Synthesis and structural study of precursors of novel methylsilanediols by IR and Raman spectroscopies, single-crystal X-ray diffraction and DFT calculations

Article abstract of DOI:10.1016/j.saa.2013.09.032

On the way towards the development of a synthetic route aimed at obtaining new methylsilanediol derivatives with an aminocarbonyl group in β to silicon (which may have a potential biological interest), we have synthesized, isolated and purified five diphe

Full text of DOI:10.1016/j.saa.2013.09.032

Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy 118 (2014) 828–834
Contents lists available at ScienceDirect
Spectrochimica Acta Part A: Molecular and
Biomolecular Spectroscopy
journal homepage: www.elsevier.com/locate/saa
Synthesis and structural study of precursors of novel methylsilanediols
by IR and Raman spectroscopies, single-crystal X-ray diffraction and DFT
calculations
M.P.G. Rodríguez Ortega a, M.L. Docampo b,c, L.H. Thomas d, M. Montejo a, A. Marchal Ingraín c,
C.C. Wilson d, J.J. López González a,
⇑
a Physical and Analytical Chemistry Department, University of Jaén, Campus Las Lagunillas, Ed. B3, Jaén E-23071, Spain
b General Chemistry Department, La Habana University, 10400 Havana, Cuba
c Inorganic and Organic Chemistry Department, University of Jaén, Campus Las Lagunillas, Ed. B3, Jaén E-23071, Spain
d Department of Chemistry, University of Bath, Bath BA2 7AY, UK
h i g h l i g h t s
g r a p h i c a l a b s t r a c t
ꢀ
ꢀ
ꢀ
ꢀ
Five diphenylic precursors of
methylsilanediols derivatives were
synthesized.
Their molecular structures were
studied using IR, Raman and single
crystal XRD.
Their vibrational spectra were
assigned with the support of DFT
calculations.
Some experimental features gave
evidence of the conformational
mixture in the samples.
a r t i c l e i n f o
a b s t r a c t
Article history:
Received 15 April 2013
Received in revised form 2 September 2013
Accepted 7 September 2013
Available online 18 September 2013
On the way towards the development of a synthetic route aimed at obtaining new methylsilanediol
derivatives with an aminocarbonyl group in b to silicon (which may have a potential biological interest),
we have synthesized, isolated and purified five diphenylic possible precursors, namely chloromethyl
(methyl)diphenylsilane, 2-{[methyl(diphenyl)silyl]methyl}-1H-isoindole-1,3(2H)-dione, N-[(methyl
(diphenyl)silanyl)-methyl]-benzamide, N-[(methyl(diphenyl)silyl)-methyl]-acetamide and N-[(methyl
(diphenyl)silyl)-methyl]-formamide.
The conformational landscape of the five species in this study are explored by means of DFT calcula-
tions at the B3LYP/6-311++G⁄⁄ level. The theoretical molecular structures predicted are confirmed by
the reproduction of their respective IR and Raman spectral profiles, that are completely assigned. Some
evidence in the vibrational spectra points to the occurrence of conformational mixtures in the samples.
Further, single-crystal X-ray diffraction has allowed the elucidation of the crystalline structure of
2-{[methyl(diphenyl)silyl]methyl}-1H-isoindole-1,3(2H)-dione.
Keywords:
Organosilanes
Synthesis
IR
Raman
Single-crystal X-ray diffraction
DFT
Ó 2013 Elsevier B.V. All rights reserved.
Introduction
replacement for carbon, particularly in biologically active
molecules [1,2]. The most notable example of this is the claim of
Silicon is the second most abundant element on earth and the
one most similar to carbon. This close chemical analogy has been
silanediols as bioisosteres of the hydrated amido group and their
application in the development of peptidomimetics as protease
inhibitors [3,4]. The gem-silanediol group is most stable in its tet-
rahedral configuration than the corresponding geminal carbinol
that readily undergo dehydration and, therefore, interaction with
active site of protease is favored through hydroxyl groups which
the inspiration for many studies of silicon as
a potential
⇑
Corresponding author. Tel.: +34 953212754.
E-mail address: jjlopez@ujaen.es (J.J. López González).
