DFT calculation, biological activity, anion sensing studies and crystal structure of (E)-4-chloro-2-[(pyridin-2-ylimino)- methyl]phenol

Article abstract of DOI:10.2298/JSC171001009Y

(E)-4-Chloro-2-[(pyridin-2-ylimino)methyl]phenol was synthesized in the reaction of 2-aminopyridine with 5-chlorosalicylaldehyde. The structure of compound was investigated by FTIR, UV-Vis, 1H-NMR, 13C-NMR and X-ray data. In addition, characterization of

Full text of DOI:10.2298/JSC171001009Y

J. Serb. Chem. Soc. 83 (6) 707–721 (2018)
JSCS–5106
UDC 547.233’821+547.56:519.677:577.213.3+
543.422–76:57–188
Original scientific paper
DFT calculation, biological activity, anion sensing studies and
crystal structure of (E)-4-chloro-2-[(pyridin-2-ylimino)-
methyl]phenol
1
2
3
NURAY YILDIRIM , NESLİHAN DEMİR , GÖKHAN ALPASLAN , BAHADIR
4
5
6
BOYACIOĞLU , MUSTAFA YILDIZ * and HÜSEYİN ÜNVER
1
Health Services Vocational School, Çanakkale Onsekiz Mart University, TR-17100
2
Çanakkale, Turkey, Department of Biology, Faculty of Arts and Sciences, Çanakkale Onsekiz
3
Mart University, TR-17100 Çanakkale, Turkey, Department of Medical Services and
Techniques, Vocational School of Health Services, Giresun University, TR-28200 Giresun,
4
Turkey, Vocational School of Health Services, Ankara University, TR-06290
5
Keçioren-Ankara, Turkey, Department of Chemistry, Faculty of Arts and Sciences,
6
Çanakkale Onsekiz Mart University, TR-17100 Çanakkale, Turkey and Department of
Physics, Faculty of Science, Ankara University, 06100 Beşevler-Ankara, Turkey
(
Received 2 October, revised 28 November, accepted 25 December 2017)
Abstract: (E)-4-Chloro-2-[(pyridin-2-ylimino)methyl]phenol was synthesized
in the reaction of 2-aminopyridine with 5-chlorosalicylaldehyde. The structure
1
13
of compound was investigated by FTIR, UV–Vis, H-NMR, C-NMR and
X-ray data. In addition, characterization of the compound was realized using
theoretical quantum mechanical calculations and experimental spectroscopic
methods. The molecular structure of the compound was confirmed using X-ray
single-crystal data, NMR, FTIR and UV–Vis, which were in good agreement
with the structure predicted by the theoretical calculations using the density
functional theory (DFT). Moreover, the antimicrobial activity of the compound
was investigated against some bacteria and yeast cultures by the broth micro-
dilution test. UV–Vis spectroscopy studies of the interactions between the
Schiff base and calf thymus DNA (CT-DNA) showed that the compound inter-
acts with CT-DNA via electrostatic binding. The colorimetric response of the
compound receptors was investigated before and after the addition of an equiv-
alent amount of each anion to evaluate anion recognition properties.
Keywords: UV–Vis spectroscopy; 2-aminopyridine; anti-microbial activity;
DNA binding; X-ray crystallography.
INTRODUCTION
Schiff bases and their metal complexes have attracted curiosity due to their
1
–5
DNA binding and cleavage properties.
Applications of them as chemical nuc-
*
Corresponding author. E-mail: myildiz@comu.edu.tr
https://doi.org/10.2298/JSC171001009Y
7
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YILDIRIM et al.
leases is the focus of current research. It has been demonstrated that they could
be used in some studies as sequence specific DNA binding agents, and diagnostic
6
–9
agents in medicinal applications and for genomic research.
They were used as
10–12
ligands and their complexes were used in a wide range of medicinal chemistry.
The tautomeric balance and intramolecular hydrogen bond in Schiff bases
occur through proton transfer, leading the compound to exhibit interesting phys-
ical and biological properties that have attracted the attention of researchers.
Studies on the physical and chemical properties of Schiff bases in solid state and
1
3
in solution continue. Molecules creating intramolecular bonds are used in
1
4
highly specific systems because of their high thermodynamic stability.
Schiff bases are important to synthesize sensors for recognizing and sensing
anions, and to enlarge their areas of use. The intramolecular hydrogen bond and
15–17
proton transfer explained above are thought to affect anion-sensory properties.
It could be specifically stated that the keto-amine and enol-imine tautomer bal-
ances contribute to the bonding and selection of anions. Undoubtedly, colorimet-
ric anion sensors are of more importance, because such materials are useful as
they provide visual information more readily. Various studies have been per-
1
8,19
formed in order to develop these materials.
