The molecular structure of N,N′-disulfinyl-3,4,5,6-tetrafluoro-1,2-diaminobenzene: A computational and X-ray diffraction study

Article abstract of DOI:10.1016/j.molstruc.2010.01.070

According to the results of quantum chemical calculations at various levels of theory, an isolated molecule of the title compound prefers a non-planar Z,Z configuration, which is very similar to the configuration observed in the crystal. This is in contra

Full text of DOI:10.1016/j.molstruc.2010.01.070

Journal of Molecular Structure 978 (2010) 158–162
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Journal of Molecular Structure
journal homepage: www.elsevier.com/locate/molstruc
The molecular structure of N,N0-disulfinyl-3,4,5,6-tetrafluoro-1,2-diaminobenzene:
A computational and X-ray diffraction study
Arkady G. Makarov a, Irina Yu. Bagryanskaya a, Yuri V. Gatilov a, Alexander Yu. Makarov a, Karla Tersago b,
a,c,
Christian Van Alsenoy b, Frank Blockhuys b, , Andrey V. Zibarev
*
*
a Institute of Organic Chemistry, Russian Academy of Sciences, 630090 Novosibirsk, Russia
b University of Antwerp, Department of Chemistry, Universiteitsplein 1, BE-2610 Wilrijk, Belgium
c Department of Physics, Novosibirsk State University, 630090 Novosibirsk, Russia
a r t i c l e i n f o
a b s t r a c t
Article history:
According to the results of quantum chemical calculations at various levels of theory, an isolated mole-
cule of the title compound prefers a non-planar Z,Z configuration, which is very similar to the configura-
tion observed in the crystal. This is in contrast to its previously studied hydrocarbon analogue which
features a planar Z,Z configuration, both in the crystal and as a calculated structure. Thus, the gas-phase
molecular structures of these flexible compounds are resistant to the numerous intermolecular interac-
tions in the solid state. The results obtained for the different molecular configurations and conformations
of these compounds are in line with the qualitative bonding model suggested earlier for the isoelectronic
[RNSN]ꢀ anions, taking into account of the anomeric interactions and the electron-acceptor strength of R.
A number of additional factors operating on the molecular conformations of the title compound and its
hydrocarbon analogue, such as the van der Waals volume of the ortho-substituents X (X = H,F) and impro-
per H. . .O hydrogen bonds, are also discussed.
Received 30 November 2009
Received in revised form 27 January 2010
Accepted 27 January 2010
Available online 1 February 2010
Dedicated to Prof. Dr. Heinz Oberhammer
on the occasion of his 70th birthday.
Keywords:
N-Sulfinylaminobenzene
Configuration
Conformation
X-ray diffraction
Ó 2010 Elsevier B.V. All rights reserved.
Quantum chemical calculations
1. Introduction
R = Me3Si [16–18]. The latter can be explained by anion-cation
interactions in the crystal lattice [17,18].
Aza-analogues of sulfur dioxide (O@S@O), such as N-sulfinyli-
mines (RAN@S@O) and sulfur diimides (R@N@S@NAR), remain
interesting systems due to their high and varied reactivity, ability
to coordinate and structural flexibility [1–5]. For RAN@S@O deriv-
atives, two configurations, Z and E (Scheme 1), are theoretically
possible. The experimental data summarised in Ref. [3] reveals that
the Z configuration is preferred for all studied substituents R, rang-
ing from a single atom in the gas-phase structures of HNSO [6] and
ClNSO [7] to a more bulky group in the gas-phase structure of
Me3SiNSO [8] or various aryl groups in solid-state structures
[9–14]. Similarly, only the Z,Z configuration was observed in the
solid state of O@S@NAXAN @ S @ O compounds, both with
single-atom (X = S, Se, Te) [3] or 1,2-phenylene [15] spacers.
[RNSN]– anions (R = alkyl, Ar), which are isoelectronic with
RAN@S@O compounds, also adopt the Z configuration in the solid
state [10,11,16–18], the only exception being in the case of
Quantum chemical calculations confirm the higher stability of
the Z configuration of RAN@S@O and [RNSN]– derivatives. This sta-
bility can be rationalized using a qualitative bonding model [10,17]
in terms of stereoelectronic effects: the destabilizing interaction
between the occupied nN and nS molecular orbitals (MO) is less
pronounced in the Z configuration, in which these two MOs are
coplanar, than in the E configuration (Scheme 1). At the same time,
the stabilizing anomeric interactions between the nN and the ter-
minal rꢁSNðOÞ MOs, and between the nS and rRꢁN MOs, are only signif-
icant in the Z configuration. The calculated energy difference
between the configurations depends on both the nature of R and
the applied level of theory [3,10,17].
