Browsing by Author "Abiram, A"

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EFFECT OF PEPTIDIC BACKBONE ON THE NUCLEIC ACID DIMERIC STRANDS
(Taylor & Francis Online, 2020) Indumathi, K; Abiram, A; Praveena, G
This study explores the effect of N-(2-aminoethyl)-glycine peptide chain incorporated at the backbone of nucleic acid dimeric strands on the basis of reactivity descriptors. The structures of obtained PNA dimeric strands were examined through backbone (α, β, γ, δ, ε and ω) and linker (χ1, χ2 and χ3) torsions. The calculated torsions were found to coincide well the available experimental and theoretical data. The peptidic chain incorporated nucleic acid dimers show a drastic change in global reactivity descriptor (gr) values. The vertical ionisation potential (VIP) and polarizability (α′) of peptide chain incorporated Guanine constructs are found to be higher by about 0.24 eV and 98.49 Å3 than their natural counterparts. The obtained gr along with frontier molecular orbitals depict G-containing dimeric strands to have efficient donor and acceptor capability with improved sensitivity upon peptide chain inclusion. This study in general could serve as a basic tool to understand the reactivity properties of PNA modularities, which are the possible building blocks of extended nanostructures.
EXPLORING THE STRUCTURE AND STABILITY OF Β-DIPEPTIDE – A QUANTUM CHEMICAL AND MOLECULAR DYNAMICS STUDY
(Indian Journal of Pure & Applied Physics, 2018-07) Abiram, A; Praveena, G
Density functional theory (DFT) calculations followed by molecular dynamics study has been performed to analyze the structure and stability of β-dipeptide structures in aqueous medium. From DFT study, three local minima with folded conformations and one local minimum with unfolded conformation have been identified. In gas phase, the most stable β-dipeptide has a folded conformation with a weak hydrogen bonding. The interaction of water molecules, approximated from the first solvation shell, also confirms the folded conformation to be the most stable structure. The DFT optimized β-dipeptide conformers have been simulated in explicit water to evaluate the tendency of folded and unfolded state formation. Simulations confirmed the transition of the structure from folded to unfolded and vice versa and further indicated the former to happen rapidly within a few pico second time scale.
IMPACT OF VENOMOUS AGENT X (VX) ADSORPTION ON THE STRUCTURAL AND ELECTRONIC PROPERTIES OF BN NANOSHEET, NANOTUBE AND NANOCAGE-A DFT-D3 STUDY
(Springer Link, 2024-02-26) Prince Makarios Paul, S; Parimala devi, D; Praveena, G; Selvarengan, P; Jeba Beula, R; Abiram, A
The removal and detection of harmful gases from contaminated air has received a great deal of attention in the scientific community. In this study the interaction of toxic nerve agent Venomous Agent X (VX) with boron nitride (BN) nanosheet, nanotube and nanocage is investigated using density functional theory (DFT). The findings revealed that the target gas tends to adsorb on to the boron atom through P = O bond for the considered nanostructures. The results suggested that the electronic properties of the boron nitride nanotube (BNNT) are well altered leading to reduced energy gap and thereby resulting in increased conductivity. Among the considered nanostructures the highest adsorption energy is identified for B12N12 nanocage, recording a value of -30.85 kcal/mol which in turn makes desorption an almost impossible process. Similarly, the BN nanosheet is also seen with higher recovery time and less sensitive due to its wide energy gap and henceforth not be an effective sensor. On the other hand, the study also confirms that with a small recovery time of 2.59s in average and hence could be a potentially effective sensor for the detection of the toxic gas. Our findings could deliver a basic interpretation on the behavior of these BN based nanomaterials towards adsorption of VX nerve agent. Thereby, supporting the research community towards new perspectives on the development of gas sensors in nanotechnology.
