Synthesis, spectroscopic and X-ray structural characterization, quantum chemical studies and investigation of gama-irradiated effects of the novel hydrazone compound: [(E)-3-(2-nitrophenyl)-(E)-1-(2-phenylhydrazono)]-1-phenylallylidene

Article abstract of DOI:10.1016/j.molstruc.2016.12.092

The novel hydrazone compound, [(E)-3-(2-nitrophenyl)-(E)-1-(2-phenylhydrazono)]-1-phenylallylidene (2), has been synthesized, characterized by FTIR, ¹H NMR, ¹³C NMR techniques, elemental analysis, X-ray structure analysis and has bee

Full text of DOI:10.1016/j.molstruc.2016.12.092

Accepted Manuscript
Synthesis, spectroscopic and X-ray structural characterization, quantum chemical
studies and investigation of gama-irradiated effects of the novel hydrazone
compound: [(E)-3-(2-nitrophenyl)-(E)-1-(2-phenylhydrazono)]-1-phenylallylidene
Gül Yakalı, Abban Çakıcı, Canel Eke, Günseli Turgut Cin, Muhittin Aygün
PII:
S0022-2860(16)31411-9
10.1016/j.molstruc.2016.12.092
MOLSTR 23290
DOI:
Reference:
To appear in: Journal of Molecular Structure
Received Date: 13 March 2016
Revised Date: 15 November 2016
Accepted Date: 28 December 2016
Please cite this article as: G. Yakalı, A. Çakıcı, C. Eke, G.T. Cin, M. Aygün, Synthesis, spectroscopic
and X-ray structural characterization, quantum chemical studies and investigation of gama-irradiated
effects of the novel hydrazone compound: [(E)-3-(2-nitrophenyl)-(E)-1-(2-phenylhydrazono)]-1-
phenylallylidene, Journal of Molecular Structure (2017), doi: 10.1016/j.molstruc.2016.12.092.
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Graphical Abstract
Molecular geometry scheme and molecular electrostatic potential diagram of the [3-(2-nitrophenyl)-1-
(2-phenylhydrazono)]-1-phenylallylidene

ACCEPTED MANUSCRIPT
Synthesis, Spectroscopic and X-ray Structural Characterization, Quantum Chemical Studies
and Investigation of Gama- Irradiated Effects of The Novel Hydrazone Compound: [(E)-3-(2-
nitrophenyl)-(E)-1-(2-phenylhydrazono)]-1-phenylallylidene
a,*
b
c
b,*
d
Gül Yakalı , Abban Çakıcı , Canel Eke , Günseli Turgut Cin Muhittin Aygün
aDepartment of Opticianry Program, Vocational School of Higher Education, Akdeniz University,
07070-Konyaaltı Antalya, Turkey.
bDepartment of Chemistry, Faculty of Sciences, Akdeniz University,07070-Konyaaltı Antalya, Turkey.
cDepartment of Secondary Science and Mathematics Education, Faculty of Education, Akdeniz
University, 07070-Konyaaltı, Antalya, Turkey.
dDepartment of Physics, Faculty of Sciences, Dokuz Eylül University, 35160-Buca,İzmir,Turkey.
Abstract
The
novel
hydrazone
compound,
[(E)-3-(2-nitrophenyl)-(E)-1-(2-phenylhydrazono)]-1-
1
phenylallylidene (2), has been synthesized, characterized by FTIR, H-NMR, 13C-NMR techniques,
elemental analysis, X-ray structure analysis and has been investigated gama-irradiated effect.
Additionally, the molecular geometrical parameters, frontier molecular orbital energies (HOMO,
LUMO), their energy gap (∆ꢀ), molecular electrostatic potential analysis of the compound have been
1
13
calculated by using DFT/B3LYP with 6-311G (d, p) level. Also, IR frequencies, H and C NMR
chemical shifts of the compound were calculated by using DFT calculations at the same level basis
and changing in lattice parameters, unit cell volume and density of the compound are observed after
gama irradiated at XRD data. Unirradiated state of the title compound (C21H17N3O2) crystallizes in the
monoclinic space group P21/n with a=9.1782(7) Å, b=16.1359(12) Å, c=11.9709(12) Å,
β=101.022(8)o, V=1740.2(3) Å3, Dcalc=1.3106g/cm3 and Z=4 while irradiated state of title compound
showed significant changes in lattice parameters, crystal volume and density. In contrast, the crystal
system is found to be the same at after and before irradiation. The calculated geometrical parameters,
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13
IR frequencies, H and C NMR chemical shifts of the compound were in good agreement with the
observed single crystal- XRD data, IR, 1H and 13C NMR spectra
Keywords: Hydrazone, Bifurcate interactions, Crystal structure, 1D network, DFT, gama- irradiated.
1. Introduction
Hydrazones and their derivatives, RRC=N–NRR, are an important class of organic compounds.
Due to the capability to react with electropilic and nucleophilic reagents, hydrazones are widely used
in organic synthesis, especially for the preparation of heterocyclic compounds [1–4]. These
compounds exhibit a wide variety of biological activities such as antibacterial, antifungal [5],
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antiinflammatory [6], antimalarial [7], antimycobacterial [8], antitumoral, anti-HIV, antimicrobial [9].
