Novel Ni(II) and Zn(II) complexes coordinated by 2-arylaminomethyl-1H- benzimidazole: Molecular structures, spectral, DFT studies and evaluation of biological activity

Article abstract of DOI:10.1016/j.saa.2012.11.038

[NiL^1,2Cl₂(OH₂)₃] ·zH₂O and [ZnL^1,2(CH₃CO ₂)₂] (L¹ = (1H-benzimidazol-2-ylmethyl)-N- phenyl amine, z = 0 and L² = 2-[(1H-Benzimidazol-2-ylmethyl)-amino]- benzoic acid methyl ester, z = 1) complexes have been synthesized and characterized by a variety of physico-chemical techniques. The central Ni(II) ion is coordinated by only the pyridine-type nitrogen (N_py) of benzimidazole ring, three water molecules and two chlorido ligands forming a distorted octahedral geometry. Five coordinated zinc complexes were obtained, where the coordination sphere of zinc ion is made up of secondary amino group (NH_sec), N_py and two acetate groups, one acts as a unidentate and the other as a bidentate. A theoretical DFT/UB3LYP method combined with LANL2DZ basis set shows that all the metal-ligand bonds are of the L → M type. Electronic structures have been calculated using TD-DFT method. The antibacterial activity of NiL² complexes decreases by the introduction of COOCH₃ group in the ortho-position of the aniline moiety.

Full text of DOI:10.1016/j.saa.2012.11.038

Accepted Manuscript
Novel Ni(II) and Zn(II) complexes coordinated by 2-arylaminomethyl-1H-ben‐
zimidazole: Molecular structures, spectral, DFT studies and evaluation of bio‐
logical activity
Nour T. Abdel-Ghani, Maha F. Abo El-Ghar, Ahmed M. Mansour
PII:
S1386-1425(12)01134-1
http://dx.doi.org/10.1016/j.saa.2012.11.038
SAA 9976
DOI:
Reference:
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Spectrochimica Acta Part A: Molecular and Biomo‐
lecular Spectroscopy
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Accepted Date:
8 August 2012
6 November 2012
8 November 2012
Please cite this article as: N.T. Abdel-Ghani, M.F. Abo El-Ghar, A.M. Mansour, Novel Ni(II) and Zn(II) complexes
coordinated by 2-arylaminomethyl-1H-benzimidazole: Molecular structures, spectral, DFT studies and evaluation
of biological activity, Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy (2012), doi: http://
dx.doi.org/10.1016/j.saa.2012.11.038
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Novel Ni(II) and Zn(II) complexes coordinated by 2-arylaminomethyl-1H-
benzimidazole: Molecular structures, spectral, DFT studies and evaluation of
biological activity
Nour T. Abdel-Ghani*, Maha F. Abo El-Ghar, Ahmed M. Mansour
Chemistry Department, Faculty of Science, Cairo University, Gamaa Street, Giza, 12613, Egypt
Abstract
[NiL1,2Cl2(OH2)3]·zH2O and [ZnL1,2(CH3CO2)2] (L1 = (1H-benzimidazol-2-ylmethyl)-N-phenyl
amine, z = 0 and L2 = 2-[(1H-Benzimidazol-2-ylmethyl)-amino]-benzoic acid methyl ester, z = 1)
complexes have been synthesized and characterized by a variety of physico-chemical techniques.
The central Ni(II) ion is coordinated by only the pyridine-type nitrogen (Npy) of benzimidazole ring,
three water molecules and two chlorido ligands forming a distorted octahedral geometry. Five
coordinated zinc complexes were obtained, where the coordination sphere of zinc ion is made up of
secondary amino group (NHsec), Npy and two acetate groups, one acts as a unidentate and the other
as a bidentate. A theoretical DFT/UB3LYP method combined with LANL2DZ basis set shows that
all the metal-ligand bonds are of the L→M type. Electronic structures have been calculated using
TD-DFT method. The antibacterial activity of NiL1,2 complexes decreases by the introduction of
COOCH3 group in the ortho-position of the aniline moiety
Key Words: Benzimidazole; Hydrogen bond; TD-DFT; NBO; Antimicrobial
* Corresponding author, Tel.: +20 2 01006700375;Fax: +20 2 35728843. E-mail: noureta2002@ yahoo.com
1. Introduction
Benzimidazole nucleus is a crucial pharmacophore in drug discovery. Pharmaceutical
properties including antitumor [1-2], anti-HIV [3], anti-Parkinson [4] antimicrobial [5] and anti-
HCV NS3/NS4A serine protease [6] are unique characteristics known for benzimidazole derivatives.
Moreover, benzimidazoles were used extensively as corrosion inhibitors for metal and alloy surfaces
[6]. A considerable number of metal benzimidazole complexes including Cr, Mn, Fe, Co, Ni, Zn,
Pd, Pt, Au, and Re has been reported [7-9]. Metal complexes containing benzimidazole-based
ligands are subject of intensive researches not only owing to their rich coordination chemistry, but
also due to a number of established and potential application areas e.g. production of efficient
orange light emitting devices (OLEDs), with enhanced stability and efficiency. Metal complexes of
biologically important ligands were sometimes more effective than free ligands [10]. These different
applications have attracted many experimentalists and theorists to investigate the spectroscopic and
structural properties of benzimidazole and some of its derivatives.
1