INVESTIGATION OF DIHYDROGEN BOND INTERACTION BETWEEN CYCLOALKENES AND ALKALI METAL HYDRIDES: A DFT APPROACH
(Springer Link, 2022-06-16) Parimala devi, D; Praveena, G; Jeba Beula, R; Abiram, A
In this work, intermolecular dihydrogen bonded interactions between cycloalkenes (cyclobutene (C4H6), cyclopentene (C5H8), cyclohexene (C6H10)) and alkali metal hydrides H–M (M = Li, Na and K) complexes have been studied using B3LYP/6-311++G** method. The calculated structural parameters correlate well with the interaction energies and smallest dihydrogen bonded distance is observed for C4H6⋯HK complexes. Infrared vibrational frequency analysis indicates that significant red and blue shifts are occurring in the C–H and H–M bonds of all the complexes. The analyses of natural bond orbital, topological parameters based on the quantum theory of atoms in molecule and molecular electrostatic potential aids to know the nature of dihydrogen bonded interaction. The result shows that H⋯H interaction is strengthened in the C4H6⋯HK than the other complexes and henceforth H–K interacting complexes have better dihydrogen bonded interaction.
A NON-CATALYTIC OXIDATIVE DESULFURIZATION OF THIOPHENE AND BENZOTHIOPHENE BY PEROXYACETIC ACID OXIDANT
(Springer Science and Business Media Deutschland GmbH, 2024-12) Yuvarani, S; Abiram, A; Praveena, G
Oxidative desulfurization (ODS) is one of the most efficient methods in the removal of aromatic sulfur compounds from the combustion fuels. The present study explores the potential energy surface of thiophene (TH) and benzothiophene (BTH) oxidation reaction in the presence of peroxyacetic acid (PAA) as oxidizing agent using density functional theory (DFT). The structural and thermodynamical parameters of all the stationary points are obtained and characterized at B3LYP/6–311 + + G(d,p) and ωB97X-D/6–311 + G(d,p) levels of theory. In order to study the influence of solvents (water and acetonitrile) in the considered ODS process; solvent effects are included via conductor like polarizable continuum model (CPCM). The natural bond orbital (NBO) analysis was carried out to understand the charge transfer mechanism during the oxidation process. Fukui function calculations are performed to determine the reactivity of the kth atom site, for electrophilic ({\text{f}}_{\text{k}}^{-}) and nucleophilic ({\text{f}}_{\text{k}}^{+}) attacks. Rate constant calculations considering the quantum tunneling effects are also made. The results obtained suggest that the oxidation of benzothiophene into benzothiophene sulfoxide to be more favorable than thiophene oxidation. The presence of solvent is found to have a significant effect in reducing the barrier energy of the considered ODS process. Further this study elucidates the selective reactivity of peroxyacetic acid towards the compounds of high nucleophilicity, which makes it to be an effective oxidant in the uncatalyzed ODS in both gas and solvent phases when compared to hydrogen peroxide (H2O2) oxidant in the presence of catalyst that is available in the literature.
STRUCTURAL AND INTERACTION PROPERTIES OF PORPHYRIN LAYERS — A QUANTUM CHEMICAL STUDY
(IOP Publishing Ltd, 2015) Praveena, G; Abiram, A
This paper is proposed to understand the interaction of porphyrin layers with diatomic molecules interacting at their interior regions by applying ab initio and density functional theory (DFT) methods. We have used NO, CO, and O2 diatomic molecules to interact with the porphyrin layers. The most common Fe-centered metalloporphyrin structure with tetra-pyrrlic rings having N4 core is chosen for the study. The optimization of Porphyrin-Porphyrin (PI-PII) and Porphyrin-Diatomic molecule-Porphyrin (PI-AB-PII) (AB = NO, CO, and O2) complexes are performed using HF method. In order to understand the planarity and appropriate stacking size of porphyrins and also to infer the separation of diatomic molecules between porphyrin layers the behavior of PI-AB-PII complexes (where AB = NO, CO, and O2) are analyzed using structural properties and molecular electrostatic potentials (MEP). The MEPs are calculated using hybrid exchange correlation functional B3PW91 of DFT along with 6-31+G* basis set for the PI-PII and PI-AB-PII complexes obtained from HF method.
