Structure of 5-benzoyl-4-phenyl-2-chloropyrimidine studied by X-ray diffraction, DFT calculations, NMR and FT-IR spectra

Article abstract of DOI:10.1016/j.molstruc.2012.07.010

In this work, 5-benzoyl-4-phenyl-2-chloropyrimidine (5B4P2CP) (C ₁₇H₁₁ClN₂O), was characterized by X-ray single crystal diffraction technique (XRD), IR-NMR spectroscopy and quantum chemical computational methods as both ex

Full text of DOI:10.1016/j.molstruc.2012.07.010

Journal of Molecular Structure 1030 (2012) 1–9
Contents lists available at SciVerse ScienceDirect
Journal of Molecular Structure
journal homepage: www.elsevier.com/locate/molstruc
Structure of 5-benzoyl-4-phenyl-2-chloropyrimidine studied by X-ray diffraction,
DFT calculations, NMR and FT-IR spectra
a,
a
b
b
a
⇑
_
_
Ersin Inkaya , Muharrem Dinçer , Emine Sßahan , Ismail Yıldırım , Orhan Büyükgüngör
a Department of Physics, Faculty of Arts and Sciences, Ondokuz Mayıs University, 55139 Kurupelit, Samsun, Turkey
b Department of Chemistry, Faculty of Arts and Sciences, Erciyes University, 38039 Kayseri, Turkey
h i g h l i g h t s
"
"
"
"
Pyrimidine; X-ray single crystal diffraction.
Density functional theory (DFT).
B3LYP/6-311G(d,p) and B3LYP/6-311++G(d,p).
Non-linear optical properties of the title compound have been calculated.
a r t i c l e i n f o
a b s t r a c t
Article history:
In this work, 5-benzoyl-4-phenyl-2-chloropyrimidine (5B4P2CP) (C17H11ClN2O), was characterized by
X-ray single crystal diffraction technique (XRD), IR-NMR spectroscopy and quantum chemical computa-
tional methods as both experimental and theoretically. The compound crystallizes in the orthorhombic
space group P bca with Z = 8. The molecular geometry was also optimized using density functional theory
(DFT/B3LYP) method with the 6-311G(d,p) and 6-311++G(d,p) basis sets in ground state and compared
with the experimental data. The computed vibrational frequencies are used to determine the types of
molecular motions associated with each of the experimental bands observed. From the optimized geom-
etry of the molecule, vibrational frequencies, gauge-independent atomic orbital (GIAO) 1H and 13C NMR
chemical shift values calculated for two basis sets. Also, molecular electrostatic potential (MEP) distribu-
tion, non-linear optical properties, frontier molecular orbitals (FMOs) and thermodynamic properties of
the title compound were performed at B3LYP/6-311++G(d,p) level.
Received 12 May 2012
Received in revised form 4 July 2012
Accepted 7 July 2012
Available online 20 July 2012
Keywords:
X-ray structure determination
IR and NMR spectroscopy
DFT calculations
Pyrimidine
Non-linear optical properties
Ó 2012 Elsevier B.V. All rights reserved.
1. Introduction
Vibrational spectroscopy (IR, Raman) and NMR techniques are
widely used to study structural and dynamical aspects of molecu-
Pyrimidines have been used in syntheses for many years due to
their importance about structural diversities and medicinal prop-
erties antibacterial, antifungal, antitumour, antimicrobial, antiviral
activities [1–3]. In addition, pyrimidines are also taken in consider-
ation at biologically relevant systems such as DNA, RNA, nucleic
acids, cofactors, various toxins, and other products [4,5]. The
photostability of nucleic acid bases are directly relevant to the pho-
tochemistry and photophysics of pyrimidines and their derivatives,
especially halogenated pyrimidines [6,7]. Chloropyrimidine deriva-
tive was obtained from Vilsmeier–Haack reaction of 5-benzoyl-
4-phenyl-pyrimidine-2(1H)-one with phosphorusoxychloride.
Hence, the possible benefits of the pyrimidine derivatives encour-
age us to work on these compounds [8–10]. The title compound is
a novel compound firstly synthesized in our laboratories by us.
lar systems. With the recent advances in computational methods
and common access to large-scale powerful computers and soft-
ware, it is possible to describe molecular properties of relatively
small molecules [11] with near chemical accuracy using theoretical
methods. The evolution of density functional theory (DFT) [12] has
afforded opportunities for performing normal coordinate analysis
of moderately large molecules. Among various types of density
functionals available, Becke’s three-parameter hybrid functional
(B3LYP) [13,14] has been found to be the most promising in pro-
viding excellent results of vibrational band locations (wavenumber
scale). The gauge-independent atomic orbital (GIAO) [15,16] meth-
od is one of the most common approaches for calculating nuclear
magnetic shielding tensors.