These activities are attributed to the formation of stable chelate complexes with transition metals
which catalyze physiological processes [10–12]. In analytical chemistry, hydrazones find applications
as multidentate ligands for transition metals in colorimetric or fluorimetric determinations [13-14].
Hydrazones are formed when hydrazines condense with aldehydes and ketones by the condensation
of aldehydes with phenylhydrazine and typically are crystalline compounds with sharp melting points.
These compounds can therefore be used to identify the aldehydes and ketones from which the
hydrazones have been formed [15]. The ease of preparation, increased hydrolytic stability relative to
imines, and tendency toward crystallinity are all desirable characteristics of hydrazones. Due to these
positive traits, hydrazones have been under study for a long time, but much of their basic chemistry
remains unexplored [16].
For the synthesis of pyrazoline derivatives reaction of chalcones with phenylhydrazine or other
substitued hydrazines mostly prefer by researchers. Hydrazone compound is occurred as intermediate
product during the formation of reaction. Formation of pyrazolines or hydrazones were depend on the
nature of substituents on chalcone structure and reaction conditions were reported in the literature [17].
Although hydrazones are among intensely studied compounds, surprisingly, synthesis of hydrazone
derivatives by the reaction of chalcones and hydrazines have not been encountered in the literature
because of the intermediate phenylhydrazones could very rarely be isolated. Therefore, we
investigated the synthesis and structure of novel hydrazone derivative that may have significant
biological and pharmacological activities.
In the present study, the novel hydrazone compound, [(E)-3-(2-nitrophenyl)-(E)-1-(2-
phenylhydrazono)]-1-phenylallylidene, had been synthesized and its structure was determined by the
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13
use of elemental analysis, IR and H-NMR, C-NMR spectroscopy, single crystal X-ray diffraction
techniques and DFT/B3LYP level with 6-311G (d, p) basis set. The calculated molecular geometrical
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13
parameters, IR frequencies, H and C NMR chemical shift values are compared with experimental
XRD, IR and NMR chemical shift values.
Also, the effect of gama-irradiation on single crystal was investigated in this study. The effects of
gamma irradiation on various physicochemical properties have been investigated in a few inorganic
salts, metal complexes, polymers and alloys [18–24]. Solid state irradiation of molecular crystals leads
to the production of lattice defects and chemical damage. Consequently any subsequently measured
solid state property is found to be modified beneficially or not [25]. Gamma irradiation has been
frequently used for sterilization of biomolecular materials. Structural and biological properties of
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biomolecules can be affected by gamma irradiation as well. In a dose dependent manner, gamma
irradiation is able to reduce molecular weights of materials due to radical production. Some structural
changes in material may occur after gamma irradiation like an increase in their enthalpy.
Biocompatibility and bioactivity of biomolecular materials can be affected. [26]. The goal of this
study is to develop the spectral, theoretical and crystal structure determination of the new hydrazone
for the using fields, which are new organic synthesis, medical, analytical, drug applications and
investigation of radiation effect on structure of single crystal. In the future, effect of gama irradiated
on biological activities of single crystals will be investigated.
2. Experimental
2.1 General Procedures and Materials
All starting compounds and solvents for synthesis were purchased from Fluka and Aldrich. Melting
points were taken with an electrothermal melting point apparatus. FTIR spectra were recorded on
Bruker Tensor27 FT-IR spectrometer calibrated with polystyrene film using the KBr disc. Nuclear
magnetic resonance (1H and 13C) spectra were taken on BRUKER Spectrospin Avance DPX400
Ultrashield (400 MHz) spectrometer, reference tetramethylsilane as internal standard. Elemental
analyses were performed with LECO-932 elemental analyzer.
2.2 Synthesis
The title compound, [(E)-3-(2-nitrophenyl)-(E)-1-(2-phenylhydrazono)]-1-phenylallylidene (2),
was prepared as shown in Scheme 1. Firstly, chalcone compound, 1-phenyl-3-(2-nitrophenyl)-2-
propen-1-on (1), was were prepared by base-catalyzed Claisen–Schmidt condensation of o-
nitrobenzaldehyde with acetophenone according to the procedures of the literature [27]. After then, the
chalcone (1) (1mmol, 253 mg), phenylhydrazinium hydrochloride (3 mmol, 433.5 mg) and sodium
acetate (0.15 mmol, 12.3 mg) were dissolved in glacial acetic acid aqueous solution (6 ml,
AcOH/H2O=2/1). The reaction mixture was refluxed under nitrogen atmosphere for 3 h. Reaction was
monitored by TLC. Then, it was poured into crushed ice and neutralized with Na2CO3. The
precipitates were filtered and dried, then purified by flash column chromatography on silica gel using
hexane/EtOAc (9/1) as eluent to afford 2 (Scheme 1). The red solid product was dried at room
temperature, recrystallized from methanol. Yield: 68 %, m. p. 165◦C. IR (KBr): νmax: 3304 (NH),
3140-2910 (ArCH), 1598 (C=N), 1526 (C=C), 1499 (NO2 asym.), 1438 (β NH), 1343 (NO2 sym.),
1
1249 (C-N-N), 1138 (N-N). H NMR (d6-DMSO): δ= 6.68 (d,1H),6.73 (d, 1H) 6.87 (t, 1H), 7.03 (d,
1H), 7.23-7.27 (m, 2H), 7.33-7.37 (m, 3H), 7.51-7.59 (m, 1H), 7.61-7.64 (m, 4H), 7.77 (d, 1H), 7.88-
7.90 (m, 2H). 13C-NMR (d6-DMSO): δ= 146.3 (C), 143.9 (C), 134.7 (C), 133.3 (CH), 133.2 (CH),
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131.2 (C), 130.1 (C), 129.9 (CH), 129.5 (CH), 129.1 (CH), 128.2 (CH), 128.0 (CH), 126.7 (CH),
125.0 (CH), 120.9 (CH), 113.3 (CH). Anal. Calcd for C21H17N3O2: C, 73.39; H, 4.95; N, 12.23; Found:
C, 73.27; H, 4.89; N, 12.31.
