Synthesis, crystal structure, Hirshfeld surface analysis, DFT calculations, 3D energy frameworks studies of Schiff base derivative 2,2′-((1Z,1′Z)-(1,2-phenylene bis(azanylylidene)) bis(methanylylidene)) diphenol

Article abstract of DOI:10.1016/j.molstruc.2021.130910

The title compound 2,2′-((1Z,1′Z)-(1,2-phenylene bis(azanylylidene)) bis(methanylylidene)) diphenol was synthesized with a good yield. The crude product was recrystallized using ethanol and acetonitrile as solvent. Elemental analysis and spectroscopic analysis (NMR, LC-MS) were done to elucidate the structure. The compound was characterized by single crystal X-ray diffraction. The intermolecular interaction of the type and C[sbnd]H?O between the molecules in a crystal was shown by Hirshfeld surface analysis. Intramolecular interactions of the type O[sbnd]H?N was shown by atoms in molecule (AIM) theory calculations. The energy framework calculations revealed that the dispersion energy is dominant. The orbital energy gap between HOMO and LUMO was found to be 3.9678 eV. The charge distribution in the compound is visualised using molecular electrostatic potential surface.

Full text of DOI:10.1016/j.molstruc.2021.130910

Journal of Molecular Structure 1244 (2021) 130910
Contents lists available at ScienceDirect
Journal of Molecular Structure
journal homepage: www.elsevier.com/locate/molstr
Synthesis, crystal structure, Hirshfeld surface analysis, DFT
calculations, 3D energy frameworks studies of Schiff base derivative
ꢀ
diphenol
ꢀ
2,2 -((1Z,1 Z)-(1,2-phenylene bis(azanylylidene)) bis(methanylylidene))
Chandini KMa,b, Fares Hezam Al-Ostootc,d, Eman E. Shehatae, Nuha Y. Elamine,
Hela Ferjanie, Sridhar MAa,∗, Lokanath NKa
a Department of Studies in Physics, University of Mysore, Manasagangotri, Mysuru 570 006, India
b Department of Physics, MMK and SDM Mahila Maha Vidyalaya, Mysuru 570004, India
c Department of Chemistry, Yuvaraja’s College, University of Mysore, Mysuru 570 006, India
d Department of Biochemistry, Faculty of Education & Science, Al-Baydha University, Al-Baydha, Yemen
e Department of Chemistry, College of Science, IMSIU (Imam Mohammad Ibn Saud Islamic University), Riyadh 11623, Saudi Arabia
a r t i c l e i n f o
a b s t r a c t
ꢀ
ꢀ
Article history:
The title compound 2,2 -((1Z,1 Z)-(1,2-phenylene bis(azanylylidene)) bis(methanylylidene)) diphenol was
synthesized with a good yield. The crude product was recrystallized using ethanol and acetonitrile as
solvent. Elemental analysis and spectroscopic analysis (NMR, LC-MS) were done to elucidate the struc-
ture. The compound was characterized by single crystal X-ray diffraction. The intermolecular interaction
Received 18 February 2021
Revised 11 June 2021
Accepted 13 June 2021
Available online 16 June 2021
–
of the type and C HꢀO between the molecules in a crystal was shown by Hirshfeld surface analysis. In-
–
tramolecular interactions of the type O HꢀN was shown by atoms in molecule (AIM) theory calculations.
Keywords:
Schiff base
The energy framework calculations revealed that the dispersion energy is dominant. The orbital energy
gap between HOMO and LUMO was found to be 3.9678 eV. The charge distribution in the compound is
visualised using molecular electrostatic potential surface.
Hirshfeld surface
Energy frame works
HOMO-LUMO
AIM
© 2021 Published by Elsevier B.V.
Introduction
or amino molecules and protection of these groups throughout
complex or sensitive reactions [7]. Apart from biological activities,
The emission of cations and anionic pollutants has increased
the risks to human health and the environment due to uncon-
trolled agricultural and industrial activities [1]. The need for spe-
cific and sensitive identification of pollutant species (e.g., toxins
and metal ions) is in high demand particularly in health and envi-
ronmental applications [2, 3]. Structures from the Schiff base show
incredible results for metal ion determination [4]. Schiff bases
they are used as pigments/dyes [8], catalysts [9], intermediate sub-
stances, corrosion inhibitors [10] and polymer stabilizers [11]. Re-
cent reports indicated that Schiff bases can be used as extremely
active and promising sensing materials [12–14].
