1-Methylthio-1-phenyl-1-silacyclohexane: Synthesis, conformational preferences in gas and solution by GED, NMR and theoretical calculations

Article abstract of DOI:10.1016/j.tet.2019.130677

1-Methylthio-1-phenyl-1-silacyclohexane 1, the first silacyclohexane with the sulfur atom at silicon, was synthesized and its molecular structure and conformational preferences studied by gas-phase electron diffraction (GED) and low temperature ¹³C and ²⁹Si NMR spectroscopy (LT NMR). Quantum-chemical calculations were carried out both for the isolated species and solvate complexes in gas and in polar medium. The predominance of the 1-MeS_axPh_eq conformer in gas phase (1-Ph_eq:1-Ph_ax = 55:45, ΔG° = 0.13 kcal/mol) determined from GED is consistent with that measured in the freon solution by LT NMR (1-Ph_eq:1-Ph_ax = 65:35, ΔG° = 0.12 kcal/mol), the experimentally measured ratios being close to that estimated by quantum chemical calculations at both the DFT and MP2 levels of theory.

Full text of DOI:10.1016/j.tet.2019.130677

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1-Methylthio-1-phenyl-1-silacyclohexane: Synthesis, conformational preferences in
gas and solution by GED, NMR and theoretical calculations
Bagrat A. Shainyan, Elena N. Suslova, Tran Dinh Phien, Sergey A. Shlykov, Matthias
Heydenreich, Erich Kleinpeter
PII:
S0040-4020(19)31051-8
https://doi.org/10.1016/j.tet.2019.130677
TET 130677
DOI:
Reference:
To appear in: Tetrahedron
Received Date: 8 July 2019
Revised Date: 2 October 2019
Accepted Date: 3 October 2019
Please cite this article as: Shainyan BA, Suslova EN, Phien TD, Shlykov SA, Heydenreich M, Kleinpeter
E, 1-Methylthio-1-phenyl-1-silacyclohexane: Synthesis, conformational preferences in gas and
solution by GED, NMR and theoretical calculations, Tetrahedron (2019), doi: https://doi.org/10.1016/
j.tet.2019.130677.
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1
1
-Methylthio-1-phenyl-1-silacyclohexane: Synthesis,
Conformational Preferences in Gas and Solution by GED, NMR
and Theoretical Calculations
*
,a
a
b
Bagrat A. Shainyan, Elena N. Suslova, Tran Dinh Phien,
c
d
*,d
Sergey A. Shlykov, Matthias Heydenreich, Erich Kleinpeter
a
A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Division of the Russian Academy of
Sciences, Favorsky Street, 664033 Irkutsk, Russian Federation; e-mail:
1
bagrat@irioch.irk.ru
b
Institute of Research and Development, Duy Tan University, 03 Quang Trung, Da Nang, Viet
Nam
c
Ivanovo State University of Chemistry and Technology, Sheremetievskiy ave., 7, 153000,
Ivanovo, Russian Federation
d
Chemisches Institut der Universität Potsdam, Karl-Liebknecht-Str. 24-25, D-14476 Potsdam
Golm), Germany; e-mail: ekleinp@uni-potsdam.de
(
ABSTRACT:
___________________________________________________________________________
_
1
-Methylthio-1-phenyl-1-silacyclohexane 1, the first silacyclohexane with the sulfur atom at silicon,
was synthesized and its molecular structure and conformational preferences studied by gas-phase
1
3
29
electron diffraction (GED) and low temperature C and Si NMR spectroscopy (LT NMR). Quantum-
chemical calculations were carried out both for the isolated species and solvate complexes in gas and in
polar medium. The predominance of the 1-MeS Ph conformer in gas phase (1-Ph :1-Ph = 55:45,
ax
eq
eq
ax
ꢀG° = 0.13 kcal/mol) determined from GED is consistent with that measured in the freon solution by
LT NMR (1-Ph :1-Ph = 65:35, ꢀG° = 0.12 kcal/mol), the experimentally measured ratios being close
eq
ax
to that estimated by quantum chemical calculations at both the DFT and MP2 levels of theory.
__________________________________________________________________________
Keywords: 1-Methylthio-1-phenyl-1-silacyclohexane; Conformational analysis; Gas phase electron
_
1
3
29
diffraction; Low-temperature C and Si NMR; DFT and MP2 calculations.

2
1
. Introduction
Nowadays, a large number of silacyclohexanes, mono and disubstituted at silicon, and
silaheterocyclohexanes has been studied experimentally from the viewpoint of their
1
conformational preferences both in gas phase and in a freon solution, as reviewed in 2016 and
2–13
reported later.
Among these sila(hetero)cyclohexanes the Si−Ph compounds, which possess
1
4–18,
4, 7
19
20
a second substituent at silicon such as H, Me,
OR, F, Cl, Br, Me N, are of special
2
interest for the present work because the conformational energies of substituents in
silacyclohexanes are additive (in the parent cyclohexanes they are much more distinct but non-
additive), and because steric and electrostatic effects in the two series are of different
2
1
importance.
The conformational analysis of Si−Ph silacyclohexanes having as the second substituent
4
,19,20
at silicon the O, N, F, Cl, Br heteroatoms
showed that in the gas phase at room
temperature they exist predominantly as Si−Ph conformers (GED), but in a freon solution at
ax
low temperature the Si−Ph conformers predominate (LT NMR, ~100 K). The latter result is
eq
in agreement with the conformational equilibria of the cyclohexyl derivatives and the mono-
and di-Si-substituted silacyclohexanes. Although the C−Si bonds are considerably longer than
the C−C bonds in the cyclohexyl analogues, the more bulky substituent still goes into the
equatorial, whereas the less bulky and more polar substituents into the axial position; the
differences are much less distinct as in the corresponding cyclohexyl derivatives but clearly
indicated.
The above set of substituents includes heteroatoms O, N and Hal, which all are more
electronegative than carbon. The only available heteroatom having electronegativity close to
carbon is sulfur (2.50 and 2.44), but no sila(hetero)cyclohexanes with exocyclic sulfur atom at
silicon were known in the literature. Therefore, our first task was to synthesize 1-methylthio-1-
phenyl-1-silacyclohexane, as the simplest representative, and then to investigate it in gas phase
(by GED method), in the freon solution (at low temperature by LT NMR spectroscopy) and
theoretically at the DFT and MP2 levels of theory.
2
. Results and discussion
2
.1 Synthesis.
The simplest way to the target 1-methylthio-1-phenyl-1-silacyclohexane 1 is
substitution of chlorine in 1-chloro-1-phenyl-1-silacyclohexane with sodium
2