H
O
O
CHO
NO2
N
.HCl
NH2
NO2
KOH
CH3
N
+
HN
EtOH, rt
AcOH/H2O (2:1)
NaOAc, 2 h, reflux
O2N
(1)
(2)
Scheme 1. Synthesis of [(E)-3-(2-nitrophenyl)-(E)-1-(2-phenylhydrazono)]-1-phenylallylidene (2).
2.3 X-ray data collections, structure solution, refinement
Single crystal having dimensions of 0.38 × 0.27 × 0.19 ꢁꢁꢂ for compound was chosen for X-
ray diffraction studies and were mounted on a glass fiber. X-ray diffraction intensity data for crystal
was measured on a Agilent Diffraction Xcalibur diffractometer equipped with an Eos-CCD detector,
operated at 50 kV and 40 mA with graphite monochromated Mo-Kα (λ = 0.71073 Å) radiation at
room temperature. The absorption corrections of the collected data of the compound was done using
the program CrysAlis Pro [28]. Using Olex2 [29], the structure was solved with the SHELXS structure
solution program using the Direct Methods and refined with the SHELXL using least squares
minimization [30]. All non-hydrogen atoms were refined anisotropically. The positions of the
hydrogen atoms on their respective parent carbon atoms were generated geometrically C–H= 0.93A°.
The nitrogen atoms were also refined anisotropically and were treated with hydrogen atom found from
subsequent difference Fourier electronic density maps for N-H= 0,86A°. In the absence of any
significant anomalous scatterers in the molecule. Before gama-irradiated a summary of
crystallographic data, experimental details and refinement results for the compound are given in
Table 1.
2.4 Theoretical Studies
Computational calculation of the title compound was performed by using GaussView molecular
visualized program [31] and Gaussian 09W package [32] . The molecular structure of the compound
in the ground state was optimized by Density Functional Theory (DFT) using a hybrid functional
B3LYP (Becke’s three parameter hybrid functional using the Lee–Young–Parr (LYP) correlation
functional) [33-34] at 6-311G (d, p) double-zeta basis set [31,32]. The geometrical parameters (bond
length, bond angle and dihedral angle), frontier molecular orbital energies (EHOMO, ELUMO), Molecular
Electrostatic Potential (MEP) analysis were obtained from the optimized structure. Also, the IR
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frequencies, H and C NMR chemical shifts for the compound was calculated using same level of
theory.
Table 1. Before unirradiated crystal data and structural refinement parameters for the title
compound.
Crystal Data
Empirical Formula
Formula Weight
C21H17N3O2
343.39
Cell setting / Space group
Unit cell dimensions
monoclinic, P21/n
a= 9.1782(7) Å
b= 16.1359(12) Å
c= 11.9709(12) Å
β=101.022(8)°
1740.2(3)Å3
293
Unit cell volume
Temperature (K)
Absorption coefficient ( mm-1)
Z / Density [g/cm3]
F(000)
0.086
4/ 1.3106
720.3
Crystal size (mm3)
0.375 × 0.2734 × 0.1885
3.35-26.37
−ꢃ → ꢄꢄ
θ range (°)
h range
k range
−ꢄꢅ → ꢆꢇ
−ꢄꢈ → ꢄꢆ
6490/3536
l range
Reflections collected / unique
Completeness to θmax
Goodness-of-fit on F2
Final R indices [I > 2σ(I)]
99.99%
1.009
R1 = 0.0533
wR2 = 0.0872
R1 = 0.1101
wR2 = 0.0872
R indicesall data
Large diff. peakand hole ( e Å-3) 0.31/-0.35
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2.5 Gama-ray Irradiation
60
Single crystal of hydrazone was irradiated for 170.82 min by using Co gamma-ray source. The
single crystal was exposed 300 Gy dose of from 60Co at room temperature with dose rate of about 105
Gy/h. The sample was placed about 50 cm downstream from 60Co source.
