Synthesis, crystal structure, and DNA-binding of a 3-D netlike supramolecular manganese picrate complex with 2,6-bis(benzimidazol-2-yl)pyridine

Article abstract of DOI:10.1080/00958971003728288

Manganese picrate with 2,6-bis(benzimidazol-2-yl)pyridine (L) has been prepared and characterized by elemental analysis, IR spectroscopy, and single-crystal X-ray diffraction. The complex crystallizes in the triclinic system, space group P-1 with a=14.234(3) A, b=14.324(2)A, c=15.242(2)A, α=77.569(2)°, β=63.350(3)°, γ=82.130(2)°, and Z= 2. Interaction of the complex with calf-thymus DNA (CT-DNA) has been investigated with diverse spectroscopic techniques and viscosity measurements, and the binding constant is 1.76×10^-5mol^-1. Results suggest that the complex bind to CT-DNA via intercalation.

Full text of DOI:10.1080/00958971003728288

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Synthesis, crystal structure, and DNA-
binding of a 3-D netlike supramolecular
manganese picrate complex with 2,6-
bis(benzimidazol-2-yl)pyridine
Zhen-Zhong Yan a , Zhi-Hong Xu b , Guo-Liang Dai a , Hua-Ding
Liang a & Song-Lin Zhao a
a Department of Pharmaceutics and Chemical Engineering ,
Taizhou University , Linhai 317000, PR China
b College of Chemistry and Chemical Engineering, Xuchang
University , Xuchang 461000, PR China
Published online: 25 Mar 2010.
To cite this article: Zhen-Zhong Yan , Zhi-Hong Xu , Guo-Liang Dai , Hua-Ding Liang & Song-Lin Zhao
(2010) Synthesis, crystal structure, and DNA-binding of a 3-D netlike supramolecular manganese
picrate complex with 2,6-bis(benzimidazol-2-yl)pyridine, Journal of Coordination Chemistry, 63:7,
1097-1106, DOI: 10.1080/00958971003728288
To link to this article: http://dx.doi.org/10.1080/00958971003728288
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Journal of Coordination Chemistry
Vol. 63, No. 7, 10 April 2010, 1097–1106
Synthesis, crystal structure, and DNA-binding
of a 3-D netlike supramolecular manganese picrate
complex with 2,6-bis(benzimidazol-2-yl)pyridine
ZHEN-ZHONG YAN*y, ZHI-HONG XUz, GUO-LIANG DAIy,
HUA-DING LIANGy and SONG-LIN ZHAOy
yDepartment of Pharmaceutics and Chemical Engineering,
Taizhou University, Linhai 317000, PR China
zCollege of Chemistry and Chemical Engineering,
Xuchang University, Xuchang 461000, PR China
(Received 26 June 2009; in final form 17 November 2009)
Manganese picrate with 2,6-bis(benzimidazol-2-yl)pyridine (L) has been prepared and
characterized by elemental analysis, IR spectroscopy, and single-crystal X-ray diffraction.
˚
The complex crystallizes in the triclinic system, space group P–1 with a ¼ 14.234(3) A,
ꢀ
ꢀ
ꢀ
˚
˚
b ¼ 14.324(2) A, c ¼ 15.242(2) A, ꢀ ¼ 77.569(2) , ꢁ ¼ 63.350(3) , ꢂ ¼ 82.130(2) , and Z ¼ 2.
Interaction of the complex with calf-thymus DNA (CT-DNA) has been investigated with
diverse spectroscopic techniques and viscosity measurements, and the binding constant
is 1.76 ꢁ 105 molꢂ1. Results suggest that the complex bind to CT-DNA via intercalation.
Keywords: Crystal structure; 2,6-Bis(benzimidazol-2-yl)pyridine; Manganese picrate complex;
DNA-binding
1. Introduction
Considerable attention has been given to the synthesis of bis-benzimidazole compounds
because of their properties in cancer therapy. Various studies with bis-benzimidazole
derivatives have shown that their binding affinity to calf-thymus DNA (CT-DNA)
correlates positively with the in vitro topoisomerase inhibitory potency or cytotoxicity
[1]. The chelation of 2,6-bis(benzimidazol-2-yl)pyridine (L) is depicted in scheme 1 [2–4].
Metal complexes having polypyridyl moieties have been extensively studied as DNA
structural probes and DNA-dependent electron transfer probes [5–7]. Interaction of
metal complexes with DNA has been examined due to their cationic character, water
solubility, stability in water, and spectroscopic signature. Bunzli et al. [8–11] have
¨
reported that attachment of five-membered rings to the central pyridine in extended
tridentate ligand (L) improves affinity for metal ions. Some metal complexes
of polypyridine ligands activate endonucleolytic cleavage in DNA in the presence
*Corresponding author. Email: yanzhzh@tzc.edu.cn
Journal of Coordination Chemistry
ISSN 0095-8972 print/ISSN 1029-0389 online ß 2010 Taylor & Francis
DOI: 10.1080/00958971003728288