3
methanethiolate. Compound 2 was synthesized by the known procedure employing the
reaction of the Grignard reagent prepared from 1,5-dibromopentane with
2
2
phenyltrichlorosilane. The reaction of 2 with suspension of MeSNa in benzene was
performed in an inert atmosphere under dry conditions in the presence of dibenzo-18-crown-6
as phase-transfer catalyst. Pure 1 was isolated in 55% yield by vacuum distillation (Scheme
1
).
Scheme 1. Synthesis of heterocycle 1. Reagents and conditions: (i) Et O, reflux for 5 h under Ar; (ii) MeSNa,
2
benzene, dibenzo-18-crown-6 (0.10 mol %), reflux for 3 h under Ar.
2
.2 Quantum chemical calculations.
The PES profiles of molecule 1 were obtained by scanning the CipsoSiSC (φ) and
CorthC SiS (θ) dihedral angles describing the rotation of the methylthio group about the Si–S
ipso
bond and the phenyl ring about the Si–Cipso bond are plotted in Figure 1. As follows from
these profiles, rotation of the two groups is strongly correlated, which is typical for gear
motion in molecular motors as was demonstrated in our recent works on related compounds,
3
4, 7
6
1
-X-1-phenyl-1-silacyclohexanes with X= Me, MeO, HO and Me N. In order to clarify
2
this influence, we have calculated the PES profiles at the M062X/6-311G** level for both
axial and equatorial conformers on a grid of points corresponding to the torsion angles about
the Si–Cipso and Si–S bonds scanned with a step of 10º, the rest of the molecule being
optimized (Figure 2).

4
MeS group rotation
Phenyl ring rotation
4
3
3
2
2
.0
.5
.0
.5
.0
M062X/6-311G**
Phax;
Pheq
Phax
Pheq
M062X/6-311G**
3
3
2
2
1
1
0
0
.5
.0
.5
.0
.5
.0
.5
.0
II
II
III
III
II
II
II
II
V
1.5
.0
0.5
.0
-0.5
V
1
V
V
V
I
V
IV
IV
I
0
I
I
IV
IV
-
0.5
-150 -100 -50
0
50 100 150
-150 -100 -50
0
50
100
150
ϕ, deg.
θ, deg.
Figure 1. Lowest energy pathways for 1-Ph and 1-Ph conformers by rotating the MeS group about Si–S bond
ax
eq
(
left) and the phenyl ring about Si–Cipso bond (right) calculated at M062X/6-311G** level.
Ph-Equatorial form
Ph-Axial form
V
2
II
1
1
50
00
150
3
III
4
3
3
4
3
2
4
100
1
1
1
I
5
0
0
50
0
IV
4
8
6
5
7
7
6
6
7
4
9
3
8
9
5
7
2
3
2
4
5
6
3
IV
-50
4
I
-50
-100
-150
5
1
3
1
1
2
-
100
150
2
3
3
3
4
4
4
III
-
2
II
3
V
0
30
60
90
θ, deg.
120
150
180
0
30
60
90
θ, deg.
120
150
180
Figure 2. PES profiles of 1 obtained by synchronous scanning two angles, θ and φ, M062X/6-311G**, energy in
kcal/mol.
The M062X calculations show that this compound has five possible conformers
(
neglecting the rotamers) with C symmetry, see Figure 3. Note that the energy barriers for the
1
phenyl ring rotation between conformers III→II is very low, 0.01 kcal/mol, and conformer III
–1
has the lowest frequency of 18 cm , corresponding to the phenyl ring rotation. At the same
time, from the B3LYP and MP2 results, conformer III is unstable and readily converges to
conformer II when being optimized. Thus, molecule 1 has only four conformers: two 1-Pheq

5
and two 1-Ph . Compared to the 1-methoxy- and 1-hydroxy-1-phenyl-1-silacyclohexanes, the
ax
1
-Ph conformer, in which the phenyl ring lies in the bisect plane of the silacyclohexane
ax
frame, does not exist due to orbital interaction and steric repulsion between the two
substituents at silicon.
I
II
III
IV
V
Figure 3. Conformers of compound 1, hydrogen atoms are omitted.
As a rule, for the series 1-X-1-Ph-1-silacyclohexanes (X = Me, MeO, HO, Me N), in
2
molecule 1 the methylthio group rotation induces the phenyl ring rotation in Ph forms,
eq
whereas the phenyl group rotation does not noticeably affect the methylthio group orientation.
From the M062X/6-311G** results, the energy barriers for the MeS group rotation between
conformers I→II and IV→V are ca. 3.0 and 3.2 kcal/mol, respectively. Comparing to 1-
4
methoxy-1-phenyl-1-silacyclohexane, replacement of methoxy group at silicon by the bulkier
methylthio group increases the repulsion between the two substituents and, hence, the energy
barrier.
The relative total electron and Gibbs free energies (kcal/mol) of all conformers are given
in Table 1. As follow from QC calculations, the conformers I and IV are most stable, the ꢀE
and ꢀG values of conformer II are higher by 2.20 and 2.47 kcal/mol, respectively, relative to
conformer I. According to all the DFT/6-311G** calculations, conformers I and IV have very
similar ꢀE values and are more stable than others. It should be noted, that the use of more
sophisticated basis set cc-pVTZ leads to the increase of ꢀE value of conformer IV by 0.22
kcal/mol. Since the phenyl group is a bulkier substituent than the methylthio group, the Pheq
conformers are entropically more preferable, hence, the molar fraction of Ph conformer is
eq
higher than of Ph . It is to be noted that the ∆G° values from DFT calculations show
ax
conformer IV to be less preferable than I by 0.5–0.6 kcal/mol. Of the QC computational
methods employed, the DFT calculations predict conformer I to be the most stable. Total

