Synthesis, crystal structure and ab initio studies of 5-Phenylamino-3- phenylimino-3H[1, 2]dithiole-4-carboxylic acid ethyl ester

Article abstract of DOI:10.1007/s10870-011-0196-2

5-Phenylamino-3-phenylimino-3H[1, 2]dithiole-4-carboxylic acid ethyl ester, C₁₈H₁₆N₂O₂S₂, (I), has been synthesized and the structure has been solved by X-ray diffraction. The crystals are triclinic, space group P1, with a = 5.7127(2) A, b = 12.1757(5) A, c = 14.0734(5) A, a =112.1217(16)°, b = 97.786(2)°, c = 100.694(2) °, Mr = 356.45, V = 868.11(6) A ³, Z = 2 and R = 0.0373. In the title compound there is an intramolecular N-H O hydrogen bond. The crystal structure is stabilized only by weak C-H π and π π interactions as well as by van der Waals forces. The geometry of the isolated molecule was optimized by ab initio quantum mechanical calculations, employing both molecular orbital Hartree-Fock (HF) and density functional theory (DFT) methods. In the DFT calculation the minimum energy was achieved for a conformation very similar to that of the solid-state molecule. Springer Science+Business Media, LLC 2011.

Full text of DOI:10.1007/s10870-011-0196-2

J Chem Crystallogr (2011) 41:1889–1893
DOI 10.1007/s10870-011-0196-2
ORIGINAL PAPER
Synthesis, Crystal Structure and ab Initio Studies
of 5-Phenylamino-3-phenylimino-3H[1, 2]dithiole-4-carboxylic
acid ethyl ester
•
Raza Murad Ghalib Rokiah Hashim
•
•
P. S. Pereira Silva Othman Sulaiman
Received: 21 May 2010 / Accepted: 26 September 2011 / Published online: 7 October 2011
Ó Springer Science+Business Media, LLC 2011
Abstract 5-Phenylamino-3-phenylimino-3H[1, 2]dithiole-
4-carboxylic acid ethyl ester, C18H16N2O2S2, (I), has been
synthesized and the structure has been solved by X–ray
pyrimidines and imidazoles [1, 2]. Phenyl isothiocynate
reacts with 1, 3 dicarbonyl compounds in basic media to give
substituted thiophenes [3]. Here in this reaction when phenyl
isothiocynate reacts with diethyl malonate in basic medium
it gives unexpected title compound 5-phenylamino-3-phe-
nylimino-3H[1, 2]dithiole-4-carboxylic acid ethyl ester.
ꢀ
diffraction. The crystals are triclinic, space group P1, with
˚
a = 5.7127(2) A, b = 12.1757(5) A, c = 14.0734(5) A,
˚
˚
a =112.1217(16)°, b = 97.786(2)°, c = 100.694(2)°,
3
Mr = 356.45, V = 868.11(6) A , Z = 2 and R = 0.0373.
˚
In the title compound there is an intramolecular N–HÁÁÁO
hydrogen bond. The crystal structure is stabilized only by
weak C–HÁÁÁp and pÁÁÁp interactions as well as by van der
Waals forces. The geometry of the isolated molecule was
optimized by ab initio quantum mechanical calculations,
employing both molecular orbital Hartree-Fock (HF) and
density functional theory (DFT) methods. In the DFT cal-
culation the minimum energy was achieved for a confor-
mation very similar to that of the solid-state molecule.
Experimental Methods
Preparation of the Title Compound
A mixture of phenylisothiocyanate (1.19 mL, 10 mmol)
and diethylmalonate (1.51 mL, 10 mmol) in molar ratio 1:1
were refluxed in THF on water bath for 6 h in presence of
Na2CO3 (Scheme 1). The reaction mixture was dried on
rotary evaporator at low pressure and further fractionated
with chloroform. The chloroform soluble part was further
dried on rotary evaporator and chromatographed over silica
gel (Merck, 0.04–0.063 mm, 230–400 mesh ASTM)
column loaded in light petroleum ether. The column was
eluted successively with light petroleum ether and light
petroleum ether–diethylether (9:1–1:1). The elutants
obtained in solvent system light petroleum ether–diethyl-
ether (8:2–7:3), on crystallization with chloroform–dry
ethanol (1:1) gave the yellowish crystals of 5-phenylamino-
3-phenylimino-3H[1, 2]dithiole-4-carboxylic acid ethyl
ester (800 mg) (mp 138 °C). The melting point was deter-
mined on a Thermo Fisher digital melting point apparatus of
IA9000 series and is uncorrected.