In this paper, we report the synthesis, characterization and
crystal structure of 5B4P2CP, (C17H11ClN2O), as well as theoretical
studies using the DFT(B3LYP) method and 6-311G(d,p) and
6-311++G(d,p) basis sets. The aim of the present work was to
⇑
Corresponding author. Tel.: +90 362 3121919/5256; fax: +90 362 4576081.
E-mail address: ersin.inkaya@oposta.omu.edu.tr (E. Inkaya).
_
0022-2860/$ - see front matter Ó 2012 Elsevier B.V. All rights reserved.
http://dx.doi.org/10.1016/j.molstruc.2012.07.010

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2
E. Inkaya et al. / Journal of Molecular Structure 1030 (2012) 1–9
Scheme 1. The formation of the 5B4P2CP.
describe and characterize the molecular structure, vibrational
properties and chemical shifts of the title compound, both experi-
mentally and theoretically. A comparison of the experimental and
theoretical spectra can be very useful in making correct assign-
ments and understanding the basic chemical shift-molecular struc-
ture relationship. Molecular electrostatic potential (MEP), frontier
molecular orbitals (FMOs), thermodynamic parameters and non-
linear optical properties of the title compound were studied at
the B3LYP/6-311++G(d,p) level. We also make comparisons be-
tween experimental and calculated values.
from Merck, Fluka, Aldrich and used without further purification.
The starting material was prepared according to the literature
procedure that described by Altural and co-workers [17–20]. A
solution of 5-benzoyl-4-phenyl-pyrimidine-2(1H)-one (0.30 g, 1.1
mmol) in DMF and phosphorusoxychloride (2 ml) was heated un-
der reflux on a steam bath for 3 h and the reaction mixture poured
gradually on to crashed ice. The precipitate was filtered off, dried
then crystallized from ethanol. 0.26 g (75%), M.p.: 124 °C; FT-IR
(KBr, cmꢀ1): 3051 (arom. CAH), 1661 (PhAC@O), 760, 694 cmꢀ1
(CACl); 1H NMR (400 MHz, CDCl3): d 8.73 (s, 1H, HPyrimidine);
7.69–7.14 ppm (m, 10H, Harom.); 13C NMR (100 MHz, CDCl3): d
194.04 (PhAC@O)170.89 (C-2), 167.08 (C-1), 162.00 (C-4), 159.70
2. Experimental and theoretical methods
2.1. General remarks
Melting points were measured on an Electrothermal 9200 appa-
ratus and are uncorrected. The 1H and 13C NMR spectra were mea-
sured with a Bruker Avance III 400 MHz spectrometer and the
chemical shifts are expressed in ppm relatively to TMS. IR spectra
of the compound were recorded in the range of 400–4000 cmꢀ1 re-
gion with a Shimadzu FT-IR 8400 spectrophotometer.
2.2. Synthesis
Solvents were dried by refluxing with the appropriate drying
agents and distilled before use. All other reagents were purchased
Table 1
Crystal data and structure refinement parameters for the 5B4P2CP.
CCDC deposition No.
877548
Color/Shape
Colorless
Chemical formula
Formula weight
Temperature (K)
Wavelength (Å)
Crystal system
Space group
C17H11ClN2O
294.73
296
0.71073 MoK
Orthorhombic
P bca
a
Unit cell parameters
a, b, c (Å)
11.7568 (5), 16.3665 (10), 14.6611 (8)
a
, b,
c
(°)
90, 90, 90
2821.1 (3)
8
1.388
0.27
Volume (Å3)
Z
Dcalc (g/cm3)
l
(mmꢀ1
)
F(000)
1216
Crystal size (mm3)
Diffractometer/measurement
method
0.66 ꢁ 0.54 ꢁ 0.44
STOE IPDS 2/
x scan
Index ranges
ꢀ15 6 h 6 15, ꢀ21 6 k 6 21,
ꢀ18 6 l 6 19
h range for data collection (°)
Reflections collected
Independent/observed reflections
Rint
2.5 6 h 6 27.6
36228
3267/2459
0.055
Refinement method
Full-matrix least-squares on F2
3267/0/191
Data/restraints/parameters
Goodness-of-fit on F2
1.05
Fig. 1. (a) A view of the title compound showing the atom-numbering scheme.
Displacement ellipsoids are drawn at the 40% probability level and H atoms are
shown as small spheres of arbitrary radii. (b) The theoretical geometric structure of
the 5B4P2CP (B3LYP/6-311++G(d,p)level).
