A selective chemosensor for fluoride ion and its interaction with Calf Thymus DNA

Article abstract of DOI:10.1016/j.saa.2017.01.044

The amido-Schiff base 1 (N¹, N³-bis (2-nitrobenzylidene)benzene-1,3-dicabohydrazide) containing a [sbnd]CONH[sbnd] group and [sbnd]CH[dbnd]N[sbnd] linkage has been synthesized by the condensation between isophthalic acid dihydrazide

Full text of DOI:10.1016/j.saa.2017.01.044

Accepted Manuscript
A selective chemosensor for fluoride ion and its interaction with
Calf Thymus DNA
Soumen Ghosh, Abdulla Al Masum, Aniruddha Ganguly, Md.
Maidul Islam, Md. Akhtarul Alam, Nikhil Guchhait
PII:
DOI:
Reference:
S1386-1425(17)30063-X
doi: 10.1016/j.saa.2017.01.044
SAA 14897
Spectrochimica Acta Part A: Molecular and Biomolecular
Spectroscopy
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Revised date:
Accepted date:
26 July 2016
21 January 2017
23 January 2017
Please cite this article as: Soumen Ghosh, Abdulla Al Masum, Aniruddha Ganguly, Md.
Maidul Islam, Md. Akhtarul Alam, Nikhil Guchhait , A selective chemosensor for fluoride
ion and its interaction with Calf Thymus DNA. The address for the corresponding author
was captured as affiliation for all authors. Please check if appropriate. Saa(2017), doi:
10.1016/j.saa.2017.01.044
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ACCEPTED MANUSCRIPT
A selective chemosensor for fluoride ion and its interaction with Calf Thymus DNA
Soumen Ghosha, Abdulla Al Masumb, Aniruddha Gangulya, Md. Maidul Islamb, Md.
Akhtarul Alamb*and Nikhil Guchhaita*
aDepartment of Chemistry
University of Calcutta
92, A.P.C. Road, Kolkata 700 009, India
Telephone 91-33-23508386
Fax: 91-33-23519755
bDepartment of Chemistry
Aliah University
IIA/27, New Town, Kolkata-700 156, West Bengal, India
*Corresponding author, E-mail: alam_iitg@yahoo.com (M.A. A.);
and
nguchhait@yahoo.com (N.G.)
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Abstract
The amido-Schiff base
1
(N1, N3-bis (2-nitrobenzylidene)benzene-1,3-
dicabohydrazide) containing a –CONH- group and –CH=N- linkage has been
synthesized by the condensation between Isophthalic acid dihydrazide and o-
nitrobenzaldehyde. This molecule can act as a fluoride ion sensor with high selectivity
and sensitivity. Presence of nitro group in the phenyl ring may be responsible for the
detection of fluoride ion visually with a dramatic color change from colorless to deep red
in aqueous dimethylsulphoxide solution. This Schiff base can be used as test kit for
sensing of fluoride ion in the solid state. Compound 1 can detect fluoride also in
commercially available toothpaste. As the compound has adequate solubility in DMSO-
water mixture (7 : 93, v/v) and having some hydrogen bond donor and acceptor centers,
we have investigated its nature of binding with Calf Thymus-DNA (CT-DNA) using
theoretical molecular modelling and other experimental methods like UV−Vis
spectroscopy, circular dichroic and thermal melting studies. Thermodynamic parameters
have been obtained using the well known vant Hoff's equation. From both theoretical and
experimental findings it has been observed that it can interact effectively with CT-DNA
with binding energy -7.55kcal/mol to -7.50 kcal/mol.
Key Words: Colorimetric sensing, F- sensor, Schiff base, Hydrogen bonding, DNA
interaction
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1. Introduction
In recent time, the design and synthesis of artificial molecules which are capable
to interact with biologically important molecules and ions are the basis of medicinal or
clinical research activities to study the biophysical and biochemical processes. One of
them is the detection of fluoride ion because of its unique properties compared to its
congeners and its significant role for biological and industrial applications [1-2]. For
example, fluoride salts are commonly used in some biological processes to inhibit the
activity of phosphatases in serine/threonine phosphatases enzymes active sites [3-5].
Sometimes, it is used as an important constituent in most of the drug molecules for the
treatment of anesthetics, hypnotics’ psychiatric drugs and cockroach poisons [6-7].
