Syntheses, studies and crystal structure of new coordination polymers of mercury (II) with phenylcyanamide derivative ligands

Article abstract of DOI:10.1016/j.ica.2014.03.016

A series of compounds mercury (II), [Hg(CH₂COCH ₃)L]_n where L = anion of 4-NO₂pcyd (4-nitro phenylcyanamide) (1), 4-Clpcyd (4-chloro phenylcyanamide) (2), 4-Brpcyd (4-bromo phenylcyanamide) (3) were synthesized from acetone and characterized by elemental analysis, IR, ¹H NMR, ¹³C NMR and electronic absorption spectroscopies. Single crystal X ray analysis of 1 reveals coordination of phenylcyanamide ligand to Hg (II) unexpectedly occurred through amine nitrogen alone which is rare. Also the anion of acetone was coordinated to mercury by the carbon atom as well as oxygen atom from (CO) of another acetone anion. A theoretical study at DFT (B3LYP) level showed that the experimentally determined structure of the complex 1 is about 6.49 and 8.31 kcal/mol, respectively in the gas phase and solvent more stable than its other bonding modes. In addition, this phenomenon was supported by NBO interaction energies and the much orbital contribution in the HOMO of ligand to interact with Hg (II) that all of these observations were raised from the presence of nitro group as electron withdrawing group. By using TD-DFT method, electronic absorption spectra of the compound 1 have been predicted and a good agreement with the TD-DFT method and the experimental one is determined. Biological studies show the antibacterial activity of the complex 1 against Gram-positive and Gram-negative bacterial strains.

Full text of DOI:10.1016/j.ica.2014.03.016

Accepted Manuscript
Syntheses, studies and crystal structure of new coordination polymers of mer-
cury (II) with phenylcyanamide derivative ligands
Hossein Chiniforoshan, Nasimeh Pourrahim, Leila Tabrizi, Hossein Tavakol,
Mohammad R. Sabzalian, Behrouz Notash
PII:
S0020-1693(14)00161-3
http://dx.doi.org/10.1016/j.ica.2014.03.016
ICA 15916
DOI:
Reference:
Inorganica Chimica Acta
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9 March 2014
Please cite this article as: H. Chiniforoshan, N. Pourrahim, L. Tabrizi, H. Tavakol, M.R. Sabzalian, B. Notash,
Syntheses, studies and crystal structure of new coordination polymers of mercury (II) with phenylcyanamide
derivative ligands, Inorganica Chimica Acta (2014), doi: http://dx.doi.org/10.1016/j.ica.2014.03.016
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Syntheses, studies and crystal structure of new coordination polymers of
mercury (II) with phenylcyanamide derivative ligands
∗a
Hossein Chiniforoshan , Nasimeh Pourrahima, Leila Tabrizia, Hossein Tavakola, Mohammad R.
Sabzalianb Behrouz Notashc.
,
aDepartment of Chemistry, Isfahan University of Technology, Isfahan 84156-83111, Iran
bDepartment of Agronomy and Plant Breeding, College of Agriculture, Isfahan University of Technology
cDepartment of Chemistry, Shahid Beheshti University, Evin, Tehran 1983963113, Iran
Abstract
A series of compounds mercury (II), [Hg(CH2COCH3)L]n where L= anion of 4-NO2pcyd (4-
nitro phenylcyanamide) (1), 4-Clpcyd (4-chloro phenylcyanamide) (2), 4-Brpcyd (4-bromo
phenylcyanamide) (3) were synthesized from acetone and characterized by elemental
1
analysis, IR, H NMR, 13C NMR and electronic absorption spectroscopies. Single crystal X
ray analysis of 1 reveals coordination of phenylcyanamide ligand to Hg (II) unexpectedly
occurred through amine nitrogen alone which is rare. Also the anion of acetone was
coordinated to mercury by the carbon atom as well as oxygen atom from (C=O) of another
acetone anion. A theoretical study at DFT (B3LYP) level showed that the experimentally
determined structure of the complex 1 is about 6.49kcal/mol and 8.31kcal/mol, respectively
in the gas phase and solvent more stable than its other bonding modes. In addition, this
phenomenon was supported by NBO interaction energies and the much orbital contribution in
the HOMO of ligand to interact with Hg (II) that all of these observations were raised from
the presence of nitro group as electron withdrawing group. By using TD-DFT method,
electronic absorption spectra of the compound 1 have been predicted and a good agreement
with the TD-DFT method and the experimental one is determined. Biological studies show
the antibacterial activity of the complex 1 against Gram-positive and Gram-negative bacterial
strains.
∗Corresponding author: H. Chiniforoshan; Email: Chinif@cc.iut.ac.ir
Tel: +983113913261; fax: +983113912350
1