In the present work, the Schiff base (E)-4-chloro-2-[(pyridin-2-ylimino)-
methyl]phenol (Fig. S-1, of the Supplementary material to this paper) was pre-
pared and studied by experimental (UV–Vis, FTIR, NMR and X-ray diffraction)
and computational (density functional theory (DFT)) methods. The molecular
structure, HOMO–LUMO analysis, molecular electrostatic potential (MEP) and
nonlinear optical (NLO) effects of the compound were investigated using DFT
calculations. Additionally, the Schiff base was tested for its potential sensor
ability to sense anions selectively and for its interaction with DNA.
EXPERIMENTAL
Materials and methods
The H- and 13C-NMR spectra were recorded on a Bruker Avance-500 spectrometer
operating at 400 and 101.6 MHz, respectively. The infrared absorption spectra were obtained
in KBr discs using a Perkin Elmer BX II spectrometer and are reported in cm- units. The
UV–Vis spectra were measured using a Shimadzu 1800 series spectrometer. Elementary ana-
lyses were performed on a Vario EL III CHNS elemental analyzer. The melting points were
measured with an Electro Thermal IA 9100 apparatus using a capillary tube. 2-Aminopyri-
dine, 5-chlorosalicylaldehyde, DMSO, EtOH, CHCl , n-hexane, (Bu) NF, (Bu) NBr, (Bu) NI,
1
1
3
4
4
4
(
Bu) NCN, (Bu) NSCN, (Bu) NClO , (Bu) NHSO , (Bu) NCH COO, (Bu) NH PO ,
4 4 4 4 4 4 4 3 4 2 4
(
Bu) NN , (Bu) NOH and DMSO were purchased from Aldrich.
4
3
4
Analytical and spectral data are given in the Supplementary material.
Synthesis of (E)-4-chloro-2-[(pyridin-2-ylimino)methyl]phenol
-Aminopyridine (0.50 g, 5.32 mmol) was added to an EtOH (100 mL) solution of
-chlorosalicylaldehyde (0.829 g, 5.32 mmol). The mixture was stirred and refluxed for 1 h.
2
5
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CHARACTERIZATION AND APPLICATION OF (E)-4-CHLORO-2-[(PYRIDIN-2-YLIMINO)METHYL]PHENOL
709
The product was obtained by evaporation of the EtOH. It was crystallized from CHCl :n-hex-
3
ane (3:2 volume ratio) as orange crystals.
X-Ray crystallography
A suitable single crystal of the title compound was mounted on a goniometer and the
data were collected at 293 K on a Bruker Kappa APEXII CCD diffractometer using graphite
monochromated MoK radiation (λ = 0.71073 Å). The cell parameters of the compound were
α
2
0
-1
determined using SAINT software. Absorption correction (μ = 0.34 mm ) was obtained by
2
1
the multi-scan method via SADAPS V2012/1 software. The compound is solved by direct
methods using SHELXS-9722 and refined with SHELXL-97. The molecular figures were
22
2
3,24
prepared with the help of Mercury and ORTEP-3 program packages.
Details of the data
collection conditions and the parameters of the refinement process are given in Table I.
TABLE I. Crystallographic data and structure refinement for the title compound
Chemical formula
Crystal shape/color
Formula weight
Crystal system
Space group
C H ClN O
12 9 2
Prism/orange
232.66
Monoclinic
P2 /n
1
Unit cell parameters
a / 10-
10
m
m
m
4.5628 (4)
19.3486 (17)
12.0485 (11)
1059.19 (16)
-10
b / 10
c / 10-
10
3
Volume (m )
Z
4
-
3
D / mg cm
μ / mm
F
Crystal size, mm
Diffractometer/measurement method
Absorption correction
Tmin
Tmax
1.459
0.34
480
x
-
1
000
3
0.18×0.12×0.10
Bruker APEX-II CCD/w and ϕ scans
Multi-scan
0.643
0.745
No. of measured, independent and observed reflections
Observed criterion
Rint
22333, 2177, 1715
I > 2σ(I)
0.052
θmax
26.4
F
0.060, 1.03
2177
150
0.65, –0.60
2
Refinement on
2
2
R[F > 2σ (F )], S
No. of reflections
No. of parameters
∆
ρmax, ∆ρmin / e Å-3
Computational procedures
All theoretical computations were realized using Gauss-View5 molecular visualization
2
5
2
6
and the Gaussian 09W program package. For the calculation of the molecule geometry, the
atomic coordinates obtained from the X-ray geometry were used. The geometry optimization
of the title molecule was performed using the DFT method with the Becke three parameters
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YILDIRIM et al.
hybrid exchange-correlation functional (B3LYP)27 at the 6-311++G(d,p) basis set.28 To inves-
tigate the reactive sites and to identify sites of intra and intermolecular interactions of the
compound, the molecular electrostatic potential surface was evaluated using the B3LYP/6-
-
311++G(d,p) method. The HOMO–1, HOMO, LUMO and LUMO+1 energy values and their
shapes were calculated and simulated using the same basis set. The linear polarizability and
first hyperpolarizability properties of the compound were obtained from the molecular pola-
rizabilities based on theoretical calculations.