3. Results and Discussion
3.1 X-ray and Computational Analysis Studies Crystal Structure of the Compound
E,E-Configuration
of
[3-(2-nitrophenyl)-1-(2-phenylhydrazono)]-1-phenylallylidene
was
determined by our X-ray analysis and was optimized geometrical parameters (bond length, bond angle
and dihedral angle ) were investigated using DFT calculation by B3LYP method with 6-311G(d, p)
basis set. The geometrical parameters were listed in Table 2 and compared with the XRD data for the
compound. Moreover, Dikusar and Potkin calculated E–Z configuration isomers of phenylhydrazones
by using MNDO and PM3 method. They found out that E-configuration of phenylhydrazones were
more stable than Z configuration [35]. In this study, geometrical parameter of the title compound is
reported using data obtained from an X-ray crystal structure determination and compared with the
results obtained from a theoretical calculations. Experimental and calculated values of C16-N3-N2-C9
[173.56(17)0, 178.54(2)0] and C1-C7-C8-C9 [-178.05(19)0, -179.07(3)0] dihedral angles [that are in
agreement with reported by Magana et al., 2015] show evidence of the E conformation in the title
compound, respectively. The molecular structure and atom-labeling scheme are shown in Fig. 1a. The
optimized geometries of the most favourable conformation of the title compound is shown in Fig. 1b.
Fig. 1. a) Molecular geometry and atomic labeling scheme of the title compound. Displacement
ellipsoids are drawn at the 50% probability level. b). The optimized geometries of the most favourable
conformation of the title compound.
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The title compound is almost planar. So, the nitrophenyl ring (C1/C6) and phenyl ring (C16/C21)
bounded to N3 atom are essentially planar and are twisted with respect to each other by angle less than
220 with a maximum deviation from the plane of 0.006(3) Å for C5, 0.005(2) Å for C17 respectively.
The central phenyl ring (C10/C15) is almost planar with a maximum deviation from the plane of
0.003(3) A° for C11, C14, C15. It is almost ortogonal with the molecule plan and the dihedral angle
between them is 88,91(8)0. Also, the hydrazone region and phenylallylidene region in the crystal
structure essentially planar with the molecule plane with the dihedral angles of 3.05(7)o. The largest
observed deviation of the nitrophenyl ring atom from their mean plane is 0.005(2) Å for C5. The nitro
groups are oriented with respect to their attached phenyl ring (C1/C6) at dihedral angles of
30.92(11) Å.
Table 2. Experimental and optimized geometrical parameters of the title compound.
Parameter
Experimental
Calculated
Bond length (Å)
1.220(3)
1.220(3)
1.357(2)
1.295(2)
1.391(2)
1.465(3)
1.457(3)
1.330(3)
1.443(3)
1.484(3)
1.233(2)
1.232(2)
1.335(2)
1.309(2)
1.397(2)
1.472(2)
1.465(2)
1.352(2)
1.452(2)
1.497(2)
O1-N1
O2-N1
N2-N3
N2-C9
N3-C16
N1-C2
C1-C7
C7-C8
C8-C9
C9-C10
Bond Angle (0)
N3-N2-C9
N2-N3-C16
O2-N1-O1
C2-N1-O1
C2-N1-O2
C1-C2-N1
C3-C2-N1
C8-C9-N2
C10-C9-N2
C21-C16-N3
N3-C16-C17
C7-C8-C9
C1-C7-C8
117.11(16)
119.78(16)
122.6(2)
119.92(3)
121.64(2)
123.73(3)
118.74(2)
117.51(3)
121.95(3)
115.50(3)
114.87(3)
123.72(3)
121.86(2)
118.44(3)
125.83(3)
123.90(2)
119.05(17)
118.3(2)
120.65(19)
115.79(18)
116.18(19)
123.57(16)
122.27(19)
118.59(19)
124.85(19)
125.90(18)
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Dihedral angle (0)
C16-N3-N2-C9
C17-C16-N3-N2
N1-C2-C1-C7
O1-N1-C2-C1
O2-N1-C2-C3
N3-N2-C9-C10
N3-N2-C9-C8
C7-C8-C9-N2
C1-C7-C8-C9
173.56(17)
-167.40(17)
-5.5(3)
178.54(2)
178.14(2)
2.464(2)
-31.1(3)
-21.48(3)
-21.91(3)
-1.82(2)
-30.4(3)
-1.4(3)
-179.06(16)
179.25(19)
178.05(19)
-178.38(2)
-179.869(2)
179.07(3)
Table 2 reveals that calculated bond lengths are slightly higher than the experimental values an
except for N2-N3 bond. Calculated value of N2-N3 bond [1.335(2) Å] is lower than experimental
values [1.357(2) Å]. The N2-N3 single bond is in the range 1.340-1.363Å found in other similar
hydrazone compounds with (E) configuration [36-37]. The ꢉ and ꢊ bond characters of N3-C16, N2-
C9 are calculated as 1.397(2) Å , 1.309(2) Å are slightly deviated with experimental [1.391(2) Å and
1.295(2) Å ] data. The deviation of the bond length N3-C16 is about 0.006 Å it seems a good linearity
with X-ray value. Bond lengths of nitro group (O1-N1, O2-N1) are consistent with the XRD value. In
the studied molecule, due to rotation of C16-N3-N2-C9 dihedral angle there seems a little distortion in
hydrazone linkage (between the two phenyl ring), rest of the bond lengths could not been distorted
[38].