Keywords: Mercury (II) complex; Coordination polymer; Phenylcyanamide; NMR spectra,
Theoretical calculation, Antibacterial agent.
1. Introduction
Coordination polymers of organomercury derivatives are widely investigated in recent
years, not only for their potential applications [1–3] but also for their attractive flexibility in
building up extended structures [4–7]. Coordination polymers based on the soft Hg (II) ion
are much less predictable in respect to coordination number at the metal [8] and represent a
synthetic challenge to crystal engineering.
In some respects, anionic phenylcyanamides behave as pseudohalides in their ligating
properties. However, the attachment of a phenyl ring to the cyanamide group (NCN) adds an
extra dimension not present in azide or thiocyanate ligands. An extensive π conjugation
between the cyanamide group and the phenyl ring provides an energetically favorable means
by which a metal ion can couple into a conjugated organic π system [9]. And so, overall, they
are ambidentate in nature exhibiting three different coordination modes, namely (i)
monodentate via the cyano nitrogen, (ii) µ-1,3-bridging through both the amino and cyano
nitrogens and (iii) µ-1,1-bridging via the cyano nitrogen [10]. The amine nitrogen is sterically
crowded by the phenyl ring and so terminal coordination to the cyano nitrogen is expected.
There are many crystal structures of monodentate phenylcyanamide ligands showing
coordination through the cyano nitrogen but there were a few examples of amine nitrogen
coordination that coordinate through the amine alone [11]. In this study, a series of novel
polymer complexes of the of [Hg(CH2COCH3)L]n , where L=4- nitro phenylcyanamide (4-
NO2pcyd) (1), 4-chloro phenylcyanamide (4-Clpcyd) (2), 4-bromo phenylcyanamide (4-
Brpcyd) (3), a phenylcyanamide anion ligand, has been synthesized and characterized by IR,
1H NMR and 13C NMR spectroscopies and it has been shown that coordination of
phenylcyanamide ligand to Hg (II) unexpectedly occurred through amine nitrogen alone
2

which is rare [11]. Another interesting phenomenon in this study is formation of an
organometallic compound that has been produced by linkage of the terminal anionic carbon
atom of acetone to a metal ion. A crystal structure determination of the complex
[Hg(CH2COCH3)(4-NO2pcyd)]n as well as the density functional theory (DFT) has been
performed. We also make comparisons between experiments and calculations. Also
antibacterial assay over Gram-positive and Gram-negative pathogenic bacterial strains was
studied.
2. Experimental section
2.1. Materials
The phenylcyanamide ligands were prepared in air according to the literature procedure [12]
and used without further purification. All chemicals and solvents were highly pure Merck
compounds and used without any further purification.
Caution! Mercury and its compounds are toxic [13].
2.2. Methods and Instrumentation
Fourier transform infrared spectra were recorded on a FT-IR JASCO 680-PLUS spectrometer
in the region of 4000–400 cm-1 using KBr pellets. Electronic spectra were obtained using a
1
UV-JASCO-570 spectrometer. H NMR and 13C NMR spectra were recorded on a Bruker
DRX-500 MHz Avance spectrometer at 100 K in DMSO-d6 with tetramethylsilane (TMS; δ
= 0 ppm) as internal standard. Elemental analyses were performed by using a Leco, CHNS-
932 elemental analyzer.
2.3 X-ray structural determination of [Hg(CH2COCH3)(4-NO2pcyd)]n (1)
A yellow needle crystal with a dimension of 0.28×0.18×0.10 mm3 was mounted on a glass
fiber and used for data collection. All measurements were made on a STOE IPDS-II
diffractometer with graphite monochromated Mo Kα radiation. Cell constants and an
3

orientation matrix for data collection were obtained by least-squares refinement of diffraction
data from 6799 unique reflections. Data were collected at a temperature of 298(2)K to a
maximum 2ϴ value of 58.4 and in a series of ω scans in 1° oscillations and integrated using
the STOE X-AREA software package [14]. A numerical absorption correction was applied
using X-RED [15] and X-SHAPE [16] software’s. The data were corrected for Lorentz and
Polarizing effects. The structure was solved by direct methods [17] and subsequent difference
Fourier maps and then refined on F2 by a full-matrix least-squares procedure using
anisotropic displacement parameters [16]. All of hydrogen atoms were located in a difference
Fourier map and thereafter refined isotropically. Crystallographic data and details of the data
collection and structure refinements are listed in Table 1.
Table1.
2.4. Synthesis of mercury (II) complexes
2.4.1. [Hg(CH2COCH3)(4-NO2pcyd)]n (1)
The ligand of 4-NO2-pcyd (0.2 mmol, 33 mg) was deprotonated by reaction with NaOH
(0.4 mmol, 16 mg) in acetone (10 ml) with stirring at reflux temperature overnight. The
resulting solution was added to a stirred solution of Hg(NO3)2.H2O (0.2 mmol, 68 mg) in
acetone (15 ml) and the reaction mixture was stirred at reflux temperature for 4 hours and
then the resulting reaction mixture left at room temperature and allowed to air dry. Yellow
crystals of [Hg (CH2COCH3)(4-NO2pcyd)]n were grown after days. Yield: 65%. Anal. Calc.
(%): C, 28.61; H, 2.16; N, 10.01; and Found (%): C, 28.59; H, 2.14; N, 9.98. Selected FT-IR
data, ν(cm-1): ν(C≡N): 2140(vs), ν(CO): 1726.3(vs), ν(NO2):1590.02, 1310.39(s), ν(C−N):
1
1125(m) (see Supplementary material). H-NMR (DMSO): 1.18(s, 3H), 2.14 (s, 1H),
2.61 (s, 1H), 6.82 (d, 2H), 7.62(d, 2H) ppm. 13C–{1H} NMR (DMSO): 30.25(CH3),
4

