The structural peculiarities and chemical bonding in three organogermanes Cl3GeCH2OC(O)R with rigid coordination centre

Article abstract of DOI:10.1016/j.molstruc.2007.04.019

The molecular and crystal structure of three organogermanes Cl₃GeCH₂OC(O)R (where R = -NHC₆H₁₁, -C₁₀H₁₅, and -NH₂) has been determined by X-ray diffraction method in order to inv

Full text of DOI:10.1016/j.molstruc.2007.04.019

Available online at www.sciencedirect.com
Journal of Molecular Structure 875 (2008) 135–142
www.elsevier.com/locate/molstruc
The structural peculiarities and chemical bonding in three
organogermanes Cl3GeCH2OC(O)R with rigid coordination centre
a,
a
a
Alexander A. Korlyukov *, Eugen A. Komissarov , Mikhail Yu. Antipin ,
b
b
b
Nikolay V. Alekseev , Konstatntin V. Pavlov , Olga V. Krivolapova ,
b
b
Valerii G. Lahtin , Eugenii A. Chernyshev
a
Nesmeyanov Institute of Organoelement Compounds Russian Academy of Science, 117813 Moscow, Russian Federation
M.V. Lomonosov Moscow State Academy of Fine Chemical Technology, 117571 Moscow, Russian Federation1
b
Received 14 December 2006; received in revised form 10 April 2007; accepted 13 April 2007
Available online 21 April 2007
Abstract
The molecular and crystal structure of three organogermanes Cl3GeCH2OC(O)R (where R = –NHC6H11, –C10H15, and –NH2) has
been determined by X-ray diffraction method in order to investigate geometrical regularities of these molecules. The nature of Ge–O
bonding in these molecules was investigated by quantum chemistry method. It was shown that the influence of the nature of ligand,
attached to carbon atom of the carbonyl group, on Geꢀ ꢀ ꢀO interatomic distance is incidentally small in isolated molecule while in the
crystal it is much more pronounced due to the crystal packing effect. The nature of Geꢀ ꢀ ꢀO bonding corresponds to intermediate type
of interatomic interaction in terms of ‘‘Atoms in molecules’’ theory.
ꢀ 2007 Elsevier B.V. All rights reserved.
Keywords: Organogermanes; Pentacoordinated germanium; Single-crystal X-ray studies; Quantum chemical calculations; Electron density distribution
1. Introduction
For this reason we carried out the detailed study of the
crystal and molecular structures of (trichlorogermyl)
methyl N-cyclogexylcarbamate I, (trichlorogermyl)methyl
1-adamantanecarboxylate II and (trichlorogermyl)methyl
carbamate III (Fig. 1). Preliminary information about
molecular structure of II and III was already published
[4,5]. The results of single crystal X-ray experiments and
quantum chemical calculations of crystal structures and
isolated molecules of I–III were used to define the charac-
teristics of Geꢀ ꢀ ꢀO bonding and influence of crystal pack-
ing on geometrical parameters as well as peculiarities of
electron structure of those molecules.
Organogermanes X3Ge–CH2–Y–C(O)–R (where X = Cl,
CH3 or C6H5 and Y = CH2, O or N) with the pentacoordi-
nated germanium atom have attracted the attention of
researchers in synthetic and theoretical organic chemistry
for a long time. Pioneering studies of the molecular struc-
tures of these compounds was carried out in the early
1980s [1,2]. Since then, the crystal and molecular structures
of 23 such compounds (in which X = Cl or CH3, and
Y = CH2 or N) were studied by X-ray single crystal diffrac-
tion [Cambridge Structural Database (CSD, [3])]. How-
ever, the crystal and molecular structure as well as
chemical bonding in related compounds with Y = O are
not adequately studied.
2. Experimental
2.1. Preparation
*
Corresponding author. Fax: +7 095 135 5085.
Compounds I–III were prepared by interaction of
(trichlorogermyl)methanol with isocyanatocyclohexene,
1-adamantanecarboxylic acid chloride and isocyanatotri-
E-mail addresses: alex@xrlab.ineos.ac.ru (A.A. Korlyukov), nalex-
eev@stk.mmtel.ru (N.V. Alekseev).
1
Fax: +7 095 430 7983.
