Synthesis and crystal structure of nickel complex of N,N-bis(benzimidazol-2-yl-methyl)amine

Article abstract of DOI:10.1016/S0022-2860(02)00281-8

A new nickel(II) complex, [NiL₂]Cl₂ (L = N,N-bis(benzimidazol-2-yl-methyl)amine), was synthesized and its crystal structure was determined. According to X-ray crystallographic studies, each nickel(II) ion was six-coordinated with six nitrogen atoms of two L ligands. The complex crystallizes in triclinic system, space group P1?, a = 9.764(3) ?, b = 11.032(3) ?, c = 16.402(5) ?, α = 80.529(6)°, β = 79.180(7)°, γ = 74.232(6)°, and Z = 2. The title complex forms two-dimensional hydrogen bond network structures between the chlorine atoms and the nitrogens of L. The IR and UV spectroscopy were measured. The absorption bands of d-d electron transition are assigned, the values of Dq and B were calculated according to the electronic spectrum of the complex.

Full text of DOI:10.1016/S0022-2860(02)00281-8

Journal of Molecular Structure 644 (2003) 23–27
www.elsevier.com/locate/molstruc
Synthesis and crystal structure of nickel complex of N,N-
bis(benzimidazol-2-yl-methyl)amine
*
Jing-Yuan Xu, Wen Gu, Ling Li, Shi-Ping Yan , Peng Cheng, Dai-Zheng Liao,
Zong-Hui Jiang
Department of Chemistry, Nankai University, Tianjin 300071, People’s Republic of China
Received 2 January 2002; accepted 8 May 2002
Abstract
A new nickel(II) complex, [NiL2]Cl2 (L ¼ N,N-bis(benzimidazol-2-yl-methyl)amine), was synthesized and its crystal
structure was determined. According to X-ray crystallographic studies, each nickel(II) ion was six-coordinated with six
ꢁ
ꢀ
nitrogen atoms of two L ligands. The complex crystallizes in triclinic system, space group P1; a ¼ 9:764ð3Þ A; b ¼
ꢁ
ꢁ
11:032ð3Þ A; c ¼ 16:402ð5Þ A; a ¼ 80:529ð6Þ8; b ¼ 79:180ð7Þ8; g ¼ 74:232ð6Þ8; and Z ¼ 2: The title complex forms two-
dimensional hydrogen bond network structures between the chlorine atoms and the nitrogens of L. The IR and UV spectroscopy
were measured. The absorption bands of d–d electron transition are assigned, the values of Dq and B were calculated according
to the electronic spectrum of the complex.
q 2002 Elsevier Science B.V. All rights reserved.
Keywords: Crystal structure; N,N-bis(benzimidazol-2-yl-methyl)amine; Nickel(II) complex; Hydrogen bond
1. Introduction
2. Experimental
Histidine is known to be an important biological
ligand present at the active site of superoxide
dismutases (SOD) [1,2] and many metalloproteins
[3]. It appears to play a crucial role in the coordination
chemistry of numerous metalloproteins. The ligand of
N,N-bis(benzimidazol-2-yl-methyl)amine (L) has
proven to be an appropriate model compound of
histidine [4,5]. This paper reports the synthesis and
crystal structure of [NiL2]Cl2 complex which shows a
potential coordination environment in biological
system.
2.1. General
Iminodiacetic acid and o-phenylenediamine were
of analytical grade and used without further purifi-
cation. All other starting materials were purchased
from the Tianjin chemical company and were of
reagent grade. C, H, N elemental analyses were
carried out with a Perkin–Elmer analyzer model 240.
The IR spectra were recorded as KBr discs on a
Shimadzu IR-408 infrared spectrophotometer in the
4000–600 cm21 region. The electronic spectra were
measured on
spectrophotometer.
a
Perkin–Elmer Hitachi-240
*
Corresponding author. Fax: þ86-22-23502779.
E-mail address: coord@sun.nankai.edu.cn (S.P. Yan).
0022-2860/03/$ - see front matter q 2002 Elsevier Science B.V. All rights reserved.
