Advanced Journal of Chemistry-Section A, 2023, 6(4), 380-390

Advanced Journal of Chemistry-Section A

Journal homepage: www.ajchem-a.com

Original Research Article

A DFT and Molecular Dynamic (MD) Simulation on the

Adsorption of Vidarabine as a Potential Inhibitor on the Al
Metal surface
Fater Iorhuna 1 * , Abdullahi Muhammad Ayuba 1 , Thomas Aondofa Nyijime 2 ,
Muhammad Shuaibu 1
1Department of Pure and Industrial Chemistry, Faculty of Physical Sciences, Bayero University, Kano, Nigeria
2Department of Chemistry, College of Physical Sciences, Federal University of Agriculture, Makurdi, Nigeria

ARTICLE INFO ABSTRACT

Article history In this study, DFT and molecular dynamic (MD) modeling were used to
conduct a theoretical investigation of the potential inhibition of corrosion on
Submitted: 02 July 2023
Al by vidarabine. The local, global, and Fukui functions were used to calculate
Revised: 17 August 2023 the molecule's reactivity. It is hypothesized that vidarabine will display
Accepted: 27 August 2023 physisorption with Al surface based on the predicted adsorption energy of the
Available online: 30 August 2023 system and the binding energies obtained (58.923, -58.923 Kcal/mol). The
Manuscript ID: AJCA-2308-1390 negative value of the EHOMO, which is -5.050 eV, predicts the mechanism of
Checked for Plagiarism: Yes vidarabine on the surface of Al to be physisorption. The molecular dynamics
and the quantum properties suggest that the molecule vidarabine can operate
as a potent corrosion inhibitor.
DOI: 10.48309/AJCA.2023.409740.1390

KEYWORDS
Physiosorption
DFT
MD
Vidarabine
Aluminium

GRAPHICAL ABSTRACT

* Corresponding author: Iorhuna, Fater

 E-mail: uyerfater22@gmail.com
© 2023 by SPC (Sami Publishing Company)
 F. Iorhuna et al / Adv. J. Chem. A 2023, 6(4), 380-390

Introduction The theoretical method using DFT and MD

simulation is quick and significant in the study of
Corrosion of metals is a natural phenomenon corrosion because it gives researchers a
arising from their metallic state. The most relatively quick way to examine the structure and
common reason for metal failures nowadays, behavior of corrosion inhibitors in contrast to
surpassing other failure modes like fatigue, other methods like weight loss,
creep, impact, and others, is corrosion, which is potentiodynamics, and galvanic method, which
thus unavoidable for metals and alloys [1]. Loss require time and resources [1,3,6,7]. Applying
of production due to failure, high maintenance theoretical parameters enables describing
costs, adherence to consumer and environmental inhibitors' chemical structures and offers a
regulations, loss of product quality due to theory for how they interact with metal surfaces
contamination from corrosion of the materials, [2]. Molecular dynamic simulation can determine
high fuel and energy costs as a result of leakage the interaction and adsorption energy between
from corroded pipes, additional working capital, the inhibitor molecule and metal surfaces [1,5].
and more extensive inventories are just a few of Recent theoretical investigations that modeled
the areas where the cost of corrosion is compounds' electrical, structural, and molecular
overwhelming [2,3]. Corrosion can only be characteristics identified as prospective
reduced. The engineering and construction corrosion inhibitors using computational
industries are currently being disrupted by this methods found that these compounds are either
ugly phenomenon [5]. Researchers have inorganic, organic, or condensed matter [6-8].
developed various corrosion prevention Therefore, the theoretical method can be used in
approaches to combat the threat of this corrosive any form to depict the reactivity of any
impact. Altering the component or altering the compound.
environment are the two guiding ideas of the In this work, theoretical DFT and simulation (on
approaches that are now accessible. The the Al (110) surface) method were used to
component can be altered by making design explore the corrosion inhibition potential of
changes, which are particularly effective when vidarabine (VDB) (2-(6-Amino-purin-9-yl)-5-
the corrosion is influenced by fluid flow hydroxymethyl-tetrahydrofuran-3,4-diol)
properties (erosion-corrosion, cavitation), the compound. The molecule was chosen based on
presence or absence of gaseous phases the presence of glycosides with the idea that,
(cavitation, pitting), contacts between dissimilar since glycosylated compounds are a proven
metals (galvanic corrosion), and solution platform for creating many existing front-line
stagnation (crevice corrosion) [1,2]. drugs, they may also be able to treat pure metals
Before now, the use of inorganic inhibitors such produced over time [9]. Al (110)'s aluminum
as lead and painting of metals was in place for crystal surface was selected because of its closed
the inhibition of metals; however, due to the pack and density coverage [10].
toxicity of some of these inorganic inhibitors, The research of vidarabine (VDB) was aimed at
scientists began to search for alternative determining the modes of adsorption on the Al
inhibitors. The use of organic compounds surface, their adsorptive ability and the active
containing polar functions N, S, and O atoms and sites of the molecule using Molecular Dynamic
conjugated double bonds or aromatic rings in simulation. Considering properties such as
their molecular structure has become a fertile binding energy, bond length and quantum
environment for searching for suitable inhibitors chemical parameters such as energy of the
with adsorption centers [4]. highest occupied molecular orbital (EHOMO), the