0022-2860/$ - see front matter ꢀ 2007 Elsevier B.V. All rights reserved.
doi:10.1016/j.molstruc.2007.04.019

136
A.A. Korlyukov et al. / Journal of Molecular Structure 875 (2008) 135–142
anatocyclohexene in 100 ml. of diethyl ether. The reaction
mixture was stirred for 2 h and then 10.6 g (0.33 mol) of
methanol was added. Finally the triethylamine (33.4 g,
0.33 mol) was added dropwise with stirring. After 1 hour
the stirring was interrupted and reaction mixture washed
out with 30 mol of benzene two times and then triethanol-
amine (14.0 g, 0.9 mol) was added. After cooling of reac-
tion mixture the precipitated crystals (17.6 g, 46.9%, m.p.
145–155 ꢁC) were filtered and dried in vacuum. Analytical
data are as follows. Found (%): C, 28.8; H, 4.1; Cl, 31.9;
Ge, 21.5; N, 4.2; O, 9.6; C8H14Cl3GeNO2. Calcd (%): C,
28.67; H, 4.21; Cl, 31.73; Ge, 21.67; N, 4.18; O, 9.55%.
1H NMR spectra (25 ꢁC, CDCl3) d, ppm: 1.20, 1.43, 1.95,
3.58 (all m, 11H, cyclohexyl), 4.63 (s, 2H, CH2), 6.74 (d,
1H, NH).
2.1.2. (Trichlorogermyl)methyl 1-adamantanecarboxylate
(II)
Trichlorogermylmethanol (20.9 g, 0.1 mol) was added
dropwise with stirring to 1-adamantanecarboxylic acid
chloride (19.6 g, 0.1 mol). Then the reaction mixture was
heated until gas evolution completely accomplished. After
cooling of the reaction mixture to room temperature, crys-
tallization have occurred. Crystals of compound II were
obtained after recrystallization from hexane (31.7 g, 85%,
m.p. 85–88.5 ꢁC). Anal. Found (%): C, 38.75; H, 4.55; Cl,
28.60; Ge, 19.47. C12H17Cl3GeO2. Calcd (%): C, 38.72;
1
H, 4.60; Cl, 28.57; Ge, 19.51. H NMR (25 ꢁC, CDCl3),
d ppm: 1.68–1.77, 1.92, 1.93, and 2.05 (all m, 15 H,
C10H15); 4.37 (s, 2 H, CH2O).
2.1.3. (Trichlorogermyl)methyl carbamate (III)
Cooled (trichlorogermyl)methanol (38.8 g, 0.185 mol)
was added dropwise with stirring to isocyanatotrimethylsi-
lane (10.7 g, 0.093 mol). The reaction accompanied by heat
evaluation. Reactionary mixture then cooled, until a gas
emission finished completely. The crystallization of III
was very slow. In order to improve the yield of compound
III the reaction mass was kept at room temperature during
10 days, and then precipitate was filtered out. Finally, com-
pound III was flushed by chloroform (ꢁ10 ml) and dried in
a vacuum (11.7 g, 49.8%, m.p. 77–87 ꢁC). The crystals suit-
able for X-ray analysis were obtained by recrystallization
from benzene (m.p. 112–114). Anal. Found (%): C 10.0;
H 1.8; Ge 28.1; Cl 41.4; C2H4Cl3GeNO2. Calcd (%): C
Fig. 1. Molecular structure of I (a), II (b) and III (c) presented by thermal
ellipsoids with 50% probability.
1
9.5; H 1.6; Ge 28.7; Cl 42.0. H NMR (25 ꢁC, CDCl3), d
methylsilane correspondingly. All reactions accompanied
by significant heat evolution. Trichlorogermylmethanol
was prepared according to method published in literature
(see [6] and references therein). All manipulations were per-
formed under an argon atmosphere using standard Schlenk
techniques. Solvents were dried by standard methods and
distilled prior to use.
ppm: 4.28 s (2H, OCH2Ge); 7.20 s (1H, NH).
All 1H NMR spectrums were recorded on a Bruker AM-
360 spectrometer (360 MHz).
