One-pot synthesis, structure, theoretical study and vibrational spectroscopy of 5-amino-4-cyano-3H-1,2-dithiole-3-thione

Article abstract of DOI:10.1016/j.molstruc.2007.12.034

A novel D3T derivative, 5-amino-4-cyano-3H-1,2-dithiole-3-thione (compound 1) has been obtained in one-pot reaction. The crystal is orthorhombic, space group Pbca, with a = 10.3667(4) ?, b = 10.8898(4) ?, c = 11.4942(5) ?, V = 1297.60(9) ?³, and Z = 8. In the crystal, molecules are firstly self-assembled into a complex sheet parallel to the (0 0 1) plane containing centrosymmetric R₂⁴ (16) and R₄⁴ (24) rings, and then the interconnection of molecular sheets through S···S interactions forms a three-dimensional supramolecular assembly. The DFT calculations are performed for isolated molecule using the B3LYP/6-31+G(d,p) methods. The frontier orbital properties of compound 1 have been reported and discussed. Moreover, a detailed assignment of the fundamental vibrational modes is proposed on the basis of the calculated results.

Full text of DOI:10.1016/j.molstruc.2007.12.034

Available online at www.sciencedirect.com
Journal of Molecular Structure 888 (2008) 354–359
www.elsevier.com/locate/molstruc
One-pot synthesis, structure, theoretical study and vibrational
spectroscopy of 5-amino-4-cyano-3H-1,2-dithiole-3-thione
Yanning Cao a, Hanhui Zhang a,b,*, Yiji Lin a, Changcang Huang a, Yiping Chen a,
Fengli Zhang a, Jianshan Chen a
a Department of Chemistry, Fuzhou University, Fuzhou, Fujian 350002, PR China
b State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, The Chinese Academy of Sciences,
Fuzhou, Fujian 350002, PR China
Received 15 October 2007; received in revised form 19 December 2007; accepted 21 December 2007
Available online 11 January 2008
Abstract
A novel D3T derivative, 5-amino-4-cyano-3H-1,2-dithiole-3-thione (compound 1) has been obtained in one-pot reaction. The crystal
3
˚
˚
˚
˚
is orthorhombic, space group Pbca, with a = 10.3667(4) A, b = 10.8898(4) A, c = 11.4942(5) A, V = 1297.60(9) A , and Z = 8. In the
crystal, molecules are firstly self-assembled into a complex sheet parallel to the (001) plane containing centrosymmetric R42 (16) and
R44 (24) rings, and then the interconnection of molecular sheets through SÁÁÁS interactions forms a three-dimensional supramolecular
assembly. The DFT calculations are performed for isolated molecule using the B3LYP/6-31+G(d,p) methods. The frontier orbital prop-
erties of compound 1 have been reported and discussed. Moreover, a detailed assignment of the fundamental vibrational modes is pro-
posed on the basis of the calculated results.
Ó 2008 Elsevier B.V. All rights reserved.
Keywords: One-pot synthesis; X-ray diffraction; Molecular structure; FTIR spectra; DFT calculations; 3H-1,2-Dithiole-3-thione
1. Introduction
of biological activities displayed by such compounds has
been urging chemists to develop new methods for synthesis
of various substituted derivatives. Initially, those were
obtained from reactions of olefins with sulfur at high tem-
perature [10]. And subsequently the mixture of b-ketonest-
ers with sulfurising agents such as P2S5, Lawesson’s
reagent, or sulfur were commonly employed to prepare
the dithiolethiones [9,11,12]. Recently, Aimar and Rossi
reported a convenient one-pot synthesis of nR (n = 4 or
5, R = alkyl or aryl) thio-3H-1,2-dithiole-3-thiones via
dialkyl or dithiol malonic esters with P2S5/S8 in boiling
xylene and with 2-mercaptobenzothiazole/ZnO as catalyst
[13,14]. More interestingly, Adams and co-workers
described the facile synthesis of 4-mercapto-1,2-dithiole-3-
thiones by deprotonation of terminal alkynes followed by
sequential treatment with carbon disulfide, sulfur and acid
at room temperature [15].
D3T (3H-1,2-dithiole-3-thione) and its derivatives have
attracted considerable attention for several years because
of their significant biological activities. For instance, D3T
is known to enhance the detoxification of environmental
carcinogens, prevent neoplasia, and elicit other protective
effects by inducing phase 2 and antioxidative enzymes [1–
6]. Oltipraz (4-methyl-5-pyrazinyl-3H-1,2-dithiole-3-thi-
one) possesses remarkable activity against Schistosoma
mansoni and shows activity to inhibit HIV-1 (AIDS) virus
replication by irreversibly binding to the viral reverse trans-
criptase enzyme [7]. Other derivatives have been found to
be fungitoxic and bacteriostatic [8,9]. The wide spectrum
*
Corresponding author. Address: Department of Chemistry, Fuzhou
University, Fuzhou, Fujian 350002, PR China. Tel.: +86 591 87892013;
fax: +86 591 87893239.
Despite so many methods have been exploited to synthe-
size the D3T derivatives, the studies of the efficient one-pot
E-mail address: zhanghh1840@hotmail.com (H. Zhang).
0022-2860/$ - see front matter Ó 2008 Elsevier B.V. All rights reserved.
doi:10.1016/j.molstruc.2007.12.034

