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Ponmalai Kolandaivel

Bio: Ponmalai Kolandaivel is an academic researcher from Periyar University. The author has contributed to research in topics: Density functional theory & Molecule. The author has an hindex of 24, co-authored 174 publications receiving 2682 citations. Previous affiliations of Ponmalai Kolandaivel include Bharathiar University & Bhabha Atomic Research Centre.


Papers
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Journal ArticleDOI
TL;DR: A protocol to identify anti-COVID-19 candidate based on computer-aided drug design is urgently needed and the structure-based virtual screening computational approach will be used to filter the best drugs from the literature, and investigate the structural variation of CO VID-19 with the interaction of the best inhibitor.
Abstract: In the past two decades, the world has faced several infectious disease outbreaks. Ebola, Influenza A (H1N1), SARS, MERS, and Zika virus have had a massive global impact in terms of economic disruption, the strain on local and global public health. Most recently, the global outbreak of novel coronavirus 2019 (SARS-CoV-2) that causes COVID-19 is a newly discovered virus from the coronavirus family in Wuhan city, China, known to be a great threat to the public health systems. As of 15 April 2020, The Johns Hopkins University estimated that the COVID-19 affected more than two million people, resulting in a death toll above 130,000 around the world. Infected people in Europe and America correspond about 40% and 30% of the total reported cases respectively. At this moment only few Asian countries have controlled the disease, but a second wave of new infections is expected. Predicting inhibitor and target to the COVID-19 is an urgent need to protect human from the disease. Therefore, a protocol to identify anti-COVID-19 candidate based on computer-aided drug design is urgently needed. Thousands of compounds including approved drugs and drugs in the clinical trial are available in the literature. In practice, experimental techniques can measure the time and space average properties but they cannot be captured the structural variation of the COVID-19 during the interaction of inhibitor. Computer simulation is particularly suitable to complement experiments to elucidate conformational changes at the molecular level which are related to inhibition process of the COVID-19. Therefore, computational simulation is essential tool to elucidate the phenomenon. The structure-based virtual screening computational approach will be used to filter the best drugs from the literature, the investigate the structural variation of COVID-19 with the interaction of the best inhibitor is a fundamental step to design new drugs and vaccines which can combat the coronavirus. This mini-review will address novel coronavirus structure, mechanism of action, and trial test of antiviral drugs in the lab and patients with COVID-19.

404 citations

Journal ArticleDOI
TL;DR: Theoretical methods have been used to study the proper and improper hydrogen bonds, considering the hydrogen bond length, interaction energy, and charge transfer, for some hydrogen-bonded complexes as discussed by the authors.

109 citations

Journal ArticleDOI
TL;DR: In this paper, the atomic descriptors s(f)cffff kαπαρετερατε βαρααττε τετατη βαταγαγε αγεγεαγηαγγε βεγααγτεγγαβαγβγεβεγθαγ αγγγδαβεαααβγα βαγλαγἵαα βεβα
Abstract: In this paper, we have introduced the atomic descriptors s(f) k to determine the local reactive sites of the molecular systems during electrophilic, nucleophilic and radical attacks. The condensed Fukui function and the newly introduced condensed atomic descriptor have been calculated for six different systems, namely glycine, alanine, aniline, BH2Cl,trans-FC(O)OF andm-anisidine. The individual atomic charges (gross charge) calculated by the MPA scheme have been used to calculate the condensed Fukui functions (f k) and the newly derived condensed atomic descriptors (sf) k α at B1-DZP level of theory. We carried out the calculation using the “stockholders” charge partitioning technique (i.e., Hirshfeld population scheme). The newly derived quantity gives the same reactive sites as the condensed Fukui functions, and the complexities associated with the negative Fukui functions are removed.

72 citations

Journal ArticleDOI
TL;DR: In this paper, the effects of solvent on the geometrical parameters, relative stability and physical properties, such as dipole moment, have been studied for the conformers of glycine.
Abstract: Conformational stability and solvent effects on selected conformers of glycine under different environment, such as polar and apolar solvents have been studied using ab initio and density functional theory (DFT) methods. The molecular geometries have been optimized using HF/6-31+G ∗ method of ab initio and B3LYP/6-31+G ∗ and B3PW91/6-31+G ∗ hybrid DFT methods. The effects of solvent on the geometrical parameters, relative stability and physical properties, such as dipole moment, etc. have been studied for the conformers of glycine.

61 citations

Journal ArticleDOI
TL;DR: In this paper, the suitability of ab initio and density functional theory (DFT) methods for an accurate determination of ionization potential and chemical hardness is the subject of systematic analysis for a panel of molecules.
Abstract: The suitability of ab initio and density functional theory (DFT) methods for an accurate determination of ionization potential and chemical hardness is the subject of systematic analysis for a panel of molecules. Comparison of experimental ionization potential values with theoretical results indicates that using orbital energies obtained from the so-called statistical average of orbital potential (SAOP) model exchange correlation potential in Koopman's theorem is an efficient method to evaluate the correct ionization potentials. Experimental ionization potential and electron affinity values have been used to calculate the absolute chemical hardness. Comparative results show that the chemical hardness values calculated by using Hartree-Fock orbital energies in Koopman's theorem are sufficiently good rather than Moller-Plesset second order perturbation method and DFT-generalized gradient approximation (GGA) exchange correlation functional orbital energies. A new method given by Tozer et al. (J Phys Chem A 2005, 109, 8923) to calculate the chemical hardness works well with the orbital energies of DFT-GGA functionals together with the ionization potential values calculated from SAOP orbital energies. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem 109: 764 -771, 2009