Schiff bases are shown to be significant substances for the
design of different biological, medicinal, pharmacological applica-
tions [15] (Fig. 1). Schiff bases of salicylaldehyde have demon-
strated a framework that supports the development of new anti-
viral agents [16]. Schiff bases have gained prominence in the
biomedical fields due to a wide variety of pharmacological ac-
tivities such as anti-fungal [17], anti-bacterial, anthelmintic [18],
anti-malarial [19], analgesic, anti-pyretic, anti-inflammatory [20],
anti-convulsant [21], anti-cancer [22] and so forth. Formazans, 4-
thiazolidinines, benzoxazines are prepared from Schiff bases syn-
thons to have a variety of industrial and bioactive compounds [23,
24]. The researchers therefore, promoted the use of Schiff base
derivatives in developing unique eco-friendly technologies [25]. In
view of their broad spectrum of biological properties and as a part
of our ongoing work [26–28], the synthesis and characterization
=
are generally compounds bearing imines or azomethines (-CH N-
) functional group, that work as ligands in different metal com-
plexes. In several fields including analytical, biological and inor-
ganic chemistry, Schiff bases represent an important class of or-
ganic compounds [5, 6]. In addition to detection, recognition, and
identification of aldehydes or ketones, Schiff bases have a variety
of applications including preparatory use, purification of carbonyl
∗
Corresponding author at: Department of Studies in Physics, University of
Mysore, Manasagangotri, Mysuru 570 006, India.
E-mail addresses: faresalostoot@gmail.com (F.H. Al-Ostoot), mas@physics.uni-
mysore.ac.in (S. MA).
https://doi.org/10.1016/j.molstruc.2021.130910
0022-2860/© 2021 Published by Elsevier B.V.

C. KM, F.H. Al-Ostoot, E.E. Shehata et al.
Journal of Molecular Structure 1244 (2021) 130910
Fig. 1. Schiff base compounds shown different biological activities.
of title compound was carried out by single-crystal X-ray diffrac-
tion. The structure of the molecule was determined and character-
ized using different methods like NMR and elemental analysis. This
study is also supplemented by Hirshfeld surface investigations and
Density Functional Theory (DFT) calculations.
tals. The melting point (M.P) of the compound was found to be 165
°C.
2.3. Spectral data
ꢀ
ꢀ
2,2 -((1Z,1 Z)-(1,2-phenylene
bis(azanylylidene))
2. Experimental details
bis(methanylylidene)) diphenol (3). Yield 80%; M.P. 165–167
°C; 1HNMR (400 MHz, DMSO–d6) δ (ppm): 6.90–7.39 (m, 6H,
Ar-H), 8.63 (s, 1H, HC N), 13.03 (s, 1H, OH), (Fig. 2); 13C NMR
=
2.1. Materials and methods
(400 MHz, DMSO) δ: 117.55 (1C, Ar-C), 118.95 (1C, Ar-C), 119.20
(1C, Ar-C), 119.73 (1C, Ar-C), 127.66 (1C, Ar-C), 132.31 (1C, Ar-C)
142.56 (1C, Ar-C), 161.33 (1C, C = N), 163.72 (1C, Ar-C-OH) (Fig
S1); LC-MS m/z: 316 [M+]. Anal.Calcd.for C20H16 N2O2(316): C,
75.93; H, 5.11; N, 8.85. Found: C, 75.90; H, 5.08; N, 8.84%.
Chemicals were purchased from Sigma Aldrich Chemical Com-
pany and TCI Chemical Pvt.Ltd, and used without further purifi-
cation. Melting point was determined using the Chemi Line CL725
Micro Controller based melting point apparatus with a digital ther-
mometer. The NMR (1H 13C) spectrum was recorded on a VNMRS-
400 MHz Agilent-NMR spectrophotometer in DMSO, Mass spec-
trum was obtained with a VG70–70H spectrophotometer. Elemen-
tal analysis results are within 0.5% of the calculated value.
2.4. Data collection and reduction
A single crystal of about 0.18✗0.19✗0.20 mm was chosen for X-
ray diffraction data collection. X-ray intensity data were collected
on a Rigaku X-ray diffractometer equipped with radiation MoKα
ꢀ
ꢀ
2.2. Synthesis of 2,2 -((1Z,1 Z)-(1,2-phenylene bis(azanylylidene))
˚
bis(methanylylidene)) diphenol
of wavelength 0.71073 A. The data were collected at 293 K. Crys-
tal structure was solved by direct methods using SHELXS-97 pro-
gram [29]. A total of 2000 phase sets were refined, with the cor-
rect phase set having combined figure of merit CFOM=0.0661. An
E-map drawn with the correct phase set revealed all the non-
hydrogen atoms.
