.; Dickhoff, J. N.; Erb, J. M.; Jones, M. P.; Leopold, S. H.; Vollman, A. T.; Wang, Y.; 

Glover, S. A. J. Org. Chem. 2007, 72, 9954. 

[4] Glover, S. A.; Novak, M. Can. J. Chem. 2005, 83, 1372.



PP363 

Avoiding Heisenberg with Certainty 

Yves A. Bernard, Peter M. W. Gill 

Research School of Chemistry, Australian National University, Canberra, Australia 

The Heisenberg Uncertainty Principle states that we cannot simultaneously measure the position r 

and the momentum p of a particle. However, recent electron correlation models based on intracules 

require information about both the positions and the momenta of the electrons and the limitations of 

the Uncertainty Principle are therefore very inconvenient. To get around this problem, in 1932, Wigner 

proposed a phase space distribution W 1 (r,p) for a particle which gives the correct position and 

momentum space density when integrated over p or r respectively. However, because W 1 (r,p) is not 

necessarily positive, it cannot be strictly interpreted as a joint probability density of r and p. 

In this poster, we show that information about r and p can be obtained rigorously by considering a new 

variable s = r⋅p, the position-momentum dot product. This “posmom” variable, s, is a quantum 

mechanical observable and its density D(s) can be computed efficiently. We also show that the 

posmom quasi-density W(s) that is derived from the W 1 (r,p) is an approximation of D(s). We present 

results for simple systems such as the harmonic oscillator and the hydrogen atom, as well as for 

molecular systems. 

PP364 

Parallel Implementation of RI-MP2 Energy Calculations of Large Molecules 

Michio Katouda, Shigeru Nagase 

Department of Theoretical and Computational Molecular Science, Institute for Molecular Science, 

Okazaki, Japan 

The resolution-of-the-identity (RI) approximation has been developed for second-order Moller-Plesset 

perturbation theory (MP2) to reduce the computational cost [1]. To make the RI-MP2 method 

applicable to large molecules, the parallel implementation is important [2, 3]. In this study, we present 

a parallel implementation of RI-MP2 energy calculations to assess its performance. 

The most computationally demanding step in RI-MP2 energy calculations is the construction of two 

electron integrals in MO basis with simple matrix-matrix multiplications of three-center two-electron 

integral matrices. To make the parallel algorithm efficient, uniform distribution of the construction of 

two electron integrals on each processor is needed. Parallelization of the construction of two electron 

integrals with efficient load balancing is archived by dividing occupied orbitals into batches whose 

sizes are almost equal and distributing these batches on each processor. 

Benchmark calculations were performed for the taxol molecule (C 47 H 51 NO 14 ) with the 6-311G** basis 

set and the Ahlrichs’s SVP auxiliary basis set (1484 functions, 4175 auxiliary functions, and 164 

correlated orbitals). Calculations were performed on a Linux cluster of 3.2 GHz Pentium4 PCs with 4 

GB memory and 400 GB hard disk. These PCs are connected by Gigabit-Ethernet network. Table 1 

shows the elapsed times and speed-up of parallel RI-MP2 calculations. For 32 processors, the speedup 

is 29.6 and the elapsed time is only 25 minutes. Benchmark calculations were also performed for 

(C 96 H 24 ) 2 , a cluster model of two layer graphene sheets [4], with the 6-311G** basis set and the 

Ahlrichs’s SVP auxiliary basis set (3936 functions, 11280 auxiliary functions, and 408 correlated 

orbitals). By using 32 processors, calculation was finished within 43 hours. These results indicate that 

RI-MP2 energy calculations of large molecules can be performed in modest time using low-cost PC 

clusters. 

Table 1. Elapsed times and speed-up of parallel 

RI-MP2 energy calculations of taxol. 

Processors Time [m] Speed-up 

1 741.7 1.0 

2 344.9 2.2 

4 168.1 4.4 

8 86.8 8.5 

16 45.5 16.3 

32 25.1 29.6 

[1] Feyereisen, M.; Fitzgerald, G.; Komornicki, A. Chem. Phys. Lett. 1993, 208, 359. 

[2] Bernholdt, D. E.; Harrison, R. J. Chem. Phys. Lett. 1996, 250, 477. 

[3] Hättig, C.; Hellweg, A.; Köhn, A. Phys. Chem. Chem. Phys. 2006, 8, 1159. 

[4] Grimme, S.; Mück-Lichtenfeld, C.; Antony, J. J. Phys. Chem. C 2007, 111, 11199.



PP365 

Development of an Efficient Computational Scheme for Relativistic GMC-QDPT and its 

Application to Molecular Systems 

Ryo Ebisuzaki, Yoshihiro Watanabe, Haruyuki Nakano 

Department of Molecular Chemistry, Graduate School of Sciences, Kyushu University, Fukuoka, 

Japan 

In electronic structure calculations for systems that contain heavy elements, treatment of both the 

electron correlation and relativistic effects is essential for high accuracy. However, quantum chemical 

theory including relativistic effects is much complicated compared to non-relativistic theory, and 

therefore even today it is not an easy task to perform relativistic calculations. In addition, calculations 

of heavy-atom compounds require much higher computational cost than those of the systems that 

consist of first- and second-row atoms such as hydrocarbons. Thus, due to its complexity and 

computational cost, highly accurate quantum chemical calculations including both the electron 

correlation and relativistic effects are restricted to small sized molecules consisting of few atoms. 

Recently, our group has developed the general multiconfiguration quasi-degenerate perturbation 

theory (GMC-QDPT) [1] and its relativistic generalized version [2]. GMC-QDPT is a multistate 

multireference perturbation theory that is applicable to any multiconfigurational reference wave 

functions. This method enjoys both high computational accuracy and efficiency. However, even with 

this relativistic GMC-QDPT, still it is not easy to efficiently calculate heavy-atom compounds with many 

electrons to be treated. 

In this presentation, we report the following of our recent development for improving computational 

efficiency of the relativistic GMC-QDPT, 

(1) A novel computational scheme based on the matrix elements reference functions and ionized 

determinants, which is more efficient than our previous computational scheme based on Goldstone 

diagrams [3], 

PP366 

Ab Initio Benchmark Calculations on Monoligand Ca(II) Complexes and Comparison with 

Density Functional Theory Methodologies 

Víctor M Rayón 1 , Haydee Valdés 2 , Natalia Díaz 2 , Dimas Suárez 2 

1 University of Valladolid, Department of Physical Chemistry and Inorganic Chemistry, Valladolid, 

Spain, 2 University of Oviedo, Department of Physical Chemistry and Analytical Chemistry, Oviedo, 

Spain 

Calcium is an essential element to life and as such plays a crucial role in many structural and reactive 

biochemical processes [1]. The understanding of these processes at the molecular level is of course of 

particular importance. To achieve this end, the study of biomimetics, i.e. model systems that only 

include the metal and chelating ligands, is usually proposed as a first step. 

We have carried out a theoretical study employing both ab initio correlated wave function and density 

functional methods on a set of 24 monoligand Ca(II) complexes. Several basis sets ranging from 

double to quintuple-zeta quality have been used, including all-electron correlation consistent basis 

sets. We can therefore provide a reliable high-level benchmark ab initio database for a set of 1:1 

complexes of Ca(II). The performance of four different functionals, namely, PW91, PBE, B3LYP, and 

TPSS in the prediction of binding energies, metal-ligand bond distances and proton affinities has been 

also assessed. Additionally, an analysis of the metal-ligand interaction has been carried out by means 

of an energy decomposition method.This analysis provides information on the relative importance of 

the electrostatic, induction and dispersive contributions to the metal-ligand interaction energy and 

might be useful for the assessment of ‘non-bonded’ molecular mechanics potentials that are no the 

basis of many biomolecular simulations [2]. 

[1] Berg, J. M.; Tymoczko, J. L.; Stryer, L. Biochemistry, 5 th Ed. Freeman & Co., New York, 2003. 

[2] Rayón, V. M.; Valdés, H.; Díaz, N.; Suárez, D. J. Chem. Theory Comput. 2008, 4, 243-256. 

(2) The Kramers-restricted formalism corresponding to spin-adapted formalism of non-relativistic 

theory, 

(3) Parallel algorithm. 

As an application, we also report the d-d excitation energy spectra of platinum complexes [PtX n ] 2- (X = 

halogen atom) with the new computational scheme. The calculated values were in good agreement 

with experimental data. 

[1] (a) H. Nakano, R. Uchiyama, and K. Hirao, J. Comput. Chem. 2002, 23, 1166-1175. 

(b) H. Nakano, J. Chem. Phys, 1993, 99, 7983–7992. 

[2] M. Miyajima, Y. Watanabe, and H. Nakano, J. Chem. Phys. 2006, 124, 044101 

[3] R. Ebisuzaki, Y. Watanabe, and H. Nakano, Chem. Phys. Lett. 2007, 442, 164-169.



PP367 

Aldehyde Dehydrogenase Enzymatic Chemistry: Insights from Hybrid QM/MM Calculations 

Troy Wymore, James Keener, Shawn Brown 

Pittsburgh Supercomputing Center, National Resource for Biomedical Supercomputing, Pittsburgh, 

PA, United States 

Aldehyde Dehydrogenases (ALDHs) oxidize aldehydes to their corresponding carboxylic acids and 

require a cofactor, usually nicotinamide adenine dinucleotide (NAD). The catalytic cycle is initiated by 

nucleophilic attack by a cysteine residue on aldehyde substrates to form a thiohemiacetal 

intermediate. The traditional mechanism for this step fails to mention even the possibility of proton 

transfer to this intermediate. Our past, published results employing hybrid PM3/OPLS umbrellasampling 

simulations suggest a novel enzyme mechanism where a proton transfers from a main chain 

amide to the oxyanion thiohemiacetal. We hypothesize that proton transfer stabilizes the intermediate 

protecting it from forming a “dead-end” cysteine-NAD complex. Our prediction of cysteine-NAD 

complex formation in ALDH was confirmed by re-examination of already deposited electron density 

maps. 

In this presentation, we will describe our strategy for re-parameterizing the semiempirical molecular 

orbital method AM1 to calculate, with considerably improved accuracy, various intermolecular 

interactions and reactions important for simulating Aldehyde Dehydrogenase (ALDH) chemistry. The 

“fitness” of a particular AM1 parameter set was evaluated by comparison to properties collected from 

either published experimental results or high-level Quantum Mechanical (QM) calculations. This 

reference data includes geometries, dipole moments, ionization potentials, heats of formation and 

reaction energies. Various non-linear search algorithms were then employed to search for parameter 

sets that best reproduce the reference data using a modified version of the DYNAMO library 

(www.pdynamo.org). The use of these parameters in QM/MM simulations to calculate the free energy 

profiles/surfaces of reactions in ALDH facilitates examination of the hydride transfer step. The 

simulations will test the hypothesis that two mutations in two separate but related ALDHs affect the 

essential protonation of the thiohemiacetal intermediate. These two mutations are responsible for two 

metabolic diseases, Sjorgren-Larsson syndrome and Hyperprolinemia Type II. 

PP368 

Simulation Studies of the Folding and Aggregation of Model Amyloid Peptides in Solution and 

at an Interface 

Volker Knecht, Madeleine Kittner, Reinhard Lipowsky 

Max Planck Institute of Colloids and Interfaces, Theory & Bio-Systems Department, Potsdam, 

Germany 

The development of therapeutic treatments against amyloid diseases requires an understanding of the 

(mis)folding and aggregation of fibrillogenic species at a microscopic level. To study these species in 

atomic detail experimentally is difficult due to their tendency to aggregate and the transient nature of 

early oligomers. Therefore, an indispensable tool to study these systems is provided by computer 

simulations. The most accurate treatment consists of a full atomistic description of peptides and 

solvent environment. We present molecular dynamics (MD) simulations of the folding or aggregation of 

various model amyloid peptides in explicit water and at a water/vapor interface. As shown in Fig. 1, the 

18-residue amyloid peptide B18 derived from the sea urchin fertilization protein Bindin was observed 

to undergo a transition from beta-sheet/coil conformations in water to partially alpha-helical 

conformations at a water/vapor interface. Possible pathways for alpha-beta transformations in solution 

and beta-alpha transformations at the interface were suggested [1]. 

In contrast, a 12-residue amyloid peptide derived from a viral protein and denoted as LSFD was found 

to adopt the same type II’ beta-hairpin conformation in equilibrium with more disordered but also U- 

shaped conformations both in water and at a water/vapor interface [2]. This suggests that beta-sheet 

conformations suggested from previous spectroscopic measurements on LSFD immediately after 

preparation of the peptide solution may not arise from the presence of protofilaments as speculated 

previously, but, rather, indicate a property of monomers. In addition, combined with previous results 

from x-ray scattering, our findings suggest that interfacial aggregation of LSFD implies a transition 

from U-shaped to extended peptide conformations. We directly observed such U-shaped to extended 

transitions during replica exchange simulations of the dimerization of the (25-35) fragment of the 

Alzheimer A beta peptide in water. Simulations of a monolayer consisting of peptides with sequence 

G(VT)5 adopting extended intermolecular beta-sheets revealed a strong bending of the beta-sheets at 

the termini. Taken together, our results give insights to the properties of fibrillogenic or beta-sheet 

forming peptides at an atomic level important from a biophysical, medical, and nanotechnological point 

of view. 

FIG. 1: Conformational polymorphism of 

model amyloid peptide B18 in different 

environments from all-atom simulations 

[1]. The initial (left) and typical 

configurations in explicit water (middle) or 

a water/vapor interface (right) are shown. 

[1] Knecht, V., Möhwald, H., and Lipowsky, R., J. Phys. Chem. B 2007, 111, 4161-4170. 

[2] Knecht V., J. Phys. Chem. B , accepted.



PP369 

Electrophoretic Mobility Does Not always Reflect the Charge on a Particle 

Volker Knecht, H. Jelger Risselada, Alan E. Mark, Siewert-Jan Marrink 

1 Max Planck Institute of Colloids and Interfaces, Theory & Bio-Systems, Potsdam, Germany, 

2 Groningen Biomolecular Sciences and Biotechnology Institute, and Zernike Institute for Advanced 

Materials, University of Groningen, Groningen, Netherlands, 3 School of Molecular and Microbial 

Sciences, University of Queensland, Brisbane, Australia, 4 Groningen Biomolecular Sciences and 

Biotechnology Institute, and Zernike Institute for Advanced Materials, University of Groningen, 

Groningen, Netherlands 

Electrophoresis is widely used to determine the electrostatic potential of colloidal particles. 

Hydrophobic particles such as oil droplets or air bubbles in water above pH 3 show negative 

electrophoretic mobilities. This is commonly attributed to a negative surface charge due to the 

adsorption of hydroxide ions. This explanation, however, has been challenged recently by 

spectroscopic experiments and atomistic simulations indicating that hydrophobic surfaces, rather, 

adsorb hydronium but (weakly) repel hydroxide, thus being positively charged. Alternative 

explanations for negative electrophoretic mobilities of hydrophobic particles are anionic impurities at 

the interface. Here we present molecular dynamics simulations of oil droplets in water in the presence 

of an external electric field but in the absence of any ions [1]. The simulations reproduce the negative 

sign and the order of magnitude of the oil droplet mobilities at the point of zero charge in experiment. 

The electrostatic potential in the oil with respect to the water phase, induced by anisotropic dipole 

orientation at the interface, is positive. Our results suggest that, for hydrophobic interfaces, the effect 

of hydronium causing positive electrophoretic mobility is overcompensated by negative mobility arising 

from dipolar ordering. More generally, our findings suggest that electrophoretic mobility does not 

always reflect the net charge or electrostatic potential of colloidal particles, and that a fundamental 

understanding of electrokinetic phenomena requires a molecular description. 

PP370 

A Multilevel Sidechain Representation Library for Protein Structure Prediction and Docking. 

Quentin Kaas 

Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia 

Protein-protein docking and ab-initio structure prediction are nowadays the more challenging area of 

research in structural bioinformatics. The major problem of protein docking is to account for protein 

flexibility [1]. It is often done by using the soft docking method which allows a certain level of 

entanglement between the two docked structures [2]. On the other hand ab-initio structure prediction 

(loop or whole protein modelling) often uses simplified sidechain representations, with a reduced 

number of interaction centres, for faster computation and to comply with low resolution modelling [3]. 

I have developed a new method called SCHISMo that combines and extends those approaches 

thanks to a multilevel library of sidechain representations. The first level represents sidechains with 

two interaction centres, the second level uses interaction centres corresponding to a single atom or to 

a group of atoms and the third level corresponds to all the heavy atoms. The levels are implemented 

hierarchically which allows to pass from a simple to a more complex representation, or the reverse. 

The flexibility of the sidechains are modelled by mapping the positions of the interaction centres on a 

circle or on a sphere. The sidechain conformations are predicted by considering conformation 

frequency in a set of experimental structures and by considering charge and hydrophobic interactions. 

A C library allows an easy implementation of SCHISMo in other modeling programs that will be able to 

progressively complexify sidechain representations as a model is refined. Finally SCHISMo can build 

new simplified representation libraries with different centre definitions and train this library on a 

different set of experimental structures, for example corresponding to a specific class of proteins. 

FIG. 1: Electrophoresis of oil droplets in water in the absence of ions in molecular dynamics simulations. Left: 

(Periodic) simulation box (black frame) with direction of the external electric field. Middle: Heptane droplet of 

diameter 9 nm (dark gray) in water (white) moving in negative field direction. Right top: Heptane-water interface. 

Right bottom: Single heptane and water molecule. CH 3 and CH 2 groups in heptane were treated as compound 

atoms. For heptane, covalent bonds are depicted as white lines, and one of the bond torsion angles is indicated. 

For water, partial charges on oxygen and hydrogen atoms are indicated. 

[1] Lensink, M. F.; Méndez, R.; Wodak, S.J. Proteins 2007 69, 704-718 

[2] Fernandez-Recio, J.; Totrov, M.; Abagyan, R.; Protein Science 2002 11, 280-291 

[3] Maupetit, J.; Tuffery, P.; Derreumaux, P.; Proteins 2007 69, 394-408 

[1] Knecht, V; Rissela, H.J.; Mark, A.E.; and Marrink, S.J; J. Col. Int. Sc. 2008, 318, 477-486.



PP371 

In Quest of an Efficient and Accurate Modelling of the Photochemistry of Biological 

Photoreceptors: A QM/MM Approach. 

Pedro B. Coto, Israel González-Ramírez, Gloria Olaso-González, Daniel Roca-Sanjuán, Juan José 

Serrano-Pérez, Manuela Merchán 

Instituto de Ciencia Molecular (ICMOL), University of Valencia, Valencia, Spain 

Light-driven chemical reactions play a key role in different biological processes fundamental for life. 

Photoreceptors such as rhodopsins, phytochromes and xanthopsins use the energy of 

electromagnetic radiation to unleash complex biochemical processes like vision [1], photosynthesis 

[2], and phototaxis [3]. The use of hybrid Quantum Mechanics/Molecular Mechanics (QM/MM) [4] 

methods allows tackling the treatment of large biological systems in an efficient and accurate way. In 

particular, the CASPT2//CASSCF/Forcefield protocol is able to give a balanced treatment of the 

different electronic states involved in the photochemical process by including both dynamic and static 

correlation effects. We have applied this scheme to the analysis of the photochemistry of Rhodopsin 

[5,6] and PYP [7]. The different factors controlling the wavelength absorption maxima are discussed. 

PP372 

Efficient Extrapolation of Triple Excitations to the Complete Basis Set Limit 

Ericka Barnes, George Petersson 

Wesleyan University, Chemistry Department, Middletown, CT, United States 

Compound model chemistry methods (e.g. G3, CBS-QB3, and W1) designed to approximate 

CCSD(T)/CBS energies are limited by the cost of the non-iterative perturbative contribution of triple 

excitations. This component scales as O 3 V 4 and thus will ultimately determine the range of 

applicability of any such method. It is therefore imperative to make every effort to minimize the basis 

sets used for this component. There is little to be gained from reducing the error in the approximation 

of the CCSD(T)/CBS limit much below the error in the CCSD(T) energy relative to the FCI energy, 

which defines the limiting accuracy possible within this framework. We therefore sought the smallest 

basis sets for which the rms deviation in our extrapolated triple excitation component falls below this 

inherent error in the CCSD(T) energy (0.5 mE h for our test set). We find that a linear extrapolation of 

3s2p (double-ζ without diffuse or polarization functions) and 5s4p1d (triple-ζ augmented with diffuse 

valence functions and a single set of polarization functions for first-row atoms) satisfies our criterion. 

This extrapolation reduces the rms error (compared to the CBS limit of the perturbative triple excitation 

component) below 0.4 mE h for our test set of 57 bond dissociation energies, ionization potentials, and 

electron affinities. The combination of this (T) extrapolation with CCSD extrapolations employing larger 

basis sets is comparable to the overall accuracy of W1 theory (with triples extrapolated from 4s3p2d 

and 5s4p3d2f basis sets for first-row atoms) with up to two orders-of-magnitude advantage in speed. 

[1] Wald G. Nobel Lecture 1967. 

[2] Quail, P. H.; Boylan M. T.; Parks, B. M.; Xu, Y.; Wagner, D. Science 1995, 268, 675-680. 

[3] Sprenger, W. W.; Hoff, W. D.; Armitage, J. P.; Hellingwerf, K. J. J. Bacteriol. 1993, 175, 3096-3104. 

[4] Warshel, A.; Levitt, M. J. Mol. Biol. 1976, 103, 227-249. 

[5] Coto, P. B.; Strambi, A.; Ferré, N.; Olivucci, M. Proc. Natl. Acad. Sci. (USA) 2006, 103, 17154-17159. 

[6] Strambi, A.; Coto, P. B.; Frutos, L. M.; Ferré, N.; Olivucci, M. J. Am. Chem. Soc. 2008, 130, 3382-3388. 

[7] Coto, P. B.; Martí, S.; Oliva, M.; Olivucci, M.; Merchán, M.; Andrés, J. J. Phys. Chem. B. doi: 

10.1021/jp711396b.



PP373 

Decomposition of 6,7,8-Trioxybicyclo[3.2.2]nonane Prompted by Fe(II). A Model to Study the 

Fisrt Stages of the Decomposition Mechanism of Artemisinin 

Pamela Moles, V. Sixte Safont, Mónica Oliva 

Universitat Jaume I, Departament de Química Física i Analítica, Castelló de la Plana, Spain 

Artemisinin is the most effective drug against malaria at hand nowadays. The endoperoxide group that 

Artemisinin possesses has been proven to be critical for its antimalarial activity. 

By using the 6,7,8-trioxybicyclo[3.2.2]nonane as Artemisinin model, and the Fe(II)[H 2 O] 2 [OH - ] 2 as 

activator agent, we present a theoretical investigation of the decomposition mechanism of Artemisinin. 

The first step involves the reductive cleavage of the peroxidic bond prompted by Fe (II), leading to the 

formation of oxygen-centered radicals which, in turn, generate carbon-centered radicals. These can 

participate in a series of chemical reactions and form other kind of intermediates, one or more of which 

could kill the malaria parasite. The molecular structures of the free radicals and the neutral species 

that take part in the reactions have been calculated with the B3LYP method at 6-311+G** level. In 

addition an electron localization function (ELF) based study has been carried out to have a topological 

description of the bonds being broken and formed in the reported steps. 

H 3 C 

O 

O 

O 

H 

O 

H 3 C 

O 

H 

CH 3 

O 

O 

O 

PP374 

Solvation of Platinum Chloro-Complexes in 1,3-Dialkylimidazolium Ionic Liquids 

Gerhard A Venter, Kevin J Naidoo 

Department of Chemistry, University of Cape Town, Rondebosch, Western Cape, South Africa 

Room Temperature Ionic Liquids (RTILs) are fast becoming synonymous with "Green Chemistry". 

Their qualities of possessing near-negligible vapour pressure and high thermal stability are key in this 

regard—but it is their degree of tunability, afforded by mixing cation/anion combinations and varying 

individual molecular structure, that designates them "designer solvents" [1]. 

The solvation behaviour and structure of transition metal systems in ionic liquids are of direct concern 

in determining catalytic reaction pathways, even more so where charged precursors or intermediate 

species are present. The effect of strong ionic association on reaction rates has been illustrated [1]. 

The most popular class of ionic liquids are those consisting of imidazolium cations, in particular, the 1- 

alkyl-3-methylimidazolium cations. We have simulated the solvation of hexachloroplatinate(IV) in 

cations of this type, using a variety of different anions. In doing so we have developed a transferable 

CHARMM-type forcefield for the 1,3-dialkylimidazolium cations that is also consistent with our platinum 

group metal forcefield [2]. Whereas other popular CHARMM-type RTIL forcefields depend on charges 

being calculated as needed for each new ion under investigation [3], we opted for a more general 

description favouring transferability [4]. The parameterization strategy outlined by Mackerell and 

Foloppe was used as a guide [5]. 

Other than comparison with experimental properties such as densities, diffusion coefficients and pair 

distribution functions (where available) as validation of the forcefield, we also present spatial 

distribution functions (SDF) of the solvation structure of [PtCl 6 ] 2- in 1,3-dialkylimidazolium chloride. 

2- 

Cl 

Cl Cl 

CH 2 

CH 2 

Pt 

H 3 C m N N n 

Cl 

CH 3 

Cl Cl 

Cl 

Figure. Artemisinin and 6,7,8-trioxybicyclo[3.2.2]nonane 

[1] J. D. Gu, K. X. Chen, H. L. Jiang, J. Leszczynski, Journal of Physical Chemistry A. 1999, 103, 9364. 

[2] J. Gu, K. Chen, H. Jiang, J. Leszczynski, Journal of Molecular Structure-Theochem 1999, 491, 57. 

[3] P. L. Olliaro, R. K. Haynes, B. Meunier, Y. Yuthavong, Trends in Parasitology 2001, 17, 122. 

[4] M. G. B. Drew, J. Metcalfe, M. J. Dascombe, F. M. D. Ismail, Journal of Medicinal Chemistry 2006, 49, 6065. 

[5] M. G. B. Drew, J. Metcalfe, F. M. D. Ismail, Journal of Molecular Structure-Theochem 2005, 756, 87. 

[6] S. Tonmunphean, V. Parasuk, S. Kokpol, Journal of Molecular Structure-Theochem 2005, 724, 99. 

[7] J. Queiroz, J. Walkimar, M. Teixeira, F. H. Andrade, A. Gutterres, Bioorganic and Medicinal Chemistry 2008, 

16, 5021. 

[1] (a) Welton, T. Coord. Chem. Rev. 2004, 248, 2459–2477. (b) Welton, T. Chem. Rev. 1999, 99, 2071–2083. 

[2] Lienke, A.; Klatt, G.; Robinson, D. J.; Koch, K. R.; Naidoo, K. J. Inorg. Chem. 2001, 40, 2352–2357 

[3] Maginn, E. J. Acc. Chem. Res. 2007, 40, 1200–1207. 

[4] Pádua, A. A. H.; Costa Gomes, M. F.; Canongia Lopes, J. N. A. Acc. Chem. Res. 2007, 40, 1087-1096. 

[5] Foloppe, N.; MacKerell, Jr., A. D. J. Comp. Chem. 2000, 21, 86–104.



PP375 

Mechanistic Analysis of Intermolecular Arene C-H Activation 

Stuart A. Macgregor, David L. Davies, Amalia I. Poblador-Bahamonde 

Heriot-Watt University, Engineering and Physical Sciences (EPS), Edinburgh, United Kingdom 

The intermolecular C-H activation of benzene by the model complex [IrCp(PH 3 )AcO] + has been 

studied by density functional calculations. Three possible mechanisms have been considered: 

oxidative addition; σ–bond methathesis; and electrophilic activation [1]. Our results indicate 

electrophilic activation to be the most promising process. 

H 3 P 

Ir 

O 

O C CH3 

H 3 P 

Ir 

O 

O 

C CH3 

H 3 P 

Ir 

O 

OH 

C CH3 

PP376 

DFT Study on Charge Conductivity of DNA-Wrapped Carbon Nanotubes 

Noriyuki Kurita 1 , Ikuyo Komura 1 , Takayuki Tsukamoto 1 , Yasuyuki Ishikawa 2 

1 Toyohashi University of Technology, Toyohashi, Aichi, Japan, 2 University of Puerto Rico, San Juan, 

PR, United States 

1. Introduction 

Recently, Zheng et al. [1] reported that single-walled carbon nanotubes (SWNTs) can be wrapped by 

single-stranded DNAs (ssDNA), and that the ssDNA-SWNT complexes formed can be used in 

chromatographic techniques to allow the separation of SWNTs by length, conductivity type and 

diameter. In the present study, we investigated the stable structures, electronic and charge-conductive 

properties of the ssDNA-wrapped SWNTs by molecular simulations based on classical molecular 

mechanics (MM) and ab initio molecular orbital (MO) methods. Because the previous experiment [1] 

indicated that the (GT) 14 ssDNA wraps SWNTs, we employed the ssDNAs with the sequence 5’- 

d(GTGTGT)-3’ and 5’-d(GGCC)-3’, while the semiconducting (10,0) and metallic (6,6) SWNTs with 30 

Å in length were employed, in order to elucidate the difference in the effect of ssDNA wrapping on the 

electronic properties between the semiconducting and metallic SWNTs. 

base displacement H-transfer 

Electrophilic activation is computed to proceed by a two-step mechanism, where the initial 

displacement of acetate is rate determining. Replacing acetate with a more weakly coordinating 

species such as triflate therefore reduces the barrier to C-H activation. Comparisons with other 

systems show that the presence of an intramolecular chelating base greatly facilitates C-H activation. 

2. Method of calculations 

A standard B-form ssDNA was docked to SWNT by using the automated ligand-docking program 

AutoDock3. A total of 100 candidate structures for ssDNA-SWNT were produced and fully optimized 

by the AMBER-MM method. In density-functional theory calculations using the Dmol³ program, the 

electronic properties of these ssDNA-SWNTs were examined to elucidate the effect of ssDNA 

wrapping on the energy levels and spatial distributions of MOs, including the HOMO and LUMO. 

Based on the electronic properties, charge conductive properties of the ssDNA-SWNTs as well as 

SWNTs were probed via the charge-conductive analysis algorithm developed by Meunier et al. [2]. 

[1] Davies D. L., Donald S.M.A., Al-Duaij O., Macgregor S. A., Pölleth M., J. Am. Chem. Soc., 2006, 128, 4210. 

3. Results and discussion 

The GGCC ssDNA can wrap both the (10,0) and (6,6) SWNTs, whereas the (GT) 3 ssDNA wraps only 

the (6,6) SWNT. In the GGCC-ssDNA+SWNT complexes, the backbone of ssDNA wraps the SWNTs 

in a helical form, while the bases of ssDNA are stacked onto the surface of the SWNTs, as suggested 

by the previous molecular modeling study [1]. Therefore, it seems that the bases of the GGCC ssDNA 

contribute to the wrapping of SWNTs. 

For the most stable structures of the (GT) 3 ssDNA+SWNTs complexes, we investigated the binding 

energies between ssDNA and SWNT to find that the (GT) 3 ssDNA can bind more strongly to the 

metallic (6,6) SWNT than (10,0) SWNT. In the (GT) 3 ssDNA+(6,6) SWNT complex, some stacking 

interactions between the bases of ssDNA and the surface of (6,6) SWNT stabilize the complex. On the 

other hand, the (GT) 3 ssDNA cannot wrap the (10,0) SWNT, resulting in the weak binding between 

(GT) 3 ssDNA and (10,0) SWNT. 

The HOMO and LUMO of the (GT) 3 ssDNA+(10,0) SWNT are localized on both edges of the (10,0) 

SWNT, whereas they are distributed over the (6,6) SWNT in the (GT) 3 ssDNA+(6,6) SWNT. Therefore, 

the effects of the (GT) 3 ssDNA-wrapping on the electronic properties of the (10,0) and (6,6) SWNTs 

differ significantly. The results on the charge conductive properties of ssDNA+SWNTs will be shown in 

the poster. 

[1] Zheng, M. et al. Nature Materials 2003, 2, 338. [2] Meunier, V. et al. J. Chem. Phys. 2005, 123, 024705.



PP377 

Specific Interactions between Thermolysin and Dipeptide Ligands Obtained by Fragment 

Molecular Orbital Calculations 

Noriyuki Kurita 1 , Kenichi Dedachi 1 , Mahmud T. H. Khan 2 , Ingebrigt Sylte 2 

1 Toyohashi University of Technology, Toyohashi, Aichi, Japan, 2 University of Tromsø, Tromsø, 

Norway 


Thermolysin (TMN) is one of the widely studied zinc metalloproteases from Bacillus 

stearothermophilus. Especially, the hydrolysis mechanism of TMN has been theoretically studied for 

over a decade. Recent experimental studies indicated that the activity of TMN is largely dependent on 

the types of ligand (dipeptide) molecules. In the present study, we investigated the specific 

interactions between TMN and some kinds of dipeptides by classical molecular mechanics (MM) and 

multi-layer fragment molecular orbital (MLFMO) methods. 

2. Method of calculations 

We have obtained the X-ray structures of the complexes with TMN and IY (Ile-Tyr) or LW (Leu-Trp). 

These X-ray structures have about 350 crystal water molecules, although the positions of hydrogen 

atoms are not determined. We then added hydrogen atoms to these structures and optimized the 

positions of only hydrogen atoms by the MM method based on AMBER force field, with considering 

the crystal water molecules explicitly. 

PP378 

Characterization of Weak Interactions between Aromatic Amino Acids and the Natural 

Nucleobases 

Lesley Rutledge, Holly Durst, Stacey Wetmore 

University of Lethbridge, Department of Chemistry and Biochemistry, Lethbridge, Alberta, Canada 

Interactions between DNA and protein building blocks have been proven to be very important in 

nature, where they dictate biomolecular structure and are essential in many biological processes. For 

example, DNA replication and transcription rely on protein–DNA interactions. ‘Weak’ noncovalent 

interactions, such as hydrogen bonding and stacking have been studied extensively. However, crystal 

structures reveal that there are also T-shaped interactions in enzyme active sites, which were 

previously believed to be even weaker than stacking interactions. This study uses computational 

chemistry to characterize the gas-phase stacking and T-shaped interactions between aromatic amino 

acids (HIS, PHE, TYR, TRP) and the natural nucleobases (A, G, C, T). The MP2/6-31G*(0.25) 

potential energy surfaces of the nucleobase–amino acid dimers were calculated as a function of 

several geometrical variables and higher-level calculations were performed to determine the most 

accurate binding strengths possible. Our calculations provide valuable information about the nature 

and magnitude of these weak interactions, and our results suggest that these interactions play a more 

important role in biochemistry than initially suspected. 

The electronic properties of the optimized TMN+dipeptide structures with crystal water molecules 

were investigated by using the MLFMO method [1,2]. In this calculation, dipeptide, Zn and amino acids 

of TMN existing within a 5.0 Å distance from the dipeptide and Zn were treated by MP2/6-31G(d,p), 

while the other amino acids of TMN were treated by HF/6-31G(d,p). The crystal water molecules were 

treated in the same way. It is noted that Zn ion was included in the same fragment of Glu166, which 

exists near to Zn ion. From the comparison of interaction energies between the amino acids or water 

molecules and dipeptide, we attempted to elucidate which amino acids or water molecules are 

important for the specific interactions between TMN and dipeptide in electronic level. 

3. Results and discussion 

The obtained interaction energies between the amino acids of TMN or water molecules and IY indicate 

that Asn112, Arg203 and Glu143 amino acids have larger interaction energies. It is thus expected that 

these amino acids of TMN mainly contribute to the specific interactions between TMN and IY. In 

addition, it is elucidated that one unique water molecule has large (-13.23 kcal/mol) interaction energy 

with IY. This water molecule is directly hydrogen bonded to the NH 2 terminal of Ile of IY peptide and 

bridges between IY, Zn and Glu166 of TMN. Therefore, it can be concluded that this water molecule 

can contribute significantly to the specific interactions between TMN, Zn and IY. On the other hand, 

there is no such water molecule in the complex of TMN+LW, so that the binding energy between TMN 

and IY is smaller than that between TMN and LW. At the conference, we will also present the results 

for the complexes with TMN and other dipeptides. 

[1] Fedorov, D. G. et al., J. Phys. Chem. A 2005, 109, 2638. 

[2] Mochizuki, Y. et al., Chem. Phys. Lett. 2005, 410, 247.



PP379 

DFT Study of the Manganese Containing Ribonucleotide Reductase in Chlamydia Trachomatis 

Katarina Roos, Per E.M. Siegbahn 

Department of Physics, Stockholm University, Stockholm, Sweden 

Ribonucleotide reductase (RNR) catalyses the reduction of ribonucleotides to deoxyribonucleotides, 

the building blocks for DNA synthesis. In the pre-activating step a stable tyrosyl radical needed for 

catalysis is formed by oxygen cleavage at a di-iron site. The human pathogen Chlamydia trachomatis 

(Ct) RNR lacks the tyrosine crucial for activity in conventional RNR. Instead the active cofactor is a 

manganese(IV)/iron(III) metal center. An explanation is suggested to why the enzyme needs this 

manganese instead of a second iron to perform the same chemistry as with the tyrosyl radical. In 

normal class I RNR (e.g. from Escherichia coli) compound X has a similar oxidation state with 

iron(IV)/iron(III). This state precedes the tyrosyl radical and has not yet been structurally determined. 

In this study DFT is used to show why it is crucial to have manganese(IV) in the active center of Ct R2 

and that switching to iron(IV) would probably generate an inactive complex. The quantum chemical 

calculations performed explain experimental observations of Ct RNR and give guidance for future 

experiments. 

PP380 

Computational Studies of the Isomerisation of Nido- and Closo- 12-vertex Carboranes 

Stuart A. Macgregor, David McKay, Alan J. Welch 

Heriot-Watt University, School of Engineering and Physical Sciences, Edinburgh, United Kingdom 

The production of supraicosahedral carboranes requires the reduction of a closo 12-vertex species to 

a nido fragment followed by capitation. We have used computational methods to study the reduction 

of closo-C 2 B 10 H 12 species. The reduction of para-carborane is particularly complex and produces five 

different nido dianionic minima. We present the full characterisation of the initial products of reduction 

and the subsequent isomerisation pathways to all five nido species. 

C 

C 

para-carborane 

REDUCTION 

CAPITATION 

{ML n } 2+ 

C 

ML n 

C 

13-vertex cl oso ruthenacarborane 

C 

C 

para-carborane 

RED 

2- 

2- 

2- 

2- 

2- 

C 

C 

C 

C 

C C 

C 

+ 

+ + 

+ 

C 

C 

C 

[1,7-nido-C 2 B 10 H 12 ] 2- [3,7-nido-C 2 B 10 H 12 ] 2- [4,7-nido-C 2 B 10 H 12 ] 2- [7,9-nido-C 2 B 10 H 12 ] 2- [7,10-nido-C 2 B 10 H 12 ] 2- 

These results agree with experimental studies which have shown that reduction and capitation of 

para-carborane produces 13-vertex ruthenacarboranes derived from these nido intermediates [1]. 

Additional computational studies show the 2e reduction of ortho- and meta-carborane produces 

[7,9-nido-C 2 B 10 H 12 ] 2− , in agreement with experimental studies [2]. Reoxidation then gives a new 

species shown to be an intermediate in a new low energy route for isomerisation of ortho- to metacarborane. 

C 

C 

C 

C 

ortho-carborane 

meta-carborane 

R 

O 

C 

C 

R 

[7,9-nido-C 2 B 10 H 12 ] 2- 

[1] Zlatogorsky, S.; Edie, M. J.; Ellis, D.; Erhardt, S.; Lopez, M. E.; Macgregor, S. A.; Rosair, G. M.; Welch, A. J. 

Angew. Chem. Int. Ed. 2007, 46, 6706. 

