Results in Chemistry 5 (2023) 100763

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Results in Chemistry
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Molecular dynamic, Hirshfeld surface, molecular docking and drug likeness

studies of a potent anti-oxidant, anti-malaria and anti-Inflammatory
medicine: Pyrogallol
M. Amin Mir a, *, Farah Manzer Manhas b, Kim Andrews a, Syed M Hasnain a, Abid Iqbal c,
Shama Sehar d, Adnan Younis e
a
Department of Mathematics & Natural Sciences, Prince Mohammad Bin Fahd University, Al-Khobar, Saudi Arabia
b
Department of Chemistry, Shoolini University, Solan, Himachal Pradesh, India
c
Department of Electrical Engineering, University of Engineering and Technology, Peshawar, Pakistan
d
College of Science, University of Bahrain, Sakhir, Bahrain
e
Department of Physics, College of Science, University of Bahrain, Bahrain

A R T I C L E I N F O A B S T R A C T

Keywords: Pyrogallol (1, 2, 3-trihydroxybenzene) was studied by computational study analysis using density functional
Hirshfeld surface analysis theory (DFT), B3LYP method using 6-311++G (d, p) as basis set. The computational study was done involving
Molecular Electrostatic Potential IR, UV–visible, H NMR and other parameters like, AIM theory (Atoms in molecules) for ellipticity, isosurface
Drug-likeness
projection analysis, and binding energies, which run parallel to experimental values. The crystal intermolecular
Binding energy
interactions were studied by Hirshfeld surface analysis, and donor and acceptor interactions were studied by
NBO analysis. By Pyrogallol was also studied for Fukui function analysis and Molecular Electrostatic Potential
(MEP) and for the nucleophilic and electrophilic sites of interactions. As per the results of energy difference in
frontier molecular orbitals as calculated viz, HOMO and LUMO clearly shows Pyrogallol is stable molecule. The
electrophilicity index, and molecular docking studies show that Pyrogallol is biologically important and can
interact with different proteins with binding energy of 7.405 and 5.718 kcal/mol. The biomolecular stability
involves molecular dynamic simulation. The drug-likeness studies have shown that Pyrogallol as an antibiotic
shows close relationship with Ascorbic Acid, Gallic acid, Ellagic acid, Hexahydroxy, diphenic acid

Introduction temperature [1]. It is utilised by various industries and consumer

Pyrogallol also known as pyrogallic acid or 1, 2, 3-trihydroxyben­
zene, an organic phenol compound that exists naturally in many
plants such as oak, eucalyptus, Terminalia chebula and Myriophyllum spi­
catum (Fig. 1) [1,2]. People are naturally exposed to pyrogallol through
several ways including consumption of tea, use of hair colouring creams,
inhaling smoke produced during cooking mutton, fish and so on [3].
Pyrogallol was found for the first time in the natural extract of the seeds
of Abrus precatorius [4]. It is also found as a contaminant in anthocya­
nins, alkaloids, flavones and tannins and produced during its disposal,
industrial use and isolation [1]. Resorcinol, its metabolite, is produced
as a thermal breakdown material in effluents of wastewater during the
process of converting coal. Nowadays, pyrogallol is obtained commer­
cially via decarboxylation of gallic acid under high pressure and
products [1].
Nowadays, pyrogallol is obtained commercially via decarboxylation
of gallic acid under high pressure and temperature [1]. It is utilised by
various industries and consumer products [5]. Pyrogallol possesses
antibacterial, antipsoriatic, antifungal and oxidative properties [6–9]. It
is autoxidised rapidly in solutions ranging from pH 3.5 to 4.5 [10] and
generates free radicals such as molecular oxygen (O2), peroxide nitrite
(ONOO− ), hydrogen peroxide (H2O2), and hydroxyradical (OH–) by the
Haber- Weiss reaction Inui et al. [11]. Reactive oxygen species (ROS) are
produced by artemisinin in the digestive vacuole through the activation
of endoperoxide bridge and free Fe+2 can increase the production of ROS
by Fenton process; hence, it has been suggested that artemisinin-
activated ROS may induce parasite death via reducing the capability
of the parasite’s antioxidant defence system to eliminate free radicals

* Corresponding author.
E-mail address: mohdaminmir@gmail.com (M. Amin Mir).

https://doi.org/10.1016/j.rechem.2023.100763
Received 3 November 2022; Accepted 31 December 2022
Available online 2 January 2023
2211-7156/© 2023 The Authors. Published by Elsevier B.V. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-
nc-nd/4.0/).
M. Amin Mir et al. Results in Chemistry 5 (2023) 100763

other molecular parameters, HOMO, LUMO, NBO, and MEP was done
using structure of optimization. Surface parameters, like, electron den­
sity, electron localization function was studied by (AIM) Atoms in
molecule theory with the help of Multiwfn software [20], and drug-
likeness, ADME properties of Pyrogallol was carried out by Swis­
sADME Tool [21]. All graphs of the concerned compound were drawn by
Origin 8.0 software [22] and some by Multiwfn software. The concerned
research was done as per Abraham et al. [23] and Basha et al. [24].

Results and discussion

Optimized molecular geometry

The bond parameters (optimized) as obtained for the compound of

Fig. 1. Geometrically Optimized structure of Pyrogallol (1, 2, 3-trihydroxyben­
zene) brown colored are carbons and red colored are oxygens. (For interpre­
tation of the references to color in this figure legend, the reader is referred to
the web version of this article.)
[12]. pyrogallol is auto-oxidised in the pH ranging from 3.5 to 4.5, thus,
this compound can function within the parasite’s digestive vacuole as
this organelle also has the pH ranging from 3.7 to 6.5 [13].
Experimental details
The experimental data and the analysis have been done by the
comparison of the previous reported studies for this compound, Pyro­
gallol (1, 2, 3-trihydroxybenzene) [14,15].
reference with the help of B3LYP method involving a basis set of 6–311
++ G (d, p) is shown in Table 1; and the optimized structure with atoms
numbered is shown by Fig. 1. The studied compound showed C1 point
group. The comparison of an optimized Pyrogallol was done with the
(CIF) crystallographic information file downloaded [25]. The length of
bonds in terms of RMSD with B3LYP are 0.05321 and the value for R2 is
0.9756 and the experimental bond angle values have been found to be
1.324 and R2 as 0.879, and the observed low values suggest the exper­
imental and theoretical observations same. However, a small change in
values so for observed could be because the solid phase was used in
experimental set up and the computationally analyzed values are in gas
phase [26,27]. The bond angle values of C–C–C in the ring structures
have been found in 118.47–121.16◦ (exp. 118.48–121.16◦ ) and C –C
–O bond angle range in a ring system is between 116.954 and 122.095◦
(exp. 116.967–122.090◦ ). The bond lengths of O –H have constant
values because of similar oxygen environment in the ring system. The
C–C bonds ranges in between 1.37 and 1.41˚A (exp. 1.36–1.39˚A) due to

