N-(4-Nitrobenzoyl)-N′-(1,5-dimethyl-3-oxo-2-phenyl-1H-3(2H) -pyrazolyl)-thiourea hydrate: Synthesis, spectroscopic characterization, X-ray structure and DFT studies

Article abstract of DOI:10.1016/j.saa.2011.12.040

The title molecule (C₁₉H₁₇N₅O ₄S·H₂O) was synthesized and characterized by IR-NMR spectroscopy, MS and single-crystal X-ray diffraction. The molecular geometry, vibrational frequencies and gauge-independent atomic orbital (GIAO) ¹H and ¹³C NMR chemical shift values of the compound in the ground state have been calculated by using the density functional theory (DFT) method with 6-31G(d) basis set, and compared with the experimental data. All the assignments of the theoretical frequencies were performed by potential energy distributions using VEDA 4 program. The calculated results show that the optimized geometries can well reproduce the crystal structural parameters, and the theoretical vibrational frequencies and ¹H and ¹³C NMR chemical shift values show good agreement with experimental data. To determine conformational flexibility, the molecular energy profile of the title compound was obtained with respect to the selected torsion angle, which was varied from -180°to +180°in steps of 10°. Besides, molecular electrostatic potential (MEP), frontier molecular orbitals (FMO) analysis and thermodynamic properties of the compound were investigated by theoretical calculations.

Full text of DOI:10.1016/j.saa.2011.12.040

Spectrochimica Acta Part A 89 (2012) 30–38
Contents lists available at SciVerse ScienceDirect
Spectrochimica Acta Part A: Molecular and
Biomolecular Spectroscopy
journal homepage: www.elsevier.com/locate/saa
N-(4-Nitrobenzoyl)-Nꢀ-(1,5-dimethyl-3-oxo-2-phenyl-1H-3(2H)-pyrazolyl)-
thiourea hydrate: Synthesis, spectroscopic characterization, X-ray structure and
DFT studies
N. Burcu Arslana,∗, Canan Kazaka, Fatma Aydınb
a Department of Physics, Faculty of Arts and Sciences, Ondokuz Mayıs University, 55139 Samsun, Turkey
b Department of Chemistry, Faculty of Arts and Sciences, C¸ anakkale Onsekiz Mart University, 17100 C¸ anakkale, Turkey
a r t i c l e i n f o
a b s t r a c t
Article history:
Received 20 August 2011
Received in revised form 9 December 2011
Accepted 20 December 2011
The title molecule (C19H17N5O4S·H2O) was synthesized and characterized by IR-NMR spectroscopy,
MS and single-crystal X-ray diffraction. The molecular geometry, vibrational frequencies and gauge-
independent atomic orbital (GIAO) 1H and 13C NMR chemical shift values of the compound in the ground
state have been calculated by using the density functional theory (DFT) method with 6-31G(d) basis set,
and compared with the experimental data. All the assignments of the theoretical frequencies were per-
formed by potential energy distributions using VEDA 4 program. The calculated results show that the
optimized geometries can well reproduce the crystal structural parameters, and the theoretical vibra-
tional frequencies and 1H and 13C NMR chemical shift values show good agreement with experimental
data. To determine conformational flexibility, the molecular energy profile of the title compound was
obtained with respect to the selected torsion angle, which was varied from −180◦ to +180◦ in steps
of 10◦. Besides, molecular electrostatic potential (MEP), frontier molecular orbitals (FMO) analysis and
thermodynamic properties of the compound were investigated by theoretical calculations.
© 2011 Elsevier B.V. All rights reserved.
Keywords:
Thiourea
X-ray structure determination
IR and NMR spectroscopy
DFT calculations
Electronic structure properties
1. Introduction
analgesic, anti-inflammatory and antipyretic properties [12].
Pyrazolone derivatives are also widely used in preparing dyes and
N-Acyl(aroyl)-Nꢀ,Nꢀ-dialkylthioureas and N-acyl(aroyl)-Nꢀ-
alkylthioureas have been formulated as R/ArCONHCSNRꢀRꢀꢀ and
R/ArCONHCSNHRꢀ, and they are known for more than 100 years
[1–4]. They were first synthesized by Neucki in 1873 and are also
largely important in synthesis of heterocyclic compounds. Many
of these substrates have interesting biological activities [5–9].
Aroyl thioureas, which have at least three potential donor atoms
(N, O, S), are a well-known class of excellent ligands for transition
metals. These show a more varied coordination behavior than
the structurally related ␤-diketones which have been thoroughly
investigated [3,10].
pigments [13]. It can be used as an intermediate for the synthesis
of pharmaceuticals especially antipyretic and analgesic drugs [14].
4-aminoantipyrine is also used in the colorimetric determination
of phenols [15].