1386-1425/$ - see front matter Ó 2013 Elsevier B.V. All rights reserved.
http://dx.doi.org/10.1016/j.saa.2013.09.032

M.P.G. Rodríguez Ortega et al. / Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy 118 (2014) 828–834
829
are excellent hydrogen bond donors and acceptors [5–7]. Never-
theless, previous attempts to inhibit hydrolases with relatively
simple silanediols found them to be inactive [8]. This may be
attributed to the fact that dialkylsilanediols with small side chains
are prone to fast polymerization while steric effects of the bulky
groups prevent silanediols from this process through the screening
of OH groups. The structure of silanediols successfully used as
protease inhibitors, contains aminocarbonyl and amide groups in
doublet, (m) multiplet, (bs) broad singlet. Mass spectra were run
on a SHIMADZU-GCMS 2010-DI-2010 spectrometer (equipped
with a direct inlet probe) operating at 70 eV. High resolution mass
spectra were recorded using a Waters Micromass AutoSpec-Ultima
spectrometer (equipped with a direct inlet probe) operating at
70 eV.
Chloromethyl(methyl)diphenylsilane (2)
b and
c
positions to silicon [4,9].
Dichloro(chloromethyl)methylsilane (6 mL, 0.041 mol) was
added drop-wise over a period of 30 min under an argon atmo-
sphere to a stirred solution of commercial phenylmagnesium bro-
mide in diethyl ether (41 mL, 0.123 mol). The mixture was then
refluxed for 16 h and subsequently poured into ice water
(150 mL). The mixture was extracted with diethyl ether
(2 Â 100 mL) and the extract washed with three 100 mL portions
of water and then dried over anhydrous sodium sulfate. Finally,
the solvent was removed in vacuo and the residue was purified
by Flash chromatography (n-hexane) producing 2 as colorless oil
(8.13 g, 80%). 1H NMR (400 MHz, CDCl3, 25 °C) d (ppm): 7.65–
7.62 (m, 4H, Ar), 7.49–7.42 (m, 6H, Ar), 3.31 (s, 2H, ACH2), 0.78
(s, 3H, ACH3); 13C NMR (100 MHz, CDCl3) d (ppm): 134.6, 134.2,
129.9, 128.0, 28.8 (ACH2), À5.6 (ACH3); 29Si NMR (79.49 MHz,
CDCl3) d (ppm): À8.95; MS (EI, 70 eV): 246 (M+Á, 1), 197 (100),
165 (7), 105 (8); HR-MS (EI): C14H15ClSi calculated 246.0632,
found. 246.0624. Anal. Calcd for C14H15ClSi (246.81): C, 68.13; H,
6.13. Found: C, 68.16; H, 6.17.
Thus, a theoretical–experimental analysis of the molecular
structure of this type of silanediol would help achieve a better
understanding of the mechanisms of stabilization of the Si(OH)2
functionality, and which could be related to their potential biolog-
ical role. For this task, we are working on the preparation of a
significant set of relatively simple methylsilanediols which are
structurally related to those that have proven biological activity.
We report our first efforts to synthesize a new set of these
methylsilanodiols, specifically those containing an aminocarbonyl
group on the b position relative to the silicon (Fig. 1). In this work,
our goal has been to perform a thorough structural analysis of five
diphenylsilyl intermediates, obtained synthetically and isolated
and purified for the first time, which could be used as precursors
of the mentioned silanediols.
We present the joint theoretical study and experimental
characterization of the following structurally related species:
chloromethyl(methyl)diphenylsilane (intermediate 2), 2-{[methyl
(diphenyl)silyl]methyl}-1H-isoindole-1,3(2H)-dione (intermediate
3), N-[(methyl(diphenyl)silanyl)-methyl]-benzamide (intermedi-
ate 5a), N-[(methyl(diphenyl)silyl)-methyl]-acetamide (intermedi-
ate 5b) and N-[(methyl(diphenyl)silyl)-methyl]-formamide (inter
mediate 5c). We have performed a thorough theoretical (DFT)
conformational analysis of all the species. Further, the crystal
structure of the so called intermediate 3 has also been determined
using single-crystal X-ray diffraction.
2-{[Methyl(diphenyl)silyl]methyl}-1H-isoindole-1,3(2H)-dione (3)
Potassium phtalamide (8.14 g, 43.96 mmol) was added to a
solution of 2 (7.23 g, 29.31 mmol) in anhydrous DMSO (100 mL)
at room temperature and the solution was then heated to 100 °C
until no starting material was visible by TLC (ca: 18 h. Eluent: hex-
ane/ethyl acetate 8:2 v/v). After the mixture was cooled to room
temperature it was subsequently poured into ice water (300 mL).
