Synthesis, spectroscopic, computational and drug docking studies of 1-(benzenesulfonyl)-2-methyl-1H-indole-3-carbaldehyde

Article abstract of DOI:10.1016/j.molstruc.2018.12.069

An N-Substituted 1H-indole derivative having an empirical formula C₁₆H₁₃NO₃S was synthesized by the condensation of 2-Methyl-1H-Indole-3-carbaldehyde and benzene sulfonyl chloride in presence of a phase transfer catalyst of type quaternary ammonium salt in basic conditions. Then the compound was characterized by using FT-IR, UV–Visible and NMR spectroscopic methods. Thus the obtained experimental results were effectively compared with DFT studies in arriving the structural characteristics of the title compound. From vibrational analysis, it was observed that carbonyl frequency is somewhat lower than a typical aldehydic stretching frequency and it could be possible only when the formyl group is coplanar with the ring and subsequent resonance conjugation reduces its force constant. Similarly, the optical absorption behavior of a typical indole ring suffered from a bathochromic shift due to the presence of ring substituents. Finally, the molecular drug docking studies of the title compound were performed using AutoDock 4.2 tools to ascertain its binding mode, efficiency and the nature of chemical interactions with the target proteins and it has been predicted theoretically that the binding efficiency of the ligand on the target receptor surface was found to be better in the case of Gram positive bacteria S. Aureus than the Gram negative N. Meningitidis.

Full text of DOI:10.1016/j.molstruc.2018.12.069

Accepted Manuscript
Synthesis, spectroscopic, computational and drug docking studies of 1-
(benzenesulfonyl)-2-methyl-1H-indole-3-carbaldehyde
Yagna Narayana Bellomkond, S.P. Vijaya Chamundeeswari
PII:
S0022-2860(18)31502-3
DOI:
https://doi.org/10.1016/j.molstruc.2018.12.069
MOLSTR 26006
Reference:
To appear in: Journal of Molecular Structure
Received Date: 17 July 2018
Revised Date: 14 December 2018
Accepted Date: 17 December 2018
Please cite this article as: Y.N. Bellomkond, S.P. Vijaya Chamundeeswari, Synthesis, spectroscopic,
computational and drug docking studies of 1-(benzenesulfonyl)-2-methyl-1H-indole-3-carbaldehyde,
Journal of Molecular Structure (2019), doi: https://doi.org/10.1016/j.molstruc.2018.12.069.
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ACCEPTED MANUSCRIPT
Graphical Abstract
Synthesis, spectroscopic, computational and drug docking studies of
1-(Benzenesulfonyl)-2-Methyl-1H-Indole-3-Carbaldehyde
B.YAGNA NARAYANA*a and SP.VIJAYA CHAMUNDEESWARI*a
a School of Advanced Sciences, Vellore Institute of Technology, Vellore, India.

ACCEPTED MANUSCRIPT
Synthesis, spectroscopic, computational and drug docking studies of
1-(Benzenesulfonyl)-2-Methyl-1H-Indole-3-Carbaldehyde
Yagna Narayana Bellomkonda and SP.VijayaChamundeeswarib*
a School of Advanced Sciences, Vellore Institute of Technology, Vellore, India.
bCenter for crystal Growth,Vellore Institute of Technology,Vellore,India
* E-mail address:vijaya_vit64@yahoo.co.in
Mobile: +91 9003508929
Abstract
An N-Substituted 1H-indole derivative having an empirical formula
C16H13NO3S was synthesized by the condensation of 2-Methyl-1H-Indole-3-carbaldehyde
and benzene sulfonyl chloride in presence of a phase transfer catalyst of type quaternary
ammonium salt in basic conditions. Then the compound was characterized by using
FT-IR, UV-Visible and NMR spectroscopic methods. Thus the obtained experimental
results were effectively compared with DFT studies in arriving the structural
characteristics of the title compound. From vibrational analysis, it was observed that
carbonyl frequency is somewhat lower than a typical aldehydic stretching frequency and it
could be possible only when the formyl group is coplanar with the ring and subsequent
resonance conjugation reduces its force constant. Similarly, the optical absorption
behavior of a typical indole ring suffered from a bathochromic shift due to the presence of
ring substituents. Finally, the molecular drug docking studies of the title compound were
performed using AutoDock 4.2 tools to ascertain its binding mode, efficiency and the
nature of chemical interactions with the target proteins and it has been predicted
theoretically that the binding efficiency of the ligand on the target receptor surface was
found to be better in the case of Gram positive bacteria S.Aureus than the Gram negative
N.Meningitidis.

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Keywords: 1-Benzenesulfony-1H-indole; 3-formyl-1H-indole; N-substituted-1H-indole;
N-substituted sulfonamide; Skatole.
1. Introduction
In the search for safer and more potent therapeutic agents, a popular
approach is to synthesize and evaluate biologically active compounds with chemical
structures analogous to those having the desired biological activity. The approach of the
practice of medicinal field has been developed by synthesizing new compounds based
largely on modifications of structures of known activity. Literature survey reveals that
majority of the pharmacologically active agents are heterocyclic compounds [1].
Especially, the chemistry of indoles are quite rewarding from synthetic and biological
aspects [2-9]. Indole itself is found in coal-tar. Animal body contains indole which is
formed along with pus and also in liver, pancreas, the brain and bile. Human and animal
faeces are found to contain indole and its methyl homologue i.e. skatole [10].
In view of these general observations, our attention was drawn towards the
synthesis and study of biological properties of N-Heterocycles, mainly indole derivatives
of biological and pharmacological interest since it has various activities mainly shown to
exhibit anti-bacterial properties against Gram positive, Gram negative and fungi [11-12].
Of several natural products containing indole nucleus, mention may be made of the
essential amino acid L-tryptophan, the plant growth hormone indole-3-acetic acid, the
vasoconstrictor serotonin, a large number of alkaloids like abrine, reserpine, bufotenin,
brucine, yohimbine, strychnine etc. Also the medicinally important antibiotics like
mitomycin, indolomycin, gliotoxin and aparanotin. As most of the naturally occurring
heterocycles possess varities of pharmacological activities, it is not surprising to expect

