Computational evaluation of the reactivity and pharmaceutical potential of an organic amine: A DFT, molecular dynamics simulations and molecular docking approach

被引:108
作者
Abraham, Christina Susan [1 ]
Muthu, S. [2 ]
Prasana, Johanan Christian [1 ]
Armakovic, Stevan [3 ]
Armakovic, Sanja J. [4 ]
Rizwana, Fathima B. [1 ]
Geoffrey, Ben [1 ]
David, Host Antony R. [5 ]
机构
[1] Madras Christian Coll, Dept Phys, East Tambaram 600059, Tamil Nadu, India
[2] Arignar Anna Govt Arts Coll, Dept Phys, Cheyyar 604407, Tamil Nadu, India
[3] Univ Novi Sad, Fac Sci, Dept Phys, Trg D Obradovica 4, Novi Sad 21000, Serbia
[4] Univ Novi Sad, Fac Sci, Dept Chem Biochem & Environm Protect, Trg D Obradovica 3, Novi Sad 21000, Serbia
[5] Madras Christian Coll, Bioinformat Ctr BITSnet, East Tambaram 600059, Tamil Nadu, India
关键词
DFT; FT-IR; Vibrational profiling; Average local ionization energy; Solubility; H-BDE; Molecular docking; LOCAL IONIZATION ENERGIES; FT-IR; OPTOELECTRONIC PROPERTIES; SPECTROSCOPIC CHARACTERIZATION; DRUG DISCOVERY; FORCE-FIELD; RAMAN; DEGRADATION; ENERGETICS; STABILITY;
D O I
10.1016/j.saa.2019.117188
中图分类号
O433 [光谱学];
学科分类号
0703 ; 070302 ;
摘要
2-[N-(carboxymethyl)anilino] acetic acid (PIDAA) molecule has been spectroscopically characterized and computationally investigated for its fundamental reactive properties by a combination of density functional theory (DFT) calculations, molecular dynamics (MD) simulations and molecular docking procedure. A comparison drawn between the simulated and experimentally attained spectra by FT-Raman and FT-IR showed concurrence. The natural bond orbital (NBO) analysis enabled in comprehending the stability and charge delocalization in the titlemolecule. The first hyperpolarizabilitywhich is an important parameter for future studies of nonlinear optics (NLO) was calculated to check the potential of the molecule to be an NLO material. Besides, frontier molecular orbitals (FMO), electron localization function (ELF) and localized orbital locator (LOL) analysis were performed. Energy gap (Delta E), electronegativity (chi), chemical potential (mu), global hardness (eta), softness (S), Mulliken population analysis on atomic charges and thermodynamic properties of the title compound at different temperatures have been calculated. The local reactive properties of PIDAA have been addressed by MEP and ALIE surfaces, togetherwith bond dissociation energy for hydrogen abstraction (H-BDE). MD simulations have been used in order to identify atomswith pronounced interactionswithwatermolecules. The pharmaceutical potential of PIDAA has been considered by the analysis of drug likeness parameters and molecular docking procedure. The biological activity of the molecule in terms of molecular docking has been analyzed theoretically for the treatment of SARS and minimum binding energy calculated. The Ramachandran plot was used to check the stereochemistry of the protein structure. In addition, a comparison of the physiochemical parameters of PIDAA and commercially available drugs (Yu et al., 2004; Tan et al., 2004; Elshabrawy et al., 2014; Chu et al., 2004; Gopal Samy and Xavier, 2015) were carried out. (C) 2019 Elsevier B.V. All rights reserved.
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页数:16
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