Y. Cao et al. / Journal of Molecular Structure 888 (2008) 354–359
355
Table 1
synthesis of them are, nevertheless, very rare and still remain
Crystal data and structure refinement for compound 1
in urgent need. Furthermore, at present, most of the substit-
uents contained in the derivatives of D3T are various hydro-
phobic groups, while hydrophilic groups are scarcely present
in such compounds. We recently focused our attention on
the study of organic-inorganic hybrid open-framework oxa-
lates [16,17]. Meanwhile, due to the geometrical similarity
between oxalate and i-mnt (i-mnt = 1,1-dicyanoethylene-
2,2-ditholate), we extended our investigation to the hybrid
compounds with i-mnt as the organic ligands. When the i-
mnt reacted with Nb5+, surprisingly, the product obtained
was not the coordination compound with Nb5+ and i-mnt,
but is a derivative of D3T: 5-amino-4-cyano-3H-1,2-
dithiole-3-thione. Herein, we describe the novel one-pot syn-
theses, X-ray crystal structure, DFT calculations and the
FT-IR spectrum of compound 1.
Formula
C4H2N2S3
Fw
174.26
Space group
Pbca
˚
a (A)
10.3667(4)
10.8898(4)
11.4942(5)
1297.60(9)
8
1.784
1.037
704
˚
b (A)
˚
c (A)
3
˚
V (A )
Z
q (g/cmÀ3
)
l (mmÀ1
F (000)
)
h Range (°)
3.24–28.22
9046/1586/0.0211
1586/0/82
1.014
Reflections collected/unique/[R(int)]
Data/restraints/parameters
Goodness-of-fit on F2
Final R1/R2 indices [I > 2r(I)]
Largest diff. peak and hole
R1 = 0.0226, wR2 = 0.À03686
˚
0.299 and À0.193 e A
2. Experimental
2.4. Theoretical methods
2.1. Materials and apparatus
The geometric parameters of the molecule in the calcu-
lations were employed from crystal structure data. To cal-
culate optimized geometric structure, the HOMO and
LUMO orbits, the harmonic frequencies and infrared
intensities, the density functional theory (DFT) hybrid
method B3LYP methods was used. The calculation was
carried out with one functional base: 6-31G+(d,p). All the-
oretical calculations were performed using the Gaussian
03W package of programs [20] running on a PC.
K2(i-mnt) [18] was prepared as described in the litera-
ture. All reagents and solvents purchased were A.R. grade
and used without further purification. Elemental analyses
(C, H and N) were performed on a Perkin-Elmer 2400
CHN Elemental Analyzer. The FT-IR spectrum of crystal
form of the title compound in the region 400–4000 cmÀ1
was measured on a Perkin-Elmer FT-IR spectrum 2000
spectrometers using KBr pellets.
2.2. Synthesis
3. Results and discussion
K2(i-mnt) (0.1 g, 0.46 mmol), the ethanol solution of
NbCl5 (0.5 mL, 0.5 M) and tetraethylammonium iodide
(0.03 g, 0.12 mmol) were dissolved in 16 mL ethanol–glycol
(1:1, v/v) solvent. The mixture were stirred for about
30 min at room temperature and filtered. Orange crystals
suitable for X-ray diffraction were obtained by slow evap-
oration of the filtrate (1 month approximately). Yield: 21%
(based on K2(i-mnt)). Anal. for C4H2N2S3, Calc C, 27.57;
H, 1.16; N, 16.08. Found: C, 27.73; H, 1.19; N, 16.12.
3.1. Synthesis
A novel D3T derivative, compound 1 has been obtained
in one-pot reaction, simply by mixing K2(i-mnt), the
2.3. Crystal structure determination
The X-ray intensity data were collected at 293(2) K on a
Bruker SMART APEX II X-ray diffractometer system
with graphite-monochromated Mo Ka radiation
˚
(0.71073 A), using the u and x-scan technique. The struc-
ture was solved by direct methods using the SHELXTL
6.1 bundled software package [19]. Absorption corrections
were applied with SADABS. All non-hydrogen atoms were
refined anisotropically. The hydrogen atoms were placed in
geometrically idealized positions and refined as riding
atoms, with Uiso(H) = 1.2Ueq(N). Crystallographic data
and the processing parameters are given in Table 1. The
crystallographic information file is deposited in the Cam-
bridge Crystallographic Data Center as CCDC 660472.
Fig. 1. The molecular structure of compound 1, showing the atom-
numbering scheme. Displacement ellipsoids are drawn at the 50%
probability level.