Recently, structural studies, antimicrobial activity, in vitro cytotoxicity, and structure-activity
relationship for some derivatives of 2-arylaminomethylbenzimidazole and their Pd(II) and Pt(II)
complexes have been reported [8-9]. In the earlier studies, it was found that, the Pd(II) complexes
were inactive against all the tested microorganisms, whatever the nature of the substituent on the
para-position of the aniline ring [11]. As a continuation of our recent studies on synthesis, biological
studies, and density functional theory (DFT) calculations of some benzimidazole metal complexes
[8-9,11], the main aspects of the present work are: (i) discussing the coordination modes of bi- and
tridentate 2-arylaminomethyl-1H-benzimidazoles (L1,2) ligands (Fig. 1) towards Ni(II) and Zn(II)
ions, (ii) how far the introduction of methyl ester group in aniline moiety affects geometry and
biological activity of the titled complexes, (iii) discussing theoretically the molecular geometries,
vibrational spectra and, electronic absorption spectra, as well as natural bond orbital (NBO)
analysis, and frontier molecular orbital (FMO).
2. Experimental
2.1. Synthesis and characterization
One mmole hot ethanolic solution of ligands L1,2 [11-13] was added to one mmole hot
ethanolic solution of either NiCl2∙6H2O or Zn(CH3CO2)2∙2H2O, and refluxed for 6 h, whereupon the
complexes precipitated. The low conductance values of NiL1,2 complexes (10-3 M, DMF) indicated
their non-electrolytic nature, while zinc complexes are insoluble in most common solvents such as
DMSO and DMF. The elemental analyses data are in a good agreement with those calculated for the
suggested formula.
. Data for NiL1 (C14H19Cl2N3NiO3) (1). Color: Buff. Yield: 68%. MS: M+ = 407 (calcd. 406). Anal.
Calcd. %C, 42.32; %H, 4.71; %Cl, 17.42; %N, 10.33; %Ni, 14.42. Found: %C, 42.97; %H, 4.56;
%Cl, 18.08; %N, 10.59; %Ni, 14.56. FT IR: 3399, ν(NH)sec; 3054, ν(C-H)Ar; 2922, ν(C-H)Aliph
;
1602, ν(C=N) + ν(C=C); 1499, ν(C=C); and 1429 cm-1, β(NH)sec. Molar Cond. (10-3 M, DMF):
8.22 Ω-1 cm2 mole-1. μeff = 3.82 B.M.. UV-Vis. (DMF): 274, 280, 351, 456, 608, and 824 nm.
. Data for ZnL1 (C18H19N3O4Zn) (2). Color: Yellow. Yield: 50%. MS: M+ = 406 (calcd. 406). Anal.
Calc. %C, 53.15; %H, 4.71; %N, 10.33; %Zn, 16.08. Found: %C, 52.98; %H, 4.58; %N, 10.26;
%Zn, 15.97. FT-IR: 3070, ν(C-H)Ar; 2975, ν(C-H)Aliph; 2924, ν(C-H)Aliph; 1602, ν(C=N) + ν(C=C);
1545, νass(COO-); 1494, ν(C=C); 1431, ν(C=C); 1470, νass(COO-); 1385, υss(COO-); 1277,
νss(COO-), 938, 828, and 640 (COO unidentate deformation) and 596 cm-1 [π(CO2)].
2

. Data for NiL2 (C16H23Cl2N3NiO6) (3). Color: Pale yellow. Yield: 62%. MS: M+ = 477 (calcd.
477). Anal. Calc. %C, 39.79; %H, 4.80; %Cl, 14.68; %N, 8.70; %Ni, 12.15. Found: %C, 39.41;
%H, 4.56; %Cl, 15.12; %N, 8.68; %Ni, 12.06. FT IR: 3564, ν(NH)im; 3363, ν(NH)sec; 3061,
ν(C-H)Ar; 1682, ν(C=O); 1610, ν(C=N); 1582, ν(C=C); 1510, ν(C=C), and 1269 cm-1; ν(C-O).
Molar Cond. (10-3 M, DMF): 17.57 Ω-1 cm2 mole-1. μeff = 3.41 B.M.. UV-Vis. (DMF): 276, 281,
342, 457, 609, and 824 nm.
. Data for ZnL2 (C20H21N3O6Zn) (4). Color: White. Yield: 70% MS: M+ = 464 (calcd. 464). Anal.
Calc. %C, 51.68; %H, 4.55; %N, 9.04; %Zn, 14.07. Found: %C, 51.59; %H, 4.51; %N, 8.97;
%Zn, 13.99. FT IR: 3587, ν(NH)im; 3361, ν(NH)sec; 2951, ν(C-H)Aliph; 1687, ν(C=O); 1634,
νass(COO-); 1580, ν(C=C); 1513, ν(C=C); 1438, νass(COO-); 1264, νss(COO-), 920, 697 and 616
cm-1 (COO unidentate deformation).
2.2. Instruments
Infrared spectra (4000-200 cm-1) were recorded in KBr discs using FTIR-460 plus, JASCO.
Thermogravimetric analysis was carried out in dynamic nitrogen and air atmospheres (20 mL min-1)
with a heating rate of 10 ºC min-1 in platinum crucible using DTG-60H SIMULTANEOUS DTA-TG
APPARATUS-SHIMADZU. Mass spectra were recorded at 70 eV using SHIMADZU QP-2010 plus
mass spectrometer. Elemental microanalyses were performed at Micro-analytical Center, Cairo
University. The analyses were repeated twice to check the accuracy of the obtained data. The metal
content was determined complexometry [13]. X-ray powder diffraction patterns were studied over
2θ = 5-60 º range using Philips X-ray diffractometer model PW 1840. Radiation was provided by
copper anode (Kα, λ = 1.54056 Å) operated at 40 kV and 25 mA. Spectrophotometric measurements
were carried out using UV-Vis. SHIMADZU Lambda 4B. Magnetic measurements were carried out
on a Sherwood Scientific magnetic balance using Gouy method [14]. Diamagnetic corrections were
made by Pascal's constant and Hg[Co(SCN)4] was used as a calibrant. Digital Jenway 4330
Conductivity-pH meter with (1.02) cell constant was used for pH and molar conductance
measurements.
2.3. Computational details
Gas phase geometries of [NiL1,2Cl2(OH2)3] and [ZnL1,2(CH3CO2)2] complexes were optimized
by DFT/B3LYP method [15] combined with LANL2DZ basis set [9] using Gaussian 03 package
[16]. The optimized geometries were verified by performing frequency calculation. Vibrational
modes were analyzed via Gaussview software [17]. Electronic spectra were obtained by using time-
dependent density functional theory (TD-DFT) [18] method. Net atomic charges had been obtained
3

