Synthesis, crystal structure and DNA interaction studies of three coordination polymers with mixed ligand

Article abstract of DOI:10.1080/10610278.2012.695791

Three coordination polymers [Mn(Nip)(Pbim)]_n (1), [Co(Nip)(Pbim)]_n (2) and [Zn(Nip)(Pbim)]_n (3) [5-nitroisophthalate (Nip) and 2-(2-pyridyl)benzimidazole (Pbim)] were synthesised and characterised by elemental analysis, IR

Full text of DOI:10.1080/10610278.2012.695791

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Supramolecular Chemistry
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Synthesis, crystal structure and DNA interaction studies
of three coordination polymers with mixed ligand
Yan Yang a b , Liu-Ting Yan b , Wen-Gui Duan b , Xiao Li a & Rong-Huan Qin a
a School of Chemistry and Material, Yulin Normal University , Yulin , 537000 , P.R. China
b School of Chemistry and Chemical Engineering, Guangxi University , Nanning , 530004 ,
P.R. China
Published online: 20 Jun 2012.
To cite this article: Yan Yang , Liu-Ting Yan , Wen-Gui Duan , Xiao Li & Rong-Huan Qin (2012) Synthesis, crystal structure and
DNA interaction studies of three coordination polymers with mixed ligand, Supramolecular Chemistry, 24:10, 707-712, DOI:
10.1080/10610278.2012.695791
To link to this article: http://dx.doi.org/10.1080/10610278.2012.695791
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Supramolecular Chemistry
Vol. 24, No. 10, October 2012, 707–712
Synthesis, crystal structure and DNA interaction studies of three coordination polymers
with mixed ligand
Yan Yangab*, Liu-Ting Yanb, Wen-Gui Duanb, Xiao Lia and Rong-Huan Qina
aSchool of Chemistry and Material, Yulin Normal University, Yulin 537000, P.R. China; bSchool of Chemistry and Chemical Engineering,
Guangxi University, Nanning 530004, P.R. China
(Received 18 December 2011; final version received 9 May 2012)
Three coordination polymers [Mn(Nip)(Pbim)]n (1), [Co(Nip)(Pbim)]n (2) and [Zn(Nip)(Pbim)]n (3) [5-nitroisophthalate
(Nip) and 2-(2-pyridyl)benzimidazole (Pbim)] were synthesised and characterised by elemental analysis, IR and
single-crystal X-ray diffraction. Single-crystal X-ray diffraction analysis reveals that 1, 2 and 3 have 1-D ladder chain
structures constructed from m3-bridge Nip ligands and metal atoms. All of these chain-like structures are finally packed into
supramolecular networks through hydrogen bonds and p–p stacking interactions. Fluorescence spectral method has been
used for the study on the interaction of film sperm DNA with complexes. The results show that the corresponding
fluorescence spectrum appeared and the intensity was enhanced with the growth of the concentration of DNA. All of the
results indicate that there exists strong interaction of the complexes with DNA.
Keywords: crystal structure; mixed ligand; supramolecular network; fluorescence; DNA interaction
Introduction
Herein, we report the synthesis, structural character-
isations and photoluminescence properties of three
coordination polymers constructed from Nip and Pbim.
Significant intermolecular hydrogen bonding and p–p
stacking interactions extend the 1-D arrangement into the
supramolecular framework. And, we mainly focused on
exploring the trend in DNA-binding affinities of three
complexes with mixed ligands and the spectroscopic
properties of these complexes in response to pH changes.
The interaction of transition metal complexes with DNA
has been extensively studied for their usage as probes for
DNA structure and their potential application in molecular
light switches, DNA footprinting agents, nucleic acid
probes, chemotherapy and photodynamic therapy (1–3).