Moreover, fluoride is an essential element in human diet due to its significant role in bone
and teeth mineralization [8-9]. But excessive fluoride intake may cause bone disorders,
thyroid activity, collagen breakdown depression and immune system disruption [10-11].
This dual functionality of fluoride ion has acquired interest to the chemists. For this
purpose a number of procedures have been reported for the detection of fluoride [12-16].
Among them the use of electrode is very familiar. However, this procedure is too much
laborious, time consuming and costly [16-19]. On the other hand, fluorescence based
sensors require some instrumental assistance and they are less useful in real-time
application [20]. In contrast, colorimetric receptors received much attraction to the
analyst because of simplicity, sensitivity, selectivity and real-time ‘naked eye’ detection
without help of any instrument.
The visual detection of fluoride can be achieved by designing a host molecule
which can change its color during the detection process and colorimetric sensors are the
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best for this purpose. Generally a colorimetric sensor contains a binding site (H-bond
donors) to interact with anions and a signaling unit (e.g. –NO2 group) to show the color
changes during the interaction of the sensor and the anions. Based on this concept, lots of
sensors have been reported. However very few of them are able to detect fluoride
selectively [21-23]. Furthurmore most of them are unable to detect fluoride in solid state
which is no doubt a restriction of their application.
Another interesting field is the study of the interaction between synthetic organic
small molecules/drugs/drug templates with DNA, because it provides the opportunity to
develop a new efficient therapeutic agent to control gene expression [24-25]. The
interaction of small molecules with DNA involves mainly three modes- (i) intercalation
of the molecule within the base pairs of nucleic acid to distort the DNA backbone (ii)
groove binding in the deep major groove or the shallow minor groove of the DNA helix
by some non-bonding interactions (like hydrogen bonding or van der Waals interaction)
and (iii) electrostatic binding between the negatively charged DNA phosphate backbone
and cationic or positive end of the molecules [26-27]. These studies can provide
significant information about various important biological processes and to design and
develop of new and more efficient therapeutic agents targeted to DNA.
Considering the above facts we have synthesized and characterized a amido-Schiff base
1, as molecular sensor for fluoride and studied its interaction with DNA. Here, the
compound 1 detects fluoride ion selectively in semi-aqueous medium as well as in solid
state by a naked-eye color change from colorless to deep red. Interestingly, it has been
found that the position of –NO2 group in the compund has an effect on the sensitivity as
well as on the color change. Furthuemore, compound 1 has been found to interact
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effectively with calf-thymus DNA established by both experimental and theoritical
results.
2. Experimental
2.1. Instrumentation
Electronic absorption spectra have been recorded by a Hitachi UV-Vis (Model U–
3501) spectrophotometer. IR spectra (KBr pellet, 4000–400 cm–1) have been recorded on
1
a Parkin Elmer modal 883 infrared spectrophotometer. H NMR spectra have been
recorded on a Bruker, Avance 300 spectrometer, where chemical shifts (δ in ppm) have
been determined with respect to tetramethylsilane (TMS) as internal standards. The
intrinsic circular dichroism (CD) spectra have been recorded on a JASCO J-815
spectropolarimeter using a cylindrical cuvette of 0.1 cm path length at 25 0C.
2.2. Reagents
All reagents and solvents required for synthesis have been used as received from
commercial sources without further purification. All anions in the form of
tetrabutylammonium salts have been purchased from Sigma-Aldrich Chemical Company.
All solvents used for the spectroscopic studies are spectroscopic grade. Calf-thymus
DNA from Sigma-Aldrich, USA, has been used as received. Disodium hydrogen
phosphate and citric acid have been purchased from SRL, India, and citrate-phosphate
buffer of pH 7.4 was prepared in triply distilled deionized water from a Milli-Q water
purification system (Millipore).
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2.3. Syntheses
The Isophthalic acid dihydrazide (A) has been synthesized accroding to the
literature procedure [28].