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energy of the lowest unoccupied molecular Fukui function and Fukui functions f(r), at the
orbital (ELUMO), energy gap (ΔE), total energy (E), lower possible energy with moderate
electron affinity (A), ionization potential (I), temperature.
global hardness (ƞ), global softness (S), Second

Scheme 1. Molecular structure of vidarabine

Computational Methods energy of the lowest unoccupied molecular

orbital (ELUMO) [14–17].
Sketching and Geometric Optimization of the
IE= - EHOMO (1)
Molecules
EA= - ELUMO (2)
Chem-Draw CambridgeSoft Ultra 7.0.3 was used
to draw diagrams of the examined compound; to According to Pearson, the global hardness (ƞ)
get a stable configuration, the molecular value is approximated as shown in Equation (3).
structure needs to be adjusted after construction. Equation 4 demonstrates that the system's global
In order to achieve a stable state for the softness (S) is the opposite of the global
structure's energy or a state where the forces hardness. While Equations 5 and 6 derive the
acting on the atoms are zero, the coordinates of global electrophilicity index and nucleophilicity,
the atoms are modified during this process. respectively [7,9].
When the system is in equilibrium, it is predicted (3)
that the geometry corresponding to this
structure would closely lower the system's actual S (4)
physical structure [6–8]. To optimize the
compound, the DMol3 optimization model, a
ω= (5)
function of BIOVIA Materials Studio 8.0 (Accelrys,
Inc.), was used to lower the torsional and
ε= (6)
conformational energies of the molecules. Before
the optimization, the compound was imported Using the relationship provided in Equation 7,
into Materials Studio from ChemDraw. The the energy gap of the molecules is computed. The
optimization used the following variables: DFT- energy gap is a factor that determines both the
D's restricted spin polarization DNP+ base. In the stability and reactivity of an inhibitor molecular
water solvent as B3LYP was selected as the local structure.
density functional [11–13].
(7)
Quantum Chemical Parameters Calculations Hence aluminum has a predicted
electronegativity value of (𝜒Al=5.6eV) and a
Per Koopman's theory, Equations (2) and (3),
global hardness of 0 eV. Half-electron transfer
respectively, relate the energy of the border
(ΔN) in Equation 8 was computed, which shows
molecular orbital, the energy of the highest
the proportion of electrons transported from the
occupied molecular orbital (EHOMO), and the

