UNIVERSITY OF CALIFORNIA, SAN DIEGO

CALIFORNIA, SAN DIEGO 1 

UNIVERSITY OF 

CALIFORNIA, SAN DIEGO 

La Jolla, CA 92093-0332 

5149 FAX: (858) 822-5407 

Web: www.sdsc.edu/~kimb 

Email: kimb@oci.uzh.ch 

kimb@sdsc.edu 

Tirath Ramdas, Gerald Egan, David Abramson and Kim K. 

Baldridge, Towards a special purpose computer for Hartree- 

Fock computations, Theor. Chem. Acc, 120, 133-135 (2008). 

Kim K. Baldridge and Jay S. Siegel, Quantum chemical 

prediction of the 13 TEL: (858) 534-5489 

FAX: (858) 534-6693 

Web: www-chem.ucsd.edu 

Email: chair@chem.ucsd.edu 

Department of Chemistry and Biochemistry 

Robert E. Continetti, Chair. 

Degrees Offered: B.A, B.S, M.S, Ph.D. 

Fields of Specialization: MS and PhD in Chemistry 

fields include Biochemistry, Biophysics, Analytical 

Florian P. Seebeck, Angelo Guainazzi, Celine Amoreira 

and Donald Hilvert, Stereoselectivity and expanded substrate 

scope of an engineered PLP-dependent aldolase, Angewante. 

Chemie. Int. Engl, 45, 6824-6826 (2006). 

Toshiyuki Hamura, Yousuke Ibusuki, Hidehiro Uekusa, 

Takashi Matsumoto, Jay S. Siegel and Kim K. Baldridge, 

Dodecamethoxy- and Hexaoxo-tricyclobutabenzene: Synthesis 

and characterization, J. Am. Chem. Soc, 128, 10032- 

10033 (2006). 

Jay S. Siegel, Kim K. Baldridge, Anthony Linden and Reto 

Dorta, D8 Rhodium and Iridium complexes of corannulene, 

J. Am. Chem. Soc, 128, 10644-10645 (2006). 

Michale DeClue, Kim K. Baldridge, Peter Kast and Donald 

C NMR shifts in alkyl and chlorocorannulenes: 

correction of chlorine effects, Theor. Chem. 

Acc, 120, 95-106 (2008). 

L. Gregerson, Outlying charge, stability, efficiency, and 

extensibility in quantum mechanical solvation methods: The 

COSAB-GAMESS method. (D) 

BERTRAM, TIMOTHY (b.1978) Assistant Professor. 

B.A, 2000, Colby College; Ph.D, 2006, UC Berkeley. 

NOAA C&GC; Postdoctoral Fellow, 2007-2009, 

University of Washington. Atmospheric Chemistry; Environmental 

Chemistry. My research interests, in the field 

Chemistry, Environmental and Atmospheric Chemistry, 

Inorganic Chemistry, Organic Chemistry, Com- 

putational Chemistry, Theoretical Chemistry, Materials 

Chemistry, and Physical Chemistry PhD in 

Chemistry with specialization in Bioinformatics. 

Interdisciplinary Program: Joint Doctoral Program 

in Chemistry and San Diego State University and 

University of California San Diego. 

ALLISON, WILLIAM S. (b.1935) Professor, Emeri- 

Hilvert, Experimental and computational investigatin of the 

uncatalyzed elimination and rearrangement reactions of isochorismate, 

J. Am. Chem. Soc, 128, 2043 (2006). 

Yao-Ting Wu, Tomoharu Hayama, Kim K. Baldridge, Anthony 

Linden and Jay S. Siegel, Synthesis of fluoranthenes 

and indenocorannulenes: Elucidation of chrial stereoisomers 

on the basis of static molecular bowls, J. Am. Chem. Soc, 

128, 6870-6884 (2006). 

Roie Yerushalmi, Alexander Brandis, Vada Rosenbach- 

Belkin, Kim K. Baldridge and Avigdor Scherz, Modulation 

of fragmental charge transfer via hydrogen bonds; direct 

measurement of electronic contributions, J. Phys. Chem, 110, 

of atmospheric chemistry, utilize both laboratory and 

field-based approaches to provide constraints on chemi- 

cal processes occurring in the atmosphere. Specifically, 

my research focuses on providing measures of speciated 

reactive nitrogen from various platforms (ground, aircraft 

and satellite). These observations are used to direct- 

ly constrain both chemical mechanisms and transport 

processes in the atmosphere. TEL: (510) 388-7600 FAX: 

(858) 534-1697 

Web: bertramgroup.ucsd.edu 

Email: thbertram@ucsd.edu 

tus. A.B, 1957, Dartmouth College; M.A, 1959, Dart- 412 (2006). E. C. Wood, T. H. Bertram, P. J. Wooldridge and R. C. 

mouth College; Ph.D, 1963, Brandeis University. 

USPHS Fellow, 1964-1965, MRC, Laboratory Molecular 

Biology, Cambridge, England. The molecular mecha- 

nism of ATP synthase. TEL: (858) 534-3057 FAX: (858) 

822-0079 

Web: www.chem.ucsd.edu 

Email: wallison@ucsd.edu 

wsa@checfs2.ucsd.edu 

No publication information submitted for this edition. 

Jose N. Onuchic, Chiguas Kobayashi, Osamu Miyashita, 

Patricia Jennings and Kim K. Baldridge, Exploring biomolecular 

machines; energy landscape control of biological reactions, 

Philosophical Transactions of the Royal Society of 

London, 361, 1439-1443 (2006). 

Tomoharu Hayama, Yao-Ting Wu, Anthony Linden, Kim 

K. Baldridge and Jay S. Siegel, Synthesis, Structure, and 

Isomerization of Decapentynylcorannulene: Enediyne Cyclization/Interconversion 

of C40R10 Isomers, J. Am. Chem. Soc, 

129, 12612-12613 (2007). 

Cohen, Measurements of N2O5, NO2 and O3 East of the San 

Francisco Bay, Atmos. Chem Phys, 5, 483-491 (2005). 

T. H. Bertram, A. Heckel, A. Richter, J. Burrows and R. C. 

Cohen, Satellite measurements of daily variations in soil 

NOx emissions, Geophys. Res. Lett, (2005). 

T. H. Bertram, P. M. Chu and R. C. Cohen, Comparison of 

NIST ozone, nitric oxide and nitrogen dioxide standards, J. 

Air and Waste Management Assoc, 55, 1473-1479 (2005). 

C. S. Boxe, A. J. Colussi, M. R. Hoffman, J. G. Murphy, P. 

J. Wooldridge, T. H. Bertram and R. C. Cohen, Photochemi- 

ARNOLD, JAMES R. 


Giancarlo Terraneo, Donatella Potenza, Angeles Canales, 

Jesus Jimenez-Barbero, Kim K. Baldridge and Anna Bernardi, 

A Simple Model System for the Study of Carbohydratecal 

production and release of gaseous NO2 from nitrate 

doped water ice, J. Phys. Chem. B, (2005). 

R. V. Martin, C. E. Sirois, K Chance, T. B. Ryerson, T. H. 

BAKER, TIMOTHY S. (b.1949) Professor. B.S, 

1971, Duke University; Ph.D, 1976, University of California, 

Los Angeles. Jane Coffin Childs Fellow, 1976- 

1978; NIH Postdoc Fellow, 1979-1980; Charles A. King 

Trust Postdoctoral Fellow, 1980-1982. Biochemistry. 

Macromolecular, cryoelectron microscopy and three-dimensional, 

image-reconstruction techniques are used in 

our research to visualize viruses and to determine how 

Aromatic Interactions, J. Am. Chem. Soc, 129, 2890-2900 

(2007). 

Jan Andzelm, Adam M. Rawlett, Joshua A. Orlicki, James 

F. Snyder and Kim K. Baldridge, Optical Properties of 

Phthalocyanine and Naphthalocyanine Compounds, J. Chem. 

Theory Comput, 3, 870-877 (2007). 

He-Ping Wu, Daniel H. Ess, Seren Lanza, Timothy J. R. 

Weakley, K. N. Houk, Kim K. Baldridge and Michael M. 

Haley, Rearrangement of Iridabenzvalenes to Iridabenzenes 

and/or � 

Bertram, P. J. Wooldridge, R. C. Cohen, A. A. Neuman, A. 

Swanson and F. M. Flocke, Evaluation of space based constraints 

on nitrogen oxide emissions with regional aircraft 

measurements over and downwind of eastern North America, 

J. Geophys. Res, (2006). 

O. R. Cooper, A. Stohl, M. Trainer, A. Thompson, J. C. 

Witte, S. J. Oltmans, B. J. Johnson, J. Merrill, J. L. Moody, 

G. Morris, D. Tarasick, G. Forbes, P. Nedelec, F. C. Fehsen- 

feld, J. Meagher, M. J. Newchurch, F. J. Schmidlin, S. Tur- 

5-Cyclopentadienyliridium(I) 

viruses interact with their hosts. TEL: (858) 534-5845 

FAX: (858) 534-5846 

Web: www-biology.ucsd.edu/faculty/baker.html 

Email: tsb@ucsd.edu 

Complexes: Experimental 

and Computational Analysis of the Influence of Silyl 

Ring Substituents and Phosphine Ligands, Organometallics, 

26, 3957-3968 (2007). 

Simon Duttwyler, Quyen-Quyen Do, Anthony Linden, 

quety, J. H. Crawford, G. Chen, K. E. Pickering, S. L. 

Baughcum, R. C. Cohen, T. H. Bertram, P. Wooldridge, A. 

Perring, W. H. Brune, N. Spichtinger and C. C. Brown, 

Large upper tropospheric enhancements above mid-latitude 

North America during summer: In situ evidence from the 

Said A. Ghabrial, Wendy F. Ochoa, Timothy S. Baker and Kim K. Baldridge and Jay S. Siegel, Synthesis of 2,6- IONS and MOZAIC ozone monitoring networks, J. Geophys. 

Max L. Nibert, Partitiviruses: General features, Encyclopedia diarylphenyldimethylsilyl cations: polar-� distribution of cat- Res, (2006). 

of Virology, 4, 68-75 (2008). 

ion character, Angew. Chem., Int. Ed, 47, 1719-1722 (2008). S. Kim, L. G. Huey, R. E. Stickel, D. J. Tanner, J. H. 

Xiaodong Yan, Zeyun Yu, Ping Zhang, Anthony J. Battisti, Vincent Lemieux, M. Daniel Spantulescu, Kim K. Bal- Crawford, J. R. Olson, G. Chen, W. H. Brune, X. Ren, R. 

Heather A. Holdaway, Paul R. Chipman, Chandrajit Bajaj, dridge and Neil R. Branda, Modulating the Lewis acidity of Lesher, P. J. Wooldridge, T. H. Bertram, A. Perring, R. C. 

Max Bergoin, Michael G. Rossmann and Timothy S. Baker, boron using a photoswitch, Angew. Chem., Int. Ed, 47, 5034- Cohen, B., B. Lefer, R. E. Shetter, M. Avery, G. Diskin and 

The capsid proteins of a large icosahedral dsRNA virus, J. 5037 (2008). I. Sokolik, Measurement of HO2NO2 in the upper tropo- 

Mol. Bio, 385, 1287-1299 (2008). 

Tirath Ramdas, Gregory K. Egan, David Abramson and sphere during ICARRT-INTEX-NA, J. Geophys. Res, 

Hazel C. Levy, Valorie D. Bowman, Lakshmanan Govin- Kim K. Baldridge, Uniting extrinsic vectorization and shell (2007). 

dasamy, Robert McKenna, Kevin Nash, Kenneth Warringstructure for efficient SIMD evaluation of electron repulsion R. C. Hudman, D. J. Jacob, S. Turquety, E. M. Leibensper- 

ton, Weijun Chen, Nicholas Muzyczka, Xiaodong Yan, Tim- integrals, Chem. Phys, 349, 147-157 (2008). ger, L. T. Murray, S. Wu, A. B. Gilliland, M. A. Avery, G. 

othy S. Baker and Mavis Agbandje-McKenna, Heparin bind- Tirath Ramdas, Gerald Egan, David Abramson and Kim K. W. Sachse, T. H. Bertram, R. C. Cohen, P. J. Wooldridge, A. 

ing induces conformational changes in Adeno-associated vi- Baldridge, On ERI sorting for SIMD execution of large-scale E. Perring, W. H. Brune, X. R. Ren, J. E. Dibb, F. M. Flocke, 

rus serotype 2, J. Struct. Bio, 165, 146-156 (2008). 

Hartree-Fock SCF, Comp. Phys. Comm, 178, 817-834 A. Fried, J. S. Holloway, A. Newman, T. B. Ryerson, R. Or- 

Jinghua Tang, Wendy F. Ochoa, Robert S. Sinkovits, Bon- (2008). ville and H. B. Singh, Surface and lightning sources of nitronie 

T. Poulos, Said A. Ghabrial, Donald V. Lightner, Timo- Ryan L. Holland, Kevin D. Bunker, Christopher H. Chen, gen oxides in the United States: Magnitudes, chemical evolu- 

thy S. Baker and Max L. Nibert, Infectious myonecrosis vi- Antonio G. Di Pasquale, Arnold L. Rheingold, Kim K. Bal- tion and outflow, J. Geophys. Res, (2007). 

rus has a totivirus-like, 120-subunit capsid, but with fiber dridge and Joseph M. O’Connor, Reactions of a Metallacy- H. B. Singh, L. Salas, D. Herlth, E. Czech, M. Avery, J. H. 

complexes at the fivefold axes, Proc. Natl. Acad. Sci. U. S. A, clobutene Complex with Alkenes, J. Am. Chem. Soc, 130, Crawford, R. B. Pierce, G. W. Sachse, D. R. Blake, R. C. Co- 

105, 17526-17531 (2008). 

10093-10095 (2008). hen, T. H. Bertram, A. Perring, P. J. Wooldridge, J. Dibb, G. 

Wendy F. Ochoa, Wendy M. Havens, Robert S. Sinkovits, Yao-Ting Wu, Davide Bandera, Roman Maag, Anthony Huey, R. C. Hudman, S. Turquety, L. K. Emmons, F. Flocke, 

Max L. Nibert, Said A. Ghabrial and Timothy S. Baker, Par- Linden, Kim K. Baldridge and Jay S. Siegel, Multiethynyl Y. Tang, G. R. Carmichael and L. W. Horowitz, Reactive nititivirus 

structure reveals a 120-subunit, helix-rich capsid Corannulenes: Synthesis, Structure, and Properties, J. Am. trogen distribution and partitioning in the north american tro- 

with distinctive surface arches formed by quasisymmetric Chem. Soc, 130, 10729-10739 (2008). posphere and lowermost stratosphere, J. Geophys. Res, 

coat-protein dimers, Structure (Cambridge, MA, U. S.), 16, Tomoharu Hayama, Kim K. Baldridge, Yao-Ting Wu, An- (2007). 

776-786 (2008). 

thony Linden and Jay S. Siegel, Steric Isotope Effects A. Fried, J. Walega, J. Olson, J. Crawford, G. Chen, P. 

Jinghua Tang, Norman Olson, Paul J. Jardine, Shelley Gauged by the Bowl-Inversion Barrier in Selectively Deuter- Weibring, D. Richter, C. Roller, F. Tittel, M. Porter, H. Fuel- 

Grimes, Dwight L. Anderson and Timothy S. Baker, DNA ated Pentaarylcorannulenes, J. Am. Chem. Soc, 130, 1583- berg, J. Halland, T. H. Bertram, R. Cohen, K. Pickering, B. 

poised for release in bacteriophage �29, Structure (Cam- 1591 (2008). Heikes, J. Snow, H. Shen, D. O’Sullivan, W. Brune, X. Ren, 

bridge, MA, U. S.), 16, 935-943 (2008). 

Jose N. Onuchic, Chigusa Kobayashi and Kim K. Bal- D. Blake, N. Blake, G. Sachse, G. Diskin, J. Podolski, S. 

dridge, Quantum tunneling in biological reactions: the inter- Vay, R. Shetter, B. Anderson, L. Thornhill, A. Clarke, C. 

BALDRIDGE, KIM K. (b.1960) Adjunct Professor. 

B.S, 1982, Minot State University; M.A, 1985, North 

Dakota State University; Ph.D, 1988, North Dakota State 

University. Postdoctoral Fellow, 1989, Wesleyan. Theoretical 

Chemistry. Direct application of quantum chemical 

software to problems in biomedical research and materials 

chemistry; development of new quantum chemical 

algorithms for study of reaction processes including effects 

of the environment; development of visualization, 

database, and grid middleware technologies for computational 

chemistry and biochemistry ; development of instructional 

codes for chemical curricula. TEL: (858) 534play 

between theory and experiments, J. Braz. Chem. Soc, 

19, 206-210 (2008). 

Roberto Peverati and Kim K. Baldridge, Implementation 

and Performance of DFT-D with Respect to Basis Set and 

Functional for Study of Dispersion Interactions in Nanoscale 

Aromatic Hydrocarbons, J. Chem. Theory Comput, 4, 2030- 

2048 (2008). 

Franco Cozzi, Rita Annunziata, Maurizio Benaglia, Kim 

K. Baldridge, Gerardo Aguirre, Jesus Estrada, Yongsak Sritana-Anant 

and Jay S. Siegel, Through-space interactions between 

parallel-offset arenes at the van der Waals distance: 

1,8-diarylbiphenylene syntheses, structure and QM computations, 

Phys. Chem. Chem. Phys, 10, 2686-2694 (2008). 

McNaughton, H. Singh, M. Avery, G. Huey, D. Millet and D. 

Jacob, The role of convection in redistributing formaldehyde 

to the upper troposphere over North America and the North 

Atlantic during the Summer 2004 INTEX Campaign, J. Geophys. 

Res, (2007). 

T. H. Bertram, A. E. Perring, P. J. Wooldridge, J. D. 

Crounse, A. J. Kwan, P. O. Wennberg, E. Scheuer, J. Dibb, 

M. Avery, G. Sachse, S. A. Vay, J. H. Crawford, C. S. 

McNaughton, A. Clarke, K. E. Pickering, H. Fuelberg, G. 

Huey, D. R. Blake, H. B. Singh, S. R. Hall, R. E. Shetter, A. 

Fried, B. G. Heikes and R. C. Cohen, Direct measurement of 

the convective recycling of the upper troposphere, Science, 

(2007).

2 CALIFORNIA, SAN DIEGO 

K. F. Boersma, D. J. Jacob, E. J. Buscela, A. E. Perring, R. nior Research Fellow, 1958, California Institute of Tech- dynamics. Charge exchange and dissociative recombina- 

Dirsken, R. J. can der, A. R. M. Yantosca, R. J. Park, M. O. nology. Ion-molecule reactions in the gas phase; organo- tion dynamics of molecular and cluster cations. TEL: 

Wenig, T. H. Bertram and R. C. Cohen, Validation of OMI sulfur chemistry; reaction mechanisms. TEL: (619) 534- (858) 534-5559 FAX: (858) 534-9856 

Tropospheric NO2 observations during INTEX-B and appli- 3130 FAX: (619) 534-5211 Web: checont6.ucsd.edu 

cation to constrain NOx emissions over the Eastern United Email: mcaserio@ucsd.edu Email: rcontinetti@ucsd.edu 

States and Mexico, Atmos. Environment, (2008). 

O. R. Cooper, S. Eckhardt, J. H. Crawford, C. C. Brown, 

No publication information submitted for this edition. Zhou Lu, Qichi Hu, Jonathan E. Oakman and Robert E. 

R. C. Cohen, T. H. Bertram, P. Wooldridge, A. Perring, W. 

Continetti, Dynamics on the HOCO potential energy surface 

CLARK, LEIGH B. (b.1934) Professor Emeritus. B.S, studied by dissociative photodetachment of HOCO- H. Brune, X. Ren, D. Brunner and S. Baughcum, The sum- 

and 

DOCO-, mertime buildup and decay of lightning NOx and aged thun- 1957, University of California, Berkeley; Ph.D, 1963, 

J. Chem. Phys, 126, 194305/1-194305/11 (2007). 

derstorm outflow above North America, J. Geophys. Res, University of Washington. Research Fellowship, 1963, Silvia De Dea, Dominic Graziani, David R. Miller and 

(2008). 

University of California, Berkeley. Electronic states of Robert E. Continetti, Growth of magnetic thin films using 

molecules; exciton states of crystals; reflection spectros- CO2 RESS expansions, J. Supercrit. Fluids, 42, 410-418 

BOND, F. THOMAS 

copy; optical properties of polynucleotides; optical prop- (2007). 

No publication information submitted for this edition. erties of liquids. TEL: (619) 534-2156 

Zhou Lu and Robert E. Continetti, Alignment of a Molecu- 

Email: lclark@ucsd.edu 

lar Anion via a Shape Resonance in Near-Threshold Photodetachment, 

Phys. Rev. Lett, 99, 113005/1-113005/4 (2007). 

BRYDGES, STACEY (b.1972) Lecturer, Potential Se- 


Jennifer E. Mann, Zhen Xie, John D. Savee, Bastiaan J. 

curity of Employment (LPSOE). B.Sc, 1996, McMaster 

University; Ph.D, 2003, McMaster University. Chemistry COHEN, SETH M. (b.1972) Associate Professor. B.S, 

Braams, Joel M. Bowman and Robert E. Continetti, Probing 

the Structure of CH5 + Education. TEL: (858) 246-0993 FAX: (858) 534-7042 

Web: www-chem.ucsd.edu/research/profile.cfm?cid= 

C22509 

Email: sbrydges@ucsd.edu 


1994, Stanford University; B.A, 1994, Stanford University; 

Ph.D, 1998, University of California, Berkeley. NIH 

Postdoctoral Fellow, 1999-2001, M. I. T. Bioinorganic 

Chemistry; Inorganic Chemistry. Metalloenzyme inhibitor 

design, metal-organic frameworks. TEL: (858) 822- 

5596 FAX: (858) 822-5598 

by Dissociative Charge Exchange, J. 

Am. Chem. Soc, 130, 3730-3731 (2008). 

Vadim A. Mozhayskiy, John D. Savee, Jennifer E. Mann, 

Robert E. Continetti and Anna I. Krylov, Conical for Stepwise, 

Glancing for Concerted: The Role of the Excited-State 

Topology in the Three-Body Dissociation of sym-Triazine, J. 

Phys. Chem. A, 112, 12345-12354 (2008). 

BURKART, MICHAEL D. (b.1972) Associate Professor. 

B.A, 1994, Rice University; Ph.D, 1999, The 

Scripps Research Institute. NIH Postdoctoral Fellow, 

1999-2002, Harvard Medical School. Bioorganic Chemistry. 

Bioorganic chemistry; natural product biosynthesis; 

natural product synthesis; molecular diagnostics. TEL: 

Web: www.checohen0.ucsd.edu/ 

Email: scohen@ucsd.edu 

Publication list has not been verified by the department. 

Sergio J. Garibay, Jay R. Stork, Zhenqiang Wang, Seth M. 

Cohen and Shane G. Telfer, Enantiopure vs. racemic metalloligands: 

impact on metal-organic framework structure and 

Silvia De Dea, David R. Miller and Robert E. Continetti, 

Growth of Nanoscale Magnetic Films Using a Supercritical 

CO2/Ferric Acetylacetonate Batch Process Near Room Temperature, 

J. Phys. Chem. C, 112, 17102-17108 (2008). 

Zhou Lu, Jonathan E. Oakman, Qichi Hu and Robert E. 

Continetti, Photoelectron-photofragment angular correlations 

in the dissociative photodetachment of HOCO- (858) 534-5673 FAX: (858) 822-2182 


C04373 

Email: mburkart@ucsd.edu 

K. M. Clarke, A. C. Mercer, J. J. La Clair and M. D. Burkart, 

In vivo reporter labeling of proteins via metabolic deliv- 

ery of Coenzyme A Analogues, J. Am. Chem. Soc, 127, 

11234-11235 (2005). 

M. D. Alexander, S. D. Fontaine, J. J. La Clair, A. G. Di- 

Pasquale, A. L. Rheingold and M. D. Burkart, Synthesis of 

the mycolactone core by ring-closing metathesis, Chem. 

Comm, 44, 4602-4604 (2006). 

Andrew S. Worthington and Michael D. Burkart, The old 

is new again: Asparagine oxidation in calcium-dependent antibiotic 

biosynthesis, ACS Chem. Biol, 2, 152-154 (2007). 

Alexander L. Mandel, Brian D. Jones, James J. La Clair 

and Michael D. Burkart, A synthetic entry to pladienolide B 

and FD-895, Bioorg. Med. Chem. Lett, 17, 5159-5164 

(2007). 

Timothy L. Foley and Michael D. Burkart, Site-specific 

protein modification: Advances and applications, Curr. Opin. 

Chem. Biol, 11, 12-19 (2007). 

Andrew C. Mercer and Michael D. Burkart, The ubiquitous 

carrier protein-a window to metabolite biosynthesis, Nat. 

Prod. Rep, 24, 750-773 (2007). 

Peyman Najmabadi, James J. La Clair and Michael D. Burkart, 

A systems perspective to digital structures in molecular 

analysis, Org. Biomol. Chem, 5, 214-222 (2007). 

A. C. Mercer, J. L. Meier, G. H. Hur, A. R. Smith and M. 

D. Burkart, Antibiotic evaluation and in vivo analysis of alkynyl 

Coenzyme A antimetabolites in Escherichia coli, Bioorg 

Med Chem Lett, 18, 5991-5994 (2008). 

Shiven Kapur, Andrew Worthington, Yinyan Tang, David 

E. Cane, Michael D. Burkart and Chaitan Khosla, Mechanism 

based protein crosslinking of domains from the 6-deoxyerythronolide 

B synthase, Bioorg. Med. Chem. Lett, 18, 

3034-3038 (2008). 

Robert W. Haushalter, Andrew S. Worthington, Gene H. 

Hur and Michael D. Burkart, An orthogonal purification 

strategy for isolating crosslinked domains of modular synthases, 

Bioorg. Med. Chem. Lett, 18, 3039-3042 (2008). 

A. S. Worthington, G. H. Hur, J. L. Meier, Q. Cheng, B. S. 

Moore and M. D. Burkart, Probing the compatibility of type 

II ketosynthase-carrier protein partners, Chembiochem, 9, 

2096-2103 (2008). 

Jordan L. Meier, Andrew C. Mercer and Michael D. Burkart, 

Fluorescent Profiling of Modular Biosynthetic Enzymes 

by Complementary Metabolic and Activity Based Probes, J. 

Am. Chem. Soc, 130, 5443-5445 (2008). 

J. L. Meier, T. Barrows-Yano, T. L. Foley, C. L. Wike and 

M. D. Burkart, The unusual macrocycle forming thioesterase 

of mycolactone, Mol Biosyst, 4, 663-671 (2008). 

Alexander Mandel, Synthetic studies applied to polyketide 

natural products. (D) 

Andrew Mercer, Co-opting CoA biosynthesis for the in 

vivo modification of carrier proteins. (D) 

Andrew Worthington, Chemoenzymatic investigations of 

protein-protein interactions in carrier protein-mediated bio- 

synthesis. (D) 

synthesis, Chem. Commun. (Cambridge, U. K.), 4881-4883 

(2007). 

Faith E. Jacobsen, Jana A. Lewis and Seth M. Cohen, The 

design of inhibitors for medicinally relevant metalloproteins, 

ChemMedChem, 2, 152-171 (2007). 

Seth M. Cohen, New approaches for medicinal applications 

of bioinorganic chemistry, Curr. Opin. Chem. Biol, 11, 

115-120 (2007). 

Sara R. Halper, Jay R. Stork and Seth M. Cohen, Preparation 

and characterization of asymmetric �-alkoxy dipyrrin ligands 

and their metal complexes, Dalton Trans, 1067-1074 

(2007). 

Jay R. Stork, Van S. Thoi and Seth M. Cohen, Rare Examples 

of Transition-Metal-Main-Group Metal Heterometallic 

Metal-Organic Frameworks from Gallium and Indium Dipyr- 

rinato Complexes and Silver Salts: Synthesis and Framework 

Variability, Inorg. Chem. (Washington, DC, U. S.), 46, 

11213-11223 (2007). 

Faith E. Jacobsen, Jana A. Lewis, Katie J. Heroux and Seth 

M. Cohen, Characterization and evaluation of pyrone and 

tropolone chelators for use in metalloprotein inhibitors, 

Inorg. Chim. Acta, 360, 264-272 (2007). 

Zhenqiang Wang and Seth M. Cohen, Postsynthetic Covalent 

Modification of a Neutral Metal-Organic Framework, J. 

Am. Chem. Soc, 129, 12368-12369 (2007). 

Stephane Petoud, Gilles Muller, Evan G. Moore, Jide Xu, 

Jurek Sokolnicki, James P. Riehl, Uyen N. Le, Seth M. Cohen 

and Kenneth N. Raymond, Brilliant Sm, Eu, Tb, and Dy 

Chiral Lanthanide Complexes with Strong Circularly Polarized 

Luminescence, J. Am. Chem. Soc, 129, 77-83 (2007). 

Misha Golynskiy, Sheng Li, Virgil L. Woods, Jr. and Seth 

M. Cohen, Conformational studies of the manganese transport 

regulator (MntR) from Bacillus subtilis using deuterium 

exchange mass spectrometry, JBIC, J. Biol. Inorg. Chem, 12, 

699-709 (2007). 

Yi-Long Yan and Seth M. Cohen, Efficient Synthesis of 5- 

Amido-3-hydroxy-4-pyrones as Inhibitors of Matrix Metalloproteinases, 

Org. Lett, 9, 2517-2520 (2007). 

Zhenqiang Wang and Seth M. Cohen, Tandem modification 

of metal-organic frameworks by a postsynthetic approach, 

Angew. Chem., Int. Ed, 47, 4699-4702 (2008). 

Emily Dugan, Zhenqiang Wang, Marilyn Okamura, Annette 

Medina and Seth M. Cohen, Covalent modification of a 

metal-organic framework with isocyanates: probing substrate 

scope and reactivity, Chem. Commun. (Cambridge, U. K.), 

3366-3368 (2008). 

Arpita Agrawal, Diego Romero-Perez, Jennifer A. Jacob- 

sen, Francisco J. Villarreal and Seth M. Cohen, Zinc-binding 

groups modulate selective inhibition of MMPs, ChemMed- 

Chem, 3, 812-820 (2008). 

Van S. Thoi, Jay R. Stork, Edwards T. Niles, Ezra C. Depperman, 

David L. Tierney and Seth M. Cohen, Diamidodi- 

pyrrins: Versatile Bipyrrolic Ligands with Multiple Metal 

Binding Modes, Inorg. Chem. (Washington, DC, U. S.), 47, 

10533-10541 (2008). 

Kristine K. Tanabe, Zhenqiang Wang and Seth M. Cohen, 

Systematic Functionalization of a Metal-Organic Framework 

via a Postsynthetic Modification Approach, J. Am. Chem. 

Soc, 130, 8508-8517 (2008). 

, Mol. Phys, 

106, 595-606 (2008). 

John D. Savee, Vadim A. Mozhayskiy, Jennifer E. Mann, 

Anna I. Krylov and Robert E. Continetti, The Role of Excited-State 

Topology in Three-Body Dissociation of sym-Triazine, 

Science (Washington, DC, U. S.), 321, 826-830 (2008). 

J. E. Mann, Probing the potential energy surface of elementary 

neutral reactions using dissociative charge exchange. 

(D) 

S. De Dea, Nano-scale magnetic film formation by decom- 

pression of supercritical CO2/ferric acetylacetonate solutions. 

(D) 

Z. Lu, Dynamics of gas phase transient species studied by 

dissociative photodetachment of molecular anions. (D) 

CROWELL, JOHN E. (b.1956) Professor. B.S, 1979, 

University of Illinois, Urbana; Ph.D, 1984, University of 

California, Berkeley. Postdoctoral Research Associate, 

1984-1986, University of Pittsburgh. Bioanalytical 

Chemistry; Physical Chemistry. Spectroscopic studies of 

surface chemistry at well-defined interfaces and surfaces; 

kinetic and mechanistic studies of elementary surface 

processes, thin film growth by atomic layer deposition, 

chemical vapor deposition, and photo-induced surface 

chemistry; development of in-situ spectroscopic probes 

of surface reactions; surface infrared spectroscopy; de- 

sorption / ionization mass spectrometry; nanofunctionalization 

and patterning for bioanalysis; microfluidics, pro- 

teomics and microanalysis. TEL: (858) 534-5441 FAX: 

(858) 534-7244 


C00906 

Email: jcrowell@ucsd.edu 


CZWORKOWSKI, JOHN (b.1963) Lecturer PSOE. 

B.A, 1985, University of Pennsylvania; Ph.D, 1991, Uni- 

versity of Texas at Austin. Postdoctoral Associate, 1991- 

1996, Yale University; Associate Research Scientist, 

1996-1998, Yale University. Chemistry Education. TEL: 

(858) 822-6665 FAX: (858) 534-7687 


C20691 

Email: jczworkowski@ucsd.edu 


DENNIS, EDWARD A. (b.1941) Professor. B.A, 

1963, Yale University; M.A, 1965, Harvard University; 

Ph.D, 1968, Harvard University; Ph.D.(Hon.), 2008, 

Goethe University of Frankfurt Germany. Research Fellowship, 

1967-1969, Harvard Medical School. Biochemistry; 

Pharmacology. Phospholipases-catalytic mechanism, 

regulation function and mutagenesis; prostaglandin 

control in macrophage cell cultures; phospholipid metab- 

olism and enzyme mechanism; NMR of phospholipids; 

membrane and micelle structure and function; signal 

Jordan Meier, Synthetic active site probes for PKS and 

CONTINETTI, ROBERT E. (b.1962) Professor. transduction; LIPID MAPS; mass spec of lipids and pro- 

NRPS biosynthetic enzymes. (D) B.A, 1983, John Hopkins University; Ph.D, 1989, Uni- teins. TEL: (858) 534-3055 FAX: (858) 534-7390 

versity of California, Berkeley. Postdoctoral Fellowship, Web: www.cobra.uscd.edu 

CASERIO, MARJORIE C. (b.1929) Professor Emer- 1989-1992, University of California, Berkeley. Chemical Email: edennis@ucsd.edu 

itus. B.Sc, 1950, Chelsea College, University of London; Physics; Physical Chemistry. Energetics and dissociation Matthew W. Buczynski, Daren L. Stephens, Rebecca C. 

M.A, 1951, Bryn Mawr College, Pennsylvania; Ph.D, dynamics of reactive intermediates; photodissociation Bowers-Gentry, Andrej Grkovich, Raymond A. Deems and 

1956, Bryn Mawr College, Pennsylvania. Postdoctoral and photodetachment dynamics; photoelectron-photo- Edward A. Dennis, TLR-4 and Sustained Calcium Agonists 

Fellowship, 1956, California Institute of Technology; Se- fragment coincidence spectroscopy; three-body reaction Synergistically Produce Eicosanoids Independent of Protein


Synthesis in RAW264.7 Cells, J. Biol. Chem, 282, 22834- Oswald Quehenberger, Aaron Armando, Darren Dumlao, rin-related phosphatase Mtmr13 leads to a Charcot-Marie- 

22847 (2007). Daren Stephens and Edward A. Dennis, Lipidomics analysis Tooth 4B2-like peripheral neuropathy in mice, Proc. Natl. 

Richard Harkewicz, Eoin Fahy, Alexander Andreyev and of essential fatty acids in macrophages, Prostaglandins Leu- Acad. Sci. U. S. A, 105, 4916-4921 (2008). 

Edward A. Dennis, Arachidonate-derived Dihomoprostaglan- kotrienses and Essential Fatty Acids, 79, 123-129 (2008). Shaun W. Lee, Douglas A. Mitchell, Andrew L. Markley, 

din Production Observed in Endotoxin-stimulated Macrophage-like 

Cells, J. Biol. Chem, 282, 2899-2910 (2007). 

Richard Harkewicz, Eoin Fahy, Alexander Andreyev and 

Edward A. Dennis, Arachidonate-derived dihomoprostaglandin 

production observed in endotoxin-stimulated macro- 

phage-like cells. [Erratum to document cited in CA146: 

314968], J. Biol. Chem, 282, 29068 (2007). 

David A. Six, Efrosini Barbayianni, Vassilios Loukas, 

Violetta Constantinou-Kokotou, Dimitra Hadjipavlou-Litina, 

Daren Stephens, Alan C. Wong, Victoria Magrioti, Panagiota 

Moutevelis-Minakakis, Sharon F. Baker, Edward A. Dennis 

and George Kokotos, Structure-Activity Relationship of 2- 

Oxoamide Inhibition of Group IVA Cytosolic Phospholipase 

A2 and Group V Secreted Phospholipase A2, J. Med. Chem, 

50, 4222-4235 (2007). 

Panagiota Moutevelis-Minakakis, Afroditi Neokosmidi, 

Maria Filippakou, Daren Stephens, Edward A. Dennis and 

George Kokotos, Synthesis of lipophilic 2-oxoamides based 

on �-aminobutyric and �-aminovaleric analogues and their 

activity against phospholipase A2, J. Pept. Sci, 13, 634-641 

(2007). 

Kara Schmelzer, Eoin Fahy, Shankar Subramaniam and 

Edward A. Dennis, The lipid maps initiative in lipidomics, 

Methods Enzymol, 432, 171-183 (2007). 

Raymond Deems, Matthew W. Buczynski, Rebecca Bowers-Gentry, 

Richard Harkewicz and Edward A. Dennis, Detection 

and quantitation of eicosanoids via high performance 

liquid chromatography-electrospray ionization-mass spectrometry, 


Manish Sud, Eoin Fahy, Dawn Cotter, Alex Brown, Edward 

A. Dennis, Christopher K. Glass, Alfred H. Merrill, Jr., 

Robert C. Murphy, Christian R. H. Raetz, David W. Russell 

and Shankar Subramaniam, LMSD: LIPID MAPS structure 

database, Nucleic Acids Res, 35, D527-D532 (2007). 

John E. Burke, Mark J. Karbarz, Raymond A. Deems, 

Sheng Li, Virgil L. Woods, Jr. and Edward A. Dennis, Interaction 

of Group IA Phospholipase A2 with Metal Ions and 

Phospholipid Vesicles Probed with Deuterium Exchange 

Mass Spectrometry, Biochemistry, 47, 6451-6459 (2008). 

Georgia Antonopoulou, Efrosini Barbayianni, Victoria 

Magrioti, Naomi Cotton, Daren L. Stephens, Violetta Constantinou-Kokotou, 

Edward A. Dennis and George Kokotos, 

Structure-activity relationships of natural and non-natural 

amino acid-based Amide and 2-oxoamide inhibitors of human 

Phospholipase A2 enzymes, Bioorg.Med.Chem, 16, 

10257-10269 (2008). 

Ruben Lopez-Vales, Xavier Navarro, Takao Shimizu, Con- 

Andrej Grkovich, The function, activation and inhibition of 

phosphatidic acid phosphohydrolase-1 and group IVA phospholipase 

A2 in toll-like receptor activated macrophages. (D) 

John E. Burke, Deuterium exchange mass spectrometry 

studies of the phospholipase A2 superfamily. (D) 

Matthew W. Buczynski, Lipidomic analysis of eicosanoid 

synamics in inflammation and disease. (D) 

DIXON, JACK E. (b.1943) Professor. B.A, 1966, University 

of California, Los Angeles; Ph.D, 1971, Universi- 

ty of California, Santa Barbara. TEL: (858) 822-3522 

FAX: (858) 822-0084 

Email: jedixon@ucsd.edu 


Seema Mattoo, Yvonne M. Lee and Jack E. Dixon, Interactions 

of bacterial effector proteins with host proteins, Curr. 

Opin. Immunol, 19, 392-401 (2007). 

Alan Cheng, Mei Zhang, Matthew S. Gentry, Carolyn A. 