2.3.1. Compound 1: Sythesis of N1, N3-bis (2-nitrobenzylidene)benzene-1,3-
dicabohydrazide
Compound A (1 mmol, 0.200 g) has been reacted with 2-nitrobenzaldehyde (2.3
mmol, 0.350 g) in methanol at room temperature for 30 minutes and a very light yellow
solid has been obtained. The product thus obtained has been filtered and then dried under
vacuum (yield: 0.330 g, 70%). 1H NMR in d6-DMSO, 300MHz, δ (ppm): 12.37 (s, 2H, –
CONH–), 8.88 (s, 2H, –CH=N–), 8.49 (s, 1H), 8.15-8.06 (m, 6H), 7.82 (t, J=7.5 Hz, 2H),
7.7-7.65 (m, 3H). 13C NMR (75.5 MHz, d6-DMSO, 20 ºC) δ (ppm): 124.89, 128.28,
128.85, 131.03, 131.42, 133.54, 133.99, 143.76, 148.52, 163.03. Anal. calcd for
C22H16N6O6: C, 57.39; H, 3.50; N, 18.25. Found: C, 57.32; H, 3.58; N, 18.20. IR
(KBr): 3235, 3190, 3049, 1677, 1644, 1541, 1517, 1361, 1339, 1282, 1262, 1160, 1126
cm–1.
3. Results and discussion
The compound 1 has been synthesized following two steps (Scheme I). In the first
step isophthalic acid dihydrazide has been prepared from diethyl isophthalate, then
condensation was done with o-nitro benzaldehyde, Compound 1 has been characterized
1
by H, 13C NMR and IR spectroscopic methods. The FT-IR spectrum provides the
information about the presence of two functional groups (amido (–CONH–) and imino (–
CH=N–) group) by the absorption peaks in the range of 1677 to 1665 and 1660-1644 cm-
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1
1 respectively [29]. In the H-NMR spectra, two characteristic peaks at 12.37 ppm and
8.88 ppm have been found which also support the presence of (–CONH–) and imino (–
CH=N–) groups in compound 1 [30].
3.1. Visual sensing of anions
The colorimetric sensing ability of compound 1 (10–4 M) has been investigated by
naked eye in aqueous dimethyl sulphoxide solvent (DMSO:H2O =7:3, v/v). When F– ion
is added to the solution of 1, an intense red coloration occurs, which can be visualized by
naked eye (Fig. 1 ). Now to rationalize the reason behind the color change of compound
1, we have synthesized two copounds (2 and 3, Scheme 1). Compound 2 contains the
nitro group in the meta position of the aldehyde ring and compound 3 does not contain
nitro group. On treatment of F- with the aqueous DMSO solution of 2 and 3 (1.0  10–4
M) , 2 shows a color change from colorless to light yellow (Fig. S9), but 3 does not show
any color change (Fig. S10). So, the colour change of the compound are most probably
due to hydrogen bonding interaction between the amide groups and fluoride ion. The
formation of these hydrogen bonds affects the electronic properties of the chromophore,
leading to a subsequent intramolecular charge-transfer from electron rich fluoride-bound
amide to the electron deficient nitrobenzene group in compounds 1 and 2 [31-32].
–
Under similar experimental condition, other anions, such as CH3COO–, H2PO4 ,
–
Cl–, Br–, HSO3 and CN– do not exhibit any visual color change which attributes either
very negligible or no interaction of these anions with the compounds. Based on the above
obervations, it can be said that compound 1 can detect fluoride ion selectively.
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3.2. UV–Vis spectroscopic titration
The colorimetric sensing ability of compound 1 (10–6 M) with anions has also
been monitored by UV-Visible spectroscopy in aqueous dimethyl sulphoxide solution.
Compound 1 exhibits a strong absorption band at 300 nm and a hump at 335 nm (Fig. 2
and Fig. S11). With the addition of increasing amount of F– ion to the aqueous dimethyl
sulphoxide solution of 1 (10–6 M), the peak at 300 nm gradually decreases with the
generation of a shoulder band slightly shifted to red with increasing intensity and a new
broad absorption band appears at 456 nm with a clear isosbestic point at 345 nm. The
presence of one isosbestic point indicates one type of interaction takes place between 1
and F- which is obviously the formation of complex between 1 and the fluoride ion via H-
bonding interaction. As a result the –N centre of the amide becomes electron rich
resulting a intramolecular charge transfer from the electron rich amidic nitrogen to the
electron deficient –NO2 group and this is the reason for the appearance of the new band at
at 456 nm. To cross check our assumption, i.e. the effect of nitro group on the color
change of the compound 1 towards fluoride, we have studied the UV-Vis responses of
compound 2 and 3 in presence of fluoride in aqueous DMSO solution. The UV-Vis
spectra of compound 2 (10–6 M) also show an observable change during titration with F–
ion. Upon addition of F– ion, the peak at 274 nm decreases its intensity, while a new band
at 343 nm appears with an isosbestic point at 317 nm (Fig. S12). These spectral changes
take place accompanied by visual color change from colorless to yellow color. As
expected, the UV-Vis spectrum of compound 3 does not show any notable spectral
changes with addition of increasing amount of F- ion (Fig. S13). These spectral changes
also gives the evidence for the formation of H-bonded complex between the two amide
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protons of the compound and F– ion followed by deprotonation of the protons which gets
stabilized by resonance with the –NO2 group [33-34]. The compound 1 containing the
nitro group in ortho position shows red shifted band for fluoride complex than fluoride
complex of 2 where the nitro group is in the meta position. This is because the nitro
group in the ortho position makes the amide proton more acidic and at the same time it
makes more stable fluoride complex by resonance stabilization (Scheme 2 and S1).
