Synthesis, structure and DNA binding studies of 1,4-bis((4-nitrophenoxy) methyl)benzene and its reduction derivative

Article abstract of DOI:10.1016/j.molstruc.2011.03.026

The dinitrocompound, 1,4-bis((4-nitrophenoxy)methyl)benzene (NMB) and its derivative 1,4-bis((4-aminophenoxy)methyl)benzene (AMB), a potential monomer for polymeric materials have been synthesized and characterized by elemental and spectral studies. AMB w

Full text of DOI:10.1016/j.molstruc.2011.03.026

Journal of Molecular Structure 994 (2011) 242–247
Contents lists available at ScienceDirect
Journal of Molecular Structure
journal homepage: www.elsevier.com/locate/molstruc
Synthesis, structure and DNA binding studies of
1,4-bis((4-nitrophenoxy)methyl)benzene and its reduction derivative
a
a
b
Ali Haider a, Zareen Akhter a, , Fariya Jabeen , Naveed Kausar Janjua , Michael Bolte
⇑
a Department of Chemistry, Quaid-i-Azam University, Islamabad 45320, Pakistan
b Institut für Anorganische Chemie, J.W. Goethe-Universität Frankfurt, Max-Von-Laue-Strasse 7, Frankfurt/Main 60438, Germany
a r t i c l e i n f o
a b s t r a c t
Article history:
The dinitrocompound, 1,4-bis((4-nitrophenoxy)methyl)benzene (NMB) and its derivative 1,4-bis((4-ami-
nophenoxy)methyl)benzene (AMB), a potential monomer for polymeric materials have been synthesized
and characterized by elemental and spectral studies. AMB was also characterized by single crystal anal-
ysis as the monoclinic space group C2/c with unit cell parameters a = 40.858(6) Å, b = 5.4606(8) Å,
Received 16 February 2011
Accepted 9 March 2011
Available online 13 March 2011
c = 7.7741(15) Å;
a = 90°, b = 100.471(7)°, c = 90° and Z = 4. The molecule is located on a centre of inver-
Keywords:
sion and the water molecule on a twofold rotation axis. The cyclic voltammetric (CV) investigations
showed the precursor and its amino-analogue to be strong ds.DNA binder and replication quencher.
The threading intercalation mode of binding is proposed on the basis of positive peak potential shift
and molecular structures.
Dinitro compound
Reduction derivative
Single crystal analysis
Cyclic voltammetry
ds.DNA binding
Ó 2011 Elsevier B.V. All rights reserved.
1. Introduction
solubility, processability and toughness of the resulting polymers
without deteriorating their inherent excellent properties [19–23].
The design of novel, functional, conjugated monomers and olig-
omers remains an area of intense interest that can induce a num-
ber of properties in the polymeric material. These properties
include heat resistance, solvent resistance, good mechanical
strength, electroactivity in cyclic voltammetry [1], electrochemical
interaction with DNA [2], good toughness, excellent dimensional
stability, low coefficient of friction, outstanding radiation resis-
tance and resistance to creep and wear [3,4].
Electrochemical studies of the aromatic amines and their pre-
cursors i.e., nitroaromatic compounds have a long history in chem-
ical literature since the beginning of the twentieth century [5], but
still there is a great interest in these types of molecules due to their
use in pharmaceutical products. They are mainly used as antibac-
terial, antiprotozoal and anticancer agents [6]. A variety of small
molecules of drugs interact reversibly with ds.DNA either through
electrostatic interaction with anionic oxygen of phosphate struc-
tures, fitting into the grooves of DNA double helix or intercalation
between stacked base pairs in the core of DNA [7,8].
Such soluble polymers have also found a range of application in
electrochemistry, coatings and can be processed for nano-compos-
ite preparation using sol–gel and solution intercalation techniques
[24,1–3].
The synthesized compounds, being electroactive in cyclic vol-
tammetry having flexible methylene spacers between the aryl
ether moieties are an outcome of the efforts for the modification
of the aromatic diamine monomers by incorporating the flexible
linkages. Furthermore, their redox chemistry and their electro-
chemical interactions with ds.DNA have also been evaluated which
could be related with their symmetric structures and DNA binding
capabilities.
2. Experimental
2.1. General
K2CO3 anhydrous, p-nitrophenol,
a,
a0-dicholoro-p-xylene,
For most of the polymers difficulties are encountered in pro-
cessing due to their poor solubilities and high processing temper-
atures. The incorporation of bulky [9–14], rotatable and flexible
segments [15–17] such as ether moiety, sulphone linkages, meth-
ylene spacers and structurally similar groups [18] into the polymer
backbones greatly influence the redox potentials and enhance the
hydrazine 80%, 10% Pd/C were purchased from Aldrich (Germany)
and used as received. Solvents DMF and ethanol were obtained
from Merck (Germany), dried and distilled prior to use.
The elemental analyses were obtained from Perkin Elmer CHNS/
O 2400. The melting points were determined on melting point
apparatus Mel-Temp., Mitamura Riken Kogyo, Inc., Tokyo, Japan,
using open capillary tubes. Infrared measurements were
performed by ATR technique using a TGA/SDTA 851e, Metller
⇑
Corresponding author. Tel.: +92 51 9064 2111; fax: +92 51 9064 2241.
E-mail address: zareenakhter@yahoo.com (Z. Akhter).
0022-2860/$ - see front matter Ó 2011 Elsevier B.V. All rights reserved.
doi:10.1016/j.molstruc.2011.03.026