In this study, we present results of a detailed investigation of
the synthesis and structural characterization of the title compound
using single crystal X-ray diffraction, MS, IR-NMR spectroscopy and
quantum chemical methods. The geometrical parameters, funda-
mental frequencies and GIAO 1H and 13C NMR chemical shift values
of the title compound in the ground state have been calculated by
using DFT (B3LYP) method with 6-31G(d) basis set. This calculation
is valuable for providing insight into molecular parameters and the
vibrational spectrum and NMR spectrum. The aim of this work is to
explore the molecular dynamics and the structural parameters that
govern the chemical behavior, and to compare predictions made
from theory with experimental observations.
In addition, pyrazolone such as Ampyrone or 4-aminoantipyrine
(2,3-dimethyl-1-phenyl-3-pyrazolin-5-one),
a
five-membered-
ring lactam containing two nitrogens, is a derivative of pyrazole
that has an additional carbonyl group (C O) in the same molecule.
It is an active moiety as a pharmaceutical ingredient, especially
in the class of nonsteroidal antiinflammatory agents used in
the treatment of arthritis and other musculoskeletal and joint
disorders [11]. Ampyrone has a metabolite of aminopyrine with
2. Materials and methods
2.1. General remarks
∗
The melting point was measured on an Electro Thermal IA 9100
apparatus using a capillary tube and uncorrected. Reactions were
Corresponding author. Tel.: +90 362 3121919/5257; fax: +90 362 4576081.
E-mail address: barslan@omu.edu.tr (N.B. Arslan).
1386-1425/$ – see front matter © 2011 Elsevier B.V. All rights reserved.
doi:10.1016/j.saa.2011.12.040

N.B. Arslan et al. / Spectrochimica Acta Part A 89 (2012) 30–38
31
Table 1
monitored by thin-layer chromatography (TLC) on silica-gel 60
Crystal data and structure refinement parameters for the title compound.
F254 plates (Merck) and an UV lamp. The IR spectrum of the title
compound was recorded in the range 4000–400 cm−1 with a Perkin
Elmer spectrum BX II (100-83634) FT-IR spectrometer. The 1H NMR
and 13C NMR spectra were recorded on a Bruker AVANCE DPX NMR
spectrometer operating at 400 and 101.6 MHz, respectively, using
TMS as an internal standard and DMSO-d6 as solvent. LC mass spec-
tra were obtained on an AGILENT 1100 MSD spectrometer with an
ion source temperature of 240 ◦C. All the chemicals and solvents
used were in analytical grade.
Color/shape
Light yellow/prism
Chemical formula
Formula weight
Temperature (K)
C19H17N5O4S·H2O
411.44
296
˚
Wavelength (A)
0.71073 Mo K˛
Monoclinic
C2/c (No. 15)
Crystal system
Space group
Unit cell parameters
˚
a, b, c (A)
29.270(7), 7.4963(13),
26.006(9)
4009(2)
3
˚
Volume (A )
2.2. Synthesis
Z
8
Calculated density (Mg/m3)
1.423
0.204
ꢁ (mm−1
)
A mixture of 4-nitrobenzoyl chloride (0.370 g, 2 mmol), KSCN
(0.194 g, 2 mmol) in 20 ml of acetone were heated under reflux with
stirring for 2 h, then a solution of 4-amino-1,5-dimethyl-3-oxo-2-
phenyl-1H-3(2H)-pyrazole (0.406 g, 2 mmol) in 20 ml acetone was
added dropwise to 4-nitrobenzoyl isothiocyanate within 15 min.
When the solution was added completely, the resulting solution
was mixed for 4 h at the reflux temperature and the progress of the
reaction was controlled by TLC. After the reaction was complete, the
solution was poured into a beaker containing ice-water mixture.
The yellowish precipitate was filtered off and washed with distilled
water several times and then dried under vacuum. Recrystalization
from THF yielded a pure product, N-(4-nitrobenzoyl)-Nꢀ-(1,5-
dimethyl-3-oxo-2-phenyl-1H-3(2H)-pyrazolyl)-thiourea hydrate
(C19H17N5O4S·H2O) (Scheme 1), as yellowish crystals (87%). M.p.:
214–216 ◦C. MS (m/z): 411.43 (M+).
