Anagostic interactions, revisiting the crystal structure of nickel dithiocarbamate complex and its antibacterial and antifungal studies

Article abstract of DOI:10.1016/j.poly.2010.09.023

The synthesis of Ni(dtc)₂ [dtc = diethyldithiocarbamate] has been achieved by the interaction of NiL(ClO₄)₂ with sodium diethyldithiocarbamate. Although single crystal structure of this complex was already reported (R = 10.6%), we were able to refine crystal structure up to R = 2.99%. We also observed rare C-H?Ni anagostic interactions generally exhibited by d⁸ complexes which were overlooked previously. To investigate the structure of Ni(dtc)₂ in solution, variable temperature NMR spectra in solution have also been recorded between 25 and -50 °C. Ni(dtc)₂ was also tested for antibacterial and antifungal activities. It showed higher activity against the bacteria and fungi than the known antibiotics.

Full text of DOI:10.1016/j.poly.2010.09.023

Polyhedron 30 (2011) 33–40
Contents lists available at ScienceDirect
Polyhedron
journal homepage: www.elsevier.com/locate/poly
Anagostic interactions, revisiting the crystal structure of nickel
dithiocarbamate complex and its antibacterial and antifungal studies
Ahmad Husain a, Shahab A.A. Nami b, Suneel P. Singh c, M. Oves d, K.S. Siddiqi a,
⇑
a Department of Chemistry, Aligarh Muslim University, Aligarh 202002, India
b Department of Kulliyat, Faculty of Unani Medicine, Aligarh Muslim University, Aligarh 202002, India
c Department of Chemistry, University of Guelph, Guelph, Ontario, Canada N1G 2W1
d Department of Microbiology, Faculty of Agriculture, Aligarh Muslim University, Aligarh 202002, India
a r t i c l e i n f o
a b s t r a c t
Article history:
Received 27 July 2010
Accepted 21 September 2010
Available online 29 September 2010
The synthesis of Ni(dtc)2 [dtc = diethyldithiocarbamate] has been achieved by the interaction of
NiL(ClO4)2 with sodium diethyldithiocarbamate. Although single crystal structure of this complex was
already reported (R = 10.6%), we were able to refine crystal structure up to R = 2.99%. We also observed
rare C–Hꢀ ꢀ ꢀNi anagostic interactions generally exhibited by d8 complexes which were overlooked previ-
ously. To investigate the structure of Ni(dtc)2 in solution, variable temperature NMR spectra in solution
have also been recorded between 25 and ꢁ50 °C. Ni(dtc)2 was also tested for antibacterial and antifungal
activities. It showed higher activity against the bacteria and fungi than the known antibiotics.
Ó 2010 Elsevier Ltd. All rights reserved.
Keywords:
Anagostic interactions
Crystal structure
Square planar Ni(II) dithiocarbamate
Supramolecular synthons
1. Introduction
diethyldithiocarbamate which resulted in a ligand transfer reac-
tion. The resulting compound was characterized as Ni(dtc)2 by sin-
Dithiocarbamate based coordination complexes have been thor-
oughly studied because of their ability to coordinate many com-
mon metal ions in different binding modes [1]. They have been
shown to possess a broad spectrum of biological activities such
as fungicidal [2,3] and bactericidal [4,5]. The antibacterial and anti-
fungal activities of dithiocarbamates were reported to arise by the
reaction with HS-groups of the physiologically important enzymes
by transferring the alkyl group of the dithioester to the HS-function
of the enzyme [5]. All dithiocarbamates contain the characteristic
disulfur moiety that binds metal ions in monodentate or bidentate
fashion. The nitrogen may be functionalized in various ways to
modify the physico-chemical properties of the ensuing metal com-
plex, particularly its solubility and lipophilicity [6]. The dithiocar-
bamate core, M–S2CNR2 (M = Metal, R = Alkyl) could prove to be
of great synthetic utility since a wide variety of organic substitu-
ents can be incorporated in this stable bidentate ligand system. It
gives rise to the chemical ‘fine-tuning’ of the biological properties
of the complex by variation of the substituent R in M–S2CNR2 [7].
Recently, we have explored the chemistry of [Ni(L)][CoCl4]
gle crystal X-ray diffraction and other spectroscopic studies and
evaluated for antibacterial and antimicrobial properties.
2. Experimental
2.1. Materials and methods
Reagent grade sample of NiCl2.6H2O, sodium diethyldithiocar-
bamate (Fluka), ethylenediamine (Acros), Ammonia solution
(25%) and formaldehyde (S.D. Fine) were used as received and all
experiments were carried out in an open atmosphere. All solvents
were purchased from Merck India and used after purification. Ele-
mental analyses (C, H, N and S) were carried out with a Carlo Erba
EA-1108 analyzer. IR spectra (4000–400 cmꢁ1) were recorded with
a RXI FT-IR spectrometer as KBr disc. The NMR spectra were re-
corded with a BRUKER AV-400 in CDCl3.Caution! Although our
samples never exploded during handling, perchlorate metal com-
plexes are potentially explosive: they should be handled with care.
[where
L = 3,7-bis(2-aminoethyl)-1,3,5,7-tetraazabicyclo(3.3.1)-
2.2. Synthesis
nonane] complex [8]. As an extension of our previous findings,
we report in this paper the reaction of NiL(ClO4)2 with sodium
[Ni(L)(ClO4)2] [where L = 3,7-bis(2-aminoethyl)-1,3,5,7-tetraaz-
abicyclo(3.3.1)nonane] was synthesized as reported earlier [9].
To an aqueous solution of [Ni(L)(ClO4)2] (5 mM, 2.36 g) an etha-
nolic solution of sodium diethyldithiocarbamate (10 mM, 1.69 g)
were added dropwise with continuous stirring. The solution
⇑
Corresponding author.
E-mail addresses: ahmad.chem786@hotmail.com (A. Husain), ks_siddiqi@yahoo.
co.in (K.S. Siddiqi).
0277-5387/$ - see front matter Ó 2010 Elsevier Ltd. All rights reserved.
doi:10.1016/j.poly.2010.09.023

