Molecular complexes of octafluoronaphthalene with catenated.pdf

Journal of Fluorine Chemistry 127 (2006) 437–442
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Molecular complexes of octafluoronaphthalene with catenated
chalcogen–nitrogen compounds C 6 H 5 –X–N S N–SiMe 3 (X = S, Se)
Alexander Yu. Makarov a , Enno Lork b , Ruediger Mews b, *,
Andrey V. Zibarev a,c, **
a Institute of Organic Chemistry, Russian Academy of Sciences, 630090 Novosibirsk, Russia
b Institute for Inorganic and Physical Chemistry, University of Bremen, 28334 Bremen, Germany
c Department of Physics, Novosibirsk State University, 630090 Novosibirsk, Russia
Received 20 September 2005; received in revised form 31 October 2005; accepted 2 November 2005
Available online 6 March 2006
Abstract
Mismatched molecular 1:1 complexes of C 10 F 8 with catenated chalcogen–nitrogen compounds C 6 H 5 –X–N S N–SiMe 3 (X = S, Se) were
prepared and characterized by X-ray crystallography. The complexes provide examples of structurally non-rigid polyheteroatom molecules
involved in non-covalent arene–polyfluoroarene p-stacking interactions. In going from homocrystals to the co-crystals, the molecular Z, E
configuration of the catenated compounds changes from noticeably non-planar to perfectly planar, i.e. C 10 F 8 acts as ‘‘molecular iron’’. On the other
hand, C 10 H 8 does not produce complexes with C 6 F 5 –X–N S N–SiMe 3 (X = S, Se).
# 2006 Elsevier B.V. All rights reserved.
Keywords: Octafluoronaphthalene; Chalcogen–nitrogen compounds; Molecular complexes; p-Stacking interactions; X-ray structure determination
1. Introduction
It is well recognized that non-covalent arene–polyfluoroarene
p-stacking interactions [1] are important for both
fundamental and applied chemistry. In particular, these
interactions are successfully used in the design and synthesis
of various advanced functional materials (for representative
examples, see [2] and references therein).
The majority of the described binary complexes bonded by
p-stacking interactions are those between structurally rigid
hydrocarbons and fluorocarbons (for selected references, see
[2,3] and references therein), examples of the participation of
polyheteroatom molecules are rare ([4] and references therein).
In the context of supramolecular chemistry and crystal
engineering, it is of obvious interest to investigate how broad
the molecular diversity of the compounds involved in the
arene–polyfluoroarene p-stacking interactions can be, and
whether geometrical matching of the interacting molecules is
* Corresponding author. Tel.: +49 421 218 3354; fax: +49 421 218 4267.
** Corresponding author. Fax: +7 383 330 9752.
E-mail addresses: mews@chemie.uni-bremen.de (R. Mews),
zibarev@nioch.nsc.ru (A.V. Zibarev).
a significant structural requirement. Aryl-substituted chalcogen–nitrogen
compounds, i.e. polyheteroatom chains and
cycles (frequently non-rigid) of variable size, are especially
promising for further research in this direction.
Recently, 1:1 molecular complexes between octafluoronaphthalene
and acyclic (Ar–N S N–Ar, Ar–N S N–
SiMe 3 ) and heterocyclic (7-methyl-2,1-benzothiazole) sulfur–nitrogen
compounds featuring p-stacking interactions of
the arene–polyfluoroarene type were synthesized [5,6]. Also,
2:1 inclusion complexes of the bicyclic sulfur–nitrogen
compounds Ar–CN 5 S 3 (including polyfluorinated derivatives)
and fluorocarbon and hydrocarbon aromatics were prepared,
the inclusion is driven by arene–polyfluoroarene p-stacking
interactions [4]. These investigations [4–6] showed that the
molecular geometries of the sulfur–nitrogen derivatives
were practically not affected by these interactions. In some
cases, the co-crystals were much better suited for X-ray
crystallography than the crystals of the individual compounds.
Based on these findings, a methodology was
suggested [4] which uses arene–polyfluoroarene co-crystals
for the structural characterization of aromatic compounds
(including liquids [5,6]) for which good quality homocrystals
are not available.