Screening for antimicrobial activities
Bacillus subtilis ATCC 6633, Staphylococcus aureus ATCC 25923, Escherichia coli
ATCC 25922, Enterococcus faecalis ATCC 29212, Pseudomonas aeruginosa ATCC 27853,
Escherichia coli ATCC 35218, Bacillus cereus NRRL B-3711, Proteus hauseri ATCC 13315,
Candida albicans ATCC 60193 and Candida tropicalis ATCC 13803 were used as the test
microorganisms. The MIC tests were performed by the broth microdilution method in tri-
2
9
plicate as outlined in the CLSI guidelines. The inocula were adjusted to a turbidity of 0.5
5
5
-1
McFarland standard and diluted to a final concentration from 4×10 to 8×10 CFU mL . The
compound was dissolved in DMSO (dimethyl sulfoxide) and serially diluted in cation-adjusted
Mueller–Hinton broth for the bacteria or RPMI medium for the yeasts in 96 well plates to a
final volume of 100 µL in each well. Then, an equal volume of inocula was added to each
well. The concentration of the compound, including control antibiotics ampicillin and antifun-
-
1
gal fluconazole ranged between 0.5–256 µg mL . The plates were incubated at 37 °C and the
results were evaluated after 16–20 h for the bacteria and 24±2 h for the fungi and the MIC
values were recorded.
DNA-binding experiments
The UV–Vis spectra titrations were performed in Tris–HCl/NaCl buffer at room tempe-
rature to investigate the binding affinity between CT-DNA and the Schiff base. The UV–Vis
absorbance at 260 and 280 nm of the CT-DNA solution in Tris buffer give a ratio of 1.8–1.9,
30
indicating that the DNA was sufficiently free of protein. Tris–HCl/NaCl buffer (3 mL) and
the solutions of Schiff base of buffered CT-DNA solution were added to each cuvette in order
to eliminate the absorbance of DNA itself. Before the absorption spectra were recorded, the
Schiff base–DNA solutions were incubated at room temperature for 5 min.
Anion sensors measurements
Schiff base (0.006 mmol) was dissolved in DMSO (50 mL). Tetrabutylammonium salts
-
-
-
-
-
-
-
-
-
-
-
(
F , Br , I , CN , SCN , ClO , HSO , CH COO , H PO , N and OH , 0.006 mmol) were
4 4 3 2 4 3
dissolved in DMSO (50 mL). Each solution of a tetrabutylammonium salt was added to the
Schiff base solution (1:1) in the tube. After mixing, the UV absorption spectra and a photo-
graph were taken at room temperature.
RESULTS AND DISCUSSION
Description of the crystal structure
The title compound crystallizes in the monoclinic space group P2 /n with
1
Z = 4 in the unit cell. The asymmetric unit in the crystal structure contains only
one molecule. It is known that tautomeric forms of Schiff base compounds have
…
two types of intramolecular hydrogen bonds, which belong to O–H N in
…
phenol-imine form and N–H O in the keto-amine form. The single-crystal
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CHARACTERIZATION AND APPLICATION OF (E)-4-CHLORO-2-[(PYRIDIN-2-YLIMINO)METHYL]PHENOL
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X-ray study showed that the title compound adopts the phenol-imine tautomeric
form. The C7–N1 and C2–O1 bond lengths have a significant influence in deter-
mining the tautomeric form. The C7–N1 bond distance (1.278(3) Å) is consistent
with a C=N double bond and the C2–O1 bond (1.353(3) Å) is consistent with a
C–O single bond. These bond distances are comparable with those of compounds
3
1–33
previously reported as phenol-imine.
The dihedral angle between the
C1–C6 and pyridine rings (C8–N2) is 4.38(8)°. The molecular structure is stabi-
…
lized by an intra-molecular O1–H1 N1 hydrogen bond (Fig. 1). In the crystal
…
structure, molecules are linked to each other by an intermolecular C–H O hyd-
rogen bond. Atom C7 in the reference molecule at (x, y, z) acts as a hydrogen-
-
bond donor, via H7, to atom O1 in the molecule at (x–1/2, –y+3/2, z–1/2), so
forming a C(5) chain running parallel to the [001] direction (Fig. S-6 of the Sup-
plementary material). Details of the hydrogen bonds are summarized in Table II.