6
contribution of the Ph conformers summed over all its rotamers varies within 31–39% at the
ax
DFT level. At the same time, at the MP2/6-311G** level of theory, conformer IV is lower in
energy E by 0.43 kcal/mol and in free energy G° only 0.02 kcal/mol higher in energy than
conformer I, suggesting the predominance of 1-Ph conformer (from ∆E) or practically equal
ax
contribution of the two conformers (from ∆G°). However, the use of a higher-level basis set
cc-pVTZ for MP2 calculations inverts this result so that the most stable rotamers of 1-Ph and
ax
1
-Ph conformers become practically identical in energy (∆E = 0.023 kcal/mol in favor of 1-
eq
Ph ). Vibrational calculations at MP2/cc-pVTZ level are too costly, so the ZPE and entropy
eq
corrections to ∆E were taken from MP2/6-311G** calculations resulting in ∆G° for equation
(
1) of –0.47 kcal/mol and the 1-Ph :1-Ph ratio of 64:36 (Table 1). This ratio virtually
eq ax
coincides with the calculated at various DFT levels (Table 1) as well as with those measured
experimentally in gas phase [I:IV:V=55(15):35(15):10(10), GED] and in the freon solution (1-
Ph :1-Ph = 65:35, LT NMR) – vide infra.
eq
ax
Table 1. Relative total electron energies ꢀE [E(1-Ph ) – E(1-Ph )] and Gibbs free energies ∆G° [G°(1-Ph ) –
ax
eq
ax
G°(1-Ph ), kcal/mol] and predicted contribution X of conformers of 1.
eq
–
ꢀE
–ꢀG° (298 K)
X, %
Method/basis set
I II
III IV
V
I II
III IV
V
I:IV:V
B3LYPD3/6–311G** 0 2.20
–
–
–0.01 0.84 0 2.47
0.22 0.95 0 2.60
–
–
0.47 1.17 63:28:9
0.45 1.06 61:29:10
B3LYPD3/cc–pVTZ
M062X/6–311G**
M062X/cc–pVTZ
MP2/6–311G**
0 2.32
0 2.62 2.84 0.02 1.11 0 3.16 3.40 0.45 1.41 64:30:6
0 2.68 2.70 0.22 1.14 0 3.38 3.34 0.62 1.39 69:24:7
0 2.70
–
–
–0.43 0.59 0 2.80
0.023
–
–
0.02 0.87 46:44:10
(0.47) 64:36
MP2/cc–pVTZ
0
–
–
0
–
–
2
.3 Gas Electron Diffraction (GED) analysis.
Based on the ∆G° values in Table 1, conformer I is favorable with respect to
conformers IV and V because of strong steric repulsion between the phenyl and
silacyclohexane ring (1,3-diaxial interactions). Conformers II and III are much higher in
terms of ꢀE and ∆G° values and, thus, may be excluded from further consideration. For this

7
reason, we assume the investigated vapor over liquid at 333(3) K to consist of three
conformers, namely I, IV and V (cf. Figure 3).
The following independent geometric parameters were used to describe the geometry:
bond distances Si–C2, C2–C3, C7–C8, Si–S, C–S and C2–H; bond angles SiC2C3, C7SiC2,
C8C7Si, SSiC2, CSSi, HC2Si, HC2C3, HC8C7, HCS and HC14H; dihedral angles SiC2C3C4,
C2C3C4C5, C8C7SiC2, CSSiC7 and HCSSi for conformer I; C8C7SiC2 and CSSiC7 for
conformers IV and V. All other geometrical parameters for the conformers were described by
parameters analogous to those in conformer I and corrected by adding the differences adopted
from M062X/6-311G** calculations. For the three studied conformers, the benzene ring was
fixed to be planar since the QC calculations showed very small deviations from planarity.
The experimental and theoretical molecular scattering intensities sM(s) and radial
distribution curves f(r) with the corresponding differences “Experim.–Theor.” are plotted in
Figure 4. Vibrational amplitudes for all three conformers were refined in nine groups
according to the specific regions in the radial distribution: 0–1.20; 1.20–1.70; 1.70–2.02; 2.02–
2
.30; 2.30–2.64; 2.64–3.02; 3.02–3.91; 3.91–6.06 and 6.06–10.0 Å. The differences between
the amplitudes within each group were constrained to the calculated values. Vibrational
corrections ∆r = r – r and starting root-mean square amplitudes were calculated with the
h
a
1
2
3
Vibmodule program using the so-called second approximation, in which a harmonic
approach with nonlinear relation between Cartesian and internal coordinates was applied on
the basis of the force field estimated in the QC calculations at the M062X/6-311G** level.