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that synthetic hetorocycles may also exhibit interesting pharmacological properties. For
example, the discovery of indomethacin 950, a very important nonsteriodal anti-
inflammatory and antipyretic agent gave an impetus to synthesize large number of its
structural analogues [13]. Keasling et al. have reported that a considerable number of 3-
acylindole possessed anticonvulsant action that can be compared to the activity of
phenobarbital [14]. Similarly, the various 3-carboxamido-1-phenylindoles also shown to
have exhibited analgesic, anti-inflammatory, hypotensive, vaso-dilator, anti-convulsant,
sedative, muscle relaxant and para sympatholytic activities. Because of varied biodynamic
properties of indole and its derivatives, today the scope of indole research is multifarious
extending from rather simple molecules to highly complex molecules. Design and
developing a procedure for the transformation of simple molecules in to a bioactive
molecule with different functionalities is a worthwhile contribution in organic synthesis
and thereby we can enhances some important physiochemical properties demanded for a
targeted drug delivery. The physicochemical properties of the lead molecule play a critical
role in drug formulation. The two most relevant physicochemical properties to drug
delivery is solubility and stability. There are several parameters that affect the solubility
and chemical stability of a drug in solution. The pH of the solution can dramatically affect
both the solubility and chemical stability of the drug. Buffer concentration/composition
and ionic strength can also have an effect, especially on chemical stability. The
hydrophobic/hydrophilic nature of the drug influences solubility.
A
typical
characterization of a drug will start with a study of the chemical stability of the drug as a
function of pH. First, we presented hare a report of valid synthetic procedure and the
structural analysis drawn out of both experimental and theoretical outcomes. Then, we
presented only the theoretical docking results for future considerations regarding
biological activity of the title compound.

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2. Experimental methods
2.1. Synthesis of 1-(Benzenesulfonyl)-2-Methyl-1H-Indole-3-Carbaldehyde
To a solution of 2-Methyl-indole-3-carbaldehyde (1) (2.1g, 10.0mmoles) in
Benzene (50 mL) containing 50% NaOH solution (25 mL), tetrabutylammonium
hydrogensulphate (100 mg) and P-Toluenesulfonyl chloride (1.31g, 10.0mmoles) were
added. The mixture was stirred well for 4 h. Then it was poured over crushed ice and
extracted with ethyl acetate (3x50mL). The organic layer was separated, washed with
water (3x25mL) and dried (MgSO4). Crystallization process by slow solvent evaporation
technique using ethyl acetate gave the desired product in 87% yield. The above proposed
reaction scheme is presented in Figure 1.
CHO
N
CHO
CH3
DMF
50% NaOH
N
CH3
POCL3
C6H6
O
O
S
N
N
H
O
H
Cl
S
O
Figure 1. Reaction scheme for the synthesis of 1-(Benzenesulfonyl)-2-Methyl-1-H-Indole-
3-Carbaldehyde
2.2. FT-IR spectroscopy
The FT-IR spectrum was recorded with Perkin Elmer spectrum One FT-IR
spectrometer and the scan range was maintained within the standard limit between the
sample and the reference.
2.3. UV-Visible spectroscopy
UV-Visible spectrum of an aqueous solution of the title compound, and deionized
water as an internal standard, was recorded over a range of 200–800 nm with a JASCO

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V-670 PC spectrophotometer, operated at a resolution of 0.5 nm. The sampling were made
in a quartz cuvette having a path length of 1.0 cm.
2.4. 1H NMR spectroscopy
1
The H NMR spectrum of the title compound was recorded on Bruker 400 MHz
Avance NMR spectrometer using TMS as an internal standard. Sampling of the compound
was done by employing polar aprotic solvent, CDCl3.
2.5. 13C NMR spectroscopy
The proton decoupled 13C NMR spectrum was recorded on Bruker 400 MHz
Avance NMR spectrometer, by using deuterated Chloroform (CDCl3) as a solvent and
TMS was used as an internal standard.
3. Computational methods
3.1. Density Functional Theoretical method
The Density functional theoretical (DFT) calculations were performed using
Gaussian-03 quantum-chemical software package [15]. The CAM-B3LYP/B3LYP hybrid
density function and triple split valence 6-311++G (d p) basis set has been used [16-18]. It
is noteworthy to mention that the original CAMB3LYP functional is defined with a
coulomb-attenuating parameter of α+β=0.65 and, therefore, exhibits a -0.65/r dependence
for the exchange potential. As a result, the CAMB3LYP functional becomes different
when compared to other LC functionals like LC-BLYP, Wb97xD etc., and it does not
incorporate a full 100% HF exchange at large inter-electronic distances [19-20]. The
electronic absorption spectrum and the nuclear magnetic shielding tensors were simulated
by employing Time-dependent self-consistent field (TD-SCF) and Gauss independent
atomic orbital (GIAO) methods [21-22] respectively.

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3.2. Molecular drug-docking studies
Docking calculations were carried out using AutoDock 4.1 tools [23]. Gasteiger
partial atomic charges were added to the ligand atoms. Non-polar H-atoms were merged,
and rotatable bonds were defined. Docking calculations were carried out on appropriate
protein targets. Essential hydrogen atoms, Kollman united atom type charges, and
solvation parameter were added with the aid of AutoDock tools. Affinity grid maps of xx
Å grid points and 0.375 Å spacing were generated by customizing and running the
Autogrid program. AutoDock parameter set- and distance-dependent dielectric functions
were used in the calculation of the van der Waals and the electrostatic terms, respectively.
Docking simulations were performed using the Lamarckian genetic algorithm (LGA) and
local search method. Initial position, orientation, and torsion of the ligand molecules were
set accordingly. All rotatable torsion were released during docking. Each docking
experiment was derived from 10 different runs that were set to terminate after a max. of
250000 energy evaluation. The population size was set to 150. During the search, a
translational step of 0.2 Å, and quaternion and torsion steps of 5 were applied. Docking
results were analyzed and the high-resolution images were generated with the help of
CHIMERA molecular visualization program [24].
4. Results and discussion
4.1. Optimized molecular geometry
The geometry minimization, of pre-optimized
structure of
1-(Benzenesulfonyl)-2-Methyl-1H-Indole-3-Carbaldehyde by semi-empirical method, is
carried out using the DFT model CAM-B3LYP/6-311++G (d p) incorporating water as a
solvent molecules by utilizing the polar continuum model (PCM) [25-26]. The optimized
geometry is shown in the Figure 2. Calculated geometrical parameters viz. Bond lengths