R indices [I > 2
R indices (all data)
qmin (e/Å3)
r
(I)]
R1 = 0.0674, wR2 = 0.0988
R1 = 0.0427, wR2 = 0.0906
0.16, ꢀ0.21
D
qmax, D

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E. Inkaya et al. / Journal of Molecular Structure 1030 (2012) 1–9
3
Table 3
Experimental and optimized geometrical parameters of the 5B4P2CP.
Parameters
Experimental
Calculated DFT/B3LYP
6-311G(d,p)
6-311++G(d,p)
Bond lengths (Å)
Cl1AC1
N1AC1
N1AC2
N2AC1
N2AC4
O1AC11
C2AC3
C3AC4
C2AC5
1.735 (17)
1.319 (2)
1.343 (19)
1.314 (2)
1.332 (2)
1.213 (2)
1.399 (2)
1.383 (2)
1.485 (2)
1.505 (2)
1.483 (2)
1.756
1.318
1.345
1.324
1.335
1.215
1.413
1.395
1.482
1.510
1.496
0.006
0.021
1.754
1.319
1.345
1.324
1.336
1.217
1.413
1.395
1.482
1.509
1.495
0.005
0.019
C3AC11
C11AC12
RMSEa
Max. differencea
Bond angles (°)
C1AN1AC2
C1AN2AC4
N2AC1AN1
N2AC1ACl1
N1AC1ACl1
N1AC2AC3
N1AC2AC5
N2AC4AC3
O1AC11AC12
O1AC11AC3
C12AC11AC3
RMSEa
115.93 (14)
113.59 (14)
129.64 (15)
115.82 (12)
114.53 (13)
120.43 (14)
115.09 (13)
123.84 (16)
121.96 (15)
118.15 (15)
119.87 (14)
117.68
114.37
128.24
115.88
115.88
119.69
115.59
123.76
121.65
119.24
119.07
0.16
117.71
114.53
128.08
115.96
115.97
119.71
115.75
123.67
121.69
119.24
119.02
0.16
Fig. 2. Part of the crystal structure of the 5B4P2CP, showing the CAHꢂ ꢂ ꢂ
p
interactions. For the sake of clarity, H atoms not involved in H-bonds have been
omitted.
Table 2
Max. differencea
1.75
1.78
Hydrogen bonding geometry for the 5B4P2CP.
Torsion angles (°)
C4AN2AC1AN1
C4AN2AC1ACl1
C2AN1AC1AN2
C2AN1AC1ACl1
N1AC2AC3AC11
O1AC11AC12AC17
O1AC11AC12AC13
DAHꢂ ꢂ ꢂA
DAH (Å)
0.93
Hꢂ ꢂ ꢂA (Å)
Dꢂ ꢂ ꢂA (Å)
DAHꢂꢂꢂA (°)
2.6 (3)
2.79
2.69
C4AH4ꢂ ꢂ ꢂCg2i
2.740
3.614
156
ꢀ178.29 (13)
ꢀ177.76
ꢀ177.90
i
ꢀ2.4 (3)
ꢀ1.76
ꢀ1.83
Symmetry code: x ꢀ 1/2, y, ꢀz ꢀ 1/2. Cg2: Centroid of the C5AC10.
178.46 (11)
ꢀ168.22 (14)
ꢀ173.64 (17)
6.0 (3)
178.79
ꢀ167.63
ꢀ166.61
11.35
178.77
ꢀ168.07
ꢀ165.80
12.36
(C-3), 135.72, 135.30, 134.21, 131.30, 130.03, 129.74, 129.42,
128.77 ppm (C-Ph). C17H11N2O4Cl (234.74 g/mol) (Scheme 1).
a
RMSE and maximum differences between the bond lengths and angles com-
2.3. Crystallography
puted using theoretical methods and those obtained from X-ray diffraction.