A. Haider et al. / Journal of Molecular Structure 994 (2011) 242–247
243
Toledo Swiss apparatus. 1H NMR spectral analysis was carried out
by using a 300 MHz and 13C NMR at 75 MHz Bruker ultra-shield
instrument (in DMSO as solvent) using TMS (tetramethyl silane
as standard). Eco Chemie Auto lab. PGSTAT 12 potentiostat/galva-
nostat with three electrode cell was used for cyclic voltammetric
studies. Glassy carbon (GC, 0.071 cm2), SCE/3M KCl and Pt wire
(0.1 cm thickness) were employed as working electrode, reference
electrode and counter electrode, respectively. Ar gas was purged
for 10–15 min in each measurement.
to precipitate a yellow solid which was washed thoroughly with
water and then separated by filtration. Elemental analysis. Found:
C = 62.75, H = 4.19, N = 7.45%.
H = 4.21, N = 7.37%. IR (KBr pellet) in cmꢀ1: 1491, 1330
Asy.st, Sym. st.), 3081 (Ar–H st), 2864
(–CH2 st). 1H NMR
C
20H16O6N2 requires C = 63.14,
t
(NO2
t
t
(DMSO-d6) in d (ppm) and J (Hz): 8.24 (9.0) (2H, d, 2, 20), 7.25
(9.0) (2H, d, 3, 30), 5.29 (2H, s, 5), 7.52 (2H, s, 7, 70), (see scheme
for atom labelling). In the second step a 250 ml two neck flask
was charged with 1.00 g (2.84 mmol) of the yellow solid and was
refluxed in ethanol as solvent with 0.06 g of 5% palladium on car-
bon (Pd/C), followed by the drop wise addition of hydrated hydra-
zine diluted in ethanol. The mixture was refluxed for 8 h and then
filtered to remove Pd/C. The solvent was evaporated and the result-
ing crude solid was recrystallized from ethanol to afford crystals
suitable for X-ray analysis (yield: 70%, m.p.: 142 °C), which was
then analyzed by single crystal technique. Elemental analysis,
Crystal structure data were collected on a STOE-IPDS-II two-cir-
cle diffractometer employing graphite-monochromated Mo K
a
radiation (k = 0.71073 Å) with -scans. Data reduction was per-
x
formed with the X-Area software [25]. The structures was solved
by direct methods with SHELXS-90 [26] and refined by full-matrix
least-squares techniques with SHELXL-97 [26]. All non-H atoms
were refined with anisotropic displacement parameters. Hydro-
gen’s bonded to C were included at calculated positions and al-
lowed to ride on their parent atoms. H atoms bonded to N were
freely refined. The water H atom was refined with U(H) set to 1.2
found: C = 74.56, H = 6.15, N = 8.50%.
C = 75.0, H = 6.25, N = 8.75%. IR (KBr pellet) in cmꢀ1: 3367
st), 3142
(Ar–H st), 2909 (–CH2 st). 1H NMR (DMSO-d6) in d
C
20H20O2N2 requires
t
(NH2
t
U
eq(O).
(ppm) and J (Hz): 4.63 (2H, s, –NH2), 6.52 (8.81) (2H, d, 2, 20),
6.73 (8.81) (2H, d, 3, 30), 4.92 (2H, s, 5), 7.40 (2H, s, 7, 70), (see
Scheme 1 for atom labelling). 13C NMR in d (ppm) in DMSO-d6
and J (Hz): 142.6 (1), 116.2 (2, 20), 115.6 (3, 30), 150.3 (4), 70.0
(5), 137.6 (6), 128.0 (7, 70).
2.2. General procedure for NMB and AMB synthesis
1,4-Bis((4-aminophenoxy)methyl)benzene (AMB) was synthe-
sized in two steps. In the first step
a mixture of 2.00 g
(0.0114 mol) of
a,
a0-dicholoro-p-xylene, 3.154 g (0.0229 mol) of
3. Results and discussion
anhydrous K2CO3 and 3.181 g (0.0229 mol) of p-nitrophenol in a
two neck round bottom flask having 50 ml of DMF was heated at
120 °C for 12 h under nitrogen atmosphere. After cooling to room
temperature, the reaction mixture was poured in 800 ml of water
1,4-Bis((4-aminophenoxy)methyl)benzene (AMB) compound
was synthesized in two step reaction (Scheme 1). The first step
was the Williamson etherification for synthesis of 1,4-bis((4-nitro-
ClH2C
CH2Cl
O2N
OH
DMF
120ºC
K2CO3 anhy.
7
7
6
3
2
3
2
6
H2
C
H2
1
4
1
4
O2N
O
C
O
NO2
5
5
7'
2'
2'
7'
3'
3'
NMB
i) 80% Hydrazine
ii) 5% Pd/C
EtOH
7
7
3
2
3
2
6
6
H2
H2
1
4
1
4
H2N
O
C
C
O
NH2
5
5
7'
3'
2'
2'
7'
AMB
3'
Scheme 1. Synthesis of NMB and AMB.