8
sM(s)
5
98 mm
3
38 mm
∆sM(s)
0
5
10
115
20
25
30
−
s, Å
EXP
I:IV:V=55+35+10%
Conf V
Conf IV
Conf I
0
1
2
3
4
5
r, Å
6
7
8
9
10
Figure 4. Molecular scattering intensities sM(s) (above) and radial distribution curves f(r) (below): experimental
dots) and theoretical (black line) for refined mixture of the conformers I:IV:V=55(15):35(15):10(10)%; colored
lines correspond to refinement of all parameters under assumptions of individual conformers; the differences
(
“Experim.-Theor.” are given at the bottom.
The optimal conformer ratio of compound 1 was found to be I:IV:V=55(15):35(15):10(10)%
[
Ph :Ph =55(15):45(15)%] with the uncertainty estimated using Hamilton’s criterion at 0.05
ax eq
significance level (Rf,min= 4.17%), see Figure 5. Thus, from GED analysis, relative Gibbs free
energies between the Ph and Ph conformers were estimated as ∆G°(333K) = G° – G° =
ax
eq
ax
eq
0
.13(40) kcal/mol [the values of ꢀG(333K) of conformers I:IV:V are 0:0.30:1.13 kcal/mol].
Clearly, the theoretical results very well agree with experimental GED data. For comparison,

9
the ratios Ph :Ph of 1-phenyl-1-(X)-silacyclohexanes are 62(10):38(10), 42(15):58(15),
eq
ax
1
4
14
6
4
2
0(15):80(15), 30(15):70(15) and 50(20):50(15) for X of H, Me, Me N, MeO and HO
2
4
group, respectively.
0
1
00
10
M
90
o
l
2
0
%
a
,
r
8
0
f
V
r
a
3
0
r
6.0
5
e
c
t
i
o
7
0
m
r
4
0
6.6
n
o
f
o
n
o
f
.0
60
c
c
50
o
f
n
o
f
50
o
r
n
6
0
6.2
o
m
i
t
4.4
c
5
.2
40
e
a
r
r
70
6.4
I
V
f
r
,
a
30
l
%
o
80
M
4.8
5
.4
.6
20
.4 10
9
0
5
4.6
5
1
00
6
.8 5.8
5.2 5.8
6
.4
0
0
10 20 30 40 50 60 70 80 90 100
Molar fraction of conformer I, %
Figure 5. Agreement factor R as a function of molar fraction of the most stable conformers of compound 1.
f
In addition, a goodness of fit was checked by running the KCED program with no
refinement of geometry and vibrational parameters of all three conformers of the compounds
for the theoretical models built on the M062X/6-311G** calculations; the tests resulted in the
following R-factors: 7.1, 8.1 and 12.4% in the case of individual conformers I, IV and V,
respectively.
Geometry and NBO analysis. Selected experimental (GED) along with the calculated (QC)
geometric parameters of the three most stable conformers I, IV and V of compound 1 are
compiled in Table 2. As follows from QC results, the C–C bond distances of silacyclohexane
ring do not depend on position and orientation of the substituents. Due to steric repulsion
between the two rings, the Si–Cipso bond distance in conformer IV is longer by 0.005 Å than
that in conformer I. The MP2 method predicts shorter Si−S and S−C bond distances by 0.008-
0
.009 Å and longer C−C bond distances of phenyl ring by 0.007-0.010 Å than the M062X
calculations. In conformers I and IV, the steric repulsion between the methyl group and two

1
0
rings leads to increase of the C(7)−Si−S bond angle by ca. 3º. The θ angles of both Phax
conformers IV and V differ by 4–6º, i.e. the rotation of the methylthio group does not strongly
influence the orientation of the phenyl ring.
The calculated bond distances and bond angles are in good agreement with the GED
values. The MP2 calculations very well predict Si–S, S–C and sesquialteral C–C bond
distances. The experimental dihedral angles φ and θ were refined for the conformers I, IV and
V with big uncertainty, in agreement with the theoretical predictions. The Si–S bond is not
perpendicular to the phenyl ring plane in the axial and equatorial forms. The bond length of
the term Si−S, despite low multiplicity, was derived reliably with high precision (standard
deviation 0.0008 Å) due to it is quite well resolved in the radial distribution, see Figure 4 at
ca. 2.15Å and Table 2. Experimental and theoretical geometric and vibrational parameters of
all conformers are summarized in Supplementary data, Tables S4–S6.
As follows from the NBO analysis, the orbital interaction between the electron lone pairs
of sulfur atom and Si–Cipso bond leads to the Si–Cipso bond distance elongation in conformer
IV by 0.005 Å, comparing to that in conformer V. This orbital interaction LP(S)→ σ*(Si–C7)
also leads to stability of conformers I and IV. In addition, the NBO analysis shows that the
steric effect stabilizes the equatorial form I at M062X/6-311G** level of theory. However, as
concluded from the MP2/6-311G** results, the steric effect stabilizes the axial conformer IV.

1
1
a
Table 2. Theoretical (with 6-311G** basis set) and experimental parameters, the second-order
(2)
(ST)
perturbation energy E LP(S)→σ*(Si–C), relative total steric energy ꢀE
at the M062X and MP2 levels with
6
-311G** basis set of three conformers (MP2/cc-pVTZ values are given in brackets).
Conformer
Method
I
IV
V
M062X MP2
GED M062X MP2
GED M062X MP2
GED
Bond distance, Å
Si–C2
Si–C7
Si–S
1.875 1.874 1.872(4) 1.874
1.878)
1.873 1.871(4) 1.879 1.878 1.876(4)
(1.877)
(
1.875 1.873 1.872(4) 1.881
1.876)
1.877 1.878(4) 1.876 1.872 1.872(4)
(1.879)
(
2.157 2.148 2.158(5) 2.151
2.150)
2.143 2.152(5) 2.152 2.143 2.152(5)
(2.145)
(
C2–C3
C7–C8
C–S
1.542 1.542 1.542(3) 1.542
1.538)
1.543 1.542(3) 1.542 1.543 1.543(3)
(1.539)
(
1.401 1.408 1.406(4) 1.399
1.404)
1.408 1.404(4) 1.399 1.409 1.404(4)
(1.404)
(
1.831 1.824 1.828(4) 1.832
1.827)
1.825 1.829(4) 1.831 1.825 1.828(4)
(1.828)
(
Bond and torsion angles, º
C7SiS
SiSC
φ
108.4 108.9 106.8(8) 108.5
108.7 108.1(8) 105.7 105.7 111.1(8)
(108.3)
(108.3)
98.9
52.1
60.2
98.4
99.5(6)
48(17)
59(13)
99.0
48.1
63.8
98.7
99.5(6) 100.0 99.8 100.6(6)
(98.5)
(98.5)
52.4
46.5
(49.8)
58(25)
55(32)
170.1 171.5 152(57)
68.0 74.2 85(30)
(54.6)
θ
65.4
68.3
(43.8)
(61.5)
Second-order perturbation energy and total steric energy, kcal/mol
LP(S)→
σ*(SiC6)
9
6
.76
11.30
10.69
12.46
10.02 11.32
LP(S)→
.83
0
7.91
0
6.29
6.85
1.15
–
–
σ*(SiC7)
ST
ꢀE
–0.75
–0.50 –0.11
a)
See Figure 3 for atom numbering and text above for angles φ and θ definition. Values in parentheses for the
2
2 ½
GED data are full errors estimated as σ(r )=[σ
+(2.5σ ) ] and as 3σ for angles, where σscale =0.002r and
LS LS
h1
scale
σLS is a standard deviation in least-squares refinement for internuclear distances