Computational details

The quantum calculations, Density functional theory (DFT) shows

comprehensive machinery mechanism and nice pictorial information
about the charged bonds, and the lower basis set was chosen, also by
using B3LYP method and 6–311 ++ G (d, p) with higher basis order set
chosen for calculations [16]. The analysis was done by using Gaussian
03 W [17] program set-up using personal system [18]. The Geometrical
parameter, vibrational analysis was computed by geometry optimiza­
tion of Pyrogallol using B3LYP method and 6–311 ++ G (d, p) basis set
Fig. 2. Molecular orbitals (HOMO and LUMO) of Pyrogallol.
[19], in which the parameters, like, wavenumbers (vibrational) and

Table 1
Optimized geometrical parameters of Pyrogallol: bond length (Å) and bond angles (◦ ).
Parameter Parameter

Bond length (Å) B3LYP/6–311++G(d, p) Experimental Bond angle (◦ ) B3LYP/6–311++G(d, p) Experimental

C1-C2 1.3879 1.3885 C2-C1-C3 120.4073 120.411

C1-C3 1.3837 1.3840 C2-C1-O4 120.3743 120.354
C1-O4 1.3771 1.3767 C3-C1-O4 119.2182 119.235
C2-C5 1.3882 1.3881 C1-C2-C5 119.6002 119.568
C2-O6 1.3782 1.3776 C1-C2-O6 117.8862 117.889
C3-C7 1.3857 1.3854 C5-C2-O6 122.5104 122.540
C3-H8 0.9509 0.9503 C1-C3-C7 119.4274 119.392
O4-H9 0.8483 0.8482 C1-C3-H8 120.3746 120.348
C5-C10 1.3881 1.3875 C7-C3-H8 120.1979 120.260
C5-O11 1.3715 1.3721 C1-O4-H9 107.8624 107.884
O6-H12 0.8668 0.8667 C2-C5-C10 120.3912 120.430
C7-C10 1.3841 1.3841 C2-C5-O11 115.6671 115.631
C7-H13 0.9486 0.9491 C10-C5-O11 123.9426 123.939
C10-H14 0.9497 0.9499 C2-O6-H12 110.7899 110.808
O11-H15 0.8672 0.8670 C3-C7-C10 120.8813 120.926
C3-C7-H13 119.5783 119.542
Bond angle (◦ ) B3LYP/6-311þþG(d, p) Experimental C10-C7-H13 119.5403 119.533
C7-C10-H14 120.4536 120.423 C5-C10-C7 119.2673 119.246
C5-O11-H15 112.3759 112.371 C5-C10-H14 120.2791 120.330

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M. Amin Mir et al. Results in Chemistry 5 (2023) 100763

Table 2
Pyrogallol vibrational (calculated) frequencies (cm− 1) on B3LYP/6–311++G (d, p) basis set.
Mode no Experimental wave number (cm¡1) Theoretical wave number (cm¡1) IcIR IdRAMAN Assignments (PED)a, b

FTIR Unscaled Scaled

39 3800 3852 3702 58.72 105.38 γOH(48), γOH(52)

38 – 3806 3658 84.04 60.43 γOH(53), γOH(46)
37 – 3788 3640 71.70 63.75 γOH(51), γOH(47)
36 3300 3203 3078 6.91 142.20 γCH(47), γCH(11), γCH(41)
35 – 3186 3062 12.38 89.95 γCH(62), γCH(36)
34 – 3163 3040 10.73 74.48 γCH(52), γCH(27), γCH(21),
33 1700 1664 1599 76.25 12.68 γCC(41), γCC(12)
32 – 1655 1590 27.99 14.07 γCC(24), γCC(12), γCC(18), β CCC(13),
31 1500 1549 1489 101.01 1.83 γOC(20), β HCC(10), β HCC(16), β CCC(15)
30 – 1522 1463 48.97 1.45 γCC(34), β HCC(20), β HCC(12)
29 1350 1395 1341 18.81 0.75 γCC(35), β HOC(27), β HCC(12)
28 — 1375 1321 65.36 1.31 γCC(22), γOC(10), β HOC(12), β HOC(20),), β HCC(17)
27 – 1328 1276 250.00 6.32 γCC(10), γOC(24), β HOC(25), β HCC(14)
26 1290 1276 1226 107.42 1.64 γOC(44), β CCC(15), β HOC(19)
25 – 1257 1208 100.97 0.16 γOC(29), β HOC(22), β HCC(15)
24 – 1200 1153 77.571 1.97 γCC(11),), β HOC(11), β HOC(28),
23 1150 1177 1131 42.86 3.10 γCC(10), β HCC(16), β HCC(32), β HCC(27)
22 – 1162 1117 46.16 4.99 γCC(12), β HOC(32), β HOC(23)
21 1040 1080 1038 26.20 11.58 γCC(10), γCC(24), β HCC(19), β HCC(16)
20 – 1007 968 131.38 0.90 γCC(18), γOC(39)
19 950 933 897 0.394 0.49 –
18 880 843 810 1.98 3.27 τHCCC(25), τHCCC(63)
17 – 837 804 10.36 3.38 γOC(20),), β CCC(52),
16 790 748 719 51.27 2.37 τHCCC(42), τCCCC(15)
15 – 707 679 12.71 27.80 γCC(37), γOC(31)
14 – 701 674 0.422 0.23 τHCCC(44)
13 570 585 562 0.43 0.04 –
12 – 583 560 12.13 2.59 β CCC(24), β CCC(21), β OCC(15), β OCC(18)
11 – 547 526 2.83 0.09 τCCCC(27), τCCCC(17)
10 – 513 493 4.036 2.74 γCC(10),), β OCC(39)
9 – 507 487 0.394 3.81 γOC(12), β CCC(17), β CCC(44)
8 420 428 411 64.38 1.53 τHOCC(18), τHOCC(68)
7 300 323 310 88.44 3.70 τHOCC(36), τHOCC(13), τHOCC(26)
6 – 312 300 11.41 0.30 β CCC(10), β OCC(38), β OCC(33)
5 290 300 288 0.15 0.72 τHOCC(16)
4 250 294 283 1.75 0.08 β CCC(13), β OCC(46), β OCC(13), β OCC(16),
3 – 250 240 1.15 2.04 τCCCC(82)
2 150 156 150 205.81 4.71 τHOCC(10), τCCCC(16), τCCCC(62)
1 – 152 146 1.89 0.22 –