244
A. Haider et al. / Journal of Molecular Structure 994 (2011) 242–247
Table 1
phenoxy)methyl)benzene (NMB) and was characterized by ele-
mental, IR, and 1H NMR analysis. It was then hydrogenated to
AMB using 5% Pd/C and 80% hydrazine. The disappearance of the
nitro peak and appearance of –NH2 vibrational band in IR spectra
and appearance of signal at 4.63 ppm in 1H NMR spectra confirmed
the formation of titled compound. However, the shift in the 1H
NMR signal for 2,20 and 3,30 protons in diamine NMR spectrum is
due to the electron donating nature of the –NH2 moiety.
Crystal data and structure refinement for za34.
Identification code
za34
Empirical formula
Formula weight
Temperature
Wavelength
Crystal system
Space group
C
20H20N2O2
338.40
173(2) K
0.71073 Å
Monoclinic
C2/c
Finally, 1,4-bis((4-aminophenoxy)methyl)benzene (AMB) was
characterized by single crystal analysis to be crystallized in the
monoclinic space group C2/c with unit cell parameters
Unit cell dimensions
a = 40.858(6) Å, a = 90°
b = 5.4606(8) Å, b = 100.471(14)°
c = 7.7741(15) Å, g = 90°
1705.6(5) Å3
Volume
Z
Density (calculated)
Absorption coefficient
F(0 0 0)
Crystal size
Theta range for data collection
Index ranges
Reflections collected
Independent reflections
Completeness to theta
Absorption correction
Data/restraints/parameters
Goodness-of-fit on F2
Final R indices [I > 2sigma(I)]
R indices (all data)
Largest diff. peak and hole
a = 40.858(6) Å, b = 5.4606(8) Å, c = 7.7741(15) Å;
a = 90°, b =
4
100.471(7)°, = 90° and Z = 4. The molecule is located on a centre
c
1.318 Mg/m3
0.089 mmꢀ1
of inversion and the water molecule on a twofold rotation axis. The
box and ORTEP diagram is shown in Figs. 1a and 1b, respectively.
The crystal data and structure refinement for AMB are shown in
Table 1, where as some important Bond lengths (Å) and angles
(°) are shown in Table 2.
720
0.32 ꢁ 0.28 ꢁ 0.25 mm3
1.01–25.01°
ꢀ48 ꢂ h ꢂ 47, 0 ꢂ k ꢂ 6, 0 ꢂ l ꢂ 9
3601
1517 [R(int) = 0.0898]
=25.00°, 100.0%
None
1517/2/125
1.029
R1 = 0.0589, wR2 = 0.1355
R1 = 0.0847, wR2 = 0.1430
0.251 and ꢀ0.248 e Åꢀ3
3.1. Electrochemical investigations of AMB and NMB
The intermediate precursor and the final product were analyzed
electrochemically on GC working electrode in a buffered medium
at pH 4.7 and 37 °C.
3.1.1. NMB
1,4-Bis((4-nitrophenoxy)methyl)benzene is observed to be
electroactive in ꢀ1.5 to +0.2 V potential window with only catho-
dic (reduction) peak. The peak current, Ipc is found to increase with
the scan rate but not exponentially which can be correlated with
the irreversible electron transfer followed by chemical reaction
(EC) as shown in Fig. 2.
of NMB reduction product increased with the addition of 1–6 lM
ds.DNA which is a measure of decrease in free NMB concentration
due to intercalation within DNA. Intercalation is an interactive
phenomenon of any drug or potential drug due to hydrophobicity
which can rupture hydrogen-bonding between the base pairs, thus
deforming DNA and ultimately preventing its replication [30–32].
The irreversible behaviour of NMB system is also confirmed by
plotting ip/t1/2 vs. log
t as shown in inset B of Fig. 2 [27–29]. This
ðIp ꢀ IpoÞ
% Decrease in current ¼
ꢁ 100
ð1Þ
Ipo
phenomenon is similar to adsorption process which may hinder
fast electron redox exchange, therefore rendering the resulting
peak current low.
where Ip and Ipo are the peak currents with and without DNA,
respectively.
3.1.2. NMB as DNA-quencher
The electrochemical behaviour of NMB was also investigated
with chicken blood DNA (ds.DNA) and its current profile was found
to decrease with added DNA (Fig. 3). The %decrease in peak current
3.1.3. AMB
Both the anodic and cathodic peaks appeared in 1,4-bis((4-ami-
nophenoxy)methyl)benzene (AMB) in a potential window of ꢀ1.5
Fig. 1a. Box diagram.
Fig. 1b. ORTEP diagram.