1098
Z.-Z. Yan et al.
Scheme 1. The structure of L.
of external agents or footprinting agents and as models for the reactivity of some
antitumor antibiotics [12].
In this work, an organic picrate possessing relatively weak coordination activity was
chosen as a counter anion for manganese complex with 2,6-bis(benzimidazol-2-yl)-
pyridine (L). Elemental analyses indicate a 1 : 2 : 2 : 1 metal-to-L-to-picrate-to-ethanol
stoichiometry, MnL2(Pic)2(C2H6O). The crystal structure indicates that [MnL2](Pic)2
link to each other by intermolecular hydrogen bonds and ꢃ–ꢃ stacking interactions to
form a three-dimensional (3-D) netlike supermolecule. The interactions of DNA with
the complex have been investigated to evaluate biological activity.
2. Experimental
2.1. Materials and methods
All reagents and solvents were purchased commercially and used without purification
unless otherwise noted. Mn(Pic)2 was prepared by the reaction of manganese carbonate
and picric acid in hot water. Calf-thymus DNA (CT-DNA) was obtained from Sigma
Chemicals Co. (USA) and used as received. The solutions of CT-DNA in 50 mmol
NaCl, 5 mmol Tris-HCl (tris(hydroxymethyl) aminomethane hydrochloride) (pH 7.2)
gave a ratio of UV-Vis absorbance of 1.8–1.9 : 1 at 260 and 280 nm, indicating that the
DNA was sufficiently free of protein [13]. The concentration of DNA was determined
spectrophotometrically using a molar absorptivity of 6600 molꢂ1 cmꢂ1 (260 nm) [14].
Doubly distilled water was used to prepare buffers.
Carbon, nitrogen, and hydrogen analyses were determined using an Elementar Vario
EL. The IR spectra were recorded on a Nicolet 360 FT-IR instrument using KBr discs
from 4000–400 cmꢂ1. The 1H NMR spectrum was measured on a Varian Mercury-300B
spectrometer in CDCl3 solution with TMS as internal standard. The luminescence and
phosphorescence spectra were obtained on a Hitachi RF-4500 spectrophotometer at
room temperature.
2.1.1. Preparation of L. The ligand 2,6-bis(benzimidazol-2-yl)pyridine was prepared
by reaction of pyridine-2,6-dicarboxylic acid and O-phenylenediamine in syrupy
phosphoric acid (40 mL) at ca 230ꢀ for 4 h as described previously [15], yield 55%,
m.p. 4 250ꢀ (Found: C, 70.86; H, 4.05; N, 22.06. Calcd for L (%): C, 70.27; H, 4.03;
N, 21.40). IR(cmꢂ1) in KBr pellet: ꢄ(C¼N) 1459s; ꢄ(C¼C): 1436s; ꢄ(C–N):1274s;