A γ-stretching, γa-Symmetrical stretching, γas-asymmetrical stretching, β-bending, τ -torsion, Vout- Out of plane vibration, vs-very strong, s-strong, m-medium, w-
weak. b scaling factor: 0.961 for B3LYP/6-311++ G (d, p).
c
Relative absorption intensities normalized with highest peak absorption equal to 100.
d
Relative Raman intensities normalized to 100.

oxygen atom in the ring. All C –H bond lengths have same values of
1.08˚A, exp. 1.07˚A) and C1-O1 and C1- O8 have similar length of (1.37˚A
exp. 1.370). An electron withdrawing nature of oxygen atom in the ring
makes the heterocyclic ring electron deficient and the six-membered
heterocyclic ring thus have slight distortion in their bond angles from
the perfect hexagonal structure. The HOMO, LUMO structures of Pyro­
gallol are represented in Fig. 2.

Vibrational spectral analysis

The IR spectroscopic analysis determination in terms of FT-IR and

FT-Raman spectrum of Pyrogallol (1, 2, 3-trihydroxybenzene) was done
and [15] and the comparison was done with computational spectra Fig. 3. The experimental IR Spectra of Pyrogallol.
using B3LYP-6–311 ++ G (d, p) as base with the addition of a small
correction factor of 0.961 being used for small deviation to have a good
energy distribution was estimated [19] in which the fundamental modes
relation for the experimental to theoretical values because of different
of vibrations are recognized by their PED. With C1 symmetry the cor­
phase form analysis of Pyrogallol. As per the results no imaginary fre­
responding structure of Pyrogallol are more frequent due to high ground
quencies have been observed which makes it clear that the optimized
state Energy Distribution related to the fundamental modes of vibration.
geometry gets situated at lowest local point on ground state energy
The vibrational frequencies observed in IR and Raman along with
surface. The Pyrogallol is constituted of 17 atoms and therefore show 45
experimentally determined [15] vibrational frequencies of Pyrogallol
fundamental vibrations corresponding to Centre of Symmetry and C1-
are shown in Table 2. For the comparing and predicting the exact Raman
point group symmetry. All constituted vibrations seem active in IR
and IR spectra a Lorentzian band shape was used and corresponding
and Raman spectra. With the help of VEDA programme the (PED) partial

3
M. Amin Mir et al.
Fig. 4. The calculated IR Spectra of Pyrogallol based on B3LYP/6-311++G (d, p) basis set.
Fig. 5. The experimental Raman spectra of Pyrogallol.
Fig. 6. The calculated Raman spectra of Pyrogallol based on B3LYP/6-311++G
(d, p) basis set.
graphs are shown in figures Figs. 3, 4, 5 and 6. The vibrational fre­
quencies calculated and experimentally determined corresponding to IR
and Raman spectra possess correlation coefficients nearby to each other
(R2 = 0.988 and 0.979 respectively).
C–O vibrations: The C–O bond vibrations in Pyrogallol in the
heterocyclic ring have vibrational stretching range in between 837 and
1549 which is the most observed range of frequencies in the compounds
with C–O group 830–2000 cm− 1 [26]. Pyrogallol have two C–O bonds
so possess two one symmetric and two asymmetric vibrations as ex­
pected. Also, the asymmetric stretching vibrations have higher (mode
no. 20) magnitude than the symmetric stretching (mode no. 29) which is
as per the reference [27] which appeared between 1543 and 1664 cm− 1
4
Results in Chemistry 5 (2023) 100763
Fig. 7. The experimental spectra of Pyrogallol.
[28,29]. The wavenumbers calculated theoretically by B3LYP/6–311
++ G (d, p) for C–O possesses the values in between 310 and 8 cm− 1
which correspond to torsion and bending. As per the results of PED the
mode with 100 % frequency corresponding to C–O stretching at
wavelength of 1843 cm− 1.
C –H vibrations The C –H ring stretching vibrations of the Pyro­
gallol have been found in the range 3186–3203 in the structure. The
spectral range is also characterized as the region with strong Raman
intensity vibrations, and electronegative atoms does not affect the in­
tensity of the bonds apparently [30]. The compound of reference has
eight C–H vibrational frequencies within the ring and have 47, 11, 41,
62, 36, 52, 27 and 21 PED values as is shown in the Table 2. The
stretching frequencies observed so far for C–H bonds have been found
to be 3203, 3186, 3163 which agree with the experimentally determined
values, of 3300, 3050 cm− 1. The bending oscillations of C–H–C were
observed to have the frequencies values 950 and 850 cm− 1. All the
bending and the torsional vibrational observed agree with the experi­
mentally determined values. So far it had been observed that the vi­
brations corresponding to C–H are slightly different because of
functional group vibrations like, C–C, C–O, in-plane and out-of-plane
bending oscillations which effect the vibrational values with low PED
percentage.
C –C vibrations: The vibrational bands corresponding to C–C have
been found between 1522 and 1655 cm− 1 in cyclic ring [31]. It is the
form of interaction between C–C which leads to the type of vibrational
M. Amin Mir et al. Results in Chemistry 5 (2023) 100763

chemical softness was found to be 0.21, so is considered as nontoxic in

particular. The total (TDOS), partial (PDOS), and overlap population
(OPDOS or COOP (Crystal Orbital Overlap Population) density of states
were analyzed by Mulliken population analysis. The three λcal (nm)
value of 285.20, 269.92 and 258.10 have been found as per the
computational analysis of Pyrogallol and the energy difference in
ground and excited state for transitions have been found to be 4.1858
(eV), 4.5596 (eV), 4.7305(eV). Similarly, the experimental determined
λmax (nm) was found to be 265.20, while the energy gap was found 4.321
(eV). The Calculated Energy Parameters of Pyrogallol are shown in
Table 4.

