Computational Study for Molecular Properties of Some of the Isolated Chemicals from Leaves Extract of Guiera Senegalensis as Aluminium Corrosion Inhibitor

2021 ◽  
Vol 13 (1) ◽  
Author(s):  
A. M. Ayuba ◽  
◽  
M. Abubakar ◽  
Keyword(s):  
Molecular Dynamics ◽  
Quantum Chemical ◽  
Energy Gap ◽  
Computational Study ◽  
Physical Adsorption ◽  
Chemical Constituents ◽  
Molecular Size ◽  
Structural Features ◽  
Inhibitor Molecule ◽  
Fukui Indices

The present work describes the computational methods for the corrosion inhibition of aluminium using three selected chemical constituents (5-methyldihydroflavasperone, 5-methylflavasperone and methoxylated naphthyl butanone) reportedly obtained from the leaves extract of Guirea senegalensis. Quantum chemical calculations including EHOMO, ELUMO, energy gap (ΔE), electronegativity (χ), global hardness (η) and fraction of electrons transfer from the inhibitor molecule to the aluminium surface (ΔN) were calculated. The local reactive sites through Fukui indices which explain the effect of structural features of these components in relation to electrophilic and nucleophilic point of attack were evaluated. The similarities in quantum chemical parameters for the compounds obtained revealed that the adsorption strengths of the molecules will be mostly determined by molecular size rather than electronic structure parameters. Fukui indices showed that the point of interaction of inhibitor molecule with the Al(l10) surface were through aromatic carbon atom rich in pi-electrons and oxygen atom of the alkanone functional group in the inhibitor molecules. Molecular dynamics simulations describing the adsorption behavior of the inhibitor molecule on Al(110) surface through Forcite quench molecular dynamics were carried out. The compounds were found to all obey the mechanism of physical adsorption because of their relatively low adsorption energies.

Rational design of novel fluorescent analogues of cholesterol: a “step-by-step” computational study

2019 ◽  
Vol 21 (28) ◽  
pp. 15487-15503 ◽  
Author(s):  
Andrea Bonvicini ◽  
Peter Reinholdt ◽  
Vincent Tognetti ◽  
Laurent Joubert ◽  
Daniel Wüstner ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Quantum Chemical ◽  
Rational Design ◽  
State Of The Art ◽  
Computational Study ◽  
Dynamics Simulations ◽  
Fluorescent Analogues

State-of-the-art quantum chemical and molecular dynamics simulations are used as guidelines in design of novel fluorescent analogues of cholesterol.

Discovery of RTA ricin subunit inhibitors: a computational study using PM7 quantum chemical method and steered molecular dynamics

2021 ◽  
pp. 1-19
Author(s):  
Elton José Ferreira Chaves ◽  
Luiz Eduardo Gomes da Cruz ◽  
Itácio Queiroz Mello Padilha ◽  
Carlos Henrique Silveira ◽  
Demetrius Antônio Machado Araujo ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Quantum Chemical ◽  
Chemical Method ◽  
Computational Study ◽  
Steered Molecular Dynamics ◽  
Quantum Chemical Method

Can modified DNA base pairs with chalcogen bonding expand the genetic alphabet? A combined quantum chemical and molecular dynamics simulation study

2020 ◽  
Vol 22 (41) ◽  
pp. 23754-23765
Author(s):  
Karan Deep Sharma ◽  
Preetleen Kathuria ◽  
Stacey D. Wetmore ◽  
Purshotam Sharma
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Hydrogen Bonds ◽  
Quantum Chemical ◽  
Computational Study ◽  
Dynamics Simulation ◽  
Base Pairs ◽  
Dna Base ◽  
Modified Dna ◽  
Dna Base Pairs

A comprehesive computational study is presented with the goal to design and analyze model chalcogen-bonded modified nucleobase pairs that replace one or two Watson–Crick hydrogen bonds of the canonical A:T or G:C pair with chalcogen bond(s).

Probing the binding mechanism of novel dual NF-κB/AP-1 inhibitors by 3D-QSAR, docking and molecular dynamics simulations

RSC Advances ◽  
2015 ◽  
Vol 5 (99) ◽  
pp. 81523-81532 ◽  
Author(s):  
Shaojie Ma ◽  
Shepei Tan ◽  
Danqing Fang ◽  
Rong Zhang ◽  
Shengfu Zhou ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Binding Sites ◽  
Computational Study ◽  
3D Qsar ◽  
Structural Features ◽  
Binding Mechanism ◽  
Interaction Mechanisms ◽  
Dynamics Simulations

Potent dual NF-κB/AP-1 inhibitors could effectively treat immunoinflammatory diseases. An integrated computational study was carried out to identify the most favourable binding sites, the structural features and the interaction mechanisms.