using natural bond orbital (NBO) analysis of Weinhold and Carpenter [19]. Frontier molecular
orbitals (FMO) were performed at the same level of theory.
2.4. Biological studies
The antimicrobial activities of the tested samples were determined by a modified Kirby-Bauer
disc diffusion method [20] under standard conditions using Mueller-Hinton agar medium (tested for
composition and pH), as described by NCCLS [21]. The antimicrobial activities were carried out
using culture of Bacillus subtilis, Staphylococcus aureus, and Streptococcus faecalis as Gram-
positive bacteria and Escherichia coli, Pseudomonas aeruginosa, and Neisseria gonorrhea as Gram-
negative bacteria. The solution of 20 mg/ml of each compound (free ligand, metal complexes and
standard drug Tetracycline) in DMSO was prepared. Centrifuged pellets of bacteria from a 24 h old
culture containing approximately 104-106 CFU/ml (colony forming unit) were spread on the surface
of Mueller Hinton Agar plates. Then the wells were seeded with 10 ml of prepared inocula to have
106 CFU/ml. Petri plates were prepared by pouring 100 ml of seeded nutrient agar. DMSO (0.1 ml)
alone was used as control under the same conditions for each microorganism. The antimicrobial
activities could be calculated as a mean of three replicates.
3. Results and discussion
3.1. Geometry optimization and NBO analysis
3.1.1. [NiL1,2Cl2(OH2)2] complexes
The fully optimized geometries of [NiL1,2Cl2(OH2)3] complexes and numbering of atoms are
shown in Fig. 2. Selected bond distances and angles are listed in Table 1. The molecular structures
of these complexes show a distorted octahedral geometry around Ni(II) centre as revealed from the
spreading in their calculated bond distances (1.907-3.126 Å), and bond angles (89.79-107.40°). As
shown in Fig. 2, the benzimidazoles L1,2 interact with metal ion through only the pyridine-type
nitrogen (N11) as the aniline moiety is bent out of the coordination plane and becomes far from the
Ni(II) ion. Table 1, summarizes the details of H-bond interactions. Two types of H-bond are known
[22], the first one is the conventional, defined as A-H…B where A, and B are electronegative atoms
such as nitrogen, oxygen or halogen. Another type of H-bonding is the blue-shifting hydrogen bond,
usually C-H…B, where B is either an electronegative atom carrying lone pair or a region of excess
electron density (π electrons of an aromatic system). Each water molecule in the axial position of
octahedral structure is involved in three H-bonds of different strength, and this leads to a distorted
geometry. For example, (O33H2) in NiL1 complex interacts with the methylene proton (H24) and
two chlorine atoms (Cl31 and Cl38) with D…A distances 2.12, 2.38, and 2.76 Å, respectively
4

