Two germatranes with bulky substituents

Article abstract of DOI:10.1107/S0108270106019317

In 1-adamantyl-2,8,9-trioxa-5-aza-1-germabicyclo[3.3.3]un-decane or 1-adamantylgermatrane, [Ge(C₁₀H₁₅)(C₆H ₁₂NO₃)], (I), and (2,8,9-trioxa-5-aza-1-germabicyclo[3.3. 3]undecan-1-yl)methyl N-cyclohexylcarbamate or [(germatran-1-yl)methyl]- cyclohexylcarbamate, [Ge(C₆H₁₂NO₃)(C ₈H₈NO₂)], (II), the Ge atoms are characterized by trigonal-bypiramidal configurations. The Ge...N distances [2.266 (3) and 2.206 (3) A in (I) and (II), respectively] are among the longest observed in germatranes. The significant distortion of the apical N-Ge-C angle in (II) is caused by crystal packing effects.

Full text of DOI:10.1107/S0108270106019317

metal-organic compounds
Acta Crystallographica Section C
Crystal Structure
carbamate, (II), have been studied by X-ray diffraction and
the results are presented here (Figs. 1 and 2).
Communications
The coordination around atom Ge1 in (I) and (II) is
trigonal±bipyramidal. Atom N1 of the atrane framework and
the organic R group occupy the axial positions, while three O
atoms occupy the equatorial positions. The Ge1 atoms deviate
ISSN 0108-2701
Two germatranes with bulky substitu-
ents
Ê
from the plane of the equatorial O atoms towards R by 0.28 A
Ê
in (I) and 0.24 A in (II). Analysis of the Cambridge Structural
Database (CSD, Version 5.27; Allen, 2002) reveals that the
interatomic Ge1Á Á ÁN1 distance in (I) is among the longest
observed for this class of compounds. According to the CSD,
Alexander A. Korlyukov,a* Eugene A. Komissarov,a
Nikolay V. Alekseev,b Konstantin V. Pavlov,b Olga V.
Krivolapovab and Valentin G. Lachtinb
Ê
the Ge1Á Á ÁN1 distance varies in the range 2.01±2.32 A (for 85
examined structures). The longest Ge1Á Á ÁN1 distances are
observed in 1-(1-trimethylsylilcyclopropyl)germatrane (Kor-
lyukov et al., 2003) and 1-(germatranylmethyl)germatrane
aA. N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of
Science, 28 Vavilov Street, Moscow 119991, Russian Federation, and bState
Research Institute of Chemistry and Technology of Organoelement Compounds, 38
Entuziastov Sh., Moscow 111123, Russian Federation
Ê
(Gurkova et al., 1982) (2.300 and 2.315 A). The presence of
the electron-withdrawing carbamate group in (II) leads to a
Correspondence e-mail: alex@xrlab.ineos.ac.ru
Ê
decrease in this interatomic distance by 0.06 A compared with
the corresponding value in (I). The absence of a greater
shortening of the Ge1Á Á ÁN1 interatomic distance in (II) can be
explained by a signi®cant delocalization of electron density in
the N2/C8/O4/O5 carbamate fragment. Indeed, the N2ÐC8
and C8ÐO4 bonds are shorter than the respective standard
single bonds, but they are noticeably longer than the corre-
sponding double bonds (Allen et al., 1987). Thus, in both (I)
Received 28 April 2006
Accepted 23 May 2006
Online 23 June 2006
In 1-adamantyl-2,8,9-trioxa-5-aza-1-germabicyclo[3.3.3]un-
decane or 1-adamantylgermatrane, [Ge(C10H15)(C6H12NO3)],
(I), and (2,8,9-trioxa-5-aza-1-germabicyclo[3.3.3]undecan-1-
yl)methyl N-cyclohexylcarbamate or [(germatran-1-yl)methyl]
-cyclohexylcarbamate, [Ge(C6H12NO3)(C8H14NO2)], (II), the
Ge atoms are characterized by trigonal±bypiramidal con®g-
Ê
urations. The GeÁ Á ÁN distances [2.266 (3) and 2.206 (3) A in
(I) and (II), respectively] are among the longest observed in
germatranes. The signi®cant distortion of the apical NÐGeÐ
C angle in (II) is caused by crystal packing effects.
Comment
Figure 1
Organogermanic compounds with expanded coordination
spheres around the metal, such as substituted germatranes,
have been of interest since 1970. Most probably, this is due to
their potential use as biologically active substances (Lukevics
et al., 1990, 1992). The wide spectrum of pharmacological
action of organogermanic compounds, their low toxicity and
other useful properties have created favourable conditions
The molecular structure of (I), showing the atom-numbering scheme.
Displacement ellipsoids are drawn at the 50% probability level and H
atoms have been omitted for clarity.
for the development of bioorganogermanic chemistry.