The calculated bond angles are also closer to the XRD values. The bond angle N2-N3-C16 is
calculated 121.64(2)0. Similarly the bond angle N3-N2-C9 is calculated as 119.92(3)0 which nearly
matches with experimental value of 117.11 (16)0 [39] .The calculated dihedral angles of C16-N3-N2-
C9, N3-N2-C9-C8, C1-C7-C8-C9, C7-C8-C9-N2 are 178.540(2)0, -178.380(2)0, 179.070(3)0,
-179.869(2)0 respectively and are these values are closer to be XRD values. According to our
theoretical investigation, there is not appreciable changes in the parameters by the presence of ring
substitution. However, during the rotation of the bond, the hydrazone region gets disturbed and the
properties of this region also changes [38].
The atoms associated with the N-N=C linkage display interaxial angles that deviate only slightly
from that expected ideal trigonal planar geometries ranging from 116.18 (19)0 to 124.85(19)0. Trigonal
planar geometries is occurred as a result of N2 atom have sp2 hybritization [40]. This state requires
that the remaining electrons are in a pz orbital. Delocalization of these pz orbital electrons with the π
orbitals on the adjacent phenyl rings and C=N atoms have a significant perturbing effect on the
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observed pattern of bond lengths in the hydrazone region [39-40]. The N2=C9 bond length in this
structure is observed 1.295(2) Å (this value agree with reported by Annie et al., 2015) but is longer
than the 1.278-1.285 (Å) value typically observed in similar compounds [29] and is shorter than
theoretical computational values [1.309(2) (Å)]. Also, C8-C9 bond length is shortened 1.443(3) Å
[computational values 1.452(2) Å] that linking the double bonds is consistent with conjugation in this
part of the compound [41]. The O2-N1-O1 angle in the NO2 group is 122.6(2)0 that is significantly
greater than 1200 for the compound as a result of the steric effect of the lone pair of electrons on each
of the O atoms; this effect is predicted by the valance- shell electron-pair repulsion theory [42].
Generally the average bond lengths and angles (experimental and theoretical) in the title compound are
comparable to those observed in other similar hydrazone compounds. These values are in good
aggrement with reported [43,44].
In the crystal structure, bifurcated interactions (three centered interactions) are formed by
N3-H3….O2 and C17-H17….O2 short intermolecular contacts (showing Fig 2, Table 3) leading to
the formation chains propagating along the b axis. Three centered interactions may describe instance
in which two H-bond donors are bound to a single acceptor [45]. These short interactions are less than
the sum of the van de Waals radio. Distance of H17…O2 and H3…O2 are 2.66 Å, 2.69 Å,
respectively [symetry code: -1/2-x,1/2+y,1/2-z] (showing Table 3). These values are less than 2.72 Å
which is van de Waals radius33. The six membered ring motifs S(6) is occurred by these interactions
[46] .
Fig 2. Three centered interactions (dashed lines) of the title compound by C-H…O and N-H…O short
interactions.
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The title compound are linked into chains by the combination of weak intermolecular and
intramolecular C-H…O hydrogen bonds (Table 3). Atom C6 in the molecule at (x, y, z) acts as a
hydrogen-bond donor, via atom H6, to atom O1 in the molecule at (-1/2+x,1/2-y,-1/2+z), forming
chain along the a axis. Atom C7 in the molecule at (x, y, z) serves as a hydrogen-bond donor, via
atom H7, to atom O1 in the molecule at (x, y, x), forming a S (6) ring motif (showing Fig. 3) [46].
Fig.3 Intermolecular and intramolecular C-H…O hydrogen bonding of the title compound
Table 3. Hydrogen-bond and short bifurcate interactions geometry(Å, °) for compound.
Bond
D – H
0.930(3)
0.930(3)
0.930(3)
0.86
H…A
2.546(3)
2.321(3)
2.66
D…A
D – H…A
134.7(2)
110.98(19)
124
C6-H6…O1i
C7-H7…O1
C17-H17…O2ii
N3-H3…O2ii
3.268(3)
2.792(3)
………
………
2.69
144
Symetry code: (i) -1/2+x,1/2-y,-1/2+z; (ii) -1/2-x,1/2+y,1/2-z
There are also parallel slipped π…π interactions present (Fig. 4) with 3.9946(12) Å distance
between the centroids Cg1 Cg2 ( Cg1: C1/C6; Cg2: C16/C21; symetry code: (ii): 2-x,3-y,-1-z) and N-
O…π [N1-O2…Cg3; Cg3=C10/C15; symetrycode (iii): 3/2-x,1/2+y,1/2-z; O…Cg3 distance is
3.573(2) Å] interactions in the crystal structure. The result of these interactions leads to the formation
of sheets lying parallel to (100) plane and 1D supramolecular network (showing Fig.4).
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Fig. 4 The formation of the sheets and 1D supramolecular network lying parallel to (100) plane in the
crystal structure of the title compound by intermolecular ꢊ … ꢊ and N-O … ꢊ interactions. H atoms
omitted.