Worby, Jack E. Dixon and Alan R. Saltiel, A role for AGL 

ubiquitination in the glycogen storage disorders of Lafora 

and Cori’s disease, Genes Dev, 21, 2399-2409 (2007). 

Sandra E. Wiley, Mark L. Paddock, Edward C. Abresch, 

Larry Gross, Peter van der Geer, Rachel Nechushtai, Anne N. 

Murphy, Patricia A. Jennings and Jack E. Dixon, The outer 

mitochondrial membrane protein mitoNEET contains a novel 

redox-active 2Fe-2S cluster, J. Biol. Chem, 282, 23745- 

23749 (2007). 

Neal M. Alto, Andrew W. Weflen, Matthew J. Rardin, 

Defne Yarar, Cheri S. Lazar, Raffi Tonikian, Antonius Koller, 

Susan S. Taylor, Charles Boone, Sachdev S. Sidhu, Sandra 

L. Schmid, Gail A. Hecht and Jack E. Dixon, The type III 

effector EspF coordinates membrane trafficking by the spa- 

tiotemporal activation of two eukaryotic signaling pathways, 

J. Cell Biol, 178, 1265-1278 (2007). 

Matthew S. Gentry, Robert H. Dowen, III, Carolyn A. 

Worby, Seema Mattoo, Joseph R. Ecker and Jack E. Dixon, 

The phosphatase laforin crosses evolutionary boundaries and 

links carbohydrate metabolism to neuronal disease, J. Cell 

Biol, 178, 477-488 (2007). 

Lorena Navarro, Antonius Koller, Roland Nordfelth, Hans 

Wolf-Watz, Susan Taylor and Jack E. Dixon, Identification 

of a molecular target for the Yersinia protein kinase A, Mol. 

Cell, 26, 465-477 (2007). 

Shibu Yooseph, Granger Sutton, Douglas B. Rusch, Aaron 

L. Halpern, Shannon J. Williamson, Karin Remington, Jona- 

Mary E. Hensler, David Gonzalez, Aaron Wohlrab, Pieter C. 

Dorrestein, Victor Nizet and Jack E. Dixon, Discovery of a 

widely distributed toxin biosynthetic gene cluster, Proc. Natl. 

Acad. Sci. U. S. A, 105, 5879-5884 (2008). 

Hirohide Iwasaki, Yoshimichi Murata, Youngjun Kim, Is- 

rail Hossain, Carolyn A. Worby, Jack E. Dixon, Thomas 

McCormack, Takehiko Sasaki and Yasushi Okamura, A voltage-sensing 

phosphatase, Ci-VSP, which shares sequence 

identity with PTEN, dephosphorylates phosphatidylinositol 

4,5-bisphosphate, Proc. Natl. Acad. Sci. U. S. A, 105, 7970- 

7975 (2008). 

DONOGHUE, DANIEL J. (b.1952) Professor. B.Sc, 

1974, University of Wisconsin; Ph.D, 1979, M.I.T. Postdoctoral 

Fellowship, 1980-1982, Salk Institute. Molecular 

Biology. FGFR2 signaling and FGFR3 activation of 

MCF-7 in breast cancer. Nordihydroguaiaretic acid 

(NDGA) and FGFR3 in multiple myeloma cells FGFR4 

signaling and NF-kappaB regulation in prostate cancer. 

Androgen-Independence (AI) cell proliferation, and acquisition 

of invasiveness and metastatic properties in 

prostate cancer cells. Spy1 interaction with p27 and 

CDK2 in cell cycle progression, DNA damage, apoptosis, 

and checkpoint activation. TEL: (858) 534-2463 

FAX: (858) 534-7481 

Web: cancer.ucsd.edu/summaries/ddonoghue.asp 

Email: ddonoghue@ucsd.edu 

Randy F. Gastwirt, Christopher W. McAndrew and Daniel 

J. Donoghue, Speedy/RINGO regulation of CDKs in cell cycle, 

checkpoint activation and apoptosis, Cell Cycle, 6, 1188- 

1193 (2007). 

Christopher W. McAndrew, Randy F. Gastwirt, April N. 

Meyer, Lisa A. Porter and Daniel J. Donoghue, Spy1 enhances 

phosphorylation and degradation of the cell cycle inhibitor 

p27, Cell Cycle, 6, 1937-1945 (2007). 

Azadeh Golipour, Dorothy Myers, Tiffany Seagroves, 

Daniel Murphy, Gerard I. Evan, Daniel J. Donoghue, Roger 

A. Moorehead and Lisa A. Porter, The Spy1/RINGO Family 

Represents a Novel Mechanism Regulating Mammary 

Growth and Tumorigenesis, Cancer Res, 68, 3591-3600 

(2008). 

April N. Meyer, Christopher W. McAndrew and Daniel J. 

Donoghue, Nordihydroguaiaretic Acid Inhibits an Activated 

Fibroblast Growth Factor Receptor 3 Mutant and Blocks 

Downstream Signaling in Multiple Myeloma Cells, Cancer 

Res, 68, 7362-7370 (2008). 

stantinos Baskakis, George Kokotos, Violetta Constantinou- 

Kokotou, Daren L. Stephens, Edward A. Dennis and Sameul 

David, Intracellular Phospholipase A2 group IVA and group 

than A. Eisen, Karla B. Heidelberg, Gerard Manning, Weizhong 

Li, Lukasz Jaroszewski, Piotr Cieplak, Christopher S. 

Miller, Huiying Li, Susan T. Mashiyama, Marcin P. Joachim- 

Randy Francis Gastwirt, Spy1 regulation of the cell cycle, 

checkpoint activation and apoptosis. (D) 

VIA play important roles in wallerian degeneration and axon 

regeneration after peripheral nerve injury, Brain, 131, 2620iak, 

Christopher van Belle, John-Marc Chandonia, David A. 

Soergel, Yufeng Zhai, Kannan Natarajan, Shaun Lee, Benja- DOOLITTLE, RUSSELL F. (b.1931) Research Pro- 

2631 (2008). 

Faith E. Jacobsen, Mathew W. Buczynski, Edward A. Dennis 

and Seth M. Cohen, A macrophage cell model for selective 

metalloprotein inhibitor design, Chem.Bio.Chem, 9, 

2087-2095 (2008). 

Georgia Antonopoulou, Victoria Magrioti, Daren L. Stephens, 

Violetta Constantinou-Kokotou, Edward A. Dennis and 

George Kokotos, Synthesis of 2-oxoamides based on sulfonamide 

analogues of gamma-amino acids and their activity on 

min J. Raphael, Vineet Bafna, Robert Friedman, Steven E. 

Brenner, Adam Godzik, David Eisenberg, Jack E. Dixon, Susan 

S. Taylor, Robert L. Strausberg, Marvin Frazier and J. 

Craig Venter, The Sorcerer II global ocean sampling expedition: 

expanding the universe of protein families, PLoS Biol, 

5, 432-466 (2007). 

Mark L. Paddock, Sandra E. Wiley, Herbert L. Axelrod, 

Aina E. Cohen, Melinda Roy, Edward C. Abresch, Dominique 

Capraro, Anne N. Murphy, Rachel Nechushtai, Jack E. 

fessor. B.A, 1952, Wesleyan University; M.A, 1957, 

Trinity College; Ph.D, 1961, Harvard University. Post- 

doctoral Fellowship, 1962-1964, Karolinska Institute. 

Structure and function of fibrinogen; fibrin formation. 

Evolution of proteins; peptide synthesis; x-ray crystallography. 

TEL: (858) 534-4417 

Email: rdoolittle@ucsd.edu 


Phospholipase A2, J Pept Sci, 10, 1111-1120 (2008). 

John E. Burke, Yuan-Hao Hsu, Raymond A. Deems, 

Sheng Li, Virgil L. Woods Jr. and Edward A. Dennis, A 

phospholipid substrate molecule residing in the membrane 

surface mediates opening of the lid region in group IVA cytosolic 

Phospholipase A2, J. Biol Chem, 283, 31227-31236 

(2008). 

Yuan-Hao Hsu, John E. Burke, Daren L. Stephens, Raymond 

A. Deems, Sheng Li, Kyle M. Asmus, Virgil L. Woods 

Jr. and Edward A. Dennis, Calcium binding rigidifies the C2 

domain of GIVA Phospholipase A2 as revealed by hydrogen/ 

deuterium exchange mass spectrometry, J. Biol Chem, 283, 

9820-9827 (2008). 

Richard Harkewicz, Karsten Hartvigsen, Felicidad Almazan, 

Edward A. Dennis, Joseph L. Witztum and Yury I. Miller, 

Cholesteryl Ester Hydroperoxides Are Biologically Active 

Components of Minimally Oxidized Low Density Lipoprotein, 

J. Biol. Chem, 283, 10241-10251 (2008). 

Dixon and Patricia A. Jennings, MitoNEET is a uniquely 

folded 2Fe-2S outer mitochondrial membrane protein stabilized 

by pioglitazone, Proc. Natl. Acad. Sci. U. S. A, 104, 

14342-14347 (2007). 

Sandra E. Wiley, Anne N. Murphy, Stuart A. Ross, Peter 

van der Geer and Jack E. Dixon, MitoNEET is an iron-containing 

outer mitochondrial membrane protein that regulates 

oxidative capacity, Proc. Natl. Acad. Sci. U. S. A, 104, 5318- 

5323 (2007). 

Youngjun Kim, Matthew S. Gentry, Thurl E. Harris, Sandra 

E. Wiley, John C. Lawrence, Jr. and Jack E. Dixon, A 

conserved phosphatase cascade that regulates nuclear membrane 

biogenesis, Proc. Natl. Acad. Sci. U. S. A, 104, 6596- 

6601 (2007). 

Seema Mattoo, Neal M. Alto and Jack E. Dixon, Subver- 

sion of myosin function by E. coli, Dev. Cell, 14, 8-10 

(2008). 

Stephen J. Juris, Kavita Shah, Kevan Shokat, Jack E. Dix- 

Russell F. Doolittle and Leela Pandi, Probing the �-Chain 

Hole of Fibrinogen with Synthetic Peptides That Differ at 

Their Amino Termini, Biochemistry, 46, 10033-10038 

(2007). 

Russell F. Doolittle, Searching for differences between fi- 

brinogen and fibrin that affect the initiation of fibrinolysis, 

Cardiovasc. Hematol. Agents Med. Chem, 6, 181-189 (2008). 

Russell F. Doolittle, Yong Jiang and Justin Nand, Genomic 

Evidence for a Simpler Clotting Scheme in Jawless Vertebrates, 

J. Mol. Evol, 66, 185-196 (2008). 

DORRESTEIN, PIETER C. B.S, 1998, Northern 

Arizona University; Ph.D, 2004, Cornell University. NIH 

NRSA Fellow, 2004-2006, University of Illinois. Chemical 

Biology; Mass Spectrometry. TEL: (858) 534-6607 

Web: chem-faculty.ucsd.edu/dorrestein/ 

Email: pdorrestein@ucsd.edu 

John E. Burke, Yuan-Hao Hsu, Raymond A. Deems, on and Panayiotis O. Vacratsis, Identification of otubain 1 as Jun Yin, Paul D. Straight, Sinisa Hrvatin, Pieter C. Dorre- 

Sheng Li, Virgil L. Woods, Jr. and Edward A. Dennis, A a novel substrate for the Yersinia protein kinase using chemi- stein, Stefanie B. Bumpus, Cindy Jao, Neil L. Kelleher, Ro- 

Phospholipid Substrate Molecule Residing in the Membrane cal genetics and mass spectrometry. [Erratum to document berto Kolter and Christopher T. Walsh, Genome-wide high- 

Surface Mediates Opening of the Lid Region in Group IVA cited in CA144:145397], FEBS Lett, 582, 3159 (2008). throughput mining of natural-product biosynthetic gene clus- 

Cytosolic Phospholipase A2, J. Biol. Chem, 283, 31227- Matthew J. Rardin, Sandra E. Wiley, Anne N. Murphy, ters by phage display, Chem. Biol. (Cambridge, MA, U. S.), 

31236 (2008). David J. Pagliarini and Jack E. Dixon, Dual Specificity Phos- 14, 303-312 (2007). 

Yuan-Hao Hsu, John E. Burke, Daren L. Stephens, Ray- phatases 18 and 21 Target to Opposing Sides of the Mito- Christopher T. Calderone, David F. Iwig, Pieter C. Dorremond 

A. Deems, Sheng Li, Kyle M. Asmus, Virgil L. chondrial Inner Membrane, J. Biol. Chem, 283, 15440-15450 stein, Neil L. Kelleher and Christopher T. Walsh, Incorpora- 

Woods, Jr. and Edward A. Dennis, Calcium Binding Rigidi- (2008). tion of Nonmethyl Branches by Isoprenoid-like Logic: Multifies 

the C2 Domain and the Intradomain Interaction of GIVA Carolyn A. Worby, Matthew S. Gentry and Jack E. Dixon, ple �-Alkylation Events in the Biosynthesis of Myxovirescin 

Phospholipase A2 as Revealed by Hydrogen/Deuterium Ex- Malin Decreases Glycogen Accumulation by Promoting the A1, Chem. Biol. (Cambridge, MA, U. S.), 14, 835-846 

change Mass Spectrometry, J. Biol. Chem, 283, 9820-9827 Degradation of Protein Targeting to Glycogen (PTG), J. Biol. (2007). 

(2008). Chem, 283, 4069-4076 (2008). Jaclyn M. Winter, Michelle C. Moffitt, Emmanuel Zazo- 

Constantinos Baskakis, Victoria Magrioti, Naomi Cotton, Neal M. Alto and Jack E. Dixon, Analysis of Rho-GTPase poulos, James B. McAlpine, Pieter C. Dorrestein and Bradley 

Daren L. Stephens, Violetta Constantinou-Kokotou, Edward mimicry by a family of bacterial type III effector proteins, S. Moore, Molecular Basis for Chloronium-mediated Mero- 

A. Dennis and George Kokotos, Synthesis of Polyfluoro Ke- Methods Enzymol, 439, 131-143 (2008). terpene Cyclization: Cloning, sequencing, and the heterolotones 

for selective inhibition of human Phospholipase A2 en- Fred L. Robinson, Ingrid R. Niesman, Kristina K. Beis- gous expression of the napyradiomycin biosynthetic gene 

zymes, J. Med. Chem, 51, 8027-8037 (2008). wenger and Jack E. Dixon, Loss of the inactive myotubula- cluster, J. Biol. Chem, 282, 16362-16368 (2007).


Lauren J. Pouwels, Liping Zhang, Nam H. Chan, Pieter C. 

Dorrestein and Rebekka M. Wachter, Kinetic Isotope Effect 

Studies on the de Novo Rate of Chromophore Formation in 

Fast- and Slow-Maturing GFP Variants, Biochemistry, 47, 

10111-10122 (2008). 

Dario Meluzzi, Wei Hao Zheng, Mary Hensler, Victor Niz- 

et and Pieter C. Dorrestein, Top-down mass spectrometry on 

low-resolution instruments: Characterization of phosphopantetheinylated 

carrier domains in polyketide and non-ribosomal 

biosynthetic pathways, Bioorg. Med. Chem. Lett, 18, 

3107-3111 (2008). 

Jeremiah W. Hanes, Kristin E. Burns, David G. Hilmey, 

Abhishek Chatterjee, Pieter C. Dorrestein and Tadhg P. Begley, 

Mechanistic Studies on Pyridoxal Phosphate Synthase: 

The Reaction Pathway Leading to a Chromophoric Intermediate, 

J. Am. Chem. Soc, 130, 3043-3052 (2008). 

Eduardo Esquenazi, Cameron Coates, Luke Simmons, David 

Gonzalez, William H. Gerwick and Pieter C. Dorrestein, 

Visualizing the spatial distribution of secondary metabolites 

produced by marine cyanobacteria and sponges via MALDI- 

TOF imaging, Mol. BioSyst, 4, 562-570 (2008). 

Jacky Chi Ki Ngo, Kayla Giang, Sutapa Chakrabarti, 

Chen-Ting Ma, Nhat Huynh, Jonathan C. Hagopian, Pieter C. 

Dorrestein, Xiang-Dong Fu, Joseph A. Adams and Gourisankar 

Ghosh, A sliding docking interaction is essential for sequential 

and processive phosphorylation of an SR protein by 

SRPK1, Mol. Cell, 29, 563-576 (2008). 

Jian Zhang, Steven G. Van Lanen, Jianhua Ju, Wen Liu, 

Pieter C. Dorrestein, Wenli Li, Neil L. Kelleher and Ben 

Shen, A phosphopantetheinylating polyketide synthase producing 

a linear polyene to initiate enediyne antitumor antibiotic 

biosynthesis, Proc. Natl. Acad. Sci. U. S. A, 105, 1460- 

1465 (2008). 

T. Luke Simmons, R. Cameron Coates, Benjamin R. Clark, 

Niclas Engene, David Gonzalez, Eduardo Esquenazi, Pieter 

C. Dorrestein and William H. Gerwick, Biosynthetic origin 

of natural products isolated from marine microorganism-in- 

vertebrate assemblages, Proc. Natl. Acad. Sci. U. S. A, 105, 

4587-4594 (2008). 

Shaun W. Lee, Douglas A. Mitchell, Andrew L. Markley, 

Mary E. Hensler, David Gonzalez, Aaron Wohlrab, Pieter C. 

Dorrestein, Victor Nizet and Jack E. Dixon, Discovery of a 

widely distributed toxin biosynthetic gene cluster, Proc. Natl. 

Acad. Sci. U. S. A, 105, 5879-5884 (2008). 

ELLIS, ARTHUR B. (b.1951) Professor. B.Sc, 1973, 

Caltech; Ph.D, 1977, MIT. Materials Chemistry. TEL: 

(858) 534-3526 FAX: (858) 534-3868 

Email: abellis@ucsd.edu 

Arthur B. Ellis, Integrating research and education to 

create a dynamic physical chemistry curriculum, ACS Symp. 

Ser, 973, 40-43 (2007). 

FAHEY, ROBERT C. (b.1936) Professor Emeritus. 

B.S, 1957, University of California, Berkeley; Ph.D, 

1963, University of Chicago. Guggenheim Foundation 

Fellowship, 1970-1971, Laboratory Molecular Biology, 

Medical Research Council, Cambridge, England; American 

Cancer Society, Cancer Scholar, 1988-1989, Cancer 

Research Campaign Gray Laboratory, Northwood, England. 

Biochemistry. Thiol biochemistry; current emphasis 

is on the biosynthesis and metabolism of mycothiol in 

Mycobacterium tuberculosis and of bacillithiol in Staphylococcus 

aureus as targets for new antibiotics. TEL: 

(858) 534-2163 FAX: (858) 534-4864 

Email: rcfahey@ucsd.edu 

Nathan I. Nicely, Derek Parsonage, Carleitta Paige, Gerald 

L. Newton, Robert C. Fahey, Roberta Leonardi, Suzanne 

Jackowski, T. Conn Mallett and Al Claiborne, Structure of 

the Type III Pantothenate Kinase from Bacillus anthracis at 

2.0 Å Resolution: Implications for Coenzyme A-Dependent 

Redox Biology, Biochemistry, 46, 3234-3245 (2007). 

Krzysztof P. Bzymek, Gerald L. Newton, Philong Ta and 

Robert C. Fahey, Mycothiol import by Mycobacterium smegmatis 

and function as a resource for metabolic precursors and 

energy production, J. Bacteriol, 189, 6796-6805 (2007). 

Gerald L. Newton, Paul R. Jensen, John B. MacMillan, 

William Fenical and Robert C. Fahey, An N-acyl homolog of 

mycothiol is produced in marine actinomycetes, , 190, 547- 

557 (2008). 

Todd Johnson, Gerald L. Newton, Robert C. Fahey and 

Mamta Rawat, Unusual production of glutathione in Actinobacteria, 

Arch. Microbiol, 191, 89-93 (2008). 

Gerald L. Newton, Nancy Buchmeier and Robert C. Fahey, 

Biosynthesis and functions of mycothiol, the unique protective 

thiol of Actinobacteria, Microbiol. Mol. Biol. Rev, 72, 

471-494 (2008). 

Gerald L. Newton and Robert C. Fahey, Regulation of mycothiol 

metabolism by � 

the stabilization of reactive transition metal fragments. 

Modulation and control of redox equivalents for chemical 

transformations through the explicit use of redox-active 

ligands and/or spectator agents. Construction of novel 

transition metal-stabilized main group species. TEL: 

(858) 822-7478 FAX: (858) 822-4222 

Web: figueroagroup.ucsd.edu/home.htm 

Email: jsfig@ucsd.edu 

Brian J. Fox, Queena Y. Sun, Antonio G. DiPasquale, 

Alexander R. Fox, Arnold L. Rheingold and Joshua S. Figueroa, 

Solution Behavior and Structural Properties of Cu(I) 

Complexes Featuring m-Terphenyl Isocyanides, Inorg. 

Chem. (Washington, DC, U. S.), 47, 9010-9020 (2008). 

FOX, MARYE ANNE (b.1947) Professor, Chancellor. 

B.S, 1969, Notre Dame College; M.S, 1970, Cleveland 

State University; Ph.D, 1974, Dartmouth College. Postdoctoral 

fellow, 1974-1976, University of Maryland. Organic 

Chemistry; Photochemistry. Physical organic 

chemsitry at surfaces; self-assembled monolayers; 

photoelectrochemistry; spectroscopy of dendrimers. 

TEL: (858) 534-3135 FAX: (858) 534-6523 

Web: www.chancellor-ucsd.edu 

Email: mafox@ucsd.edu 


GALPERIN, M. (b.1969) Assistant Professor. M.Sc, 

1991, Ural State University; Ph.D, 2003, Tel Aviv University. 

Postdoctoral Fellow, 2002-2003, Duke University; 

Senior Research Associate, 2003-2007, Northwestern 

University; Director’s Postdoctoral Fellow, 2007-2008, 

Los Alamos National Laboratory. Chemical Physics; 

Theoretical Chemistry. Electron transport in condensed 

phases. Dissipation and relaxation processes. Open quan- 

tum systems out of equilibrium. Molecular electronics. 

TEL: (858) 246-0511 FAX: (858) 534-7244 

Web: galperingroup.ucsd.edu/ 

Email: migalperin@ucsd.edu 

M. Galperin and D. N. Beratan, Simulation of scanning 

tunneling microscope images of 1,3-cyclohexadiene bound to 

a silicon surface, Journal of Physical Chemistry B, 109, 

1473-1480 (2005). 

M. Galperin, A. Nitzan, M. A. Ratner and D. R. Stewart, 

Molecular transport junctions: Asymmetry in inelastic tunneling 

processes, Journal of Physical Chemistry B, 109, 

8519-8522 (2005). 

M. Galperin, M. A. Ratner and A. Nitzan, Hysteresis, 

switching and negative differential resistance in molecular 

junctions: A polaron model, Nano Letters, 5, 125-130 (2005). 

M. Galperin and A. Nitzan, Current-induced light emission 

and light-induced current in molecular-tunneling junctions, 

Physical Review Letters, 95, 206802 (2005). 

M. Galperin and A. Nitzan, Optical properties of current 

carrying molecular wires, Journal of Chemical Physics, 124, 

234709 (2006). 

M. Galperin, A. Nitzan and M. A. Ratner, Resonant inelastic 

tunneling in molecular junctions, Physical Review B, 73, 

045314 (2006). 

M. Galperin, A. Nitzan and M. A. Ratner, Inelastic tunnel- 

ing effects on noise properties of molecular junctions, Physical 

Review B, 74, 075326 (2006). 

M. Galperin, A. Nitzan and M. A. Ratner, Molecular transport 

junctions: Current from electronic excitations in the 

leads, Physical Review Letters, 96, 166803 (2006). 

S. Yeganeh, M. Galperin and M. A. Ratner, Switching in 

molecular transport junctions: Polarization response, Journal 

of American Chemical Society, 129, 13313-13320 (2007). 

M. Galperin, M. A. Ratner and A. Nitzan, Molecular transport 

junctions: Vibrational effects, Journal of Physics: Condensed 

Matter, 19, 103201 (2007). 

M. Galperin, A. Nitzan and M. A. Ratner, Inelastic effects 

in molecular junctions in the Coulomb and Kondo regimes: 

Nonequilibrium equation-of-motion approach, Physical Review 

B, 76, 035301 (2007). 

M. Galperin, A. Nitzan and M. A. Ratner, Heat conduction 

in molecular transport junctions, Physical Review B, 75, 

155312 (2007). 

M. Galperin and S. Tretiak, Linear optical response of current-carrying 

molecular junction: A NEGF-TDDFT approach, 

Journal of Chemical Physics, 128, 124705 (2008). 

M. Galperin, A. Nitzan and M. A. Ratner, The non-linear 

response of molecular junctions: The polaron model revisited, 

Journal of Physics: Condensed Matter, 20, 374107 

(2008). 

M. Galperin, A. Nitzan and M. A. Ratner, Inelastic effects 

in molecular junction transport: scattering and self-consistent 

calculations for the Seebeck coefficient, Molecular Physics, 

University; M.S, 1988, Albert Einstein College of Medicine; 

Ph.D, 1991, Albert Einstein College of Medicine. 

Postdoctoral Fellow, 1991-1995, Yale University. Regu- 

lation of gene expression; high resolution x-ray crystal- 

lography, mutational and biochemical approaches to 

study biologically active protein/DNA and protein/RNA 

complexes. TEL: (858) 822-0469 FAX: (858) 534-7042 

Email: gghosh@ucsd.edu 


Devin Drew, Eriko Shimada, Kim Huynh, Simon 

Bergqvist, Rashmi Talwar, Michael Karin and Gourisankar 

Ghosh, Inhibitor �B Kinase � Binding by Inhibitor �B Kinase 

�, Biochemistry, 46, 12482-12490 (2007). 

Soumen Basak, Hana Kim, Jeffrey D. Kearns, Vinay Ter- 

gaonkar, Ellen O’Dea, Shannon L. Werner, Chris A. Benedict, 

Carl F. Ware, Gourisankar Ghosh, Inder M. Verma and 

Alexander Hoffmann, A fourth I�B protein within the NF-�B 

signaling module, Cell (Cambridge, MA, U. S.), 128, 369- 

381 (2007). 

Anu K. Moorthy, Tom Huxford and Gourisankar Ghosh, 

Structural aspects of NF-�B and I�B proteins, Handb. 

Transcr. Factor NF-kappaB, 9-24 (2007). 

Randall Lukasiewicz, Adolfo Velazquez-Dones, Nhat 

Huynh, Jonathan Hagopian, Xiang-Dong Fu, Joseph Adams 

and Gourisankar Ghosh, Structurally Unique Yeast and 

Mammalian Serine-Arginine Protein Kinases Catalyze Evolutionarily 

Conserved Phosphorylation Reactions, J. Biol. 

Chem, 282, 23036-23043 (2007). 

Randall Lukasiewicz, Bradley Nolen, Joseph A. Adams 

and Gourisankar Ghosh, The RGG Domain of Npl3p Recruits 

Sky1p Through Docking Interactions, J. Mol. Biol, 

367, 249-261 (2007). 

Anu K. Moorthy, De-Bin Huang, Vivien Ya-Fan Wang, 

Don Vu and Gourisankar Ghosh, X-ray Structure of a NF-�B 

p50/RelB/DNA Complex Reveals Assembly of Multiple Dimers 

on Tandem �B Sites, J. Mol. Biol, 373, 723-734 (2007). 

Stephanie D. Shaw, Sutapa Chakrabarti, Gourisankar 

Ghosh and Adrian R. Krainer, Deletion of the N-terminus of 

SF2/ASF permits RS-domain-independent pre-mRNA splicing, 

PLoS One, 2, No pp. given (2007). 

Jacky Chi Ki Ngo, Justin Gullingsrud, Kayla Giang, Me- 

linda Jean Yeh, Xiang-Dong Fu, Joseph A. Adams, J. Andrew 

McCammon and Gourisankar Ghosh, SR Protein Kinase 

1 Is Resilient to Inactivation, Structure (Cambridge, 

MA, U. S.), 15, 123-133 (2007). 

Erika Mathes, Ellen L. O’Dea, Alexander Hoffmann and 

Gourisankar Ghosh, NF-�B dictates the degradation pathway 

of I�B�, EMBO J, 27, 1357-1367 (2008). 

Erika Mathes, Ellen L. O’Dea, Alexander Hoffmann and 

Gourisankar Ghosh, NF-�B dictates the degradation pathway 

of I�B�. [Erratum to document cited in CA148:555634], 

EMBO J, 27, 1421 (2008). 

Eileen J. Kennedy, Gourisankar Ghosh and Lorraine Pillus, 

Identification of Functionally Distinct Regions That Mediate 

Biological Activity of the Protein Kinase A Homolog Tpk2, 

J. Biol. Chem, 283, 1084-1093 (2008). 

Amanda J. Fusco, Olga V. Savinova, Rashmi Talwar, Jeffrey 

D. Kearns, Alexander Hoffmann and Gourisankar 

Ghosh, Stabilization of RelB Requires Multidomain Interactions 

with p100/p52, J. Biol. Chem, 283, 12324-12332 

(2008). 

Malini Sen and Gourisankar Ghosh, Transcriptional Out- 

come of Wnt-Frizzled Signal Transduction in Inflammation: 

Evolving Concepts, J. Immunol, 181, 4441-4445 (2008). 

Chen-Ting Ma, Adolfo Velazquez-Dones, Jonathan C. Hagopian, 

Gourisankar Ghosh, Xiang-Dong Fu and Joseph A. 

Adams, Ordered Multi-site Phosphorylation of the Splicing 

Factor ASF/SF2 By SRPK1, J. Mol. Biol, 376, 55-68 (2008). 

Stephanie M. E. Truhlar, Erika Mathes, Carla F. Cervantes, 

Gourisankar Ghosh and Elizabeth A. Komives, Pre-folding 

I�B� Alters Control of NF-�B Signaling, J. Mol. Biol, 380, 

67-82 (2008). 

Jonathan C. Hagopian, Chen-Ting Ma, Bryan R. Meade, 

Claudio P. Albuquerque, Jacky Chi Ki Ngo, Gourisankar 

Ghosh, Patricia A. Jennings, Xiang-Dong Fu and Joseph A. 

Adams, Adaptable Molecular Interactions Guide Phosphoryl- 

ation of the SR Protein ASF/SF2 by SRPK1, J. Mol. Biol, 

382, 894-909 (2008). 

Jacky Chi Ki Ngo, Kayla Giang, Sutapa Chakrabarti, 

Chen-Ting Ma, Nhat Huynh, Jonathan C. Hagopian, Pieter C. 

Dorrestein, Xiang-Dong Fu, Joseph A. Adams and Gourisankar 

Ghosh, A sliding docking interaction is essential for sequential 

and processive phosphorylation of an SR protein by 

SRPK1, Mol. Cell, 29, 563-576 (2008). 

GHOSH, PARTHO (b.1962) Professor. B.S, 1985, 

Yale University; Ph.D, 1992, University of California, 

San Francisco. Irvington Institute for Medical Research, 

1993-1997, Harvard University. Biochemistry; Structural 

R and the thiol redox sensor anti-sigma 

factor RsrA, Mol. Microbiol, 68, 805-809 (2008). 

FIGUEROA, JOSHUA S. (b.1978) Assistant Professor. 

B.Sc, 2000, University of Delaware; Ph.D, 2005, 

M.I.T. NIH Postdoctoral Resarch Fellow, 2005-2007, 

Columbia University. Inorganic Chemistry; Organome- 

106, 397-404 (2008). 

M. Galperin, A. Nitzan and M. A. Ratner, Inelastic trans- 

port in the Coulomb blockade regime within a nonequilibrium 

atomic limit, Physical Review B, 78, 125320 (2008). 

M. Galperin, M. A. Ratner, A. Nitzan and A. Troisi, Nuclear 

coupling and polarization in molecular transport junctions: 

Beyond tunneling to function, Science, 319, 1056-1060 

Biology. We are interested in understanding the interactions 

between microbial pathogens and targets on host 

mammalian cells. We are studying these interactions us- 

ing the tools of biochemistry and structural biology. In 

understanding the detailed interaction of pathogen and 

host macromolecules, we aim to probe fundamental istallic 

Chemistry. Research in the Figueroa Group broadly (2008). 

sues in mammalian cell biology and to provide informaencompasses 

aspects of synthetic inorganic and organometallic 

chemistry. Areas of interest include: Design and GHOSH, GOURISANKAR (b.1959) Asst. Professor. 

tion for the design of antimicrobial therapeutics. TEL: 

(858) 822-1139 FAX: (858) 822-2871 

implementation of highly tailored ancillary ligands for B.Sc, 1983, St. Xaviers’ College; M.Sc, 1985, Calcutta Web: pghosh.ucsd.edu


Email: pghosh@ucsd.edu 

Sybil C. Lang Hrtska, Melissa M. Kemp, Eva M. Munoz, 

Omaira Azizad, Mani Banerjee, Catarina Raposo, Jyothi Kumaran, 

Partho Ghosh and Robert J. Linhardt, Investigation of 

the Mechanism of Binding between Internalin B and Heparin 

Using Surface Plasmon Resonance, Biochemistry, 46, 2697- 

2706 (2007). 

Loren Rodgers, Alicia Gamez, Roland Riek and Partho 

Ghosh, The Type III Secretion Chaperone SycE Promotes a 

Localized Disorder-to-Order Transition in the Natively Unfolded 

Effector YopE, J. Biol. Chem, 283, 20857-20863 

(2008). 

Jason L. Miller, Johanne Le Coq, Asher Hodes, Roman 

Barbalat, Jeff F. Miller and Partho Ghosh, Selective ligand 

recognition by a diversity-generating retroelement variable 

protein, PLoS Biol, 6, 1195-1207 (2008). 

Case McNamara, Annelies S. Zinkernagel, Pauline Macheboeuf, 

Madeleine W. Cunningham, Victor Nizet and Partho 

Ghosh, Coiled-Coil Irregularities and Instabilities in Group A 

Streptococcus M1 Are Required for Virulence, Science 

(Washington, DC, U. S.), 319, 1405-1408 (2008). 

GIANNESCHI, NATHAN CLAUDE Assistant Professor. 

B.Sc, 1999, University of Adelaide; Ph.D, 2005, 

Northwestern University. Dow Chemical Foundation 

Fellow, 2005-2008, The Scripps Research Institute. 

Biomaterials; Bioorganic Chemistry. TEL: (858) 246- 

0857 FAX: (858) 534-0202 

Web: gianneschigroup.ucsd.edu/home.htm 

Nathan C. Gianneschi and M. Reza Ghadiri, Design of mo- 

lecular logic devices based on a programmable DNA-regulated 

semisynthetic enzyme, Angew. Chem., Int. Ed, 46, 3955- 

3958 (2007). 

Martin S. Masar, III, Nathan C. Gianneschi, Christopher G. 

Oliveri, Charlotte L. Stern, SonBinh T. Nguyen and Chad A. 

Mirkin, Allosterically Regulated Supramolecular Catalysis of 

Acyl Transfer Reactions for Signal Amplification and Detection 

of Small Molecules, J. Am. Chem. Soc, 129, 10149- 

10158 (2007). 

Nathan C. Gianneschi, Supramolecular allosteric catalysts. 

(D) 

HARPER, E. (b.1930) Professor Emeritus. B.S, 1952, 

City College of New York; M.A, 1961, Brooklyn College; 

Ph.D, 1966, Albert Einstein College of Medicine. 

Postdoctoral Fellowship, 1966-1967, Weizmann Institute 

of Science, Rehovot, Israel; Resident Fellow, Medicine, 

1967-1968, Harvard Medical School. Collagen metabolism; 

structure-function aspects of the collagenases. 

TEL: (619) 534-4177 TEL: (619) 534-4861 

Email: eharper@ucsd 

droxyethyl)ethylenediamine, Inorg. Chem. (Washington, DC, 

U. S.), 46, 8111-8113 (2007). 

Patrick L. Feng, Christopher C. Beedle, Wolfgang Wernsdorfer, 

Changhyun Koo, Motohiro Nakano, Stephen Hill and 

David N. Hendrickson, Heterometallic Cubane Single-Molecule 

Magnets, Inorg. Chem. (Washington, DC, U. S.), 46, 

8126-8128 (2007). 

Wen-Guo Wang, Ai-Ju Zhou, Wei-Xiong Zhang, Ming- 

Liang Tong, Xiao-Ming Chen, Motohiro Nakano, Christopher 

C. Beedle and David N. Hendrickson, Giant Heterometallic 

Cu17Mn28 Cluster with Td Symmetry and High-Spin 

Ground State, J. Am. Chem. Soc, 129, 1014-1015 (2007). 

G. de Loubens, A. D. Kent, V. Krymov, G. J. Gerfen, C. C. 

Beedle and D. N. Hendrickson, High frequency EPR on dilute 

solutions of the single molecule magnet Ni4, J. Appl. 

Phys, 103, 07B910-1-07B910-3 (2007). 

G. de Loubens, G. D. Chaves-O’Flynn, A. D. Kent, C. 

Ramsey, E. del Barco, C. Beedle and D. N. Hendrickson, 

Magnetization and EPR studies of the single molecule magnet 

Ni4 with integrated sensors, J. Appl. Phys, 101, 09E104- 

1-09E104-3 (2007). 

Anthony Wilson, En-Che Yang, David N. Hendrickson 

and Stephen Hill, On the validity of the giant spin approximation 

and its application to single-molecule magnets, Polyhedron, 

26, 2065-2068 (2007). 

Christopher C. Beedle, Katie J. Heroux, Motohiro Nakano, 

Antonio G. DiPasquale, Arnold L. Rheingold and David N. 

Hendrickson, Antiferromagnetic tetranuclear manganese 

complex: Wheel or dicubane?, Polyhedron, 26, 2200-2206 

(2007). 

Jon Lawrence, Chris C. Beedle, En-Che Yang, James Ma, 

Stephen Hill and David N. Hendrickson, High frequency 

electron paramagnetic resonance (HFEPR) study of a high 

spin Co(II) complex, Polyhedron, 26, 2299-2303 (2007). 

M. Bal, J. R. Friedman, W. Chen, M. T. Tuominen, C. C. 

Beedle, E. M. Rumberger and D. N. Hendrickson, Radiationand 

phonon-bottleneck-induced tunneling in the Fe8 singlemolecule 

magnet, EPL, 82, 17005 (2008). 

G. de Loubens, D. A. Garanin, C. C. Beedle, D. N. Hendrickson 

and A. D. Kent, Magnetization relaxation in the single-molecule 

magnet Ni4 under continuous microwave irra- 

diation, EPL, 83, 83, 37006 (2008). 

Christopher C. Beedle, Casey J. Stephenson, Katie J. Heroux, 

Wolfgang Wernsdorfer and David N. Hendrickson, Pho- 

toluminescent Mn4 Single-Molecule Magnet, Inorg. Chem. 


Jon Lawrence, En-Che Yang, Rachel Edwards, Marilyn M. 

Olmstead, Chris Ramsey, Naresh S. Dalal, Peter K. Gantzel, 

Stephen Hill and David N. Hendrickson, Disorder and Inter- 

molecular Interactions in a Family of Tetranuclear Ni(II) 

Complexes Probed by High-Frequency Electron Paramagnetic 

Resonance, Inorg. Chem. (Washington, DC, U. S.), 47, 

1965-1974 (2008). 

Patrick L. Feng, Christopher C. Beedle, Changhyun Koo, 

sity of Ulm, Germany; Ph.D, 1996, Max-Planck-Institute 

for Biochemistry/Ludwig-Maximilians-University, Munich. 

