A V-shaped ligand Bis(2-benzimidazolymethyl)amine (bba) and its nickel(II) picrate (pic) complex, with composition [Ni(bba)2](pic)2·3MeOH, have been synthesized and characterized on the basis of elemental analyses, molar conductivities, IR spectra, and UV/vis measurements. In the complex, the Ni(II) ion is six-coordinated with a N2O4 ligand set, resulting in a distorted octahedron coordination geometry. In addition, the DNA-binding properties of the Ni(II) complex have been investigated by electronic absorption, fluorescence, and viscosity measurements. The experimental results suggest that the nickel(II) complex binds to DNA by partial intercalation binding mode.
Binding studies of small molecules to DNA are very important in the development of DNA molecular probes and new therapeutic reagents [
Since the benzimidazole unit is the key-building block for a variety of compounds which have crucial roles in the functions of biologically important molecules, there is a constant and growing interest over the past few years for the synthesis and biological studies of benzimidazole derivatives [
In this context, we synthesized and characterized a novel Ni(II) complex. Moreover, we describe the interaction of the novel Ni(II) complex with DNA using electronic absorption and fluorescence spectroscopy and viscosity measurements.
Calf thymus DNA (CT-DNA) and Ethidium bromide (EB) were purchased from Sigma Chemicals Co. (USA). All chemicals used were of analytical grade. All the experiments involving interaction of the ligand and the complexes 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 [
Elemental analyses were performed on Carlo Erba 1106 elemental analyzer. The IR spectra were recorded in the 4000–400 cm−1 region with a Nicolet FT-VERTEX 70 spectrometer using KBr pellets. Electronic spectra were taken on a Lab-Tech UV Bluestar spectrophotometer. The fluorescence spectra were recorded on a 970-CRT spectrofluorophotometer. 1H
Absorption titration experiment was performed with fixed concentrations of the complexes while gradually increasing concentration of CT-DNA. While measuring the absorption spectra, a proper amount of CT-DNA was added to both compound solution and the reference solution to eliminate the absorbance of CT-DNA itself. From the absorption titration data, the binding constant (
EB emits intense fluoresence 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 [
Viscosity experiments were conducted on an Ubbelohde viscometer, immersed in a thermostated water-bath maintained at 25.0 ± 0.1°C. DNA samples approximately 200 bp in average length were prepared by sonicating in order to minimize complexities arising from DNA flexibility [
The synthetic route for the ligand bba and its Ni(II) complex are shown in Scheme
The synthesis of ligand bba and its Ni(II) complex.
The ligand bba was synthesized according to the procedure reported by Berends and Stephan [
The ligand bba (0.4 mmol) and Ni(II) picrate (0.2 mmol) were dissolved in methanol (15 mL). A blue-green crystalline product which formed rapidly was filtered off, washed with methanol and absolute Et2O, and dried in vacuo. The dried precipitate was dissolved in DMF resulting in a blue-green solution that was allowed to evaporate at room temperature. Blue-green crystals suitable for X-ray diffraction studies were obtained after one week. C47H36N16Ni O17 (Mr = 1155.63 g·mol−1) calcd: C 48.85; H 3.14; N 19.39%; found: C 48.79; H 3.16; N 19.53%. IR (KBr, pellet, cm−1): 1272s (
A suitable single crystal was mounted on a glass fiber and the intensity data were collected on a Bruker Smart CCD diffractometer with graphite-monochromated Mo K
Crystallographic data and data collection parameters for the Ni(II) complex.