3.2 Experimental and Theoratical IR Sspectral Analysis of the Compound
Theoretical description of vibrational spectra is practical importance for the identification of
compounds. There is no negative frequency in the calculated IR spectrum which indicates the stable
optimized geometry. DFT calculations were used to gain insight into properly understanding
degenerated vibration modes which are observed at the same frequency, but not the same vibrational
mode. The calculated wave numbers are slightly different from their observed values of the normal
modes. Two factors may be responsible for the discrepancies between the experimental and computed
spectra of this compound. The first is originated from the environment effects and the second reason
for these discrepancies is the fact that the experimental values are anharmonic while the calculated
ones are harmonic [47]. The selected harmonic vibrational wave numbers computed at the B3LYP/6-
311+G(d,p) level and the corresponding experimental values are listed in Table 4.
The harmonic frequencies by DFT calculations are usually higher than the corresponding
experimental ones due to the fact of the electron correlation approximate treatment, anharmonicity
effects and basis set deficiencie [48]. Besides, the interactions between the molecules make the
frequencies shift to the lower frequencies. The FTIR spectrum of the hydrazone showed a strong N-H
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stretching band at 3304 cm-1. The same band was calculated as 3512 cm-1. Another important band
occurred at 1499 cm-1 for N=O asymmetric bond and at 1343 cm-1 for N=O symetric bond . Theirs
theoretical values were calculated as 1602.02 and 1390.71 respectively.The lower values of the N=O
bands were exhibited intermolecular and intramolecular hydrogen bonding [49]. Also the lower value
of the N-H bands was exhibit short strong intermolecular interactions. Other IR data aromatic CH,
aliphatic CH, C=N and C=C were observed in the expected regions. For the correction of theoretical
errors in this work, the theoretical harmonic frequencies above 1700 cm−1 were scaled by a scaling
factor of 0.958, and frequencies less than 1700 cm−1 were scaled by 0.9627 [47]. In this study we
found that correlation coefficient is R2=0.99657 (R2: correlatin coefficient). This value showed that
experimental values is good aggreement with calculated values. R2 is showed at regression analysis as
below (Fig. 5)
ꢎ∑
)
ꢎ∑ )ꢎ∑ )
ꢍ
ꢌ
ꢏꢐ −
ꢏ
ꢐ
ꢋꢌ =
ꢌ
ꢒ ꢎ∑
ꢑ ꢍ
)
ꢎ∑ )ꢌꢓꢒ ꢎ∑
)
ꢎ∑ )ꢌꢓ
− ꢐ
ꢏ
−
ꢏ
ꢍ
ꢐ
n: number of data; X: values of calculated axis; Y: values of experimental axis.
Table 4. Experimental and theoretical frequences for the compound.
Experimental frequency
Calculated frequency
Assignment
(cm-1)
(cm-1)
3304
3512
ν (N-H)
3.140-2910
1598
3217.66-3192.64
1659.69
ν(C-H) Ar1, Ar2, Ar3
ν(C=N)
1526
1604.58
ν (C7=C8)
1499
1602.02
νasym (N=O)
νsym(N=O)
1343
1390.71
1249
1293.73
ν(C16-N3-N2)
1138
1438
1192.92
1537.39
ν(N-N)
β(N-H)
Vibration mode: v; stretching, β; bending, sym; symmetric, asym; asymmetric. (Ar1, Ar2, Ar3=
aromatic rings)
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4000
3500
3000
2500
2000
1500
1000
500
IR frequencies
B3LYP/6-311G (d,p)
y = 0.996x+78.253
R2= 0.99657
0
0
500
1000
1500
2000
2500
3000
3500
Calculated (cm-1)
Fig. 5. Correlation graph of calculated and experimental frequencies of the title compound (R2:
correlation coefficient)
3.3 Experimental and Theoratical 1H and 13C NMR Spectral Analysis of the Compound
The 1H and 13C NMR chemical shifts are determined theoretically by the DFT method in using the
basis set B3LYP/6-311G (d,p). The geometry of the compound, together with that of tetramethylsilane
1
13
(TMS) were fully optimized. The H and C NMR chemical shifts were converted to the TMS scale
by subtracting the calculated absolute chemical shielding of TMS (ꢔ = ∑ꢕ − ∑, where ꢔ is the
chemical shift, ∑ is the absolute shielding and ∑ꢕ is the absolute shielding of TMS), with values of
31.88 ppm (1H) and 182.46 ppm (13C) for B3LYP/6-311G(d,p). The experimental and theoretical
1
chemical shift values are displayed in Table 5. At H NMR spectrum, while H17 and H21 protons of
hydrazone compound is expected as the same, it is observed that H17 shifted lower fields. The reason
is that H17 engaged in a strong short interaction with nitro group (O2 atom). Similarly, H3 proton
(bounded to N3 atom) shifted lower fields. As can be seen in Table 5, also H7 proton shifted lower
fields than expected because it engaged in intramolecular hydrogen bonds with nitro group (O1 atom).
The calculated values show good agreement with measured values of 1H NMR and 13CNMR chemical
shifts. The small shifts can be explained as a consequence of the change in the molecular environment.
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Table 5. Experimental and theoretical 13C and 1H chemical shifts (ppm) for the compound.