34
A. Husain et al. / Polyhedron 30 (2011) 33–40
Scheme 1. Synthesis of Ni(dtc)2.
immediately turned green followed by the formation of dark green
precipitate which was filtered and washed several times with dis-
tilled water and dried in vacuo. The resulting compound was char-
acterized as Ni(dtc)2 (Scheme 1) by spectroscopic studies. In a
competing process, the Ni(L)(ClO4)2 complex undergoes demetala-
tion immediately due to sodium diethyldithiocarbamate to yield
nickel(II) bis(N,N-diethyldithiocarbamate). X-ray quality crystals
of Ni(dtc)2 were grown by slow evaporation of chloroform solution
at room temperature. Yield: 58%. M.p. 537 K. 1H NMR (CDCl3;
400 MHz, d ppm): 1.23 (t, J = 7.2 Hz, 12H, CH3), 3.6 (q, J = 14.4 Hz,
100(2) K using graphite monochromated Mo Ka radiation (k )
a
0.71073 Å. The frames were indexed, integrated, and scaled using
the SMART and SAINT software package [10] and the data were cor-
rected for absorption using the SADABS [11] program. The structure
was solved by direct method and refined using the SHELX-97 [12]
suite of programs, while additional crystallographic calculations
were performed by the program PLATON [13]. Figures were drawn
using ORTEP-3.2 [14a] and MERCURY-2.3 [14b]. The hydrogen
atoms were included at geometrically calculated positions in the fi-
nal stages of the refinement and were refined according to the ‘‘rid-
ing model”. All non-hydrogen atoms were refined with anisotropic
thermal parameters.
8H, CH2). IR (
m
cmꢁ1, KBr):
m
(CSS) 993,
m
(Cꢀ ꢀ ꢀN) 1517; Anal. Calc.
for C10H20N2NiS4: C, 33.83; H, 5.68; N, 7.89; S, 36.06; Ni, 16.54.
Found: C, 33.40; H, 5.45; N, 7.76; S, 35.95; Ni, 16.65%.
3. Results and discussion
2.3. Crystal structure determination
3.1. Crystal structure description of [Ni(dtc)2]
Single-crystal X-ray structural study was performed on a CCD
Bruker SMART APEX Diffractometer equipped with an Oxford
Instrument low-temperature attachment. Data were collected at
The molecular structure of the [Ni(dtc)2] complex along with
the atomic numbering scheme is shown in Fig. 1, Crystallographic
Fig. 1. Molecular structure of Ni(dtc)2 depicting the Niꢀ ꢀ ꢀH and Sꢀ ꢀ ꢀH interactions. (MERCURY software has been used for the drawing, bond lengths have been measured in
angstrom; only the atoms involving in the interactions are labeled for clarity).