The structure was refined using SHELXL-97 [29] against F2 by
full matrix least-squares method. All the non-hydrogen atoms were
refined anisotropically. The hydrogen atoms were placed at chemi-
cally acceptable positions, and were allowed to ride on their parent
atoms. A total of 2926 parameters were refined with 298 unique
reflections which converged the R value to 0.0780. The final weight
factor wR2 was 0.1808, and goodness-of-fit S was 1.099. The geo-
metrical calculations were performed using PLATON [30]. The OR-
ꢀ
ꢀ
The compound 2,2 -((1Z,1 Z)-(1,2-phenylene bis(azanylylidene))
bis(methanylylidene)) diphenol (3) was accomplished by a syn-
thetic procedure as shown in Scheme 1.
A solution of 2-
hydroxybezaldehyde (1, 5 ml) was mixed with 60 ml of ethano-
lic solution of o-phenylene diamine (2, 2 mmol, 0.223 gm) in mo-
lar ratio 1:2. The reaction mixture was stirred and refluxed for
30 min and monitored by TLC using mobile phase system [hex-
ane: ethyl acetate (3:1)]. The yellow precipitate formed was then
cooled to room temperature, filtered, washed several times with
mixture of water and ethanol. The precipitate was dried to ob-
tain a crude product, which on recrystallization with system of
ethanol:acetonitrile (6:2) formed the compound as colourless crys-
2

C. KM, F.H. Al-Ostoot, E.E. Shehata et al.
Journal of Molecular Structure 1244 (2021) 130910
Scheme 1. Schematic representation of the synthesis of the title compound (3).
Fig. 2. 1HNMR spectrum of title compound (3).
TEP and molecular packing diagrams were generated using MER-
CURY software [31].
3. Results and discussion
3.1. Synthesis
The title compound (3) was accomplished by
a synthetic
procedure as shown in Scheme 1. Initially a solution of 2-
hydroxybezaldehyde (1), was mixed with ethanolic solution of o-
phenylene diamine (2). The reaction mixture was then stirred and
refluxed for 30 min and monitored by TLC. Finally, the precipitate
of compound (3) was formed and then cooled to room temper-
ature, filtered, washed several times with mixture of water and
ethanol. The structure of the newly synthesised compound was as-
signed on the basis NMR, LC-MS spectroscopic data and also by
C, H, and N analysis. The 1H NMR spectrum of compound (3) has
shown the disappearance of protons of both NH2 groups of com-
pound (2), and the appearance of two protons at δ 8.63 corre-
=
sponding for the imine group -CH N. Besides, the mass spectrum
gave significant stable M + peak at m/z 316, which clearly affirmed
the formation of compound (3).
Fig. 3. ORTEP of the molecule with thermal ellipsoids drawn at 50% probability.
3.2. X-ray diffraction
The title compound C 20H16 N2O2 is crystallized in the mono-
clinic crystal system with space group P 21/c. The unit cell pa-
˚
The crystal structure comprises three six membered rings. The
phenyl rings are connected to benzene ring by schiff bases (-C = N-
). The carbon atoms in the phenyl rings (C1-C2-C3-C4-C5-C6) and
(C18-C19-C20-C21-C22-C23) are sp2 hybridized and has nearly pla-
nar trigonal geometry evident from bond angle values C2-C3-
C4 = 121.3(4)°, C3-C4-C5 = 120.6(4)°C18-C19-C20 = 120.7(4)°. The
planarity of the rings can be understood by torsion angle val-
˚
rameters are a = 6.002(8) A, b = 16.55(2) A, and c = 16.33(2)
˚
A and β = 91.60 ° The crystal data and structure refinement de-
tails are listed in Table 1. The ORTEP of the molecule with thermal
ellipsoids drawn at 50% probability is shown in Fig. 3. The bond
lengths, bond angles and torsion angles are listed in Tables 2, 3,
and 4 respectively.
3

C. KM, F.H. Al-Ostoot, E.E. Shehata et al.
Journal of Molecular Structure 1244 (2021) 130910
Table 1
Crystal data and structure refinement details.