Successful progress in this area is impossible without a wide
search for the most active substances and discovering the
correlation between their structure and biological activity. As
a continuation and development of our work in this area
(Gurkova et al., 1984; Knyazev et al., 2000; Korlyukov et al.,
2003), the crystal and molecular structures of 1-germanyla-
damantane, (I), and [1-(germathranyl)methyl]cyclohexyl-
Figure 2
The molecular structure of (II), showing the atom-numbering scheme.
Displacement ellipsoids are drawn at the 50% probability level and H
atoms have been omitted for clarity.
Acta Cryst. (2006). C62, m303±m305
DOI: 10.1107/S0108270106019317
# 2006 International Union of Crystallography m303

metal-organic compounds
ꢀ
Ê
Ê
and (II), the interatomic Ge1Á Á ÁN1 distances are typical
(CÁ Á ÁF ' 3.4 A, HÁ Á ÁF ' 2.5 A and CÐHÁ Á ÁF = 138±164 ) and
ꢀ
Ê
for germatranes with donor substituents (for instance, in
Ê
one CÐHÁ Á Áꢀ contact (HÁ Á ÁCg ' 2.8 A and CÐHÁ Á Áꢀ = 116 ,
where Cg is the centroid of the C6F5 ring) are observed. Of
course, all the above contacts are weak, but their total energy
is suf®cient for the distortion of the N1ÐGe1ÐC7 angle. In
(II), one may see that the N1ÐGe1ÐC7 angle deviates
further from the ideal value of 180ꢀ than in other germatranes.
Such a deviation is related to the in¯uence of crystal packing.
Actually, atom N2 of the carbamate group participates in an
1-ethylgermatrane, the Ge1Á Á ÁN1 distance is 2.24 A; Atov-
myan et al., 1970).
In the present compounds, the Ge atoms are bonded to
bulky carbamate and adamantane substituents. In (II), the
N1ÐGe1ÐC7 angle is 173.73 (13)ꢀ, while in the majority of
germatranes, the relative values are in the range 175±179ꢀ. In
the case of the adamantane group in (I), the N1ÐGe1ÐC7
angle remains almost undistorted [178.69 (11)ꢀ]. It is of
interest to study the reason for the decrease in the N1ÐGe1Ð
C7 angle in (II).
We have found that the distortion of the N1ÐGe1ÐC7
angle is related to the formation of intra- and intermolecular
contacts between the O atoms of the atrane framework and
the substituents (Allen et al., 1987). For a more reliable
analysis of the intramolecular contacts, we normalize all CÐH
Ê
N2ÐH2Á Á ÁO1 hydrogen bond [H2CÁ Á ÁO1 = 2.077 A, N2Á Á Á
ꢀ
Ê
O1 = 2.951 (4) A and N2ÐH2CÐO1 = 172 ; symmetry code:
x, 32 y, z 12], while atom O5 forms a contact with the atrane
framework (Fig. 3). Taking into account the noticeable ¯ex-
ibility of the Ge coordination polyhedron, one may conclude
that the formation of the NÐHÁ Á ÁO interaction leads to
distortion of the N1ÐGe1ÐC7 angle.
In (I), the presence of the adamantane fragment does not
lead to a signi®cant deviation of N1ÐGe1ÐC7 from ideal
linearity. The adamantane hydrocarbon does not afford the O
atoms of the atrane cage the opportunity to form inter-
molecular contacts. In turn, the intramolecular contacts of the
methylene groups of the adamantane fragment to the O atoms
of the atrane cage are unfavourable, due to large OÁ Á ÁH
Ê
bonds to 1.08 A according to single-crystal neutron diffraction
data. The germatranes with R1C CR2R3 substituents (R1 = H,
I or Br, R2 = H, Br or Cl and R3 = Ph; N1ÐGe1ÐC7 angles in
the range 173.5±178.1ꢀ; Karlov et al., 2001; Faller & Kultyshev,
2003; Selina, Karlov et al., 2004; Selina, Zhachkina et al., 2004)
may serve as examples of the in¯uence of intramolecular
contacts on the linearity of the N1ÐGe1ÐC7 angle. In these
compounds, short CÐHÁ Á ÁO contacts between an O atom and
a phenyl group are always observed. In addition, the Br and I
atoms also form short intermolecular contacts with O atoms of
the atrane framework (torsion angle OÐSiÐCÐHal ' 22ꢀ,
where Hal = Br or I).
The in¯uence of the intermolecular contacts can be
demonstrated by methyl (germatranyl)trimethylsilylacetate
(Zaitseva et al., 1997) and (penta¯uorophenyl)germatrane
(Kultyshev et al., 2004) (N1ÐGe1ÐC7 = 175.73 and 176.29ꢀ,
respectively). In the case of the former compound, the acetate
ꢀ
Ê
distances (2.7±2.9 A) and small CÐHÁ Á ÁO angles (106±110 ).