Synthesis, crystal structure, and DNA-binding of manganese picrate complex
1099
1
ꢄ(N–H) 3083 m, 3058 m and ꢄ(O–H) 3180 m. H NMR (CDCl3, 300 MHz): 7.3–8.5
(m, aromatic), 13.2 (s, imino).
2.1.2. Synthesis of the manganese picrate complex. The manganese picrate complex
was prepared as yellow powder by the reaction of Mn(Pic)2 and L at 1 : 1 molar ratio
in ethanol (Found: C, 52.47; H, 2.802; N, 19.47. Calcd for MnL2(Pic)2(C2H6O) (%):
C, 52.93; H, 3.08; N, 18.99). IR(cmꢂ1, KBr): ꢄ(C¼N): 1610; ꢄ(C¼C): 1441; ꢄ(C–N):
1274; ꢄas(–NO2): 1555; ꢄs(–NO2): 1342.
2.2. DNA-binding experiments
Absorption titration experiments were performed by maintaining the metal complex
concentration as constant at 10 mmol while varying the concentration of CT-DNA
within 0.5–10 mmol. While measuring absorption spectra, equal quantity of CT-DNA
was added to both the complex and the reference solution to eliminate the absorbance
of DNA itself.
For fluorescence measurements, fixed amounts (10 mmol) of the complex were
titrated with increasing amounts (0–50 mmol) of CT-DNA. The excitation wavelength
was 415 nm, scan speed ¼ 240 nm minꢂ1, and slit width 2.5/2.5 nm.
Viscosity experiments were conducted on an Ubbelohde viscometer immersed in a
thermostatted water bath maintained at 25 ꢃ 0.1ꢀC. The data were presented as (ꢅ/ꢅ0)1/3
versus the ratio of the concentration of the compound to CT-DNA, where ꢅ is
the viscosity of CT-DNA in the presence of the compound and ꢅ0 is the viscosity of
CT-DNA alone. The viscosity values were calculated from the observed flow time
of CT-DNA containing solutions corrected from the flow time of buffer alone (t0),
ꢅ ¼ t ꢂ t0 [16].
2.3. Crystal structure determination
Yellow crystals suitable for X-ray diffraction were obtained by slow evaporation of
the ethanol solution of the Mn complex. Single-crystal X-ray diffraction was performed
on a Bruker SMART CCD diffractometer equipped with a graphite crystal
monochromator situated in the incident beam for data collection. A single crystal
with dimensions 0.30 ꢁ 0.19 ꢁ 0.17 mm3 was chosen for X-ray diffraction studies.
The determination of unit cell parameters and data collection were performed
˚
with Mo-Ka radiation (ꢆ ¼ 0.71073 A) at 298(2) K on a Bruker SMART diffractometer.
The structure was solved by direct methods using SHELXS program of the
SHELXL-97 package and refined with SHELXL [17]. Manganese centers were located
from the E-map and other non-hydrogen atoms were located in successive difference
Fourier syntheses. The final refinement was performed by full matrix least
squares with anisotropic thermal parameters for non-hydrogen atoms on F2. The
hydrogens were added geometrically and not refined. The final R ¼ 0.0885 and
wR ¼ 0.2046
(w ¼ 1/[ꢇ2(Fo2) þ (0.0477P)2 þ 0.1617P],
where
P ¼ (Fo2 þ 2Fc2)/3),
S ¼ 1.001, (Dꢈ)max ¼ 0.794, (Dꢈ)min ¼ ꢂ0.417 e Aꢂ3, and (D/ꢇ)max ¼ 0.000.
˚

