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A combined experimental and theoretical analysis of the solid-state supramolecular
self-assembly of N-(2,4-dichlorophenyl)-1-naphthamide: Synthesis, anticholinesterase
potential and molecular docking analysis
Madiha Kazmi, Aliya Ibrar, Hafiz Saqib Ali, Mehreen Ghufran, Abdul Wadood, Ulrich
Flörke, Jim Simpson, Aamer Saeed, Antonio Frontera, Imtiaz Khan
PII: S0022-2860(19)30921-4
DOI: https://doi.org/10.1016/j.molstruc.2019.07.077
Reference: MOLSTR 26830
To appear in: Journal of Molecular Structure
Received Date: 23 April 2019
Revised Date: 18 June 2019
Accepted Date: 17 July 2019
Please cite this article as: M. Kazmi, A. Ibrar, H.S. Ali, M. Ghufran, A. Wadood, U. Flörke, J. Simpson,
A. Saeed, A. Frontera, I. Khan, A combined experimental and theoretical analysis of the solid-state
supramolecular self-assembly of N-(2,4-dichlorophenyl)-1-naphthamide: Synthesis, anticholinesterase
potential and molecular docking analysis, Journal of Molecular Structure (2019), doi: https://
doi.org/10.1016/j.molstruc.2019.07.077.
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Graphical Abstract

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A combined experimental and theoretical analysis of the solid-state
supramolecular self-assembly of N-(2,4-dichlorophenyl)-1-naphthamide:
Synthesis, anticholinesterase potential and molecular docking analysis
Madiha Kazmi,
a,b
Aliya Ibrar,
c
Hafiz Saqib Ali,
d
Mehreen Ghufran,
e
Abdul Wadood,
e
Ulrich
Flörke,
f
Jim Simpson,
g
Aamer Saeed,
a,
* Antonio Frontera,
h,
* Imtiaz Khan,
d,
*
a
Department of Chemistry, Quaid-i-Azam University, Islamabad-45320, Pakistan
b
Department of Chemistry, University of Gujrat, Rawalpindi Sub-campus, Satellite Town,
Rawalpindi, Pakistan
c
Department of Chemistry, Abbottabad University of Science and Technology, Havelian,
Abbottabad, Pakistan
d
School of Chemistry & Manchester Institute of Biotechnology, The University of Manchester
131 Princess Street, Manchester M1 7DN, United Kingdom
e
Department of Biochemistry, Computational Medicinal Chemistry Laboratory, UCSS, Abdul
Wali Khan University, Mardan, Pakistan
f
Department of Chemistry, University of Paderborn, 33098 Paderborn, Germany
g
Department of Chemistry, University of Otago, P.O. Box 56, Dunedin, 9054, New Zealand
h
Departament de Química, Universitat de les Illes Balears, Crta. de Valldemossa km 7.5, 07122
Palma de Mallorca (Baleares), Spain
*Corresponding authors. E-mail: aamersaeed@yahoo.com (A. Saeed); toni.frontera@uib.es
(A. Frontera); imtiaz.khan@manchester.ac.uk (I. Khan).

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Abstract
In the present report, we describe the synthesis of the amide derivative, N-(2,4-dichlorophenyl)-
1-naphthamide, 3, via a facile chemical route. The title compound was isolated in 86% yield. The
structure of compound 3 was established using spectroscopic methods and X-ray
crystallography. In the crystal structure of 3, supramolecular assembly is dominated by classical
N–H…O hydrogen bonding and C–Cl…π halogen bonding interactions which were examined in
detail using several theoretical methods and DFT calculations. The optimized geometric
parameters of compound 3 were calculated using density functional theory (DFT/B3LYP and
DFT/M06-2X) quantum chemical methods with the 6-311++G(d,p) basis set using the
crystallographic coordinates. Additionally, fragments contributing to the HOMO and LUMO
molecular orbitals were investigated at the same level of theory. The nature and various types of
intermolecular interactions in the crystal structure were also realized by Hirshfeld surface
analysis. The biological properties such as anti-Alzheimer’s potential were also assessed which
reveals strong acetylcholinesterase (AChE) and butyrylcholinesterase (BChE) inhibitory effects.
Compound 3 was 16-fold more active inhibitor of acetylcholinesterase compared to neostigmine
with an IC
50
value of 1.044 ± 0.76 µM in addition to 21-fold strong inhibition against
butyrylcholinesterase. The in vitro bioactivity results were further strengthened by the molecular
docking analysis revealing the presence of several important interactions with the active site
residues from cholinesterase (AChE & BChE) enzymes.
Keywords: N-(2,4-dichlorophenyl)-1-naphthamide; Noncovalent interactions; Theoretical
analysis; Halogen bonding; Alzheimer’s potential.

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1. Introduction
The amide functionality is a well-recognized synthetic motif widely encountered in numerous
natural products, pharmaceuticals, and potential drug candidates [1]. The prevalence of an amide
linkage in various drugs with useful biological profiles including acetaminophen, lidocaine,
loperamide [2,3], atorvastatin [4], lisinopril [5], valsartan [6], and diltiazem [7] clearly signals
the importance of this functionality. Several literature reports have documented the close
association of amide derivatives with many biological functions including their use in cytotoxic
[8], analgesic [3], anti-inflammatory [9], antimalarial [10], antitumor [11], anti-HSV [12],
antimicrobial [13], anticancer [14], anticonvulsant [15] and enzyme inhibitory applications [16]
in addition to their industrial and agricultural uses [17].
Alzheimer’s disease (AD) is an age-related irreversible neurodegenerative disorder characterized
by a progressive memory loss, a decline in language skills and other cognitive impairments [18-
23], thus affecting the activity and quality of daily life. The percentage of people with AD is
increasing dramatically with a prediction to witness rise in number to 131 million by 2050 [24].
Neuropathological evidence has proved that the low level of acetylcholine (ACh) is mainly
responsible for the memory impairment and behavioural abnormalities in patients with AD.
Therefore, AChE inhibitors have remained the frontline approach to develop AD drugs, allowing
an increase in the acetylcholine level in the synapses between cholinergic neurons, thus
enhancing the cholinergic function [25].
The cooperative nature of noncovalent interactions resulting in the facile construction of
supramolecular assemblies with numerous interesting properties remains highly intriguing
concept. Such systems are often used in the exploration of new chemical synthons in crystal
engineering [26]. Examples of noncovalent interactions include electrostatic forces, hydrogen

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bonding, halogen bonding, CH–π contacts, π–π stacking, cation–π, anion–π, and lone pair–π
contacts. Such contacts have been at the center point of supramolecular chemistry for a number
of years [27-37]. The ubiquitous and critical roles played by these common interactions are
widely accepted by chemists working in the fields of biology, supramolecular chemistry, crystal
engineering, drug design, pharmaceuticals and materials science [38-45]. Therefore, a deep
understanding of weak interactions is essential to expand the field of supramolecular chemistry
to new applications, particularly in the pharmaceutical industry where an understanding of the
solid-state properties of potential drugs remains imperative.
In this context and in a continuation of our work [46-50] on the importance of noncovalent
interactions and structural assemblies of various synthons, and identification of structural leads
for cholinesterase inhibition [21-23], we have synthesized N-(2,4-dichlorophenyl)-1-
naphthamide and characterized it using numerous readily available spectro-analytical techniques
and X-ray crystallography. Supramolecular assemblies of this compound were dominated by
classical and non-classical hydrogen bonds together with C–Cl…π halogen bonding interactions.
These contacts were examined in detail using several theoretical methods and DFT calculations.
Biological properties such as anti-Alzheimer’s potential were also assessed and these properties
were further investigated by molecular docking analysis.
2. Experimental
2.1. General considerations
All the reagents and solvents were procured from commercial suppliers (Sigma Aldrich, Merck,
Lab Scan) and used without further purification. All solvents used were either anhydrous or dried
using standard procedures. The reaction progress was monitored by thin layer chromatography
(TLC) using Merck DF-Alufoilien 60F
254
0.2 mm pre-coated plates. Compounds were visualized