Fig. 1. Ortep-3 diagram of the title compound. Displacement ellipsoids are drawn at the 30 %
probability level. The intramolecular hydrogen bond is shown as a dashed line.
TABLE II. Hydrogen-bond geometry (Å, °); symmetry code, i: x–1/2, –y+3/2, z–1/2
…
…
…
…
D–H
A
D–H
0.88(5)
0.93
H
A
D
A
D–H A
…
O1–H1 N1
1.92(5)
2.61
2.622(3)
3.487(3)
135(4)
158
C7–H7 O1i
…
Optimized structure
Geometric optimization of the investigated compound was performed using
the DFT/B3LYP method with the 6-311++G(d,p) basis set (Fig. S-7 of the
Supplementary material). Some of the bond lengths, bond angles and torsion
angles of the optimized structure are listed in Table III and compared with the
experimental data of the compound. As can be seen from Table III, most of the
molecular geometric parameters are slightly different from the experimental
ones. The biggest differences between experimental and calculated bond lengths
and angles are 0.058 Å for the C10–C11 bond and 5.3° for the C10–C9–C8
angle, respectively. According to crystallographic studies, the dihedral angle
between the C1–C6 and pyridine rings is 4.38(8)°, while this angle was calcul-
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YILDIRIM et al.
ated as 41.75° for optimized structure. In order to compare the theoretical results
with the experimental values, the root mean square error (RMSE) was used. The
calculated RMSE for bond lengths and bond angles are 0.026 Å and 2.34°, res-
pectively. These differences could result from the environments in which experi-
mental and theoretical data were obtained. Namely, the theoretical computations
were performed in gaseous phase for isolated molecules, whereas the experimen-
tal analyses were recorded in the solid phase of the title molecule. The inter-
…
-
molecular hydrogen bonding interactions in the solid phase (the C7–H7 O1
hydrogen bonds depicted in Fig. S-6) were ignored in the theoretical calculations.
…
Due to the O1–H1 N1 intra-molecular hydrogen bonding interaction, the
C2–C1–C7–N1 torsional angle was recorded and calculated as –2.3 and 0.6°,
respectively. However, the N2–C8–N1–C7 torsional angles between other groups
and pyridine ring (do not exposure any interaction within the theoretical calcul-
ations) were measured and computed as 178.0 and 140.4°, respectively.
TABLE III. Some selected molecular structure parameters
Bond distance, Å
Experimental B3LYP
Bond angle, °
Experimental B3LYP
Parameter
Parameter
C1–C6
C1–C2
C2–O1
C3–C4
C5–Cl1
C7–N1
C8–N2
C8–N1
C9–C10
C10–C11
C12–N2
C11–C12
Max. Dif.
RMSE
1.403 (4)
1.411 (3)
1.353 (3)
1.373 (4)
1.743 (3)
1.278 (3)
1.381 (4)
1.418 (3)
1.343 (4)
1.334 (4)
1.383 (4)
1.372 (4)
1.407
1.420
1.337
1.385
1.760
1.285
1.336
1.406
1.389
1.392
1.333
1.393
0.058
0.026
C6–C1–C2
C6–C1–C7
O1–C2–C1
O1–C2–C3
C6–C5–Cl1
N1–C7–C1
N2–C8–C9
N2–C8–N1
C10–C9–C8
C11–C12–N2
C7–N1–C8
C8–N2–C12
118.6 (2)
119.5 (2)
121. 2 (2)
118.8 (2)
119.6 (2)
122.2 (2)
117.5 (2)
118.1 (2)
123.7 (3)
119.4 (3)
121.7 (2)
119.1 (3)
119.3
119.3
122.3
118.5
119.9
121. 9
122.7
115.1
118.4
123.8
121.1
117.8
5.3
2.34
Experimental B3LYP
Torsion angle, °
C1–C7–N1–C8
O1–C2–C1–C7
C7–N1–C8–N2
N1–C8–C9–C10
–179.1 (2)
1.0 (4)
177.7
0
178.0 (2)
–179.6 (3)
140.4
–178.8
HOMO–LUMO analyses and tautomeric stability
The highest occupied molecular orbital (HOMO) represents the outermost
orbital filled by electrons and behaves as an electron donor, while the lowest
unoccupied molecular orbital (LUMO), considered as the first empty innermost
orbital unfilled by electron, behaves as an electron acceptor. In this study, the
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CHARACTERIZATION AND APPLICATION OF (E)-4-CHLORO-2-[(PYRIDIN-2-YLIMINO)METHYL]PHENOL
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HOMO–1, HOMO, LUMO and LUMO+1 energies and their shapes in the com-
pound are shown in Fig. 2. As seen from Fig. 2, HOMO–1, HOMO and LUMO
electrons are localized over almost the whole molecule, whereas LUMO+1 ones
are placed on other groups, excepting the 5-chloro-2-hydroxyphenyl ring. The
concept of chemical hardness is quite useful in explaining chemical stability.