The single-crystal X-ray data was collected on a STOE diffrac-
tometer with an IPDS(II) image plate detector. All diffraction mea-
surements were performed at room temperature (296 K) using
method with the 6-311G(d,p) [27] and 6-311++G(d,p) [28] basis
sets. All the calculations were performed without specifying any
symmetry for the title molecule by using Gauss View molecular
visualization program [29] and Gaussian 03 program package
[30]. For modeling, the initial guess of the compound was first ob-
tained from the X-ray coordinates. The harmonic vibrational fre-
quencies were calculated at the same level of theory for the
optimized structure the obtained frequencies were scaled by
0.9679 [31] and 0.9668 [32], respectively. The geometry of the
compound, together with that of tetramethylsilane (TMS), was
fully optimized. 1H and 13C NMR chemical shifts were calculated
within GIAO approach applying the same method and the basis
sets as used for geometry optimization. The predicted 1H and 13C
graphite monochromated MoK
tion data was recorded in the rotation mode using the
a
radiation (k = 0.71073 Å). Reflec-
scan tech-
x
nique by using X-AREA software [21]. Unit cell parameters were
determined from least-squares refinement of setting angels with
h in the range 2.5 6 h 6 27.6. The structure was solved by direct
methods using SHELXS-97 [22] implemented in WinGX [23] pro-
gram 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 191 crystallographic parameters, using SHELXL-97
[24]. All H atoms were positioned geometrically and treated using
a riding model, fixing the bond lengths at 0.93 CH atoms. Data col-
lection: X-AREA, cell refinement: X-AREA, data reduction: X-RED32
[25]. Details of the data col-lection conditions and the parameters
of refinement process are given in Table 1. The general-purpose
crystallographic tool PLATON [26] was used for the structure anal-
ysis and presentation of the results. The molecular graphic were
done using ORTEP-3 for Windows [23]. Details of the data collec-
tion conditions and the parameters of the refinement process are
given in Table 1.
NMR chemical shifts were derived from the equation d = R0
ꢀ
R,
where d is the chemical shift, is the absolute shielding and R0
R
is the absolute shielding of the standard (TMS), whose values are
31.99 and 184.79 ppm for B3LYP/6-311G(d,p), 31.97 and 184.66
ppm for B3LYP/6-311++G(d,p), respectively. The effect of solvent
on the theoretical NMR parameters was included using the default
model IEF-PCM (Integral-Equation-Formalism Polarizable Contin-
uum Model) [33] provided by Gaussian 03. The mean linear polar-
isability and mean first hyperpolarisability properties of the title
compound were obtained using molecular polarisabilities based
on theoretical calculations. The thermodynamic properties of the
title compound at different temperatures were calculated on the
basis of vibrational analyses.
2.4. Theoretical
The molecular structure of the 5B4P2CP in the ground state (in
vacuo) was optimized using density functional theory DFT (B3LYP)

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E. Inkaya et al. / Journal of Molecular Structure 1030 (2012) 1–9
Fig. 4. (a) Experimental and (b) Theoretical FT-IR spectra of the 5B4P2CP.
Fig. 3. Atom-by-atom superimposition of the calculated structures (yellow) on the
X-ray structures (blue) for molecule. (a) DFT/B3LYP/6-311G(d,p) and (b) DFT/
B3LYP/6-311++G(d,p).
Table 4
Comparison of the observed and calculated vibrational spectra of the 5B4P2CP.
Assignments
Experimental
Calculated (cmꢀ1
)
(cmꢀ1
)
6-311G(d,p)
6-
311++G(d,p)
3. Results and discussion
Scal.
freq.
I (km/ Scal.
I (km/
mol)
mol)
freq.
3.1. Description of crystal structure
m
m
m
m
m
m
m
m
m
m
c
c
sCAH(phenyl)
sCAH(benzoyl)
asCAH(phenyl)
asCAH(phenyl)
sCAH(pyrimidine)
C@O
C@C(phenyl)
C@C(benzoyl)
C@N(pyrimidine)
3051
–
–
–
3105
3099
3092
3083 17
3059 12
1683 173
4
8
7
3099
3093
3088
3087 12
3056 11
1670 194
4
8
7
The title compound 5B4P2CP, an ORTEP and theoretical view of
which is shown in Fig. 1, is a crystallizing in the orthorhombic
space group P bca with eight molecules in unit cell. The asymmet-
ric unit in the structure contains only one molecule. In the
5B4P2CP compound, C17H11ClN2O, the molecule contains essen-
tially planar pyrimidine ring with the 5- and 4-positions substi-
tuted by benzoyl and phenyl groups, respectively. The phenyl
ring and the planar part of benzoyl moiety form dihedral angles
of 34.15 (7)° and 64.34 (4)°, respectively, with the pyrimidine ring.
The two phenyl rings are inclined at an angle of 66.60 (7)° with re-
spect to one other. In the crystal structure, phenyl and benzoyl
rings are cis position with respect to the pyrimidine ring.