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by exposure to UV light at 254 nm. The melting point was recorded in open capillary using
Gallenkamp melting point apparatus (MP-D) and is uncorrected. The FTIR spectrum was
recorded on a Thermoscientific Fourier Transform Infra-Red Spectrophotometer USA model
Nicolet 6700 using the attenuated total refraction (ATR) technique. NMR spectra were acquired
on Bruker AV300 spectrometer at room temperature.
1
H and
13
C NMR spectra were referenced
to external tetramethylsilane via the residual protonated solvent (
1
H) or the solvent itself (
13
C).
All chemical shifts are reported in parts per million (ppm). The chemical shifts are referenced to
7.26 ppm for
1
H NMR spectroscopy and 77.16 ppm for
13
C NMR spectroscopy for CDCl
3
. A
Leco CHNS-932 Elemental Analyzer from Leco Corporation (USA) was used for the elemental
analysis of the synthesized compound.
2.2. Preparation of N-(2,4-dichlorophenyl)-1-naphthamide (3)
A few drops of DMF were added to a stirred solution of naphthalene-1-carboxylic acid (1 mmol)
and thionyl chloride (1.2 mmol) and the reaction mixture was heated to reflux for 3 h to afford
the corresponding acid chloride which was used in the next step without further purification.
Subsequently, freshly prepared 1-naphthoyl chloride was slowly added to a stirred solution of
2,4-dichloroaniline (1 mmol) in acetone (10 mL) and the resulting mixture was heated to reflux
for 3 h. After completion of the reaction (monitored by thin layer chromatography), the reaction
mixture was poured onto crushed ice. The precipitated solid was filtered off, washed with cold
distilled water, dried and recrystallized from ethanol to afford N-(2,4-dichlorophenyl)-1-
naphthamide 3.
Colourless crystalline solid (86%): m.p 200–202 °C; IR (ATR, cm
‒1
): 3265 (N‒H), 3033 (C
sp2
‒
H), 1684 (C=O), 1605, 1556 (C=C);
1
H NMR (300 MHz, CDCl
3
) δ
H
8.10 (1H, d, J = 8.3 Hz,
ArH), 8.03‒8.00 (1H, m, ArH), 7.99–7.94 (2H, m, ArH), 7.71‒7.69 (1H, m, ArH), 7.61‒7.54

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(4H, m, ArH), 7.17–7.16 (1H, m, ArH);
13
C NMR (75 MHz, CDCl
3
) δ
C
166.24, 138.40 (2 × C),
133.74, 133.07, 133.06, 131.29, 130.51, 129.74, 128.84, 128.35, 128.02, 127.33, 124.71, 124.47
(2 × C), 117.79; Anal. Calcd. for C
17
H
11
Cl
2
NO (315.02): C, 64.58; H, 3.51; N, 4.43; found: C,
64.39; H, 3.29; N, 4.37.
2.3. Crystal growth development
Good quality single crystals of compound 3 suitable for X-ray diffraction analysis were grown
from ethanolic solution by slow evaporation at ambient temperature.
2.4. X-ray data collection and structure refinement
Data were collected at 130(2) K using Mo-K
α
radiation (λ = 0.71073 Å) on a Bruker APEXII
CCD diffractometer, processed using APEX2 and SAINT [51] with multi-scan absorption
corrections applied using SADABS [51].
The structure was solved by direct methods (SHELXS-
97) [52] and refined using full-matrix least-squares procedures with SHELXL-2013-4 [53] and
TITAN2000 [54]. All non-hydrogen atoms were refined anisotropically and hydrogen atoms were
placed in calculated positions with their thermal parameters refined isotropically and U
eq
(H) =
1.2—1.5 U
eq
(C). Molecular plots and packing diagrams were drawn using Mercury [55] and
additional metrical data were calculated using PLATON [56].
Tables were prepared using
WINGX [57].
Details of the X-ray measurements and crystal data for compound 3 are given in
Table 1.
Table 1. Crystallographic data for compound 3.
Empirical formula C
17
H
11
Cl
2
NO
Formula weight 316.17
Temperature 130(2) K
Wavelength 0.71073 Å
Crystal system Orthorhombic
Space group P c a 21

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Unit cell dimensions a = 9.8820(10) Å, α = 90°
b = 5.5866(6) Å, β = 90°
c = 25.365(3) Å, γ = 90°
Volume 1400.3(3) Å
3
Z 4
Density (calculated) 1.500 Mg/m
3
Absorption coefficient 0.460 mm
‒1
F(000) 648
Crystal size 0.360 × 0.240 × 0.200 mm
3
Theta range for data collection 1.606 to 27.877°
Index ranges ‒12<=h<=13, ‒7<=k<=6, ‒33<=l<=33
Reflections collected 12030
Independent reflections 3338 [R(int) = 0.0219]
Completeness to theta = 25.242° 100.0 %
Absorption correction Semi-empirical from equivalents
Max. and min. transmission 0.9136 and 0.8519
Refinement method Full-matrix least-squares on F
2
Data / restraints / parameters 3338 / 1 / 190
Goodness-of-fit on F
2
1.059
Final R indices [I>2sigma(I)] R
1
= 0.0282, wR
2
= 0.0704
R indices (all data) R
1
= 0.0292, wR
2
= 0.0711
Absolute structure parameter 0.022(17)
Extinction coefficient n/a
Largest diff. peak and hole 0.332 and -0.166 e.Å
‒3
CCDC reference number 1884623
2.5. Theoretical methods
The geometries of the complexes and single compound included in this study were computed at
the DFT/M06-2X and DFT/B3LYP with the 6-311++G(d,p) level of theory using the
crystallographic coordinates, unless otherwise noted. For all calculations, we have used the
GAUSSIAN-09 program [58]. We have also used the Grimme’s dispersion [59] correction as
implemented in GAUSSIAN-09 program since it is adequate for the evaluation of noncovalent

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interactions where dispersion effects are relevant like σ-hole interactions. The basis set
superposition error for the calculation of interaction energies has been corrected using the
counterpoise method [60]. The NCIplots [61] isosurfaces have been used to characterize
noncovalent interactions. They correspond to both favorable and unfavorable interactions, as
differentiated by the sign of the second density Hessian eigenvalue and defined by the isosurface
color. The color scheme is a red-yellow-green-blue scale with red for ρ
+cut
(repulsive) and blue
for ρ
−cut
(attractive). The thermodynamic parameters and temperature effects on them were
computed by using Moltran [62] software. The Bader’s “atoms in molecules” (AIM) analysis
[63] has been carried out using the AIMAll software and the M06-2X/6-311++G(d,p) wave
function [64]. Further details of the intermolecular architecture of this molecule were obtained
using Hirshfeld surface analysis [65] with surfaces and two-dimensional fingerprint plots
generated by CrystalExplorer [66].
2.6. Enzyme inhibitory protocols
2.6.1. Cholinesterase inhibition
Ellman’s spectrophotometric method was used to determine the AChE and BChE inhibitory
activity with a slight modification [67]. The compounds were prepared in DMSO (end
concentration was 1%). The assays were carried out in 96 well-plate in triplicate. The reaction
mixture consisted of 20 µL of buffer (tris HCl 50 mM, 0.02 M MgCl
2
.6H
2
O, 0.1 mM NaCl) at
pH 8, 10 µL of the test compound, 10 µL enzyme acetylcholine or butyrylcholinesterase of 0.03
U/mL (500 U/mg) of AChE and 700 U/mg of BChE). The contents were incubated for 10 min at
25 °C followed by the addition of 1 mM of 10 µL of substrate acetylcholine iodide for AChE and
butyrylthiocholine iodide for BChE and incubated again at 25 °C for 15 min. 50 µL of 3 mM
DTNB as a coloring agent was added and incubated at 25 °C for further 10 min. The amount of