The solid was filtered off, washed with water and n-hexane and
recrystallized from EtOH to produce compound 3 as a yellow solid
(7.54 g, 72%). M.p. 91–93 °C; 1H NMR (400 MHz, DMSO-d6, 25 °C) d
(ppm): 7.73 (m, 4H, Ar), 7.52 (m, 4H, Ar), 7.34 (m, 6H, Ar), 3.61 (s,
2H, ACH2), 0.68 (s, 3H, ACH3); 13C NMR (100 MHz, DMSO-d6) d
(ppm): 167.7 (C@O), 134.6, 134.2, 134.1, 131.4, 129.6, 127.8,
122.6, 26.6 (ACH2), À4,2 (ACH3); 29Si NMR (79.49 MHz, DMSO-
d6) d (ppm): À8.65; MS (EI, 70 eV): 356 (M-HÁ, 9), 342 (8), 280
(100), 266 (31), 197 (66), 105 (11); HR-MS (EI): C22H18NO2Si-H cal-
culated 356.1107 [M-H], found 356.1112 [M-H]. Anal. Calcd for
IR and Raman spectra of the five species have also been mea-
sured and the bands assigned showing, in some cases, evidence
of conformational mixtures in the samples.
Materials and methods
Synthesis
Reagents were purchased from commercial sources and used
without further purification. Solvents were dried as described
elsewhere [10]. Reactions were followed by thin layer chromatog-
raphy (TLC). This was performed on Merck Silica Gel 60GF254 alu-
minium precoated foils (0.2 mm) using fluorescent indicator and
spots were visualized using ultraviolet radiation or using the nin-
hydrin test. Flash chromatography was performed using silica gel
Merck 60 (particle size 0.040–0.063 mm). Melting points (m.p.)
were determined in open capillaries in a Electrothermal IA9000
series digital melting point apparatus and are uncorrected. 1H,
13C and 29Si NMR spectra were recorded on a Bruker Avance 400
spectrophotometer operating at 400 MHz, 100 and 79.49 MHz
respectively, using CDCl3 and [D6] DMSO as solvents and tetra-
methylsilane as the internal standard. The following abbreviations
were used for the multiplicity of signals in 1H NMR: (s) singlet, (d)
C22H19NO2Si (357.48): C, 73.92; H, 5.36; N, 3.92. Found: C, 73.89;
H, 5.40; N, 3.88.
[(Methyl(diphenyl)silyl)]-methanamine (4)
Hydrazine monohydrate (5.9 mL, 78.67 mmol) was added to a
solution of 3 (3.00 g, 8.39 mmol) in a mixture of THF and methanol
(40 ml, 1:1, v/v) under an argon atmosphere. The solution was
heated to 65 °C until no starting material was observable using
TLC (ca: 4 h. Eluent: hexane/ethyl acetate 8:2, v/v) and then was
cooled, filtered, washed with THF and finally concentrated in vacuo.
The residue was washed with water and extracted with four 20 mL
portions of toluene. Organic extract was dried over Na2SO4, filtered
and the solvent removed in vacuo to give compound 4 as a colorless
oil (1.73 g, 90%). 1H NMR (400 MHz, DMSO-d6, 25 °C) d (ppm): 7.49
(m, 4H, Ar), 7.36 (m, 6H, Ar), 2.55 (s, 2H, CH2), 0.53 (s, 3H, CH3); 13
C
NMR (100 MHz, DMSO-d6) d (ppm): 136.1, 134.3, 129.2, 127.8, 28.4
(ACH2), À5.9 (ACH3); 29Si NMR (79.49 MHz, DMSO-d6) d (ppm):
À9.51.
N-[(methyl(diphenyl)silanyl)-methyl]-benzamide (5a)
Benzoyl chloride (0.8 mL, 7.26 mmol) in dry toluene (5 mL) was
added drop-wise to a solution of freshly obtained 4 (1.10 g,
Fig. 1. Molecular scheme of methylsilanediols with an aminocarbonyl group in the
b position relative to the silicon.

830
M.P.G. Rodríguez Ortega et al. / Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy 118 (2014) 828–834
4.85 mmol) and Et3N (6.1 mL, 43.54 mmol) in dry toluene (10 mL)
at 0 °C under an argon atmosphere. The mixture was stirred and
warmed to reflux until no starting material was observable using
TLC (ca: 5 h. Eluent: CH2Cl2/MeOH 9:1, v/v) and then, 20% aqueous
K2CO3 (20 mL) was added at room temperature. The organic layer
was separated and aqueous layer extracted twice with toluene
(10 mL). The combined organic extracts were washed with satu-
rated aqueous NaCl, dried over Na2SO4, and finally the solvent
was removed in vacuo. Flash chromatography (CH2Cl2/MeOH,
99:1, v/v) resulted in 5a as a pure pale yellow solid (0.52 g, 32%).