PII: S0022-2860(02)00281-8

24
J.-Y. Xu et al. / Journal of Molecular Structure 644 (2003) 23–27
Table 1
Experimental data
Empirical formula
Formula weight
Temperature
C
32H30Cl2N10Ni
684.27
293(2) K
˚
0.71073 A
Wavelength
Crystal system
Space group
Triclinic
ꢀ
P1
ꢁ
Unit cell dimensions
a ¼ 9:764ð3Þ A; a ¼ 80:529ð6Þ8
ꢁ
b ¼ 11:032ð3Þ A; b ¼ 79:180ð7Þ8
ꢁ
c ¼ 16:402ð5Þ A; g ¼ 74:232ð6Þ8
3
1658.0(9) A , 2
˚
Volume, Z
Density (calculated)
Absorption coefficient
Fð000Þ
1.371 g cm23
0.785 mm21
708
0.30 £ 0.25 £ 0.20 mm3
Crystal size
u Range for data collection
Limiting indices
2.36–25.038
211 # h # 8; 212 # k # 13; 219 # l # 11
6820
Reflections collected
Independent reflections
Max. and min. transmission
Refinement method
Data/restraints/parameters
Goodness-of-fit on F2
Final R indices ½I . 2sðIÞꢀ
R indices (all data)
Largest diff. peak and hole
5770 ½RðintÞ ¼ 0:0422ꢀ
0.8588 and 0.7986
Full-matrix least-squares on F2
5770=0=406
0.950
R1 ¼ 0:0544; wR2 ¼ 0:0870
R1 ¼ 0:1504; wR2 ¼ 0:1037
23
˚
0.815 and 20.268 e A
2.2. Preparation of N,N-bis(benzimidazol-2-yl-
methyl)amine (L)
H and N contents were determined by elemental
analysis (calcd for C.56.16; H.4.42; N.20.47. Found:
C.55.71; H.4.28; N.20.32).
The ligand L was prepared by using a literature
procedure described earlier [5]. A mixture of o-
phenylenediamine (0.2 mol) and iminodiacetic acid
(0.1 mol) in 1,2-ethandiol was refluxed for 24 h. After
cooling, 450 ml of water was added with stirring. The
resulting pink precipitate was filtered and dried under
vacuum. The obtained solid was recrystallised three
times from the mixed solvent of water and propanone
in volume 1:1 to give white powder of N,N-
bis(benzimidazol-2-yl-methyl)amine. The yield was
19.24 g (70%) and mp 249–251 8C.
3. Structure determination
Determination of the unit cell and data collection
were performed on a Bruker Smart 1000 diffract-
ometer using graphite monochromated Mo Ka radi-
ation. The intensity data collected by v-scan
technique were corrected for Lorentz and polarisation
factors. An absorption correction was performed
using SADABS program [6]. Experimental data,
methods and the procedures used to elucidate the
structure and other related parameters are given in
Table 1. The structure was solved by direct methods,
SHELXS97 [7].