1100
Z.-Z. Yan et al.
3. Results and discussion
3.1. Crystal structure of the title complex
A summary of crystallographic data and details of the structure refinements are listed in
table 1; selected bond lengths and angles are given in table 2.
As shown in figure 1, in MnL2(Pic)2(C2H6O), Mn(II) is coordinated with six
nitrogens from two tridentate L in a distorted octahedron. Two picrates are counter
anions and one ethanol is in the outer coordination sphere. All atoms of the same L are
almost in a plane, and the dihedral angle between two planes is 80.50ꢀ.
A 3-D netlike supramolecule (figure 2) was further formed through hydrogen bonds
and ꢃ–ꢃ interactions. The ꢃ–ꢃ interactions between the picrate groups, which are
formed between two benzene rings of the benzimidazole rings [the centroid (C14, C15,
˚
C16, C17, C18, and C19) to centroid distances are 3.800 A (symmetry code: 1 ꢂ x, 1 ꢂ y,
1 ꢂ z); the centroid (C33, C34, C35, C36, C37, and C38) to centroid (C26, C33, C34,
˚
N9, and N10) distances are 3.909 A (symmetry code: 1 ꢂ x, ꢂy, 1 ꢂ z)] form a 2-D layer
supramolecule [18]. In addition, the layers are linked by ꢃ–ꢃ interactions between two
picrate ions [the centroid (C39, C40, C41, C42, C43, and C44) to centroid distances are
˚
4.004 A (symmetry code: x, y, z)] and intermolecular N–H ꢄ ꢄ ꢄ O and C–H ꢄ ꢄ ꢄ O hydrogen
bonds between nitrogens of L and picrate. All of the relevant hydrogen-bonding values
and symmetry codes are listed in table 3.
Table 1. Crystal and experimental data.
Empirical formula
Formula weight
Temperature (K)
C52H36N16O15Mn
1179.91
298(2)
˚
Wavelength (A)
Crystal system
Unit cell dimensions (A, )
0.71073
Triclinic
ꢀ
˚
a
b
c
ꢀ
ꢁ
ꢂ
14.234(3)
14.324(2)
15.242(2)
77.569(2)
63.350(3)
82.130(2)
2709.5(8), 2
1.446
3
˚
Volume (A ), Z
Calculated density (mg mꢂ3
)
Absorption coefficient (mmꢂ1
F(000)
)
0.328
1210
Crystal size (mm3)
0.30 ꢁ 0.19 ꢁ 0.17
ꢉ range for data collection (ꢀ)
Limiting indices
2.12–25.01
ꢂ8 ꢅ h ꢅ 16; ꢂ17 ꢅ k ꢅ 17; ꢂ17 ꢅ l ꢅ 18
13,771
Reflections collected
Independent reflection
9136 [R(int) ¼ 0.0618]
Completeness to ꢉ ¼ 25.00 (%)
95.8
Absorption correction
Semi-empirical from equivalents
0.9464 and 0.9080
9136/451/835
Max. and min. transmission
Data/restraints/parameters
Goodness-of-fit on F 2
1.001
Final R indices [I 4 2ꢇ(I )]
R indices (all data)
Largest difference peak and hole (e A
Refinement method
R1 ¼ 0.0885, wR2 ¼ 0.2046
R1 ¼ 0.2379, wR2 ¼ 0.2985
0.794 and 0.079
Full-matrix least-squares on F 2
ꢂ3
˚
)