(Table 1). It is seen that C14-H24…O33 interaction is the strongest one (155.8 º) among the latter
interactions, since the angle of interaction approaches linearity [23]. It is worthy to mention that the
H25 proton of NHsec (N21) group in NiL2 is participated in H-bond with the oxygen atom (O43, -
0.668e) of the ester group [13], while the imidazolic proton (H22) interacts with the nitrogen atom
(N21) of NHsec group through another H-bond with distance of 2.51 Å.
Natural bond orbital (NBO) analysis [19] and second order perturbation theory analysis of Fock
Matrix provide details about the type of hybridization, nature of bonding and strength of the
interactions between metal ion and donor sites [24]. According to NBO results, the electronic
configuration of Ni in NiL2 (as representative example) is: [core]4s0.343d8.724p0.334d0.015p0.20, 17.996
core electrons, 9.573 valence electrons, and 0.018 Rydberg electrons with 27.587 electrons as a total
electrons that is in agreement with the calculated natural charge (+0.413e) on nickel atom. The
strength of interaction between Ni(II) and active binding sites has been assigned by second order
interaction energy (E2). The E2 values are 2.77, 1.20, 0.64, 0.44, 1.81, and 1.57 kcal/mol for
LP(1)N11→RY*(9)Ni, LP(2)Cl31→σ*(Ni-Cl31), LP(2)O32→σ*(Ni-Cl31),LP(2)O33→σ*(Ni-Cl31)
,LP(4)Cl38→RY*(9)Ni and LP(2)O39→RY*(9)Ni, respectively. In addition, the lone pair
interaction (∼29 kcal/mol) of oxygen (O43) atom of the carbonyl group with anti-bonding σ*(C42-
O44) is an evidence for charge transfer in the H-bonded system. The π(C16-C17) is conjugated with
the π*(C42-O43) anti-bonding orbital in the aniline ring and this leads to a strong π-electron
delocalization with an energy difference ~ 220 kcal/mol.
3.1.2. [ZnL1,2(CH3CO2)2] complexes
The fully optimized geometries of [ZnL1,2(CH3CO2)2] complexes and numbering of atoms are
shown in Fig. 3 and their selected geometric parameters are listed in Table 1. The local coordination
environment of Zn(II) ion can be described as a distorted square pyramidal completed by two N
atoms, N11 and N21, and two oxygen atoms of a bidentate acetate group in the base of the pyramid
and an oxygen atom from a monodentate acetate in the axial position. This geometry prevents the
participation of COOCH3 group in the coordination sphere of ZnL2 complex as was experimentally
found [12]. It was found that, C13N11 and C14N21 bond lengths in ZnL1 complex were increased
upon the coordination of N11 and N21 to metal ion. In ZnL1 complex, the bond length of ZnN11
(2.091 Å) is in agreement with the average zinc-imidazole bond distances (2.02-2.08 Å) [25]. On the
same manner, the bond distance of ZnN21 (2.36 Å) is comparable to the average value of 2.27 Å
which was previously observed for sec-NH donors in five-coordinated zinc(II) complexes [25]. The
Zn-O32 and Zn-O38 bond distances of the bidentate acetate anion are 2.126 and 2.222 Å,
5

respectively [26]. Zn-N21 bond length in ZnL2 complex is longer than that of ZnL1 due to
participation of NHsec in H-bond. The unidentate acetate interacts with methylene group forming H-
bond with D…A distances, 2.085, and 2.115 Å, for ZnL1,2 complexes. According to NBO, the
electronic configuration of Zn in ZnL1 is [core]4s0.303d9.984p0.31: 18 core electrons, 10.59 valence
electrons (on 4s, 3d, and 4p atomic orbitals), and 0.0078 Rydberg electrons with 28.605 as a total
electrons and +1.395e as a natural charge. The E2 values were found to be 32, 12, 20, 36, and 10
kcal/mol for LP(1)N11→RY*(6)Zn, LP(1)N21→RY*(6)Zn, LP(2)O32→RY*(6)Zn, LP(2)O37→
RY*(6)Zn and LP(2)O38→RY*(6)Zn, respectively [27].
3.2.Electronic structure, frontier molecular orbitals and magnetic susceptibility
Frontier molecular orbitals play an important role in electric and optical properties [28]. The
frontier orbital gap can be used to characterize the chemical reactivity and kinetic stability of the
molecule. Fig. 4 shows the electronic distributions and energy levels of HOMO and LUMO orbitals
for the titled complexes. The values of the energy gap between HOMO and LUMO are 0.84, 0.51,
4.75 and 3.48 eV for NiL1,2 and ZnL1,2 complexes, respectively.
The absorption spectra of many octahedral Ni(II) complexes can be easily interpreted using
3
Tanabe-Sugano diagram for d8 electron configuration [29]. The electronic ground state is A2g and
spin-allowed transitions to three triplet-excited states are expected and can be easily observed in
solution absorption spectra. The most important excited states for octahedral Ni(II) complexes are
3
3
3
3
1Eg, T2g, and T1g(3F) [30]. The T2g, and T1g(3F) excited states are close in their energy at all
1
ligand-field strengths. The energy of the first singlet excited state Eg is almost independent of
6
2
ligand-field strength as it arises from the same t2g eg electronic ground state. Here, the two bands
between 275 and 282 nm in NiL1,2 are assigned to π-π* in benzimidazole ring [8-9], while the band
at 342 nm is attributed to intra-molecular H-bond ring [13] (Fig. S1, supplementary materials). The
3
3
three bands at 457, 608 and 824 nm, are assigned to A2g→3T2g (ν1), A2g→3T1g (3F) (ν2) and
3A2g→1Eg (ν3), respectively.
The values of the effective magnetic moment (μeff) of NiL1,2 complexes at 296 K were found
to be 3.82 and 3.41 B.M. with orbital angular momentum contribution (spin-orbital coupling) [30]
for octahedral Ni(II) complexes. Generally, experimental values differ from the spin-only ones (2.83
B.M.), usually being somewhat greater. This is because the orbital motion of the electrons also
contributes to the magnetic moment. The theoretical magnitude of spin only μeff (μs) for an
octahedral nickel complex is 2.83 B.M., whereas orbital contribution (μs+L) raises this value to 4.47
6