A. Husain et al. / Polyhedron 30 (2011) 33–40
35
Table 1
units of Ni(dtc)2 (Fig. 2). The unit cell parameters were found to
0
Crystallographic data for nickel(II) bis(N,N-diethyldithiocarbamate).
be a = 6.0080 (12), b = 11.441 (2), c = 11.543 (2) ÅA, b = 95.98 (3)°
which are considerably different from that reported by Bonamico
et al. [15], Selvaraju and Panchanatheswaran [16] Khan et al. [17]
and Hogarth et al. [1]. The major change takes place in the refine-
ment factor, R which is improved from 10.6% to 2.99%. Two inde-
pendent dithiocarbamate moiety coordinate to the nickel atom to
form the complex. The nickel atom is four-coordinated with two
sulfur atoms of each diethyldithiocarbamate ligand giving rise to
a square planar arrangement. The bond angle of four-membered
chelate rings around the Ni(II) is 109.75° which is in close proxim-
ity with a square planar Ni(II) ion. The near equality of the two Ni–
S and two C–S distances confirm the isobidentate coordination of
the dithiocarbamate group. The difference between the Ni–S1
and Ni–S2 bond lengths is only 0.001 (6). For comparison, the cor-
responding differences were 0.012 in the previous determination.
The accuracy in the C1–N bond length of 1.317 (3) is an order of
magnitude higher than that reported earlier [1.33 (10)/ꢂ]. The Ni
Empirical formula
Formula weight
Melting point (K)
Crystal system
Space group
T (K)
a (Å)
b (Å)
c (Å)
C10H20N2NiS4
355.25
537
monoclinic
P21/c
298
6.0080 (12)
11.441 (2)
11.543 (2)
95.98 (3)
789.1 (3)
2
b (°)
V (Å3)
Z
qcalc (g cmꢁ3
)
1.495
1.74
372
l
(mmꢁ1
F(0 0 0)
)
Crystal size (mm)
h Range for data collection (°)
Index ranges
0.25 ꢄ 0.12 ꢄ 0.09
2.2–25.5
ꢁ7 ꢅ h ꢅ 6; ꢁ13 ꢅ k ꢅ 13;
ꢁ9 ꢅ l ꢅ 13
4127
Number of reflections collected
Number of independent reflections
atom lies on a centre of symmetry and participates in two short
0
1460 (0.038)
symmetrically related Niꢀ ꢀ ꢀH contacts of 2.665 ÅA with H3A atoms
attached to C3 [symmetry code: (i) ꢁx + 1, ꢁy + 1, ꢁz + 1]. The tor-
sion angles C1–N1–C5–S2 [ꢁ5.2 (3)°], C1–N1–C5–S1 [174.6 (2)°],
C3–N1–C5–S1 [ꢁ2.1 (3)°] and C3–N1–C5–S2 [178.0 (2)°] confirm
the near planarity of the S2CNR2 moiety.
In an attempt to understand the supramolecular arrangement of
the Ni(dtc)2 molecules, the packing and hydrogen bonding interac-
tions between the molecules were analyzed in detail. The packing
and Niꢀ ꢀ ꢀH bonding interactions viewed along the a-axis are shown
in Fig. 3. In addition to this, the hydrogen H3A of the methyl group
is also involved in an Sꢀ ꢀ ꢀH–C interaction propagating into a three
dimensional hydrogen bonded network (Figs. 4–7).
(Rint
)
Number of observed [I > 2
reflections
r
(I)]
1361
Number of data/restraints/parameters
1460/0/81
1.14
0.029
Goodness-of-fit (GOF) on F2
R[F2 > 2
r
(F2)]
wR(F2)
0.075
D
qmax and
Data completeness
D
qmin (e Åꢁ3
)
0.45 and ꢁ0.45
0.993
Table 2
Generally, there are three forms of C–Hꢀ ꢀ ꢀM interactions includ-
ing (i) hydrogen bond, (ii) agostic and (iii) anagostic [18]. Hydrogen
bonds (i) are 3-center-4-electron interactions with an almost linear
geometry accompanied by a downfield 1H NMR shift of the partic-
ipating H atom. Agostic Mꢀ ꢀ ꢀH–C interactions are usually referred