2.2. X-ray crystallographic study
X-ray diffraction measurements of I–III were carried out
with a SMART 1000 CCD diffractometer at 100 K and
monitored by SMART program [7]. The frames were inte-
grated and corrected for absorption by the SAINT and
SADABS programs [7]. The details of crystallographic
2.1.1. (Trichlorogermyl)methyl N-cyclogexylcarbamate (I)
The trichlorogermylmethanol (21.0 g, 0.1 mol) was
added dropwise to the solution (12.5 g, 0.1 mol) of isocy-

A.A. Korlyukov et al. / Journal of Molecular Structure 875 (2008) 135–142
137
Table 2
data and experimental conditions are presented in Table 1.
Important experimental bond lengths and angles in compounds I–III
Important structural parameters of structures I–III are
summarized in Table 2.
Bond lengths and angles
Ia
II
III
The structures were solved by the direct method and
refined by full-matrix least-squares technique against F2
in the anisotropic approximation. The hydrogen atoms
were located from difference electron density syntheses
and refined in rigid body model. All calculations were per-
formed using the SHELXTL PLUS 5.10 program package
[8]. Atomic coordinates, bond lengths, bond angles and
thermal parameters of I–III have been deposed at the Cam-
bridge Crystallographic DataBase (Deposition Nos.:
264020, 606570 and 629736).
Ge(1)ꢀ ꢀ ꢀO(1)
2.188(2)
2.324(3) (A)
2.376(3) (B)
2.190(1) (A)
2.189(1) (B)
2.136(1)
2.126(1)
1.950(3)
1.228(4)
1.437(4)
2.251(2)
Ge(1)–Cl(1)
2.2172(7)
2.2082(8)
Ge(1)–Cl(2)
Ge(1)–Cl(3)
Ge(1)–C(1)
O(1)–C(2)
O(2)–C(1)
O(2)–C(2)
2.1416(8)
2.1322(7)
1.950(2)
1.253(3)
1.433(3)
2.1264(8)
2.1320(8)
1.942(3)
1.223(3)
1.430(3)
1.339(4)
N(1)–C(2)
Cl(1)–Ge(1)–O(1)
1.321(3)
173.55(5)
1.319(4)
173.95(5)
173.15(7) (A)
172.81(6) (B)
115.4(3)
O(2)–C(1)–Ge(1)
O(1)–C(2)–O(2)
C(2)–N(1)–C(3)
O(1)–C(2)–N(1)
a
113.94(15)
121.5(2)
125.20(19)
123.7(2)
114.9(2)
121.7(2)
120.0(3)
2.3. Calculations
125.1(3)
The quantum chemical calculations of I–III structures in
the crystal were carried out using the VASP 4.6.28 code [9].
Conjugated gradient technique was used for optimizations
of the atomic positions (started from experimental data)
and minimization of total energy. Projected augmented
wave (PAW) method was applied to account for core elec-
trons while valence electrons were approximated by plane-
wave expansion with 400 eV cutoff [9]. Exchange and cor-
relation terms of total energy were described by PBE [10]
exchange-correlation functional. In case of crystals I and
II Kohn–Sham equations were integrated using C-point
The values for independent molecules A and B are presented, otherwise
averaged values are shown.
approximation, while for crystal of III, 4 · 4 · 4 Monk-
horst-Pack k-point mesh [11] have been applied. We believe
that C-point approximation is sufficient for I and II
because of their large crystal unit cells. Using DFT method
it’s not possible to take into account dispersion interac-
tions. For this reason calculated cell parameters may be
Table 1
Crystal data and experimental conditions for compounds I–III
I
II
III
Molecular formula
Formula weight
Color, shape
C8H14Cl3GeNO2
335.14
cube
C12H17Cl3GeO2
372.20
Plate
C2H4Cl3GeNO2
253.00
prism
Dimension (mm)
Crystal system
Space group
0.3 · 0.3 · 0.3
Orthorombic
Pbca
0.3 · 0.3 · 0.02
Monoclinic
P21/n
0.3 · 0.3 · 0.2
Monoclinic
P21/n
˚
a (A)
10.599(3)
13.682(4)
17.854(5)
17.997(5)
9.049(2)
18.335(4)
90.043(7)
2985.7(13)
8
8.1768(10)
10.0604(13)
9.7887(11)
91.086(3)
805.09(17)
4
˚
b (A)
˚
c (A)
b (ꢁ)
3
˚
V (A )
2589.0(13)
8
1.72
Z
qcalc (g cmꢂ1
)
1.656
2.087
Temperature (K)
Scan type
120
x
120
x
120
x
2hmax (ꢁ)
60.14
0.71073
29.66
SADABS
0.53/0.53
1344
60.06
0.71073
25.80
SADABS
0.51/0.95
1504
59.92
0.71073
47.32
SADABS
0.45/0.33
488
˚
Radiation, k(Mo-Ka) (A)
Linear absorption (l) (cmꢂ)
Absorption correction
Tmin/Tmax
F(000)
Total refl. (Rint
Number of independent refl.
