ORIGINAL PAPER

Synthesis, Crystal Structure and DNA-Binding Propertiesof a Zinc(II) Complex with 1,3-Bis(1-propylbenzimidazol-2-yl)-2-oxapropane

Huilu Wu • Fan Kou • Fei Jia • Bin Liu •

Jingkun Yuan • Ying Bai

Received: 12 August 2011 / Accepted: 6 June 2012 / Published online: 19 June 2012

� Springer Science+Business Media, LLC 2012

Abstract A complex of formula [Zn(pobb)2]�2pic, (pobb

= 1,3-bis(1-propylbenzimidazol-2-yl)-2-oxapropane, pic =

2,4,6-trinitrophenol), has been synthesized and structurally

characterized by elemental analysis, IR, UV–Vis spectral

measurements. The crystals crystallize in the monoclinic

system, space group C2/c, a = 25.77(2) A, b = 15.227(13)

A, c = 19.281(17) A, a = 90�, b = 129.544(7)�, c = 90�,

Z = 4. The coordination environment around zinc(II) atom

can be described as a distorted octahedral geometry. The

interactions of the ligand pobb and the zinc(II) complex

with calf thymus DNA (CT-DNA) are investigated by

using electronic absorption titration, ethidium bromide-

DNA displacement experiments and viscosity measure-

ments. The experimental evidence indicated the pobb and

the zinc(II) complex interact with CT-DNA through

intercalation.

Keywords 1,3-Bis(1-propylbenzimidazol-2-yl)-2-

oxopropane � Zinc(II) complex � Crystal structure � DNA

binding property

Introduction

Benzimidazoles have a wide variety of pharmacological

applications including fungicides or antihelminthics [1].

The benzimidazole ring, classed as a privileged structure

[2–4], is present in clinically approved anthelmintics,

antiulcers, antivirals, and antihistamines [5, 6].

The interaction of transition metal complexes with DNA

have been an active area of research at the interface of

chemistry and biology [7–9]. Numerous biological exper-

iments have demonstrated that DNA is the primary intra-

cellular target of anticancer drugs; interaction between

small molecules and DNA can cause damage in cancer

cells, blocking the division and resulting in cell death

[10–12]. Studies on the interaction of transition metal

complexes with nucleic acid have gained prominence,

because of their relevance in the development of new

reagents for biotechnology and medicine [13, 14]. Zinc is

an element of great biological interest [15]. Zinc plays an

important role in various biological systems; it is critical

for numerous cell processes and is a major regulatory ion in

the metabolism of cells [16]. In the literature, diverse zinc

complexes with biological activity are reported, but only

zinc complexes with drugs used for the treatment of Alz-

heimer disease [17] and others showing antibacterial [18],

anticonvulsant [19], antidiabetic [20], anti-inflammatory

[21], antimicrobial [22] and antiproliferative–antitumor

[23] activity are structurally characterized [24].

In this study, a new ligand and its Zn(II) complex have

been synthesized and characterized. The DNA-binding

behaviors were investigated.

Experimental

The C, H and N elemental analyses were determined using

a Carlo Erba 1106 elemental analyzer. Electrolytic con-

ductance measurements were made with a DDS-11A type

conductivity bridge using 10-3 mol L-1 solutions in DMF

at room temperature. The IR spectra were recorded in the

4,000–400 cm-1 region with a Nicolet FT-VERTEX 70

spectrometer using KBr pellets. Electronic spectra were

H. Wu (&) � F. Kou � F. Jia � B. Liu � J. Yuan � Y. Bai

School of Chemical and Biological Engineering, Lanzhou

Jiaotong University, Lanzhou 730070, Gansu,

People’s Republic of China

e-mail: wuhuilu@163.com

123

J Chem Crystallogr (2012) 42:884–890

DOI 10.1007/s10870-012-0331-8

taken on a Lab-Tech UV Bluestar spectrophotometer. 1H

NMR spectra were obtained with a Mercury plus 400 MHz

NMR spectrometer with TMS as internal standard and

DMSO-d6 as solvent. The fluorescence spectra were

recorded on a LS-45 spectrofluorophotometer.

Synthesis of the Ligand and Complex

1, 3-Bis(1-propylbenzimidazol-2-yl)-2-oxopropane (pobb)

The 1, 3-bis(1-benzimidazol-2-yl)-2-oxopropane (5.56 g,

0.020 mol)(synthesized by the literature method [25]) was

suspended in dry tetrahydrofuran (170 mL) and stirred

under reflux with potassium (1.56 g). Iodopropane (6.80 g,

0.040 mol) was added, and the solution was stirred for 2 h.