Molecules having a large HOMO–LUMO energy gap will be more stable and
3
4,35
less reactive than soft molecules having a small HOMO–LUMO energy gap.
To investigate the tautomeric stability, optimization calculations at B3LYP/6-
311++G(d,p) level were performed for O–H···N in the phenol-imine (OH) and
-
for N–H···O in the keto-amine (NH) forms of the compound. In addition, the
total energy, I (ionization potential), A (electron affinity), χ (electronegativity),
3
6
ζ (softness), ψ (electrophilicity index) and η (chemical hardness) were calcul-
ated at the same level and the results are given in Table IV. The total energy of
the OH form is lower than that of the NH form, while the chemical hardness of
the OH form is greater than that of the NH form, which indicates that the OH
1
5,37
form of the compound is more stable than its NH form in the gas phase.
Fig. 2. The molecular orbital surfaces and
their energy values of the title compound.
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YILDIRIM et al.
TABLE IV. The calculated quantum molecular descriptors of the title compound
Phenol-imine
B3LYP/6-311++G(d,p) B3LYP/6-311++G(d,p)
Keto-amine
Parameter
Etotal / Hartree (atomic unit of energy)
EHOMO / eV
ELUMO / eV
–1107.81804145
–6.399
–2.425
3.974
–1107.81351026
–5.885
–2.765
3.120
EHOMO–ELUMO / eV
Ionization potential [I = −EHOMO], eV
Electron affinity [A = −ELUMO], eV
Chemical hardness [η =(I − A)/2], eV
Electronegativity [χ = −(I + A)/2], eV
Softness [ζ = 1/2η], eV
6.399
2.425
1.987
–4.412
0.251
5.885
2.765
1.560
–4.325
0.320
2
Electrophilicity index [ψ = χ /2η], eV
4.898
5.995
The molecular electrostatic potential V(r) is created in the space around a
molecule by its nuclei and electrons. It is defined by Eq. (1):
ZA
ρ(r′)
V (r) =
−
dr′
(1)

r′ − r
RA − r
A
in which Z is the charge of nucleus A, located at R , ρ(r′) is the electronic
A
A
3
8
density function of the molecule, and r′is the dummy integration variable.
MEP is related to the electronic density and is a very useful descriptor in deter-
mining sites for electrophilic and nucleophilic reactions as well as hydrogen
3
9,40
bonding interactions.
geometry was calculated.
The MEP at the B3LYP/6-311++G(d,p) optimized
The red color parts represent the negative electrostatic potential regions or
electrophilic reactivity, while blue ones represent the positive ones or nucleo-
4
1
philic reactivity. As could be seen in Fig. 3, a negative region of the compound
was observed around the pyridine rings N2 atom. The negative V(r) value is
–
0.048 a.u. for the N2 atom. A maximum positive region localized on the C7–H7
Fig. 3. Molecular electrostatic potential map calculated at the B3LYP/6-311++G(d,p) level.
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CHARACTERIZATION AND APPLICATION OF (E)-4-CHLORO-2-[(PYRIDIN-2-YLIMINO)METHYL]PHENOL
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bond, indicates a possible site for nucleophilic attack. These values give inform-
ation about the region from where the compound could have intermolecular inter-
…
actions. Thus, Fig. 3 confirms the existence of the intermolecular C–H O hyd-
rogen bond interactions.
Non-linear optical effects
NLO materials have potential applications in optical technology and indus-
4
2
trial applications. The NLO values for the compound were calculated at the
B3LYP/6-311++G(d,p) level using the Gaussian 09W program package. The
equations for calculating the magnitude of total static dipole moment μtotal, the
mean polarizability <α>, the anisotropy of the polarizability ∆α, and the mean
4
3,44
first hyperpolarizability (β) using the x, y, z components are defined as:
2
2
2
μ = μ + μ + μ
z
(2)
(3)
x
y
αxx +αyy +αzz
<
α > =
3
1
Δα ={ [
2
2
2
(
αxx −αyy
)
+
(
αxx −αzz
)
+
(4)
2
2
2
2
]}1/2
+
(
αyy −αzz
)
+ 6
αxy +αxz +αyz
(
)
2
2
2
β =
(
βxxx + βxyy + βxzz
)
+
(
βyyy + βxxy + βyzz
)
+
(
βzzz + βxxz + βyyz
)
( 5 )
It is well known that higher values of the linear polarizability and the first
hyperpolarizability are important key factors for molecules with effective NLO
properties. The polarizabilities and first hyperpolarizability are reported in terms
of atomic units (a.u.) and the calculated values were converted using 1 a.u =
–24
–33
=
0.1482×10
electrostatic unit (esu) for α and 1 a.u = 8.6393×10
esu for β.