The molecular conformations of the Z configuration vary from
perfectly planar to essentially non-planar, also depending on the
nature of R. For example, for RAN@S@O derivatives with aromatic
groups R, a planar conformation was observed in the crystal for
R = C6H5 [9], whereas for R = 2,6-F2C6H3 [11], 2,6-(C2H5)2C6H3 [9]
and 2,4,6-[(CH3)3C]3C6H2 [12] the N@S@O group is twisted by
about 44°, 53° and 88° out of the plane of the ring, respectively.
For [RNSN]– anions, a planar conformation is found for R = C6H5
[18], but twisted conformations featuring dihedral angles of about
* Corresponding authors. Fax: +32 3 265 23 10 (F. Blockhuys), Fax: +7 383 330 97
52 (A.V. Zibarev).
E-mail addresses: frank.blockhuys@ua.ac.be (F. Blockhuys), zibarev@nioch.n-
sc.ru (A.V. Zibarev).
0022-2860/$ - see front matter Ó 2010 Elsevier B.V. All rights reserved.
doi:10.1016/j.molstruc.2010.01.070

A.G. Makarov et al. / Journal of Molecular Structure 978 (2010) 158–162
159
graphite monochromator. The structure was solved by direct
methods and refined by full-matrix least-squares methods on all
F2 in the anisotropic approximation using the SHELX-97 program
[21]. The obtained crystal structure was analyzed for short contacts
between non-bonded atoms using the PLATON program [22].
Crystal structure data for 2 C6F4N2O2S2, M = 272.20, triclinic,
R
N
S
N
S
R
O
O
Z
E
Scheme 1.
a = 4.745(1) Å, b = 7.510(1) Å, c = 12.497(2) Å,
a = 87.168(13)°,
b = 89.442(15)°,
P1, Z = 2, Dc = 2.033 g cm
c
= 89.87ꢀ73(14)°, V = 444.76(14) Å3, space group
, l(Mo Ka
) = 0.649 mmꢀ1, F(000) =
ꢀ
78° and 70° between the NSN and carbocycle planes are observed
for R = 2,6-F2C6H3 and 2,6-(C2H5)2C6H3 [10,11], respectively. It has
been suggested that planar conformations of aromatic RAN@S@O
derivatives possessing a hydrogen atom positioned ortho to the
NSO moiety are stabilized by a blue-shifting (or anti or improper)
CH. . .O hydrogen bond [19]. For [RNSN]– anions, the precise molec-
ular conformation correlates with the electron-acceptor strength of
R [10]. Estimates based on quantum chemical calculations led to
conclusion that the deviations from planarity are energetically
more favorable than a change in the configuration [3,10,17].
Preliminary calculations on N,N0-disulfinyl-1,2-diaminobenzene
(1) unexpectedly revealed that its gas-phase molecular conforma-
tion is very similar to that observed in the solid state using X-ray
diffraction, despite the presence of numerous intermolecular inter-
actions [15]. For an in-depth study of these effects, the molecular
conformation and solid-state intermolecular interactions of 1 were
perturbed by completely substituting the hydrogen atoms in 1 by
fluorine atoms, and in this paper we report a quantum chemical
and X-ray diffraction study on N,N0-disulfinyl-3,4,5,6-tetrafluoro-
1,2-diaminobenzene (2) (Chart 1).
268, crystal size 0.8 ꢂ 0.2 ꢂ 0.1 mm, 2hmax = 54°, 2205 reflections
measured, 1933 unique reflections (Rint = 0.0184) measured, empir-
ical method (psi-scans) transmission 0.83 and 0.87, 146 parame-
ters, R1 [1521 F0 P 2
r(F)] = 0.0404, wR2 = 0.1122, S = 1.033 for all
data, residual electron density peaks of + 0.312 and –0.320e Åꢀ3
.
Tables listing detailed crystallographic data, atomic positional
parameters, and bond lengths and angles are available as CCDC
747702 from the Cambridge Crystallographic Data Centre.
2.3. Quantum chemical calculations
DFT/PBE/3z calculations were performed using the PRIRODA
program [23]. DFT/B3LYP/6–311 + G(d,p) and MP2/6–311G(d,p)
calculations were performed with the GAMESS program [24].