1
2
2
.4 Low-temperature dynamic NMR study.
1
13
29
Room temperature H, C and Si NMR spectra of compound 1 in CD Cl confirm
2
2
the structure of the compound (see Supplementary Data). The dynamic ring interconversion of
1
13
the silacyclohexane ring is fast on the NMR time scale; thus, averaged H/ C signals and a
2
9
single Si signal of conformers 1-Ph and 1-Ph are observed. On cooling the solution of
ax
eq
compound 1 in the freon mixture CD Cl : CHFCl : CHF Cl = 1 : 1 : 3, which remains liquid
2
2
2
2
below 100 K, the dynamic silacyclohexane ring interconversion process gets slow on the
1
13
29
NMR time scale; the H, C and Si NMR signals partly or completely split into separate
signals of conformers 1-Ph SMe and 1-Ph ,SMe (cf. Scheme 2). This allowed full
ax,
eq
eq
ax
2
9
conformational analysis to be performed. Note, that until very recently the Si NMR was not
used for conformational analysis of silacyclohexane or any related Si-containing compounds.
The first and so far the only example is our recent work on (1,1′-phenyl-1,1′-silacyclohex-1-
2
4
yl)disiloxane.
Scheme 2. Conformational equilibrium of 1-Methylthio-1-phenyl-1-silacyclohexane 1.
1-Methylthio-1-phenyl-1-silacyclohexane 1 is the first compound which can be
employed to study the influence of the C −Si−S−CH motif on both the barrier to ring
2
3
interconversion and on the conformational equilibrium of the Si-disubstituted silacylohexanes.
So far, monosubstituted silacyclohexanes (X = Me, CF , SiH , CN, F, Cl, Br, I, OMe, NMe )
3
3
2
8
−10, 12, 25–30
31
2
,
disubstituted analogues 3 containing a methyl group at silicon (X = F, CF ) and
3
disubstituted silacyclohexanes 4 (H, CH , F, Cl, OMe, NMe ) with the phenyl group at
3
2
2
, 4, 6, 14,17
silicon
have been studied (cf. Scheme 3); the corresponding conformational equilibria
have been investigated in the gas phase by GED, otherwise in solution by vibrational
spectroscopy and/or low temperature NMR spectroscopy.

1
3
Scheme 3. Conformational equilibria of various mono- and di-Si-substituted silacyclohexanes.
In series 2, CH , SiH and C≡N prefer the equatorial conformation. The substituents F,
3
3
CF , Cl, Br, I, OMe and NMe in 2, however, were found as preferred axial conformers
3
2
(unlike in the corresponding cyclohexanes, where they still remain equatorial). This trend is
continuing in the di-substituted derivatives 3: the methyl group remains in the equatorial, the
more polar substituents (CF , F and Cl) change to the axial position. Finally, the phenyl
3
analogues 4: Depending on temperature in the gas phase (GED) and in the freon solution (LT
NMR spectroscopy) the conformational preferences may be different. At room temperature in
the gas phase the Ph conformer is the preferred one, whereas in the freon solution at ca. 100
ax
K the corresponding Ph conformer predominates. The latter result is in agreement with the
eq
evident trend of a more bulky substituent (Ph) to occupy the equatorial position and the other
substituent – less bulky and/or more electronegative – to go to the axial position; the
differences are much less distinct as in the corresponding cyclohexyl derivatives but clearly
indicating.
First, we calculated the free energy of activation of the silacyclohexane ring
≠
13
interconversion (ꢀG ) of compound 1. In Figure 6 are given the relevant C NMR data for
the Cipso carbon signal. The coalescence temperature (T ) was found at 123 K, the chemical
c
13
shift difference (ꢀν = 317 Hz) of the C NMR signals of the two conformers was measured at
9
8 K, the lowest temperature obtained with the local NMR facility. Together with the rate
≠
constant k = π ꢀν/√2 = 704.2 via ꢀG = 19.14 T (10.32 + log T /k ) the barrier to ring
c
c
c
c
interconversion of 5.8 kcal/mol was obtained, quite normal for the ring interconversion in the
2
–19
so-far studied Si-disubstituted silacyclohexanes.
The barrier to the 6-membered ring interconversion was also calculated by the same
29
13
3,5
procedure examining the Si NMR signal, and the C NMR signals of C and of the SMe
1
carbon of 1. As to the H NMR spectra, in spite of splitting of some signals at low temperature
(not the SMe singlet), even at 98 K there are too many poorly resolved and overlapping
signals, so that the assignments could not be easily done (see Supplementary data).
Theoretical estimation of the barrier to ring inversion by calculating the transition state
(TS) at the same MP2 level as for conformers of 1 are too time-consuming, so, it was done at
the MP2/6-311G**//MP2/6-31G** level, that is, on the geometry optimized with a slightly