Under the same experimental condition, on addition of other anions such as AcO–,
–
–
H2PO4 , Cl–, Br–, I– and HSO3 notable spectral or colour changes have not been
observed with 1, 2 and 3 indicating no interaction or complexation of these anions with
the above the compounds (Fig. S8, S9a, S10).
As shown in Fig. 2 (inset), the Benesi–Hildebrand (B–H) plot of 1/[A-A0] vs 1/ [F–] for
the titration of 1 with F– ion provides a strignt line, indicating 1:1 complex formation
with association constant (K) 1.3  103 M–1 [35-36]. The detection limit of sensor 1
towards F- ion has been calculated using UV–Visible titration data (Fig. S14). Sensor 1 is
found to have a detection limit of 1.2 × 10−6 M for F- in semi aqueous solvent system
[37].
3.3. 1H NMR titration
1
To investigate the nature of binding of compound with fluoride ion, H NMR
1
titration experiments have been performed in d6-DMSO. H NMR spectra of 1 shows
characteristic peak of amide proton (Ha) at  12.37 ppm (Fig. 3). During titration when 1
equiv. of TBAF has been added the –NH peak becomes broad due to the formation of H-
bonded complex. On further addition of 2 equiv. of F ions the –NH peak of receptor 1
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disappears and the Hc proton of isophthalate undergoes an downfield shift. At 5
equivalent of F- ions the Hc proton is further shifted to downfield direction, at the same
time the signal at  8.88 corresponding to imine proton Hb is slowly upfielded owing to
the formation of exocyclic double bond during detection process. The downfield shift of
Hc proton of isophthalate may be explained in terms of hydrogen bonding interaction
between the Hc proton and the fluoride ion (Scheme II) [38-39].
The above results of 1H NMR titration and UV–Vis titration indicate that the
binding mechanism of compound 1 with fluoride may be a two step process. Firstly, 1:1
adduct formation has been taken place between compound 1 and fluoride ion through
hydrogen bonding interaction and then deprotonation of –NH- proton which increases
electron density over the receptor. As a result charge separation is introduced in the
receptor which triggers intramolecular charge transfer (ICT) between the electron
deficient –NO2 group and electron rich –N of amide to show the UV-Vis and colorimetric
changes. In case of compound 1 the electron deficient –NO2 group is in the ortho position
of the phenyl ring which results better charge seperation between the donor moiety
(electron rich –N of amide) and the acceptor moeity ( electron deficient –NO2 group)
consequently the ICT process becomes energiticaly more favourable. As a result the
compound 1 absorbs the longer wavelength resulting a color change from colorless to
deep red (Scheme II and Scheme S2). In contrast, compound 2 has the –NO2 group in the
meta position. So extent of charge seperation will be less, therefore, the ICT process is
comperatively less energiticaly favourable than 1. That is why it absorbs comperatively
shorter wave length than 1 showing a yellow coloration (Scheme S1). As compound 3
does not contain –NO2 group in the phenyl ring, the amide protons are not sufficiently
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acidic. So the extent of interaction of it with F- will be less than the above two. If it
interacts with F- , due to absence of –NO2 group there will be no effective charge
seperation to favour ICT process. As a result no color change has been observed for it.
3.4. Practical Application
3.4.1. Visual color changes on test papers
By considering the above observations, we have tried to investigate practical
applications of compound 1 as anion sensor. To explore this, we have prepared test kits
by coating a test paper (Whatman-40) with aqueous DMSO solution of 1 (1× 10–4 M) and
then dried it in air for long time because it is hard to be dried in air. For the detection of
anion, the aqueous solution of anions (1× 10–4 M) have been added on the test paper and
dried in hot air. Interestingly, only that spot which contains F– ion shows a bright red
color (Fig. 4) and no color changes was observed in other spots containing anions like
–
–
AcO–, Cl–, Br–, I–, CN–, HSO3 and H2PO4 . This experiment supports that compounds 1
has the capability to detect F– ion both in solution and solid state. It is noteworthy to
mention that compound 2 can also detect fluoride ion in solid state exhibiting light yellow
color on the test paper (Fig. S15).