to as a 3-centre-2-electron interaction, resulting in a pronounced
highfield chemical shift of the corresponding H atom and charac-
terized by relatively short Mꢀ ꢀ ꢀH distances of ꢃ1.8–2.2 Å and C–
Hꢀ ꢀ ꢀM bond angles of ꢃ90–130°. Such interactions are often found
in d6 complexes. Anagostic interactions [18–25] occurring (Fig. 3)
in square planar d8 systems are of broad general interest due to
possible implications for the mechanism of C–H activation [26–
27]. Anagostic interactions are characterized by relatively long
Mꢀ ꢀ ꢀH distances (ꢃ2.3–2.9 Å) and large Mꢀ ꢀ ꢀH–C bond angles
(ꢃ110–170°). In the present case Mꢀ ꢀ ꢀH distances is 2.665 Å and
Mꢀ ꢀ ꢀH–C bond angle is 142.4°. They are in between the hydrogen
bonds and agostic interactions, with characteristic downfield shifts
of the anagostic protons. Although the origin of these interactions
is still under debate it may involve donation of filled d2z or dxz/yz
Selected bond lengths (Å) and angles (°).
Bond lengths
Ni1–S2i
Ni1–S2
Ni1–S1
Ni1–S1i
S1–C5
2.2026 (8)
2.2026 (8)
2.2042 (6)
2.2042 (6)
1.719 (2)
1.724 (2)
1.317 (3)
1.467 (3)
1.478 (3)
1.525 (3)
0.9700
C1–H1B
C2–H2A
C2–H2B
C2–H2C
C3–C4
C3–H3A
C3–H3B
C4–H4A
C4–H4B
C4–H4C
0.9700
0.9600
0.9600
0.9600
1.515 (3)
0.9700
0.9700
0.9600
0.9600
0.9600
S2–C5
N1–C5
N1–C1
N1–C3
C1–C2
C1–H1A
Bond angles
S2i–Ni1–S2
S2i–Ni1–S1
S2–Ni1–S1
S2i–Ni1–S1i
S2–Ni1–S1i
S1–Ni1–S1i
C5–S1–Ni1
C5–S2–Ni1
C5–N1–C1
C5–N1–C3
C1–N1–C3
N1–C1–C2
N1–C1–H1A
C2–C1–H1A
N1–C1–H1B
C2–C1–H1B
H1A–C1–H1B
C1–C2–H2A
C1–C2–H2B
180.0
H2A–C2–H2B
C1–C2–H2C
H2A–C2–H2C
H2B–C2–H2C
N1–C3–C4
N1–C3–H3A
C4–C3–H3A
N1–C3–H3B
C4–C3–H3B
H3A–C3–H3B
C3–C4–H4A
C3–C4–H4B
H4A–C4–H4B
C3–C4–H4C
H4A–C4–H4C
H4B–C4–H4C
N1–C5–S1
109.5
109.5
109.5
109.5
111.62 (17)
109.3
109.3
109.3
109.3
108.0
109.5
109.5
109.5
109.5
109.5
109.5
100.57 (2)
79.43 (2)
79.43 (2)
100.57 (2)
180.0
85.38 (7)
85.31 (7)
121.19 (17)
121.42 (18)
117.31 (16)
111.15 (18)
109.4
109.4
109.4
109.4
108.0
109.5
109.5
orbitals of the metal center into the C–H
r* orbital [28]. The nature
of the anagostic Mꢀ ꢀ ꢀH–C interaction in a variety of square planar
d8 compounds was recently addressed theoretically by Zhang
et al. [29].
The methylene group to which the metal is attached through
anagostic-type bond, can be envisaged as a dative bond from the
X–H
a back-donation from the valence electron pairs of the metal into
the X–H * antibonding orbital of the neutral species.
r bonding orbital to the empty 4s orbital of the metal, and
124.82 (16)
125.44 (16)
109.74 (11)
N1–C5–S2
S1–C5–S2
r
A specific interaction C–Hꢀ ꢀ ꢀS (Figs. 4–6) apparently takes place
between the hydrogen atom of the second methylene group and
the thioureide sulfur. The existence of specific interactions C–
Hꢀ ꢀ ꢀS is manifested by anomalous downfield shift of the signal
from the corresponding proton. This observed shift may be due
to specific interaction C–Hꢀ ꢀ ꢀS, or it may be due to the influence
of anisotropy of the –CSS group [30], the interatomic Sꢀ ꢀ ꢀH distance
Symmetry code: (i) ꢁx + 1, ꢁy + 1, ꢁz + 1.
data, selected bond lengths and bond angles are given in Tables 1
and 2. [Ni(dtc)2] was crystallized in monoclinic system with P21/
c space group in body centered lattice. The unit cell contains two