Parameter
Value
CCDC number
2060415
C20 H16 N2 O2
316.35
Empirical formula
Formula weight
Temperature
293 K
˚
Wavelength
0.71073 A
Crystal system
Space group
Monoclinic
P 21 /c
˚
˚
˚
Cell Dimensions
Volume
a = 6.002 (8)Ab = 16.55 (2) Ac = 16.33 (2) Aβ = 91.60 °
3
˚
1622 (4) A
Z
4
Density(calculated)
Absorption coefficient
F000
1.296 Mg m−3
0.085 mm−1
664
Crystal size
0.18 mm × 0.19 mm × 0.20 mm
3.51° to 27.57°
θ range for data collection
Index ranges
−4 ≤ h ≤ 7−20 ≤ k ≤ 20−10 ≤ l ≤ 20
6042
Reflections collected
Independent reflections
Absorption correction
Refinement method
Data / restraints/ parameters
2926 [Rint = 0.066]
Multi-scan
2
Full matrix least-squares on F
2926 / 0 / 218
2
Goodness-of-fit on F
1.099
Final [I > 2σ(I)]
R1 = 0.0780, wR2 = 0.1808
R1 = 0.1375, wR2 = 0.2152
0.003(3)
R indices (all data)
Extinction coefficient
Largest diff. peak and hole
−
˚
0.153 and −0.217 e A
³
Table 2
Table 3
Bond lengths.
Bond angles.
˚
˚
Angle (°)
Angle (°)
Length (A)
Length (A)
Atoms
XRD
DFT
Atoms
XRD
DFT
Atoms
XRD
DFT
Atoms
XRD
DFT
C8-N9-C10
C15-N16-C17
C2-C1-C6
123.7(3)
119.3(3)
122.3(3)
118.2(4)
121.3(4)
120.6(4)
121.1(3)
119.8(3)
119.1(3)
121.0(3)
117.8(3)
121.2(3)
122.1(3)
116.4(3)
118.0(3)
125.6(3)
120.9(4)
121.19
121.19
121.27
119.09
121.11
120.16
121.88
199.37
188.75
121.19
119.00
119.82
122.13
124.31
118.81
116.87
121.47
C11-C12-C13
C12-C13-C14
C13-C14-C15
C10-C15-C14
N16-C15-C14
N16-C15-C10
N16-C17-C18
C19-C18-C23
C17-C18-C19
C17-C18-C23
C18-C19-C20
C19-C20-C21
C20-C21-C22
C21-C22-C23
C18-C23-C22
O24-C23-C18
O24-C23-C22
120.9(4)
119.5(4)
120.8(3)
120.0(3)
121.3(3)
118.6(3)
121.8(3)
119.4(3)
119.0(3)
121.6(3)
120.7(4)
119.3(4)
120.8(4)
120.0(4)
119.8(3)
121.9(3)
118.3(3)
199.67
119.67
121.47
118.82
116.87
124.31
122.12
119.00
119.81
121.19
121.26
119.10
121.11
120.17
119.36
121.88
118.76
O7-C5
O24-C23
N9-C8
N16-C17
N16-C15
C1-C6
1.347(5)
1.355(5)
1.273(5)
1.275(5)
1.420(5)
1.404(5)
1.385(6)
1.389(7)
1.369(7)
1.397(6)
1.406(5)
1.446(5)
1.3408
1.3407
1.2930
1.2930
1.4129
1.4092
1.3856
1.4037
1.3888
1.4033
1.4237
1.4490
C10-C15
C10-C11
C11-C12
C13-C14
C14-C15
C17-C18
C18-C23
C18-C19
C19-C20
C20-C21
C21-C22
C22-C23
1.404(5)
1.398(5)
1.380(6)
1.380(5)
1.392(5)
1.456(5)
1.400(5)
1.389(5)
1.382(6)
1.390(7)
1.376(6)
1.385(5)
1.4198
1.4033
1.3907
1.3907
1.4033
1.4491
1.4237
1.4093
1.3855
1.4038
1.3887
1.4033
C1-C2-C3
C2-C3-C4
C3-C4-C5
O7-C5-C6
C4-C5-C6
C1-C2
C2-C3
O7-C5-C4
C5-C6-C8
C3-C4
C4-C5
C1-C6-C5
C5-C6
C1-C6-C8
C6-C8
N9-C8-C6
N9-C10-C15
C11-C10-C15
N9-C10-C11
C10-C11-C12
ues C2-C3-C4-C5 = 0.6(7)°, C3-C4-C5-C6 = 0.3(6)°, C19-C20-C21-
C22 = 1.0(6)°, C20-C21-C22-C23 = −0.1(6)°.