One of the important DNA-related activity of the transition
metal complexes is that some of the complexes show the
ability to insert DNA (4). As the functional groups of the
active sites of a number of enzymes, benzimidazole and its
derivative can participate in many important biochemical
reactions (5). So, the 2-(2-pyridyl)benzimidazole (Pbim)
steps into our visions. In fact, as a chelate ligand Pbim has
multiple coordination modes in forming metal coordi-
nation polymers. It can not only be chelate end blocking
ligand but also be bridging ligand when it is deprotonated
(6–8), which is different from the benzimidazole ligand
(9). On the other hand, the containing N atoms derived
from the ligand can act as hydrogen-bond acceptors or can
play important roles in the construction of supermolecular
structures. With the aim of extending the coordination
chemistry based on mixed ligands, we add 5-nitroi-
sophthalate (Nip) in the reactions. Nip is a versatile ligand
in the synthesis of coordination polymers because its
two carboxylic groups can bond with metal centres and
the nitro group as an electron-withdrawing group
coexisting in isophthalic acid, which can not only act as
a hydrogen-bond acceptor, but also take on some spatial
effects (10–18).
Experimental
Materials and methods
Film sperm DNA (FS-DNA) was purchased from the Sino-
American Biotechnology Company. Other reagents were
bought from commercial sources and used without further
purification. IR spectra were recorded in the range of
4000–400 cm21 on Perkin-Elmer Spectrum One FT/IR
spectrometer using a KBr pellet. Elemental analysis (C, H,
N) was carried out on a Perkin-Elemer 2400II CHN
elemental analyzer. Emission spectra were measured on
Ls55 spectrofluorophotometer. The crystal structure was
determined by a Bruker APEX area-detector diffract-
ometer and employing the SHELXTL crystallographic
software. Buffer [5 mM tris(hydroxymethyl)amino-
methane (Tris) hydrochloride, 50 mM NaCl, pH 7.5] was
used for emission titration experiments. The concentration
of FS-DNA was determined spectrophotometrically
assuming a molar absorption of 6600 M21 cm21
*Corresponding author. Email: yy135175@163.com
ISSN 1061-0278 print/ISSN 1029-0478 online
q 2012 Taylor & Francis
http://dx.doi.org/10.1080/10610278.2012.695791
http://www.tandfonline.com

708
Y. Yang et al.
(260 nm) (19, 20). The emission titration of three
complexes was carried out by using a fixed complex
concentration to which increments of the DNA stock
solution were added. The concentration of complexes
solution was 10 mM. Complex-DNA solutions were
allowed to incubate for 15 min before the emission spectra
were recorded. The pH dependence of the excited state
properties of these complexes is investigated by fluor-
escence spectra. Fluorescence pH spectroscopic titrations
of these complexes are carried out in dimethyl sulfoxide
(DMSO)–Tris buffer (1:1) solution with 0.2 M NaCl to
maintain a constant ionic strength. All spectral changes
with pH are reversible.
with distilled water and dried in air. Elemental analysis
(%): Anal. Calcd C 47.92, H 3.62, N 11.18; found C 47.59,
H 4.01, N 10.81. IR (KBr pellets, cm21): n ¼ 3434, 3082,
1629, 1611, 1572, 1542, 1455, 1421, 1380, 1358, 1347,
1303, 1152, 1075, 982, 784, 747, 551.
X-ray crystallography
The diffraction data were collected on a Bruker Smart
Apex CZN diffractometer with graphite-monochromated
˚
Mo Ka radiation (l ¼ 0.71073 A) at 296 K. Absorption
correction was applied by SADABS (21). The structure
was solved by Direct Methods and refined with full-matrix
least-squares technique using SHELXTL (22). All non-
hydrogen atoms were refined with anisotropic displace-
ment parameters. The crystal data, details on the data
collection and refinement are summarised in Table 1, and
selected bond lengths and angles are presented in Table 2;
Synthesis of [Mn(Nip)(Pbim)]n (1)
For the hydrothermal reaction of MnCl2·4H2O (0.5 mmol),
Hpbim (0.25 mmol), H2nip (0.25 mmol) and water (15 ml),
the mixture was stirred for 10 min in air, then transferred
and sealed into a 23 ml Teflon reactor, which was heated at
1008C for 2 days and then cooled to room temperature.