Absorption correction
Tmin, Tmax
F0 0 0
Crystal size (mm3)
Diffractometer/measurement method
Index ranges
Integration (X-RED32)
0.8823, 0.9671
1792.0
0.450 × 0.290 × 0.130
STOE IPDS II/rotation (ω scan)
−36 ≤ h ≤ 36, −8 ≤ k ≤ 9,
−32 ≤ l ≤ 32
Theta range for data collection (◦)
Measured reflections
Independent/observed reflections
Rint
Refinement method
Data/restraints/parameters
Goodness-of-fit on F2
R indices [I > 2ꢂ(I)]
2.77 ≤ Â ≤ 26.43
10,765
3521/2080
0.0899
Full-matrix least-squares on F2
3521/2/281
0.7210
R1 = 0.0409, wR2 = 0.0660
R1 = 0.1117, wR2 = 0.0769
w = 1/[ꢂ2(Fo2) + (0.0152P)2];
P = (Fo2 + 2Fc2)/3
0.16, −0.24
R indices (all data)
Weighting scheme
3
˚
ꢃꢄmax, ꢃꢄmin (e/A )
2.3. Crystallography
The single-crystal X-ray data was collected on a STOE diffrac-
tometer with an IPDS(II) image plate detector. All diffraction
measurements were performed at room temperature (296 K) using
levels of theory revealed no imaginary frequencies, indicating that
an optimal geometry at these levels of approximation was found
for the title compound. Additionally, the calculated vibrational
frequencies were clarified by means of the potential energy dis-
tribution (PED) analysis and assignments of all the fundamental
vibrational modes using VEDA 4 program [26]. The geometry of
the title compound, together with that of tetramethylsilane (TMS),
is fully optimized. 1H and 13C NMR chemical shifts are calcu-
lated within GIAO approach [27,28] applying DFT method and the
basis set as that used for geometry optimization. The 1H and 13C
NMR chemical shifts are converted to the TMS scale by subtract-
ing the calculated absolute chemical shielding of TMS (ı = ˙0 − ˙,
where ı is the chemical shift, ˙ is the absolute shielding and
˚
graphite monochromated Mo K˛ radiation (ꢀ = 0.71073 A). Reflec-
tion data was recorded in the rotation mode using the ω scan
technique by using X-AREA software [16]. Unit cell parameters
were determined from least-squares refinement of setting angels
with  in the range 2.77 ≤  ≤ 26.43. The structure was solved by
direct methods using SHELXS-97 [17] implemented in WinGX [18]
program suit. The refinement was carried out by full-matrix least-
squares method on the positional and anisotropic temperature
parameters of the non-hydrogen atoms, or equivalently corre-
sponding to 281 crystallographic parameters, using SHELXL-97
[19]. Water hydrogen atoms got from the difference Fourier map
˙
is the absolute shielding of TMS), whose value is 32.10 and
0
˚
were refined isotropically with 0.82(4) and 0.91(4) A. All other H
189.40 ppm, respectively. All the calculations are performed by
using GaussView Molecular Visualization program [29] and Gaus-
sian 03 program package [30] on a personal computer without
specifying any symmetry for the title molecule. The effect of solvent
on the theoretical NMR parameters was included using the default
model IEF-PCM (Integral-Equation-Formalism Polarizable Contin-
uum Model) [31] provided by Gaussian 03. A preliminary search
of low-energy structures has been carried out with the B3LYP/6-
31G(d) computations. Conformational energies were calculated as
a one-dimensional scan by varying the ϕ(C13 N4 C12 N3) dihe-
dral angle from −180◦ to +180◦ in steps of 10◦, and the molecular
energy profile was obtained.
atoms were positioned geometrically and treated using a riding
model, fixing the bond lengths at 0.86, 0.93 and 0.96 A for NH,
˚
CH and CH3 atoms, respectively. The displacement parameters of
the H atoms were fixed at Uiso(H) = 1.2 Ueq (1.5 Ueq for methyl)
of their parent atoms. Data collection: X-AREA, cell refinement:
X-AREA, data reduction: X-RED32 [20]. Details of the data col-
lection conditions and the parameters of refinement process are
given in Table 1. The general-purpose crystallographic tool PLA-
TON [21] was used for the structure analysis and presentation of the
results.
2.4. Theoretical
The molecular structure of the title compound in the ground
state (in vacuo) was optimized using DFT(B3LYP) [22,23] method
with the 6-31G(d) [24] basis set. The experimental X-ray crystal-
lographic coordinates for corresponding atoms in the compound
were used as a starting point. Then, vibrational frequencies for the
optimized molecular structures are calculated with this method
and then scaled by 0.9613 [25]. Frequency calculations at the same
3. Results and discussion
3.1. Crystallographic results
The title compound, which the atom labeling Ortep-3 diagram
is depicted in Fig. 1, crystallizes in the monoclinic space group C2/c.
X-ray crystal structure analysis indicates that the asymmetric unit

32
N.B. Arslan et al. / Spectrochimica Acta Part A 89 (2012) 30–38
Scheme 1. The formation of the title compound.
contains one discrete molecule while the unit cell contains eight
molecules.
The dihedral angles between the thiourea moiety and
the N-(4-nitrobenzoyl) and Nꢀ-(1,5-dimethyl-3-oxo-2-phenyl-1H-
3(2H)-pyrazolyl rings are 133.6 (3)◦ and −114.9 (3)◦, respectively.
In the molecule of the crystal, the C N bond such as C12 N4
of this species confirmed by establishing one to one correlation
between observed and theoretically calculated frequencies [32].