3.4.2. Detection of fluoride in toothpaste by the compound 1
As we have mentioned above, compound 1 can quantitatively detect F– in a very
wide concentration range, we have checked the sensitivity of compound 1 towards
fluoride ion in commercially available toothpaste. For this purpose we have prepared an
aqueous DMSO solution of commercially available toothpaste as sample. With the
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addition of the toothpaste solution to the aqueous DMSO solution of compound 1 (1×10−4
M) a deep yellow color generates which is comparable to the color of the receptor in
presence of bare fluoride (Fig.S16, inset). The UV-Vis spectra of compound 1 (1×10−5
M) in presence of toothpaste solution shows a broad band at 465 nm which is
resemblance to the UV-Vis spectra of sensor 1 in presence of fluoride (Fig.S13). Thus the
sensor 1 can detect F− in commercially available toothpaste.
3.5. Theoretical structure
To know the most stable conformers of 1 and the reference compound 3 the
ground state optimization has been carried out in vacuum using Gaussian 03 software
with B3LYP hybride functional and 6-31++G(d,p) basis set at Density Functional Theory
level [40]. The optimized global minimum structure of 1 shows that the two nitro-
benzene moieties and the isophthalic moiety are not in the same plane and is twisted by
an angle of 57.4o (Fig. 5). The optimized structure of 1 also shows that each amide C=O
is intramolecularly H-bonded with the N= C-H (distances H1….O1 and H2…O2 are
2.180Å and 2.180Å respectively, Table 1). Furthermore, the O atom of the NO2 groups is
also H-bonded with the N= C-H (distances H1….O3 and H2….O4 are 2.277Å and
2.277Å respectively, Table 1). Importantly the two amide N-H moieties are pointing
upward with respect to the isophthalic moiety. The isophthalic moiety and the amide N-H
are not in the same plane and are deviated by the tortional angle of 41.5o. In case of
compound 3 also the benzene moieties and the isophthalic moiety are not in the same
plane (Fig. S17a). Unlike 1, the immine hydrogens of 3 are pointed towards inside,
perhaps the absence of -NO2 group may be reason. That is why, there is no H-bonding
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interactions between the carbonyl oxygens and the immine hydrogens. Now, the
optimized structure 1.F– complex shows that fluoride ion can fit in-between the twisted
structure of 1, and thus can form 1:1 stable complex (Fig. S17b), where donor-acceptor
distances are N-H3...F– = 2.220 Å , N-H4...F– = 1.692 Å and C-H5….F– = 2.106 Å
(Table 1). It is important to note that in 1.F– complex the O1-H1 and O2-H2 distances are
changed compare to the bare compound 1 (Table 1). Furthermore, after complex
formation the tortional angle between the isophthalic moiety and the anime N-H reduces
to 22.59o. Interestingly, the predicted stoichiometry from theoretical structural
optimization corroborates with the outcome of UV-Vis titration experiment and B–H
plot. On the other hand the optimized structure of 3.F- complex shows that between two
amidic hydrogen only H4 is in same plane with fluoride and there is a partial double bond
character between N2 and the carbonyl carbon (Fig. S17c). That means only H4 forms
effective H-bond with fluoride where the donor-acceptor distances are N-H3...F– = 2.74
Å , N-H4...F– = 2.12 Å and C-H5….F– = 2.22 Å (Table S1). So it can be said that
between compound 1 and 3, compound 1 form strong complex with fluoride ion.
3.6. DNA binding Study
As compound 1 contains several H-bond donor acceptor units and most
importantly it is soluble in water-DMSO solvent mixture (water : DMSO =93:7), we have
investigated its interaction with calf-thymus DNA in Citrate Phosphate Bufffer
containing 7% DMSO, [Na+] 10 mM, pH 7.0).