56.41(CH2), 120.10(C7), 124.13(C2,6), 126.75(C4), 131.90(C3,5), 153.04(C1) and
216.90(CO) ppm (Scheme1).
2.4.2. [Hg(CH2COCH3)(4-Clpcyd)]n (2)
Complex 2 was prepared in a similar way to 1 with the use of ligand of 4-Cl-pcyd (0.2
mmol, 30.5mg) instead of 4-NO2-pcyd. The white solid obtained was vacuum filtered,
washed with acetone, and dried in desiccator over CaCl2. Yield: 77%. Anal. Calc. (%): C,
29.35; H, 2.22; N, 6.85; and Found (%): C, 29.33; H, 2.19; N, 6.81. Selected FT-IR data,
ν(cm-1): ν(C≡N): 2190(vs), ν(CO): 1728.2(vs), ν(C−N): 1165(m) (see Supplementary
1
material). H-NMR (DMSO): 1.15(s, 3H), 2.12 (s, 1H), 2.49 (s, 1H), 6.65 (d, 2H),
6.98(d, 2H) ppm. 13C–{1H} NMR (DMSO): 30.20(CH3), 56.38(CH2), 119.03(C7),
120.12(C2,6), 126.56(C4), 128.66(C3,5), 152.70(C1) and 216.65(CO) ppm (Scheme1).
2.4.3. [Hg(CH2COCH3)(4-Brpcyd)]n (3)
Complex 3 was prepared in a similar way to 1 with the use of ligand of 4-Br-pcyd (0.2
mmol, 39.4mg) instead of 4-NO2-pcyd. The white solid obtained was vacuum filtered,
washed with acetone, and dried in desiccator over CaCl2. Yield: 70%. Anal. Calc. (%): C,
26.47; H, 2.00; N, 6.17; and Found (%): C, 26.45; H, 1.97; N, 6.14. Selected FT-IR data, ν
(cm-1): ν(C≡N): 2183(vs), ν(CO): 1725.4(vs), ν(C−N): 1070(m) (see Supplementary
1
material). H-NMR (DMSO): 1.16(s, 3H), 2.10 (s, 1H), 2.57 (s, 1H), 6.68 (d, 2H),
7.14(d, 2H) ppm. 13C–{1H} NMR (DMSO): 30.21(CH3), 56.29(CH2), 107.57(C7),
120.96(C2,6), 126.44(C4), 131.64(C3,5), 151.94(C1) and 216.10(CO) ppm (Scheme1).
2.5. Computational methods
The geometry optimizations, frequency calculations (including energies) and population
analyses were performed employing Gaussian 09 program package [18]. In addition, natural
5

bond orbital calculations (NBO) were used to obtain the natural atomic charges and second-
order perturbation energies (to estimate the values of intermolecular interactions) [19]; this
method is implemented in the Gaussian program package. Solvent effects in acetone (reaction
solvent) were determined by calculation of free energies of solvation using SCRF keyword at
Tomasi's polarized continuum (PCM) model [20]. All calculations were performed using
DFT calculations at CAM-B3LYP/6-311+G* level of theory and carried out at room
temperature and standard pressure. Time-dependent density functional theory (TD-DFT)
calculations were employed to obtain the computational UV-Vis spectra of complex 1 and
these calculations were performed at TD CAM-B3LYP/6-311+G* level of theory. The
theoretical data were obtained after optimization of the molecular geometry without any
symmetry restriction.
2.6. Anti bactericidal assay
The free ligand of 4-NO2-pcyd and metal complex (1) were screened for their antimicrobial
activities against E.coli (Enterobacteriaceae) as the model from Gram-negative bacteria and
Salmonella aureus (Staphylococcaceae) as the model from Gram-positive bacteria by the disc
diffusion method. The method was designed to test the ability of antimicrobial agents quickly
and qualitatively in order to inhibit the growth of microorganisms over a short period of time.
After incubation, usually overnight or after a few days, a circular inhibition zone of microbial
growth appears around the disc of material as a result of antibiotic diffusion into the agar and
growth inhibition of the bacterial isolates. The zone sizes are compared and the bacterial
isolate is recorded as sensitive, intermediate or resistant to the applied material [21-23].
2.6.1. Preparation of Nutrient - Agar Medium
To prepare one litre of Nutrient-Agar (NA) medium, 5 g of peptone, 3 g of meat extract, 5 g
NaCl and 15 g agar were dissolved in 1000 ml of distilled water. The solution was sterilized
at 120 ° C for 20 min in an autoclave, and then 20 ml of culture medium was solidified in
6