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and angles are listed in the Table 1. The CAM-B3LYP model predicted a ground state
energy of about -1295.90 Hartrees in aqueous phase. The gas phase single point energy
state of the above mentioned optimized structure of 1-(Benzenesulfonyl)-2-Methyl-1H-
Indole-3-Carbaldehyde is found to be less stabler than the solvated title compound by
means of 100.4 kcal. After 23 states of minimization process in aqueous solution, the
stationary point was found and the optimization convergence plot of energy E vs N steps is
given in the Figure 3. Criteria for convergence to a stationary point is given in the
Table 2. Similarly, the frequency calculation has no imaginary frequencies which also
confirmed that the optimized geometry of the title compound become the stationary point
for the molecular system [27].
Figure 2. Optimized geometry of 1-(Benzenesulfonyl)-2-Methyl-1H-Indole-3-
Carbaldehyde showing numbering scheme according to DFT model
The optimized structure shows a co-planar formyl group with an indole ring which
could result in an extensive conjugation and it is confirmed from the bond length of 1.45 Å
between C7-C19 atoms. The predicted bond length reveals a partial double bond character
between the above mentioned atoms. Furthermore, the C=O bond of formyl group also
shows a slight increase in its length, and strongly added support to the bond resonance. Of
all C-H bonds, the formyl C-H bond length is found to be higher i.e. proton become
deshielded and will expected to have higher chemical shift value compared to other

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protons in the title compound. Similarly, an intermediate value of 1.4 Å for C-N bond
lengths of indole ring also confirmed the resonance delocalization. The bond lengths of C-
S and S=O are found to be 1.8 and 1.4 Å, respectively and showed a good correlation with
that of literature value [28] corresponding to σ
and π
bonds. Moreover, both the
S=O
C-S
phenyl and indole ring systems are almost perpendicular to each other, which is evident
from the calculate bond angle of about 105˚ between the C6-S19-N7 atoms.
Table 1. Optimized geometrical parameters of 1-(Benzenesulfonyl)-2-Methyl-1H-Indole-
3-Carbaldehyde by using the CAM-B3LYP/6-311++G (d p) model
Parameters
Parameters
Obtained
values (Å)
1.388
1.388
1.082
1.388
1.082
1.391
1.083
1.385
1.082
1.39
Obtained
values (°)
1.219
1.101
1.448
1.447
118.5
121
120.1
119.6
120.4
122.2
118.9
120.3
120.5
119.8
119.7
120.1
120.2
119.6
118.5
120.5
121
118.9
104.7
109.5
109.1
109.2
125.3
108.3
123.4
124.9
106.9
131.3
Parameters
Obtained
values (ν)
105.3
106.8
128.4
108.3
125.2
109.9
111.2
111.4
126.5
132.7
107.3
124.1
116.4
119.9
118.6
119.9
121.8
121.4
120.7
119.8
119.5
121.6
119.6
118.9
117.4
120.7
121.9
108.9
107.8
107.6
119.5
120.3
R(1-2)
R(1-6)
R(1-22)
R(2-3)
R(2-23)
R(3-4)
R(3-24)
R(4-5)
R(4-25)
R(5-6)
R(5-26)
R(6-19)
R(7-8)
R(7-15)
R(7-19)
R(8-9)
R(8-16)
R(9-10)
R(9-17)
R(10-11)
R(10-15)
R(11-12)
R(11-27)
R(12-13)
R(12-28)
R(13-14)
R(13-29)
R(14-15)
R(14-30)
R(16-31)
R(16-32)
R(16-33)
R(17-18)
R(17-34)
R(19-20)
R(19-21)
A(2-1-6)
A(2-1-22)
A(1-2-3)
A(1-2-23)
A(6-1-22)
A(1-6-5)
A(1-6-19)
A(3-2-23)
A(2-3-4)
A(2-3-24)
A(4-3-24)
A(3-4-5)
A(3-4-25)
A(5-4-25)
A(4-5-6)
A(4-5-26)
A(6-5-26)
A(5-6-19)
A(6-19-7)
A(6-19-20)
A(6-19-21)
A(8-7-15)
A(8-7-19)
A(7-8-9)
A(7-8-16)
A(15-7-19)
A(7-15-10)
A(7-15-14)
A(7-19-20)
A(7-19-21)
A(9-8-16)
A(8-9-10)
A(8-9-17)
A(8-16-31)
A(8-16-32)
A(8-16-33)
A(10-9-17)
A(9-10-11)
A(9-10-15)
A(9-17-18)
A(9-17-34)
A(11-10-15)
A(10-11-12)
A(10-11-27)
A(10-15-14)
A(12-11-27)
A(11-12-13)
A(11-12-28)
A(13-12-28)
A(12-13-14)
A(12-13-29)
A(14-13-29)
A(13-14-15)
A(13-14-30)
A(15-14-30)
A(31-16-32)
A(31-16-33)
A(32-16-33)
A(18-17-34)
A(20-19-21)
1.082
1.775
1.396
1.42
1.712
1.373
1.489
1.446
1.447
1.396
1.401
1.383
1.081
1.398
1.083
1.385
1.083
1.391
1.078
1.086
1.089
1.091
R – bond length (Å); A – bond angle (°); W – vibrational frequencies (ν).