Keywords Crystal structure Á 5-Phenylamino-3-
phenylimino-3H[1, 2]dithiole-4-carboxylic acid ethyl
ester Á DFT calculations Á Molecular orbital Hartree-Fock
calculations
Introduction
Phenyl isothiocynate is a useful reagent for the synthesis
several heterocyclic molecules such as thiophenes, pyrroles,
R. M. Ghalib (&) Á R. Hashim Á O. Sulaiman
School of Industrial Technology, Universiti Sains Malaysia,
Pulau Pinang 11800, Malaysia
e-mail: raza2005communications@gmail.com
Crystal Structure Determination
P. S. P. Silva
CEMDRX, Physics Department, University of Coimbra,
P-3004-516 Coimbra, Portugal
A crystal of (I) with a thick plate shape and having
approximate dimensions of 0.42 9 0.36 9 0.21 mm was
123

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J Chem Crystallogr (2011) 41:1889–1893
S
S
Scheme 1 Route of synthesis
of (I)
C
C
NH
N
C
C
COOC2H5
COOC2H5
Na2CO3
Reflux
THF
N
C
S
H2C
O
O
6 Hours
CH2
CH3
Diethyl malonate
Phenyl isothiocyanate
5-phenylamino-3-phenylimino-3H[1,2]dithiole-4-carboxylic acid ethyl (1)
glued on a glass fibre and mounted on a Bruker Apex II
diffractometer. Diffraction data were collected at room
temperature 293(2) K using graphite monochromated Mo
basis set. Each self-consistent field calculation was iter-
ated until a D of less than 10-5 Bohr-3 was achieved. The
final equilibrium geometries at the minimum energy had a
maximum gradient in internal coordinates of 10-5 Hartree
Bohr-1 or Hartree rad-1. At the end of these geometry
optimizations we conducted Hessian calculations to
guarantee that the final structures correspond to true
minima, using the same level of theory as in the geometry
optimizations.
˚
Ka (k = 0.71073 A). Data reduction was performed with
APEX II [4]. Lorentz and polarization corrections were
applied. Absorption correction was applied using SADABS
[5]. The crystallographic structure was solved by direct
methods (SHELXS-97) [6]. Refinements were carried out
with SHELXL-97 package [6]. All refinements were made
by full-matrix least-squares on F2, with anisotropic dis-
placement parameters for all non-hydrogen atoms. All the
hydrogen atoms were located in a difference Fourier syn-
thesis, placed at calculated positions and then, included in
the structure factor calculation in a riding model using
SHELXL-97 defaults. We have chosen to model the posi-
tional disorder of the methyl substituent with two groups.
The methyl C atoms were refined anisotropically with the
Uij values restrained to behave more isotropically, with the
ISOR instruction, and the C atom of one group was given
the same displacement parameters as the corresponding
atom of the other group with the EADP instruction. The C5–
C6 bond lengths of the two groups were made equivalent
with the SADI instruction. The final least-squares cycle was
based on 4533/13/221 observed reflections [I [ 2r(I)],
221 variable parameters, 13 restraints, converged with
R = 0.0373 and wR = 0.0995. Additional informations to
the structure determination are given in Table 1. Selected
structural parameters can be seen in Table 2. Supplemen-
tary data have been deposited at the Cambridge Crystallo-
graphic Data Centre (CCDC No. 775631).