The benzene ring (C10-C11-C12-C13-C14-C15) is also sp2 hy-
bridized and has trigonal planar geometry. The bond angles C10-
C11-C12 = 120.9(4)°, C11-C12-C13 = 120.9(4)° and torsion angle
values are C10-C11-C12-C13 = 0.3(6)°, C12-C13-C14-C15 = 0.7(6)°.
The crystal structure shows intramolecular interactions of the
type O7-H7ꢀN9, O24-H24ꢀN16 and intermolecular hydrogen bond
–
of the type C17-H17ꢀO7 (Table 5). The structure has C Hꢀπ and
π-π interactions. The interaction details are given in Tables 6 and
7 respectively. The molecular packing viewed down b axis is shown
in Fig. 4.
Table 8
Fig. 4. Packing the molecules viewed down the b-axis.
3.3. Hirshfeld surface analysis
fined as
Hirshfeld surface analysis is a valuable tool to elucidate the in-
termolecular interactions in a crystal structure. CrystalExplorer 17.5
[32] software was used to generate the Hirshfeld surface mapped
over dnorm (Fig. 5). The normalized contact distance dnorm is de-
vdw
vdw
di − ri
de − re
dnorm
=
+
,
vdw
vdw
ri
re
4

C. KM, F.H. Al-Ostoot, E.E. Shehata et al.
Journal of Molecular Structure 1244 (2021) 130910
Table 4
Torsion angles.
Angle (°)
Angle (°)
Atoms
XRD
DFT
Atoms
XRD
DFT
C10-N9-C8-C6
C8-N9-C10-C11
C8-N9-C10-C15
C17-N16-C15-C10
C15-N16-C17-C18
C6-C1-C2-C3
179.8(3)
−1.6(6
179.85
−128.90
52.2
N9-C10-C15-C14
C11-C10-C15-N16
C11-C10-C15-C14
C10-C11-C12-C13
C11-C12-C13-C14
C12-C13-C14-C15
C13-C14-C15-N16
C13-C14-C15-C10
N16-C17-C18-C19
N16-C17-C18-C23
C17-C18-C19-C20
C23-C18-C19C20
C17-C18-C23-O24
C17-C18-C23-C22
C19-C18-C23-O24
C19-C18-C23-C22
C18-C19-C20-C21
C19-C20-C21-C22
C20-C21-C22-C23
C21-C22-C23-O24
C21-C22-C23-C18
175.7(3)
175.1(3)
1.1(5)
−177.19
−177.19
3.75
−178.1(3
131.7(3
176.3(3
−0.7(6)
1.0(5)
52.2
0.3(6)
0.5
179.85
−0.04
0.09
−1.1(6)
0.7(6)
0.64
0.50
C2-C1-C6-C5
−175.8(3)
0.4(5)
178.16
−2.71
179.77
−0.35
179.98
0.10
C2-C1-C6-C8
−176.9(4)
−0.1(7)
0.6(7)
179.98
−0.02
0.04
C1-C2-C3-C4
175.8(3)
−4.6(5)
178.1(3)
−1.5(5)
1.9(5)
C2-C3-C4-C5
C3-C4-C5-O7
C3-C4-C5-C6
179.7(4)
−0.3(6)
179.5(3)
−2.5(5)
−0.5(5)
177.5(3)
175.5(3)
−2.4(5)
−175.7(4)
0.8(6)
−179.97
0.01
O7-C5-C6-C1
O7-C5-C6-C8
C4-C5-C6-C1
179.91
0.02
0.02
−177.2(3)
−178.5(3)
2.4(5
−179.96
179.90
−0.08
−0.05
−0.02
0.04
−0.08
−179.96
179.77
−0.34
178.16
−2.71
1.88
C4-C5-C6-C8
C1-C6-C8-N9
C5-C6-C8-N9
N9-C10-C11-C12
C15-C10-C11-C12
N9-C10-C15-N16
−0.2(6)
1.0(6)
−0.1(6)
179.3(3)
−1.6(5)
−179.97
0.01
−8.0(5)
Table 5
nucleus outside and inside the surface respectively [33]. The red
highlighted spots and blue regions on the dnorm surface are from
the short contacts and longer contacts less than the sum of van
der Waals radii respectively.
