Z. Kristallogr. NCS 230 (2015) 9-10 / DOI 10.1515/ncrs-2014-0217
9
© 2015 Walter de Gruyter GmbH, Berlin/Munich/Boston
Crystal structure of 3,5-diaza-methyl-2-methyl-6-oxo-6-phenyl-4thioxohexanoate, at 200 K, C12H14N2O3S
Felix Odame, Eric C. Hosten, Zenixole R. Tshentu and Richard Betz*
Nelson Mandela Metropolitan University, Summerstrand Campus, Department of Chemistry, University Way, Summerstrand, PO Box 77000,
Port Elizabeth 6031, South Africa
Received October 15, 2014, accepted October 24, 2014, available online December 17, 2014, CCDC no. 1267/4205
Abstract
C12H14N2O3S, triclinic, P1 (no. 2), a = 7.4237(4) Å,
b = 8.7173(5) Å, c = 11.3227(6) Å, ' = 73.411(2)°,
% = 72.173(3)°, ! = 68.967(3)°, V = 638.2 Å3, Z = 2,
Rgt(F) = 0.0426, wRref(F2) = 0.1158, T = 200 K.
Table 1. Data collection and handling.
Crystal:
Wavelength:
$:
Diffractometer, scan mode:
2#max:
N(hkl)measured, N(hkl)unique:
Criterion for Iobs, N(hkl)gt:
N(param)refined:
Programs:
colourless platelets,
size 0.182#0.207#0.244 mm
Mo K( radiation (0.71073 Å)
2.56 cm&1
Bruker APEX-II CCD, ) and (
56.68°
11208, 3154
Iobs > 2 "(Iobs), 2519
173
SHELX, WinGX, MERCURY,
PLATON [7–10]
Source of material
The compound was synthesized upon reacting the free hexanoic
acid with TMSCl in methanol. Crystals suitable for the diffraction
study were obtained upon free evaporation of the solvent at room
temperature.
Experimental details
Carbon-bound H atoms were placed in calculated positions (C–H
0.95 Å for aromatic carbon atoms, C–H 1.00 Å for methine
groups) and were included in the refinement in the riding model
approximation, with Uiso(H) set to 1.2Ueq(C). The H atoms of the
methyl groups were allowed to rotate with a fixed angle around
the C–C bond to best fit the experimental electron density (HFIX
137 in the SHELX program suite [7], with Uiso(H) set to
1.5Ueq(C). Both nitrogen-bound H atoms were located on a difference Fourier map and refined freely.
Discussion
Chelate ligans have found widespread use in coordination chemistry as coordination compounds formed by them show a markedly higher stability than coordination compounds formed from
comparable but exclusively monodentate ligand systems. Mixed
_____________
* Correspondence author (e-mail: [email protected])
N,S,O ligand systems are especially interesting in this aspect as
they offer a set of donor atoms of variable Lewis acidity and can,
therefore, probe for prefereable binding sites. The incorporation
of the aforementioned set of atoms in a mixed keto-thioketo-amide environment, in addition, offers the possibility of N–H tautomerization involving the two double-bonded atoms, thus enhancing the versatility of the ligand system. In continuation of our ongoing research on the field of N,S,O ligands, the title compound
was synthesized and its crystal and molecular structure was determined. Two similar compounds – namely syn,anti-O,O'dimethyl N,N'-(m-phenylenedicarbonyl)bis(dithiocarbamate)
and anti,anti-O,O'-dimethyl N,N'-(m-phenylenedicarbonyl)bis(thiocarbamate) – have been reported in the literature [1]. The
structures of two compounds featuring the title compound's scaffold as moiety of a partially cyclic structure are also apparent in
the literature [2]. Due to amide-type resonance the N,S,O moiety
shows widespread planarization (r.m.s of all fitted non-hydrogen
atoms = 0.0902 Å) with the carbonyl-type oxygen atom deviating
most from the common least-squares plane by 0.1472(10) Å.
However, the aromatic system does not seem to take part in this
resonance as the least-squares plane defined by its carbon atoms
intersects at an angle of 27.64(4)° with the least-squares plane
just described. This observation is in good agreement with the situation found for a comparable compound recently synthesized
and characterized in our group [3]. The length of the C–S bond is
supportive of involving the latter in resonance as its value of
1.6760(17) Å is found slightly towards longer values than the
most common ones reported for molecular structures featuring
comparable O–(C=S)–N moieties in the Cambridge Structural
Database [4]. In the crystal, a classical intramolecular hydrogen
bond of the N–H)))O type is observed next to C–H)))O and
C–H)))S contacts whose range invariably falls below the sum of
van-der-Waals radii of the atoms participating in them. While the
N–H)))O contact is intramolecular, the N–H)))S contact is
intermolecular and fosters the formation of centrosymmetric
dimers. While the C–H)))S contact is supported by a hydrogen
atom of the phenyl group in ortho-position to the chain-type
substituent, the C–H)))O contacts stem from the hydrogen atom of
the methine group as well as one hydrogen atom each of both
methyl groups. All oxygen atoms present in the molecule serve as
acceptor for one of the latter contacts. In terms of graph-set analysis [5,6], the descriptor for the classical hydrogen bonds is S(6) on
the unary level while the C–H)))O contacts necessitate a
R22(8)R22(10)R22(20) descriptor on the same level. The unary
descriptor for the C–H)))S contacts is R22(14). In total, the molecules are connected to planes perpendicular to the crystallographic a axis. The shortest intercentroid distance between two
centers of gravity was measured at 4.4181(12) Å.