M.p. 82–84 °C; 1H NMR (400 MHz, CDCl3, 25 °C) d (ppm): 7.60–
7.24 (m, 15H, Ar), 5.85 (bs, 1H, ANH), 3.48 (d, J = 5.6 Hz, 2H,
ACH2), 0.67 (s, 3H, ACH3); 13C NMR (100 MHz, CDCl3) d (ppm):
167.8 (C@O), 134.8, 134.6, 134.3, 133.9, 131.1, 130.0, 129.8,
128.5, 128.3, 127.8, 126.6, 27.6 (ACH2), À5.0 (ACH3); 29Si NMR
(79.49 MHz, CDCl3) d (ppm): À8.54; MS (EI, 70 eV): 331 (M, 13),
330 (M-HÁ, 43), 316 (14), 254 (93), 240 (69); 197 (100), 105 (42),
77 (29); HR-MS (EI): C21H20NOSi-H calculated 330.1314 [M-H],
found 330.1320 [M-H].
equipped with a ceramic internal air cooled source, KBr optics
(for MIR) and polyethylene optics (for FIR) and a DLaTGS detector.
Raman spectra of the samples were recorded using a MultiRAM
Stand Alone FT-Raman spectrometer, equipped with an Nd:YAG la-
ser (excitation line at 1064 nm) and a Ge detector cooled at liquid
nitrogen temperature. All spectra were recorded with a resolution
of 1 cmÀ1 and 100 scans.
Single-crystal X-ray diffraction analysis
Crystals of 2-{[methyl(diphenyl)silyl]methyl}-1H-isoindole-
1,3(2H)-dione (intermediate 3) were grown by slow evaporation
(at 40 °C) of dissolutions of the sample in diethylether/hexane
(1:1) mixtures. Small, pale orange block crystals of the sample
were obtained. X-ray diffraction data were collected at 100 K on
a Rigaku R-axis/RAPID image plate diffractometer equipped with
an Oxford cryosystems N2 low temperature device, using graphite
monochromated Mo K
a radiation (k = 0.71075 Å). The crystal
structure was solved using direct methods and the program SHEL-
XS-97 [11] and refined using SHELXL-97 [12] against |F2| using all
data, as implemented in the WinGX program suite [13]. Non-
hydrogen atoms were refined with anisotropic thermal parame-
ters. Hydrogen atoms were identified in a Fourier difference map
and were allowed to refine freely. Crystal data at 100 K: formula
N-[(methyl(diphenyl)silyl)-methyl]-acetamide (5b)
A mixture of freshly obtained compound 4 (0.63 g, 2.77 mmol)
and acetic anhydride (6 mL) was stirred at room temperature until
no starting material was observable using TLC (ca: 2 h. Eluent: CH2-
Cl2/MeOH 9:1, v/v) and then CH2Cl2 (15 mL) and water (15 mL)
were added. The aqueous layer was extracted twice with CH2Cl2
(15 mL) and then all the organic extracts were put together,
washed with 20% aqueous K2CO3 (20 mL) and dried over MgSO4.
Finally, the solvent was removed in vacuo and the residue was
purified by Flash chromatography (CH2Cl2/MeOH, 95:5, v/v) to give
5b as a colorless oil (0.45 g, 60%).
C
22H19NO2Si, M = 357.48 g/mol, X-ray (100 K): Monoclinic, space
group P21/c, a = 7.8360(6), b = 29.6480(3), c = 7.9145(8) Å, = 90,
b = 92.247(7),
= 90, V = 1837.3(3) Å3, Z = 4, = 1.292 g cmÀ3
= 0.144 mmÀ1
F(000) = 752. total of 20,901 reflections
(3.3° < h < 27.5) were collected, 4199 unique (Rint = 0.0352),
R = 0.0381 for 3452 reflections with I > 2 (I), and R = 0.0488 for
a
c
,
q
,
l
A
r
all reflections, wR2 = 0.0992, qel (max, min) = 0.389 and
À0.273 e ÅÀ3, GOOF(S) = 1.069. All other refinement details are
available in the CIF (CCDC: 922163).
