Browsing by Author "G, Praveena"

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EFFECT OF PEPTIDIC BACKBONE ON THE NUCLEIC ACID DIMERIC STRANDS
(Taylor & Francis, 2019-03-01) K, Indumathi; A, Abiram; G, Praveena
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.
EXCITED STATES OF PNA BASE PAIRS – A THEORETICAL APPROACH
(PSGR Krishnammal College for Women, 2018-07-21) K, Indumathi; G, Praveena
Time dependent density functional theory (TDDFT) calculations using B3LYP/6-311++G** level of theory were presented to understand the basic structural properties of peptidic chain added Watson Crick base pairs and compared to their natural counterparts. The excitation energy, oscillator strength, energy gap and wavelength of the all the base pairs were taken for the analysis. This study would pave way to understand the electronic excitation properties of all the Peptide Nucleic Acid (PNA) base pairs for the better understanding of the transitions and the luminescence properties of synthetic oligonucleotides structures.
EXPLORING THE STRUCTURE AND STABILITY OF Β-DIPEPTIDE – A QUANTUM CHEMICAL AND MOLECULAR DYNAMICS STUDY
(NISCAIR-CSIR, India, 2018-07) A, Abiram; G, Praveena
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.
INTERACTION OF HYDROGEN HALIDES AND WATER MOLECULES WITH THE ISOMERS OF C20 FULLERENE – A THEORETICAL STUDY
(Elsevier, 2007-02-28) G, Praveena; P, Kolandaivel
Density functional theory calculations have been carried out to analyze the effect of hydrogen halides and H2O molecule interactions with the three lowest energy isomers the ring, bowl and cage of C20 fullerene. The single-point energy calculations have also been performed at MP2/6-31+G*//B3LYP/6-31G* level of theory. The complexes (C20⋯H–X and H2O, where X = F, Cl, and Br) are bounded by two interactions namely: (i) very weak X–H⋯π H-bond interactions and (ii) long range van der Waals interactions of H–X⋯C type. These interactions produced negligible distortion in the structures and a good correlation between electron density and stabilization energy of the complexes is found. The counterpoise correction to the interaction energies and the study of topology of the electron density for all the complexes have been performed. The charge transfer and the maneuver of resonance interaction in the interacting orbitals have been investigated by natural bond orbital (NBO) approach.
INTERACTION OF METAL IONS WITH CYCLO [(1R, 3S)-Γ-ACC-GLY]3 HEXAPEPTIDE – A THEORETICAL STUDY
(Elsevier, 2009-04-30) G, Praveena; P, Kolandaivel
The interaction of monovalent metal ions with cyclo[(1R,3S)-γ-Acc-Gly]3 hexapeptide ((TAG)3) is studied using density functional theory calculations. The (TAG)3 and its Li+, Na+ and K+ metal ionic complexes are optimized at B3LYP/6-311+G∗ level of theory. The optimized structure of (TAG)3 ionic complexes agrees well with the various cyclic peptide cationic complexes that are obtained experimentally. The valence, peptide deformation and Ramachandran angles clearly explain the structural effects in (TAG)3 upon ionic interaction. The dependability of cavity size towards the size of ions is noted. The molecular electrostatic potential (MEP) map effectively illustrates the weak interaction between metal ion and (TAG)3, and further confirms carbonyl oxygens to be the active sites. The binding energy of (TAG)3 towards metal ion increases as Li+ > Na+ > K+, which is consistent with the electron density at bond critical points. The significant binding energies and the symmetric nature of (TAG)3 upon Na+ and K+ enclosures in turn shows that its nanotubular structures might act as the ion channels of biological interest.
INTERACTION OF METAL IONS WITH CYCLO[(1R,3S)-Γ-ACC-GLY]3 HEXAPEPTIDE
(Elsevier B.V, 2008-12-29) G, Praveena; P, Kolandaivel
The interaction of monovalent metal ions with cyclo[(1R,3S)-γ-Acc-Gly]3 hexapeptide ((TAG)3) is studied using density functional theory calculations. The (TAG)3 and its Li+, Na+ and K+ metal ionic complexes are optimized at B3LYP/6-311+G∗ level of theory. The optimized structure of (TAG)3 ionic complexes agrees well with the various cyclic peptide cationic complexes that are obtained experimentally. The valence, peptide deformation and Ramachandran angles clearly explain the structural effects in (TAG)3 upon ionic interaction. The dependability of cavity size towards the size of ions is noted. The molecular electrostatic potential (MEP) map effectively illustrates the weak interaction between metal ion and (TAG)3, and further confirms carbonyl oxygens to be the active sites. The binding energy of (TAG)3 towards metal ion increases as Li+ > Na+ > K+, which is consistent with the electron density at bond critical points. The significant binding energies and the symmetric nature of (TAG)3 upon Na+ and K+ enclosures in turn shows that its nanotubular structures might act as the ion channels of biological interest.