2.3. Preparation of the title complex
To 110.8 mg (0.4 mmol) of L stirred in 10 cm3 of
methanol, 95.2 mg (0.4 mmol) of NiCl2·6H2O in
10 cm3 of methanol was added and the mixture was
continuously stirred for about 2 h. Blue single crystals
suitable for X-ray investigation were obtained by
slowly evaporating the resulting solution in air. The C,
Since the difference synthesis did not clarify the
position of the H atoms, they were placed in
calculated positions at distances of 0.970, 0.930,
˚
0.910 and 0.860 A for CH2, CH, NH (alkylamino) and
NH (imidazolyl) bonds, respectively, from the

J.-Y. Xu et al. / Journal of Molecular Structure 644 (2003) 23–27
25
Table 2
Fractional atomic coordinates ( £ 104) and equivalent isotropic
2
3
˚
displacement parameters (A £ 10 )
Atom
x
y
z
UðeqÞ
Ni(1)
N(1)
7097(1)
5382(4)
8341(4)
8311(4)
6843(4)
5544(4)
8666(4)
7975(1)
7721(4)
6558(3)
7081(3)
6209(4)
4810(4)
8389(4)
9547(4)
9184(4)
6853(1)
6282(3)
4604(3)
5856(2)
7495(2)
7610(3)
7359(3)
7256(3)
7620(3)
7798(3)
6105(3)
5534(3)
5323(3)
4636(3)
4066(3)
4314(4)
5108(4)
5676(3)
5423(3)
6942(3)
7369(3)
7813(3)
7972(3)
8223(4)
8305(4)
8140(3)
7886(3)
6100(3)
6903(4)
8011(4)
8629(5)
9323(5)
9416(4)
8804(3)
8080(4)
6417(4)
7279(4)
8541(4)
9287(5)
9924(5)
9822(4)
9074(4)
8418(4)
3142(1)
4137(1)
33(1)
38(1)
38(1)
32(1)
34(1)
44(1)
37(1)
64(2)
37(1)
51(1)
42(1)
41(1)
30(1)
31(1)
44(2)
49(2)
47(2)
43(1)
34(1)
47(2)
40(1)
34(1)
49(2)
68(2)
66(2)
60(2)
41(1)
52(2)
45(2)
54(2)
87(2)
92(3)
68(2)
47(2)
40(1)
52(2)
41(1)
45(2)
69(2)
77(2)
71(2)
50(2)
40(1)
74(1)
60(1)
N(2)
N(3)
N(4)
N(5)
N(6)
N(7)
10,212(5)
5646(4)
4487(5)
7237(4)
5961(5)
7548(5)
9753(6)
10,976(6)
12,223(6)
12,235(6)
11,006(6)
9732(6)
4556(5)
5622(5)
7636(6)
9052(6)
9577(7)
8756(8)
7378(7)
6823(6)
8712(6)
9202(6)
10,319(6)
11,132(7)
10,915(8)
9885(7)
9074(6)
9317(5)
6026(6)
5373(5)
4139(6)
3281(6)
3201(7)
3952(7)
4804(5)
4874(5)
6665(2)
7160(1)
N(8)
N(9)
11,184(4)
9765(4)
7071(5)
6902(4)
6537(4)
6306(4)
6364(5)
6639(5)
6888(5)
6851(4)
7008(5)
6012(5)
5039(5)
4658(5)
3371(6)
2493(6)
2865(5)
4150(5)
9904(5)
9280(5)
8785(6)
8692(7)
7857(8)
7164(6)
7242(5)
8078(5)
10,788(5)
10,370(6)
10,471(6)
10,803(7)
9829(8)
8603(8)
8253(6)
9240(5)
6100(1)
9827(1)
N(10)
C(1)
C(2)
Fig. 1. An ORTEP [10] drawing of the title complex with the atom-
numbering scheme. The displacement ellipsoids are drawn at 30%
probability level.
C(3)
C(4)
C(5)
C(6)
C(7)
corresponding atoms and a riding model was used
during the refinement process by SHELXL97 [7].
Positional parameters and selected bond lengths and
angles are presented in Tables 2 and 3, respectively.
C(8)
C(9)
C(10)
C(11)
C(12)
C(13)
C(14)
C(15)
C(16)
C(17)
C(18)
C(19)
C(20)
C(21)
C(22)
C(23)
C(24)
C(25)
C(26)
C(27)
C(28)
C(29)
C(30)
C(31)
C(32)
Cl(1)
Cl(2)
4. Results and discussion
4.1. Crystal study
The title complex (Fig. 1) consists of one [NiL2]2þ
cation and two Cl2 anions. Two alkylamino and four
imidazolyls N atoms from two ligands are coordinated
to nickel ion to form a slightly distorted octahedron.