NMR analysis

NMR studies related to 13C and 1H of Pyrogallol was done by using

Tri-chloromethane as a reference with the help of Bruker Advance 400/
Avll HD-300 (FT- NMR) instrument and the results obtained are shown
Fig. 8. The calculated Raman spectra of Pyrogallol based on B3LYP/6-311++G
(d, p) basis set. Table 4
The Calculated Energy Parameters of Pyrogallol by B3LYP/
frequency and not the substituent around [32]. Also, the ring stretching 6–311++G (d, p).
– C) were observed in range of 1375–1007 cm − 1 [33]. The
vibrations (C– Parameters Values
C–C frequencies which have been observed theoretically assigned to EHomo (eV) − 5.2314562
C–C stretching vibrations are 1522, 1395, 1375, 1328 cm− 1 corre­ ELumo (eV) − 1.2314322
sponding to stretching vibrations and their respective PED values are Ionization potential − 5.2314562
mentioned in Table 2. All C–C, C– – C and C–O bands are within the Electron affinity 1.2314322
Energy gap (eV) 4.0000242
expected ranges. Some weak C–C torsional vibrational corresponding
Electronegativity 2.5437862
to 790 cm− 1 wave length and bending vibrations corresponding to 300 Chemical potential − 2.5437862
cm− 1 have also been observed in the IR spectra of Pyrogallol [34]. Chemical hardness 2.54378642
chemical softness 0.19765434
Electrophilicity index 1.01651534
Frontier molecular orbital and UV–Visible spectral analysis

The experimentally determined and DFT/B3LYP analyzed UV–Vis

spectrum of Pyrogallol are represented in Figs. 7 and 8, analyzed in gas
phase and in Dimethyl sulphoxide solvent. The theoretically calculated
and experimentally observed wavelengths values are shown in Table 3.
The values of wavelengths in gas phase and in solvent are nearby to each
other making it clear that there is less effect of solvent on the transitions.
As shown in Table 8, the difference of energy between highest occupied
and lowest unoccupied molecular orbitals is 4.5 eV, which clearly in­
dicates electron conductivity parameter. The Electronegativity of Py­
rogallol was found to be 2.33 as per B3LYP technique, and indicates
clearly that there is big difference between highest occupied and lowest
unoccupied orbitals. More information about Pyrogallol like, electro­
philicity, hardness, and potential (chemical) was analyzed by Concep­
tual Density Functional Theory (CDFT), due to which the biological
properties of a molecule and identification of reactive sites for attack by
other molecules are analyzed [26] and the values are shown in Table 4.
The electrophilic reactivity of Pyrogallol as determined for Pyrogallol
Fig. 9. The Experimentally determined 1H NMR spectra of Pyrogallol.
help in predicting the hazardous effect [28], and for Pyrogallol, the

Table 3
Calculated UV–Visible frequencies (cm− 1) assignments of Pyrogallol based on B3LYP/6-311++G (d, p) basis set.
Experimentally determined TD-B3LYP/6-311++G (d, p)

Solvent λmax (nm) Frequency Band gap (eV) λcal (nm) Frequency Band gap (eV) Singlet Excitation state value Assignments

Gas 285.20 0.121 4.0981 0.21337 H →L (90 %)

0.12649 H →L + 1(89 %)
0.11549 H →L + 2 (85 %)
269.92 0.214 4.3261 0.21521 H →L (92 %)
0.22160 H →L + 1(90 %)
0.13250 H →L + 2 (89 %)
258.10 0.011 4.5101 0.58142 H →L (91 %)
0.15568 H →L + 1(89 %)
DMSO 265.20 0.2514 4.321 0.61345 H →L (92 %)
0.21890 H →L + 1(90 %)
0.13789 H →L + 2 (87 %)

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M. Amin Mir et al. Results in Chemistry 5 (2023) 100763

Fig. 10. The calculated 1H NMR spectra of Pyrogallol based on B3LYP/6-311++G (d, p) basis set.

148.69, 137.00, 118.77, 111.86, 107.74 respectively, and the experi­

mental values for the respective carbons have been found to be, 149.22,
147.32, 135.54, 117.45, 110.23, 105.45 ppm, respectively. The Dipole
moment (field-independent basis, Debye): along X- axis was found to be
− 4.2178 Y-axis, 3.2456, Z-axis − 0.0001 and Total was 5.543 Debye.
However, the Quadrupole moment (field-independent basis, Debye-
Ang) along various axis’s have been found to be XX = − 65.5, YY =
− 52.5, ZZ = − 61.2, XY = 7.3, XZ = − 0.0018, YZ = 0.0013. So, for the
results are taken into consideration it could be found that the observed
and the experimental values show good resemblance.

Table 5
13
C and 1H chemical shift values of Pyrogallol (ppm) (Experimental and
theoretical).
Atoms Chemical shift (ppm) Chemical shift (ppm) B3LYP
13
Fig. 11. The experimentally determined C NMR spectra of Pyrogallol. (Experimental) (Calculated)

13-H 7.75 7.65

in Figs. 9 and 10 (1H NMR) and the NMR analysis was done by GIAO 8-H 7.61 7.53
(Gaussian with Gauge Independent Atomic Orbital) method [35] as 14-H 7.31 7.25
9-H 5.51 5.51
shown in Figs. 11 & 12 (13C NMR). In Table 5 the experimentally and 12-H, 5.05 4.95
theoretically determined values related to 1H NMR and 13C data of Py­ 15-H 4.21 4.10
rogallol, are shown using TMS as standard. The chemical shifts values 1-C 149.22 151.54
for 13-H, 8-H, 14-H, 9-H, 12-H, 15-H in the pyrogallol ring system have 5-C 147.32 148.69
2-C 135.54 137.00
been found to be 7.75, 7.61, 7.31, 5.51, 5.05, 4.21 experimentally and
7-C 117.45 118.77
the observed values by computation system have been found to be, 7.65, 3-C 110.2 111.86
7.53, 7.25, 5.51, 4.95, 4.10 ppm respectively. The 13C NMR of the ring 10-C 105.45 107.74
carbons viz, 1-C, 5-C, 2-C, 7-C, 3-C, 10-C was observed at 151.54,

13
Fig. 12. The calculated C NMR spectra of Pyrogallol based on B3LYP/6-311++G (d, p) basis set.

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M. Amin Mir et al. Results in Chemistry 5 (2023) 100763

Fig. 13. ELF of Pyrogallol (1, 2, 3-trihydroxybenzene) (hydrogen bonding region are shaded and projection areas).