1
4
smaller basis set. The energy of TS is higher than that of conformers 1-Ph SMe and 1-
ax,
eq
Ph ,SMe by 3.9 and 3.4 kcal/mol, respectively, which is in satisfactory agreement both with
eq
ax
2
1
the experiment and the barriers for the previously studied related silacyclohexanes. However,
it must be mentioned that the imaginary frequency from MP2/6-31G** vibrational calculations
–
1
is as low as –41 cm and, moreover, this vibrational mode corresponds not only to the
distortion of the silacyclohexane ring from the chair conformation but mainly to rotational
vibrations of the phenyl ring about the Si–Cipso bond, so, it cannot be considered as a reliable
TS for the ring interconversion.
1
73 K
23 K
1
9
8 K
33
32 31 30 29 28 27 26 25 24 23 22 21 20 19 18 17 16 15 14 13 12 11 10
9
8
7
ppm
137
136
135
134
133
132
131
130
129
128
ppm
1
3
Figure 6. C NMR spectra of 1-phenyl-1-SMe-1-silacylohexane 1 at various temperatures (above: 173 K, 123 K,
9
8 K; below: at 98 K, all in the freon solution).

1
5
2
9
Figure 7. Si NMR spectrum of 1-methylthio-1-phenyl-1-silacyclohexane 1 at 98 K in the freon solution.
Second, the different contribution of the two conformers in the present conformational
2
9
13
3,5
equilibrium was determined. The Si (cf. Figure 7), C signals of Cipso, C and the SMe
carbon atom at 98 K (cf. Figure 6) were integrated (K = [65.7]/[34.3] = 1.90 and evaluated
accordingly –∆G° = RT lnK = ±0.12 kcal/mol). To determine the sign of ∆G° and, hence, the
c
structure predominating in the conformational equilibrium (cf. Scheme 2), it is necessary to
1
3
29
assign the C and Si signals in the low temperature NMR spectra to specific conformers.
Based on the comparison of theoretically calculated and experimental chemical shifts (Table
3
), as well as on the above brief analysis of conformational preferences of the Si(Ph,X)
disubstituted silacyclohexanes, the major conformer was assigned to the 1-Ph conformer
eq
(65.5%, ∆G° = 0.12 kcal/mol). This is in agreement with the conformational equilibria of the
other so far studied disubstituted silacyclohexanes as obtained by low temperature NMR
spectra. The differences in ∆G° are only minor: for 1-X-1-Ph-silacyclohexanes (X = Me, F, Cl,
OMe, NMe , SMe) they vary from −0.15 to −0.1 kcal/mol, but, as compared with the
2
cyclohexyl analogues, there are parallel conformational dependences. The most bulky
substituent Ph goes into the equatorial position (the 1-Pheq conformer predominates), the
others go into the axial position. (ii) In doing so, the most bulky among the other substituents
(
Me) shows the lowest percentage of 1-Ph conformer (63%), while and the least bulky and
eq
most polar ones (H, F, Cl) – the highest percentage of 1-Ph (76−82%). In between are X =
eq
NMe (77%), OMe (69%) and SMe (66% of 1-Ph conformer), which are unsymmetrical
2
eq
rotors and can adopt the least hindered conformation by rotating their methyl group(s) away

1
6
from the ring. (iii) When comparing X = OMe and SMe, a slightly larger axial preference of
more polar OMe group is evident (69 vs. 66%). So, all together, the conformational behavior
of substituted cyclohexanes persists for the same substituents in silacyclohexanes; the effects
are only less pronounced due to the longer C−Si bond distances.
29
13
Table 3. Calculated (MP2/6-311G**) and experimental (bold) Si and C chemical shifts, δ,
a)
of 1-Ph and 1-Ph conformers of compound 1 and their difference ꢀ (ppm).
ax
eq
eq–a
2
9
3,5
Conformer
Si
ꢀeq–ax Cipso ꢀeq–ax Cmeta ꢀeq–ax
C
ꢀeq–ax SCH3 ꢀeq–ax
1
1
a)
-Phax
12.19
.62
13.03 2.31
.93
134.3
133.0
136.9
134.1
130.3
29.7
8.5
5
0.84
2.6
1.1
135.1 –0.4
129.9 –1.4
133.7
23.9 –1.0
28.7 –0.7
23.2
7.9
7.9
7.4
–0.6
–0.5
-Pheq
7
2,4,6
1
The remaining carbon atoms (Cortho, Cpara, C , as well as all H NMR signals] do not split at 98 K.
In Table 3, the most convincing evidence of correct assignment is the calculated values
of ꢀeq–ax, which vary in parallel with the experimental ones and prove the predominance of the
-Ph conformer. Note, that the relative Gibbs free energies in Table 1 cannot strongly depend
1
eq
on the polarity of the medium because the 1-Ph and 1-Ph conformers have very close
eq
ax
calculated dipole moments differing by ~0.1 D (depending on the method used). Therefore,
the predominance of the 1-Ph conformer in gas phase, which is retained in the Freon mixture
eq
used should probably retain in other solvents of different polarity.
3
. Conclusions
In conclusion, we have synthesized 1-methylthio-1-phenylsilacyclohexane 1, the first
silacyclohexane with the sulfur atom at silicon and performed its conformational analysis by
GED, low-temperature NMR and theoretical calculations. In gas phase, the three lowest-lying
conformers were found to be 1-Ph and 1-Ph (two rotamers about the Si–S bonds) in the
eq
ax
ratio of 55:45% corresponding to ∆G°(333K) = 0.13 kcal/mol. In the freon solution, LT NMR
1
3
29
spectroscopy showed decoalescence of some C and Si signals at ca. 100 K, allowing to
measure a somewhat larger 1-Ph :1-Ph ratio of 65:35% corresponding to ∆G°(98K) = 0.12
eq
ax
kcal/mol. The signals were assigned to specific conformers based on quantum-chemical
calculations, including both the energy and NMR calculations, as well as by comparison to the
earlier studied analogues. The dynamic NMR analysis also allowed to determine the barrier to
≠
interconversion of the silacyclohexane ring (ꢀG = 5.8 kcal/mol), which is typical for barriers