0022-1139/$ – see front matter # 2006 Elsevier B.V. All rights reserved.
doi:10.1016/j.jfluchem.2005.11.021

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A.Y. Makarov et al. / Journal of Fluorine Chemistry 127 (2006) 437–442
Table 1
Crystal data and structure refinement for 1–4
Compounds 1 2 3 * 4
Empirical formula C 9 H 14 N 2 S 2 Si C 9 H 14 N 2 SSeSi C 19 H 14 F 8 N 2 S 2 Si C 19 H 14 F 8 N 2 SSeSi
Formula weight 242.43 289.33 514.53 561.43
Temperature (K) 173 (2) 173 (2) 173 (2) 173 (2)
Wavelength (pm) 71.073 71.073 71.073 71.073
Crystal system Monoclinic Monoclinic Monoclinic Monoclinic
Space group P 2 1 /n P 2 1 /n P 2 1 P2 1 /c
Unit cell dimensions
a (pm) 583.7(2) 580.70(10) 692.0(3) 1361.2(3)
b (pm) 1654.1(3) 1654.5(3) 1211.7(2) 1207.7(2)
c (pm) 1359.9(2) 1379.4(2) 1340.1(4) 1397.0(3)
b (8) 100.84(3) 99.630(10) 193.73(3) 106.440(10)
Volume (nm 3 ) 1.2896(2) 1.3066(4) 1.0932(6) 2.2027(8)
Z 4 4 2 4
Density (calculated) (Mg/m 3 ) 1.249 1.471 1.563 1.693
Absorption coefficient (mm 1 ) 0.473 3.093 0.375 1.930
F(0 0 0) 512 584 520 1112
Crystal size (mm 3 ) 0.80 0.70 0.50 0.70 0.50 0.50 0.70 0.30 0.10 0.40 0.40 0.30
u range for data collection (8) 2.90–27.50 2.88–27.50 3.03–27.52 2.99–27.51
Index ranges 7 h 1,
21 k 21,
17 l 17
7 h 7,
21 k 21,
17 l 17
8 h 1,
15 k 15,
17 l 17
1 h 17,
15 k 1,
18 l 17
Reflections collected 7607 11870 6324 6261
Independent reflections 2967 [R(int) = 0.0455] 3007 [R(int) = 0.0403] 4861 [R(int) = 0.0249] 5026 [R(int) = 0.0266]
Completeness to u8 (%) 99.9 99.9 99.7 99.2
Absorption correction None Empirical (DIFABS) None None
Maximum and
0.7978 and 0.7034 0.3069 and 0.2207 0.9634 and 0.7790 0.5951 and 0.5923
minimum transmission
Refinement method
Full-matrix
least squares on F 2
Full-matrix least
squares on F 2
Full-matrix least
squares on F 2
Full-matrix least
squares on F 2
Data/restraints/parameters 2967/5/170 3007/0/133 4861/5/324 5026/0/313
Goodness-of-fit on F 2 1.074 1.066 1.031 1.069
Final R indices [I > 2s(I)] R1 = 0.0275,
wR2 = 0.070
R1 = 0.0350,
wR2 = 0.0878
R1 = 0.0469,
wR2 = 0.1098
R1 = 0.0314,
wR2 = 0.0733
R indices (all data) R1 = 0.0305,
wR2 = 0.0770
R1 = 0.0427,
wR2 = 0.0922
R1 = 0.0610
wR2 = 0.1175
R1 = 0.0411,
wR2 = 0.0773
Extinction coefficient 0.0313 (18) 0.0068 (11) 0.011 (2) 0.0115 (5)
Largest diff. peak and hole 0.273 and 0.185 0.677 and 0.888 0.237 and 0.395 0.343 and 0.748
* The structure was refined as a ‘‘racemic twin’’ (73%:27%).
With the present work we continue our investigations
[4–6] on the ability of aryl-substituted chalcogen–nitrogen
compounds to produce co-crystals with polyfluoroaromatic
derivatives. Two new 1:1 complexes between octafluoronaphtalene
and C 6 H 5 –X–N S N–SiMe 3 (1, X = S; 2, X = Se),
i.e. between molecules with very different shape and
composition, are prepared and structurally characterized. The
molecular structures of the individual catenated compounds
1 and 2 are also pre-sented and discussed in comparison with
those in the co-crystals.