[2] (a) Dunks, G. B.; Wiersema, R. J.; Hawthorne, M. F. J. Am. Chem. Soc. 1973, 95, 3174. (b) Zakharkin, L. I.; 

Kalinin, V. N.; Podvisotskaya, L. S. Bull. Acad. Sci. USSR, Div. Chem. Sci. 1966, 1444.



PP381 

Short Intramolecular Hydrogen Bonds: Derivatives of Malonaldehyde with Symmetrical 

Substituents 

Jacqueline Hargis, Francesco Evangelista, Justin Ingels, Henry Schaefer 

Center of Computational Chemistry, University of Georgia, Athens, GA, United States 

A systematic study of various derivatives of malonaldehyde has been carried out to explore very short 

hydrogen bonds (r OO < 2.450 Å). Various electron withdrawing groups, including CN, NO 2 , and BH 2 

have been attached to the central carbon atom, C 2 . To C 1 and C 3 , strong electron donors and/or steric 

hindered substituents were used to strengthen the intramolecular hydrogen bond, including but not 

limited to NH 2 , N(CH 3 ) 2 , and C(CH 3 ) 3 . Six molecules (Figure 2) were found to have extremely short 

intramolecular hydrogen bonds. 

The chemical systems investigated are intriguing due to their low energetic barrier for the 

intramolecular hydrogen atom transfers. Energy barriers were predicted using correlated methods 

including second-order perturbation theory and coupled cluster theory in conjunction with the Dunning 

hierarchy of correlation consistent basis sets, cc-pVXZ (X=D, T, Q, 5). Focal point analyse allowed for 

the barriers to be evaluated at the CBS limit including core correlation and zero-point vibrational 

energy corrections. 

B3LYP energies are benchmarked against highly accurate correlated energies for intramolecular 

hydrogen bonded systems. The focal point extrapolated value including coupled cluster full triple 

excitation contributions give a hydrogen transfer barrier for malonaldehyde of 3.9 kcal mol -1 . We also 

describe two compounds with extremely low barriers; nitromalonamide (0.44 kcal mol -1 ) and 

2-borylmalonamide (0.62 kcal mol -1 ). An empirical relationship was drawn between the underestimated 

B3LYP energetic barriers and the predicted barriers at the CBS limit. By relating these two quantities, 

barrier heights for larger systems may be estimated for systems that possess too many atoms to use 

highly correlated electronic structure methods. 

PP382 

Structural Effects of DNA Modification at the C8 site of Purine Nucleobases 

Andrea Millen 1 , Cassandra Churchill 1 , Lex Navarro-Whyte 1 , Jenny Shim 1 , Katie Schlitt 2 , Chris 

McLaughlin 2 , Richard Manderville 2 , Stacey Wetmore 1 

1 Department of Chemistry & Biochemistry, University of Lethbridge, Lethbridge, Alberta, Canada, 

2 Departments of Chemistry & Toxicology, University of Guelph, Guelph, Ontario, Canada 

Modification at the C8 site of the purines can occur when molecules such as phenols are oxidized into 

phenoxyl radicals by peroxidase enzymes or redox-active transition metals. These C-bonded DNA 

adducts can lead to abasic site formation, and thus increase the vulnerability of the cell to the 

carcinogenic process [1,2]. Conversely, the unique properties of DNA modified in this way can be 

exploited, where for example the structures can be used as bioprobes [3]. Our research uses 

computational methods to understand the structure and reactivity of these modified nucleobases [4]. 

R O 

2 

R 

12 11 7 6 

2 

N 

5 

NH 

N 

13 

R 1 1 R 

10 8 

1 

14 θ N 4 

15 

2 

9 N NH N 

HO 

3 2 

HO 

5′ χ 

O 

O 

4′ 

3′ 

OH 

1′ 

2′ 

OH 

NH 2 

N 

N 

O 

O 

1a 7 6 

N 5 

2a 7 6 

X 

8 NH 

N 5 

5a 2a 

1a X 3a 

8 NH 

1 

1 

4a 

9 

5a 

9 

HO 3a θ N 4 N 2 

4a 

NH 2 HO θ N 4 N 2 

5' 

NH 2 

5' 3 

O χ 

3 

O χ 

4' 

1' 

4' 

1' 

3' 2' 

3' 2' 

OH X=O,NH,orS OH 

Scheme 1 Scheme 2 

Experimental work has proposed that the preferred conformation of ortho phenoxyl purine adducts 

(Scheme 1, R 2 =OH, R 1 =H) fluctuates between twisted and planar structures depending on the solvent, 

while the para adducts (Scheme 1, R 2 =H, R 1 =OH) adopt only twisted conformations. To better 

understand the structures of these adducts, the gas-phase potential energy surfaces of the 

deoxyguanosine and deoxyadenosine ortho and para carbon-bonded adducts (Scheme 1) were 

systematically studied using DFT by varying the orientation about the glycosidic bond (χ) and phenoxyl 

substituent (θ) for two orientations of the C5′-hydroxyl group. The effects of various phenyl 

substituents on the adduct structure and the barrier for glycosidic bond cleavage have also been 

performed for comparison to experimental deglycosylation studies. Additionally, the structures of a 

series of five-membered ring adducts (Scheme 2) with interesting fluorescent properties that could be 

used as bioprobes have been studied for their conformational properties. This poster will summarize 

some of our important findings about the structures of these important DNA nucleosides and the 

implications of these findings for their biological activity and use as bioprobes. 

[1] Manderville, R. A. Can. J. Chem.-Rev. Can. Chim. 2005, 83, 1261-1267. 

[2] McLaughlin, C. K.; Lantero, D. R.; Manderville, R. A. J. Phys. Chem. A 2006, 110, 6224-6230. 

[3] Sun, K. M.; McLaughlin, C. K.; Lantero, D. R.; Manderville, R. A. J. Am. Chem. Soc. 2007, 129, 1894-1895. 

[4] Millen, A. L.; McLaughlin, C. K.; Sun, K. M.; Manderville, R. A.; Wetmore, S. D. J. Phys. Chem. A 2008, 112, 

3742-3753.



PP383 

Chlorine-π Interactions: New Methods for Old Problems 

Anna K. Croft, Helen M. Howard-Jones, Chris C. Wood 

School of Chemistry, University of Wales Bangor, Bangor, Gwynedd LL57 2UW, United Kingdom 

PP384 

The Importance of Solvent Reorganisation in Reactions Performed in Ionic Liquids 

Hon Man Yau 2 , Susan A. Barnes 1 , James M. Hook 2 , Tristan G. A. Youngs 3 , Jason B. Harper 2 , Anna K. 

Croft 1 

1 School of Chemistry, University of Wales Bangor, Bangor, Gwynedd LL57 2UW, United Kingdom, 

2 School of Chemistry, University of New South Wales, Sydney, NSW 2052, Australia, 3 Atomistic 

Simulation Centre, Queen's University Belfast, Belfast, BT7 1NN, United Kingdom 

The structure of the chlorine-atom benzene complex has been a topic of significant controversy for 

more than 50 years. We have re-examined the structure of this and related complexes with new 

density functional methods especially designed for non-covalent complexes [1], and compared the 

structures and energetics to those obtained using standard DFT and high accuracy composite 

methods [2]. We find that the popular B3LYP functional fails to identify stationary points revealed by 

other functionals [3], and that the η 1 -σ complex appears to be more stable than the η 1 -π complex, 

highlighting the careful selection of methods required in non-covalent radical systems. 

[1] Zhao, Y. and Truhlar D. G., J. Phys. Chem. A, 2004, 108, 6908-6918. 

[2] (a) Henry, D. J., Sullivan, M. B. and Radom, L., J. Chem. Phys., 2003, 118, 4849-4860. (b) Mayer, P. M., 

Parkinson, C. J., Smith D. M., and Radom, L., J. Chem. Phys., 1998, 108, 604-615. 

[3] Croft, A. K. and Howard-Jones, H. M., Phys. Chem. Chem. Phys., 2007, 9, 5649-5655. 

Ionic liquids have been touted as potential alternatives to environmentally damaging volatile organic 

solvents [1]. These salts, typically made up of a bulky organic cation and a charge diffuse anion, are 

attractive as alternative solvents due to their negligible vapour pressures and the ability to 'tune' the 

properties of the solvent based on the modification of the component ions. Temperature dependent 

rate studies demonstrate an enthalpic benefit and an entropic cost associated with the change in the 

rate of unimolecular substitution process on addition of a high proportion of an ionic liquid [2]. 

Molecular dynamics simulations have supported this latter effect by showing a large change in the 

degree of organisation around reaction intermediates, compared with that seen for the starting 

materials. 

[1] Rogers, R. D., and Seddon, K. R., Science, 2003, 302, 792. 

[2] Yau, H. M., Barnes, S. A., Hook, J. M., Youngs, T. G. A., Croft, A. K and Harper, J. B., Chem. Commun., 2008, 

in press.



PP385 

Quantum Chemical Study on the Promotion Effect of H 2 in the Selective Catalytic Reduction of 

NOx over Ag-MFI Zeolite 

Kyoichi Sawabe, Ken-ichi Shimizu, Atsushi Satsuma 

Department of Molecular Design and Engineering, Nagoya University, Chikusa-ku, Nagoya, Japan 

The selective catalytic reduction of NOx to N 2 with hydrocarbons (HC-SCR) is a promising technique 

for removing NOx from lean-burn and diesel exhausts. Recently, it was reported that the addition of 

hydrogen drastically increases the catalytic activity of Ag/Al 2 O 3 and Ag-exchanged zeolites, such as 

Ag/MFI for the HC-SCR [1-3]. Although numerous spectroscopic studies have focused on the 

hydrogen promotion effect, the role of hydrogen is still under debate. We have proposed that the Ag n 

cluster formed by the hydrogen addition is a key to improve the catalytic activity [2]. On the other 

hand, several spectroscopic studies by other groups have indicated no linkage between the high NOx 

conversion and the formation of Ag n cluster [3]. In order to sheds light on the controversial reaction 

mechanisms ever reported, we have carried out the density functional calculation on the promotion 

effect of H 2 addition in the HC-SCR reaction over the Ag-MFI system. 

PP386 

Towards a 32-electron Principle: Pu@Pb 12 and Related Systems 

Jean-Pierre Dognon, Carine Clavaguéra, Pekka Pyykkö 

1 CEA/Saclay, DSM/IRAMIS/SCM, Gif sur Yvette, France, 2 CNRS/Ecole Polytechnique, Palaiseau, 

France, 3 University of Helsinki, Helsinki, Finland 

The 18-electron principle goes back to Langmuir [1]. Formally it would correspond to fully occupying at 

a central atom its ns, np and (n-1)d orbitals. For early 5f-elements the f-shell becomes chemically 

available and remains so until about Am. Theoretically it could be filled with 14 further electrons, 

bringing the total to 32, a theoretical possibility already evoked by Langmuir. How far towards that limit 

can one go? Thorocene, Th(C 8 H 8 ) 2 , was classified as a ’20e’ case. In the ’metalloactinyl’ compounds, 

like the linear IrThIr 2- , one could potentially reach ’24e’ [2]. 

We now find that the 6p valence band of the recently discovered icosahedral [Pb 12 ] 2- shells forms a 

perfect partner for the 5f shell of an enclosed actinide atom, like plutonium [3]. Detailed DFT 

calculations suggest that the system is viable. It could be on good grounds characterised as a ’32e’ 

system. 

The calculated molecular geometries, an orbital analysis and a bonding energy analysis in term of 

Morokuma-type decomposition will be presented for [Pb 12 ] 2- and [M@Pb 12 ] x- with M=Yb, Th, U, Np, Pu, 

Am, Cm. The orbital-energy spectra, the densities of states and the ELF distribution for [An@Pb 12 ] x- 

(An=Pu, Am, Cm) will be given. Finally, we will propose computed electronic and spectroscopic 

properties for some systems. 

We perform now more studies to extend this concept to the search of new 5f-element clusters in a 

nanoscience context (biology or materials) [4]. 

NBO analysis shows that an Ag atom on the MFI is completely ionic. Therefore, the Ag diffusion on 

the MFI for the cluster formation requires the neutralization of Ag + . Since hydrogen molecule 

heterolytically dissociates between Ag + and oxygen of the MFI with a low activation barrier of 10.7 

kcal/mol, one of the roles of the H 2 addition is to promote the Ag diffusion through the formation of 

AgH. With this process assumed, a HHAg 4 /MFI system 

(Fig.1a) should be an intermediate to form a Ag 4 /MFI 

system (Fig1.b). TD-DFT calculation predicts that three 

strong absorption bands are observed for the Ag 4 /MFI but 

the weak UV absorption for the HHAg 4 /MFI (Fig.2). This 

result indicates that the UV-vis measurements are not 

adequate for the study of the reaction mechanisms if the 

HHAg 4 cluster plays an important role in the HC-SCR 

reaction. 

Several experiments suggest that oxygen should be 

activated for the HC-SCR reaction. No stable structure of 

the activated oxygen on the Ag 4 /MFI system has been 

found in the geometry optimization. On the other hand, the 

HOO - species is exothermically formed from the 

HHAg 4 /MFI + O 2 system (Fig.1c). Since the catalytic cycle 

of the HC-SCR reaction leads to the formation of Ag 4 

cluster, hydrogen addition is essential to reproduce the 

HHAg 4 cluster. This conclusion explains the discrepancies 

ever reported. 

[1]. Langmuir, I. Science 1921, 54, 59-67, this paper mentions the 8, 18 and 32-electron closed shells and uses 

on pp. 65-66 Fe(CO)5, Ni(CO)4 and Mo(CO)6 as examples on 18e. 

[2]. Hrobárik, P.; Straka, M.; Pyykkö, P. Chem. Phys. Lett. 2006, 431, 6-12. 

[3]. Dognon, J. P.; Clavaguéra C.; Pyykkö P. Angew. Chem. Int. Ed. 2007, 46, 1-5 

[4]. Dognon, J. P.; Clavaguéra C.; Pyykkö P. in preparation. 

[1] Satokawa, S. Chem. Lett. 2000, 29, 294-295. 

[2] Shimizu, K; Satsuma, A. Phys. Chem. Chem. Phys. 2006, 8, 2677-2695 and references there in. 

[3] Breen, J.P.; Burch, R. Top. Catal. 2006, 39, 53-58 and references there in.



PP387 

Spin-Orbit Effects on Structures and Vibrational Frequencies of Haloiodomethane Cations and 

Halogentriflorides 

Hyoseok Kim, Yoon Sup Lee 

KAIST, Daejeon, Korea, Republic of 

We have been working on ab initio molecular orbital methods that take spin-orbit and other relativistic 

effects into account without too much computational effort by using two-component relativistic effective 

core potentials (RECPs). The inclusion of spin-orbit effects in the calculations may be important for 

molecules containing halogen atoms, especially for cations containing heavy halogen atoms. 

Calculated structures and vibrational frequencies of haloiodomethane cations CH 2 XI + (X=Cl and Br) 

from conventional density functional theory (DFT) methods without spin-orbit interactions are not in 

agreement with experimental ones which have been determined from MATI experiments by Kim et al. 

[1,2,3]. While, calculated structures and vibrational frequencies of haloiodomethane cations from DFT 

methods with spin-orbit interactions are qualitatively agree well with experimental ones. DFT 

calculations using various functionals with various RECPs and the corresponding basis sets were 

computed to achieve more accurate calculated results compared to experimental results. Other 

halogen series of haloiodomethane cations CH 2 XI + (X=F, I, and At) were also calculated to compare 

the extent of spin-orbit effects on cations containing iodine atoms. 

The effects of spin-orbit interactions and electron correlations on molecular structures and vibrational 

frequencies of halogenflurorides XF 3 (X=I, At, and element 117) were described. Considering spinorbit 

effects and other relativistic effects as well as electron correlations, the structure of IF 3 is found to 

be a C 2v symmetry and the structure of (117)F 3 is found to be a planar D 3h symmetry, which are in 

good agreement with the available estimated data[4,5]. The calculated stable structure of AtF 3 is 

critically dependent upon the basis set and electron correlations applied. AtF 3 is a borderline case 

between the VSEPR structure of IF 3 and the non-VSEPR structure of (117)F 3 . AtF 3 has a local 

minimum in the D 3h symmetry when scalar relativistic effects, spin-orbit interactions, and electron 

correlations are considered together. 

PP388 

Interference Partitioning of the Energy for Generalized Product Functions: N 2 as a Test Case. 

Thiago Messias Cardozo, Marco Antonio Chaer Nascimento 

Instituto de Química - UFRJ, Rio de Janeiro, RJ, Brazil 

The role of quantum mechanical effects in the formation of the chemical bond was first made clear by 

recognizing that interference among one-electron states was the driving force for the bonding 

phenomena [1]. Although the problem of partitioning the energy to obtain the interference contributions 

has been thoroughly discussed [1a], the actual application of the method has been limited to a few 

cases. This has to do with the difficulty in partitioning the density of complex molecules in a chemically 

intuitive and physically meaningful way. 

Here we propose the use of Generalized Product Functions (GPFs) [2] for such an analysis. GPFs are 

a natural choice, since their first order reduced density matrices are blocked by electron group and 

their second order reduced density matrices are neatly partitioned in intergroup and intragroup blocks. 

In particular, by describing valence electron groups with modern Valence Bond methods (GVB, SC, 

etc.), the arbitrariness of the choice for atomic orbitals inherent to the interference partition is removed. 

We derived the conservation relations for the reduced density matrices and the equations for the 

interference partitioning for this type of wavefunction allowing, for instance, in the scope of the σ-π 

separation approximation, the separate analysis of interference contributions of σ and π electrons to 

the molecular energy. We present the interference energy partition for the N 2 molecule as a test case. 

The results were obtained for a wavefunction describing the core and lone-pair electrons at the HF 

level, and the bonding electrons at the GVB-PP level, with a cc-pVTZ basis. 

The interference contribution to the kinetic energy (KX) has a negative sign for both the σ and π 

electron groups, and is the dominant quantum-mechanical term, while the interference potential 

energy (VX) is positive, in agreement with previous calculations of simpler molecules. At equilibrium 

distance, both σ and π electrons are responsible for stabilizing the bond, with the σ electrons total 

interference contribution (EX) being greater than the π electrons EX in module by approximately 

0.07hartree. 

[1] Lee, M.; Kim, H.; Lee, Y. S.; Kim, M. S. Angew. Chem. Int. Ed. 2005, 49, 2929-2931. 

[2] Lee, M.; Kim, H.; Lee, Y. S.; Kim, M. S. J. Chem. Phys. 2005, 122, 244319-1-9. 

[3] Lee, M.; Kim, H.; Lee, Y. S.; Kim, M. S. J. Chem. Phys. 2005, 123, 024310-1-9. 

[4] Schwerdtfeger, P., J. Phys. Chem. 1996, 103, 2968-2973. 

[5] Bae, C.; Han, Y. K.; Lee, Y. S. J. Phys. Chem. A, 2003, 107, 852-858. 

0,1 

0,4 

0,0 

0,2 

A20 

-0,1 

-0,2 

-0,3 

EX(pi bond) 

EX(sigma bond) 

Energy(adj.) 

Energy(hartree) 

0,0 

-0,2 

-0,4 

VX(sigma) 

VX(pi) 

Energy(adj) 

KX(sigma) 

KX(pi) 

-0,4 

1 2 3 4 5 

-0,6 

1 2 3 4 5 

A1 

Internuclear distance (Angstrom) 

[1] (a) Ruedenberg, K. Rev. Mod. Phys. 1962, 34, 326-376. (b) Wilson, C. W.; Goddard III, W. A. Theoret. Chim. 

Acta 1972, 26, 195-210 

[2] (a) McWeeny, R. Proc. Roy. Soc. Lond. 1959, A253, 242-259. (b) Li, J.; McWeeny, R. Int. J. Quantum Chem. 

2002, 89, 208-216



PP389 

Canonical Transformation Theory: Review and Application to Transition Metal Oxides 

Eric Neuscamman, Takeshi Yanai, Garnet Chan 

1 Cornell Department of Chemistry and Chemical Biology, Ithaca, NY, United States, 2 Institute for 

Molecular Science, Nishigo-Naka, Myodaiji, Okazaki, Japan, 3 Cornell Department of Chemistry and 

Chemical Biology, Ithaca, NY, United States 

Canonical Transformation (CT) Theory [1,2] is a new approach for treating dynamic correlation in 

multireference systems. Based on a unitary, multireference, exponential ansatz, its accuracy for 

calculations on water, nitrogen, and metal-oxides is competitive with state-of-the-art multireference 

methods, while its cost is proportional to second order multireference perturbation theory. CT theory’s 

central approach is to approximate three and higher body operators produced by the Baker-Campbell- 

Hausdorff expansion using one and two body operators. Through the framework of extended normal 

ordering [3], this approximation is similar to neglecting the effect of three and higher body connected 

excitations. The result is an energy expression that contains no reduced density matrices higher than 

second order. Natural connections exist between CT and state-specific multireference coupled cluster 

theory [3] as well as recent formulations of the anti-hermitian contracted Schroedinger equation [4]. 

Absolute energies for TiO, MnO, FeO, and NiO are comparable to those produced by the MRCI+Q, 

ACPF, and AQCC methods, much more so than energies computed by CASPT2 and CASPT3. 

Current work focuses on developing a straightforward solution condition to overcome the numerical 

difficulties presented by a highly linearly dependent first order interaction space. 

[1] Yanai, T. and Chan, G. J. Chem. Phys. 2006, 124, 194106 

[2] Yanai, T. and Chan, G. J. Chem. Phys. 2007, 127, 104107 

[3] Kutzelnigg, W. and Mukherjee D. J. Chem. Phys. 1997, 107, 432-449 

[4] Mazziotti, D. Phys. Rev. Lett. 2006, 97, 143002 

PP390 

Temperature and Isotope Effects on Water Cluster Ions with Path Integral Molecular Dynamics 

Suzuki Kimichi 1 , Shiga Motoyuki 2 , Tachikawa Masanori 1 

1 Quantum Chemistry Division, Graduate School of Science, Yokohama-City University, Seto 22-2, 

Kanazawa-ku, Yokohama, Japan, 2 CCSE, Japan Atomic Energy Agency, Higashi-Ueno 6-9-3, Taitoku, 

Tokyo, Japan 

To analyze the temperature dependency of geometrical isotope effect (GIE) on water cluster ions, we 

have combined path integral molecular dynamics (PIMD) and 4th order correction of Trotter expansion 

[1,2]. Although quiet huge number of beads is required at low temperature in the conventional PIMD 

method, our approach can provide accurate description of the quantum system with less number of 

- 

+ 

beads. In this paper, we show the results of temperature dependency of GIE on H 3 O 2 and H 5 O 2 

species. 

Figure 1 shows schematic illustration of H 3 O - 2 . Figure 2 

δ OH* = r 1 – r 2 

- 

shows one-dimensional distribution on H 3 O 2 with 

R 

respect to the δ OH* at 50 and 400K, where δ OH* is 

OO 

defined as the difference of r 1 and r 2 . Apart from the 

r 1 r 

“quantum simulation” by PIMD calculation, the 

H* 

2 

“classical simulation” has been also performed with the 

Figure 1. Schematic illustration of H 3 O 2- . 

condition of 1 bead. For convenience, proton and triton substitutions are labeled as “H-species” and 

“T-species” in quantum simulation, respectively. In Figure 2 a), the distribution of classical simulation 

has double peaks, since it is difficult for the central proton to go over the potential barrier at δ OH* =0. As 

the temperature becomes higher, the distribution at δ OH* =0 is gradually increased as shown Figure 2 

b). 

On the other hand, in the quantum simulation we can find that 

distributions of H and T species have single peak at 50K, since 

these species completely go over the potential barrier at δ OH* =0 

by both thermal and nuclear quantum effects. Figure 2 b) shows 

distribution of T-species is double peaks at 400K, while that of 

H-species is still single peak. This result means that hydrogen 

bonded triton is located at closer to either oxygen atoms, since 

the potential barrier height at δ OH* =0 becomes higher as the 

elongation of bond length between two oxygen atoms (R OO ). 

Actually, GIE with respect to the R OO is clearly different between 

low and high temperatures. Average bond length between two 

oxygen atoms () of H-species is longer than that of T- 

species at low temperature, while the inverse relation is 

observed at high temperature. We have found that GIE at low 

temperatures is due to the difference of zero point vibration, 

while multidimensional effect which is coupled between proton 

transferring and oxygen-oxygen stretching motions should be 

indispensable at high temperatures. Further detail will be 

presented on my poster session. 

Distribution 

a) 50K 

b) 400K 

H-species 

T-species 

classical 

-1.2 -0.6 0.0 0.6 1.2 

δ OH* (Å) 

Figure 2. 1D distributions of δ OH* 

in H 3 O 2- at a) 50K and b) 400K. 

[1] Takahashi, M.; Imada, M. J. Phys. Soc. Jpn., 1984, 53, 3765. 

[2] Li, X-P.; Broughton, J. Q. J. Chem. Phys., 1987, 86, 5094.



PP391 

Molecular Dynamics Simulation of Photodesorption Process of CO Ice 

Junko Takahashi 1 , Marc van Hemert 2 

1 Meiji Gakuin University, Tokyo, Japan, 2 Leiden Institute of Chemistry, University of Leiden, Leiden, 

Netherlands 

At such a low density and temperature in interstellar space, gaseous CO is still detected, although all 

molecules other than H 2 should be kept frozen on dust grains within the timescale shorter than the 

cloud lifetime. Since thermal desorption is negligible, photodesorption has been suggested as a 

possible mechanism to explain the abundance of CO in interstellar gas phase. In the laboratory, this 

process has been simulated by depositing CO on a 10 K surface and following CO desorption upon 

irradiation of a D 2 discharge lamp [1]. 

In order to analyze this process theoretically, we have performed a classical molecular dynamics 

simulation on CO photodesorption from an amorphous cluster of a few hundred CO molecules as a 

model of a piece of interstellar dust grain. All simulations were performed on the non-periodic systems. 

The equations of motion were integrated according to the velocity-Verlet algorithm. The system 

temperature was set at 10-40 K, the typical temperatures in interstellar clouds. 

We have constructed a force field by performing ab initio coupled cluster calculations for the CO dimer 

on a large grid of orientations and inter- and intramolecular distances. In order to get a potential 

energy surface in a useful form for MD simulation, we fit about 15000 data points to a potential energy 

function consisting of Lennard-Jones parameters and site point charges. We also fit the intramolecular 

potential of the individual CO molecule to a Morse-type function. 

At the first step of MD simulation, we made amorphous CO clusters. The initial loose geometries were 

generated on a one by one basis by minimizing the interaction energy of the newly arriving CO with 

the CO molecules already present with a simplex method. After about 50 ps MD simulation, we 

obtained stable amorphous CO clusters. 

At the second step, we excited a selected CO molecule in a CO 

cluster with a 9-10 eV photon. This energy is insufficient to break the 

C-O bond, but there are several electronically excited states in this 

energy region. The dominant excitation is X 1 Σ + to A 1 Π. We translated 

the photon energy into ground or excited state vibration by extending 

the intramolecular distance of the CO molecule to a value 

corresponding to the outer turning point of the Morse oscillator. 

We assumed the following two mechanisms; (1) Instantaneous internal conversion; (2) Internal 

conversion with a relaxation period. In the first mechanism, the excited CO molecule does not 

propagate on the excited state potential energy surface, and there were no resulting trajectories of CO 

desorption. On the other hand, in the second mechanism, the excited CO propagates on the excited 

state potential energy surface, and we observed several trajectories of CO desorption where the 

excited CO or a neighbouring CO molecule was kicked out from the CO cluster. The latter case 

severely depends on the pair potential for the ground state CO and the excited state CO. We are still 

developing this potential energy function. In the poster, we will show the latest results of the potential 

energy functions and the MD simulation. 

[1] Öberg, K. I.; Fuchs, G. W.; Awad, Z.; Fraser, H. J.; Schlemmer, S.; van Dishoeck, E. F.; Linnartz, H. 

Astrophys. J., 2007, 662, L23-L26. 

PP392 

HERON Reaction of N-Acyloxy-N-alkoxyamides — Theoretical and Experimental Study 

Stephen Glover 

School of Science and Technology, University of New England, Armidale, N.S.W., Australia 

Anomeric amides 1 are amides bearing two heteroatoms at the amide nitrogen [1-3]. They are 

pyramidal at nitrogen and behave as N-acylamines in all respects. They undergo the HERON 

rearrangement, which is anomerically driven by a lone pair destabilisation of the N-Y bond by the less 

electronegative atom X [4, 5]. 

R 

O 

C N 

1 

X 

Y 

R C O 

X 

N Y N Y 

Figure 1. HERON reaction of an anomeric amide. 

HERON has mainly been observed for NNO, systems. However, ONO systems in the form of N- 

acyloxy-N-alkoxyamides (1, Y=OR, X=Oacyl) have recently been found to undergo the rearrangement 

affording anhydrides and alkoxynitrenes. 6 

The reaction has been modelled at the B3LYP/6-31G* level using N-formyloxy-N-methoxyformamide 2 

and DFT calculations predict the rearrangement to favour migration of the formyloxy group over the 

methoxyl group. The energetics of reaction pathways have been deduced and are in line with the 

significant energy requirement of the reaction, which with N-acyloxy-N-alkoxyamides is found to occur 

above 90°C in non-polar toluene. 

H 

O 

E 

O 

A =39 kcal mol -1 

O 

O 

O 

N OMe 

H 

H H 

H 

O 

N 

O C 

C H 

O 

MeO 

N OMe 

O 

(2) (3) (4) 

[1] Glover, S. A.; Rauk, A. J. Org. Chem. 1996, 61, 2337. 

[2] Glover, S. A. Tetrahedron 1998, 54, 7229. 

[3]Glover, S. A.; Rauk, A. J. Org. Chem. 1999, 64, 2340. 

[4] Glover, S. A.; Rauk, A.; Buccigross, J. M.; Campbell, J. J.; Hammond, G. P.; Mo, G.; Andrews, L. E.; Gillson, 

A.-M. E. Can. J. Chem. 2005, 83, 1492. 

[5] Glover, S. A., HERON Rearrangement. In Merck Index, Organic Name Reactions ONR-43, 14 ed.; O'Neil, M. 

J., Ed. Merck & Co., Inc.: Whitehouse Station, N.J., 2006. 

[6] Glover, S. A., N-Acyloxy-N-alkoxyamides —Structure, Properties, Reactivity and Biological Activity. In Adv. 

Phys. Org. Chem., Richard, J., Ed. Elsevier: London, 2007; Vol. 42, p35.



PP393 

A Linear-Scaling Spectral-Element Method for Computing Electrostatic Potentials 

Mark A. Watson, Kimihiko Hirao 

Department of Applied Chemistry, The University of Tokyo, Tokyo, Japan 

A new linear-scaling method for the fast numerical evaluation of the electronic Coulomb potential is 

presented. Our work is an extension of the low-scaling algorithm introduced by Sundholm 

[J.Chem.Phys.122, 194107 (2005), J.Chem.Phys.126, 094101 (2007)] which obtains the electrostatic 

potential of an arbitrary density by direct summation of differential contributions avoiding the solution 

of Poisson's equation. The current work describes three main improvements. Firstly, we replace the 

uniform finite-element (FE) representation with a high-order spectral expansion in a tensorial basis of 

Chebyshev polynomials. We show that the new basis can converge the Coulomb energy to an 

accuracy 1000 times higher than the FE representation for the same number of expansion 

coefficients, or, alternatively, for a target accuracy of one part per million, 8 times fewer coefficients 

are required, which implies a 16-fold reduction in CPU time when using the basic O(N 4/3 ) algorithm. 

Secondly, we reduce the scaling to the true O(N) regime by combining the numerical algorithm with 

the fast multipole method for distant interactions. Thirdly, we explore further ways to increase the 

efficiency using adaptive resolution for different regions of space. Finally, benchmark calculations to 

demonstrate the above improvements are reported. 

PP394 

Automatized Derivation and String-Based Evaluation of Explicitly Correlated Wavefunctions 

Andreas Köhn, Gareth Richings 

University of Mainz, Institute of Physical Chemistry, D-55099 Mainz, Germany, Germany 

The inclusion of terms in the wavefunction ansatz that explicitly take into account the interelectronic 

cusp condition has been shown to greatly improve the basis-set convergence of the correlation 

energy, for a review see e.g. [1]. One draw-back of such methods, however, is the increasing 

complexity of the final expressions. This makes it difficult to implement new wavefunction models “by 

hand” in a computer code which is both sufficiently fast and error-free. 

Here, we present the program GeCCo, which provides tools to set up and manipulate the explicit 

expressions that arise from wavefunction models that can be treated in second quantization. In 

particular, the program features a compact, yet considerably efficient kernel for the numerical 

evaluation of these expressions which uses the string-based approach [2,3] for addressing arbitrarily 

indexed quantities with high permutational symmetry. 

As applications, we will discuss the implementation of explicitly correlated higher-order coupled-cluster 

methods and the development of explicitly correlated excited-state methods. 

[1] W. Klopper, F. R. Manby, S. Ten-no, and E. F. Valeev, Int. Rev. Phys. Chem. 2006, 3, 427 

[2] W. Duch, J. Phys. A. 1985, 18, 3283 

[3] (a) M. Kállay and P. R. Surján, J. Chem. Phys. 2001, 115, 2945; (b) A. Köhn and J. Olsen, J. Chem. Phys. 

2006, 125, 17411



PP395 

Conical for Stepwise, Glancing for Concerted: The Role of Excited State Topology in Threebody 

Dissociation of sym-Triazine 

Vadim Mozhayskiy, Anna I. Krylov 

University of Southern California, Chemistry Department, Los Angeles, CA, United States 

We investigated the highly debated three-body dissociation of sym-triazine to three HCN products. 

Two dissociation channels are present in the experiment: stepwise and concerted. Calculated state 

energies and electronic couplings suggest that sym-triazine is produced in the 3s Rydberg and π*←n 

and manifolds. Analysis of the topology of these manifolds along with momentum correlation in the 

dissociation products suggest that the 3s Rydberg manifold is characterized by a conical intersection 

of two potential energy surfaces and leads to stepwise dissociation, while the π*←n manifold consists 

of a four-fold glancing intersection that leads to a symmetric concerted reaction. 

PP396 

Enzymic H-Tunnelling – A Role for Promoting Vibrations? 

Linus O. Johannissen 1 , Micheal J. Sutcliffe 1 , Nigel S. Scrutton 2 

1 School of Chemical Engineering and Analytical Science, Manchester Interdisciplinary Biocentre, 

University of Manchester, Manchester, United Kingdom, 2 Faculty of Life Sciences, Manchester 

Interdisciplinary Biocentre, University of Manchester, Manchester, United Kingdom 

Our understanding of enzyme catalysis has evolved tremendously since the early lock-and-key model. 

It is now well established that enzymes are inherently dynamic molecules, undergoing a wide range of 

internal motions – from sub-picosecond atomic fluctuations to nanosecond domain motions and even 

millisecond conformational rearrangements. Nevertheless, the current text-book picture of enzyme 

catalysis – transition state complementarity – is still very much static, and the role of such motions in 

the catalytic process is currently the centre of heated debates. In particular, it has come to light over 

the past decade or so that enzymically-catalysed H-transfers, which involve nuclear quantum 

tunnelling to varying degrees, are influenced by thermally activated vibrations, but the nature and role 

of these vibrations are not well established. According to one school of thought, collective, thermally 

equilibrated motions are required to attain quantum degeneracy between the reactant and product 

states, while faster “promoting” vibrations can enhance the probability of tunneling by compressing the 

donor-acceptor distance once such a state has been achieved. The concept of promoting vibrations is 

contentious, however, and their involvement in the catalytic effect unclear. For example, donoracceptor 

compressions might be caused by stochastic fluctuations rather than a specific vibrational 

mode; additionally, similar compressions might occur in solution-based reactions. We present results 

from molecular modelling studies of the role of promoting vibrations, using the H-transfer steps from 

the reactions catalysed by aromatic amine dehydrogenase and morphinone reductase as examples. In 

particular, molecular dynamics simulations are used to observe how enzyme motions impact the active 

site, and hybrid molecular mechanical / quantum mechanical methods are used to analyse how these 

motions affect the H-transfer barrier. 

[1]. Johannissen, L.O., Scrutton, N.S., Sutcliffe, M.J. The enzyme aromatic amine dehydrogenase induces a 

substrate conformation crucial for a promoting vibration that significantly reduces the effective potential energy 

barrier to proton transfer. J. Roy. Soc. Interface. In press. 

[2]. Johannissen, L.O., Hay, S., Scrutton, N.S., Sutcliffe, M.J. Proton tunneling in aromatic amine dehydrogenase 

is driven by a short-range sub-picosecond promoting vibration: Consistency of simulation and theory with 

experiment. J. Phys. Chem. B 2007, 111, 2631-2638. 

[3]. Masgrau L., Roujeinikova A., Johannissen L.O., Hothi P., Basran J., Ranaghan K.E., Mulholland A.J., Sutcliffe 

M.J., Scrutton N.S., Leys D. Atomic description of an enzyme reaction dominated by proton tunneling. Science 

2006, 312, 237-241.



PP397 

Calculation of the Effective Chemical Shielding Anisotropy in L-alanyl-L-alanine, 

Conformational and Charge dependence study 

Ladislav Benda 1 , Petr Bouř 1 , Norbert Müller 2 , Vladimír Sychrovský 1 

1 Institute of Organic Chemistry and Biochemistry, Molecular Spectroscopy Group, Praha, Czech 

Republic, 2 Johannes Kepler University, Institute of Organic Chemistry, Linz, Austria 

The high-resolution nuclear magnetic resonance (NMR) spectroscopy is a powerful tool for the 

molecular structure determination. Theoretical modeling of NMR parameters can complement the 

NMR experiment and allows accurate predictions of structural parameters and dynamical behavior of 

biomolecular compounds. Recently we determined the structure of the L-alanyl-L-alanine di-peptide 

(A) on the basis of complete assignment of isotropic chemical shifts and scalar coupling constants [1]. 

There is, however, additional structural information contained in the anisotropy of the chemical 

shielding tensor (CSA) that can be accessed through the measurement of NMR relaxation 

parameters. The cross-correlated relaxation rates (CCRR) are important NMR relaxation parameters 

that depend on both CSA and local geometry. A reliable structural interpretation of the CCRRs still 

requires theoretical modeling [2]. 

In this work we correlated the effective CSAs calculated for atoms along the peptide backbone with its 

major descriptors, the torsion angles phi, psi (A, B). Further we investigated the dependence of the 

effective CSAs on total charge of the di-peptide (anion, zwitterion, cation) that can be experimentally 

accessed at different pH (~12, ~7, ~2, respectively). The geometries were optimized at the BPW91 / 6- 

311++G** level employing the PCM solvent model for all three forms of the di-peptide. The NMR 

parameters were calculated using the B3LYP / IGLO-III / PCM approach. The calculated surfaces of 

effective CSA can improve interpretation of the cross-correlated relaxation rates in peptides. 

PP398 

Insights into the Structural Basis of N2 and O6 Substituted Guanine Derivatives as Cyclin- 

Dependent Kinase 2 (CDK2) Inhibitors: Prediction of the Binding Modes and Potency by 

Docking and ONIOM Calculations 

Jans Alzate-Morales, Julio Caballero Ruiz, Ariela Vergara, Fernando Danilo González Nilo 

Bioinformatics and Molecular Simulation Centre, University of Talca, Talca, Region VII, Chile 

The cyclin dependent kinases (CDKs) are a class of enzymes which play a fundamental role in cell 

cycle regulation [1]. The aberrant CDK control and consequent loss of cell cycle checkpoint function 

have been directly linked to the molecular pathology of cancer [2]. One of the medical strategies to 

face this pathology is using synthetic inhibitors. For example, N2 and O6 substituted guanine 

derivatives are well known as potent and selective CDK2 inhibitors [3]. The ability of molecular 

docking, using the program AutoDock3 [4], and the hybrid method ONIOM [5] to obtain some quantum 

chemical descriptors, with the aim to successfully rank these inhibitors (80 compounds), was 

assessed. The quantum chemical descriptors were used to explain the affinity, of the series studied, 

by a model of the CDK2 binding site. The initial structures were obtained from docking studies and 

the ONIOM method was applied with only a single point energy calculation on the protein-ligand 

structure. We obtained a good correlation model between the ONIOM derived quantum chemical 

descriptor “H-bond Energy” and the experimental biological activity, with a correlation coefficient value 

of R = 0.80 for 75 compounds. To the best of our knowledge, this is the first time that both 

methodologies are used in conjunction in order to obtain a correlation model. The model suggests that 

electrostatic interactions are the principal driving forces in this protein-ligand interaction. Overall, the 

approach was successful for the cases considered and suggests that this may be useful for the design 

of inhibitors in the lead optimization phase of drug discovery. 