The solvents were stripped to dryness and the resulting

powder dissolved in distilled water. The soluble KI was

removed by filtration. The undissolved substances were

recrystallized from MeOH and a colorless powder was

deposited. Yield: 3.84 g (53 %); M. p. 54–56 �C. Anal.

Calcd for C22H26N4O (%): C 72.90; H 7.23; N 15.46.

Found (%): C 72.87; H 7.20; N 15.45. 1H NMR (400 MHz,

DMSO-d6, d/ppm): d = 7.59–7.68 (4H, m, Ph-H), 7.23–

7.30 (4H, m, Ph-H), 4.92 (2H, s, –CH2–O), 4.20–4.27 (2H,

m, –CH2CH2CH3), 1.70–1.80 (2H, m, –CH2CH2CH3),

0.79–0.86 (3H, m, –CH2CH2CH3). IR (selected data, KBr):

m = 746 m(o–Ar), 1112 (mC–O), 1443 (mC=N), 1623 m(C=C).

UV/Vis (DMF): k = 280, 288 nm.

Preparation of Zn(II) Complex

The synthesis of the ligand pobb and the Zn(II) complex are

shown in Scheme 1. To a stirred solution of 1,3-bis(1-pro-

pylbenzimidazol-2-yl)-2-oxopropane (0.145 g, 0.40 mmol)

in hot MeOH (5 mL) was added Zn(II) picrate (0.104 g,

0.20 mmol) in MeOH (5 mL). A deep white precipitate

product formed rapidly. The precipitate was filtered off,

washed with MeOH and absolute Et2O, and dried in vacuo.

The dried precipitate was dissolved in DMF resulting in a

yellow solution. The white crystals suitable for X-ray dif-

fraction studies were obtained by ether diffusion into DMF

after several days at room temperature. Yield: 0.182 g

(72 %). Anal. Calcd for C56H56N14O16Zn (%): C, 53.96; H,

4.53; N, 15.73. Found (%): C, 53.95; H, 4.56; N, 15.70. IR

(selected data, KBr): 748 m(o–Ar), 1076 m(C–O), 1494 m(C=N),

1635 m(C=C). UV/Vis (DMF): k = 281, 289, 383 nm.

X-ray Crystal Structure Determination

A suitable single crystal was mounted on a glass fiber, and

the intensity data were collected on a Bruker APEX-II

CCD (Japan) diffractometer with graphite-monochroma-

tized Mo Ka radiation (k = 0.71073 A) at 293(2) K. Data

reduction and cell refinement were performed using Saint

programs [26]. The absorption correction was carried out

by empirical methods. The structure was solved by Direct

Methods and refined by full-matrix least-squares against F2

using SHELXTL software [27]. All H atoms were found in

difference electron maps and were subsequently refined in

a riding model approximation with C–H distances ranging

from 0.95 to 0.99 A. The crystal data and experimental

parameters relevant to the structure determination are listed

in Table 1. Selected bond distances and angles are pre-

sented in Table 2.

DNA-Binding Studies

Calf thymus DNA (CT-DNA) and ethidium bromide (EB)

were obtained from Sigma-Aldrich Co. (USA). Other

reagents and solvents were reagent grade obtained from

commercial sources and used without further purification.

Tris–HCl buffer were prepared using bidistilled water. The

stock solution of complex was dissolved in DMF at

3 9 10-3 mol L-1. All chemicals used were of analytical

Scheme 1 The synthesis of the

ligand pobb and the Zn(II)

complex (pic = picrate)

J Chem Crystallogr (2012) 42:884–890 885

123

grade. The experiments involving interaction of the ligand

and the complex with CT-DNA were carried out in doubly

distilled water buffer containing 5 mM Tris and 50 mM

NaCl and adjusted to pH 7.2 with hydrochloric acid. A

solution of CT-DNA gave a ratio of UV absorbance at 260

and 280 nm of about 1.8–1.9, indicating that the CT-DNA

was sufficiently free of protein [28]. The CT-DNA con-

centration per nucleotide was determined spectrophoto-

metrically by employing an extinction coefficient of

6,600 M-1 cm-1 at 260 nm [29].