Atom
Experimental (ppm)
Calculated (ppm)
124.01
C1
C3
C2
C4
130.1
126.7
146.3
128.2
128.0
120.9
131.1
128.2
128.2
134.7
129.5
129.5
134.02
114.43
113.93
121.40
118.11
115.94
113.93
127.41
113,93
115.25
98.40
113.38
118.30
114.27
130.30
117.34
114.52
113.77
98.01
C5
C6
133.2
C7
C8
133.3
C9
C10
C12
C14
C16
C18
C20
143.9
C11
C13
C15
C17
C19
C21
H3A
H5
129.1
129.9
129.1
113.3
125.0
106.08
113.3
H4
H6
7.88-7.90
7.61-7.64
7.88-7.90
7.77
7.51-7.59
7.61-7.64
8.40
7.64
7.85
7.29
8.06
7.74
7.57
7.29
7.47
7.36
7.85
H3(N3)
H7
H8
7.03
7.33-7.37
7.33-7.37
6.73
7.24
8.01
7.74
6.34
7.01
7.85
H11
H13
H15
H18
H20
H12
H14
H17
H19
H21
7.61-7.64
7.33-7.37
7.61-7.64
7.23-7.27
7.23-7.27
6.87
6.68
3.4 Frontier molecular orbitals
The highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital
(LUMO) are the main orbitals that take part in chemical stability. The HOMO represents the ability to
donate an electron, LUMO as an electron acceptor represents the ability to obtain an electron. This
also predicted that the nature of electrophiles and nucleophiles to the atom where the HOMO and
LUMO are stronger [50]. The energy gap of the compound was calculated using B3LYP/6-311G(d, p)
level. In this title compound, highest electronic energy which exhibited at 90th orbital lies hydrazone
linkage and phenyl ring (C16/C21) and the HOMO is calculated about -5.13 eV. The lowest electronic
energy appeared in the nitrophenyl ring, which exhibited at 91th virtual orbital and measured as
LUMO value -2.317 eV. The energy gap of HOMO and LUMO could be determined about 2.827 eV,
which leads the molecule becomes less stability and more reactivity.
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Small HOMO-LUMO energy gaps is precisely why long conjugated molecules usually have color
(such as beta carotene in carrots). This is because they can be modeled as a particle in a box which has
ꢗ
ꢗ
ℏ ꢘ
energy levels according to ꢀꢖ = ꢌꢙꢚꢗ ꢍꢌ where L is the length of the box. Also, lower the HOMO–
LUMO energy gap explains the eventual charge transfer interactions taking place within the molecule,
which influences the biological activity of the molecule. The larger the HOMO–LUMO energy gap,
the molecule will be harder, more stable and less reactive. Corresponding frontier molecular orbitals
are shown in Fig 6.
Fig 6. Frontier molecular orbital surfaces and energy levels for the HOMO and LUMO of the
compound computed at B3LYP/6-311G(d,p) level.
3.5 Molecular Electrostatic Potential
The molecular electrostatic potential (MEP) is very useful as a reactivity map displaying probable
region for the electrophilic attack, nucleophilic reaction and hydrogen bonding interaction of organic
molecules. In order to predict the reactive site of the electrophilic and nucleophilic attack of the title
compound MEP was also calculated from B3LYP/6-311G (d,p) optimized geometry. The negative
region (red) of MEP was related to electrophilic reactivity and positive region (blue) correspond to
nucleophilic reactivity (Fig. 7). Negative regions in the studied molecule were found around the NO2
15

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group. This region showed point to the existence of intramolecular and intermolecular hydrogen
bonding. However maximum positive regions are localized on the C16-N3 hydrazone region which
can be considered as possible sites for nucleophilic attack. Mathematically, MEP can be defined by the
following equation:
ꢟ
ꢥꢎꢜꢦ)
ꢛ ꢜ = ꢝ ꢞ ꢠꢡ
ꢎ )
ꢢ − ꢣ ꢤ
ꢧ ꢨꢜꢦ
ꢡ
ꢋꢠ − ꢜ
ꢜꢦ − ꢜ
Summation (Σ) runs over all nuclei, ZA is charge of nucleus which is located at RA and ρ(r') is electron
density.
Fig. 7 Molecular electrostatic potential diagram of the title compound.
3.6 Gama- Irradiated Results
The results of gama-irradiated single crystal studies are presented in Table 6. The unit cell
parameters, lattice constants, unit cell volume and density were evaluated and these values are found
to be changed upon irradiation. Studied single crystal has 0.38 × 0.27 × 0.19 ꢁꢁꢂ dimensions.
Avarage crystallite size is increased implying aggregation of particle upon irradiation. The increase in
the cell volume (about 0,6 %) of irradiated sample suggests precence of Schottky defects [51]. This
will result in a decrease intensity which is related to the number of such defects. Defects in a crystal
give rise to a distortion of the crystal structure. In addition a shift of the bragg maxima according to an
avarege lattice parameter change, local deviations from that avarage lattice parameters should cause as
reduction of bragg maxima intensities and diffuse scattering [52]. Moreover a change in lattice
parameters suggests, the relaxation around the vacancy is significant [53]. The presence of defects in
a crystalline lattice may change both the unit cell size and the physical size of the crystal.