(A) (B) 

9 

R = 0.80 

N = 75 

Figure could 

not be 

loaded 

Log (10 6 /IC 50 

) 

8 

7 

6 

5 

4 

-10 -15 -20 -25 -30 -35 -40 -45 

ONIOM[(High, A)+(Mid, AB-A)] Energy (kcal/mol) 

[1] (a) Bouř, P.; Buděšínský, M.; Špirko, V.; Kapitán, J.; Šebestík, J.; Sychrovský, V. J. Am. Chem. Soc. 2005, 

127, 17079-17089. (b) Sychrovský, V.; Buděšínský, M.; Benda, L.; Špirko, V.; Vokáčová, Z.; Šebestík, J.; Bouř, P. 

J. Phys. Chem. B 2008, 112, 1796-1805. 

[2] (a) Reif, B.; Diener, A.; Hennig, M.; Maurer, M.; Griesinger, C. J. Magn. Reson. 2000, 143, 45–68. (b) 

Sychrovský, V.; Müller, N.; Schneider, B.; Smrečki, V.; Špirko, V.; Šponer, J; Trantírek, L. J. Am. Chem. Soc. 

2005, 127, 14663-14667. 

[1] Morgan, D. O. Nature 1995, 374, 131-134. 

[2] Hall, M.; Peters, G. Adv Cancer Res 1996, 68, 67-108. 

[3] Hardcastle, I. R.; Arris, C. E.; Bentley, J.; Boyle, F. T.; Chen, Y. et al. J Med Chem 2004, 47, 3710-3722. 

[4] Garrett M. Morris, D. S. G., Robert S. Halliday, Ruth Huey, William E. Hart, Richard K. Belew, Arthur J. Olson. 

Journal of Computational Chemistry 1998, 19, 1639-1662. 

[5] Dapprich, S.; Komaromi, I.; Byun, K. S.; Morokuma, K.; Frisch, M. J. Journal of Molecular Structure: 

THEOCHEM 1999, 461-462, 1-21.



PP399 

New Implementation and Parallelization of DMRG: Towards Large-Scale Multireference 

Electronic-Structure Calculations 

Yuki Kurashige, Takeshi Yanai 

Institute for Molecular Science, Okazaki, Aichi, Japan 

Recently, Density Matrix Renormalization Group (DMRG) algorithm, which was invented to solve 

quantum lattice problems, has been applied to solution of the electronic Schrodinger equation with ab 

initio Hamiltonian [1]. Ab initio DMRG is especially expected to be a robust alternative to CASCI 

method for large-scale multireference problems that cannot be handled by the conventional CI. As can 

be seen in past ab initio DMRG studies by Chan's group [2], the DMRG approach is successful in 

dealing with large-scale multireference correlation, particularly, in long chain π-conjugated molecules 

that are spatially quasi-one-dimensional. For the π-conjugated systems, the one-dimensional 

correlation in π space is easily described by a small number of the renormalized correlation basis, the 

number of which interestingly remains small (e.g. 300-500) for yielding the certain accuracy no matter 

how long the system grows. Targeting the large-scale multireference problems for general molecular 

systems, say the polyatomic complexes containing transition metals, however, it seems to be still an 

open question whether ab initio DMRG can accurately describe the complicated strong electron 

correlation in such systems where the one-dimensionality of the correlation structure is absent while 

the exponentially-growing number of necessary renormalized correlation basis is marked contrast to 

one-dimensional situation. To investigate and extend the applicability of ab initio DMRG to such 

problems, we have developed a highly efficient algorithm which can take full advantage of point-group 

symmetry and have exploited a new parallelism that allows for maintaining a large number of 

renormalized basis for the correlation space. 

[1] (a) White, S. R.; Martin, R. L. J. Chem. Phys. 1999, 110, 4127. (b) Mitrushenkov, A. O.; Fano, G.; Ortolani, F.; 

Linguerri, R.; Palmieri, P. J. Chem. Phys. 2001, 115, 6815. (c) Chan, G. K.-L.; Head-Gordon, M. J. Chem. Phys. 

2002, 116 4462. (d) Legeza, Ö; Röder, J.; Hess, B. A. Phys. Rev. B 2003, 67, 125114. (e) Moritz, G; Reiher, M. 

J. Chem. Phys. 2007, 126, 244109. (f) Zgid, D.; Nooijen, M. J. Chem. Phys. 2008, 128, 014107. 

[2] (a) Hachmann, J.; Cardoen, W.; Chan, G. K.-L. J. Chem. Phys. 2006, 125, 144101. (b) Hachmann, J.; 

Dorando, J. J.; Avilés, M.; Chan, G. K.-L. J. Chem. Phys. 2007, 127, 134309. (c) Ghosh,D.; Hachmann, J.; Yanai, 

T.; Chan, G. K.-L. J. Chem. Phys. 2008, 128, 144117. 

PP400 

Hybrid Functionals and Møller-Plesset Perturbation Theory applied to Extended Systems 

Joachim Paier, Andreas Grueneis, Martijn Marsman, Georg Kresse 

University of Vienna, Computational Materials Physics, Vienna, Austria 

The main advantage of density functional theory (DFT) is its computational efficiency, i.e., at the 

moment no other ab-initio method provides results at such low computational cost combined with 

reasonable accuracy. Therefore, DFT has found its undisputed place for many applications in solid 

state physics as well as quantum chemistry. 

Of course, DFT in its LDA and GGA flavours still does not provide final and decisive answers to some 

of the most delicate problems in computational physics and chemistry: E.g., reaction energies and 

barriers of chemical reactions are wrong by up to 100 kJ/mol (= 1 eV/f.u.), some semiconductors are 

predicted to be metals, correlated oxides are not well described, equilibrium volumes and elastic 

constants are generally wrong by several percent and dispersion interactions are not properly 

accounted for. In order to improve and to include the yet lacking physics a possible strategy seems to 

be the inclusion of (exact) Hartree-Fock exchange together with a compatible correlation energy, e.g., 

by N th -order Møller-Plesset (MPN) perturbation theory. Note that MP2 is almost routine in quantum 

chemistry but due to the computational cost involved hardly ever applied to extended systems. 

Recently, the nonlocal Fock operator as well as 2 nd -order Møller-Plesset perturbation theory (MP2) 

were implemented within the framework of the full-potential projector augmented plane-wave using 

periodic boundary conditions and a plane-wave basis set. 

The poster summarizes some of the latest post-DFT results obtained using the projector augmented 

plane-wave code VASP (Vienna ab-initio simulation package). We present lattice constants, bulk 

moduli, atomization energies and band gaps obtained using the HSE06 Hartree-Fock/DFT hybrid 

functional applied to several representative semiconducting and insulating systems. Secondly, 

emphasis is put on the performance of hybrid functionals when applied to metallic systems. Finally, 

lattice constants, bulk moduli, atomization energies and band gaps of several semiconductors and 

insulators obtained using MP2 are presented.



PP401 

Molecular Docking with Accurate Polarizable Charges: A QM/MM Approach in Discovery Studio 

Jiabo Li, Al Maynard, Jurgen Koska, George Fitzgerald, Dipesh Risal, Paul Kung, Jon Sutter, Paul 

Flook 

Accelrys Inc, San Diego, United States 

The importance of using accurate polarizable charges in molecular docking has been recognized in 

recent studies. A major defect of using fixed force field charges in docking is that it lacks the flexibility 

to reflect the electrostatic polarization of proteins and ligands. In this study, a novel docking method 

using accurate electric charges of ligands derived from quantum mechanical calculations has been 

reported. This method has been implemented in Discovery Studio 2.1, the most comprehensive 

platform for life science applications [1]. Validation studies are also reported. 

PP402 

Ionization Energy of 1-Hydroxyethyl Radical: The Effects of Hyperconjugation 

Boris Karpichev, Hanna Reisler, Anna Krylov, Kadir Diri 

University of Southern California, Department of Chemistry, Los Angeles, CA, United States 

Experimental studies on the hydroxymethyl and 1-hydroxyethyl radicals have revealed an unusually 

large difference in their ionization energies (IE). The expected decrease in the IE of the latter radical 

due to its larger size does not fully account for the experimentally observed difference of 0.92 eV. In 

this work we investigated the problem with the aid of electronic structure calculations. It is found that 

the large drop in the IE of 1-hydroxyethyl radical stems from the combined effects of the 

destabilization of its highest occupied molecular orbital and the stabilization of the corresponding 

cation due to hyperconjugation. This qualitative picture is in agreement with a simple Hückel-like 

approach and is also verified with Natural Bond Orbital calculations. 

[1] Discovery Studio 2.1, Accelrys Inc, San Diego, 2008



PP403 

Oxidase Catalysis Beyond Biology: A Density Functional Theory Investigation of 

N-Methyl-Imidazole (and Acetate) Complexes of First-Row Transition Metal Ions 

Ivan Taylor, Stephen Colbran, Gary Willett 

School of Chemistry, University of New South Wales, Sydney NSW, Australia 

Imidazolyl (His) and carboxylate (Asp or Glu) ligand environments distinguish the active sites of many 

metalloproteins that activate dioxygen for constructive biological reactions or deactivate reactive 

reduced oxygen species which are deleterious in living systems. Examples include the characteristic 2 

His + 1 carboxylate triad of non-heme iron oxygenases, the iron and copper centres within soluble and 

particulate methane monooxygenases, respectively, and the manganese, iron and nickel centres in 

the respective superoxide dismutase [1]. The study of metal centres with imidazole and carboxylate 

ligands is the key to understanding the physical processes behind catalysis by the aforementioned 

metalloproteins. Looking more widely, questions about how analogous complexes of transition metal 

ions not utilised in biological systems would behave in dioxygen activation reactions have not before 

been addressed. 

Using N-methyl imidazole (N-MeIm) and acetic acid (HOAc) as analogues for histidine and for aspartic 

and glutamic acids, respectively, the first-row transition metal (Sc through Zn) complexes [M(N- 

MeIm)] n+ , [M(N-MeIm) 2 ] n+ , [M(N-MeIm) 3 ] n+ , [M(N-MeIm)(OAc)] n+ and [M(N-MeIm) 2 (OAc)] n+ have been 

modelled using Density Functional Theory. These species and their reactions can also be observed 

and studied in the gas phase by mass spectrometry. The geometric and electronic structures of these 

metal complexes and, in addition, the charge balance between the metal ion and its ligand(s) [2] have 

been studied in order to elucidate the chemical reasons for the prolific utilisation of such species in 

metalloprotein active sites. 

Periodic trends are observed in the charge donation across the first-row transition metal complexes, 

possibly correlating with the catalytic activity of these metal centres. 

[1] See, for example: Kovacs, J. A. Science, 2003, 299, 1024-1025. Schwartz, J. K.; Rosenzweig, A. C.; 

Frederick, C. A.; Lippard, S. J.; Nordlund, P. Nature 1993, 366, 537-543. Solomon E. I. et al. J. Am. Chem. Soc. 

2008, 130, 7098-7109. Yoshizawa K.; Shiota Y. J. Am. Chem. Soc., 128, 9873 -9881. Gherman B.F. et al. J. Am. 

Chem. Soc. 2001, 123, 3836-3837. Lieberman, R. L.; Rosenzweig, A. C. Nature, 2005, 434, 177-182. Miller, A.- 

F., and Sorkin, D. L. Comments Mol. Cell. Biophys. 1997, 9, 1-48. 

[2] Solomon E. I.; Gorelsky S. I.; Dey A. J. Comp. Chem. 2006, 27, 1415-1428. 

PP404 

Development of the Translational and Rotational Free Quantum Monte Carlo Method 

Yukiumi Kita 1 , Ryo Maezono 2 , Masanori Tachikawa 1 

1 Yokohama city University, Yokohama, Kanagawa, Japan, 2 School of Information Science, Japan 

Advanced Institute of Science and Technology, Nomi, Ishikawa, Japan 

The quantum nature of the light particle (proton and deuteron etc.) has important effects on the many 

research fields. Representative topics include the hydrogen/deuterium isotope effect observed in redshift 

of vibrational frequencies [1], shift of chemical reaction rates [2], the Ubbelohde effect [3], and 

drastic shift in the structural phase transition temperature for hydrogen-bonded dielectric materials [4]. 

Especially, hydrogen cluster and its isotope (H 2 , HD and H 3 + etc.) are one of the system in which the 

nuclear quantum effect appears in dominantly. 

For such systems in which we cannot use the Born–Oppenheimer approximation for nuclei, two 

distinct theoretical approaches are available. One is the method using the internal coordinate which 

allows us to analyze theoretically only physical quantities depending on internal coordinates [5]. The 

other approach is the method using the modified Hamiltonian defined by, 

where the first two terms are the kinetic and Coulomb interaction energies for N-particle system, 

respectively. The last two terms are the kinetic energy of the center of mass of N-particle system and 

the rotational energy of the system around the center of mass, respectively. Thus, H TRF means the 

internal energy of the N-particle system. This theoretical approach using H TRF , which was first 

proposed by Nakai et al. with the ab initio molecular orbital technique [6], has the generalized 

frameworks for various systems containing only quantum particles and the ease for generating the trial 

wave function used in quantum Monte Carlo method in contrast to the former. 

In this study, we developed the translational and rotational free quantum Monte Carlo [TRF-QMC] 

method which means the variational and diffusion Monte Carlo method under the Hamiltonian H TRF 

using the trial wave function obtained by ab initio Multi-Component Molecular Orbital method [7], and 

applied to the system of the positronium and 

HD as benchmark models for this method, and 

H + -0.18908(4) 

3 system. 

TF: translational free 

VMC 

TRF: translational & rotational free 

Figure 1 shows the total energy of the 

positronium obtained by our methods. From 

this figure, we found that the diffusion Monte 

-0.249476(9) 

Carlo method with the translational and 

TF-VMC 

rotational free technique gives the exact 

-0.249627(7) 

internal energy of this system. The results of 

TRF-VMC -0.24992(6) 

HD and H + -0.25 

3 will be shown in the presentation. 

TRF-DMC exact 

Energy [a.u.] 

Fig.1: Total energy of positronium by TRF-QMC method 

[1] N. D. Sokolov, M. V. Vener, and V. A. Savel’ev, J. Mol. Struct. 1990, 222, 365. 

[2] Reaction Rate of Isotopic Molecules, edited by L. Melander and W. H. Saunders (Wiley, New York, 1980). 

[3] A. R. Ubbelohde and K. J. Gallagher, Acta. Cryst. 1995, 8, 71. 

[4] N. Dalal, A. Klymachyov, and A. Bussmann-Holder, Phys. Rev. Lett. 1998, 81, 5924. 

[5] D. B. Kinghorn and L. Adamowicz, J. Chem. Phys. 2000, 113, 4203. 

[6] H. Nakai, M. Hoshino, K. Miyamoto and S. Hyodo, J. Chem. Phys. 2005, 122, 164101. 

[7] M.Tachikawa; Chem. Phys. Lett. 2001, 350, 269.



PP405 

Fragmentation of Peptide Radical Cations: Proton Scissors vs. Proton Patches 

Galina Orlova, Matthew MacLennan 

St. Francis Xavier University, Department of Chemistry, Antigonish, NS, Canada 

Collision-induced dissociation (CID) of peptide radical cations is becoming a powerful mean in mass 

spectrometry for structural determination and proteomics. The fragmentation behaviour of radical 

cations is different from that of protonated species. The fragmentation mechanism of protonated 

peptides is based on the “proton scissors” model developed over the last two decades [1]. According 

to this model, a proton hops with low activation barriers between the basic centres of a peptide 

weakening the skeletal bonds. For example, the cleavage of an amide bond is rationalized by the 

protonation at the nitrogen of the peptide bond followed by low-barrier dissociation. 

The fragmentation mechanism of peptide radical cations is not yet fully understood. There exist 

competitive radical-induced and charge-directed fragmentations observed experimentally, the latter is 

rationalized in terms of “proton scissors” model [2]. We performed QM/CPMD study of spontaneous 

and low-barrier (ca. 10 kcal/mol) fragmentations of radical-cationic amino acids Thr +• (loss of CH 2 C=O 

and CH 2 C=OH + ), Arg +• and Asn +• (loss of CO 2 ), and Trp +• (loss of cationic side chain, 3-methylene 

indolenine). QM at the B3LYP/6-311+G(d,p) level predicts that loss of neutral fragments is driven by 

proton transfer, in accord with the proton scissors model. However, molecular dynamics simulations 

showed that the C-C bonds break first followed by proton transfer as shown below. Moreover, proton 

PP406 

A Molecular Dynamics study of Protein-Protein Binding between a K + Channel and Peptide 

Toxin 

Po-Chia Chen, Serdar Kuyucak 

School of Physics, The University of Sydney, NSW, Australia 

Potassium channels have become a popular topic of study due to the complex features of the 

selectivity filter essential to its function in vivo, clinical relevance, and complex structural-functional 

relationships [1]. Prediction of binding poses and binding energy have become a major focus of some 

computational studies [2]. 

For this latter purpose, umbrella sampling (US) is a straightforward process of calculating the PMF 

(and by extension an estimation of energy of binding) of protein-ligand interactions. Our study 

represents a novel investigation into its use on protein toxins and K+ channels, a magnitude larger in 

size to its previous applications, with the aim of verifying whether the essentials characteristics of 

binding can be replicated for a larger system. 

We studied the unbinding process between a complex of KcsA and charybdotoxin (ChTX), the 

structure of which has been previously elucidated [3]. The toxin was pulled away from its binding site 

in the direction along the channel axis, and 1D Umbrella sampling (US) was applied in order to predict 

the PMF for this interaction, with the choice of backbone COM as the reaction coordinate. 

It was found that the essential features of the underlying PMF have been observed, and key positions 

along the reaction coordinate correlated with e.g. the breaking of ionic interactions between charged 

side-chains of the participants. We further showed that the final PMF score is unaffected by the 

strength of umbrella potential, provided that the windows overlap. Transient differences between the 

PMFs deduced for umbrella potential 20 kcal/mol and 40 kcal/mol have been attributed to the stronger 

strain produced between the backbone and the side-chains, reducing the entropic gain of the toxin. 

CPMD trajectory snapshots of Arg +• fragmenting to lose CO 2 . 

[1] See, for example: Mitcheson, J. S. Chem. Res. Toxicol., 2008, 21, 1005-1010. 

[2] e.g. Recanatini, M; Cavalli, A; Masetti, M. Chem. Med.Chem., 2008, 3, 523-535. 

[3] Yu, L.; Sun, C.; Song, D.; Shen, J.; Xu, N.; Gunasekera, A.; Hajduk, P.J.; Olejniczak, E.T. Biochemistry, 2005, 

44, 15834-15841. 

transfer affects thermochemistry making fragmentations more exothermic but it does not notably affect 

the reaction barriers to fragmentation, which is important since CID is kinetically controlled. When 

proton transfer is sterically hindered the C-C bond still cleaves spontaneously or with a low barrier to 

produce a radical and a cation (for example, CH 2 C=OH + and [Gly-H] • for Thr +• ) 

The proton scissors model therefore might be modified to the “proton patches” model when applied to 

the radical cations. 

[1]. Wysocki, V.H.; Cheng, G.; Zhang, Q.; Herrmann, K.; Beardsley, R. L., Hilderbrand, A. E., in Principles of Mass 

Spectrometry Applied to Biochemistry; Laskin J., Lifshitz, C., Eds.; John Wiley and Sons;NJ, 2006, chapter 8. 

[2]. see for example, Chu, I.K.; Zhao, J.; Xu, M.; Siu, S.O.; Hopkinson, A.C.; Siu, K.W.M. JACS, 2008, ASAP 

Article; DOI: 10.1021/ja801108j



PP407 

A Molecule Search System Using Ajax 

Lizhu LIU, Shin-ya TAKANE 

Department of Information Systems Engineering, Daito, Osaka, Japan 

With the spread of the Internet, we have freely accessed to the immense amount of information on the 

Internet. However, it is slightly difficult to find out necessary information quickly. Although search 

engines such as Google are useful tools when the keywords contain rather general phrases, it is still 

difficult to search scientific or technical terms efficiently. 

In this study, we present a prototype of the search system for molecular information (structures and 

properties) getting from the temporary database which is constructed from the results of the primary 

(keyword) search using a spider program. The results are followed by the secondary search, which 

refines by filter program. For the usability of the system, we used Ajax (Asynchronous JavaScript + 

XML) as an interface between the search page and the database. This is all done asynchronously 

without reloading the page and interrupting user activity. 

PP408 

Ab Initio Calculation of the Coherent 2D Infrared Response Function for Two-Dimensional 

Vibrational Spectroscopy 

Sangjoon Hahn 1 , Minhaeng Cho 2 

1 Korea Science Academy, Busan, Korea, Republic of, 2 Korea University, Seoul, Korea, Republic of 

The two-dimensional vibrational spectroscopy involving two infrared pulses and a single optical pulse 

[1] is studied by using the ab initio calculation method. By obtaining the first- and second-order 

derivatives of the molecular dipole moment as well as the polarizability, the coherent 2D IR response 

function and its spectrum are calculated with an assumption that the vibrational dynamics can be 

described by the Brownian oscillator model. 

Internet 

Access 

Page 

Spider 

Database 

Filter 

The origin of each peak in the entire coherent 2D IR spectrum is discussed in detail, and is directly 

compared with the coherent 2D Raman scattering spectrum. This comparison demonstrates the 

complementary nature between the coherent 2D IR and Raman spectroscopies. A brief discussion on 

the coupling patterns is also presented. 

User 

Keyword 

Ajax 

Control 

Search page 

[1] Park, Kisam; Cho, Minhaeng. J. Chem. Phys. 1998, 109, 10559–10569. 

Result



PP409 

Ab Initio Density Matrix Renormalization Group with Orbital Optimisation and its Application to 

β-Carotene 

Debashree Ghosh 1 , Johannes Hachmann 1 , Takeshi Yanai 2 , Garnet Chan 1 

1 Department of Chemistry and Chemical Biology, Cornell University, Ithaca, United States, 

2 Department of Theoretical and Computational Molecular Science, Institute for Molecular Science, 

Okazaki, Japan 

We have implemented orbital optimisation within our local ab-initio Density Matrix Renormalization 

Group method. This has allowed us to carry out DMRG-CASSCF with active spaces as big as (24,24). 

We demonstrate our algorithm with full-valence space CASSCF studies on β-carotene [1]. These yield 

new insight into the nature of the low-lying excited states of carotenoids involved in photosynthetic 

light-harvesting. 

[1] D. Ghosh, J. Hachmann, T. Yanai, G.K.-L. Chan, J. Chem. Phys. 2008, 128, 144117 

PP410 

Excited State Dynamics of Molecules by Using Gaussian Wave Packet 

Takashi Kuchitsu 1 , Motoyuki Shiga 2 , Masanori Tachikawa 1 

1 International Graduate School of Arts and Sciences, Yokohama City University, Seto 22-2, 

Kangazawa-ku, Yokohama, Kanagawa 236-0027, Japan, 2 Center for Computational Science and E- 

Systems, Japan Atomic Energy Agency (JAEA), Higashi-Ueno 6-9-3, Taito-ku, Tokyo 110-0015, 

Japan 

By recent development of intense laser technology, it is nowadays a realistic challenge to probe the 

electron rearrangement within a molecule [1]. For instance, new ideas have been proposed to control 

bond breaking/creating processes and charge transfer reactions using ultrafast laser pulses. In 

attosecond to femtosecond time region, photo-released electron comes back to the molecule by 

oscillating laser field, and this recolliding electronic wavepacket gives many informations of the 

molecule. In such femtosecond/attosecond phenomena, electron dynamics is usually important, since 

the electronic excited state may not settle in a certain stationary state for an instantaneous nuclear 

configuration. In femtosecond to picosecond time region, ultrafast spectroscopies give information of 

nuclear motion in electronically excited state. In some experiment, unexpectedly fast decay of excitedstate 

spectra are observed, for such as DNA bases. Although it is considered that the molecule is 

relaxed by passing through a crossing of adiabatic surface, its dynamical aspect is not yet studied 

sufficiently. Especially, it is a difficult challenge to describe electron-nuclear entanglement. 

Recently, we have developed a general time-dependent framework to excited state dynamics of 

molecular system [2], combining ab initio molecular orbital scheme and Gaussian wave packet 

dynamics. Our purpose is to adopt and modify our framework to the dynamics of attosecond, 

femtosecond, and picosecond time region given above. 

In our approach, similar to Deumens and Öhrn [3], the many-particle wavefunctions are described by 

Slater determinants constructed from time-dependent molecular orbitals, that are usually expanded as 

the linear combination of atomic orbitals (LCAO). If only LCAO coefficients are chosen as the timedependent 

parameters, our approach corresponds to the conventional real-time time-dependent 

Hartree-Fock approach. In addition, the center coordinates of Gaussian basis functions can be set to 

time-dependent, giving the traveling basis function. Traveling basis function is expected for electronic 

basis function which follows nuclear motion, or describing polarization [2] or ionization [4]. The 

remaining parameter, the exponent values of Gaussian basis functions can also be time-dependent, 

giving the thawed basis function. This thawed basis function makes possible the distribution of the 

wavefunction to diffuse or shrink as electron cloud moves [4]. These time-dependent parameters 

of the wavefunction are time-developed by the equation of motion 

obtained by applying the time-dependent variational principle. We are expecting our approach to be 

developed for multiconfigurational wavefunction and electron nuclear dynamics. 

[1] Gagnon, E.; Ranitovic, P.; Tong, X.-M.; Cocke, C. L.; Murnane, M. M.; Kapteyn, H. C.; Sandhu, A. S. Science 

2007, 317, 1374. 

[2] Kuchitsu, T.; Tachikawa, M.; Shiga, M. Chem. Phys. Lett., 2006, 433, 193. 

[3] Deumens, E.; Öhrn, Y. J. Phys. Chem. A 2001, 105, 2660. 

[4] Kuchitsu, T.; Okuda, J.; Tachikawa, M. Int. J. Quantum Chem., 2008, accepted.



PP411 

Spin Transition Mechanism and New Necessary Condition of LIESST: DFT Study of 

[Fe(2-pic) 3 ] 2+ 

Hideo Ando, Yoshihide Nakao, Hirofumi Sato, Shigeyoshi Sakaki 

Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto, 

Japan 

Photo-induced spin transition between low-spin (LS) and high-spin (HS) 

states, called Light-induced excited spin state trapping (LIESST), was 

discovered by Decurtins et al. in 1984 [1]. Since then, this phenomenon has 

drawn considerable attention. We theoretically investigated the electronic 

structures and the potential energy curves (PECs) of LS, HS, and 

intermediate-spin (IS) states of a well-known LIESST complex, mer-[Fe(2- 

pic) 3 ] 2+ (pic = picolylamine, Scheme 1). Our study aims to clarify the spin 

transition mechanism in terms of relative positions of PECs and to present 

new guidelines for designing LIESST complexes. 

Geometry optimization and evaluation of PECs were carried out with the 

DFT method, using either the B3LYP or the B3LYP* functional [2]. PECs 

were evaluated along the linear internal coordinate [3] which connects the 

LS, HS, and IS equilibrium geometries. Excitation energies were calculated by using the TD-DFT 

method with B3LYP functional. 

The HS state is as stable as the LS state, which is consistent with experimental results [4]. Spin 

transition from LS to HS causes elongation of all Fe-N bonds by about 0.2 Å because anti-bonding d 

orbitals become occupied in the HS state. In the IS 

state, we found three different structures in which 

four Fe-N bonds are elongated by Jahn-Teller 

distortion. These structures are close in energy to 

each other (within 1 kcal/mol). As shown in Figure 

1, the IS potential minimum is above the LS and 

the HS state at the same geometry, indicating that 

both ISLS intersystem crossing (ISC) and 

ISHS ISC can occur. This is one of the 

important conditions required for LIESST 

complexes [5]. The activation barrier is large 

enough to suppress thermal spin transition and 

tunneling between LS and HS states. The 

excitation energies are different between LS and 

HS complexes; the d-d transitions appear at 2.05, 

2.07, and 2.09 eV in LS state and at 1.46 and 1.64 

eV in HS state. Thus, the LSHS and the 

HSLS spin transitions can be induced selectively 

by different lights. All these results are consistent 

with the fact that both LIESST and reverse-LIESST 

are observed in mer-[Fe(2-pic) 3 ] 2+ . 

Scheme 1. 

mer-[Fe(2-pic) 3 ] 2+ 

0.0 

LS (singlet) 

-0.2 

HS (quintet) 

-0.4 

LS geometry IS geometry HS geometry 

[1] Decurtins, S.; Gütlich, P.; Köhler, C. P.; Spiering, H.; Hauser, A. Chem. Phys. Lett. 1984, 105, 1-4. 

[2] Reiher, M.; Salomon, O.; Hess, B. A. Theor. Chem. Acc. 2001, 107, 48-55. 

[3] Komornicki, A.; McIver, J. W., Jr. J. Am. Chem. Soc. 1974, 96, 5798-5800. 

[4] (a) Goodwin, H. A. Coord. Chem. Rev. 1976, 18, 293-325. (b) Halcrow, M. A. Polyhedron 2007, 26, 3523- 

3576. 

[5] Ando, H.; Nakao, Y.; Sato, H.; Sakaki, S. J. Phys. Chem. A 2007, 111, 5515-5522. 

Energy /eV 

1.0 

0.8 

0.6 

0.4 

0.2 

IS (triplet) 

Figure 

Li 

1. 

i 

Potential 

l 

energy 

di 

curves 

obtained by DFT(B3LYP*) method 

PP412 

Molecular Dynamics Simulation for the Protonation Process in Matrix-Assisted Laser 

Desorption Ionization 

Makoto Hatakeyama, Masanori Tachikawa 

Graduate School of Integrated Science, Yokohama-City University, Yokohama, Japan 

In the MALDI (Matrix-Assisted Laser Desorption Ionization), protonated target molecules, produced by 

proton transfer from matrix molecules of condensed phase to target species, are detected sharply in 

the mass spectrum. The ion yields in the MALDI procedure tend to depend on the proton affinity of 

matrix molecules. However, the ion yields of molecules such as Lysine et al. are known to be 

independent of the proton affinity [1]. We note here that the experimental process of MALDI begins 

from the condensed phase, while a proton affinity is a characteristic value in the gas phase. Thus, we 

can easily assume that the protonation of Lysine in the condensed phase may be different from that in 

the gas phase. In this paper, we will analyze the protonation reaction on the condensed phase in the 

MALDI process by using quantum mechanics and molecular mechanics (QM/MM) molecular 

dynamics. 

First, we focus on the dynamics of only matrix molecules of α-cyano-4-hydroxy-cinnamic acid (CHCA) 

as shown in Figure 1. We have employed HF/STO-3G molecular orbital theory and the general Amber 

Force Field as QM and MM parts, respectively. Molecular desorption is simulated as the temperature 

in the matrix surface is heated up instantly from 300 K to 1300 K. 

When quantum molecules desorbed from the matrix surface, proton transfer sometimes occurs in the 

intermolecular hydrogen bond at the =O・・・HO- part. Since these protonated molecules are unstable, 

these species return to the neutral molecule. Figure 2 shows the potential energy map of =O・・・HO-, 

in which the lower left valley corresponds to the optimized structure and the protonation barrier is 

greater than 50 kJ/mol. Figure 2 clearly indicates that molecular translational motion is needed for the 

protonation, as well as simple HO bonding vibrational motion. However, we have observed that 

molecular translational motion is much slower than HO vibrational motion at the early desorption 

process in our QM/MM simulation. We will show more detailed results in our poster session. 

H 

O 

N 

C 

C 

× 

C 

H 

O 

C H 

O 

O H 

H C C 

× 

r 

O C 

C 

R 

Fig 1. Hydrogen bonding CHCA pair. R and r refer to 

the molecular center of mass dis-tance and H-O 

bond length respectively. 

N 

[1] Nishikaze T.; Takayama M. Rapid Commun. Mass Spectrom. 2006, 20, 376-382. 

O 

H 

Fig 2. =O・・・HO- potential energy difference 

from optimized structure by UHF/STO-3G. 

Contour interval is defined 20 kJ/mol.



PP413 

Tungsten η 3 -Silaallyl/Vinylsilyl, η 3 -Silapropargyl/Alkynylsilyl, and Silylene Complexes: New 

Insight of their Bonding Nature and Electronic Structure 

Mausumi Ray, Yoshihide Nakao, Hirofumi Sato, Shigeyoshi Sakaki 

Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Nishikyo-ku, 

Kyoto 615-8510, Japan 

Multiple bonds involving Si are interesting because 

Si is considerably different from its carbon 

analogue. Syntheses of such chemical species 

are interesting and challenging in recent chemistry. 

Silaallyl and silapropargyl species are silicon 

analogues of allyl and propargyl, respectively 

(Scheme 1). They would be reactive, but the 

interaction with transition metal (TM) complex is 

expected to stabilize them. Also, the interaction 

between the TM complex and these Si species is 

interesting because it is very much different from 

carbon analogues. Hence, bonding nature and 

electronic structure of TM silaallyl and silapropargyl 

complexes are attractive research subject in 

theoretical/computational chemistry. 

We theoretically investigated the bonding nature 

and stability of tungsten η 3 -silaallyl complex 

Cp(CO) 2 W(η 3 -H 2 SiCHCH 2 ) 1, tungsten η 3 - 

silapropargyl complex Cp(CO) 2 W(η 3 -H 2 SiCCH) 2, 

and tungsten acetylide-silylene complex 

Cp(CO) 2 W(CCH)(SiH 2 ) 3 (Scheme 2), using DFT, 

MP4, and CCSD(T) methods with triple zeta quality 

basis sets. 

Our theoretical study presents fundamental 

understanding about the electronic structures of 1, 

2, and 3 and the interaction between the TM 

complex and silicon species, as follows: Though 

the non-bonding π orbital (HOMO) of 1 and 2 are 

similar to those of TM-allyl and propargyl 

complexes, the π orbital (HOMO-1) is much 

different from those of the TM-allyl and propargyl 

complexes, indicating that the electronic structures 

of 1 and 2 are intermediate between those of 

completely conjugated 4 and non-conjugated 5 

(Scheme 3) [1,2]. 3 exhibits interesting chargetransfer 

(CT) interactions; one is the CT from the 

lone pair orbital of silylene to the π* orbital of 

acetylide and the other is the CT from the π orbital 

of acetylide to the empty p orbital of silylene. 1 

Detailed discussions will be presented in the 

poster. 

Allyl Propargyl 

Silaallyl Silapropargyl 

Scheme 1 

1 2 3 

H 

Si 

H 

W H 

C C 

H 

H 

Scheme 2 

H 

Si 

H 

[1] Ray, M.; Nakao, Y.; Sato, H.; Sakaba, H.; Sakaki, S. J. Am. Chem. Soc. 2006, 128, 11927. 

[2] Ray, M.; Nakao, Y.; Sato, H.; Sakaki, S. Organometallics 2007, 26, 4413. 

H 

H 

W 

C 

C 

H 

H 

H 

4 5 

Scheme 3 

W 

H 

C C H 

H 

W 

C 

C 

H 

PP414 

Theoretical Analysis on Positron Halide Complexes by Multi-Component Quantum Monte Carlo 

Method 

Tomohiro Takeda 1 , Yukiumi Kita 1 , Ryo Maezono 2 , Masanori Tachikawa 1 

1 Graduate School of Integrated Science, Yokohama City University, Yokohama, Japan, 2 School of 

Information Science, Japan Advanced Institute of Science and Technology, Isikawa, Japan 

It is well known experimentally that positron injecting into liquid/solid forms the positron-molecular 

complex which is the temporary bound state between a positron and atom/molecule. The positronium 

halides complexes [X - ;e + ] (X=F, Cl, Br, and I), which are typical positron-molecular complexes, has 

been detected experimentally except for [F - ;e + ]. It is found that the order of the positronium (Ps) 

binding energies (X BE ) in aqueous solutions is Cl BE 

known theoretically to be Cl BE > Br BE > I BE [2]. In order to make this inconsistency clear, we evaluate 

Ps binding energies by using the more quantitatively accurate multi-component quantum Monte Carlo 

[3] (MC_QMC) method. MC_QMC method can handle the correlation not only between electrons but 

also the electron-positron in more reliable manner, latter of which is known as a difficult quantity to be 

evaluated by conventional quantum chemical methods. 

In this paper, we analyze the total energy of positronium halides by MC_QMC method as the first 

attempt to reveal the inconsistency between the experimental and theoretical results with respect to 

the order of X BE . 

We used the Slater-Jastrow wave function, 

Ψ ( R) 

= e 

T 

J ( R ) ↑ 

↓ 

× De 

( R 

↑ 

) × De 

( R 

↓ 

) × φp( 

rp 

) , 

e 

e 

as a trial/guiding wave function for VMC (variational Monte Carlo) and DMC (diffusion Monte Carlo) 

methods. D e ↑↓ , φ p , and J(R) denote single Slater determinant of up/down spin electron, a positron 

orbital, and Jastrow factor, respectively. Variational parameters in the Jastrow factor are optimized by 

the variance minimization [4, 5] under the cusp condition between each charged particles. Tables 1 

and 2 show the total energy of [F - ;e + ], F - , and [Cl - ;e + ] systems with various schemes, respectively. Our 

results give variationally improved (lower) energy than those by conventional one (MRCISD), as well 

as the smaller statistical error than the previous work by Bressanini [6]. 

Table 1. Total energy (a.u.) of 

Table 2. Total energy (a.u.) of 

[F - ;e + ] system 

[Cl - ;e + ] system Method Energy 

Method Energy 

VMC -99.9881(9) 

MC_MO -459.7085 

DMC -100.0713(2) 

VMC -460.257(2) 

MRCISD [2] -100.0175 

MRCISD [2] -460.0378 

DMC [6] -100.0719(8) 

[1] Mogensen, O. E.; et al. Chem. Phys. 1979, 37, 139. 

[2] Saito, S. L.; et al. J. Chem. Phys. 2005, 122, 054302. 

[3] Hammond, B. L.; et al. Monte Carlo Methods in Ab Initio Quantum Chemistry; World Scientific: Singapore, 

1994 

[4] Umrigar, C. J.; et al. J. Chem. Phys. 1988, 60, 1719. 

[5] Drummond, N. D.; et al. Phys. Rev. B, 2005, 72, 085124. 

[6] Bressanini, D.; et al. J. Chem. Phys. 1998, 108, 12, 22.



PP415 

New Developments in Spin-Flip Methods 

David Casanova 1 , Lyudmila V. Slipchenko 2 , Anna I. Krylov 3 , Martin Head-Gordon 1 

1 University of California, Berkeley, Berkeley, California, United States, 2 Purdue University, West, 

Lafayette, Indiana, United States, 3 University of Southern California, Los Angeles, California, United 

States 

One of the main reasons for the introduction of the spin-flip methods was the idea that triplet states 

are often easier to model across a potential energy surface than singlets. As a result, these methods 

have been shown to be very reliable in the formation/breaking of chemical bounds [1] and in the 

description of diradical systems [2, 3] as well. For these reasons, in recent years the spin-flip methods 

have become a common tool for molecular electronic structure studies. 