The two L ligands are tridentately bonded to Ni,
forming five-membered chelate rings. Each ligand
coordinated to Ni ion exhibits two distorted big planes
whose dihedral angles are 91.2 and 85.88 for the two
ligands, respectively. Each basal plane positions of
the nickel atoms is occupied by seven carbon atoms
and two nitrogen atoms of benzimidazol ring, one
alkylamino N atom and one methene C atom from the
L ligand. For the four planes of the [NiL2]2þ cation
unit, the basal atoms deviate from their mean plane by
˚
ca. ^0.0923, ^0.1971, ^0.0691 and ^0.1117 A,
respectively, and the metal atom is displaced out of
˚
the plane by 0.1658, 0.0355, 0.0596 and 0.1702 A,
P P
i
UðeqÞ ¼ ð1=3Þ
j Uijapi apj aiaj:

26
J.-Y. Xu et al. / Journal of Molecular Structure 644 (2003) 23–27
Table 3
˚
Selected bond lengths (A) and angles (8)
Bond lengths
Bond angles
Bond angles
Ni(1)–N(3)
Ni(1)–N(8)
Ni(1)–N(6)
Ni(1)–N(4)
Ni(1)–N(1)
Ni(1)–N(10)
2.054(4)
2.055(4)
2.056(4)
2.111(4)
2.165(4)
2.170(4)
N(3)–Ni(1)–N(8)
N(3)–Ni(1)–N(6)
N(8)–Ni(1)–N(6)
N(3)–Ni(1)–N(4)
N(8)–Ni(1)–N(4)
N(6)–Ni(1)–N(4)
N(3)–Ni(1)–N(1)
N(8)–Ni(1)–N(1)
165.65(16)
100.88(16)
86.22(15)
89.87(15)
100.32(17)
105.54(16)
80.77(16)
91.12(16)
N(6)–Ni(1)–N(1)
N(4)–Ni(1)–N(1)
N(3)–Ni(1)–N(10)
N(8)–Ni(1)–N(10)
N(6)–Ni(1)–N(10)
N(4)–Ni(1)–N(10)
N(1)–Ni(1)–N(10)
174.78(17)
79.35(15)
87.76(16)
81.16(17)
79.95(16)
174.36(16)
95.21(15)
respectively. The Ni–N bonds of alkylamino
˚
(average 2.168(4) A) are slightly longer than those
4.2. Spectroscopic properties
˚
of imidazolyls (average 2.069(4) A), (Table 2). As
The infrared spectra of the title complex display
the characteristic bands of the ligand. The n(–CyN)
absorption of the benzimidazole is observed at
1621s cm21, and n(C–N) at 1450s cm21, and they
are slightly shifted to higher wavenumbers than those
of the free ligand. The n(N–H) is at 3350s,b and
3100s,b cm21. The absorption bands, near 900w,
740m cm21, are due to out-of-plane bend vibration
correlating with aryl ring, where s, b, m and w refer to
strong, broad, medium and weak, respectively.
can be seen from the packing diagram (Fig. 2)
there are intermolecular hydrogen bonds between
the Cl2 anions and the N atoms of [NiL2]2þ
cations of neighbouring molecules. Hydrogen
bonding distances and angles are grouped in
Table 4. For clarity the conventional description
of hydrogen bonding structural parameters has been
adopted: D(H)· · ·A (D ¼ N(1), N(2), N(5), N(7),
N(9), N(10); A ¼ Cl(1), Cl(2)) indicates the
distance between a donor D atom and acceptor A
atom, (D)H· · ·A the distance between a donor
hydrogen atom bound to D and acceptor, while
D–H· · ·A indicates the angle. The Cl(1) anion
forms hydrogen bond network with N(2), N(5) and
N(9) atoms from imidazolyls rings at 3.316, 3.125
The ultraviolet and visible spectra were measured
in the 200–900 nm range. The spectra show a very
strong absorption band over 46,730 cm21 ð1 ¼
3:00 £ 104 L mol21 cm21Þ; and three strong absorp-
tions at 41,152 cm21 ð1 ¼ 1:69 £ 104 L mol21 cm21Þ;
36,630 cm21 ð1 ¼ 2:08 £ 104 L mol21 cm21
Þ
and
35,714 cm21 ðe ¼ 2:02 £ 104 L mol21 cm21Þ; which
may be attributed to charge transfer and the transition of
the ligand itself. In addition, three very weak absorp-
tions at 27,240 cm21 (n1, 1 < 84 L mol21 cm21Þ,
˚
and 3.149 A of D(H)· · ·A distances, and the Cl(2)
anion with imidazolyls N(7) atom, and two
alkylamino N atoms: N(1) and N(10) at 3.244,
˚
3.214 and 3.232 A, respectively. All these hydrogen
bonds connect [NiL2]2þ and Cl2 to form a two-
dimensional network along a and b axes.