each 35 cm Petri plate.
2.5.2. The inhibition zone test (disc diffusion method)
A microbial suspension (1 ml) of E. coli and Salmonella aureus was spread evenly over the
surface of nutrient agar plate (bacterial concentration was measured to be 108 per 50 micro-
liters). The ligand of 4-NO2-pcyd or metal complex (1) was separately applied to the centre of
agar plates as a disc with 12 mm diameter (10 mg of each) in three replicates (in a fashion
that the material doesn't spread out from the centre). Agar plates were then incubated for one
week at 25 2 ˚C and inhibition zone was monitored. The size of inhibition zone (diameter of
inhibition) was related to the level of antimicrobial activity present in the products.
3. Results and discussion
3.1. Synthesis and characterization
Phenylcyanamide derivatives can be readily prepared in high yields from the corresponding
anilines [12]. The polymer complexes of [Hg(CH2COCH3)L]n, (L=4-NO2pcyd, 4-Clpcyd, 4-
Brpcyd), have been prepared by the deprotonation of phenylcyanamide with sodium
hydroxide in acetone and the addition of this solution to a solution of Hg(NO3)2.H2O in
acetone. The infrared data for the anion of phenylcyanamide ligands and complexes of Hg
(II) are listed in Table 2 (data provided as Supplementary material). The identification of C-N
vibrations is a very difficult task, since mixing of several bands is possible in this region.
Silverstein and Webster [24] assigned C-N stretching absorption in the region 1382–1266 cm-
1 for aromatic amines. In the present, the bands observed in the region 1300–1100 cm-1 in FT-
IR spectrum have been assigned to C-N stretching vibrations. When the anion of
phenylcyanamide ligand coordinates to Hg (II), ν(C-N) is shifted to lower energies. The
ν(C≡N) bands observed in the region 2140–2190 cm-1 (Table 2) but there is no much
difference between the bands of the anion of ligand and the complexes suggesting the
7

importance of coordination of cyanamide via the amine nitrogen and locking in the negative
charge on the amine nitrogen. The ν (CO) appears at higher frequencies in comparison with
the parent acetone (1716 cm-1) which is in agreement with the shortening observed in the
C=O distance in complexes [25-27].
The protons NMR spectra of the pcyd ligands and complexes 1-3 (see Table 3) in DMSO-
d6 were clean and easily assigned. Up on coordination of pcyd ligands to Hg (II) the proton
chemical shifts decrease with respect to the free ligands. The protons of the methylene group
are not equivalent due to differences in their chemical environment when carbon is bonded to
mercury.
Table2.
Table3.
The 13C NMR spectrum of ligands and complexes in DMSO-d6 were also recorded (see
13
Table 4). The numbering for C-NMR data and pcyd- derivatives is shown in scheme 1. The
most interesting aspect of the 13C NMR spectra of the complexes is the shifts observed in the
carbons of nitrile and amine signals with respect to the free ligands, which indicate
coordination through the NCN group. The 13C NMR shifts of the CO group in complexes are
around 216 ppm, at a lower field than around 206 ppm noted for the same carbon in the
parent acetone, indicating much lower shielding of carbon of the CO group in these
complexes.
Electronic spectral data for the Hg (II) complexes in DMF are assembled in Table 5. The
bands in the region 260-270 and 400-450 nm correspond closely to ligand-centered π→π*
transitions [9,28,29]. In this study, the experimentally observed spectra of complex 1 showed
two bands at 267 nm (log ɛ = 3.18) and 451 (log ɛ = 3.85) nm. Electronic absorption spectra
of the compound 1 was calculated by the TD-DFT method based on the TD CAM-B3LYP/6-
311+G* level optimized structure in gas phase. For TD-DFT calculations, the theoretical
8

absorption bands are obtained at 446 nm with oscillator strength being 0.0195 and 274nm
with oscillator strength being 0.024 and can easily be seen that they correspond to the
experimental absorption ones.
scheme1
Table4.
Table5.
3.2. Structure description of 1
A crystal structure determination of the complex [Hg(CH2COCH3)(4-NO2pcyd)]n has been
performed and ORTEP diagram of the complex is shown in Fig.1. The anions of the
phenylcyanamide ligand and acetone solvent are coordinated to the Hg (II) ion. The
cyanamide group binds to Hg (II) only through the amine nitrogen and the acetone is
coordinated via carbon atom [C(8)]. The cyanamide groups are almost in the plane of the
benzene ring due to strong π-coupling between them. In addition, a bond length of 1.37(2)Å
between the amine nitrogen of cyanamides and aromatic carbon [C(2)-N(2)] suggests a great
deal of double-bond character and strong π interaction between the cyanamide groups and the
benzene ring. The bond angle formed by those atoms [C(8)-Hg-N(2)] is 175.6(7)˚ and the
NCN moiety is almost linear with the [N(1)-C (1)-N(2)] angle of 174(2)˚. Bond angles around
[C(2)-N(2)-C(1)], [C(2)-N(2)-Hg], [C(1)-N(2)-Hg] are 118.8(17)˚, 124.2(13)˚, 116.2 (13)˚
respectively and are close to 120˚ with the summation of the angles being 359.2˚ which it has
been in-plane. The dihedral angle between two planes of phenyl ring and [C(2)-C(1)-N(2)-
Hg] equals to 4.99˚ which shows an approximately planar structure. This suggests that the
amine nitrogen atoms make the connection by the double bond. Bond angle around [C(2)-
N(2)-Hg] is 124.2(13)˚, but as we expected bond angle around [C(1)-N(1)-Hg] unit is almost
linear with an angle close to 180˚ [11] that has less inhibition than the first. So we defined
two isomer b1 (bond of N(2)-Hg) and b2 (bond of N(1)-Hg) for determining theoretically
9