This contribution focuses on two recent developments. First, a general extension of the SF method 

with multiple spin-flip excitations is introduced [4]. The extension includes all configurations in which 

no more than one virtual level of the high spin reference becomes occupied and no more than one 

doubly occupied level becomes vacant. As a result, the ground and low-lying states are treated at the 

same level. Therefore, these methods appear to be specially suitable in some challenging situations 

like bond breaking, multiradiacaloid systems, avoided crossings or conical intersections. This 

expansion takes care of the unbalanced treatment of alpha and beta spaces of the standard SF 

models, removing the common noticeable presence of spin contamination in some of the computed 

states. 

PP416 

Fullerene Formation from a Benzene Source: Density Functional Tight-Binding Molecular 

Dynamics Simulations 

Biswajit Saha 1 , Stephan Irle 2 , Keiji Morokuma 1 

1 Fukui Institute for Fundamental Chemistry, Kyoto University, Kyoto 606-8103, Japan, 2 Institute for 

Advanced Research and Department of Chemistry, Nagoya University, Nagoya 464-8602, Japan 

Molecular dynamics simulations using the density functional tight-binding (DFTB) quantum chemical 

method are reported for the fullerene formation mechanism with benzene molecules as carbon 

feedstock. We observed that the presence of hydrogen slows down the cluster growth process as well 

as fullerene formation. Reactive polycyclic aromatic hydrocarbons (PAHs) without complete saturation 

of their edges by hydrogen form in the early stage, and these PAHs aggregate to form giant fullerenes. 

The dynamic self-assembly goes through four distinct stages, i.e., ring breaking, nucleation, ring 

condensation and cage closure. The effect of temperature on the formation mechanism is discussed, 

and the trajectories are analyzed in terms of pentagon/hexagon/heptagon ring count and sp/sp 2 ratio 

evolution. As in the case of fullerene formation from C 2 molecules as feedstock, only giant fullerenes 

are created, which are expected to shrink following the “Shrinking Hot Giant” road of fullerene 

formation, described earlier by our group. 

The second part of this work introduces the double spin-flip (2SF) family of methods. The 

implementation and application of 2SF within EOM-CC and CI formalism show their capability of 

describing several low-lying electronic states. This approach appears to be particularly suitable in the 

computation of double bond breaking and tetraradical systems. 

[1] Krylov, A. I.; Sherrill, C. D. J. Chem. Phys. 2002, 116, 3194. 

[2] Shao, Y.; Head-Gordon, M.; Krylov, A. I. J. Chem. Phys. 2003, 118, 4807. 

[3] Levchenko, S. V.; Krylov, A. I. J. Chem. Phys. 2002, 117, 4694. 

[4] Casanova, D.; Head-Gordon, M. J. Chem. Phys. 2008, 129, 64104.



PP417 

The Electronic Structure of Gold Clusters: A Study by Coupled Cluster Calculation with a 

Newly Developed Relativistic Model Core Potential 

Hirotoshi Mori 1 , Hisaki Nakashima 2 , Eisaku Miyoshi 2 

1 Division of Advanced Sciences, Ochadai Academic Production, Ochanomizu University, Bunkyo-ku, 

Ohtsuka 2-1-1, Tokyo 112-8610, Japan, 2 Interdisciplinary Graduate School of Engineering Sciences, 

Kyushu University, 6-1 Kasuga Park, Fukuoka 816-8580, Japan 

After the discovery of gold cluster’s amazingly high catalytic function by Haruta et al. [1], the clusters 

have been considered as a future’s new ecological material and studied by many scientists [2]. For 

example, small gold clusters supported on MgO substrates show remarkable catalytic activity for the 

oxidation of CO. The partial hydrogenation of acetylene on supported gold clusters is another 

example for the catalytic activity of gold nano clusters. Now, gold’s chemistry is considered as one of 

the nano science. 

In the past decade, many theoretical studies were done to understand the mechanism of catalytic 

function of gold clusters. Most of them were done on the basis of density functional theory (DFT) from 

the computational costs point of view, and gave many basic and important information of gold’s 

chemistry [3]. On the other hand, recently, Olson et al. did ab initio post-HF based study with 

CCSD(T) level of theory instead DFT, and they discussed the effect of semi-core electrons’ correlation 

effect [3]. Their results gave new insights of gold chemistry, which cannot be discussed with simple 

DFT. However, since their CCSD(T) study was done just for Au 6 and Au 8 , there seems to be still 

unresolved chemical problems of gold nano clusters. 

In this study, the electronic structure of gold nano clusters (Au n ; n=2-10) was studied by using highlevel 

ab initio molecular orbital calculations at the MP2, CCSD, CCSD(T) and CR-CCSD(T) L level of 

theories with newly developed small core type relativistic model core potentials (spdsMCP) [4]. MCP 

is a kind of effective core potential (ECP) methods which is originally proposed by Huzinaga et al. and 

unique in that they are naturally capable of producing valence orbitals with nodal structure [5]. Since 

MCP reproduces the valence nodal structure, which is important to describe electron-electron 

correlation effect, the choice of the combination of MCP and highly correlated post-HF methods shown 

above should be reasonable and reliable one. For comparison, corresponding copper and silver 

clusters’ electronic structures were also investigated. The electronic structures of gold clusters, 

difference from Cu n or Ag n , will be discussed in detail. 

PP418 

Density Functional Theory Study on the Stacking and Excitation of Metal Ion Containing 

Artificial DNA 

Hideaki Miyachi 1 , Toru Matsui 1 , Yasuteru Shigeta 2 , Kimihiko Hirao 1 

1 Department of Applied Chemitry, School of Engineering, The University of Tokyo, Tokyo, Japan, 

2 Institute of Picobiology, Graduate School of Lifescience, University of Hyogo, Hyogo, Japan 

These days, DNA has become attractive again to chemists as molecules having flexible functions. 

Recently, Tanaka et al. and many others have succeeded in developing metal ion containing artificial 

DNA systems [1]. While having similar structure as natural DNA nucleobases, the artificial DNA 

nucleobases posses distinctive shape, size and function. Furthermore, various metal ions in nature 

coordinate to DNA in unique ways [2]. Thus, the combination of metal ions and artificial DNA greatly 

improves the flexibility of DNA which will lead to progress in nano material science. 

After the pioneering work by Tanaka et al., there has been much effort by experimentalists to further 

understand the systems. There are also important contributions by theoretical chemists as well. For 

example, Voityuk [3] predicted that [T-Hg 2+ -T] paring plays important role in an excess electron 

transfer in DNA duplex, which was later experimentally reported. However, there are not many 

detailed molecular level analysis by X-ray crystal structures or theoretical calculations. Therefore, our 

present research aims to give understandings of these systems. 

Among various artificial DNA and metal ion systems, we focused on a system consisted of 

hydroxypyridone nucleobase (H) and Cu 2+ ion, [H-Cu 2+ -H] (Fig. 1). The Density Functional Theory 

(DFT) and Time-Dependent (TD)-DFT methods was used to calculate the ground state and excited 

states. First, we calculated the distance between two [H-Cu 2+ -H] units (Fig. 2). 

Fig. 1 The structure of [H-Cu 2+ -H] Fig. 2 Two stacking [H-Cu 2+ -H] 

Fig.1 One of the stable geometries of Au 7 and Au 8 predicted by CCSD(T)/spdsMCP. 

[1] M. Haruta et al., J. Catal. 1989, 115, 301. 

[2] G. C. Bond et al., Catalysis by gold, Imperial College Press (2006)., 

[3] R. M. Olson and M. S. Gordon, J. Chem. Phys., 2007, 126, 214310, and references there in. 

[4] Y. Osanai et al., Chem. Phys. Lett., 452, 210 (2008)., Y. Osanai et al., Chem. Phys. Lett., submitted (2008). 

[5] V. Bonifacic, S. Huzinaga, J. Chem. Phys., 1974, 60, 2779. 

Acknowledgement This research was primarily supported by the Ochadai Academic Production project 

operated by Japan Science and Technology agency (JST). H.M. and E.M. also should acknowledge JST-CREST 

for their great support. Some parts of the calculations were performed on CPU resources on RCCS (research 

center for computational science) at Institute for Molecular Science. Authors were grateful to the research center 

for giving us enough CPU time for this research. 

With the conventional DFT functional, there was no 

minimum when the distance was elongated. This result 

implies that the van del Waals interaction missing in the 

conventional functional is necessary. We confirmed this 

by adding the Andersson-Langreth-Lundqvist van del 

Waals correlation functional (ALL) [4]. The calculated 

result shown in Fig. 2 agrees with 3.7±0.1 Å obtained by 

EPR measurement (Fig. 3). In addition, the triplet and 

singlet states were nearly degenerate which also suggest 

that the stacking interaction between H is more important 

than the interaction between Cu 2+ . In the poster 

presentation, additional results on ground state properties 

and results on excited state of the system [5] will be 

presented in detail. 

Fig. 3 PES with and without ALL 

[1] Tanaka, K.; Clever, G. H.; Takezawa, Y.; Yamada, Y.; Kaul, C.; Shinoya, M.; Carell, T. Nature Nanotech. 

2006, 2, 190. 

[2] Matsui, T; Shigeta, Y.; Hirao, K. Chem. Phys. Lett. 2006, 423, 331. 

[3] Voityuk, A. A. J. Phys. Chem. B 2006, 110, 21010. 

[4] Sato, T.; Tsuneda, T.; Hirao, K.; J. Chem. Phys. 2007, 126, 234114. 

[5] Matsui,T.; Miyachi, H.; Shigeta, Y.; Hirao, K. submitting.



PP419 

Diels-Alder Reaction of Crotonyl Phosphonate: Cylopentadiene versus Cyclohexadiene 

Nihan Çelebi-Ölçüm 1 , Viktorya Aviyente 1 , K. N. Houk 2 

1 Bogaziçi University, Department of Chemistry, Istanbul, Turkey, 2 University of California, Los Angeles 

Department of Chemistry and Biochemistry, CA, United States 

Diels-Alder reactions between a diene and a hetero-diene provide a good example for the 

periselectivity of the cycloadditions yielding two different products. We have recently found that in the 

thermal and SnCl 4 catalyzed reactions of crotonyl phosphonate with cyclopentadiene, the bispericyclic 

transition states lead to the formation of both Diels-Alder (DA) and hetero-Diels-Alder (HDA) 

products. The Lewis acid catalyst alters the shape of the potential energy surface, ultimately shifting 

the product distribution toward the hetero-Diels-Alder product. [1] 

H 3 C 

O 

P(OCH 3 ) 2 

O 

O 

CH 3 

O 

+ 

P(OCH 3 ) 2 

O P(OCH 3 ) 2 

CH 3 

DA HDA 

In this study, the potential energy surface of the reaction between crotonyl phosphonate and 

cyclohexadiene is explored using Density Functional Theory in order to understand the poor 

periselectivity of the cycloaddition in contrast to the reaction between crotonyl phosphonate and 

cyclopentadiene [2]. 

[1] Çelebi-Ölçüm, N.; Ess, D. H.; Aviyente, V.; Houk, K. N. J. Am. Chem. Soc. 2007, 129, 4528. 

[2] Hanessian, S.; Compain, P. Tetrahedron 2002, 58, 6521. 

O 

PP420 

Solving the Schrödinger Equation of the Hydrogen Molecular Ion in a Magnetic Field by the 

Free ICI (Iterative Complement Interaction) Method 

Atushi Ishikawa 1 , Hiroyuki Nakashima 2 , Hiroshi Nakatsuji 2 

1 Kyoto University, Kyoto, Japan, 2 Quantum Chemistry Research Institute, JST-CREST, Kyoto, Japan 

The free iterative complement interaction (ICI) method is applied to the hydrogen molecular ion (H 2 + ), 

previously in non-magnetic field [1], and here in a strong magnetic field. H 2 + in a strong magnetic field 

is interesting from both chemical and astronomical viewpoints, since it is considered to be a interstellar 

molecule that maybe in a strong magnetic field. The direction of the applied magnetic field is assumed 

to be parallel or perpendicular to the internuclear axis. The ground state total energies are calculated 

under various strengths of magnetic fields, and calculated energies are highly accurate for all field 

strengths, both parallel and perpendicular cases. 

The generated wave function forms depend on the direction of the magnetic field. Under the 

perpendicular magnetic field, our ICI wave function is represented by the mixture of various angular 

momentum quantum numbers. This clearly indicates that ICI method automatically takes into account 

the symmetry-breaking brought about by the applied magnetic field: our ICI procedure automatically 

generates the wave functions appropriate for the environment. 

The gauge-origin problem is also investigated. We have shown that the gauge-origin dependence of 

energy is removed by introducing the gauge-including initial function. This initial function holds its 

gauge-including property during the free ICI cycle. Consequently, our highly-accurate method can be 

applied to various atoms and 

molecules in the magnetic field 

without gauge-dependence problem. 

This problem is also investigated with 

the use of the gauge-dependent type 

initial function. The calculated 

energy, which is initially gauge-origin 

dependent, converges to the gaugeindependent 

result when a sufficient 

ICI order is applied. This property is 

also confirmed by the electron 

density plot (see FIGURE). These 

results indicate that the wave 

functions generated by the ICI 

method properly converges 

automatically to the exact wave 

function, from both energetic and 

gauge-dependent point of view. 

[1] Ishikawa, A.; Nakashima, H.; Nakatsuji, H.; J. Chem. Phys. 2008, 128, 124103



PP421 

Oxygen Atom Transfer Reactions of Iridium and Osmium Complexes: Theoretical Study of 

Significantly Large Differences between these Two Complexes 

Atsushi Ishikawa, Yoshihide Nakao, Hirofumi Sato, Shigeyoshi Sakaki 

Kyoto University, Kyoto, Japan 

Oxygen atom transfer reaction between O=ML 3 and ML 3 (eq. 1) (L=2,4,6-trimethylphenyl (mes) for 

M=Ir and L=tris(2,6-diisopropylphenyl)imide (TIPI) for M=Os) [1] was theoretically investigated by DFT 

method. The optimized geometry of the µ-oxo intermediate, (CH 3 ) 3 Ir-O-Ir(CH 3 ) 3 , is considerably 

different from the experimental one but that of (mes)Ir-O-Ir(mes) agrees well with the experimental 

one. 

ML 3 =O + ML 3 →ML 3 + O=ML 3 (1) 

Our computational results indicate that the bulky substituent of the ligand plays important rules to 

determine the geometry. The calculated activation barriers of the iridium and osmium systems are 2.8 

and 33.0 kcal/mol, respectively, which are consistent with the experimental results that the reaction 

easily occurs in the iridium system but with difficulty in the osmium system. 

The large difference in activation barriers arises from the nuclear and electronic factors. 

The nuclear factor is the sum of 

re-organization energies of ML 3 

and O=ML 3 which are defined as 

the energy difference between the 

reactant geometry and the 

transition state one. This nuclear 

factor is much larger in the 

osmium system than in the iridium 

system because the osmium 

reactants take trigonal planar 

structure. Therefore, significant 

geometrical change is needed for 

the osmium reactants to reach the 

transition state structure. 

Electronic factor arises from 

donor-acceptor interaction 

between O=ML 3 and ML 3 , and the 

energy gap between the donor 

orbital of ML 3 and the acceptor orbital of O=ML 3 is much larger in the osmium system than in the 

iridium system. 

[1] Fortner, K. C.; Laiter D. S.; Muldoon, J; Pu, L.; Braun-Sand, S. B.; Wiest, O.; Brown, S. N. J. Am Chem. Soc. 

2007, 129, 588–600. 

PP422 

Elucidating the Photoelectron Spectrum of CS by Molecular Vibration Calculations of CS + 

Nobumitsu Honjou 

Oita University, Oita, Japan 

The objectives of this study are (i) to determine vibrational frequency ω e and anharmonicity constant 

ω e x e for the C 2 Σ + state of CS + to investigate the cause of the discrepancy (64 cm -1 ) in the ω e value of 

the C state between the photoelectron (PE) spectroscopy value [1] and a recent theoretical value [2] 

obtained from polynomial fitting of ab initio configuration interaction (CI) energies, and (ii) to interpret 

the vibrational structure on the fourth band in the observed PE spectrum of CS [1] because there has 

been no detailed interpretation of the vibrational structure on the fourth band. We calculated potential 

energies for low-lying electronic states of CS + , and the 1 1 Σ + state of CS by the ab initio CI method and 

also calculated molecular vibrations for the electronic states in which the vibrational Schrödinger 

equation was solved using the potential energy functions [3]. The calculated results were used to 

deduce spectroscopic constants, including the vibrational constants for the CS + electronic states, and 

to compute Franck-Condon factors so as to provide the PE vibrational intensity distributions (VID) for 

ionization from the CS 1 1 Σ + state to the CS + electronic states. The VID allows comparison of both the 

energy levels and intensities of vibrational components with the experimental vibrational structure. The 

ALCHEMY II computer program [4] was used for the CI calculations. 

The present study reveals the following information [3]. 

(1) The calculated potential energies and vibrational term values for the X 1 2 Σ + , A 1 2 Π, and B 2 2 Σ + 

states of CS + are accurate because the theoretical spectroscopic constants (electronic term value 

T e , equilibrium internuclear distance R e , ω e , and ω e x e ) for the three states are in good agreement 

with experiment. 

(2) The C 3 2 Σ + state has a double potential well, whose inner well accommodates essentially two 

vibrational states with a significant anharmonicity of vibration. The ω e and ω e x e values for the innerwell 

are calculated to be 1101 cm -1 and 46.7 cm -1 , respectively. The present ω e value is 46 cm -1 

larger than the PE spectroscopy value [1]. No experimental ω e x e value for the C state has been 

available. The discrepancy in ω e might be partly due to the experimental determination of ω e from 

only the observed PE spectrum because of an insufficient number of inner-well vibrational states to 

estimate the anharmonicity constant. 

(3) The first and second components of the fourth band in the observed PE spectrum are respectively 

assigned to the transitions to the C 3 2 Σ + v’=0 and v’=1 states occupying essentially the inner-well, 

where v’ denotes vibrational quantum number. Two transitions to the C 3 2 Σ + v’=4 and v’=5 states 

extending across both wells are responsible for the third component. Experiments to resolving the 

splitting of the third component into two peaks should provide evidence of the double potential well. 

[1] Frost D.C.; Lee S.T.; and McDowell C.A., Chem. Phys. Letters 1972, 17, 153-156. 

[2] Honjou N., Chem. Phys. 2006, 324, 413-419. 

[3] Honjou N., Chem. Phys. 2008, 344, 128-134. 

[4] McLean A.D.; Yoshimine M.; Lengsfield B.H.; Bagus P.S.; and Liu B., in: E. Clementi (Ed.), Modern 

Techniques in Computational Chemistry, Escom, Leiden, 1990, 593-638.



PP423 

DFT Studies into Conjugate Transfer Hydrogentations of Hantzsch Esters 

Robert S Paton, Jonathan M Goodman 

University of Cambridge, Cambridge, United Kingdom 

Recent experimental studies have shown that the creation of new C-H stereogenic centres can be 

accomplished using the blueprints of biochemical reductions [1]. Nature’s reducing agents can be 

mimicked synthetically by small molecule amine catalysts and Hantzsch ester pyridines. The use of 

chiral amines, and more recently, chiral amine salts results in highly regio- and stereoselective 

hydrogenations of unsaturated enals and enones. The mechanism and competing transition structures 

for this process have been studied using DFT calculations. 

Calculations show that formation of reactive iminium species leads to a significant reduction in the 

energetic barrier to conjugate hydrogenation. The nature of the competing transition structures have 

been probed using a variety of spin-restricted and unrestricted density functionals and van der Waals 

corrected functionals. The effects of continuum solvation on TS geometries and energies have also 

been studied. The stereoinduction observed due to chiral amines is explained in terms of competing 

transition structures in which the participation of the amine’s counterion is also critical. For reactions 

that employ a chiral phosphate counterion, our calculations show the lowest energy pathway involves 

bidentate coordination to protons in the Hantzsch ester and also in the iminium substrate. This “three 

point contact model” (which can also be applied to the direct hydrogenation of imines [2]) leads to a 

successful explanation for the observed enantioselectivity. 

PP424 

Theory of Paramagnetic NMR Chemical Shift in the Presence of Zero-Field Splitting 

Teemu O. Pennanen, Juha Vaara 

Laboratory of Physical Chemistry, Department of Chemistry, University of Helsinki, Helsinki, Finland 

NMR spectroscopy of open-shell, paramagnetic molecules is of interest when studying, e.g. 

,metalloprotein systems in natural solution environment. Computational determination of NMR 

shielding tensor is a valuable tool to help structure determination, but until recently, theory only existed 

for the special cases of double systems [1] and (as an approximate a posteriori correction) cylindrically 

symmetric systems of higher multiplicity [2]. 

We have developed a general and systematic theory of paramagnetic NMR shielding tensor for 

paramagnetic systems in arbitrary spin state and spatial symmetry [3]. As a result of including zerofield 

splitting of energy levels, all the contributions [1] to paramagnetic part of shielding tensor have 

contributions of more than one tensorial rank, e.g., the contact shift has an anisotropic part, anad there 

is an isotropic leading-order dipolar shift. 

The theory was implemented into a program that acquires the g-, hyperfine and zero-field splitting 

tensors from a calculation with ORCA [4] software and the orbital shielding tensor from calculation with 

Gaussian 03 [5]. This program is easily adaptable to use tensor data from any quantum chemistry 

code available. 

[1] Pennanen, T.O.; Vaara, J. J. Chem. Phys. 2005, 123, 174102. 

[2] Hrobarik, P.; Reviakine, R.; Arbuznikov, A. V.; Malkina, O.; Malkin, V. G.; Köhler, F. H.; Kaupp, M. J. Chem. 

Phys. 2007, 126, 024107. 

[3] Pennanen, T. O.; Vaara, J. Phys. Rev. Lett. 2008, 100, 133002. 

[4] Neese, F. Orca, Version 2.6.4; University of Bonn, 2007. 

[5] Frisch, M. J. et al., Gaussian 03, Revision C.02; Gaussian Inc.; Wallingford CT, 2004. 

[1] Ouellet, S. G.; Walji, A. M.; Macmillan, D. W. C. Acc. Chem. Res. 2007, 40, 1327-1339. 

[2] Simón, L.; Goodman, J. M. J. Am. Chem. Soc. 2008, ASAP article.



PP425 

Reversible Interconversion of H 2 and H 2 O by Hydroxo/Sulfido-Bridged Dinuclear Ruthenium- 

Germanium Complex. Theoretical Study 

Noriaki Ochi, Hirofumi Sato, Yoshihide Nakao, Shigeyoshi Sakaki 

Kyoto University, Department of Molecular Engineering, Kyoto, Japan 

The activation of dihydrogen molecule with transition metal complex is interesting as a model of the 

hydrogen metabolism reaction mediated by enzyme such as hydrogenases, in which H 2 is reversibly 

converted to two electrons and two protons. Although several activations of H 2 by enzyme models 

were reported, the reversible interconversion between H 2 and H 2 O has been limited. Recently, the 

reversible interconversion by [(Dmp)(Dep)Ge(µ-S)(µ-OH)Ru(PPh 3 )] + (Dmp=2,6-dimesitylphenyl, 

Dep=2,6-diethylphenyl) 1 was experimentally reported by Matsumoto and Tatsumi et at [1]. 

We theoretically investigated the interconversion with ONIOM(DFT:MM) method, to understand the 

reaction mechanism and the reason why 1 efficiently catalyzes this reaction. Because 1 contains the 

reactive µ-OH and µ-S groups, there are two possible reaction courses, as shown in Figure 1. In path I, 

the reaction occurs on the µ-OH, in which the rate determining step is dissociation of H 2 O (TS OH ), and 

its activation barrier is 19.6 kcal/mol. In path II, the reaction occurs on the µ-S, in which the rate 

determining step is isomerization (TS S ) of the H atom concomitant with PPh 3 dissociation and its 

activation barrier is 32.1 kcal/mol. These results indicate that the interconversion takes place on the 

µ-OH. 

In TS OH , H 2 O recedes from the Ge atom to afford the product complex (PRD), which indicates the 

important role of the Ge atom in the interconversion reaction. To shed some light on the role of the Ge 

atom in 1, we investigated the same reaction with the Si analogue [(Dmp)(Dep)Si(µ-S)(µ-OH)Ru 

(PPh 3 )] + 2, in which the Ge atom is replaced with Si atom. Except for the transition state (TS Si ) of 

dissociation of H 2 O, the energy changes of 2 are similar to those of 1. The activation barrier for TS Si is 

30.8 kcal/mol, which is considerably larger than that of 1. This difference is interpreted in the term of 

E-OH 2 (E=Ge and Si) bond energy; Ge-OH 2 and Si-OH 2 bond energies are estimated 26.6 and 36.9 

kcal/mol, respectively. Because the Ge-OH 2 bond energy is moderate, 1 efficiently catalyzes the 

interconversion of H 2 and H 2 O. 

PP426 

Theoretical Study of the Hydrogen Bonds in Functionalized Molecules using Multi-Component 

Molecular Orbital (mc_mo) Method 

Masato Kaneko 1 , Taro Udagawa 2 , Masanori Tachikawa 1 

1 Graduate School of Integrated Science, Yokohama-City University, Yokohama, Japan, 2 Faculty of 

Engineering, Gifu University, Gifu, Japan 

We have recently developed the multi-component molecular 

orbital (MC_MO) methods [1], which can directly include nuclear 

quantum effect of light particles such as proton. We have clearly 

demonstrated that the nuclear quantum effect is important for 

adequate description of the various systems in which hydrogen 

atom or hydrogen nucleus (proton) takes an important role. In this 

research, we applied MC_MO method to hydrogen bonds in HIV-1 

Protease (HP) and Naphthalocyanine molecule to theoretically 

analyze a role of hydrogen bonds for such systems. 

HP is an important enzyme for AIDS therapeutics, because it 

dominates the replication of HIV. Porter et al. theoretically found 

that one water molecule exists between two Asp residues in HP’s 

active site, and three hydrogen bonds stabilize the geometry [2]. 

Although the water molecule is thought to be important for 

electronic state and enzymatic reaction in HP’s active site, the 

active site has not been theoretically analyzed sufficiently, and it 

has not been revealed which of three bonds is directly involved in 

its reaction. 

On the other hands, Naphthalocyanine (Figure 1) is expected as a monomeric device owing to double 

proton transfer reaction in the center of molecule. Liljeroth et al. [3] found current-induced hydrogen 

tautomerization using STM. By this reaction, the shape of molecular orbital and direction of electrical 

current in Naphthalocyanine change, and this molecule may serve as single-molecule switch. 

Additionally, it is well known that quantum mechanical treatment of proton is important for hydrogen 

(or proton) tautomerization. However, there are no theoretical reports on this tautomerization with 

using multi-component methods. 

r1 

r2 

Figure 1. Optimized structure of 

Naphthalocyanine 

In order to reveal a role of nuclear quantum nature of proton for these systems, we have theoretically 

analyzed the geometrical isotope effect on these systems with our MC_MO method. In addition, we 

have calculated the potential energy surface for Naphthalocyanine molecule for detailed analysis of 

hydrogen(proton) tautomerization reaction. 

The optimized covalent bond lengths and GIEs of Naphthalocyanine are shown below. As a result of 

anharmonicity of the potential, which is included by MC_MO method, N-H covalent bond length in HH 

is longer than that in conventional. Detailed results will be presented on the day. 

Figure 1. Rate determining step in the interconversion of H 2 and H 2O on µ-OH and µ-S calculated with 

ONIOM(DFT:MM). The geometry in square bracket means the transition state of rate determining step. 

The energies are in parenthesis (kcal/mol). 

TABLE: Optimized Covalent Bond Length and Calculated GIEs a . 

HF DFT 

MC_HF 

(HH) (HH) HH HD DD 

r1 0.999 1.019 1.018 1.018 (H→D) 1.012 

r2 0.998 1.019 1.015 (H→D) 1.008 1.008 

(HH: non-substituted HD: mono-substituted DD: di-substituted) 

a Basis sets: 6-31g**(center)/6-31g(outer) for electron, 1sGTF for proton/deuteron 

[1] Matsumoto, T.; Nakaya, Y.; Itakura, N.; Tatsumi, K. J. Am. Chem. Soc., 2008, 130, 2458-2459. 

[1] Tachikawa, M.; Mori, K.; Nakai, H.; Iguchi, K. Chem. Phys. Lett.1998, 290, 437-442. 

[2] Porter, M. A.; Molina, P. A. J. Chem. Theor. Comp. 2006, 2, 1675-1684. 

[3] Liljeroth, P.; Repp, J.; Meyer, G. Nature, 2007, 317, 1203-1206.



PP427 

Role of Electrodes in Characterizing Transport Properties of a Molecular Device 

Yeonchoo Cho, Woo Youn Kim, Kwang Soo Kim 

Center for Superfunctional Materials, Department of Chemistry, Pohang University of Science and 

Technology, Pohang, Korea, Republic of 

Current-voltage (I-V) characteristics of a molecular device have been extensively studied. To design 

novel devices, it is important to manipulate transport properties of the system composed of a 

molecular core, electrodes sandwiching the molecule, and linkers connecting them. Although there are 

various studies focusing on the role of molecular cores and linkers, few studies have focused on the 

role of electrodes in characterizing transport properties. 

We have made first principles calculations on systems with different electrodes using the density 

functional theory code where the non-equilibrium Green function formalism is implemented [1]. Gold, 

ruthenium, and carbon nanotube electrodes are studied, each representing s, d, and p valence metals, 

respectively. Using the simplest alkyne molecule, the transmission coefficients and the I-V curves are 

calculated. We have found that the transport properties considerably depend on electrode materials. 

The gold electrode, with the s valence, shows high conductance due to highly broadened transmission 

peaks, whereas the ruthenium electrode having the d valence is less effectively coupled to the 

molecule than the gold electrode regardless of linkers. In contrast, the carbon nanotube electrode, 

with the p valence, displays discrete bands reflecting molecular features. 

PP428 

The CASPT2 Method: Current Limitations and Benchmarks. 

Valera Veryazov 

Lund University, Theoretical Chemistry, Lund, Sweden 

Multiconfigurational second-order perturbation method CASPT2 is known as a reliable computational 

tool for the electronic structure calculations. However, quite often this method is associated with 

calculations of very small molecules. 

Recent development of CASSCF and CASPT2 codes in Molcas 7 package allows us to extend the 

limits for the calculations which can be produced with these methods. The purpose of this study is to 

demonstrate the possibility to use CASSCF/CASPT2 approach for relatively large molecules, and 

molecular systems. Benchmark tests for CASSCF and CASPT2 implementation in Molcas 7 package 

are also presented. 

[1] Kim, W. Y.; Kim, K. S. J. Comput. Chem. 2008, 29, 1073-1083.



PP429 

Cycloaddition Reactions of ICNO: A Theoretical and Experimental Study 

Melinda Krebsz 1 , Tibor Pasinszki 1 , Balázs Hajgató 2 

1 Department of Inorganic Chemistry, Institute of Chemistry, Eötvös Loránd University Budapest, 

Budapest, Hungary, 2 Department SBG, Hasselt University, Diepenbeek, Belgium 

Small nitrile oxides (X―C≡N→O) are important molecules in synthetic organic chemistry, and are 

widely utilized for dipolar cycloaddition reactions, in particular for the formation of various substituted 

heterocycles. They are unstable in the pure state and solutions, thus they are generated in situ at the 

presence of the appropriate dipolarophile. ICNO is a promising precursor for cycloaddition reactions, 

however, its generation is not known so far. 

This paper discusses the theoretical investigation of cycloaddition reactions of ICNO with various 

dipolarophiles (see below) and the dimerisation process, as well as our first experimental results for 

the same reactions. The mechanism of the cycloaddition rections have been studied using single- and 

multi-reference coupled-cluster methods, as well as density functional theory. Our results indicate a 

multi-step dimerisation process for ICNO, but a synchronous cycloaddition with nitriles and ethynyl 

derivatives. 

PP430 

Charge-State Dependent Hydrogen Diffusion on Silicon (001) 

Oliver Warschkow 

Centre for Quantum Computer Technology, School of Physics, The University of Sydney, Sydney, 

NSW, Australia 

The diffusion of hydrogen atoms is an important reaction in a number of chemical and technological 

processes of the silicon (001) surface. This includes the dissociative adsorption of molecules, the 

growth of overlayers by chemical vapor deposition (CVD), thermal desorption of various molecules 

(including H 2 ) from the surface, and the directed atomic-scale functionalization of the surface by 

scanning tunnelling microscopy (STM) hydrogen lithography. The basic inter- and intradimer hydrogen 

shift reactions are well studied theoretically (e.g. Refs. 1, 2). STM measurements [2, 3] have yielded 

experimental activation energies of ~1.7 eV and between 1.0 and 1.4 eV for inter- and intradimer H- 

shift, respectively. With this poster we pose and discuss two pertinent questions: (1) Are single energy 

barriers adequate to describe these H-shift reactions, and (2) are STM measurements of H-diffusion 

truly representative for hydrogen desorption in the absence an STM tip. These two questions warrant 

examination because hydrogen adatoms on Si(001) are known [5-7] to adopt a variety of charge 

states depending on factors such as the doping level of the bulk, the defect density on the surface, 

and – critical to the STM diffusion measurements – the STM tip to surface bias voltage. Using a highlevel 

“cluster compound model” [8] approach which delivers approximate formation energies at the 

B3LYP/6-311++(2df,2pd)//B3LYP/6-311++(d,p) level for a large Si 53 H 44 surface cluster, we report 

activation energies of diffusion of hydrogen adatoms in positive, neutral, and negative charge states. 

We correlate our results with the experimental literature and discuss the effects of charging on 

diffusion rates. 

[1] Vittadini, A.; Selloni, A.; Casarin, M. Phys. Rev. B 1995, 52, 5885. 

[2] Nachtigall, P.; Jordan, K.D. J. Chem. Phys. 1995, 102, 8249. 

[3] Owen, J.H.G; Bowler, D.R.; Goringe, C.M.; Miki, K.; Briggs, G.A.D. Phys. Rev. B 1996, 54, 14153. 

[4] Hill, E.; Freelon, B.; Ganz, E. Phys. Rev. B 1999, 60, 15896. 

[5] Reusch, T.C.G.; Warschkow, O.; Radny, M.W.; Smith, P.V.; Marks, N.A.; Curson, N.J.; McKenzie, D.R.; 

Simmons, M.Y. Surf. Sci. 2007, 601, 4036. 

[6] Radny, M.W.; Smith, P.V.; Reusch, T.C.G,; Warschkow, O.; Marks, N.A.; Wilson, H.F.; Schofield, S.R.; 

Curson, N.J.; McKenzie, D.R.; Simmons, M.Y. Phys. Rev. B 2007, 76, 155302. 

[7] See also the gating of a prototype molecular transistor by a change of charge-state of a missing hydrogen 

defect on a hydrogenated Si(001) surface reported in Piva, P.G.; DiLabio, G.A; Pitters, J.L.; Zikovsky, J.; Rezeq, 

M.; Dogel, S.; Hofer, W.A.; Wolkow, R.A. Nature 2005, 435, 658 

[8] Warschkow, O.; McDonnell; T.L.; Marks, N.A. Surf. Sci. 2007, 601, 3020. 

Acknowledgement: Hungarian Scientific Research Fund (OTKA T049148)



PP431 

Exploiting Next-Gen Computers for Computational Quantum Chemistry 

Tirath Ramdas 1 , Gregory Egan 1 , David Abramson 2 , Kim Baldridge 3 

1 Monash University, Center for Telecommunications and Information Engineering, Melbourne, VIC, 

Australia, 2 Monash University, Center for Distributed Systems and Software Engineering, Melbourne, 

VIC, Australia, 3 University of Zürich, Organic Chemistry Institute, Zürich, Switzerland 

The merit of the Cell BE (e.g. Playstation 3), graphics processing units (GPUs), and fieldprogrammable 

gate arrays (FPGAs) for scientific applications are now sufficiently hyped [1]. That 

these devices are capable of impressive performance is widely accepted – the difficulty is in exploiting 

this capability. The best performance is usually only obtained with a highly detailed understanding of 

the specific architecture of the targeted device. However, there is a common feature to these 

architectures (and this a key feature of the Cell BE and GPU, in particular) that may be exploited in 

general: data-parallel processing, commonly known as single-instruction multiple-data (SIMD) 

processing. 

Data-parallelism is a highly efficient form of parallelism; more efficient that the ubiquitous threadparallelism 

that is exploited by computational clusters and other conventional parallel processors. 

Unfortunately, data-parallelism is not available to many applications. Ab initio computational quantum 

chemistry tools (such as GAMESS, Gaussian, etc.) contain computational bottlenecks that belong to a 

general class of operations called tensor contractions [2]: these are SIMD-friendly. However, there is 

another bottleneck – electron repulsion integrals – which are not SIMD-friendly. 

A key thrust of our research has been to overcome this problem through a run-time dynamic workload 

reordering approach, where it has been shown that substantial SIMD processing of ERIs is possible 

[3]. With that basic issue addressed, we expand our scope of interest to consider other issues, such 

as: 

1. How to best exploit the large internal bandwidth in next-generation architectures? 

PP432 

Thermal Isomerization of 11-cis-Retinal. An Unexpected Manifold 

Carlos Silva Lopez, Rosana Alvarez Rodriguez, Marta Dominguez Seoane, Olalla Nieto Faza, Angel 

R. de Lera 

Universidade de Vigo, Galicia, Spain 

The native chromophore responsible for vision in vertebrates, 11-cis-retinal, responds very distinctively 

to photochemical and thermal conditions. In the vertebrate eye, ligated as a protonated Schiff base to 

the opsin apoprotein, and under UV-vis irradiation, 11-cis-retinal undergoes double bond isomerization 

to yield efficiently and quantitatively the protonated Schiff base of all-trans-retinal [1]. In solution, under 

thermal conditions, 11-cis-retinal is transformed into a mixture of two isomers, namely 13-cis-retinal 

and all-trans-retinal in a ~65:35 ratio. 

all-trans-retinal 

CHO 

hν 

11-cis-retinal 

CHO 

80 ºC 

+ 

CHO 



13-cis/all-trans ~ 65:35 

Control experiments on 13-cis and all-trans-retinal suggest that these two compounds do not 

interconvert under thermal conditions, indicating that two independent reaction pathways are operating 

to furnish each isomer. Furthermore, deuterium labeling experiments devised to probe if sigmatropic 

rearrangements are involved in the product formation provide an intriguing inversion in product 

distribution and, to some extent, deuterium scrambling. 

CHO 

2. How to overcome constraints such as limited memory size in off-load compute engines? 

Note that this is a significant reversal in conventional thinking; in the past the implicit assumption has 

always been that processors have access to a large memory space but that bandwidth was limited! 

We also consider the impact internal interconnection topologies would have on dataflow at a finer 

granularity than we have become accustomed to with conventional coarse-grained parallelism. We 

pose many of these questions, and consider their implications on the way ab initio computational 

quantum chemistry codes should be designed and/or augmented. 

CD 3 


CHO 

80 ºC 

CD 3-y (H) y 


CD 3 

D(H) 

+ 

CHO 


13-cis/all-trans ~ 30:70 

CHO 

[1] See, for example: Williams et al.; Proceedings of ACM Computing Frontiers, 2006, 9-20. 

[2] Baumgartner et al; Proceedings of the IEEE, 2005, 93, 276-292. 

[3] See, for example, Ramdas, T; Egan, GK; Abramson, D; Baldridge, KK; Comp Phys Commun, 2008, 178, 817- 

834. 

Experimental kinetic studies and computational modeling are employed to unveil a complex 

mechanistic manifold implicated in the thermal isomerization of 11-cis-retinal. The absence or 

presence of label scrambling and the inversion of populations upon deuterium substitution can also be 

explained via synergistic NMR monitoring experiments and molecular modeling. 