1H NMR (400 MHz, CDCl3, 25 °C) d (ppm): 7.51 (m, 4H, Ar), 7.38
(m, 6H, Ar), 5.19 (bs, 1H, NH), 3.29 (d, J = 5.6 Hz, 2H, CH2), 1.88 (s,
3H, CH3), 0.61 (s, 3H, CH3); 13C NMR (100 MHz, CDCl3) d (ppm):
170.3 (C@O), 134.5, 134.3, 129.9, 128.2, 27.3 (ACH2), 23.1
(ACH3), À5.1 (ACH3); 29Si NMR (79.49 MHz, CDCl3) d (ppm):
À8.99; MS (EI, 70 eV): 268 (M-HÁ, 7), 254 (17), 197 (94), 192
(100), 178 (58), 137 (28); 105 (21), 43 (7). HR-MS (EI): C16H18-
NOSi-H calculated 268.1158 [M-H], found 268.1163 [M-H].
Computational details
All DFT calculations were performed using the Gaussian 09
suite of programs [14]. Geometry optimizations and frequency
calculations were carried out using the Becke’s three-parametric
hybrid exchange functional (B3) [15] combined with the
Lee–Yang–Parr correlation functional (LYP) [16] in conjunction
with the 6-311++G⁄⁄ basis set [17]. Each stationary point obtained
was characterized by the computation of the harmonic vibrational
spectra at the same level of theory.
N-[(methyl(diphenyl)silyl)-methyl]-formamide (5c)
A mixture of freshly obtained compound 4 (1.00 g; 4.40 mmol),
aqueous 95% formic acid (0.67 mL, 17.59 mmol) and sodium
formate (0.072 g, 0.88 mmol) in toluene (10 mL) was heated under
reflux using MS 3 Å until no starting material was observable using
TLC (ca: 24 h. Eluent:) and then, 30% aqueous K2CO3 (20 mL) was
added. The organic layer was separated and the aqueous layer ex-
tracted twice with toluene (10 mL). The combined organic extracts
were washed with saturated aqueous NaCl and dried over MgSO4.
Finally, the solvent was removed in vacuo and the residue was
purified by Flash chromatography (CH2Cl2/MeOH 95:5, v/v) to give
5c as a yellow oil (0.60 g, 53%).
Results and discussion
Synthesis
Along the synthesis route towards 6 (see Fig. 1S in the Supple-
mental material) with an aminocarbonyl group in b to silicon, five
apparently simple silanodiol derivatives have been generated from
the common starting point of treating commercial chlorosilane 1
with 1.5 eq of phenylmagnesium bromide in diethyl ether accord-
ing with the procedure reported by Hu et al. [18] and improved by
Larson et al. [19].
The preparation of any silanol typically requires that the hydro-
xyl groups be masked or protected along the synthetic route in
order to avoid self-condensation. Phenyl groups were selected for
this purpose because of their ability to assist in stabilizing interme-
diates and the possibility of removing these groups at the end
under acid conditions compatible with amide groups. Then, the
1H NMR (400 MHz, CDCl3, 25 °C) d (ppm): 8.10 (s, 1H, CH), 7.52–
7.38 (m, 10H, Ar), 5.28 (bs, 1H, NH), 3.32 (d, J = 5.8 Hz, 2H, CH2),
0.62 (s 3H, CH3); 13C NMR (100 MHz, CDCl3) d (ppm): 161.4
(C@O), 134.5, 134.0, 130.0, 128.3, 25.8 (ACH2), A5.2 (ACH3); 29Si
NMR (79.49 MHz, CDCl3) d (ppm): À9.08. MS (EI, 70 eV): 254 (M-
HÁ, 4), 240 (9); 197 (100); 178 (66); 164 (37); 137 (16), 105 (18).
HR-MS (EI): C15H16NOSi-H calculated 254.1001 [M-H], found.
254.0995 [M-H].
Infrared and Raman spectra
nitrogen was introduced as
a
phtalimide. Treatment of
IR spectra of the samples were recorded in the MIR and FIR
chloromethylsilane 2 with potassium phthalimide gave 3 in 72%
regions using
a
FT-IR Bruker Vertex 70 spectrophotometer
and removal of the phthalimide group with hydrazine under

M.P.G. Rodríguez Ortega et al. / Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy 118 (2014) 828–834
831
Table 1
standard Gabriel conditions gave the corresponding amine 4 as a
Calculated molecular population and zero point corrected relative energies (
D
E0/kcal/
colorless oil in an excellent yield [9].
mol) for the molecular conformations of intermediates 2, 3, 5a, 5b and 5c at the
This amine decomposes easily, and therefore must be stored in
a dark place and under inert atmosphere and fresh samples used in
further synthesis steps.
B3LYP/6-311++G⁄⁄ level of theory.