)
28811
3777
18550
8485
7325
2304
Number of indepent refl. with I > 2(r)
3128
4435
1623
Parameters
wR2
136
325
0.0847
0.0442
0.988
82
0.0487
0.0308
0.982
0.0795
0.0333
0.965
1.05/ꢂ0.54
R1 [I > 2(r)]
GOF
ꢂ3
˚
qmax/qmin (e A
)
1.39/ꢂ0.51
0.45/ꢂ0.45

138
A.A. Korlyukov et al. / Journal of Molecular Structure 875 (2008) 135–142
systematically overestimated or underestimated up to 5%.
Thus, the experimental values of cell parameters were used
in the calculations. At a final step of our calculations
atomic displacements converged were better than
the axial Ge–Cl bond is more prone to the elongation in the
case of CGeCl3 fragment.
Cl Ge-C-Y-C(O)-R
The form of five-membered rings
in
3
I–III correspond to neither the former nor the latter type.
These rings adopt an envelope conformation with the Ge
atoms deviating from the plane of the OAC@O fragment
0.02 eV Aꢂ1, as well as energy variations were less than
˚
10ꢂ3 eV. In order to carry out the topological analysis of
electron density distribution function in terms of R.F Bad-
er’s theory ‘‘Atoms in molecules’’ (AIM) [12] the dense
FFT (fast Fourier transformation) grid was used (corre-
sponding to cutoff 1360 eV). The latter was obtained by
separate single point calculation of optimized geometry
with hard PAWs for each atom type. The topological anal-
ysis of electron density distribution function was carried
out using AIM program – part of ABINIT software pack-
age [13].
The isolated molecules of I–III were simulated utilizing
the Gaussian 98 Release A7 software [14]. Optimization
of atomic positions was carried out using B3LYP hybrid
functional and 6-311G(d,p) local basis set. The structures
of isolated molecules of I–III were tested on stability by
calculation of vibrational frequencies. The topological
analysis of electron density distribution function of isolated
molecules was carried out utilizing AIMPAC program
package [15].
˚
(the deviation is within ꢁ0.02 A). The corresponding val-
˚
ues of Ge atom deviation are equal to 0.08 A in I, 0.45–
˚
˚
0.56 A in II and 0.24 A in III. Therefore the shortest
Geꢀ ꢀ ꢀO distance correspond the most planar five-mem-
bered ring.
Such conformations of five-membered rings in mole-
cules under consideration are due to the fact that the C–
H and equatorial Ge–Cl bonds tend to arrange so as to
minimize the torsion strain in the Cl–Ge–C–H fragments.
This can be achieved if either the C or Ge atom deviates
from the plane of the ring. However, the C atom is a part
of the ester fragment R–C(O)OCH2– in which all the atoms
appear, as a rule, in the same plane (for example, in methyl
acetate [18] and methyl (3-chloro-4-hydroxyphenyl)glyoxy-
late [19]). Therefore, Ge atoms deviates significantly from
the plane of the ring. As a result, the Cl–Ge–C–H torsion
angles are close to those observed in methyltrichloroger-
mane, in which the Ge–Cl bond is staggered with respect
to the C–H bond (60ꢁ). It is also necessary to mention, that
one cannot exclude the influence of crystal packing on con-
formation of five-membered ring in I–III. Hovewer, based
only on structural data it is impossible to study this influ-
ence in detail.