16

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When atoms have finite size, there is a little path difference between X-rays scattered by electron
cloud on opposite sides of atom and this difference increases with increasing 2ꢩ. Since atoms vibrate
about a mean position, effective size of atoms will be larger and this leads to a further decrease in
scattering power with increase in 2ꢩ. When the crystal is exposed to gamma radiation, atoms in the
crystal vibrate more vigorously so that scattering power decreases and hence intensities will be more
pronounced. Irradiation can create defects in the crystal. Consequently, the crystal structure factor
(F:structure factor) will vary, and it can lead to changes in unit cell parameters (a,b,c).
In our study, the sample was exposed to 60Co gamma ray at a dose rate of 300 Grey at room
temperature. The cause of irradiation of crystal with 60Co is investigated that influence of single
crystal structure of gama rays. Studies in the literature, the crystals were irradiated in different dose
values (600 kGy [51], 0.4–2.4 kGy [54] ) and the values of the applied dose are 2-3 times higher than
ours. We applied dose which these more lower than these values and observed change of the unit cell
parameters, lattice constants, unit cell volume and density of single crystal.
Table 6. Changing parameters of the gama- irradiated compound.
Unit Cell
Unirradiated
Irradiated
9.1782(7)
16.1359(2)
11.9709(2)
90
9.1955(5)
16.1678(8)
11.9934(6)
90
a(Å)
b(Å)
c(Å)
α(0)
β(0)
γ(0)
101.022(8)
90
100.986(5)
90
1740.2(3)
Monoclinic
1.3106
1750.39(15)
Monoclinic
1.3030
V(Å3)
Crystal System
Density (g/cm3)
4. Conclusion
1
13
The single crystal of hydrazone has been characterized by elemental analysis, IR, H NMR, C
NMR and X-ray diffraction method. The X-ray results show that the compound exists in
E-configuration and is stabilized by the combination of weak C-H…O hydrogen bonds, strong π…π
and N-O…π interactions. All theoretical calculations are performed with B3LYP/6-31G(d,p) level by
1
13
DFT method. Geometrical parameters, IR frequencies, H and C NMR chemical shifts further have
been calculated theoretically for the compound and they are found to be in good agreement with the
experimental XRD structural parameters, IR frequencies and NMR chemical shift values. Also frontier
17

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molecular orbital energies (HOMO, LUMO), their energy gap (∆ꢀ), molecular electrostatic potential
analysis of the compound have been calculated by same theorerical method. Moreover the effect of
gama-irradiated on single crystal is investigated. The crystal was exposed to 60Co gamma ray at a dose
rate of 100 Grey. Although this dose rate is lower, the crystal defects are observed in single crystal
structure. Irradiation does not change the geometry of the system and changes in lattice parameters,
unit cell volume and density significant. In the future, we will apply dose values of higher than 300 Gy
and more lower than 300 Gy on the single crystal periodically and we will investigate that structure of
single crystal is changed what dose value. In addition these, we will investigate that effect of gama
irradiated on biological activities of single crystal material and structure of gama irradiated material
will have been illuminate by UV-vis, IR (infrared), Raman, and Mass spectra in conjunction with
quantum theory. These results of relevant gamma-irradiation are the first step for studies in the future.
Acknowledgements
This work has been completed at Dokuz Eylül University and Akdeniz University. The authors
acknowledge Dokuz Eylül University for the use of the Agilent Xcalibur Eos diffractometer
(purchased under University Research Grant No: 2010.KB.FEN.13), Akdeniz University Research
Fund (grand no BAP-2007.01.0105.001 and BAP 2008.02.0121.006) for their financial support and
Akdeniz University for Nuclear Sciences Research and Application Center (NUBA) (60Co source).
Supplementary material
Crystallographic data as .cif files for the structures reported in this paper have been deposited at the
Cambridge Crystallographic Data Center with CCDC 1453180 for the unirradiated compound and
with CCDC 1453210 irradiated compound. Copies of the data can be obtained free of charge at
www.ccdc.cam.ac.uk/conts/retrieving.html (or from the Cambridge Crystallographic Data Center, 12,
Union Road, Cambridge CB2 1EZ, UK). Email: deposit@ccdc.cam.ac.uk. Also, supplementary
material contains FT-IR, 1H and 13C NMR spectra.
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Research Highlights
‹ The novel hydrazone compound, [(E)-3-(2-nitrophenyl)-(E)-1-(2-phenylhydrazono)]-
1-phenylallylidene, has been synthesized and fully characterized by FTIR, 1H-NMR,
13C-NMR techniques, elemental analysis, X-ray crystal structure analysis and
investigated gama-irradiated effect.
‹ The molecular geometrical parameters, frontier molecular orbital energies (HOMO,
LUMO), their energy gap (∆E), molecular electrostatic potential analysis of the
compound have been calculated by using DFT/B3LYP with 6-311G (d, p) level.
‹ IR frequencies, 1H and 13C NMR chemical shifts of the compound were calculated by
using DFT calculations at the same level basis and changing in lattice parameters, unit
cell volume and density of the compound upon gama irradiation are observed after
irradiated at XRD data.
‹ The crystal system of the compound is found same at after and before irradiation while
irradiated state of the compound showed significant changes lattice parameters, crystal
volume and density.