The pyrimidine ring is planar with a maximum deviation of
0.0056 (10) Å for atom N1. The NAC bond lengths in the pyrimi-
dine ring [1.319 (2)–1.343 (19) Å] and the ClAC distance [1.735
(17) Å] are comparable with those reported for similar structures
[34,35]. The chloro substitution at the 2-position of the pyrimidine
ring introduces a considerable in-plane distortion, which is re-
flected in the widening of the N1AC1AN2 bond angle to 129.64
(15)° compared with the other angles. The conformation of the
–
1661
1595
–
–
1545
1516
1592
4
1587
4
1586 36
1536 348
1495 242
1431
1389 283
1101 101
987
985
984
968
958
804
1581 36
1533 358
1493 239
1425
1387 250
1100 95
982
981
980
956
952
824
C@C +
m
C@N(pyrimidine)
CAH(phenyl)
5
4
CAH(pyrimidine)
+
m
CANAC 1283
h(pyrimidine)
bCAH(benzoyl)
h(phenyl)
h(benzoyl)
bCAH(phenyl)
bCAH(pyrimidine)
1119
–
918
–
–
–
2
3
4
3
2
11
2
2
3
3
3
25
mCACl
760
Vibrational modes:
Abbreviations: s, symmetric; as, asymmetric.
m
, stretching; c, rocking; b, in-plane bending; h, ring breathing.
molecule is described by the torsion angles C3AC2AC12AC11
and C3AC2AC5AC6 of ꢀ126.59 (16) and ꢀ147.69 (15)°, respec-

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E. Inkaya et al. / Journal of Molecular Structure 1030 (2012) 1–9
5
Fig. 5. Experimental (a) 1H and (b) 13C chemical shift spectra of the 5B4P2CP.
tively. The C2AC5 bond length of 1.485 (2) Å is slightly longer than
average Csp2ꢀCar bond length of 1.476 (14) Å in conjugated
CarAC@NAC systems [36]. The C11AO1 bond length is indicative
of a significant double bond character [1.213 (2) Å].

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E. Inkaya et al. / Journal of Molecular Structure 1030 (2012) 1–9
Perspective view of the crystal packing in the unit cell is shown
in Fig. 2. The crystal structure further stabilized by an intermolec-
ring is agreement with the literature value of 1528 cmꢀ1 [39].
The mCACl stretching vibration is characterized by a medium peak
ular CAHꢂ ꢂ ꢂ
p
(p-ring) stacking interaction (C4AH4ꢂ ꢂ ꢂCg2 with
appearing at 804 cmꢀ1 in FT-IR spectrum, while the theoretically
calculated value of 804 and 824 cmꢀ1 show a positive deviation
of 44 and 64 cmꢀ1, thus, it is partly due to the fact that calculated
CACl bond distance is longer than experimental value.
symmetry code: 1/2 + x, y, 1/2 ꢀ z; the Cg2 ring is consistent with
C5AC10). A detail of this interaction is given Table 2. The crystal
structure of molecule does not exhibit any intramolecular and
intermolecular hydrogen bond interactions.
3.4. NMR spectra
3.2. Optimized structures
The characterization of the 5B4P2CP was further enhanced by
the use of 1H and 13C NMR spectroscopy. The 1H and 13C NMR spec-
tra of the tittle compound recorded using TMS as an internal stan-
dard and chloroform (CDCl3) as solvent are shown Fig. 5. GIAO 1H
and 13C chemical shift values (with respect to TMS) were calcu-
lated using the DFT (B3LYP) method with the 6-311G(d,p) and 6-
311++G(d,p) basis sets and compared with experimental 1H and
13C chemical shift values. The results of this calculation are shown
in Table 5 together with the experimental values.
The first task for the computational work is to determine the
optimized geometry of the 5B4P2CP. The starting coordinates were
those obtained from the X-ray structure determination. The opti-
mized parameters (bond lengths, bond angles and dihedral angles)
of the 5B4P2CP were obtained using the (DFT/B3LYP) method with
the 6-311G(d,p) and 6-311++G(d,p) basis sets. The results are listed
in Table 3 and compared with the experimental data for the title
compound.
As seen from Table 3, agreement between the calculated struc-
tures and the experimentally determined X-ray crystal structure is
quite satisfactory. According to X-ray study, the dihedral angles be-
tween the phenyl ring and the planar part of benzoyl moiety form
are 34.15 (7)° and 64.34 (4)°, respectively, with the pyrimidine
ring, whereas the dihedral angles have been calculated at 32.40°
and 65.21° for 6-311G(d,p) level and 33.87° and 66.40° for 6-
311++G(d,p) level.
The biggest difference between experimental and calculated
bond lengths is about 0.021 Å for B3LYP/6-311G(d,p) level, the root
mean square error (RMSE) is found to be 0.006 Å, indicating that
the bond lengths obtained by B3LYP method show strong correla-
tion with the experimental values. For bond angles, the biggest dif-
ference and RMSE is about 1.78° and 0.16 for B3LYP/6-311++G(d,p)
level, respectively.