whether b1 is the major isomer and the reasons for this preference. The bond length [C(1)-
N(1)] and [C(2)-N(2)] is, respectively, 1.17 and 1.37Å. The C ≡ N bond length of nitrile and
the C = N bond length of imine group are respectively 1.136 and 1.279Å [30]. So, the bond
C(1)-N (1) is a quasi-triple bond and C(2)-N(2) is a quasi-double which is due to resonance
between the phenyl ring and N(2)-C(1)-N(1) moiety. Packing diagram of complex1 indicates
1D polymeric structure which Hg (II) centers in the polymers is three coordinated but with T-
shape coordination environment (see Fig.2), which is a common coordination type in mercury
chemistry [31,32]. The mercury atom is surrounded by one nitrogen atom of imine from
phenylcyanamide ligand with Hg–N distance of 2.120(17) Å and one carbon atom of the
acetone ligand with Hg–C distances of 2.097(19) Å and also one oxygen atom of from (C=O)
of another acetone anion with Hg–O distances of 2.820 (17) Å. The resulting Hg-O distance
of 2.820(17) Å is much shorter than the sum of the van der Waals radii for mercury (rvdw =
1.75 Å) [33] and oxygen (rvdw = 1.54 Å) [34] which indicating the presence of significant
bonding interactions between the mercury atom and the oxygen atom of acetone in the
molecular structure. Fractional atomic coordinates and equivalent isotropic displacement
coefficients (Ueq) for the non-hydrogen atoms of complex 1 are shown in Table S1
(Supplementary material).Table 6 lists key bond lengths and angles for complex1.
Fig.1.
Fig.2.
Table6.
3.3. Theoretical studies
Complex 1 has two isomers, b1 and b2, that are presented in Fig.3 in attendant with the
numbering scheme of the studied molecules. The isomer b1 is the unique isomer that was
characterized by X-ray crystal structure analysis. Of interest will be to determine theoretically
whether this is the major isomer and the reasons for this preference. In the b1 isomer, the
10

ligand (4-NO2pcyd, a) acts via amine nitrogen (N2) and in b2 isomer, the cyano nitrogen
(N1) binds to the metal. Our calculation showed that in gas phase and solvent (acetone, the
solvent of the reaction), b1 is the major isomer and it is more stable than b2 by 6.49kcal/mol
and 8.31kcal/mol, respectively in the gas phase and solvent. In addition to the calculated
stabilities, the para-nitro group is electron withdrawing group and adsorbs the electron
density of NCN toward the benzene ring and electron density is located on N2 more than N1
and the N2 is complexed to Hg, not N1. To make more insight about these isomers,
molecular parameters (bond lengths (Å) and bond angles) were extracted from the optimized
structures and compared with the observed X-Ray data in Table 7. Table shows that
calculated parameters of isomer b1 are in better agreement with the structure observed by X-
ray crystallography, although the calculated bond lengths are slightly different from measured
ones. Moreover, the value of the C(1)-N(2)-C(2)-C(3) dihedral angle (shown in the last rows
of the table) confirm planarity of the molecules.
NBO calculations are useful tools to calculate molecular properties such as precise atomic
charges (Table 8) and the interactions between important parts of molecules (second-order
perturbation energies, Table 9) with high precision. Table 8 presents natural atomic charges
in ligand (a) in addition to those for both isomers of complex 1 (b1 and b2). It is noticeable
that in ligand, more negative charge placed on N2 (-0.362 au) versus N1 (-0.337) that shows
why the complexation occurred at N2. In addition, in isomer b1, the absolute value of the
charge placed on the N2 atom is larger than that in the isomer b2. This shows that there is a
more effective interaction between the N2 atom and mercury rather than the N1 atom and
mercury. In Table 9, the most important interaction between ligand and mercury, obtained
from NBO second order perturbation energies (E2) are listed. These types of data are a
criterion of interaction strength in studied molecules. In our molecules, both important
interactions (lone pair of N to Hg and lone pair of N to σ*(Hg-C)) have remarkable larger
11