The resulting vibrational wavenumbers for the optimized geometry
and the proposed assignments are given in Table 3. The vibrational
bands assignments have been made by using Gauss View molecular
visualization program [29]. Experimental infrared spectra, and the
simulated infrared spectra, where the intensity (km/mol) is plotted
against the harmonic vibrational frequencies are shown in Fig. 2.
The proposed vibrational assignments with PED’s analysis of the
molecule were performed with VEDA 4 program for the frequencies
calculated by B3LYP method. As seen from the table, the calcu-
lated frequencies are in good agreement with the experimental
data.
˚
˚
˚
˚
(1.400 A), C12 N3 (1.340 A), C13 N4 (1.358 A) and N3-C2 (1.414 A)
˚
is shorter than the normal C N bond length (1.479 A), which
revealed that C N bond is of the character of double bond.
˚
Also C12-S1 (1.664 A) bond is slightly shorter than a C S dou-
˚
ble bond (1.681 A), indicating partial electron delocalization in the
N(H) C(S) N(H) C(O) structural segment. It is deduced that this
thiourea makes up a multi-electron conjugated ␲-bond.
The crystal structure is stabilized by various types of hydro-
gen bondings. One is the intramolecular hydrogen bond between
enamine N3 and carbonyl oxygen O2. Others are the O H· · ·O
hydrogen bonds between the unligated water molecule and both
unprotaneted nitro oxygen atom O4, amide N4 and carbonyl oxy-
gen O1 on pyrazole ring. Additionally, non-conventional weak
intermolecular C H· · ·S hydrogen bond is present between thio-
carbonyl S1 and C15 on nitrobenzene ring system. Details of the
hydrogen bonding geometry are shown Table 2.
The title compound named as N1-aroyl N2-alkylthiourea has
two different N H bonds. The characteristic IR bands of the syn-
thesized compound appear two peaks in the 3317 and 3270 cm−1
regions due to the ꢅ(N H) stretching vibrations. This is interpreted
as a result of its conjugated resonance with the p-nitrophenyl
ring, besides the carbonyl group is connected to the imine group.
In addition, this difference between the ꢅ(N H) stretching vibra-
tion frequencies is due to an intra-molecular hydrogen bond with
N
H (see Table 2). The calculated ꢅ(N H) stretching vibrations are
observed at 3233 and 3220 cm−1. There are aromatic and methyl
moieties in the compound. The strong ꢅ(C H, Ar H) and ꢅ(C H,
CH3) stretching bands appear at 3106 and 2946 cm−1, respec-
3.2. Vibrational spectra
tively. These values have been calculated as 3129 and 2994 cm−1
.
Vibrational spectroscopy is used extensively in organic chem-
istry for the identification of functional groups of organic
compounds, the study of molecular conformations, reaction kinet-
ics, etc. Assignment of complex systems can be proposed on the
basis of frequency agreement between the computed harmonics
and the observed fundamental modes. The vibrational spectral data
obtained from the solid phase FT-IR spectra are assigned based on
the results of the normal coordinate calculations. The observed
and the calculated spectra are found to be in good agreement
with each other. Based on the comparison between the calculated
and experimental results, assignments of fundamental modes were
carried out. The assignment of the experimental frequencies is
based on the observed band frequencies in the infrared spectra
The compound also has two carbonyl groups, as aroyl and pyra-
zolone carbonyl. The strong ꢅ(C O) stretching band appears at
1644 and 1607 cm−1, apparently decreasing in frequencies com-
pared with the ordinary carbonyl absorption (1710 cm−1), while
they are calculated at 1727 and 1680 cm−1. The IR spectra of
the compound do not display the S H mode at about 2600 cm−1
indicating that in the solid state this compound remains in the
thioketo-amine form [33].
To make a comparison with the experimental observation, it is
presented correlation graphic in Fig. 3 based on the calculation. As
can be seen from correlation graphic in Fig. 3, obtained correlation
coefficient is 0.99513 for B3LYP/6-31G(d).
Fig. 1. A view of the title compound showing the atom-numbering scheme. Displacement ellipsoids are drawn at the 30% probability level. For the sake of clarity, H atoms
not involved in H-bonds have been omitted. Intra-molecular hydrogen bondings are indicated by broken lines.

N.B. Arslan et al. / Spectrochimica Acta Part A 89 (2012) 30–38
33
Table 2
◦
˚
Hydrogen bonding geometry for the title compound (A, ).