Postdoctoral Fellow, 1996-1998, IBMC/CNRS, 

Strasbourg, France; Research Associate, 1999-2000, Me- 

morial Sloan-Kettering Cancer Center, New York, NY; 

Senior Research Scientist, 2001, Memorial Sloan-Kettering 

Cancer Center, New York, NY. Bioorganic Chemistry; 

Crystallography. TEL: (858) 534-4467 FAX: (858) 

534-0202 

Web: tch.ucsd.edu 

Email: tch@ucsd.edu 

Sergey M. Dibrov, Hillary Johnston-Cox, Yi-Hsin Weng 

and Thomas Hermann, Functional architecture of HCV IRES 

domain II stabilized by divalent metal ions in the crystal and 

in solution, Angew. Chem., Int. Ed, 46, 226-229 (2007). 

Christopher M. Barbieri, Malvika Kaul, Melanie Bozza- 

Hingos, Fang Zhao, Yitzhak Tor, Thomas Hermann and Daniel 

S. Pilch, Defining the molecular forces that determine the 

impact of neomycin on bacterial protein synthesis: impor- 

tance of the 2’-amino functionality, Antimicrob. Agents Chemother, 

51, 1760-1769 (2007). 

Yuefen Zhou, Vlad E. Gregor, Benjamin K. Ayida, Geof- 

frey C. Winters, Zhongxiang Sun, Douglas Murphy, Greg 

Haley, Dwight Bailey, Jamie M. Froelich, Sarah Fish, Steph- 

en E. Webber, Thomas Hermann and Daniel Wall, Synthesis 

and SAR of 3,5-diamino-piperidine derivatives: novel antibacterial 

translation inhibitors as aminoglycoside mimetics, 


Thomas Hermann, Valentina Tereshko, Eugene Skripkin 

and Dinshaw J. Patel, Apramycin recognition by the human 

ribosomal decoding site, Blood Cells, Mol., Dis, 38, 193-198 

(2007). 

Konstantin H. Dragnev, W. Jeffrey Petty, Sumit J. Shah, 

Lionel D. Lewis, Candice C. Black, Vincent Memoli, William 

C. Nugent, Thomas Hermann, Andres Negro-Vilar, 

James R. Rigas and Ethan Dmitrovsky, A Proof-of-Principle 

Clinical Trial of Bexarotene in Patients with Non-Small Cell 

Lung Cancer, Clin. Cancer Res, 13, 1794-1800 (2007). 

Jerod Parsons and Thomas Hermann, Conformational flex- 

ibility of ribosomal decoding-site RNA monitored by fluorescent 

pteridine base analogues, Tetrahedron, 63, 3548-3552 

(2007). 

Qiang Zhao, Qing Han, Charles R. Kissinger, Thomas Hermann 

and Peggy A. Thompson, Structure of hepatitis C virus 

IRES subdomain IIa, Acta Crystallogr., Sect. D: Biol. Crystallogr, 

D64, 436-443, S436/1-S436/3 (2008). 

Yuefen Zhou, Stephen E. Webber, Douglas E. Murphy, 

Lian-Sheng Li, Peter S. Dragovich, Chinh V. Tran, Zhongxiang 

Sun, Frank Ruebsam, Amit M. Shah, Mei Tsan, Richard 

E. Showalter, Rupal Patel, Bin Li, Qiang Zhao, Qing Han, 

Thomas Hermann, Charles R. Kissinger, Laurie LeBrun, Ma- 

ria V. Sergeeva and Leo Kirkovsky, Novel HCV NS5B polymerase 

inhibitors derived from 4-(1’,1’-dioxo-1’,4’-dihydro- 

1’�6-benzo[1’,2’,4’]thiadiazin-3’-yl)-5-hydroxy-2H-pyrida- No publication information submitted for this edition. Wolfgang Wernsdorfer, Motohiro Nakano, Stephen Hill and 

David N. Hendrickson, Heterometallic Integer-Spin Ana- 

logues of S = 

zin-3-ones. Part 1: Exploration of 7’-substitution of benzothiadiazine, 


9/2 

HAYMET, A. D. J. Vice Chancellor and Dean, Marine 

Sciences. B.Sc, 1978, University of Sydney; Ph.D, 1981, 

University of Chicago; D.Sc, 1997, University of Sydney. 

Physical Chemistry. Nucleation, clathrates, freezing, 

anti-freeze proteins in fish. TEL: (858) 534-2827 FAX: 

(858) 453-0167 

Mn4 Cubane Single-Molecule Magnets, 

Inorg. Chem. (Washington, DC, U. S.), 47, 3188-3204 

(2008). 

Sonali J. Shah, Christopher M. Ramsey, Katie J. Heroux, 

James R. O’Brien, Antonio G. DiPasquale, Arnold L. Rhein- 

gold, Enrique del Barco and David N. Hendrickson, Wheel- 

Shaped Mn16 Single-Molecule Magnets, Inorg. Chem. 

Yuefen Zhou, Lian-Sheng Li, Peter S. Dragovich, Douglas 

E. Murphy, Chinh V. Tran, Frank Ruebsam, Stephen E. 

Webber, Amit M. Shah, Mei Tsan, April Averill, Richard E. 

Showalter, Rupal Patel, Qing Han, Qiang Zhao, Thomas Hermann, 

Charles R. Kissinger, Laurie LeBrun and Maria V. 

Sergeeva, Novel HCV NS5B polymerase inhibitors derived 

from 4-(1’,1’-dioxo-1’,4’-dihydro-1’�6-benzo[1’,2’,4’]thia- Web: sio.ucsd.edu/About/Director/ 

Email: haymet@ucsd.edu 


Andrzej Wierzbicki, Pranav Dalal, Thomas E. Cheatham, 

III, Jared E. Knickelbein, A. D. J. Haymet and Jeffry D. Madura, 

Antifreeze proteins at the ice/water interface: Three calculated 

discriminating properties for orientation of type I 

proteins, Biophys. J, 93, 1442-1451 (2007). 

E. J. Smith, T. Bryk and A. D. J. Haymet, Reply to “Comment 

on Molecular dynamics study of solvation of Cl 


Patrick L. Feng, Changhyun Koo, John J. Henderson, Motohiro 

Nakano, Stephen Hill, Enrique del Barco and David N. 

Hendrickson, Single-Molecule-Magnet Behavior and Spin 

Changes Affected by Crystal Packing Effects, Inorg. Chem. 



Antonio G. DiPasquale, Naresh S. Dalal, Arnold L. Rhein- 

gold, Enrique del Barco and David N. Hendrickson, Molecu- 

lar Wheels: New Mn12 Complexes as Single-Molecule Magnets, 


diazin-3’-yl)-5-hydroxy-2H-pyridazin-3-ones. Part 2: Variation 

of the 2- and 6-pyridazinone substituents, Bioorg. Med. 

Chem. Lett, 18, 1419-1424 (2008). 

Yuefen Zhou, Chun Chow, Douglas E. Murphy, Zhongxiang 

Sun, Thomas Bertolini, Jamie M. Froelich, Stephen E. 

Webber, Thomas Hermann and Daniel Wall, Antibacterial 

activity in serum of the 3,5-diamino-piperidine translation inhibitors, 


HOFFMANN, ALEXANDER (b.1966) Assistant 

- and 

Na (2008). Professor. B.A, 1988, Cambridge University; M.Ph, 

+ in the ice/water interface’ [J. Chem. Phys. 123, 034706 

(2005)], J. Chem. Phys, 126, 237102/1-237102/2 (2007). 

P. W. Wilson and A. D. J. Haymet, Workman-Reynolds 

Freezing Potential Measurements between Ice and Dilute Salt 

Solutions for Single Ice Crystal Faces, J. Phys. Chem. B, 

112, 11750-11755 (2008). 

P. W. Wilson and A. D. J. Haymet, Comment on “Workman-Reynolds 

Freezing Potential Measurements between Ice 

and Dilute Salt Solutions for Single Ice Crystal Faces, J. 

Phys. Chem. B, 112, 15260 (2008). 

HENDRICKSON, DAVID N. (b.1943) Professor. 

B.S, 1966, University of California, L.A; Ph.D, 1969, 

University of California, Berkeley. Fellowship, 1970, 

California Institute of Technology. Inorganic Chemistry; 

Nanochemistry. Magnetic bistability in single-molecule 

magnets; resonant magnetization quantum tunneling; dynamics 

in transition metal complexes; optical bistability 

in valence tautomeric and spin-crossover complexes; 

magnetic exchange in polynuclear complexes. TEL: 

(858) 534-5580 FAX: (858) 534-5383 

Email: dhendrickson@ucsd.edu 

Ai-Ju Zhou, Lian-Jing Qin, Christopher C. Beedle, Shu 

Emi Evangelio, David N. Hendrickson and Daniel Ruiz- 

Molina, Intramolecular electron transfer in the mixed-valence 

[Co(3,5-DTBCat)(3,5-DTBSQ)(bpy)] complex: Beyond valence 

tautomerism, Inorg. Chim. Acta, 361, 3403-3409 

(2008). 

Patrick L. Feng, Christopher C. Beedle, Changhyun Koo, 

Jon Lawrence, Stephen Hill and David N. Hendrickson, Origin 

of magnetization tunneling in single-molecule magnets as 

determined by single-crystal high-frequency EPR, Inorg. 

Chim. Acta, 361, 3465-3480 (2008). 

Michio Sorai, Ramon Burriel, Edgar F. Westrum, Jr. and 

David N. Hendrickson, Mechanochemical Effect in the Iron 

(III) Spin Crossover Complex [Fe(3-MeO-salenEt)2]PF6 as 

Studied by Heat Capacity Calorimetry, J. Phys. Chem. B, 

112, 4344-4350 (2008). 

Christopher M. Ramsey, Enrique del Barco, Stephen Hill, 

Sonali J. Shah, Christopher C. Beedle and David N. Hendrickson, 

Quantum interference of tunnel trajectories between 

states of different spin length in a dimeric molecular 

nanomagnet, Nat. Phys, 4, 277-281 (2008). 

Sonali J. Shah, Single-molecule magnets: Polynuclear 

manganese wheels and clusters. (D) 

1991, Cambridge University; Ph.D, 1994, Rockefeller 

University. Postdoctoral Associate, 1995-1998, M. I. T; 

Postdoctoral Associate, 1998-2003, CalTech. Biochemis- 

try. Eukaryotic gene expression is regulated by a circuitry 

of signaling pathways. My research is focused on NFkB 

signaling that controls mammalian immune and stress 

responses. Using computational modeling, I aim to con- 

nect biochemical results from in vitro studies and from 

genetically altered cells and mice. Constructing a computational 

model of this signaling pathway leads to quantitative 

understanding, novel hypotheses, and exploration 

of novel therapeutic agents for a host of human diseases. 

TEL: (858) 822-0212 FAX: (858) 534-6693 


C04518 

Email: ahoffmann@ucsd.edu 

Alexander Hoffmann, Yifeng Xia and Inder M. Verma, In- 

flammatory tales of liver cancer, Cancer Cell, 11, 99-101 

(2007). 

Soumen Basak, Hana Kim, Jeffrey D. Kearns, Vinay Tergaonkar, 

Ellen O’Dea, Shannon L. Werner, Chris A. Bened- 

ict, Carl F. Ware, Gourisankar Ghosh, Inder M. Verma and 

Ding, Motohiro Nakano, Ji-Dong Leng, Ming-Liang Tong 

and David N. Hendrickson, New Mn12 Clusters with Tunable 

Oxidation States via the Use of N,N,N’,N’-Tetrakis(2-hy- 

HERMANN, THOMAS Assistant Professor. B.S, 

1988, University of Ulm, Germany; M.S, 1992, Univer- 

Alexander Hoffmann, A fourth I�B protein within the NF-�B 

signaling module, Cell (Cambridge, MA, U. S.), 128, 369- 

381 (2007).


E. L. O’Dea, D. Barken, R. Q. Peralta, K. T. Tran, S. L. Benjamin T. Andrews, Shachi Gosavi, John M. Finke, Jose makrishnan, Structures of tRNAs with an expanded antico- 

Werner, J. D. Kearns, A. Levchenko and A. Hoffmann, A ho- N. Onuchic and Patricia A. Jennings, The dual-basin land- don loop in the decoding center of the 30S ribosomal subunit, 

meostatic model of IkappaB metabolism to control constitu- scape in GFP folding, Proc. Natl. Acad. Sci. U. S. A, 105, RNA, 13, 817-823 (2007). 

tive activity, Molecular Systems Biology, 3, 111 (2007). 12283-12288 (2008). Lucia Garcia-Ortega, Jenise Stephen and Simpson Joseph, 

Soumen Basak and Alexander Hoffmann, Crosstalk via the Dominique T. Capraro, Melinda Roy, Jose N. Onuchic and Precise alignment of peptidyl tRNA by the decoding center is 

NF-�B signaling system, Cytokine Growth Factor Rev, 19, Patricia A. Jennings, Backtracking on the folding landscape essential for EF-G-dependent translocation, Mol. Cell, 32, 

187-197 (2008). 

of the �-trefoil protein interleukin-1�?, Proc. Natl. Acad. Sci. 292-299 (2008). 

Erika Mathes, Ellen L. O’Dea, Alexander Hoffmann and U. S. A, 105, 14844-14848 (2008). 

Gourisankar Ghosh, NF-�B dictates the degradation pathway Shachi Gosavi, Paul C. Whitford, Patricia A. Jennings and J. S. Feinberg, Interactions between the acceptor arm of 

of I�B�, EMBO J, 27, 1357-1367 (2008). 

Jose N. Onuchic, Extracting function from a �-trefoil folding tRNA and the large subunit of the bacterial ribosome impor- 

Tomohisa Kato, Jr., Yusuke Gotoh, Alexander Hoffmann motif. [Erratum to document cited in CA149:240950], Proc. tant for translocation. (D) 

and Yoshitaka Ono, Negative regulation of constitutive NF- Natl. Acad. Sci. U. S. A, 105, 16057 (2008). S. M. Studer, MRNA interaction with the bacterial ribo- 

�B and JNK signaling by PKN1-mediated phosphorylation 

some during initiation and translocation. (D) 

of TRAF1, Genes Cells, 13, 509-520 (2008). 

Christine S. Cheng, Tracy L. Johnson and Alexander Hoffmann, 

Epigenetic control: slow and global, nimble and local, 

Genes Dev, 22, 1110-1114 (2008). 

Shannon L. Werner, Jeffrey D. Kearns, Victoria Zadorozhnaya, 

Candace Lynch, Ellen O’Dea, Mark P. Boldin, Averil 

Ma, David Baltimore and Alexander Hoffmann, Encoding 

NF-�B temporal control in response to TNF: distinct roles 

for the negative regulators I�B� and A20, Genes Dev, 22, 

2093-2101 (2008). 

Amanda J. Fusco, Olga V. Savinova, Rashmi Talwar, Jeffrey 

D. Kearns, Alexander Hoffmann and Gourisankar 

Ghosh, Stabilization of RelB Requires Multidomain Interactions 

with p100/p52, J. Biol. Chem, 283, 12324-12332 

(2008). 

Irene L. Ch’en, Stephen M. Hedrick and Alexander Hoffmann, 

NF-�B as a determinant of distinct cell death pathways, 


Ellen L. O’Dea, Jeffrey D. Kearns and Alexander Hoffmann, 

UV as an amplifier rather than inducer of NF-�B activity, 

Mol. Cell, 30, 632-641 (2008). 

Soumen Basak, Vincent Feng-Sheng Shih and Alexander 

Hoffmann, Generation and activation of multiple dimeric 

transcription factors within the NF-�B signaling system, Mol. 

Cell. Biol, 28, 3139-3150 (2008). 

Irene L. Ch’en, Daniel R. Beisner, Alexei Degterev, Candace 

Lynch, Junying Yuan, Alexander Hoffmann and Stephen 

M. Hedrick, Antigen-mediated T cell expansion regulated 

by parallel pathways of death, Proc. Natl. Acad. Sci. U. S. A, 

105, 17463-17468 (2008). 

James Lee, Regulation of the ISRE by NFkB: A novel role 

for the P50 homodimer. (M) 

D. Barken, Temporal encoding and homeostatic control in 

the IKK-IkB-NFkB signaling system. (D) 

JENNINGS, PATRICIA A. (b.1962) Professor. B.S, 

1985, Rutgers University; Ph.D, 1991, Pennsylvania 

State University. Postdoctoral Research Fellowship, 

1991-1993, Scripps Research Institute. Biochemistry; 

NMR Spectroscopy. Biophysical chemistry: protein 

structure, function, dynamics and folding; multinuclear 

(1H, 15N, 13C, 2H)-multidimensional (2, 3 and 4D) 

NMR spectroscopy; cloning and site-specific mutagenesis 

by PCR; equilibrium and kinetic-fluorescence, UVabsorbance. 

TEL: (858) 534-6417 FAX: (858) 534-7042 

Web: www.chem/Faculty/Research_txt/jennings.html 

Email: pajennin@ucsd.edu 

pajennings@ucsd.edu 


John M. Finke, Patricia A. Jennings, Jennifer C. Lee, Jose 

N. Onuchic and Jay R. Winkler, Equilibrium unfolding of the 

poly(glutamic acid)20 helix, Biopolymers, 86, 193-211 

(2007). 

Sandra E. Wiley, Mark L. Paddock, Edward C. Abresch, 

Larry Gross, Peter van der Geer, Rachel Nechushtai, Anne N. 

Murphy, Patricia A. Jennings and Jack E. Dixon, The outer 

mitochondrial membrane protein mitoNEET contains a novel 

redox-active 2Fe-2S cluster, J. Biol. Chem, 282, 23745- 

23749 (2007). 

Jamie E. Mills, Paul C. Whitford, Jennifer Shaffer, Jose N. 

Onuchic, Joseph A. Adams and Patricia A. Jennings, A Novel 

Disulfide Bond in the SH2 Domain of the C-terminal Src 

Kinase Controls Catalytic Activity, J. Mol. Biol, 365, 1460- 

1468 (2007). 

Benjamin T. Andrews, Andrea R. Schoenfish, Melinda 

Roy, Geoffrey Waldo and Patricia A. Jennings, The Rough 

Energy Landscape of Superfolder GFP Is Linked to the Chromophore, 

J. Mol. Biol, 373, 476-490 (2007). 

Mark L. Paddock, Sandra E. Wiley, Herbert L. Axelrod, 

Aina E. Cohen, Melinda Roy, Edward C. Abresch, Domi- 

nique Capraro, Anne N. Murphy, Rachel Nechushtai, Jack E. 

Dixon and Patricia A. Jennings, MitoNEET is a uniquely 

folded 2Fe-2S outer mitochondrial membrane protein stabilized 

by pioglitazone, Proc. Natl. Acad. Sci. U. S. A, 104, 

14342-14347 (2007). 

Jonathan C. Hagopian, Chen-Ting Ma, Bryan R. Meade, 

Claudio P. Albuquerque, Jacky Chi Ki Ngo, Gourisankar 

Ghosh, Patricia A. Jennings, Xiang-Dong Fu and Joseph A. 

Adams, Adaptable Molecular Interactions Guide Phosphorylation 

of the SR Protein ASF/SF2 by SRPK1, J. Mol. Biol, 

JOHNSON, JOHN E. (b.1945) Professor. B.A, 1967, 

Carthage College, Kenosha, WI; Ph.D, 1972, Iowa State 

University, Ames, Iowa. National Cancer Institute Fellowship, 

1974-1976, Purdue University; NATO Travel 

Fellowship, 1978, Purdue Unversity; Travel Fellowship, 

2000, Japanese Society for the Promotion of Science; 

Travel Fellowship, 2001, Taiwan National Science Committee. 

TEL: (858) 784-9705 FAX: (858) 784-8660 

Web: www.noda.scripps.edu 

Email: jackj@scripps.edu 


John E. Johnson and Wah Chiu, DNA packaging and delivery 

machines in tailed bacteriophages, Curr. Opin. Struct. 

Biol, 17, 237-243 (2007). 

Blair R. Szymczyna, Lu Gan, John E. Johnson and James 

R. Williamson, Solution NMR Studies of the Maturation Intermediates 

of a 13 MDa Viral Capsid, J. Am. Chem. Soc, 

129, 7867-7876 (2007). 

Anton Poliakov, Esther van Duijn, Gabriel Lander, Chi-yu 

Fu, John E. Johnson, Peter E. Prevelige and Albert J. R. 

Heck, Macromolecular mass spectrometry and electron microscopy 

as complementary tools for investigation of the heterogeneity 

of bacteriophage portal assemblies, J. Struct. Biol, 

157, 371-383 (2007). 

Sebyung Kang, Gabriel C. Lander, John E. Johnson and 

Peter E. Prevelige, Development of bacteriophage P22 as a 

platform for molecular display: genetic and chemical modifications 

of the procapsid exterior surface, ChemBioChem, 9, 

514-518 (2008). 

Manidipa Banerjee and John E. Johnson, Activation, exposure 

and penetration of virally encoded, membrane-active 

polypeptides during nonenveloped virus entry, Curr. Protein 

Pept. Sci, 9, 16-27 (2008). 

Daniel Nemecek, Gabriel C. Lander, John E. Johnson, 

Sherwood R. Casjens and George J. Thomas, Assembly Architecture 

and DNA Binding of the Bacteriophage P22 Terminase 

Small Subunit, J. Mol. Biol, 383, 494-501 (2008). 

Gina E. Sosinsky, John Crum, Ying Z. Jones, Jason Lanman, 

Benjamin Smarr, Masako Terada, Maryann E. Martone, 

Thomas J. Deerinck, John E. Johnson and Mark H. Ellisman, 

The combination of chemical fixation procedures with high 

pressure freezing and freeze substitution preserves highly labile 

tissue ultrastructure for electron tomography applications, 

J. Struct. Biol, 161, 359-371 (2008). 

Jason Lanman, John Crum, Thomas J. Deerinck, Guido M. 

Gaietta, Anette Schneemann, Gina E. Sosinsky, Mark H. Ellisman 

and John E. Johnson, Visualizing flock house virus 

infection in Drosophila cells with correlated fluorescence and 

electron microscopy, J. Struct. Biol, 161, 439-446 (2008). 

Lu Gan and John E. Johnson, An optimal exposure strategy 

for cryoprotected virus crystals with lattice constants greater 

than 1000 Å, J. Synchrotron Radiat, 15, 223-226 (2008). 

Hanna E. Walukiewicz, Manidipa Banerjee, Anette 

Schneemann and John E. Johnson, Rescue of maturation-defective 

flock house virus infectivity with noninfectious, mature, 

viruslike particles, J. Virol, 82, 2025-2027 (2008). 

Reed B. Wickner, Jinghua Tang, Nora A. Gardner and 

John E. Johnson, The yeast dsRNA virus L-A resembles 

mammalian dsRNA virus cores, Segmented Double-Stranded 

RNA Viruses, 105-114 (2008). 

Gabriel C. Lander, Alex Evilevitch, Meerim Jeembaeva, 

Clinton S. Potter, Bridget Carragher and John E. Johnson, 

Bacteriophage Lambda Stabilization by Auxiliary Protein 

gpD: Timing, Location, and Mechanism of Attachment Determined 

by Cryo-EM, Structure (Cambridge, MA, U. S.), 16, 

1399-1406 (2008). 

Kelly K. Lee, Lu Gan, Hiro Tsuruta, Crystal Moyer, James 

F. Conway, Robert L. Duda, Roger W. Hendrix, Alasdair C. 

Steven and John E. Johnson, Virus Capsid Expansion Driven 

by the Capture of Mobile Surface Loops, Structure (Cam- 

bridge, MA, U. S.), 16, 1491-1502 (2008). 

JOSEPH, SIMPSON (b.1966) Full Professor. Ph.D, 

1994, University of Vermont. American Cancer Society 

Fellowship, 1994-1998, University of California, Santa 

Cruz. Biochemistry; Biophysics/Biophysical Chemistry. 

Ribosome structure, function and dynamics; role of 

rRNA in translation; mechanism of translocation; interaction 

of antibiotics with ribosomes. TEL: (858) 822- 

2957 FAX: (858) 534-7042 

Email: sjoseph@chem.ucsd.edu 

KEARNS, DAVID R. (b.1935) Professor Emeritus. 

B.S, 1956, University of Illinois; Ph.D, 1960, University 

of California, Berkeley. NAS Postdoctoral Fellow, 1960- 

1961, University of Chicago; NAS Postdoctoral Fellow, 

1961-1962, M. I. T; Guggenheim Fellowship, 1969- 

1970. Physical chemistry of polynucleotides; dynamics 

and structural studies by one-, two-, three-dimensional 

NMR; drug-DNA, metal-DNA, protein-DNA interactions, 

unusual DNA structures, and protein structure. 

TEL: (858) 534-2760 FAX: (858) 534-0202 

Web: www.chem.ucsd.edu/Faculty/emeritus.html# 

kearns 

Email: dkearns@ucsd.edu 


KIM, JUDY E. Assistant Professor. M.S, 1994, M.I.T; 

Ph.D, 2001, University of California, Berkeley. NIH 

Postdoc Fellow, 2003-2005, California Institute of Technology. 

Biophysics/Biophysical Chemistry; Physical 

Chemistry. Integral membrane proteins comprise ~30% 

of all cell proteins, and play essential roles in cellular 

functions as gates, pumps, receptors, energy transducers, 

and enzymes. Despite recent progress towards understanding 

the structure and function of membrane pro- 

teins, a more complex and fundamental question persists: 

What are the molecular mechanisms for the folding, in- 

sertion, and assembly of integral membrane proteins that 

give rise to functional structures? TEL: (858) 534-5598 

FAX: (858) 534-7042 


C04912 

Email: judyk@ucsd.edu 

Arneh Babakhani, Alemayehu A. Gorfe, Justin Gullingsrud, 

Judy E. Kim and J. Andrew McCammon, Peptide inser- 

tion, positioning, and stabilization in a membrane: insight 

from an all-atom molecular dynamics simulation, Biopolymers, 

85, 490-497 (2007). 

Katheryn M. Sanchez, Jonathan E. Gable, Diana E. Schlamadinger 

and Judy E. Kim, Effects of Tryptophan Microenvironment, 

Soluble Domain, and Vesicle Size on the Ther- 

modynamics of Membrane Protein Folding: Lessons from the 

Transmembrane Protein OmpA, Biochemistry, 47, 12844- 

12852 (2008). 

Arneh Babakhani, Alemayehu A. Gorfe, Judy E. Kim and 

J. Andrew McCammon, Thermodynamics of Peptide Inser- 

tion and Aggregation in a Lipid Bilayer, J. Phys. Chem. B, 

112, 10528-10534 (2008). 

Katheryn M. Sanchez, Tiffany J. Neary and Judy E. Kim, 

Ultraviolet Resonance Raman Spectroscopy of Folded and 

Unfolded States of an Integral Membrane Protein, J. Phys. 

Chem. B, 112, 9507-9511 (2008). 

K. M. Sanchez, D. E. Schlamadinger, J. E. Gable and J. E. 

Kim, Forster resonance energy transfer and conformational 

stability of proteins: An advanced biophysical module for 

physical chemistry students, Journal of Chemical Education, 

85, 1253-1256 (2008). 

Tiffany J. Neary, Ultraviolet resonance raman spectroscopy 

of the integral membrane protein OmpA: Elucidating 

structure and tryptophan microenvironment of folded and unfolded 

states. (M) 

KOBAYASHI, YOSHIHISA (b.1970) Assistant Professor. 

B.A, 1994, The University of Tokyo; M.A, 1996, 

The University of Tokyo; Ph.D, 1999, The University of 

Tokyo. Postdoctoral Fellow, 1999-2002, Harvard University; 

Research Associate, 2002-2003, Harvard University. 

Natural Products Chemistry; Synthesis. Total 

synthesis of natural products, heterocycles, development 

of methodology of synthetic organic chemistry. TEL: 

(858) 822-5870 FAX: (858) 822-5870 

Web: www.chem-faculty.ucsd.edu/kobayashi/index.html 

Email: ykoba@chem.ucsd.edu 

Matthew J. Buller, Travis G. Cook and Yoshihisa Kobayashi, 

Versatile synthesis of 2,2-disubstituted indolinones via 

protected indolones generated by one-pot multi-oxidation of 

2-substituted indoles, Heterocycles, 72, 163-166 (2007). 

Jerry Isaacson, Cynthia B. Gilley and Yoshihisa Kobayashi, 

Expeditious access to unprotected racemic pyroglutamic 

382, 894-909 (2008). Sean M. Studer and Simpson Joseph, Binding of mRNA to acids, J. Org. Chem, 72, 3913-3916 (2007). 

Shachi Gosavi, Paul C. Whitford, Patricia A. Jennings and the bacterial translation initiation complex, Methods Enzy- Jerry Isaacson, Cynthia B. Gilley and Yoshihisa Kobaya- 

Jose N. Onuchic, Extracting function from a �-trefoil folding mol, 430, 31-44 (2007). shi, Expeditious access to unprotected racemic pyroglutamic 

motif, Proc. Natl. Acad. Sci. U. S. A, 105, 10384-10389 Christine M. Dunham, Maria Selmer, Steven S. Phelps, acids. [Erratum to document cited in CA147:031335], J. Org. 

(2008). Ann C. Kelley, Tsutomu Suzuki, Simpson Joseph and V. Ra- Chem, 72, 5024 (2007).


Cynthia B. Gilley, Matthew J. Buller and Yoshihisa Koba- ments meet theory, Curr. Opin. Struct. Biol, 18, 27-34 Jonathan B. Caballero, Chemical sensor development leadyashi, 

New Entry to Convertible Isocyanides for the Ugi Re- (2008). ing to an alternative glucose detection method. (D) 

action and Its Application to the Stereocontrolled Formal To- Gina N. Betts, Peter van der Geer and Elizabeth A. Kotal 

Synthesis of the Proteasome Inhibitor Omuralide, Org. 

Lett, 9, 3631-3634 (2007). 

Mitchell Vamos, Kerem Ozboya and Yoshihisa Kobayashi, 

Synthesis of bicyclic pyroglutamic acid featuring the Ugi reaction 

and a unique stereoisomerization at the angular position 

by Grob fragmentation followed by a transannular ke- 

tene [2+2] cycloaddition reaction, Synlett, 1595-1599 (2007). 

Mitchell Vamos and Yoshihisa Kobayashi, Scalable Preparation 

of Both Enantiomers of 2-(1-Hydroxy-2-oxocyclo- 

hexyl)acetic Acid, J. Org. Chem, 73, 3938-3941 (2008). 

Cynthia B. Gilley and Yoshihisa Kobayashi, 2-Nitrophenyl 

Isocyanide as a Versatile Convertible Isocyanide: Rapid Access 

to a Fused �-Lactam �-Lactone Bicycle, J. Org. Chem, 

73, 4198-4204 (2008). 

Thong X. Nguyen and Yoshihisa Kobayashi, Synthesis of 

the Common Propellane Core Structure of the Hasubanan Alkaloids, 

J. Org. Chem, 73, 5536-5541 (2008). 

Jerry Isaacson, Mandy Loo and Yoshihisa Kobayashi, To- 

tal Synthesis of (±)-Dysibetaine, Org. Lett, 10, 1461-1463 

(2008). 

M. J. Buller, C. B. Gilley, B. Nguyen, L. Olshansky, B. 

Fraga and Y. Kobayashi, Synthesis of functionalized pyro- 

glutamic acids. Part 1: The synthetic utility of N-Acylindole 

and the ugi reaction with a chiral levulinic acid, Synlett, 

2244-2248 (2008). 

mives, Structural and Functional Consequences of Tyrosine 

Phosphorylation in the LRP1 Cytoplasmic Domain, J. Biol. 

Chem, 283, 15656-15664 (2008). 

Stephanie M. E. Truhlar, Erika Mathes, Carla F. Cervantes, 

Gourisankar Ghosh and Elizabeth A. Komives, Pre-folding 

I�B� Alters Control of NF-�B Signaling, J. Mol. Biol, 380, 

67-82 (2008). 

Shih-Che Sue, Carla Cervantes, Elizabeth A. Komives and 

H. Jane Dyson, Transfer of Flexibility between Ankyrin Re- 

peats in I�B� upon Formation of the NF-�B Complex, J. 

Mol. Biol, 380, 917-931 (2008). 

David G. Mendoza-Cozatl, Emerald Butko, Franziska 

Springer, Justin W. Torpey, Elizabeth A. Komives, Julia 

Kehr and Julian I. Schroeder, Identification of high levels of 

phytochelatins, glutathione and cadmium in the phloem sap 

of Brassica napus. A role for thiol-peptides in the long-dis- 

tance transport of cadmium and the effect of cadmium on 

iron translocation, Plant J, 54, 249-259 (2008). 

Diego U. Ferreiro, Aleksandra M. Walczak, Elizabeth A. 

Komives and Peter G. Wolynes, The energy landscapes of repeat-containing 

proteins: topology, cooperativity, and the 

folding funnels of one-dimensional architectures, PLoS Comput. 

Biol, 4, No pp. given (2008). 

Stephanie M. E. Truhlar, Carla F. Cervantes, Justin W. 

Torpey, Magnus Kjaergaard and Elizabeth A. Komives, Rapid 

mass spectrometric analysis of 

KUMMEL, A. C. (b.1959) Professor. B.S, 1981, Yale 

University; M.S, 1984, Stanford University; Ph.D, 1988, 

Stanford University. 1988, Cornell University. Deposition 

of oxides on compound semiconductors to form passive 

interfaces for use in MOSFETs: STM/STS structure 

determination of the oxide/semiconductor interface; 

Computational modeling of absorbates, oxides, and defects 

on compounds semiconductor surfaces; Deposition 

of organo-metallic films for use in ChemFET sensors; 

Chemical Dynamics of gas-surface reaction. TEL: (858) 

534-3368 FAX: (858) 534-2063 

Web: www.chem-faculty.ucsd.edu/kummel/ 

Email: ack@chem.ucsd.edu 

akummel@ucsd.edu 


D. L. Winn, T. J. Grassman and A. C. Kummel, Electronic 

properties of adsorbates on In0.37Ga0.63As(001)-(2 × 4), ECS 

Trans, 11, 441-449 (2007). 

M. J. Hale, S. I. Yi, J. Z. Sexton, A. C. Kummel and M. 

Passlack, Scanning tunneling microscopy and spectroscopy 

of gallium oxide deposition and oxidation on GaAs(001)-c 

(2×8)/(2×4). [Erratum to document cited in CA140:009103], 

J. Chem. Phys, 127, 049902/1 (2007). 

15 C. B. Gilley, M. J. Buller and Y. Kobayashi, Synthesis of 

functionalized pyroglutamic acids. Part 2: The stereoselective 

condensation of multi-functional groups with chiral levulinic 

acids, Synlett, 2249-2252 (2008). 

S. Born and Y. Kobayashi, A stable synthetic equivalent of 

2,3-Dihydropyridine, Synlett, 2479-2482 (2008). 

S. Born, G. Bacani, E. E. Olson and Y. Kobayashi, Microwave-assisted 

intramolecular diels-alder reaction towards the 

total synthesis of symbioimine, Synlett, 2877-2881 (2008). 

N-Leu incorporation fidelity 

during preparation of specifically labeled NMR sam- 

ples, Protein Sci, 17, 1636-1639 (2008). 

S. Bergqvist, G. Ghosh and E. A. Komives, The IkBa /NFkB 

complex has two hot-spots, one at either end of the interface, 

Protein Science, 17, 2051-2058 (2008). 

Stephanie M. E. Truhlar and Elizabeth A. Komives, LRR 

Domain Folding: Just Put a Cap on It, Structure (Cambridge, 

MA, U. S.), 16, 655-657 (2008). 

KYTE, JACK (b.1946) Professor Emeritus. B.A, 1967, 

Carleton College; Ph.D, 1972, Harvard University. Post- 

doctoral Fellowship, 1972-1974, University of Califor- 

nia, San Diego. Enzymology, active transport, biomem- 

brane, membrane proteins, pharmacological receptors. 

TEL: (858) 534-3281 FAX: (858) 534-4864 

Email: jkyte@ucsd.edu 


C. B. Gilley, New convertible isocyanides for the ugi reaction; 

application to the stereoselective synthesis of omuralide. 

(D) 

KOMIVES, ELIZABETH A. (b.1960) Professor. 

B.S, 1982, M.I.T; M.S, 1982, M.I.T; Ph.D, 1987, Uni- 

versity of California, San Francisco. NIH Postdoctoral 

Fellowship, 1987-1990, Harvard University. Biochemistry; 

Biophysics/Biophysical Chemistry. Protein-protein 

interactions of multidomain proteins; disulfide bonded 

domains; thrombomodulin, LRP, IkappaB; NMR, binding 

kinetics, binding thermodynamics, H/D exchange, 

Muneera Beach, Thermodynamics and the role of allostery 

in the thrombin-thrombomodulin interaction. (D) 

KRAUT, JOSEPH (b.1926) Research Professor. B.S, 

1950, Bucknell University; Ph.D, 1954, California Institute 

of Technology. Fellowship, 1955-1956, Howard 

Hughes Medical Institute. Molecular structure, function 

and evolution of proteins and other biologically important 

molecules; x-ray diffraction crystallography; site di- 

rected mutagenesis. TEL: (626) 794-6352 FAX: (858) 

534-4864 

Email: jkraut@ucsd.edu 

LINDENBERG, KATJA (b.1941) Distinguished Professor. 

B.A, 1962, Alfred University; Ph.D, 1967, Cor- 

nell University. Postdoctoral Fellowship, 1967-1969, 

University of Rochester. Chemical Physics; Theoretical 

Chemistry. Stochastic processes and their applications, 

nonlinear systems, nonequilibrium statistical mechanics, 

pulse propagation in granular materials. TEL: (858) 534- 

3285 FAX: (858) 534-7244 

Web: hypatia.ucsd.edu 

Email: klindenberg@ucsd.edu 

A. H. Romero, A. M. Lacasta, J. M. Sancho and Katja Lindenberg, 

Numerical study of A + A � 0 and A + B � 0re- 

mass spectrometry. TEL: (858) 534-3058 FAX: (858) 

joek@chem.ucsd.edu 

actions with inertia, J. Chem. Phys, 127, 174506/1-174506/7 

534-6174 

Web: www.chem.ucsd.edu/Faculty/bios/komives.html 

Email: ekomives@ucsd.edu 


KUBIAK, CLIFFORD P. (b.1953) Harold C. Urey 

(2007). 

J. M. Sancho, A. H. Romero, A. M. Lacasta and Katja Lindenberg, 

Langevin dynamics of A + A reactions in one di- 

Xiaohua Wu, Zhi-fang Li, Randolph Brooks, Elizabeth A. 

Komives, Justin W. Torpey, Eva Engvall, Steven L. Gonias 

and G. Diane Shelton, Autoantibodies in Canine Masticatory 

Muscle Myositis Recognize a Novel Myosin Binding Protein-C 

Family Member, J. Immunol, 179, 4939-4944 (2007). 

Diego U. Ferreiro, Carla F. Cervantes, Stephanie M. E. 

Truhlar, Samuel S. Cho, Peter G. Wolynes and Elizabeth A. 

Komives, Stabilizing I�B� by “Consensus” Design, J. Mol. 

Biol, 365, 1201-1216 (2007). 

Joachim Laetzer, Garegin A. Papoian, Michael C. Prentiss, 

Elizabeth A. Komives and Peter G. Wolynes, Induced Fit, 

Professor. B.Sc, 1975, Brown University; Ph.D, 1980, 

University of Rochester. Postdoctoral Associate, 1980- 

1981, M. I. T. Inorganic Chemistry; Materials Chemistry. 

Inorganic and materials chemistry. Electron and 

atom transfer chemistry. Effects of ultrafast intramolecular 

reactions on IR spectra. Molecular electronics and nanoscience. 

Energy conversion. Carbon dioxide conversion. 

TEL: (858) 822-2665 FAX: (858) 822-4442 

Web: kubiak.ucsd.edu 

Email: ckubiak@ucsd.edu 

mension, J. Phys.: Condens. Matter, 19, 065108/1-065108/ 

12 (2007). 