The expansion of coordination polyhedron of Ge in
molecules under consideration occurs as a result of addi-
tional Geꢀ ꢀ ꢀO interaction. Unfortunately the analysis of
structural parameters could not give the necessary informa-
tion about the nature of this interaction. Using the quan-
tum chemical methods allows one to get the information
on this problem. Previously the chemical bonding in tri-
chloroorganogermanes was studied using only semi-empir-
ical (PM3 and AM1) level [20]. In this study we carried out
quantum chemical calculations of the crystal packing of I–
III using PBE exchange correlation functional and plane
wave basis set as well as quantum chemical calculations
of the isolated molecules I–III based on B3LYP/6-
311G(d,p) level of theory. R.F. Bader’s theory ‘‘Atoms in
molecules’’ (AIM) [12] was chosen as theoretical approach
to analyze the electronic structures of I–III. Previously, we
successfully utilized such a methodological background for
studying series of silicon compounds with expanded coor-
dination polyhedron of the Si atom [21–23].
3. Results and discussion
Previously investigated trichloroorganogermane mole-
cules can be classified into two groups according to the nat-
ure of the substituent Y. In compounds, with Y = CH2, the
˚
Ge–O distances vary over a wide range from 2.123 A (in
3-(trichlorogermyl)-N,N0-dimethylpropan-amide) [2] to
˚
3.228 A (in 3-(trichlorogermyl)propionic acid [1]). The
Cl Ge-C-Y-C(O)-R
five-membered rings
in these molecules
3
adopt an envelope conformation where the carbon atom
adjacent to the Ge atom deviates from the plane formed
other four atoms. In the molecules with Y = N, the Ge–
O distances vary over a much smaller range, from 2.080
˚
˚
to 2.354 A (in most cases, ca. 2.2 A). The above-mentioned
five-membered rings (Y = N) in are nearly planar (for
example, in N-methyl-4-N-trichlorogermylmethyl methylb-
enzamide [16]).
The elongation of the axial Ge(1)–Cl(1) bond in com-
parison with equatorial Ge–Cl bonds does not exceed
˚
0.1 A in all trichloroorganogermanes investigated earlier.
Therefore the CGeCl3-coordination centre in the above-
mentioned compounds can be described as rigid. This fea-
ture makes a distinguish between CGeCl3 and C3GeCl
coordination centers. The compounds with C3GeCl coordi-
nation centre are investigated extensively [17]. In their mol-
ecules, Oꢀ ꢀ ꢀGe and Ge–Cl axial distances vary in much
wider ranges and so that the C3GeCl coordination centre
can be described as soft (non-rigid). Such difference can
be explained in terms of Lewis acidity of the CGeCl3 and
C3GeCl fragments. The softness of the C3GeCl moiety as
Lewis base is more than that of CGeCl3 moiety. Therefore
The experimental and calculated structural parameters
of the crystals I–III are in satisfactory agreement. The main
differences are observed for intermolecular distances corre-
sponding to weak N–Hꢀ ꢀ ꢀO, C–Hꢀ ꢀ ꢀO bonds and Clꢀ ꢀ ꢀCl
˚
interatomic contacts which are equal, on average 0.1 A.
All the bonds formed by Ge atom are elongated up to
˚
0.03 A compared to experimental ones. Probably, the rea-
sons of such a deviations are disadvantages of the DFT
theory which cannot account for weak van der Waals inter-

A.A. Korlyukov et al. / Journal of Molecular Structure 875 (2008) 135–142
139
actions. Nevertheless the calculations reproduced well the
differences between two independent molecules in structure
of II.
ory. In turn, all bonds formed by the Ge atom are charac-
terized by positive value of $2q(r) and negative one of
Ee(r), that is typical for interatomic interactions of interme-
diate type. Weak intermolecular interactions found in crys-
tal may be described as closed shell interactions (for them
$2q(r) > 0, Ee(r) > 0, in CP(3,ꢂ1)).
The geometry of isolated molecules I–III agrees well
with experimental one (except for Geꢀ ꢀ ꢀO distances).