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inhibitor to the surface of the metal. An indicator A simulation box measuring 17 x 12 x 28 with a
of the type of electron transfer between the periodic boundary condition was used to conduct
inhibitor molecule and the metal surface. a computational simulation to mimic the reality
of the reaction between the molecule and the
Δ𝑁 = (8) surface. To separate Al along the (110) plane, a
fractional depth of 3.0 was utilized. The lower
Back donation is determined with the help of
layers' form was constrained prior to iron
Equation (9)
surface optimization. Then, the Al surface was
ΔEbd = (µ+- µ-)2 = (9) expanded into a 10 × 10 supercell [1,4,19] to
reduce edge effects. Setting the temperature to
χ = Absolute electronegativity (eV) χ= = quench the molecule on the surface at 350 K [1-2,
21]. With a time step of 1 fs and a simulation
(EHOM0 ELUMO) (10)
runtime of 5 ps, the temperature was established
ω-: electron donating power (eV) using the NVE (microcanonical) ensemble. The
system was set up to quench every 250 steps on
(11)
both surfaces to get statistical data for the
energies on the surface of Al. Forcite-specific
ω+: electron accepting power (eV)
models and surface designs were used to create
(12) various interactions. The binding energy
between the inhibitors and the metal surfaces is
The donating and acceptance of the molecule calculated using Equation 16 [22,31-34].
and the metal were described using the second-
Binding Energy= Etotal – (Einhibitor+EFe surface) (16)
order Fukui function (f2), also known as the dual
descriptor f(k) [2,5,31]. The distinction between Eadsorption= -Ebinding (17)
the electrophilic and nucleophilic Fukui
functions, as seen in Equation (15), is the second Result and Discussion
Fukui function (f2) [14] where site + favors a
Molecular Dynamic Simulation
nucleophilic attack when f2(r) is greater than
zero, as opposed to an electrophilic assault when The close contacts between the inhibitor and
f2(r) is less than zero. This demonstrates that the aluminum surface were evaluated using the
f2(r) is a selectivity index for nucleophilic or Forcite model in the BOVIA Material Studio
electrophilic assaults [14,19,20]. (Accelrys, Inc.), where each step was quenched at
350 K [1]. Using the parameters of interaction
+: (for nucleophilic attack) such as binding energy, surface energy, total
(13) kinetic energy and adsorption energies, the
nature of the interaction between the molecule
-: (for electrophilic attack) and the surface was calculated with the aid of
(14) Equation (16) and the result was presented as
shown in Table 1. The result depicts that the
(r) +- - 2 (Fukui function) (15) compound exhibits low binding and negative
adsorption energy.
Molecular Dynamics Simulation Ayuba and Umar reported that a more negative
value of adsorption energy of the inhibitor-metal
surface interaction, the better the adsorption of

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the inhibitor onto the metal surface, the better and Bello et al., in their various research, stated
the adsorption of the inhibitor onto the metal that chemical adsorption would occur on the
surface and, subsequently, the higher the metal surface if the binding energy is >100
inhibition. Ebinding is equivalent to -Eadsorption kcalmol-1 [19,20,31]. Thus, it is confirmed from
as presented in Equation (17). This indicates that the Molecular Dynamic simulation result in Table
the molecule VDB had mild adsorption on the 1 that the binding energy is just 58.923 kcalmol-1,
aluminum surface; hence the binding energy less than 100kcalmol-1. This implies that the
exhibited by the interaction is -58 kJmol-1[2, 22, aluminum and vidarabine (Al-VDB) interaction
25]. This is also per Belghiti et al., Nyijime et al., was physical.

Figure 1. Mode of adsorption of VDB on the surface of the aluminum

Table 1. The energy of the interaction between Al(110) and VDB

Properties VDB Al (kJ.mol-1)
Total Potential Energy -9.722±0.1
Energy of the Molecule 49.200±0.0
Total kinetic energy 16.884±2.2
Energy of Al (110) 0.000 ±0.0
Adsorption energy -58.923±0.1
Binding energy 58.923±0.1

Frontier Molecular Orbitals that such bonds did not require much energy for
the breakdown [1,2]. Figure 3 depicts that the
When the bond lengths of the compound were molecule interacted with the aluminum surface
compared before and after simulation, the and that electrons had undoubtedly been
molecules with double bonds were shorter, transferred between the surface and the
demonstrating that high energy is required for molecule [4]. The bond locations N10-C11, C1-
such a bond to break down, while the molecules N2, N2=C3, C14-C12, O12-C13, C13-C16, C16-
with single bonds were longer, demonstrating O17, and C11-C15 all exhibit a noticeable change