J. J. Ruiz-Lorenzo, Santos B. Yuste and Katja Lindenberg, 

Simulations for trapping reactions with subdiffusive traps 

and subdiffusive particles, J. Phys.: Condens. Matter, 19, 

065120/1-065120/12 (2007). 

Kevin Wood, C. Van den Broeck, V. Kawai and Katja Lin- 

denberg, Continuous and discontinuous phase transitions and 

partial synchronization in stochastic three-state oscillators, 

Los Alamos Natl. Lab., Prepr. Arch., Condens. Matter, 1-10 

(2007). 

Folding, and Recognition of the NF-�B-Nuclear Localization Clifford P. Kubiak and Eugenio Simon-Manso, Nickel Santos Bravo Yuste, J. Klafter and Katja Lindenberg, 

Signals by I�B� and I�B�, J. Mol. Biol, 367, 262-274 complexes with carbonyl, isocyanide and carbene ligands, Number of distinct sites visited by a subdiffusive random 

(2007). Comprehensive Organometallic Chemistry III, 8, 1-26 walker, Los Alamos Natl. Lab., Prepr. Arch., Condens. Mat- 

Ganesh S. Anand, Matthew Hotchko, Simon H. J. Brown, (2007). ter, 1-4 (2007). 

Lynn F. Ten Eyck, Elizabeth A. Komives and Susan S. Tay- Benjamin J. Lear, Starla D. Glover, J. Catherine Salsman, S. B. Yuste and Katja Lindenberg, The subdiffusive target 

lor, R-subunit Isoform Specificity in Protein Kinase A: Dis- Casey H. Londergan and Clifford P. Kubiak, Solvent dynam- problem: Survival probability, Los Alamos Natl. Lab., Prepr. 

tinct Features of Protein Interfaces in PKA Types I and II by ical control of ultrafast ground state electron transfer: impli- Arch., Condens. Matter, 1-5 (2007). 

Amide H/ 2H Exchange Mass Spectrometry, J. Mol. Biol, 374, cations for class II-III mixed valency, J. Am. Chem. Soc, 129, Francisco J. Cao, Kevin Wood and Katja Lindenberg, 

487-499 (2007). 12772-12779 (2007). Noise-induced phase transitions in field-dependent relaxa- 

Dong-Yul Sung, David Lee, Hugh Harris, Andrea Raab, Benjamin J. Lear and Clifford P. Kubiak, Origins of coop- tional dynamics: the Gaussian ansatz, Los Alamos Natl. Lab., 

Jorg Feldmann, Andrew Meharg, Bryan Kumabe, Elizabeth erative noncovalent host-guest chemistry in mixed valence Prepr. Arch., Condens. Matter, 1-9 (2007). 

A. Komives and Julian I. Schroeder, Identification of an arse- complexes, J. Phys. Chem. B, 111, 6766-6771 (2007). Kevin Wood, C. Van den Broeck, R. Kawai and Katja Linnic 

tolerant double mutant with a thiol-mediated component Timi P. Singa, Antonio G. DiPasquale, Arnold L. Rhein- denberg, Effects of disorder on synchronization of discrete 

and increased arsenic tolerance in phyA mutants, Plant J, 49, gold and Clifford P. Kubiak, Bis(2, 6-dimethyphenyl isocya- phase-coupled oscillators, Phys. Rev. E: Stat., Nonlinear, Soft 

1064-1075 (2007). nide) gold (I) tetrafluoridoborate, Acta Cryst, E64, m1221 Matter Phys, 75, 041107/1-041107/11 (2007). 

Diego U. Ferreiro, Joseph A. Hegler, Elizabeth A. Ko- (2008). Kevin Wood, C. Van den Broeck, R. Kawai and Katja Linmives 

and Peter G. Wolynes, Localizing frustration in native John C. Goeltz and Clifford P. Kubiak, Mixed Valence denberg, Continuous and discontinuous phase transitions and 

proteins and protein assemblies, Proc. Natl. Acad. Sci. U. S. Self-Assembled Monolayers: Electrostatic Polarizabilities of partial synchronization in stochastic three-state oscillators, 

A, 104, 19819-19824 (2007). the Mixed Valence States, J. Phys. Chem. C, 112, 8114-8116 Phys. Rev. E: Stat., Nonlinear, Soft Matter Phys, 76, 041132/ 

Diego U. Ferreiro and Elizabeth A. Komives, The plastic (2008). 1-041132/9 (2007). 

landscape of repeat proteins, Proc. Natl. Acad. Sci. U. S. A, Starla D. Glover, Benjamin J. Lear, Jennifer C. Salsman, Francisco J. Cao, Kevin Wood and Katja Lindenberg, 

104, 7735-7736 (2007). Casey H. Londergan and Clifford P. Kubiak, Electron trans- Noise-induced phase transitions in field-dependent relaxa- 

Chun-Ming Huang, Justin W. Torpey, Yu-Tseung Liu, fer at the class II/III borderline of mixed valency: Depen- tional dynamics: the Gaussian ansatz, Phys. Rev. E: Stat., 

Yun-Ru Chen, Katherine E. Williams, Elizabeth A. Komives dence of rates on solvent dynamics and observation of a lo- Nonlinear, Soft Matter Phys, 76, 051111/1-051111/9 (2007). 

and Richard L. Gallo, A peptide with a ProGln C terminus in calized-to-delocalized transitioin in freezing solvents, Phil. S. B. Yuste and Katja Lindenberg, Subdiffusive target 

the human saliva peptidome exerts bactericidal activity Trans. Roy. Soc. A, 366, 177-185 (2008). problem: survival probability, Phys. Rev. E: Stat., Nonlinear, 

against Propionibacterium acnes, Antimicrob. Agents Che- J. Catherine Salsman and Clifford P. Kubiak, Infrared Soft Matter Phys, 76, 051114/1-051114/6 (2007). 

mother, 52, 1834-1836 (2008). spectroelectrochemical investigations of ultrafast electron Kevin Wood, C. Van den Broeck, R. Kawai and Katja Lin- 

Julia R. Koeppe, Muneera A. Beach, Abel Baerga-Ortiz, S. transfer in mixed-valence complexes, Spectroelectrochem, denberg, Continuous and discontinuous phase transitions and 

Jordan Kerns and Elizabeth A. Komives, Mutations in the 123-144 (2008). partial synchronization in stochastic three-state oscillators. 

Fourth EGF-like Domain Affect Thrombomodulin-Induced [Erratum to document cited in CA148:086141], Phys. Rev. E: 

Changes in the Active Site of Thrombin, Biochemistry, 47, Benjamin J. Lear, The effects of electronic delocalization Stat., Nonlinear, Soft Matter Phys, 76, 059901/1 (2007). 

10933-10939 (2008). in highly coupled mixed valence systems. (D) Kevin Wood, C. Van den Broeck, R. Kawai and Katja Lin- 

Doug Barrick, Diego U. Ferreiro and Elizabeth A. Ko- John C. Stires IV, Charge transfer complexes in molecular denberg, Fluctuation theorem for entropy production during 

mives, Folding landscapes of ankyrin repeat proteins: Experi- electronics: Approaching metallic conduction. (D) effusion of an ideal gas with momentum transfer, Phys. Rev.


E: Stat., Nonlinear, Soft Matter Phys, 75, 061116/1-061116/8 

(2007). 

Katja Lindenberg, J. M. Sancho, A. M. Lacasta and I. M. 

Sokolov, Dispersionless Transport in a Washboard Potential, 

Phys. Rev. Lett, 98, 020602/1-020602/4 (2007). 

Alexandre Rosas, Aldo H. Romero, Vitali F. Nesterenko 

and Katja Lindenberg, Observation of Two-Wave Structure 

in Strongly Nonlinear Dissipative Granular Chains, Phys. 

Rev. Lett, 98, 164301/1-164301/4 (2007). 

Massimiliano Esposito and Katja Lindenberg, Continuous 

time random walk for open systems: fluctuation theorems 

and counting statistics, arXiv.org, e-Print Arch., Condens. 

Matter, 1-13 (2008). 

Alexandre Rosas, Aldo H. Romero, Vitali F. Nesterenko 

and Katja Lindenberg, Short pulse dynamics in strongly nonlinear 

dissipative granular chains, arXiv.org, e-Print Arch., 

Condens. Matter, 1-16 (2008). 

I. M. Sokolov, S. B. Yuste, J. J. Ruiz-Lorenzo and Katja 

Lindenberg, Mean field model of coagulation and annihilation 

reactions of a subdiffusive species, arXiv.org, e-Print 

Arch., Condens. Matter, 1-9 (2008). 

Ramon Reigada, Javier Buceta, Jordi Gomez, Francesc Sagues 

and Katja Lindenberg, Phase separation in three-component 

lipid membranes: From Monte Carlo simulations to 

Ginzburg-Landau equations, J. Chem. Phys, 128, 025102/1- 

025102/10 (2008). 

M. Khoury, A. M. Lacasta, J. M. Sancho, A. H. Romero 

and Katja Lindenberg, Charged particle transport in antidot 

lattices in the presence of magnetic and electric fields: Langevin 

approach, Phys. Rev. B, 78, 155433/1-155433/9 

(2008). 

S. B. Yuste, G. Oshanin, Katja Lindenberg, O. Benichou 

and J. Klafter, Survival probability of a particle in a sea of 

mobile traps: A tale of tails, Phys. Rev. E, 78, 021105/1- 

021105/7 (2008). 

S. B. Yuste, J. Klafter and Katja Lindenberg, Number of 

distinct sites visited by a subdiffusive random walker, Phys. 

Rev. E, 77, 032101/1-032101/3 (2008). 

A. Rosas, A. H. Romero, V. F. Nesterenko and Katja Lindenberg, 

Short-pulse dynamics in strongly nonlinear dissipative 

granular chains, Phys. Rev. E, 78, 051303/1-051303/10 

(2008). 

Massimiliano Esposito and Katja Lindenberg, Continuoustime 

random walk for open systems: Fluctuation theorems 

and counting statistics, Phys. Rev. E: Stat., Nonlinear, Soft 

Matter Phys, 77, 051119/1-051119/12 (2008). 

Kevin Wood, Nonequilibrium phase transitions in stochastic 

spatially extended systems. (D) 

MAGDE, DOUGLAS (b.1942) Professor. B.S, 1963, 

Boston College; M.S, 1968, Cornell University; Ph.D, 

1970, Cornell University. Postdoctoral Resident Associate, 

1970-1972, Cornell University; Postdoctoral Resident 

Associate, 1972-1974, Washington State University. 

Biophysics/Biophysical Chemistry; Physical Chemistry. 

work. The studies show, for example, how a substrate 

may be attracted to the active site of an enzyme by electrostatic 

interactions. We also use these methods for 

computer-aided drug discovery. TEL: (858) 534-2905 

FAX: (858) 534-4974 

Web: mccammon.ucsd.edu/ 

Email: jmccammon@ucsd.edu 

Alemayehu A. Gorfe, Arneh Babakhani and J. Andrew 

McCammon, Free energy profile of H-ras membrane anchor 

upon membrane insertion, Angew. Chem., Int. Ed, 46, 8234- 

8237 (2007). 

Riccardo Baron and J. Andrew McCammon, Dynamics, 

Hydration, and Motional Averaging of a Loop-Gated Artificial 

Protein Cavity: The W191G Mutant of Cytochrome c 

Peroxidase in Water as Revealed by Molecular Dynamics 

Simulations, Biochemistry, 46, 10629-10642 (2007). 

Yuhui Cheng, Jason K. Suen, Zoran Radic, Stephen D. 

Bond, Michael J. Holst and J. Andrew McCammon, Continuum 

simulations of acetylcholine diffusion with reaction-determined 

boundaries in neuromuscular junction models, Biophys. 

Chem, 127, 129-139 (2007). 

Xiaolin Cheng, Ivaylo Ivanov, Hailong Wang, Steven M. 

Sine and J. Andrew McCammon, Nanosecond-timescale conformational 

dynamics of the human �7 nicotinic acetylcholine 

receptor, Biophys. J, 93, 2622-2634 (2007). 

Yuhui Cheng, Jason K. Suen, Deqiang Zhang, Stephen D. 

Bond, Yongjie Zhang, Yuhua Song, Nathan A. Baker, Chandrajit 

L. Bajaj, Michael J. Holst and J. Andrew McCammon, 

Finite element analysis of the time-dependent Smoluchowski 

equation for acetylcholinesterase reaction rate calculations, 

Biophys. J, 92, 3397-3406 (2007). 

Joanna Trylska, Valentina Tozzini, Chia-en A. Chang and 

J. Andrew McCammon, HIV-1 protease substrate binding 

and product release pathways explored with coarse-grained 

molecular dynamics, Biophys. J, 92, 4179-4187 (2007). 

Arneh Babakhani, Alemayehu A. Gorfe, Justin Gullingsrud, 

Judy E. Kim and J. Andrew McCammon, Peptide insertion, 

positioning, and stabilization in a membrane: insight 

from an all-atom molecular dynamics simulation, Biopolymers, 

85, 490-497 (2007). 

Jesper Soerensen, Donald Hamelberg, Birgit Schioett and 

J. Andrew McCammon, Comparative MD analysis of the stability 

of transthyretin providing insight into the fibrillation 

mechanism, Biopolymers, 86, 73-82 (2007). 

Chia-En A. Chang, Joanna Trylska, Valentina Tozzini and 

J. Andrew McCammon, Binding pathways of ligands to 

HIV-1 protease: coarse-grained and atomistic simulations, 

Chem. Biol. Drug Des, 69, 5-13 (2007). 

Cesar Augusto F. de Oliveira, Maurice Zissen, John Mongon 

and J. Andrew Mccammon, Molecular dynamics simulations 

of metalloproteinases types 2 and 3 reveal differences 

in the dynamic behavior of the S1’ binding pocket, Curr. 

Pharm. Des, 13, 3471-3475 (2007). 

Richard H. Henchman and J. Andrew McCammon, Protein 

structural flexibility: molecular motions, Handb. Proteins, 1, 

Cesar Augusto F. de Oliveira, Donald Hamelberg and J. 

Andrew McCammon, Estimating kinetic rates from acceler- 

ated molecular dynamics simulations: Alanine dipeptide in 

explicit solvent as a case study, J. Chem. Phys, 127, 175105/ 

1-175105/8 (2007). 

Benzhuo Lu and J. Andrew McCammon, Improved 

Boundary Element Methods for Poisson-Boltzmann Electrostatic 

Potential and Force Calculations, J. Chem. Theory 

Comput, 3, 1134-1142 (2007). 

John Mongan, Carlos Simmerling, J. Andrew McCammon, 

David A. Case and Alexey Onufriev, Generalized Born Model 

with a Simple, Robust Molecular Volume Correction, J. 

Chem. Theory Comput, 3, 156-169 (2007). 

J. Swanson, J. Wagoner, N. Baker and J. A. McCammon, 

Optimizing the poisson dielectric boundary with explicit solvent 

simulations: lessons learned with atom-centered dielectric 

functions, J. Chem. Theory Comput, 3, 170-183 (2007). 

Benzhuo Lu, Xiaolin Cheng and J. Andrew McCammon, 

New-version-fast-multipole-method” accelerated electrostat- 

ic calculations in biomolecular systems, J. Comput. Phys, 

226, 1348-1366 (2007). 

Alemayehu A. Gorfe, Michael Hanzal-Bayer, Daniel 

Abankwa, John F. Hancock and J. Andrew McCammon, 

Structure and Dynamics of the Full-Length Lipid-Modified 

H-Ras Protein in a 1,2-Dimyristoylglycero-3-phosphocholine 

Bilayer, J. Med. Chem, 50, 674-684 (2007). 

Barry J. Grant, J. Andrew McCammon, Leo S. D. Caves 

and Robert A. Cross, Multivariate Analysis of Conserved Se- 

quence-Structure Relationships in Kinesins: Coupling of the 

Active Site and a Tubulin-binding Sub-domain, J. Mol. Biol, 

368, 1231-1248 (2007). 

Valentina Tozzini, Joanna Trylska, Chia-en Chang and J. 

Andrew McCammon, Flap opening dynamics in HIV-1 pro- 

tease explored with a coarse-grained model, J. Struct. Biol, 

157, 606-615 (2007). 

Philip R. Leduc, Michael S. Wong, Placid M. Ferreira, 

Richard E. Groff, Kiryn Haslinger, Michael P. Koonce, Woo 

Y. Lee, J. Christopher Love, J. Andrew McCammon, Nancy 

A. Monteiro-Riviere, Vincent M. Rotello, Gary W. Rubloff, 

Robert Westervelt and Minami Yoda, Towards an in vivo bi- 

ologically inspired nanofactory, Nat. Nanotechnol, 2, 3-7 

(2007). 

Rommie E. Amaro, Robert V. Swift and J. Andrew 

McCammon, Functional and structural insights revealed by 

molecular dynamics simulations of an essential RNA editing 

ligase in Trypanosoma brucei, PLoS Neglected Trop. Dis, 1, 

No pp. given (2007). 

Ivaylo Ivanov, John A. Tainer and J. Andrew McCammon, 

Unraveling the three-metal-ion catalytic mechanism of the 

DNA repair enzyme endonuclease IV, Proc. Natl. Acad. Sci. 

U. S. A, 104, 1465-1470 (2007). 

Donald Hamelberg, Tongye Shen and J. Andrew McCammon, 

A proposed signaling motif for nuclear import in 

mRNA processing via the formation of arginine claw, Proc. 

Natl. Acad. Sci. U. S. A, 104, 14947-14951 (2007). 

Jacky Chi Ki Ngo, Justin Gullingsrud, Kayla Giang, Me- 

Femtosecond lasers; hemoglobin, guanylatecyclase and 166-171 (2007). linda Jean Yeh, Xiang-Dong Fu, Joseph A. Adams, J. Another 

heme enzymes; inorganic photochemistry, chemi- Alemayehu A. Gorfe, Arneh Babakhani and J. Andrew drew McCammon and Gourisankar Ghosh, SR Protein Ki- 

cal sensors, and general photophysical chemistry. TEL: 

(858) 534-3199 FAX: (858) 822-2563 

Email: dmagde@ucsd.edu 

Edith C. Glazer, Douglas Magde and Yitzhak Tor, Ruthenium 

Complexes That Break the Rules: Structural Features 

Controlling Dual Emission, J. Am. Chem. Soc, 129, 8544- 

8551 (2007). 

McCammon, H-ras Protein in a Bilayer: Interaction and 

Structure Perturbation, J. Am. Chem. Soc, 129, 12280-12286 

(2007). 

Yuhui Cheng, Xiaolin Cheng, Zoran Radic and J. Andrew 

McCammon, Acetylcholinesterase: Mechanisms of Covalent 

Inhibition of Wild-Type and H447I Mutant Determined by 

Computational Analyses, J. Am. Chem. Soc, 129, 6562-6570 

(2007). 

nase 1 Is Resilient to Inactivation, Structure (Cambridge, 

MA, U. S.), 15, 123-133 (2007). 

Robert V. Swift and J. Andrew McCammon, Catalytically 

Requisite Conformational Dynamics in the mRNA-Capping 

Enzyme Probed by Targeted Molecular Dynamics, Biochem- 

istry, 47, 4102-4111 (2008). 

Alemayehu A. Gorfe, Chia-en A. Chang, Ivaylo Ivanov 

and J. Andrew McCammon, Dynamics of the acetylcholin- 

MARTI, K. (b.1936) Professor Emeritus. M.S, 1963, 

University of Berne; Ph.D, 1965, University of Berne. 

Postgraduate Resident Chemist, 1965-1968, University 

of California, San Diego; Guggenheim Fellowship, 1976. 

Variations in isotopic compositions and origin of the 

Rommie E. Amaro, David D. L. Minh, Lily S. Cheng, William 

M. Lindstrom, Jr., Arthur J. Olson, Jung-Hsin Lin, 

Wilfred W. Li and J. Andrew McCammon, Remarkable Loop 

Flexibility in Avian Influenza N1 and Its Implications for 

Antiviral Drug Design, J. Am. Chem. Soc, 129, 7764-7765 

(2007). 

esterase tetramer, Biophys. J, 94, 1144-1154 (2008). 

Alemayehu A. Gorfe, Riccardo Baron and J. Andrew 

McCammon, Water-membrane partition thermodynamics of 

an amphiphilic lipopeptide: an enthalpy-driven hydrophobic 

effect, Biophys. J, 95, 3269-3277 (2008). 

Yuhui Cheng, Chia-en A. Chang, Zeyun Yu, Yongjie 

chemical elements; extinct elements; nuclear reactions Ivaylo Ivanov, Xiaolin Cheng, Steven M. Sine and J. An- Zhang, Meihao Sun, Thomas S. Leyh, Michael J. Holst and J. 

induced by cosmic rays; history of the moon, history of drew McCammon, Barriers to Ion Translocation in Cationic Andrew McCammon, Diffusional channeling in the sulfate- 

Mars, the meteorites and the solar system. TEL: (858) 

534-2939 FAX: (858) 534-7441 

Email: kmarti@ucsd.edu 


and Anionic Receptors from the Cys-Loop Family, J. Am. 

Chem. Soc, 129, 8217-8224 (2007). 

Li-Tien Cheng, Joachim Dzubiella, J. Andrew McCammon 

and Bo Li, Application of the level-set method to the implicit 

solvation of nonpolar molecules, J. Chem. Phys, 127, 

activating complex: combined continuum modeling and 

coarse-grained Brownian dynamics studies, Biophys. J, 95, 

4659-4667 (2008). 

Sergio E. Wong, Riccardo Baron and J. Andrew McCammon, 

Hot-spot residues at the E9/Im9 interface help binding 

A. J. T. Jull, D. Lal, S. Taylor, R. Wieler, A. Grimberg, L. 084503/1-084503/10 (2007). via different mechanisms, Biopolymers, 89, 916-920 (2008). 

Vacher, L. R. McHargue, S. P. H. T. Freeman, C. Maden, C. Ilja V. Khavrutskii and J. Andrew McCammon, General- Melissa R. Landon, Rommie E. Amaro, Riccardo Baron, 

Schnabel, S. Xu, R. C. Finkel, K. J. Kim and K. Marti, ized gradient-augmented harmonic Fourier beads method Chi Ho Ngan, David Ozonoff, J. Andrew McCammon and 

3He, 20,21,22Ne, 14C, 10Be, 26Al, and 36Cl in magnetic fractions of with multiple atomic and/or center-of-mass positional re- Sandor Vajda, Novel druggable hot spots in avian influenza 

cosmic dust from Greenland and Antarctica, Meteorit. Plan- straints, J. Chem. Phys, 127, 124901/1-124901/12 (2007). neuraminidase H5N1 revealed by computational solvent 

et. Sci, 42, 1831-1840 (2007). 

Benzhuo Lu, Y. C. Zhou, Gary A. Huber, Stephen D. mapping of a reduced and representative receptor ensemble, 

K. V. Ponganis and K. Marti, Nitrogen components in Bond, Michael J. Holst and J. Andrew McCammon, Electro- Chem. Biol. Drug Des, 71, 106-116 (2008). 

IAB/IIICD iron meteorites, Meteorit. Planet. Sci, 42, 331- diffusion: A continuum modeling framework for biomolecu- Benzhuo Lu and J. Andrew McCammon, Molecular sur- 

346 (2007). 

lar systems with realistic spatiotemporal resolution, J. Chem. face-free continuum model for electrodiffusion processes, 

Phys, 127, 135102/1-135102/17 (2007). Chem. Phys. Lett, 451, 282-286 (2008). 

MCCAMMON, J. ANDREW (b.1947) Joseph E. 

Mayer Professor of Theoretical Chemistry. A.B, 1969, 

Pomona College; A.M, 1970, Harvard University; Ph.D, 

1976, Harvard University. NSF Postdoctoral Fellowship, 

1976-1977, Harvard University; NIH Postdoctoral Fel- 

lowship, 1977-1978, Harvard University. Biophysics/ 

Biophysical Chemistry; Chemical Physics. We use theoretical 

and computational methods to study biological 

molecules. Most of our work uses methods from statistical 

mechanics. These methods range from computer simulations 

of molecular behavior to purely theoretical 

David D. L. Minh, Donald Hamelberg and J. Andrew 

McCammon, Accelerated entropy estimates with accelerated 

dynamics, J. Chem. Phys, 127, 154105/1-154105/5 (2007). 

David S. Cerutti, Nathan A. Baker and J. Andrew McCammon, 

Solvent reaction field potential inside an uncharged 

globular protein: A bridge between implicit and explicit solvent 

models?, J. Chem. Phys, 127, 155101/1-155101/12 

(2007). 

Donald Hamelberg, Cesar Augusto F. de Oliveira and J. 

Andrew McCammon, Sampling of slow diffusive conformational 

transitions with accelerated molecular dynamics, J. 

Chem. Phys, 127, 155102/1-155102/9 (2007). 

Jennifer M. Bui and J. Andrew McCammon, Intrinsic conformational 

flexibility of acetylcholinesterase, Chem.-Biol. 

Interact, 175, 303-304 (2008). 

Riccardo Baron and J. Andrew McCammon, (Thermo)dynamic 

role of receptor flexibility, entropy, and motional 

correlation in protein-ligand binding, ChemPhysChem, 9, 

983-988 (2008). 

B. Z. Lu, Y. C. Zhou, M. J. Holst and J. A. McCammon, 

Recent progress in numerical methods for the Poisson-Boltz- 

mann equation in biophysical applications, Commun. Comp. 

Physics, 3, 973-1009 (2008). 

Donald Hamelberg and J. Andrew McCammon, Dealing


with bound waters in a site: do they leave or stay?, Comput. dent Structural and Dynamical Features of Ras Proteins, Phorbas sp. Assignment of the Configurations of Phorbasides 

Struct. Approaches Drug Discovery, 95-110 (2008). 

Structure (Cambridge, MA, U. S.), 16, 885-896 (2008). A and B by Quantitative CD, J. Am. Chem. Soc, 129, 4150- 

Daniel Abankwa, Michael Hanzal-Bayer, Nicolas Ariotti, 

4151 (2007). 

Sarah J. Plowman, Alemayehu A. Gorfe, Robert G. Parton, J. David Cerutti, Models for solvated biomolecular struc- Evan W. Rogers and Tadeusz F. Molinski, Highly Polar 

Andrew McCammon and John F. Hancock, A novel switch 

region regulates H-ras membrane orientation and signal out- 

put, EMBO J, 27, 727-735 (2008). 

Z. Yu, M. Holst and J. A. McCammon, High-fidelity geo- 

metric modelling for biomedicine and other applications, Finite 

Elements in Analysis and Design, 44, 715-723 (2008). 

Alemayehu A. Gorfe and J. Andrew McCammon, Similar 

Membrane Affinity of Mono- and Di-S-acylated Ras Mem- 

brane Anchors: A New Twist in the Role of Protein Lipidation, 

J. Am. Chem. Soc, 130, 12624-12625 (2008). 

Ilja V. Khavrutskii, Joachim Dzubiella and J. Andrew 

McCammon, Computing accurate potentials of mean force in 

electrolyte solutions with the generalized gradient-augmented 

harmonic Fourier beads method, J. Chem. Phys, 128, 

044106/1-044106/13 (2008). 

Cesar Augusto F. de Oliveira, Donald Hamelberg and J. 

Andrew McCammon, Coupling Accelerated Molecular Dynamics 

Methods with Thermodynamic Integration Simulations, 

J. Chem. Theory Comput, 4, 1516-1525 (2008). 

Ilja V. Khavrutskii, Mikolai Fajer and J. Andrew McCam- 

mon, Intrinsic Free Energy of the Conformational Transition 

of the KcsA Signature Peptide from Conducting to Nonconducting 

State, J. Chem. Theory Comput, 4, 1541-1554 

(2008). 

Mikolai Fajer, Donald Hamelberg and J. Andrew McCammon, 

Replica-Exchange Accelerated Molecular Dynamics 

(REXAMD) Applied to Thermodynamic Integration, J. 

Chem. Theory Comput, 4, 1565-1569 (2008). 

Rommie E. Amaro, Riccardo Baron and J. Andrew 

McCammon, An improved relaxed complex scheme for receptor 

flexibility in computer-aided drug design, J. Comput.tures. 

(D) 

David Minh, Free energy reconstruction from irreversible 

single-molecule pulling experiments. (D) 

Yuhui Cheng, Multiscale simulations of biochemically reacting 

systems. (D) 

MCMORRIS, TREVOR C. (b.1930) Professor. B.S, 

1952, London University; M.Sc, 1955, London University; 

Ph.D, 1958, London University. Interuniversity Fellow, 

Organic Chemistry, 1958-1959, London University, 

Imperial College; Fellowship, Organic Chemistry, 1959- 

1960, University of Western Ontario. Chemistry of steroids 

and other natural products; isolation, structure elucidation 

and synthesis of sex hormones and other biologically 

active substances in fungi and higher plants; illudin 

analogs as new anticancer drugs. TEL: (858) 534- 

4178 FAX: (858) 534-4864 

Email: tmcmorris@ucsd.edu 


Trevor C. McMorris, Ramesh Chimmani, Mahender Gurram, 

Michael D. Staake and Michael J. Kelner, Synthesis and 

antitumor activity of amine analogs of irofulven, Bioorg. 

Med. Chem. Lett, 17, 6770-6772 (2007). 

MOLINA, MARIO J. (b.1943) Professor. Nobel 

Prize, 1995, University of California, Berkeley. TEL: 

(858) 534-1696 FAX: (858) 534-4864 


C04871 

Email: mjmolina@ucsd.edu 

Spiroisoxazolines from the Sponge Aplysina fulva, J. Nat. 

Prod, 70, 1191-1194 (2007). 

Tatyana N. Makarieva, Pavel S. Dmitrenok, Alexander M. 

Zakharenko, Vladimir A. Denisenko, Alla G. Guzii, Ronghua 

Li, Colin K. Skepper, Tadeusz F. Molinski and Valentin A. 

Stonik, Rhizochalins C and D from the Sponge Rhizochalina 

incrustata. A Rare threo-Sphingolipid and a Facile Method 

for Determination of the Carbonyl Position in �,�-Bifunctionalized 

Ketosphingolipids, J. Nat. Prod, 70, 1991-1998 

(2007). 

Jonel P. Saludes, Sarah C. Lievens and Tadeusz F. Molinski, 

Occurrence of the �-Glucosidase Inhibitor 1,4-Dideoxy- 

1,4-imino-D-arabinitol and Related Iminopentitols in Marine 

Sponges, J. Nat. Prod, 70, 436-438 (2007). 

Brandon I. Morinaka, Colin K. Skepper and Tadeusz F. 

Molinski, Ene-yne Tetrahydrofurans from the Sponge Xestospongia 

muta. Exploiting a Weak CD Effect for Assignment 

of Configuration, Org. Lett, 9, 1975-1978 (2007). 

Evan W. Rogers and Tadeusz F. Molinski, Asymmetric 

Synthesis of Diastereomeric Diaminoheptanetetraols. A Proposal 

for the Configuration of (+)-Zwittermicin A, Org. Lett, 

9, 437-440 (2007). 

Brandon I. Morinaka, Makoto N. Masuno, Joseph R. Paw- 

lik and Tadeusz F. Molinski, Amaranzole A, a New N-Imidazolyl 

Steroid from Phorbas amaranthus, Org. Lett, 9, 5219- 

5222 (2007). 

Brandon I. Morinaka and Tadeusz F. Molinski, Exciton 

coupling circular dichroism of an allylic N-imidazolyl group 

in amaranzole A, a marine natural product from Phorbas 

amaranthus, Chirality, 20, 1066-1070 (2008). 

Sepehr Dadsetan, Liudmila Zakharova, Tadeusz F. Molin- 

ski and Alla F. Fomina, Store-operated Ca2+ Aided Mol. Des, 22, 693-705 (2008). 


Influx Causes 

Ca2+ Release from the Intracellular Ca2+ Y. Zhou, M. Holst and J. A. McCammon, A nonlinear 

elasticity model of macromolecular conformational change 

induced by electrostatic forces, J. Math. Analysis Applic, 

340, 135-164 (2008). 

Lily S. Cheng, Rommie E. Amaro, Dong Xu, Wilfred W. 

Li, Peter W. Arzberger and J. Andrew McCammon, Ensemble-Based 

Virtual Screening Reveals Potential Novel Antiviral 

Compounds for Avian Influenza Neuraminidase, J. Med. 

Chem, 51, 3878-3894 (2008). 

Zeyun Yu, Michael J. Holst, Yuhui Cheng and J. Andrew 

McCammon, Feature-preserving adaptive mesh generation 

for molecular shape modeling and simulation, J. Mol. Graphics 

Modell, 26, 1370-1380 (2008). 

Arneh Babakhani, Alemayehu A. Gorfe, Judy E. Kim and 

J. Andrew McCammon, Thermodynamics of Peptide Insertion 

and Aggregation in a Lipid Bilayer, J. Phys. Chem. B, 

112, 10528-10534 (2008). 

Riccardo Baron, Sergio E. Wong, Cesar A. F. de Oliveira 

and J. Andrew McCammon, E9-Im9 Colicin DNase-Immunity 

Protein Biomolecular Association in Water: A Multiple- 

Copy and Accelerated Molecular Dynamics Simulation 

Study, J. Phys. Chem. B, 112, 16802-16814 (2008). 

Y. C. Zhou, Benzhuo Lu, Gary A. Huber, Michael J. Holst 

and J. Andrew McCammon, Continuum Simulations of Acetylcholine 

Consumption by Acetylcholinesterase: A Poisson- 

Nernst-Planck Approach, J. Phys. Chem. B, 112, 270-275 

(2008). 

Jianwei Che, Joachim Dzubiella, Bo Li and J. Andrew 

McCammon, Electrostatic Free Energy and Its Variations in 

Implicit Solvent Models, J. Phys. Chem. B, 112, 3058-3069 

(2008). 

Rainer Volkamer, Federico San Martini, Luisa T. Molina, 

Dara Salcedo, Jose L. Jimenez and Mario J. Molina, A missing 

sink for gas-phase glyoxal in Mexico City: formation of 

secondary organic aerosol, Geophys. Res. Lett, 34, L19807/1- 

L19807/5 (2007). 

Katja Dzepina, Janet Arey, Linsey C. Marr, Douglas R. 

Worsnop, Dara Salcedo, Qi Zhang, Timothy B. Onasch, Lui- 

sa T. Molina, Mario J. Molina and Jose L. Jimenez, Detection 

of particle-phase polycyclic aromatic hydrocarbons in 

Mexico City using an aerosol mass spectrometer, Int. J. Mass 

Spectrom, 263, 152-170 (2007). 

Andrey V. Ivanov, Sofia Trakhtenberg, Allan K. Bertram, 

Yulii M. Gershenzon and Mario J. Molina, OH, HO2, and 

Ozone Gaseous Diffusion Coefficients, J. Phys. Chem. A, 

111, 1632-1637 (2007). 

V. Faye McNeill, Franz M. Geiger, Thomas Loerting, 

Bernhardt L. Trout, Luisa T. Molina and Mario J. Molina, Interaction 

of Hydrogen Chloride with Ice Surfaces: The Effects 

of Grain Size, Surface Roughness, and Surface Disor- 

der, J. Phys. Chem. A, 111, 6274-6284 (2007). 

Ryan C. Moffet, Yury Desyaterik, Rebecca J. Hopkins, 

Alexei V. Tivanski, Mary K. Gilles, Y. Wang, V. Shutthan- 

andan, Luisa T. Molina, Rodrigo Gonzalez Abraham, Kirsten 

S. Johnson, Violeta Mugica, Mario J. Molina, Alexander 

Laskin and Kimberly A. Prather, Characterization of Aerosols 

Containing Zn, Pb, and Cl from an Industrial Region of 

Mexico City, Environ. Sci. Technol, 42, 7091-7097 (2008). 

Jong-Ho Park, Andrey V. Ivanov and Mario J. Molina, Effect 

of Relative Humidity on OH Uptake by Surfaces of Atmospheric 

Importance, J. Phys. Chem. A, 112, 6968-6977 

Channels That Is 

Required for T Cell Activation, J. Biol. Chem, 283, 12512- 

12519 (2008). 

Colin K. Skepper and Tadeusz F. Molinski, Long-Chain 

2H-Azirines with Heterogeneous Terminal Halogenation 

from the Marine Sponge Dysidea fragilis, J. Org. Chem, 73, 

2592-2597 (2008). 

John B. MacMillan, Xiong-Zhou Guang, Colin K. Skepper 

and Tadeusz F. Molinski, Phorbasides A-E, Cytotoxic 

Chlorocyclopropane Macrolide Glycosides from the Marine 

Sponge Phorbas sp. CD Determination of C-Methyl Sugar 

Configurations, J. Org. Chem, 73, 3699-3706 (2008). 

Colin K. Skepper, Doralyn S. Dalisay and Tadeusz F. Mo- 

linski, Synthesis and Antifungal Activity of (-)-(Z)-Dysidazirine, 

Org. Lett, 10, 5269-5271 (2008). 

Evan W. Rogers, Zwittermicin A: Determination of its 

complete configuration and total synthesis of its enantiomer. 

(D) 

Makoto N. Masuno, Synthesis and biological evaluation of 

brominated marine natural product analogs that modulate teh 

skeletal muscle FKBP12/calcium channel complex. (D) 

MÜLLER, ULRICH F. (b.1969) Assistant Professor. 

Ph.D, 2000, Darmstadt University of Technology. Postdoctoral 

Fellow, 2001-2006, Whitehead Institute. Biochemistry. 

TEL: (858) 534-6823 FAX: (858) 822-4442 

Web: www-chem.ucsd.edu/Faculty/bios/muller.html 

Email: ufmuller@ucsd.edu 


David D. L. Minh and J. Andrew McCammon, Springs and 

Speeds in Free Energy Reconstruction from Irreversible Single-Molecule 

Pulling Experiments, J. Phys. Chem. B, 112, 

5892-5897 (2008). 

Z. Yu, M. Holst, T. Hayashi, C. L. Bajaj, M. H. Ellisman, 

J. A. McCammon and M. Hoshijima, Three-dimensional geometric 

modeling of membrane-bound organelles in ventricular 

myocytes: Bridging the gap between microscopic imaging 

and mathematical simulation, J. Struct. Biol, 164, 304-313 

(2008). 

Shamila S. Gunatilleke, Cesar Augusto F. Oliveira, J. Andrew 

McCammon and Amy M. Barrios, Inhibition of cathepsin 

B by Au(I) complexes: a kinetic and computational study, 

JBIC, J. Biol. Inorg. Chem, 13, 555-561 (2008). 

Cameron Mura and J. Andrew McCammon, Molecular dynamics 

of a �B DNA element: base flipping via cross-strand 

intercalative stacking in a microsecond-scale simulation, 

Nucl. Acids Res, 36, 4941-4955 (2008). 

Hai-Long Wang, Xiaolin Cheng, Palmer Taylor, J. Andrew 

McCammon and Steven M. Sine, Control of cation permeation 

through the nicotinic receptor channel, PLoS Comput. 

Biol, 4, No pp. given (2008). 

(2008). 

MOLINSKI, TADEUSZ F. (b.1957) Professor. B.Sc, 

1978, Monash University; Ph.D, 1985, Australian National 

University. Postdoctoral Fellow, 1984-1987, 

Scripps Institution of Oceanography; Postdoctoral Fellow, 

1987-1988, University of Utah; Visiting Chemist, 

1988, UC San Diego; Assistant Professor, 1989-1995, 

UC Davis; Associate Professor, 1995-1997, UC Davis; 

Professor, 1997-2005, UC Davis. Natural Products 

Chemistry; Organic Chemistry. Structure and synthesis 

of marine natural products. Chiroptical methods in or- 

ganic stereochemistry. NMR. ‘Nanomole-scale’ natural 

products. Biological chemistry. Discovery of therapeutics 

for AIDS-related disease and cancer. TEL: (858) 

534-7115 FAX: (858) 822-0386 

Web: www-chem.ucsd.edu/Faculty/bios/molinski.html 

Email: tmolinski@ucsd.edu 

Tianzhong Yang, Eric Esteve, Isaac N. Pessah, Tadeusz F. 