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Table 2. Criteria for the convergence of minimization process
S.No
PARAMETERS
Max. force
VALUE
THRESHOLD
0.000450
0.000300
0.001800
0.001200
CONVERGED
1
2
3
4
0.000020
0.000004
0.001474
0.000411
yes
yes
yes
yes
RMS force
Max. displacement
RMS displacement
4.2. Molecular properties
4.2.1 Dipole moment
Dipole moment of 1-(Benzenesulfonyl)-2-Methyl-1H-Indole-3-Carbaldehyde is
found to be 7.9 D in water, and the respective dipole moment vector components are given
in the Table 3. In the gas phase, the dipole moment of single point geometry of the title
compound is only about 6.0 D which is appreciably lesser than that of the same in aqueous
phase and far greater than that of water (ꢀtotal=1.85 D). Its seem that the dipole moment of

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the title compound could increase with increasing the solvent polarity. Moreover, the
overall dipole moment vector is found to be bisecting the XZ-plane from the origin at an
approximate angle of 45˚ and very much perpendicular to Y-axis, is shown in Figure 4.
Table 3. Theoretical dipole moment and dipole moment components of
1-(Benzenesulfonyl)-2-Methyl-1H-Indole-3-Carbaldehyde
Dipole vector components
Dipole moment, µ(Debye)
–6.89
0.47
µx
µy
-3.82
7.90
µz
µtotal
4.2.2 Molecular electrostatic potential (MEP)
Molecular electrostatic potential map provides versatile information about the
molecular reactivities such as nucleophilicity, electrophilicity, protonation/deprotonation,
H-bonding’s and various other possible molecular interactions [29]. The MEP surfaces of
1-(Benzenesulfonyl)-2-Methyl-1H-Indole-3-Carbaldehyde is shown in Figure 5. As
expected, most electronegative atoms viz. C and N-atoms has a negative potential surface
indicated by bright red colored surface. Indole N-atom has comparatively less negative

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potential than that of O-atoms, since its lone pair of electrons involved in an aromatic
delocalization. Hence, the three O-atoms only expected to be participate in any kind of
inter-molecular interactions. The sulfonyl S-atom seems buried inside the highest possible
positive potential surface of the title compound.
Figure 5. MEP Surface of 1-(Benzenesulfonyl)-2-Methyl-1H-Indole-3-Carbaldehyde
4.2.3 FMO Analysis
Frontier molecular orbital analysis of the title compound is carried by using the
same DFT model as mentioned earlier for geometry optimization. The molecular system
found to have 219 molecular orbitals. Among them only 156 orbitals are comprising of
bonding and anti-bonding orbital. Rest of them are Rydberg and Non-bonding lone pair
orbitals. Both HOMO and LUMO has anti-symmetric properties with energy of about
-7.9 and -0.76 e V, respectively. The calculated energy gap is found to be quiet large,
7.13 e V. Figure 6a & b, shows the frontier molecular orbitals of 1-(Benzenesulfonyl)-2-
Methyl-1H-Indole-3-Carbaldehyde. Evidently, the HOMO is a pi-bonding molecular
orbital with occupancy of 1.69 on the C-atoms of the indole ring at position-11 and 12.
Whereas LUMO mainly centered on the Rydberg orbitals of the ring carbon atoms with p-

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character at position-1 and 2. It seems very hard for an excitation to happen between these
two states due to an unfavorable energy criteria under ordinary conditions.
4.3. NPA and NBO Analysis
For NPA and NBO analysis [30], the pre-optimized structure of
1-(Benzenesulfonyl)-2-Methyl-1H-Indole-3-Carbaldehyde obtained from CAM-B3LYP/6-
311++G (d p) is utilized. The chosen triple split valence basis model consists of 219 AOs
( 9 AOs each on C,N and O; 13 on S-atom; 2 on each H-atom ) extended by 93 AOs
beyond the minimum basis level.
4.3.1 NPA Analysis
From NAO population, it is observed that carbonyl C-atom possesses a minimum
valence 2s orbital Lewis pair occupancy of only about 0.9 whereas the valence 2s orbital
of O-atom contains a maximum orbital occupancy of about 1.70. Here, the carbonyl
C-atom showed a depletion of 6% of its electron density which can make it as a potent
nucleophilic center and the carbonyl O-atom gains an extra population of about 7.25% of
its own electron density. Also, the formyl H-atom contains a least energetic valence 1s

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orbital of maximum occupancy 0.82. Similarly, the N-atom of indole ring has a total
occupancy of 7.61 which is slightly greater than its actual occupancy. Here the N-atom
could gained its extra population during aromatic delocalization of pi-electrons. The
S-atom of sulfonyl group found to have a total occupancy of only about 13.73 out of 16.
Depletion of electron densities could arise due to the presence of two more electronegative
O-atoms.
The summary of NPA in terms of atomic charge distribution is shown in Figure 7.
The sulfonyl S-atom has nuclear charge of about 2.265 which is far greater than the charge
on the nucleophilic carbonyl C-atom having the value of 0.36. Higher nuclear charge on
the S-atom could arise due to more electronegative O-and N-atom to which the former is
attached terahedrally. All the ring C-atoms, except those attached directly to the more
electronegative N-atom, have negative atomic charges reflecting extra population on their
corresponding atomic orbitals. As expected, all electronegative atoms viz. N and O’s
possess negative atomic charges. Amongst the sulfonyl O-atoms has large negative value.
Similarly, the Natural Minimal Basis (NMB) and Natural Rydberg Basis (NRB)
populations of 1-(Benzenesulfonyl)-2-Methyl-1H-Indole-3-Carbaldehyde are presented in
the Table 4. It is evident that ninety three Rydberg orbitals of the NRB set contribute only
0.2% of electron density. As expected, NMB account for a maximum of 97.79% of
electron densities in the molecule.
Table 4. Summary of the NMB and NRB populations
S.No
TYPE
Core
TOTAL POPULATION
99.96% of 50
1
2
3
4
Valence
99.71% of 106
99.79% of 156
0.21% of 156
Natural Minimal Basis
Natural Rydberg Basis