Colourless crystals were obtained (yield 52% based on
Mn), filtered off, washed with distilled water and dried in
air. Elemental analysis (%): Anal. Calcd C 52.30, H 2.63,
N 12.20; found C 51.96, H 2.91, N 11.87. IR (KBr pellets,
cm21): n ¼ 3445, 3089, 1626, 1609, 1569, 1539, 1451,
1421, 1377, 1365, 1347, 1322, 1149, 1075, 976, 792,
747, 548.
˚
the hydrogen bond lengths (A) and bond angles (deg) are
listed in Table 3.
Crystal structures of complexes 1, 2 and 3
Single-crystal X-ray diffraction analysis reveals that
compounds 2 and 3 are isostructural and crystallise in
the monoclinic C2/c space group. Only structure 2 is
described here in detail. Compound 2 has a supramole-
cular framework structure formed by 1-D ladder chains.
Asymmetric unit contains one Co atom, one Pbim ligand
and one Nip ligand (Figure 1(a)). Each Co atom is
coordinated to two N atoms from one Pbim ligand and
three O atoms from three Nip ligands, and adopts a
distorted square-pyramidal coordination environment. The
Synthesis of [Co(Nip)(Pbim)]n (2)
Complex 2 was obtained by a similar procedure described
as complex 1. For the hydrothermal reaction of
Co(NO3)2·6H2O (0.5 mmol), Hpbim (0.25 mmol), H2nip
(0.25 mmol) and water (15 ml), the mixture was stirred for
20 min in air, then transferred and sealed into a 23 ml
Teflon reactor, which was heated at 1108C for 4 days and
then cooled to room temperature. Red needle-shaped
crystals were obtained (yield 48% based on Co), filtered
off, washed with distilled water and dried in air. Elemental
analysis (%): Anal. Calcd C 51.14, H 2.57, N 11.93; found
C 50.72, H 2.89, N 11.81. IR (KBr pellets, cm21):
n ¼ 3434, 3082, 1626, 1608, 1566, 1541, 1454, 1421,
1379, 1360, 1347, 1300, 1157, 1075, 984, 781, 747, 554.
˚
Co–O distances are in the range of 1.968(3)–2.055(3) A,
and the Co–N distances are in the range of 2.052(3)–
˚
2.136(3) A, respectively. In the structure, the Nip ligand
adopts m3-bridge coordination fashion: one carboxylate
group adopts bis-monodentate coordination mode to
bridge two Co(II) centres, and another carboxylate group
acts as a monodentate ligand. The adjacent Co(II) is
connected by m3-bridged Nip into 1-D ladder chain
(Figure 1(b)). It should be noted that the uncoordinated O
atoms of Nip ligand act as hydrogen-bonding acceptors to
form hydrogen bonds with N of Pbim ligands, in which
˚
O···N separations of 3.350(5) A, and OZH···N angles of
154.008 (Figure 2(a)). And Pbim ligand still acts as a
chelating ligand and alternately decorated at both sides of
the chains. The 1-D chains mentioned above are
interconnected through these hydrogen bonds and p–p
stacking interactions between the adjacent Pbim groups
Synthesis of [Zn(Nip)(Pbim)]n (3)
Complex 3 was also obtained by a similar procedure
described as complex 1. For the hydrothermal reaction of
Zn(NO3)2·6H2O (0.5 mmol), Hpbim (0.25 mmol), H2nip
(0.25 mmol) and water (15 ml), the mixture was stirred for
30 min in air, then transferred and sealed into a 23 ml
Teflon reactor, which was heated at 1208C for 3 days and
then cooled to room temperature. Colourless crystals were
obtained (yield 42% based on Zn), filtered off, washed
˚
(the distance is 3.578(2) A) to result in a layer structure
(Figure 2(b)) and further stabilise the supramolecular
network. The structure of 1 is very similar to complexes 2
and 3, which may be attributed to the influence of different
coordination geometries of metal ions (6).

Supramolecular Chemistry
Table 1. Crystal data and structure refinement for 1–3.