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3.6.1. Absorption spectral modification of 1 in presence of DNA
The absorption profile of compound 1 shows a strong absorption band at 300 nm
and a hump at 335 nm. On addition of CT-DNA the absorption intensity decreases with
slight red shift, indicating modification of the environment of compound 1 suggesting
binding interaction of 1 and CT-DNA (Fig. 6). Non-cooperative Scatchard analysis
(Fig.6, inset) has been used to determine binding constant and the number of excluded
base pair during binding process [41]. Analysis of data shows that binding constant is
5
1
–
2.99×10 M , while the number of excluded base pair is 9.5. These data shows that
compound 1 binds strongly to DNA .
3.6.2. Conformation investigation: circular dichroism spectroscopy
To further study the binding of compound 1 with CT-DNA, intrinsic CD spectra of CT-
DNA has been measured at increasing volume of DMSO in water to examine its stability
in water-DMSO mixture. The CD spectra reveal that the conformation of CT- DNA
remains unchanged upto 50% DMSO (Fig. 7a ). So we have studied the binding
interaction of 1 with CT-DNA in 7% DMSO–water mixture which is very less than the
permisiable level of stability of CT-DNA.
The CD spectra of CT-DNA in 7% DMSO exhibit a typical shape (Fig. 7b),
revealing a minimum at ~ 247 nm and a maximum at ~ 276 nm corresponding to the right
handed B-form. On addition of compound 1, it has been found that molar ellipticity of
positive band increases gradually. Two very weak isoelliptic points have also been
observed at 292 and 262 nm which indicate strong binding of ligand to CT-DNA helix
and change in conformation of CT-DNA due to binding with 1 (Fig. 7b) [42].
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3.6.3. Thermodynamic parameters and nature of the acting forces
There are different types of binding interaction between small molecules and
DNA such as hydrogen bond, van der Walls force, electrostatic and hydrophobic
interaction. Since the sign and magnitude of the thermodynamic parameters (H, S,
G) can account for the main driving forces for these interactions, we have estimated
these parameters from the plot of ln Kb vs 1/T (Fig. 8) according to the van’t Hoff Eq.
(Table S2). Ross and Subramanian have explained the thermodynamic law to evaluate the
primary mode of binding forces between small molecules and biological molecules: (1)
H > 0 and S > 0 are associated with hydrophobic interaction; (2) electrostatic force are
more dominant when H= 0 and S > 0; (3) H < 0 and S < 0 are frequently taken for
hydrogen bond and van der Waals force [43]. From the fitted data it has been observed
that the enthalpy of binding (ΔH) is -1.3 kcal where as the entropy change (S) during
the binding is 20.8 cal/mol/K (Fig. 8). These data clearly shows that the binding is
favored by negative enthalpy and positive entropy change. This infers groove binding
between the molecule and DNA through hydrogen bonding and van der Waals
interaction. As seen in Table S1, the negative values of G signify that the process of
probe-DNA interaction is spontaneous in nature.
3.6.4. DNA Denaturation Temperature Studies.
DNA melting experiment provides characteristic melting temperature (Tm) at which DNA
double helix strands separates as a result of breaking of all type of non-bonding
interactions. Depending on the strength of interaction between the molecule and DNA
melting temperature varies. Here, the change in absorbance at 260 nm for the DNA in the
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absence and presence of compound 1 has been measured. The values of Tm of DNA and
the 1-DNA system have obtained from the transition midpoint of the melting curves
based on fss versus temperature (T),
fss = (A - A0)/(Af - A0)
where A0 is the initial absorbance intensity, A is the absorbance intensity corresponding
to its temperature, and Af is the final absorbance intensity [44]. The melting curves of
DNA in the absence and presence of 1 is shown in Figure 9. As seen in the figure, the Tm
of DNA in the absence of 1 is 71oC, whereas Tm of DNA in the presence of 1 is 72.02oC.
The melting data indicates that the DNA helix stabilizes moderately on binding with 1.
3.6.3. Molecular docking studies
To study the binding of compound 1 with CT-DNA docking calculations using
MOE program have been conducted using Alpha PMI as the placement methodology
with four CT-DNA sequences (Table 2). The docked poses obtained thus have been
further refined using force field method available in the MOE program. The calculation
setup has been approached by placing the compound 1 in the minor groove of CT-DNA
and the search space has set to the pocket. This enabled the MOE program to search the
binding poses in the minor groove only. Once compound 1 has been placed, the docking
run has been initiated with the input parameters described above.