Mean-square deviations of calculated and experimental
˚
values of bond lengths are equal to ca. 0.02A. For bond
One of the useful advantages of AIM theory is the pos-
sibility to evaluate the energy of closed shell interactions as
well as interactions of intermediate type using correlation
formula proposed by Espinosa, Mollins and Lecomte [28]:
angles, this value is equal to ca. 2.0ꢁ. The discrepancy
between experimental and calculated values of Geꢀ ꢀ ꢀO dis-
tances is expected as result of influence of crystal field. It’s
very probably, that Ge–O bonds in studied molecules are
similar to Siꢀ ꢀ ꢀN and Geꢀ ꢀ ꢀN bonds in silatranes and ger-
matranes. As it is known at transferring from solid to gas
phase Siꢀ ꢀ ꢀN and Geꢀ ꢀ ꢀN interatomic distances in this mol-
EA–B ꢃ 1=2V eðrÞ
ð1Þ
where EA–B is the energy of weak interatomic contacts or
coordination bond and Ve(r) is potential energy density
in CP(3,ꢂ1). The value of Ve(r) can be calculated from val-
ues q(r) and $2q(r) in CP(3,ꢂ1) using Kirzhnitz formula
for kinetic energy density and local virial theorem expres-
sion [29]. We utilized this methodological background for
detailed analysis the influence of the crystal packing on
geometry and electron structure.
˚
ecules are enlarged by ꢁ0.2–0.3 A [24–27]. Apparently, the
behavior of Geꢀ ꢀ ꢀO interatomic distances in molecules
under consideration appears to be similar. And really, cal-
culated values of Geꢀ ꢀ ꢀO interatomic distances in I–III
˚
exceed the experimental ones by ꢁ0.2A as it is possible
to see from data of the Table 3. It should be noted that
in isolated molecules I–III the variation of Geꢀ ꢀ ꢀO inter-
Both in experimental and calculated crystal packing, the
molecules of I are assembled into centrosymmetric dimers
via N(2)–H(2B)ꢀ ꢀ ꢀO(1) hydrogen bonds (Fig. 2). The
energy of latter bond is equal to 4.84 kcal/mol (calculated
˚
atomic distances (0.07 A) is less pronounced than in crys-
tal. So one can expect that in isolated molecules I–III
Geꢀ ꢀ ꢀO bonds have almost equal energies (Table 4).
˚
Both in crystals and isolated molecules I–III the topo-
logical analysis of electron density distribution function
q(r) have shown the presence of critical points CP(3,ꢂ1)
in region of all expected bonds as well as for Geꢀ ꢀ ꢀO coor-
dination bonds. Besides, the CP(3,ꢂ1) critical points corre-
sponding to the N–Hꢀ ꢀ ꢀO, C–Hꢀ ꢀ ꢀO, C–Hꢀ ꢀ ꢀCl weak
hydrogen bonds and Clꢀ ꢀ ꢀCl, Clꢀ ꢀ ꢀO, Clꢀ ꢀ ꢀN contacts were
also found. The C–O, N–C, C–C, C–H and N–H bonds are
characterized by negative values of laplacian $2q(r) and
local energy density Ee(r). These bonds correspond to
shared type (ordinary covalent bonds) in terms of AIM the-
Nꢀ ꢀ ꢀO, Hꢀ ꢀ ꢀO distances are equal to 2.02 and 3.041 A,
˚
the experimental Nꢀ ꢀ ꢀO distance is 3.074(4) A). Similar
dimers in crystal packing of III are formed by more strong
N(2)–H(2)ꢀ ꢀ ꢀO(1) bonds (5.65 kcal/mol), the calculated
˚
Hꢀ ꢀ ꢀO and Nꢀ ꢀ ꢀO distances are 1.96 and 2.979 A (the
˚
experimental value of latter distance is larger by 0.06 A).