A. Haider et al. / Journal of Molecular Structure 994 (2011) 242–247
245
Table 2
to +1.5 V. The major effect of scan rate is observed on the oxidation
peak, Ipa(II). AMB system is also found to be irreversible as a prom-
inent peak shift is observed upon increasing scan rate from 20 to
1000 mV sꢀ1 (Fig. 4).
Some important bond lengths (Å) and angles (°).
Bond
Angle (°) and length (Å) measurement
C11 O1 C1
C14 N1 H1A
C14 N1 H1B
H1A N1 H1B
O1 C1 C2
117.59 (15)
120 (3)
112.1 (14)
120 (3)
107.34 (17)
121.0 (2)
179.45 (17)
ꢀ177.72 (18)
177.91 (17)
1.375 (3)
1.441 (3)
1.431 (3)
0.930 (5)
3.1.4. AMB as DNA-quencher
C3 C2 C1
The effect of DNA concentration on voltammetric response of
AMB (1 mM) is shown in Fig. 5. The %decrease in oxidation peak
current, Ipa (II) increased with added DNA and became constant
O1 C11 C12 C13
C12 C13 C14 N1
N1 C14 C15 C16
O1 C11
O1 C1
N1 C14
N1 H1A
N1 H1B
O1W H1W
at 6 lM which is maximum DNA concentration quenched with
1 mM AMB. This DNA concentration also corresponds to the max-
imum interaction of AMB with DNA. The %decrease in the peak cur-
rent upon the addition of DNA is also indicative of decreased
concentration of free AMB (because of intercalation phenomenon)
and formation of AMBꢀDNA complex [33].
0.970 (3)
0.832 (10)
N M B
B
A
10
8
R = 0.99
6
4
log ν
ν/Vs-1
2
0
-2
-4
-6
-8
a
↓
k
-1.6
-1.4
-1.2
-1.0
-0.8
-0.6
-0.4
-0.2
0.0
0.2
E / V vs. SCE
Fig. 2. Effect of scan rate on current–voltage profile of NMB (1 mM) in a buffer of pH 4.7 (3:7 H2O:Ethanol mixture) at 37 °C and GC vs. SCE. Scan rates were: (a) 20 (b) 50 (c)
100 (d) 200 (e) 300 (f) 400 (g) 500 (h) 800 (i) 1000 (j) 1200 (k) 1500 mV sꢀ1; Irreversibility is depicted from Ep vs. Scan rate (inset A), and ip/t1/2 vs. log
t (inset B).
3
NMB
2
1
0
-1
N M B
g
-2
a
-3
-4
-5
DNA conc. in μΜ
-1.6
-1.4
-1.2
-1.0
-0.8
-0.6
-0.4
-0.2
0.0
0.2
E / V vs. SCE
Fig. 3. Effect of DNA on voltammetric response of 1 mM NMB at 100 mV sꢀ1; inset, %decrease in peak current with added DNA (
lM): (a) 0.0 (b) 1.0 (c) 2.0 (d) 3.0 (e) 4.0 (f) 5.0
(g) 6.0. Other experimental conditions are same as in Fig. 2.