356
Y. Cao et al. / Journal of Molecular Structure 888 (2008) 354–359
ethanol solution of NbCl5 and tetraethylammonium iodide
in ethanol–glycol (1:1, v/v) solvent at room temperature.
Compound 1 is soluble not only in common organic sol-
vents (e.g., ethanol, acetone, acetonitrile) but also in water.
A series of experimental results show that compound 1 can
be synthesized in several different reaction medium (e.g.,
methanol, methanol–glycol, methanol-n-butanol, ethanol,
and ethanol–acetonitrile). But as the NbCl5 is absent, com-
pound 1 cannot be obtained, which indicates the NbCl5
plays an essential role during the generation of compound
1. Further investigations of the reaction mechanism are
continuing.
and atom-numbering scheme for 1 are shown in Fig. 1.
Selected bond distances and angles are given in Table 2.
As shown in Fig. 1, the molecule is essentially planar:
the maximum deviation from the least squares plane
˚
defined by the dithiolethione ring is 0.065(2) A for S3.
The absolute planarity of the dithiolethione ring is the
structural characteristic of this kind of compounds [21].
˚
The exocyclic S3–Cl bond length, 1.670(1) A, is longer than
˚
the value expected for the double-bond length of 1.61 A,
but is consistent with that for 4-methyl-5-(2-pyrazinyl)-
3H-1,2-dithiole-3-thione [22]; The C4–C2 bond connecting
˚
the cyano group and the five-membered ring is 1.421(2) A,
which is shorter than the single-bond C–C length of
˚
1.544 A. Two endocyclic S1–C3 and S2–C1 bond distances
are nearly identical. The C1–C2 and C2–C3 bond lengths
are 1.408(2) and 1.404(2) A, respectively, which are inter-
3.2. Description of the structure
˚
mediate in length between single and double bonds. The
Compound 1 crystallizes in Pbca with one independent
molecule in the asymmetric unit. The molecular structure
˚
S1–S2 bond distance, 2.070(1) A, is comparable with the
˚
longest distances: 2.050 A found in related structure [21]
Table 2
˚
and shorter than the length of 2.08 A given by Pauling
˚
Selected bond lengths (A) and angles (°) for compound 1
for an S–S single bond [23]. All the observed intramolecu-
lar bond lengths in the molecule indicate the delocalization
of the conjugated p-electron system.
S(1)–C(3)
S(2)–C(1)
N(1)–C(3)
C(1)–C(2)
C(2)–C(4)
1.737(1)
1.736(1)
1.314(2)
1.408(2)
1.421(2)
S(1)–S(2)
S(3)–C(1)
N(2)–C(4)
C(2)–C(3)
2.071(1)
1.670(1)
1.144(2)
1.404(2)
Supramolecular interactions play an important role in
crystal packing and stabilization of compound 1. Two
kinds of intermolecular hydrogen bonds, N1-H1AÁÁÁS3#1
(a) and N1-H1BÁÁÁN2#2 (b), are present in the crystal struc-
ture of compound 1 (Fig. 2 and Table 3). The N1-
H1BÁÁÁN2#2 hydrogen bonds link the molecules into C(6)
chains running parallel to the [010] direction. Meanwhile,
the N1–H1AÁÁÁS3#1 hydrogen bonds connect the molecules
C(3)–S(1)–S(2)
C(2)–C(1)–S(2)
C(3)–C(2)–C(1)
C(1)–C(2)–C(4)
N(1)–C(3)–S(1)
N(2)–C(4)–C(2)
94.8(1)
113.6(1)
119.2(1)
120.3(1)
118.8(1)
178.2(1)
C(1)–S(2)–S(1)
C(2)–C(1)–S(3)
S(3)–C(1)–S(2)
C(3)–C(2)–C(4)
N(1)–C(3)–C(2)
C(2)–C(3)–S(1)
96.9(1)
128.9(1)
117.4(1)
120.6(1)
125.7(1)
115.5(1)
Fig. 2. Presentation of the two-dimensional hydrogen-bonded network, as well as the R42 (16) and R44 (24) ring motifs generated. N1–H1AÁÁÁS3#1 (a) and
N1–H1BÁÁÁN2#2 (b) hydrogen bonds are shown as red and blue dashed lines, respectively. Symmetry code for the generated atoms: #1, x + 1/2, Ày + 3/2,
Àz + 1; #2, Àx + 1/2, y À 1/2, z.