values in b1 versus b2. Therefore, since the strength of interaction between metal ion and
ligand is one of the factors that helpful in determining the stability of the studied complex,
these values confirm that in b1, the efficiency of this interaction is greater than that in b2.
In order to reveal the further coordinating interaction behaviors between ligand and Hg (II),
the frontier molecular orbitals and their density distribution analysis in ligand and two
isomers were presented. In the coordination process, the ligand is a Lewis base (electron pair
donor), while the Hg (II) acts as a Lewis acid (an electron pair acceptor). According to the
Frontier Molecular Orbital Theory (FMO theory) [35–37], the occupied orbitals of ligand
interact with the unoccupied orbitals of the Hg (II). EHOMO measures the electron donating
character of a compound, while ELUMO measures its electron accepting character. Thus, the
greater the EHOMO is, the greater the electron donating capability will be, and the smaller the
ELUMO is, the smaller the resistance to accept electrons will be. Fig.4 shows HOMO and
LUMO molecular orbitals for ligand and both isomers of complex 1. For the more stable
isomer (b1), ELUMO is low (-0.015 eV), whereas in the unstable isomer b2 has large value, -
0.024 eV. As a result, two isomers (b1 and b2) have the same HOMO level and since the
LUMO level of b1 is lower than b2, so isomer b1 is more stable than b2. Also our calculation
shows that in the HOMO of ligand, the contribution of the 2p orbital of nitrogen for N1 is
0.438 and for N2 is 0.608 and hence N2 has more contribution in HOMO. We know that
based on basic fundamentals of chemistry, each atom (or orbital) has the much contribution
in HOMO, this atom is the major place to start the nucleophilic attack and therefore it has
more effective interaction with Hg (II). All of these observations were raised from the
presence of nitro group as electron withdrawing group and show why b1 is the major isomer.
Fig.3
Fig.4
Table7.
12

Table8.
Table9.
3.4. Antibacterial assay
The results of the antibactericidal assay showed that the 4-NO2pcyd and complex1
exhibited a large inhibition zone indicating their antibacterial properties (Fig.5) and the
inhibitory zone values (mm) are summarized in Table 10. Generally, the diameter of
inhibition zone was more than 30 mm in both of 4-NO2-pcyd and Hg (II) complex (1) in E-
coli and Salmonella (Table 10), which represent probable sensitiveness of both Gram-
negative and Gram-positive bacteria to the compounds. Gwaram et al. [38] studying
antibacterial effects of some synthetic Schiff bases derived from 2-Acetylpyridine and their
metal complexes against Salmonella aureus showed that the diameter of inhibition zone
around the impregnated discs was more than 20 mm in some compounds.
Fig.5
Table10.
4. Conclusion
In the present work, we have synthesized and characterized three Hg (II) complexes of
phenylcyanamide derivatives, 1–3, and emphasis has been given to coordination of
phenylcyanamide ligand to Hg (II) through amine nitrogen alone which is rare. Also, the
anion of acetone was coordinated to mercury by the carbon atom as well as oxygen atom
from (C=O) of another acetone anion. X-ray crystal structure indicates 1D polymeric
structure with the Hg (II) centers in the polymers having a three coordinated T-shape
environment with the third position being taken up by an oxygen atom. The resulting Hg-O
distance is much shorter than the sum of the van der Waals radii for mercury and oxygen
indicating the presence of significant bonding interactions between the mercury atom and the
13

oxygen atom of acetone in the molecular structure. The result of theoretical study on the gas
and solvent phase showed that the experimentally determined structure of the complex 1 is
more stable than its other bonding modes that the para-nitro group as electron withdrawing
group is responsible for this phenomenon. The TD-DFT calculations of complex 1 lead to a
close agreement with the experimental absorption spectra in gas phase. The ligand of 4-
NO2pcyd and its complex were tested against Gram-positive (Salmonella aureus) and Gram-
negative bacteria (E.coli).The growth inhibition ring of E.coli and Salmonella was observed
in both, showing dramatic antibacterial effectiveness of complex 1 against two bacterial
species.
Acknowledgements
We are grateful for the financial support from the Department of Chemistry, Isfahan
University of Technology (IUT).
Appendix A. Supplementary data
CCDC 974122 contains the supplementary crystallographic data for compound 1. 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.
References
[1]
[2]
[3]
[4]
A.A.Khandar, V.T.Yilmaz, F.Costantino, S.Gumus, S.A.Hosseini-Yazdi, G.
Mahmoudi,Inorganica Chimica Acta 394 (2013) 36–44.
S.J.Sabounchei, H.Nemattalab, S.Salehzadeh, M.Bayat, H.R.Khavasi, H.Adams,
Journal of Organometallic Chemistry 693 (2008) 1975–1985.
F.Mendizabal, D.Burgos, C.Olea-Azar, Chemical Physics Letters 463 (2008) 272–
277.
B.Moulton, M.J.Zaworotko, Chem. Rev. 101 (2001) 1629-1658.
14