61 citations


Cited by
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Journal ArticleDOI
TL;DR: This chapter discusses the development of DFT as a tool for Calculating Atomic andMolecular Properties and its applications, as well as some of the fundamental and Computational aspects.
Abstract: I. Introduction: Conceptual vs Fundamental andComputational Aspects of DFT1793II. Fundamental and Computational Aspects of DFT 1795A. The Basics of DFT: The Hohenberg−KohnTheorems1795B. DFT as a Tool for Calculating Atomic andMolecular Properties: The Kohn−ShamEquations1796C. Electronic Chemical Potential andElectronegativity: Bridging Computational andConceptual DFT1797III. DFT-Based Concepts and Principles 1798A. General Scheme: Nalewajski’s ChargeSensitivity Analysis1798B. Concepts and Their Calculation 18001. Electronegativity and the ElectronicChemical Potential18002. Global Hardness and Softness 18023. The Electronic Fukui Function, LocalSoftness, and Softness Kernel18074. Local Hardness and Hardness Kernel 18135. The Molecular Shape FunctionsSimilarity 18146. The Nuclear Fukui Function and ItsDerivatives18167. Spin-Polarized Generalizations 18198. Solvent Effects 18209. Time Evolution of Reactivity Indices 1821C. Principles 18221. Sanderson’s Electronegativity EqualizationPrinciple18222. Pearson’s Hard and Soft Acids andBases Principle18253. The Maximum Hardness Principle 1829IV. Applications 1833A. Atoms and Functional Groups 1833B. Molecular Properties 18381. Dipole Moment, Hardness, Softness, andRelated Properties18382. Conformation 18403. Aromaticity 1840C. Reactivity 18421. Introduction 18422. Comparison of Intramolecular ReactivitySequences18443. Comparison of Intermolecular ReactivitySequences18494. Excited States 1857D. Clusters and Catalysis 1858V. Conclusions 1860VI. Glossary of Most Important Symbols andAcronyms1860VII. Acknowledgments 1861VIII. Note Added in Proof 1862IX. References 1865

3,890 citations

01 Jan 2016
TL;DR: The principles of fluorescence spectroscopy is universally compatible with any devices to read and is available in the digital library an online access to it is set as public so you can download it instantly.
Abstract: Thank you very much for downloading principles of fluorescence spectroscopy. As you may know, people have look hundreds times for their favorite novels like this principles of fluorescence spectroscopy, but end up in malicious downloads. Rather than reading a good book with a cup of tea in the afternoon, instead they cope with some harmful bugs inside their desktop computer. principles of fluorescence spectroscopy is available in our digital library an online access to it is set as public so you can download it instantly. Our digital library spans in multiple locations, allowing you to get the most less latency time to download any of our books like this one. Kindly say, the principles of fluorescence spectroscopy is universally compatible with any devices to read.

2,960 citations

01 Dec 1991
TL;DR: In this article, self-assembly is defined as the spontaneous association of molecules under equilibrium conditions into stable, structurally well-defined aggregates joined by noncovalent bonds.
Abstract: Molecular self-assembly is the spontaneous association of molecules under equilibrium conditions into stable, structurally well-defined aggregates joined by noncovalent bonds. Molecular self-assembly is ubiquitous in biological systems and underlies the formation of a wide variety of complex biological structures. Understanding self-assembly and the associated noncovalent interactions that connect complementary interacting molecular surfaces in biological aggregates is a central concern in structural biochemistry. Self-assembly is also emerging as a new strategy in chemical synthesis, with the potential of generating nonbiological structures with dimensions of 1 to 10(2) nanometers (with molecular weights of 10(4) to 10(10) daltons). Structures in the upper part of this range of sizes are presently inaccessible through chemical synthesis, and the ability to prepare them would open a route to structures comparable in size (and perhaps complementary in function) to those that can be prepared by microlithography and other techniques of microfabrication.

2,591 citations

Journal ArticleDOI
TL;DR: The specific advantages brought up by a design based on the use of the halogen bond will be demonstrated in quite different fields spanning from material sciences to biomolecular recognition and drug design.
Abstract: The halogen bond occurs when there is evidence of a net attractive interaction between an electrophilic region associated with a halogen atom in a molecular entity and a nucleophilic region in another, or the same, molecular entity. In this fairly extensive review, after a brief history of the interaction, we will provide the reader with a snapshot of where the research on the halogen bond is now, and, perhaps, where it is going. The specific advantages brought up by a design based on the use of the halogen bond will be demonstrated in quite different fields spanning from material sciences to biomolecular recognition and drug design.

2,582 citations

01 Feb 1995
TL;DR: In this paper, the unpolarized absorption and circular dichroism spectra of the fundamental vibrational transitions of the chiral molecule, 4-methyl-2-oxetanone, are calculated ab initio using DFT, MP2, and SCF methodologies and a 5S4P2D/3S2P (TZ2P) basis set.
Abstract: : The unpolarized absorption and circular dichroism spectra of the fundamental vibrational transitions of the chiral molecule, 4-methyl-2-oxetanone, are calculated ab initio. Harmonic force fields are obtained using Density Functional Theory (DFT), MP2, and SCF methodologies and a 5S4P2D/3S2P (TZ2P) basis set. DFT calculations use the Local Spin Density Approximation (LSDA), BLYP, and Becke3LYP (B3LYP) density functionals. Mid-IR spectra predicted using LSDA, BLYP, and B3LYP force fields are of significantly different quality, the B3LYP force field yielding spectra in clearly superior, and overall excellent, agreement with experiment. The MP2 force field yields spectra in slightly worse agreement with experiment than the B3LYP force field. The SCF force field yields spectra in poor agreement with experiment.The basis set dependence of B3LYP force fields is also explored: the 6-31G* and TZ2P basis sets give very similar results while the 3-21G basis set yields spectra in substantially worse agreements with experiment. jg

1,652 citations