Table 6
Calculated Milliken atomic charges, Fukui Functions and Local softness values of Pyrogallol by B3LYP/6–311++G (d, p).
Atom Mullikan atomic charges Fukui Functions Local softness

N (0, 1) N-1 (+1, 2) N + 1 (-1, 2) fr+ fr- Δf fr0 sr+ fr+ sr- fr- sr0 fr0

C1 − 0.19 − 0.17 − 0.14 0.05 − 0.01 0.07 − 0.2 − 0.01 0.02 − 0.3
C2 − 0.12 − 0.04 0.97 1.10 − 0.08 1.18 − 0.1 − 0.01 0.01 − 0.04
C3 − 0.08 − 0.058 0.15 0.22 − 0.01 0.25 0 − 0.03 0.00 − 0.02
O4 − 0.26 − 0.11 − 0.27 − 0.02 − 0.14 0.12 0 − 0.023 0.01 − 0.01
C5 0.07 0.10 0.85 0.80 − 0.03 0.83 0.15 0.03 0.01 0.12
O6 − 0.31 − 0.17 − 0.27 0.047 − 0.14 0.19 0.15 0.04 − 0.1 0.07
C7 − 0.12 − 0.06 0.17 0.30 − 0.05 0.35 − 0.3 − 0.06 0.02 − 0.22
C10 0.01 0.10 − 0.40 − 0.41 − 0.09 − 0.32 − 0.4 − 0.02 0.01 − 0.25
O11 − 0.31 − 0.26 − 0.30 0.007 − 0.05 0.062 0.3 0.01 0.04 0.20

Electron localization function (ELF) Population analysis

Electron localization function is a good instrumental technique to
determine the electron repulsion of reference electron to the nearby
electron cloud with same spin at a particular locus. The ELF technique
emerges as great weapon to analyze the electron density of a particular
area in their nuclear system quantitively. An ELF value of 1 is considered
as an area of high Pauling repulsion, shows an area of high electron
density in the nearby area with opposite spin, and an ELF value of 0 zero
shows minimum Pauling repulsion. All those electrons are considered to
be localized, with an effective involvement in bonding, atomic shells or
as lone pairs which have high Pauling repulsion value, so give a concrete
evidence about the molecular bond formation, chemical reactivity of a
region, and in determining the aromaticity of a ring structure [36]. The
values of ELF (as shown in rainbow color scale shows a geographical
map) characterized by 2 and 3- dimensional graphical representations as
shown in Fig. 13. The highest ELF (approximately 1) value is represented
by red color and with decrease in ELF value the color changes from
yellow to green, so the least ELF value region is shown by sky blue
followed by royal blue. The hydrogen areas with Maximum Pauli
repulsion as represented by red color, as hydrogen does possess a single
electron so an area with maximum repulsion. The oxygen atoms in Py­
rogallol are shown in orange color and the blue regions are represent
Carbon area. The Shaded surface map for ELF is in the form of projection
is the three-dimensional graph of Pyrogallol and is shown in Fig. 13.
Also, the C–O and C–C bond regions (covalent) with high ELF values,
shows maximum electron localization, whereas the low electron local­
ization zones are shown by brown-colored area around each nucleus
which exists in between the valence and inner orbitals of heavier atoms.
The atomic charges are very important in the determination of mo­
lecular polarizability, dipole moment, chemical reactivity and electronic
structure and also help in NMR chemical shift value determination.
Muliken population analysis method with the help of B3LYP method in
the analysis of charges determination on the atoms of the Pyrogallol and
the obtained data is shown in Table 6. As per the results shown in table
the C1, C2, C3, C4, O6, C7 and C8 have negative values and C5, C10 have
positive. As the molecule have one ring and contain 6 carbon atoms and
three oxygen atoms, in which C1, C2 and C3 are directly attached with
electronegative oxygen atom, so are electron deficient which is shown
by Mulliken population analysis (MPA).
Similarly, C3, C7 and C10 are least positive and the hydrogen atoms
(H8, H13, and H14) possess same charge and H9, H12, H15 are little more
electropositive as being attached with oxygen directly attached, as per
inductive effect. Fukui function [24] values determined by NBO charges
are presented in Table 7. The density of electrons increases with the
addition of an electron to the molecule as shown with positive value of
Fukui function and the electron density decreases with the removal of an
electron from the molecule with Fukui function showing negative value.
As per the calculated values, the activity order for electrophilic attack
follows the order, O4 = O6 = O11. The polarization of hybrids and the
atomic orbital charge in natural orbital bonds is shown in Table 8.
Similarly, the nucleophilic attack follows the C3 = C7 = C10 > C1 = C2 =
C5. The chemical reactivity, the point of electrophilic and nucleophilic
attack is in accordance with electron concentration. On examining the
reactivity interactions, it can be mentioned that electrophilic attack has
high influence as compared to nucleophilic and radical attacks. Fukui
function can provide information about the local softness and can help
in the study of biology of protein–ligand interactions, proteins set-up .

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M. Amin Mir et al. Results in Chemistry 5 (2023) 100763

Table 7
Second Order Perturbation theory of the Fock matrix NBO (deviations from line of nuclear centers) of Pyrogallol (1, 2, 3-trihydroxybenzene).
DONOR TYPE ED/e ACCEPTOR TYPE ED/e E(2) kcal/mol E(j)-E(i) a.u. F(i,j) a.u.