DFT/B3LYP/aug-cc-pVTZ calculations were performed with the
Gaussian 03 suite of programs [25]. In all cases, the basis sets were
used as they are implemented in the programs. Force-field
calculations were used to ascertain whether the resulting struc-
tures are energy minima. Different conformers are denoted as
anti,anti, anti,syn, syn,anti or syn,syn according to the torsion angles
u1 = C2–C1–N1–S1 and u2 = C1–C2–N2–S2 (see Chart 1).
2. Experimental
High-resolution mass-spectra (EI, 70 eV) were recorded on a
DFS Thermo Electron Corporation instrument. The 13C, 15N and
17O NMR spectra were recorded on a Bruker DRX-500 machine,
and the 19F spectra on a Bruker AV-300 machine, at frequencies
of 125.8, 50.7, 67.8 and 282.4 MHz, respectively. The standards
were TMS, NH3 (liq.), D2O and C6F6 (d = –162.2 ppm with respect
to CFCl3), respectively.
3. Results and discussion
3.1. Solid-state structure
For compound 2, the cell setting, space group and number of
molecules in the unit cell are the same as for compound 1 [15],
ꢀ
i.e., triclinic, P1 and 2, respectively. At the same time, the molecular
conformations and modes of crystal packing are very different for
these two related systems. According to the X-ray diffraction data,
compound 1 displays a planar Z,Z configuration in the solid state,
the torsion angles u1 and u2 being 175.2(3)° and 178.9(3)° [15].
The structure of molecule 2 in the crystal is presented in Fig. 1.
Here too, both N@S@O groups have the Z configuration and are ro-
2.1. Preparation of compound 2
A mixture of 1.8 g (0.01 mol) of 3,4,5,6-tetrafluoro-1,2-diamino-
benzene [20] and 3.5 ml (0.05 mol) of SOCl2 was refluxed for 4 h.
The excess SOCl2 was distilled off and the residue was recrystal-
lized from hexane. 2 was obtained in the form of moisture-sensi-
tive yellow crystals in a yield of 2.1 g (78%). M.p. 40–41 °C. MS
(m/z) measured (calculated) for C6F4N2O2S2:
M
271.9326
(271.9337). NMR (CDCl3, d): 13C 140.3, 139.8, 119.9; 15N 330.3;
17O 436; 19F 24.9, 7.7. Found (calculated) for C6F4N2O2S2 (%): C
26.19 (26.47), F 27.99 (27.92), N 10.15 (10.29), S 23.38 (23.56).
2.2. X-ray structure determination
Crystal structure data for 2 were collected at 193 K on a Bruker
P4 diffractometer using Mo K
a radiation (k = 0.71073 Å) with a
S
O
N
N
S
O
ϕ2
S
O
F
N
F
N
F
S
O
F
ϕ1
1
2
Fig. 1. X-ray molecular structure of compound 2. Thermal ellipsoids are drawn at
Chart 1.
the 30% probability level.

160
A.G. Makarov et al. / Journal of Molecular Structure 978 (2010) 158–162
Table 1
Table 3
Selected geometrical data comparing solid-state 0(XRD) and calculated geometries of
Calculated relative energies (D
E in kJ molꢀ1) of the nine possible conformers of Z,Z-2,
the Z,Z isomer of compound 1; bond lengths in ÅA and angles in degrees.
at the DFT/B3LYP/aug-cc-pVTZ level of theory.
PBE/3z
(C2v
anti,anti) (C2v-anti,anti)
B3LYP/6–
311 + G(d,p)
MP2/6–
311G(d,p)
(C1-syn,anti)
XRD [15]
Conformer
D
E
-
C2v-syn,syn
–
–
–
–
4.1
3.8
4.0
0.0
7.1
Cs-syn,syn
Cs-syn,anti
C2v-anti,anti
C2-syn,syn
C2-anti,anti
Cs-anti,anti
C1-syn,anti
C1-syn,anti
C1–C2
C1–N1
N1–S1
S1–O1
C2–N2
N2–S2
S2–O2
C2–C1–N1
C1–N1–S1
N1–S1–O1
C1–C2–N2
C2–N2–S2
N2–S2–O2
C2–C1–N1–S1
C1–C2–N2–S2
1.442
1.381
1.566
1.509
1.381
1.566
1.509
116.5
131.0
120.6
116.5
131.0
120.6
180.0
180.0
1.434
1.383
1.543
1.491
1.383
1.543
1.491
117.0
132.0
119.8
117.0
132.0
119.8
180.0
180.0
1.418
1.399
1.560
1.482
1.405
1.563
1.481
116.1
126.6
120.1
122.1
123.7
120.2
ꢀ151.2
50.0
1.423(4)
1.387(4)
1.511(3)
1.449(3)
1.385(4)
1.521(3)
1.443(3)
116.7(3)
133.1(2)
121.52(17)
116.1(3)
132.6(2)
120.74(17)
175.2(2)
178.9(2)
tated by –53.4(3)° and 129.8(2)° out of the carbocycle plane. At
first glance, the driving forces behind this twisted conformation
must be the increased electron-acceptor strength of the carbocycle
upon going from 1 to 2, the disappearance of the CH. . .O intramo-
lecular interaction, and steric strain caused by the increased van
der Waals radius of the ortho-substituents (being 1.10 and 1.46 Å
for hydrogen and fluorine, respectively [26]).