The energy of numerous weak C–Hꢀ ꢀ ꢀO(Cl) bonds and
Clꢀ ꢀ ꢀCl, Clꢀ ꢀ ꢀO, Clꢀ ꢀ ꢀN contacts vary in range
0.2 ‚ 1.5 kcal/mol. The topological analysis of q(r) allowed
us to found in II rather strong C(2)ꢀ ꢀ ꢀCl(30) and
C(20)ꢀ ꢀ ꢀCl(3) contacts with energies being equal to
Table 3
Structural parameters of calculated crystal structures and isolated molecules of I–III
Bond lengths and angles
Crystal
Isolated molecules
Ia
II
III
I
II
III
˚
Atomic bondings (A)
Ge(1)ꢀ ꢀ ꢀO(1)
2.222
2.242
2.300 (A)
2.362 (B)
2.230 (A)
2.217 (B)
2.164
2.168
1.976
1.243
1.429
2.255
2.252
2.403
2.220
2.443
2.207
2.377
2.224
Ge(1)–Cl(1)
Ge(1)–Cl(2)
Ge(1)–Cl(3)
Ge(1)–C(1)
O(1)–C(2)
O(2)–C(1)
O(2)–C(2)
N(1)–C(2)
2.176
2.164
1.978
1.267
1.424
1.351
1.325
2.167
2.168
1.975
1.261
1.429
1.354
1.326
2.167
2.167
1.991
1.223
1.434
1.343
1.349
2.167
2.167
1.969
1.225
1.402
1.360
2.164
2.164
1.990
1.222
1.429
1.344
1.339
1.346
Valence angles (ꢁ)
Cl(1)–Ge(1)–O(1)
O(2)–C(1)–Ge(1)
O(1)–C(2)–O(2)
C(2)–N(1)–C(3)
O(1)–C(2)–N(1)
a
174.07
113.69
121.18
125.33
123.94
172.29
115.17
120.95
174.79
114.15
121.25
170.2
117.5
123.3
125.5
122.9
174.0
117.5
117.4
170.6
116.9
123.0
124.84
124.8
The values for independent molecules A and B are presented, otherwise averaged values are shown.

140
A.A. Korlyukov et al. / Journal of Molecular Structure 875 (2008) 135–142
Table 4
Topological properties of selected chemical bonds in crystal and isolated molecules of I–III
Chemical bond
Compound
I
II
III
q(r)
$2q(r)
Ee(r)
Ve(r)
q(r)
$2q(r)
Ee(r)
Ve(r)
q(r)
$2q(r)
Ee(r)
Ve(r)
Crystal
Ge(1)ꢀ ꢀ ꢀO(1)
0.43
4.23
ꢂ0.10
ꢂ0.49
0.37
0.32
0.71
0.80
0.95
3.38
2.84
3.57
3.88
0.69
ꢂ0.07
ꢂ0.06
ꢂ0.37
ꢂ0.46
ꢂ0.73
ꢂ0.38 (A)
ꢂ0.31 (B)
ꢂ0.99
0.40
3.89
ꢂ0.09
ꢂ0.44
Ge(1)–Cl(1)
Ge–Cleq
Ge(1)–C(1)
N(1) –H(1)ꢀ ꢀ ꢀO(1)
0.68
0.80
0.95
0.15
3.61
3.74
0.22
0.46
ꢂ0.34
ꢂ0.46
ꢂ0.72
0.005
ꢂ0.93
ꢂ1.18
ꢂ1.50
ꢂ0.10
0.67
0.80
0.96
0.17
3.52
3.90
0.73?
1.79
ꢂ0.34
ꢂ0.47
ꢂ0.73
0.002
ꢂ0.92
ꢂ1.21
ꢂ1.51
ꢂ0.12
ꢂ1.20
ꢂ1.50
Isolated molecule
Ge(1)ꢀ ꢀ ꢀO(1)
Ge(1)–Cl(1)
Ge–Cleq
0.23
0.61
0.68
0.87
2.42
2.67
2.66
0.12
ꢂ0.02
ꢂ0.29
ꢂ0.34
ꢂ0.54
e
ꢂ0.22
ꢂ0.75
ꢂ0.86
ꢂ1.07
2
0.24
0.56
0.59
0.78
2.20
3.42
3.41
1.27
ꢂ0.01
ꢂ0.18
ꢂ0.19
ꢂ0.35
ꢂ0.17
ꢂ0.59
ꢂ0.62
ꢂ0.79
0.25
0.58
0.65
0.83
2.54
3.47
3.77
2.03
ꢂ0.03
ꢂ0.26
ꢂ0.30
ꢂ0.47
ꢂ0.24
ꢂ0.75
ꢂ0.87
ꢂ1.08
Ge(1)–C(1)
e
The values of V (r) are given in a.u. while q(r), E (r) and $ q(r) are given in e A and Aꢂ5, respectively.
ꢂ3
˚
˚
Fig. 2. H-bonded dimers in crystal structure of III.