Absorption titration experiments were performed with

fixed concentrations of the compounds, while gradually

increasing the concentration of CT-DNA. To obtain the

absorption spectra, the required amount of CT-DNA was

added to both compound solution and the reference solu-

tion to eliminate the absorbance of CT-DNA itself. From

the absorption titration data, the binding constant (Kb) was

determined using the equation [30]:

DNA½ �=ðea � efÞ ¼ DNA½ �=ðeb � efÞ þ 1=Kbðeb � efÞ

where [DNA] is the concentration of CT-DNA in base

pairs, ea corresponds to the extinction coefficient observed

(Aobsd/[M]), ef corresponds to the extinction coefficient of

the free compound, eb is the extinction coefficient of the

compound when fully bound to CT-DNA, and Kb is the

intrinsic binding constant. The ratio of slope to intercept in

the plot of [DNA]/(ea - ef) versus [DNA] gave the value of

Kb.

EB emits intense fluorescence in the presence of CT-

DNA, due to its strong intercalation between the adjacent

CT-DNA base pairs. It was previously reported that the

enhanced fluorescence can be quenched by the addition of

a second molecule [31, 32]. The extent of fluorescence

quenching of EB bound to CT-DNA can be used to

determine the extent of binding between the second mol-

ecule and CT-DNA. The competitive binding experiments

were carried out in the buffer by keeping [DNA]/

[EB] = 1.13 and varying the concentrations of the com-

pounds. The fluorescence spectra of EB were measured

using an excitation wavelength of 520 nm and the emission

range was set between 550 and 750 nm. The spectra were

analyzed according to the classical Stern–Volmer equation

[33],

I0= I ¼ 1þ Ksv Q½ �

where I0 and I are the fluorescence intensities at 604 nm in

the absence and presence of the quencher, respectively, Ksv

is the linear Stern–Volmer quenching constant, [Q] is the

concentration of the quencher.

Viscosity experiments were conducted on an Ubbelodhe

viscometer, immersed in a water bath maintained at

25.0 ± 0.1 �C. Titrations were performed for the com-

pound (3 lM), and each compound was introduced into

Table 1 Crystal data and structure refinement for the Zn(II) complex

Formula C56H56N14O16Zn

M 1246.52

System Monoclinic

Space group C2/c

a (A) 25.77(2)

b (A) 15.227(13)

c (A) 19.281(17)

b/(�) 129.544(7)

V/A3 5834(8)

Z 4

qcaled (g/cm3) 1.419

Limiting indices -30,25/-18,18/-21,21

Crystal size (mm) 0.25 9 0.23 9 0.21

Absorption correction Semi-empirical from equivalents

Min. and max. transmission 0.9018/0.8846

q range for data collection (�) 2.55 \ h\ 25.00

Data/restraints/parameters 4,985/6/396

F(000) 2,592

Final R indices [I [ 2sigma(I)] R1 = 0.0688, wR2 = 0.1822

R indices (all data) 0.1822

Dq(max) and Dq(min), (e A -3) 1.376 and -0.733

Table 2 Selected bond lengths (A) and angles (�) for the Zn(II)

complex

Bond lengths

Zn(1)–N(3)#1 2.078(4)

Zn(1)–N(1)#1 2.100(4)

Zn(1)–O(1) 2.336(5)

Zn(1)–N(3) 2.078(4)

Zn(1)–N(1) 2.100(4)

Zn(1)–O(2) 2.426(8)

Bond angles

N(3)#1–Zn(1)–N(3) 137.5(2)

N(3)–Zn(1)–N(1)#1 95.67(13)

N(3)–Zn(1)–N(1) 98.61(14)

N(3)#1–Zn(1)–O(1) 111.25(11)

N(1)#1–Zn(1)–O(1) 69.94(11)

N(3)#1–Zn(1)–O(2) 68.75(11)

N(1)#1–Zn(1)–O(2) 110.06(11)

N(3)#1–Zn(1)–N(1) 95.67(13)

N(1)#1–Zn(1)–N(1) 139.9(2)

N(3)–Zn(1)–O(1) 111.25(11)

N(1)–Zn(1)–O(1) 69.94(11)

N(3)–Zn(1)–O(2) 68.75(11)

N(1)–Zn(1)–O(2) 110.06(11)

O(1)–Zn(1)–O(2) 180.000(1)

Symmetry transformations used to generate equivalent atoms:

#1 - x ? 1, y, -z ? 1/2

886 J Chem Crystallogr (2012) 42:884–890

123

CT-DNA solution (50 lM) present in the viscometer. Data

were presented as (g/g0)1/3 versus the ratio of the concen-

tration of the compound to CT-DNA, where g is the vis-

cosity of CT-DNA in the presence of the compound and g0

is the viscosity of CT-DNA alone. Viscosity values were

calculated from the observed flow time of CT-DNA con-

taining solutions corrected from the flow time of buffer

alone (t0), g = (t - t0) [34].

