F-KCW-Department Publications
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Item EFFECT OF PEPTIDIC BACKBONE ON THE NUCLEIC ACID DIMERIC STRANDS(Taylor & Francis, 2019-03-01) K, Indumathi; A, Abiram; G, PraveenaThis 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.Item EXPLORING THE STRUCTURE AND STABILITY OF Β-DIPEPTIDE – A QUANTUM CHEMICAL AND MOLECULAR DYNAMICS STUDY(NISCAIR-CSIR, India, 2018-07) A, Abiram; G, PraveenaDensity 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.Item STRUCTURAL AND INTERACTION PROPERTIES OF PORPHYRIN LAYERS — A QUANTUM CHEMICAL STUDY(IOP Science, 2015) G, Praveena; A, AbiramThis 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.