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Figure 7. Summary of atomic charge distribution in terms of NPA
4.3.1 NBO Analysis
The search for a natural Lewis structure of 1-(Benzenesulfonyl)-2-Methyl-1H-
Indole-3-Carbaldehyde is carried out by the same DFT model as mentioned earlier for
NPA and it has been predicted that the title compund contains 40 and 13 Lewis type 2-
centered bond pairs and 1-centered lone pairs, respectively. The valence Lewis-type
NBO’s contribute only 97% of its total electron densities to the natural Lewis structure
which is slightly lesser than expected. Significantly, the anti-bonding orbitals 176 to 219
has an occupancies of about 2.7% in the natural Lewis structure.
4.3.1.1 Perturbation theory energy Analysis
The possible electronic perturbation between ‘filled’ Lewis-type NBO’s and
‘unfilled’ acceptor Non-Lewis NBO’s and energy associated with the same are presented
in the Table 5. Delocalization of anti-bonding electron pair from C10-C15 to an
anti-bonding orbital of C13-C14 provides a higher stabilization energy of about
222.8 kcal/mol. Also, the anti-bonding orbitals of C8-C9 accepts an anti-bonding electron
from the Carbonyl C=O group results in an electronic delocalization energy of 127.6
kcal/mol. It is noteworthy to mention that an electronic interactions between the lone pair

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of N-atom and the anti-bonding orbitals of C8-C9 and C10-C15 provides a delocalization
energies of about 44.5 and 29.7 kcal, respectively. Similarly, the three lone pair
occupancies on each O-atom of sulfonyl bond found to be involved in a transition to an
anti-bonding orbitals of N7-S19 and contributing an energy about 40 kcal towards the
molecular stabilization of 1-(Benzenesulfonyl)-2-Methyl-1H-Indole-3-Carbaldehyde.
Table 5. Energies associated with delocalization of electron density using
the second order Perturbation theory
S.No
Donor NBO (i)
LP(1)N7
Acceptor NBO (j)
BD*(2)C8-C9
E(2) kcal/mol
44.49
E(j)-E(i) a.u
0.42
F(i,j) a.u
0.122
0.102
0.115
0.121
0.095
0.084
1
2
3
4
5
6
LP(1)N7
BD*(2)C10-C15
BD*(1)N7-S19
BD*(1)N7-S19
BD*(2)C13-C14
BD*(2)C8-C9
29.67
0.41
LP(3)O20
36.98
0.42
LP(3)O21
40.68
0.42
BD*(2)C10-C15
BD*(2)C17-C18
222.76
127.56
0.02
0.01
4.4. FT-IR spectral analysis
The representative FT-IR spectrum of 1-(Benzenesulfonyl)-2-Methyl-1H-
Indole-3-Carbaldehyde is shown in the Figure 8a. Similarly, the simulated vibrational
spectrum of the same by using the DFT model CAM-B3LYP/6-311++G (d p)
in aqueous phase is shown in Figure 8b. Another DFT model
B3LYP/6-311++G (d p) also been utilized for the frequency calculations. The former
model produces a result almost similar to that of experimental observations [31-32]. The
calculated harmonic vibrational frequencies are scaled down by a factor of 0.9613 in order
to attain a reasonable agreement between those observed and theoretically estimated
vibrational frequencies [33]. Most prominent vibrational frequencies and their assignments
are presented in the Table 6a. Similarly, the complete vibrational frequency assignments
are presented in the Table 6b.

16
ACCEPTED MANUSCRIPT

17
ACCEPTED MANUSCRIPT
Table 6a. Most prominent vibrational frequencies and their assignments by comparing
both experimental and theoretical methods
S.No
FT-IR (cm–1)
CAM-B3LYP/6-311++G (d p) in
H2O
B3LYP/6-311++G (d p)
in H2O
Assignment
1
2
3
4
5
6
3066
2926
1664
1246
920
3090
2891
1668
1280
969
3073
2864
1656
1294
961
Aliphatic CH stretching
Formyl CH stretching
C=O stretching
C-N stretching
Indole breathing mode
Sulfonyl scissoring
555
554
540
4.4.1 C=O stretching
The FT-IR spectrum of the title compound clearly shows an intense IR
absorption peak at 1664 cm–1 corresponds to the stretching vibrational mode of the
aldehydic carbonyl group and the CAM-B3LYP model also produces the similar
vibrational frequency at 1668 cm–1. The observed carbonyl frequency is somewhat
lower than a typical aldehydic stretching frequency and this can be explained on the
basis of bond resonance which can be possible only when the formyl group is
coplanar with the indole ring. The DFT model also predicted the same and it is shown
evident from the optimized molecular geometry of the title compound.
4.4.2 Formyl C-H and Aliphatic C-H stretching
Similarly, the two distinct vibrational peaks at 3066 and 2926 cm–1 must be
the vibrational stretching modes of –CH3 and -CHO protons, respectively. As
expected, the vibrational frequency of aldehydic proton observed in a lower frequency
range than the methyl protons. The similar observations are also presented by the
chosen DFT models. The CAM-B3LYP model predicts a value of 3090 and 2891 cm–1
for the vibrational stretching modes of –CH3 and -CHO protons respectively.