So one may therefore conclude that the bulky adamantane
group preserves the N1ÐGe1ÐC7 angle from distortion due
to crystal packing.
Experimental
The synthesis of (I) was carried out according to the previously
published method of Gar et al. (1985). The compound was recrys-
tallized from hexane. Compound (II) was prepared from (trichloro-
germyl)methanol (21.0 g, 0.1 mol), isocyanocyclohexane (12.5 g,
0.1 mol) and triethanolamine (14.0 g, 0.9 mol). The reaction mixture
was heated until gas evolution ceased. After cooling to room
temperature, crystals of (II) appeared (yield 17.6 g, 46.9%; m.p. 421±
Ê
group forms four CÐHÁ Á ÁO contacts (CÁ Á ÁO ' 3.5 A, HÁ Á Á
ꢀ
Ê
O ' 2.6 A and CÐHÁ Á ÁO = 107±146 ) as well as three HÁ Á ÁH
Ê
Ê
1
and CÁ Á ÁH contacts (HÁ Á ÁH ' 2.2 A and CÁ Á ÁH ' 3.1 A). In
(penta¯uorophenyl)germatrane, four CÐHÁ Á ÁF contacts
425 K). H NMR (Bruker AM-360 spectrometer; 360 MHz, DMSO-
d6): ꢁ 1.53±1.92 (m, 11H, C6H11), 1.96 (t, 6H, CH2), 3.50 (t, 6H, CH2O),
4.42 (s, 1H, NH), 4.64 (s, 2H, OCH2Ge); IR (Bruker IFS-113V
spectrometer; KBr tablet, ꢂ, cm 1): 3283 (NH), 1707 (C O), 1103,
1074, 1045, 1022 [Ge(OCH2CH2)3N].
Compound (I)
Crystal data
[Ge(C10H15)(C6H12NO3)]
Mr = 353.98
Z = 4
Dx = 1.520 Mg m
Mo Kꢄ radiation
ꢅ = 1.99 mm
T = 120 (2) K
Prism, colourless
0.30 Â 0.10 Â 0.10 mm
3
Monoclinic, P21=c
1
Ê
a = 10.641 (6) A
Ê
b = 7.292 (4) A
Ê
c = 19.943 (11) A
ꢃ = 90.001 (12)ꢀ
V = 1547.3 (14) A
3
Ê
Data collection
Bruker SMART 1000 CCD area-
detector diffractometer
' and ! scans
Absorption correction: multi-scan
(SADABS; Sheldrick, 1998)
Tmin = 0.587, Tmax = 0.826
15300 measured re¯ections
4396 independent re¯ections
3193 re¯ections with I > 2ꢆ(I)
Rint = 0.059
Figure 3
The crystal packing of (II). H atoms have been omitted for clarity, with
the exception of atom H2C. The N2ÐH2CÁ Á ÁO1 hydrogen bonds are
shown as dashed lines.
ꢇmax = 30.0ꢀ
ꢁ
m304 Korlyukov et al. [Ge(C10H15)(C6H12NO3)] and [Ge(C6H12NO3)(C8H14NO2)]
Acta Cryst. (2006). C62, m303±m305

metal-organic compounds
Re®nement
(1982) with a TWIN matrix de®ned as TWIN 100 010 001, which is the
default for a monoclinic type with ꢃ approximately 90ꢀ. All calcula-
tions were carried out using SHELXTL (Version 5.10; Sheldrick,
1998).
Re®nement on F2
R[F2 > 2ꢆ(F2)] = 0.038
wR(F2) = 0.108
S = 0.97
4396 re¯ections
191 parameters
H-atom parameters constrained
w = 1/[ꢆ2(Fo2) + (0.0517P)2]
where P = (Fo2 + 2Fc2)/3
(Á/ꢆ)max < 0.001
For both compounds, data collection: SMART (Bruker, 1998); cell
re®nement: SAINT-Plus (Bruker, 1998); data reduction: SAINT-
Plus; program(s) used to solve structure: SHELXTL (Sheldrick,
1998); program(s) used to re®ne structure: SHELXTL; molecular
graphics: SHELXTL; software used to prepare material for publi-
cation: SHELXTL.
3
Ê
Áꢈmax = 1.02 e A
3
Ê
0.56 e A
Áꢈmin
=
Compound (II)
Crystal data
[Ge(C6H12NO3)(C8H14NO2)]
Mr = 374.96
Z = 4
Dx = 1.543 Mg m
Mo Kꢄ radiation
ꢅ = 1.92 mm
T = 120 (2) K
Plate, colourless
0.20 Â 0.10 Â 0.03 mm
3
This work was supported by the Russian Foundation for
Basic Research (grant No. 04-03-32662) and the Programme
for State Support of Young Scientists (grant No. MK-
3578.2005.3).