1
7
measured by us earlier for other silacyclohexanes. Theoretical calculations are consistent with
the experiment, proving a higher stability of 1-Ph conformer by up to 0.5 kcal/mol depending
eq
on the method and basis set used.
4
. Experimental Section
4
.1 General.
IR spectra were taken on a Bruker Vertex 70 instrument. Chemicals and technical
grade solvents (hexane, triethylamine) were distilled prior to use over CaH . Room
2
1
13
29
temperature H, C and Si NMR spectra were registered on a Bruker DPX 400 spectrometer
1
13
29
29
at working frequencies 400 ( H), 100 ( C) and 79 MHz ( Si) in CDCl . Low temperature Si
3
1
3
and C NMR spectra were recorded on a Bruker AVANCE-600 instrument (at 119.2 MHz
and 150.95 MHz, respectively). Chemical shifts were determined relative to residual CHCl3
1
13
13
(
H, 7.27 ppm), internal CDCl ( C, 77.0 ppm), and internal CD Cl ( C, 53.73 ppm).
3 2 2
1
Analysis and assignment of the H NMR data were supported by homonuclear (COSY) and
heteronuclear (HSQC and HMBC) correlation experiments. A solvent mixture of CD Cl ,
2
2
CHFCl , and CHF Cl in a ratio of 1:1:3 was employed for the low temperature measurements
2
2
because of being still liquid at around 100 K. The probe temperature was calibrated by means
of a thermocouple PT 100 inserted into a dummy tube. The low temperature measurements
were estimated to be accurate to ±1°. EI mass spectra (70 eV) were obtained on a GC-MS-
QP5050A Shimadzu chromatomass spectrometer with quadruple mass analyzer, capillary
column Ultra 2, 0.2 mm × 50 m, gas carrier – helium. Solvents were purified and dried by
standard procedures and stored over molecular sieves 4Å. All reactions were performed in
flame-dried glassware under argon atmosphere.
4
.2 Synthesis.
Three-neck flask equipped with condenser, dropping funnel, thermometer and
protected from air moisture was filled with argon and charged with 1 g (0.014 mol) of MeSNa
Acros Organics), 1.061 g (0.10 mol%) of dibenzo-18-crown-6 and 15 ml of benzene. Then,
.011 g (0.014 mol) of 1-chloro-1-phenyl-1-silacyclohexane 2 was added dropwise during 15
(
3
min at vigorous stirring, the mixture refluxed for 3 h, cooled to room temperature,
concentrated in vacuum (45 mm Hg). The residue was treated with hexane and filtered through

1
8
Schott filter under Ar. After vacuum distillation 1.745 g (55%) of 1-methylthio-1-phenyl-1-
о
–1
silacyclohexane 1 (b.p. 148–9 С/1 mm Hg) was isolated. IR spectrum (film), ν, cm : 3062
1
А
(
Ph), 2919 (CH ), 2852, 1433 (SiCH ), 1109 (SiPh). Н NMR, δ, ppm: 1.13 dd (2Н, SiСН , J
2 2
В
4А
5
.2, 1.9 Hz), 1.16 d (2Н, SiСН , J 6.1 Hz), 1.44 dtt (1H, СH , J 13.6, 9.1, 3.0 Hz) 1.55–1.65
4В
3,5
2
m,p
m (1H, СH ), 1.73–1.87 m (4Н, СН ), 1.90 s (3Н, SМе), 7.41–7.43 m (3Н, H ), 7.65–
o
13
2,6
3,5
4
7
.67 m (2Н, H ). С NMR, δ , ppm: 8.20 (SMe), 12.63 (C ), 24.12 (C ), 29.62 (C ), 127.99
С
p
m
o
i
29
(
C ), 129.75 (C ), 134.06 (C ), 135.10 (C ). Si NMR, δ : 6.61 ppm. Mass spectrum, m/z (I ,
Si rel
+
+
+
+
%
): 222(83) [M] , 175(100) [M–CH S] , 145(68) [M–Ph] , 121(70) [C H SiHCH ] , 105 (86)
3 6 5 3
+
+
[
PhSi] , 96(80) [C H Si] . Found, %: С, 64.25; H, 7.91; Si, 12. 80; S 14.23. C H SSi.
5 10 12 18
Calculated, %: C, 64.63; H, 8.05; Si, 12.61; S 14.41.
.4 GED-MS experiments.
4
The diffraction patterns were recorded during a combined gas-phase electron
diffraction and mass spectrometric experiment carried out using the EMR-100/APDM-1 unit
3
2, 33
at ISUCT.
pieces of Schott filter (the details of the experiment see in the Supplementary data) and kept at
33(3) K in the course of the experiments for compound 1. All operations with the sample
The samples were loaded into molybdenum effusion cell filled with crushed
3
were done in a glove box under argon atmosphere. The conditions of the GED/MS experiment
and data refinement details are given in Supplementary data, Table S1 and related chapters.
The EI mass spectra recorded simultaneously with the diffraction patterns showed at
Uioniz. = 50 V, a noticeable molecular peak m/z = 222 a.m.u.(36), and a set of fragmented ions,
such as: [M–SMe], m/z = 175 (90), [M–Ph] m/z = 146 (62), [C H SiH], m/z = 106 (100), see
6
5
also Table S3 in Supplementary Data. In order to check whether the daughter ions originated
from the same molecule 1, a set of mass spectra were recorded at lower electron energies: the
molecular ion was left the only species at Uioniz. as low as ca.10 V.
4
.5 Computational details.
All calculations were performed with Gaussian 09 program suite. The geometry and
3
4
vibrational calculations were performed using DFT (with B3LYP-D3 and M062X functionals)
and MP2 methods with the 6-311G** and cc-pVTZ basic sets. The potential energy surface
(
PES) profiles were obtained by scanning Corth–Cipso–Si–S (θ) and Cipso–Si–S–С (φ) dihedral
angles with a step of 5º and optimization of all other geometrical parameters at the M062X/6-
11G** level of theory. Also, the energies at the M062X/6-311G** level for both conformers
3
have been calculated on a grid of points corresponding to the Si–Cipso and Si–S torsion angles
varied with a step of 10º with optimizations of all other geometric parameters.