D
H· · ·A
D
H (A)
H· · ·A (A)
D· · ·A (A)
D
H· · ·A (◦)
˚
˚
˚
O5W H5W1· · ·O1i
O5W H5W2· · ·O4ii
N3 H3· · ·O2
0.84 (7)
0.88 (7)
0.86
0.86
0.86
1.94 (7)
2.48 (6)
1.98
2.56
1.99
2.776 (6)
3.188 (4)
2.666 (6)
3.155 (4)
2.830 (4)
3.560 (4)
174(4)
137(6)
136
127
164
N3 H3· · ·O2iii
N4 H4· · ·O5Wiv
C15 H15· · ·S1ii
0.93
2.83
136
Symmetry codes: i x, −y, z−1/2; ii x+3/2, y+3/2, z+1; iii x+3/2, y+1/2, z+1; iv x+1/2, −y+3/2, z−1/2.
Note: The atom numbering according to Fig. 1 used.
3.3. NMR spectra
average values for these protons are determined as 2.91 and
2.10 ppm.
The characterization of compound was further enhanced by use
of 13C and 1H NMR spectroscopy. The 13C and 1H NMR spectroscopy
using TMS as an internal standard and DMSO-d6 as solvent are
shown in Fig. 4. GIAO 13C and 1H chemical shift calculations have
been carried out using B3LYP method with 6-31G(d) basis set for the
optimized geometry. The results of this calculation are tabulated in
Table 4.
The carbonyl and thione carbons can be clearly observed at
between ∼167.30–182.22 ppm and more slightly deshielded in the
13C NMR spectra. Formation of intramolecular hydrogen bonding,
the increasing electronegativity of oxygen and sulfur atoms and
different environments such as 4-nitrophenyl and pyrazolyl and
conformations cause a deshielding effect for these signals. The sig-
nal of thione carbon (C=S) has been calculated as 176.78 ppm. The
compound has two different carbonyl groups. The 13C NMR signal
of the carbonyl groups is appeared at ∼167.30–161.47 ppm. The
existence of the intramolecular hydrogen bond owing to the car-
bonyl oxygen atom is confirmed at ∼167.30 ppm [35]. Due to this
interaction, the experimental and theoretical chemical shift differ-
ence for atom C13 is more than 10 ppm. The peak at 161.47 ppm is
confirmed the carbonyl group on pyrazolone ring. The calculated
13C NMR signal values of these carbonyl groups are determined as
152.14–158.66 ppm.
The experimental 1H NMR data of the title compound cor-
respond to those of similar compounds [34]. The 1H NMR
signals for H3(N3) and H4(N4) protons shifted downfield to 12.04
and 11.38 ppm, while that N H appeared at about ∼8.00 and
∼4.00 ppm, respectively. Title compound has thiourea protons
(N H). These shifts result from variety parameters, such as the
p-nitro substituted group and pyrazolone, which release and with-
draw electron density in each ring, their positions and intra- and
intermolecular hydrogen bondings [3]. The calculated chemical
shift values for these N H protons are 11.07–10.63. The compound
has aromatic moieties such as p-nitrophenyl and phenyl rings,
and their peaks are observed at ∼8.80–7.85 and ∼7.53–7.35 ppm,
respectively. These signals have been calculated as 8.75–8.41
and 7.64–7.06. The chemical shifts (8.80, 7.86 ppm) of hydrogen
atoms on the benzene rings are in a lower field than the average
chemical shift (7.270 ppm) of the hydrogen atoms on the non-
3.4. Theoretical structures
The molecular structure of the title compound was also stud-
ied theoretically. The starting coordinates were obtained from the
X-ray structure determination. Some selected geometric parame-
ters experimentally obtained and theoretically calculated by B3LYP
with 6-31G(d) as the basis set are listed in Table 5 comparing with
experimental data.
substituted benzene ring due to the substituted NO2 and C
O
groups of the benzene ring. The peaks belonging to the methyl
protons on pyrazolone ring are observed at ∼3.34 and ∼3.14 ppm
while methyl protons generally appear at ∼1.0 ppm. The theoretical
The agreement between the theoretically calculated and the
experimentally obtained structure parameters for this thiourea is
Table 3
Comparison of the observed and calculated vibrational spectra of the title compound.
Assignments (%PEDa)
Experimental IR
Calculated (cm−1
)
with KBr (cm−1
)
B3LYP/6-31G(d)
Scaled freq.
I (km/mol)
ꢅas
ꢅs
O
O
H2 (97)
H2 (92)
3426
3364
3317
3270
3106
2946
1644
1607
1575
1511
1410
1317
1259
1116
977
3637
3379
3233
3220
3129
2994
1727
1680
1581
1552
1421
1316
1162
1123
1073
943
73.42
542.08
409.05
215.70
1.43
ꢅ N H (96)
␯ N H (89)
ꢅs
C H (97)
ꢅ C H3 (98)
ꢅ C O (82) + ˇCNN (10)
ꢅ C O (68) + ꢆ N H (10)
␯ C C (54) + ␤CCC (13)
ꢆ N H (40) + ꢅ N O2 (15) + ꢅ C N (13)
ω C H3 (62)
ꢆ C H (36) + ꢅ C N (20)
ꢆ C H (48) + ␯ C C (14) + ␯ C N (11)
ı C H3 (40)
␯ C C (24) + ꢆ C N (22)
ı C H3 (16) + ˇCNC (12)
␣ N O2 (31) + ␯ N O2 (14) + ␯ C N (13)
ω N H (22) + ꢅ C S (13)
8.80
308.31
87.38
2.59
390.26
14.60
74.65
92.77
25.90
17.61
14.51
65.11
61.42
926
830
744
838
748
Vibrational modes: ꢅ, stretching; s, symmetric; as, asymmetric; ˛, scissoring; ꢆ, rocking; ω, wagging; ı, twisting; ˇ, in-plane bending.
a
PEDs are expressed in %; values lower than 10% are neglected.