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product formed was measured by using micro plate reader (Bio-Tek ELx 800, Instruments Inc.,
Winooski, VT, USA) at 405 nm. The enzyme dilutions were made by using buffer at pH 8 (tris
base 50 mM and having 0.1% BSA). As compound showed >50% inhibition, 9–12 serial
dilutions in the assay buffer were prepared and IC
50
values were calculated by graph pad prism.
2.7. Docking studies
Molecular docking is an important tool for exploring the interactions
between a potential inhibitor molecule and the protein target [68]. To find the binding
interactions of the compound 3 in the active sites of acetyl- and butyrylcholinesterase, the MOE-
Dock program (www.chemcomp.com) was used to perform molecular docking. 3D crystal
structures with their PDB codes, 4M0E (AChE), 1P0P (BChE) of these enzymes were retrieved
from the Protein Databank (PDB). All water molecules were removed from the retrieved crystal
structures using the Molecular Operating Environment (MOE) software (www.chemcomp.com).
The hydrogen atoms were added to the protein structures by 3D protonation and then energy
minimization was carried out by using the default parameters of the MOE program. The structure
of the synthesized compound 3 was built in the MOE program and energy minimized using the
MOE default parameters. The synthesized compound 3 was docked into the active sites of the
target enzymes in MOE (www.chemcomp.com) using the default parameters i-e Placement:
Triangle Matcher, Rescoring 1: London dG, Refinement: Forcefield, Rescoring 2: London dG.
For the described ligand, ten conformations were generated and the top ranked conformation
based on the docking score was selected for further molecular docking studies. After the
molecular docking, the best poses with polar, H-pi and pi-H interactions were analyzed using the
Pymol software. Before docking the docking protocol was validated by re-docking the co-
crystalized ligands of AChE and BChE.

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3. Results and discussion
3.1. Synthesis and spectroscopic characterization
The synthetic route to the target compound 3 is illustrated in Scheme 1. The slow addition of 1-
naphthoyl chloride 2 (prepared from 1-naphthoic acid and thionyl chloride) to a mixture of 2,4-
dichloroaniline in acetone produced the title compound in 86% yield. In the FTIR spectrum, the
presence of distinctive peaks for the N–H and carbonyl functionalities at 3265 and 1684 cm
–1
,
respectively, indicated the formation of compound 3.
1
H NMR analysis further confirmed the
formation of amide bond and the resonance for aniline protons was not observed.
13
C NMR data
was also in agreement to the structure 3 where diagnostic peak for the amide carbonyl appeared
at 166.24 ppm.
Scheme 1. Synthesis of N-(2,4-dichlorophenyl)-1-naphthamide 3.
3.2. X-ray crystallography
3.3. Structural description
The compound N-(2,4-dichlorophenyl)-1-naphthamide, C
17
H
11
Cl
2
NO (3), comprises a
naphthamide unit with a 2,4-dichlorophenyl substituent of the amide N1 atom (Fig. 1). The
naphthamide and benzene rings are inclined to one another by only 1.56(11)° but are displaced
by approximately 0.8 Å from one another as the C2,C1,O1,N1,C12 plane subtends angles of
51.94(8)° and 53.42(9)° to the naphthalene and benzene ring planes respectively. Interestingly,
this inclination does not appear to be significantly influenced by the formation of an
intramolecular C4—H4A…O1 hydrogen bond which does not impose planarity on the

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O1,C1…C4 segment of the molecule. Bond distances and angles in 3 are normal and closely
similar to those found in the four discrete phenyl-1-naphthamide derivatives found in the
Cambridge structural database [69]. Of these N-(4-fluorophenyl)-1-naphthamide
and N-(4-
chlorophenyl)-1-naphthamide [70] are closely related to the compound reported here with the
other representatives having methoxy and dimethylamino substituents on the 8-position of the
naphthamide ring system [71].
Fig. 1. The structure of 3 showing the atom-numbering with ellipsoids drawn at the 50%
probability level. An intramolecular hydrogen bond is shown as a dashed line.
In the crystal structure, classical N1—H1A…O1 hydrogen bonds form C5 chains [72] of
molecules along the a axis direction. These chains are further stabilized by C17—Cl2…π
halogen bonds [73] with the C12…C17 benzene ring acting as the halogen bond acceptor (Fig.
2). Although relatively unusual, these C‒X…π contacts (X = halogen) are increasingly found to
be important in stabilizing the packing in both organic and organometallic small molecule
[74,75] and protein structures [76,77]. Non-classical C10—H10A…O1 hydrogen bonds also
form C6 chains [72]
along a (Fig. 3). These contacts combine to stack along the b axis direction,

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with individual stacks linked into chain-like columns along a. There are no close contacts
between the individual columnar chains (Fig. 4).
Fig. 2. Chains of molecules of 3 formed along a by N—H…O hydrogen bonds (blue dashed
lines) and C—Cl…π halogen bonds (green dotted lines).

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Fig. 3. Chains of molecules of 3 formed along the a axis direction by C—H…O hydrogen bonds.
Fig. 4. Overall packing of 3 viewed along the b axis direction.

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3.4. Theoretical structure
The optimization of structure 3, N-(2,4-dichlorophenyl)-1-naphthamide (Fig. 1) was performed
at B3LYP/6-311++G(d,p) level of theory. The different geometric parameters, bond length,
selected bond angles and dihedral angles were calculated and are listed and compared with the
values found crystallographically in Table 2. The calculated lengths of C‒N bonds (N1‒C1
[1.389 Å], N1‒C12 [1.412 Å]) were in close agreement to those with the experimental as well as
values reported in the literature [78]. The dihedral angle between the two rings (benzene and
naphthalene) is 20.615°. These were also in close agreement to with the experimental values with
only a slight difference in the computed bond lengths and angles which is probably because the
experimental results were obtained in the solid state with a possible existence of weak hydrogen
bonding and the van der Waals interactions that may affect these parameters. In contrast, the
theoretical calculations were performed in the gas phase.
Table 2. Some selected geometrical parameters compared with crystallographic data.
Bond lengths (Å) Bond & Dihedral Angles (°)
Atom Calculated
Expt. Atom Calculated Expt.
C
1
‒C
2
1.493 1.497(3) C
1
‒N
1
‒C
12
130.380 121.96(19)
C
2
‒C
3
1.435 1.436(3) O
1
‒C
1
‒N
1
119.373 123.10(2)
C
3
‒C
4
1.425 1.416(4) O
1
‒C
1
‒C
2
122.410 122.10(2)
O
1
‒C
1
1.251 1.226(3) N
1
‒C
1
‒C
2
118.906 114.70(2)
N
1
‒C
1
1.389 1.358(3) C
4
‒C
3
‒C
8
118.391 118.80(2)
N
1
‒C
12
1.412 1.417(3) C
4
‒C
3
‒C
2
123.383 123.10(2)
C
2
‒C
11
1.385 1.374(3) C
8
‒C
3
‒C
2
118.231 118.10(2)
C
3
‒C
8
1.438 1.425(3) C
6
‒C
7
‒C
8
120.918 121.10(2)
C
4
‒C
5
1.379 1.377(4) C
9
‒C
8
‒C
3
119.464 119.60(2)
C
5
‒C
6
1.417 1.411(4) C
7
‒C
8
‒C
3
119.174 118.80(2)
C
6
‒C
7
1.377 1.361(4) C
9
‒C
10
‒C
11
119.997 119.70(2)
C
7
‒C
8
1.424 1.421(3) C
17
‒C
12
‒N
1
120.271 121.00(2)
C
8
‒C
9
1.422 1.416(4) Cl
1
‒C
2
‒C
1
119.503 119.20(2)
C
9
‒C
10
1.377 1.368(4) C
15
‒C
16
‒C
17
119.128 118.50(2)
C
10
‒C
11
1.413 1.409(3) O
1
‒C
1
‒C
2
‒C
11
‒126.108 ‒125.60(3)
C
12
‒C
13
1.393 1.394(3) N
1
‒C
1
‒C
2
‒C
3
‒133.844 ‒132.60(2)

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C
12
‒C
17
1.403 1.400(3) C
4
‒C
3
‒C
8
‒C
9
179.966 178.90(2)
Cl‒C
15
1.826 1.738(2) N
1
‒C
12
‒C
13
‒C
14
‒179.367 ‒179.60(2)
C
15
‒C
16
1.389 1.384(4) C
12
‒C
13
‒C
14
‒C
15
‒0.3482 ‒0.30(4)
C
16
‒C
17
1.390 1.386(3) C
13
‒C
12
‒C
17
‒C
16
1.046 0.90(3)
3.5. HOMO
‒
LUMO energy
There are many ways of calculating excitation energy. The simplest is to find the difference
between the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular
orbital (LUMO), called frontier orbitals, used for the determination of chemical reactivity of the
molecule [79]. The HOMO and LUMO orbitals for the title compound 3, their energy and the
energy gap between them were calculated by using B3LYP/6-311++G level of the density
functional theory and its 3D plots are shown in the Fig. 5. Both orbitals (HOMO and LUMO) are
the main chemical participants in a reaction. The HOMO orbital has an ability to give electrons,
on the other hand LUMO has the capacity to accept these electrons, and their energy gap
determines the chemical stability and the reactivity of a compound. If the energy gap between
both orbitals is low, it indicates high reactivity and low stability of the compound and vice versa
[80]. For the title compound 3, the HOMO and LUMO orbitals are localized on the 2,4-
dichlorophenyl and naphthalene rings respectively demonstrating that these are π antibonding
orbitals with an energy gap of 2.69 eV, hence an
݊ → ߨ∗
electronic transition is possible [81].
The other electronic properties, for instance, chemical potential (µ), ionization potential (I.P),
electron affinity (E.A), electrophilicity index (ψ), chemical hardness (
ߟ
) and softness (ɛ) have
been calculated from HOMO-LUMO energies [82] and are tabulated in Table 3. The small value
of chemical potential and electrophilicity index indicates the reactive nature of the title
compound which is confirmed by the positive value of chemical softness [83].

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Fig. 5. The Frontier molecular orbitals for N-(2,4-dichlorophenyl)-1-naphthamide 3.
Table 3. Molecular properties (a.u.) of compound 3.
Molecular properties B3LYP/6-311++G(d,p)
Free Energy ‒1704.65
Ionization potential (I.P) 0.3142
Electron affinity (E.A) 0.2156
Chemical potential (µ) ‒0.2649
Chemical Hardness (
ߟ
) 0.0494
Chemical softness (ɛ) 0.0247
Electrophilicity index (ψ) 0.0017
Dipole moment (Debye) 3.1757
3.6. Hirshfeld surface analysis
In order to visualize the intermolecular interactions in the crystal of the title compound, a
Hirshfeld surface analysis [65] was performed using Crystal Explorer [66]. Hirshfeld surfaces
viewed for opposite faces (a) and (b) of 3 are shown in Fig. 6. The red circles on the surfaces
correspond to the strong N—H…O hydrogen bond, the most prominent circles, and the weaker
C‒H…O hydrogen bond and the Cl…π(ring) halogen bond. As indicated previously, these
contacts play a considerable role in stabilizing the packing in this structure.

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(a) (b)
Fig. 6. Hirshfeld surfaces for 3 mapped over d
norm
showing opposite faces (a) and (b) of the
molecule.
Fingerprint plots of the principal contacts on the Hirshfeld surface of 3 are shown in Fig. 7.
These comprise H…C/C…H, H…H, H…Cl/Cl…H, Cl…C/C…Cl, H…O/O…H and Cl…Cl
contacts. The much less significant H…N/N…H, C…C, N…C/C…N and O…C/C…O
contributions, that together contribute only 2% to the Hirshfeld surface, are not shown in the
figure but for completeness are detailed in Table 4. An interesting feature of the contributions of
interatomic contacts to the Hirshfeld surface in this structure is the dominance of contacts
involving carbon that make up more than 40% of the surface contacts. Normally for organic
compounds, van der Waals H…H interactions are the most extensive [84,85] but here the
H…C/C…H contacts top the list. The significant contributions of contacts involving chlorine are
also a feature for 3.

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Fig. 7. (a) The full two-dimensional fingerprint plot for 3. (b)-(g) The principal individual
contact types for 3 that in descending contact order are found to be H…C/C…H, H…H,
H…Cl/Cl…H, Cl…C/C…Cl, H…O/O…H and Cl…Cl contacts.

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Table 4. Percentage contributions of interatomic contacts to the Hirshfeld surface of 3.
# Contact %
1 H…C/C…H 33.3
2 H…H 25.3
3 H…Cl/Cl…H 20.2
4 Cl…C/C…Cl 9.1
5 H…O/O…H 8.5
6 Cl…Cl 1.5
7 H…N/N…H 0.8
8 C…C 0.7
9 N…C/C…N 0.4
10 O…C/C…O 0.1
3.7. Theoretical (DFT) study
The DFT study seeks to analyze the physical nature of the Cl…π interaction described above
(Fig. 2). Due to the anisotropic nature of the Cl atom (negative belt and positive σ-hole), the Cl
atom can act as either an electron donor or an acceptor. Therefore, we intend to differentiate
between two possible interaction modes, which are σ-hole…π and lone pair(lp)…π. In Fig. 8 we
show the molecular electrostatic potential (MEP) plotted onto the van der Waals surface of
compound 3. It shows that the most positive region corresponds to the amidic N–H group and the
most negative to the amidic C=O group. In fact, the intermolecular C=O…H–N H-bonding
interaction is crucial in the solid state of 3 as evidenced in the crystal packing shown in Figs. 2
and 4 in good agreement with the MEP analysis. Moreover, the MEP surface also shows the
existence of a σ-hole at a Cl atom at the extension of the C–Cl bond (+10 kcal/mol) and a
negative belt with a minimum MEP value of –10 kcal/mol. The isosurface also reveals that the
MEP values over the naphthalene and dichlorophenyl ring planes are negative (–17 and –9
kcal/mol, respectively). The fact that the MEP value over the dichlorophenyl ring is negative
supports the description of the Cl…π interaction in 3 as a σ-hole interaction (electrostatically
attractive) instead of a lp…π contact (electrostatically repulsive).

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Fig. 8. MEP surface (isosurface = 0.001 a.u.) of compound 3. The MEP values at selected points
of the surface are indicated.
In Fig. 9 we show two theoretical models that we have used to evaluate the N–H…O hydrogen
bonding and C–Cl…π halogen bonding interactions that govern the formation of the infinite 1D
chains of molecules of 3 formed along a, as indicated in Fig. 2. The dimerization energy of 3
(Fig. 9a) is very favorable ∆E
1
= –19.9 kcal/mol due to the concurrent formation of both
interactions in addition to long‒range van der Waals forces due to the proximity of the
naphthalene rings. In an effort to estimate the contribution of the halogen bonding interaction, we
have used a theoretical model where the Cl atom has been replaced by a hydrogen (Fig. 9b).
Consequently, the halogen bonding is not established and the interaction energy is reduced to
∆E
2
= –16.4 kcal/mol, which represents the contribution of the hydrogen bond and the rest of van
der Waals interactions due to the proximity of the bulk of both molecules. The halogen bonding
contribution can thus be estimated by difference to be –3.5 kcal/mol.

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Fig. 9. Theoretical models used to evaluate the halogen bonding interaction in compound 3.
We have also computed the “noncovalent Interaction plot” (NCIplot) index in order to further
characterize the interactions in the dimer of compounds 3. The NCIplot is an intuitive
visualization index that enables the identification of noncovalent interactions easily and
efficiently since it clearly shows which molecular regions interact. The colour scheme has a red-
yellow-green-blue scale with red (repulsive) and blue (attractive). Yellow and green surfaces
correspond to weak repulsive and weak attractive interactions, respectively. The representation
of the NCIplot index is shown in Fig. 10a. The NCIplot reveals the existence of a green
isosurface between the π-system of the dichlorophenyl ring and the Cl atom thus confirming the
existence of the halogen bonding interaction. Moreover, a small and blue isosurface characterizes
the strong H-bonding interaction. Finally, an extended green isosurface is located between both
naphthalene rings, thus confirming the existence of weak van der Waals contacts that further
contribute to the stabilization of the assembly.
Finally, we have used the Bader’s theory of atoms in molecules to further characterize the
noncovalent interactions described above. The presence of a bond critical point and bond path
connecting two atoms is a clear indication of interaction [86]. In Fig. 10b we show the

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distribution of bond CP and bond paths of the dimer of compound 3. It can be observed the
presence of a bond CP and bond path interconnecting the O and H atoms of the amide group,
thus characterizing the H‒bond. Moreover, the C–Cl…π interaction is characterized by a bond
CP and bond path connecting the Cl atom to one C atom of the aromatic ring, thus confirming
the existence of the interaction. Finally, the van der Waals interaction revealed by the NCIplot
can be also described as C–H…π interactions since they are characterized by a bond CP and
bond path connecting the C–H groups to the aromatic ring. In Fig. 10b, we have also indicated
the values of ρ(r) at the bond CPs. It is well known that these values correlate with the strength
of the interaction [87]. It can be observed that the value of ρ(r) at the bond CP that characterizes
the HB is the largest one, in agreement with the NCI analysis that shows an intense blue color
and also energetic results.
Fig. 10. (a) NCI surface of the dimer of compound 3. The gradient cut-off is s = 0.35 au, and the
color scale is −0.04 < ρ < 0.04 au. (b) Distribution of bond and ring critical points (green and
yellow spheres, respectively) and bond paths for the dimer of 3. The values of ρ(r) at the bond
CPs that characterize the noncovalent interactions are given in a.u.

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3.8. Thermodynamic analysis
The total energy of a molecule is the sum of vibrational, rotational, electronic and translational
energies. The statistical thermochemical analysis of the title compound 3 was carried out
considering the molecule to be at standard temperature and pressure (298.15 K & 1 atm). The
thermodynamic properties such as heat capacity (Cp), enthalpy
(ܪ − ܧ)/ܶ
, Gibb’s free energy
(ܩ − ܧ)/ܶ
and entropy (S
0
) are calculated using DFT/B3LPY with the 6-311++G (d,p) basis set.
The thermodynamic quantities of compound 3 for various ranges (10-500 K) of temperatures
were calculated using the Moltran software [62] and are listed in Table 5. From the results, it can
be predicted that the thermodynamic parameter increases on increasing temperature from 10-500
K because the vibrational intensities of 3 changes with temperature [88]. The variation in the
thermodynamic parameters with temperature can be seen in Fig. 11. All the thermodynamic data
provide helpful information for further study on the title compound. The correlation equations
between these thermodynamic properties and temperature were fitted by a parabolic formula.
The regression coefficient is also given in the parabolic equation.
(Cp
o
)
total
= 7.728 + 0.183T – 6.913E-6T
2
(R
2
= 0.999)
(S
o
)
total
= 53.882 + 0.314T – 0.0001645T
2
(R
2
= 0.995)
(ܪ − ܧ)/ܶ
= 539.410 + 0.02563T + 0.0003045T
2
(R
2
= 0.999)
(ܩ − ܧ)/ܶ
= 540.822 – 0.218T – 0.000369T
2
(R
2
= 0.999)
The partition function is one of the most important thermodynamic parameters that link
thermodynamics, spectroscopy and quantum theory. The partition function can be calculated
either by internuclear potential energy wall or the first vibrational level [89]. The partition

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function can be used to calculate equilibrium constant, rate constant, entropies and heat
capacities.
Table 5. Thermodynamic parameters calculated for 3 using B3LYP/6-311++G(d,p).
Temperature
(K)
Thermodynamic parameters
S (Cal/mol/K) C
p
(Cal/mol/K) (H‒E)/T
(Cal/mol/K) (G‒E)/T
(Cal/mol/K) Q/VPF
10.0 51.571 9.690 539.610 537.881 2.76328E+09
50.0 72.455 17.373 541.478 529.327 1.10028E+13
100.0 87.151 25.954 545.117 515.886 1.92794E+15
150.0 99.276 34.478 550.180 500.233 9.86148E+16
200.0 110.408 43.418 556.705 482.643 3.02237E+18
250.0 121.095 52.766 564.765 463.227 7.04914E+19
300.0 131.558 62.306 574.414 442.039 1.39648E+21
350.0 141.873 71.721 585.656 419.110 2.48820E+22
400.0 152.043 80.720 598.446 394.463 4.11213E+23
450.0 162.042 89.105 612.695 368.124 6.40691E+24
500.0 171.833 96.784 628.292 340.126 9.48789E+25
0 100 200 300 400 500
0
100
200
300
400
500
600
Thermodynamic Parameters (Cal/ mol K)
Temperature (K)
Cp
H
S
G
Fig. 11. Variation of thermodynamic parameters with temperatures for N-(2,4-dichlorophenyl)-1-
naphthamide 3.
3.9. Enzyme inhibition studies
N-(2,4-dichlorophenyl)-1-naphthamide, 3, was investigated for the assessment of its anti-
neurodegenerative potential using cholinesterase (AChE & BChE) enzymes. Neostigmine and

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donepezil were used as standard inhibitors. The data presented in Table 6 demonstrated the
remarkable potential of compound 3 as an anticholinesterase inhibitor. The inhibition efficacy
was several folds higher compared to the standard drugs. Compound 3 demonstrated an IC
50
value of 1.044 ± 0.76 µM against AChE whereas 0.343 ± 0.012 µM against BChE enzyme. This
inhibitory efficacy demonstrated by compound 3 was compared to literature data where other
benzamide molecules containing isoquinoline, phthalimide and dimethylamine fragments are
reported [90-92]. The results were remarkably much superior, thus giving a promising
opportunity to develop new small-molecule inhibitors for the treatment of Alzheimer’s disease.
Table 6. Anti-Alzheimer’s potential of N-(2,4-dichlorophenyl)-1-naphthamide 3.
Compound AChE BChE Docking Score Binding Affinity
(Kcal/mol)
IC
50
± SEM (µM) AChE BChE AChE BChE
3 1.044 ± 0.76 0.343 ± 0.012 ‒12.5268 –10.3123 –6.85 –6.67
Neostigmine
16.3 ± 1.12 ―
–
8.9232
–
7.8734
–
2.69
–
1.09
Donepezil ― 7.23 ± 0.12
–
12.6109
–
9.8918
–
5.38
–
3.61
3.10.
Molecular docking analysis
The docking protocol was validated by re-docking the co-crystallized ligands in the active sites
of AChE and BChE. In both cases the RMSD between the co-crystallized ligand and re-docked
conformation was within acceptable range (Fig. 12). By using molecular docking analysis, we
investigated the interaction of compound 3
with the
AChE as well as BChE. The docking results
showed that the compound 3 was well accommodated in the active sites of both the AChE and
BChE enzymes. From the docking conformation of compound 3 (docking score = ‒12.5268), it
was observed that this compound formed two hydrogen bonds with the active site residues of

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AChE. Tyr124 formed a polar interaction with the hydrogen of the NH moiety of the compound
3. Ser293 was observed to form a hydrogen bond with a chloro group of the dichlorophenyl
moiety of the compound 3 (Fig. 13). One arene-cation linkage with the benzene moiety of the
compound was also found. Furthermore, hydrophobic interactions between compound 3 and
active site residue Phe338 were observed.
For BChE compound 3 has a docking score of –10.3123 and is bound to the BChE enzyme in an
adequate manner through one hydrogen bond and several hydrophobic interactions (Fig. 14).
Trp82 forms a polar bond and arene-arene linkages with both the carbonyl oxygen unit and the
dichlorophenyl moiety respectively. Ala328 and Trp430 form arene-cation interactions with the
aromatic rings of the compound. The potency of the compound might be due to the existence of
the electron-withdrawing chloro-substituents.
Fig. 12. Superposition of co-crystallized ligand conformation and docked conformations. (a)
AChE; (b) BChE target proteins. The co-crystallized ligand conformations are shown in red
color whereas the re-docked conformations are shown in yellow color.

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Fig. 13. Binding mode of compound 3 with the active residues of AChE.
Fig. 14. Binding mode of compound 3 with the active residues of BChE.
4.
Conclusions
In summary, we have described the synthesis of a new amide derivative, namely N-(2,4-
dichlorophenyl)-1-naphthamide. The supramolecular assemblies of the title compound 3 were
stabilized by classical and non-classical hydrogen bonding and halogen bond interactions. These

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noncovalent interactions were further investigated by DFT calculations, Hirshfeld surface
analysis and “noncovalent interaction plots” (NCIplot) index. The NCIplot reveals the existence
of a green isosurface between the π-system of the dichlorophenyl ring and the Cl atom thus
confirming the existence of the halogen bonding interaction. The molecular geometry and
thermodynamic properties of compound 3 have been calculated using the density functional
theory with 6-311++G (d,p) basis set which show that compound is fairly stable at high
temperature. The optimized geometric parameters show good consistency with the experimental
data. Anti-Alzheimer’s potential was also assessed by evaluating the inhibitory efficacy of
compound 3 against acetyl- and butyryl-cholinesterase enzymes. The results were remarkably
intriguing with several folds stronger inhibition compared to standard drugs.
Acknowledgements
M.K is grateful to the Higher Education Commission of Pakistan for financial support. We also
thank the MINECO/AEI from Spain for financial support (project numbers CTQ2017-85821-R,
FEDER funds).
Supplementary data
CCDC 1884623 contains the supplementary crystallographic data for this paper. These data can
be obtained free of charge via www.ccdc.cam.ac.uk/data_request/cif, or by emailing
data_request@ccdc.cam.ac.uk, or by contacting The Cambridge Crystallographic Data Centre,
12, Union Road, Cambridge CB2 1EZ, UK; fax: +44 1223 336033.
1
H- &
13
C-NMR spectra of
compound 3 reported in this study can be found online at…..
References
[1] (a) E. Valeur, M. Bradley, Chem. Soc. Rev. 38 (2009) 606-631; (b) A. Khalafi-Nezhad, A.
Parhami, M.N. Soltani Rad, A. Zarea, Tetrahedron Lett. 46 (2005) 6879-6882; (c) R.M. Lanigan,

MANUS CRIP T
ACCEP TED
ACCEPTED MANUSCRIPT
P. Starkov, T.D. Sheppard, J. Org. Chem. 78 (2013) 4512-4523; (d) V.R. Pattabiraman, J.W.
Bode, Nature 480 (2011) 471-479; (e) J. Clayden, N. Greeves, S. Warren, P. Wothers, Organic
Chemistry, New York, Oxford, 2001; (f) G.S. Singh, Tetrahedron 59 (2003) 7631-7649; (g) C.R.
Kemnitz, M.J. Loewen, J. Am. Chem. Soc. 129 (2007) 2521-2528.
[2] N. Kanışkan, Ş. Kökten, İ. Çelik, ARKIVOC viii (2012) 198-213.
[3] F.A. Bettelheim, J. March, Introduction to General, Organic and Biochemistry, 5
th
ed.,
Sounders College Publishing, Fort Worth, 1998, pp. 492-508.
[4] A. Graul, J. Castaner, Drugs Future 22 (1997) 956-968.
[5] A.A. Patchett, J. Med. Chem. 36 (1993) 2051-2058.
[6] M. Gasparo, S. Whitebread, Regul. Pept. 59 (1995) 303-311.
[7] V.S. Ananthanarayanan, S. Tetreault, A. Saint-Jean, J. Med. Chem. 36 (1993) 1324-1332.
[8] K.A. Shaaban, M.D. Shepherd, T.A. Ahmed, S.E. Nybo, M. Leggas, J. Rohr, J. Antibiot. 65
(2012) 615-622.
[9] G. Caliendo, V. Santagada, E. Perissutti, B. Severino, F. Fiorino, T.D. Warner, J. Wallace,
D.R. Ifa, E. Antunes, G. Cirino, G.D. Nucci, Eur. J. Med. Chem. 36 (2001) 517-530.
[10] T. Wu, A. Nagle, T. Sakata, K. Henson, R. Borboa, Z. Chen, K. Kuhen, D. Plouffe, E.
Winzeler, F. Adrian, Bioorg. Med. Chem. Lett. 19 (2009) 6970-6974.
[11] Y. Nagaoka, T. Maeda, Y. Kawai, D. Nakashima, T. Oikawa, K. Shimoke, T. Ikeuchi, H.
Kuwajima, S. Uesato, Eur. J. Med. Chem. 41 (2006) 697-708.
[12] Y.F. Xiang, C.W. Qian, G.W. Xing, J. Hao, M. Xia, Y.F. Wang, Bioorg. Med. Chem. Lett.
22 (2012) 4703-4706.
[13] N. Kushwaha, R.K. Saini, S.K.S. Kushwaha, Int. J. Chem. Tech. Res. 3 (2011) 203-209.

MANUS CRIP T
ACCEP TED
ACCEPTED MANUSCRIPT
[14] K. Suzuki, H. Nagasawa, Y. Uto, Y. Sugimoto, K. Noguchi, M. Wakida, K. Wierzba, T.
Terada, T. Asao, Y. Yamada, K. Kitazato, H. Hori, Bioorg. Med. Chem. 13 (2005) 4014-4021.
[15] S. Nadeem, M. Shamsher-Alam, W. Ahsan, ActaPharma 58 (2008) 445-454.
[16] M.A. Abbasi, A. Rehman, M. Irshad, S.Z. Siddiqui, M. Ashraf, Pak. J. Chem. 4 (2014) 26-
30.
[17] Y. Liu, G.Y. Zhang, Y. Li, Y.N. Zhang, S.Z. Zheng, Z.X. Zhou, S.J. An, Y.H. Jin, Heteroat.
Chem. 24 (2013) 9-17.
[18] Alzheimer’s Association, Alzheimer’s & Dementia 15 (2019) 321‒387.
[19] L. Xiang, Y. Xu, Y. Zhang, X. Meng, P. Wang, J. Mol. Struct. 1086 (2015) 207‒215.
[20] Ü. Demirbas¸ B. Barut, A. Özel, H. Kantekin, J. Mol. Struct. 1187 (2019) 8‒13.
[21] I. Khan, S.M. Bakht, A. Ibrar, S. Abbas, S. Hameed, J.M. White, U.A. Rana, S. Zaib, M.
Shahid, J. Iqbal, RSC Adv. 5 (2015) 21249–21267.
[22] I. Khan, A. Ibrar, S. Zaib, S. Ahmad, N. Furtmann, S. Hameed, J. Simpson, J. Bajorath, J.
Iqbal, Bioorg. Med. Chem. 22 (2014) 6163–6173.
[23] I. Khan, M. Hanif, M.T. Hussain, A.A. Khan, M.A.S. Aslam, N.H. Rama, J. Iqbal, Aust. J.
Chem. 65 (2012) 1413–1419.
[24] B. Zhou, B. Zhang, X. Li, X. Liu, H. Li, D. Li, Z. Cui, H. Geng, L. Zhou, Sci. Rep. 8 (2018)
1559.
[25] J.L. Cummings, Lancet 356 (2000) 2024–2025.
[26] H.J. Schneider, Angew. Chem. Int. Ed. (48) 2009 3924–3977.
[27] J.S. Murray, K.E. Riley, P. Politzer, T. Clark, Aust. J. Chem. 63 (2010) 1598–1607.
[28] P. Politzer, J.S. Murray, ChemPhysChem 14 (2013) 278–294.
[29] P. Metrangolo, G. Resnati, Cryst. Growth Des. 12 (2012) 5835–5838.

MANUS CRIP T
ACCEP TED
ACCEPTED MANUSCRIPT
[30] A Bauzá, T.J. Mooibroek, A. Frontera, Angew. Chem. Int. Ed. 52 (2013) 12317-12321.
[31] A. Bauza, T.J. Mooibroek, A. Frontera, Chem. Eur. J. 20 (2014) 10245–10248.
[32] G.R. Desiraju, T. Steiner, The Weak Hydrogen Bond in Structural Chemistry and Biology,
Oxford University Press, Oxford, 1999.
[33] J.C. Ma, D.A. Dougherty, Chem. Rev. 97 (1997) 1303-1324.
[34] A. Frontera, P. Gamez, M. Mascal, T.J. Mooibroek, J. Reedijk, Angew. Chem. Int. Ed. 50
(2011) 9564-9583.
[35] A. Bauzá, D. Quiñonero, P.M. Deyà, A. Frontera, New J. Chem. 37 (2013) 2636–2641.
[36] A. Bauzá, D. Quiñonero, P.M. Deyà, A. Frontera, Chem. Phys. Lett. 37 (2013) 2636–2641.
[37] P. Gamez, T.J. Mooibroek, S.J. Teat, J. Reedijk, Acc. Chem. Res. 40 (2007) 435-444.
[38] K.E. Riley, P. Hobza, Acc. Chem. Res. 46 (2013) 927-936.
[39] S. Goyal, A. Chattopadhyay, K. Kasavajhala, U.D. Priyakumar, J. Am. Chem. Soc. 139
(2017) 14931-14946.
[40] K.C. Ryan, A.I. Guce, O.E. Johnson, T.C. Brunold, D.E. Cabelli, S.C. Garman, M.J.
Maroney, Biochemistry 54 (2015) 1016-1027.
[41] S.K. Seth, I. Saha, C. Estarellas, A. Frontera, T. Kar, S. Mukhopadhyay, Cryst. Growth Des.
11 (2011) 3250-3265.
[42] B.R. Beno, K.-S. Yeung, M.D. Bartberger, L.D. Pennington, N.A. Meanwell, J. Med. Chem.
58 (2015) 4383-4438.
[43] M. Raynal, P. Ballester, A. Vidal-Ferran, P.W.N.M. van Leeuwen, Chem. Soc. Rev. 43
(2014) 1660-1733.
[44] G.R. Desiraju, T. Steiner, The Weak Hydrogen Bond in Structural Chemistry and Biology,
Oxford University Press, Oxford, 2001.

MANUS CRIP T
ACCEP TED
ACCEPTED MANUSCRIPT
[45] J.W. Steed, J.L. Atwood, Supramolecular Chemistry, second ed., Wiley, Chichester, 2009.
[46] H. Andleeb, I. Khan, A. Bauzá, M.N. Tahir, J. Simpson, S. Hameed, A. Frontera, Acta
Cryst. C74 (2018) 816–829.
[47] H. Andleeb, I. Khan, A. Bauzá, M.N. Tahir, J. Simpson, S. Hameed, A. Frontera, J. Mol.
Struct. 1139 (2017) 209-221.
[48] R. Shukla, I. Khan, A. Ibrar, J. Simpson, D. Chopra, CrystEngComm 19 (2017) 3485–3498.
[49] I. Khan, P. Panini, S.U.-D. Khan, U.A. Rana, H. Andleeb, D. Chopra, S. Hameed, J.
Simpson, Cryst. Growth Des. 16 (2016) 1371−1386.
[50] I. Khan, A. Ibrar, J. Simpson, CrystEngComm 16 (2014) 164–174.
[51] Bruker, APEX2, SAINT, SADABS. Bruker AXS Inc., Madison, Wisconsin, USA, 2009.
[52] G.M. Sheldrick, Acta Cryst. A64 (2008) 112-122.
[53] G.M. Sheldrick, SHELXL Acta Cryst. C71 (2014) 3-8.
[54] K.A. Hunter, J. Simpson, TITAN2000. University of Otago, New Zealand, 1999.
[55] C.F. Macrae, I.J. Bruno, J.A. Chisholm, P.R. Edgington, P. McCabe, E. Pidcock, L.
Rodriguez-Monge, R. Taylor, J. van de Streek, P. A. Wood, J Appl. Cryst 41 (2008) 466-470.
[56] A.L. Spek, Acta Cryst. D65 (2009) 148-155.
[57] L.J. Farrugia, J. Appl. Cryst. 45 (2012) 849-854.
[58] M.J. Frisch, G.W. Trucks, H.B. Schlegel, G.E. Scuseria, M.A. Robb, J.R. Cheeseman, G.
Scalmani, V. Barone, B. Mennucci, G.A. Petersson, H. Nakatsuji, M. Caricato, X. Li, H.P.
Hratchian, A.F. Izmaylov, J. Bloino, G. Zheng, J.L. Sonnenberg, M. Hada, M. Ehara, K. Toyota,
R. Fukuda, J. Hasegawa, M. Ishida, T. Nakajima, Y. Honda, O. Kitao, H. Nakai, T. Vreven, J.A.
Montgomery, Jr., J.E. Peralta, F. Ogliaro, M. Bearpark, J.J. Heyd, E. Brothers, K.N. Kudin, V.N.
Staroverov, R. Kobayashi, J. Normand, K. Raghavachari, A. Rendell, J.C. Burant, S.S. Iyengar,

MANUS CRIP T
ACCEP TED
ACCEPTED MANUSCRIPT
J. Tomasi, M. Cossi, N. Rega, J.M. Millam, M. Klene, J.E. Knox, J.B. Cross, V. Bakken, C.
Adamo, J. Jaramillo, R. Gomperts, R.E. Stratmann, O. Yazyev, A.J. Austin, R. Cammi, C.
Pomelli, J.W. Ochterski, R.L. Martin, K. Morokuma, V.G. Zakrzewski, G.A. Voth, P. Salvador,
J.J. Dannenberg, S. Dapprich, A.D. Daniels, Ö. Farkas, J.B. Foresman, J.V. Ortiz, J. Cioslowski,
D.J. Fox, Gaussian 09 (Gaussian, Inc., Wallingford CT, 2009).
[59] S. Grimme, J. Antony, S. Ehrlich, H. Krieg, J. Chem. Phys. 132 (2010) 154104.
[60] S.F. Boys, F. Bernardi, Mol. Phys. 19 (1970) 553–566.
[61] J. Contreras-García, E.R. Johnson, S. Keinan, R. Chaudret, J.-P. Piquemal, D.N. Beratan,
W. Yang, J. Chem. Theory Comput. 7 (2011) 625-632.
[62] S.K. Ignatov, Moltran v.2.5 — Program for molecular visualization and thermodynamic
calculations, University of Nizhny Novgorod, 2004, http://www.qchem.unn.ru/moltran.
[63] R.F.W. Bader, Atoms in Molecules: A Quantum Theory", Oxford University Press, Oxford,
1990.
[64] T.A. Keith, T.K Gristmill, AIMAll (Version 19.02.13), Gristmill Software, Overland Park
KS, USA, 2019 (aim.tkgristmill.com).
[65] M.A. Spackman, D. Jayatilaka, CrystEngComm, 11 (2009) 19–32.
[66] M.J. Turner, J.J. McKinnon, S.K. Wolff, D.J. Grimwood, P.R. Spackman, D. Jayatilaka,
M.A. Spackman, 2017, CrystalExplorer17. University of Western Australia, Nedlands, Western
Australia; http://hirshfeldsurface.net.
[67] G.L. Ellman, K.D. Courtney, V. Andres, Jr; R.M. Feather-Stone, Biochem. Pharmacol. 7
(1961) 88-90.
[68] A.R. Leach, B.K. Shoichet, C. Peishoff, J. Med. Chem. 49 (2006) 5851–5855.
[69] C.R. Groom, I.J. Bruno, M.P. Lightfoot, S.C. Ward, Acta Cryst. B72 (2016) 171-179.

MANUS CRIP T
ACCEP TED
ACCEPTED MANUSCRIPT
[70] V. Strukil, B. Bartolec, T. Portada, I. Dilovic, I. Halasz, D. Margetic, Chem. Commun. 48
(2012) 12100-12102.
[71] J. O'Leary, X. Formosa, W. Skranc, J.D. Wallis, Org. Biomol. Chem. 3 (2005) 3273-3283
[72] J. Bernstein, R.E. Davis, L. Shimoni, N.-L. Chang, Angew. Chem. Int. Ed. Engl. 34 (1995)
1555-1573.
[73] G.R. Desiraju, P.S. Ho, L. Kloo, A.C. Legon, R. Marquardt, P. Metrangolo, P. A. Politzer,
G. Resnati, K. Rissanen, Pure Appl. Chem. 85 (2013) 1711–1713.
[74] M.D. Prasana, T.N. Guru Row, Cryst. Eng. 3 (2000) 135-154.
[75] R. Shukla, P. Panini, C.J. McAdam, B.H. Robinson, J. Simpson, T. Tagg, D. Chopra, J.
Mol. Struct. 1131 (2017) 16-24.
[76] I. Saraogi, V.G. Vijay, S. Das. K. Sekar, T.N. Guru Row, Cryst. Eng. 6 (2003) 69-77.
[77] H. Matter, M. Nazaré, S. Güssregen, D.W. Will, H. Schreuder, A. Bauer, M. Urmann, K.
Ritter, M. Wagner, V. Wehner, Angew. Chem. Int. Ed. 48 (2009) 2911-2916.
[78] H.T. Akçay, R. Bayrak, E. Şahin, K. Karaoğlu, Ü. Demirbaş, Spectrochim. Acta A Mol.
Biomol. Spectrosc. 114 (2013) 531-540.
[79] X.-Q. Gao, Q.-J. Pan, L. Li, Y.-R. Guo, H.-X. Zhang, H.-G. Fu, Chem. Phys. Lett. 506
(2011) 146-151.
[80] M. Ponikvar-Svet, D.N. Zeiger, L.R. Keating, J.F. Liebman, Struct. Chem. 25 (2014) 1581-
1592.
[81] A. Galstyan, K. Riehemann, M. Schafers, A. Faust, J. Mater. Chem. B 4 (2016) 5683-5691.
[82] T. Koopmans, Physica 1 (1934) 104-113.
[83] V. Balachandran, G. Mahalakshmi, A. Lakshmi, A. Janaki, Spectrochim. Acta A Mol.
Biomol. Spectrosc. 97 (2012) 1101-1110.

MANUS CRIP T
ACCEP TED
ACCEPTED MANUSCRIPT
[84] E.T. Farkhani, M. Pourayoubi, M. Izadyar, P.V. Andreev, E.S. Shchegravina, Acta Cryst.
C74 (2018) 847–855.
[85] C.J. McAdam, L.R. Hanton, S.C. Moratti, J. Simpson, R.N. Wickramasinhage, Acta Cryst.
E75 (2019) 946–950.
[86] R.F.W. Bader J. Phys. Chem. A 102 (1998) 7314‒7323.
[87] F. Cortes-Guzman, R.F.W. Bader, Coord. Chem. Rev. 249 (2005) 633‒662.
[88] V. Balachandran, G. Santhi, V. Karpagam, A. Lakshmi, Spectrochim. Acta A Mol. Biomol.
Spectrosc. 110 (2013) 130-140.
[89] V. Balachandran, S. Lalitha, S. Rajeswari, Spectrochim. Acta A Mol. Biomol. Spectrosc. 97
(2012) 1023-1032.
[90] D.-Y. Peng, Q. Sun, X.-L. Zhu, H.-Y. Lin, Q. Chen, N.-X. Yu, W.-C. Yang, G.-F. Yang,
Bioorg. Med. Chem. 20 (2012) 6739–6750.
[91] A. Mohammadi-Farani, S.S. Darbandi, A. Aliabadi, Iran. J. Pharm. Res. 15 (2016) 313‒320.
[92] X.-H. Gao, L.-B. Liu, H.-R. Liu, J.-J. Tang, L. Kang, H. Wu, P. Cui, J. Yan, J. Enzyme
Inhib. Med. Chem. 33 (2018) 110‒114.

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ACCEPTED MANUSCRIPT
Highlights
• Synthesis of N-(2,4-dichlorophenyl)-1-naphthamide 3
• Theoretical and experimental analysis of noncovalent interactions
• Analysis of thermodynamic and biological properties
• Identification of strong anti-Alzheimer efficacy