709
Identification code
Empirical formula
1
C20H12MnN4O6
2
C20H12CoN4O6
3
C20H12ZnN4O6
Formula weight
Temp (K)
Crystal system
459.28
296(2)
Monoclinic
C2/c
463.27
296(2)
Monoclinic
C2/c
469.37
296(2)
Monoclinic
C2/c
Space group
˚
a (A)
˚
20.336(7)
14.315(5)
19.477(6)
138.12(2)
3785(3)
0.18 £ 0.20 £ 0.22
8
20.073(17)
14.070(11)
13.944(12)
113.034(11)
3624(5)
0.26 £ 0.26 £ 0.28
8
20.167(7)
14.008(3)
13.909(3)
113.86(2)
3593.5(17)
0.16 £ 0.16 £ 0.18
8
b (A)
˚
c (A)
b (8)
3
V (A )
˚
Cryst size (mm)
Z
Dc (g cm23
’ (mm21
F (000)
)
)
1.612
0.746
1864
1.698
0.998
1880
1.499
0.905
1643
Limiting indices
221 # h # 24
–17 # k # 17
2 23 # l # 11
9894
–18 # h # 23
–15 # k # 16
2 15 # l # 16
9536
3194
2443
280
0.041
1.03
0.0375
0.1006
0.38/–0.41
1.8, 25.0
–22 # h # 23
–16 # k # 16
2 15 # l # 16
9430
Reflections
Independent
Observed data
Npar
3337
2541
280
0.096
1.83
0.0605
0.0905
0.56/–0.55
1.8, 25.0
3160
877
126
0.238
Rint
GOF
0.85
0.1477
0.4040
2.34/–3.51
1.8, 25.0
R1a (I . 2s(I))
wR2 (all data)
b
23
)
˚
Max/min electron density (e A
Theta range (8)
a R1 ¼ SkFoj–jFck/SjFoj.
b wR2 ¼ [Sw(Fo2 2 Fc2)2/Sw(Fo2)2]1/2
.
˚
Table 2. Selected bond lengths (A) and bond angles (8) for complexes 1–3.
Complex 1
Complex 2
Complex 3
Mn1ZO1
Mn1ZN1
Mn1ZN2
Mn1ZO8b
Mn1ZO7d
O1ZMn1ZN1
O1ZMn1ZN2
O1ZMn1ZO8b
O1ZMn1ZO7d
N1ZMn1ZN2
O8bZMn1ZN1
O7dZMn1ZN1
O8bZMn1ZN2
O7dZMn1ZN2
O7dZMn1ZO8b
2.038(3)
2.264(3)
2.207(3)
2.095(3)
2.159(4)
100.16(11)
114.61(13)
101.77(12)
99.22(13)
74.13(14)
158.08(11)
88.76(14)
96.47(12)
144.03(13)
87.84(14)
Co1ZO1
Co1ZO2
Co1ZO3
Co1ZN1
Co1ZN2
O1-Co1ZO2
O1ZCo1ZO3
O1ZCo1ZN1
O1ZCo1ZN2
O2ZCo1ZO3
O2ZCo1ZN1
O2ZCo1ZN2
O3ZCo1ZN1
O3ZCo1ZN2
N1ZCo1ZN2
2.031(3)
Zn1ZO1
Zn1ZN1
Zn1ZN2
Zn1ZO2a
Zn1ZO6b
O1ZZn1ZN1
O1ZZn1ZN2
O1ZZn1ZO2a
O1ZZn1ZO6b
N1ZZn1ZN2
O2aZZn1ZN1
O6bZZn1ZN1
O2aZZn1ZN2
O6bZZn1ZN2
O2aZZn1ZO6b
2.003(12)
2.155(15)
2.066(14)
2.082(13)
1.916(13)
162.3(5)
97.7(5)
87.2(5)
96.8(5)
76.7(6)
88.1(6)
2.055(3)
1.968(3)
2.136(3)
2.052(3)
87.28(9)
95.92(9)
168.52(9)
97.91(9)
100.68(9)
89.79(9)
143.74(9)
95.53(9)
114.30(9)
78.07(9)
100.8(5)
144.3(5)
116.8(6)
97.5(5)
Symmetry transformations used to generate equivalent atoms: Complex 1, b ¼ 1/2 2 x, 21/2 2 y, 1 2 z; d ¼ 1/2 þ x, 21/2 2 y, 1/2 þ z. Complex 3, a ¼ 2x, y, 1/2 2 z;
b ¼ 2x, 1 2 y, 2z.