Y. Cao et al. / Journal of Molecular Structure 888 (2008) 354–359
357
to form the C(6) chains along [100]. The combined effect of
the two kinds of hydrogen bonds is the formation of a com-
plex sheet parallel to the (001) plane containing centrosym-
metric R42 (16) and R44 (24) rings [24]. Finally, the
interconnection of molecular sheets through SÁÁÁS interac-
tions between S1ÁÁÁS3#3 (3.260(1) A) and S2ÁÁÁS3#3
˚
˚
(3.536(5) A) (#3, Àx, y À 0.5, Àz + 0.5), respectively,
forms
a
three-dimensional supramolecular assembly
(Fig. 3). The solid-state packing with rather short SÁÁÁS
intermolecular distances appears to be the other character-
istic of compounds containing the dithiole–thione ring [25].
3.3. The B3LYP/6-31+G(d,p) calculations
3.3.1. The HOMO and LUMO orbits
The contour plots of the p-like frontier orbitals for the
ground state of compound 1 are shown in Fig. 4, including
the highest occupied molecular orbital (HOMO) and low-
est unoccupied molecular orbital (LUMO). From the plots,
one can find that the HOMO mainly concentrates on S3
and the dithiolethione ring with some delocalization along
S1–C3 and S2–C1–C2, whereas, the LUMO distributes
over the whole molecule with some delocalization along
Table 3
˚
Hydrogen bonds distances (A) and angles (°) in compound 1
D–HÁÁÁA
D–H
HÁÁÁA
2.66
DÁÁÁA
3.487(1)
<(DHA)
N1–H1AÁÁÁS3#1
0.86
0.86
162.7
160.2
N1–H1BÁÁÁN2#2
2.16
2.989(2)
Symmetry transformations used to generate equivalent atoms. #1, x + 1/2,
Ày + 3/2, Àz + 1; #2, Àx + 1/2, y À 1/2, z.
Fig. 4. Schematic drawings of the HOMO and LUMO of compound 1.
Fig. 3. View of the three-dimensional supramolecular assembly of compound 1. The SÁÁÁS interactions are shown by green dashed lines. Symmetry code for
the generated atoms: #3, Àx, y À 0.5, Àz + 0.5.