Hydrogen bond geometry.
˚
˚
˚
Atoms
D - H (A)
HꢀA (A)
D - A (A)
D - HꢀA (°)
O7-H7ꢀN9a
O24-H24ꢀN16a
C17-H17ꢀO7i
0.82
0.82
0.93
1.85
1.89
2.46
2.579(3)
2.618(3)
3.315(4)
148
147
152
Hirshfeld surface mapped for shape index and curvedness is
shown in Fig. 6. The planar stacking arrangements and contact
with the adjacent molecule are visualized from the shape index
and the curvedness mapping. The complementary hollows which is
red in color and blue bumps shows the molecular surfaces touch-
ing each other [34]
i: 1 + x, y, z.
a: intramolecular interactions.
The percentage contribution of intermolecular interactions to
the total surface area of the molecule is visualized by two dimen-
sional fingerprint plots [35]. The fingerprint plots of di and de are
–
–
shown in Fig. 7. The significant contributions are from C H, H H,
–
and O H contacts. The blue - green regions on the fingerprint plots
indicate the π-π interactions.
3.4. Energy frameworks
The interaction energies between the molecular pairs in
a
crystal structure is visualized by energy frameworks. The energy
˚
frameworks were generated for molecules within 3.8 A radius from
the central molecule using CrystalExplorer 17.5 [32] software with
the functional basis set B3LYP/6 −31 G(d, p) [36]. The molecular
pairs involved in the interaction energy calculations are shown in
figure S2. The energy frameworks generated for Coulomb, disper-
sion and total energy are represented by different color cylinders
joining the center of mass of the molecules with cutoff energy 5 kJ
mol−1 (Fig. 8).
Fig. 5. Hirshfeld surface of the molecule mapped for dnorm.
The elecrostatic (−51.89 kJ mol−1), polarization (−10.656 kJ
mol−1), dispersion (−187.87 kJ mol−1), and repulsive (83.61 kJ
mol−1) energy terms gives the total interaction energy (−166.7 kJ
mol−1). Dispersion energy is dominant over electrostatic and polar-
where ri and re are the van der Waals (vdw) radii of the appro-
priate atom internal and external to the surface respectively; de
and di are the distance from a point on the surface to the nearest
Table 6
–
C
Hꢀπ interaction involved in the molecular structure.
˚
˚
˚
–
C Hꢀπ (°)
CꢀH
CgJ
HꢀCg (A)
H⊥ (A)
γ (°)
C-HꢀCg (°)
CꢀCg (A)
C3 – H3
Cg3ii
2.84
2.89
2.83
4.84
9.18
140
163
3.603(7)
3.796(7)
48
73
iii
C21 –H21
Cg2
−2.86
ii: − x, 1 − y, 2 − z
Cg2: C10-C11-C12-C13-C14-C15
iii: 1 − x, 1/2 + y, 3/2 − z
Cg3: C18-C19-C20-C21-C22-C23
5

C. KM, F.H. Al-Ostoot, E.E. Shehata et al.
Journal of Molecular Structure 1244 (2021) 130910
Fig. 6. Hirshfeld surface of the molecule mapped for shape index (a) and curvedness (b).
Fig. 7. Fingerprint plots of the compound showing percentage contributions for the total Hirshfeld surface.
6

C. KM, F.H. Al-Ostoot, E.E. Shehata et al.
Journal of Molecular Structure 1244 (2021) 130910
Table 7
π -π interaction involved in the molecular structure.
˚
˚
˚
CgI
CgJ
CgI-CgJ
α (°)
β(°)
γ (°)
CgI⊥ (A)
CgJ⊥ (A)
Slippage (A)
Cg1
Cg1
Cg2
Cg2
Cg3
Cg3
Cg2iv
Cg3v
Cg1vi
Cg3vii
Cg1viii
Cg2ix
3.769(5)
4.900(7)
3.769(5)
5.150(7)
4.849(7)
5.132(7)
3.30(19)
23.7
8.3
22.1
63.6
23.7
88.4
70.9
85.4
3.4921(16)
2.1823(16)
−3.4510(16)
−0.1441(16)
1.5899(16)
0.4117(16)
−3.4511(16)
4.8495(16)
3.4919(16)
−5.0677(16)
4.5636(16)
−5.0207(16)
1.515
56.84(18)
3.30(19)
–
22.1
10.2
19.7
11.9
1.418
83.42(18)
56.84(18)
83.42(18)
–
–
–
iv: −1 + x, y, z
vii: 1 + x, y,
v: 1 − x, 1 − y, 2 − z
vi: − x, 1- y, 2 − z
viii: 1 + x, 1/2 + y, 3/2 − z
ix: 1 − x, −1/2 + y, 3/ 2 − z
Cg2:C10-C11-C12-C13-C14-C15
Cg1:C1-C2-C3-C4-C5-C6
Cg3: C18-C19-C20-C21-C22-C23
Fig. 8. Graphical representation of the interaction energies Coulomb energy, Dispersion energy and Total energy along a,b, c axes.