C1 - C2(1) σ 1.97283 C1 - C3 (1) σ* 0.02107 3.85 1.28 0.063

– C2 - C5 (1) 0.03383 3.88 1.27 0.063
– C2 - O6 (1) 0.01823 0.62 1.05 0.023
– C3 - H8 (1) 0.01200 1.92 1.17 0.042
– C5 - O11 (1) 0.02297 2.89 1.04 0.049
– O6 - H12(1) 0.00885 1.57 1.13 0.038
C1 - C2(2) σ 1.64540 C3 - C7 (2) π* 0.36787 16.96 0.30 0.064
– C5 - C10 (2) 0.43533 23.51 0.29 0.075
C1 - C3(1) σ 1.97385 C1 - C2(1) σ* 0.03348 3.63 1.25 0.060
– C1 - O4 0.01918 0.76 1.06 0.025
– C2 - O6 0.01823 3.43 1.04 0.053
– C3 - C7 0.01263 2.59 1.29 0.052
– C3 - H8 0.01200 0.87 1.15 0.028
– O4 - H9 0.00893 1.47 1.12 0.036
– C7 - H13 0.01255 2.26 1.15 0.046
C1 - O4(1) σ 1.99357 C1 - C2(1) σ* 0.03348 0.65 1.46 0.028
– C1 - C3 0.02107 1.00 1.48 0.034
– C2 - C5 0.03383 1.27 1.46 0.039
– C3 - C7 0.01263 1.20 1.50 0.038
C2 - C5(1) σ 1.97105 C1 - C2 (1) σ* 0.03348 4.00 1.28 0.064
– C1 - O4 0.01918 3.03 1.08 0.051
– C2 - O6 0.01823 0.50 1.06 0.021
– C5 - C10 0.02355 4.13 1.28 0.065
– C10 - H14 0.01311 2.09 1.15 0.044
– O11 - H15 0.00719 1.83 1.12 0.041
C2 - O6(1) σ 1.99268 C1 - C2(1) σ* 0.03348 0.63 1.46 0.027
– C1 - C3 0.02107 1.52 1.48 0.042
– C2 - C5 0.03383 0.93 1.46 0.033
– C5 - C10 0.02355 1.36 1.47 0.040
C3 - C7(1) σ 1.97531 C1 - C3(1) σ* 0.02107 2.52 1.26 0.050
– C1 - O4 0.01918 4.15 1.05 0.059
– C3 - H8 0.01200 1.35 1.14 0.035
– C7 - C10 0.01452 2.70 1.28 0.053
– C7 - H13 0.01255 0.93 1.15 0.029
– C10 - H14 0.01311 2.63 1.12 0.049
C3 - C7(2) σ 1.71463 C1 - C2(2) π* 0.43413 22.09 0.27 0.071
– C5 - C10 0.43533 16.99 0.27 0.063
C5 - C10(1) σ 1.97654 C2 - C5(1) σ* 0.03383 4.41 1.27 0.067
– C2 - O6 0.01823 3.72 1.05 0.056
– C7 - C10 0.01452 2.88 1.30 0.055
– C7 - H13 0.01255 2.13 1.17 0.045
– C10 - H14 0.01311 0.88 1.14 0.028
C5 - C10(2) σ 1.70315 C1- C2 (2) π* 0.43413 16.60 0.29 0.064
– C3 - C7 0.36787 20.48 0.30 0.071
– C5 - C10 0.43533 0.66 0.28 0.013
C5 - O11(1) σ 1.99385 C1 - C2(1) σ* 0.03348 1.55 1.47 0.043
– C5 - C10 0.02355 1.08 1.48 0.036
– C7 - C10 0.01452 1.03 1.50 0.035
C7 - C10(1) σ 1.97354 C3 - C7(1) σ* 0.01263 2.62 1.29 0.052
– C3 - H8 0.01200 2.43 1.14 0.047
– C5 - C10 0.02355 2.90 1.26 0.054
– C5 - O11 0.02297 5.17 1.02 0.065
– C7 - H13 0.01255 0.88 1.15 0.028
– C10 - H14 0.01311 1.41 1.12 0.036
LP(1) - O4 σ 1.97820 C1 - C2(1) σ* 0.03348 5.09 1.16 0.069
LP(2) - O4 1.87393 C1 - C2(2) π* 0.43413 28.03 0.34 0.095
LP(1) - O6 σ 1.97656 C1 - C2(1) σ* 0.03348 0.58 1.18 0.023
– C2 - C5 0.03383 5.27 1.18 0.071
– O4 - H9 0.00893 0.69 1.04 0.024
LP(2) - O6 σ 1.89626 C1 - C2(2) π* 0.43413 22.16 0.36 0.087
LP(1) - O11 σ 1.97783 C2 - C5(1) σ* 0.03383 0.84 1.18 0.028
– C5 - C10 0.02355 5.97 1.19 0.075
– O6 - H12 0.00885 0.60 1.04 0.022
LP(2) - O11 σ 1.89861 C5 - C10(2) π* 0.43533 23.96 0.36 0.091

Molecular docking
Table 8
H-bonding, docking with centromere-associated protein inhibitor protein Molecular docking analysis helps to design the role of drugs and is an
targets. important step pharmaceuticals industry. An online drug predictor in
Protein No. of Bond Inhibition Binding Energy the name of SWISS ADME-Target chooses a suitable protein for inter­
(PDB ID) Residues distance (Å) constant (10− 6) (kcal/mol) action with a specific ligand viz, reference compound. By using soft­
6TUG 2 2.230, 2.041 0.17 − 7.405 ware’s like Chimera 1.14 [29] and Auto dock-vina [30], Pyrogallol was
7TBV 3 2.142, 1.981 0.19 5.718 docked with two proteins, viz, 6tug protein is a part of hydrolase domain

8
M. Amin Mir et al. Results in Chemistry 5 (2023) 100763

Fig. 14. 3D and 2D docking of Ligand Pyrogallol (2 methyl-1, 4 nathoquinone) embedded in active site of 6TUG and 7TBV02 protein.

with binding energy of 7.405 kcal/- mol and the hydrogen bond distance shows the interactions between the protein and the ligand.
of 2.230 Å, 2.041 Å. 7tbv protein which belongs to immune system
domain [29,30] possess the binding energy as 5.718 kcal/mol with
Drug-likeness
hydrogen bond distance of 2.142 Å and 1.981 Å. The values obtained are
mentioned in table and the figures show the binding and other inter­
An important structural property related to ligands, also called as
active relationships. The low binding energies values, shows that the
drug-likeness, and does possess a crucial role in achieving an efficient
molecule is relatively more bioactive in nature as the results are shown
and complete way in the formation of medicines. The parameters
in Table 8 and the Graphs showing interaction between ligand and
include Lipinski’s rule, HBD, GBA, MR, TPSA, GI absorption, BBB rule,
protein are shown in Fig. 14. The H-bonding between the residue and the
CYP1A2, and bioavailability [26] in the calculations. As Pyrogallol and
ligand (compound) as found, shows that the ligand has a protein re­
its derivatives have wide range of physicochemical and biomedical
ceptor. The molecular structure as per docking of Pyrogallol clearly
importance which include anti-malarial, antidiabetic and anti-

Table 9
ADME properties of Pyrogallol.
Derivatives HBD HBA MR TPSA GI BBB permeability CYPIA 2 Log Kp Lipinski violations Bioavailability score
A2 Absorption Inhibitor (cm/s)

Pyrogallol 3 3 32.51 60.69 High Yes No − 6.20 Yes; 0.55

Ascorbic Acid 4 6 35.12 107.22 High no no − 8.54 Yes 0.56
Gallic acid 4 5 39.47 39.47 High no no − 6.84 Yes 0.56
Ellagic acid 4 8 75.31 141.34 High No Yes − 6.39 Yes 0.55
Hexahydroxy diphenic acid 8 10 7.93 195.98 Low No Yes − 8.03 Yes 0.11

HBD - Hydrogen Bond Donor, HBA - Hydrogen bond acceptor, MR - Molar refractivity, TPSA - Topological polar surface area, GI - Gastrointestinal, BBB – blood–brain
barrier penetration, log kp – skin permeability.

9
M. Amin Mir et al.
inflammatory medicine. The anti-inflammatory property associated
with Pyrogallol have influence on many body parts which include, gall-
bladder, liver cell, blood tissues, breast and oral cells, and ADME pa­
rameters like, hydrogen bond donors (HBD), hydrogen bond acceptors
(HBA), topological polar surface area (TPSA), blood–brain barrier
penetration (BBB), molar refractivity (MR), log kp and bioavailability
score as calculated are mentioned in Table 9. As per the reference the
values of HBD and HBA for any drug molecule must be less than 10, and
Pyrogallol have been found to have the same with HBD 3 and HBA 3
showing Pyrogallol a good medicine in comparison to the other mole­
cules shown in Table 9. Also, the value of TPSA is 60.69 Å2, which in­
dicates that Pyrogallol can be considered as better medicine than
Ascorbic Acid, Ellagic acid, Hexahydroxy diphenic acid. Also, the
bioavailability score of pyrogallol is as same for the mentioned drugs.
The molar refractivity of Pyrogallol is less 32.48 and for a drug molecule
must be in between 40 and 130 [29]. Also, as shown in the table the GI
absorption value is high, BBB permeability is fine, skin permeability (log
Kp) is − 6.20. All these values are good and are fine which a drug
molecule must possess, so the reference molecule can be considered as
good medicine against various diseases.
Conclusion
The Pyrogallol (1,2,3-trihydroxybenzene) a ring system, exists in
many natural products and also a precursor for many interesting phar­
macological important molecules, have been explored as medicinally
and naturally occurring medicine and a more potential drug. The Py­
rogallol have been explored experimentally and theoretically and the
analysis includes 1H, 13C NMR, FT-IR, UV–Vis, DFT study method, and
6–311+ +G (d, p) basis set. Spectral analysis which include IR, UV–vi­
sible spectra obtained by computational analysis have been compared
with the experimentally obtained spectra’s and the obtained results run
parallel to each other. The binding energy values show hydrogen bond
energies are high making it suitable for covalent bond formation. The
energy gap between HOMO-LUMO was found to be 2.14 eV which shows
that Pyrogallol is more stable and is biologically important as a medicine
supported by FMO theoretical examination. Hirshfeld surface analysis
viz, dnorm, di, de, Shape index, and curvedness, and 2D fingerprint plots
studied show that Pyrogallol have good and easy intermolecular in­
teractions. The RMSD and hydrogen bonds which are formed in between
the ligands and the protein residues are molecular dynamic studies
which show complex’s strength, and the study surely showed an in­
crease of knowledge for scientific community for the generation of new
drugs. The drug-likeness studies have shown that Pyrogallol as an
antibiotic shows close relationship with Ascorbic Acid, Gallic acid,
Ellagic acid, Hexahydroxy, diphenic acid. So over it could be concluded
that Pyrogallol as whole or as a part could be considered as good anti­
biotic, anti-inflammatory, anti-malarial medicine.
Declaration of Competing Interest
The authors declare that they have no known competing financial
interests or personal relationships that could have appeared to influence
the work reported in this paper.
Data availability
No data was used for the research described in the article.
References
[1] H. Wang, H. Kang, L. Zhang, S. Cheng, H. Liu, et al., Composition of ethyl acetate
extracts from three plant materials (shaddock peel, pomegranate peel,
pomegranate seed) and their algicidal activities, Pol. J. Environ. Stud. 24 (4)
(2015) 1803–1807.
10
Results in Chemistry 5 (2023) 100763
[2] J. Shao, Z. Wu, G. Yu, X. Peng, R. Li, Allelopathic mechanism of pyrogallol to
Microcystis aeruginosa PCC7806 (Cyanobacteria): from views of gene expression
and antioxidant system, Chemosphere 75 (7) (2009) 924–928.
[3] G. Upadhyay, A. Kumar, M.P. Singh, Effect of silymarin on pyrogallol-and
rifampicin-induced hepatotoxicity in mouse, Eur. J. Pharmacol. 565 (1–3) (2007)
190–201.
[4] S. Selvaraj, P. Rajkumar, K. Thirunavukkarasu, S. Gunasekaran, S. Kumaresan,
Vibrational (FT-IR and FT-Raman), electronic (UV–vis) and quantum chemical
investigations on pyrogallol: a study on benzenetriol dimers, Vib. Spectrosc. 95
(2018) 16–22.
[5] G. Upadhyay, S.P. Gupta, O. Prakash, M.P. Singh, Pyrogallol-mediated toxicity and
natural antioxidants: triumphs and pitfalls of preclinical findings and their
translational limitations, Chemico-Biol. Interact. 183 (3) (2010) 333–340.
[6] G. Singh, P. Kumar, Extraction, gas chromatography–mass spectrometry analysis
and screening of fruits of Terminalia chebula Retz. For its antimicrobial potential,
Pharmacognosy Res. 5 (3) (2013) 162–168.
[7] M. Shahzad, E. Millhouse, S. Culshaw, C.A. Edwards, G. Ramage, E. Combet,
Selected dietary (poly) phenols inhibit periodontal pathogen growth and biofilm
formation, Food Funct. 6 (3) (2015) 719–729.
[8] L. Panzella, A. Napolitano, Natural phenol polymers: Recent advances in food and
health applications, Antioxidants 6 (2) (2017) 30.
[9] M.A. Bianco, A. Handaji, H. Savolainen, Quantitative analysis of ellagic acid in
hardwood samples, Sci. Total Environ. 222 (1–2) (1998) 123–126.
[10] T. Inui, K. Nakahara, M. Uchida, W. Miki, K. Unoura, Y. Kokeguchi, T. Hosokawa,
Oxidation of ethanol induced by simple polyphenols: Prooxidant property of
polyphenols, Bull. Chem. Soc. Jpn. 77 (6) (2004) 1201–1207.
[11] Y. Torii, H. Saito, N. Matsuki, Induction of emesis in Suncusmurinus by pyrogallol,
a generator of free radicals, Br. J. Pharmacol. 111 (2) (1994) 431–434.
[12] H.M. Ismail, V. Barton, M. Phanchana, S. Charoensutthivarakul, M.H.L. Wong,
J. Hemingway, G.A. Biagini, P.M. O’Neill, S.A. Ward, Artemisinin activity-based
probes identify multiple molecular targets within the asexual stage of the malaria
parasites Plasmodium falciparum 3D7, Proc. Natl. Acad. Sci. USA 113 (8) (2016)
2080–2085.
[13] R. Hayward, K.J. Saliba, K. Kirk, The pH of the digestive vacuole of Plasmodium
falciparum is not associated with chloroquine resistance, J. Cell Sci. 119 (Pt 6)
(2006) 1016–1025.
[14] G.A. Petersson, A. Bennet, T.G. Tensfeldt, M.A. Al-Laham, W.A. Shirley,
J. Mantzaris, J. Chem. Phys. 89 (4) (1988) 2193–2218.
[15] F. Neese, The ORCA program system, Wiley Interdiscip. Rev.: Comput. Mol. Sci. 2
(2012) 73–78.
[16] T. Lu, F. Chen, Multiwfn: (2012) A multifunctional wavefunction analyzer, J.
Comp. Chem. 33: 580–592.
[17] A. Daina, O. Michielin, V. Zoete, SwissADME: a free web tool to evaluate
pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small
molecules, Sci. Rep. 7 (2017) 42717.
[18] Origin 8.0, Origin Lab Corp., Northampton, MA.
[19] T. Lu, F. Chen, Multiwfn: a multifunctional wavefunction analyzer, J. Comput.
Chem. 33 (2012) 580–592.
[20] M.H. Jomroz (2004) Vibrational Energy Distribution Analysis, VEDA4, Warsaw.
[21] T.C. Lu, F.-W. Chen, Calculation of molecular orbital composition, Acta Chim.
Sinica 69 (2011) 2393–2406.
[22] S. Rezazadeh, A. Ebrahimi, A computational study on the hydride transfer
mechanism between nicotinamide and menadione, Chemistry Select 3 (42) (2018)
11977–11985.
[23] J.S. Murry, K. Sen, Molecular Electrostatic Potential Concepts and Applications,
Elsevier, Amesterdam, 1996.
[24] H. Nowell, J.P. Attfield, X-Ray and neutron powder diffraction studies of the crystal
structure of vitamin K3Electronic supplementary information (ESI) available: X-ray
powder diffraction data, New J. Chem. 28 (2004) 406.
[25] F.L. Hirshfeld, Theor. Chim. Acta 44 (1977) 129–138.
[26] W. Wang, Y. Ling, L.-J. Yang, Q.-L. Liu, Y.-H. Luo, B.-W. Sun, Crystal structure,
topology, DFT and hirshfeld surface analysis of a novel charge transfer complex
(L3) of Anthraquinone and 4-{[(anthracen-9-yl) meth-yl] amino}-benzoic acid (L2)
exhibiting photocatalytic properties: an experimental and theoretical approach,
Res. Chem. Intermed. 42 (4) (2016) 3157–3168.
[27] I. Jomaa, O. Noureddine, S. Gatfaoui, N. Issaoui, T. Roisnel, H. Marouani,
Experimental, computational, and in silico analysis of (C8H14N2) 2 [CdCl6]
compound, J. Mol. Str. 1213 (2020), 128186.
[28] J. Poater, M. Duran, M. Solà, B. Silvi, Theoretical evaluation of electron
delocalization in aromatic molecules by means of atoms in molecules (AIM) and
electron localization function (ELF) topological approaches, Chem. Rev. 105 (10)
(2005) 3911–3947.
[29] J.P. Hermann, D. Ricard, J. Ducuing, Z-scan measurements of the nonlinear
refraction in retinal derivatives, Appl. Phys. Lett. 23 (4) (1973) 178–180.
[30] F. Weinhold, L.C. Randis, Valency and Bonding: A Natural Bond Orbital Donor
Acceptor Perspective, Cambridge University Press, 2005.
[31] K. Fukui, Role of frontier orbitals in chemical reactions, Science 218 (4574) (1982)
747–754.
[32] A. Shalini, H. Tandon, T. Chakraborty, Molecular electrophilicity index - A
promising descriptor for predicting toxicological property, J. Bioequiv, Availab. 9
(6) (2017) 518–527.
[33] R. Parthasarathi, V. Subramanian, D.R. Roy, P.K. Chattaraj, Electrophilicity index
as a possible descriptor of biological activity, Bioorg. Med. Chem. 12 (21) (2004)
5566–15543.
M. Amin Mir et al. Results in Chemistry 5 (2023) 100763

[34] D.R. Roy, R. Parthasarathi, B. Maiti, V. Subramanian, P.K. Chattaraj, [36] G.M. Morris, R. Huey, W. Lindstrom, M.F. Sanner, R.K. Belew, D.S. Goodsell, A.
Electrophilicity as a possible descriptor for toxicity prediction, Med. Chem. 13 J. Olson, AutoDock4 and AutoDockTools4: automated docking with selective
(2005) 3405–3412. receptor flexiblity, J. Comput. Chem. 30 (2009) 2785–2791.
[35] E.F. Pettersen, T.D. Goddard, C.C. Huang, G.S. Couch, D.M. Greenblatt, E.C. Meng,
T.E. Ferrin, UCSF Chimera–a visualization system for exploratory research and
analysis, J. Comput. Chem. 25 (2004) 1605–1612.

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