34
N.B. Arslan et al. / Spectrochimica Acta Part A 89 (2012) 30–38
Table 4
Experimental and theoretical 13C and 1H isotropic chemical shifts (ppm) for the title
compound.
Atom
Experimental
Calculated
(DMSO-d6)
(DMSO-d6)
B3LYP/6-31G(d)
C1
C2
C3
C4
C5
C6
C7
C8
161.47
108.70
153.54
11.95
36.14
138.53
123.31
130.79
126.98
130.79
123.31
182.22
167.30
135.44
129.62
124.31
150.29
124.31
129.62
12.04
11.38
2.22
152.14
106.73
148.91
14.14
35.08
129.45
113.15
122.64
118.49
122.31
116.13
176.78
158.66
131.60
126.71
118.53
144.43
119.05
123.33
11.07
10.63
3.08a
C9
C10
C11
C12
C13
C14
C15
C16
C17
C18
C19
H3N3
H4N4
H5W
H4
3.34
3.14
2.10a
H5
2.91a
H7
7.35
7.06
H8
7.53
7.53
H9
7.39
7.32
H10
H11
H15
H16
H18
H19
7.53
7.51
7.86
7.85
8.80
8.79
7.50
7.64
8.42
8.43
8.41
8.75
Note: The atom numbering according to Fig. 1 used in the assignment of chemical
shifts.
a
Average.
Fig. 2. (a) FT-IR spectrum of the title compound and (b) simulated IR spectra of the
title compound.
obtained by B3LYP method shows strong correlation with the
experimental values. The same trend was also observed in bond
angles. The largest difference between experimental and calculated
bond angels is about 1.433◦ and the root mean square error (RMSE)
is found about 2.949◦ indicating that the bond angles obtained by
B3LPY method shows strong correlation with the experimental val-
ues.
very good. The main differences of conformations between by X-
ray and by calculation are manifested that the bond lengths of the
calculation are usually larger than those of the X-ray. According to
our calculations, B3LYP method correlates well for the bond length.
Although the largest difference between experimental and calcu-
˚
lated bond lengths is about 0.166 A, the root mean square error
A logical method for globally comparing the structures obtained
with the theoretical calculations is by superimposing the molecular
skeleton with that obtained from X-ray diffraction, giving an RMSE
˚
(RMSE) is found about 0.092 A, indicating that the bond lengths
˚
of 0.158 A (Fig. 5). As a result, there is a good agreement between
the experimental and theoretical geometrical parameters.
3.5. Conformational analysis
To determine the most stable energy conformation of the
title compound, a conformation analysis was performed between
nitrobenzene and antipyrine ring system on C13 N4 C12 N3
atoms. While this ϕ(C13 N4 C12 N3) torsion angle is obtained as
4.0(4)◦ in the X-ray structure, the computational value is −3.98041◦
for B3LYP/6-31G(d).
Molecular energy profile with respect to rotations about the
selected torsion angle is presented in Fig. 6. In order to define the
conformational energy profiles, energy values of the density func-
tional theory (DFT) using Becke’s three-parameter hybrid method
with the Lee, Yang, and Parr correlation functional (B3LYP) are cal-
culated as a functions of the torsion angles ϕ(C13 N4 C12 N3)
Fig. 3. Correlation graphic of calculated and experimental frequencies of title com-
pound.
from
0
to 360◦ varied every 10◦ using 6-31G(d) basis set

N.B. Arslan et al. / Spectrochimica Acta Part A 89 (2012) 30–38
35
Fig. 4. (a) 13C NMR spectrum of the title compound and (b) 1H NMR spectrum of the title compound.
keeping the other torsional angle constant. The standard conver-
gence criteria are used. The zero-point energies of each point are
carried out by the performance of frequency calculation using
the same model. Results showed that low energy domains for
ϕ(C13 N4 C12 N3) are located at 20◦ and 30◦ with −1783.44038
and −1783.44032 hartree, respectively. In the meantime, the high-
energy conformer located at −100◦ with −1783.42228 hartree.