17,540 cm21 (n2, 1 < 26 L mol21 cm21
)
and
11,792 cm21 (n3, 1 < 12 L mol21 cm21) may be
Table 4
˚
Relevant intermolecular hydrogen bonds parameters (distances in A, angles in degrees)
D–H
(D)H· · ·A
D–H· · ·A
D(H)· · ·A
A
Symm.
N(1)–H(1C)
N(2)–H(2A)
N(5)–H(5B)
N(7)–H(7B)
N(9)–H(9C)
N(10)–H(10A)
2.328
2.469
2.343
2.580
2.345
2.333
164.45
168.69
151.34
134.84
155.84
169.57
3.214
3.316
3.125
3.244
3.149
3.232
Cl(2)
Cl(1)
Cl(1)
Cl(2)
Cl(1)
Cl(2)
½2x þ 1; 2y þ 2; 2z þ 1ꢀ
½2x þ 1; 2y þ 1; 2z þ 1ꢀ
½2x þ 2; 2y þ 2; 2z þ 1ꢀ
½2x þ 1; 2y þ 2; 2z þ 1ꢀ
D: Donor; A: Acceptor; Symm.: Symmetry applied in acceptor.

J.-Y. Xu et al. / Journal of Molecular Structure 644 (2003) 23–27
27
observed in the concentrated solution. They are
tentatively attributed to the electronic transitions
3
3
n1 : 3A2g ! T1gðPÞ; n2 : 3A2g ! T1g and n3 : 3A2g
!
3T2g: The values of the parameter Dq, B were 1179 and
626, respectively, and n2 ¼ 17; 526 cm21; which
calculated from the values of n1 and n3 according to
the formula of electronic transitions energy [8], and the
assignment was checked by comparing the predicted
and observed positions of the second band. The
agreement is very satisfactory. This spectrum is typical
d–d charge-transfer bands in the octahedral Ni(II)
surrounding [9].
Acknowledgments
This work was supported by the National Natural
Science Foundation of China (No. 20171026) and
Tianjin Natural Science Foundation (No. 013605811).
References
[1] Y. Kitagawa, N. Tanaka, Y. Hata, M. Kusonoki, G.P. Lee, Y.
Katsube, K. Asada, J. Biochem. 109 (1991) 477.
[2] J.B. Cooper, H.P.C. Driessen, S.P. Wood, Y. Zhang, D.
Young, J. Mol. Biol. 235 (1994) 1156.
[3] W.R. Scheidt, C.A. Reed, Chem. Rev. 81 (1981) 543.
[4] C. Piguet, B. Bocquet, E. Mu¨ller, A.F. Williams, Helv. Chim.
Acta 72 (1989) 323–337.
[5] X.L. Liu, Q.Y. Cheng, W.H. Zhou, R. Zhao, X.H. Liu, F.M.
Miao, Acta Chim. Sinica. 59 (2001) 1045.
[6] G.M. Sheldrick, SADABS: Program for the Empirical correc-
¨
tion of Area-Detector Data; University of Gottingen:
Germany, 1996.
[7] G.M. Sheldrick, SHELXS97 and SHELXL97, University of
¨
Gottingen, Germany, 1996.
[8] G.L. Wang, S.P. Yan, D.Z. Liao, F.L. Yin, Acta Chim. Sinica.
44 (1986) 196 and references cited therein.
[9] M. Schro¨eder, in: R.B. King (Ed.), Encyclopedia of Inorgnic
Chemistry: Nickel: Inorganic and Coordination Compounds,
vol. 5, Wiley, New York, 1994, pp. 2392–2412, and
references cited therein.
Fig. 2. The packing diagram of the title complex viewed along (a) a-
axis and (b) b-axis. Hydrogen bonds are shown as dotted lines and H
atoms not involved in hydrogen bonding and phenyl rings have been
omitted for clarity.
[10] C.K. Johnson, ORTEP II, Report ORNL-5138, Oak Ridge
National Laboratory, TN, 1976.