Molecular docking of compound 1 clearly reveals that due to the curve shape of
compound 1 it prefers to bind to the narrower and deeper shape of the minor groove of
CT-DNA and binding further stabilizes through hydrogen bonding and van der Waals
forces (Fig. S18). The free energy of binding is in the range of -9.53 to -7.16 kcal/mol
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which collaborates with the experimental value (Table S2). From the docking picture and
two dimensional binding studies it is observed that the N-H group and the carbonyl group
played a significant role during binding process forming hydrogen bond with bases
present in DNA (Fig.10a and Fig. S19).
The orientation of compound 1 in the minor groove is such that its nitro group ring
is orthogonal to the rest of the molecule and is exposed to the outside of the minor groove
and in contact with solvent environment. It is also observed that the molecule occupied 5
to 7 base pair during binding to CT-DNA (Fig.10) which was supported by Scatchard
plot.
4. Conclusion
In summary, we have described that isophthalic acid dihydrazide derived Schiff
bases 1 containing electron deficent –NO2 group can selectively detect F– ion by changing
color, which could be visible by “naked-eye” without any spectroscopic instrumentation
both in solution phase and in solid phase. Interestingly, compound 1 interacts effectively
with CT-DNA. Docking study, CD spectral analysis and thermal denaturation study
suggest that binding of compound 1 to DNA is mainly groove binding in nature.
Thermodynamic parameters show that the binding of 1 to DNA is favored by both
negative enthalpy and positive entropy changes. So the compound 1 can be used as a
colorimetric fluoride sensor in both solid and solution phase as well as it can act as a
good DNA intercalater.
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Acknowledgment
SG & AG would like to acknowledge UGC for Fellowship. MAA thanks DST,
Govt. of West Bengal, India (Project No. 376(Sanc.)/ST/P/S&T/9G-16/2013) for
financial support.
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Figure captions
Fig.1. Naked-eye color changes of compound 1 (1.0  10–4 M) after addition of 2
equivalent of various anions in aqueous dimethyl sulphoxide solvent (DMSO:H2O =7:3,
v/v).
Fig. 2. UV-Vis spectral changes of compound 1 (1.0  10–6 M) upon addition of F– ion
(0–5 equiv.) in aqueous dimethyl sulphoxide solvent (DMSO:H2O =7:3, v/v)..
1
Fig. 3. H NMR spectra of compound 1 in DMSO-d6 after addition of 0-5 equivalent of
fluoride ion.
Fig. 4. Color change of test paper containing 1 (10–4 M) in presence of different anions.
Fig. 5. Ground state optimized structure of compound 1.
Fig. 6. a) Circular dichroic spectral profile of DNA in different ratio of DMSO and water
(v/v) Inset: change of ellipticity vs concentration of DMSO b) Circular dichroic spectral
profile of DNA (40 mM) with increasing compound 1 concentration.
Fig. 7. Absorption of compound 1 in the presence of increasing concentration of DNA
(Scatchard analysis inset).
Fig. 8. Van’t Hoff plot for the binding of 1 with CT-DNA.
Fig. 9. Thermal melting profiles of DNA and the 1–DNA complex as constructed by
observing the relative absorbance at abs = 260 nm as a function of temperature.
Fig. 10. Molecular docking using MOE. (a) Docking picture of 1 to the minor groove of
DNA, (b) Hydrogen bonds between compound 1 and DNA bases (indicated with the
distances), (c) Two-dimensional interaction diagram of compound 1−DNA system
(buttons with A and T represent adenine and thymine bases in DNA.
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Table 1. Some useful Some useful bond lengths (Å )of compound 3 and 3. F– complex
of compound 1 and 1. F– complex
Substrates H1…O1 H1–O3 H2…O2 H2–O4 N-
N-
C-
H3...F- H4...F- H5...F-
2.108
2.066
2.277
2.260
2.108
2.575
2.277
2.144
---
---
---
1
1 + F-
2.220
1.692
2.106
Table 2. List of four DNA Decamer Sequences used for Docking Study
S.No. DNA Sequence
1
2
3
4
S1
S2
S3
S4
5'-d(GATGGCCATC)2
5'-d(GATCCGGATC)2
5'-d(GGCAATTGCC)2
5'-d(GGCTTAAGCC)2
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Fig. 1
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Fig. 2
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Fig. 3
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I–
Br–
AcO–
Cl–
1
F–
–
HSO3
–
H2PO4
CN–
Fig. 4
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O1
O3
O2
H1
N1
H2
O4
N2
H3
H4
Fig. 5
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Fig. 6
29