[1] This is one of the fastest and most efficient reactions recorded, taking place in only 200 fs. with a quantum 

yield of 0.65. Yan, E. C. Y.; Ganim, Z.; Kazmi, M. A.; Chang, B. S. W.; Sakmar, T. P.; Mathies, R. A. Biochemistry 

2004, 43, 10867-10876.



PP433 

Structures and Infrared Spectra of the Topology-Distinct Protonated Water Clusters 

H 3 O + (H 2 O) n-1 (n ≤ 6) 

Maihemutijiang Jieli, Misako Aida 

Center for Quantum Life Sciences & Graduate School of Science, Hiroshima University, Higashi- 

Hiroshima, Hiroshima, Japan 


Rooted digraphs were used to represent the features of the hydrogen bond (HB) and we enumerated 

all possible topology-distinct patterns corresponding to protonated water (PW) clusters containing up 

to 8 water molecules by means of the graph theory. From close investigation of the structural patterns 

obtained, several restrictions which should be satisfied in the stable structures of PW clusters were 

found. The generated hydrogen bond (HB) matrices of the restrictive rooted digraph were used as the 

theoretical framework; the local minima on the potential energy surfaces of those PW clusters are 

obtained using ab initio MO method and DFT method. For PW pentamers and hexamers we found 

some new local minimum structures which had not been obtained previously. The characteristic IR 

harmonic vibrational frequencies of stretching modes of different HB types of OH in PW clusters are 

generated systematically using the MP2/aug-cc-pVDZ level of theory. 

2. Computational Methods and Results 

The H-B matrix is used to enumerate all the possible structures, in which the hydrogen bonding 

patterns are different. We found several restrictions which should be satisfied in the stable structures 

of PW clusters given belove (we call a vertex which corresponds to a protonated water molecule P- 

vertex, and a vertex which corresponds to a water molecule W-vertex): 

(1) There is no arrow directed toward the P-vertex. 

(2) The number of the arrows directed from the P-vertex is 2 or 3. 

(3) When two arrows are directed from the P-vertex, a W-vertex which accepts an arrow from the 

P-vertex cannot accept any arrow from other vertex. 

(4) When three arrows are directed from the P-vertex, all of the three W-vertices, each of which 

accepts an arrow from the P-vertex, cannot accept other arrow from other vertex. 

The OH stretching modes are divided into eight types by analyzing the characteristic IR frequencies of 

local minimum structures of PW clusters H 3 O + (H 2 O) n-1 (n=2~7). 

3. Conclusion 

We showed here the systematical method to find all possible structures of PW clusters. Combination 

of graph theoretical enumerations with ab initio MO calculations allows us to find all topology-distinct 

stable structures for PW clusters. We found some new PW pentamer and hexamer structures. 

Stretching modes of different OH bonds in local minima of PW clusters are generated systematically at 

the MP2/aug-cc-pVDZ level of theory. The vibrational frequencies distribution and their changing order 

of different types of OH in PW clusters are classified systematically. Vibrational frequencies of different 

OH types agree reasonably well with the recent experimental and theoretical results. 

PP434 

The Bonding Nature of Dinuclear Cr(II) Complexes. A Theoretical Study with the MRMP2 

Method 

Yusaku Kurokawa, Yoshihide Nakao, Shigeyoshi Sakaki 

Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto City, 

Japan 

Metal-Metal multiple bond is one of the interesting and challenging research targets in inorganic, 

physical, and theoretical chemistries.[1] Chromium dimer, Cr 2 , is of considerable interest because it is 

believed to bear a hextuple Cr-Cr bond, in a formal sense, which is the largest bond order at this 

moment. Also, theoretical calculation of similar Cr dinuclear complex is very challenging because of 

the presence of very large static correlation effects. 

In this study, recently synthesized open-lantern type dinuclear chromium complex, [Cr(R 1 - 

NC(R 2 )NR 3 ) 2 ] 2 (R 1 = Et, R 2 = CH 3 , R 3 = t Bu, 1) [2], was theoretically investigated with DFT, CASSCF, 

and MRMP2 methods. 

R 2 

R 

R 2 

1 

N 

R 1 

R 

N 

N N R 3 

3 

Cr Cr 

R 1 

N 

N R 

R 3 

1 

N 

R 2 

NR R3 2 

1 

First, we optimized the structure of 1 with the DFT method at various Cr-Cr distances. In the DEToptimized 

geometry, the potential energy surface (PES) smoothly decreases as the Cr-Cr distance 

decreases, whereas the optimized Cr-Cr distance (1.76 Å) is too short. On the other hand, that of 

CASSCF does not present a minimum in the range of the Cr-Cr distance from 1.75 to 2.15 Å. The 

MRMP2 method successfully presents a minimum at Cr-Cr distance of 1.851 Å, as shown in Fig. 1, 

though it is a little shorter than the experimental value. These suggest that both static and dynamical 

correlations are important in this complex. 

The occupation numbers of d σ , d π1 , and d π2 orbitals are evaluated to be 1.72, 1.70, and 1.69, 

respectively, and that of d δ was 1.30. The bond order between two Cr atoms is 2.40 with the CASSCF 

method, which is much smaller than the formal bond order (4) of this complex. 

Significantly large differences are observed between this dinuclear chromium complex and Mo 

analogue. In the Mo analogue, the DFT, CASSCF, and MRMP2 methods present almost the same 

Mo-Mo equilibrium distance, as shown in Fig. 2. The Mo-Mo bond order was evaluated to be 3.41, 

which is considerably smaller than the formal value but much larger than the Cr-Cr bond order. The 

reason of the differences will be discussed. 

Fig. 1 Fig. 2 

Jieli M.; Miyake, T.; Aida, M. Bull. Chem. Soc. Jpn. 2007, 80, 2131–2136. 

[1] F. Weinhold and C. R. Landis Science, 2007, 316, 61. 

[2] A. R. Sadique; M. J. Heeg; C. H. Winter; J. Am. Chem. Soc., 2003, 125, 7774.



PP435 

Sampling Enhancement for Ab Initio Monte Carlo Calculations of Molecular Clusters 

Akira Nakayama, Tetsuya Taketsugu 

Division of Chemistry, Graduate School of Science, Hokkaido University, Sapporo, Japan 

An approach is developed to enhance sampling for ab initio Monte Carlo and ab initio path integral 

Monte Carlo calculations of molecular clusters by employing an auxiliary Markov chain to move 

configuration space efficiently. In this scheme, an auxiliary Markov chain moves on an approximate 

and computationally cheap potential constructed by the interpolation method. The ab initio potential 

energies at previous steps are used as reference points for interpolation and these reference points 

are updated dynamically in the simulation. 

We apply this scheme to protonated water clusters and demonstrate its dramatic enhancement in 

sampling efficiency. Also, combination of this technique with other methods, such as umbrella 

sampling and parallel tempering, is presented in order to further speed up the convergence. 

PP436 

Complexity under Control: A Theoretical Mechanistic Study of Gold and Platinum Catalyzed 

Rearrangements 

Olalla Nieto Faza, Adán Gonzalez Perez, Carlos Silva Lopez, Angel R. de Lera 

Universidade de Vigo, Vigo, Spain 

The use of gold and platinum as homogeneous catalysts in organic transformations has exploded in 

the last years. Their dual activity as electron donors and acceptors, which can be attributed to 

relativistic effects [1], provides an excellent scaffold for facile transformations involving the activation of 

diverse functional groups. As a result, they have been extensively used to mediate in complex 

rearrangements that sometimes coexist with an exquisite stereocontrol. 

We have used Density Functional Theory calculations to study the mechanism of two of these 

remarkable transformations, namely the Pt-catalyzed pentannulation of propargylic esters containing 

oxirane or aziridine moieties reported by Sarpong et al. and the Au-catalyzed 

carboalkoxylation/Claisen rearrangement reported by Toste et al. [2]. The theoretical study highlights 

the role of the metal in mediating complex, multistep rearrangements of polyfunctionalized substrates, 

occurring with chirality transfer. 

[1] Gorin, D. J.; Toste, F. D. Nature, 2007, 446, 395-403. 

[2] (a) Pujanauski, B. G.; Bhanu Prasad, B. A.; Sarpong, R. J. Am. Chem. Soc., 2006, 128, 6786-6787. (b) 

Motamed, M.; Bunnelle, E. M.; Singaram, S. W.; Sarpong, R. Org. Lett., 2007, 9, 2167-2170. (c) Dubé, P.; Toste, 

F. D. J. Am. Chem. Soc., 2006, 128, 12062-12063.



PP437 

Hartree-Fock and Kohn-Sham Response Theory in a Second-Quantization Atomic-Orbital 

Formalism Suitable for Linear Scaling 

Thomas Kjaergaard 1 , Poul Jørgensen 1 , Jeppe Olsen 1 , Sonia Coriani 2 , Trygve Helgaker 3 

1 Aarhus University Department of Chemistry, Aarhus C, Denmark, 2 Dipartimento di Scienze Chimiche 

Universita degli Studi di Trieste, Trieste, Italy, 3 Department of Chemistry, University of Oslo, Oslo, 

Norway 

We present a second-quantization based atomic-orbital method for the computation of response 

functions within Hartree–Fock and Kohn–Sham density-functional theories. The method scales linearly 

with the size of the system. Illustrative results are presented for excitation energies, one- and twophoton 

transition moments, polarizabilities and hyper-polarizabilities for hexagonal BN sheets with 

upto 180 atoms. 

PP438 

Scrutiny of the Mean-Field Approximation to the Two-Electron Spin-Dependent Terms in the 

Two-Component Pseudo-Relativistic Hamiltonian 

Mojmir Kyvala 

Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, 

Flemingovo namesti 2, 166 10 Praha 6, Czech Republic 

A series of ab initio one-electron approximations to the Breit−Pauli two-electron spin-spin Hamiltonian 

has been developed under the well established scheme for the derivation of the mean-field spin-orbit 

Hamiltonian [1]. Mainly for comparison, similar approximations to the two-electron part of the 

nonrelativistic Hamiltonian have also been defined. It is shown that the single-determinant 

approximation to the diagonal matrix elements of the spin-spin Hamiltonian (corresponding to the 

single-determinant open-shell Hartree−Fock approximation to the expectation values of the 

nonrelativistic Hamiltonian) introduced almost fifty years ago [2] and exploited recently in both density 

functional theory and correlated ab initio calculations [3] represents the simplest but the least accurate 

element in the series. 

All the discussed one-electron approximations to the two-electron terms in the two-component 

pseudo-relativistic Hamiltonian have been put to the test: several types of matrix elements among 

multiconfiguration nonrelativistic states have been evaluated for various small and medium-sized 

molecules (biradicals). As a reference, both the matrix elements of the corresponding “exact” twoelectron 

operators and the known experimental values of the zero-field splitting parameters D and E 

have been used. 

[1] Hess, B. A.; Marian, C. M.; Wahlgren, U.; Gropen, O. Chem. Phys. Lett. 1996, 251, 365−371. 

[2] McWeeny, R.; Mizuno, Y. Proc. R. Soc. (London) 1961, A259, 554−577. 

[3] (a) Petrenko, T. T.; Petrenko, T. L.; Bratus, V. Y. J. Phys: Condens. Matter 2002, 14, 12433−12440. (b) Neese, 

F. J. Am. Chem. Soc. 2006, 128, 10213−10222.



PP439 

Theoretical Study of Multi-Nuclear Complexes, [Pt 2 X 4 (Me 2 pz) 8 ] (X=Ag, Cu, H): Metallophilic 

LUMO Participation in Strong Luminescence 

Yoshihide Nakao, Shigeyoshi Sakaki 

Kyoto University, Kyoto, Japan 

[Pt 2 Ag 4 (Me 2 pz) 8 ] (1), [Pt 2 Cu 4 (Me 2 pz) 8 ] (2), and [Pt 2 H 4 (Me 2 pz) 8 ] (3) are strongly luminescent 

complexes, and luminescent colors are blue(497 nm), orange(625 nm), and yellow(556 nm), 

respectively, in the solid state. They have no color in the ground singlet state and their luminescence 

exhibits remarkably large Stokes shift. Sasaki et. al. explained that strong luminescence requires the 

small geometrical relaxation in the excited state.[1] Recently, [Cu 3 (X 2 pz) 3 ] (X=H, CH 3 , CF 3 ) 

synthesized by Dias et. al. have large Stokes shifts and metal-metal bonding interaction in the excited 

triplet states.[2] Due to creating the metal-metal bonding interaction in excited states, they have very 

large geometrical difference between the ground and excited states. We theoretically studied relation 

between metal-metal bonding interaction and luminescence of three complexes. 

We carried out the geometry optimization of the ground singlet and excited triplet states and evaluated 

emission energies from vertical excitation energies by the B3LYP method. Absorption spectrum was 

evaluated by the TD-B3LYP method. The Pt-Pt distance of the singlet and triplet states are 5.439 and 

5.914 Å, respectively, and the Ag-Ag distance of those are 3.407 and 2.870 Å, respectively. Since 

other complexes have large geometrical relaxation in excited states, it considers they should exhibit 

large Stokes shifts. Complexes 1 and 2 have very interesting LUMO, which consists of in-phase 

bonding interaction among all of 6p orbitals of two Pt atoms and either 5p orbitals of four Ag atoms or 

4p orbitals of four Cu atoms, respectively. Luminescence of 1 corresponds with transition from these 

LUMO to Pt(d-sigma) and the calculated emission energy, 2.54 eV, agrees with the experimental 

value, 2.34 eV, in CH 2 Cl 2 . The calculated and experimental emission energies of 2 are 1.53 and 1.51 

eV, respectively. The calculated emission energies are in good agreement with the experimental 

values. 

Pt II 

Pt 2.5 

PP440 

New Approaches to Large-Scale Multiconfigurational Perturbation Theory Calculations 

Francesco Aquilante 1 , Tanya Todorova 1 , Laura Gagliardi 1 , Björn Olof Roos 2 

1 Department of Physical Chemistry, Geneva University, Geneva, Switzerland, 2 Department of 

Theoretical Chemistry, Lund University, Lund, Sweden 

Two complementary approaches are described which further extend the capabilities of Cholesky 

decomposition-based multiconfigurational perturbation theory (CD-CASPT2) calculations [1] to treat 

large systems and with high-quality atomic orbital basis sets. 

For situations where the active orbitals are localized within a small region of the molecule, a suitable 

“active site'” can be identified as the collection of atoms where the active orbitals effectively extend. 

Accordingly, the inactive and secondary orbitals can be separately localized and partitioned between 

this active site and the remaining atoms (environment). From the basic assumptions of our approach, 

these two regions are assumed to be uncoupled, and therefore two separate sets of canonical orbitals 

can be deduced for the active site and the environment. It is shown that accurate relative energies can 

be computed by performing CD-CASPT2 calculations in which the correlating orbitals are restricted to 

only those assigned to the active site. This allows for substantial savings in computational costs – not 

uncommonly, of 1-2 orders of magnitude. 

For systems with delocalized active orbitals, instead, a method is suggested which allows to truncate 

the virtual space in CD-CASPT2 calculations with systematic improvability of the resulting 

approximation. The method is based upon a modified version of the Frozen Natural Orbital (FNO) 

approach used in coupled cluster theory [2] – similarly, the idea is to exploit approximate linear 

dependences among the eigenvectors of the virtual-virtual block of the MP2 density matrix. It is shown 

that FNO-CASPT2 recovers more than 95% of the full CD-CASPT2 correlation energy while requiring 

only a fraction of the total virtual space, especially when large atomic orbital basis sets are in use. 

Tests on various properties commonly investigated with CASPT2 demonstrate the reliability of the 

approach and the corresponding dump in computational costs and storage demands of the 

calculations. 

Ag I Ag I 

Ag I Ag I 

Ag I 

Ag I Ag I 

Ag I 

[1] Aquilante, F.; Malmqvist, P-Å.; Pedersen, T. B.; Ghosh, A.; Roos, B. O. J. Chem. Theory Comp. 2008, 4, 694- 

702 

[2] See, for example: Taube, A. G.; Bartlett, R. J. Collect. Czech. Chem. Commun. 2005, 70, 837-850 

Pt II 

Pt 2.5 

singlet 

triplet 

r(Pt-Pt) = 5.439 Å 

r(Pt-Ag) = 3.633 Å 

r(Ag-Ag) = 3.407 Å 

r(Pt-Pt) = 5.914 Å 

r(Pt-Ag) = 3.587 Å 

r(Ag-Ag) = 2.870 Å 

Figure 1. Geometrical changes between ground singlet 

and excited triplet states in 1 

HOMO 

LUMO 

Figure 2. HOMO and LUMO of singlet state in 1 

[1] Sasaki, Y. Bull. Jpn. Soc. Coord. Chem. 2006, 48, 50. 

[2] Dias, H. V. R.; Diyabalanage, H. V. K.; Eldabaja, M. G. ; Elbjeirami, O.; Rawashdeh-Omary, M.; Omary, M. A. 

J. Am. Chem. Soc. 2005, 127, 7489.



PP441 

Spin-Orbit Coupling Effects in Rhenium Tetra-Hydrides 

Shiro Koseki, Toshio Asada, Taka-aki Hisashima 

Department of Chemistry, Osaka Prefecture University, Sakai, Osaka, Japan 

In the series of our research projects, the spin-orbit coupling effects upon the shapes of potential 

energy surfaces are analyzed for transition metal compounds. The present poster will report 

dissociation potential energy curves of several low-lying electronic states in rhenium tetra-hydride 

(ReH4). Since the tetra-hydride at the most stable structure is very close in energy to its corresponding 

dissociation limits, the spin-orbit coupling effects must become very important in exploring the 

potential energy surfaces of low-lying electronic states and investigating Jahn-Teller and pseudo- 

Jahn-Teller deformation paths. 

In the present theoretical calculations, the SBKJC basis set was used after augmented by a set of 

polarization functions for each atom including hydrogen atoms. The orbitals were optimized by using 

full-optimized reaction space (FORS) multi-configuration self-consistent field (MCSCF) method, where 

its MCSCF active space includes the orbitals correlating to Re’s 5d and 6sp orbitals and hydrogen’s 1s 

orbitals in the dissociation limit. Namely, the active space includes 13 orbitals and 11 electrons. Using 

these optimized orbitals, first-order configuration interaction (FOCI) wave functions were constructed 

for the purpose of spin-orbit coupling calculations. 

The most stable structure of ReH 4 has a planar C 2v structure and its ground state belongs to 4 B 2 . The 

ground state in the dissociation limit is sextet, ReH 2 ( 6 Σ + g ) + H 2 ,( 1 Σ + g ), and the energy difference 

between these is smaller than 10 kcal/mol. Additionally, the highest symmetric T d 

structure has a 2 E ground state and this is distorted into two different D 2d 

structures ( 2 A 1 and 2 B 1 ) by the Jahn-Teller effect. The energy differences are very 

small between these D 2d structures and the most stable planar C 2v structure and, 

as a result, the D 2d structures are very close in energy to the dissociation limit. It is 

apparently necessary to carry out more sophisticated calculations in order to 

obtain conclusive results. Another highest symmetric D 4h structure has 6 E u ground 

state. However, this is considerably higher in energy than the structures described above. This is 

distorted into D 2h structures ( 6 B 2u , 6 B 3u ) by the Jahn-Teller effect and into C 2v planar structures ( 6 A 1 , 

6 B 2 ) by the pseudo-Jahn-Teller effect, where the geometry optimization of the C 2v structures derives 

the dissociation into ReH 2 + H 2 . As long as the adiabatic approximation is used, this molecular system 

has never reached the C 2v structure ( 4 B 2 ) or the T d structure ( 2 E) because of different spin multiplicity. 

In order to explain the paths from the D 4h structure to the T d and C 2v structures, the spin-orbit coupling 

effects need to be included for calculating the potential energy surfaces of low-lying electronic states 

in this molecule. The details of the calculated results will be reported at the symposium. Additionally, 

the dissociation of ReH 2 into Re ( 6 S) + H 2 is now being investigated. A large energy barrier exists on 

the ground-state sextet potential energy curve along the C 2v path, as previously reported by 

Balasubramanian et al. This barrier could be remarkably reduced if a C s path and spin-orbit coupling 

effects are considered. 

PP442 

Chromium-Complexes of Furoxan and Benzofuroxan 

Tibor Pasinszki 

Department of Chemistry, Institute of Chemistry, Eötvös Loránd University of Budapest, Budapest, 

Hungary 

Furoxans (1,2,5-oxadiazole 2-oxides) are potential organic ligands in organometallic chemistry. They 

are aromatic molecules, and may form π-donor and n-donor complexes via the π-system and oxygen 

and nitrogen lone electron pairs, respectively. Furoxan-complexes, however, are unknown, so far. 

The original aim of the present work was to study structures of potential furoxan and benzofuroxan 

complexes of chromium(0), which could be derived by substitution reactions from the stable and easily 

accessible Cr(CO) 6 , Cr(CO) 3 (CH 3 CN) 3 , (η 6 -benzene)Cr(CO) 3 , and (η 6 -benzene) 2 Cr complexes. 

Another aim was to study the thermodynamics of the formation reactions prior to experimental work. 

The studied reactions are as follows: 

Cr(CO) 6 + furoxan → Cr(CO) 5 (κ N -furoxan) 

Cr(CO) 6 + furoxan → Cr(CO) 5 (κ O -furoxan) 

Cr(CO) 5 (CH 3 CN) + furoxan → Cr(CO) 5 (κ N -furoxan) 

Cr(CO) 5 (CH 3 CN) + furoxan → Cr(CO) 5 (κ O -furoxan) 

Cr(CO) 3 (CH 3 CN) 3 + furoxan → Cr(CO) 3 (η 5 -furoxan) 

(η 6 -benzene)Cr(CO) 3 + furoxan → Cr(CO) 3 (η 5 -furoxan) 

Cr(η 6 -benzene) 2 + furoxan → Cr(η 5 -furoxan) 2 

The structure and formation of target molecules have been studied using density functional theory. As 

test systems, the experimentally well known Cr(CO) 6 and (η 6 -benzene)Cr(CO) 3 molecules have been 

studied using various DFT functionals, and finally the B3PW91 functional is selected for this study. 

Calculations have predicted the formation of n-donor complexes, but unexpectedly indicated the 

furoxan-ring opening in hypothetical π-donor mode, leading to novel dinitrosoethylene-derivatives. 

Structures and energetics of potential formation reactions have been calculated for all furoxan- and 

dinitrosoethylene-complexes. 

Acknowledgement: Hungarian Scientific Research Fund (OTKA T049148) 

[1] T. Hisashima, T. Matsushita, T. Asada, S. Koseki, and A. Toyota, Theoret. Chem. Acc., 2008, 120, 85. 

[2] S. Koseki, Computational Methods in Sciences and Engineering, Theory and Computation: Old Problems and 

New Challenges, edited by G. Maroulis and T. Simos, 2008, CP963, Vol. 1, page 257. 

[3] D. Dai and K. Balasubramaniana, J. Chem. Phys. 1991, 95, 4284.



PP443 

Crowding Effects on Protein Folding: A Binary System Simulation 

Jian Yin 1 , Jianwen Jiang 2 , Raj Rajagopalan 3 

1 Singapore-MIT Alliance, Singapore, Singapore, 

2 Department of Chemical & Biomolecular 

Engineering, National University of Singapore, Singapore, Singapore, 3 Singapore-MIT Alliance and 

Department of Chemical & Biomolecular Engineering, National University of Singapore, Singapore, 

Singapore 

It has been broadly recognized only during this recent decade in biological community that crowding 

effect plays an important role in the process of protein refolding and aggregation [1]. The crowding 

effect is a result of multi-body interaction. It is created thermodynamically from the difference of 

volume exclusion of the macromolecules around the neighbourhoods of a target macromolecule. The 

so called depletion force due to the depletion zones as the overlaps of the excluded volumes is one of 

these crowding effects. 

We are investigating the crowding effect as a function of crowder size and effective volume fraction on 

a single peptide with molecular dynamics simulation using coarse-grained model. The attribute feature 

of this work is that our simulation system is simple binary system consisting of one coarse-grained 

peptide and hundreds of Lennard-Jones crowders. Our major conclusions: 1) Crowding enhances 

extraordinarily conformational fluctuation of peptide. It is generally believed that larger conformational 

fluctuations are necessary for and favourite to conformational transitions. 2) Crowding raises the van 

der Waals energy of the peptide. This will imply an acceleration of the rate of conformational transition 

of peptides, which will be beneficial to protein refolding. 3) Crowding enhances the correlation 

between its van der Waals energy and its radius of gyration. 4) Crowding enhances the solvent 

accessible surface area by enhance its hydrophobic portions. 5) The crowder-excluded space creates 

hydrophobic cavities. This will result in the depletion attraction taking over the dominating position of 

driving force exerted on the peptide. The major support of this proposal is coming from the works of 

Wenner and Bloomfield, etc [2]. 

PP444 

The Free Energy Change of Glycine Tautomerization in Aqueous Solution 

Miyamoto Hidenori, Misako Aida 

Center for Quantum Life Sciences & Graduate School of Science, Hiroshima University, Higashihiroshima, 

Japan 

Introduction 

Glycine, the simplest amino acid, is a compound with an intramolecular hydrogen bond. A glycine 

molecule gets converted from neutral form (NF) to zwitterionic form (ZW) in aqueous solution, via 

intramolecular hydrogen transfer. In this study, we calculate the relative free energy of this process of 

the tautomerization of glycine. 

Method 

A Monte Carlo simulation with the free energy perturbation method was employed to determine the 

relative stability between the glycine neutral form and the zwitterionic form in aqueous solution. The 

difference in free energy between solute structures i and j is given by: 

∆A ij = – kT ln[〈exp{– (E j – E i ) / kT}〉 (i) ] 

The bracket (i) denotes the ensemble average of the difference in total QM/MM energies E i and E j 

of the system with solute in the i and j structures respectively. To calculate ensemble average of 

energy, MM water molecules were arranged around a glycine molecule, and 20200000 configurations 

of MM water molecules were generated using MC method at 298K with the glycine molecule fixed, 

and 2020 configurations from those 20200000 configurations were selected randomly. Selected 2020 

configurations were calculated by means of QM/MM method, where the QM part was the glycine 

molecule and the MM part was the water molecules, and MM water molecules within 2.45 angstrom of 

the glycine were treated as QM molecules. 

[1] (a) Minton, A. P. Mol. Cell Biochem., 1983, 55: 119-140. (b) Zimmerman, S. B., and Minton, A. P. Annu. Rev. 

Biophys. Biomol. Struct., 1993, 22, 27-65. (c) Ellis, R. J. Curr. Opin. Struct. Biol., 2001, 11: 114-119. (d) Hall, D., 

and Minton, A. P. Biochim. Biophys. Acta, 2003, 1649: 127-139. 

[2] (a) Wenner, J. R., and Bloomfield, V. A. Biophysical J. 1999, 77, 3234 – 3241. (b) Record, M. T., Courtenay, E. 

S., Cayley, D. S., and Guttman, H. J., Trends Biochem. Sci., 1998, 23: 143-148. (c) Dinnbier, U., Limpinsel, E., 

Schmid, R., and Bakker, E. P., Arch. Microbiol., 1988, 150: 348-357; (d) Shepherd, V. A., Curr Top Develop Biol., 

2006, 75:171–223. 

The program packages used were HONDO, 

GAMESS, Gaussion03 and AIM2000. 

Results and discussion 

The free energy difference between the NF and 

the ZW in water and the activation free energy 

barriers are plotted in Fig.1. The solute molecule 

was calculated using MP2/6-31G* basis set, 

solvent molecules within 2.45 angstrom of the 

glycine molecule were treated with HF/6-31G* 

basis set, and other solvent molecules were 

treated with TIP3P, at each point along the 

course of hydrogen atom transfer. The blue line 

is the free energy hydration, the black line is the 

free energy of the system, and the red line is the 

potential energy of the solute (glycine). The sign 

of free energy of hydration is inverted: it's 

actually with minus sign. The available 

experimental values for the NF → ZW 

transformation compare with our computational 

result. The agreement between the experimental 

(7.3 kcal/mol) and our results (7.2kcal/mol) is 

fairly good, which may indicate that our method 

is effective to calculate solvation effect. 

∆A ( kcal/mol ) 

energy of solute ( glycine) 

free energy of hydration 

35 

30 

25 

20 

15 

10 

5 

0 

-5 

-10 

Fig. 1 g(MP2) + nw(HF) + (101−n)w(MM) 

NF 

ZW



PP445 

Locating Multiple SCF Solutions: an Approach Inspired by Metadynamics 

Alexander Thom, Martin Head-Gordon 

University of California, Berkeley, Berkeley, California, United States 

The SCF equations are non-linear in the electron density and their solutions, which are stationary 

points of the energy with respect to changes of the occupied orbitals, are usually located iteratively. 

The non-linearity of the equations presents a difficult mathematical challenge, as the number of 

solutions is not known, and so there is no guarantee that any solution which has been located is an 

appropriate global minimum. Furthermore, in systems with many minima close in energy, the solution 

located is extremely dependent on the initial guess used for the iterative procedure. 

We propose a method to locate the solutions to the Self-Consistent Field equations, using an 

approach based upon metadynamics. Within an SCF calculation, when a solution is found, a biasing 

potential is added to the energy to avoid reconvergence to the same solution. Multiple solutions can 

therefore be relatively easily found with relatively trivial modifications to existing algorithms. Using this 

method we locate all known solutions and one unknown solution of the H4 model [1], one of the few 

systems whose many solutions have been investigated, and also apply it to a number of small 

molecules. 

PP446 

Theoretical Study of the Electric Conductivity in Nb-Doped TiO 2 

Takahiro Suenaga, Hideyuki Kamisaka, Hisao Nakamura, Koichi Yamashita 

University of Tokyo, Department of Chemical System Engineering, Tokyo, Japan 

Transparent conductive oxides are key components in flat-panel display (FPD), photovoltaic cells and 

light emitting diodes (LED). Sn-doped In 2 O 3 (ITO) is the most widely used, but the supply of indium is 

expected to be depleted because of its worldwide consumption. So we need to seek the alternative to 

ITO. The alternative needs to have wide band gap which leads transparency in visible range and a lot 

of carrier which leads high conductivity. T. Hasegawa found that Nb-doped anatase (TNO) has high 

conductivity and transparency in visible range. The aim of our research is to clarify the micro 

mechanism of TNO by investigating band structure, chemical bond and effective mass. 

The structural and electronic properties of TNO have been investigated by a DFT-based first-principle 

method using PW91 functional and ultrasoft pseudopotential (USPP). When we first construct a TNO 

model, we prepare pure anatase cell containing Ti 16 O 32 and one of Ti atoms is replaced by Nb atom. 

Then we optimize it. The lattice constant of the optimized structure corresponds to the experimental 

data [1]. From the optimized structure, the chemical properties of the Nb dopant were analyzed. 

[1] Kowalski, K.; Jankowski K Phys. Rev. Lett. 1998, 81, 1195-1198 

Table 1. Lattice constant of antase and TNO 

anatase TNO TNO 

(calc.) (calc.) (exp. [1]) 

a (Å) 7.564 7.647 7.596 

c (Å) 9.502 9.560 9.561 

We calculate the band structure, density of state, charge density and electron effective mass of the 

optimized TNO model and compare with pure anatase. From the band structure, we find that there is 

little effect of Nb as a dopant. From the density of state, we confirm that valence band is constructed 

by O 2p electron and conduction band is constructed Ti 3d and Nb 4d electron which they are hybrid 

and there is no impurity band between valence band and conduction band, so TNO keep transparent. 

From the electron effective mass, we find that TNO has anisotropy; z-axis direction’s is ten times as 

much as x-axis one. In the theoretical analysis by H. Furubayashi, the effective mass of TNO is 0.4m 0 . 

So the result of out calculation accord with the analysis. 

Table 2. Effective mass of antase and TNO 

anatase TNO Exp. [2] 

x-axis direction 0.421 0.419 

z-axis direction 4.053 4.053 

about 1 

[1] Y. Furubayashi et al. Appl. Phys. Lett. 2005, 86, 252101 

[2] H. Tang et al. J. Appl. Phys. 1994, 75, 2042



PP447 

Understanding Nucleation Phenomena Near the Spinodal 

Suman Chakrabarty, Mantu Santra, Prabhakar Bhimalapuram, Biman Bagchi 

Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore, Karnataka, India 

We have revisited the apparently well-studied problem of nucleation and growth of a stable phase 

inside a parent metastable phase, particularly near the spinodal curve. We have undertaken extensive 

computer simulation studies to probe the molecular mechanism for the onset of instability in a wide 

range of systems (both Lennard-Jones fluid and nearest neighbour Ising model in 2- and 3- 

dimensions). We have constructed the multidimensional free energy surface of nucleation as a 

function of multiple reaction coordinates using a very efficient non-Boltzmann sampling scheme. While 

the classical Becker-Döring (BD) picture of homogenous nucleation, that assumes the growth of a 

single nucleus by single particle addition, holds good at low to moderate supersaturation, the 

formation of the new stable phase becomes more collective and spread over the whole system at 

large supersaturation. As the spinodal curve is approached from the coexistence line, the free energy, 

as a function of the size of the largest liquid-like cluster, develops a minimum at sub-critical cluster 

size. We find the emergence of an alternative free energy pathway (with a barrier less than that in the 

BD picture) that involves participation of many sub-critical liquid-like clusters and the growth is 

promoted by coalescence with intermediate sized clusters present in the neighbourhood of the largest 

cluster. Very close to the spinodal the free energy surface becomes quite flat and the significance of a 

‘critical’ nucleus is lost. The scenario seems to be mostly independent of the model chosen. 

[1] Bhimalapuram, P.; Chakrabarty, S.; Bagchi, B. Phys. Rev. Lett. 2007, 98, 206104. 

[2] Reply to a comment against the Ref. 1: Chakrabarty, S.; Santra, M.; Bagchi, B. Phys. Rev. Lett. 2008 (in 

press). 

PP448 

DFT and Multinuclear NMR ( 17 O, 13 C) Studies of Diazenedicarboxylates and Related 

Compounds 

Francesca Mocci, Michele Usai, Giovanni Cerion 

Università di Cagliari, Dipartimento di Scienze Chimiche, Cagliari, Italy 

Few widely employed organic compounds, diazenedicarboxylates (1a) and related maleic (2a) and 

fumaric (3a) dimethyl diesters, have been studied by a combined computational and multinuclear NMR 

(O-17, C-13) approach. Theoretical calculations were carried out at the density functional theory level 

employing the PBE0 functional, which has been shown to give very good results in the prediction of 

the chemical shielding, together with the 6-311G(d,p) basis set for geometry optimization, and the 6- 

311+G(2d,p) basis set for calculating the NMR shielding. The polarizable continuum model (PCM) was 

employed both for geometry optimization and for calculating the NMR shielding constants using the 

gauge-including atomic orbitals method. 

This combined approach afforded important information about the preferred conformations in 

chloroform and their influence on the NMR isotropic shielding, indicating that all of the studied 

compounds exist in solution as a mixture of two or more conformations in fast exchange, and that for 

1a and 2a most of the conformations have the plane of carboxylate groups deviating from planarity 

with respect to the system of delocalized electrons to which they are bound. 

The results show how an “exotic” magnetic nucleus such as oxygen-17 can be of great help in the 

determination of conformational preferences of molecules in solution. 

The lowest energy conformations of 1a, 2a and 3a



PP449 

The Double-helical → Ladder Structural Transition in the B-DNA is Induced by a Loss of 

Dispersion Energy 

Jiri Cerny, Pavel Hobza 


Prague, Czech Republic 

Noncovalent interactions play a unique role in biology since they are responsible for the structure of 

biomacromolecules. The double-helical structure of DNA which is responsible for storing and transfer 

of genetic information and its structure is governed from the subtle balance of noncovalent interactions 

among DNA building blocks. The most prominent role is played by interactions between DNA bases 

and two binding motifs can be recognized: planar hydrogen bonding and vertical stacking. 

In this work we investigate separately the roles of the dispersion energy and electrostatic energy on 

the geometry and stability of B-DNA helix. We performed series of molecular dynamics simulations 

with empirical force field and hybrid QM/MM molecular dynamics simulations where the dispersion or 

electrostatics term are suppressed or increased. We show that the decrease of the dispersion term 

leads to increase of vertical separation of the bases as well as loss of helicity and thus resulting in 

ladder–like structure. A decrease of the electrostatic term produces the unwinding of the DNA strands. 

We can conclude that the simulations clearly show that the dispersion energy is responsible for the 

helical structure of the DNA. 

PP450 

Enzymatic Reaction Mechanism Revealed by Molecular Docking and QM/MM-MD 

Yohsuke Hagiwara 1 , Osamu Nureki 2 , Masaru Tateno 3 

1 Graduate School of Pure and Applied Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan, 

2 Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo, Japan, 3 Center for Computational 

Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan 

Aminoacyl-tRNA synthetases (aaRS’s) play a critical role in decoding genetic information located on 

genome DNA sequence, through catalyzing attachment of their cognate amino acid to 3’-end of the 

specific tRNA (aminoacylation). The fidelity of translation is assured by their strict discrimination of the 

cognate amino acids from non-cognate ones. However, in the case of valine, isoleucine, and leucine, 

all of which are similar to each other in their sizes and hydrophobicity, the cognate enzymes, i.e. 

leucyl-, valyl-, and isoleucyl-tRNA synthetases (LeuRS, ValRS, and IleRS, respectively), have 

difficulties in the strict discrimination of their specific amino acid if they perform only the single catalytic 

reaction, producing mis-aminoacylated tRNA’s, such as Ile-tRNA Leu . To avoid generating such 

incorrect products, the enzymes accomplish another reaction, i.e. ‘editing’, through which those 

enzymes hydrolyze mis-products by themselves. Although several crystal structures of those aaRS 

systems have been determined in complex with the cognate tRNAs, reaction mechanisms of editing 

have not yet been clarified. The reasons are as follows: (i) no crystal structures of the enzymes in 

complex with the substrate, i.e. the cognate tRNA of which the 3’-terminus is bound to nonspecific 

amino acid. (ii) nucleophile to trigger the reaction has not yet been identified in the crystal structures 

due to lower quality of X-ray crystallographic data. 

Our goal is to elucidate reaction mechanisms of editing by those aaRS systems; in this presentation, 

we focus on the LeuRS system. First, in order to carry out molecular docking of the LeuRS•ValtRNA 

Leu complex, we adopted our novel molecular docking algorithm. Characteristic features of our 

docking scheme are to enable to predict conformational changes of protein induced by interaction with 

a substrate and waters (induced fitting), and also, to identify configuration of ordered water molecules 

located in the substrate-binding site. In the case of the LeuRS•Val-tRNA Leu complex, structural water 

molecules in the active site have not yet been identified experimentally so far, as mentioned above. 

This docking simulation is coupled to molecular dynamics (MD) calculations with explicit solvent water 

molecules, thus being referred to as the “Fully Solvated Dynamical Docking” (FSDD) scheme [1]. 

Thereby, we have successfully identified ordered water molecules forming stable hydrogen bond 

networks in the active site composed of LeuRS, Val-tRNA Leu . It should be noted here that one of such 

waters is located at an appropriate position as nucleophile in our modelled structure. 

Thus, for the entire structure of the LeuRS•Val-tRNA Leu complex constructed by the FSDD calculation, 

we performed ab initio electronic structure calculations to elucidate the first phase in reaction of 

editing. For the purpose, we used our QM/MM program recently developed, which connects QM 

(gamess) and MM (amber) engines [2, 3]. For QM regions composed of about 120 atoms, HF/DFT 

hybrid all-electron calculations were adopted with use of the B3LYP functional. Thereby, it has been 

found that LUMO is located on the reaction point of the substrate, suggesting that the water identified 

attacks LUMO as nucleophile. Therefore, we next performed QM/MM MD calculations to simulate 

reaction processes. In the poster session, we discuss detailed reaction mechanisms of editing by the 

LeuRS system, which is elucidated for the first time. 