A global comparison was performed by superimposing the
molecular skeletons obtained from X-ray diffraction and the theo-
retical calculations atom by atom (Fig. 3), obtaining RMSE’s values
of 0.102 and 0.103 for 6-311G(d,p) and 6-311++G(d,p) levels. Con-
sequently, 6-311G(d,p) level correlates a little well for the geomet-
rical parameters when compared with 6-311++G(d,p) level.
We have calculated 1H chemical shift values (with respect to
TMS) of 8.62–7.33 ppm for the B3LYP/6-311G(d,p) level and
8.72–7.42 ppm for B3LYP/6-311++G(d,p) level, however, the exper-
imental results were observed to be 8.73-7.14 ppm. The C-H pro-
ton in the pyrimidine ring appears at 8.73 ppm, while this signal
is observed computationally at 8.60 and 8.72 ppm for two basis
sets, respectively. This CAH proton in pyrimidine ring is shown a
little different with literature values of 8.16 [40] and 8.08 [41]
ppm. There is no significant difference between literature values
and other 1H chemical shifts of the title compound.
We have calculated 13C chemical shift values (with respect to
TMS) of 200.75–134.04 ppm for 6-311G(d,p) level and 203.66–
134.79 ppm for 6-311++G(d,p) level, however, the experimental
results were observed to be 194.04-128.77 ppm. 13C NMR spectra
of tittle compound show signal at 194.04 ppm due to the C11 atom
Table 5
Experimental and theoretical 13C and 1H isotropic chemical shifts (ppm) for the
5B4P2CP.
Atom
Experimental (ppm) (CDCl3)
Calculated (ppm) DFT/B3LYP
6-311G(d,p)
6-311G++(d,p)
3.3. Vibrational spectra
C1
C2
C3
C4
C5
C6
C7
C8
167.08
170.89
159.70
162.00
135.72
129.74
131.30
129.42
130.03
134.21
194.04
135.30
134.21
130.03
128.77
131.30
129.74
8.73
174.58
176.56
137.44
165.85
142.32
137.33
135.55
138.21
134.04
137.00
200.75
142.93
136.25
135.70
142.25
134.84
138.57
8.60
177.40
178.28
138.61
166.76
143.78
138.97
136.55
139.33
134.79
137.95
203.66
144.92
137.63
136.26
143.22
135.82
139.71
8.72
The experimental and theoretical simulated FT-IR spectra are
shown in Fig. 4. Harmonic vibrational frequencies of the tittle com-
pound were calculated using DFT (B3LYP) method with 6-
311G(d,p) and 6-311++G(d,p) basis sets and obtained frequencies
were scaled by 0.9679 [31] and 0.9668 [32], respectively. The ob-
served and calculated frequencies in FT-IR spectra of the
5B4P2CP and their relative infrared intensities and probable
assignments are given Table 4. The agreement between experi-
mental and calculated frequencies is satisfactory general.
C9
C10
C11
C12
C13
C14
C15
C16
C17
H4
The
mCAH aromatic stretching vibrations were observed at
3051 cmꢀ1 and these modes have been calculated at 3105–3059
cmꢀ1 and 3099–3056 cmꢀ1 for 6-311G(d,p) and 6-311++G(d,p) lev-
els, respectively. The mC@O stretching vibration is characterized by
a strong peak appearing at 1661 cmꢀ1 in FT-IR spectrum, while the
theoretically calculated values of 1683 cmꢀ1 and 1670 cmꢀ1 for
H6
H7
7.52
7.32
8.51
7.93
8.67
8.04
H8
H9
7.28
7.38
7.69
7.68
7.36
7.14
7.31
7.50
7.86
7.54
7.33
8.62
8.02
8.13
7.91
7.96
7.88
7.61
7.42
8.73
8.05
8.21
8.15
8.08
same levels, respectively. The mC@O stretching mode in benzoyl
moiety is shown good agreement with the literature values of
H10
H13
H14
H15
H16
H17
1681 cmꢀ1 [37] and 1657 cmꢀ1 [38].