IR spectra
Supplementary Information, available online). As repre-
sentative, only the IR and Raman spectra of 2 are described
here in details. The strong and broad absorption at
3445cm21 suggests the presence of N–H stretch vibrations.
Compared with the free H2nip, the disappearance of band at
For the coordination modes of carboxylate group, the
difference between the asymmetric (nas) and symmetric (ns)
carboxylate stretches (D ¼ nas–ns) is often used (23).
The IR spectra of 1–3 are similar (Figure S1 of the

710
Y. Yang et al.
˚
Table 3. Distances (A) and angles (8) of hydrogen bonds for complexes 1–3.
DZH···A
d(DZH)
d(H···A)
d(D···A)
,(DZH···A)
Complex 1
O2ZH17···N1
C47ZH47···O6
0.8200
0.9300
2.6000
2.4300
3.350(5)
3.078(4)
154.00
127.00 (1/2 þ x, 1/2 2 y, 1/2 þ z)
Complex 2
N3ZH3···O4
C3ZH3A···O5
0.8600
0.9300
1.8700
2.4800
2.707(4)
3.116(4)
165.00 (x, 1 þ y, z)
126.00 (2 2 x, 1 þ y, 1/2 2 z)
Complex 3
N3ZH3···O5
C4ZH4···O4
0.8600
0.9300
1.9000
2.3700
2.75(2)
3.04(3)
164.00 (x, 21 þ y, z)
129.00 (2x, 21 þ y, 1/2–z)
Figure 1. (a) Coordination environment of complex 2 and (b) 1-D chain of complex 2, hydrogen atoms are omitted for clarity.
Figure 2. (a) p–p Stacking and hydrogen-bonding interactions and (b) 2-D layers along ab plane.
1718cm21 in 2 is indicative of the full deprotonation of
aromatic acid. The characteristic absorptions for the
asymmetric and symmetric vibrations of the carboxylate
of the ligand are observed at 1626, 1569, 1451 and
1347cm21, respectively. And their difference (Dv ¼ vas 2
vs ¼ 175 and 222 cm21) suggests the coexistence of the bi-
and monodentate modes of Nip anion (23). These
conclusions are also supported from the results obtained
from X-ray diffraction measurements. The weak bands
observed in the 450–554 cm21 region are due to Co–O and
Co–N stretching vibrations (24).
Raman spectra
Raman spectrum of complex 2 in the frequency region
(100–2000 cm21) is shown in Figure 3. The relative strong
bands are observed when excited with the line at 514 nm.
The peaks with frequency lower than 300 cm21 may be the
vibration of CoII, which is relatively weak as observed in
Raman spectrum. The peak at 570 and 709 cm21 may be
the wagging and rocking modes of the coordinate nitrogen
atoms, respectively (23, 24). The COO2 symmetric and
asymmetric stretching mode at 1434 and 1525 cm21
respectively, and 1564 cm21 is assigned to C ¼ O
,

Supramolecular Chemistry
711
200
1525
Blank
8000
6000
4000
2000
0
DNA
[2]/[DNA] = 0.4
[2]/[DNA] = 0.6
[2]/[DNA] = 0.8
[2]/[DNA] = 1.0
[2]/[DNA] = 1.2
[2]/[DNA] = 1.4
150
100
50
1269
1564
1618
1434
1330
1015
1150
570
709
0
500
1000
1500
2000
Wavenumber (cm–1
)
350
400
450
500
550
Wavelength (nm)
Figure 3. Raman spectrum of complex 2 at room temperature.