Monoclinic, P21=c
1
Ê
a = 9.4398 (13) A
Ê
b = 16.690 (2) A
Ê
c = 10.3361 (16) A
ꢃ = 97.740 (3)ꢀ
V = 1613.6 (4) A
3
Ê
Data collection
Supplementary data for this paper are available from the IUCr electronic
archives (Reference: SQ3019). Services for accessing these data are
described at the back of the journal.
Bruker SMART CCD 1000 area-
detector diffractometer
' and ! scans
Absorption correction: multi-scan
(SADABS; Sheldrick, 1998)
Tmin = 0.700, Tmax = 0.945
8957 measured re¯ections
3487 independent re¯ections
2310 re¯ections with I > 2ꢆ(I)
Rint = 0.048
ꢇmax = 27.1ꢀ
References
Allen, F. H. (2002). Acta Cryst. B58, 380±388.
Allen, F. H., Kennard, O., Watson, D. G., Brammer, L., Orpen, A. G. & Taylor,
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Re®nement
Re®nement on F2
R[F2 > 2ꢆ(F2)] = 0.047
wR(F2) = 0.108
S = 1.05
3487 re¯ections
199 parameters
H-atom parameters constrained
w = 1/[ꢆ2(Fo2) + (0.0462P)2]
where P = (Fo2 + 2Fc2)/3
(Á/ꢆ)max = 0.001
3
Ê
Áꢈmax = 1.53 e A
3
Ê
0.39 e A
Áꢈmin
=
Table 1
Selected bond lengths (A) in (I) and (II).
Ê
Bond
(I)
(II)
Ge1Á Á ÁN1
Ge1ÐO1
Ge1ÐO2
Ge1ÐO3
Ge1ÐC7
2.206 (3)
1.817 (2)
1.794 (2)
1.791 (2)
1.957 (4)
1.471 (4)
1.415 (4)
2.266 (3)
1.822 (3)
1.825 (3)
1.820 (3)
1.966 (3)
1.473 (5)
1.416 (3)
Jameson, G. B. (1982). Acta Cryst. A38, 817±820.
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(2001). J. Organomet. Chem. 627, 1±5.
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I. A., Chernyshev, E. A., Lysenko, K. A. & Antipin, M. Yu. (2000). Dokl.
Akad. Nauk, 371, 50±54.
Korlyukov, A. A., Lyssenko, K. A., Antipin, M. Yu., Alekseev, N. V., Knyazev,
S. P. & Chernyshev, E. A. (2003). J. Mol. Struct. 655, 215±220.
Kultyshev, R. G., Prakash, G. K. S., Olah, G. A., Faller, J. W. & Parr, J. (2004).
Organometallics, 23, 3184±3188.
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Biologicheskaja aktivnost' soedinenii germaniya (Biological Activity of
Germanium Compounds). Riga: Zinatne. (In Russian.)
NÐC (mean)
OÐC (mean)
Table 2
Selected bond angles (ꢀ) in (I) and (II).
Angle
(I)
(II)
Lukevics, E. Ya., Germane, S. & Ignatovich, L. V. (1992). Appl. Organomet.
Chem. 6, 543±564.
Pratt, C. S., Coyle, B. A. & Ibers, J. A. (1971). J. Chem. Soc. pp. 2146±2151.
Selina, A. A., Karlov, S. S., Gauchenova, E. V., Churakov, A. V., Kuz'mina,
L. G., Howard, J. A. K., Lorberth, J. & Zaitseva, G. S. (2004). Heteroatom
Chem. 15, 43±56.
N1ÐGe1ÐC7
104.5 (2)
118.26 (12)
114.0 (3)
114.3 (3)
104.4 (3)
117.65 (14)
114.0 (3)
OÐGeÐO (mean)
CÐNÐC (mean)
C7ÐO4ÐC8
Selina, A. A., Zhachkina, A. E., Karlov, S. S., Churakov, A. V. & Zaitseva, G. S.
(2004). Heteroatom Chem. 15, 169±174.
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5.10). Bruker AXS Inc., Madison, Wisconsin, USA.
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Howard, J. A. K., Avtomonov, E. V. & Lorberth, J. (1997). Chem. Ber. 130,
739±796.
The H atoms were calculated geometrically and re®ned using a
Ê
rigid-body model, with CÐH = 0.99±1.00 A and Uiso(H) = 1.2Ueq(C).
The crystals of (I) were found to be twinned. The structure was
re®ned in XL using the method of Pratt et al. (1971) and Jameson
ꢁ
Acta Cryst. (2006). C62, m303±m305
Korlyukov et al.
[Ge(C10H15)(C6H12NO3)] and [Ge(C6H12NO3)(C8H14NO2)] m305