THEORETICAL INSIGHTS ON THE INTERACTION BETWEEN P-SYNEPHRINE AND METFORMIN: A DFT, QTAIM AND DRUG-LIKENESS INVESTIGATION
(Elsevier, 2024-03) Prince Makarios Paul, S; Parimala Devi, D; Abisha Nancy, Sukumar; Praveena, G; Jeba Beula, R; Abiram, A
Metformin (MET) known to be an effective drug for type 2 diabetes is interacted with a well known herb P-synephrine (P-SNY) applying density functional theory (DFT) method for combinational drug therapy. Analysis on the geometry and vibrational characteristics confirmed the presence of non-covalent interaction between the hydroxyl and amine groups of herb and drug respectively. The quantum theory of atoms in molecule (QTAIM) is implied to understand the nature of bonds and strength of the interaction. In order to identify the donor, acceptor and further estimate the amount of charges transferred between the herb and drug, natural bond analysis is performed. Furthermore, in order to understand the drug actions, adsorption, distribution, metabolism and excretion (ADME) properties are studied using the SwissADME online tool. The overall study confirms the interaction between MET and P-SNY and additionally these findings can support the experimental community in the design of a new novel hybrid drug combination for the treatment of type 2 diabetes.
THEORETICAL INVESTIGATION OF INTERMOLECULAR DIHYDROGEN BONDS IN C2H2•••HM AND C2H4•••HM (M = LI, NA AND K) COMPLEXES: A DFT AND AB INITIO STUDY
(Asian Journal of Chemistry, 2021-07-26) Parimala Devi, D; Tom, Giju; Praveena, G; Abiram, A
This study aims to investigate the dihydrogen bond formation in ethyne (C2H2) and ethene (C2H4) with alkali metal hydrides (HM; M = Li, Na and K) complexes using density functional theory (DFT) and ab initio methods. It mainly focuses on the comparison of the performances of different functionals of DFT and ab initio method on the intermolecular dihydrogen bonded complexes. The geometrical parameter and energy values agree with the formation of dihydrogen bonds in the complexes. Among the ethyne and ethene complexes, the smallest dihydrogen bond distance was formed by C2H2···HK and C2H4···HK, respectively. The C2H2 is found to form better dihydrogen bond (DHB) with alkali metal hydrides than C2H4. Among all the functionals, M06L was observed to predict shortest H···H bond distance, while M062X the longest. Natural bond orbital (NBO), quantum theory of atom in molecules (QTAIM) along with molecular electrostatic potential (MEP) analysis further confirms the dihydrogen bond formation.
THEORETICAL INVESTIGATION OF INTERMOLECULAR DIHYDROGEN BONDS IN C2H2•••HM AND C2H4•••HM (M = LI, NA AND K) COMPLEXES: A DFT AND AB INITIO STUDY
(Asian Journal of Chemistry, 2021-07-26) Parimala devi, D; Tom, Giju; Praveena, G; Abiram, A
This study aims to investigate the dihydrogen bond formation in ethyne (C2H2) and ethene (C2H4) with alkali metal hydrides (HM; M = Li, Na and K) complexes using density functional theory (DFT) and ab initio methods. It mainly focuses on the comparison of the performances of different functionals of DFT and ab initio method on the intermolecular dihydrogen bonded complexes. The geometrical parameter and energy values agree with the formation of dihydrogen bonds in the complexes. Among the ethyne and ethene complexes, the smallest dihydrogen bond distance was formed by C2H2···HK and C2H4···HK, respectively. The C2H2 is found to form better dihydrogen bond (DHB) with alkali metal hydrides than C2H4. Among all the functionals, M06L was observed to predict shortest H···H bond distance, while M062X the longest. Natural bond orbital (NBO), quantum theory of atom in molecules (QTAIM) along with molecular electrostatic potential (MEP) analysis further confirms the dihydrogen bond formation.
THEORETICAL INVESTIGATION ON THE INTERACTION BETWEEN METFORMIN AND FERULIC ACID - A DFT APPROACH
(Elsevier, 2022-03-03) Prince Makarios Paul, S; Parimala Devi, D; Praveena, G; Jeba Beula, R; Haris, M; Abiram, A
We have theoretically studied the interaction of a commonly used drug, Metformin, with the herb, Ferulic acid, applying density functional theory (DFT). The complex was optimized at various positions and confirmed to be in their local minima through vibrational analysis at B3LYP/6–311++G∗∗ level. Study on the molecular geometry along with the interaction energy of the complexes confirmed the presence of interaction between the hydroxyl and amine group of the herb and drug respectively. The calculation of Gibbs free energy and entropy exhibited the stability of the interacting structures along with the vibrational assignment which showed significant red and blue shifts in the complexes. Additionally, NBO analysis and molecular electrostatic potential (MEP) revealed the charge transfer between the complexes identifying an electrostatic interaction prevailing between the herb and drug.