Molinski, Paul D. Allen and Jose R. Lopez, Elevated resting 

[Ca 

NAKAGAWA, TERUNAGA Assistant Professor. 

M.D, 1996, University of Tokyo; Ph.D, 2000, University 

of Tokyo. HFSP long term fellow, 2000-2001, MGH, 

Harvard Medical School; HFSP long term fellow, 2001- 

2003, MIT; HHMI post-doctoral fellow, 2003-2005, 

MIT. Biochemistry; Neuroscience. Structure and func- 

tion of glutamate receptors. TEL: (858) 534-2974 FAX: 

(858) 534-7042 

K. Takao, K. Okamoto, T. Nakagawa, R. L. Neve, T. Nagai, 

A. Miyawaki, T. Hashikawa, S. Kobayashi and Y. Hayashi, 

Visualization of synaptic Ca2+ /calmodulin-dependent 

protein kinase II activity in living neurons, J. Neurosci, 25, 

3107-3112 (2005). 

T. Nakagawa, Y. Cheng, E. Ramm, M. Sheng and T. Walz, 

Structure and different conformational states of native 

AMPA receptor complexes, Nature, 433, 545-549 (2005). 

X. Chen, L. Vinade, R. D. Leapman, J. D. Petersen, T. 

Nakagawa, T. M. Phillips, M. Sheng and T. S. Reese, Mass 

of the post synaptic density and enumeration of three key 

molecules, PNAS, 102, 11551-11556 (2005). 

2+]i 

Chia-en A. Chang, William A. McLaughlin, Riccardo Baron, 

Wei Wang and J. Andrew McCammon, Entropic contributions 

and the influence of the hydrophobic environment in 

promiscuous protein-protein association, Proc. Natl. Acad. 

Sci. U. S. A, 105, 7456-7461 (2008). 

R. Amaro, A. Schnaufer, W. Hol, K. Stuart and J. A. 

McCammon, Discovery of drug-like inhibitors of an essential 

RNA editing ligase in Trypanosoma brucei, Proc. Natl. 

in myotubes expressing malignant hyperthermia 

RyR1 cDNAs is partially restored by modulation of passive 

calcium leak from the SR, Am. J. Physiol, 292, C1591-C1598 

(2007). 

Anne Schuetz, Jochen Junker, Andrei Leonov, Oliver F. 

Lange, Tadeusz F. Molinski and Christian Griesinger, 

Stereochemistry of sagittamide A from residual dipolar coupling 

enhanced NMR, J. Am. Chem. Soc, 129, 15114-15115 

(2007). 

T. Nakagawa, Y. Cheng, M. Sheng and T. Walz, Three-dimensional 

structure of an AMPA receptor without associated 

stargazin/TARP proteins, Biol. Chem, 387, 179-187 (2006). 

T. Nakagawa, M. I. Feliu-Mojer, P. Wulf, C. Lois, M. 

Sheng and C. C. Hoogenraad, Generation of lentiviral transgenic 

rats expressing glutamate receptor binding protein 1 

(GRIP1) in brain, spinal cord, and testis, J. Neurosci. Methods, 

152, 1-9 (2006). 

D. Cheng, C. C. Hoogenraad, J. Rush, E. Ramm, M. A. 

Acad. Sci. USA, 106, 17278–17283 (2008). Colin K. Skepper, John B. MacMillan, Guang-Xiong Schlager, D. M. Duong, P. Xu, S. R. Wijayawardana, J. Han- 

Alemayehu A. Gorfe, Barry J. Grant and J. Andrew Zhou, Makoto N. Masuno and Tadeusz F. Molinski, felt, T. Nakagawa, M. Sheng and J. Peng, Relative and abso- 

McCammon, Mapping the Nucleotide and Isoform-Depen- Chlorocyclopropane Macrolides from the Marine Sponge lute quantification of postsynaptic density proteome isolated


from rat forebrain and cerebellum, Mol. Cell. Proteomics, Wenyuan Wang, Jeffrey K. Takimoto, Gordon V. Louie, tion and Chemical Transformation, J. Am. Chem. Soc, 130, 

5(6), 1158-1170 (2006). Thomas J. Baiga, Joseph P. Noel, Kuo-Fen Lee, Paul A. Sle- 2806-2816 (2008). 

Audrey Fischer, Consuelo Garcia-Rodriguez, Isin Geren, singer and Lei Wang, Genetically encoding unnatural amino Oanh P. Lam, Christian Anthon, Frank W. Heinemann, Jo- 

Jianlong Lou, James D. Marks, Terunaga Nakagawa and 

Mauricio Montal, Molecular Architecture of Botulinum Neurotoxin 

E Revealed by Single Particle Electron Microscopy, 

J. Biol. Chem, 283, 3997-4003 (2008). 

Terunaga Nakagawa, Identification and characterization of 

novel kinesin super family (KIF) proteins. (D) 

NEWSAM, JOHN M. Adjunct Professor. B.A, 1976, 

acids for cellular and neuronal studies, Nat. Neurosci, 10, 

1063-1072 (2007). 

Marina Varbanova, Shinjiro Yamaguchi, Yue Yang, 

Katherine McKelvey, Atsushi Hanada, Roy Borochov, Fei 

Yu, Yusuke Jikumaru, Jeannine Ross, Diego Cortes, Choong 

Je Ma, Joseph P. Noel, Lew Mander, Vladimir Shulaev, Yuji 

Kamiya, Steve Rodermel, David Weiss and Eran Pichersky, 

Methylation of gibberellins by Arabidopsis GAMT1 and 

GAMT2, Plant Cell, 19, 32-45 (2007). 

seph M. O’Connor and Karsten Meyer, Structural and Spec- 

troscopic Characterization of a Charge-Separated Uranium 

Benzophenone Ketyl Radical Complex, J. Am. Chem. Soc, 

130, 6567-6576 (2008). 

Joseph M. O’Connor and Seth J. Friese, Transition-Metal 

Hydrides as Hydrogen Atom Donors: Stronger Metal-Hydrogen 

Bonds Can Be Advantageous, Organometallics, 27, 

4280-4281 (2008). 

Oxford University; M.A, 1980, Oxford University; 

D.Phil, 1980, Oxford University. Biomaterials; Materials 

Chemistry. Development and application of high 

throughput experimentation for materials applications. 

Use of HTE in discovery of catalytic materials. Use of 

HTE in development of novel drug and other products 

for application to the skin. Innovation. TEL: (858) 677- 

6732 FAX: (858) 677-6737 

Email: jnewsam@ucsd,edu 

J. M. Newsam, R. D. King-Smith, A. Jain, P. Karande, I. 

Feygin, J. Burbaum, T. R. Gowrishankar, M. Sergeeva and S. 

Mitragotri, Screening soft materials for their effect on skin 

barrier function by high throughput experimentation, J. Ma- 

terials Chemistry, 15, 3061-3068 (2005). 

R. D. King-Smith and J. M. Newsam, Accelerated development 

of topical and transdermal delivery systems, Skin Delivery 

Systems: Cosmetics, Dermatologicals, and Transder- 

Gordon V. Louie, Thomas J. Baiga, Marianne E. Bowman, 

Takao Koeduka, John H. Taylor, Snejina M. Spassova, Eran 

Pichersky and Joseph P. Noel, Structure and reaction mecha- 

nism of basil eugenol synthase, PLoS One, 2, No pp. given 

(2007). 

Thomas J. Baiga, Haibing Guo, Yalan Xing, George A. 

O’Doherty, Andrew Dillin, Michael B. Austin, Joseph P. 

Noel and James J. La Clair, Metabolite Induction of Caenorhabditis 

elegans Dauer Larvae Arises via Transport in the 

Pharynx, ACS Chem. Biol, 3, 294-304 (2008). 

Takuto Kumano, Stephane B. Richard, Joseph P. Noel, 

Makoto Nishiyama and Tomohisa Kuzuyama, Chemoenzymatic 

syntheses of prenylated aromatic small molecules using 

Streptomyces prenyltransferases with relaxed substrate 

specificities, Bioorg. Med. Chem, 16, 8117-8126 (2008). 

Yi Tao, Jean-Luc Ferrer, Karin Ljung, Florence Pojer, 

Fangxin Hong, Jeff A. Long, Lin Li, Javier E. Moreno, Mar- 

OESTERREICHER, H. (b.1939) Professor. Ph.D, 

1965, University of Vienna. Resident Associate, 1965- 

1966, University of Pittsburgh; Resident Associate, 

1966-1967, Brookhaven National Laboratory; Resident 

Associate, 1967, Cornell University. Structural, magnetic 

and superconducting properties of metallic and semiconducting 

systems. TEL: (858) 534-4179 FAX: (858) 534- 

4864 

Email: joesterreicher@ucsd.edu 


H. Oesterreicher, Superconductivity and Structure, J. Supercond. 

Novel Magn, 20, 201-213 (2007). 

H. Oesterreicher, Phenomenological laws and charge order 

concepts in high Tc superconductors, Phys. C (Amsterdam, 

Neth.), 460, 362-363 (2007). 

H. Oesterreicher, Plane isolation model for superconduct- 

mals, 297-308 (2006). 

ianne E. Bowman, Lauren J. Ivans, Youfa Cheng, Jason Lim, ing Tc prediction using an parent-calibration’ obtained for 

Yunde Zhao, Carlos L. Ballare, Goran Sandberg, Joseph P. YBa2CuCu2Oy and applied to other model systems, Solid 

Noel and Joanne Chory, Rapid synthesis of auxin via a new 

NGUYEN-HUU, XUONG (b.1933) Professor Emeri- State Commun, 142, 583-586 (2007). 

tryptophan-dependent pathway is required for shade avoidtus. 

B.S, 1955, Marseille EE Sch; M.S, 1958, Paris EE ance in plants, Cell (Cambridge, MA, U. S.), 133, 164-176 

Sch. and University of Paris; M.A, 1961, University of (2008). 

OPELLA, STANLEY J. (b.1947) Professor. B.S, 

California, Berkeley; Ph.D, 1962, University of Califor- Alessandra S. Eustaquio, Johannes Harle, Joseph P. Noel 1969, University of Kentucky; Ph.D, 1974, Stanford 

nia, Berkeley. Determination of 3-dimensional structures and Bradley S. Moore, S-adenosyl-L-methionine hydrolase University. Postdoctoral Fellow, 1975-1976, M. I. T. 

of protein using x-ray diffraction method; development (adenosine-forming), a conserved bacterial and archeal pro- NMR Spectroscopy; Structural Biology. Development 

of new instruments. TEL: (858) 534-2501 FAX: (858) tein related to SAM-dependent halogenases, ChemBioChem, and application of NMR spectroscopy for the study of 

534-7042 

9, 2215-2219 (2008). 

proteins. TEL: (858) 822-4820 FAX: (858) 822-4821 

Email: nxuong@ucsd.edu 

Michael B. Austin, Paul E. O’Maille and Joseph P. Noel, Web: www-chem.ucsd.edu/research/profile.cfm?cid= 

No publication information submitted for this edition. Evolving biosynthetic tangos negotiate mechanistic land- C03864 

scapes, Nat. Chem. Biol, 4, 217-222 (2008). Email: sopella@ucsd.edu 

Paul E. O’Maille, Arthur Malone, Nikki Dellas, B. Andes 

NICOLAOU, K. C. —See Chemistry Section, The 


Scripps Research Institute, Department of Chemistry. 

Hess, Jr., Lidia Smentek, Iseult Sheehan, Bryan T. Greenha- 

NICOLAOU, KYRIACOS 


gen, Joe Chappell, Gerard Manning and Joseph P. Noel, 

Quantitative exploration of the catalytic landscape separating 

divergent plant sesquiterpene synthases, Nat. Chem. Biol, 4, 

617-623 (2008). 

Alessandra S. Eustaquio, Florence Pojer, Joseph P. Noel 

Sonja D. Mueller, Anna A. De Angelis, Torsten H. Walther, 

Stephan L. Grage, Christian Lange, Stanley J. Opella and 

Anne S. Ulrich, Structural characterization of the pore forming 

protein TatAd of the twin-arginine translocase in membranes 

by solid-state 15N-NMR, 

NOEL, JOSEPH P. (b.1964) Adjunct Assistant Professor. 

B.S, 1985, University of Pittsburgh at Johnstown; 

Ph.D, 1990, The Ohio State University. NSF Chemistry 

Fellowship, 1990-1992, Yale University; NIH Fellowship, 

1993-1994, Yale University. Structural and stereochemical 

analysis of signal transduction cascade and 

cyclic terpenoid biosynthesis. TEL: (619) 453-4100 Ext. 

1442 FAX: (619) 452-3683 

Email: noel@sbl.salk.edu 


Yan Zhang, Sebastian Daum, Dirk Wildemann, Xiao Zhen 

Zhou, Mark A. Verdecia, Marianne E. Bowman, Christian 

Lucke, Tony Hunter, Kun-Ping Lu, Gunter Fischer and Joseph 

P. Noel, Structural basis for high-affinity peptide inhibition 

of human Pin1, ACS Chem. Biol, 2, 320-328 (2007). 

Michael B. Austin and Joseph P. Noel, Mechanisms of 

type III polyketide synthase functional diversity: from ‘steric 

modulation’ to the ‘reaction partitioning’ model, ACS Symp. 

Ser, 955, 185-197 (2007). 

Michelle C. Moffitt, Gordon V. Louie, Marianne E. Bowman, 

Janelle Pence, Joseph P. Noel and Bradley S. Moore, 

and Bradley S. Moore, Discovery and characterization of a 

marine bacterial SAM-dependent chlorinase, Nat. Chem. 

Biol, 4, 69-74 (2008). 

Takao Koeduka, Gordon V. Louie, Irina Orlova, Christine 

M. Kish, Mwafaq Ibdah, Curtis G. Wilkerson, Marianne E. 

Bowman, Thomas J. Baiga, Joseph P. Noel, Natalia Dudareva 

and Eran Pichersky, The multiple phenylpropene synthases 

in both Clarkia breweri and Petunia hybrida represent 

two distinct protein lineages, Plant J, 54, 362-374 (2008). 

Nan Zhao, Jean-Luc Ferrer, Jeannine Ross, Ju Guan, Yue 

Yang, Eran Pichersky, Joseph P. Noel and Feng Chen, Structural, 

biochemical, and phylogenetic analyses suggest that indole-3-acetic 

acid methyltransferase is an evolutionarily ancient 

member of the SABATH family, Plant Physiol, 146, 

455-467 (2008). 

Sigal Savaldi-Goldstein, Thomas J. Baiga, Florence Pojer, 

Tsegeye Dabi, Cristina Butterfield, Geraint Parry, Aaron 

Santner, Nihal Dharmasiri, Yi Tao, Mark Estelle, Joseph P. 

Noel and Joanne Chory, New auxin analogs with growth-pro- 

moting effects in intact plants reveal a chemical strategy to 

improve hormone delivery, Proc. Natl. Acad. Sci. U. S. A, 

105, 15190-15195 (2008). 

Biochim. Biophys. Acta, 

Biomembr, 1768, 3071-3079 (2007). 

Sangwon Lee, Stephen B. Howell and Stanley J. Opella, 

NMR and mutagenesis of human copper transporter 1 

(hCtr1) show that Cys-189 is required for correct folding and 

dimerization, Biochim. Biophys. Acta, Biomembr, 1768, 

3127-3134 (2007). 

Stanley J. Opella and Francesca M. Marassi, Nuclear mag- 

netic resonance (NMR): solid state, Handb. Proteins, 2, 

1129-1133 (2007). 

Min-Ju Kim, Sang Ho Park, Stanley J. Opella, Thomas H. 

Marsilje, Pierre-Yves Michellys, H. Martin Seidel and Shin- 

Shay Tian, NMR Structural Studies of Interactions of a 

Small, Nonpeptidyl Tpo Mimic with the Thrombopoietin Re- 

ceptor Extracellular Juxtamembrane and Transmembrane 

Domains, J. Biol. Chem, 282, 14253-14261 (2007). 

Alexander A. Nevzorov, Sang Ho Park and Stanley J. 

Opella, Three-dimensional experiment for solid-state NMR 

of aligned protein samples in high field magnets, J. Biomol. 

NMR, 37, 113-116 (2007). 

Christopher V. Grant, Siu-Ling Sit, Anna A. De Angelis, 

Kelli S. Khuong, Chin H. Wu, Leigh A. Plesniak and Stanley 

J. Opella, An efficient 1H/ 31P double-resonance solid-state 

Discovery of Two Cyanobacterial Phenylalanine Ammonia NMR probe that utilizes a scroll coil, J. Magn. Reson, 188, 

Lyases: Kinetic and Structural Characterization, Biochemistry, 

46, 1004-1012 (2007). 

Shunji Takahashi, Yunsoo Yeo, Bryan T. Greenhagen, 

Tom McMullin, Linsheng Song, Julie Maurina-Brunker, Reinhardt 

Rosson, Joseph P. Noel and Joe Chappell, Metabolic 

engineering of sesquiterpene metabolism in yeast, Biotechnol. 

Bioeng, 97, 170-181 (2007). 

Juan A. Faraldos, Yuxin Zhao, Paul E. O’Maille, Joseph P. 

Noel and Robert M. Coates, Interception of the enzymatic 

O’CONNOR, JOSEPH M. Professor. Ph.D, 1984, 

University of Wisconsin, Madison. Postdoctoral Fellowship, 

1984, University of California, Berkeley. Organic 

Chemistry; Organometallic Chemistry. Bioorganometallic 

chemistry; transition metal catalysts; alkyne and me- 

tallacycle chemistry; mechanistic and synthetic organometallic 

chemistry; metal-mediated organic trasformations. 

TEL: (858) 534-5836 FAX: (858) 534-5383 

279-284 (2007). 

Bibhuti B. Das, T. G. Ajithkumar, Neeraj Sinha, Stanley J. 

Opella and K. V. Ramanathan, Cross- and axial-peak intensi- 

ties in 2D-SLF experiments based on cross-polarization-The 

role of the initial density matrix, J. Magn. Reson, 185, 308- 

317 (2007). 

Neeraj Sinha, Christopher V. Grant, Sang Ho Park, Jona- 

than Miles Brown and Stanley J. Opella, Triple resonance ex- 

periments for aligned sample solid-state NMR of 13C and 15 conversion of farnesyl diphosphate to 5-epi-aristolochene by Email: jmoconno@ucsd.edu 

N 

labeled proteins, J. Magn. Reson, 186, 51-64 (2007). 

using a fluoro substrate analogue: 1-fluorogermacrene a from Charles L. Perrin, Betsy L. Rodgers and Joseph M. Alexander A. Nevzorov and Stanley J. Opella, Selective 

(2E,6Z)-6-fluorofarnesyl diphosphate, ChemBioChem, 8, O’Connor, Nucleophilic Addition to a p-Benzyne Derived averaging for high-resolution solid-state NMR spectroscopy 

1826-1833 (2007). from an Enediyne: A New Mechanism for Halide Incorpora- of aligned samples, J. Magn. Reson, 185, 59-70 (2007). 

Yvonne Haagen, Inge Unsoeld, Lucia Westrich, Bertolt tion into Biomolecules, J. Am. Chem. Soc, 129, 4795-4799 Neeraj Sinha, Fabian V. Filipp, Lena Jairam, Sang Ho 

Gust, Stephane B. Richard, Joseph P. Noel and Lutz Heide, (2007). Park, Joel Bradley and Stanley J. Opella, Tailoring 13C label- 

A soluble, magnesium-independent prenyltransferase cata- Joseph M. O’Connor, Anna G. Wenzel and Kristin Hiib- ing for triple-resonance solid-state NMR experiments on 

lyzes reverse and regular C-prenylations and O-prenylations ner, Iridium(III)-vinylidene chemistry: conversion of an aligned samples of proteins, Magn. Reson. Chem, 45, S107of 

aromatic substrates, FEBS Lett, 581, 2889-2893 (2007). iridacyclopentadiene-chlorido complex and terminal alkynes S115 (2007). 

Shunji Takahashi, Yun-Soo Yeo, Yuxin Zhao, Paul E. to iridacyclopentadiene-vinyl complexes, Inorg. Chim. Acta, Anna A. De Angelis and Stanley J. Opella, Bicelle samples 

O’Maille, Bryan T. Greenhagen, Joseph P. Noel, Robert M. 361, 3033-3041 (2008). for solid-state NMR of membrane proteins, Nat. Protoc, 2, 

Coates and Joe Chappell, Functional Characterization of Ryan L. Holland, Kevin D. Bunker, Christopher H. Chen, 2332-2338 (2007). 

Premnaspirodiene Oxygenase, a Cytochrome P450 Catalyz- Antonio G. Di Pasquale, Arnold L. Rheingold, Kim K. Bal- Sang Ho Park and Stanley J. Opella, Conformational 

ing Regio- and Stereo-specific Hydroxylations of Diverse dridge and Joseph M. O’Connor, Reactions of a Metallacy- changes induced by a single amino acid substitution in the 

Sesquiterpene Substrates, J. Biol. Chem, 282, 31744-31754 clobutene Complex with Alkenes, J. Am. Chem. Soc, 130, trans-membrane domain of Vpu: implications for HIV-1 sus- 

(2007). 10093-10095 (2008). ceptibility to channel blocking drugs, Protein Sci, 16, 2205- 

Joseph P. Noel, Digging for answers, smelling a hint of Oanh P. Lam, Patrick L. Feng, Frank W. Heinemann, Jo- 2215 (2007). 

success and tasting triumph, Nat. Chem. Biol, 3, 690-691 seph M. O’Connor and Karsten Meyer, Charge-Separation in Stanley J. Opella, Ana Carolina Zeri and Sang Ho Park, 

(2007). Uranium Diazomethane Complexes Leading to C-H Activa- Structure, dynamics, and assembly of filamentous bacterio-


phages by nuclear magnetic resonance spectroscopy, Annu. 

Rev. Phys. Chem, 59, 635-657 (2008). 

Vitaly V. Vostrikov, Christopher V. Grant, Anna E. Daily, 

Stanley J. Opella and Roger E. Koeppe, II, Comparison of 

“Polarization Inversion with Spin Exchange at Magic Angle” 

and “Geometric Analysis of Labeled Alanines” Methods for 

Transmembrane Helix Alignment, J. Am. Chem. Soc, 130, 

12584-12585 (2008). 

Chin H. Wu and Stanley J. Opella, Shiftless nuclear magnetic 

resonance spectroscopy, J. Chem. Phys, 128, 052312/1- 

052312/5 (2008). 

Chin H. Wu and Stanley J. Opella, Proton-detected separated 

local field spectroscopy, J. Magn. Reson, 190, 165-170 

(2008). 

PAESANI, FRANCESCO (b.1971) Assistant Professor. 

Ph.D, 2000, University of Rome “La Sapienza”. 

Postdoctoral Fellow, 2002-2005, University of California, 

Berkeley; Postdoctoral Researcher, 2005-2009, University 

of Utah. Physical Chemistry; Theoretical Chemistry. 

TEL: (858) 534-5658 FAX: (858) 534-7244 

Web: paesanigroup.ucsd.edu 

Email: fpaesani@ucsd.edu 

R. E. Zillich, F. Paesani, Y. Kwon and K. B. Whaley, Path 

integral methods for rotating molecules in superfluids, J. 

Chem. Phys, 123, 114301 (2005). 

F. Paesani, R. E. Zillich, Y. Kown and K. B. Whaley, OCS 

in para-hydrogen clusters: Rotational dynamics and super- 

fluidity, J. Chem. Phys, 122, 181106 (2005). 

F. Paesani, Y. Kwon and K. B. Whaley, Onset of superfluidity 

in small CO2( 

1990-1992, Scripps Institution of Oceanography. Analytical 

Chemistry. Forensic science. I interact with a group 

of colleagues interested in the application of Real Time 

PCR to forensic analyses. Determining SNP genotype 

frequencies in different ethnic groups, and most recently 

the use of the BioTrove Open Array Platform for the 

analysis of a SNP panel for use in human identification. 

TEL: (858) 822-5736 FAX: (858) 534-7687 

Email: rpomeroy@ucsd.edu 


PRATHER, KIMBERLY A. (b.1962) Professor. 

B.Sc, 1985, University of California, Davis; Ph.D, 1990, 

University of California, Davis. Postdoctoral Fellow, 

1990-1992, University of California, Berkeley. Analytical 

Chemistry; Atmospheric Chemistry. Atmospheric, 

physical, analytical chemistry: Field and laboratory in- 

vestigations of gas/particle (heterogeneous) reaction processes 

of tropospheric significance using mass spectrom- 

etry and laser-based techniques. Understanding the role 

of aerosols and their impacts on climate, regional weather 

and water supply, and human health. TEL: (858) 822- 

5312 FAX: (858) 534-7042 

Web: www.chem.ucsd.edu/Faculty/bios/prather.html 

Email: kprather@ucsd.edu 

Thomas P. Rebotier and Kimberly A. Prather, Aerosol 

time-of-flight mass spectrometry data analysis: A benchmark 

of clustering algorithms, Anal. Chim. Acta, 585, 38-54 

(2007). 

of aerosol particles during a monsoonal transition period over 

the Indian Ocean, J. Geophy. Res, 113 (2008). 

R. C. Moffet, X. Y. Qin, T. Rebotier, H. Furutani and K. 

A. Prather, Chemically segregated optical and microphysical 

properties of ambient aerosols measured in a single-particle 

mass spectrometer, J. Geophy. Res, 113 (2008). 

Matthew T. Spencer, Hiroshi Furutani, Steven J. Olden- 

burg, Thomas K. Darlington and Kimberly A. Prather, Gold 

Nanoparticles as a Matrix for Visible-Wavelength Single- 

Particle Matrix-Assisted Laser Desorption/Ionization Mass 

Spectrometry of Small Biomolecules, J. Phys. Chem. C, 112, 

4083-4090 (2008). 

Laura Shields, Single particle characterization, source apportionment, 

and aging effects of ambient aerosols in Southern 

California. (D) 

Matthew Spencer, Approaches for the chemical and physi- 

cal characterization of aerosols using a single particle mass 

spectrometry based technique. (D) 

Ryan Moffet, Measurements of the chemical, physical, and 

optical properties of single aerosol particles. (D) 

Ryan Sullivan, Heterogeneous chemistry of atmospheric 

mineral dust particles and their resulting cloud-nucleation 

properties. (D) 

Stephen Toner, Anthropogenic particulate source charac- 

terization and source apportionment using aerosol time-offlight 

mass spectrometry. (D) 

Xueying (Sharon) Qin, Characterization of ambient aerosol 

composition and formation mechanisms and development of 

quantification methodologies utilizing ATOFMS. (D) 

4He)N clusters, Phys. Rev. Lett, 94, 

153401 (2005). 

F. Paesani, W. Zhang, T. E. Cheatham III, D. A. Case and 

G. A. Voth, An accurate and simple quantum model for liquid 

water, J. Chem. Phys, 125, 184507 (2006). 

F. Paesani and K. B. Whaley, Vibrational shifts of OCS in 

mixed clusters of parahydrogen and helium, J. Chem. Phys, 

124, 234310 (2006). 

F. Paesani and K. B. Whaley, Potential energy surface and 

infrared spectra of OCS hydrogen complexes, Mol. Phys, 

104, 61 (2006). 

Y. Kwon, F. Paesani and K. B. Whaley, Local superfluidi- 

ty in inhomogeneous systems, Phys. Rev. B, 74, 174522 

(2006). 

F. Paesani, S. Iuchi and G. A. Voth, Quantum effects in 

liquid water from an ab initio-based polarizable force field, J. 

Chem. Phys, 127, 074506 (2007). 

F. Paesani, K. B. Whaley, G. E. Douberly and R. E. Miller, 

Rovibrational spectra for the HCCCN HCN and 

HCN HCCCN binary complexes in 

R. C. Sullivan, S. A. Guazzotti, D. A. Sodeman and K. A. 

Prather, Direct observations of the atmospheric processing of 

Asian mineral dust, Atmos. Chem. Phys, 7, 1213-1236 

(2007). 

Laura G. Shields, David T. Suess and Kimberly A. Prather, 

Determination of single particle mass spectral signatures 

from heavy-duty diesel vehicle emissions for PM2.5 source 

apportionment, Atmos. Environ, 41, 3841-3852 (2007). 

Ryan C. Sullivan, Sergio A. Guazzotti, David A. Sodeman, 

Youhua Tang, Gregory R. Carmichael and Kimberly A. 

Prather, Mineral dust is a sink for chlorine in the marine 

boundary layer, Atmos. Environ, 41, 7166-7179 (2007). 

Matthew T. Spencer, Laura G. Shields and Kimberly A. 

Prather, Simultaneous Measurement of the Effective Density 

and Chemical Composition of Ambient Aerosol Particles, 

Environ. Sci. Technol, 41, 1303-1309 (2007). 

Kerri A. Denkenberger, Ryan C. Moffet, John C. Holecek, 

Thomas P. Rebotier and Kimberly A. Prather, Real-Time, 

Single-Particle Measurements of Oligomers in Aged Ambi- 

RHEINGOLD, ARNOLD L. (b.1940) Professor. 

A.B, 1962, Western Reserve University; M.S, 1963, 

Western Reserve University; Ph.D, 1969, University of 

Maryland. Research Associate, 1970, Virginia Polytech- 

nic Institute. Inorganic Chemistry. Main-group organometallic 

chemistry; metal/main-group clusters; small- 

molecule crystallography; polymorphism; thermoelectric 

materials. TEL: (858) 822-3870 FAX: (858) 822-3872 

Web: www-chem.ucsd.edu/Faculty/bios/rheingold.html 

Email: arheingold@ucsd.edu 

Christina S. Angle, Kathryn J. Woolard, Michael I. Kahn, 

James A. Golen, Arnold L. Rheingold and Linda H. Doerrer, 

Metallophilic interactions in iodido(2,2’:6’,2’’-terpyridine) 

platinum(II) diiodidoaurate(I), Acta Crystallogr., Sect. C: 

Cryst. Struct. Commun, C63, m231-m234 (2007). 

Jason C. Sanchez, Antonio G. DiPasquale, Arnold L. 

Rheingold and William C. Trogler, Synthesis, Luminescence 

Properties, and Explosives Sensing with 1,1-Tetraphenyl- 

4He droplets, J. Phys. 

Chem. A, 111, 7516 (2007). 

F. Paesani and G. A. Voth, Nonlinear quantum time correlation 

functions from centroid molecular dynamics and the 

maximum entropy method, J. Chem. Phys, 129, 194113 

ent Aerosol Particles, Environ. Sci. Technol, 41, 5439-5446 

(2007). 

Ryan C. Sullivan and Kimberly A. Prather, Investigations 

of the Diurnal Cycle and Mixing State of Oxalic Acid in Individual 

Particles in Asian Aerosol Outflow, Environ. Sci. 

silole- and 1,1-Silafluorene-vinylene Polymers, Chem. Mater, 

19, 6459-6470 (2007). 

Pirmin A. Ulmann, Aaron M. Brown, Maxim V. Ovchinni- 

kov, Chad A. Mirkin, Antonio G. DiPasquale and Arnold L. 

Rheingold, Spontaneous formation of heteroligated PtII (2008). 

Y. Wu, H. Chen, F. Wang, F. Paesani and G. A. Voth, An 

improved multistate empirical valence bond model for aqueous 

proton transport, J. Phys. Chem. B, 112, 467 (2008). 

O. Markovitch, H. Chen, S. Izvekov, F. Paesani, G. A. 

Voth and N. Agmon, Statistical validation of the mechanism 

of proton mobility, J. Phys. Chem. B, 112, 9456 (2008). 

F. Paesani and G. A. Voth, Quantum effects strongly influ- 

ence the surface premelting of ice, J. Phys. Chem. C, 112, 

324 (2008). 

Technol, 41, 8062-8069 (2007). 

J. Muhle, T. J. Lueker, Y. Su, B. R. Miller, K. A. Prather 

and R. F. Weiss, Trace gas and particulate emissions from 

the 2003 southern California wildfires, J. Geophy. Res, 112 

(2007). 

J. C. Holecek, M. T. Spencer and K. A. Prather, Analysis 

of rainwater samples: Comparison of single particle residues 

with ambient particle chemistry from the northeast Pacific 

and Indian Oceans, J. Geophy. Res, 112 (2007). 

L. G. Shields, X. Y. Qin, S. M. Toner and K. A. Prather, 

complexes 

with chelating hemilabile ligands, Chem.—Eur. J, 13, 

4529-4534 (2007). 

Katie J. Heroux, Katrina S. Woodin, David J. Tranchemon- 

tagne, Peter C. B. Widger, Evan Southwick, Edward H. 

Wong, Gary R. Weisman, Sterling A. Tomellini, Thaddeus J. 

Wadas, Carolyn J. Anderson, Scott Kassel, James A. Golen 

and Arnold L. Rheingold, The long and short of it: the influence 

of N-carboxyethyl versus N-carboxymethyl pendant 

arms on in vitro and in vivo behavior of copper complexes of 

cross-bridged tetraamine macrocycles, Dalton Trans, 2150- 

PERRIN, CHARLES L. (b.1938) Professor. A.B, 

1959, Harvard University; Ph.D, 1963, Harvard University. 

NSF Postdoctoral Fellowship, 1963, University of 

California, Berkeley. Organic Chemistry; Physical Organic 

Chemistry. Physical-Organic Chemistry (Molecular 

Structure, and Mechanisms of Organic Reactions): 

Substituent effects, proton exchange, dynamic NMR, 

anomeric effects, isotope effects, stereoelectronic control, 

hydrogen bonding, conformational analysis, steric 

hindrance to ionic solvation, malonic anhydrides, nonradical 

reactions of para-benzynes. TEL: (858) 534-2164 

FAX: (858) 822-0386 


C00389 

Email: cperrin@ucsd.edu 

Charles L. Perrin and Yanmei Dong, Secondary Deuterium 

Isotope Effects on the Acidity of Carboxylic Acids and Phe- 

Detection of ambient ultrafine aerosols by single particle 

techniques during the SOAR 2005 campaign, Aer. Sci. Technol, 

42, 674-684 (2008). 

K. A. Prather, C. D. Hatch and V. H. Grassian, Analysis of 

atmospheric aerosols, Annual Review of Analytical Chemistry, 

1, 485-514 (2008). 

R. C. Moffet, B. de Foy, L. T. Molina, M. J. Molina and K. 

A. Prather, Measurement of ambient aerosols in northern 

Mexico City by single particle mass spectrometry, Atmos. 

Chem. Phys, 8, 4499-4516 (2008). 

M. J. Cubison, B. Ervens, G. Feingold, K. S. Docherty, I. 

M. Ulbrich, L. Shields, K. Prather, S. Hering and J. L. Jimenez, 

The influence of chemical composition and mixing state 

of Los Angeles urban aerosol on CCN number and cloud 

properties, Atmos. Chem. Phys, 8, 5649-5667 (2008). 

H. Furutani, M. Dall’osto, G. C. Roberts and K. A. Prather, 

Assessment of the relative importance of atmospheric aging 

on CCN activity derived from field observations, Atmos. Environ, 

42, 3130-3142 (2008). 

2162 (2007). 

Jacky Chen, Robert Russo, Wilson Chao, Lawrence D. 

Margerum, Mitchell R. Malachowski, Ryan White, Zachary 

Thawley, Angelina Thayer, Arnold L. Rheingold and Lev N. 

Zakharov, Synthesis, structure, redox properties and azide 

binding for a series of biphenyl-based Cu(II) complexes, 

Dalton Trans, 2571-2579 (2007). 

John J. Eisch, Yun Qian and Arnold L. Rheingold, Nickel 

(II)-carbene intermediates in reactions of geminal dihaloal- 

kanes with nickel(0) reagents and the corresponding carbene 

capture as the phosphonium ylide, Eur. J. Inorg. Chem, 

1576-1584 (2007). 

Jian Yuan, Russell P. Hughes and Arnold L. Rheingold, 

The first example of a bis(trifluoromethyl)carbene transitionmetal 

complex and its reduction to a perfluoroallene complex, 

Eur. J. Inorg. Chem, 4723-4725 (2007). 

Kil Sik Min, Antonio DiPasquale, Arnold L. Rheingold 

and Joel S. Miller, Room-Temperature Spin Crossover Observed 

for [(TPyA)FeII(DBQ2-)FeII(TPyA)] 2+ nols, J. Am. Chem. Soc, 129, 4490-4497 (2007). Stephen M. Toner, Laura G. Shields, David A. Sodeman 

[TPyA = Tris 

(2-pyridylmethyl)amine; DBQ2- Charles L. Perrin, Betsy L. Rodgers and Joseph M. 

O’Connor, Nucleophilic Addition to a p-Benzyne Derived 

from an Enediyne: A New Mechanism for Halide Incorporation 

into Biomolecules, J. Am. Chem. Soc, 129, 4795-4799 

(2007). 

Charles L. Perrin and Yanmei Dong, Nonadditivity of Secondary 

Deuterium Isotope Effects on Basicity of Trimethylamine, 

J. Am. Chem. Soc, 130, 11143-11148 (2008). 

Charles L. Perrin and Chen Zhao, Intramolecular kinetic 

isotope effect in hydride transfer from dihydroacridine to a 

quinolinium ion. Rejection of a proposed two-step mechanism 

with a kinetically significant intermediate, Org. Biomol. 

and Kimberly A. Prather, Using mass spectral source signatures 

to apportion exhaust particles from gasoline and diesel 

powered vehicles in a freeway study using UF-ATOFMS, 

Atmos. Environ, 42, 568-581 (2008). 

Weixiang Zhao, Philip K. Hopke and Kimberly A. Prather, 

Comparison of two cluster analysis methods using single particle 

mass spectra, Atmos. Environ, 42, 881-892 (2008). 

Ryan C. Moffet, Yury Desyaterik, Rebecca J. Hopkins, 

Alexei V. Tivanski, Mary K. Gilles, Y. Wang, V. Shutthanandan, 

Luisa T. Molina, Rodrigo Gonzalez Abraham, Kirsten 

S. Johnson, Violeta Mugica, Mario J. Molina, Alexander 

Laskin and Kimberly A. Prather, Characterization of Aero- 

= 2,5-Di-tert-butyl-3,6-dihydroxy-1,4-benzoquinonate], 

Inorg. Chem, 46, 1048-1050 

(2007). 

Konstantin I. Pokhodnya, Michael Bonner, Antonio G. Di- 

Pasquale, Arnold L. Rheingold, Jae-Hyuk Her, Peter W. 

Stephens, Jong-Won Park, Bretni S. Kennon, Atta M. Arif 

and Joel S. Miller, Structural and Magnetic Properties of 

MCl2 (M = Fe, Mn, Co): Acetonitrile Solvates, Inorg. Chem. 


Eduardo E. Chufan, Claudio N. Verani, Simona C. Puiu, 

Eva Rentschler, Ulrich Schatzschneider, Christopher Incarvi- 

to, Arnold L. Rheingold and Kenneth D. Karlin, Generation 

and Characterization of [(P)M-(X)-Co(TMPA)] n+ Chem, 6, 3349-3353 (2008). sols Containing Zn, Pb, and Cl from an Industrial Region of 

Assemblies; 

P = Porphyrinate, M = FeIII and CoIII ,X=O2- ,OH- , 

Mexico City, Environ. Sci. Technol, 42, 7091-7097 (2008). O2 2- POMEROY, ROBERT S. (b.1958) LPSOE. Ph.D, 

1990, University of Arizona. Post-doctoral Researcher, 

M. T. Spencer, J. C. Holecek, C. E. Corrigan, V. Ramanathan 

and K. A. Prather, Size-resolved chemical composition 

, and TMPA = Tris(2-pyridylmethyl)amine, Inorg. Chem. 