Results and Discussion

The ligand pobb and the Zn(II) complex are very stable in

the air. The ligand pobb is soluble in organic solvents but

insoluble is water. The Zn(II) complex is soluble in DMF

and DMSO but insoluble in water and others organic sol-

vents, such as methanol, ethanol, acetone, petroleum ether,

trichloromethane, etc.

The results of the elemental analyses show that the

composition is [Zn(pobb)2](pic)2. The IR spectra of the free

ligand pobb and the Zn(II) complex were compared. The IR

spectrum of the Zn(II) complex shows that the strong

absorption mC=N in the free ligand, which is shifted to lower

wave numbers in the Zn(II) complex. The redshift indicates

that the nitrogen atoms of the ligand are coordinated to the

Zn(II) atom. They are the preferred nitrogen atoms for

coordination, as found in other metal complexes with

benzimidazole open chain crown ether derivatives [35]. This

fact agrees with the result determined by X-ray diffraction.

In the UV/Vis spectra, the band of free ligand are red-shifted

in the Zn(II) complex and show clear evidence of C=N

coordination to the copper atom. The absorption band is

assigned to p–p* (imidazole) transition [36].

X-ray Crystallography

Complex crystallizes in the monoclinic space group C2/

c and its structure along with the atomic numbering scheme

is shown in Fig. 1, consists of a [Zn(pobb)2]2? cation

and two trinitrophenol anions. The central metal ion of

[Zn(pobb)2]2? cation, adopting a distorted octahedral

geometry, is six-coordinated with an N4O2 ligand set which

four N atoms (N(1), N(3), N(1)A, N(3)A) are afforded by

the benzimidazole rings and other two O atoms (O(1),

O(1)A) are supplied by the pobb. The complex is fairly

symmetrical and symmetry transformations #1 -x ? 1, y,

-z ? 1/2 were used to generate equivalent atoms. An

equatorial plane is formed by atoms N(1), N(3), N(1)A,

N(3)A and Zn(1), where the deviation for four N atoms is

0.737 A and the Zn(1) atom is in the mean plane. The bond

angles of ideal 90� are range from 98.61(14)� [N(3)–Zn(1)–

N(1)] to 95.67(13)� [N(3)#1–Zn(1)–N(1)] and from 69.94

(11)� [N(1)–Zn(1)–O(1)] to 111.25(11)� [N(3)–Zn(1)–

O(1)]. The bond lengths of ideal are equally, but the bond

lengths are 2.336(5) A [Zn(1)–O(1)] to 2.426(8) A [Zn(1)–

O(2)]. With regard to a regular octahedron, the angles and

lengths show a certain distortion.

CT-DNA Binding Studies

Electronic Absorption Titration

Electronic absorption spectroscopy is universally employed

to determine the binding characteristics of metal complexes

with DNA [37–39]. The absorption spectra of the ligand

pobb and the Zn(II) complex in the absence and presence

of CT-DNA are given in Fig. 2a, c, respectively. As for the

Fig. 1 The molecular structure

of complex Zn(II) showing

displacement ellipsoids at the

30 % probability level

J Chem Crystallogr (2012) 42:884–890 887

123

ligand pobb with two well-resolved band at 258 nm and

278 nm in Fig. 2a, there is also a well-resolved band at

about 277 nm in Fig. 2c for the Zn(II) complex. With

increasing DNA concentrations, the hypochromism are

12.5 % at 276 nm for the ligand pobb, and 13.1 % at

277 nm for the Zn(II) complex. The hypochromism sug-

gest that the ligand pobb and the Zn(II) complex interact

with DNA [40].

The binding constant Kb for the Zn(II) complex have

been determined from the plot of [DNA]/(eA - ef) versus

[DNA] and found to be 1.1 9 105 M-1 (R = 0.97 for 10

points). Kb for the ligand (8.2 9 103 M-1) (R = 0.97 for

10 points) is thus smaller than for the Zn(II) complex.

Compared with those of a so-called DNA-intercalative

ruthenium complexes (1.1 9 104–4.8 9 105 M-1) [41],

the binding constants (Kb) of the ligand pobb and the Zn(II)

complex suggest that the compounds most probably bind to

DNA in an intercalation mode. With the above intrinsic

binding constant values, the binding affinity of the Zn(II)

complex is stronger than that of the free ligand pobb.