The calculated mean polarizability <α>, the anisotropy of the polarizability (∆α)
and the first hyperpolarizability (β) for the studied compound are
–
24
–24
–31
2
8.5354266×10 , 55.741745×10
and 77.5621354×10
esu, respectively
(Table V). Urea is one of the essential molecules used for the determination of
the NLO properties of molecular systems. Therefore, it is usually used as a refer-
ence molecule in NLO studies. The calculated values of urea with the same basis
–24
–31
set are 4.9066694×10
esu for <α> and 7.8781964×10
esu for β. According
to these results, the mean polarizability and first hyperpolarizability of the stu-
died compound are approximately 5.81 and 9.845 times greater than those of
urea, which implies that the title compound is a good candidate material for NLO
applications.
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YILDIRIM et al.
TABLE V. The computed dipole moments, polarizability and first hyperpolarizability values
of the title compound
Parameter
a.u.
esu×1024
Parameter
a.u.
esu×1031
αxx
αxy
αxz
αyy
αyz
αzz
αtotal
Δα
μx
311.1872364
4.4930217
–4.7262655
167.2074794
5.6208234
99.2454993
192.5467383
376.12331457
–2.1621
46.1179484
0.6658658
0.7004325
24.7801484
0.8330060
14.7081829
28.5354266
55.741745
βxxx
–722.1630436 62.3898318
–285.766783 24.6882496
β
xxy
β
–72.2753195
–71.7018625
84.4473294
26.8613951
–15.1811256
–15.7126661
–5.1689098
6.2440816
6.1945390
7.2956581
2.3206365
1.3115429
1.3574643
0.4465576
xyy
β
yyy
β
xxz
β
yyz
β
xzz
β
yzz
β
zzz
μy
μz
–2.7821
–0.8375
β
897.7826375 77.5621354
μtotal
3.6216
FTIR, H-NMR, 13C-NMR and UV spectroscopy
1
–1
The vibration bands with the wave numbers 3433 cm (broad strong, O–H);
–
1
–1
–1
3
107–3046 cm (weak, Ar-H); 1560 cm (strong, C=C); 1478 cm (strong, C–N)
–
1
and 1356 cm (strong, Ar–O) were observed for the compound (Fig. S-2). The
–
1
C=N bond was observed at 1616 cm for the compound. The stretching fre-
quency observed at 2852–2750 cm in the spectrum of the compound showed
the presence of O–H N intramolecular hydrogen bonds.
–1
…
45,46
The C=N bond,
which is partially accountable for the existence of the phenol-imine form, can
also be inferred from the IR spectrum of the compound. A compound with strong
–1
band at 1274 cm possessed high percentages of the phenol-imine tautomer due
4
7
to stabilization of the phenolic C–O bond.
1
The H-NMR data for the compound show that the tautomeric equilibrium
favors the phenol-imine form in DMSO (Fig. S-3). The OH proton was observed
as a singlet at 12.49 ppm for the compound. The azomethine proton was obs-
erved as a singlet at 8.94 ppm for the compound. The phenyl protons of the com-
pound resonated as multiplet between 8.60–6.96 ppm.
According to the proton de-coupled 13C-NMR spectra, the compound has 12
signals in deutero-DMSO (Fig. S-4). The azomethine carbon (ArCH=N–) is obs-
erved at δ = 164.15 ppm for the Schiff base. In the investigated compound, the
aromatic-C chemical shifts (δ / ppm) are 164.15, 158.80, 148.73, 144.89, 144.24,
1
33.60, 130.99, 128.17, 124.64, 123.05, 121.20 and 119.61.
The UV–Vis spectra of the compound were studied in DMSO (Fig. S-5).
Schiff bases exhibited absorptions in the range greater than 400 nm in polar and
nonpolar solvents. The UV–Vis spectrum of ortho hydroxylated Schiff-bases that
exist mainly as the phenol-imine structure is indicated by the presence of a band
at < 400 nm, while compounds existing either as keto-amine or as mixture of
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CHARACTERIZATION AND APPLICATION OF (E)-4-CHLORO-2-[(PYRIDIN-2-YLIMINO)METHYL]PHENOL
717
phenol-imine/keto-amine forms show a new band, especially in polar and non-
polar solvents in both acidic and basic media, at >400 nm. 4
5–47
The title com-
pound showed no absorption above 400 nm in DMSO, indicating that the com-
1
pound exists in the phenol-imine form in DMSO. In conclusion, UV-Vis, H-NMR
13
and C-NMR results showed that the compound existed in the phenol-imine
form in DMSO.