B.M. [31]. In the present work, it was found that the observed values of μ exceed μs, but are not high
as μs+L [31]. This is because the electric fields of other atoms, ions, and molecules surrounding metal
ion in its compounds which can restrict the orbital motion of the electrons so that the orbital angular
momentum and hence the orbital moments are partially quenched.
To gain detailed insight into the charge transitions, TD-DFT calculations were performed. The
absorption spectra were simulated using GAUSSSUM software [32] based on the obtained TD-DFT
results. Each excited state was interpolated by a Gaussian convolution with the full-width at half-
maximum (FWHM) of 3000 cm-1. The calculated d-d excitation wavelengths of the nickel
complexes and their assignments are given in Table 2 as representative example, while those of zinc
complexes are included in supplementary material section (Table S1). The intensity of these
transitions has been assessed from the oscillator strength (f). The d-d transitions are forbidden and
their oscillators’ strengths are very small (close to 0.0) [33].
3.3. Vibrational assignments
The theoretical FT IR spectra of the titled complexes were obtained at B3LYP/LANL2DZ
level of theory. The calculated harmonic frequencies were found to be higher than the experimental
values due to electron correlation approximate treatment, anharmonicity effects and basis set
deficiencies, etc. [34-35]. Scale factors were introduced [8] to overcome these shortcomings. Herein,
a uniform scaling method with a value of 0.970 has been introduced. Benzimidazoles (L1,2) have a
strong intermolecular hydrogen bond [13] with a broad band (3500-2200 cm-1) in their vibrational
spectra [11-13]. Therefore, it is experimentally difficult to assign the benzimidazolic NH (N12)
band. In complexes, this group remains intact and is observed at 3566 and 3564 cm-1 in NiL1,2 and at
3587 cm-1 in ZnL2. This is theoretically confirmed, since the position of ν(NHBz) band remains
virtually unaltered in L1,2 and their complexes. The sharp bands at 3427 (L1) [11] and 3345 cm-1 (L2)
[13] are assigned to ν(NHsec). The discrepancy between the latter values is attributed to intra H-
bond. For NiL1, the NHsec group is not involved in chelation, but it participates in H-bond with axial
chlorido atom (Fig. 2) giving a band at 3399 cm-1. Alternatively, the NHsec of L2 in NiL2 remains
also intact, but it is liberated from the effect of intra H-bond and is shifted to a higher value (3363
cm-1) with respect to the free ligand. On the same manner, the scaled ν(NHsec) mode (NiL2) is
assigned at 3381 and 3367 cm-1 in NiL2 and L2, respectively. On the other hand, the ν(NHsec) mode
is observed at low wavenumber, 3350 cm-1 in ZnL1 complex and becomes broad indicating its
involvement in coordination sphere. For ZnL2 complex, the NHsec group suffers from two
antagonistic effects, the withdrawal effect of the nitrogen atom, as a result of complex formation,
7

and the intra H-bond. These two effects compensate each other, lead to appearance of this group at
higher wavenumber than that of the free ligand, 3361 cm-1 [12].
The ν(C=N) mode is observed at 1682 cm−1 [11] in L1. In complexes, this group is shifted to
low frequencies and is overlapped with C=C bands to give a band at 1601 cm-1 in NiL1 and ZnL1. In
L2, the ν(C=N) is overlapped with ν(C=O) and ν(C=C) modes due to H-bond [13]. In complexes, the
C=N group is liberated from H-bond with increasing of double bond characters and is observed at
1634 cm-1 (ZnL2), while it is overlapped with ν(C=C) giving a band at 1610 cm-1 in NiL2. Moreover,
the band at 1674 cm-1 in L2 is assigned to ν(C=O). In complexes, the carbonyl group is not involved
in chelation, since its stretching mode is located at a higher wavenumber, 1682 and 1687 cm-1 for
NiL2 and ZnL2, respectively.
Deacon and Phillips [36] studied and assigned three binding modes of the carboxylate group in
the IR spectra of many acetates and trifluoroacetates complexes, and arrived the following
conclusions according to the value of Δν, Δν = [νass(COO-)- νss(COO-)]: (i) unidentate complexes
exhibit Δν > 200 cm-1 that are much greater than ionic complexes. (ii) chelating (bidentate)
complexes exhibit Δν < 100 cm-1 that are significantly less than ionic values. (iii) the Δ values for
bridging complexes (Δν) are greater than those of chelating (bidentate) complexes, and close to the
ionic values. Here, the new bands at 1591-1419 cm-1 and 1385-1250 cm-1 in the ZnL1,2 are assigned
to asymmetric and symmetric stretching vibrations of coordinated carboxylate group, respectively
[37]. For ZnL1 complex, the νass(COO-) and νss(COO-) modes of the unidentate acetate group appear
at 1545 and 1277 cm-1, respectively. The lower values of these modes may be attributed to
participation of this group in intra H-bond with methylene group of ligand (Fig. 3). In addition, this
complex exhibits three bands (COO deformation) of the unidentate acetate group at 933, 828 and
640 cm-1 and [π(CO2)] at 596 cm-1 [37]. Also, this complex shows new bands corresponding to
bidentate acetate group at 1470 and 1385 cm-1 (Δν = 85 cm-1). Similarly, ZnL2 complex exhibits
νass(COO-) and νss(COO-) modes at 1634 and 1264 cm-1 for unidentate group, while the band at 1438
cm-1 is assigned to νass(COO-) of bidentate group. The bands at 920, 794, and 616 cm-1 are allocated
to COO deformation of the unidentate group. The detail assignments of the remaining bands in the
theoretical vibrational spectra of the studied complexes are shown in Table S2 as supplementary
materials.
3.4. Mass spectrometry
8