Table 1 Crystallographic data and structure refinement of compound
(I)
Empirical formula
Formula weight
Temperature (K)
C18H16N2O2S2
356.45
293(2)
˚
Wavelength (A)
0.71073
Crystal system
Space group
Triclinic
ꢀ
P1
˚
a (A)
5.7127(2)
12.1757(5)
14.0734(5)
112.1217(16)
97.786(2)
100.694(2)
868.11(6)
2
˚
b (A)
˚
c (A)
a (°)
b (°)
c (°)
3
˚
Volume (A )
Z
Calculated density (g/cm3)
Absorption coefficient (mm-1
F(000)
1.364
)
0.319
372
Crystal size (mm)
0.42 9 0.36 9 0.21
1.60–28.81
Ab Initio Calculations
h Range for data collection (°)
Index ranges
-7 \ h \ 7, -16 \ k \ 16,
-19 \ l \ 19
23007/4533 [R(int) = 0.0169]
The geometry optimization was performed using the
Firefly QC package [7], which is partially based on the
GAMESS (US) source code [8], starting from the exper-
imental X-ray geometry. We performed two calculations,
one with the molecular orbital Hartree-Fock (MO-HF)
method and the other within density functional theory
(DFT) using B3LYP (Becke three-parameter Lee–Yang–
Parr) for exchange and correlation, which combines
the hybrid exchange functional of Becke [9, 10] with the
correlation functional of Lee, Yang and Parr [11]. The
calculations were performed with an extended 6-31G(d,p)
Reflections collected/unique
Completeness to h = 25.00°
Refinement method
100%
Full-matrix least-squares on F2
4533/13/221
Data/restraints/parameters
Goodness-of-fit on F2
Final R indices [I [ 2r(I)]
R indices (all data)
1.099
R1 = 0.0373 wR2 = 0.0995
R1 = 0.0449 wR2 = 0.1064
0.470 and -0.274
Largest different peak
-3
˚
and hole (e A
)
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J Chem Crystallogr (2011) 41:1889–1893
1891
Table 2 Comparison of selected geometrical parameters for (I) as
determined by X-ray diffraction and from DFT and HF calculations
˚
(A, °)
Experimental
DFT
2.103
HF
S1–S2
2.0573(5)
1.747(1)
1.807(1)
1.384(2)
1.451(2)
1.464(2)
1.215(2)
1.318(2)
1.459(2)
1.487(5)
1.337(2)
1.425(2)
1.262(2)
1.414(2)
96.46(5)
94.98(5)
118.35(10)
112.42(10)
117.20(12)
121.68(14)
3.57(13)
7.69(11)
-5.85(7)
121.05(18)
113.15(18)
2.4(2)
2.066
1.759
1.817
1.379
1.467
1.471
1.209
1.307
1.426
1.516
1.332
1.427
1.248
1.405
S1–C1
1.768
1.856
1.401
1.459
1.470
1.239
1.336
1.448
1.521
1.347
1.416
1.269
1.402
95.47
95.39
118.26
112.57
117.96
121.71
1.99
S2–C3
C1–C2
C2–C3
C2–C4
C4–O1
C4–O2
O2–C5
Fig. 1 ORTEP diagram of the title compound with the ellipsoids
drawn at the 50% probability level, with the atomic labelling scheme.
For the sake of clarity, in the disordered methyl group, only the
orientation with the highest occupancy is shown
C5–C6A
N1–C1
N1–C7
N2–C3
N2–C13
S1–S2–C3
S2–S1–C1
S1–C1–C2
S2–C3–C2
C1–C2–C3
O1–C4–O2
S2–S1–C1–C2
S1–S2–C3–C2
C1–S1–S2–C3
C1–N1–C7–C8
C3–N2–C13–C14
C3–C2–C4–O2
C4–O2–C5–C6A
C4–O2–C5–C6B
96.18
95.50
118.24
112.76
117.26
122.09
0.34
5.81
2.33
-4.05
136.25
119.48
0.22
-1.41
90.09
97.66
-3.68
-83.82
-71.3(7)
-96.8(8)
-84.45
Results and Discussion
Fig. 2 A view down the a axis of the unit cell of (I), with the
H-bonds shown as dashed lines
ꢀ
Compound (I) crystallizes in the space group P1 with one
molecule in the asymmetric unit (Fig. 1). The 1,2-dithiole
ring is essentially planar, with a maximum deviation from
Etter’s graph-set theory [14, 15]. This hydrogen bond may
control the conformation of the carboxyl fragment, which
is almost coplanar with the 1,2-dithiole ring, as shown by
the small value of the torsion angle C3–C2–C4–O2:
2.4(2)°. In the ethoxycarbonyl group the terminal methyl is
disordered over two sites with refined occupancies of
0.64(2) and 0.36(2). The crystal packing is stabilized only
by weak interactions: C–HÁÁÁp and pÁÁÁp interactions and
van der Waals forces.