Synthesis, crystal structure, and DNA-binding of manganese picrate complex
3.2. Absorption titration
1101
The electronic absorption spectroscopy in DNA-binding studies is one of the most
useful techniques [19, 20]; absorption spectra of the complex in the absence and
presence of CT-DNA (at a constant concentration of the complex) are given in figure 3.
In the presence of DNA, absorption bands of the complex at 333 nm exhibit
hypochromism of about 26.1% and bathochromism of about 13 nm. These spectral
characteristics suggest that the complex interacts with DNA most likely through a mode
that involves a stacking interaction between the aromatic chromophore and the base
pairs of DNA.
ꢀ
˚
Table 2. Selected bond lengths (A) and angles ( ).
Mn(1)–N(1)
Mn(1)–N(6)
Mn(1)–N(2)
Mn(1)–N(7)
Mn(1)–N(4)
Mn(1)–N(9)
2.228(7)
2.238(7)
2.253(7)
2.261(7)
2.262(7)
2.307(7)
N(1)–Mn(1)–N(2)
N(1)–Mn(1)–N(4)
N(1)–Mn(1)–N(6)
N(1)–Mn(1)–N(7)
N(1)–Mn(1)–N(9)
N(2)–Mn(1)–N(4)
N(2)–Mn(1)–N(6)
N(2)–Mn(1)–N(7)
N(2)–Mn(1)–N(9)
N(4)–Mn(1)–N(6)
N(4)–Mn(1)–N(7)
N(4)–Mn(1)–N(9)
N(6)–Mn(1)–N(7)
N(6)–Mn(1)–N(9)
N(7)–Mn(1)–N(9)
72.0(3)
71.6(2)
162.4(3)
123.7(2)
93.2(3)
142.2(3)
118.6(2)
91.6(2)
99.3(2)
99.2(2)
100.4(2)
92.4(2)
71.9(3)
71.8(3)
143.0(3)
Figure 1. ORTEP diagram (30% probability ellipsoids) showing the molecular structure of the Mn complex
(the free ethanol is omitted for clarity).

1102
Z.-Z. Yan et al.
The absorption data were analyzed to evaluate the intrinsic binding constant Kb,
which can be determined from [16]:
½DNAꢆ=ð"a ꢂ "fÞ ¼ ½DNAꢆ=ð"b ꢂ "fÞ þ 1=Kbð"b ꢂ "fÞ
where [DNA] is the concentration of DNA in base pairs, the apparent absorption
coefficient "a, "f, and "b correspond to Aobsd/[M], the extinction coefficient of the
free compound and the extinction coefficient of the compound when fully bound
to DNA, respectively. In plots of [DNA]/("a ꢂ "f) versus [DNA], Kb is given by the
ratio of slope to the intercept. The intrinsic binding constant Kb of the complex
was 1.76 ꢁ 105 molꢂ1
.
Figure 2. 3-D netlike supermolecule generated by intermolecular hydrogen bonds and ꢃ–ꢃ interactions
in the title complex (hydrogen bonds are indicated by the yellow dashed lines).
ꢀ
˚
Table 3. Hydrogen bonds in crystal packing (A, ).
D–H ꢄ ꢄ ꢄ A
d(D–H)
d(H ꢄ ꢄ ꢄ A)
d(D ꢄ ꢄ ꢄ A)
ff DHA
Symmetry
N(3)–H(3) ꢄ ꢄ ꢄ O(15)
N(5)–H(5) ꢄ ꢄ ꢄ O(1)
N(8)–H(8) ꢄ ꢄ ꢄ O(3)
N(10)–H(10) ꢄ ꢄ ꢄ O(8)
C(5)–H(5A) ꢄ ꢄ ꢄ O(1)
C(16)–H(16) ꢄ ꢄ ꢄ O(2)
C(23)–H(23) ꢄ ꢄ ꢄ O(10)
C(24)–H(24) ꢄ ꢄ ꢄ O(9)
0.86
0.86
0.86
0.86
0.93
0.93
0.93
0.93
1.90
2.17
2.08
1.90
2.28
2.36
2.41
2.43
2.7452
2.9981
2.9369
2.7545
3.1621
3.1517
3.3393
3.2123
168
160
178
171
159
142
174
142
ꢂ1 þ x, y, 1 þ z
1 ꢂ x, 1 ꢂ y, 1 ꢂ z
1 ꢂ x, ꢂy, 1 ꢂ z
1 þ x, y, z
1 ꢂ x, ꢂy, 1 ꢂ z