Comparison of the molecular structures of 1 and 2 (given in Ta-
bles 1 and 2, respectively) reveals that besides a change in the ori-
entation of the N@S@O groups, substitution of hydrogen by
fluorine affects the geometries of these functionalities, including
a lengthening of the C–N bonds by about 0.03 Å and a narrowing
of the CNS bond angles by about 6.5° on average.
The crystal lattice of 1 reveals a layered structure formed by in-
plane intermolecular CH. . .S [2.85(5) Å] and S. . .O [3.265(4) Å] con-
tacts [15], which are shorter than the corresponding van der Waals
contacts [26] by about 0.07 and 0.13 Å, respectively. The crystal
packing of 2 is very different (Fig. 2). It displays stacks formed by
Table 2
Selected geometrical data comparing solid-state (XRD) and calculated geometries of
the Z,Z isomer of compound 2 (C1-syn,anti); bond lengths in ÅA and angles in degrees.
0
PBE/
3z
B3LYP/6–
311 + G(d,p)
MP2/6–
311G(d,p)
XRD
C1–C2
C1–N1
N1–S1
S1–O1
C2–N2
N2–S2
S2–O2
C2–C1–N1
C1–N1–S1
N1–S1–O1
C1–C2–N2
C2–N2–S2
N2–S2–O2
C2–C1–N1–S1
C1–C2–N2–S2
1.436 1.425
1.381 1.384
1.571 1.547
1.417
1.400
1.567
1.479
1.398
1.564
1.481
122.8
123.6
119.5
118. 4
122.3
118.7
ꢀ49.9
133.5
1.404(3)
1.416(3)
1.519(3)
1.448(3)
1.410(3)
1.517(2)
1.447(2)
122.1(2)
125.7(2)
119.29(14)
119.1(2)
127.1(2)
118.87(13)
ꢀ53.4(3)
129.8(2)
1.500
1.475
1.381 1.383
1.572 1.545
1.495 1.483
123.7 123.9
128.7 130.5
120.2 119.5
118.2 118.4
128.8 130.0
119.7 119.2
ꢀ42.3 ꢀ42.4
141.9 137.2
N. . .
p and F. . .p interactions with an N1. . .Cg distance of 3.352(5)
Å and an F2. . .Cg distance of 3.405(4) Å (Cg denotes the centroid
of the ring); the separation of the ring planes is 3.189 Å. The neigh-
bouring stacks are connected into layers parallel to the [0 3 1]
plane by S2...O2 contacts of 3.235(3) Å (the sum of van der Waals
radii is 3.39 Å [26]), and bifurcate S1...F4 contacts of 3.220(2) and
3.202(2) Å (the sum of van der Waals radii is 3.27 Å [26]). The
Fig. 2. A view of the packing of 2 along the [1 1 0] direction. Dashed lines indicate selected intermolecular interactions (see text for details).

A.G. Makarov et al. / Journal of Molecular Structure 978 (2010) 158–162
161
Table 4
Relative energies (
D
E in kJ molꢀ1) of the three different isomers of compounds 1 and 2 at various levels of theory.