The bands observed at 1595 and 1545 cmꢀ1, which can be
attributed to the
1592 and 1587 cmꢀ1 for 6-311G(d,p) level and 1495 and 1493
cmꢀ1 for 6-311++G(d,p) level, respectively. The
C@N stretching
mode in pyrimidine ring observed at 1545 cmꢀ1 with
C@C
stretching. The C@C + C@N stretching vibrations in pyrimidine
mC@C stretching vibrations, were calculated at
m
m
Note: The atom numbering according to Fig. 1 used in the assignment of chemical
shifts.
m
m

_
E. Inkaya et al. / Journal of Molecular Structure 1030 (2012) 1–9
7
of carbonyl group. This signal has been calculated at 200.75 and
203.66 ppm for 6-311G(d,p) and 6-311++G(d,p) levels, respec-
tively. In the pyrimidine ring C1, C2, C3 and C4 signal were ob-
served at 167.08, 170.89, 159.70 and 162 ppm, that have been
calculated at 174.58, 176.56, 137.44 and 165.85 ppm for 6-
311G(d,p) level and at 177.40, 178.28, 138.61 and 166.76 ppm
for 6-311++G(d,p) level, respectively.
As can be seen from Table 5, the theoretical 1H and 13C chemical
shift results for the 5B4P2CP are generally closer to the experimen-
tal 1H and 13C shift data. To make comparison with experimental
observations, we present correlation graphs in Fig. 6 based on
the calculations. As can be seen from the correlation graphs, 1H
and 13C the correlation coefficients are 0.99299 for B3LYP/6-
311G(d,p) and 0.992988 for B3LYP/6-311++G(d,p) levels.
3.5. Molecular electrostatic potential
The molecular electrostatic potential (MEP) is related to the
electronic density and is a very useful descriptor in understanding
sites for electrophilic attack and nucleophilic reactions as well as
hydrogen-bonding interactions [42–44]. The electrostatic potential
V(r) are also well suited for analyzing processes based on the ‘‘rec-
ognition’’ of one molecule by another, as in drug–receptor, and en-
zyme-substrate interactions, because it is through their potentials
that the two species first ‘‘see’’ each other [45,46]. Being a real
physical property V(r) can be determined experimentally by dif-
fraction or by computational methods [47].
To visually consider the most probable sites of the title mole-
cule for an interaction with electrophilic and nucleophilic species,
MEP was calculated at the DFT/B3LYP/6-311++G(d,p) optimized
geometry. While electrophilic reactivities visualized by red color
which indicate the negative regions of the molecule, the nucleo-
philic reactivities colored by blue1
of the molecule as shown in Fig. 7.
, indicating the positive regions
As can be seen in from Fig. 7, O1 atom in carbonyl group is sur-
rounded by a greater surface of negative charge, becoming these
sites potentially more favorable for a possible coordination point.
The maximum value of the negative region on the O1 atom in car-
bonyl is determined as ꢀ0.027 a.u. A maximum positive region
localized on the phenyl ring has value of +0.028 a.u. indicating a
possible site for nucleophilic attack. Considering these calculated
results, the MEP map shows that the negative potential sites are
on electronegative, and positive potential sites around hydrogen
atoms, respectively. These sites give the information about the re-
gion from where the compound may have intermolecular
interactions.
Fig. 6. Correlation graphics between the experimental and theoretical NMR
chemical shift values of the 5B4P2CP.
3.6. Frontier molecular orbitals
By examining the frontier orbitals of a molecule the optical
properties and the steps to react with other molecules can be
determined. Distributions and energy levels of HOMO and LUMO
orbitals computed with B3LYP/6-311++G(d,p) level for the title
compound are shown in Fig. 8. The calculations indicate that the
5B4P2CP has 76 occupied molecular orbitals.
It is clear from the figure that while the LUMO orbital is delocal-
ized all over the compound HOMO electrons are mainly delocal-
ized on the pyrimidine, phenyl rings and carbonyl group. The
value of the energy separation between the HOMO and LUMO is
4.6 eV. This large HOMO–LUMO gap automatically means high
excitation energies for many of the excited states, good stability
and a large chemical hardness for the 5B4P2CP.
Fig. 7. Molecular electrostatic potential map calculated at B3LYP/6-311++G(d,p)
level.
3.7. Non-linear optical effects
Non-linear optical (NLO) effects arise from the interactions of
electromagnetic fields in various media to produce new fields al-
tered in phase, frequency, amplitude or other propagation charac-
teristics from the incident fields [48]. NLO is at the forefront of
current research because of its importance in providing the key
1
For interpretation of color in Figs. 1–4 and 6–8, the reader is referred to the web
version of this article.

_
8
E. Inkaya et al. / Journal of Molecular Structure 1030 (2012) 1–9
Table 6
Thermodynamic properties of the 5B4P2CP at different temperatures at the B3LYP/6-
311++G(d,p) level.