The mass spectrum of NiL1 complex (1) gives rise to M+ at m/z 407 due to [NiL1Cl2(OH2)3]
with two fragmentation pathways (scheme S1, supplementary materials). The first route is traced by
a peak (m/z 371) due to removal of 2H2O from M+ followed by loss of 2 Cl to offer a fragment at
m/z 301 ([NiL1(OH2)]) and then loss H2O to give peak at m/z 281, [NiL1]. The second way involves
loss of 2Cl to provide a fragment at m/z 336, [NiL1(OH2)3]. It was found that the involvement of
C=Npy in chelation introduces a weakness point through which the benzimidazole ring decomposes
to imidazole moiety with a fragment at m/z 181, [(imidazole)NiCl(OH2)] [9]. The NiL2 complex (3)
has a strong M+ peak at m/z 477 corresponding to [NiLCl2(OH2)3]·H2O and decomposes through
four fragmentation routes (scheme S2, supplementary materials). There were no evidences revealed
the participation of carbonyl group in chelation.
The mass spectra of Zn-L1,2 complexes give rise to M+ at m/z 406 and 464, respectively due to
[ZnL1,2(CH3CO2)2]. For Zn-L1 complex (2), (scheme S3, supplementary materials), the first pathway
involves removal of CH3 to give a fragment at m/z 391, followed by loss of oxygen atom (m/z 375)
and then CH3CO to provide a peak at m/z 331. The second route is typical as ligand itself with
fragments due to L1 (m/z 223), 2-methylene benzimidazole (m/z 131), and benzimidazole (m/z 118).
Fragmentation pattern of Zn-L2 complex (4) goes under four complicated fragmentation routes as
demonstrated in (scheme S4, supplementary materials). The peak at m/z 242 confirms the presence
of two acetate groups around metal ion, [(Benzimidazole)Zn(CH3CO2)].
3.5. Thermal analyses and kinetics studies
The thermal degradation of NiL1 (1) proceeds via four main stages maximized at 160, 325,
445, and 570 ºC in nitrogen atmosphere. The 1st stage is assigned to elimination of 2H2O with a
mass loss amounts to 8.78 % (calcd. 8.85 %). The 2nd event is attributed to removal of 2HCl
molecules with a mass loss 18.26 % (calcd. 17.95%). The 3rd and 4th stages are assigned to
decomposition of L1 giving NiO as a final residue with a total mass loss, 72.96% (calcd. 73.20%).
Regarding the TG curve constructed for ZnL1 complex (2), one can observe mainly one peak
maximized at 514 ºC. This stage is attributed to elimination of L1, C2H6, CO and CO2 leaving ZnO
with overall mass loss amounts to 80.27 % (calcd. 80.05 %).
For NiL2 complex (3), the thermal degradation starts at 100 ºC, with two peaks at 331 and 409
ºC in nitrogen atmosphere with overall mass loss amounts to 68.96% (calcd. 84.48 %) assuming
NiO as a final residue as no other nickel compounds can present at 1200 ºC. Similar, degradation of
ZnL2 complex (4) is also incomplete [38] up to 1200 ºC with four peaks at 75, 289, 418, and 550 ºC
9

and total mass loss amounts to 64.18% (calcd. 82.87 %) with ZnO as residue. This behavior [9]
reflects the high stability of these complexes comparing with those of ligand L1. However, the
thermal decomposition of ZnL2 complex in air shows two degradation stages at 289 and 458 ºC with
overall mass loss amounting to 82.62%. Coats-Redfern equation [39] was used to calculate the
thermo-dynamic parameters from TG curves (Table S3 as supplementary materials). The positive
ΔH* values mean endothermic processes, while the negative ΔS* values indicate that the complexes
are spontaneously formed and are highly ordered in their activated states [8]. The activation energies
of the decomposition stages were found to be in the range of 40-666 kJ/mole indicating the high
stability of these complexes in terms of their H-bonds.
3.6. X-ray powder diffraction
Single crystals of the reported complexes could not be obtained since these complexes are
amorphous in their nature. The X-ray powder diffraction patterns were recorded over 2θ = 5-60 º
range in order to obtain an idea about the lattice dynamics of these compounds. The values of 2θ,
interplanar spacing d (Å) and the relative intensities (I/I°) were tabulated in (supplementary
material, table (S4)). The comparison between the obtained XRD patterns of the title complexes
(supplementary material, figure S2), revealed that the pronounced effect of metal type on the
crystallinity of these compounds. The identification of the complexes was done by the known
method [9]. There are five strong diffraction peaks in NiL2 complex at 6.73º, 19.88º, 21.08º, 26.72º,
and 28.98º and the interstices of the corresponding crystal faces are 13.12, 4.46, 4.21, 3.33, and 3.07
Å, respectively. The interstice 6.73 Å at 2θ = 13.12º is the interlayer spacing of NiL2 complex.
Moreover, the similarity between nickel complexes, with an interlayer spacing at 6.73 Å, suggests
that both complexes have the same phase structure. This behavior has been also found between the
zinc complexes with nearly the same interstice 10.74 Å at 2θ = 8.24º.
3.7. Biological activity
The antimicrobial activity data of NiL1,2 complexes were compared with those of the free
ligands and the corresponding Pd(II) and Pt(II) complexes [11,13]. The results revealed the capacity
of the titled complexes for inhibiting the metabolic growth of the investigated bacteria to different
extents and especially the Staphylococcus aureus (Fig. 5). The variation in the effectiveness of the
studied compounds against different organisms depends either on the impermeability of the cells of
the microbes or on differences in ribosome of microbial cells. Here, the nickel complexes are active
against both types of the bacteria, which may indicate broad-spectrum properties [40].
10