[5]
[6]
[7]
L.Carlucci, G.Ciani, D.M.Proserpio, Coord.Chem. Rev. 246 (2003) 247-289.
D.Braga, L.Brammer, N.R.Champness, Cryst.Eng.Comm. 7 (2005) 1-19.
S.Kitagawa, R.Matsuda, Coord.Chem. Rev. 251 (2007) 2490-2509.
[8]
[9]
C.Hu, I.Kalf, U.Englert, Cryst.Eng.Comm. 9 (2007) 603-610.
R.J.Crutchley, Coordination Chemistry Reviews 219–221 (2001) 125–155
[10] E.W.Ainscough, A.M.Brodie, R.J.Cresswell, J.C.Turnbull, J.M.Waters Croatica
Chemica Acta 72 (1999) 377-394.
[11] H.Brand, P.Mayer, A.Schulz, T.Soller, A.Villinger, Chem. Asian. J. 3(2008)1050 –
1058.
[12] R.J.Letcher, W.Zhang, C.Bensimon, R.J.Crutchley, Inorg.chimica. Acta 20(1993)183-
191.
[13] A.M.Florea, D.Busselberg, BioMetals. 19 (2006) 419-427.
[14] Stoe & Cie, X-AREA, version 1.30: Program for the Acquisition and Analysis of
Data, Stoe & Cie GmbH, Darmatadt, Germany, 2005.
[15] Stoe & Cie, X-RED, version 1.28b: Program for Data Reduction and Absorption
Correction, Stoe & Cie GmbH, Darmatadt, Germany, 2005.
[16] G.M.Sheldrik, SHELX97. Program for Crystal Structure Solution and Refinement,
University of Gottingen, Germany, 1997.
[17] Stoe & Cie, X-SHAP, version 2.05: Program for Crystal Optimization for Numerical
Absorption Correction, Stoe & Cie GmbH, Darmatadt, Germany, 2004.
[18] Gaussian 09, Revision A.1, M. J. Frisch, et al. Gaussian, Inc., Wallingford CT, 2009.
[19] E.D.Glendening, A.E. Reed, E.J.Carpenter, F.Weinhold, NBO Version 3.1, 2005.
[20] S.Mietrus, E.Scrocco, J. Chem. Phys. 55 (1981) 117-122.
[21] KF.Barker, J. Clin. Pharmacol. 48(1999)109–124.
15

[22] Y.Li,P. Leung, L.Yao,Q.W.Song, E. Newton, J. Hosp. Infect. 62(2006)58–63.
[23] Q.L.Feng, J.Wu, G.Q.Chen, F.Z.Cui, T.N.Kim, J.O.Kim, J. Biomed. Mater. Res. 52(
2000)662-668.
[24] M. Silverstein, F.X. Webster, Spectrometric Identification of Organic Compounds,
sixth ed., John Wiley, Asia, 2003.
[25] J.Vicente, A.Arcas, J.M.Fernandez-Hernandez, D.Bautista, Organometallics, 27(
2008) 3978–3985.
[26] K. Nakamoto, Infrared and Raman Spectra of Inorganic and Coordination
Compounds, Wiley, New York, 1978.
[27] J.B.King, M.R.Haneline, M.Tsunoda, F.P.Gabbai, J. AM. CHEM. SOC., 124 ( 2002)
9350-9351.
[28] A.B.P.Lever, Inorganic Electronic Spectroscopy, Elsevier publishing Co., Amsterdam
(1984).
[29] H. Hadadzadeh, A.R.Rezvani, F.Belanger-Gariepy, Journal of Molecular Structure 740
(2005) 165–168
[30] F.H.Allen, O.Kennard, D.G.Watson, L.Brammer, A.G.Orpen, J.Chem. Soc. Perkin
Trans. II (1987) S1-S19.
[31] E.López-Torres, M.A.Mendiola, J.Organomet.Chem. 725 (2013) 28-33
[32] G.B.Deacon, P.W.Felder, P.C.Junk, K. Müller-Buschbaum, T.J.Ness, C.C.Quitmann,
Inorg.chimica. Acta 358(2005) 4389-4393
[33] P.Pyykko,M.Straka, Phys. Chem. Chem. Phys. 2(2000) 2489-2493.
[34] S.C.Nyburg, C.H.Faerman, Acta Crystallogr., Sect. B 41(1985) 274-279.
[35] I.Fleming, Frontier Orbitals and Organic Chemical Reactions, Wiley, London,1978.
16

[36] M.M.El-Nahass, M.A.Kamel, A.F.El-Deeb, A.A.Atta, S.Y.Huthaily, Spectrochim.
Acta A 79 (2011) 1499–1504.
[37] K.Dedachi, T.Hirakawa, S.Fujita, M.T.H.Khan, I.Sylte, N.Kurita, J.Comput.
Chem. 32 (2011) 3047–3057.
[38] N.S.Gwaram, H.M.Ali, H.Khaledi, M.A.Abdulla, A.H.A.Hadi, T.K.Lin, C.L.Ching,
C.L.Ooi, Molecules 17(2012) 5952-5971.
17

Scheme1. X= -NO2, -Cl, -Br
18

Table1.Crystallographic data for 1.
1
Empirical Formula
C10H9HgN3O3
Formula weight
419.79
T/K
298 (2) K
Crystal system
Monoclinic
Space group
P21
a/Å
13.1294 (8)
b/Å
9.0851 (5)
c/Å
10.8288 (7)
α/°
90.00
β/°
94.01
γ/°
90.00
V/Å3
593.5 (2)
Z
2
µ (mm-1)
Dcal/Mg m-3
12.97
2.349
F(000)
388
ƟRange/°
2.5–29.2
Independent reflections
3183
Data/restraints/parameters
3183/0/156
Goodness-of-fit on F2
Final R indices
1.13
R1 = 0.0743, wR2 = 0.1925
R1 = 0.0840, wR2 = 0.2059
5.08 ,-7.16
R indices (all data)
Largest difference peak and hole (e Å−3)
19