36
A. Husain et al. / Polyhedron 30 (2011) 33–40
Fig. 2. Unit cell of Ni(dtc)2. Molecules have been shown as ORTEP diagram with 50% thermal ellipsoids. All hydrogen atoms have been omitted for clarity.
Fig. 3. Two dimensional packing diagram depicting the Niꢀ ꢀ ꢀH interactions bonded network along a-axis.
corresponding to the equilibrium geometry was found to be 3.0 Å,
equal to the sum of the van der Waals radii of the hydrogen
and sulfur atoms [31] and Sꢀ ꢀ ꢀH–C bond angle was found to be
171.7°.
sition data processing was performed with the MestReC NMR soft-
ware package [32]. The 1H NMR spectrum at room temperature
shows only a single set of signals, suggesting that the two ligands
are equivalent in solution. In the 1H NMR spectrum of Ni(dtc)2 the
–CH2– protons were observed at 3.54 ppm while in case of ligand it
was reported at 4.02 ppm. Interestingly, upon cooling the sample
to ꢁ50 °C the signals start to broaden. Similar observations have
also been reported for C–Hꢀ ꢀ ꢀM interactions in d8 square-planar
complexes of Pd(II) [33], Pt(II) [34] and Ni(II) [27,35] have been re-
ported recently.
3.2. 1H NMR studies
To investigate the structure of Ni(dtc)2 in solution, 1H NMR
spectra of the complex was recorded in CDCl3 solution at variable
temperatures ranging from 25 °C to ꢁ50 °C (Fig. 8). All post acqui-