Minimum inhibitory concentration (MIC)
The MIC was evaluated by the broth micro dilution test. The MIC values
were read as the lowest concentration of the drug in the series that prevents the
development of visible growth of the test organism. The data reported in Table
VI are the average from three experiments.
The antimicrobial activity spectrum of the Schiff base varied in the concen-
–1
tration range 32–128 µg mL . It could be observed from Table VI that the Schiff
base exhibited a high antifungal effect on C. albicans and C. tropicalis, while the
compound had a low effect on the bacteria. However, the compound had stronger
antibacterial effect against S. aureus, E. faecalis, B. cereus NRRL B-3711, E.
coli ATCC 25922, E. coli ATCC 35218, P. aeruginosa and P. hauseri compared
to B. subtilis. Furthermore, this compound showed similar activity against the
tested microorganisms, despite the fact that the cell wall in Gram-positive bac-
teria have a single layer, whereas the Gram-negative cell wall is a multi-layered
structure, and the yeast cell wall is quite complex. The antifungal activity of the
–1
compound was found to be dose dependent with MIC of 32 µg mL .
-
1
TABLE VI. MIC value (µg mL ) of the compound
Compound
Schiff base
Antibiotic
Microorganism
Ampicillin
Fluconazole
S. aureus ATCC 25923
E. faecalis ATCC 29212
B. cereus NRRL B-3711
B. subtilis ATCC 6633
E. coli ATCC 25922
64
64
64
128
64
64
64
64
32
32
1
2
2
–
–
–
–
–
–
–
–
16
32
1
16
32
2
2
–
E. coli ATCC 35218
P. aeruginosa ATCC 27853
P. hauseri ATCC 13315
C. albicans ATCC 60193
C. tropicalis ATCC 13803
–
DNA-binding
The potential binding ability of the compound to CT-DNA was characterized
by UV spectroscopy. The absorption spectra of the ligand in the absence and
presence of CT-DNA at different concentrations are given in Fig. 4. Absorption
spectroscopy is one of the most used methods for investigating the effects of any
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7
18
YILDIRIM et al.
material on DNA. If it has an intercalation effect against DNA, generally a hypo-
chromic effect is observed. However, if the interaction of a material with DNA is
electrostatic or partially intercalative, a hyperchromic effect is observed.4
Moreover, a red shift of the absorption maximum indicates that the difference
between HOMO and LUMO energy levels decreases, and that the complex
,5,15
4
interacts with DNA. The absorption spectra of the Schiff base in the absence
and the presence of CT-DNA are shown in Fig. 4. In the UV region, two intense
bands absorbed at 269 and 386 nm for the ligand. In the presence of CT-DNA, an
increase in the peak intensities was observed in the absorption spectra of Schiff
base. In addition to the increase in intensity, a small red shift (bathochromism;
1
–7 nm) was also observed in the spectra for Schiff base. The absorption inten-
sity of the band at 269 nm of the ligand increased (hyperchromism) evidently
after the addition of CT-DNA (0, 0.5, 1, 2, 3, 4, 5, 6, 7 and 8 µL), which indi-
cated the interactions between DNA and the Schiff base (Fig. 4). The extent of
red shift and hyperchromism are commonly found to correlate with the electro-
static binding strength. Consequently, the observation of hyperchromic effect in
the absorption spectra implies that the ligand established an electrostatic bond
with DNA. In the electrostatic binding, DNA breaks phenol protons from the
more acidic Schiff base. As a result, the negative charge distribution is changed
in the DNA chain, thereby, leading to disruption of the DNA molecules.
Fig. 4. Absorption spectra of the compound in the absence and presence of increasing amounts
of CT-DNA at room temperature in Tris–HCl/NaCl buffer (pH 7.2).
Colorimetric anion-sensing
In order to investigate whether the Schiff base could be used for visual con-
firmation of anions in a sample, real color photographs of the corresponding
–
–
–
–
–
–
–
DMSO solutions of the compound with F , Br , I , CN , SCN , ClO , HSO ,
4
4
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CHARACTERIZATION AND APPLICATION OF (E)-4-CHLORO-2-[(PYRIDIN-2-YLIMINO)METHYL]PHENOL
719
–
–
–
–
N , AcO , H PO and OH as tetrabutylammonium salts were taken and are
3
2
4
shown in Fig. 5. After addition of the anions to the Schiff base in DMSO, the
–
–
color of the solution changed from colorless to yellow and orange with F , AcO ,
–
–
OH and CN with fast response time (< 1 s), indicating that receptors in the title
compound could serve as a “naked-eye” indicator for F , AcO , OH and CN .