1
9
The Natural Bond Orbital (NBO) analysis was performed at the M062X/6-311G**
3
5
levels using the GenNBO program version 5.0.
Appendix A. Supplementary data
Supplementary data related to this article can be found at https://doi ...
Acknowledgements
S.A.S. is thankful to the Ministry of Education and Science of the Russian Federation
through Project Supporting Program (Project No. 4.3232.2017/4.6). GED/MS experiments
were performed on the equipment at the Center of collective use at ISUCT (see
https://www.isuct.ru/department/ckp/structure/ged-ms).
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2
2
1
-Methylthio-1-phenylsilacyclohexane: Synthesis, Conformational Preferences in Gas and
Solution by GED, NMR and Theoretical Calculations
*
Bagrat A. Shainyan, Elena N. Suslova, Tran Dinh Phien, Sergey A. Shlykov, Matthias
Heydenreich and Erich Kleinpeter*
Graphical Abstract
Ph
Si
SMe
Si
SMe
Ph
Ph MeS
Ph MeS
ax
eq
eq
ax
GED
NMR
Theory
Ph MeS : Ph MeS
ax
45 : 55 35 : 65 33 : 67
ax
eq
eq

2
3
1
-Methylthio-1-phenylsilacyclohexane: Synthesis, Conformational Preferences in Gas and
Solution by GED, NMR and Theoretical Calculations
*
Bagrat A. Shainyan, Elena N. Suslova, Tran Dinh Phien, Sergey A. Shlykov, Matthias
Heydenreich and Erich Kleinpeter*
Highlights
-
-
-
1-Methylthio-1-phenylsilacyclohexane 1, the first silacyclohexane with the sulfur atom
at silicon was synthesized.
The conformational analysis of 1 was performed by GED, low-temperature NMR
spectroscopy and theoretical calculations.
In gas phase, the three lowest-lying conformers were found to be 1-Ph and 1-Phax
eq
(two rotamers about the Si–S bons) in the ratio of 55:45% corresponding to ∆G°(333K)
=
0.13 kcal/mol.
-
-
-
In a freon solution, LT NMR spectroscopy showed at ca. 100 K a conformational
equilibrium 1-Ph :1-Ph ratio of 65:35% corresponding to ∆G°(98K) = 0.12 kcal/mol.
eq
ax
The dynamic NMR analysis also allowed to determine the barrier to interconversion of
≠
the silacyclohexane ring (ꢀG = 5.8 kcal/mol).
Theoretical calculations are consistent with the experiment, proving a higher stability
of 1-Ph conformer by up to 0.5 kcal/mol depending on the method and basis set used.
eq

1
1
-Methylthio-1-phenyl-1-silacyclohexane: Synthesis,
Conformational Preferences in Gas and Solution by GED, NMR
and Theoretical Calculations
*
,a
a
b
Bagrat A. Shainyan, Elena N. Suslova, Tran Dinh Phien,
c
d
*,d
Sergey A. Shlykov, Matthias Heydenreich, Erich Kleinpeter
a
A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Division of the Russian Academy of
Sciences, Favorsky Street, 664033 Irkutsk, Russian Federation; e-mail:
1
bagrat@irioch.irk.ru
b
Institute of Research and Development, Duy Tan University, 03 Quang Trung, Da Nang, Viet
Nam
c
Ivanovo State University of Chemistry and Technology, Sheremetievskiy ave., 7, 153000,
Ivanovo, Russian Federation
d
Chemisches Institut der Universität Potsdam, Karl-Liebknecht-Str. 24-25, D-14476 Potsdam
Golm), Germany; e-mail: ekleinp@uni-potsdam.de
(
ABSTRACT:
___________________________________________________________________________
_
1
-Methylthio-1-phenyl-1-silacyclohexane 1, the first silacyclohexane with the sulfur atom at silicon,
was synthesized and its molecular structure and conformational preferences studied by gas-phase
1
3
29
electron diffraction (GED) and low temperature C and Si NMR spectroscopy (LT NMR). Quantum-
chemical calculations were carried out both for the isolated species and solvate complexes in gas and in
polar medium. The predominance of the 1-MeS Ph conformer in gas phase (1-Ph :1-Ph = 55:45,
ax
eq
eq
ax
∆G° = 0.13 kcal/mol) determined from GED is consistent with that measured in the freon solution by
LT NMR (1-Ph :1-Ph = 65:35, ∆G° = 0.12 kcal/mol), the experimentally measured ratios being close
eq
ax
to that estimated by quantum chemical calculations at both the DFT and MP2 levels of theory.
__________________________________________________________________________
Keywords: 1-Methylthio-1-phenyl-1-silacyclohexane; Conformational analysis; Gas phase electron
_
1
3
29
diffraction; Low-temperature C and Si NMR; DFT and MP2 calculations.

2
Declaration of interests
X The authors declare that they have no known competing financial interests or personal
relationships that could have appeared to influence the work reported in this paper.
☐
The authors declare the following financial interests/personal relationships which may be
considered as potential competing interests: