Novel 1,3,4-oxadiazole linked benzopyrimidinones conjugates: Synthesis, DFT study and antimicrobial evaluation

Article abstract of DOI:10.1016/j.molstruc.2020.128357

This work describes the synthesis, characterization and antimicrobial evaluation of a series of new 1,3,4-oxadiazole linked benzopyrimidinones. Their structures were confirmed on the basis of ¹H, ¹³C NMR and ES-HRMS analysis. Their molecular geometry are also studied theoretically by the Density Functional Theory (DFT) method with B3LYP/6–31++G (d,p). All the calculations were done in DMSO, using conductor like polarizable continuum (CPCM). The target compounds were screened for their antimicrobial activity against four types of pathogenic bacteria and three fungal strains. Biological results revealed that some of these compounds demonstrated excellent to moderate antimicrobial activities with minimum inhibitory concentration (MIC) values ranging from 10.8 to 140.7 μM. Notably, compounds 5g and 5h showed the highest inhibitory activity against all bacterial strains with MIC values ranging from 111.3 to 10.8 μM against S. aureus, E. coli and P. aeruginosa, and displayed a good antifungal activity against C. albicans with MIC values of 10.8 and 27,8 μM, respectively. The structure-activity relationship (SAR) was discussed.

Full text of DOI:10.1016/j.molstruc.2020.128357

Journal Pre-proof
Novel 1,3,4-oxadiazole linked benzopyrimidinones conjugates: Synthesis, DFT study
and antimicrobial evaluation
Sarra Chortani, Hayet Edziri, Marwa Manachou, Youssef O. Al-Ghamdi, Sami G.
Almalki, Yaser E. Alqurashi, Hichem Ben Jannet, Anis Romdhane
PII:
S0022-2860(20)30682-7
DOI:
https://doi.org/10.1016/j.molstruc.2020.128357
MOLSTR 128357
Reference:
To appear in: Journal of Molecular Structure
Received Date: 12 March 2020
Revised Date: 12 April 2020
Accepted Date: 27 April 2020
Please cite this article as: S. Chortani, H. Edziri, M. Manachou, Y.O. Al-Ghamdi, S.G. Almalki, Y.E.
Alqurashi, H. Ben Jannet, A. Romdhane, Novel 1,3,4-oxadiazole linked benzopyrimidinones conjugates:
Synthesis, DFT study and antimicrobial evaluation, Journal of Molecular Structure (2020), doi: https://
doi.org/10.1016/j.molstruc.2020.128357.
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© 2020 Published by Elsevier B.V.

Sarra Chortani did the synthesis work. Hayet Edziri tested the antimicrobial activity. Marwa
Manachouperformed the DFT study. Youssef O. Al-Ghamdi helped in the structure analysis. Sami G.
Almalki helped in the interpretation of biological results. Yaser E. Alqurashi guided some biological
assays. Hichem Ben Jannet contributed to the discussion of the results and completed the redaction
of the manuscript. Anis Romdhane was the supervisor of the present work, he also checked the
structure determination of the synthesized compounds and the biological study, and he completed
the redaction of the article.

Graphical abstract

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Novel 1,3,4-oxadiazole linked benzopyrimidinones conjugates:
Synthesis, DFT study and antimicrobial evaluation
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Sarra Chortania, Hayet Edzirib, Marwa Manachouc, Youssef O. Al-Ghamdid,*, Sami G.
Almalkie, Yaser E. Alqurashie, Hichem Ben Janneta, Anis Romdhanea,*
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aLaboratory of Heterocyclic Chemistry, Natural Products and Reactivity, Team: Medicinal
Chemistry and Natural Products (LR11ES39), Department of Chemistry, Faculty of Science
of Monastir, University of Monastir, Avenue of Environment, 5019 Monastir, Tunisia.
bLaboratory of Transmissible Diseases and Biologically Active Substances, Faculty of
Pharmacy, 5000 Monastir, Tunisia
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cLaboratory of Material Characterization, Applications and Modeling,
Faculty of Science of Tunis, University of Tunis El Manar, 2092, Tunis, Tunisia
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dDepartment of Chemistry, College of Science Al-zulfi, Majmaah University, Al-Majmaah,
11952, Saudi Arabia
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eDepartment of Biology, College of Science Al-zulfi, Majmaah University, Al-Majmaah,
11952, Saudi Arabia
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*Corresponding authors. A. Romdhane (T Tel.: +21673500279, Fax: +21673500278; E-mail:
anis_romdhane@yahoo.fr). Y O. Al-Ghamdi (Tel.: +966164044094, Fax: +966164044094; E-
mail: yo.alghamdi@mu.edu.sa).
Abstract:
This work describes the synthesis, characterization and antimicrobial evaluation of a series of
new 1,3,4-oxadiazole linked benzopyrimidinones. Their structures were confirmed on the
1
basis of H, 13C NMR and ES-HRMS analysis. Their molecular geometry are also studied
theoretically by the Density Functional Theory (DFT) method with B3LYP/6-31++G(d,p). All
the calculations were done in DMSO, using conductor like polarizable continuum (CPCM).
The target compounds were screened for their antimicrobial activity against four types of
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pathogenic bacteria and three fungal strains. Biological results revealed that some of these
compounds demonstrated excellent to moderate antimicrobial activities with minimum
inhibitory concentration (MIC) values ranging from 10.8 to 140.7 µM. Notably, compounds
5g and 5h showed the highest inhibitory activity against all bacterial strains with MIC values
ranging from 111.3 and 10.8 µM against S. aureus, E. coli and P. aeruginosa, and displayed a
good antifungal activity against C. albicans with MIC values of 10.8 and 27,8 µM,
respectively. The structure-activity relationship (SAR) was discussed.
Keywords: benzopyrimidinone, 1,3,4-oxadiazole, antibacterial, antifungal, DFT
1. Introduction
Heterocyclic compounds furnish a basic platform for the building of newer entities and have
captured wide spread interest because of their abundance in natural products and their diverse
biological properties [1]. Amongst all, heterocyclic molecules containing nitrogen and oxygen
are known to display interesting biological activities [2]. In this framwork, pyrimidinones
cores have demonstrated a broad spectrum of biological properties including anticancer [3],
anti-acetylcholinesterase [4], antityrosinase [5], antibacterial [6] and antifungal [7].
Furthermore, pyrimidine molecules have become an important building blocks for the
development of new commercial drugs such as Trimethoprim (antimicrobial) (Fig. 1),
Metioprim (antibacterial) (Fig. 1) and Flucytosine (antifungal) (Fig. 1)[8].
In the other hand, oxadiazoles and their derivatives are very attractive targets on account of
their diverse biological properties such as cytotoxic [9], antibacterial [10], antioxidant [11]
and anti-inflammatory activities [12]. Particularly, 1,3,4-oxadiazoles core has aroused
considerable attentions on account of its derivatives are characterized with a wide range of
biological activities, including anti-diabetic [13], anti-malarial [14], antimicrobial [15],
anticancer [16], analgesic [17] and anti-inflammatory [18]. Moreover, this fragment is present
in skeleton of several important commercialized medicinal derivatives such as Raltegravir
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(antiretroviral agent) [19] (Fig. 1), Zibotentan (anticancer drug) [20](Fig.1), Fenadiazole
(hypnotic drug) [21] (Fig. 1), and Nesapidil (antihypertensive agent) [22](Fig. 1).
The diverse biological properties of these heterocyclic scaffolds prompted us to continue to
the development of highly antimicrobial bioactive molecules. In this context, a new series of
1,3,4-oxadiazole linked benzopyrimidinones were synthesized and evaluated for their in vitro
antimicrobial activity. To support the experimental results, the synthesis of these new hybrid
molecules is described through DFT calculations at the B3LYP/6–31 ++G(d,p) level of
theory. The reactivity of these series of compounds was studied using hardness, softness and
global electrophilicity index as well as the FMO theory.
O
HN
N
O
NH2
N
S
N
NH2
O
O
NH2
N
F
N
O
H2N
flucytosine
NH2
O
metioprim
Trimethoprim
R1
H3CO
N
N
N
O
N
N
O
N
CH3
N
O
S O
N
O
O
N
NH
N
O
N
N
HO
N
O
R
N
Design prototype
Zibotentan
Nesapidil
O
N
OH
N
OH
F
N
N
O
H
H
N
N
O
N
O
Fenadiazole
Raltegravir
61
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63
Fig. 1. Representative examples of biologically active drugs containing pyrimidine and 1,3,4-
oxadiazole derivatives.
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2. Experimental section
2.1. General information
All reactions were monitored by TLC using aluminium sheets of Merck silica gel 60 F254,
0.2 mm. Melting temperatures were determined on an electrothermal 9002 apparatus and were
reported uncorrected. NMR spectra were recorded on a Bruker AC-300 spectrometer at 300
MHz (1H) and 75 MHz (13C). All chemical shifts were reported as δ values (ppm) relative to
residual non deuterated solvent. High Resolution Mass Spectra (ES-HRMS) were obtained
with Micromass LCT (ESI technique, positive mode) spectrometers.
2.1.1. General procedure for the synthesis of 2-aryl-benzopyrimidinone 2
A mixture of 2-aminobenzamide 1 (5 mmol) and substituted aromatic aldehydes (5 mmol)
was heated under reflux for 24 h in dry acetonitrile (50 mL) in the presence of equimolar
molecular of iodine. After the reaction was completed, the mixture was cooled to room
temperature. A solution of sodium thiosulphate (5%) was added and the resulted solid was
filtered off and washed with water. The crude product was recrystallized from ethanol.
2.1.2. General procedure for preparation of hydrazides 3
Equimolar solution 1mmol of 2-arylbenzopyrimidinones 2, anhydrous potassium carbonate
and ethyl chloroacetate was refluxed in dry DMF (40 mL) with continuous stirring for 6 h.
The reaction mixture was allowed to cool and then it was poured in water and extracted using
EtOAc. The organic layer was dried over anhydrous MgSO4. After evaporation of the solvent,
the residual was treated with an excess of hydrazine hydrate in ethanol at room temperature
for 1 hour. The precipitated solid formed was filtered, washed with ethanol, and dried to
obtain compounds 3a-c.
2.1.3. General procedure for the synthesis of compounds 5
Equimolar solution (1mmol) of hydrazide 3 and the arylaldehyde was refluxed in dry ethanol
(15 mL) for 2 h under argon atmosphere. The white precipitate formed thus obtained was
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filtered to afford compounds 4 which were refluxed by potassium carbonate (1mmol) in
dimethyl sulphoxide at 100°C in the presence of catalytic amount of iodine for 8 h. After the
reaction was completed, the solvent was evaporated and the residue thus obtained was
purified by column chromatography (silica gel, PE /EtOAc 8:2) to give compounds 5a-o.
2.2. In vitro Antimicrobial Activity
2.2.1. Microorganisms
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The microorganisms tested in this work were S. aureus (ATCC 25923), E. coli (ATCC25922),
P. aeruginosa (ATCC 27950), and E. faecalis (ATCC 29212). The antifungal activity was
tested against three pathogenic reference yeasts including Candida albicans ATCC 90028, C.
glabrata ATCC 90030 and C. parapsilosis ATCC 22019.
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2.2.2. Micro-well dilution assay
Minimum inhibitory concentration (MIC) values were determined by a micro dilution method
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[23]. All product stock solutions were dissolved in 10% dimethyl sulfoxide (DMSO). The
inocula of the bacteria and yeasts were prepared from 12 h broth cultures and suspensions
were adjusted to 0.5 McFarland standard turbidity. Media were placed into each 96 wells of
the microplates. Test solutions at 500 µg/mL were added in the first rows of the microplates
and two-fold dilution of the compounds (250–0.125 µg/mL) were made by dispensing the
solutions to the remaining wells. Ten microliter culture suspensions were inoculated into all
the wells. The plate was covered with a sterile plate sealer and then incubated for 18 h at 37
°C. Ampicillin and Griseofulvin (for bacteria and fungi), and Amoxicillin (for bacteria) were
used as standard antibiotics. All tests were performed in triplicate. The MIC was defined as
the lowest concentration of the compounds that inhibits the growth of microorganisms after
incubation.
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2.3. Computational details
The optimization of all geometries was performed by density functional theory using the
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Gaussian 09 set of programs [24]. Geometry optimization of all products was carried out
using DFT methods at the B3LYP/6-31++G(d,p) level of theory [25]. For these systems, we
carried out full geometry optimization in the C1 point group, followed by harmonic
frequencies simulations to confirm that they correspond to true minima (all positive
frequencies). All the calculations were done in DMSO, using conductor like polarizable
continuum (CPCM). The conceptual DFT descriptors [26-28] have been computed using the
so-called frozen core approximation and the Koopmans’ theorem [29]. Thus, global indexes
have been calculated using frontier densities, frontier energies[30-32] such as the chemical
potential μ ≅ (Eꢀꢁꢂꢁ + Eꢃꢄꢂꢁ)/2 [33], hardness η ≅ (Eꢃꢄꢂꢁ − Eꢀꢁꢂꢁ) and the
electrophilicity index ω= μꢅ/2η[34-36]. Molecular structure drawings and spin densities
plots were generated using the ADF-GUI auxiliary program [37a,b,c,d].
3. Results and discussion
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3.1. Synthesis
The synthetic route, used for the synthesis of a new 1,3,4-oxadiazoles linked
benzopyrimidinones is depicted in Scheme 1. Initially, the first step involved the formation of
benzopyrimidinones derivatives, which were efficiently generated by the condensation
reaction of 2-aminobenzamide 1 with various substituted aromatic aldehydes in the presence
of equimolar molecular iodinein acetonitrile [3]. The structures of the formed
benzopyrimidinones 2a-c were characterized by their 1H NMR and 13C NMR spectra. In fact,
1
the H NMR spectra showed, in addition of the signals corresponding to the protons
introduced by the arylaldehyde and the 2-aminobenzamide moiety, the presence of the singlet
at 12.26 - 12.53 ppm due to the NH proton. Unambiguous proofs for the obtained compounds
aroused from their 13C NMR data. Particularly the shift-values attributed to the quaternary
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152
153
154
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158
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161
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163
carbons C-2 (151.4 - 151.9 ppm) and C-4 (162.2 - 162.3 ppm) were consistent with the strong
deshielding effects caused by heteroatom's proximity.
Esterification of benzopyrimidinones 2a-c with ethyl chloroacetate in DMF in the presence of
potassium carbonate gave the synthesized esters, which were converted to the corresponding
hydrazides 3a-3c by stiring with hydrazine hydrate in ethanol at room temperature, in good
1
yields [38-39]. The structures of 3a-3c were ascertained by their H NMR spectra showing a
new singlet at 5.11-5.14 ppm relative to the methylene group (N-CH2-) and the presence of a
new two singlets due to mobile protons NH and NH2 at 9.48-950 and 3.65-4.32 ppm,
respectively. The 13C NMR spectra of compounds 3a-3c showed the appearance of new
signals at 64.1-64.3 and 166.1-166.3 ppm attributed to the methylene carbon (CH2) and C=O,
respectively.
In addition, the synthetic hydrazides 3a-3c were reacted with substituted aromatic aldehydes
in dioxane affording the hydrazones 4a-4o which were cyclized in situ, in presence of iodine
and potassium carbonate in dimethyl sulphoxide, to give the desired 1,3,4-oxadiazole
derivatives 5a-5o [40]. The physical properties of compounds 5a-5o are shown in Table 1.
The structures of the target compounds 5a-5o were confirmed by their spectral data (1H and
1
13C NMR and ES-HRMS). In fact, the H NMR spectra of these compounds exhibited the
absence of two singlets related to the mobile protons (NH and NH2), the presence of a singlet
corresponding to the methylene group (CH2) at 5.91-6.06 ppm and the appearance of a new
characteristic signals at 6.61-8.56 ppm attributable to the aromatic protons introduced by
aromatic aldehyde. In the 13C-NMR spectra of these products, we observed essentially the
appearance of two new signals attributable to C-2 and C-5 carbons of the oxadiazole ring at
158.5-165.9 ppm and the disappearance of a signal at 166.1-166.3 ppm corresponding to the
carbonyl of the hydrazid group (C-16). Moreover, high resolution mass spectrometry (ES-
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HRMS) data of all the examined compounds 5a-5o were also in agreement with the proposed
structures.
O
4
O
O
5
4a
3
6
NH2
NH2
NH
H
CH3CN
I2
10
13
+
9
7
11
12
8a
N
1
R
2
8
1
14
R1
R
2a-c
NH2
NH
1. Cl-CH2COOEt
K2CO3 / DMF
N
O
O
O
NH
O
16
15
2. NH2-NH2
EtOH
O
16
15
5
3
N
4a
5
R1
H
6
4
4a
3
6
7
4
N
10
ETOH
7
9
10
11
12
2
N
1
9
8a
11
12
2
8
N
1
8a
8
14
R
14
13
R
3a-c
4a-o
13
R1
R= H, Cl, OCH3
5'
2'
4'
N
K2CO3/ I2
DMSO
3'
N
O
1'
7'
O
4
6'
8'
9'
R2
5
8
4a
8a
H
15
10
3
6
7
N
11'
CH3
Cl
10'
O
R1
R2
9
11
12
2
N
1
6'
7'
9'
8'
OCH3
14
R
13
5a-o
166
167
Scheme 1. Synthetic route of benzopyrimidinones linked 1,3,4-oxadiazoles 5a-o.
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Table 1. Structures and yields of compounds 5a-o.
Substituent
Compounds
R
H
H
H
H
H
Cl
Cl
R1
C6H5
Yields %
66
74
60
77
63
65
74
5a
5b
5c
5d
5e
5f
4-CH3-C6H4
4-Cl-C6H4
4-OCH3-C6H4
furyl
C6H5
4-CH3-C6H4
5g
8

Cl
4-Cl-C6H4
4-OCH3-C6H4
furyl
61
78
62
69
79
64
80
68
5h
5i
Cl
Cl
5j
OCH3
OCH3
OCH3
OCH3
OCH3
C6H5
5k
5l
4-CH3-C6H4
4-Cl-C6H4
4-OCH3-C6H4
furyl
5m
5n
5o
170
171
172
173
174
3.2. Biological activity
The synthesized compounds 2a-c, 3a-c and 5a-o were screened for their in vitro antibacterial
and antifungal activity.
3.2.1 In vitro Antibacterial activity
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The antibacterial activity of the target compounds was assayed in vitro against Gram-positive
bacteria, namely, Staphylococcus aureus (S. aureus) and Enterococcus faecalis (E. faecalis),
and Gram-negative bacteria, namely, Pseudomonas aeruginosa (P. aeruginosa), and
Escherichia coli (E. coli). The minimum inhibitory concentration (MIC) was defined as the
lowest concentration of the product inhibiting the visible growth of each microorganism
which was ascertained by the broth microdilution method.
The results presented in Table 2 showed that most compounds from the series 2a-c and 3a-c
were found to have slight to moderate antibacterial against the four tested bacteria compared
to the reference antibiotics (Ampicillin and Amoxicillin).On the other hand, compounds 5a-o
showed in most cases interesting antibacterial potential. The compound 5c displayed
significant antibacterial activity against E. coli and P. aeruginosa with MIC values of 45 and
22.5 µM, respectively compared to the reference antibiotics. The results showed that
compound 5g exhibited a good activity against all the strains used with MIC values ranging
from 10.8 to 21.7µM. This finding shows that the presence of a chlorine atom in para position
in the phenyl group introduced by the arylaldehyde, used in the first step of the synthesis,
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seems at the origin of the high activity. This conclusion was reinforced by the weak activity of
the derivative 5b where only the chlorine atom has been changed by a hydrogen atom. The
compound 5h displayed an interesting activity against S. aureus and E. faecalis with MIC
value of 27.8µM. The existence of two chlorine atoms in this molecule may be at the origin of
the noted antibacterial activity. The activity of this derivative compared to that of 5c (MIC =
90.1µM against S. aureus and E. faecalis) where the chlorine atom introduced by the
arylaldehyde is replaced by a hydrogen atom can explain the effect of this halogen on the
antibacterial activity. Compounds 5j and 5o were found to be active towards S. aureus and E.
faecalis with MIC values of 71.3 and 87.4, respectively. The activity of these two derivatives
(5j and 5o), compared to certain analogs, could be explained by the presence in each one of a
furyl ring.
Table 2. In vitro Antibacterial activity of synthesized compounds 2a-c, 3a-c and 5a-o
MIC(µM)
Gram-positive bacteria
Gram-negative bacteria
Staphylococcus
aureus
ATCC 25923
Enterococus Eschericha Pseudomonas
faecalis
ATCC
29212
337.7
390.5
247.9
255.0
106.6
192.8
131.5
253.7
90.1
coli
ATCC
25922
337.7
390.5
123.9
255.0
106.6
192.8
263.0
253.7
45.0
aeruginosa
ATCC 27853
Compounds
337.7
390.5
247.9
255.0
106.6
192.8
131.5
253.7
90.1
337.7
195.2
123.9
255.0
106.6
96.4
131.5
126.8
22.5
2a
2b
2c
3a
3b
3c
5a
5b
5c
5d
5e
5f
5g
5h
5i
5j
5k
5l
121.8
135
181.1
10.8
27.8
140.7
121.8
135.0
181.1
10.8
27.8
140.7
121.8
135.0
181.1
21.7
111.3
140.7
154.6
152.3
117.8
140.7
113.5
121.8
67.5
181.1
10.8
27.8
70.3
154.6
152.3
117.8
140.7
113.5
77.3
77.3
152.3
117.8
140.7
113.5
152.3
117.8
140.7
113.5
5m
5n
10

87.4
71.5
-
87.4
-
0.27
174.9
28.62
70.0
87.4
28.62
-
5o
Ampicillina
Amoxicillina
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203
a positive control
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222
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3.2.2 In vitro Antifungal activity
The in vivo fungicidal results of the synthesized compounds 2a-c, 3a-c and 5a-o against
Candida parapsilosis (C. parapsilosis), Candida albicans (C. albicans) and Candida glabrata
(C. glabrata) were presented in Table 3. The most synthesized compounds displayed variable
degrees of inhibition against the three yeasts used. Griseofulvin and Ampicillin were used as
standard antifungal agents.
However, Compounds 2a-c, and 3a-c did not show any interesting activity towards the used
fungal strains by comparison with the positive controls employed.
On the other hand, certain derivatives from the series 5a-o exhibited a promising antifungal
activity against C. albicans with MIC values ranging from of 140.7 (5n) and 10.8 (5g) µM
compared to Griseofulvin (MIC = 141.7µM).
Compound 5g, the only derivative among those having R = chlorine, has a fairly high activity
(MIC = 10.8µM) against the three fungi used. The coexistence of this chlorine atom and the
4-CH3-C6H4- group in the same molecule can explain this strong activity compared to other
analogs bearing in each case a chlorine with a C6H5-(5f), 4-Cl-C6H4-(5h), 4-OCH3-C6H4- (5i)
and furyl (5j). The substitution of the chlorine atom in 5g by a hydrogen atom in compound
5b significantly attenuated this activity which goes from 10.8 µM to 45.0 µM against C.
parapsilosis, C. albicans and to 90.1µM towards C. glabrata. The activity of compound 5h
against C. albicans with an MIC value of 27.8 µM can be also interpreted by the coexistence
of the two chlorine atoms in both aromatic rings.
With respect to the structure-activity relationship (SAR), The results indicated that the
presence of a chlorine atom in the aromatic ring and the introduction of methyl or chlorine
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group in the phenyl ring of the 1,3,4-oxadiazole system were in favor of the high activity of
compounds 5g and 5h.
Table 3. In vitro Antifungal activity of synthesized compounds 2a-c, 3a-c and 5a-o
229
230
231
MIC(µM)
C. parapsilosis
ATCC 22019
337.7
C. albicans
ATCC 90028
337.7
C. glabrata
ATCC 90030
337.7
Compounds
2a
2b
195.2
195.2
195.2
123.9
255.0
106.6
123.9
255.0
106.6
247.9
255.0
106.6
2c
3a
3b
192.8
131.5
96.4
131.5
192.8
131.5
3c
5a
45.0
63.4
121.8
67.5
45.0
126.8
121.8
67.5
90.1
126.8
5121.8
67.5
5b
5c
5d
5e
5f
181.1
181.1
181.1
10.8
55.6
140.7
77.3
152.3
117.8
10.8
27.8
70.3
154.6
152.3
117.8
10.8
55.6
140.7
77.3
76.1
117.8
5g
5h
5i
5j
5k
5l
140.7
113.5
87.4
-
140.7
113.5
87.4
141.7
-
140.7
113.5
174.9
-
5n
5m
5o
Griseofulvina
Ampicillina
0.143
0.143
232
233
apositive control
234
235
236
237
238
239
3.3. DFT study
In order to understand the behavior of molecules in reactions, it is advisable to use reliable
theoretical reactivity indices based on computational chemistry methods to interpret
experimental data. The density functional theory DFT [41] is the most often used quantum
chemical methods because of its low cost and satisfactory performance.
Equilibrium structure and Vibrational analysis of benzopyrimidinone:
12

240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
Figure 2 and Table 4 show the main geometrical parameters of the optimized equilibrium
geometry of benzopyrimidinone considered as the core of the prepared molecules. These data
are obtained using B3LYP method in conjunction with the 6-31G++ (d,p) basis sets. Close
examination of these structures shows that the benzopyrimidinone moiety within these
compounds has very close structure. Indeed, C=O, C-C, C-N and N-H distances of 1.23, 1.46,
1.39, 1.01 (all values are in Å), respectively, have been computed. The deviations between
the distances and the angles calculated using B3LYP are less than 0.01 Å and less than 1°.
Thus, the functionalization of this heterocycle (benzopyrimidinone) slightly disturbs its
structure. This is confirmed by the vibrational analysis performed for this series. Anharmonic
frequencies can be obtained after scaling the corresponding harmonic frequencies by the
appropriate scaling factor (by 0.9662 for ω> 1000 cm-1 and by 0.9833 for ω< 1000 cm-1) as
discussed in Ref. [42]. Table 5 presents the respective data for C=N, C=O and NH
elongations. This table shows that similar C=N (of~1557 cm-1), C=O (of ~1641 cm-1), NH (of
~3476 cm-1) elongations values are computed for all the compounds. Indeed, these differ by
less than 5 cm-1 within the series. This little difference cannot be considered as significant for
reactivity.
2a
2b
2c
Figure 2. 3D structures and bond lengths (in Å) of benzopyrimidinone obtained using B3LYP/6-31G++ (d,p)
13

Table 4. Valence angles (in degree) of benzopyrimidinone derivatives computed using B3LYP/6-31G++
(d,p)
Angles
2a
2b
2c
C3-N15-C12 118.1 118.1 118.2
N15-C12-N14 122.2 122.3 121.9
C12-N14-C9 124.8 124.7 124.9
N14-C9-C4
C9-C4-C3
113.4 113.4 113.5
118.5 118.5 118.4
O13-C9-N14 120.3 120.3 120.3
256
257
258
259
Table 5. Scaled anharmonic vibrational frequencies (in cm-1) (scaling factor 0.9662 42) of
some elongation modes of benzopyrimidinone derivatives as computed using B3LYP/6-
31++G(d,p).
Compounds
2a
2b
2c
Assignement
C=O
NH
1641.3
3476.5
1557.8
1643.6
3477.6
1542.4
1640.1
3475.8
1541.0
C=O stretching
N–H stretching
C=N stretching
C12=N
260
261
262
263
264
265
266
Chemical reactivity of synthesized compounds 2a-c, 3a-c and 5a-o
To investigate the relation between electronic parameters and experimental results, the
electronic parameters of these compounds have been calculated. The energies of HOMO and
LUMO are related to the reactivity of the molecule. For instance, molecules with electrons at
accessible (near-zero) HOMO levels tend to be good nucleophiles because donation of these
electrons toward making a new bond is easy. Similarly, molecules with low LUMO energies
14

267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
tend to be good electrophiles because placing an electron into such an orbital is facilitated.
Both properties can be connected via the energy gap (∆E) between the HOMO and the
LUMO.ΔE = ELUMO − EHOMO showkinetically stability of the molecules. Figures 3-5 shows
the dispersion of the HOMO, LUMO orbitals calculated with DFT methods at the B3LYP/6-
31++G(d,p) level of theory.
The HOMO and LUMO distributions of phenylquinazolinone and their derivatives of group I
II and III are illustrated in Figures 3-5. As shown in this figures, the LUMO distributions are
almost the same, while the HOMO distributions are different. The HOMO distributions are
localized around quinazolinone, which is most important part among involving constituents in
the antibacterial and antifungal activity. These characteristics may be helpful for a qualitative
understanding of the electrostatic interactions that may take place between reagents or
enzyme active sites and the phenylbenzopyrimidinone derivatives under study.
On the other hand, electron-donating like (Cl, CH3…) groups delocalize the HOMO all over
the molecules, which support, in most cases, the activity of the corresponding compounds.
Concerning the value of the energy of the gap ΔE, the larger values of the energy difference
will provide the low reactivity to a chemical species. The chemical hardness, electronic
chemical potential and electronegativity are also important tools to study stability or reactivity
of species. Regarding to the Pearson’s maximum hardness principle [43] which shows the
relation between energy and chemical hardness. All structures, which have the lowest value of
chemical hardness and energy gap, are the highest reactivity species.
In this context, Table 6 shows that 2-phenylbenzopyrimidin-4(3H)-one 2a has a large energy
gap (4.530 eV) compared to 2c (4.381 eV). According to these data we can conclude that the
2-(4-methoxyphenyl) benzopyrimidin-4(3H)-one 2c is softer and more reactive and less stable
in comparison with the other analogsfrom the series 2. The result is the same for the other
series. Indeed, as shown in Tables 7-9, the compounds 3c, 5m (R=OCH3, R1=4-Cl-C6H4) and
15

292
293
294
295
296
297
298
299
300
301
302
303
5o (R=OCH3, R1=furyl)) have the lowest energy gap (4.653, 4.360 and 4.521eV, respectively)
and the lowest hardness (2.326, 2.180 and 2.260 eV, respectively) compared to the other
derivatives in their respective series. These findings were found to being agreement with the
results of biological activity. Therefore, the lowest chemical hardness, the energy gap, and the
highest chemical potential for these molecules, make these them a most active species in their
respective groups. All other descriptors converge to the same result.
A distinct feature of the systems containing electron-donating group is the small HOMO-
LUMO gap which can be correlated with a stronger reactivity [44] as was observed in the
antibacterial and antifungal activity. This small interval is always related to the substitution of
a donor group whatever the series studied in our case we find it at the level of 2c, 3c and 5o
(Figures 3-5). Indeed, energy gap descreases when a electro-donor group is substituted at the
radicals, in a case of 3a-c (∆E= 4.87, 4.82, 4.65 eV, respectively). As can be seen, compound
304
305
306
307
308
309
310
311
312
313
3c has the smallest energy gap (∆E= 4.65 eV). Thus, this compound is the most reactive one
in this series.
Therefore, electron-donating like (Cl, OCH3…) groups substituted in para position of the
phenylquinazolinone core, according to their softness improve the antimicrobial activity and
their reactivity [45]. This order is proportion to the reaction yield and to the biological activity
noted. In fact, compounds 5g shows a good activity against all the strains used with MIC
values ranging from 10.8 to 21.7 µM. In overall, this result supports the experimental trend.
So to increase the value of the activity, we can decrease the ELUMO value, for which we
suggest the substitution of the phenylquinazolinone core with a stronger donor electron ability
group.
16

2a
2b
2c
Figure 3. The frontier molecular orbitals of group (I)
17

3a
3b
3c
Figure 4. The frontier molecular orbitals of group (II)
18

LUMO
(-1.86 eV)
eV
(-6.57 eV)
HOMO
5 e
5 j
5 o
Figure 5. The frontier molecular orbitals of group (III)
19