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in bond length, showing that the molecule has in Figure 1. This demonstrates that molecules
surface contact with the metal [25,32,33]. Both tend to adsorb to metal surfaces in a flat
versions of all the examined molecules are orientation, maximizing the surface coverage
entirely planar, as evidenced by the torsional [10]. Salient bond lengths in the molecules were
angles in Table 2 of optimized structures and the compared between the simulated and optimized
simulated structure values [27]. This is also versions to explain the molecule's impact on the
shown in the horizontal orientation of the surface during interaction [27].
molecule encounter with the surface as depicted

Figure 2. Calculated link length (Å) of the molecule VDB before and after simulation
Table 2. Rotational constants of H2, DH, and D2
Torsion Atoms Before simulation (φ°) After stimulation (φ°)
C1-N2=C3-N4 -0.562 1.245
N4-C5-C6-N8 179.932 178.785
N8-C6-C5-N7 -0.512 1.328
N8-C9-N10-C11 166.177 163.463
C9-N10-C11-O12 28.974 35.472
O12-C13-C16-O17 63.178 66.208
O17-C16-C13-C14 77.826 169.304
O19-C15-C14-O18 16.744 48.616

Active site all reveal a molecule's point of attack [10,15,19].

The only Fukui functions studied in this work
Molecules' local reactivity improves efficiently were the nucleophilic (f+) and electrophilic (f-).
during electron transfer by picking where the The findings of those with the most significant
reaction is most likely to occur, either by values are displayed in Figure 3 [4]. Figure 4
providing or absorbing electrons [4,5]. The demonstrates the results of the Fukui second
radical Fukui function (fo), electrophilic Fukui function, which computes the nucleophilic and
function (f-), and nucleophilic Fukui function (f+) electrophilic nature of the molecule.

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Figure 3. The Fukui functions of the Molecule VDB

Figure 4. The calculated Fukui function of the molecule

According to Figure 3, N7 had the highest F- the HOMO and the LUMO orbitals, the quantum
function for electron transport per atom, while chemical parameters were obtained through
N2 had the highest F+ function. This suggests that equations 1-12 as presented in Table 3.
electrons are transferred to the metallic surface Ionization energy is the amount of energy a
at position N2 and that the molecule gains extra molecule requires to liberate one electron from
electrons at position N7 [29,30]. The second the surface of an atom when it is in a gaseous
Fukui function in Figure 4 shows that the state, while electron affinity is the measure of an
molecule is nucleophilic, meaning that it atom's ability to absorb an electron [10]. In other
transfers electrons to aluminIum's p-orbital words, an examination of the ionization potential
faster than it returns them to the inhibitor from (IE) and electron affinity (EA) may be used to
the p-orbitals [20]. anticipate the amount of energy that is released
by a molecule during the inhibitor-metal
Quantum Chemical Parameters adsorption process when an electron is lost and
gained [20,34]. Both the measurements for the
Figure 5 demonstrated the Optimized molecule,
electron affinity and the ionization potential for
HOMO orbitals, Electron Density and LUMO
the VDB molecule under study were in good
orbitals of the molecule under study. Through
agreement. According to the estimated quantum

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parameters results, the molecule VDB has a half- However, if ΔN is greater, the effectiveness of the
electron transfer value of less than 3.6. According inhibition decreases as the inhibitor's ability to
to the literature, if ΔN is less than 3.6, the donate electrons rises [1,10,21]. The formal
effectiveness of the inhibition increases as the scenario for the structure under study is one
molecules' ability to donate electrons rises. with a VDB molecule on an aluminum surface.

a c

b d

Figure 5. (a) Optimized molecule (b) HOMO orbitals (c) Electron Density (d) LUMO orbital

Table 3. Energy parameters of the molecule VDB

Parameters studied VDB
EHOMO (eV) -5.050
ELUMO (eV) -1.158
IP (eV 5.050
EA (eV) 1.158
∆E(eV) 3.892
electronegativity(χ) 3.104
Global hardness ( 1.946
Global softness(S) 0.514
Global electrophilicity index 2.476
Nucleophilicity 0.404
Half-electron transfer(∆N) Al 0.641
(ω-) Electron donating power 4.271
(ω+) Electron accepting power 1.167
(ΔEbd) Back donation -0.487