18
ACCEPTED MANUSCRIPT
Table 6b. Complete vibrational frequency assignments of 1-(Benzenesulfonyl)-2-Methyl-
1H-Indole-3-Carbaldehyde by comparing both experimental and theoretical methods
S.
No.
Calculated vibrational frequencies (cm-1)
Experimental
IR (cm-1)
ASSIGNMENTS
CAM-B3LYP/6-
311++G (d p)
B3LYP/6-311++G
(dp)
1.
2.
3.
4.
5.
6.
7.
8.
µ
π
µ
ω
µ
ω
µ
ω
ω
ω
-phenyl ring
-C6-S-N
-phenyl ring
-methyl oop
-indole ring
-methyl oop
-methyl
-formyl C-H oop
-formyl C-H oop
-indole ring in-plane
11.03274397
24.93766008
44.06128163
79.14267544
105.8844072
134.428192
-52.3110621
-38.17476108
-4.21991474
49.95674227
78.89725555
113.4454163
140.4963983
151.9797997
158.4550203
173.9256058
188.7813437
206.2651797
259.8598657
276.7853787
300.2140861
303.8901935
319.2568624
325.3827466
386.4058783
392.010738
410.109037
415.260163
448.0378014
478.7144225
515.8607848
540.2315663
554.8898532
556.8651324
161.7287275
165.9705599
174.7746259
184.4400168
203.9255678
218.0555242
269.4972827
283.5643701
304.3307573
318.6928676
322.6945673
337.3935172
400.3010853
401.5741349
416.3318203
430.4185182
460.8419329
481.6363899
530.2038614
554.7103785
562.9930354
573.5747374
9.
10.
11.
12.
13.
14.
15.
16.
17.
18.
19.
20.
21.
22.
23.
24.
25.
26.
27.
28.
29.
µ-methyl
µ-phenyl ring
ω
ω
-SO2
-methyl in-plane
C-S deformation
ω
ω
ω
ω
-S-N
-methyl
-indole ring oop
-C-S
µ-phenyl ring
µ-indole ring in-plane
ω
ω
-phenyl C-H oop
-phenyl C-H oop
Indole ring deformation
-SO2
π
ω
ω
555
-S-O
-formyl C-H
µ-indole ring
µ-indole ring
µ-C8-C9
607.8733446
634.0489669
650.3535762
682.9870195
690.7117379
711.9420484
740.8023893
745.3771199
748.3870463
763.3419904
839.4459965
869.2531218
904.5149516
935.47208
957.9255486
969.0013588
985.390178
986.5222049
988.0905658
988.8960391
1006.444763
1012.519218
1016.115056
1019.487201
1025.416499
1057.508827
603.1480745
614.85046
30.
31.
32.
33.
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
ω
ω
-indole C-C in-plane
-phenyl C-C oop
644.5435751
668.946464
684.0230125
703.3519678
728.6314661
731.7488659
735.1811875
744.2601854
823.7796904
850.7147396
897.3313489
917.2619818
936.2900502
961.3523909
964.50036
965.273149
967.9733446
979.8630875
984.5258732
1005.170367
1010.742255
1012.852308
1014.246001
1050.852689
All ring deformation
π
π
- phenyl C-C-C
- indole C-C-C
ω
ω
ω
ω
ω
-indole C-H oop
-phenyl C-H oop
-indole C-C oop
-phenyl C-H oop
-indole C-H oop
Indole breathing mode
ω
ω
Indole breathing mode
Phenyl C-H deformation
Phenyl breathing
ω
ω
ω
-phenyl C-H oop
-indole C-H oop
920
-formyl C-H
-indole C-H oop
-phenyl C-H oop
All ring breathing
Phenyl breathing
Indole ring deformation
ω
-methyl
C-S deformation
ρ – rocking; ω – wagging; π – scissoring; µ – twisting; oop – out-of-plane.

19
ACCEPTED MANUSCRIPT
S.
No.
Calculated vibrational frequencies (cm-1)
Experimental
IR (cm-1)
ASSIGNMENTS
CAM-B3LYP/6-
311++G (d p)
B3LYP/6-311+G
(dp)
55.
56.
57.
58.
59.
60.
61.
62.
63.
64.
65.
66.
67.
68.
69.
70.
71.
72.
73.
74.
75.
76.
77.
78.
79.
80.
81.
82.
83.
ω
ω
-phenyl in-plane
-indole in-plane
1075.51609
1102.91737
1113.585397
1133.450277
1144.229142
1155.351286
1162.740319
1199.584352
1235.192058
1277.59577
1280.738356
1299.563301
1306.261063
1309.76827
1360.959898
1381.63054
1395.420581
1415.749961
1428.034125
1439.416013
1441.054934
1468.394594
1471.273111
1557.083747
1590.976878
1593.841745
1598.198933
1614.62332
1071.702037
1096.908572
1109.085071
1131.592084
1145.849509
1149.557243
1160.018206
1188.807122
1226.420195
1274.627564
1294.307778
1294.488406
1318.899082
1336.391666
1351.82476
1368.864572
1385.932165
1407.707052
1419.886146
1430.209835
1430.909566
1458.240478
1459.535253
1547.497375
1575.514368
1576.164687
1581.897111
1594.754114
C-S vibration
ω
ω
-phenyl C-H in-plane
-indole C-H in-plane
π
ω
-N-C8-C9
-phenyl C-H
C-N deformation
C8-N-C15 stretching
SO2 asymmetric stretch
C15-N stretching
ω
ω
Indole deformation
Methyl deformation
ω
1246
-C-H all in-plane
-phenyl C-H in-plane
-methyl
Formyl C-H vibration
Methyl deformation
µ-methyl
µ-phenyl in-plane
Indole ring vibration
Phenyl deformation
All ring deformation
C8-C9 stretching
ω
-C-H all in-plane
Phenyl C-C stretching
Phenyl C-C stretching
Indole C-C stretching
Carbonyl stretching
1664
2926
1668.321538
2891.436207
2964.981329
3024.803797
3063.426236
3076.223061
3079.144067
3086.598949
3090.038000
3094.278198
3100.800715
3104.907292
3111.743289
3140.177004
1656.856402
2864.492699
2948.568477
3004.286675
3044.626861
3059.100866
3061.931318
3069.399177
3073.129309
3077.357876
3084.029106
3088.025518
3095.076269
3123.210636
84.
85.
86.
87.
88.
89.
90.
91.
92.
93.
94.
95.
96.
Formyl C-H stretching
Aliphatic C-H stretching
Aliphatic C-H asymmetric
Aliphatic C-H asymmetric
Aromatic C-H stretching
Aromatic C-H stretching
Aromatic C-H asymmetric
Aromatic C-H asymmetric
Phenyl C-H vibration
3066
Indole C-H vibration
Phenyl C-H asymmetric
Phenyl C-H asymmetric
Indole C14-H stretching
_________________________________________________________________________________________________
ρ – rocking; ω – wagging; π – scissoring; µ – twisting; oop – out-of-plane.
4.4.2 Formyl C-H and Aliphatic C-H stretching
Similarly, the two distinct vibrational peaks at 3066 and 2926 cm–1 must be
the vibrational stretching modes of –CH3 and -CHO protons, respectively. As
expected, the vibrational frequency of aldehydic proton observed in a lower frequency
range than the methyl protons. The similar observations are also presented by the
chosen DFT models. The CAM-B3LYP model predicts a value of 3090 and 2891 cm–1
for the vibrational stretching modes of –CH3 and -CHO protons respectively.