It was found that NiL1 complex is more toxic against the tested organisms than NiL2 that is in
agreement with the previously reported data of the free ligands [11,13] as the introduction of
COOCH3 in the aniline ring decreases distinctly the antibacterial activity of NiL2 complex. As
shown in Fig. 5, the nickel complexes exhibit slightly lower toxicity than their free ligands. This
may be attributed to their inability to chelate metals, which are essential for the metabolism of
microorganisms, low lipophilicity and/or to form hydrogen bonds with the active centers of cell
structures, resulting in an interference with the normal cell cycle. Finally, the nickel complexes are
toxic than the inactive palladium complexes [11,13] at the same concentration. This may be
interpreted in terms of the strength of the M-L bonds, besides other factors such as size of the cation,
receptor sites, diffusion, and a combined effect of the metal and the ligands for inactivation of the
bio-molecules.
4. Conclusion
Better approaches to the synthesis of Ni(II) and Zn(II) complexes coordinated by 2-arylamino-
methylbenzimidazole derivatives as potential antimicrobial agents have been developed. The
reasonable agreement between the theoretical and experimental data reflects to great extent the
suitability of the applied basis set, LANL2DZ for this type of work and confirms the suggested
structures. The obtained results seem to suggest the different ligational behavior of such ligands
towards the metal ion. TD-DFT calculations help to assign the electronic transitions. Vibrational
assignments revealed the presence of two types of coordinated acetate groups in the zinc complexes.
The calculated values of the second order interaction energy showed strong coordination bonds
between the ligands and metal ions. The EI mass spectra indicated the involvement of pyridine-type
nitrogen in chelation and decomposition of benzimidazole ring into imidazole moiety. The
introduction of substituent in the ortho-position of the aniline ring decreases markedly the
antibacterial activity of the investigated nickel complexes. The strength of the M-L bonds, besides
other factors such as size of the cation, receptor sites, diffusion, and a combined effect of the metal
and the ligands affect the biological activity of this type of compounds.
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14

Figure(s)
Figure-caption list
Figure (1): The optimized structures of benzimidazole ligands L1,2.
Figure (2): The optimized structures of (a) Ni-L1 (1) and (b) Ni-L2 (2) complexes.
Figure (3): The optimized structures of (a) Zn-L1 (1) and (b) Zn-L2 (2) complexes.
Figure (4): Molecular orbital surfaces and energy levels of (a) Ni-L1, (b) Ni-L2, (c) Zn-L1
and (d) Zn-L2 complexes.
Figure (5): Antibacterial activities of L1,2 and their Ni-L1,2 complexes and tetracycline
against B. subtilis, S. aureus, and S. faecalis as Gram-positive, P. aeruginosa, E. coli, and N.
Gonorrhea as Gram-negative bacteria.
1

L1
L2
Figure (1)
2

(a)
(b)
Figure (2)
3

(a)
(b)
Figure (3)
4

(a)(HOMO, -5.90 eV)
(LUMO, -5.06 eV)
(b)(HOMO, -5.92 eV)
(LUMO, -5.41 eV)
5

(c) (HOMO, -6.11 eV)
(LUMO, -1.36 eV)
(d)(HOMO, -8.91 eV)
(LUMO, -5.43 eV)
Figure (4)
6

33
35
30
30
27
27
26
25
30
25
20
15
10
22.66
15
19
18
16
19.33
17
16
16
14
14
17
14
14
15.66
15.66
13
11
10
10.33
10.66
10.33
10.33
Tetracycline
5
L1
L2
Ni-L1
Ni-L2
0
Ni-L2
Ni-L1
L2
B. subtilis (G+)
S. aureus (G+)
S. faecalis (G+)
P. aeruginosa
(G-)
L1
E. coli (G-)
N. Gonorrhoeae
(G-)
Tetracycline
Figure (5)
7