5.65 kcal/mol, on average. The calculated C(2)ꢀ ꢀ ꢀCl(30) and
Thus, the presence of C(2)ꢀ ꢀ ꢀCl(30) contacts and C–
Hꢀ ꢀ ꢀO(2) weak hydrogen bonds causes the distortion of
planarity of five-membered helate cycle in comparison to
the form of latter in isolated molecule II. Actually, in iso-
lated molecule of II the conformation of such cycle is con-
siderably flattened in comparison to molecule in crystal.
On the base of AIM theory it is of interest to analyze the
differences between two independent molecules in the crys-
tal structure of II. This can be done by the summation of the
0
˚
C(2 )ꢀ ꢀ ꢀCl(3) distances are 3.378 and 3.331 A are less than
˚
sum of van der Waals radii of C and Cl atoms (3.57 A) [30].
The experimental values for such distances are 3.419(3) and
0
˚
3.400(3) A. In terms of AIM theory C(2)ꢀ ꢀ ꢀCl(3 ) and
C(20)ꢀ ꢀ ꢀCl(3) contacts corresponds to so-called ‘‘peak and
hole’’ interactions, that is interaction of a lone electron pair
of Cl atom with antibonding orbital of C(20)–O(20) bond
(Fig. 3).

A.A. Korlyukov et al. / Journal of Molecular Structure 875 (2008) 135–142
141
described as weak interatomic interaction with high ionic
contribution. The energy of such bonds mostly depends
on crystal packing effects in more extent than the nature
of ligand. In isolated molecules I–III the geometrical
parameters and peculiarities of electron structure are nearly
the same as in case of those crystal structures. The only sig-
nificant difference is the strengthening of Geꢀ ꢀ ꢀO coordina-
tive bonds to 5–11 kcal/mol in crystal compared to those in
isolated molecules. In addition the influence of crystal
packing lead to some distortion of five-membered Ge-con-
taining ring.
Thus, the usage quantum chemical calculations both for
crystal structures obtained by single crystal X-ray diffrac-
tion and isolated molecules I–III allowed one to study in
details the nature of Geꢀ ꢀ ꢀO bond and describe the role
of crystal packing.
Acknowledgements
Fig. 3. The section of electron localization function illustrating the
interaction of lone electron pair of the Cl(2) with antibonding orbital of
the C(20)–O(20) bond of adjacent molecule in crystal structure of II.
This study was financially supported by the Russian
Foundation
for
Basic
Research
(Project
No.
99_07_90133) and the Council on Grants of the President
of the Russian Federation (Program for State Support of
Leading Scientific Schools of the Russian Federation,
Grant NSh_3894.2007.3).
energies of contacts of each independent molecule consider-
ing them separately. The sum of contacts energies for mol-
ecule A is 21.2 kcal/mol while for B this value is equal to
22.6 kcal/mol. Indeed the difference is rather small, but
one should keep in mind that potential function of Geꢀ ꢀ ꢀO
interatomic distance is very flat therefore weak intermolec-
ular contacts can significantly affect it. The evaluation of the
energy of Geꢀ ꢀ ꢀO coordination bond in crystal of I–III have
revealed that it vary in rather narrow range (14.4–22.9 kcal/
mol). Unfortunately in literature we could not find the
results of evaluation of Geꢀ ꢀ ꢀO(N) coordinative bonds ener-
gies by means of theoretical or spectral methods. Hovewer,
for comparison we can use the articles describing the silatr-
anes [31,32]. According to this literature data the energy of
Siꢀ ꢀ ꢀN coordination bonds in different silatranes vary in the
range of 10–20 kcal/mol that is close to calculated values for
I–III. The strongest Geꢀ ꢀ ꢀO bond found in I, while the weak-
est one is observed in II (14.4 kcal/mol in molecule B). It is
interesting to note that the energies of Ge(1)ꢀ ꢀ ꢀO(1)
(17.71 kcal/mol) and Ge(10)ꢀ ꢀ ꢀO(10) bonds differs by
ꢁ3 kcal/mol, the discrepancy in interatomic distance
Appendix A. Supplementary data
Supplementary data associated with this article can be
found, in the online version, at doi:10.1016/j.molstruc.
2007.04 .019.
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