Table2. Infrared spectra of the anion of ligands and the complexes of 1 – 3 (cm-1).
4-NO2pcyd-
4-Clpcyd-
4-Brpcyd-
Assigments
1
2
3
−N)
ν(C
1150,1295
2145
1125
2140
1185,1245
2194
1165
2190
1260,1100
2186
1070
2183
ν(C≡N)
ν(NO2)
ν(CO)
1590.0
1310.4
1597.7
1337.4
1726.3
1728.2
1725.4
20

Table3. 1H-NMR of ligands and the complexes of 1-3 (ppm).
Observed
protons
4-NO2pcyd
1
4-Clpcyd
2
4-Brpcyd
3
Phenyl
7.06(d)
7.92(d)
6.82(d)
7.62(d)
1.18(s)
6.91(d)
7.28(d)
6.65(d)
6.98(d)
1.15(s)
6.91(d)
7.28(d)
6.68(d)
7.14(d)
-CH3
-CH2
1.16(s)
2.61(d)
2.14(d)
2.49(d)
2.12(d)
2.57(d)
2.10(d)
d (doublet), s (singlet)
21

Table4. 13C-NMR of ligands and the complexes of 1-3 (ppm).
Observed
4-NO2pcyd
1
4-Clpcyd
2
4-Brpcyd
3
carbons
C(H3)
C(H2)
C7
30.2
56.4
30.2
56.4
30.2
56.3
112.5
120.0
129.0
132.5
136.6
120.1
124.1
126.7
131.9
153.0
216.9
111.7
116.9
128.9
129.9
136.2
119.0
120.1
126.6
128.7
152.7
216.6
100.7
115.5
128.6
132.1
135.5
107.6
121.0
126.4
131.6
151.9
216.1
C2,6
C4
C3,5
C1
C(=O)
22

Table5. Electronic absorption data for [Hg(CH2COCH3)L]n complexes.
Experimental
Calculated
Assignment
L
λmax(f)b
λmax(log ɛ)a
451(3.85)
267(3.18)
446(0.0195)
274(0.024)
π→π*
π→π*
4-NO2pcyd
π→π*
π→π*
−
−
418(3.98)
267(3.58)
4-Clpcyd
4-Brpcyd
π→π*
π→π*
−
−
404(4.17)
266(3.97)
a λ in nm (log ɛ), in DMF solution.
b the oscillator strength (f)
23

Table6. Selected bond lengths (Å) and bond angles (˚) for the compound 1.
Bond lengths
N(1)-C(1)
N(2)-C(1)
N(2)-C(2)
N(3)-C(5)
Hg(1)-N(2)
Hg(1)-C(8)
Hg(1)-O(3)
Bond angles
1.17(2)
1.29(2)
1.37(2)
1.39(3)
2.120(17)
2.097(19)
2.820 (17)
C(8)-Hg(1)-N(2)
C(1)-N(2)-C(2)
175.6(7)
118.8(17)
116.2(13)
124.2(13)
174(2)
C(1)-N(2)-Hg(1)
C(2)-N(2)-Hg(1)
N(1)-C(1)-N(2)
H(8A)-C(8)-H(8B)
C(9)-C(8)-H(8A)
C(9)-C(8)-H(8B)
Hg(1)-C(8)-H(8B)
Hg(1)-C(8)-H(8A)
C(9)-C(8)-Hg(1)
108.2
109.7
109.7
109.7
109.7
110.0(13)
24

Table7. A comparison between the selected calculated bond lengths (Å) and bond angles (˚)
and corresponding experimental values for 1.
b1
b2
X-ray
Bond lengths (Å)
N(1)-C(1)
1.161 1.193 1.17(2)
1.381 1.269 1.29(2)
1.436 1.420 1.37(2)
2.076 2.013 2.120(17)
C(1)-N(2)
N(2)-C(2)
N-Hg
Bond angles (˚)
N(1)-C(1)-N(2)
C(1)-N(2)-C(2)
Hg-N-C(2)
178.3 171.1
174(2)
116.0 120.8 118.8(17)
116.3 176.6 124.2(13)
C(1)-N(2)-C(2)-C(3)
0.0
0.0
---
25

Table8. Calculated NBO charges on selected atoms of ligand (4-NO2pcyd) and isomers of
complex 1.
a
b1
b2
N1
C1
N2
C2
Hg
-0.337
0.089
-0.362
0.114
------
-0.198
0.126
-0.314
0.137
0.234
-0.317
0.252
-0.271
0.12
0.197
26

Table9. Most important occupancies of NBOs in atomic units (LP: lone pair)
b1
b2
acceptor
Hg
donor
N2(LP)
N2(LP)
acceptor
Hg
energy donor
105.88 N1(LP)
energy
90.73
16.48
σ*(Hg-C)
46.21 N1(LP) σ*(Hg-C)
27

Table10. Inhibition zone values from disk diffusion tests for free ligand of 4-NO2pcyd and
the complex 1.
Inhibition zone diameter (mm)
Compound
Salmonella
> 30 mm
> 30 mm
Ecoli
> 30 mm
> 30 mm
4-NO2pcyd
1
28

Fig.1. ORTEP structure of the [Hg(CH2COCH3)(4-NO2pcyd)]n complex.
29