20
ACCEPTED MANUSCRIPT
4.4.3 S=O stretching
The vibrational frequency observed at 555 cm–1 could be the bending mode of
sulfonyl S=O bond which is further confirmed from the predicted vibrational frequency.
4.4. UV-Visible spectral analysis
The experimental UV-Visible spectrum of the title compound shows a
two distinct absorption maxima at 290 and 227 nm. The former has the least intensity
compared to that of the later. The absorption spectrum of 1-(Benzenesulfonyl)-2-
Methyl-1H-Indole-3-Carbaldehyde shown in Figure 9a. Absorbance maxima at 290 nm
could more probably be due to the π-π* transition involving the indole moeity. The
characteristics absorption of indole is centered at 270 nm. In this case, λmax shifts towards
longer wave-length which could be due to the bathochromic effect of the methyl
substituent at position-2 and as well as due to an extension of pi-conjugation over the
formyl group at position-3 on the indole ring.

21
ACCEPTED MANUSCRIPT
Similarly, the absorbance peak at 227 nm could arise from the π-π* transition involving
the phenyl ring. The high peak intensity suggested that n-π* transition involving the lone
pair of electrons on the Hetero-atoms viz. O and N becomes least favorable. Since, the n-
π* transitions are generally known to be forbidden transitions with very less intensities
associated with it.
The theoretical absorbance spectrum of the title compound is derived out of
Time-dependent DFT model CAM-B3LYP6-311++G (d p) in aqueous phase. Also, two
more DFT models are employed for the same purpose viz. B3LYP6-311++G (2d p) and
BVP86/6-311++G (d p) methods. But the later models shows large deviation from the
observed experimental results. The CAM-B3LYP model predicts a fairly good absorption
maxima for the title compound which has also some deviation from the experimental
results. The simulated absorption spectrum, shown in Figure 9b, has maximum peak
intensities at 271 and 250 nm corresponding to that of experimental absorbance maxima at
290 and 227 nm, respectively. Moreover, the molecular orbitals invovling the transition
corresponding to λmax at 271 nm are found to be the HOMO/LUMO and HOMO/SUMO.
Similarly, the absorption at 250 nm is found to be more complex to account for and it
comprises of several molecular orbitals viz. HOMO, LUMO, SUMO and other higher
anti-bonding orbitals having pi-symmetry. Nevertheless, the model produces a good
correlation with that of experimental results. The discrepency between the experimental
and theoretical values could be due to the shortsightedness of the chosen DFT model and
expected a tolerance limit of 15 nm. The predicted electronic excitation from CAM-
B3LYP model can be visualized from the charge densities between ground and excited
state. Figure 10 shows a representation of the difference electron density between the
excited and ground state [34].

22
ACCEPTED MANUSCRIPT
It can be easily seen that the electron density moves from the pale green region to the blue
region when moving from the ground state to the first excited state. Thus, for most part,
the predicted electronic transition can be stated as an excitation of electrons originating
mainly from the formyl substituent on the indole ring and also arriving mainly at the same
indole ring.
4.5 NMR Spectroscopy
4.5.1 1H NMR spectrum
1
The obtained experimental H NMR spectrum of 1-(Benzenesulfonyl)-2-
Methyl-1H-Indole-3-Carbaldehyde in CDCl3 is shown in the Figure 11a. Similarly, the
NMR shielding tensors of single point geometry of the title compound is calculated by
GIAO method employing the same DFT model as mentioned earlier for geometry
optimizatin and also by using another DFT model B3LYP/6-31+G (2d p) in DMSO as
solvent. The predicted NMR spectrum of the title compound is shown in Figure 11b.
For comparison, the CAM-B3LYP shows a very good correlation with the experimental
results. Standard reference of TMS shielding tensors computed at B3LYP/6-31+G (2d p)
level is utilized in the calculations.

23
ACCEPTED MANUSCRIPT
The experimental spectrum of 1-(Benzenesulfonyl)-2-Methyl-1H-Indole-3-
Carbaldehyde shows a clusters of absorption peaks over the region 7.0 to 8.5 ppm which
must arise due to the presence of aromatic protons on the periphery of both the phenyl and
indole ring. Similar observations are also predicted by the theoretical methods. Most
importantly, the proton resonating at 2.94 ppm with peak area integrated to 3 unit must be
the CH3 protons at position-2 on the indole ring. Also, the CAM-B3LYP model predicted
a shielding tensor value of 3.08 ppm for the same. Similarly, the more strongly deshielded
proton resonating at 10.30 ppm must be the aldehydic proton of formyl moeity at
position-3 on the indole ring. Here also the chosen theoretical model predicted a value of
10.4 ppm for the same proton which is almost equivalent to the experimental result.
From these observations, it is clearly seen that the proposed CAM-B3LYP model for the
title compound and its derivatives is an appropriate choice of theoretical method for such
NMR predictions. The experimental and theoretical values computed at CAM-B3LYP and
B3LYP model for the title compound is presented in the Table 7.