[1] Hagiwara, Y.; Tateno, M. to be published. 

[2] Ohta, T.; Hagiwara, Y.; Kang, J.Y.; Nagao, H.; Tateno, M. submitted. 

[3] Hagiwara, Y.; Tateno, M. to be published.



PP451 

Density Functional Theory Augmented with an Empirical Dispersion Term – DFT-D – What is 

the Effect of the Many-Body Terms and Higher Order Contributions to Dispersion? 

Petr Jurecka 1 , Mikulas Kocman 1 , Pavel Hobza 2 

1 Palacky University, Olomouc, Czech Republic, 2 Institute of Organic Chemistry and Biochemistry, 

Academy of Sciences of the Czech Republic, Prague, Czech Republic 

Recently it was shown that one of the major drawbacks of current density functionals – their inability to 

describe the long-range dispersion interaction – can be mitigated by adding an empirical dispersion 

correction [1]. With the growing number of the DFT-D applications we are gradually gaining the 

necessary validation of the newly developed dispersion parametrization [2]. Fairly good accuracy 

comparable with the results of much more demanding wave-function based methods was found for the 

interaction energies of various intermolecular complexes as well as for their geometries. DFT-D, 

although designed for the intermolecular interactions, succeeded in predicting the lowest energy 

conformers of the single peptide molecules, such as phenylalanyl-glycyl-glycine. The dispersion 

correction improves also the DFT force constants calculated for small peptides [3]. 

Here, we investigated whether the DFT-D accuracy can be improved by adding the many-body terms 

and C8 contributions to dispersion. Results are judged based on the RMS error for the S22 reference 

set of molecules [4] and other small complexes. The effect of the three-body terms is in most cases 

rather small. Contribution of the C8 term, which is known to be non-negligible, improves the accuracy 

of the original dispersion parametrization only slightly, most likely because in the C6-only scheme it is 

in part fitted into the damping function. This explains why the dispersion correction based on the C6 

term only is usually fairly successful, in spite of its simplicity. 

PP452 

The Vibrational Band Origins and Potential Energy Surface of Fluorine Isocyanate and its 

Isomers 

Frank Pickard, Yukio Yamaguchi, Henry Schaefer III 

The University of Georgia, Center for Computational Chemistry, Athens, GA, United States 

The isomerisation pathways of fluorine isocyanate (FNCO) have been studied using coupled-cluster 

theory incorporating all single and double excitations (CCSD), along with the perturbative inclusion of 

connected triple excitations [CCSD(T)]. These calculations employed large one particle correlation 

consistent basis sets (cc-pVQZ). The final potential energy surface (PES) of this system was 

computed using valence focal point extrapolations [1]. Accurate vibrational band origin (VBO) 

predictions were made for all minima on the PES. Excellent agreement was found between the 

predicted and observed [2] VBOs for FNCO. The VBO predictions for the heretofore unsynthesized 

high energy isomers of FNCO should assist in their eventual experimental characterization. The 

calculated PES also demonstrates that several high energy isomers should be viable synthetic targets. 

[1]. Császár, A. G.; Allen, W. D.; Schaefer, H. F. J. Chem. Phys. 1998, 108, 9751. 

[2]. Jacobs, J.; Juelicher, B.; Schatte, G.; Willner, H.; Mack, H. G. Chem. Ber. 1993, 126, 2167. 

[1] Grimme, S. J. Comput. Chem. 2004, 25, 1463-1473. 

[2] Jurečka, P.; Černý, J.; Hobza, P.; Salahub, D. R. J. Comput. Chem. 2007, 28, 555-569. 

[3] Černý, J.; Jurečka, P.; Hobza, P.; Valdés H. J. Phys. Chem. A 2007, 111, 1146-1154. 

[4] Jurečka, P.; Šponer, J.; Černý, J.; Hobza, P. Phys. Chem. Chem. Phys. 2006, 8, 1985-1993.



PP453 

Exploration of Matrix Exponentiation Issues Involved with Non-Reversible Rate Matrices Used 

in the Modelling of DNA Sequence Evolution 

Harold Schranz 

Computational Genomics, John Curtin School of Medical Research, ANU, Canberra, ACT, Australia 

Modelling DNA sequence evolution involves the exponentiation of instantaneous rate matrices [1]. The 

most commonly employed rate matrices impose the restriction that evolutionary processes are timereversible. 

Relaxing the assumption of time-reversibility requires consideration of non-reversible 

matrices. 

For particular classes of matrices, the most popular eigendecomposition based matrix exponentiation 

algorithm is sometimes inaccurate and may even fail completely [2]. Predicting the conditions for 

failure is of considerable practical interest as is the application of more robust exponentiation 

methods. Eigendecomposition works well for normal matrices (that commute with their conjugate 

transposes) but breaks down when the matrix does not have a complete set of linearly independent 

eigenvectors or when the condition number of the matrix of eigenvectors is large (near singular) [3]. 

Here we tested whether such pathological rate matrices exist in nature by constructing them 

from concatenated protein coding gene alignments from microbial genomes, primate genomes 

and independent intron alignments from primate genomes. The Taylor series expansion and 

eigendecomposition matrix exponentiation algorithms were compared to the less widely employed, but 

more robust, Padé with scaling and squaring algorithm for nucleotide, dinucleotide and trinucleotide 

rate matrices. Our results [4] indicate that development of robust software for computing nonreversible 

dinucleotide, codon and higher evolutionary models requires implementation of the Padé 

with scaling and squaring algorithm. 

[1] Lio P, Goldman N. Genome Res 1998, 8,1233–44. 

[2] (a) Moler CB, Van Loan CF. SIAM Review 2003, 45, 3–49. (b) Golub GH, Loan CFV: Matrix computations (3rd 

ed.). Baltimore, MD, USA: Johns Hopkins University Press, 1996. 

[3] (a) Smith R. Numerische Mathematik 1967,10, 232–240. (b) Demmel J: On condition numbers and the 

distance to the nearest ill-posed problem. Numerische Mathematik 1987, 51, 251–289. (c) Bai Z, Demmel J, 

McKenney A. ACM Trans. Math. Softw. 1993, 19, 202–223. 

[4] Harold W. Schranz, Von Bing Yap, Simon Easteal, Rob Knight and Gavin A. Huttley, in preparation. 

PP454 

The Electronic State of Blue Cu Protein Revealed by the New QM/MM Interface Program 

Takehiro Ohta 1 , Yohsuke Hagiwara 2 , Masaru Tateno 3 

1 Institute for Materials Chemistry and Engineering, Kyushu University, Kasuga, Fukuoka, Japan, 

2 Graduate School of Pure and Applied Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan, 

3 Center for Computational Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan 

Metalloenzymes are involved in various biological functions such as electron transfer, storage of 

metals, binding of dioxygen, turnover of substrates, and configuration of protein structure. 

Understanding the coordination geometry and electronic structure of metal active sites in the 

metalloenzymes is of fundamental biophysical importance to gain insight into the structure/function 

correlation of those biological macromolecules. Azurin 

is one of the metalloenzymes, for which biological 

function is related to electron transfer. The copper ion 

bound to its active site is coordinated by five amino acid 

residues, cystein (Cys), two histidines (His), methionine 

(Met), and a backbone carbonyl oxygen of glycine 

(Gly). Here, we present a QM/MM study of azurin, in 

which our newly developed program that interfaces the 

quantum mechanical (QM) calculation program gamess 

with the molecular mechanics (MM) simulation program 

amber is used [1, 2]. 

Our QM/MM energy evaluation method is based on an additive scheme, in which we consider 

polarization of the QM region induced by surrounding MM atoms. In this study the spin-unrestricted 

Hartree-Fock (UHF) / density functional theory (DFT) hybrid all-electron calculation with the B3LYP 

functional was adopted as the QM Hamiltonian. To assess the accuracy of the additive energy 

scheme, we employed two computational models, referred to as Model I and Model II. In Model I, 

electrostatic interactions between the QM and MM atoms were calculated by incorporating partial point 

charges of MM atoms into one-electron integration of QM Hamiltonian. In Model II, the electrostatic 

interactions between the QM and MM atoms were calculated at MM level, and thus, the electron 

density of the QM region was not allowed to be polarized by the partial point charges: this is referred 

to as the subtractive scheme. 

In order to obtain equilibrated structure in solvent, we first performed classical molecular dynamics 

(MD) simulation for 1ns with explicit solvent water molecules, started from a high resolution crystal 

structure of azurin. During the simulation, the protein structure was quite stable; the final snapshot was 

subjected to energy minimization at MM level. Then, started from the minimized structure, we 

performed QM/MM geometry optimization by using each calculation scheme of Models I or II. 

Comparison of the optimized structures obtained through two schemes showed that Model I provided 

the electronic property more consistent with spectroscopic experiments than that of the Model II 

calculation. This indicates that the explicit inclusion of electrostatic interaction into the QM Hamiltonian 

is essential for accurate descriptions of the copper site. With respect to the geometries, different 

descriptions of the copper coordination geometry were obtained between Models I and II, particularly 

for the coordinated bonds including a large dipole. Thus, it is suggested that modification of the QM 

Hamiltonian so as to interact with long-distance partial point charges of the environment is crucial for 

an accurate QM/MM description of both the geometrical and electronic properties of metal active sites. 

[1] Ohta, T., Hagiwara, Y., Kang, J.Y., Nagao, H., and Tateno, M., to be published. 

[2] Hagiwara, Y, Ohta, T., and Tateno, M., to be published.



PP455 

Investigation of the Invisible Water Effect for Quantitative Docking Analysis of Protein-Ligand 

Complexes 

Hitoshi Goto 1 , Shigeaki Obata 1 , Taku Sugiyama 1 , Naofumi Nakayama 1 , Kouichi Nishigaki 2 

1 Toyohashi University of Technology, Toyohashi, Japan, 2 Saitama University, Saitama, Japan 

X-ray crystal structure analysis of the target protein with specific ligand is very important for 

pharmaceutical developments and the drug-discoveries, such as investigation of the protein function, 

hypothetical formation for the activation mechanism, purification of the binding compound, the binding 

site determination, and etc. Although we can expect the experimental fact provides us the most 

appropriate structure for quantitative evaluation of the binding energy with protein-ligand docking 

calculations, in many practical cases, we know it is very very difficult. 

Part of the problem is, we call, “invisible water effect”, that is, the role of the water molecules and/or 

the water cluster not determined in the X-ray crystal structure analysis. In this paper, as the practical 

examples of the effect, we introduce our recent observations in the studies on two pharmaceutical 

important enzymes with both molecular mechanics and molecular dynamics calculations: 1) the 

unfolding transition on HIV-1 protease-inhibitor complexes during crystal structure optimization, and 2) 

deformation of A-B domains of cathepsin E crystal structure. 

PP456 

Density-Functional Study of Acyclic and Cyclic Phosphoryl Transfer Reactions in Solution: 

Comparison with Experimental Thio and Isotope Effect Measurements 

Francesca Guerra, Jiali Gao, Darrin M. York 

Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, MN, 

United States 

Phosphoryl transfer reactions are ubiquitous in biology, and are important in cell signaling, energy 

transfer and the synthesis and breakdown of DNA and RNA. Of particular importance is in the 

unraveling of the mechanisms whereby RNA enzymes, or ribozymes, are able to catalyze fairly 

intricate reactions with efficiency that rival many protein enzymes. Experimentally, common methods 

used to probe mechanism and the nature of the rate-controlling transition state involve the study of 

chemically modified and/or isotopically labeled model reactions. Typically, sulfur is used to study socalled 

thio effects, and 18 O and 34 S are used to measure isotope effects, both of which provide 

information about the reaction. In order to translate experimental measurements into a detailed picture 

of mechanism requires the use of a theoretical model. Density-functional theory provides a powerful 

tool to aid in the interpretation of experimental thio and isotope effects, and provide detailed insight 

into the molecular mechanisms of phosphoryl transfer reactions. In the present work, DFT is used to 

study a series of acyclic and cyclic phosphoryl transfer reactions, including sulfur-substitutions, for 

which kinetic isotope measurements have been made. A comparison of the performance of modern 

DFT functionals for these reactions, including B3LYP and M06-2X, and implicit solvation methods 

including COSMO, PCM and SM6, has been made and used to assess the overall reliability and 

accuracy of the models and to establish reliable benchmarks in the gas phase and in solution. These 

benchmarks serve as key data in the development of new-generation semiempirical quantum models, 

such as the AM1/d-PhoT Hamiltonian, that can be used in combined QM/MM simulations in more 

complex aqueous and solvated macromolecular environments. Together with experiments, the 

present results provide new insight into the mechanisms of phosphoryl transfer reactions in solution, 

and catalyzed by enzymes and ribozymes. 

Fig. 1 X-ray structure of HIV-1 protease-inhibitor complex and 

the optimized structure with appearance of invisible water molecules



PP457 

Photodissociation of the Water Dimer: A 12-D Quasiclassical Study 

Gustavo Avila, Geert-Jan Kroes, Marc Van Hemert 

Leiden University, Leiden Institute of Chemistry, Leiden, Netherlands 

The ab initio study of the photodissociation of the water dimer in its first absorption band is the first 

step in the understanding of the VUV liquid water absorption spectrum that is so remarkably shifted 

towards the blue by around 1 eV with respect to the gas phase spectrum. 

PP458 

Generator Coordinate Gaussian Basis Sets for the First-row Atoms: A New Alternative for 

Pople’s and Dunning’s Basis Sets 

Moacyr Comar Jr. 1 , Francisco Lima 2 , Albérico Da Silva 3 

1 Instituto de Ciências Exatas - UFAM, Manaus, Amazonas, Brazil, 2 Instituto de Química de São Carlos 

- USP, Instituto de Química de São Carlos - USP, Brazil, 3 Instituto de Química de São Carlos - USP, 

Instituto de Química de São Carlos - USP, Brazil 

Since its development in the eighties, the Generator Coordinate Hartree-Fock (GCHF) method [1] has 

been used as an important tool to generate universal and adapted Gaussian basis sets to be used in 

atomic and molecular calculations. In 2003, we published a new way to discretize the integral equation 

of the GCHF method [2] so that we could improve the efficiency of the GCHF method in generating 

Gaussian basis sets. This new way of discretizing the integral equation of the GCHF method is done 

by a polynomial and the name of the method was then changed to polynomial version of the Generate 

Coordinate Hartree-Fock (pGCHF) method. Here, we now present Gaussian basis sets for the firstrow 

atoms of the periodic table that are an excellent alternative for the well-known Pople´s and 

Dunning´s Gaussian basis sets since with our first-row basis sets one is able to get results comparable 

or better than the Pople´s and Dunning´s Gaussian basis sets but with a lower computational cost, 

mainly when compared to the Dunning´s correlation consistent Gaussian basis sets. 

[1] Da Silva, A.B.F.; Da Costa, H.F.M. and Trsic, M., Mol. Phys. 1989, 68, 433-445. 

[2] Barbosa, R.C. and Da Silva, A.B.F., Mol. Phys. 2003, 101, 1073-1077. 

water absorption spectrum in the gas phase, 1:50 Ar matrix, liquid and solid (20K) 

(MCvH ~1975). 

The basic ingredients in the ab initio calculation of absorption spectra are potential energy surfaces for 

all degrees of freedom for both ground and excited states and subsequently the complete description 

of the nuclear motion on these potential energy surfaces. For the water monomer such a calculation 

has been performed successfully and perfect agreement between the theoretical and experimental 

spectrum was obtained [1]. 

For the water dimer the situation is complicated by the high dimensionality. Our strategy in this case 

initially has been a reduced dimensionality treatment [2]. That treatment was able to explain the blue 

shift but lacked detail. Afterwards a full 12-dimensional study was performed [3] where the essential 

parts of the ground and excited state potentials were calculated on the MRCI level using the grow 

approach of the Collins group [4]. The necessary first and second order derivatives were calculated at 

a lower level of electron correlation, i.e. MCSCF, in order to avoid prohibitive computer times. The 

spectra were calculated using the quasiclassical approximation. This appeared to be a successful 

approach since now, among others, the predicted ‘red tail’ of the dimer spectrum could be reproduced. 

In this contribution we will show how the spectra can still be further improved by calculating the first 

and second order derivatives at the same level of electron correlation as the energies. 

[1] R. van Harrevelt and M.C. van Hemert, J. Chem. Phys. 2001, 114, 9453. 

[2] L. Valenzano, M.C. van Hemert and G.J. Kroes, J. Chem. Phys., 2005, 123, 034303. 

[3] G. Avila, G.J. Kroes and M.C. van Hemert, J. Chem. Phys. 2008, 128, 144313. 

[4] M. A. Collins, Theor. Chem. Acc., 2002, 108, 313.



PP459 

Three-Body Corrections to Scaled Opposite Spin Second-Order Møller-Plesset Perturbation 

Theory 

Robert DiStasio, Alex Thom, David Casanova, Martin Head-Gordon 

University of California at Berkeley Department of Chemistry, Berkeley, CA, United States 

In this work, we present several theoretical frameworks in which three-body electron correlation can be 

included within scaled opposite spin second-order Møller-Plesset (SOS-MP2) perturbation theory [1]. 

We derive these three-body corrections by considering a subset of the triples contribution in fourthorder 

Møller-Plesset perturbation theory that only includes excitations involving opposite spin 

electrons. These new models include two empirical parameters based on extensive benchmarking 

with respect to highly accurate coupled cluster models. As a result, this approach provides a simple 

and economical electronic structure method that has the potential of achieving chemical accuracy in 

the prediction of thermochemical properties for systems that are currently too large to be treated using 

highly-accurate methods like CCSD(T). 

PP460 

Structures of the Mono-hydrated Guanine-Cytosine Cation 

Heather Jaeger, Henry Schaefer III 

University of Georgia, Center for Computational Chemistry, Athens, GA, United States 

A detailed study of the mono-hydrated guanine-cytosine cation potential energy surface, using B3LYP 

with a DZP++ basis, reveals seven local minima. Structural changes from the isolated guaninecytosine 

cation geometry upon hydration have been observed and are dependent on the location of 

the water molecule. The preferred binding site of the water molecule is at the hydrogen atom on 

guanine which replaces the deoxyribose in DNA. At this geometry water binds to the base pair with 13 

kcal/mol and is the global minimum. Four local minima were found having binding energies 3 kcal/mol 

above the global minimum, and two others were found with energies 7 kcal/mol above the global 

minimum. The positive charge of the complex is localized on the guanine molecule which agrees with 

experimental evidence that guanine has a lower ionization potential than cytosine. 

[1] Jung, Y.; Lochan, R. C.; Dutoi, A. D.; Head-Gordon, M. J. Chem. Phys. 2004, 121, 9793-9802.



PP461 

Application of Ab Initio DMRG to the Physics of Conjugated π-Electron Systems 

Johannes Hachmann, Jonathan J. Dorando, Debashree Ghosh, Garnet Kin-Lic Chan 

Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, United States 

We present some recent developments in the ab initio density matrix renormalization group (DMRG) 

method for quantum chemical problems, in particular our local, quadratic scaling algorithm [1] for lowdimensional 

systems. This method is particularly suited for the description of strong nondynamic 

correlation, and allows us to compute numerically exact (FCI) correlated energies for large active 

spaces, up to one order of magnitude larger then can be obtained by conventional CASCI techniques. 

PP462 

Molecular Conductance through a Graphene Sheet 

Haitao Wang, Garnet Chan 

Department of Chemistry and Chemical Biology, Cornell University, Ithaca,NY, United States 

Graphene, as a single layer of carbon planner sheet, draws great attention since its experimental 

realization. Its interesting linear energy dispersion relationship offers a unique platform for the study of 

the electronic transport problem. In this poster, we will investigate the conductance through a 

graphene sheet when potassium is added on the top to charge the sheet. 

We will review the problems, predominantly in the field of organic electronic materials, which we 

studied with the ab initio DMRG: 

1) metal-insulator transition in hydrogen chains [1] 

2) all-trans polyacetylene oligomers [1] 

3) acenes [2] 

4) polydiacetylene oligomers [3] 

5) graphene nanopatches [3]. 

Organic electronic materials and the correlation in their quasi-1D-conjugated π-backbone pose are 

serious challenge to conventional quantum chemical methods. With the ab initio DMRG we can 

correlate the complete π-valence space, which determines the qualitative physics of these molecules, 

and obtain numerically exact results. 

In our studies we stress the analysis of the obtained ground and excited states with respect to 

particular physical regimes in order to categorize their inherent nature. 

[1] Hachmann, J.; Cardoen, W.; Chan, G. K.-L. J. Chem. Phys. 2006, 125, 144101. 

[2] Hachmann, J.; Dorando, J. J.; Aviles, M.; Chan, G. K.-L. J. Chem. Phys. 2007, 127, 134309. 

[3] unpublished.



PP463 

The Role of Ligands in Developing Mn 4 -based Single-Molecule Magnets and Single-chain 

Magnets 

Nguyen Anh Tuan, Shin-ichi Katayama, Dam Hieu Chi 

1 School of Materials Science, Japan Advanced Institute of Science and Technology, 1-1, Asahidai, 

Nomi, Ishikawa, 923-1292, Japan, 2 Faculty of Physics, Hanoi University of Science, 334 Nguyen Trai, 

Thanh Xuan, Hanoi, Viet Nam 

Distorted cubane Mn 4 clusters have been known as single-domain nanoscale magnetic particles 

(single-molecules magnets, SMMs) [1]. They display slow magnetization relaxation below their 

blocking temperature. This behavior results from a significant ground spin state (S T ≈ 9/2) combined 

with a large and negative Ising (or easy-axis) type of magnetoanisotropy, as measured by the axial 

zero-field splitting parameter, D ≈ −(0.65~0.75) K. This combination leads to a significant barrier (U) to 

magnetization reversal, whose maximum value is given by (S T 2 − 1/4)|D| = 20|D|. There are various 

distorted cubane [Mn 4 (µ 3 -O 3 )(µ 3 -X)(O 2 CR) 3 (L1,L2) 3 ] (X, R, L1, and L2 = various) have been 

synthesized [1]. Each Mn 4 SMM is distinguished from the other by its ligands and also exhibits 

different characteristics due to the function by ligands. Besides, the existence of the dimer structure of 

distorted cubane Mn 4 O 3 Cl 4 (O 2 CEt) 3 (py) 3 [2] shows that distorted cubane Mn 4 can become building 

block for developing new manganese SMMs and single-chain magnets (SCMs). Here the particular 

ligand structure in Mn 4 O 3 Cl 4 (O 2 CEt) 3 (py) 3 was observed to be responsible for the dimer formation. 

Based on these observations, we realize that ligands must play an important role in determining 

magnetic behavior of distorted cubane Mn 4 , as well as in combining Mn 4 building blocks to develop 

new manganese SMMs and SCMs. Therefore, we explore systematically the role of ligands in 

determining the geometric structure, electronic structure, and magnetic properties of distorted cubane 

Mn 4 SMMs by using first-principles calculations based on density-functional theory, in order to support 

for designing new Mn 4 SMMs, as well as to look for new Mn 4 building blocks for developing new SMMs 

and SCMs. Our results show that the distorted cubane geometry and the ground spin state of Mn 4 

SMMs are preserved even if the µ 3 -O atoms are changed by X 2 -type ligand complexes such as NCH 3 . 

The results reveal more possibilities of designing new Mn 4 SMMs and combining them for developing 

new manganese SMMs. Our results also show that the distorted cubane geometry and the ground 

spin state of Mn 4 SMMs are preserved even if the O atoms of O 2 CR are changed by X 2 -type ligand 

complexes. The results also give more possibilities of designing new Mn 4 building blocks and 

combining them. Our results show that the ground spin states of distorted cubane Mn 4 molecules can 

be controlled by substituting L1 and L2 [3]. Besides, the mechanism of exchange couplings between 

manganese ions in distorted cubane Mn 4 SMMs is elucidated. The results show the correlation among 

the charge and spin states of manganese ions and the magnetic structure of distorted cubane Mn 4 

SMMs [3]. These results also reveal the possibility of designing new distorted cubane Mn 4 SMMs with 

S T = 15/2. Finally, we observe significant spin polarizations on peripheral ligands L1 and L2 in 

distorted cubane Mn 4 SMMs [3]. These spin polarizations can enhance the exchange couplings 

between Mn 4 building blocks for developing Mn 4 -based SMMs and SCMs. 

PP464 

Ring Molecules as Basic Modules in Metamaterials? 

Stephan Bernadotte 1,3 , Wim Klopper 1,2,3 , Ferdiand Evers 1,2 

1 Institut für Nanotechnologie, Karlsruhe, Germany, 2 Institut für Physikalische Chemie, Universität, 

Karlsruhe, Germany, 3 Institut für Theorie der Kondensierten Materie, Universität, Karlsruhe, Germany 

An important research direction in material sciences is the design of ''metamaterials''. Metamaterials 

exhibit an artificial unit cell, for instance a split ring resonator that is embedded in a crystalline 

superstructure consisting of many other such cells. The design of split ring resonators aims at 

customizing the electromagnetic properties. Most notably one would like to create a material with an 

index of refraction that is negative at optical frequencies. In order to go to such high frequencies the 

current resonator size is too large; whether ring molecules may a viable alternative, is a very important 

motivation of our research. 

The dynamical electromagnetic response of electrons on a one-dimensional ring is studied in the 

present work. The applicability of this model reaches from π-systems of organic ring molecules to 

clean metal rings. The electrons are treated with a parabolic (''free'') dispersion as well with a tight 

binding one. First we calculate the density and current response with the Kubo formula. The 

corresponding response kernels are dressed at the RPA level. From this the permittivity, the 

permeability and the index of refraction of an array of such rings are calculated. 

By introducing a slit on the ring we observe that the resonance of the magnetic response is shifted 

near to the electric resonance so that the real part of the index of refraction may become negative. We 

study the analytic structure of the index of refraction and its dependency on damping, screening, the 

size of the system, the number of electrons on the ring and the fill factor respectively. Finally, 

implications for the material design are discussed. 

[1] S. M. J. Aubin, M. W. Wemple, D. M. Adams, H.-L. Tsai, G. Christou, and D. N. Hendrickson, J. Am. Chem. 

Soc. 1996, 118, 7746-7754. 

[2] W. Wernsdorfer, N. Aliaga-Alcalde, D. N. Hendrickson, and G. Christou, Nature (London) 2002, 416, 406. 

[3] N. A. Tuan, S. Katayama, D. H. Chi, A Systematic Study of Influence of Ligand Substitutions on the Electronic 

Structure and Magnetic Properties of Mn 4 Single-Molecule Magnets, Phys. Chem. Chem. Phys. 2008, B806661B.



PP465 

Role of Solvent and Dispersion Forces on the Stability of the DNA Double-Helix 

Martin Kabelác, Pavel Hobza 


Prague, Czech Republic 

A role of dispersion and presence of the solvent on the stability and geometry of short sequences of DNA (up to 

tetramers) was calculated for the first time at ab initio quantum chemical level. The systems were fully relaxed 

using the resolution of identity DFT method with/without empirical dispersion term fitted to the CCSD(T) data. The 

optimizations were performed in the presence/absence of water which was modelled implicitly using the 

conductor-like screening model (COSMO) as well as counterions. The final stabilization energies and geometries 

were mutually compared. The absence of dispersion forces leads to significant distortion of the structure of DNA 

and separation of stacked bases in comparison with canonical form of DNA. The presence of the solvent leads to 

the destabilization of the double-helical structure, however the optimized structure is pretty close to the canonical 

form of B-DNA. 

PP466 

Design of a Synthetic Catalytic Pore for Cation-Olefin Cyclizations; DFT and MD-Simulations 

Approach 

Daniel Emery, Guillaume Bollot, Jiri Mareda 

Department of Organic Chemistry, University of Geneva, Geneva, Switzerland 

Cation-olefin cyclizations are very useful, albeit complex, carbon-carbon bond forming reactions. For 

such cyclizations a high degree of stereocontrol is often achieved by cyclases and antibodies in 

biogenesis of natural products. [1] In the laboratory the cation-olefin cyclizations are accomplished by 

solvolysis of an appropriate substrate, although with lesser stereocontrol. Here we describe computer 

modeling studies of cation-olefin reactions aimed at elucidating the mechanism of the cyclization at the 

active site of the catalytic antibody and design of a new synthetic catalyst able to mimic the action of 

the antibody. 

The electronic structures, energies, and equilibrium geometries of reaction intermediates involved in 

the cation-olefin cyclizations were studied first by density functional theory (DFT) methods. Thus, 

obtained stationary point geometries were then docked into the active site of the catalytic antibody 

4C6. [2] Subsequent MD simulations on the protein part of the complex led to average geometry that 

was used to establish the theoretical model of the antibody active site where only the key residues of 

the biocatalyst were retained for further investigation by quantum mechanics. Using the ONIOM 

method and several density functionals, the theozyme model was used to investigate the key 

pathways of antibody catalyzed cation-olefin cyclizations. 

Understanding of the cyclization mechanism and mapping of the antibody’s active site provided 

necessary data to propose the structure of an artificial chiral catalyst. Based on the concept of rigidrod 

β-barrels developed [3], the internal hollow space of the β-barrel was populated with the 

appropriate residues in order to mimic the catalytic effect of the antibody. The predicted catalytic 

activity of the proposed rigid-rod β-barrel was evaluated by the DFT model calculations. 

[1] (a) T. Li; K. D. Janda; R. A. Lerner: Acc. Chem. Res. 30, 115, 1997 ; (b) J. Hasserodt; K. D. Janda: 

Tetrahedron 53, 11237, 1997 ; (c) K. Wendt; G. Schulz; E. J. Corey; D. Liu: Angew. Chem. Int. Ed. 2000, 39, 

2813. 

[2] X. Zhu; A. Heine; F. Monnat; K. N. Houk; K. D. Janda; I. A. Wilson: J. Mol. Biol. 2003, 329, 69. 

[3] N. Sakai; J. Mareda; S. Matile : Acc. Chem. Res. 2005, 38, 79.



PP467 

Projected Entangled Pair States as a Multi-Dimensional Ansatz for Non-Dynamic Correlation in 

Huge Active Spaces 

Dominika Zgid, Garnet Chan 

Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14850, United States 

Modern quantum chemistry methods have become very efficient in addressing dynamic correlation. 

However, the success of quantum chemical approaches is still limited if one considers the treatment of 

non-dynamic correlation. For example, many inorganic systems with many closely degenerate states 

still cannot be qualitatively described by current methods. Although the Density Matrix 

Renormalization Group (DMRG) has proven to be very successful for the treatment of the 

multireference effects in systems with pseudo-one-dimensional connectivity, extended multidimensional 

systems with large active spaces are still too demanding for DMRG. Here, we present 

generalization of the DMRG ansatz to higher dimensions that is able to effectively recover nondynamic 

correlation in two-dimensional lattices. This ansatz is known in physics as the Projected 

Entangled Pair State (PEPS) ansatz and has been proven to work successfully in two-dimensional 

model systems. We present the theory of PEPS listing possible advantages and problems arising from 

such a treatment. Additionally, preliminary applications of our PEPS code are presented, such as to 

multi-center molecular magnets which both require very large active spaces and which possess 

intrinsic two-dimensional lattice connectivity. 

PP468 

Self-Cleavage Catalysis of the Hepatitis Delta Virus Ribozyme Investigated by QM/MM 

Calculations 

Pavel Banáš 1 , Lubomír Rulíšek 2 , Daniel Svozil 2 , Nils Walter 3 , Jiri Šponer 4 , Michal Otyepka 1 

1 Palacky University, Department of Physical Chemistry, Olomouc, Czech Republic, 2 Institute of 

Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Czech 

Republic, 3 Department of Chemistry, Single Molecule Analysis Group, University of Michigan, Ann 

Arbor, United States, 4 Institute of Biophysics, Academy of Science of the Czech Republic, Brno, 

Czech Republic 

The hepatitis delta virus (HDV) ribozyme is a catalytic RNA embedded in human pathogenic HDV 

RNA. Published experimental studies have established that the nucleotide C75 is essential for selfcleavage 

of the ribozyme. The exact catalytic role of C75 in the self-cleavage reaction remains 

debated. Structural data from X-ray indicate that C75 can act as the general base that initiates 

catalysis by deprotonating the 2’-OH nucleophile at the cleavage site, while a hydrated magnesium ion 

likely protonates the 5’-oxygen leaving group. In contrast, some mechanistic studies support the 

hypothesis that C75 may be protonated and acts as the general acid. We report combined quantum 

chemical/molecular mechanical calculations (ONIOM: MPW1K/6-31+G(d,p)/parm99) for the C75 

general base pathway, utilizing the available structural data for the wt-HDV genomic ribozyme as a 

starting point. Several starting configurations differing in magnesium ion position were considered and 

both one-dimensional and two-dimensional potential energy surface scans were used to explore 

plausible reaction paths. Our calculations show that C75 is readily capable of acting as the general 

base, in concert with the hydrated magnesium ion as the general acid. The calculated energy barrier 

of the proposed mechanism, ~20 kcal/mol, would lower the reaction barrier by ~15 kcal/mol compared 

to the uncatalyzed reaction and is in good agreement with experimental data. Thus, the hypothesis 

that C75 serves as the general base has to be considered chemically feasible. Due to the absence of 

suitable experimental starting structures that would be consistent with the general acid mechanism we 

could not evaluate the alternative pathway in which C75 is protonated and acts as the general acid.



PP469 

MOLEONLINE: An Interactive Web-Based Tool to Find and Analyze Molecular Channels, 

Tunnels and Pores. 

Martin Petřek 1 , Jaroslav Koča 1 , Michal Otyepka 2 

1 National Centre for Biomolecular Research, Masaryk University, Brno, Czech Republic, 2 Department 

of Physical Chemistry, Palacky University, Olomouc, Czech Republic 

MOLEOnline provides interactive and easy-to-use web interface to analyze molecular channels by 

MOLE, which is an universal toolkit for rapid and fully automated location and characterization of 

channels, tunnels and pores in molecular structures [1]. This tool is freely available on the Internet 

(http://mole.chemi.muni.cz) and overcomes many of the shortcomings and limitations of the recently 

developed CAVER software [2]. The core of MOLE algorithm is a Dijsktra’s path search algorithm, 

which is applied to a Voronoi mesh. Robust tests on a variety of molecular structures show that MOLE 

is a powerful software for exploring large molecular channels, complex networks of channels and 

molecular dynamics trajectories (AMBER) in which analysis of a large number of snapshots is 

required. 

PP470 

A Systematic Study of UVA Chemical Sunscreen Filters. 

Jacqueline Cawthray, Mark Buntine, Stephen Lincoln 

Department of Chemistry, University of Adelaide, Adelaide, South Australia, Australia 

Sunscreens are a popular and effective method of protecting against the damaging effects of solar 

radiation including skin cancer and immune system suppression. Chemical sunscreen filters achieve 

this by absorbing ultraviolet radiation and are classified as UVB (280 – 320 nm) or UVA (320 – 400 

nm) sunscreens depending on the wavelengths in which they absorb energy. An efficient sunscreen 

must afford protection against both UVB and UVA. The majority of chemical filters approved for use 

worldwide are UVB absorbers and the few UVA filters approved provide minimal UVA protection or 

show only moderate photostability. For example, the enol form of the β-diketone, BMDBM (I), absorbs 

strongly in the UVA region but is prone to photodegradation via the keto form (II). 

H 

O 

O 

O 

O 

O 

O 

I 

II 

We have been exploring the use of theoretical methods as a tool in the design of potentially new 

sunscreens. In particular, we have investigated the ability of the SAC-CI method to represent the 

trends and properties important to the photochemistry of a series of known β-diketones. In most 

cases, the SAC-CI theoretical spectra accurately describe the experimental spectra. This information 

can then be applied to the design of potentially new sunscreen filters having the desired properties. 

Our latest results will be presented. 

[1]. Petrek, M., Kosinova, P., Koca, J., Otyepka, M. Structure 2007, 15, 1357. 

[2]. Petrek, M., Otyepka, M., Banas, P., Kosinova, P., Koca, J., and Damborsky, J. BMC Bioinformatics 2006, 7, 

316.



PP471 

Quantum Chemical Simulations of Acetone Adsorption on SWCNTs 

Yoshifumi Nishimura 1 , Dmitry Kazachkin 2 , Eric Borguet 2 , Stephan Irle 1 

1 Institute for Advanced Research and Department of Chemistry, Nagoya University, Nagoya, Japan, 

2 Department of Chemistry, Temple University, Philadelphia, United States 

Many studies of the interaction between single walled carbon nanotubes (SWCNTs) and small 

molecules such as acetone have already been reported both experimentally and theoretically, aiming 

at the development of advanced SWCNT-based nanosensors [1,2]. However, many aspects of such 

interactions are unknown as of yet. Therefore, using the dispersion-augmented self-consistent-charge 

density functional tight binding (SCC-DFTB-D) method, we performed quantum chemical model 

studies of acetone molecules physisorbed on SWCNTs. 

First, we performed a rigorous benchmark of the SCC-DFTB-D method against ab initio MP2 and 

higher levels of theory using large basis sets for a coronene-acetone model system. We found that 

physisorption energy differences between SCC-DFTB-D and counter-poise corrected 

MP2/QZVPP//MP2/SVP (MP2 with highly polarized quadruple zeta basis set single point energies for 

MP2 with polarized split valence basis set geometries) adsorption energies are typically smaller than 2 

kJ/mol, which is an excellent agreement. 

Second, we applied SCC-DFTB-D to the study of the physisorption of acetone on 10 Å long (6,5) and 

(11,9) open-ended SWCNT fragments, terminated by hydrogen atoms. We considered adsorption at 

three distinct sites – exohedral, endohedral, and at the groove sites of two tubes. We found a clear 

correlation between sidewall curvature and physisorption energy (See Figure 1). In addition, 

adsorption at the groove sites was found to be about 1.9 times stronger than exohedral adsorption at a 

single tube. The acetone-SWCNT interactions are largely dominated by dispersion. Conformations 

where the carbonyl group of acetone is parallel to the six membered rings are energetically most 

favorable, since these have the largest molecule-surface contact areas. Three distinct desorption 

peaks are observed experimentally in temperature-programmed desorption mass spectroscopy (TPD- 

MS) experiments, suggesting three distinct sites [3]. The magnitude of experimentally determined 

interaction energies can be compared with the computational studies. We will further quantify our 

results by presenting molecular dynamics simulations for the motion of acetone on pristine and 

oxidized tubes. 

PP472 

Acid-Base Properties of Sterically Demanding Borane–Phosphine Pairs and Implications for 

Metal-Free Hydrogen Activation 

Tibor András Rokob, Andrea Hamza, András Stirling, Imre Pápai 

Chemical Research Center of HAS, Budapest, Hungary 

The impossibility of Lewis adduct formation due to steric bulk opens promising synthetic pathways. 

Among others, metal-free hydrogen activation and catalytic hydrogenation have been achieved using 

unquenched donor/acceptor pairs, termed frustrated Lewis pairs (FLPs) [1]. Our recent computational 

mechanistic studies on the P(tBu) 3 + B(C 6 F 5 ) 3 + H 2 → [(tBu) 3 PH] + [HB(C 6 F 5 ) 3 ] − reaction have revealed 

that a weakly bound (tBu) 3 P···B(C 6 F 5 ) 3 complex enables simultaneous interaction of acidic and basic 

functionalities with H 2 , yielding the product in a strongly exothermic reaction [2]. We suggested 

reactant-side destabilization owing to frustration to be the key of this remarkable transformation. 

To promote understanding of the factors governing this reactivity, we now present systematic studies 

[3] on the heterolytic hydrogen splitting by various phosphine/borane pairs that were studied 

experimentally [4]. Structures and binding energies of weak R 3 P···BR′ 3 complexes have been 

determined and their structural features discussed. Net reaction energies have been calculated; their 

decomposition into terms including proton and hydride affinities (see Figure) confirms the importance 

of appropriate cumulative strength of the acid and base. Reaction profile and strain analysis of a 

frustrated and a classical system of comparable strength demonstrate quantitatively the role of 

frustration. 