H2O and H2S adsorption by assistance of a heterogeneous carbon-boron-nitrogen nanocage: Computational study

2021 ◽  
pp. 1-9
Author(s):  
Xin Liu ◽  
Zahra Ahmadi
Keyword(s):  
Quantum Chemical ◽  
Energy Gap ◽  
Computational Study ◽  
Hydrogen Atoms ◽  
Acid Base ◽  
H2s Adsorption ◽  
Adsorbed Substance ◽  
Complex Formations ◽  
Boron Nitrogen ◽  
Activated Surface

A model of heterogeneous carbon-boron-nitrogen (C-B-N) nanocage was investigated in this work for adsorbing H2O and H2S substances. To achieve this goal, quantum chemical calculations were performed to obtain optimized configurations of substances towards the surface of nanocage. The calculations yielded three possible configurations for relaxing each of substances towards the surface. Formation of acid-base interactions between vacant orbitals of boron atom and full orbitals of each of oxygen and sulfur atoms yielded the strongest complexes of substance-nanocage in comparison with orientation of substances through their hydrogen atoms towards the surface of nanocage. As a consequence, formations of interacting H2O@C-B-N and H2S@C-B-N complexes were achievable, in which mechanism of action showed different strengths for the obtained complexes. Variations of molecular orbital features and corresponding energy gap and Fermi energy for the models before/after adsorption could help for detection of adsorbed substance through a sensor function. And finally, such C-B-N nanocage showed benefit of providing activated surface for efficient adsorption of each of H2O and H2S substance with possibility of differential adsorption regarding the strength of complex formations.

Prediction of Alkanolamine pKa Values by Combined Molecular Dynamics Free Energy Simulations and ab initio Calculations

2019 ◽  
Author(s):  
Javad Noroozi ◽  
William Smith
Keyword(s):  
Molecular Dynamics ◽  
Free Energy ◽  
Ab Initio Calculations ◽  
Gas Phase ◽  
Quantum Chemical ◽  
Phase Reaction ◽  
Pka Values ◽  
Gas Phase Reaction ◽  
Reaction Free Energy ◽  
Energy Simulations

We use molecular dynamics free energy simulations in conjunction with quantum chemical calculations of gas phase reaction free energy to predict alkanolamines pka values. <br>

Bonded Force Constant Derivation of Lysine-Arginine Cross-linked Advanced Glycation End-Products

2018 ◽  
Author(s):  
Anthony Nash ◽  
Nora H de Leeuw ◽  
Helen L Birch
Keyword(s):  
Molecular Dynamics ◽  
Force Constant ◽  
Computational Study ◽  
Force Constants ◽  
Quantum Mechanical ◽  
Advanced Glycation ◽  
Partial Charges ◽  
Cross Links ◽  
Complete Set ◽  
Dynamics Simulations

<div> <div> <div> <p>The computational study of advanced glycation end-product cross- links remains largely unexplored given the limited availability of bonded force constants and equilibrium values for molecular dynamics force fields. In this article, we present the bonded force constants, atomic partial charges and equilibrium values of the arginine-lysine cross-links DOGDIC, GODIC and MODIC. The Hessian was derived from a series of <i>ab initio</i> quantum mechanical electronic structure calculations and from which a complete set of force constant and equilibrium values were generated using our publicly available software, ForceGen. Short <i>in vacuo</i> molecular dynamics simulations were performed to validate their implementation against quantum mechanical frequency calculations. </p> </div> </div> </div>

Accelerated Discovery of High-Refractive-Index Polyimides via First-Principles Molecular Modeling, Virtual High-Throughput Screening, and Data Mining

2019 ◽  
Author(s):  
Mohammad Atif Faiz Afzal ◽  
Mojtaba Haghighatlari ◽  
Sai Prasad Ganesh ◽  
Chong Cheng ◽  
Johannes Hachmann
Keyword(s):  
Data Mining ◽  
Refractive Index ◽  
High Throughput ◽  
First Principles ◽  
High Throughput Screening ◽  
Large Scale ◽  
Computational Study ◽  
High Refractive Index ◽  
Structural Features ◽  
Learning Program

<div>We present a high-throughput computational study to identify novel polyimides (PIs) with exceptional refractive index (RI) values for use as optic or optoelectronic materials. Our study utilizes an RI prediction protocol based on a combination of first-principles and data modeling developed in previous work, which we employ on a large-scale PI candidate library generated with the ChemLG code. We deploy the virtual screening software ChemHTPS to automate the assessment of this extensive pool of PI structures in order to determine the performance potential of each candidate. This rapid and efficient approach yields a number of highly promising leads compounds. Using the data mining and machine learning program package ChemML, we analyze the top candidates with respect to prevalent structural features and feature combinations that distinguish them from less promising ones. In particular, we explore the utility of various strategies that introduce highly polarizable moieties into the PI backbone to increase its RI yield. The derived insights provide a foundation for rational and targeted design that goes beyond traditional trial-and-error searches.</div>

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