Energy difference between the most favorable and unfavorable
conformer, which arises from the rotational potential barrier cal-
culated with respect to the selected torsion angle, is calculated as
0.0181 hartree (1,007,3011.35 kcal mol−1).
sites for electrophilic attack and nucleophilic reactions as well as
hydrogen bonding interactions [36–38]. The electrostatic poten-
tial V(r) are also well suited for analyzing processes based on the
“recognition” of one molecule by another, as in drug–receptor and
3.6. Molecular electrostatic potential
Fig. 5. Atom-by-atom superposition of the calculated (purple) over the X-ray struc-
ture (black) for the title compound. (For interpretation of the references to color in
this figure legend, the reader is referred to the web version of this article.)
Molecular electrostatic potential (MEP) is related to the elec-
tronic density and is a very useful descriptor in understanding

36
N.B. Arslan et al. / Spectrochimica Acta Part A 89 (2012) 30–38
Table 5
Some selected experimental and optimized geometrical parameters of the title
compound.
Parameters
Experimental
Calculated
B3LYP/6-31G(d)
˚
Bond lengths (A)
C1 O1
C1 N1
C2 N3
C3 N2
C3 C4
C5 N2
C6 N1
C12 N3
C12 N4
C12 S1
C13 O2
C13 N4
C13 C14
C17 N5
N1 N2
1.240 (3)
1.392 (3)
1.414 (3)
1.374 (4)
1.486 (4)
1.478 (4)
1.431 (3)
1.343 (4)
1.400 (3)
1.661 (3)
1.219 (3)
1.359 (3)
1.516 (4)
1.494 (4)
1.394 (3)
1.223 (3)
1.208(3)
1.22211
1.41484
1.40482
1.39097
1.49267
1.46838
1.42195
1.34717
1.40084
1.69022
1.23162
1.38452
1.50285
1.47526
1.41596
1.22989
1.22988
0.09159
0.16646
Fig. 6. Molecular energy profile against the selected torsional degree of freedom at
B3LYP/6-31G(d) level.
N5 O3
N5 O4
RMSEa
shown in Fig. 7. In this case, as can be seen in Fig. 7, the nitro and
carbonyl oxygen atoms are surrounded by a greater surface of neg-
ative charge, becoming these sites potentially more favorable for
a possible coordination point. The maximum value of the negative
region on the carbonyl oxygen atom is determined as −0.598 a.u.
On the other hand, it was founded that free located water molecule
is surrounded by a greater surface of positive charge, which can
be considered as possible sites for nucleophilic attack. The maxi-
mum value for this positive region is 0.632 a.u. These results obtain
information about the region from where the compound can have
intra- or intermolecular interaction and metallic bonding. As can
be seen from the results, the MEP map confirms the existence
of intra- and intermolecular interactions observed in the solid
state.
Max. Differencea
Bond angles (◦)
O1 C1 N1
C1 C2 N3
N3 C12 N4
N3 C12 S1
N4 C12 S1
O2 C13 N4
C16 C17 N5
C18 C17 N5
C1 N1 C6
N2 N1 C6
C3 N2 C5
N1 N2 C5
C12 N3 C2
C13 N4 C12
O4 N5 O3
O4 N5 C17
O3 N5 C17
RMSEa
123.9 (3)
123.2 (3)
114.9 (3)
126.1 (2)
119.0 (2)
124.4 (3)
119.0 (3)
117.9 (3)
125.2 (2)
119.4 (2)
119.1 (3)
115.7 (3)
123.9 (2)
128.5 (3)
124.6 (3)
118.7 (3)
116.8 (3)
125.87217
120.28025
115.66271
125.04271
119.29318
122.93881
118.93657
118.91991
123.44335
119.15719
119.44431
113.86582
126.84912
127.85788
124.87107
117.59575
117.53309
2.94912
3.7. Frontier molecular orbitals analysis
By examining the frontier orbitals of a molecule the optical
properties and the steps to react with other molecules can be deter-
mined. Distributions and energy levels of HOMO-1, HOMO, LUMO
and LUMO+1 orbitals computed with B3LYP/6-31G(d) level for the
title compound are shown in Fig. 8.
Max. Differencea
1.43338
Torsion angles (◦)
O2 C13 C14 C19
N4 C13 C14 C19
O1 C1 N1 C6
132.2 (3)
−47.5 (4)
21.0 (5)
−164.19091
16.53693
26.34628
C11 C6 N1 C1
C7 C6 N1 N2
−53.5 (4)
−21.7 (4)
156.6 (3)
−174.9 (3)
3.3 (4)
−114.7 (3)
−11.7 (5)
168.0 (3)
4.0 (4)
−54.70087
−21.09139
159.16107
172.45155
−7.98439
Calculations indicate that 112 of 118 molecular orbital have
been occupied. As observed form the Fig. 8, while the highest
occupied molecular orbital (HOMO) of the title compound is prin-
cipally delocalized among the 4-nitrobenzamide ring system, the
lowest-lying unoccupied molecular orbital (LUMO) is delocalized
among the antipyridine ring system. In addition to this HOMO-
1 and LUMO+1 orbitals partially delocalized opposite side of the
molecule according to each other. Both of the HOMOs and LUMOs
are mostly the ␲-antibonding type orbitals. The energy difference
between the HOMO and LUMO, being 2.98 eV, showed that the
molecule is in the steady state.