Table 6. Frontier orbital energy HOMO, LUMO, energy gap (∆E), the global reactivity descriptors (µ, η, S, w) in eV, and yields of reaction for
group (I)
S(eV-1)
0.220
0.225
0.228
entry
2a
yield %
55
R
H
EHOMO
-6.515
-6.529
-6.226
ELUMO
-1.984
-2.092
-1.845
χ
µ
η
ω
4.250
4.310
4.036
-4.250
-4.310
-4.036
2.265
2.218
2.190
3.987
4.187
3.718
Cl
2b
60
OMe
2c
68
Table 7. Frontier orbital energy HOMO, LUMO, energy gap (∆E), the global reactivity descriptors (µ, η, S, w) in eV, and yields of reaction for
group (II)
yield
S(eV-1)
entry
R
EHOMO
ELUMO
χ
µ
η
ω
%
58
64
72
-6.588
-6.688
-6.303
-1.717
-1.865
-1.650
4.152
4.276
3.976
-4.152
-4.277
-3.977
2.435
2.411
2.326
0.205
0.207
0.214
3.540
3.793
3.398
3a
3b
3c
H
Cl
OMe
Table 8. Frontier orbital energy HOMO, LUMO, energy gap (∆E), the global reactivity descriptors (µ, η, S, w) in eV, and yields of reaction for
group (III)
S(eV-1)
entry
5e
yield %
63
R
H
EHOMO
-6.572
-6.580
-6.353
ELUMO
-1.860
-1.911
-1.832
χ
µ
η
ω
4.216
4.245
4.093
-4.216
-4.246
-4.093
2.355
2.334
2.260
0.212
0.214
0.221
3.773
3.861
3.705
Cl
5j
62
OMe
5o
68
20

Table 9. Frontier orbital energy HOMO, LUMO, energy gap (∆E), the global reactivity descriptors (µ, η, S, w) in eV, and yields of reaction
R
entry yield %
R1
EHOMO
ELUMO
S(eV-1)
∆E
χ
µ
η
ω
C6H5
66
74
60
77
65
74
61
78
69
79
64
80
5a
5b
5c
5d
5f
-6.727
-6.681
-6.701
-1.862
-1.789
-1.993
4.864
4.892
4.708
4.295
4.235
4.347
-4.295
-4.235
-4.347
2.432
2.446
2.354
0.205
0.204
0.212
3.792
3.666
4.014
4-CH3-C6H4
4-Cl-C6H4
4-OMe-C6H4
H
Cl
-6.360
-6.661
-6.705
-6.725
-6.368
-6.354
-6.351
-6.356
-6.333
-1.760
-1.922
-1.820
-2.007
-1.783
-1.865
-1.792
-1.995
-1.737
4.600
4.738
4.885
4.718
4.585
4.488
4.559
4.360
4.596
4.060
4.291
4.262
4.366
4.075
4.109
4.071
4.176
4.035
-4.060
-4.291
-4.262
-4.366
-4.075
-4.109
-4.071
-4.176
-4.035
2.300
2.369
2.442
2.359
2.292
2.244
2.279
2.180
2.298
0.217
0.211
0.204
0.211
0.218
0.222
0.219
0.229
0.217
3.584
3.887
3.719
4.041
3.622
3.763
3.636
3.999
3.543
C6H5
4-CH3-C6H4
4-Cl-C6H4
4-OMe-C6H4
C6H5
5g
5h
5i
5k
5l
4-CH3-C6H4
4-Cl-C6H4
4-OMe-C6H4
OMe
5m
5n
21

4. Conclusion
In conclusion, a new series of benzopyrimidinones linked 1,3,4-oxadiazoles were designed
and synthesized by reacting the hydrazide 3a-c,
previously prepared from
2-aminobenzamide 1 in two steps, with various substituted aromatic aldehydes provided the
N-substituted hydrazides 4a-c, which were cyclized in presence of iodine and potassium
carbonate. The newly prepared compounds 2-5 have been tested for in vitro antimicrobial
activity. Amongst all the tested compounds 5g and 5h exhibited excellent antibacterial
activity particularly against S. aureus, E. coli and P. aeruginosa and showed the highest
antifungal activity against C. albicans. The study of the SAR permitted to conclude in most
cases the presence of chlorine atom attached to aromatic ring and the importance of the nature
of the substituents attached the aryl group on the 1,3,4-oxadiazoles moiety improved the
activity against fungi and some bacterial organisms tested. Theoretical DFT/B3LYP study
has been carried out in order to explain the reactivityof the different product and to understand
the experimental findings. The energies of HOMO and LUMO are related to the reactivity and
the biological activity of the molecule and this properties can be connected via the energy gap
(∆E) between the HOMO and the LUMO. As we saw previously, 5m and 5o have the lowest
energy gap in comparison with the other molecules their respective groups. Further, the
lowest chemical hardness, and the highest chemical potential for these molecules, make these
compounds a most active species in their respective groups.
Conflict of interest
None declared.
22

Acknowledgments
The authors are grateful to the Ministry of Higher Education and Scientific Research of
Tunisia for financial support. The authors also would like to thank Deanship of Scientific
Research at Majmaah University, Saudi Arabia, for supporting this work.
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