Sonia Nieto, Julio Perez, Lucia Riera, Victor Riera, Daniel


Miguel, James A. Golen and Arnold L. Rheingold, Pyrazole X- Complexes as Anion Receptors: Effects of Changing the 

[n=1,2,3,5,7,9,11;X=I,OTf], Organometallics, 26, 

264-271 (2007). 

trile-facilitated reductive dimerization of TCNE to octacyanobutanediide, 

[C4(CN)8] 2- Metal, the Pyrazole Substitution Pattern, and the Number of Douglas B. Grotjahn, Xi Zeng, Andrew L. Cooksy, W. 

, by iron(II) chloride, Chem.—Eur. 

J, 14, 714-720 (2008). 

Pyrazole Ligands, Inorg. Chem. (Washington, DC, U. S.), 46, Scott Kassel, Antonio G. DiPasquale, Lev. N. Zakharov and Peter M. Iovine, Charles R. Gyselbrecht, Emily K. Perttu, 

3407-3418 (2007). 

Helen W. Richter, Gerald F. Koser, Christopher D. Incarvito 

and Arnold L. Rheingold, Preparation and Structure of a 

Solid-State Hypervalent-Iodine Polymer Containing Iodine 

and Oxygen Atoms in Fused 12-Atom Hexagonal Rings, 


(2007). 

Dong-Heon Lee, Lanying Q. Hatcher, Michael A. Vance, 

Ritimukta Sarangi, Ashley E. Milligan, Amy A. Narducci 

Sarjeant, Christopher D. Incarvito, Arnold L. Rheingold, 

Keith O. Hodgson, Britt Hedman, Edward I. Solomon and 

Kenneth D. Karlin, Copper(I) Complex O2-Reactivity with a 

N3S Thioether Ligand: a Copper-Dioxygen Adduct Including 

Sulfur Ligation, Ligand Oxygenation, and Comparisons with 

Arnold L. Rheingold, Experimental and Computational 

Study of the Transformation of Terminal Alkynes to Vinylidene 

Ligands on trans-(Chloro)bis(phosphine)Rh Fragments 

and Effects of Phosphine Substituents, Organometallics, 26, 

3385-3402 (2007). 

William J. Evans, Kevin A. Miller, Stosh A. Kozimor, Joseph 

W. Ziller, Antonio G. DiPasquale and Arnold L. Rheingold, 

Actinide Hydride Complexes as Multielectron Reductants: 

Analogous Reduction Chemistry from [(C5Me5)2UH]2, 

[(C5Me5)2UH2]2, and [(C5Me5)2ThH2]2, Organometallics, 26, 

3568-3576 (2007). 

William J. Evans, Kevin A. Miller, Joseph W. Ziller, Antonio 

G. DiPasquale, Katie J. Heroux and Arnold L. Rheingold, 

Formation of (C5Me5)2U(EPh)Me, (C5Me5)2U(EPh)2, and 

(C5Me5)2U(� 

Cole Klick, Alexander Neuwelt, Jason Loera, Antonio G. Di 

Pasquale, Arnold L. Rheingold and Jeremy Kua, Hetero-aryl- 

boroxines: the first rational synthesis, X-ray crystallographic 

and computational analysis, Dalton Trans, 3791-3794 

(2008). 

Roman Dembinski, Pablo Espinet, Sergio Lentijo, Marcin 

W. Makowicz, Jose M. Martin-Alvarez, Arnold L. Rhein- 

gold, Daniel J. Schmidt and Adam Sniady, Fluorophobic ef- 

fect in metallomesogens the synthesis and mesomorphism of 

Ag, Au, Cu, Fe, Pd, and Pt fluorous isocyanide complexes, 

European Journal of Inorganic Chemistry, 1565-1572 

(2008). 

Harry W. Gibson, Hong Wang, Chin P. Chng, Thomas E. 

Glass, Daniel Schoonover, Lev N. Zakharov and Arnold L. 

2-TeC6H4) All Nitrogen Ligand Analogues, Inorg. Chem. (Washington, 

DC, U. S.), 46, 6056-6068 (2007). 

Anthony E. Wetherby, Jr., Lindy R. Goeller, Antonio G. 

DiPasquale, Arnold L. Rheingold and Charles S. Weinert, 

Synthesis and Structures of an Unusual Germanium(II) Calix 

from (C5Me5)2UMe2 and PhEEPh (E 

= S, Se, Te), Organometallics, 26, 4287-4293 (2007). 

William J. Evans, Daniel B. Rego, Joseph W. Ziller, Antonio 

G. DiPasquale and Arnold L. Rheingold, Facile Insertion 

of CO2 into Tetra- and Pentamethylcyclopentadienyl Lanthanide 

Moieties To Form (C5Me4RCO2) 

Rheingold, Synthesis and conformational analysis of a small 

meta-cyclophane, bis(5-carbomethoxy-1,3-phenylene)-14crown-4, 

Heteroatom Chemistry, 19, 48-54 (2008). 

William J. Evans, Justin R. Walensky, Filipp Furche, Jo- 

seph W. Ziller, Antonio G. DiPasquale and Arnold L. Rhein- 

- [4]arene Complex and the First Germanium(II) Calix[8]arene 

Complex and Their Reactivity with Diiron Nonacarbonyl, 


(2007). 

Julie A. Cissell, Thomas P. Vaid, Antonio G. DiPasquale 

Carboxylate Ligands 

(R = H, Me), Organometallics, 26, 4737-4745 (2007). 

K. Brian Davis, T. David Harris, Michael P. Castellani, 

James A. Golen and Arnold L. Rheingold, Synthesis and x- 

ray Crystal Structure of [(C5Ph5)CrCl(�-Cl)2Tl]2: An Example 

of the Rare M-X-Tl 

gold, Synthesis of (C5Me5)2(C5Me4H)UMe, (C5Me5)2(C5H5) 

UMe, and (C5Me5)2UMe[CH(SiMe3)2] from Cationic Metallocenes 

for the Evaluation of Sterically Induced Reduction, 


(2008). 

I and Arnold L. Rheingold, Germanium Phthalocyanine, GePc, 

and the Reduced Complexes SiPc(pyridine)2 and GePc(pyridine)2 

Containing Antiaromatic �-Electron Circuits, Inorg. 


Yonglian Zhang, Hong-Chang Liang, Lev N. Zakharov, 

Sanjib K. Das, Marcel M. Hetu and Arnold L. Rheingold, 

Carboxyester hydrolysis promoted by Cu(II) complexes of 

pyridyl-amine carboxylate-pendant ligands, Inorg. Chim. 

Acta, 360, 1691-1701 (2007). 

Jose L. Lamboy, Antonio Pasquale, Arnold L. Rheingold 

and Enrique Melendez, Synthesis, solution and solid state 

structure of titanium-maltol complex, Inorganica Chimica 

Acta, 360, 2115-2120 (2007). 

Kil Sik Min, Antonio G. DiPasquale, James A. Golen, Arnold 

L. Rheingold and Joel S. Miller, Synthesis, Structure, 

and Magnetic Properties of Valence Ambiguous Dinuclear 

Antiferromagnetically Coupled Cobalt and Ferromagnetically 

Coupled Iron Complexes Containing the Chloranilate(2-) 

and the Significantly Stronger Coupling Chloranilate( 3-) 

Radical Trianion, J. Am. Chem. Soc, 129, 2360-2368 (2007). 

Kil Sik Min, Antonio G. DiPasqual, James A. Golen, Arnold 

L. Rheingold, Atta M. Arif and Joel S. Miller, Synthesis, 

structure, and magnetic properties of valence ambiguous 

dinuclear antiferromagnetically coupled cobalt and ferromagnetically 

coupled iron complexes containing the chloranilate 

(2-) and the significantly stronger coupling chloranilate( 3-) 

Linkage (X = Halide), Organometal- 

lics, 26, 4843-4845 (2007). 

Corina Scriban, David S. Glueck, James A. Golen and Arnold 

L. Rheingold, Platinum-catalyzed asymmetric alkylation 

of a secondary phosphine: Mechanism and origin of enantioselectivity. 

[Erratum to document cited in CA146: 

422111], Organometallics, 26, 5124 (2007). 

Nicole A. Ketterer, Joseph W. Ziller, Arnold L. Rheingold 

and Alan F. Heyduk, Imido and Organometallic-Amido Titanium(IV) 

Complexes of a Chelating Phenanthrenediamide 

Ligand, Organometallics, 26, 5330-5338 (2007). 

Gerd W. Rabe, Florian A. Riederer, Mei Zhang-Presse and 

Arnold L. Rheingold, A Partially Demethylated Donor-Functionalized 

Terphenyl Lanthanide Compound, Organometallics, 

26, 5724-5726 (2007). 

Lyudmila Leontyeva, Russell P. Hughes and Arnold L. 

Rheingold, An Unusual Migratory Insertion of CO into a 

Pentamethylcyclopentadienyl-Platinum Bond, Organometal- 

lics, 26, 5735-5736 (2007). 

Anand Sundararaman, Resmi Varughese, Haiyan Li, Lev 

N. Zakharov, Arnold L. Rheingold and Frieder Jaekle, A Donor-Acceptor 

Dyad with a Highly Lewis Acidic Boryl Group, 

Organometallics, 26, 6126-6131 (2007). 

Julie A. DuPont, Michael B. Coxey, Peter J. Schebler, 

Christopher D. Incarvito, William B. Dougherty, Glenn P. A. 

Yap, Arnold L. Rheingold and Charles G. Riordan, High- 

Lihua Liu, Lev N. Zakharov, James A. Golen, Arnold L. 

Rheingold and Tracy A. Hanna, Synthesis and Characterization 

of Bismuth(III) and Antimony(III) Calixarene Com- 

plexes, Inorg. Chem. (Washington, DC, U. S.), 47, 11143- 

11153 (2008). 

William J. Evans, Elizabeth Montalvo, Dustin J. Dixon, Joseph 

W. Ziller, Antonio G. DiPasquale and Arnold L. Rheingold, 

Lanthanide metallocene complexes of the 1,3,4,6,7,8- 

Hexahydro-2H-pyrimido[1,2-a]pyrimidinato ligand, (hpp)1-, 


(2008). 

Anthony E. Wetherby, Jr., Lindy R. Goeller, Antonio G. 

DiPasquale, Arnold L. Rheingold and Charles S. Weinert, 

Metal-dependent reactions of bulky metal(II) amides M[N 

(SiMe3)2]2 with 3,3’-disubstituted binaphthols 

(HO)2C20H10(SiR3)2-3,3’: selective conversion of one equivalent 

-OH group to a silyl ether -OSiMe3, Inorg. Chem. 



James R. O’Brien, Antonio G. DiPasquale, Arnold L. Rheingold, 

Enrique del Barco and David N. Hendrickson, Wheel- 

Shaped Mn16 Single-Molecule Magnets, Inorg. Chem. 


Kendric J. Nelson, Antonio G. DiPasquale, Arnold L. 

Rheingold, Matthew C. Daniels and Joel S. Miller, Structure 

and Properties of [CrIIIF(NCMe)5](BF4)2·MeCN: radical trianion. [Erratum to document cited in CA146: Spin Organocobalt(II) Complexes in a Thioether Coordina- 

A Nonaqueous 

Source of CrIIIF2+ 393663], J. Am. Chem. Soc, 129, 6056 (2007). 

Natalia F. Blank, Jillian R. Moncarz, Tim J. Brunker, Corina 

Scriban, Brian J. Anderson, Omar Amir, David S. Glueck, 

Lev N. Zakharov, James A. Golen, Christopher D. Incarvito 

and Arnold L. Rheingold, Palladium-Catalyzed Asymmetric 

Phosphination. Scope, Mechanism, and Origin of Enantioselectivity, 

J. Am. Chem. Soc, 129, 6847-6858 (2007). 

Jennifer E. Sprague, Yijie Peng, Ashley L. Fiamengo, Katrina 

S. Woodin, Evan A. Southwick, Gary R. Weisman, Edward 

H. Wong, James A. Golen, Arnold L. Rheingold and 

Carolyn J. Anderson, Synthesis, Characterization and In 

Vivo Studies of Cu(II)-64-Labeled Cross-Bridged Tetraazamacrocycle-amide 

Complexes as Models of Peptide Conjugate 

Imaging Agents, J. Med. Chem, 50, 2527-2535 (2007). 

Harry W. Gibson, Hong Wang, Carla Slebodnick, Joseph 

Merola, W. Scott Kassel and Arnold L. Rheingold, Isomeric 

tion Environment, Organometallics, 26, 971-979 (2007). 

Daniel P. Kennedy, Antonio G. DiPasquale, Arnold L. 

Rheingold and Roy P. Planalp, Ni(II)-mediated synthesis of 

the novel tripodal aminopyridyl ligand tamepyr: Coordination 

geometry and rigidity of complexes with the divalent 3d 

metals Fe-Zn and with In(III), Polyhedron, 26, 197-203 

(2007). 

Christopher C. Beedle, Katie J. Heroux, Motohiro Nakano, 

Antonio G. DiPasquale, Arnold L. Rheingold and David N. 

Hendrickson, Antiferromagnetic tetranuclear manganese 

complex: Wheel or dicubane?, Polyhedron, 26, 2200-2206 

(2007). 

Timi P. Singa, Antonio G. DiPasquale, Arnold L. Rhein- 

gold and Clifford P. Kubiak, Bis(2,6-dimethylphenyl isocya- 

nide-.kappa.C)gold(I) tetrafluoridoborate, Acta Crystallographica, 

Section E: Structure Reports Online, E64, m1221/1and 

a Building Block for New Prus- 

sian-Blue-Like Magnetic Materials, Inorg. Chem. (Washington, 

DC, U. S.), 47, 7768-7774 (2008). 

Brian J. Fox, Queena Y. Sun, Antonio G. DiPasquale, 

Alexander R. Fox, Arnold L. Rheingold and Joshua S. Fi- 

gueroa, Solution Behavior and Structural Properties of Cu(I) 

Complexes Featuring m-Terphenyl Isocyanides, Inorg. 



Antonio G. DiPasquale, Naresh S. Dalal, Arnold L. Rheingold, 

Enrique del Barco and David N. Hendrickson, Molecu- 

lar Wheels: New Mn12 Complexes as Single-Molecule Magnets, 


(2008). 

Hyojong Yoo, Chad A. Mirkin, Antonio G. DiPasquale, 

Arnold L. Rheingold and Charlotte L. Stern, Reversible CO- 

Induced Chloride Shuttling in RhI 2,6-Pyridino-Cryptands Based on Dibenzo-24-crown-8, J. 

Org. Chem, 72, 3381-3393 (2007). 

Jinqiang Zhang, Feihe Huang, Ning Li, Hong Wang, Harry 

W. Gibson, Peter Gantzel and Arnold L. Rheingold, Paraquat 

Substituent Effect on Complexation with a Dibenzo-24crown-8-Based 

Cryptand, J. Org. Chem, 72, 8935-8938 

(2007). 

Brenna L. Ghent, Sarah L. Martinak, Lauren A. Sites, 

James A. Golen, Arnold L. Rheingold and Chip Nataro, Elecm1221/7 

(2008). 

William J. Evans, Kevin A. Miller, Antonio G. DiPasquale, 

Arnold L. Rheingold, Timothy J. Stewart and Robert 

Bau, A crystallizable f-element tuck-in complex: the tuck-in 

tuck-over uranium metallocene [(C5Me5)U{�-�5:�1:�1- C5Me3(CH2)2}(�-H)2U(C5Me5)2], Angew. Chem., Int. Ed, 47, 

5075-5078 (2008). 

Kil Sik Min, Krzysztof Swierczek, Antonio G. DiPasquale, 

Arnold L. Rheingold, William M. Reiff, Atta M. Arif and 

Joel S. Miller, A dinuclear iron(ii) complex, [(TPyA)Fe 

Tweezer Complexes Con- 

taining Urea-Functionalized Hemilabile Ligands, Inorg. 


H. Christopher Fry, Heather R. Lucas, Lev N. Zakharov, 

Arnold L. Rheingold, Gerald J. Meyer and Kenneth D. Kar- 

lin, Intermolecular versus intramolecular electron-/atom- (Cl) 

transfer in heme-iron and copper pyridylalkylamine complexes, 

Inorg. Chim. Acta, 361, 1100-1115 (2008). 

Annalese F. Maddox, Arnold L. Rheingold, James A. Golen, 

W. Scott Kassel and Chip Nataro, Taniaphos and Wal- 

II 

trochemistry and complexation of Josiphos ligands, J. Orga- (THBQ phos ligands: Oxidative electrochemistry and complexation. 

2-)FeII(TPyA)](BF4)2 nomet. Chem, 692, 2365-2374 (2007). 

[TPyA = tris(2-pyridylmethyl) 

amine; THBQ Synthesis, characterization, oxidative electrochemistry and 

2- Tim J. Brunker, Brian J. Anderson, Natalia F. Blank, David 

S. Glueck and Arnold L. Rheingold, Enantioselective 

Synthesis of P-Stereogenic Benzophospholanes via Palladium-Catalyzed 

Intramolecular Cyclization, Org. Lett, 9, 1109- 

1112 (2007). 

Cameron K. Gren, Timothy P. Hanusa and Arnold L. 

Rheingold, Threefold Cation-� Bonding in Trimethylsilylated 

Allyl Complexes, Organometallics, 26, 1643-1649 

(2007). 

Corina Scriban, David S. Glueck, James A. Golen and Arnold 

L. Rheingold, Platinum-Catalyzed Asymmetric Alkylation 

of a Secondary Phosphine: Mechanism and Origin of 

Enantioselectivity, Organometallics, 26, 1788-1800 (2007). 

Cheryl J. Bourgeois, Hui Huang, Roman B. Larichev, Lev 

N. Zakharov, Arnold L. Rheingold and Russell P. Hughes, 

= 2,3,5,6-tetrahydroxy-1,4-benzoquinonate] 

exhibiting both spin crossover with hysteresis and ferromag- 

netic exchange, Chem. Commun. (Cambridge, U. K.), 317- 

319 (2008). 

Ami Doshi, Krishnan Venkatasubbaiah, Arnold L. Rheingold 

and Frieder Jaekle, Binary stacks of [CuC6F5]4 with arenes, 

Chem. Commun. (Cambridge, U. K.), 4264-4266 

(2008). 

Arnold L. Rheingold, Antonio G. DiPasquale and Peter A. 

Beckmann, The relationship between crystal structure and 

NMR relaxation in molecular solids with tert-butyl groups, 

Chem. Phys, 345, 116-118 (2008). 

Krishnan Venkatasubbaiah, Ami Doshi, Israel Nowik, 

Rolfe H. Herber, Arnold L. Rheingold and Frieder Jakle, Examination 

of the mixed-valence state of the doubly boron- 

X-ray structures of [(Taniaphos/Walphos)MCl2] (M = Pd or 

Pt), Inorg. Chim. Acta, 361, 3283-3293 (2008). 

Phillip Moheno, Wolfgang Pfleiderer, Antonio G. DiPasquale, 

Arnold L. Rheingold and Dietmar Fuchs, Cytokine and 

IDO metabolite changes effected by calcium pterin during in- 

hibition of MDA-MB-231 xenograph tumors in nude mice, 

Int. J. Pharm, 355, 238-248 (2008). 

Ryan L. Holland, Kevin D. Bunker, Christopher H. Chen, 

Antonio G. Di Pasquale, Arnold L. Rheingold, Kim K. Baldridge 

and Joseph M. O’Connor, Reactions of a Metallacyclobutene 

Complex with Alkenes, J. Am. Chem. Soc, 130, 

10093-10095 (2008). 

Valentin Miranda-Soto, Douglas B. Grotjahn, Antonio G. 

DiPasquale and Arnold L. Rheingold, Imidazol-2-yl Com- 

plexes of Cp * bridged diferrocene cation [(FeCp)2{�-C10H6(BPh)2}] Ir as Bifunctional Ambident Reactants, J. Am. 

+ Variable-Temperature NMR Determination of the Barriers to 

, 

Chem.—Eur. J, 14, 444-458 (2008). 

Chem. Soc, 130, 13200-13201 (2008). 

Rotation about the Ir-C �-Bond in a Series of Primary Per- Konstantin I. Pokhodnya, Michael Bonner, Antonio G. Di- Dayna L. Turner, Thomas P. Vaid, Peter W. Stephens, 

fluoroalkyl Iridium Complexes [IrCp * {(CF2)nCF3}(PMe3)2] + Pasquale, Arnold L. Rheingold and Joel S. Miller, Acetoni- Kevin H. Stone, Antonio G. DiPasquale and Arnold L.


Rheingold, Semiconducting Lead-Sulfur-Organic Network Theodor Agapie, Lawrence M. Henling, Antonio G. Di- of freestanding porous silicon particles containing spectral 

Solids, J. Am. Chem. Soc, 130, 14-15 (2008). Pasquale, Arnold L. Rheingold and John E. Bercaw, Zirconi- barcodes, Phys. Status Solidi RRL, 1, R71-R73 (2007). 

William J. Evans, Elizabeth Montalvo, Timothy M. Cham- um and Titanium Complexes supported by tridentate LX2 li- Dmitri Simberga, Tasmia Duza, Ji Ho Park, Markus Essler, 

pagne, Joseph W. Ziller, Antonio G. DiPasquale and Arnold gands having two phenolates linked to Furan, Thiophene, and Jan Pilch, Lianglin Zhang, Austin M. Derfus, Meng Yang, 

L. Rheingold, Organolanthanide-Based Synthesis of 1,2,3- Pyridine donors: Precatalysts for propylene polymerization Robert M. Hoffman, Sangeeta Bhatia, Michael J. Sailor and 

Triazoles from Nitriles and Diazo Compounds, J. Am. Chem. and oligomerization, Organometallics, 27, 6245-6256 Erkki Ruoslahti, Biomimetic amplification of nanoparticle 

Soc, 130, 16-17 (2008). (2008). homing to tumors, Proc. Natl. Acad. Sci. U. S. A, 104, 932- 

Daesung Chong, Derek R. Laws, Ayman Nafady, Paulo Joerg Eppinger, Katharina R. Nikolaides, Mei Zhang- 936 (2007). 

Jorge Costa, Arnold L. Rheingold, Maria Jose Calhorda and Presse, Florian A. Riederer, Gerd W. Rabe and Arnold L. Frederique Cunin, Pierre-Emmanuel Milhiet, Emily Ang- 

William E. Geiger, [Re(� lin, Michael J. Sailor, Cedric Espenel, Christian Le Grimel- 

5-C5H5)(CO)3] + Family of 17-Elec- Rheingold, Alkyl Complexes of Rare-Earth Metal Centers 

tron Compounds: Monomer/Dimer Equilibria and Other Re- Supported by Chelating 1,1’-Diamidoferrocene Ligands: lec, Daniel Brunel and Jean-Marie Devoisselle, Continuous 

actions, J. Am. Chem. Soc, 130, 2692-2703 (2008). 

William J. Evans, Benjamin M. Schmiege, Sara E. Lorenz, 

Kevin A. Miller, Timothy M. Champagne, Joseph W. Ziller, 

Antonio G. Di Pasquale and Arnold L. Rheingold, Reductive 

Reactivity of the Organolanthanide Hydrides, [ 

(C5Me5)2LnH]x, Leads to ansa-Allyl Cyclopentadienyl (� 

Synthesis, Structure, and Application in Methacrylate Poly- 

merization, Organometallics, 27, 736-740 (2008). 

Anthony E. Wetherby, Arnold L. Rheingold, Christa L. 

Feasley and Charles S. Weinert, Synthesis and crystal struc- 

ture of a germanium(II) calix[6]arene containing unusual 

planar phospholipid bilayer supported on porous silicon thin 

film reflector, Ultramicroscopy, 107, 1048-1052 (2007). 

Emily J. Anglin, Lingyun Cheng, William R. Freeman and 

Michael J. Sailor, Porous silicon in drug delivery devices and 

materials, Adv. Drug Delivery Rev, 60, 1266-1277 (2008). 

J.-H. Park, G. A. V. Maltzahn, L. Zhang, M. P. Schwartz, 

5- C5Me4CH2-C5Me4CH2-� 

diamidosilyl ether groups, Polyhedron, 27, 1841-1847 

S. N. Bhatia, E. Ruoslahti and M. J. Sailor, Magnetic iron ox- 

3 ) 2- and Trianionic Cyclooctatetraenyl 

(C8H7) 

(2008). 

ide nanoworms for tumor targeting and imaging, Adv. Mater, 

3- Ligands, J. Am. Chem. Soc, 130, 8555-8563 

(2008). 

Derek R. Laws, Daesung Chong, Karen Nash, Arnold L. 

Hui Huang, Russell P. Hughes and Arnold L. Rheingold, 

Synthesis and structural characterization of a coordinatively 

unsaturated ruthenium complex, Cp 

20, (9), 1630-1635 (2008). 

Ji-Ho Park, Geoffrey von Maltzahn, Lianglin Zhang, Mi- 

* Rheingold and William E. Geiger, Cymantrene radical cation 

family: spectral and structural characterization of the halfsandwich 

analogues of ferrocenium ion, J. Am. Chem. Soc, 

130, 9859-9870 (2008). 

Xianlong Wang, Arnold L. Rheingold, Antonio G. DiPasquale, 

Frank B. Mallory, Clelia W. Mallory and Peter A. 

Beckmann, The quenching of isopropyl group rotation in van 

der Waals molecular solids, J. Chem. Phys, 128, 124502/1- 

124502/3 (2008). 

Matt L. Childers, Joonhyung Cho, Celeste A. S. Regino, 

Martin W. Brechbiel, Antonio G. DiPasquale, Arnold L. 

Rheingold, Suzy V. Torti, Frank M. Torti and Roy P. Planalp, 

Influence of ligand structure on Fe(II) spin-state and redox 

rate in cytotoxic tripodal chelators, J. Inorg. Biochem, 

102, 150-156 (2008). 

Zhenfu Han, Thomas P. Vaid and Arnold L. Rheingold, 

Hexakis(4-(N-butylpyridylium))benzene: A Six-Electron Organic 

Redox System, J. Org. Chem, 73, 445-450 (2008). 

Monika L. Amadoruge, Antonio G. DiPasquale, Arnold L. 

Rheingold and Charles S. Weinert, Hydrogermolysis reactions 

involving the �-germylated nitriles R3GeCH2CN (R = 

Ru(Ph2nacnac), and its 

CO adduct, Polyhedron, 27, 734-738 (2008). 

You-Moon Jeon, Dongwoo Kim, Chad A. Mirkin, James 

A. Golen and Arnold L. Rheingold, Pyrene-appended fluorescent 

tweezers generated via the Weak-Link Approach and 

their halide recognition properties, Tetrahedron, 64, 8428- 

8434 (2008). 

SAILOR, MICHAEL J. (b.1961) Professor. B.S, 

1983, Harvey Mudd College; Ph.D, 1988, Northwestern 

University. Postdoctoral Associate, 1988, Stanford University; 

Postdoctoral Associate, 1988-1990, California 

Institute of Technology. Bioengineering; Materials Science. 

Synthesis and study of nanophase materials with 

unusual optical, magnetic, or electronic properties, with 

emphasis on silicon-based systems. Current projects are 

directed at problems in nanoparticle-based diagnosis and 

treatment of disease, remote sensing of toxins and pollu- 

tants, high-throughput screening of biomarkers, point detectors 

for chemical or biological warfare agents, and mi- 

crofluidic technologies. TEL: (858) 534-8188 FAX: 

chael P. Schwartz, Erkki Ruoslahti, Sangeeta N. Bhatia and 

Michael J. Sailor, Magnetic iron oxide nanoworms for tumor 

targeting and imaging, Adv. Mater. (Weinheim, Ger.), 20, 

1630-1635 (2008). 

Ji-Ho Park, Geoffrey von Maltzahn, Erkki Ruoslahti, Sangeeta 

N. Bhatia and Michael J. Sailor, Micellar hybrid nano- 

particles for simultaneous magnetofluorescent imaging and 

drug delivery, Angew. Chem., Int. Ed, 47, 7284-7288 (2008). 

Geoffrey von Maltzahn, Yin Ren, Ji-Ho Park, Dal-Hee 

Min, Venkata Ramana Kotamraju, Jayanthi Jayakumar, Valentina 

Fogal, Michael J. Sailor, Erkki Ruoslahti and Sangeeta 

N. Bhatia, In Vivo Tumor Cell Targeting with “Click” Nanoparticles, 

Bioconjugate Chem, 19, 1570-1578 (2008). 

Jason R. Dorvee, Michael J. Sailor and Gordon M. Miskel- 

ly, Digital microfluidics and delivery of molecular payloads 

with magnetic porous silicon chaperones, Dalton Trans, 721- 

730 (2008). 

Loren A. Perelman, Claudia Pacholski, Yang Yang Li, Mi- 

chael S. VanNiewenhze and Michael J. Sailor, pH-triggered 

release of vancomycin from protein-capped porous silicon 

films, Nanomedicine (London, U. K.), 3, 31-43 (2008). 

Felix Casanova, Casey E. Chiang, Chang-Peng Li, Igor V. 

Ph, Pr i,Bu t) and germanium amides R3GeNMe2 (R = Pr 

i,Bu t 

(858) 534-5383 Roshchin, Anne M. Ruminski, Michael J. Sailor and Ivan K. 

) with Ph3GeH: Substituent-dependent reactivity and crystal 

structures of Pr 

Web: www.chem-faculty.ucsd.edu/sailor/ Schuller, Gas adsorption and capillary condensation in nano- 

i 3GeGePh3 and But 3Ge[NHC(CH3)CHCN], J. 

Organomet. Chem, 693, 1771-1778 (2008). 

Katherine A. McArthur, Scott S. Mitchell, Ginger Tsueng, 

Arnold Rheingold, Donald J. White, Jennifer Grodberg, Kin 

S. Lam and Barbara C. M. Potts, Lynamicins A-E, chlorinated 

bisindole pyrrole antibiotics from a novel marine actino- 

mycete, Journal of Natural Products, 71, 1732-1737 (2008). 

Jason C. Sanchez, Sara A. Urbas, Sarah J. Toal, Antonio 

G. DiPasquale, Arnold L. Rheingold and William C. Trogler, 

Catalytic Hydrosilylation Routes to Divinylbenzene Bridged 

Silole and Silafluorene Polymers. Applications to Surface 

Imaging of Explosive Particulates, Macromolecules (Washington, 

DC, U. S.), 41, 1237-1245 (2008). 

Craig D. Sergeant, Ingo Ott, Adam Sniady, Srinivasarao 

Meneni, Ronald Gust, Arnold L. Rheingold and Roman 

Dembinski, Metallo-nucleosides: synthesis and biological 

evaluation of hexacarbonyl dicobalt 5-alkynyl-2’-deoxyuridines, 

Org. Biomol. Chem, 6, 73-80 (2008). 

Brian J. Anderson, Marites A. Guino-o, David S. Glueck, 

James A. Golen, Antonio G. DiPasquale, Louise M. Liable- 

Sands and Arnold L. Rheingold, Platinum-Catalyzed Enan- 

tioselective Tandem Alkylation/Arylation of Primary Phosphines. 

Asymmetric Synthesis of P-Stereogenic 1-Phosphaacenaphthenes, 

Org. Lett, 10, 4425-4428 (2008). 

Thomas M. Cameron, Chongying Xu, Antonio G. Dipasquale 

and Arnold L. Rheingold, Synthesis and Structure of 

Strontium and Barium Guanidinates and Mixed-Ligand 

Guanidinate Pentamethylcyclopentadienyl Complexes, Or- 

Email: msailor@ucsd.edu 

Michael J. Sailor, Color Me Sensitive: Amplification and 

Discrimination in Photonic Silicon Nanostructures, ACS 

Nano, 1, 248-252 (2007). 

Ester Segal, Loren A. Perelman, Frederique Cunin, Francesco 

Di Renzo, Jean-Marie Devoisselle, Yang Yang Li and 

Michael J. Sailor, Confinement of thermoresponsive hydrogels 

in nanostructured porous silicon dioxide templates, Adv. 

Funct. Mater, 17, 1153-1162 (2007). 

B. H. King, A. M. Ruminski, J. L. Snyder and M. J. Sailor, 

Optical fiber-mounted porous silicon photonic crystals for 

sensing of organic vapor breakthrough in activated carbon, 

Adv. Mater, 19, (24), 4530—4534 (2007). 

Brian H. King, Andrei Gramada, Jamie R. Link and Michael 

J. Sailor, Internally referenced ammonia sensor based 

on an electrochemically prepared porous SiO2 photonic crys- 

tal, Adv. Mater. (Weinheim, Ger.), 19, 4044-4048 (2007). 

Brian H. King, Anne M. Ruminski, Jay L. Synder and Michael 

J. Sailor, Optical-fiber-mounted porous silicon photonic 

crystals for sensing organic vapor breakthrough in activated 

carbon, Adv. Mater. (Weinheim, Ger.), 19, 4530-4534 

(2007). 

Michael P. Schwartz, Sara D. Alvarez and Michael J. Sail- 

or, Porous SiO2 Interferometric Biosensor for Quantitative 

Determination of Protein Interactions: Binding of Protein A 

to Immunoglobulins Derived from Different Species, Anal. 

Chem, 79, 327-334 (2007). 

porous alumina films, Nanotechnology, 19, 315709/1- 

315709/6 (2008). 

SAWREY, B. A. (b.1951) Associate Vice Chancellor/ 

Undergraduate Education. B.S, 1973, Baldwin-Wallace 

College; M.A, 1982, San Diego State University; Ph.D, 

1983, University of California, San Diego. Chemistry 

Education. Cognition and understanding in college-level 

chemistry courses. TEL: (858) 822-4358 FAX: (858) 

822-3044 


C00298 

Email: bsawrey@ucsd.edu 


SCHRAUZER, G. N. 


G. N. Schrauzer, Interactive Effects of Selenium and Cadmium 

on Mammary Tumor Development and Growth in 

MMTV-Infected Female Mice. A Model Study on the Roles 

of Cadmium and Selenium in Human Breast Cancer, Biol. 

Trace Elem. Res, 123, 27-34 (2008). 

G. N. Schrauzer, Antioxidant supplementation increases 

skin cancer risk, or, why zinc should not be considered an antioxidant. 

Comments, J. Nutr, 138, 820 (2008). 

ganometallics, 27, 1596-1604 (2008). 

Monika L. Amadoruge, James A. Golen, Arnold L. Rheingold 

and Charles S. Weinert, Preparation, Structure, and Reactivity 

of Discrete Branched Oligogermanes, Organometallics, 

27, 1979-1984 (2008). 

Thilagar Pakkirisamy, Krishnan Venkatasubbaiah, W. 

Scott Kassel, Arnold L. Rheingold and Frieder Jakle, Examination 

of the Pyridine Binding to the Bifunctional Lewis 

Acid B,B’-Diphenyldiboradiferrocene, Organometallics, 27, 

3056-3064 (2008). 

William J. Evans, Elizabeth Montalvo, Timothy M. Champagne, 

Joseph W. Ziller, Antonio G. DiPasquale and Arnold 

Geoffrey Von Maltzahn, Todd J. Harris, Ji-Ho Park, Dal- 

Hee Min, Alexander J. Schmidt, Michael J. Sailor and Sangeeta 

N. Bhatia, Nanoparticle Self-Assembly Gated by Logical 

Proteolytic Triggers, J. Am. Chem. Soc, 129, 6064-6065 

(2007). 

Jennifer S. Park, Shawn O. Meade, Ester Segal and Michael 

J. Sailor, Porous silicon-based polymer replicas formed 

by bead patterning, Phys. Status Solidi A, 204, 1383-1387 

(2007). 

Loren A. Perelman, Michael P. Schwartz, Aaron M. Wohlrab, 

Michael S. VanNieuwenhze and Michael J. Sailor, A 

simplified biomolecule attachment strategy for biosensing 

SHULER, K. E. (b.1922) Professor Emeritus. B.S, 

1942, Georgia Institute of Technology; Ph.D, 1949, 

Catholic University of America. AEC Postdoctoral Fel- 

low, 1949-1951, Johns Hopkins University, Applied 

Physics Laboratory. Non-equilibrium statistical mechanics, 

relaxation phenomena, stochastic processes, theory 

of random walks. Transport in inhomogeneous media. 

TEL: (858) 822-4136 FAX: (858) 756-2359 

Email: kshuler@ucsd 


L. Rheingold, Diazomethane Insertion into Lanthanide- and 

Yttrium-C(allyl) Bonds To Form the � 

using a porous Si oxide interferometer, Phys. Status Solidi A, 

2-Hydrazonato Com- 204, 1394-1398 (2007). SINHA, AMITABHA (b.1956) Professor. B.S, 1978, 

plexes (C5Me5)2Ln[�2(N,N’)-RNN=CHSiMe3] (R=C3H5), 

Organometallics, 27, 3582-3586 (2008). 

Douglas B. Grotjahn, Xi Zeng, Andrew L. Cooksy, W. 

Scott Kassel, Antonio G. DiPasquale, Lev N. Zakharov and 

Arnold L. Rheingold, Experimental and Computational 

Study of the Transformation of Terminal Alkynes to Vinylidene 

Ligands on trans-(Chloro)bis(phosphine)Rh Fragments 

and Effects of Phosphine Substituents. [Erratum to document 

cited in CA147:212016], Organometallics, 27, 3626 (2008). 

Brian J. Anderson, David S. Glueck, Antonio G. DiPasquale 

and Arnold L. Rheingold, Substrate and Catalyst 

Screening in Platinum-Catalyzed Asymmetric Alkylation of 

Sara D. Alvarez, Michael P. Schwartz, Ben Migliori, Camilla 

U. Rang, Lin Chao and Michael J. Sailor, Using a porous 

silicon photonic crystal for bacterial cell-based biosensing, 

Phys. Status Solidi A, 204, 1439-1443 (2007). 

Michael P. Schwartz, Christine Yu, Sara D. Alvarez, Benjamin 

Migliori, Denis Godin, Lin Chao and Michael J. Sailor, 

Using an oxidized porous silicon interferometer for determi- 

nation of relative protein binding affinity through non-cova- 

lent capture probe immobilization, Phys. Status Solidi A, 204, 

1444-1448 (2007). 

Claudia Pacholski and Michael J. Sailor, Sensing with porous 

silicon double layers: a general approach for back- 

Case Western Reserve University; Ph.D, 1985, M.I.T. 

Postdoctoral Fellowship, 1985-1987, National Oceanic 

and Atmospheric Administration Boulder, CO; Postdoctoral 

Fellowship, 1987-1992, University of Wisconsin, 

Madison. Physical Chemistry. Laser spectroscopy, reaction 

dynamics and photochemistry of vibrationally excited 

molecules, laser control of chemical reactions, kinetics 

and photochemistry of free radicals and transient 

molecules occurring in atmospheric and combustion 

chemistry. TEL: (858) 534-5593 FAX: (858) 534-7042 

Email: asinha@ucsd.edu 

Bis(secondary) Phosphines. Synthesis of an Enantiomerically ground suppression, Phys. Status Solidi C, 4, 2088-2092 Jamie Matthews, Monica Martinez-Aviles, Joseph S. Fran- 

Pure C2-Symmetric 

4992-5001 (2008). 

Diphosphine, Organometallics, 27, (2007). 

Shawn O. Meade and Michael J. Sailor, Microfabrication 

cisco and Amitabha Sinha, Probing OH stretching overtones 

of CH3OOH through action spectroscopy: Influence of dipole


moment dependence on HOOC torsion, J. Chem. Phys, 129, Sergiy Markutsya, Shankar Subramaniam, R. Dennis Vigil Dynamics Revealed by Dye-Triggered Aggregation and DA- 

074316/1-074316/16 (2008). and Rodney O. Fox, On Brownian Dynamics Simulation of KAP1�-Mediated Localization in Living Cells, Chem. Biol. 