C11 C6 N1 N2
N4 C12 N3 C2
S1 C12 N3 C2
C1 C2 N3 C12
O2 C13 N4 C12
C14 C13 N4 C12
N3 C12 N4 C13
S1 C12 N4 C13
C16 C17 N5 O4
C18 C17 N5 O3
−119.94573
3.77120
−176.97867
−3.98041
−174.3 (3)
−172.1 (3)
−170.0 (3)
176.42883
−179.93536
−179.94744
a
RMSE and maximum differences between the bond lengths and angles com-
puted by the theoretical methods and those obtained from X-ray diffraction.
3.8. Thermodynamic properties
enzyme–substrate interactions, because it is through their poten-
tials that the two species first “see” each other [39,40]. Being a
real physical property V(r)s can be determined experimentally by
diffraction or by computational methods [41].
To visually consider the most probable sites of the title molecule
for an interaction with electrophilic and nucleophilic species, MEP
was calculated at the B3LYP/6-31G(d) optimized geometry. While
electrophilic reactivities visualized by red color which indicate the
negative regions of the molecule, the nucleophilic reactivities col-
ored by blue, indicating the positive regions of the molecule as
The vibrational analysis and statistical thermodynamics based
on, the standard thermodynamic functions which are standard heat
capacities (Cpo,m), standard entropies (Smo ), and standard enthalpy
changes (ꢃHmo (0 → T)) were obtained and listed in Table 6. The
scale factor for frequencies is 0.9613, which is a typical value for
the B3LYP/6-31G(d) level of calculations.
From Table 6, it can be observed that the standard heat capac-
ities, entropies and enthalpy changes increase at any temperature
from 100.00 K to 1000.00 K since increasing temperature causes
an increase in the intensities of molecular vibration. For the title

N.B. Arslan et al. / Spectrochimica Acta Part A 89 (2012) 30–38
37
Fig. 7. Molecular electrostatic potential map calculated at B3LYP/6-31G(d) level.
Fig. 8. Molecular orbital surfaces and energy levels given in parentheses for the HOMO-1, HOMO, LUMO, LUMO+1 of the title compound at B3LYP/6-31G(d).
compound, the correlation equations between these thermody-
namic properties and temperature T, which can be used for the
further studies of the title compound, are as follows:
4. Conclusions
In this study, a novel thiourea compound, C19H17N5O4S·H2O has
been synthesized and characterized by elemental analysis, FT-IR,
1H NMR, 13C NMR spectroscopy, mass spectrometry and structural
(XRD) techniques. The theoretical calculations of this compound
have been performed by using the density functional theory (DFT)
method with the 6-31G(d) basis set. Although the differences
observed in the geometric parameters, the general agreement is in a
good range and the theoretical calculations support the solid-state
structures. The experimental vibrational frequencies and chemi-
cal shift values are in a good agreement with the results of B3LYP
method. The calculated MEP map verifies the solid-state interac-
tions.
Cp0,m = 11.25038 + 0.38166T − 1.69255 × 10−4 T2 (R2 = 0.99959)
Sm0 = 74.21691 + 0.45185T − 1.20945 × 10−4 T2 (R2 = 0.99988)
ꢃHm0 = −5.34681 + 0.05688T + 9.74114 × 10−5 T2 (R2 = 0.99936)
Table 6
Thermodynamic properties of the title compound at different temperatures at
B3LYP/6-31G(d) level.
T (K)
100.00
Cp0,m(cal mol−1 K−1
)
Sm0 (cal mol−1 K−1
)
ꢃHm0 (kcal mol−1
)
48.043
79.599
116.371
160.828
199.068
199.761
235.976
269.808
301.261
330.431
357.502
382.683
406.177
3.060
9.655
200.00
298.15
300.00
400.00
500.00
600.00
700.00
800.00
900.00
1000.0
Supplementary material
109.761
110.312
138.109
161.197
179.728
194.614
206.739
216.762
225.147
19.153
19.360
32.016
47.221
64.499
83.442
103.728
125.117
147.423
CCDC 815263 contains the supplementary crystallographic
data (excluding structure factors) for the structure reported
in this article. These data can be obtained free of charge via
http://www.ccdc.cam.ac.uk/data request/cif, by e-mailing or by
contacting The Cambridge Crystallographic Data Centre, 12, Union
Road, Cambridge CB2 1EZ, UK; fax: +44 1223 336033.

38
N.B. Arslan et al. / Spectrochimica Acta Part A 89 (2012) 30–38
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