358
Y. Cao et al. / Journal of Molecular Structure 888 (2008) 354–359
C3–C2–C4. These further demonstrate that there exists the
delocalization of the conjugated p-electron system in the
molecule of compound 1.
3.3.2. The observed and calculated fundamental modes of
vibrations
Vibrational spectroscopy has not only contributed to
structural studies of molecules, but also provides additional
insight into other properties such as molecular conforma-
tional behavior, interaction with the solvent and other mol-
ecules, and even biological activity [26]. Whereas, the
achievements of these objectives must be dependent on
the veracious vibrational assignment of the title com-
pounds. To the best of our knowledge, there have been
no complete experimental vibrational data and no quan-
tum mechanical calculations on the molecule with dithiol-
ethione ring to examine the proposed vibrational
assignments.
Fig. 5. The experimental and simulated infrared spectra of compound 1.
Here, we report the vibrational analysis of compound 1.
The experimental and theoretical vibrational wavenumbers
as well as the assignments (based on the scaled B3LYP/6-
31+G(d,p) force field) are listed in Table 4. The calculated
and stimulated absorption spectra are shown in Fig. 5.
As shown in Fig. 5, the assignments of frequencies
show a one-to-one correspondence and good agreement
between the observed and calculated fundamentals except
those of the t(N–H) and t(C„N). According to the cal-
culation, the asymmetric and symmetric N–H stretching
modes are predicated at 3718 and 3578 cmÀ1, whereas
the observed corresponding bands are at 3270 and
3174 cmÀ1 in the IR spectrum. The great differences
between the calculated and observed frequencies are due
to the significant environmental dependence of the N–H
stretching vibration. In other words, the calculated fre-
quencies were obtained from an isolated molecule, with-
out taking into account the strong intermolecular
hydrogen bonds existing in crystal, which caused the
remarkable differences. The stretching mode of C„N
bond is observed at 2215 cmÀ1 and calculated at
2318 cmÀ1. As discussed above, the difference is also
caused by the hydrogen bonding in the experimental sys-
tem. The observed bands at 1627 and 1206 cmÀ1 are
assignment to the in-plane scissoring and rocking vibra-
tion modes of N-H, which are associated with the simu-
lated signal at 1657 and 1168 cmÀ1
,
respectively.
According to the point of Rimai et al., the C=C stretch-
ing mode is a sensitive indication of charge delocalization
[27]. Thus, the bond alternation should results in a shift
of the C@C bond stretching mode to lower frequency.
For compound 1, the predicated C@C bond stretching
mode is at 1527 cmÀ1, while the observed C@C bond
stretching mode is at a rather lower frequency (1505
cmÀ1). The experimental IR band at 501 cmÀ1 is due to
the stretching mode of the S–S bond [28,29], which corre-
sponds to the calculated frequency at 460 cmÀ1. The rest
stretching modes are delocalized over several atoms and
thus cannot be assigned to the local bonds. This is a
characteristic feature of cyclic compounds, particularly
aromatic compounds [30]. Therefore the tentative assign-
ments were provided in Table 4.
Table 4
Comparison of the experimental and calculated vibrational frequencies
(cmÀ1) and tentative assignment for compound 1 (vs, very strong; s,
strong; m, medium; w, weak; vw, very weak)
Assignment
Observed
Calculated
tas(N–H)
ts(N–H)
t(C„N)
r(N–H)
t(C@C)
tas(C@C–C)
ts(C@C–C)
3270 w
3147 m
2215 m
1627 s
1505 vs
1398 m
1322 s
1206 w
1006 s
892 m
797 w
3718
3578
2318
1657
1527
1398
1335
1168
1046
870
4. Conclusion
In summary, we have discovered an one-pot reaction
leading to a novel derivative of D3T, compound 1, starting
from K2(i-mnt) and NbCl5 at room temperature. In the
compound, molecules are self-assembled into a 3D infinite
supramolecular architecture by intermolecular hydrogen
bonding and SÁÁÁS interactions. The structure of isolated
molecule has been optimized by DFT method using 6-
31G+(d,p) basis set. The frontier orbital properties of com-
pound 1 have been reported and discussed. A detailed
q(N–H)
t(C@S) + q(N–H)
t(C–S) + q(N–H)
q(N–H) + q(C@CAC)
c(C@CAC)
d(C„N) + d(C–S)
ts (S–S)
795
637
547
460
611 m
552 w
501 w
x(N–H) + s(C@S)
440 vw
432

Y. Cao et al. / Journal of Molecular Structure 888 (2008) 354–359
359
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assignment of the fundamental vibrational modes is pro-
posed on the basis of the DFT calculations.
Acknowledgements
[18] S.G. Liu, Y.Q. Liu, Y.F. Li, D.B. Zhu, Synthetic Met. 83 (1996)
131.
We thank Dr. Zhi Ji for many useful suggestions in the
DFT calculations. This work was financially supported by
the State Key Laboratory of Structure Chemistry, Fujian
Institute of Research on the Structure of Matter, Chinese
Academy of Sciences, and the Young Talent Programmed
of Fujian Province (Project No. 2006F3072).
[19] G.M. Sheldrick, shelxtl 6.1, Crystallographic Computing System,
Bruker Analytical X-Ray System, Madison, WI, 2000.
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Appendix A. Supplementary data
Supplementary data associated with this article can be
found, in the online version, at doi:10.1016/j.molstruc.
2007.12.034.
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