The more acidic phenol proton would deprotonate upon exposure to more
basic OH , F and AcO and therefore, intramolecular proton transfer occurs into
the keto-amine form. In contrast, CN has much weaker hydrogen bonding abil-
–
–
–
–
–
–
–
–
–
–
–
ity in comparison with OH , F and AcO with a stronger nucleophilicity toward
the imine group, which results in the addition reaction of CN to the carbon atom
–
of an electron deficient imine group and, subsequently, fast proton transfer of the
phenol hydrogen to the neighboring nitrogen anion through an intramolecular
15
hydrogen bond. The formation of the keto-amine form of the compound leads
to higher wavelength absorptions.
Fig. 5. The color changes of the compound (1 equiv.) upon addition of various anions
(
1 equiv.) of the compound.
CONCLUSIONS
In this study, (E)-4-chloro-2-[(pyridin-2-ylimino)methyl]phenol is reported.
The molecular structure of the compound was confirmed by X-ray crystallogra-
phic, elemental analysis, UV–Vis, NMR and FTIR studies. Theoretical calcul-
ations were employed to determine the molecular structure, spectroscopic values,
and HOMO and LUMO levels of the title compound. The theoretical calculations
were found to be in good agreement with the experimental data. The theoretical
evaluation of the NLO properties showed that the title compound has larger pola-
rizability and hyperpolarizability values than urea, which denotes its use in pot-
ential NLO applications. The ligand was found to act as anti-microbial, DNA-
-
binding and anion sensor agent.
Acknowledgement. The authors are grateful to the Scientific and Technical Research Council
of Turkey (TÜBİTAK) for the financial support of this work, Grant No. TÜBİTAK 115F253.
SUPPLEMENTARY MATERIAL
Further information may be obtained from Cambridge Crystallographic Data Centre
(
1
CCDC), 12 Union Road, Cambridge CB21EZ, UK, by quoting the depository number CCDC
564849, e-mail: deposit@ccdc.cam. ac.uk.
Available on line at www.shd.org.rs/JSCS/
________________________________________________________________________________________________________________________
(CC) 2018 SCS.

7
20
YILDIRIM et al.
Theoretical and spectral data of the title compound are available electronically at the pages
of journal website: http://www.shd.org.rs/JSCS/, or from the corresponding author on request.
И З В О Д
DFT ИЗРАЧУНАВАЊЕ, БИОЛОШКА АКТИВНОСТ, ПРОУЧАВАЊЕ ДЕТЕКЦИЈЕ
АНЈОНА И КРИСТАЛНА СТРУКТУРА (E)-4-ХЛОРО-2-[(ПИРИДИН-2-ИЛИМИНО)-
МЕТИЛ]ФЕНОЛА
1
2
3
4
5
NURAY YILDIRIM , NESLİHAN DEMİR , GÖKHAN ALPASLAN , BAHADIR BOYACIOĞLU , MUSTAFA YILDIZ
6
и HÜSEYİN ÜNVER
1
Health Services Vocational School, Çanakkale Onsekiz Mart University, TR-17100 Çanakkale, Turkey,
2
Department of Biology, Faculty of Arts and Sciences, Çanakkale Onsekiz Mart University, TR-17100
3
Çanakkale, Turkey, Department of Medical Services and Techniques, Vocational School of Health Services,
Giresun University, TR-28200 Giresun, Turkey, Vocational School of Health Services, Ankara University,
TR-06290 Keçioren-Ankara, Turkey, Department of Chemistry, Faculty of Arts and Sciences, Çanakkale
Onsekiz Mart University, TR-17100 Çanakkale, Turkey and Department of Physics, Faculty of Science,
4
5
6
Ankara University, 06100 Beşevler-Ankara, Turkey
(
E)-4-Хлоро-2-[(пиридин-2-илимино)метил]фенол је синтетисан реакцијом 2-ами-
нопиридина са 5-хлоросалицилалдхидом. Структура једињења је истраживана са FTIR,
1
13
UV–Vis, H-NMR, C-NMR и дифракцијом X-зрака (XRD). Карактеризација једињења је
такође урађена коришћењем теоријских квантномеханичких израчунавања и експери-
менталних спектроскопских метода. Молекулска структура једињења је потврђена XRD,
NMR, FTIR и UV–Vis подацима који су били у доброј сагласности са структуром прет-
сказаном теоријским израчунавањем, коришћењем методе функционала густине (DFT).
Надаље, истраживана је антимикробна активност једињења на културама бактерија и
квасца тестом разблаживања хранљивог медијума. UV–Vis спектроскопске студије
интеракција између Шифових (Schiff) база и DNK говеђег тимуса (CT-DNA), показала су
да једињење интерагује са CT-DNA путем електростатског везивања. Колориметријски
одговор рецептора овог једињења истражен је пре и након додатка еквивалентне коли-
чине разних анјона како би се процениле особине препознавања анјона.
(
Примљено 2. октобра, ревидирано 28. новембра, прихваћено 25. децембра 2017)
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