Table 8
3.5. Density functional theory
Percentage contributions to the total Hirshfeld
surface area from various intermolecular con-
tacts .
3.5.1. Frontier molecular orbitals
Density functional theory (DFT) calculations were performed
using Gaussian 09 [37] package with B3LYP hybrid functional and
6–31 G (d, p) basis set in gas phase. Molecular orbitals were vi-
sualized in GaussView [38]. The bond length, bond angle, torsion
angles calculated from DFT calculations are in good agreement
with results from single crystal Xray diffraction. Highest occupied
molecular orbital (HOMO) and lowest unoccupied molecular orbital
(LUMO) of the compound are shown in Fig. 9. The energy gap be-
tween LUMO and HOMO is 3.9678 eV.
Intermolecular Contacts
Contribution (%)
H – H
C – H
O – H
C – C
N – H
C – N
45.1
32.3
12.19
5.5
2.3
1.9
The global parameters such as ionization potential, electron
affinity, chemical potential, chemical hardness, electronegativity,
electrophilicity, global softness are listed in Table 10.
ization energies. The lattice energy of the molecule is −137.85 kJ
mol−1
The molecular interaction energies are calculated and
.
The total density of states (TDOS) are created by convoluting
the molecular orbital information with Gaussian curves of unit
listed in table 9 with scale factor k_ele = 1.057, k_pol =0.740,
k_disp=0.871, k_rep =0.618.
7

C. KM, F.H. Al-Ostoot, E.E. Shehata et al.
Journal of Molecular Structure 1244 (2021) 130910
Table 9
Interaction energies of the molecular pairs involved in energy calculation in kJ/mol. R is the distance betweeen molecular
˚
centroids in A and N is the number of molecular pairs involved.
Fig. 10. Molecular Electrostatic Potential Surface.
Fig. 9. HOMO and LUMO of the title compound.
height and full width at half maximum (FWHM) [39] by using the
Gauss-Sum 2.2 program [40]. The plot of TDOS gives the graphical
representation of compositions of the molecular orbital’s and their
contributions to chemical bonding figure S3.
Table 10
Calculated energy values of HOMO, LUMO
and electronic properties of the title com-
pound.
3.5.2. Molecular electrostatic potential
Parameter
Value
The electropositive and electronegative regions of the molecule
are visualized as molecular electrostatic potential surface. The map
gives a spectral display of increasing potential value from red to
blue (Fig. 10). The potential value ranges from −3.895e-2 a.u. (red)
to +3.895e-2 a.u. (blue) for the molecule under discussion. The red
and blue regions on the molecular electrostatic potential surface
indicate electrophilic and nucleophilic regions respectively [41].
Mulliken atomic charges with hydrogen atoms summed into
heavy atoms were calculated using B3LYP / 6 −31 G (d, p) basis
set and plotted (Fig. 11). The nitrogen atoms N9 and N16 are more
ELUMO
−1.8161 eV
−5.7839 eV
3.9678 eV
5.7839 eV
1.8161 eV
−3.8 eV
EHOMO
E
Ionization potential (I)
Electron affinity (A)
Chemical potential μ
Chemical Hardness η
Electronegativity χ
Electrophilicity ω
Global softness σ
1.9839 eV
3.8 eV
3.64 eV
0.50 eV−1
8

C. KM, F.H. Al-Ostoot, E.E. Shehata et al.
Journal of Molecular Structure 1244 (2021) 130910
Fig. 11. Mulliken charge distribution of the title compound.
Fig. 13. RDG plot showing non covalent bond interactions in the title compound.
using Multiwfn software and visualized in VMD (Visual Molecular
Dynamics) software [45]. From the Fig. 13 one can observe that
the title molecule displayed strong attractions around the nitrogen
atoms, strong repulsions in the six membered rings, and van der
Waals interactions occured between two nitrogen atoms.