Intermediate 2
A
G+
GÀ
0.06
35.9
Treatment of this amine freshly obtained with benzyl chloride,
acetic anhydrate and formic acid under inert atmosphere, provided
several representative amide moiety on the left-hand side of the
structure 5a–c in moderate yielded using classical substitution
chemistry [20–24].
With compounds 5 in hand, we are now working in the optimi-
zation of the final key deprotection of phenyl groups. In this
respect, a review of the literature reveals that phenyls groups could
be removed afterwards using an excess of triflic acid ATfOHA in
methylene chloride at 0 °C, followed by addition of ammonium
hydroxide [3,24–26].
a
D
E0 (kcal/mol)
0.74
27.3
0.00
36.8
Population (%)b
Intermediate 3
E
0.00
35.3
G+
0.21
32.4
GÀ
D
E0 (kcal/mol)
Population (%)
0.21
32.3
Intermediate 5a
A
0.00
37.5
G+
0.14
35.4
GÀ
D
E0 (kcal/mol)
Population (%)
0.80
27.1
Intermediate 5b
Theoretical conformational analysis and molecular structure
A
0.00
37.6
G+
0.17
35.1
GÀ
D
E0 (kcal/mol)
0.80
27.3
The search for the conformers of the five intermediates (com-
pounds 2, 3, 5a, 5b and 5c) was performed considering the relative
orientation of the side chain with respect to the SiACH3 bond. The
positions of the phenyl groups were not fixed during optimization
since their relative orientations have been proven to be fairly influ-
enced by the positions adopted by the side chains.
Three different conformations were found to be real minima
(for which no imaginary frequencies were computed) on the PES
of the corresponding molecules, which differ in the relative orien-
tation of the substituents on the silicon center. The side chains of
the mentioned systems can be arranged in anti (A, 180°), gauche+
(g+, +60°) and gaucheÀ (gÀ, À60°) geometry respect to the
Si-CH3 bond. The case of intermediate 3 is noteworthy, for which
the anti conformation was not a real minima but an eclipsed (e)
arrangement of the phthalimide and phenyl groups was found
instead. The e conformation of intermediate 3 was confirmed by
ab initio calculations (MP2/6-31+G⁄) performed for this system.
Fig. 2S (reported as Supplemental material) shows the different
structures isolated from the corresponding PES of the intermedi-
ates under study.
Population (%)
Intermediate 5c
A
0.00
37.5
G+
0.15
35.3
GÀ
D
E0 (kcal/mol)
0.80
27.1
Population (%)
a
D
E0 stand for zero point corrected relative energy.
Theoretical population calculated using the Boltzmann equation and taking
b
T = 298.16 K.
suitability of using the corresponding optimized theoretical struc-
ture (B3LYP/6-311++G⁄⁄) for the computation of the vibrational
spectra and carrying out the subsequent vibrational analysis and
spectral assignment of the sample. The slight differences found be-
tween the experimentally and theoretically determined structures
can be attributed to effects of the crystal packing. The most note-
worthy dissimilarity between the experimental and theoretical
(DFT) structures is related to the arrangement of one of the phenyl
groups attached to the silicon center. In the DFT structure the plane
containing one of the phenyl groups is 14° twisted with respect to
the plane containing the same phenyl ring in the experimental
molecular structure. The associated experimental value for the
SiACAC angle is 122.0°(1) whereas in the theoretical model it is
calculated to be 119.7°.
Table 1 shows the relatives energies (DE0, kcal/mol) for the
three conformers of each intermediate along with their relative
populations in gas phase (at room temperature) calculated from
D
E0 values (B3LYP/6-311++G⁄⁄) using the Boltzmann distribution
equation. As shown in the table, conformer gÀ is the global mini-
mum for intermediate 2 and conformer e is the most stable for
intermediate 3. For each of the remaining species (5a, 5b and
5c), conformer a represents the global minimum. Nevertheless,
The crystal packing of the structure is dominated by CH-
p
(edge-to-face stacking) and offset stacking interactions, which
p
pAp
commonly are the main forces governing the crystal structure of
aromatic systems [27]. These two types of interactions are estab-
lished by both phenyl rings and the phthalimide group. Each
the relative energy differences (DE0) among the three described
conformers of each intermediate are less than 1 kcal/mol, showing
that the contribution to the theoretical total sample composition of
each conformer is very similar within a given set of conformers of
each system.
phthalimide group interacts through offset pAp stacking with
another phthalimide group of a neighboring molecule, with a dis-
tance of 3.369 Å between the planes containing each heterocycle.