Cp0;m (cal molꢀ1 Kꢀ1
)
S0m (cal molꢀ1 Kꢀ1
)
D )
H0m (kcal molꢀ1
T (K)
100.00
200.00
298.15
300.00
400.00
500.00
26.409
45.206
60.112
66.466
86.397
102.854
89.593
114.850
137.559
137.981
160.474
184.033
1.890
5.244
11.292
11.418
19.284
28.977
ties and temperature T, which can be used for the further studies
of the 5B4P2CP, are as follows:
C0p;m ¼ 7:36715 þ 0:18614T ꢀ 1:3356 ꢁ 10ꢀ5T2ðR2 ¼ 0:98831Þ
S0m ¼ 65:00172 þ 0:25197T ꢀ 2:9107 ꢁ 10ꢀ5T2ðR2 ¼ 0:99969Þ
D
H0m ¼ 0:02561 þ 0:00725T þ 1:01604 ꢁ 10ꢀ4T2ðR2 ¼ 0:99955Þ
Based on these relationships, the values of C0p;m, Sm0 , and Hm0 can
D
be obtained at any other temperatures and be helpful for the fur-
ther studies of the 5B4P2CP.
4. Conclusions
In
this
paper,
5-benzoyl-4-phenyl-2-chloropyrimidine
Fig. 8. Molecular orbital surfaces and energy levels given in parentheses for the
(5B4P2CP) (C17H11ClN2O), was synthesized and characterized by
spectroscopic (FT-IR and NMR) and structural (single-crystal X-
ray diffraction) techniques. To support the solid state structure,
the geometric parameters, vibrational frequencies and 1H and 13C
NMR chemical shifts of the 5B4P2CP have been calculated using
the density functional theory DFT (B3LYP) method with the 6-
311G(d,p) and 6-311++G(d,p) basis sets and compared with the
experimental findings. It is seen from the theoretical results, there
is no remarkable difference between the results of the two level
used in evaluating geometrical parameters, vibrational frequen-
cies, and chemical shifts. It was noted here that the experimental
results belong to solid phase and theoretical calculations belong
to gaseous phase. In the solid state, the existence of the crystal field
along with the intermolecular interactions have connected the
molecules together, which result in the differences of bond param-
eters between the calculated and experimental values. The calcu-
lated MEP map verifies the solid-state interactions. The value of
the energy separation between the HOMO and LUMO is very large
and this energy gap gives significant information about the
5B4P2CP. The predicted non-linear optical (NLO) properties of
the 5B4P2CP are much greater than those of urea. The 5B4P2CP
is a good candidate as second-order non-linear optical material.
HOMO and LUMO of the 5B4P2CP computed at B3LYP/6-311++G(d,p) level.
functions of frequency shifting, optical modulation, optical switch-
ing, optical logic, and optical memory for the emerging technolo-
gies in areas such as telecommunications, signal processing, and
optical interconnections [49,50].
The calculations of the mean linear polarizability (atot) and the
mean first hyperpolarizability (btot) from the Gaussian output have
been explained in detail previously [51], and DFT has been exten-
sively used as an effective method to investigate the organic NLO
materials [52]. The total molecular dipole moment (
polarizability ( tot) and first-order hyperpolarizability (btot) of the
title compound were calculated at the DFT (B3LYP) method with
ltot), linear
a
6-311++G(d,p) level. The calculated values of ltot, atot and btot are
1.681 D, 31.820 Å3 and 2.705 ꢁ 10ꢀ30 cm5/esu. Urea is one of the
prototypical molecules used in the study of the NLO properties of
molecular systems. Therefore it was used frequently as a threshold
value for comparative purposes. The values of ltot, atot and btot of
urea are 3.874 D, 5.0424 Å3 and 0.7648 ꢁ 10ꢀ30 cm5/esu obtained
at the same level. Theoretically, the first-order hyperpolarizability
of the title compound is of 3.5 times magnitude of urea. According
to these results, the 5B4P2CP is a good candidate of NLO material.
Supplementary material
3.8. Thermodynamic properties
CCDC 877548 contains supplementary crystallographic data
(excluding structure factors) for the structure reported in this arti-
cle. These data can be obtained free of charge at http://
www.ccdc.cam.ac.uk/data_request/cif, by e-mailing or by contact-
ing The Cambridge Crystallographic Data Centre, 12 Union Road,
Cambridge CB2 1EZ, UK; fax: +44 1223 336033.
The vibrational analysis and statistical thermodynamics based
on, the standard thermodynamic functions which are standard
heat capacities (C0p;m), standard entropies (S0m), and standard enthal-
py changes (D
H0m (0 ? T)) were obtained and listed in Table 6. The
scale factor for frequencies is 0.9668, which is a typical value for
the B3LYP/6-311++G(d,p) 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 500.00 K since increasing temperature causes an
increase in the intensities of molecular vibration. For the 5B4P2CP,
the correlation equations between these thermodynamic proper-
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