Table(s)
Table (1): Selected bond lengths (Å), angles (º) and charge (e) for the titled complexes
[NiL1Cl2(OH2)3] (1) [ZnL1(CH3CO2)2] (2) [NiL2Cl2(OH2)3] (3)
[ZnL2(CH3CO2)2] (4)
Bond lengths
(Å)
Bond lengths (Å)
Bond Angles (º)
Bond Angles (º)
Bond lengths (Å)
Bond Angles (º)
Bond lengths (Å)
Bond Angles (º)
N11NiCl31 =
91.0
N11NiO32 =
105.3
Cl31NiCl38 =
95.6
N11Ni = 1.907
Cl32Ni = 2.258
N11NiCl32 = 91.5 N11Zn = 2.090 N11ZnN21 = 75.7
N11NiO40 = 89.8
N11Ni = 1.908
N11Zn = 2.084
N11ZnN21 = 74.9
N21Zn = 2.360 N11ZnO37 = 118.6 Cl31Ni = 2.255
Cl38Ni = 2.287
N21Zn = 2.385 N11ZnO36 = 111.8
O36Zn = 1.950 N21ZnO36 = 107.1
Cl37Ni = 2.298 Cl32NiCl39 = 95.8 O37Zn = 1.942 N21ZnO37 = 92.3
N11NiO33 =
101.0
O33Ni = 2.841 N11NiO33 = 103.4 O32Zn = 2.126 O32ZnO37 = 128.2 O32Ni = 2.883
O31Zn = 2.091
O31ZnO36 = 62.2
N11NiO39 =
90.1
O34Ni = 3.072 N11NiO34 = 107.4 O38Zn = 2.221 O38ZnO37 = 111.8 O33Ni = 3.126
O37Zn = 2.240 O36ZnO37 = 110.9
C14H23…O31
C14H23…O30
O36ZnO31 = 119.6
= 2.115
O40Ni = 1.943
O32ZnO38 = 61.9
O39Ni = 1.952
= 2.085
H-bond
Cl24H24…O33
= 2.120
C14H23…O31
C14H23…O31 =
Cl24H24…O33
C14H24…O33
N21H25O46 =
142.0
= 2.085
137.9
= 2.121
= 155.8
O33H37…Cl31
= 2.379
O33H36…Cl38
= 2.761
N12H22…N21
= 2.510
O33H37…Cl31 O33H37…Cl31
= 2.381 = 142.0
O33H36…Cl38 O33H36…Cl38
C14H23…O30 =
140.4
= 2.764
N12H22…N21
= 2.518
= 128.7
N12H22…N21
= 97.17
Charge (e)
N11 = -0.553
Ni = 0.426
N11= -0.673
N21 = -0.750
Zn = 1.394
O32 = -0.827
O37 = -0.881
O38 = -0.771
N11 = -0.563
Ni = 0.413
N11= -0.673
N21 = -0.756
Zn = 1.399
O31 = -0.816
O36 = -0.878
O37 = -0.773
Cl32 = -0.436
O33 = -0.983
O34 = -0.984
Cl39 = -0.483
O40 = -0.906
Cl31 = -0.416
O32 = -0.984
O33 = -0.991
Cl38 = -0.478
O39 = -0.907

Table (2): Selected computed d-d excitation energies (eV), electronic transition configurations, and oscillator strengths (f) of the
studied nickel complexes
nm (eV)
f
Composition
 Ni-L1
1330 (0.932)
914 (1.356)
0.0001
0.0
HOMO-1→LUMO (98%)
HOMO-3→LUMO (63%), HOMO-11→LUMO (16%)
811 (1.528)
0.0
HOMO-7→LUMO (21%), HOMO-6→LUMO (18%)
682 (1.816)
575 (2.155)
411 (3.014)
359 (3.451)
357 (3.465)
0.0005
0.0004
0.0097
0.0027
0.0804
HOMO-8→LUMO (28%), HOMO-16→LUMO (23%)
HOMO→LUMO (92%)
HOMO-2→LUMO (77%)
HOMO-7→LUMO (34%), HOMO-8→LUMO (25%)
HOMO→LUMO+1 (93%)
 Ni-L2
1221 (1.015)
873 (1.419)
0.0002
0.0
HOMO-1→LUMO (91%)
HOMO-4→LUMO (59%), HOMO-12→L (19%)
795 (1.559)
0.0001
HOMO-6→LUMO (46%), HOMO-9→LUMO (15%)
690 (1.795)
0.0002
HOMO-7→LUMO (26%), HOMO-3→LUMO (22%), HOMO-18→LUMO (21%),
446 (2.775)
418 (2.965)
375 (3.298)
358 (3.462)
0.0005
0.0111
0.0021
0.0019
HOMO→LUMO (99%)
HOMO-2→LUMO (53%), HOMO-3→LUMO (34%)
HOMO-3→LUMO (34%), HOMO-2→LUMO (27%), HOMO-7→LUMO (23%),
HOMO-5→LUMO (88%)

General significance of the obtained results:
.
.
.
.
[NiL1,2Cl2(OH2)3] and [ZnL1,2(CH3CO2)2] benzimidazole complexes were synthesized.
Biological activity is affected by the nature of the substituent on aniline ring.
Two types of coordinated acetate groups are assigned in zinc complexes.
Strong coordination bonds between ligands and metal ions as revealed by E2 values.
Best regards
Yours
Ahmed M. Mansour
Assistant Professor of Inorganic and Analytical Chemistry,
Faculty of Science,
Cairo University,
Giza,
Egypt

Graphical abstract
The obtained results confirmed the different coordinating mode of the studied benzimidazole
ligands towards Ni(II) and Zn(II) metal ion; [NiLCl2(OH2)3] and [ZnL(CH3CO2)2]