On the other hand, both phenyl groups interact through CH edge-
to-face
p stacking with adjacent molecules. However, each phenyl
Single crystal X-ray study
group interacts in a different manner within a given molecular
unit. One of the phenyl groups acts as H donor making a CH
Only intermediate 3 was suitable for study by mean of single-
crystal X-ray diffraction. 2-{[methyl(diphenyl)silyl]methyl}-1H-
isoindole-1,3(2H)-dione (intermediate 3) crystallizes in space
group P 21/c with both the g+ and gÀ forms present in the crystal
packing of the sample, as shown in Fig. 3S of the Supplemental
material. Comparison between the experimental and theoretical
(gas-phase, B3LYP/6-311++G⁄⁄) molecular structures reveals a
good match (RMS = 0.0240) between theory and experiment (see
Fig. 4S reported as Supplemental material). As shown, there is a
high level of similarity between the two molecular structures with
a slight difference in one of the phenyl rings. This fact confirms the
edge-to-face p stacking interaction with a neighboring phenyl ring
of an adjacent molecule, measuring 3.267 Å between the centroid
of the charge donor ring and the hydrogen atom involved in the
interaction. On the contrary, the other phenyl group within the
same molecular unit acts as double H acceptor and interacts
through CH edge-to-face
p stacking simultaneously with a phthali-
mide aromatic unit (2.720 Å between the centroid of the ring and
the hydrogen atom) and a phenyl group (3.267 Å between the
centroid of the ring and the hydrogen atom) of two adjacent mol-
ecules, resulting in a double T-shape
p-stacking interaction. This
double T-shape interaction corresponds to the phenyl ring with

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M.P.G. Rodríguez Ortega et al. / Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy 118 (2014) 828–834
the most significant deviation from the calculated molecular struc-
ture, which was performed under the isolated molecule approxi-
mation in which crystal packing effects such as this were not
taken into account.
Vibrational study
The IR and Raman spectra of the five compounds under study
are shown in Figs. 2 and 3, while Tables 1S–5S (that can be found
as Supplemental material) outline the proposed vibrational assign-
ments for intermediates 2, 3, 5a, 5b and 5c, respectively. Note that,
while in the case of compounds 2, 5a, 5b and 5c the vibrational
analyses have been carried out considering all the possible molec-
ular conformations predicted for the species in the gas phase, for
compound 3, only conformers g+ and gÀ were taken into account;
those which were confirmed to be present in the crystal packing, as
reported above. Fig. 4 shows the experimental IR and Raman
spectra profile of this species in comparison with the theoretical
spectra calculated for both conformers. As shown, the theoretical
spectra are in quite good agreement with the experimental profiles
of the sample since most of the experimental features are repro-
duced by the computed spectra for both conformers.
Theoretical wavenumbers have been scaled using the scale
factors recommended elsewhere [28] for harmonic vibrational
frequencies computed at the B3LYP/6-311++G⁄⁄ level in the low
and high frequency regions (1.0019 and 0.9673 respectively). As
can be seen, we have found a good correlation among the scaled
values of the computed harmonic frequencies and the observed
Fig. 3. Experimental Raman spectra of the five intermediates in this study: (a)
intermediate (2), (b) intermediate (3), (c) intermediate (5a), (d) intermediate (5b)
and (e) intermediate (5c).
vibrational bands in the whole spectral range for all the species
under study, especially in the spectral region above 700 cmÀ1
.
Nonetheless, below 700 cmÀ1, some features appearing in the
vibrational spectra of 2, 5a, 5b and 5c may point to the occurrence
of conformational mixtures in these samples.
In the case of intermediate 2, the medium intensity band cen-
tered at 623 cmÀ1 (IR) can be assigned to the symmetric stretching
of the SiC bond in conformers g+ and gÀ. However, the band at
617 cmÀ1 (IR) can be attributed to the same vibrational mode in
conformer a, in accordance with its calculated value. Similarly,
the medium intensity band centered at 368 cmÀ1 (IR) can be as-
signed to the scissoring of the SiC2 group in conformer a while
the peak observed at 373 cmÀ1 (IR) can be assigned indistinctly
to the same motion in conformers g+ and gÀ (Table 1S, in bold).
On the other hand, for 5a the most interesting feature in its
vibrational spectra is the band centered at 350 cmÀ1 (IR) which
have been assigned to the SiC2 scissoring vibrational mode of
conformer a, while the band centered at 312 cmÀ1 (IR) has been
assigned to the same vibrational mode of conformer g+ (Table 3S,
in bold), according to their computed values.