24
ACCEPTED MANUSCRIPT
Table 7. Experimental and theoretical 1H NMR chemical shifts (ppm) of
1-(Benzenesulfonyl)-2-Methyl-1H-Indole-3-Carbaldehyde
S.No
PROTON
Experimental, CDCL3
Chemical shifts (ppm)
CAM-B3LYP/
6-311++g(d,p)
B3LYP/
6-311+g(2d,p)
DMSO
3.09
DMSO
3.16
1
2
Methyl
Formyl
2.93
10.27
10.42
10.57
4.5.2 13C NMR spectrum
The experimental spectrum of 1-(Benzenesulfonyl)-2-Methyl-1H-Indole-
13
3-Carbaldehyde is shown in the Figure 12. Similarly, the C nuclear magnetic shielding
tensors are computed by utilizing a two different DFT models viz. CAM-B3LYP and
B3LYP models.
Like 1H NMR spectrum of the title compound, the theoretical model B3LYP/6-311+G
(2d p) shows a reliable correlation with that of the obtained experimental results. In this

25
ACCEPTED MANUSCRIPT
case, the CAM-B3LYP model predicts a value somewhat slightly higher for sp2 C-atom
and slightly a lower value for sp3 C-atom. The spectrum displays two distinct resonating
peaks; one at a far downfield region of about 186 ppm and another one at an up-field
region of about 12 ppm. The former is the characteristics radio-frequency absorption peak
of sp2 C-atom of the carbonyl group in aldehydic form. The peak appearing at 12 ppm
corresponds to the sp3 C-atom of the methyl substituent at position-2 on the indole ring.
DFT model B3LYP/6-311+G (2d p) predicts almost a similar value for the above
mentioned C-atoms i.e. 191 ppm for the carbonyl C-atom and 12 ppm for the methyl
substituent. Other sp2 ring C-atoms are found to be resonating between the regions 110 to
160 ppm. Similar resonating peaks are obtained experimentally for the sp2 ring C-atoms.
4.6. Docking studies
The main objective of the molecular docking studies using AUTODOCK 4.2
tools is to evaluate the nature of binding mode, efficiency and types of possible interaction
associated with the title compound, if it could become a potent anti-bacterial against Gram
positive and Gram negative pathogens. For docking purpose, the first NEAT domain of
IsdH protein of Gram positive Staphylococcus Aureus and N-terminal domain of Gram
negative Neisseiria Meningitidis PilB has been chosen and their respective PDB ID’s are
3S48 and 2FY6. The tertiary structure of the chosen receptor protein molecules are shown
in the Figure 13a & b. It is well known that the protein targets viz. 3S48 and 2FY6 are
primarily expressed during the human infection. Both can acts as a cellular adhesion to the
human ligands [35-40].

26
ACCEPTED MANUSCRIPT
Before docking, the residual water molecules are eliminated from the target receptors. All
the polar H’s are added, non-bonded atoms and non-polar H’s are allowed to merge. The
Kollman charges of 18.3 and 4.0 are added to the receptor protein 3S48 and 2FY6,
respectively. Similarly, the ligand molecule is defined and added with Gasteiger partial
charges. All possible rotatable bonds are set to be free and Torsional Degrees Of Freedom
(TORSDOF) is only 3 for the ligand molecule, 1-(Benzenesulfonyl)-2-Methyl-1H-Indole-
3-Carbaldehyde. On the other hand, the protein is considered to be a rigid substrate during
the docking processes. The individual docking results of the title compound involving the

27
ACCEPTED MANUSCRIPT
two seperate receptor proteins 3S48 and 2FY6 are given in the Table 8a & b respectively.
As given in the above table, the Gibb’s free energy of binding is found to be a large
negative value of about 6.24 kcal for the docking process between the ligand and the
receptor 2FY6 which indicate the spontaneity of the process is slightly far better than the
one between the same ligand with the protein 3S48. The later has energy value of only
about -5.69 kcal. It should be mentioned that the docking conformation of the ligand with
the receptor protein 2FY6 has no H-bonding interactions though it has large negative value
of binding when compared to that of the binding energy between the same ligand and the
NEAT domain of S.Aureus.

28
ACCEPTED MANUSCRIPT
on residue Leucine-83 of the receptor protein, shown in the Figure 14. Bond length
between the donor and an acceptor atom is found to be 3.172 Å. Here, it should be
emphasized that an active pharmacological ingredient must exert both kind of binding
forces viz. polar and non-polar interactions.
Table 8a. Estimated free energy, inhibition constant, electrostatic energy and total
intermolecular energy obtained from ligand-protein interactions between the target
receptor 3S48 and 1-(Benzenesulfonyl)-2-Methyl-1H-Indole-3-Carbaldehyde.
Binding
energy
(Kcal/Mol)
Ligand
efficiency
Inhibition
constant
Ki (µM)
Intermolecular
energy
(Kcal/Mol)
Vdw + H-bonding
+ desolv. Energy
(Kcal/Mol)
Electrostatic
energy
(Kcal/Mol)
Total
internal
energy
Torsion.
energy
(Kcal/Mol)
S.NO
-5.69
-5.38
-5.29
-5.22
-5.00
-4.78
-4.54
-4.46
-4.38
-4.01
-0.27
-0.26
-0.25
-0.25
-0.24
-0.23
-0.22
-0.21
-0.21
-0.19
67.47
113.13
133.54
148.55
217.59
315.50
473.26
539.17
610.94
1.15 (mM)
-6.59
-6.28
-6.18
-6.12
-5.89
-5.67
-5.43
-5.35
-5.28
-4.91
-6.29
-6.17
-6.26
-6.06
-5.85
-5.58
-5.28
-5.36
-5.19
-4.88
-0.3
-0.11
0.08
-0.81
-0.85
-0.83
-0.78
-0.96
-0.93
-0.86
-0.81
-0.95
-1.00
0.89
0.89
0.89
0.89
0.89
0.89
0.89
0.89
0.89
0.89
1
2
3
-0.05
-0.04
-0.09
-0.16
0.00
4
5
6
7
8
-0.09
-0.02
9
10
On the basis of inter-molecular interactions as mentioned earlier, it has been
concluded that the binding efficiency of the ligand on the receptor surface is found to be
better in the case of Gram positive bacteria S.Aureus than the Gram negative
N.Meningitidis.