Jamie Matthews, Juliane L. Fry, Coleen M. Roehl, Paul O. Nanoparticle Aggregation, Ind. Eng. Chem. Res, 47, 3338- (Cambridge, MA, U. S.), 14, 1031-1042 (2007). 

Wennberg and Amitabha Sinha, Vibrational overtone initiated 

unimolecular dissociation of HOCH2OOH and 

HOCD2OOH: Evidence for mode selective behavior, J. 

Chem. Phys, 128, 184306/1-184306/12 (2008). 

Shuping Li, Jamie Matthews and Amitabha Sinha, Atmo- 

3345 (2008). 

Brian Saunders, Stephen Lyon, Matthew Day, Brenda Riley, 

Emily Chenette and Shankar Subramaniam, The Molecule 

Pages database, Nucleic Acids Res, 36, D700-D706 

(2008). 

Natarajan Kannan, Jian Wu, Ganesh S. Anand, Shibu Yooseph, 

Andrew F. Neuwald, J. Craig Venter and Susan S. Tay- 

lor, Evolution of allostery in the cyclic nucleotide binding 

module, GenomeBiology, 8, No pp. given (2007). 

Sharmin Schauble, Charles C. King, Manjula Darshi, Anspheric 

Hydroxyl Radical Production from Electronically Ex- tonius Koller, Kavita Shah and Susan S. Taylor, Identificacited 

NO2 and H2O, Science (Washington, DC, U. S.), 319, 

1657-1660 (2008). 

Jamie Matthews, State-resolved photochemistry and spectroscopic 

charecterization of atmospherically relevant hydroperoxides. 

(D) 

SUBRAMANIAM, SHANKAR (b.1953) Professor. 

B.Sc, 1972, Osmania University; M.A.Sc, 1974, Osmania 

University; Ph.D, 1982, Indian Institute of Technology 

Kanpur. His present research focuses several important 

aspects of computational biology. These include 

web-based approaches to bioinformatics, going from 

protein sequence to structure and function and studying 

protein recognition and function. TEL: (858) 822-0986 

FAX: (858) 534-5722 

Web: www.chem.ucsd.edu/Faculty/bios/subramaniam. 

html 

TAUBER, MICHAEL J. Assistant Professor. B.A, 

1992, Cornell University; Ph.D, 2002, University of California, 

Berkeley. Postdoctoral researcher, 2002-2003, 

University of California, Berkeley; ACS-PRF Research 

Associate, 2003-2006, Northwestern University. Physi- 

cal Chemistry. Our group investigates charge sharing and 

excited state dynamics in organic molecular assemblies, 

including self-assembled systems, by a variety of spectroscopic 

techniques including pump-probe Raman & 

resonance Raman, EPR, and transient absorption. Other 

topics of current research are new 3-dimensional architectures 

for dye-sensitized solar cells, and solvation 

structure/dynamics. TEL: (858) 534-7334 FAX: (858) 

000-0000 

Email: mtauber@ucsd.edu 

E. A. Weiss, M. J. Tauber, R. F. Kelley, M. J. Ahrens, M. 

A. Ratner and M. R. Wasielewski, Conformationally gated 

tion of ChChd3 as a Novel Substrate of the cAMP-dependent 

Protein Kinase (PKA) Using an Analog-sensitive Catalytic 

Subunit, J. Biol. Chem, 282, 14952-14959 (2007). 

Kenneth M. Humphries, Juniper K. Pennypacker and Susan 

S. Taylor, Redox Regulation of cAMP-dependent Protein 

Kinase Signaling: kinase versus phosphatase inactivation, J. 

Biol. Chem, 282, 22072-22079 (2007). 

Neal M. Alto, Andrew W. Weflen, Matthew J. Rardin, 

Defne Yarar, Cheri S. Lazar, Raffi Tonikian, Antonius Koller, 

Susan S. Taylor, Charles Boone, Sachdev S. Sidhu, San- 

dra L. Schmid, Gail A. Hecht and Jack E. Dixon, The type III 

effector EspF coordinates membrane trafficking by the spa- 

tiotemporal activation of two eukaryotic signaling pathways, 

J. Cell Biol, 178, 1265-1278 (2007). 

Ganesh S. Anand, Matthew Hotchko, Simon H. J. Brown, 

Lynn F. Ten Eyck, Elizabeth A. Komives and Susan S. Taylor, 

R-subunit Isoform Specificity in Protein Kinase A: Distinct 

Features of Protein Interfaces in PKA Types I and II by 

Amide H/ 2 Email: shsubramaniam@ucsd.edu 


Jayesh Pandey, Mehmet Koyutuerk, Yohan Kim, Wojciech 

Szpankowski, Shankar Subramaniam and Ananth Grama, 

Functional annotation of regulatory pathways, 

Bioinformatics, 23, i377-i386 (2007). 

Mano Ram Maurya and Shankar Subramaniam, A kinetic 

switching between superexchange and hopping within oligop-phenylene-based 

molecular wires, J. Am. Chem. Soc, 127, 

11842-11850 (2005). 

E. A. Weiss, M. J. Tauber, M. A. Ratner and M. R. Wasie- 

lewski, Electron spin dynamics as a probe of molecular dynamics: 

Temperature-dependent magnetic field effects on 

charge recombination within a covalent radical ion pair, J. 

Am. Chem. Soc, 127, 6052-6061 (2005). 

R. F. Kelley, M. J. Tauber and M. R. Wasielewski, Linker- 

H Exchange Mass Spectrometry, J. Mol. Biol, 374, 

487-499 (2007). 

Marat Valiev, Jie Yang, Joseph A. Adams, Susan S. Taylor 

and John H. Weare, Phosphorylation Reaction in cAPK Protein 

Kinase-Free Energy Quantum Mechanical/Molecular 

Mechanics Simulations, J. Phys. Chem. B, 111, 13455-13464 

(2007). 

Chinten James Lim, Jaewon Han, Nima Yousefi, Yuliang 

Ma, Paul S. Amieux, G. Stanley McKnight, Susan S. Taylor 

model for calcium dynamics in RAW 264.7 cells: 1. Mecha- controlled energy and charge transfer within chlorophyll treand Mark H. Ginsberg, �4 Integrins are type I cAMP-depen- 

nisms, parameters, and subpopulational variability, Biophys. foils, Angew. Chem. Int. Ed, 45, 7979-7982 (2006). 

dent protein kinase-anchoring proteins, Nat. Cell Biol, 9, 

J, 93, 709-728 (2007). 

M. J. Tauber, R. F. Kelley, J. M. Giaimo, B. Rybtchinski 415-421 (2007). 

Mano Ram Maurya and Shankar Subramaniam, A kinetic and M. R. Wasielewski, Electron hopping in pi-stacked cova- Shibu Yooseph, Granger Sutton, Douglas B. Rusch, Aaron 

model for calcium dynamics in RAW 264.7 cells: 2. Knock- lent and self-assembled perylene diimides observed by EN- L. Halpern, Shannon J. Williamson, Karin Remington, Jonadown 

response and long-term response, Biophys. J, 93, 729- DOR spectroscopy, J. Am. Chem. Soc, 128, 1782-1783 than A. Eisen, Karla B. Heidelberg, Gerard Manning, Wei- 

740 (2007). (2006). 

zhong Li, Lukasz Jaroszewski, Piotr Cieplak, Christopher S. 

Andrea L. Hevener, Jerrold M. Olefsky, Donna Reichart, R. F. Kelley, M. J. Tauber and M. R. Wasielewski, Intra- Miller, Huiying Li, Susan T. Mashiyama, Marcin P. Joachim- 

M. T. Audrey Nguyen, Gautam Bandyopadyhay, Ho-Yin molecular electron transfer through the 20-position of a iak, Christopher van Belle, John-Marc Chandonia, David A. 

Leung, Matthew J. Watt, Chris Benner, Mark A. Febbraio, chlorophyll-a derivative: An unexpectedly efficient conduit Soergel, Yufeng Zhai, Kannan Natarajan, Shaun Lee, Benja- 

Anh-Khoi Nguyen, Brian Folian, Shankar Subramaniam, for charge transport, J. Am. Chem. Soc, 128, 4779-4791 min J. Raphael, Vineet Bafna, Robert Friedman, Steven E. 

Frank J. Gonzalez, Christopher K. Glass and Mercedes Ri- (2006). 

Brenner, Adam Godzik, David Eisenberg, Jack E. Dixon, Sucote, 

Macrophage PPAR� is required for normal skeletal M. J. Ahrens, M. J. Tauber and M. R. Wasielewski, Bis(n- san S. Taylor, Robert L. Strausberg, Marvin Frazier and J. 

muscle and hepatic insulin sensitivity and full antidiabetic ef- octylamino)perylene-3,4:9,10-bis(dicarboximide)s and their Craig Venter, The Sorcerer II global ocean sampling expedi- 

fects of thiazolidinediones, J. Clin. Invest, 117, 1658-1669 radical cations: Synthesis, electrochemistry, and ENDOR tion: expanding the universe of protein families, PLoS Biol, 

(2007). spectroscopy, J. Org. Chem, 71, 2107-2114 (2006). 

5, 432-466 (2007). 

Jin Sun, Francine Battaglia and Shankar Subramaniam, Richard F. Kelley, Michael J. Tauber, Thea M. Wilson and Natarajan Kannan, Susan S. Taylor, Yufeng Zhai, J. Craig 

Hybrid two-fluid DEM simulation of gas-solid fluidized Michael R. Wasielewski, Controlling energy and charge Venter and Gerard Manning, Structural and functional diverbeds, 

J. Fluids Eng, 129, 1394-1403 (2007). transfer in linear chlorophyll dimers, Chem. Commun. (Cam- sity of the microbial kinome, PLoS Biol, 5, 467-478 (2007). 

Robert W. Byrnes, Eoin Fahy and Shankar Subramaniam, bridge, U. K.), 42, 4407-4409 (2007). 

Natarajan Kannan, Nina Haste, Susan S. Taylor and An- 

A laboratory information management system for high- Christina M. Stuart, Michael J. Tauber and Richard A. Ma- drew F. Neuwald, The hallmark of AGC kinase functional dithroughput 

experimental lipidomics: Minimal information re- thies, Structure and Dynamics of the Solvated Electron in Al- vergence is its C-terminal tail, a cis-acting regulatory mod- 

quired for the analysis of lipidomics experiments (MIALE), cohols from Resonance Raman Spectroscopy, J. Phys. Chem. ule, Proc. Natl. Acad. Sci. U. S. A, 104, 1272-1277 (2007). 

JALA, 12, 230-238 (2007). A, 111, 8390-8400 (2007). 

Rahul Das, Veronica Esposito, Mona Abu-Abed, Ganesh 

Kara Schmelzer, Eoin Fahy, Shankar Subramaniam and S. Anand, Susan S. Taylor and Giuseppe Melacini, cAMP ac- 

Edward A. Dennis, The lipid maps initiative in lipidomics, 


Eoin Fahy, Dawn Cotter, Robert Byrnes, Manish Sud, Andrea 

Maer, Joshua Li, David Nadeau, Yihua Zhau and Shankar 

Subramaniam, Bioinformatics for lipidomics, Methods 

Enzymol, 432, 247-273 (2007). 

Purnima Guda, Shankar Subramaniam and Chittibabu 

Guda, Mitoproteome: human heart mitochondrial protein sequence 

database, Methods Mol. Biol. (Totowa, NJ, U. S.), 

357, 375-383 (2007). 

Joelle R. Zavzavadjian, Sam Couture, Wei Sun Park, 

James Whalen, Stephen Lyon, Genie Lee, Eileen Fung, 

Qingli Mi, Jamie Liu, Estelle Wall, Leah Santat, Kavitha 

Dhandapani, Christine Kivork, Adrienne Driver, Xiaocui 

Zhu, Mi Sook Chang, Baljinder Randhawa, Elizabeth Gehrig, 

Heather Bryan, Mary Verghese, Andreia Maer, Brian Saunders, 

Yuhong Ning, Shankar Subramaniam, Tobias Meyer, 

Melvin I. Simon, Nancy O’Rourke, Grischa Chandy and Iain 

D. C. Fraser, The alliance for cellular signaling plasmid collection: 

a flexible resource for protein localization studies 

and signaling pathway analysis, Mol. Cell. Proteomics, 6, 

413-424 (2007). 

Manish Sud, Eoin Fahy, Dawn Cotter, Alex Brown, Edward 

A. Dennis, Christopher K. Glass, Alfred H. Merrill, Jr., 

Robert C. Murphy, Christian R. H. Raetz, David W. Russell 

and Shankar Subramaniam, LMSD: LIPID MAPS structure 

database, Nucleic Acids Res, 35, D527-D532 (2007). 

Ying Xu and Shankar Subramaniam, Consistent modeling 

TAYLOR, SUSAN S. (b.1942) Professor. B.A, 1964, 

University of Wisconsin; Ph.D, 1968, The Johns Hopkins 

University. Postdoctoral Fellowship, 1969-1971, 

Laboratory of Molecular Biology, Cambridge, England; 

Postdoctoral Fellowship, 1971-1972, University of California, 

San Diego. Biochemistry; Crystallography. 

CAMP-dependent Protein Kinase: Dynamics of Structures 

and Localization cAMP-dependent protein kinase 

(cAPK) serves as a prototype for the entire protein kinase 

superfamily. Crystal structures of the RIa and RIIb 

cAMP binding domains of the R subunits show clear isoform 

differences. From these structures we can more fully 

appreciate the conformational versatility of this ancient 

signaling module that binds cAMP and mediates a 

biological response. This stable module binds with high 

affinity to scaffold proteins. The molecular basis for targeting 

has been elucidated by solving high-resolution 

structures of two D/D domains by hetero nuclear NMR 

in collaboration with Dr. Patricia Jennings. Isoform dif- 

ferences in PKA targeting are being explored. We have 

identified two novel AKAPs that bind to both RIa and 

RIIb. Both target cAPK to mitochondria. We are beginning 

to elucidate the molecular basis for this targeting. 

TEL: (858) 534-3677 FAX: (858) 534-8193 

Web: susantaylorlab.ucsd.edu/ 

Email: staylor@ucsd.edu 

tivation of PKA defines an ancient signaling mechanism, 

Proc. Natl. Acad. Sci. U. S. A, 104, 93-98 (2007). 

Jian Wu, Simon H. J. Brown, Sventja von Daake and Su- 

san S. Taylor, PKA Type II� Holoenzyme Reveals a Combinatorial 

Strategy for Isoform Diversity, Science (Washington, 

DC, U. S.), 318, 274-279 (2007). 

Susan S. Taylor, Choel Kim, Cecilia Y. Cheng, Simon H. 

J. Brown, Jian Wu and Natarajan Kannan, Signaling through 

cAMP and cAMP-dependent protein kinase: Diverse strategies 

for drug design, Biochim. Biophys. Acta, Proteins Pro- 

teomics, 1784, 16-26 (2008). 

Lynn F. Ten Eyck, Susan S. Taylor and Alexandr P. Kornev, 

Conserved spatial patterns across the protein kinase 

family, Biochim. Biophys. Acta, Proteins Proteomics, 1784, 

238-243 (2008). 

Natarajan Kannan, Andrew F. Neuwald and Susan S. Tay- 

lor, Analogous regulatory sites within the �C-�4 loop re- 

gions of ZAP-70 tyrosine kinase and AGC kinases, Biochim. 

Biophys. Acta, Proteins Proteomics, 1784, 27-32 (2008). 

Natarajan Kannan and Susan S. Taylor, Rethinking pseu- 

dokinases, Cell (Cambridge, MA, U. S.), 133, 204-205 

(2008). 

Yuliang Ma and Susan S. Taylor, A Molecular Switch for 

Targeting between Endoplasmic Reticulum (ER) and Mito- 

chondria: Conversion of a mitochondria-targeting element 

into an er-targeting signal in DAKAP1, J. Biol. Chem, 283, 

11743-11751 (2008). 

Alexandr P. Kornev, Susan S. Taylor and Lynn F. Ten 

of interphase turbulent kinetic energy transfer in particle-laden 

turbulent flows, Phys. Fluids, 19, 085101/1-085101/9 

Publication list has not been verified by the department. Eyck, A generalized allosteric mechanism for cis-regulated 

cyclic nucleotide binding domains, PLoS Comput. Biol, 4, 

(2007). Ganesh Anand, Susan S. Taylor and David A. Johnson, No pp. given (2008). 

Srinivasan Ramachandran, Lai-Hua Xie, Scott A. John, Cyclic-AMP and Pseudosubstrate Effects on Type-I A-Ki- Alexandr P. Kornev, Susan S. Taylor and Lynn F. Ten 

Shankar Subramaniam and Ratnesh Lal, A novel role for nase Regulatory and Catalytic Subunit Binding Kinetics, Bio- Eyck, A helix scaffold for the assembly of active protein kiconnexin 

hemichannel in oxidative stress and smoking-in- chemistry, 46, 9283-9291 (2007). nases, Proc. Natl. Acad. Sci. U. S. A, 105, 14377-14382 

duced cell injury, PLoS One, 2, No pp. given (2007). Choel Kim, Cecilia Y. Cheng, S. Adrian Saldanha and Su- (2008). 

Colin T. Walsh, Julie Radeff-Huang, Rosalia Matteo, Al- san S. Taylor, PKA-I holoenzyme structure reveals a mecha- Larry R. Masterson, Alessandro Mascioni, Nathaniel J. 

bert Hsiao, Shankar Subramaniam, Dwayne Stupack and nism for cAMP-dependent activation, Cell (Cambridge, MA, Traaseth, Susan S. Taylor and Gianluigi Veglia, Allosteric 

Joan Heller Brown, Thrombin receptor and RhoA mediate U. S.), 130, 1032-1043 (2007). cooperativity in protein kinase A, Proc. Natl. Acad. Sci. U. S. 

cell proliferation through integrins and cysteine-rich protein Brent R. Martin, Thomas J. Deerinck, Mark H. Ellisman, A, 105, 506-511 (2008). 

61, FASEB J, 22, 4011-4021 (2008). Susan S. Taylor and Roger Y. Tsien, Isoform-Specific PKA Ali Torkamani, Natarajan Kannan, Susan S. Taylor and


Nicholas J. Schork, Congenital disease SNPs target lineage Email: mht@chem.ucsd.edu 

of a transcriptional terminator, Nucleic Acids Research, 34, 

specific structural elements in protein kinases, Proc. Natl. mthiemens@ucsd.edu 

6461-6471 (2006). 

Acad. Sci. U. S. A, 105, 9011-9016 (2008). S. A. Aireau, J. Farquhar, M. H. Thiemens, L. A. Leshin, K. S. Keating, N. Toor and A. M. Pyle, The GANC tetra- 

Natarajan Kannan, Nina Haste, Susan S. Taylor and An- H. Bao and E. Young, Planetesimal sulfate and aqueous al- loop receptor interaction, Journal of Molecular Biology, 383, 

drew F. Neuwald, The hallmark of AGC kinase functional di- teration in CM and CI carbonaceous chondrites, Geochinica 475-481 (2008). 

vergence is its C-terminal tail, a cis-acting regulatory mod- Cosmochimica Acta, 69, 4166-4171 (2005). 

N. Toor, K. Rajashankar, K. S. Keating and A. M. Pyle, 

ule. [Erratum to document cited in CA146:333062], Proc. R. Jost, G. Michalski and M. H. Thiemens, Comparison of Structural basis of exon recognition by a group II intron, Na- 

Natl. Acad. Sci. U. S. A, 105, 9130 (2008). rovibronic density of symmetric versus symmetric NO2 iso- ture Structural and Molecular Biology, 15, 1221-1222 

topologues at dissociation threshold: Broken symmetry ef- (2008). 

TEZCAN, F. AKIF (b.1972) Assistant Professor. A.B, fects, J. (Chemistry). Physics, 123, 054230 (2005). 

N. Toor, K. S. Keating, S. D. Taylor and A. M. Pyle, Crys- 

1995, Macalester College; Ph.D, 2001, Caltech. Re- J. R. McCabe, C. S. Boxe, A. J. Colussi, M. R. Hoffmann tal structure of a self-spliced group II intron, Science, 320, 

search Fellow, 2001-2005, Caltech. Bioinorganic Chem- and M. H. Thiemens, Oxygen isotopic fractionation in the 77-82 (2008). 

istry. Metal-Protein and Protein-Protein Interactions photochemistry of nitrate and ice, J. Geophys. Res, 110, D15- 

Metal-Directed Protein Self-Assembly Biological Nitro- D15310 (2005). TOR, YITZHAK (b.1960) Professor. B.Sc, 1982, Telgen 

Fixation. TEL: (858) 534-4862 FAX: (858) 534- B. Alexander, R. J. Park, D. J. Jacob, Q. B. Li, R. M. Yan- Aviv University, Israel; Ph.D, 1990, The Weizmann In- 

6157 

tosca, J. Savarino, C. C. W. Lee and M. H. Thiemens, Sulfate stitute of Science, Israel. Weizmann Postdoctoral Fel- 

Web: tezcan.ucsd.edu 

formation in sea-salt aerosols: Constraints from oxygen iso- lowship, 1990-1993, California Institute of Technology. 

topes, J. Geophys. Res. Atmospheres). J. Geophys. Res, 110, 

Email: tezcan@ucsd.edu 

Bioorganic Chemistry; Organic Chemistry. RNA–small 

D10307 (2005). 

Eric N. Salgado, Jasmin Faraone-Mennella and F. Akif V. K. Rai, T. L. Jackson and M. H. Thiemens, Photochem- 

molecule interactions; antiviral and antibacterial agents; 

Tezcan, Controlling Protein-Protein Interactions through ical mass independent sulfur isotopes in achondritic meteornew emissive nucleosides and oligonucleotides; novel 

Metal Coordination: Assembly of a 16-Helix Bundle Protein, ites, Science, 309, 1062-1065 (2005). 

cellular delivery agents. TEL: (858) 534-6401 FAX: 

J. Am. Chem. Soc, 129, 13374-13375 (2007). Mark H. Thiemens, History and applications of mass inde- (858) 534-0202 

Eric N. Salgado, Richard A. Lewis, Jasmin Faraone-Men- pendent isotope effects, Annual Reviews of Earth and Plane- Web: www-chem.ucsd.edu/research/profile.cfm?cid= 

nella and F. Akif Tezcan, Metal-Mediated Self-Assembly of tary Sciences, 34, 217-262 (2006). 

C02218 

Protein Superstructures: Influence of Secondary Interactions T. A. Mather, J. R. McCabe, V. K. Rai, M. K. Thiemens, Email: ytor@ucsd.edu 

on Protein Oligomerization and Aggregation, J. Am. Chem. D. M. Pyle, T. H. E. Heaton, H. J. Sloane and G. Fern, Oxy- 

Soc, 130, 6082-6084 (2008). 

Lev Elson-Schwab and Yitzhak Tor, Targeting HIV-1 

gen and sulfur isotopic composition of volcanic sulfate aero- RNA with aminoglycoside antibiotics and their derivatives, 

sol at the point of emission, J. Geophys. Res, 111, D18205 

Aminoglycoside Antibiot, 267-287, 2 plates (2007). 

THEODORAKIS, EMMANUEL A. (b.1964) Pro- (2006). 

Christopher M. Barbieri, Malvika Kaul, Melanie Bozzafessor. 

B.S, 1987, University of Athens, Greece; M.S, J. Savarino, J. Kaiser, S. Morin, D. M. Sigman and M. H. 

Hingos, Fang Zhao, Yitzhak Tor, Thomas Hermann and Dan- 

1989, University of Paris XI, France; Ph.D, 1993, Uni- Thiemens, Nitrogen and oxygen isotopic constraints on the 

iel S. Pilch, Defining the molecular forces that determine the 

versity of Paris XI, France. Postdoctoral, 1993-1995, origin of atmospheric nitrate in coastal Antarctica, Atmos. 

impact of neomycin on bacterial protein synthesis: impor- 

Scripps Research Institute. Bioorganic Chemistry; Or- Chem. Phys, 7, 1925-1945 (2007). 

tance of the 2’-amino functionality, Antimicrob. Agents Cheganic 

Chemistry. Synthesis of natural products; develop- M. De Angelis, M. H. Thiemens, J. Savarino and J. R. Pet- 

mother, 51, 1760-1769 (2007). 

it, Contributions of an ancient evaporitic-type reservoir to 

ment of synthetic methodology; and interaction of organ- Seergazhi G. Srivatsan and Yitzhak Tor, Fluorescent Py- 

Lake Vostok chemistry, Earth and Planetary Science Letters, 

ic molecules with biomolecules. TEL: (858) 822-0456 

rimidine Ribonucleotide: Synthesis, Enzymatic Incorpora- 

222, 751-765 (2007). 

FAX: (858) 822-0386 Tetsuya Yokoyama, Vinai K. Rai, Conel M. O’D. Alexantion, 

and Utilization, J. Am. Chem. Soc, 129, 2044-2053 

Web: www.chem-faculty.ucsd.edu/Theodorakis/index. der, Roy S. Lewis, Richard W. Carlson, Steven B. Shirey, 

(2007). 

html Mark H. Thiemens and Richard J. Walker, Osmium isotope 

Victor K. Tam, Denise Kwong and Yitzhak Tor, Fluores- 

Email: etheodor@ucsd.edu evidence for uniform distribution of s- and r-process compo- 

cent HIV-1 Dimerization Initiation Site: Design, Properties, 

nents in the early Solar system, Earth Planet. Sci. Lett, 259, 

and Use for Ligand Discovery, J. Am. Chem. Soc, 129, 3257- 

Gianni Guizzunti, Thomas P. Brady, Vivek Malhotra and 

567-580 (2007). 

3266 (2007). 

Emmanuel A. Theodorakis, Trifunctional norrisolide probes 

Vinai K. Rai and Mark H. Thiemens, Mass independently 

Edith C. Glazer, Douglas Magde and Yitzhak Tor, Ruthefor 

the study of Golgi vesiculation, Bioorg. Med. Chem. Lett, 

fractionated sulfur components in chondrites, Geochim. Cosnium 

Complexes That Break the Rules: Structural Features 

17, 320-325 (2007). 

mochim. Acta, 71, 1341-1354 (2007). 

Controlling Dual Emission, J. Am. Chem. Soc, 129, 8544- 

Derek Fischer and Emmanuel A. Theodorakis, Studies on 

M. A. Tyra, J. Farquhar, B. A. Wing, G. K. Benedix, A. J. 

8551 (2007). 

the synthesis of Schisandraceae natural products: exploring a 

T. Jull, T. Jackson and M. H. Thiemens, Terrestrial alteration 

Lev Elson-Schwab, Omai B. Garner, Manuela Schuksz, 

cyclopropylcarbinol ring expansion strategy, Eur. J. Org. 

of Antarctic CM chondrite meteorites in a suite of Antarctic 

Brett E. Crawford, Jeffrey D. Esko and Yitzhak Tor, Guani- 

Chem, 4193-4196 (2007). 

CM chondrites: Evidence from oxygen and carbon isotopes, 

dinylated Neomycin Delivers Large, Bioactive Cargo into 

Paqui G. Traves, Sonsoles Hortelano, Miriam Zeini, Ta- 

Geochimica Cosmochimica Acta, 71, 782-795 (2007). 

Cells through a Heparan Sulfate-dependent Pathway, J. Biol. 

Hsiang Chao, Thanh Lam, Saskia T. Neuteboom, Emmanuel 

S. A. Ewing, G. Michalski, M. Thiemens, R. C. Quinn, J. 

Chem, 282, 13585-13591 (2007). 

A. Theodorakis, Michael A. Palladino, Antonio Castrillo and 

L. Macalady, S. Kohl, S. D. Wankel, C. Kendall, C. P. 

Seergazhi G. Srivatsan and Yitzhak Tor, Synthesis and en- 

Lisardo Bosca, Selective activation of liver X receptors by 

McKay and R. Amundson, Rainfall limit of the N cycle on 

zymatic incorporation of a fluorescent pyrimidine ribonuacanthoic 

acid-related diterpenes, Mol. Pharmacol, 71, 1545- 

Earth, Global Biogeochemical Cycles, 21, GB3009 (2007). 

cleotide, Nat. Protoc, 2, 1547-1555 (2007). 

1553 (2007). 

Justin R. McCabe, Mark H. Thiemens and Joel Savarino, A 

Nicholas J. Greco and Yitzhak Tor, Synthesis and site-spe- 

Derek Fischer, Emmanuel A. Theodorakis and Mark A. 

record of ozone variability in South Pole Antarctic snow: role 

cific incorporation of a simple fluorescent pyrimidine, Nat. 

Haidekker, Synthesis and use of an in-solution ratiometric 

of nitrate oxygen isotopes, J. Geophys. Res., [Atmos.], 112, 

Protoc, 2, 305-316 (2007). 

fluorescent viscosity sensor, Nat. Protoc, 2, 227-236 (2007). 

D12303/1-D12303/9 (2007). 

Renatus W. Sinkeldam and Yitzhak Tor, To D or not to D? 

Mark A. Haidekker and Emmanuel A. Theodorakis, Mo- 

N. Patris, S. S. Cliff, P. K. Quinn, M. Kasem and M. H. 

On estimating the microenvironment polarity of biomoleculecular 

rotors-fluorescent biosensors for viscosity and flow, 

Thiemens, Isotopic analysis of aerosol sulfate and nitrate durlar 

cavities, Org. Biomol. Chem, 5, 2523-2528 (2007). 

Org. Biomol. Chem, 5, 1669-1678 (2007). 

ing ICT-2k2: Determination of different formation pathways 

Nicholas J. Greco and Yitzhak Tor, Furan decorated nucle- 

Ayse Batova, Thanh Lam, Veit Wascholowski, Alice L. 

as a function of particle size, J. Geophysical Research, 112, 

oside analogues as fluorescent probes: synthesis, photophysi- 

Yu, Athanassios Giannis and Emmanuel A. Theodorakis, 

D23301 (2007). 

cal evaluation, and site-specific incorporation, Tetrahedron, 

Synthesis and evaluation of caged Garcinia xanthones, Org. 

Yuki Kimura, Joseph A. Nuth, III, Subrata Chakraborty 

63, 3515-3527 (2007). 

Biomol. Chem, 5, 494-500 (2007). 

and Mark H. Thiemens, Non-mass-dependent oxygen isoto- 

Seergazhi G. Srivatsan and Yitzhak Tor, Using an emissive 

Matthew E. Nipper, Sheereen Majd, Michael Mayer, James 

pic fractionation in smokes produced in an electrical disuridine 

analogue for assembling fluorescent HIV-1 TAR con- 

C.-M. Lee, Emmanuel A. Theodorakis and Mark A. Hai- 

charge, Meteorit. Planet. Sci, 42, 1429-1439 (2007). 

structs, Tetrahedron, 63, 3601-3607 (2007). 

dekker, Characterization of changes in the viscosity of lipid 

Melanie Baroni, Mark H. Thiemens, Robert J. Delmas and 

Yitzhak Tor, Susan Del Valle, David Jaramillo, Seergazhi 

membranes with the molecular rotor FCVJ, Biochim. Bio- 

Joel Savarino, Mass-independent sulfur isotopic composi- 

G. Srivatsan, Andro Rios and Haim Weizman, Designing 

phys. Acta, Biomembr, 1778, 1148-1153 (2008). 

tions in stratospheric volcanic eruptions, Science (Washingnew 

isomorphic fluorescent nucleobase analogues: the thieno 

Alba Diaz-Rodriguez, Susana Fernandez, Yogesh S. 

ton, DC, U. S.), 315, 84-87 (2007). 

[3,2-d]pyrimidine core, Tetrahedron, 63, 3608-3614 (2007). 

Sanghvi, Emmanuel A. Theodorakis, Vicente Gotor and Mi- 

Gerardo Dominguez, Terri Jackson, Burton Brothers, 

Seergazhi Srivatsan, Nicholas J. Greco and Yitzhak Tor, A 

guel Ferrero, Synthesis of 2’,3’-cyclohexene bicyclic nucleo- 

Bryan Nguyen and Mark H. Thiemens, Discovery and meahighly 

emissive fluorescent nucleoside that signals the activiside 

analogues as antiviral compounds, Nucleic Acids Symp. 

surement of an isotopically distinct source of sulfate in 

ty of toxic ribosome-inactivation proteins, Angew. Chem., 

Ser, 52, 99-100 (2008). 

Earth’s atmosphere, Proc. Natl. Acad. Sci. U. S. A, 105, 

Int. Ed, 47, 6661-6665 (2008). 

12769-12773 (2008). 

Renatus W. Sinkeldam, Nicholas J. Greco and Yitzhak 

Derek A. Fischer, Synthetic studies toward complex natu- 

Subrata Chakraborty, Musahid Ahmed, Teresa L. Jackson 

Tor, Polarity of major grooves explored by using isosteric 

ral products. (D) 

and Mark H. Thiemens, Experimental Test of Self-Shielding 

emissive nucleoside, ChemBioChem, 9, 706-709 (2008). 

Fatima R. Rivas, Synthetic studies towards the total synin 

Vacuum Ultraviolet Photodissociation of CO, Science 

Seergazhi G. Srivatsan, Haim Weizman and Yitzhak Tor, 

thesis of norzoanthamine. (D) 


A highly fluorescent nucleoside analog based on thieno[3,4- 

Thanh T. Lam, synthetic studies towards diterpenes; synd]pyrimidine 

senses mismatched pairing, Org. Biomol. 

thetic studies towards the caged garcinia xanthones. (D) 

Chem, 6, 1334-1338 (2008). 

Thomas Patrick Brady, Total synthesis of norrisolide, syn- TOOR, NAVTEJ SINGH (b.1973) Assistant Profes- 

Manuela Schuksz, Mark M. Fuster, Jillian R. Brown, Brett 

thesis of norrisolide analogues, and biological evaluation of sor. B.Sc, 1996, University of Calgary; Ph.D, 2004, Uni- E. Crawford, David P. Ditto, Roger Lawrence, Charles A. 

norrisolide probes. (D) versity of Calgary. Howard Hughes Medical Institute Glass, Lianxhun Wang, Yitzhak Tor and Jeffrey D. Esko, 

Postdoctoral Fellow, 2004-2009, Yale University. Bio- Surfen, a small molecule antagonist of heparan sulfate, Proc. 

THIEMENS, MARK H. (b.1950) Professor and chemistry; Structural Biology. Group II introns are self- Natl. Acad. Sci. U. S. A, 105, 13075-13080 (2008). 

Dean. B.S, 1972, University of Miami; M.S, 1974, Old splicing RNAs which are thought to be the ancestors of 

Dominion University; Ph.D, 1977, Florida State Univer- both retrotransposons and spliceosomal introns, which Nicholas J. Greco, Design, synthesis and application of 

sity. Postdoctoral Fellowship, 1977-1980, University of together make up more than 50% of the human genome. novel fluorescent nucleosides. (D) 

Chicago. Atmospheric Chemistry; Physical Chemistry. My research interests include studying the structure and Victor K. Tam, Targeting unique nucleic acid structures 

Measurement of isotope ratios in atmospheric species; function of group II introns, as well as the spliceosome, with small molecules. (D) 

application of high precision stable isotope ratio mea- using a combination of x-ray crystallography and 

surement to resolve quantum chemical astrophysical and biochemistry. TEL: (858) 534-3211 FAX: (858) 534- TROGLER, WILLIAM C. Professor. B.A, 1974, 

atmospheric processes; studies on the evolution of the 6255 

Johns Hopkins; M.A, 1974, Johns Hopkins; Ph.D, 1977, 

solar system and nucleosynthesis. Paleoclimatology and Email: ntoor@ucsd.edu 

California Institute of Technology. Materials Chemistry; 

ice core studies. Investigations of the origin and evolu- N. Toor, A. R. Robart, J. Christianson and S. Zimmerly, Nanochemistry. Inorganic polymers and nanoparticles as 

tion of planets and life. TEL: (858) 534-6882 FAX: Self-splicing of a group IIC intron: 5’ exon recognition and luminescent and electronic sensors for explosives. Char- 

(858) 822-0389 alternative 5’ splicing events implicate the stem-loop motif acterization of the chemoselectivity of field effect tran-


sistor and interdigitated electrode chemical sensors based 

on metallophthalocyanines. Use of hollow porous silica 

and titania nanoparticles in drug and gene delivery. TEL: 

(858) 534-6175 FAX: (858) 534-5383 


C02165 

Email: wtrogler@ucsd.edu 

Richard D. Yang, T. Gredig, Corneliu N. Colesniuc, Jenase 

D Revealed by a Genetically Encoded Kinase Activity 

Reporter, J. Biol. Chem, 282, 6733-6742 (2007). 

Oded Tour, Stephen R. Adams, Rex A. Kerr, Rene M. Meijer, 

Terrence J. Sejnowski, Richard W. Tsien and Roger Y. 

Tsien, Calcium Green FlAsH as a genetically targeted smallmolecule 

calcium indicator, Nat. Chem. Biol, 3, 423-431 

(2007). 

Christina T. Hauser and Roger Y. Tsien, A hexahistidine- 

Zn 

live cells and in vivo. Study the origin and evolution of 

the genetic code using genetic engineering and synthetic 

biology methods. TEL: (858) 453-4100 FAX: (858) 597- 

0855 

Web: wang.salk.edu 

Email: lwang@salk.edu 

L. Wang and P. G. Schultz, Expanding the genetic code, 

Angewandte Chemie International Edition, 44, 34-66 (2005). 

2+-dye 

ongwon Park, Ivan K. Schuller, William C. Trogler and Andrew 

C. Kummel, Ultrathin organic transistors for chemical 

sensing, Appl. Phys. Lett, 90, 263506/1-263506/3 (2007). 

Jason C. Sanchez, Antonio G. DiPasquale, Arnold L. 

Rheingold and William C. Trogler, Synthesis, Luminescence 

Properties, and Explosives Sensing with 1,1-Tetraphenylsilole- 

and 1,1-Silafluorene-vinylene Polymers, Chem. Mater, 

19, 6459-6470 (2007). 

Forest I. Bohrer, Amos Sharoni, Corneliu Colesniuc, Jeongwon 

Park, Ivan K. Schuller, Andrew C. Kummel and 

label reveals STIM1 surface exposure, Proc. Natl. 

Acad. Sci. U. S. A, 104, 3693-3697 (2007). 

Nathan C. Shaner, Michael Z. Lin, Michael R. McKeown, 

Paul A. Steinbach, Kristin L. Hazelwood, Michael W. Davidson 

and Roger Y. Tsien, Improving the photostability of 

bright monomeric orange and red fluorescent proteins, Nat. 

Methods, 5, 545-551 (2008). 

Damian J. Wallace, Stephan Meyer zum Alten Borgloh, Simone 

Astori, Ying Yang, Melanie Bausen, Sebastian Kue- 

gler, Amy E. Palmer, Roger Y. Tsien, Rolf Sprengel, Jason 

N. D. Kerr, Winfried Denk and Mazahir T. Hasan, Single- 

spike detection in vitro and in vivo with a genetic Ca 

Y. Zhang, L. Wang, P. G. Schultz and I. A. Wilson, Crys- 

tal structures of apo Wild-Type M. jannaschii TyrRS and a 

mutant synthetase specific for O-Methyl-L-Tyrosine, Protein 

Science, 14, 1340-1349 (2005). 

L. Wang, J. Xie and P. G. Schultz, Exanding the genetic 

code, Annual Review of Biophysics and Biomolecular Structure, 

35, 225-249 (2006). 

A. R. Parrish, W. Wang and L. Wang, Manipulating pro- 

teins for neuroscience, Current Opinion in Neurobiology, 16, 

585-592 (2006). 

L. Wang and R. Y. Tsien, Evolving proteins in mammalian 

2+ William C. Trogler, Gas Sensing Mechanism in Chemiresis- 

tive Cobalt and Metal-Free Phthalocyanine Thin Films, J. 

Am. Chem. Soc, 129, 5640-5646 (2007). 