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10
C12H14N2O3S
Table 2. Atomic coordinates and displacement parameters (in Å2).
Table 2. continued.
Atom
Site
x
Uiso
Atom
Site
x
y
H(71)
H(72)
H(3)
H(5A)
H(5B)
H(5C)
H(6A)
2i
2i
2i
2i
2i
2i
2i
0.890(3)
0.885(3)
0.9640
1.4370
1.5037
1.5327
0.6958
0.037(6)
0.020(4)
0.037
0.075
0.075
0.075
0.058
H(6B)
H(6C)
H(12)
H(13)
H(14)
H(15)
H(16)
2i
2i
2i
2i
2i
2i
2i
0.8746
0.8274
0.7987
0.6897
0.5773
0.5649
0.6755
0.2540
0.4195
0.7411
0.8572
0.7021
0.4339
0.3154
y
z
0.220(3)
0.384(2)
0.0864
0.1747
&0.0247
0.0917
0.2942
0.449(2)
0.158(2)
0.0878
&0.2408
&0.1951
&0.1200
0.0155
z
Uiso
&0.1044
&0.0516
0.3987
0.5795
0.7760
0.7919
0.6120
0.058
0.058
0.040
0.050
0.051
0.043
0.034
U13
U23
Table 3. Atomic coordinates and displacement parameters (in Å2).
Atom
Site
x
S(1)
O(1)
O(2)
O(3)
N(1)
N(2)
C(1)
C(2)
C(3)
C(4)
C(5)
C(6)
C(11)
C(12)
C(13)
C(14)
C(15)
C(16)
2i
2i
2i
2i
2i
2i
2i
2i
2i
2i
2i
2i
2i
2i
2i
2i
2i
2i
1.02963(8)
0.8261(2)
1.2520(2)
1.2703(2)
0.8736(2)
0.9123(2)
0.8195(2)
0.9356(2)
0.9702(3)
1.1806(3)
1.4471(3)
0.8295(3)
0.7507(2)
0.7528(3)
0.6877(3)
0.6199(3)
0.6140(3)
0.6794(2)
y
&0.01855(6)
0.5456(2)
0.0921(2)
0.2855(2)
0.2793(2)
0.2788(2)
0.4509(2)
0.1906(2)
0.2044(2)
0.2023(2)
0.0827(3)
0.3017(3)
0.5159(2)
0.6778(2)
0.7467(3)
0.6551(3)
0.4957(2)
0.4254(2)
z
0.31690(4)
0.2661(1)
&0.0859(1)
0.0005(1)
0.3806(1)
0.1705(1)
0.3689(2)
0.2835(2)
0.0596(2)
&0.0099(2)
&0.1670(2)
&0.0280(2)
0.4885(2)
0.4788(2)
0.5860(2)
0.7024(2)
0.7120(2)
0.6052(2)
U11
U22
U33
0.0604(3)
0.0566(8)
0.0511(8)
0.0464(8)
0.0343(8)
0.0430(9)
0.0285(8)
0.0269(8)
0.043(1)
0.0400(9)
0.050(1)
0.043(1)
0.0235(8)
0.0359(9)
0.046(1)
0.046(1)
0.038(1)
0.0300(8)
0.0251(2)
0.0280(6)
0.0307(7)
0.0460(8)
0.0247(7)
0.0254(8)
0.0270(8)
0.0271(8)
0.0279(8)
0.0238(8)
0.038(1)
0.043(1)
0.0243(8)
0.0297(9)
0.035(1)
0.048(1)
0.040(1)
0.0258(8)
0.0293(2)
0.0257(6)
0.0335(7)
0.0424(8)
0.0202(6)
0.0224(7)
0.0255(8)
0.0242(7)
0.0224(7)
0.0226(7)
0.042(1)
0.0319(9)
0.0274(8)
0.0371(9)
0.052(1)
0.040(1)
0.0277(8)
0.0272(8)
Acknowledgments. The authors thank Mr Jacques van Ree for helpful discussions.
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&0.0070(2)
&0.0120(6)
&0.0111(6)
&0.0187(7)
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&0.0135(5)
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&0.0073(6)
&0.0037(6)
&0.0109(9)
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&0.0074(6)
&0.0090(7)
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&0.0103(7)
&0.0063(6)
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