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A lower value of ELUMO produces a higher et al. and Nyijime et al. [18,20]. The power of the
electron-acceptance capacity of molecules from electron donator and acceptor estimated from
the surface of aluminum. The ability of the the molecule obtained from the computation was
inhibitor to assign electrons to the open d-orbital high, indicating that the molecule has a greater
on the metal surface improves the efficiency of capacity to donate an electron to the aluminum
the inhibition process [1,2]. The fact that EHOMO surface, as previously demonstrated by the
values are negative suggests that physical Second Fukui function in a system's ability to
adsorption is preferred when molecules and accept charge is strengthened by a higher
metals are adsorbed to their surfaces [1,9,15,18]. electron accepting power (ω+) value. In contrast,
Additionally, molecules with higher EHOMO values a lower electron-donating power (ω-) value
have a higher propensity to transfer electrons to improves its ability to donate charge [7].
the surface of aluminum. The ELUMO and EHOMO
levels must differ for the molecule's stability Conclusion
indicator to function correctly. A compound with
As determined by the values of
a low energy gap (ΔEg) has higher inhibition
interaction/binding energy, bond length, and
efficiency, which lowers the excitation energy
quantum chemical parameters such as the
required to remove an electron from the last
energy of the highest occupied molecular orbital
occupied orbital [1,10]. In its most basic form,
(EHOMO), the energy of the lowest unoccupied
chemical hardness refers to resistance to
molecular orbital (ELUMO), energy gap (E), total
polarization or distortion of the electron cloud of
energy (E), electron affinity (A), ionization
atoms, ions, and molecules in the presence of
potential (I), and others, from the result it can be
minute chemical reaction disturbances. In
concluded that: (a) The inhibition process was
contrast to the large energy gap of a hard
driven by the transfer of electrons between the
molecule, soft molecules have a smaller energy
metal crystal surface and the molecule, as shown
gap. The molecule's energy gap can be used to
by the number of electron transfer (ΔN) values
determine its softness [16,17,28].
for the surface; (b) According to a molecular
The back donation Eb-d energy was also used to
dynamic simulation, the adsorption happened by
discuss the contact effect between the inhibitor
a process called physisorption, which accounts
VDB and the aluminum surface. If the global
for the low value of binding energy between the
hardness is positive and the energy of back
surface and the molecule; (c) Molecular Dynamic
donation (Eb-d) value is negative, the back
(MD) and Density Functional Theory (DFT)
donation process is favored so that the molecule
simulations may be particularly effective
transmits the charge to the aluminum metal
techniques for rationalizing various potential
when they come in contact with the surface of
corrosion inhibitors; (d) Vidarabine is a suitable
the Al. In contrast, the electrophilicity index
corrosion inhibitor for aluminum metal.
indicates a molecule's ability to accept electrons
(ω). The ability of a molecule to provide or
Acknowledgment
receive electrons is referred to as nucleophilicity
(ε), which is the opposite of electrophilicity The authors wish to acknowledge the
(1/ω). According to research, compounds with contribution of Dr. A. M. Ayuba of Pure and
high nucleophilicity values successfully prevent Industrial Chemistry Bayero University, Kano,
corrosion compared to molecules with high Nigeria. for the success of this research.
electrophilicity indices. This finding was in line
with a study on a related compound by Iorhuna Disclosure statement

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 F. Iorhuna et al / Adv. J. Chem. A 2023, 6(4), 380-390

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HOW TO CITE THIS ARTICLE

Fater Iorhuna*, Ayuba Abdullahi Muhammad, Thomas Aondofa Nyijime, Muhammad Shuaibu. A DFT and Molecular
Dynamic (MD) Simulation on the Adsorption of Vidarabine as a Potential Inhibitor on the Al Metal surface, Adv. J.
Chem. A, 2023, 6(4), 380-390.
DOI: 10.48309/AJCA.2023.409740.1390
URL: https://www.ajchem-a.com/article_178007.html

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