Fig. 12. Intramolecular interactions of the title compound from AIM theory.
Multiple spikes are found in the scatter density plot (Fig. 13).
These spikes are divided in to three regions according to the values
of sign (λ2)ρ. These regions are identified by different colours. The
spikes that lie in the low density region indicates the H-bond inter-
action present in the molecule. Blue colored isosurfaces which lie
between H7 and N9, H24 and N16 atoms respectively signify the
characteristics of strong H-bond interaction. Due to the high elec-
tronegative nature of oxygen and electropositive nature of nitro-
gen, a strong interaction which is attractive in nature, is observed
in the molecule. In Fig. 13, green colored isosurface lies between
the two nitrogen atoms and signifies the presence of weak H-bond
interaction. The red colored isosurfaces indicate the steric effect
present in the ring due to strong repulsions.
electronegative and carbon atoms C5, C17, C8 are more electropos-
itive [42].
3.5.3. Atoms in molecule (AIM) theory
The topological analysis of atoms in molecule (AIM) gives the
information about the presence of strong and weak hydrogen
bonds. AIM analysis is used to find the intramolecular hydro-
gen bond interactions through bond critical paths. AIM analysis
was performed using Multiwfn 3.7 [43] program to examine the
non-covalent interactions of the title molecule. Neighboring atoms
which are chemically bonded or those atoms that have weak in-
teractions appear in the Bond Critical Paths (BCP). The topology
analysis of AIM was done to search all the bond critical points.
The paths generated are shown in Fig. 12. The presence of BCP
validates the O7-H7ꢀN9 and O24-H24ꢀN16 intramolecular inter-
actions which are also obtained from XRD analysis.
4. Conclusion
The title compound exhibits short intermolecular interactions
C17-H17ꢀO7 and intramolecular interactions O7-H7ꢀN9 and O24-
–
3.5.4. Reduced density gradient (RDG) analysis
H24ꢀN16. The packing of the molecules is reinforced by C Hꢀπ
RDG analysis is used to explore the non-covalent bond interac-
tions present in the molecule [44]. The non -covalent bond inter-
actions are visualized by plotting RDG vs electron density (ρ). The
strong attractions, van der Waals interactions, and strong repul-
sions are distinguished in Fig. 13. The calculations were performed
and π- π interactions. From Hirshfeld surface analysis fingerprint
plot shows that the major contribution for total Hirshfeld surface
–
area is from H H contacts (45.1%). Interaction energy calculations
reveal that dispersion energy is dominant. Density function theory
calculations show that the energy gap between HOMO and LUMO
9

C. KM, F.H. Al-Ostoot, E.E. Shehata et al.
Journal of Molecular Structure 1244 (2021) 130910
is 3.9678 eV. MEP map and Mulliken charge analyses show reactive
sites present in the molecule. The intramolecular interactions are
validated using AIM calculations. RDG analysis reveals the presence
of weak interactions, strong attractions, and strong repulsions in
the title compound.
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Declaration of Competing Interest
The authors declare that they have no known competing finan-
cial interests or personal relationships that could have appeared to
influence the work reported in this paper. This manuscript has not
been submitted to, nor is under review at, another journal or other
publishing venue. The authors have no affiliation with any orga-
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CRediT authorship contribution statement
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Chandini KM: Formal analysis, Writing - review & editing.
Fares Hezam Al-Ostoot: Formal analysis, Writing - original draft.
Eman E. Shehata: Investigation, Methodology. Nuha Y. Elamin: In-
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Acknowledgment
Chandini K.M. thanks to MMK and SDM Mahila Maha Vidyalaya
for their support. Fares Hezam Al-Ostoot is thankful to the gov-
ernment of Yemen and Al-Baydha University, Al-Baydha, Yemen,
for providing financial assistance under the teacher’s fellowship
and University of Mysore, Mysuru, India, Eman E. Shehata, Nuha
Y. Elamin and Hela Ferjaniare thankful to the Imam Mohammad
Ibn Saud Islamic University, Riyadh, Saudi Arabia for providing fi-
nancial support.
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Supplementary materials
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M.B. Gawande, S.N. Shelke, Synthesis and evaluation of anticonvulsant activ-
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Supplementary material associated with this article can be
found, in the online version, at doi:10.1016/j.molstruc.2021.130910.
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