2. Results and discussion
The chalcogen–nitrogen derivatives C 6 H 5 –X–N S N–
SiMe 3 (1, X= S; 2, X = Se) were prepared from (Me 3 Si–
N ) 2 S and corresponding C 6 H 5 XCl [7]. The single crystals
of these low-melting compounds, as well as the single crystals
of their 1:1 complexes with C 10 F 8 (3 and 4, respectively),
suitable for X-ray crystallography were obtained by lowtemperature
crystallization from hexane.
Under the same conditions, C 10 H 8 and C 6 F 5 –S–N S N–
SiMe 3 [8] or C 6 F 5 –Se–N S N–SiMe 3 [9] did not produce
any co-crystals.
According to the X-ray diffraction data (Table 1), in the
solid state compounds 1 and 2 exist in the Z, E configuration
(Fig. 1, Table 2), previously observed for substituted
Ar–S–N S N–SiMe 3 derivatives of 1 (Ar = 4-O 2 NC 6 H 4 [10],
2-O 2 NC 6 H 4 [11], 2-HC 6 F 4 [12]). In both cases the XNSNSi
(X = S, Se) fragment is planar, the dihedral angle between
the XNSNSi and C 6 H 5 planes is 27.88 and 21.378 for 1 and 2,
respectively.
In the complexes 3 and 4 (Fig. 2, Table 2) the Z, E
configuration of 1 and 2 is retained but non-planar molecular
conformations turned out to be planar, i.e. C 10 F 8 acts as
‘‘molecular iron’’. Thus, the torsion angle between the NSNX
and the phenyl planes (X = S, Se) reduces from 27.808 to 2.588
and from 21.378 to 2.378, when going from 1 to 3, and from 2
to 4, respectively. At the same time, the bond lengths and bond
angles of 1 and 2 are practically not affected by complexation
with C 10 F 8 (Table 2). Interestingly, in the related complex

A.Y. Makarov et al. / Journal of Fluorine Chemistry 127 (2006) 437–442 439
Fig. 1. The structure of molecules 1 and 2. For selected bond lengths, bond and torsion angles (see Table 2).
between C 10 F 8 and C 6 H 5 –N S N–SiMe 3 (5) the catenated
molecule is also virtually planar with the exception of the
CH 3 groups at the Si center (compound 5 is a liquid under
normal conditions and had not been structurally characterized
in the individual state) [6].
The complexes 3 and 4 demonstrate a face-to-face p-
stacking of the aromatic rings of 1 and 2 with C 10 F 8 featuring
Table 2
Selected bond lengths (pm), bond and torsion angles (8) for 1–4
Bond/angle 1 (X = S) 2 (X = Se) 3 (X = S) 4 (X = Se)
C–X 177.1 (2) 191.2(2) 179.2 (3) 192.09 (19)
X–N 167.3 (2) 183.6(2) 166.5 (3) 184.2 (2)
N S 155.2 (2) 154.2(2) 156.3 (3) 154.7 (2)
S N 153.8 (2) 152.1 (2) 156.1 (2) 152.0 (2)
N–Si 176.7 (2) 175.9 (2) 176.5 (2) 176.19 (18)
C–X–N 98.4 (2) 95.96 (9) 97.37 (16) 95.60 (9)
X–N S 117.1 (4) 116.49 (12) 119.01 (18) 115.71 (12)
N S N 115.9 (4) 114.79 (12) 113.31 (15) 114.56 (11)
S N–Si 122.9 (3) 123.26 (13) 121.85 (14) 124.98 (12)
NSNX–Ph 27.80 21.37 2.58 2.73
some offset of hydrocarbon and fluorocarbon moieties
(Figs. 2–4) which is typical of the field. The dihedral angle
between the planes of the cofacial hydrocarbon and
fluorocarbonringsisalmostequaltozeroin3 (Fig. 3, view
of the stacks formed along the a-axis), while in 4 (Fig. 4,
view of the stacks formed along the c-axis) a slight
inclination is observed. The arene–polyfluoroarene separation
within the stacks is in the range of 344–347 pm for 3
and 348–350 pm for 4. For comparison, this separation is
377 pm for the lowest-temperature phase of the benzene–
hexafluorobenzene co-crystals [13], 327–352 pm for the lowtemperature
structure of the C 10 H 8 /C 10 F 8 co-crystals
[14] and 342 pm for the 5/C 10 F 8 co-crystals [6]. In the
complex 4 the Se and C atoms of the Se–C bond of molecule
2 are coordinated practically to the ring’s centroids of the
neighboring C 10 F 8 molecule (this differs from mutual
orientation of 5 and C 10 F 8 observed in their complex
[6]), the atom-to-centroid distance is 354 and 348 pm,
respectively. The complex 3 displays similar pattern with
correction for the shorter S–C bond as compared with the
Se–C bond.