Figure1. SCC-DFTB-D interaction energies for acetone-SWCNT plotted versus sidewall curvature 

[1] Stephan, D. W. Org. Biomol. Chem. 2008, 6, 1535–1539. 

[2] Rokob, T. A.; Hamza, A.; Stirling, A.; Soós, T.; Pápai, I. Angew. Chem. Int. Ed. 2008, 47, 2435–2438. 

[3] Hamza, A.; Stirling, A.; Rokob, T. A.; Pápai, I. manuscript in preparation 

[4] Welch, G. C.; Stephan, D. W. J. Am. Chem. Soc. 2007, 129, 1880–1881. 

[1] Chakrapani, N.; Zhang, Y. M.; Nayak, S. K.; Moore, J. A.; Carroll, D. L.; Choi, Y. Y.; Ajayan, P. M. J. Phys. 

Chem. B, 2003, 107, 9308-9311 

[2] Snow, E.S.; Perkins, F.K. Nano Letters, 2005, 5, 2414-2417 

[3] Kazachkin, D.; Nishimura, Y.; Irle, S.; Morokuma, K.; Vidic, R.,; Borguet, E. Langmuir, 2008, in press.



PP473 

Different Localization of Protons in the Neutral and Anionic Complexes of Cytosine with 

Guanine and 8-Oxoguanine 

Iwona Dabkowska 2 , Monika Kobylecka 1 , Piotr Storoniak 1 , Maciej Gutowski 3 , Janusz Rak 1 

1 University of Gdansk, Department of Chemistry, Gdansk, Poland, 2 Free University of Berlin, Physical 

and Theoretical Chemistry, Berlin, Germany, 3 Heriot-Watt Unviersity, Chemistry-School of Engineering 

and Physical Sciences, Edinburgh, United Kingdom 

In the past we demonstrated that an excess electron can alter localization of protons in hydrogenbonded 

complexes of nucleic acid bases with model weak acids. The excess electron typically 

localizes on a nucleic acid base and promotes an intermolecular proton transfer from the acid to the 

base, with the products being a radical of the hydrogenated nucleic acid base and the deprotonated 

acid. We also demonstrated that the hydrogenated nucleic acid base can trigger single strand breaks 

in DNA with the barrier as small as ca. 5 kcal/mol. 

Here we extend these studies to two very important complexes: Watson-Crick complexes of cytosine 

(C) with guanine (G) and 8-oxoguanine (8oG). 8oG is a common lesion that develops in consequence 

of the DNA interactions with oxidative agents. The calculations have been performed with the B3LYP 

exchange-correlation functional and at the RI-MP2/aug-cc-pVDZ level. 

PP474 

Theoretical Studies of the CO Adsorption on Pt(111) Surface Using Cluster Model 

Yu-Wei Huang, Ting-Yi Chou, Yan-Yu Chen, Shyi-Long Lee 

Department of Chemistry and Biochemistry, National Chung Cheng University, Chia-Yi, Taiwan 

Correct theoretical description of the adsorption of CO on Pt(111) has been long a challenge to 

computational chemistry community [1-3]. In this work, we would like to report the theoretical studies 

of the CO adsorption on Pt(111) surface using cluster model. In our present work, recently developed 

density functional theory method, such as BMK [4] and M06 [5], were used to study CO adsorption on 

Pt cluster. Ab initio method, such as HF and MP2 were also adopted to calculate the electronic 

structure of the adsorbed system for comparison. Model clusters 7-3, 10-6, 19-12 used in this study 

were constructed systematically and shown below. CO can then be adsorbed on atop, fcc and hcp 

position. Relationship between exchange-correlation functional and site preference is established. 

Effect of cluster shape and size on the electronic structure and bonding of CO to Pt(111) surface will 

also be discussed. Our results will also be compared to Gil’s results [2]. 

Our results indicate that the excess electron localizes on cytosine in both the G-C and 8oG-C 

complexes and the anionic complexes are adiabatically bound with respect to the corresponding 

neutral Watson-Crick pairs. Moreover, the excess electron promotes an intermolecular proton transfer 

from G or 8oG to C. There are small barriers for these intermolecular proton transfers on the potential 

energy surfaces of electronic energies: 2.6 (B3LYP) and 1.3 (MP2) kcal/mol for GC - and 1.5 (B3LYP) 

and 0.2 (MP2) kcal/mol for 8oGC - . The barriers are even smaller for electronic energies corrected for 

zero-point vibrations and thermal corrections to Gibbs free energies. 

We conclude that the anionic 8oGC complex is particularly susceptible to intermolecular proton 

transfer but the barriers are also very low for the GC - complex. 

A radical of the hydrogenated cytosine, which is a product of these elementary intermolecular proton 

transfer steps, displays an adiabatic electron affinity of ca. 0.5 eV and provides an avenue to a single 

strand break in DNA [1]. 

[1] I. Dąbkowska, J. Rak, M. Gutowski, Eur. Phys. J. D 2005, 35, 429-431. 

[1] Feibelman, P.J.; Hammer B.; Nørskov J.K.; Wagner F.; Scheffler M.; Stumpf R.; Watwe R.; Dumesic J. J. 

Phys. Chem. B 2001, 105, 4018 

[2] Gil, A.; Clotet, A.; Ricart, J.M.; Kresse, G.; Garcia-Hernandez, M.; Rosch, N.; Sautet, P. Surf. Sci 2003, 530, 

71 

[3] Hu, Q. M.; Reuter, K.; Scheffler, M. Phys. Rev. Lett. 2007, 98, 176103 

[4] Boese, A. D.; Martin, J.M.L. J. Chem. Phys. 2004, 121, 3405 

[5] Zhao, Y.; Truhlar D. G. J. Chem. Phys. 2006, 125, 194101



PP475 

In Silico and In Vitro Mutagenesis of PA-IIL Lectin – Correlation with Structure-Function 

Analysis 

Jan Adam, Martina Pokorna, Zdenek Kriz, Martin Prokop, Jaroslav Koca, Michaela Wimmerova 

Masaryk University, National Centre for Biomolecular Research, Brno, Czech Republic 

Protein-carbohydrate interactions play a crucial role in recognition and adhesion of pathogen to host 

tissue cells in the first step of their invasion and infectivity. Pseudomonas aeruginosa is an 

opportunistic pathogen, responsible for numerous nosocomial infections in immunocompromised 

patients. The bacterium colonises patients with chronic lung diseases and its infections is fatal in 

cystic fibrosis patients. P. aeruginosa produces a fucose-binding lectin PA-IIL that plays a role in 

virulence and adhesion [1]. Similar lectins have been found in other opportunistic bacteria like 

Ralstonia solanacearum [2], Chromobacterium violaceaum [3] and Burkholderia cenocepacia [4], with 

different binding preferences despite only slight sequence changes. 

Mutations of the PA-IIL lectin were designed according to these differences, cloned/modelled and 

investigated both in vitro, and in silico [5,6]. Thermodynamics of binding using isothermal titration 

microcalorimetry helped to rationalise importance of particular amino acids in PA-IIL binding site and 

to define overall enthalpy and entropy contributions to the interaction. Good correlation between 

experimentally constructed mutants and in silico prediction of their sugar specificity allowed to perform 

much wider screening of mutated proteins focusing on importance of particular amino acids for 

specificity and/or affinity. This approach significantly saves experimental time needed for construction 

of mutant protein library. 

PP476 

Theoretical Study of the minor Channel forming HNO 3 in the HO 2 + NO reaction 

Marie-Therese Rayez, Jean-Claude Rayez 

Universite Bordeaux1-ISM-groupe THEO, 33405 Talence Cedex, France 

The reaction HO 2 + NO → OH + NO 2 (1a) plays a key role in controlling the interconversion between 

OH and HO 2 radicals in the troposphere. This reaction is also a major source of tropospheric ozone 

through the conversion of NO to NO 2 followed by NO 2 photolysis. 

The observation of a minor channel (1b) forming nitric acid in the reaction channel HO 2 + NO → HNO 3 

(1b), has been reported by Butkovskaya et al [1]. This minor production of HNO 3 has been shown by 

these authors to be favoured by temperature decrease, pressure increase and the presence of water 

vapour [2]. 

The mechanism of the titled reaction has been investigated using electronic quantum chemistry 

coupled to statistical RRKM-type calculations. The first step is the formation of the HOONO cis and 

trans complexes which can decompose (channel 1a) or isomerise to HNO 3 (channel 1b). We have 

demonstrated that the formation of HNO 3 can also occur through a second path along the 

decomposition channel thanks to the presence of a loose intermediate. 

Calculations also show that the addition of H 2 O molecules makes the transition states governing the 

HNO 3 formation more accessible suggesting an explanation for the experimental increase of HNO 3 

formation in the presence of water vapour. This study allows us to suggest a mechanism which agrees 

with the experimental results described above. 

[1]. Mitchell, E.; Houles, C.; Sudakevitz, D.; Wimmerova, M.; Gautier, C.; Perez, S.; Wu, A. M.; Gilboa-Garber, N.; 

Imberty, A., Structural basis for oligosaccharide-mediated adhesion of Pseudomonas aeruginosa in the lungs of 

cystic fibrosis patients. Nature Structural Biology 2002, 9, (12), 918-921. 

[2]. Sudakevitz, D.; Kostlanova, N.; Blatman-Jan, G.; Mitchell, E. P.; Lerrer, B.; Wimmerova, M.; Katcoff, D. J.; 

Imberty, A.; Gilboa-Garber, N., A new Ralstonia solanacearum high-affinity mannose-binding lectin RS-IIL 

structurally resembling the Pseudomonas aeruginosa fucose-specific lectin PA-IIL. Molecular Microbiology 2004, 

52, (3), 691-700. 

[3]. Pokorna, M.; Cioci, G.; Perret, S.; Rebuffet, E.; Kostlanova, N.; Adam, J.; Gilboa-Garber, N.; Mitchell, E. P.; 

Imberty, A.; Wimmerova, M., Unusual entropy-driven affinity of Chromobacterium violaceum lectin CV-IIL toward 

fucose and mannose. Biochemistry 2006, 45, (24), 7501-10. 

[4]. Lameignere, E.; Malinovska, L.; Slavikova, M.; Duchaud, E.; Mitchell, E. P.; Varrot, A.; Sedo, O.; Imberty, A.; 

Wimmerova, M., Structural basis for mannose recognition by a lectin from opportunistic bacteria Burkholderia 

cenocepacia. Biochem J 2008, 411, (2), 307-18. 

[5]. Adam, J.; Pokorná, M.; Sabin, C.; Mitchell, E.; Imberty, A.; Wimmerová, M., Engineering of PA-IIL lectin from 

Pseudomonas aeruginosa – Unravelling the role of the specificity loop for sugar preference. BMC structural 

biology 2007, 7, (1), 36. 

[6]. Adam, J.; Kriz, Z.;Prokop, M.; Wimmerova, M.; Koca, J., Mutagenesis and docking studies of Pseudomonas 

aeruginosa PA-IIL lectin – predicting binding modes and energies in silico, manuscript submitted 

[1] Butkovskaya, N.; Kukui, A.; Pouvesle, N.; Le Bras, G. J. Phys. Chem. A 2005, 109, 6509 

[2] Butkovskaya, N.; Kukui, A.; Le Bras, G. J. Phys. Chem. A 2007, 111, 9047



PP477 

Solvent Effect for the Interaction of Adenine Adducts with Thymine 

Prabhat K. Sahu, Yu-Wei Huang, Shyi-Long Lee 

Department of Chemistry and Biochemistry, National Chung Cheng University, Chia –Yi, Taiwan 

The existence of DNA adducts bring the danger of carcinogenesis because of mispairing with normal 

DNA bases. Solvation free energies (∆G solv ) calculations for the 1,N 6 -ethenoadenine adducts (εA) and 

1,N 6 -ethanoadenine adducts (EA) with thymine have been achieved by using COSMO model (C-PCM) 

at B3LYP/6-31+G*, so as to predict the association energies for the adenine adducts with thymine. 

The energetic computed in solvent phase has also been compared with those reported earlier in gas 

phase 1 . The calculated Gibbs free energy corrected binding energy (aq) value for εA(2)-T(I) is 3.51 

Kcal/mol, which is highest among the etheno adduct-thymine complexes and about 0.03 Kcal/mol less 

than those obtained for Watson-Crick A-T base pair and similarly, the Gibbs free energy corrected 

binding energy (aq) value for EA(2)-T(I) is 3.94 Kcal/mol, which is highest among the ethano adductthymine 

complexes and about 0.4 Kcal/mol more than those obtained for Watson-Crick A-T base pair. 

It has also been observed that EA(2)-T(I) and εA(2)-T(I) have been identified to be best possible 

mispair out of several different stable conformers for each type of adenine adduct with thymine in 

terms of current calculated results (binding energies) and the reported gas phase results (binding 

energies and reaction entalpies) with regard to Watson-Crick A-T base pair. 

PP478 

Ab Initio Molecular Energies by Fragmentation: A Feasible Strategy for Non-Bonded 

Interactions 

M. A. Addicoat, M. A. Collins 

Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia 

Ab initio quantum chemistry can calculate the total electronic energy for small to moderate sized 

molecules with reliable accuracy. However, the computational cost of these methods becomes 

prohibitive for many larger molecules of interest to chemists. Theoretical studies of the dynamical 

mechanisms of chemical reactions have been even more severely restricted to the smallest 

molecules, partly because the electronic energy must be calculated for a large number of molecular 

geometries. We have shown how the bonding energy of large organic molecules can be estimated 

from the energies of relatively small molecular fragments. We report current progress on the 

incorporation of weak non-bonded interactions to achieve chemical accuracy for the total molecular 

energy. 

Sahu, P. K.; Kuo, C. W.; Lee, S. L. J. Phys. Chem. B 2007, 111, 2991



PP479 

Agonist Binding at the Calcium Sensing Receptor: A Computational Approach 

Susan Corley, Hoi-Ming Chan, Meredith Jordan 

School of Chemistry, The Univeristy of Sydney, Sydney, Australia 

The divalent metal cations Ca 2+ , Mg 2+ and Sr 2+ all activate the calcium sensing receptor (CaSR) with 

differing potencies. [1] Amino acid residues likely to be important to be important in the CaSR binding 

site are identified using DFT, and their interactions with the divalent cations examined. Calculations 

are performed for both gas phase interactions and using the polarized continuum model (PCM), 

whereby a dielectric constant D=4 is used to represent a partially open protein environment. The 

thermodynamics of binding indicate that charged residues glutamate and aspartate, along with the 

polar residues asparagine and glutamine, together with the protein backbone group represent the 

most likely residues for metal binding. 

Binding energies alone, however, do not account for the different observed potencies of the three 

metal cations. Ca 2+ and Sr 2+ support a coordination number of seven, whereas Mg 2+ has a maximum 

coordination number of six. Thus there is more facile migration of amino acid residues from the second 

to the first coordination shell of Ca 2+ and Sr 2+ as compared to Mg 2+ , which requires substantial 

rearrangement of water molecules in the first coordination shell and is thus kinetically unfavorable due 

to a large activation barrier. This is reflected in the significantly higher activation energies for the 

transition state between second coordinate and first coordinate shell binding for model amino acid 

residue binding to Mg 2+ compared to Ca 2+ and Sr 2+ (figure 1). 

PP480 

Performance of Density Functionals in a QM and QM/MM study of the Catalytic Mechanism of 

β-Galactosidase 

Pedro Alexandrino Fernandes, Natércia Brás, Sara Moura-Tamames, Ramos Maria 

Requimte/Faculty of Sciences, University of Porto, Porto, Portugal 

Galactooligosaccharides (GOS) are special glycosides produced by the enzyme β-galactosidase. 

They contain galactose and glucose molecules. These sugars are considered to be functional food 

ingredients because they stimulate the growth of bifidobacteria and lactobacilli, combining prebiotic 

properties beneficial to the human health with physico-chemical properties beneficial in food 

processing [1]. 

The catalytic mechanism on retaining glycosides has been largely studied experimentally [2]. These 

studies propose that occurs via a double displacement mechanism involving a glycosylation and a 

deglycosylation step, which is shown in Figure 1. 

Our goal is to perform a theoretical model, which elucidates at atomic-level detail the catalytic 

mechanism of the β-galactosidase from E.coli. A minimal gas-phase model has been used previously, 

to test the performance of a large number of density functionals [3], namely B3LYP, BHandHLYP, 

B97-2, B98, PBE1PBE, B1B95, BB1K, MPW1K and MPWB1K. A significant dispersion of results has 

been found (up to 7.6 kcal.mol -1 ) in the activation energies. Conversely, the catalytic effect of a 

fundamental hydrogen bond was well reproduced by all functionals (with a dispersion smaller than 1.1 

kcal.mol -1 ). The dispersion was also small in reaction energies. The results of selected functionals 

were recalculated with a smaller model, using DFT and higher levels of theory, namely MP2, MP4 and 

QCISD(T), for comparison. 

Once set on the adequate density functional a large model, including a radius with 15 Å around the 

lactose substrate, was used to follow the catalytic mechanism. The ONIOM method was employed to 

deal with such a large system, at the BB1K:AMBER theoretical level [4]. The results of the larger 

model captured the catalytic effect of the enzyme, lowering the barrier by more than 12 kcal.mol -1 . The 

origin of the catalytic power of the enzyme was also discussed. 

Figure 1) Energy profile diagrams for the reaction M[(H 2O) 6] 2+ .L M[(H 2O) 6L] 2+ ‡ M[(H 2O) 5L] 2+ .H 2O where L = 

formamide (left) and methanol (right). 

[1] Holzapfel, W.H.; Schillinger, U. Food Res. Int., 2002, 35, 109. 

[2] Juers, D.H.; Heightman, T.D.; Vasella, A.; MacCarter, J.D.; Mackenzie, L.; Withers, S.G.; Matthews, B.W. 

Biochemistry, 2001,40, 14781–14794. 

[3] Brás, N. F.; Moura-Tamames, S.; Fernandes, P. A.; Ramos, M. J. J. Comput. Chem., ASAP, DOI: 

10.1002/jcc.20977 

[4] Brás, N. F.; Fernandes, P. A.; Ramos, M. J. submitted. 

Similarly, the interconversion between monodentate and bidentate binding for residues modeled with 

formate was observed to have a significantly higher reaction barrier for Mg 2+ (figure not shown). 

Therefore, we suggest that the selectivity of calcium over magnesium binding at the calcium sensing 

receptor and similar proteins is due to kinetic rather than thermodynamic considerations. 

[1] Brown, E. M.; Macleod, R. J. Physiological Reviews 2001, 81, 239-297.



PP481 

Molecular Modelling of Hydrotalcite Layered Double Hydroxide Structures Intercalcated with 

Transition Metal Oxide Anions 

Vinutha Murthy 1 , Howard D Smith 2 

1 Charles Darwin University, School of Environmental & Life Sciences, Darwin, NT, Australia, 2 Curtin 

University of Technology, Nanochemistry Research Institute, Bentley, WA, Australia 

Hydrotalcite is a mineral that belongs to a class of chemicals often referred to as layered double 

hydroxides and which can be produced synthetically by reacting magnesium II and aluminium III 

solutions in the presence of a strong base. In-situ absorption of transition metal anions may occur if 

they are present at the time the hydrotalcite is prepared. Our previous experimental studies have 

shown that while some transition metal oxide anions such as VO 4 3- and CrO 4 2- may be easily absorbed 

into the mineral structure, other anions such as MoO 4 2- are not. 

Intercalation, the process where anions become contained within the interlayer spaces between the 

octahedral magnesium-aluminium hydroxy layers of hydrotalcite is one possible mechanism of in-situ 

absorption. Initial studies using Molecular modelling with empirical forcefield is being carried out in 

conjunction with X-ray Diffraction and Electron-microscope data to determine the size or orientation of 

transition metal oxide anions and their impact upon hydrotalcite crystal structure. 

PP482 

Computational Studies on the Thermal Fragmentation Reactions of 1,4,2-Oxathiazole 

Derivatives – A Convenient Synthesis of Isothiocyanates 

Robert O'Reilly, Leo Radom 

School of Chemistry, University of Sydney, Sydney, NSW, Australia 

Thermolysis of 1,4,2-oxathiazole derivatives has been shown to result in the formation of 

isothiocyanates (ITCs) and the corresponding carbonyl derivatives [1]. 

R 2 

R 1 S 

R 3 ∆ 

O 

O N R 1 

R 3 

R 2 + N C S 

ITCs are gaining increasing notoriety due to their promising anticancer properties [2]. 

Whilst relatively few reports on ITC synthesis via this fragmentation reaction exist in the literature, a 

polymer-supported synthesis of ITCs has recently been published [3]. Given the potentially useful 

applications of this approach to ITC synthesis, and the ability to generate libraries for biological testing 

via the polymer-supported approach, a knowledge of the mechanism(s) by which the fragmentation 

proceeds is valuable. This poster outlines a mechanistic study carried out using quantum chemical 

procedures. 

[1] Huisgen, R.; Mack, W.; Anneser, E. Angew. Chem. 1961, 73, 656-657. 

[2] Conaway, C. C.; Yang, Y.; Chung, F. –L. Curr. Drug Metab. 2002, 3, 233-255. 

[3] Burkett, B. A.; Kane-Barber, J. M.; O’Reilly, R. J.; Shi, L. Tet. Lett. 2007, 48, 5355-5358. 

[1]. Smith HD, Parkinson GM and Hart RD, In situ absorption of molybdate and vanadate during precipitation of 

hydrotalcite from sodium aluminate solutions. Journal of Crystal Growth, 2005, 275 (1-2): e1665-e1671. 

[2]. P. Kovar, M. Pospisil, M. Nocchetti, P. Capkova, K. Melanova. Molecular modeling of layerd double 

hydroxides intercalcated with benzoate, modeling and experiment. J Mol Model, 2007; 13: 937-942



PP483 

Potential Energy Hypersurface for the Methane Radical Cation 

Lucas D. Speakman, Justin M. Turney, Henry F. Schaefer III 

University of Georgia, Center for Computational Chemistry, Athens, GA, United States 

The methane cation has been studied extensively because of its fundamental importance in chemistry. 

This cation is 

1) prevalent in interstellar clouds and planetary atmospheres [1]. 

2) likely involved in the chemical evolution that must have preceded the origin of life [2]. 

3) highly reactive and leads to other fundamental molecular ions such as CH 5 + and C 2 H 5 + . 

4) a major radiation product of methane, a species involved in many chemical and biochemical 

processes. 

5) one of the simplest systems subject to Jahn-Teller distortion. 

Because of its significance, an accurate potential energy surface is required to elucidate spectroscopic 

properties. The tetrahedral configuration has a triply degenerate 2 T 2 which could lead to C 2v , D 2d , C 3v , 

or lower symmetry distortions because of Jahn-Teller splitting. Due to this degeneracy, several 

theoretical methods fail to sufficiently describe these states in the tetrahedral configuration. The 

research method utilized is an equation-of-motion ionization potential coupled cluster (EOMIP-CC) 

theory which adequately represents the three degenerate states and has not yet been applied to this 

cation. Several low lying conformers of CH 4 + will be investigated for a thorough potential energy 

hypersurface. Vibrational perturbation theory will also be computed at each stationary point to yield 

accurate fundamental frequencies. Finally, dissociation paths of the methane cation into CH 3 + + H and 

CH 2 + and H 2 will be explored. 

[1] Miller, S. L.; Urey, H. C.; Science, 1959, 130, 245. 

[2] Arents, J.; Allen, L. C.; J. Chem. Phys. 1970, 53, 73. 

PP484 

A Computational Study of Substrate Mechanism of Pyruvate-Formate Lyase 

Karmen Condic-Jurkic 1 , V. Tamara Perchyonok 2 , Hendrik Zipse 3 , David M. Smith 1 

1 Rudjer Boskovic Institute, Centre for Computational Solutions in the Life Sciences, Zagreb, Croatia, 

2 Monash University, School of Chemistry, Melbourne, Australia, 3 Ludwig-Maximilians-Universität, 

Department Chemie und Biochemie, München, Germany 

DFT and high-level quantum mechanical calculations have been performed on small model systems 

relevant to the substrate mechanism of Pyruvate Formate-Lyase (PFL), comparing the reactivity of the 

natural substrate pyruvate with that of the known inhibitor oxamate. For both substrates the presently 

accepted (consensus) mechanism, involving the addition of a cysteine-based thiyl radical to the 

carbonyl carbon of the substrate, is compared to an alternative mechanism involving hydrogen 

abstraction as the primary step. This mechanism, relevant because of the known structural homology 

between PFL and the ribonucleotide reductase family of enzymes, 

is found to display similar reaction barriers to the consensus mechanism, but is much less favorable 

with respect to the reaction energetics. The inhibitory effect of oxamate can be traced back to an 

increase in reaction barrier and reaction energy along the consensus mechanism pathway. The highlevel 

quantum results have been subsequently used as benchmarks to examine the suitability of 

applying a coupled quantum-mechanical/molecular-mechanical (QM/MM) approach to this system. 

This comparison shows that while the QM/MM technique gives reaction barriers and enthalpies in 

good agreement with the complete quantum treatment, some caution must be exercised for properties 

such as complexation energies. It also seems that DFT tends to underestimate complexation 

energies, compared to high-level results. 

[1] Condic-Jurkic, K.; Perchyonok, T.V.; Zipse, H.; Smith, D. M., On the modeling of arginine-bound carboxylates: 

A case study with Pyruvate Formate-Lyase, J. of Comp. Chem., 2008, in print 

[2] Knappe, J.; Elbert, S.; Frey., M.; Wagner, A.F.V. Biochem. Soc. Trans. 1993, 21, 731-734 

[3] Becker, A.; Kabsch W J. Biol. Chem. 2002, 277, 400036-40042 

[4] Becker, A.; Fritz,-Wolf, K.; Kabsch, W.; Schultz, S.; Wagner, A.F.V.; Knapper J. Nat. Struc. Bio. 1999, 6, 969- 

975



PP485 

The Enthalpy of Formation and Anharmonic Force Field for Diacetylene 

Andrew Simmonett, Wesley Allen, Henry F. Schaefer III 

Center for Computational Chemistry, University of Georgia, Athens, GA, United States 

The enthalpy of formation for the diacetylene molecule (C 4 H 2 ) is pinpointed using state-of-the-art 

computational methodology, accounting for high-order correlation effects, relativity, non-Born 

Oppenheimer effects and explicit consideration of vibrational anharmonicity. Molecular energies are 

obtained through the coupled cluster hierarchy of methods with singles and doubles (CCSD), 

quasiperturbative triples [CCSD(T)], full triple excitations (CCSDT) and perturbative quadruples 

[CCSDT(Q)] in concert with Dunning’s correlation consistent family of basis sets (cc-pVXZ, 

X=D,T,Q,5,6). Our fundamental vibrational frequencies are derived from an all electron CCSD(T) full 

quartic force field, computed using Dunning’s quadruple-ζ cc-pCVQZ basis, which includes tight 

functions to provide a satisfactory description of core correlation. Second order vibrational 

perturbation theory (VPT2) is used to extract the fundamental vibrational frequencies from the 

anharmonic force field; we stress that no empirical scale factors are used. 

PP486 

Perturbative Triples Correction for State-Specific Multireference Coupled Cluster 

Francesco A. Evangelista, Wesley D. Allen, Henry F. Schaefer III 

Center for Computational Chemistry, University of Georgia, Athens, Georgia, United States 

In order to generalize the single reference CCSD(T) method to the multireference case, we have 

derived a new perturbative correction scheme for triples excitations within the framework of statespecific 

multireference coupled cluster theory based on the Jeziorski-Monkhorst ansatz. Our 

derivation is based on the Lagrangian formalism and is applicable to Mukherjee (Mk-MRCC) as well as 

Brilluoin Wigner (BW-MRCC) multireference coupled cluster. When the model space consists of one 

determinant, and Hartree Fock orbitals are used, we recover the conventional CCSD(T) energy. In the 

case of Mk-MRCC, we can achieve a non-iterative implementation in two different ways: 1) neglecting 

the off diagonal elements of the Fock matrix for each reference, or 2) neglecting the coupling terms in 

the triples equations. We compare our formulations to others previously advanced and also comment 

on the possibility of treating quadruple excitations within the same scheme. 

Using this ab initio methodology, we compute the enthalpy for the isogyric reaction 

2 H–C≡C–H → H–C≡C–C≡C–H + H 2 

to be (0.03, 0.81) kcal mol -1 at (0, 298.15) K which, combined with acetylene’s enthalpy of formation 

from the literature yields ∆ f 

H o 0 

(diacetylene) = 109.4 ± 0.3 kcal mol -1 o 

and ∆ f 

H 298 

(diacetylene) = 

109.7 ± 0.3 kcal mol -1 .



PP487 

A Theoretical Study on the S 1 /S 2 Conical Intersection Along the Amino Inversion Coordinate of 

Aminonaphthalene 

Masayuki Nakagaki, Haruyuki Nakano 

Department of Molecular Chemistry, Graduate School of Sciences, Kyushu University, Fukuoka, 

Japan 

Aniline is the most basic aromatic molecule with an amino group. Many studies therefore have been 

done both theoretically and experimentally, and its electronic structure has been well elucidated so far 

in this molecule, the πσ* Rydberg-type excited state corresponds to the S 2 state and lies near the 

valence ππ* S 1 state [1, 2]. The potential energy surface of the amino group depends on the electronic 

state; that is the amino group in S 0 state has pyramid-like non-planar structure while it is almost planar 

in S 1 state [3]. 

Similar to aniline, 1-aminonaphthalene (1AN) and 2-aminonaphthalene (2AN) (Fig.1), which are 

monosubstituted acenes including amino group, are also fundamental molecules. In AN, when the 

amino group has non-planar structure, the ππ* and πσ* states belong to the same irreducible 

representation due to the lower molecular symmetry. This fact implies to us that the inversion mode of 

the amino group plays an important role in the interaction between ππ* and πσ* states. In order to 

clarify the interaction in details, we theoretically examined the potential energy surfaces of the ππ* and 

πσ* states along the stretching and inversion motions of amino group coordinates. In particular, the 

focus was on the seeking of the conical intersection and evaluation of the interaction between the two 

states. 

We first performed geometry optimization for 1AN and 2AN in ππ* and πσ* states using the complete 

active space self-consistent field (CASSCF) method with the 6-31++G(d,p) basis set. The active space 

was constructed from 12 electrons in 12 active orbitals including 6 π orbitals and 5 π* orbitals and 1 σ* 

orbital. Then we calculated the two-dimensional potential surfaces V(θ,r) for two lowest singlet excited 

states in both diabatic and adiabatic representations, using the state averaged (SA-) CASSCF 

method, where two parameters θ and r are defined in Figure 2. We evaluated also the non-adiabatic 

coupling matrix elements < Ψi | ∂ / ∂r | Ψ j > and < Ψi | ∂ / ∂θ | Ψ j > using the finite difference method. 

PP488 

Non Specific Binding of Positron Emission Tomography (PET) Ligands as Seen from an Ab 

Initio Computational Study 

Lula Rosso 1 , Antony Gee 2 , Ian Gould 1 

1 Department of Chemistry, Imperial College London, London, United Kingdom, 2 Clinical Imaging 

Centre, GlaxoSmithKline, United Kingdom 

In developing new PET radiotracers, a common reason for candidate failure is that high non-specific 

and sub cellular binding obscures the specific binding to the molecular target and, thus, reduces the 

quality of the PET scan data. Non-specific binding is thought to be correlated in part to a molecule’s 

lipophilicity, typically estimated by measuring (or calculating) octanol-water partition coefficient. This is, 

however, a gross simplification of a complex phenomenon. The purpose of this ab-initio computational 

study is to increase our understanding of non-specific binding by investigating the molecular basis of 

ligand-membrane interaction. 

Ten well-characterized central nervous system PET radiotracers acting on a variety of molecular 

targets were used as primary set. Quantum mechanical methods were used to estimate accurately the 

strength of the electronic interaction between individual drug molecules and a single phospholipid 

molecule commonly present in mammalian membranes. This was achieved by finding the lowest 

optimized ground state energy of several drug-lipid complexes at Hartree-Fock and B3LYP level of 

theory, without using experimental data. 

The computed energies showed a non-trivial correlation with the in vivo non-specific binding 

distribution volumes relative to the free tracer plasma concentration, Fig. 1. Significantly, the drugs 

with stronger lipid interaction possessed a higher non-specific binding value. While, for the drugs 

taken in consideration in this study, the water-octanol partition coefficient, logP, did not show good 

predictive power of the in vivo non-specific binding, Fig.2. 

The computational method used provided an interesting insight into non specific binding behaviour in 

terms of membrane interaction. This method was further validated on a blinded set of 9 candidate 

radiotracers and correctly identified all 3 successful drugs in the set as the molecules forming the 

weakest lipid complexes. 

We obtained the global minima of the ππ* and πσ* states. For the optimized structure of the ππ* states, 

ππ* state was the lowest excited state, while for the optimized structure of the πσ* states, πσ* state 

was the lowest excited state. The major difference of structures in two states was the C-N bond length 

r. The bond length in πσ* state is shorter by about 0.1 Ǻ than that in the ππ* state. These results 

indicate that potential energy curves along r cross each other at the CASSCF level. We also found 

that the interaction between the two states in diabatic representation is proportional to θ, whereas it is 

almost independent of r. 

Fig.1 Structures of aminonaphthalene Fig. 2 Definition of parameters θ and r 

Fig. 1 Fig. 2 

[1] Y. Honda et al. J. Chem. Phys. 2002, 117, 2045-2052. 

[2] T. Ebata et al. J. Phys. Chem. A, 2002, 106, 11070-11074. 

[3] J. C. Jiang, C. E. Lin, J. Mol. Struct. (Theochem), 1997, 392, 181-191.



PP489 

Laser Control of Photoassociation in Diatomic Molecule 

Kiyoshi Nishikawa 1 , Masatoshi Sano 1 , Atsuhito Tawada 1 , Shunichi Taniguchi 1 , Kimikazu Sugimori 2 , 

Hidemi Nagao 1 

1 Kanazawa University, Division of Mathematical and Physical Science, Kanazawa, Japan, 2 Kinjo 

University, Hakusan, Japan 

In this work, we simulate the laser-induced photoassociation of the collision reaction O + H to generate 

the OH molecule. The photoassociation process involves the continuum-discrete transition, and the 

initial wavepacket corresponding to the collision pair is generally given by a superposition of 

continuum state. By numerically solving the time-dependent Schrödinger equation (TDSE) with split 

operator method (SOM), we can take into account implicitly but completely for the continuum state in 

the photoassociation process. In our simulation, we find interestingly the above threshold dissociation 

(ATD) spectrum due to the continuum-continuum transition as well as the target bound states by the 

photoassociation. In order to analyze the continuum state involved, we show the effective method by 

means of the quasicontinuum state on the Morse potential obtained by numerically diagonalizing the 

Fourier grid Hamiltonian (FGH) of the total system. We finally find out the effective laser pulse, which 

induces the complete generation of the target bound state from the initial wavepacket. 

PP490 

Photochemistry of Fischer Carbene Complexes 

Israel Fernandez, Miguel A. Sierra 

Dpto. de Química Orgánica, Universidad Complutenses de Madrid, Madrid, Spain 

Fischer carbene complexes are irreplaceable building blocks. While the thermal reaction chemistry of 

these organometallic complexes that has been widely studied, their photochemical reactivity and the 

mechanisms of the photochemical reactions mechanisms were at the beginning of our work barely 

explored.[1] 

By means of experimental and computational tools, we shall discuss the intimacies of the photocarbonylation 

process and the reaction of the produced metalla-ketenes with imines (Figure 1).[2] 

Furthermore, we will present that other photochemical reaction pathways, which are effective also for 

tungsten carbene complexes, are possible after proper selection of the ligands surrounding the metal 

centre.[2d,e] 

CO 

CO XR 1 

OC Cr 

OC R 

CO 

hν 

∆ 

(CO) 4 Cr 

XR 1 

R 

O 

? 

R XR 1 

(CO) 4 Cr 

O 

R 2 R 4 

R 3 

N 

R 

R 1 X 

R 2 

R 3 

N 

O R 4 

Figure 1. Photocarbonylation reaction of Fischer Carbene Complexes 

( Initial wavepacket) ( target bound state and outgoing wave) 

[1] Hegedus, L. S., Tetrahedron 1997, 53, 4105. 

[2] (a) Fernández, I.; Sierra, M. A.; Mancheño, M. J.; Gómez-Gallego, M.; Cossío, F. P. Chem. Eur. J. 2005, 11, 

5988. (b) Lage, M. L.; Fernández, I.; Mancheño, M. J.; Sierra, M. A. Inorg. Chem. 2008, 47, 5253. (c) Arrieta, A.; 

Cossío, F. P.; Fernández, I.; Gómez-Gallego, M.; Lecea, B.; Mancheño, M. J.; Sierra, M. A. J. Am. Chem. Soc. 

2000, 122, 11509. (d) Sierra, M. A.; Fernández, I.; Mancheño, M. J.; Gómez-Gallego, M.; Torres, M. R.; Cossío, 

F. P.; Arrieta, A.; Lecea, B.; Poveda, A.; Jiménez-Barbero, J. J. Am. Chem. Soc. 2003, 125, 9572. (e) Fernández, 

I.; Sierra, M. A.; Gómez-Gallego, M.; Mancheño, M. J.; Cossío, F. P. Angew. Chem. Int. Ed. 2006, 45, 125. 

[1] Sugimori, K,; Ito, T.; Takata, Y.; Ichitani, K.; Nagao, H.; Nishikawa, K. Int. J. Quantum Chem. 2006, 106, 3079- 

3086. 

[2] Sugimori, K,; Ito, T.; Takata, Y.; Ichitani, K.; Nagao, H.; Nishikawa, K. J. Phys. Chem. A, 2007, 111, 9417- 

9423. 

[3] Nishikawa, K.; Sugimori, K.; Nagao, H. AIP Conference Proceedings, 2007, 963, 843-846.



PP491 

Interaction of Roxithromycin with 50s Large Ribosomal Subunit: Molecular Dynamics 

Simulation. 

Wai Keat Yam, Habibah A Wahab 

Pharmaceutical Design and Simulation Laboratory, School of Pharmaceutical Sciences, Universiti 

Sains Malaysia, Penang, Malaysia 

Roxithromycin (ROX) is a second generation, semi-synthetic macrolide antibiotic derived from 

erythromycin. It has a broader antibacterial spectrum compared to earlier generation of macrolides 

and is clinically effective towards treatment of respiratory tract infection, bacterial infection associated 

to stomach and intestinal ulcers and etc. The structure has a 14-membered lactone ring, with a 

desosamine sugar attached to the carbon at position 5 and a cladinose sugar branched from the 

carbon 3 of the lactone ring, with the addition of etheroxime chain at position 9 of the lactone ring. 

Similarly to other 14-membered macrolide, ROX acts by selectively bind to the Domain V at 23S 

ribosomal RNA of the 50S large ribosomal subunit and blocks tunnel that channels nascent peptide 

away from peptidyl transferase center (PTC). Blockage of exit tunnel induces premature dissociation 

of peptidyl-tRNAs from the ribosome, thus inhibiting bacteria’s protein elongation process. In this 

study, we used molecular dynamics (MD) simulation to elucidate the structure and dynamics of the 

complex between ROX and ribosomal 50S large subunit. MD results showed the importance of water 

molecules in hydrating the binding pocket and their participation in forming and mediating hydrogen 

bond with ROX in the binding pocket. Besides that, explicit analysis of individual direct hydrogen bond 

between ROX and the binding pocket also enabled us to study their occupancies and assignments to 

the overall drug binding mechanism in this system. Our MD simulation also showed direct interaction 

of ROX to Domains II, IV and V through the above analyses. Using insights obtained in this study, we 

believe it could contribute in understanding the detailed mechanism of action in the binding of ROX to 

the 50S large ribosomal subunit, and thus assist in the development of safer macrolide antibiotics. 