PBE/3z
B3LYP/6–311 + G(d,p)
MP2/6–311G(d,p)
u1, u2 (symmetry)
D
E
u1, u2 (symmetry)
D
E
u1, u2 (symmetry)
DE
1-Z,Z
1-Z,E
1-E,E
2-Z,Z
2-Z,E
2-E,E
0.0
180.0, 180.0 (C2v-anti,anti)
169.2, –29.9 (C1-anti,syn)
ꢀ26.0, 150.5 (C1-syn,anti)
42.3, ꢀ141.9 (C1-syn,anti)
145.9, ꢀ22.7 (C1-anti,syn)
ꢀ29.1, 165.7 (C1-syn,anti)
0.0
180.0, 180.0 (C2v-anti,anti)
173.0, ꢀ26.9 (C1-anti,syn)
ꢀ24.7, 152.1 (C1-syn,anti)
42.4, ꢀ137.2 (C1-syn,anti)
47.3, ꢀ161.7 (C1-syn,anti)
ꢀ28.6, 167.1 (C1-syn,anti)
0.0
50.0, ꢀ151.2 (C1-syn,anti)
170.3, ꢀ48.0 (C1-anti,syn)
ꢀ35.1, 143.0 (C1-syn,anti)
49.9, ꢀ133.5 (C1-syn,anti)
51.4, ꢀ134.1 (C1-syn,anti)
ꢀ38.0, 155.0 (C1-syn,anti)
15.5
36.8
0.0
12.6
22.6
16.3
43.9
0.0
18.0
33.1
26.8
55.6
0.0
25.9
56.9
slightly shortened interlayer F1. . .F2 contacts of 2.918(2) Å (the
sum of the van der Waals radii is 2.91 Å [26]) and F3. . .O1 contacts
of 2.967(3) Å (the sum of the van der Waals radii is 3.04 Å [26])
should also be mentioned.
be interpreted using the qualitative bonding model [10,17], which
is based on anomeric interactions in the Z configuration of RNSX
(X = O, N–) derivatives, and on the electron-acceptor strength of
the group R for the twisted molecular conformation. Removal of
the CH. . .O intramolecular interaction upon substitution of the
hydrogen atoms in the 3- and 6-positions in 1 by fluorine atoms
in 2, as well as the introduction of steric strain caused by this sub-
stitution, work together towards a non-planar conformation of 2.
The combination of these stereoelectronic effects allows the ratio-
nalization of the known structures of RNSX (X = O, N–) derivatives
and the prediction of as yet unknown structures.
3.2. Gas-phase structures
The relative energies of the nine different conformers of Z,Z-2
were investigated, excluding the three with unrealistic structures:
the C2v-syn,syn conformer, in which both –NSO groups are super-
imposed, and the Cs-syn,syn and Cs-syn,anti conformers, in which
there is considerable repulsion between both –NSO groups, were
omitted from these calculations. Furthermore, the C2v-anti,anti
conformer turned out to be a transition state with two imaginary
frequencies. All conformers, including two with C1 symmetry, are
listed in Table 3, together with their relative energies. Even though
the energy differences are not very large, it is clear that one of the
C1-syn,anti conformers, i.e., the one which is also found in the solid
state, is the lowest-energy conformer.
Acknowledgements
The authors are grateful to the Russian Foundation for Basic
Research (projects 06-03-32229 and 09-03-00361) and the Univer-
sity of Antwerp (project BOF UA 22296) for financial support of
their work. The authors gratefully acknowledge the University of
Antwerp for access to the university’s computer cluster CalcUA.
Based on this observation, the structures and relative energies
of the relevant conformers of the three isomers of 1 and 2 were
calculated at various levels of theory [DFT/PBE/3z, DFT/B3LYP/
6–311 + G(d,p) and MP2/6–311G(d,p)] and the results are given
in Table 4. The geometrical data of the Z,Z isomers have been gath-
ered in Tables 1 and 2 for compounds 1 and 2, respectively. PBE/3z
reproduces the results of the earlier calculations on 2 and finds the
C1-syn,anti conformer to be the lowest-energy conformer, as do
B3LYP/6–311 + G(d,p) and MP2/6–311G(d,p), and all three geome-
tries are comparable. According to the DFT calculations, the Z,Z iso-
mer of 2 is stabilized relative to the Z,E configuration by about
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15 kJ molꢀ1, while MP2 yields a difference of about 26 kJ molꢀ1
.
The E,E configuration is further destabilized by about twice as
much, for both DFT and MP2.
For 1, the lowest-energy isomer is likewise the Z,Z isomer but in
this case both DFT functionals yield planar structures; MP2, on the
other hand, produces a markedly non-planar conformation, quite
similar to the one found for the tetrafluoro derivative (2). The cal-
culated energy differences between the Z,Z and the Z,E isomers of 1
mirror those found for 2, as differences of about 16 and 27 kJ molꢀ1
are found. DFT produces somewhat large differences between the
Z,E and E,E isomers (about 40 kJ molꢀ1), but MP2 stands by the
55 kJ molꢀ1 found also for 2.
For Z,Z-1, the two DFT methods produce similar geometries and
maintain the planar conformation also found in the solid state
(Table 1). Also for 2, the gas-phase structures obtained using the
different methods are similar to each other and to the experimen-
tal solid-state structure (Table 2). One can conclude that in the case
of these two molecules, the numerous intermolecular interactions
in the solid state do not practically affect the calculated gas-phase
molecular conformations.
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