Also suggesting the presence of more than one conformer, the
band observed at 345 cmÀ1 in the Raman spectrum of compound
5b can be attributed to the scissoring of the SiC2 group in
conformer a. Nevertheless, the bands observed at 317 (Raman)
and 307 (IR) cmÀ1 can only be assigned to the same vibrational
mode in conformers g+ and gÀ (Table 4S, in bold).
Finally, in the case of the so-called compound 5c, the band
observed at 437 cmÀ1 in the IR spectrum is assigned to the CC
out-of-plane deformation mode of phenyl rings in conformer a,
Fig. 2. Experimental IR spectra of the five intermediates in this study: (a)
intermediate (2), (b) intermediate (3), (c) intermediate (5a), (d) intermediate (5b)
and (e) intermediate (5c).

M.P.G. Rodríguez Ortega et al. / Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy 118 (2014) 828–834
833
Fig. 4. Comparison of the IR (right) and Raman (left) theoretical (B3LYP/6-311++G⁄⁄) and experimental spectra of intermediate 3.
in agreement with its calculated value (Table 5S, in bold), whilst
the same vibration is calculated at 453 and 450 cmÀ1 for conform-
ers g+ and gÀ and observed at 465 cmÀ1, also in the IR spectrum.
whose packing is dominated by pAp stacking interactions
(edge-to-face and offset). The eclipsed conformation (global min-
imum in the gas phase) was not detected in the crystalline
phase.
ꢀ The Raman and infrared spectra of the five species under study
were recorded and completely assigned for each species with
the support of the DFT calculations. We have found some
evidences of the occurrence of conformational mixture in the
samples, since some of the experimental features are only
justified if different conformers are considered to be present.
Conclusions
ꢀ On the way towards a synthetic route to obtain a series of new
methylsilanediol derivatives with an aminocarbonyl group b to
silicon, five diphenylic derivatives, candidate precursors of
these species, have been prepared, isolated and purified.
ꢀ A conformational analysis was performed at the B3LYP/6-
311++G⁄⁄ level for the five diphenylic compounds yielding up
to three different molecular conformations for each system,
which differ in the arrangement of the side chain, that can adopt
either gauche (g+ and gÀ) or anti orientation with respect to the
SiACH3 bond in the case of compounds 2, 5a, 5b and 5c. As
concerns compound 3, the eclipsed orientation was discarded
following X-ray structural analysis, albeit it was found to be
the global minimum in gas phase.
Acknowledgements
P.G.R.O. thanks MEC for a research fellowship (AP2009-3949)
from the Spanish Ministerio de Educación supporting this work.
M.L.D. thanks Cuban Science Academy, Iberoamerican Postgrade
University Association (AUIP) and University of Jaén for financial
support and accommodation. The authors are grateful to
Andalusian Regional Goverment and the Universty of Bath for
financial support and CICT-UJA staff for technical assistance.
ꢀ Only intermediate (3) was suitable for study by single-crystal
X-ray diffraction. The so-called conformers gauche+ and
gaucheÀ are both present in the crystal structure of the sample,

834
M.P.G. Rodríguez Ortega et al. / Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy 118 (2014) 828–834
X. Li, H.P. Hratchian, A.F. Izmaylov, J. Bloino, G. Zheng, J.L. Sonnenberg, M.
Hada, M. Ehara, K. Toyota, R. Fukuda, J. Hasegawa, M. Ishida, T. Nakajima, Y.
Honda, O. Kitao, H. Nakai, T. Vreven, J.A. Montgomery Jr, J.E. Peralta, F. Ogliaro,
M. Bearpark, J.J. Heyd, E. Brothers, K.N. Kudin, V.N. Staroverov, R. Kobayashi, J.
Normand, K. Raghavachari, A. Rendell, J.C. Burant, S.S. Iyengar, J. Tomasi, M.
Cossi, N. Rega, J.M. Millam, M. Klene, J.E. Knox, J.B. Cross, V. Bakken, C. Adamo,
J. Jaramillo, R. Gomperts, R.E. Stratmann, O. Yazyev, A.J. Austin, R. Cammi, C.
Pomelli, J.W. Ochterski, R.L. Martin, K. Morokuma, V.G. Zakrzewski, G.A. Voth,
P. Salvador, J.J. Dannenberg, S. Dapprich, A.D. Daniels, Ö. Farkas, J.B. Foresman,
J.V. Ortiz, J. Cioslowski, D.J. Fox, Gaussian 09 Revision B.1. Gaussian Inc.,
Wallingford, 2009.
Appendix A. Supplementary material
Supplementary data associated with this article can be found, in
the online version, at http://dx.doi.org/10.1016/j.saa.2013.09.032.
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