PP492 

Computational Studies on Bimetallic Clusters 

Ying-Chan Lin 1 , Li-Feng Cui 2 , Lai-Sheng Wang 3 , Dage Sundholm 1 

1 Department of Chemistry, University of Helsinki, Helsinki, Finland, 

2 Department of Physics, 

Washington State University, Pullman, United States, 3 Sciences Laboratory and Chemical Sciences 

Division, Pacific Northwest National Laboratory, Richland, United States 

Aromaticity is a concept introduced to account for the unusual stability of an important class of organic 

aromatic compounds. In recent times the concept of aromaticity has been extended to all metal 

molecules in order to explain the stability of some small clusters observed in laser vaporization 

experiments. Although much studied, the exact nature of their aromaticity has still not been completely 

determined. 

In the present work, we first report the generation of Cu 4 Na - and Au 4 Na - clusters in the gas phase and 

their characterizations experimentally using PES and computationally at correlated ab initio levels [1]. 

The molecular structures of Cu 4 Na - and Au 4 Na - are found to be pyramidal of D 4h symmetry and planar 

cluster of D 2v symmetry, respectively. It shows the importance of both PES experiments and 

computational spectrum in order to identify the molecular structures of observed clusters. 

Moreover, we have applied the GIMIC method [2] to three different metallic systems for understanding 

their nature of aromaticity: Al 4 2- , Al 4 4- , and Cu 4 2- [1,3]. The magnetically induced current is invariant to 

transformations of the magnetic gauge origin. In practice, however, gauge invariance is hard to 

achieve. GIMIC is a method for calculating the components of the magnetically induced current tensor 

using gauge-including atomic orbitals (GIAO). The use of GIAOs represents an elegant solution to 

remedy the gauge-origin problem. The ring-current strengths are obtained directly via explicit 

numerical integration over the net current flow through one of the bond cross -section within the 

considered molecular ring. 

[1] Lin, Y.-C.; Jusélius, J.; Sundholm, D.; Gauss, J. J. Chem. Phys. 2004, 122, 214308. 

[2] Jusélius, J.; Sundholm, D.; Gauss, J. J. Chem. Phys. 2004, 121, 3952. 

[3] Lin, Y.-C.; Sundholm, D.; Jusélius, J.; Cui, Li-Feng; Li, Xi; Zhai, Hua-Jin; Wang, Lai-Sheng J. Phys. Chem. A 

2005, 110, 4244.



PP493 

Are Isomers of the Vinyl Cyanide Ion Missing Links for Interstellar Pyrimidine Formation? 

Partha P. Bera 1 , Timthy J. Lee 1 , Henry F. Schaefer III 2 

1 NASA Ames Research Center, Space Science and Astrobiology, Moffett Field, CA, United States, 

2 University of Georgia, Center for Computational Chemistry, Athens, GA, United States 

The low energy isomers of the acrylonitrile ion (C 3 H 3 N + ) have been investigated using high level ab 

initio quantum mechanical methods, coupled cluster single and double [CCSD], and CCSD with 

perturbative triples [CCSD(T)], in conjunction with correlation consistent valence triple zeta and 

quadruple zeta cc-pVXZ [X=T,Q] basis sets, as well as simple density functional methods. An 

automated stochastic search procedure, Kick, has been employed to find isomers on the ground state 

doublet potential energy surface of the C 3 H 3 N + ion. Several new structures, along with all the 

previously reported minima, have been found. The global minimum H 2 CCCNH + is energetically much 

lower than either H 2 CC(H)CN + the acrylonitrile ion, or HCC(H)NCH + , the most likely intermediate of the 

reaction between HCCH + and HCN. These isomers are connected to the global minimum via several 

transition states and intermediates. The results indicate that not only the global minimum, but also 

several higher energy isomers of C 3 H 3 N + ion, could be important in interstellar pyrimidine formation. 

The isomeric molecules have the necessary CCNC backbone needed for the reaction with HCN to 

form the cyclic pyrimidine framework. The structural and rotational parameters of the isomers 

previously investigated, as well as newly identified by this work, have been predicted at the ccpVQZ/CCSD(T) 

level of theory with the hope that it will expedite their laboratory as well as 

astronomical identification. 

PP494 

Molecular Shape Analysis Using Ion Probes and Its Applications 

Manabu Sugimoto 

Kumamoto University, Kumamoto, Japan 

Molecular recognition is one of the key phenomena in biochemistry, supramolecular chemistry, gas 

sorption/separation sciences. The concepts of molecular surface and volume are important in 

discussing the host-guest chemistry. In order to evaluate these parameters quantitatively, it is required 

to define the outer surface of a molecule, i.e. the shape of a molecule. Here we report a computational 

method for quantitatively evaluating the molecular surface where the interaction energy between the 

target and a probe ion is used for mapping the topology. Applications to various molecules indicate 

that the evaluated topologies reflect chemically important characteristics of the targets and provide 

useful information on the molecular interaction. The method is also applied to investigate some 

characteristics of the hydrogen molecule, leading to the design of molecules for the hydrogen sorption.



PP495 

The Hydrogen Bond in Transmembrane Proteins 

Dah-Yen Yang 

Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei, Taiwan 

In our previous work, using molecular dynamics, we showed that the strength of a given hydrogen 

bond is much stronger in the isolated molecule than it is in water hence making the latter molecularly a 

much more flexible environment, as is desirable for many biological processes. Furthermore we 

measured very large entropic changes in the rupture of hydrogen bonds in water, whereas no such 

effects were seen for the isolated molecule. Hence for the H-bond in water the low energy of rupture is 

facilitated by the presence of water, whereas on the other hand the large entropy change is seen 

to reduce the rate by some two orders of magnitude. Recent MD experiments in D 2 O substantiate this 

model and show a large solvent isotope effect. 

Here we use lipids as an environment for the hydrogen bond and discover that the energy is also 

reduced from the isolated molecule, but not as far as in water. On the other hand there is now no 

entropy penalty for breaking the hydrogen bond in lipids, as we had seen for water. The result is that 

the energy is some two times larger, but nevertheless the rate is faster than in water. This is a very 

important result for understanding the reactivity and the dynamics for proteins in lipids. 

PP496 

Molecular Dynamics of Hydrogen Bonds in Protein-D 2 O 

Sheu-Yi Sheu 

Faculty of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei, 

Taiwan 

We suggest that the H-bond in proteins is not atomistically related to the motion of hydrogen in its 

bond alone and thus does not relate directly to the strength of a hydrogen bonded to its neighbors. It 

rather has its origin in the collective motion of the hydrogen bond in a widespread surrounding lattice 

of H 2 O molecules which is being perturbed in its optimal entropic configuration by motion of the H- 

bond. It is for this reason that the H-bond energy drops from some 5 kcal/mol for the pure system in 

the absence of H 2 O, to some 1.4 kcal/mol in the presence of the H 2 O medium. This low value here is 

determined by MD calculations and corresponds to the generally accepted value for biological 

systems and the calculations are tested by changing to D 2 O as the surrounding medium. We observe 

in accordance with this model that under ambient conditions the H-bond kinetics is seriously 

depressed, hence confirming the subtle effect of the H 2 O medium as a whole interacting with the H 

bond. We observe that there is an entire ensemble of H-bond structures – rather than a single 

transition state – all of which contribute to this H-bond. 

We distinguish three different cases of the behavior of hydrogen bond/complexes, strongly depending 

on the environment.



PP497 

Atomistic Modelling of Soot Particles and of their Interaction with Surrounding Molecules 

J C Rayez 1 , M T Rayez 1 , B Collignon 2 , S Picaud 2 , P N M Hoang 2 

1 Universite Bordeaux1, Institut des Sciences Moleculaires (ISM), CNRS UMR5255, 33405, Talence 

Cedex, France, 2 Université de Franche-Comté, Institut UTINAM, CNRS UMR 6213, 25030, Besançon 

Cedex, France 

Nowadays, understanding the aviation’s impact on radiative forcing, climate change, air quality and 

human health is a challenging task of great importance. In spite of the efforts undertaken to date by 

the scientific community, there is a lack of knowledge about the structure, the morphology, the 

composition, and the physico-chemical properties of aircraft engine soot that are released in the 

atmosphere. 

We present here a modelling study of the soot particles and of their interaction with water and 

Polycyclic Aromatic Hydrocarbons (PAHs). This work may lead to a better understanding, at the 

molecular level, of the role of the soot structural and chemical characteristics on water condensation 

and on the ability of these particles to act as condensation clouds nuclei. It may also lead to a better 

understanding of the chemical reactivity at the surface of these soot particles and thus on how soot 

may influence the atmospheric chemistry. 

Molecular dynamic simulations are used to study the adsorption of water molecules on partially 

oxidized graphite containing COOH and OH sites. More specifically, the competition between the OH 

and COOH sites with respect to water adsorption is characterized at three different temperatures (200, 

250 and 300K). The simulations show a strong preferential clustering of water molecules around the 

COOH sites irrespective of the temperature. In fact water molecules can be trapped by the OH sites 

only when the temperature is sufficiently low, or when the local density of OH sites is sufficiently high. 

These results give insights into the water adsorption mechanisms on oxidized graphite surfaces 

constituting black carbons or soot particles by aircraft. 

PP498 

Phosphotriesterase-Catalyzed Hydrolysis of Toxic Organophosphorus Compounds: Modelling 

of the Enzyme-Substrate Complex 

Edyta Dyguda-Kazimierowicz 1 , Jolanta Zurek 2 , Adrian Mulholland 2 , W. Andrzej Sokalski 1 , Jerzy 

Leszczynski 3 

1 Institute of Physical and Theoretical Chemistry, Wroclaw University of Technology, Wroclaw, Poland, 

2 Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, United 

Kingdom, 3 Computational Center for Molecular Structure and Interactions, Jackson State University, 

Jackson, MS, United States 

Phosphotriesterase (PTE) is a bacterial enzyme exhibiting the most promising capability of 

biodegradation of organophosphorus pesticides and related chemical warfare agents in terms of both 

wide substrate acceptance and high turnover number. Available experimental data regarding PTE 

properties have not yet allowed us to establish the molecular basis of its action. Since the suggested 

PTE catalytic mechanism has not been unequivocally verified by means of theoretical simulation, this 

research has been aimed at computational evaluation of the way PTE achieves its enormous rate 

enhancement. The knowledge of factors affecting substrate specificity and/or catalytic efficiency would 

allow for rational engineering of PTE mutants designed specifically to suit broad range of purposes. 

Considering the essential prerequisites necessary for the reliable modeling of an enzyme-catalyzed 

reaction, a well-founded model of enzyme-substrate complex is required as a starting point. Since no 

experimental structure of the latter is available, the consecutive steps employed in building and 

validation of PTE-sarin and PTE-paraoxon systems will be the subject of this contribution. Apart from 

classical molecular dynamics simulation, hybrid quantum mechanical and molecular mechanical 

(QM/MM) methodology will be employed to reveal molecular details of enzyme-substrate recognition 

along with its implication for PTE catalytic properties. 

Soot particles are also suspected to modify the atmospheric chemistry by providing surfaces for 

heterogeneous reactions. However, because ab initio calculations on such large systems are not 

realistic, we have developed mixed classical/semi-empirical calculations (hereafter called the SE-D 

method) to characterize the oxidation by OH of PAHs on small graphite cluster modelling soot 

surfaces. 

[1] Hamad, S.; Mejias, J.A.; Lago, S.; Picaud, S.; Hoang, P.N.M. J. Phys. Chem. 2004, B 108, 5405 

[2] Picaud, S.; Hoang, P.N.M.; Hamad, S. ; Mejias, J.A. J. Phys. Chem. 2004, B 108, 5410 

[3] Collignon, B.; Hoang, P.N.M.; Picaud, S.; Rayez, J.C. Chem. Phys. Lett. 2005, 406, 431. 

[4] Collignon, B.; Hoang, P.N.M., Picaud, S.; Rayez, J.C. Comp. Lett. 2005, 1, 277 

[5] Picaud, S.; Collignon, B.; Hoang, P.N.M.; Rayez, J.C. J. Phys. Chem.2006, B 110, 8398 

[6] Collignon, B.; Hoang, P.N.M.; Picaud, S.; Liotard, D.; Rayez, M.T.; Rayez, J.C. J. Mol. Struct. Theochem 

2006, 772, 1. 

[7] Picaud, S.; Collignon, B.; Hoang, P.N.M.; Rayez J.C., Phys. Chem. Chem. Phys. 2008 submitted.



PP499 

Combining the Time Reversal Symmetry with Point Group Symmetry in Relativistic Molecular 

Calculations 

Daoling Peng, Kimihiko Hirao 

Department of Applied Chemistry, The University of Tokyo, Tokyo 113-8656, Japan 

Relativistic four components and quasi-relativistic two components quantum chemistry methods for 

molecular calculation usually employ double point group symmetry, like double point group symmetry 

adapted linear combination, to improve the computational efficiency. Time reversal symmetry reduces 

the computational cost by means of properly chose the symmetry adapted linear combination of 

electron orbitals to be time reversal pairs. A systematical method has developed for arbitrary point 

groups. It fully combine the time reversal symmetry with double point group symmetry in both SCF 

calculation (using one electron functions as basis) and post-SCF calculation (using electron pair 

functions as basis). Latter is achieved by fixed the phase factor of vector coupling coefficients 

(Clebsch-Gordan coefficients) via a simple step by step procedure. 

Visscher [1] has tried to introduce time reversal symmetry for point group D 2h and its subgroup. But he 

did not solve the whole problem of real representations which occurs in the double point group of C 2v 

and D 2 . Saue [2] successfully solved this problem within D 2h and its subgroups via quaternion algebra. 

Meyer [3] developed a systemic method for all point groups, but he only got an intermediate form. Our 

approach is valid for all point groups and can extend to the case of vector coupling. 

Standard z-axis orientation non-polyhedral point groups contain only one time reversal symmetrized 

irreducible Clebsch-Gordan coefficients for the direct product of fermion irreducible representations, 

like the properties of boson irreducible representations in Abelian point groups. This may be useful for 

the simplification of relativistic two electron repulsion integrals calculations in post-SCF methods like 

relativistic configuration interaction and couple cluster. An independent program for all point groups 

based on these methods is being developed. It will provide the symmetry adapted linear combination 

functions of a molecule with given structure, and output the time reversal symmetrized CG coefficients. 

PP500 

The FMO/EFP Energy Gradient and its Applications to Solvated Peptide Molecules 

Takeshi Nagata 1 , Dmitri Fedorov 1 , Mark Gordon 2 , Kazuo Kitaura 3 

1 AIST, Tsukuba, Japan, 2 Iowa State University, Ames, United States, 3 Kyoto University, Kyoto, Japan 

We have interfaced Fragment Molecular Orbital method (FMO) [1] and Effective Fragment Potential 

method (EFP) [2]. In this study, we developed the FMO/EFP energy gradient and then applied it to 

water-solvated glycine tetramers. It is confirmed computationally that zwitterionic glycine stabilizes in 

solution [3]. The structures and energies of the electrically neutral and the zwitterionic tetraglycine 

molecules immersed in EFP water molecules are investigated using the FMO/EFP geometry 

optimization technique. The geometries optimized at RHF/cc-pVDZ level of FMO/EFP are compared 

with the conventional MO/EFP optimized geometries by taking the superposition of their geometries 

and estimating the root mean square (RMS) deviations. We found that the number of the geometry 

optimization cycles was significantly reduced when FMO external electrostatic derivatives were 

introduced [4], and the RMS deviations of superposition were small. Using the optimized geometries, 

we discuss the stability of the zwitterionic and neutral structures with the systematic increment of water 

molecules graphically and numerically. 

[1]. Kitaura, K.; Ikeo, E.; Asada, T.; Nakano, T.; Uebayasi, M. Chem. Phys. Lett. 1999, 313, 701. 

[2]. Day, P. N.; Jensen, K. H.; Gordon, M. S.; Webb, S. P.; Stevens, W. J.; Krauss, M.; Garmer, D.; Basch, H.; 

Drora, C. J. Chem. Phys. 1996, 105, 1968. 

[3]. Aikens, C. M.; Gordon, M. S.; J. Am. Chem. Soc. 2006, 128, 12835. 

[4]. Nakano, T.; Kaminuma, T.; Sato, T.; Fukuzawa, K.; Akiyama, Y.; Uebayasi, M.; Kitaura, K. Chem. Phys. Lett. 

2002, 351, 475. 

[1] Visscher, L. Chem Phys Lett 1996, 253, 20. 

[2] Saue, T.; Jensen, H. J. A. J Chem Phys 1999, 111, 6211. 

[3] (a) Meyer, J. Int J Quantum Chem 1988, 33, 445. (b) Meyer, J. Int J Quantum Chem 1994, 52, 1369. (c) 

Meyer, J.; Sepp, W.-D.; Fricke, B.; Rosen, A. Comput Phys Commun 1996, 96, 263.



PP501 

Dense Packing of Binary Spheres 

Gavin Marshall, Jonathan Kummerfeld, Toby Hudson, Peter Harrowell 

School of Chemistry, The University of Sydney, NSW, Australia 

The structure of close packed uniform spheres is an essential reference structure in numerous 

materials problems where high density is desirable. This work presents analogous dense packing 

reference structures for systems of binary spheres. They are obtained by data mining all known 

inorganic crystal structures, simulated annealing, and geometrical methods. Solutions are given for 

two subproblems: the case of homogeneous equimolar compound structures; and the case of particle 

filling of uniform honeycombs. The structures found include previously unknown structures, as well as 

known structures that were not identified as special by previous studies of packing. 

PP502 

Spectroscopic and Electric Properties of Tungsten Carbide 

Ivan Černušák, Miroslav Urban, Vladimír Kellö, Martina Čurkovičová 

Department of Physical and Theoretical Chemistry, Comenius University, Bratislava, Slovakia 

We have investigated the ground X 3 ∆ electronic state and the first excited 5 Σ electronic state of WC 

using Coupled Cluster (CC) approximation with single and double excitations corrected for the triple 

excitations (CCSD(T)) with the inclusion of scalar relativistic effects within the Douglas-Kroll-Hess 

formalism (DK-CCSD(T) in spin-free approximation). Molecular orbitals for tungsten carbide were 

expanded in terms of relativistic ANO-RCC atomic sets (triple-zeta, quadruple zeta and large 

contractions). The spectroscopic properties are calculated from the DK-CCSD(T) energies using 

Dunham sixth degree polynomial. In addition, fir the large contraction the dipole moments and dipole 

polarizabilities were evaluated within finite-field scheme. Comparison with the experimental [1] and 

previous theoretical [2] data is given. 

[1] S. M. Sickafoose, A. W. Smith, M. D. Morse, J. Chem. Phys. 2002, 116, 993. 

[2] K. Balasubramanian, J. Chem. Phys. 2000, 112, 7425.



PP503 

Acyl Radical Addition to Pyridine: Multiorbital Interactions. 

Ruth Amos 1,2 , Carl Schiesser 2,3,4 , Jason Smith 1,2 , Brian Yates 1,2 

1 School of Chemistry, University of Tasmania, Hobart, Tasmania, Australia, 2 ARC Centre of 

Excellence for Free-Radical Chemistry and Biotechnology, Country wide, Australia, 3 School of 

Chemistry, The University of Melbourne, Melbourne, Victoria, Australia, 4 Bio21 Molecular Science and 

Biotechnology Institute , The University of Melbourne, Melbourne, Victoria, Australia 

O 

N1 

H 

N 

NH2 

N 

NH 2 

N 

N 

N 

OH HO 

O 

O 

O 

P 

OHO 

O 

O 

P 

Isoniazid, the hydrazide of isonicotinic acid (1) is an important antibiotic used to combat tuberculosis 

(TB). Isoniazid is a prodrug which is activated to form a reactive intermediate. Recently we reported 

studies supporting the hypothesis that the reactive intermediate formed is an acyl radical produced by 

oxidation of the hydrazide. An important step in the chemistry of isoniazid is the addition of this acyl 

radical to the pyridinium ion in NAD + to form the true drug (2). We present results from a 

computational study into the addition of acyl radicals to both pyridine and the pyridinium ion. Natural 

bond orbital analysis predicts simultaneous SOMO→π*, Lone pair→SOMO and Lone pair → π* c=o 

interactions for the addition of the acetyl radical to the nitrogen in pyridine. These multiorbital 

interactions are responsible for the unusual motion vector associated with the transition state in this 

reaction and for the lowering in energy barrier. 

2 

OH 

OH 

O 

O 

OH 

N 

H 

N 

O 

NH 2 

PP504 

Selenium in Pyrite - Why is the XANES Spectrum of Iron Selenide not Observed? 

Nicholas Lambropoulos, Ken Riley, David French 

CSIRO Energy Technology, Lucas Heights, NSW, Australia 

There is much evidence for many forms of selenium in coal and the associated mineral matter. 

Examination of a number of Australian coals using the beam line at the Photon Factory did not 

produce x-ray absorption near edge structure (XANES) spectra for which there were unique fits of 

spectra from reference materials. Selenium is known to be present as organically bound forms and 

also as inorganic species including those associated with pyrite. Thus one of the likely forms is iron 

selenide, most likely FeSe 2 . The spectra of reference materials including FeSe and FeSe 2 did not fit 

the spectra of coals containing selenium associated with the sulfide fraction. 

The conundrum is not readily explained without consideration of the mineralogy of the likely sulfide 

associated selenium. With hindsight, it is obvious that the orthorhombic FeSe 2 is unlikely to present in 

the cubic FeS 2 mineral phase. Rather the Se is likely present at low concentrations as FeS 2-x Se x in the 

pyrite. 

The theoretical XANES spectrum of such a species has been calculated drawing on ab initio selfconsistent 

real space full multiple-scattering methods [1]. Outcomes from such a theoretical approach 

results in determination of optimised electronic structures and XANES spectra using built in core-hole 

effects. A comparison with the spectra obtained from coals containing selenium associated with the 

sulfide fraction is made [2]. 

[1] (a) Kresse, G.; Furthmüller, J. Phys. Rev. B. 1996, 54:11169. (b) Ankudinov, A.L.; Ravel, B.; Rehr, J.J.; 

Conradson, S.D. Phys. Rev. 1998, B58, 7565. 

[2] Riley, K. W.; French, D. H.; Lambropoulos, N. A.; Farrell, O. P.; Wood, R. A.; Huggins, F. E. Int. J. Coal 

Geology, 2007, 72(2), 72-80.



PP505 

Density Matrix Renormalization Group Response Theory 

Jon Dorando, Johannes Hachmann, Garnet Chan 

Cornell Chemistry and Chemical Biology, Cornell University, Ithaca, NY, United States 

Response theory in Density Matrix Renormalization Group (DMRG) has been formulated using two 

methods, Lanczos DMRG and the correction vector method [1]. Lanczos DMRG is considered to be 

accurate for obtaining the static response, but it gives less accurate results for the dynamic response. 

On the other hand, the correction vector method is accurate in obtaining both the static and dynamic 

response, but this method is rather expensive [2]. 

In our current work, we have formulated a new method to solve for the response analytically. This 

approach gives accurate results for both static and dynamic response, while also utilizing less 

computer resources. We compare the three dynamic response methods: the correction vector method 

without adapting the DMRG basis, the correction vector method with adapting the DMRG basis, and 

our newly formulated analytic response method. 

[1] Kuhner, T.D.; White, S.R. Phys. Rev. B 1999, 60 

[2] Jeckelmann, E. Phys. Rev. B 2002, 66 

PP506 

Things You Take For Granted in Closed-Shell MP2: The Subtleties of ROHF References in F12 

Methods 

Jeremiah Wilke, Henry F. Schaefer III, Wesley Allen 

Center of Computational Chemistry, University of Georgia, Athens, GA, United States 

The slow convergence of the correlation energy with respect to the size of the orbital basis has long 

been known. The error only decays as t -1/4 in the computational time! The slow convergence occurs 

since the orbital expansion is unable to describe the shape of the coulomb hole around the electron 

coalescence point. If two-particle basis functions that depend explicitly on the interelectronic distance 

supplement the orbital basis, the shape improves and convergence is greatly accelerated. In the last 

ten years, the F12 methods originally introduced by Kutzelnigg and Klopper have been the most 

successful in this regard. Efficient F12 codes for closed-shell molecules are now widely available. In 

contrast, F12 methods based on ROHF reference functions have only recently been investigated. In 

the context of perturbation theory, ROHF reference functions are not an eigenfunction of the Fock 

operator. The Hamiltonian partition must therefore be carefully redefined before perturbation theory 

can be applied. Properties such as orbital invariance, same orbitals for different spins, the Brillouin 

condition, and spin-restriction which are automatically true for closed shell MP2 all change in subtle 

ways for ROHF references. In the current work, we weigh the advantages of four different ROHF 

perturbation theories in the context of F12 methods - RMP, OPT1, OPT2, and ZAPT. ZAPT seems to 

provide the best balance of accuracy and efficiency, and we therefore derive a complete ZAPT2-F12 

theory, also considering future extensions to coupled-cluster methods. 

[1] Crawford, T.D. and Schaefer, H.F. Journal of Chemical Physics. 1996. 105. 1060-1069 

[2] Klopper, W., Valeev, E., Manby, F., and Ten-no, S. International Reviews in Physical Chemistry. 2006. 25. 

427-468.



PP507 

How Strong Is It? The Interpretation of Force and Compliance Constants as Bond Strength 

Descriptors 

Kai Brandhorst, Jörg Grunenberg 

Technische Universität Braunschweig, Institut für Organische Chemie, Braunschweig, Germany 

Recent developments of new descriptors for covalent and noncovalent interaction strengths based on 

potential constants are summarized. Several publications in favour and against the use of compliance 

matrices (inverse force constants matrix) appeared in the literature during the last few years [1] while 

the mathematical basis for the understanding and therefore interpretation of compliance constants is 

still not well developed. This contribution therefore summarizes the theoretical foundations and points 

to the advantages and disadvantages of force constants versus compliance constants for the 

description of both, non-covalent and covalent interactions. 

We will use simple matrix algebra to illustrate the properties of compliance constants and their 

uniqueness and will present some recent applications concerning individual covalent and non-covalent 

bond strenghts in molecules. 

A clear correlation between compliance constants and interaction energies is demonstrated based on 

a compilation of 40 base-pairs from the JSCH2005 dataset [2]. 

We find, that compliance constants or relaxed force constants offer not only a possibility to compare 

bond strengths in related molecules in a unique manner, but also allow the estimation of the overall 

interaction energies of weakly bound complexes in cases where several hydrogen-bonds are involved. 

PP508 

Efficient Computation of Inverse Hessians and Compliance Matrices in Redundant Internal 

Coordinates from Cartesian Hessians 

Kai Brandhorst, Jörg Grunenberg 

Technische Universität Braunschweig, Institut für Organische Chemie, Braunschweig, Germany 

We present a new algorithm for the computation of either the hessian or the compliance matrix [1] in 

redundant internal coordinates. We will show, that the complete redundant compliance matrix of a 

coordinate system of all N(N-1)/2 possible interatomic distances in a molecule can be computed with a 

complexity of only O(N 4 ), while the computation of the hessian itself in the same set of coordinates is 

of O(N 5 ) complexity, which nevertheless is one order of magnitude lower than the conventional 

algorithm that scales like O(N 6 ) [2]. 

The new algorithm has been implemented in our standalone computer code Compliance 2.0 which is 

able to compute the complete and redundant compliance matrix of all interatomic distances, valence 

angle bendings and dihedral torsions from a Cartesian hessian. Using our new algorithm avoids the 

time consuming and error prone definition of a non redundant set of coordinates and allows the 

straightforward computation of the complete compliance matrix even for complex molecular 

topologies. 

We will make available the code at no cost to anyone who is interested in using it. 

[1] (a) Grunenberg, J. J. Am. Chem. Soc. 2004, 126, 16310-16311. (b) Brandhorst, K.; Grunenberg, J. 

ChemPhysChem. 2007, 8, 1151-1156. (c) Baker, J. J. Chem. Phys. 2006, 125, 014103. (d) Baker, J.; Pulay, P. 

J. Am. Chem. Soc. 2006, 128, 11324-11325. 

[2] Jurecka, P.; Sponer, J.; Cerny, J.; Hobza, P. Phys. Chem. Chem. Phys., 2006, 8, 1985-1993. 

[1] (a) Decius, J. C. J. Chem. Phys. 1963, 38, 241-248. (b) Jones, L. H.; Swanson, B. I. Acc. Chem. Res. 1976, 9, 

128-134. (c) Brandhorst, K.; Grunenberg, J. ChemPhysChem, 2007, 8, 1151-1156. 

[2] (a) Pulay, P.; Fogarasi, G. J. Chem. Phys. 1992, 96, 2856-2860. (b) Peng, C.; Ayala, P. Y.; Schlegel, H. B.; 

Frisch, M. J. J. Comput. Chem. 1996, 17, 49-56.



PP509 

Quantized-Liquid Density Functional Theory of Hydrogen Adsorption in Nano-Porous 

Substrates. 

Serguei Patchkovskii 1 , Thomas Heine 2 

1 NRC Canada, Ottawa, Ontario, Canada, 2 Jacobs University, Bremen, Germany 

Compact storage of molecular hydrogen is the major obstacle to the development of practical 

hydrogen-powered vehicles. Physisorption of hydrogen in nano-porous materials (e.g. clathrates, 

metal-organic frameworks, and exfoliated graphite) is among the most practically successful 

approaches, but the fundamental limits on the storage capacities of these systems are not fully 

understood. 

Building on a recently-introduced [1] quantized ideal-gas treatment, we develop a simple method for 

estimation of the adsorption free energy of lightweight molecules in nanoporous structures: the 

quantized-liquid density functional theory (QLDFT). The approach allows direct calculation of the free 

adsorption energy in nano-scale systems, taking into account quantization of the nuclear motion of the 

guest molecules. The main ingredients of the technique are the kinetic energy of the quantized ideal 

gas, the mean-field interaction potential, and the excess free energy functional. The free-energy 

functional is constructed to reproduce the experimental equation of state for the uniform hydrogen 

fluid. 

PP510 

XUV Probing of a Recollision Electron Wavepacket: An Attosecond Electron Microscope. 

Olga Smirnova, Serguei Patchkovskii, Michael Spanner 

NRC Canada, Ottawa, Ontario, Canada 

Ionization of atoms and molecules, followed by recollision with the parent ion, is fundamental to many 

strong field phenomena. We propose a technique for direct imaging of the recolliding electron wave 

packet with sub-Å spatial and attosecond temporal resolution [1]. The approach relies on adsorption of 

an XUV photon at the time of recollision, with subsequent detection of the high-energy photoelectrons. 

Delicate numerical simulations show that the proposal is experimentally realizable, despite the very 

small cross-section of the desired process. 

[1] Smirnova, O., Patchkovskii, S., Spanner, M. Direct XUV Probing of Attosecond Electron Recollision, Phys Rev 

Lett 2007, 98, 123001 

We consider three increasingly sophisticated forms of the free-energy functionals. In the localinteraction 

expression (LIE) approximation, the exchange-correlation is in the local-densityapproximation 

form, while the mean-field interaction potential is set to zero. The LIE functional 

successfully reproduces adsorption thermodynamics in open pores, but fails to describe the 

microscopic fluid structure. Due to the large self-interaction error, it also fails for isolated adsorption 

sites. Incorporation of the mean-field interaction potential, together with a scaled-density 

approximation (SDA) non-local free energy functional, allows description of the hydrogen fluid 

structure, as well as phase transitions. However, the SDA-v12 form of QLDFT still fails for isolated 

adsorption sites. This remaining defect is corrected in the self-interaction corrected neighbour-density 

approximation form of QLDFT. 

[1] Patchkovskii, S., Heine, T. Evaluation of the adsorption free energy of light guest molecules in nanoporous 

host structures, Phys. Chem. Chem. Phys. 2007, 9, 2697



PP511 

QSPR Studies on the Prediction of Physicochemical Properties of High Energetic Materials: 

Melting Point 

Chan Kyung Kim 1 , Soo Gyeong Cho 2 , In Suk Han 1 , Junxian Chen 1 , Hyok Yoon 1 , Hai Whang Lee 1 , 

Bon-Su Lee 1 

1 Inha University, Department of Chemistry, Incheon, 402-751, Korea, Republic of, 2 Agency for 

Defense Development, P. O. Box 35-42, Yuseong, Deajeon, 305-600, Korea, Republic of 

Prediction of physicochemical properties of high energetic materials (HEM) is an important study in 

developing new energetic materials. To predict melting points of HEMs with at least one –NO 2 group, 

several methodologies based on group additivity, molecular topology and atom/specific functional 

group additivity are examined. As a continuing work on the QSPR works on HEMs, all the HEMs are 

fully optimized at B3LYP/6-31G(d) level of theory and confirmed to be genuine minima using Gaussian 

03. From the optimized structures, van der Waals surface electrostatic potentials are calculated using 

the method developed earlier [1]. QSPR studies are performed to find a good linear correlation using 

the descriptors obtained from GIPF variables [2]. Melting points predicted from this work are compared 

with the experimental values as well as other methods. 

PP512 

Theoretical Studies on Nucleophilic Substitution Reactions of Acetyl and Thioacetyl Halides 

with NH 3 in the Gas Phase and in Aqueous Solution 

In Suk Han, Chang Kon Kim, Hyok Yoon, Hai Whang Lee, Chan Kyung Kim 

Inha University, Department of Chemistry, Incheon, 402-751, Korea, Republic of 

The reactions of acetyl halides, CH 3 C(=O)X, and corresponding sulfur analogues, thioacetyl, 

CH 3 C(=S)X, where X = F and Cl with NH 3 have been studied theoretically at MP2 level of theory in the 

gas phase and in aqueous solution. All the reactions occurred via the T ± -typed species and the 

reactions through neutral intermediates might be ruled out in both phases except for the gas-phase 

reaction of acetyl fluoride. In the reaction of acetyl chloride, the tetrahedral species was a transition 

structure (TS) but a stable intermediate in the reactions of thioacetyl halides. This could be caused by 

different π-bond strengths of C=O and C=S. For acetyl fluoride, the tetrahedral species was neither a 

saddle point species nor an energy minimum in the gas phase, but existed as a stable intermediate in 

aqueous solution due to solvation effects. Moreover, in the reactions of thioacetyl halides the ratelimiting 

step was changed from the first step in the gas phase to the second step in aqueous solution, 

since the T ± -typed intermediates became much more stabilized in aqueous solution. However, 

lowering in the activation barriers ( ∆ E ≠ 

ZPE 

) in aqueous solution compared to those in the gas phase 

was not caused by the solvent effects but smaller deformation energies on going from reactants from 

TS. 

H 3 C 

Y 

C 

(Y = O or S and X = F or Cl) 

Y δ- 

H 3 C C 

δ+ 

Y- 

X + NH 3 

H 3 C 

C 

+ 

NH 3 

(T + ) 

δ- 

X 

X 

= 

Products 

Products 

(1a) 

(1b) 

NH 3 

Products (1c) 

YH 

H 3 C 

C 

NH 2 

[1] Kim, C. K.; Lee, K. A.; Hyun, K. H.; Park, H. J.; Kwack, I. Y.; Kim, C. K.; Lee, H. W.; Lee, B.-S. J. Comput. 

Chem. 2004, 25, 2073. 

[2] Politzer, P.; Murray, J. S. Quantitative Treatments of Solute/Solute Interac-tions; Elsevier: Amsterdam, 1994; 

p. 243. 

X 

(T)



PP513 

Effects of Basis Set Superposition Error on Optimized Geometries and Energies of Organo- 

Alkali Metal Cation and its Halide Complexes 

Chang Kon Kim 1 , In Suk Han 1 , Hyok Yoon 1 , Jongok Won 2 , Chan Kyung Kim 1 

1 Inha University, Department of Chemistry, Incheon, 402-751, Korea, Republic of, 2 Sejong University, 

Department of Applied Chemistry, Seoul, 134-747, Korea, Republic of 

Theoretical studies were performed to study the binding of the alkali metal cation, X + (X = Li, Na, K), to 

poly(ethylene oxide) (PEO, I), poly(ethylene amine, II) (PEA) and poly(ethylene N-methylamine) 

(PEMA, III) and dissociation processes in the same polymer electrolytes with alkali-metal iodides via 

the Hartree-Fock (HF) and B3LYP methods using the 6-31G(d) and 6-311+G(d,p) basis sets. Two 

types of complex were considered in this study: singly-coordinated system (SCS) and doublycoordinated 

system (DCS). Complexation and dissociation energies were calculated both without and 

with basis set superposition error (BSSE). Three possible counterpoise (CP) approaches were 

examined in detail. In the case of the function CP (fCP) correction, the complexation energies 

exhibited an unusual trend due to deformation of the subunits. This problem was solved by including 

geometry relaxation in the CP-corrected (GCP) interaction energy. The effects of structures and 

vibrational frequencies were small when the complexes were re-optimized on the CP-corrected, 

potential energy surface (PES). 

H 3 C 

H 2 

X C CH 3 

+ M + 

C X 

H 2 

H 3 C 

Singly-Coordinated System(SCS) 

H 2 

X C CH 3 

C X 

H 2 

M + 

PP514 

Theoretical Study of the Acid-Base Properties of Piroxicam and Isoxicam 

Marco Antonio Franco-Pérez, Rosario Moya-Hernández, Rodolfo Gómez-Balderas 

FESC-Cuautitlán, UNAM, Departamento de Química, México 

Oxicams are widely used for treatment of chronic inflammatory conditions. In this contribution, we 

report results of a theoretical study of Piroxicam (P) and Isoxicam (I). It is well known that acid-base 

properties of drugs affect their bio-availability and pharmacological action. In order to consider the 

different acid-base species we included the HP + , P, P – , I and I – species. Geometry optimizations and 

conformational scans have been done at the B3LYP/6-31G (d, p) level of theory. The gas phase 

minima were then reoptimized using the PCM scheme to include the effect of the solvent (H 2 O) at the 

B3LYP/6-311++G(d,p) level. Estimation of the H-NMR chemical shifts, including the main contributions 

pondered by energy of several conformers agrees reasonably well with the experimental observations. 

Additionally, we use Fukui functions, frontier orbital´s and ionization potentials to characterize these 

oxicams. 

O 

S 

OH 

O 

N 

CH 3 

O 

H 

N 

N 

O 

S 

OH 

O 

N 

CH 3 

O 

H 

N 

N 

O 

H 3 C 

X 

H 2 

C CH 3 + M + 

C X 

H 2 

M+ 

H 3 C X X 

H 2 C CH 2 

CH 3 

Piroxicam Isoxicam 

CH 3 

Doubly-Coordinated System(DCS) 

H 3 C 

H 2 

X C CH 3 

C X 

H 2 

M + 

Singly-Coordinated System(SCS) 

H 3 C 

H 2 C 

X 

+ 

M 

I - I - 

CH 2 

X 

CH 3 

Doubly-Coordinated System(DCS) 

where X = O (I), NH (II), and N(CH 3 ) (III) and M = Li, Na, and K



PP515 

Accurate Hartree-Fock Calculation Using Perturbation Theory 

Jia Deng, Peter Gill 

Research School of Chemistry, Australian National University, Australia 

The slow convergence of Quantum chemical methods with respect to the size of the one-electron 

Gaussian basis set is a major obstacle in computational chemistry, therefore, exploring the basis set 

limit at a relatively inexpensive cost is very desirable. Recently, we have discovered a mathematically 

rigorous approach, based on perturbation theory, to explore the basis set limit at Hartree-Fock level of 

theory. In this poster, we outline the Hartree-Fock Pertubation Theory (HFPT), and show that our 

method, at first order, exhibits quadratic convergence. We apply HFPT to several small atomic and 

molecular systems. Our numerical investigation shows that HFPT yields very accurate Hartree-Fock 

energies, and the convergence behaviour confirms our theoretical result.

Poster Session 3 - RSC - Australian National University

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