Complex | [Ni(bba)2](pic)2·3MeOH |
---|---|
Molecular formula | C47H36N16NiO17 |
Molecular weight | 1155.63 |
Crystal system | Triclinic |
Space group | P-1 |
a (Å) | 10.4758 (9) |
b (Å) | 16.1097 (13) |
c (Å) | 17.2302 (14) |
107.5590 (10) | |
107.5880 (10) | |
96.9150 (10) | |
2570.1 (4) | |
2 | |
1.493 | |
Absorption coefficient (mm−1) | 0.467 |
1188 | |
Crystal size (mm) | 0.41 × 0.38 × 0.31 |
2.04–25.00 | |
−12, 12/−16, 19/−20, 20 | |
Reflections collected | 18579 |
Independent reflections | 8974 [ |
Data/restraints/parameters | 8974/6/746 |
Goodness-of-fit on | 1.097 |
Final | 0.0383, 0.1135 |
0.0466, 0.1194 | |
Largest differences peak and hole (eÅ−3) | 0.734 and −0.384 |
The ligand bba and its Ni(II) complex are very stable in the air. They are remarkably soluble in polar solvents such as DMF, DMSO, and MeCN; slightly soluble in ethanol, methanol, ethyl acetate, and chloroform. The molar conductivities in DMF solution indicate that bba (1.29 S·cm2·mol−1) is nonelectrolyte compound and its Ni(II) complex is 1 : 2 electrolyte compound [
In the bba ligand, a strong band is found at ca. 1270 cm−1 together along with a broad band at 1436 cm−1. By analogy with the assigned bands of imidazole, the former can be attributed to
DMF solutions of ligand bba and its complexes show, as expected, almost identical UV spectra. The UV bands of bba (275, 280 nm) are only marginally blue shifted (1-2 nm) in the complexes, which is clear evidence of C=N coordination to the metal ions center. The absorption bands are assigned to
The molecular structure of the Ni(II) complex is shown in Figure
Selected bond lengths (Å) and angles (deg) of the Ni(II) complex.
Bond lengths | |||||
Ni–N(1) | 2.1647 (19) | Ni–N(4) | 2.0793(18) | Ni–N(6) | 2.1788(19) |
Ni–N(3) | 2.0899 (19) | Ni–N(7) | 2.0667 (18) | Ni–N(9) | 2.0628 (19) |
Bond angles | |||||
N(1)–Ni–N(6) | 94.12 (7) | N(9)–Ni–N(7) | 173.40 (7) | N(9)–Ni–N(4) | 98.11 (7) |
N(3)–Ni–N(7) | 173.40 (7) | N(3)–Ni–N(1) | 79.29 (7) | N(7)–Ni–N(4) | 166.55 (7) |
N(9)–Ni–N(3) | 107.52 (7) | N(7)–Ni–N(3) | 98.95 (7) | N(3)–Ni–N(4) | 89.98 (7) |
N(1)–Ni–N(9) | 173.19 (7) | N(7)–Ni–N(1) | 90.23 (7) | N(1)–Ni–N(4) | 81.52 (7) |
N(9)–Ni–N(6) | 79.07 (8) | N(7)–Ni–N(6) | 81.11 (7) | N(4)–Ni–N(6) | 88.87 (7) |
The molecular structure of the Ni(II) complex showing displacement ellipsoids at the 30% probability level. Hydrogen atoms have been omitted for clarity.
Electronic absorption spectroscopy is universally employed to determine the binding characteristics of metal complexes with DNA [
Electronic spectra of the Ni(II) complex (30
The binding constant
In general, measurement of the ability of a complex to affect the EB fluorescence intensity in the EB-DNA adduct allows determination of the affinity of the complex for DNA, whatever the binding mode may be. If a complex can replace EB from DNA-bound EB, the fluorescence of the solution will be quenched due to the fact that free EB molecules are readily quenched by the surrounding water molecules [
Emission spectra of EB bound to DNA in the presence of the complex. [Complex] =
Optical photophysical techniques are widely used to study the binding model of the ligand, metal complexes, and DNA but not to give sufficient clues to support a binding model. Therefore, viscosity measurements were carried out to further clarify the interaction of metal complexes and DNA. Hydrodynamic measurements that are sensitive to the length change (i.e., viscosity and sedimentation) are regarded as the least ambiguous and the most critical tests of a binding model in solution in the absence of crystallographic structural data [
Effect of increasing amounts of the Ni(II) complex on the relative viscosity of CT-DNA at 25.0 ± 0.1°C.
In this paper, a new Ni(II) complex has been synthesized and characterized. Moreover, the DNA-binding properties of the Ni(II) complex were investigated by electronic absorption, fluorescence, and viscosity measurements. The experimental results indicate that the Ni(II) complex can bind to CT-DNA by partial intercalation mode. Information obtained from our study will be helpful to understand the mechanism of interactions of benzimidazoles and their complexes with nucleic acids and should be useful in the development of potential probes of DNA structure and conformation.
CCDC 825141 contains the additional crystallographic data for this paper. These data can be obtained free of charge from The Cambridge Crystallographic Data Centre via
The authors acknowledge the financial support and a grant from “Qing Lan” Talent Engineering Funds by Lanzhou Jiaotong University. The grant from “Long Yuan Qing Nian” of Gansu Province is also acknowledged.