246
A. Haider et al. / Journal of Molecular Structure 994 (2011) 242–247
i
80
60
40
20
0
AMB
A
↑
a
II
/ Vs
B
-20
-40
log ν
-1.5
-1.0
-0.5
0.0
0.5
1.0
1.5
E / V vs. SCE
Fig. 4. Effect of scan rate on current–voltage profile of AMB (1 mM) at GC and 37 °C; Scan rates were: (a) 20 (b) 50 (c) 100 (d) 200 (e) 300 (f) 400 (g) 500 (h) 800
(i)1000 mV sꢀ1. Irreversibility is depicted from Ep vs. scan rate (inset A), and ip/t1/2 vs. log
t
(inset B). Other experimental conditions are same as in Fig. 2.
35
75
70
30
65
a
60
25
55
↓
50
20
45
g
40
II
15
35
30
10
1.0x10
2.0x10
3.0x10
4.0x10
5.0x10
6.0x10
Concentration of DNA (M)
5
0
-5
-10
-15
-1.5
-1.0
-0.5
0.0
0.5
1.0
1.5
E / V vs. SCE
Fig. 5. Effect of DNA on voltammetric response of AMB at 100 mV sꢀ1; inset, %decrease in current with added DNA concentration in
lM: (a) 0.00 (b) 1.00 (c) 2.00 (d) 3.00 (e)
4.00 (f) 5.00 (g) 6.00. Other experimental conditions are same as in Fig. 2.
3.1.5. Diffusion coefficients
the maximum ds.DNA concentration. The smaller diffusion coeffi-
cient values in the presence of DNA compared to those without
it, indicated interactions between these potential drugs and
ds.DNA.
Another criterion of intermolecular interactions is the diffusion
coefficient which can be calculated from the variation in peak cur-
rent, Ip in the absence and presence of DNA using Randles–Sevcik
equation at 100 mV sꢀ1 [34,35]:
The electrochemical data that is a prominent decrease in peak
current of the pure compounds accompanied by a potential shift
supported the threading intercalation (a mixed mode of groove
and intercalation binding) of AMB or NMB molecule within the
base pairs of DNA [37,38]. The intrusion of their planner hydropho-
bic parts into bases of ds.DNA which are also hydrophobic in nat-
ure, may result in the development of weak hydrogen bonding
[30,33] and compact supramolecular NMB- or AMB–DNA complex.
Thus, according to the binding data and the molecular structural
parameters (like bis-dinitro or diamino-groups with a central
methylene spacer, the threading intercalation mode of binding
may be proposed between these molecules and ds.DNA.
Ip ¼ 2:99 ꢁ 105nð
a
naÞ1=2ACꢃoD1o=2m1=2
ð2Þ
As NMB or AMB binds to DNA, bulky complex is formed, thus
resulting a decrease in the concentration of free electroactive spe-
cies at the electrode–solution interface leading to slower diffusion
processes [30,31,36]. The diffusion coefficient values calculated for
pure NMB and AMB are 1.84 ꢁ 10ꢀ7 and 3.44 ꢁ 10ꢀ7 cm2 sꢀ1
,
respectively. Upon the addition of ds.DNA, Do values decreased
gradually and these are found to be 4.69 ꢁ 10ꢀ8 and
1.99 ꢁ 10ꢀ7 cm2 sꢀ1 for NMB and AMB, respectively at 6
lM i.e.,

A. Haider et al. / Journal of Molecular Structure 994 (2011) 242–247
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elemental and spectral studies. The diamine (AMB) has also been
characterized by single crystal analysis. The cyclic voltammetric
investigations showed that both the compounds are electroactive
and their redox chemistry can be utilized as a criterion for further
applications. Moreover, NMB and AMB are found to interact elec-
trochemically with DNA via threading intercalation mode at phys-
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Supplementary data of the crystal structure and refinement, like
full bond lengths, bond angles dihedral angles, and anisotropic dis-
placement parameters, have been deposited with Cambridge crys-
tallographic data centre, CCDC No. 795267. These data can be
obtained, free of charge, using the link: www.ccdc.cam.ac.uk
<http://www.ccdc.cam.ac.uk/> or from the CCDC, 12 Union Road
Cambridge CB2 1EZ, UK, Fax: +44-1223-336033; e-mail:
deposit@ccdc.cam.ac.uk].
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