Synthesis, crystal structure, and DNA-binding of manganese picrate complex
3.3. Thermal denaturation study
1103
DNA melting is observed when double-stranded DNA molecules are heated and
separate into single strands; it occurs due to the disruption in intermolecular forces such
as ꢃ stacking and hydrogen-bonding interactions between DNA base pairs. Here, a
DNA melting experiment revealed that Tm of CT-DNA was 67 ꢃ 0.2 and 74 ꢃ 0.2ꢀC
in the absence and presence of the complex, respectively. However, for the ligand alone,
there is no change in DNA melting temperature. The DTm of 7ꢀC indicates that the
binding cannot be classical intercalative. Such DTm is generally associated with partial
intercalation binding of the metal complex [21]. One would expect a much larger
increase in Tm for classical intercalators [22–24]. A small DTm also indicates weak
binding of the complex to DNA. The change in Tm is indicative of moderate binding
of the complex with DNA.
3.4. Fluorescence study
In the absence of DNA, the complex emits fluorescence in Tris buffer at room
temperature, with a maximum at 415 nm (the excitation and emission slit widths
were 2.5 nm). Upon addition of CT-DNA, emission intensities of the complex are
quenched steadily (figure 4), implying that the complex interacts with DNA with
photoelectron transfer from DNA to the complex [25–28]; the hydrophobic environ-
ment inside the DNA helix reduces the accessibility of water to the complex and
complex mobility is restricted at the binding site, leading to the decrease of the
vibrational modes of relaxation.
Figure 3. Electronic spectra of the complex (10 mmol Lꢂ1) in the presence of 0, 1, 2, 4, 6, 8, 10, 12, 14, 16,
18, 20, 22, 25, and 30 mL 1.0 ꢁ 10ꢂ3 mol Lꢂ1 CT-DNA. Arrow shows the absorbance changes upon increasing
CT-DNA concentration. Inset shows the plots of [DNA]/("a ꢂ "f) vs. [DNA] for interaction between DNA
and the complex.

1104
Z.-Z. Yan et al.
Figure 4. The fluorescence emission spectra of the complex upon increasing CT-DNA concentration at
.
room temperature, concentration of the complex 1.0 ꢁ 10ꢂ3 mol Lꢂ1
3.5. Viscosity measurements
Spectroscopic experiments provide necessary, but not sufficient clues to support a
binding mode. The measurements of DNA viscosity sensitive to DNA length are
regarded as the least ambiguous and the most critical tests of binding in solution in the
absence of crystallographic structural data [29]. A classical intercalation mode results in
lengthening the DNA helix as base pairs are separated to accommodate the binding
ligand, leading to the increase of DNA viscosity. In contrast, a partial nonclassical
intercalation of ligand could bend (or kink) the DNA helix and reduce its effective
length [30]. Upon addition of the complex, the viscosity of rod-like CT-DNA increased
significantly, as illustrated in figure 5, which suggests that the complex binds to DNA
by intercalation.
4. Conclusions
A manganese(II) complex with symmetrical tridentate ligand (L) was synthesized and
characterized by elemental analysis, IR spectroscopy, and single-crystal X-ray
diffraction. [MnL2](Pic)2 Á C2H5OH are linked by intermolecular hydrogen bonds and
ꢃ–ꢃ interactions to form a 3-D netlike supermolecule. Sun et al. [31] reported intrinsic
binding constants Kb of 4.1 ꢁ 104 molꢂ1. DNA binding of our complex was investigated
by spectroscopic techniques and viscosity measurements, with intrinsic binding
constants Kb of 1.76 ꢁ 105 molꢂ1. The studies of metal complexes can give some
guidance to explore the possible new drugs, but further studies will be needed to
understand the selectivity of complexes.

Synthesis, crystal structure, and DNA-binding of manganese picrate complex
1105
Figure 5. Effect of increasing amounts of the complexes on the relative viscosity of DNA at 25 ꢃ 0.1ꢀC.
Supplementary material
The X-ray crystallographic file, in CIF format, has been deposited with the Cambridge
Crystallographic Data Center, CCDC No. 625773. Copy of this information may
be obtained free of charge from the Cambridge Crystallographic Data Center, 12 Union
Road, Cambridge, CB2 1EZ, UK (Email: deposit@ccdc.cam.ac.uk).
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