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A.Y. Makarov et al. / Journal of Fluorine Chemistry 127 (2006) 437–442
Fig. 2. The structure of complexes 3 and 4. For selected bond lengths, bond and torsion angles (see Table 2).
Fig. 3. View of the unit cell of 3 along the a-axis.

A.Y. Makarov et al. / Journal of Fluorine Chemistry 127 (2006) 437–442 441
Fig. 4. View of the unit cell of 4 along the c-axis.
3. Conclusions
Two novel mismatched molecular complexes of octafluoronaphtalene
with aryl-substituted catenated chalcogen–nitrogen
compounds have been prepared. Significantly, they provide
rare examples of flexible polyheteroatom molecules involved
in non-covalent arene–polyfluoroarene p-stacking interactions.
In going from the homocrystals to the co-crystals, the molecular
Z, E configuration of the catenated compounds changes from
noticeably non-planar to planar, i.e. C 10 F 8 acts as ‘‘molecular
iron’’. Since it is known that the limiting value of a torsion angle
interrupting efficient intramolecular p-overlap is only about
308 [15], this structural effect might be useful for the design and
synthesis of new materials based on p-conjugated molecules.
It should be noted that there is a general interest to p-functional
molecules engaged in anisotropic intermolecular interactions
in the solid state in the context of materials science [16].
4. Experimental
4.1. Preparations
The compounds 1 and 2 were prepared by the method
described [7]. The single crystals of these low-melting compounds
(1, orange prisms, mp 22–23 8C; 2, elongated orange
prisms, mp 33–35 8C) suitable to X-ray crystallography were
obtained by low-temperature crystallization from hexane.
4.2. Complexes of compounds 1 and 2 with
octafluoronaphtalene (3 and 4, respectively)
A mixture of 0.27 g (1 mmol) of C 10 F 8 and 1 mmol of 1 or 2
was dissolved in hexane (1, 1.5 mL; 2, 1 mL) and the solution
was placed in a cryostat at 30 8C for crystal growth. After
crystallization the solvent was removed with a syringe and the
crystals were dried in vacuum. Complexes 3 and 4 were
obtained as yellow needles: 3, 0.40 g (78%), mp 50–52 8C; 4,
0.25 g (45%), mp 49–51 8C.
4.3. Crystallographic analysis
The single crystal X-ray structure determinations (Table 1)
were carried out on a Siemens P4 diffractometer using Mo Ka
(71.073 pm) radiation. The crystals were mounted using KEL-F
oil on a thin glass fiber. The structures were solved by direct
methods and refined by full-matrix least squares against F 2 of
all data using SHELX-97 software [17].
Crystallographic data (excluding structure factors) for the
structures have been deposited with the Cambridge Crystallographic
Data Centre as supplementary publications no. CCDC
283504 (1), 283505 (2), 283506 (3), and 283507 (4). Copies of
the data can be obtained, free of charge, on application to CCDC,
12 Union Road, Cambridge CB2 1EZ, UK (fax: +44 1223
336033 or e-mail: deposit@ccdc.cam.ac.uk).
Acknowledgements
The authors are grateful to Mr. Peter Brackmann for
technical assistance, and to the Deutsche Forschungsgemeinschaft
(Germany) and the Russian Foundation for
Basic Research (Russia), for joint financial support of this
work (grants 436 RUS 113/486/0-2 R and 436 RUS 17/84/
04).
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