Richard D. Yang, Jeongwon Park, Corneliu N. Colesniuc, 

Ivan K. Schuller, William C. Trogler and Andrew C. Kum- 

mel, Ultralow drift in organic thin-film transistor chemical 

sensors by pulsed gating, J. Appl. Phys, 102, 034515/1- 

034515/7 (2007). 

Sarah J. Toal, Jason C. Sanchez, Regina E. Dugan and 

William C. Trogler, Visual detection of trace nitroaromatic 

explosive residue using photoluminescent metallole-containing 

polymers, J. Forensic Sci, 52, 79-83 (2007). 

Sarah L. Blair, Jessica Wang-Rodriguez, Maria J. Cortes, 

Davorka Messmer, Andrew C. Kummel and William C. Trogler, 

Enhanced touch preps to improve the ease of interpretation 

of intra-operative breast cancer margins, The American 

Surgeon, 73, 973-976 (2007). 

Jeongwon Park, Richard D. Yang, Corneliu N. Colesniuc, 

Amos Sharoni, Sungho Jin, Ivan K. Schuller, William C. 

Trogler and Andrew C. Kummel, Bilayer processing for an 

enhanced organic-electrode contact in ultrathin bottom contact 

organic transistors, Appl. Phys. Lett, 92, 193311/1- 

193311/3 (2008). 

Jian Yang, Johan U. Lind and William C. Trogler, Synthesis 

of Hollow Silica and Titania Nanospheres, Chem. Mater, 

20, 2875-2877 (2008). 

Forest I. Bohrer, Corneliu N. Colesniuc, Jeongwon Park, 

Ivan K. Schuller, Andrew C. Kummel and William C. Trogler, 

Selective Detection of Vapor Phase Hydrogen Peroxide 

with Phthalocyanine Chemiresistors, J. Am. Chem. Soc, 130, 

3712-3713 (2008). 

Jason C. Sanchez and William C. Trogler, Efficient blueemitting 

silafluorene-fluorene-conjugated copolymers: selective 

turn-off/turn-on detection of explosives, J. Mater. Chem, 

18, 3143-3156 (2008). 

Jason C. Sanchez and William C. Trogler, Hydrosilylation 

of diynes as a route to functional polymers delocalized 

through silicon, Macromol. Chem. Phys, 209, 1527-1540 

(2008). 

Jason C. Sanchez, Sara A. Urbas, Sarah J. Toal, Antonio 

G. DiPasquale, Arnold L. Rheingold and William C. Trogler, 

Catalytic Hydrosilylation Routes to Divinylbenzene Bridged 

Silole and Silafluorene Polymers. Applications to Surface 

Imaging of Explosive Particulates, Macromolecules (Washington, 

DC, U. S.), 41, 1237-1245 (2008). 

sensor, 

Nat. Methods, 5, 797-804 (2008). 

Stephen R. Adams and Roger Y. Tsien, Preparation of the 

membrane-permeant biarsenicals FlAsH-EDT2 and ReAsH- 

EDT2 for fluorescent labeling of tetracysteine-tagged proteins, 

Nat. Protoc, 3, 1527-1534 (2008). 

Samuel Andrew Hires, Yongling Zhu and Roger Y. Tsien, 

Optical measurement of synaptic glutamate spillover and reuptake 

by linker optimized glutamate-sensitive fluorescent 

reporters, Proc. Natl. Acad. Sci. U. S. A, 105, 4411-4416 

(2008). 

Michael Z. Lin, Jeffrey S. Glenn and Roger Y. Tsien, A 

drug-controllable tag for visualizing newly synthesized proteins 

in cells and whole animals, Proc. Natl. Acad. Sci. U. S. 

A, 105, 7744-7749 (2008). 

Emilia Olson, Detecting pathological protease activity with 

activatable cell penetrating peptides (ACPP’s). (D) 

TUKEY, ROBERT H. (b.1949) Professor. B.Sc, 

1973, University of Minnesota; Ph.D, 1980, University 

of Iowa. Pharmacology. Environmental toxicology: The 

role of environmental and chemical toxicants on gene expression. 

TEL: (858) 822-0288 FAX: (858) 822-0363 

Web: superfund.ucsd.edu/ 

Email: rtukey@ucsd.edu 

Kathy Senekeo-Effenberger, Shujuan Chen, Erin Brace- 

Sinnokrak, Jessica A. Bonzo, Mei-Fei Yueh, Upendra Argi- 

kar, Jenny Kaeding, Jocelyn Trottier, Rory P. Remmel, Jo- 

seph K. Ritter, Olivier Barbier and Robert H. Tukey, Expression 

of the human UGT1 locus in transgenic mice by 4-chloro-6-(2,3-xylidino)-2-pyrimidinylthioacetic 

acid (WY-14643) 

and implications on drug metabolism through peroxisome 

proliferator-activated receptor � activation, Drug Metab. 

Dispos, 35, 419-427 (2007). 

Jessica A. Bonzo, Alain Belanger and Robert H. Tukey, 

The role of chrysin and the Ah receptor in induction of the 

human UGT1A1 gene in vitro and in transgenic UGT1 mice, 

Hepatology (Hoboken, NJ, U. S.), 45, 349-360 (2007). 

Theresa N. Operana and Robert H. Tukey, Oligomerization 

of the UDP-glucuronosyltransferase 1A Proteins: Homo- and 

heterodimerization analysis by fluorescence resonance energy 

transfer and co-immunoprecipitation, J. Biol. Chem, 282, 

4821-4829 (2007). 

Mei-Fei Yueh and Robert H. Tukey, Nrf2-Keap1 Signaling 

cells using somatic hypermutation, Nature Protocols, 1, 

1346-1350 (2006). 

W. Wang, J. K. Takimoto, G. V. Louie, T. J. Baiga, J. P. 

Noel, K.-F. Lee, P. A. Slesinger and L. Wang, Genetically 

encoding unnatural amino acids for cellular and neuronal 

studies, Nature Neuroscience, 10, 1063-1072 (2007). 

D. B. F. Johnson, J. K. Takimoto, J. Xu and L. Wang, Unnatural 

amino acids to investigate biological processes, Wiley 

Encyclopedia of Chemical Biology, doi:10.1002/ 

9780470048672 (2007). 

Q. Wang and L. Wang, New methods enabling efficient incorporation 

of unnatural amino acids in yeast, Journal of the 

American Chemical Society, 130, 6066-6067 (2008). 

M. Z. Lin and L. Wang, Selective labeling of proteins with 

chemical probes in living cells, Physiology, 23, 131-141 

(2008). 

WANG, WEI Associate Professor. Postdoctoral Fellow, 

2001-2003, Stanoford University. Bioinformatics; 

Computational Chemistry. TEL: (858) 822-4240 FAX: 

(858) 822-4236 

Web: wanglab.ucsd.edu 

Email: wei-wang@ucsd.edu 


WATSON, JOSEPH W. 


WEARE, JOHN H. (b.1940) Professor. B.S, 1962, 

Harvey Mudd College; Ph.D, 1968, The Johns Hopkins 

University. AFOSR Fellowship, 1968-1969, M.I.T; Gug- 

genheim Fellowship, 1976-1977, Harvard University. 

Theoretical chemistry; ab initio molecular dynamics; 

theory of clusters, surfaces, and condensed matter; theory 

of geochemical processes. TEL: (858) 534-3286 FAX: 

(858) 534-7244 

Web: www.chem.ucsd.edu/Faculty/Research_text/ 

weare.html 

Email: jweare@ucsd 


Eric J. Bylaska, Marat Valiev, James R. Rustad and John 

H. Weare, Structure and dynamics of the hydration shells of 

the Al3+ Forest I. Bohrer, Gas sensing mechanisms in chemiresistive 

metal phthalocyanine nanofilms. (D) 

Jason C. Sanchez, Design and optimization of polymeric 

silole and boronate photoluminescent probes for improved 

Pathway Regulates Human UGT1A1 Expression in Vitro and 

in Transgenic UGT1 Mice, J. Biol. Chem, 282, 8749-8758 

(2007). 

Theresa N. Operana, Nghia Nguyen, Shujuan Chen, Deirdre 

Beaton and Robert H. Tukey, Human CYP1A1 

ion, J. Chem. Phys, 126, 104505/1-104505/8 (2007). 

Marat Valiev, Jie Yang, Joseph A. Adams, Susan S. Taylor 

and John H. Weare, Phosphorylation Reaction in cAPK Pro- 

tein Kinase-Free Energy Quantum Mechanical/Molecular 

Mechanics Simulations, J. Phys. Chem. B, 111, 13455-13464 

GFP explosives detection applications. (D) 

Expression 

in Transgenic Mice Serves as a Biomarker for Envi- 

(2007). 

TSIEN, ROGER Y. (b.1952) Professor. A.B, 1972, 

Harvard; Ph.D, 1977, University of Cambridge, Cambridge, 

UK. Comyns Berkeley Research Fellowship, 

1977-1981, Gonville & Caius College, Cambridge, U.K. 

Design, synth. and use of fluorescent indicators and photoreleasable 

messengers to probe intracellular signs such 

as Ca, inositol phosphates, cyclic nucleotides and nitric 

oxide; eng. of Green Fluorescent Protein; pharma’l ultrahigh-throughput 

screening. TEL: (858) 534-4891 FAX: 

(858) 534-5270 

Web: www.tsienlab.ucsd.edu 

Email: rtsien@ucsd.edu 

Hui-Wang Ai, Nathan C. Shaner, Zihao Cheng, Roger Y. 

Tsien and Robert E. Campbell, Exploration of New Chromophore 

Structures Leads to the Identification of Improved 

Blue Fluorescent Proteins, Biochemistry, 46, 5904-5910 

(2007). 

Brent R. Martin, Thomas J. Deerinck, Mark H. Ellisman, 

Susan S. Taylor and Roger Y. Tsien, Isoform-Specific PKA 

Dynamics Revealed by Dye-Triggered Aggregation and DA- 

KAP1�-Mediated Localization in Living Cells, Chem. Biol. 

(Cambridge, MA, U. S.), 14, 1031-1042 (2007). 

Stephen R. Adams and Roger Y. Tsien, Imaging the influx 

of cell-penetrating peptides into the cytosol of individual live 

cells, Handb. Cell-Penetrating Pept. (2nd Ed.), 505-513 

(2007). 

Maya T. Kunkel, Alex Toker, Roger Y. Tsien and Alexandra 

C. Newton, Calcium-dependent Regulation of Protein Kironmental 

Toxicant Exposure, Toxicol. Sci, 95, 98-107 

(2007). 

Nghia Nguyen, Jessica A. Bonzo, Shujuan Chen, Sarah 

Chouinard, Michael J. Kelner, Gary Hardiman, Alain Belan- 

ger and Robert H. Tukey, Disruption of the Ugt1 Locus in 

Mice Resembles Human Crigler-Najjar Type I Disease, J. 

Biol. Chem, 283, 7901-7911 (2008). 

Sarah Chouinard, Mei-Fei Yueh, Robert H. Tukey, Frank 

Giton, Jean Fiet, Georges Pelletier, Olivier Barbier and Alain 

Belanger, Inactivation by UDP-glucuronosyltransferase enzymes: 

The end of androgen signaling, J. Steroid Biochem. 

Mol. Biol, 109, 247-253 (2008). 

VIADIU, HECTOR Assistant Professor. TEL: (858) 

822-4486 FAX: (858) 822-4499 


C20803 

Email: viadiu@ucsd.edu 


Hector Viadiu, Tamir Gonen and Thomas Walz, Projection 

Map of Aquaporin-9 at 7 Å Resolution, J. Mol. Biol, 367, 80- 

88 (2007). 

WANG, LEI (b.1972) Assistant Professor. B.S, 1994, 

Peking University; Ph.D, 2002, University of California 

at Berkeley. Merck Fellow of the Damon Runyon Cancer 

Research Foundation, 2002-2005, University of California, 

San Diego. Chemical Biology. Genetically encoding 

novel amino acids to investigate biological processes in 

WEINBERGER, LEOR S. Assistant Professor. Ph.D, 

2004, UC Berkeley. Lewis Thomas Fellow, 2005-2007, 

Princeton University. Biochemistry. TEL: (858) 534- 

8671 FAX: (858) 246-0864 

Web: weinbergerlab.ucsd.edu 

Email: lsw@ucsd.edu 

Leor S. Weinberger and Thomas Shenk, An HIV feedback 

resistor: Auto-regulatory circuit deactivator and noise buffer, 

Los Alamos Natl. Lab., Prepr. Arch., Quant. Biol, 1-15 

(2007). 

Leor S. Weinberger and Thomas Shenk, An HIV feedback 

resistor: Auto-regulatory circuit deactivator and noise buffer, 

PLoS Biol, 5, 67-81 (2007). 

Leor S. Weinberger, Roy D. Dar and Michael L. Simpson, 

Transient-mediated fate determination in a transcriptional 

circuit of HIV, Nat. Genet, 40, 466-470 (2008). 

WEIZMAN, HAIM (b.1965) LPSOE. B.Sc, 1992, The 

Hebrew University of Jerusalem; M.S, 1994, The Weizmann 

Institute of Science; Ph.D, 1999, The Weizmann 

Institute of Science. Postdoctoral research fellow, 1999- 

2003, University of California, San Diego; Project Scientist, 

2003-2005, University of California, San Diego; 

Lecturer, 2003-2005, University of California, San Diego. 

Organic Chemistry. Chemical education: representa- 

tions, development of curriculum for organic and bioor- 

ganic chemistry, and cognitive process related to teaching 

of chemistry. TEL: (858) 534-2963 FAX: (858) 534- 

0202



C03537 

Email: hweizman@ucsd.edu 

K. C. Nguyen and H. Weizman, Greening Wittig reactions: 

Solvent –free synthesis of Ethyl trans-Cinnamate and E-3-(9- 

Anthryl)-2-Propenoic Acid Ethyl Ester, J. Chem. Ed, 84, 

119-121 (2007). 

R. Hwa and H. Weizman, Revisiting the separation of Ferrocene 

and Acetylferrocene by adsorption chromatography: 

Adding a third component, J. Chem. Ed, 84, 1497-1498 

(2007). 

Y. Tor, S. Del Valle, D. Jaramillo, S. G. Srivatsan and H. 

Weizman, Designing new isomorphic fluorescent nucleobase 

analogues: The thieno[3,2-d]pyrimidine core, Tetrahedron, 

63, 3608-3614 (2007). 

H. Weizman, Why are 

D. Schultz, E. Ben Jacob, J. N. Onuchic and P. G. Wolynes, 

Molecular level stochastic model for competence cycles 

in Bacillus subtilis, PNAS, 104, 17582-17587 (2007). 

T. Lu, T. Shen, M. Bennett, P. G. Wolynes and J. Hasty, 

Phenotypic variability of growing cellular populations, 

PNAS, 104, 18982-18987 (2007). 

D. Ferreiro, J. Hegler, E. Komives and P. G. Wolynes, Localizing 

frustration in native proteins and protein assemblies, 

PNAS, 104, 19819-19824 (2007). 

L. Sutto, J. Latzer, J. Hegler, D. Ferreiro and P. G. Wolynes, 

Consequences of localized frustration for the folding 

mechanism of the IM7 protein, PNAS, 104, 19825-19830 

(2007). 

C. Zong, C. J. Wilson, T. Shen, P. Wittung-Staffshede, S. 

Mayo and P. Wolynes, Establishing the entatic state in folding 

metallated pseudomonas aeruginosa azurin, PNAS, 104, 

and contextual or ecology data, the role of microbes in 

the environment and the impact of environments on mi- 

crobial communities. TEL: (858) 534-2494 FAX: (858) 

822-1452 


C03721 

Email: jwooley@ucsd.edu 

Y. Ye and J. Wooley, A historical perspective and overview 

of protein structure prediction, Computational Methods 

for Protein Structure Prediction and Modeling, (2007). 

Chloe Zubieta, S. Sri Krishna, Mili Kapoor, Piotr Kozbial, 

Daniel McMullan, Herbert L. Axelrod, Mitchell D. Miller, 

Polat Abdubek, Eileen Ambing, Tamara Astakhova, Dennis 

Carlton, Hsiu-Ju Chiu, Thomas Clayton, Marc C. Deller, 

Lian Duan, Marc-Andre Elsliger, Julie Feuerhelm, Slawomir 

1H NMR integrations not perfect? 

An inquiry based exercise for exploring the relationship between 

spin-dynamics and NMR integration in the organic 

laboratory, J. Chem. Ed, 85, 294-296 (2008). 

S. G. Srivatsan, H. W. Weizman and H. Y. Tor, A highly 

fluorescent nucleoside analog based on thieno[3,4-d]pyrimi- 

dine senses mismatched pairing, Org. Biomol. Chem, 6, 

1334—1338 (2008). 

WENKERT, ERNEST (b.1925) Professor Emeritus. 

B.S, 1945, University of Washington; M.S, 1947, University 

of Washington; Ph.D, 1951, Harvard University. 

Synthesis and structure analysis of organic natural products; 

development of new methods of organochemical 

synthesis; synthesis based on transition metal-mediated 

reactions. TEL: (619) 534-4942 FAX: (858) 534-4864 

Email: ewenkert@ucsd.edu 


WHEELER, JOHN C. (b.1941) Professor. B.A, 1963, 

Oberlin College; Ph.D, 1968, Cornell University. NSF 

Fellowship, 1967-1969, Harvard University; Alfred P. 

Sloan Foundation Fellowship, 1972-1976, University of 

California, San Diego; Guggenheim Foundation Fellowship, 

1983-1984, Université de Paris-Sud Centre 

d’Orsay. Theoretical chemistry: statistical mechanics, 

thermodynamics; phase transitions, critical phenomena 

in mixtures; moment analysis of spectral densities. Polymers 

and polymerization. Vibrational motion at solid 

surfaces. Phase equilibria in micellar solutions. TEL: 

(858) 534-3287 FAX: (858) 534-7244 

Web: www.chem.ucsd.edu/Faculty/Research_text/ 

wheeler.html 

Email: jwheeler@ucsd.edu 


WHITESELL, JAMES K. (b.1944) Professor. B.S, 

1966, Pennsylvania State University; Ph.D, 1971, Harvard 

University. Postdoctoral, 1971-1973, Woodward 

Research Institute. Organic Chemistry. Stereochemistry, 

both in a molecular and a supramolecular sense. Solar 

energy harvesting. Materials for photonic applications. 

TEL: (858) 534-5870 FAX: (858) 534-5383 

Email: jkw@ucsd.edu 


WOLYNES, PETER GUY (b.1953) Francis H. C. 

Crick Professor. A.B, 1971, Indiana University; A.M, 

1972, Harvard University; Ph.D, 1976, Harvard University; 

D.Sc, 1988, Indiana University. Research Associate, 

1975-1976, M. I. T. Biophysics/Biophysical Chemistry; 

Physical Chemistry. Protein folding and function; 

glasses; dynamics of biomolecules; stochastic cell biology; 

theoretical chemical physics. TEL: (858) 822-4825 

FAX: (858) 822-4560 

Web: www.chem.ucsd.edu/Faculty/bios/wolynes.html 

Email: pwolynes@ucsd.edu 

V. Lubchenko, R. J. Silbey and P. G. Wolynes, The microscopic 

quantum theory of low temperature amorphous solids, 

Adv. Chem. Phys, 136, 95-206 (2007). 

V. Lubchenko and P. G. Wolynes, Theory of structural 

3159-3164 (2007). 

P. G. Wolynes, Lectures on biomolecular energy landscapes, 

Proceedings of the International School of Physics 

“Enrico Fermi” Course CLXV, 27-46 (2007). 

J. Latzer, T. Shen and P. Wolynes, Conformational switching 

upon phosphorylation: A predictive framework based on 

energy landscape principles, Biochem, 47, 2110-2122 (2008). 

L. S. Itzhaki and P. G. Wolynes, The quest to understand 

protein folding, Curr. Op. Struct. Bio, 18, 1-3 (2008). 

J. A. Hegler, P. Weinkam and P. G. Wolynes, The spectrum 

of biomolecular states and motions, HFSP Journal, 2, 

307-313 (2008). 

P. G. Whitford, J. N. Onuchic and P. G. Wolynes, The energy 

landscape along an enzymatic reaction trajectory: 

Hinges or cracks?, HFSP Journal, 2, 61-64 (2008). 

J. D. Stevenson, A. M. Walczak, R. W. Hall and P. G. 

Wolynes, Constructing explicit magnetic analogies for the 

dynamics of glass forming liquids, J. Chem. Phys, 129, 

194505-1-6 (2008). 

M. C. Prentiss, D. J. Wales and P. G. Wolynes, Protein 

structure prediction using basin hopping, J. Chem. Phys, 128, 

225106-1-9 (2008). 

J. D. Stevenson and P. G. Wolynes, On the surface of 

glasses, J. Chem. Phys, 129, 234514-1-4 (2008). 

T. Shen, C. Zong, J. Portman and P. G. Wolynes, Variationally 

determined free energy profiles for structural models 

of proteins: Characteristic temperatures for folding and trapping, 

J. Phys. Chem .B, 112, 6074-6082 (2008). 

R. W. Hall and P. G. Wolynes, Intermolecular forces and 

the glass transition, J. Phys. Chem. B, 112, 301-312 (2008). 

P. G. Wolynes, Protein folding and beyond: Energy land- 

scapes and the organization of living matter in space and 

time, Physical Biology from Atoms to Medicine, 267-288 

(2008). 

D. U. Ferreiro, A. M. Walczak, E. A. Komives and P. G. 

Wolynes, The energy landscapes of repeat-containing proteins: 

Topology, cooperativity and the folding funnels of onedimensional 

architectures, PLOS Computational Biology, 4, 

1-12 (2008). 

S. Bhattacharyya, B. Bagchi and P. G. Wolynes, Facilitation, 

complexity growth, mode coupling and activated dynamics 

in supercooled liquids, PNAS, 105, 16067-16082 

(2008). 

D. Schultz, A. M. Walczak, J. N. Onuchic and P. G. Wol- 

ynes, Extinction and resurrection in gene networks, PNAS, 

105, 19165-19170 (2008). 

D. U. Ferreiro and P. G. Wolynes, The capillarity picture 

and the kinetics of one-dimensional protein folding, PNAS, 

105, 9853-9854 (2008). 

P. G. Wolynes, The protein folding energy landscape: A 

primer, Protein Folding, Misfolding and Aggregation, 49-69 

(2008). 

Aleksandra Walczak, Many body theory of stochastic gene 

networks. (D) 

Chenghang Zong, Theoretical studies of biomolecular self- 

assembly near equilibrium and far from equilibrium. (D) 

Joachim Laetzer, Computational tools based on energy 

landscape theory to predict structurally diverse ensembles of 

transcription factors. (D) 

Samuel S. Cho, Energy landscapes for protein folding, 

binding, and aggregation: Simple funnels and beyond. (D) 

Ting Lu, Stochasticity in biological networks: Two sides of 

a golden coin. (D) 

K. Grzechnik, Joanna Hale, Eric Hampton, Gye Won Han, 

Lukasz Jaroszewski, Kevin K. Jin, Heath E. Klock, Mark W. 

Knuth, Abhinav Kumar, David Marciano, Andrew T. Morse, 

Edward Nigoghossian, Linda Okach, Silvya Oommachen, 

Ron Reyes, Christopher L. Rife, Paul Schimmel, Henry van 

den Bedem, Dana Weekes, Aprilfawn White, Qingping Xu, 

Keith O. Hodgson, John Wooley, Ashley M. Deacon, Adam 

Godzik, Scott A. Lesley and Ian A. Wilson, Crystal struc- 

tures of two novel dye-decolorizing peroxidases reveal a �- 

barrel fold with a conserved heme-binding motif, Proteins: 

Struct., Funct., Bioinf, 69, 223-233 (2007). 

Chloe Zubieta, Rosanne Joseph, S. Sri Krishna, Daniel 

McMullan, Mili Kapoor, Herbert L. Axelrod, Mitchell D. 

Miller, Polat Abdubek, Claire Acosta, Tamara Astakhova, 

Dennis Carlton, Hsiu-Ju Chiu, Thomas Clayton, Marc C. 

Deller, Lian Duan, Ylva Elias, Marc-Andre Elsliger, Julie 

Feuerhelm, Slawomir K. Grzechnik, Joanna Hale, Gye Won 

Han, Lukasz Jaroszewski, Kevin K. Jin, Heath E. Klock, 

Mark W. Knuth, Piotr Kozbial, Abhinav Kumar, David Marciano, 

Andrew T. Morse, Kevin D. Murphy, Edward Nigoghossian, 

Linda Okach, Silvya Oommachen, Ron Reyes, 

Christopher L. Rife, Paul Schimmel, Christina V. Trout, 

Henry van den Bedem, Dana Weekes, Aprilfawn White, 

Qingping Xu, Keith O. Hodgson, John Wooley, Ashley M. 

Deacon, Adam Godzik, Scott A. Lesley and Ian A. Wilson, 

Identification and structural characterization of heme binding 

in a novel dye-decolorizing peroxidase, TyrA, Proteins: 


Dana Weekes, Mitchell D. Miller, S. Sri Krishna, Daniel 

McMullan, Timothy M. McPhillips, Claire Acosta, Jaume M. 

Canaves, Marc-Andre Elsliger, Ross Floyd, Slawomir K. 

Grzechnik, Lukasz Jaroszewski, Heath E. Klock, Eric Koese- 

ma, John S. Kovarik, Andreas Kreusch, Andrew T. Morse, 

Kevin Quijano, Glen Spraggon, Henry van den Bedem, 

Guenter Wolf, Keith O. Hodgson, John Wooley, Ashley M. 

Deacon, Adam Godzik, Scott A. Lesley and Ian A. Wilson, 

Crystal structure of a transcription regulator (TM1602) from 

Thermotoga maritima at 2.3 Å resolution, Proteins: Struct., 

Funct., Bioinf, 67, 247-252 (2007). 

S. Sri Krishna, Lutz Tautz, Qingping Xu, Daniel McMullan, 

Mitchell D. Miller, Polat Abdubek, Eileen Ambing, Ta- 

mara Astakhova, Herbert L. Axelrod, Dennis Carlton, Hsiu- 

Ju Chiu, Thomas Clayton, Michael DiDonato, Lian Duan, 

Marc-Andre Elsliger, Slawomir K. Grzechnik, Joanna Hale, 

Eric Hampton, Gye Won Han, Justin Haugen, Lukasz Jaroszewski, 

Kevin K. Jin, Heath E. Klock, Mark W. Knuth, Eric 

Koesema, Andrew T. Morse, Tomas Mustelin, Edward Ni- 

goghossian, Silvya Oommachen, Ron Reyes, Christopher L. 

Rife, Henry van den Bedem, Dana Weekes, Aprilfawn 

White, Keith O. Hodgson, John Wooley, Ashley M. Deacon, 

Adam Godzik, Scott A. Lesley and Ian A. Wilson, Crystal 

structure of NMA 1982 from Neisseria meningitidis at 1.5 Å 

resolution provides a structural scaffold for nonclassical, eukaryotic-like 

phosphatases, Proteins: Struct., Funct., Bioinf, 

69, 415-421 (2007). 

Qingping Xu, Kumar Singh Saikatendu, S. Sri Krishna, 

Daniel McMullan, Polat Abdubek, Sanjay Agarwalla, Eileen 

Ambing, Tamara Astakhova, Herbert L. Axelrod, Dennis 

Carlton, Hsiu-Ju Chiu, Thomas Clayton, Michael DiDonato, 

Lian Duan, Marc-Andre Elsliger, Julie Feuerhelm, Slawomir 

K. Grzechnik, Joanna Hale, Eric Hampton, Gye Won Han, 

Justin Haugen, Lukasz Jaroszewski, Kevin K. Jin, Heath E. 

Klock, Mark W. Knuth, Eric Koesema, Mitchell D. Miller, 

Andrew T. Morse, Edward Nigoghossian, Linda Okach, Silvglasses 

and supercooled liquids, Ann. Rev. Phys. Chem, 58, 

235-266 (2007). 

D. U. Ferreiro, C. F. Cervantes, M. E. Truhlar, S. S. Cho, 

P. G. Wolynes and E. A. Komives, Stabilizing IkBk by “consensus” 

design, J. Mol. Bio, 365, 1201-1216 (2007). 

J. Latzer, G. Papoian, M. Prentiss, E. Komives and P. G. 

WOOLEY, JOHN (b.1945) Professor. B.S, 1967, 

Michigan State University; Ph.D, 1975, The University 

of Chicago. Research Fellow/ Postdoc, 1975, G. D. 

Searle Pharmaceuticals, Ltd; research associate/Postdoc, 

1976-1977, Harvard University Dept of Biochemical 

ya Oommachen, Jessica Paulsen, Ron Reyes, Christopher L. 

Rife, Robert Schwarzenbacher, Henry van den Bedem, Aprilfawn 

White, Guenter Wolf, Keith O. Hodgson, John Wooley, 

Ashley M. Deacon, Adam Godzik, Scott A. Lesley and Ian 

A. Wilson, Crystal structure of MtnX phosphatase from Bacillus 

subtilis at 2.0 Å resolution provides a structural basis 

Wolynes, Induced fit, folding, and recognition of the NF-kBnuclear 

localization signals by IkBa and IdBb, J. Mol. Bio, 

376, 262-274 (2007). 

D. Schultz, J. N. Onuchic and P. G. Wolynes, Understanding 

stochastic simulations of the smallest genetic networks, J. 

Phys. Chem, 126, 245102-1-11 (2007). 

Y. Levy, J. N. Onuchic and P. G. Wolynes, Fly-casting in 

Protein-DNA binding: Frustration between protein folding 

and electrostatics facilitates target recognition, JACS, 3, 738- 

739 (2007). 

M. Gruebele and P. G. Wolynes, Quantizing ULam’s control 

conjecture, Phys. Rev. Lett, 99, 060201-1-4 (2007). 

S. S. Cho, P. Weinkam and P. G. Wolynes, Origins of barriers 

and barrierless folding in BBL, PNAS, 104, 112-123 

(2007). 

Sciences; Physiology Course Instructor, 1978, Marine 

Biological Labs; Assistant Professor, 1978-1983, Princeton 

University/ Dept of Biology and Dept of Biochemical 

Sciences; Program Director, 1984-1988, NSF Biological 

Instrumentation Program; Division Director, 1988- 

1992, NSF Instrumentaion and Resources Division; Deputy 

Associate Director, 1992-1999, DOE Biological and 

Environmental Research; Associate VC of Research, 

1999-2008, UC San Diego. Bioinformatics; Structural 

Biology. In structural genomics, the research focuses on 

obtaining insight, by way of experimental and computa- 

tional studies on protein structures, into the protein universe. 

In metagenomics, the research focuses on charac- 

terizing, by way of coupled analysis of sequence data 

for bipartite phosphomonoester hydrolysis of 2-hydroxy-3keto-5-methylthiopentenyl-1-phosphate, 

Proteins: Struct., 

Funct., Bioinf, 69, 433-439 (2007). 

Irimpan I. Mathews, Daniel McMullan, Mitchell D. Miller, 

Jaume M. Canaves, Marc-Andre Elsliger, Ross Floyd, Sla- 

womir K. Grzechnik, Lukasz Jaroszewski, Heath E. Klock, 

Eric Koesema, John S. Kovarik, Andreas Kreusch, Peter 

Kuhn, Timothy M. McPhillips, Andrew T. Morse, Kevin 

Quijano, Christopher L. Rife, Robert Schwarzenbacher, Glen 

Spraggon, Raymond C. Stevens, Henry van den Bedem, 

Dana Weekes, Guenter Wolf, Keith O. Hodgson, John Woo- 

ley, Ashley M. Deacon, Adam Godzik, Scott A. Lesley and 

Ian A. Wilson, Crystal structure of 2-keto-3-deoxygluconate 

kinase (TM0067) from Thermotoga maritima at 2.05 Å resolution, 

Proteins: Struct., Funct., Bioinf, 70, 603-608 (2007).


Chloe Zubieta, S. Sri Krishna, Daniel McMullan, Mitchell Based on Charged Derivatives of Gramicidin A, J. Am. 

D. Miller, Polat Abdubek, Sanjay Agarwalla, Eileen Ambing, Chem. Soc, 129, 9737-9745 (2007). 

Tamara Astakhova, Herbert L. Axelrod, Dennis Carlton, Petra Inbar, Mahealani R. Bautista, Stacy A. Takayama 

Hsiu-Ju Chiu, Thomas Clayton, Marc Deller, Michael DiDo- and Jerry Yang, Assay To Screen for Molecules That Assonato, 

Lian Duan, Marc-Andre Elsliger, Slawomir K. Grzech- ciate with Alzheimer’s Related �-Amyloid Fibrils, Anal. 

nik, Joanna Hale, Eric Hampton, Gye Won Han, Justin Hau- Chem. (Washington, DC, U. S.), 80, 3502-3506 (2008). 

gen, Lukasz Jaroszewski, Kevin K. Jin, Heath E. Klock, Steven Blake, Ricardo Capone, Michael Mayer and Jerry 

Mark W. Knuth, Eric Koesema, Abhinav Kumar, David Mar- Yang, Chemically Reactive Derivatives of Gramicidin A for 

ciano, Andrew T. Morse, Edward Nigoghossian, Silvya Developing Ion Channel-Based Nanoprobes, Bioconjugate 

Oommachen, Ron Reyes, Christopher L. Rife, Henry van den Chem, 19, 1614-1624 (2008). 

Bedem, Dana Weekes, Aprilfawn White, Qingping Xu, Keith Michael Mayer, Vincent Semetey, Irina Gitlin, Jerry Yang 

O. Hodgson, John Wooley, Ashley M. Deacon, Adam God- and George M. Whitesides, Using Ion Channel-Forming Pepzik, 

Scott A. Lesley and Ian A. Wilson, Crystal structure of tides to Quantify Protein-Ligand Interactions, J. Am. Chem. 

homoserine O-succinyltransferase from Bacillus cereus at 2.4 Soc, 130, 1453-1465 (2008). 

Å resolution, Proteins: Struct., Funct., Bioinf, 68, 999-1005 

(2007). 

Steven Blake, Designing nanosensors based on ion chan- 

K. Arima and J. Wooley, Metagenomics, Computational 

Methods for Understanding Bacterial and Archaeal Genomes, 

7, 345-396 (2008). 

L. Weizhong, J. C. Wooley and A. Godzik, Probing metagenomics 

by rapid cluster analysis of very large datasets, 

PLoS one, 3, e3375 (2008). 

Herbert L. Axelrod, Daniel McMullan, S. Sri Krishna, 

Mitchell D. Miller, Marc-Andre Elsliger, Polat Abdubek, Eileen 

Ambing, Tamara Astakhova, Dennis Carlton, Hsiu-Ju 

Chiu, Thomas Clayton, Lian Duan, Julie Feuerhelm, Slawomir 

K. Grzechnik, Joanna Hale, Gye Won Han, Justin 

Haugen, Lukasz Jaroszewski, Kevin K. Jin, Heath E. Klock, 

Mark W. Knuth, Eric Koesema, Andrew T. Morse, Edward 

Nigoghossian, Linda Okach, Silvya Oommachen, Jessica 

Paulsen, Kevin Quijano, Ron Reyes, Christopher L. Rife, 

Henry van den Bedem, Dana Weekes, Aprilfawn White, 

Guenter Wolf, Qingping Xu, Keith O. Hodgson, John Wooley, 

Ashley M. Deacon, Adam Godzik, Scott A. Lesley and 

Ian A. Wilson, Crystal structure of AICAR transformylase 

IMP cyclohydrolase (TM1249) from Thermotoga maritima at 

1.88 Å resolution, Proteins: Struct., Funct., Bioinf, 71, 1042- 

1049 (2008). 

Qingping Xu, Piotr Kozbial, Daniel McMullan, S. Sri 

Krishna, Scott M. Brittain, Scott B. Ficarro, Michael DiDonato, 

Mitchell D. Miller, Polat Abdubek, Herbert L. Axelrod, 

Hsiu-Ju Chiu, Thomas Clayton, Lian Duan, Marc-Andre Elsliger, 

Julie Feuerhelm, Slawomir K. Grzechnik, Joanna 

Hale, Gye Won Han, Lukasz Jaroszewski, Heath E. Klock, 

Andrew T. Morse, Edward Nigoghossian, Jessica Paulsen, 

Ron Reyes, Christopher L. Rife, Henry van den Bedem, 

Aprilfawn White, Keith O. Hodgson, John Wooley, Ashley 

M. Deacon, Adam Godzik, Scott A. Lesley and Ian A. Wilson, 

Crystal structure of an ADP-ribosylated protein with a 

nel-forming peptides of gramicidin A. (D) 

cytidine deaminase-like fold, but unknown function 

(TM1506), from Thermotoga maritima at 2.70 Å resolution, 

Proteins: Struct., Funct., Bioinf, 71, 1546-1552 (2008). 

Piotr Kozbial, Qingping Xu, Hsiu-Ju Chiu, Daniel McMullan, 

S. Sri Krishna, Mitchell D. Miller, Polat Abdubek, Claire 

Acosta, Tamara Astakhova, Herbert L. Axelrod, Dennis Carlton, 

Thomas Clayton, Marc Deller, Lian Duan, Ylva Elias, 

Marc-Andre Elsliger, Julie Feuerhelm, Slawomir K. Grzechnik, 

Joanna Hale, Gye Won Han, Lukasz Jaroszewski, Kevin 

K. Jin, Heath E. Klock, Mark W. Knuth, Eric Koesema, 

Abhinav Kumar, David Marciano, Andrew T. Morse, Kevin 

D. Murphy, Edward Nigoghossian, Linda Okach, Silvya 

Oommachen, Ron Reyes, Christopher L. Rife, Glen Spraggon, 

Christina V. Trout, Henry van den Bedem, Dana 

Weekes, Aprilfawn White, Guenter Wolf, Chloe Zubieta, 

Keith O. Hodgson, John Wooley, Ashley M. Deacon, Adam 

Godzik, Scott A. Lesley and Ian A. Wilson, Crystal structures 

of MW1337R and lin2004: representatives of a novel 

protein family that adopt a four-helical bundle fold, Proteins: 


L. Jaroszewski, L. Slabinski, J. Wooley, A. M. Deacon, S. 

A. Lesley, I. A. Wilson and A. Godzik, Genome pool strategy 

for structural coverage of protein families, Structure, 16, 

1659-1667 (2008). 

Lukasz Jaroszewski, Lukasz Slabinski, John Wooley, Ashley 

M. Deacon, Scott A. Lesley, Ian A. Wilson and Adam 

Godzik, Genome Pool Strategy for Structural Coverage of 

Protein Families, Structure (Cambridge, MA, U. S.), 16, 

1659-1667 (2008). 

YANG, JERRY (b.1972) Assistant Professor. B.S, 

1995, University of California, Berkeley; M.A, 1998, 

Columbia University; M.Ph, 2000, Columbia University; 

Ph.D, 2001, Columbia University. Postdoctoral Fellow, 

2001-2003, Harvard University. Bioorganic Chemistry; 

Biotechnology. Development of new therapeutics for Alzheimer’s 

disease; construction of functional nanosensors 

using artificial ion channels for use in medical and 

environmental diagnostics; design and synthesis of cancer 

drug delivery systems. TEL: (858) 534-6006 FAX: 

(858) 534-4554 


C04652 

Email: jerryyang@ucsd.edu 

Seong Deok Kong, Alice Luong, Gerald Manorek, Stephen 

B. Howell and Jerry Yang, Acidic Hydrolysis of N- 

Ethoxybenzylimidazoles (NEBIs): Potential Applications as 

pH-Sensitive Linkers for Drug Delivery, Bioconjugate Chem, 

18, 293-296 (2007). 

Ricardo Capone, Steven Blake, Marcela Rincon Restrepo, 

Jerry Yang and Michael Mayer, Designing Nanosensors

UNIVERSITY OF CALIFORNIA, SAN DIEGO

Create successful ePaper yourself

Delete template?

Save as template?