Competitive Binding with EB

For measuring the ability of a complex to affect the EB

fluorescence intensity in the EB–DNA adduct, the fluo-

rescence quenching method can be used to determine the

affinity of the complex for DNA, whatever the binding

mode may be. If a complex can remove EB from EB-

loaded DNA, the fluorescence of the solution will be

quenched due to the fact that free EB molecules are readily

quenched by the surrounding water molecules [42]. The

fluorescence quenching of EB bound to CT-DNA by the

ligand pobb and the Zn(II) complex are shown in Fig. 3.

The quenching plots illustrate that the quenching of EB

bound to DNA by the complex is in good agreement with

the linear Stern–Volmer equation, which also proves that

the complex binds to DNA. The Ksv value has been esti-

mated to be 7.8 9 102 M-1(R = 0.96 for 9 points) and

3.6 9 103 M-1 (R = 0.93 for 9 points) for the ligand pobb

and the Zn(II) complex, respectively. The fact that both the

ligand pobb and the Zn(II) complex show almost similar

Fig. 2 Electronic spectra of the free pobb (a) and complex the Zn(II)

(c) in Tris–HCl buffer upon addition of CT-DNA. [DNA] = 1 9

10-5–9 9 10-5 M. The arrow shows the emission intensity changes

upon increasing DNA concentration. [DNA]/(ea - ef) versus. [DNA]

for the titration of the free ligand pobb (b) and the Zn(II) complex

(d) with CT-DNA

888 J Chem Crystallogr (2012) 42:884–890

123

DNA binding constant indicates that pobb is the interca-

lating ligand. Moreover, the binding strength of the Zn(II)

complex is greater than the free ligand pobb.

Viscosity Studies

Optical photophysical probes generally provide necessary,

but not sufficient clues to support a binding model. Mea-

surements of DNA viscosity that is sensitive to DNA length

are regarded as the least ambiguous and the most critical

tests of binding in solution in the absence of crystallo-

graphic structural data [43, 44]. Intercalating agents are

expected to elongate the double helix to accommodate the

ligands in between the bases leading to an increase in the

viscosity of DNA. In contrast, complex that binds exclu-

sively in the DNA grooves by partial and/or non-classical

intercalation, under the same conditions, typically cause

less pronounced (positive or negative) or no change in

DNA solution viscosity [45]. The values of (g/g0)1/3 were

plotted against [Compound]/[DNA] (Fig. 4). Upon addi-

tion of the ligand and Zn(II) complex the viscosity of rod-

like CT-DNA increased significantly, which suggests

that the ligand pobb and Zn(II) complex can bind to DNA

by intercalation [43]. The results from the viscosity

Fig. 3 Emission spectra of EB bound to CT-DNA in the presence of

the free pobb (a) and the Zn(II)complex (c), kex = 520 nm,

[Compound] = 0.6 9 10-5–6 9 10-5 M. The arrows show the

intensity changes upon increasing concentrations of the complexes.

Fluorescence quenching curves of EB bound to CT-DNA by the free

pobb (b) and the Zn(II)complex (d) (Plots of I0/I versus [Compound].)

Fig. 4 Effect of increasing amounts of the compounds on the relative

viscosity at 25.0 ± 0.1 �C

J Chem Crystallogr (2012) 42:884–890 889

123

experiments confirm the mode of these compounds inter-

calating into DNA base pairs and already established

through absorption spectroscopic studies and fluorescence

spectroscopic studies.

Conclusion

In this paper, a new bis-benzimidazole base ligand, and its

Zn(II) complex were reported. The structure of the ligand

and the Zn(II) complex were determined on the basis of

elemental analyses, molar conductivities, IR spectra, 1H

NMR and UV–vis spectra. The Zn(II) complex’s crystal

structure have been determined by X-ray crystallography

method. Experimental results indicate that the ligand and

the Zn(II) complex bind to DNA via an intercalation mode

and the Zn(II) complex can bind to DNA more strongly

than the free ligand alone. Results obtained from our

present work would be useful to understand the mechanism

of interactions of the small molecule compounds binding to

DNA and helpful in the development of their potential

biological, pharmaceutical and physiological implications

in the future.

Supplementary Material

Crystallographic data for the Zn(II) complex has been

deposited with the Cambridge Crystallographic Data Cen-

ter as supplementary publication No. CCDC 837841.

Copies of the data can be obtained free of charge on

application to The Director, CCDC, 12 Union Road,

Cambridge CB2 1EZ, UK (fax: ?44 1223 336 033; e-mail:

deposit@ccdc.cam.ac.uk).

Acknowledgments The authors acknowledge the financial support

and a grant from ‘Qing Lan’ Talent Engineering Funds by Lanzhou

Jiaotong University.

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