˚
the mean plane of 0.055(2) A for the C3 atom. The least-
squares planes of the C7–C12 and C13–C18 phenyl rings
make dihedral angles of 64.50(8) and 75.25(8)°, respec-
tively, with the 1,2-dithiole ring. The geometries of the
phenyl rings show no exceptional features. The C1–C2
bond has double-bond character as evidenced by its bond
˚
length of 1.384(2) A. The two endocyclic S–C bond
lengths in the present structure are noticeably different
˚
from each other: 1.747(1) and 1.807(1) A. This is also
There are two C–HÁÁÁp interactions. In the strongest
interaction, the carbon atom C17 acts as the proton donor
to the phenyl ring C7–C12, of a neighbouring molecule
related by an inversion centre, with a H17ÁÁÁpi distance of
observed in related compounds [12, 13].
In the title compound there is an intramolecular N–HÁÁÁO
˚
hydrogen bond (Fig. 2) [DÁÁÁA: 2.613(2) A; D–HÁÁÁA:
˚
2.98 A, and a C17–H17ÁÁÁp angle of 140° [symmetry code:
132.3°] forming rings of descriptor S(6) according to
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J Chem Crystallogr (2011) 41:1889–1893
(i) -x, 2 - y, 1 - z]. The other bond is established
between carbon C11 and the p electron cloud of the C13–
C18 phenyl ring of a molecule related by an inversion
torsion angles in the free molecule differ significantly from
those of the molecule in the crystal for the case of the HF
values, however, the DFT torsion angles are very close to
the experimental values.
centre, with a H11ÁÁÁpii distance of 3.19 A, and a C11–
˚
H11ÁÁÁp angle of 130° [symmetry code: (ii) 1 - x, 2 - y,
1 - z]. In these interactions the hydrogen atoms H17 and
H11 are above the centre of the phenyl rings C7–C12 and
C13–C18, respectively, but the C–H bonds point towards
the ring edges, corresponding to C–HÁÁÁp(phenyl) interac-
tions of the type III, according to the classification of
Malone et al. [16]. There are also two non-conventional
interactions between hydrogens of the phenyl rings and the
five-membered ring.
The differences between the calculated and experimen-
˚
tal bond lengths are smaller than 0.049 and 0.033 A, for the
DFT and the HF calculations, respectively. As usually
found, the calculated DFT bond lengths are slightly longer
than the HF values. The HF values are closer to the
experimental values at room temperature, but after cor-
rection of the crystal structure model for librational motion,
the DFT values would become closer. However, for
disordered structures, this correction is not performed.
The calculated geometries of the ethyl group are inter-
mediate between the two refined positions in the crystal, as
can be seen by the experimental and calculated values of
the torsion angle C4–O2–C5–C6 (Table 2).
When looking for pÁÁÁp interactions between phenyl
rings, one finds four of these interactions with a distance
˚
between ring centroids, dc–c, smaller than 6 A and an angle
b smaller than 60° (b is the slipping angle defined by the
vector c1–c2, from the first ring centroid to the second and
the normal to the plane of the first ring), with the strongest
Overall, our data suggest that the supramolecular
aggregation does not play a major role in stabilizing the
observed geometry of (I), in agreement with the absence of
strong inter-molecular interactions, and the small differ-
ences in the orientations of the phenyl rings may be due to
the weak C–HÁÁÁp and pÁÁÁp interactions.
˚
[dc–c = 4.059(1) A] being between C7–C12 phenyl rings
of two neighbouring molecules related by an inversion
centre. The other three interactions are weaker, with dis-
˚
tances between ring centroids around 5 A.
In order to gain some insight on the influence of the
intermolecular interactions on the molecular geometry we
have performed quantum mechanical calculations of the
equilibrium geometry of the free molecule. Both HF and
DFT calculations closely reproduce the solid-state geom-
etry of the molecule (Table 2; Fig. 3). The agreement
between the experimental and calculated bond lengths and
valency angles is very good, but some of the calculated
Supplementary Material
Crystallographic data for structural analysis have been
deposited with the Cambridge Crystallographic Data
Center, CCDC 775631. Copies of this information may be
obtained free of charge on application to CCDC, 12 Union
Road, Cambridge CB2 1EZ, UK (fax: ?44 1223 336 033;
e-mail: deposit@ccdc.cam.ac.uk or http://www.ccdc.cam.
ac.uk).
Acknowledgments We would like to acknowledge Universiti Sains
Malaysia (USM) for the University Grant 1001/PTEKIND/8140152
to Dr. Raza Murad Ghalib. P. S. Pereira Silva acknowledges the
ˆ
support by Fundac¸a˜o para a Ciencia e a Tecnologia, under the
scholarship SFRH/BD/38387/2008.
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