Figure 5. Fluorescence emission spectra of the FS-DNA in
0.1 M tris buffer (pH ¼ 7.5) containing 10% DMSO in presence
of complex 2. lex ¼ 310 nm.
stretching. Both the 1015 cm21 band (C–COO2 stretching
motions) and the 1618 cm21 band (C–C stretching) are
relatively strong in Raman spectrum (23, 24).
Blank
600
DNA
DNA interaction studies
[3]/[DNA] = 0.4
[3]/[DNA] = 0.6
Upon excitation using a wavelength of 310 nm for
complexes, all of the complexes can emit fluorescence
with a maximum wavelength of about 370 nm. The results
of the emission titration for these complexes with DNA
are shown in Figures 4–6. The fluorescence intensity
of these complexes increased with the increase in DNA
concentration, reaching a maximum at the ratio of
[Complex]/[DNA] ¼ 0.4, at which there is a 3.26, 2.89
and 3.07-fold increase in the fluorescence intensity of the
complexes compared with that in the absence of DNA for
1, 2 and 3, respectively. This indicates that complexes bind
with DNA by intercalation, and such enhancement could
be ascribed to the fact that the intercalation of the complex
into DNA, which is hydrophobic inside the helix, limits the
[3]/[DNA] = 0.8
400
[3]/[DNA] = 1.0
[3]/[DNA] = 1.2
[3]/[DNA] = 1.4
200
0
350
400
450
500
550
Wavelength (nm)
Figure 6. Fluorescence emission spectra of the FS-DNA in
0.1 M tris buffer (pH ¼ 7.5) containing 10% DMSO in presence
of complex 3. lex ¼ 310 nm.
collision and energy dissipation with the environmental
water and oxygen (25–27).
1000
Blank
DNA
800
[1]/[DNA] = 0.4
[1]/[DNA] = 0.6
Effect of pH value
600
[1]/[DNA] = 0.8
The pH-dependent emission spectra of complexes upon
stepwise addition of NaOH in CH3OH are shown in
Figure 7, Figures S2 and S3 of the Supplementary
Information, available online. Addition of NaOH to
DMSO solution of complex 1 caused the weak emission
maximum at 372 nm. The same method was used and,
addition of NaOH solution to DMSO solution of
complexes 2 and 3 still caused the weak emission at 368
and 371 nm, respectively. At pH 5.7, all complexes exhibit
the highest intensity of emissions. It can come to the
conclusion that the intensity of emissions in acid solution
is higher than that in base solution. The emission energy is
[1]/[DNA] = 1.0
[1]/[DNA] = 1.2
400
[1]/[DNA] = 1.4
200
0
350
400
450
500
Wavelength (nm)
Figure 4. Fluorescence emission spectra of the FS-DNA in
0.1 M tris buffer (pH ¼ 7.5) containing 10% DMSO in presence
of complex 1. lex ¼ 310 nm.

712
Y. Yang et al.
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Summary
In conclusion, we successfully synthesised three novel
coordination polymers based on Pbim and Nip ligands
with different metals by solvothermal method. All these
compounds get the supramolecular structures through
intermolecular interactions. It demonstrates that the
weakly intermolecular interactions, such as hydrogen
bonding, p···p stacking interactions and CZH···O stacking
interactions, play a very important role in controlling the
coordination polymers, especially further linking the 1-D
entities into supramolecular networks. DNA interaction
studies were investigated by fluorescence spectral method,
and we observed a similarity in DNA binding by three
coordination polymers and the spectroscopic properties in
response to pH changes.
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Supplementary materials
CCDC Nos 827560 (1), 840879 (2) and 840880 (3),
contain the supplementary crystallographic data. These
data can be obtained via the Cambridge Crystallographic
Data Centre (deposit@ccdc.cam.ac.uk; http://www.ccdc.
cam.ac.uk/deposit).
Acknowledgements
We acknowledge financial support by the National Natural
Science Foundation of China (No. 51062016) and the Natural
Science Foundation of the Education Committee of Guangxi
Province (No. 200911MS199).