A. Husain et al. / Polyhedron 30 (2011) 33–40
37
Fig. 4. Two dimensional packing diagram depicting the Sꢀ ꢀ ꢀH interactions bonded network along a-axis. Hydrogen atoms except those involving in interaction have been
omitted for clarity. Ni – green, S – yellow, N – sky blue, C – dark grey, H – light grey. (For interpretation of the references to colour in this figure legend, the reader is referred to
the web version of this article.)
Fig. 5. 1D packing diagram depicting the Sꢀ ꢀ ꢀH interactions bonded network along b-axis.

38
A. Husain et al. / Polyhedron 30 (2011) 33–40
Fig. 6. 3D packing diagram depicting the Sꢀ ꢀ ꢀH interactions bonded network along c-axis.
Fig. 7. 3D packing diagram of the three dimensional coordination network showing the staggered arrangement of adjacent sheets depicting the Niꢀ ꢀ ꢀH and Sꢀ ꢀ ꢀH interactions.
4. Biological activity
thuringiensiso and Pseudomonas aeruginosa) and three fungal
strains (Aspergillus nigrus, Fusarium oxysporum and Penicillium
The antibacterial and antifungal activity of Ni(dtc)2 was deter-
mined against three bacterial strains (Escherichia coli, Bacillus
chrysogenum) and the concentration of the complex was kept at
0.5 mg mlꢁ1 in DMSO and compared with known antibiotics viz

A. Husain et al. / Polyhedron 30 (2011) 33–40
39
Fig. 8. 1H NMR spectrum of Ni(dtc)2 at different temperatures.
Tetracycline and Nystatin (Table 3) at the same concentration. The
biological activity of Ni(II) dithiocarbamate complexes is well doc-
umented [36–41]. The agar well-diffusion method [42] was used
for antibacterial and antifungal studies in this assay and each

40
A. Husain et al. / Polyhedron 30 (2011) 33–40
Table 3
Mean zone of inhibition (mm stdev).
Antibacterial assay
Bacteria
Antifungal assay
Ni(dtc)2
Tetracycline
Fungi
Ni(dtc)2
Nystatin
E. coli (mm stdev)
P. aeruginosa (mm stdev)
B. thuringiensis (mm stdev)
25.5 0.5
27.4 0.6
31.0 0.3
17.0 0.5
15.0 0.5
18.0 0.4
A. nigrus (mm stdev)
F. oxysporum (mm stdev)
P. chrysogenum (mm stdev)
21.5 0.5
27.4 0.6
24.0 0.3
18.0 0.4
14.2 0.4
20.0 0.5
[8] S.A.A. Nami, A. Husain, K.S. Siddiqi, B.L. Westcott, K. Kopp-Vaughn,
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of Gottingen, Gottingen, Germany, 1999.
[12] (a) SHELXTL Package v. 6.10; Bruker AXS: Madison, WI, 2000.;
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experiment was performed in triplicate. The radial growth of the
colony was recorded on completion of the incubation, and the
mean diameter was recorded. The complex showed higher activity
against the bacteria and fungi than the known antibiotics. Area of
zone of inhibition was used as a criterion to ascertain the biocidal
activity. The screening data are reported in Table 3. The 20 mm
zone of inhibition represents significant activity, for 10–12 mm
inhibition activity is good, 7–9 mm is low, and below 7 mm the
activity is insignificant. The Ni(dtc)2 shown remarkable antibacte-
rial and antifungal activity against these pathogens.
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5. Conclusion
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The crystal structure of nickel(II) bis(N,N-diethyldithiocarba-
mate) has been revisited and refine up to R = 2.99%. This paper
reports a rare Niꢀ ꢀ ꢀH anagostic interaction evidenced by the crystal
structure of Ni(dtc)2. The complex showed higher antibacterial and
antifungal activities than the slandered antibiotics. Ni(dtc)2
showed highest activity for B. thuringiensis and F. oxysporum.
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Department of Chemistry, I.I.T, Kanpur India is gratefully
acknowledged for providing single crystal X-ray facility. We are
grateful to the Council of Scientific and Industrial Research, New
Delhi (research scheme No. 21(0685)/07 EMR-II) for the financial
support. One of us (SAAN) thanks Department of Science & Tech-
nology for financial assistance under SERC FAST Scheme, No. SR/
FT/CS-031/2008, NewDelhi, India.
Appendix A. Supplementary data
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CCDC 682361 contains the supplementary crystallographic data
for Ni(dtc)2. This data can be obtained free of charge via http://
www.ccdc.cam.ac.uk/conts/retrieving.html, or from the Cambridge
Crystallographic Data Centre, 12 Union Road, Cambridge CB2 1EZ,
UK; fax: (+44) 1223-336-033; or e-mail: deposit@ccdc.cam.ac.uk.
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