THE INTERACTION OF POLYEHTYLENE WITH OXYGEN MOLECULE – A QUANTUM CHEMICAL STUDY
(PSGR Krishnammal College for Women, 2014-04-07) G, Praveena; M, Agalya; K, Nandhini
The molecular oxygen interacting properties of polyethylene (PE) chain with three different conformations (PE1, PE1 and PE3) have been explored using ab initio method. The isolated (PE) and complex PE…O2 systems were obtained using HF/6-31G level of theory. In order to understand the structural propensities of the isolated PE chains and their oxygen complexes, comparative analysis on geometrical parameters was carried out. The natural bond orbital analysis (NBO) was employed, to examine the non-bonded inter-actions that are present in the PE…O2 complexes. The calculated occupation numbers of the bond and the antibond orbitals were used, to study the nature of the non-bonded interactions of C-H…O type. The two body analysis was employed to calculate the interaction energies (∆E) of PE systems with the guest molecular oxygen, and the tendencies of ∆E, in the considered PE systems was also explored.
LOOKING BEYOND CARBON NANOTUBES: POLYPEPTIDE NANOTUBES AS ALTERNATIVES?
(American Scientific Publishers, 2007) G, Praveena; P, Kolandaivel; N, Santhanamoorthi; V, Renugopalakrishnan; Seeram Ramakrishna
Since the discovery of CNT by Iijima, Nature 354, 56 (1991). CNT’s have surged to the forefront as a versatile nanostructured material in nanoelectronic applications. Polypeptides nanotubular structures with tunable properties offer a challenging alternative to CNT. Earlier experimental studies on L-Alanyl-L-Valine (AV) and L-Valyl-L-Alanine (VA) have demonstrated their potential as novel porous materials, which form channel-like structure (Soldatov et al., Angew. Chem. Int. Ed. 43, 6308 (2004)). In the study reported here, DFT calculations on two closely related cyclic dipeptides cyclo[Lalanyl-L-valine]3 and cyclo[L-valyl-L-alanine]3 and on their linear correlates, [L-alanyl-L-valine]3 and [L-valyl-L-alanine]3 have been performed. This paper presents the generalstructuraland electronic properties of cyclic and linear correlates of the nanotubular oligomeric dipeptides constructs, AV, and VA. We have compared the energy gaps of these cyclic rings and their linear correlates with that of other nanotubular constructs. The calculated HOMO–LUMO gap of these isolated ring structures is significantly larger than CNT’s. Further research is required to reduce the band gaps to be comparable to CNT’s and other inorganic tubular structures. Polypeptide design promises to be a major toolin engineering desirable band gap for the creation of novelnanostructured polypeptide nanotubes.
QUANTUM CHEMICAL STUDY ON THE XH…HM (X=-C2 H, -C2 H3 AND M= LI, NA, K, FE, ZN) DIHYDROGEN BOND SYSTEMS
(PSGR Krishnammal College for Women, 2018-07-21) J, Pavithra; G, Praveena
The structure and electronic properties of dihydrogen bond complexes that form between H of M-H (where M-H=LiH, NaH, KH, FeH2, and ZnH2) and H of acetylene HC≡ CHand H of ethylene HCH=HCH compounds was predicted employing density functional theory. The ground state dihydrogen bond complexes were optimized at B3LYP-6-311++G** level of theory. The geometrical parameters, energies, entropies, and AIM analysis of the considered complexes were calculated and analyzed.
RUMEN ACIDOSIS IN GOATS
(Indian Journals.com, 2012-01-24) K, Padmaja; G, Praveena
The majority of health problems encountered in caprines reared in peri-urban areas are rumen related. Rumen acidosis in goats can be life threatening and treatment must begin immediately. In the present study, a flock of 18 goats with an accidental ingestion of left-over ceremonial waste were examined clinically and diagnosed as suffering with rumen acidosis. Rumen liquor was collected at random from 6 goats by ruminal paracentesis and analyzed. Rumen fluid analysis confirmed ruminal acidosis, as the colour was dark brown, acidic in odour, acidic pH (4.5 to 5.0) and protozoal activity was nil. Staining by Gram's stain revealed gram positive cocci. The flock was treated successfully with antihistamincs, rumen buffer and vitamins. Two goats of the flock with sternal recumbency were administered ringers lactate and calcium in addition to the above treatment.
STRUCTURAL AND DYNAMICAL STUDIES OF ALL-TRANS AND ALL-CIS CYCLO [(1R, 3S)-Γ-ACC-GLY] 3 PEPTIDES
(Springer-Verlag, 2008-12-01) G, Praveena; P, Kolandaivel
The quantum chemical and molecular dynamics studies have been performed to infer the structural changes of all-trans and all-cis forms of cyclo[(1R,3S)-3-aminocyclohexanecarboxylicacid(γ-Acc)-α- Glycine(Gly)]3 hexapeptide. The backbone conformations of the above peptide have been analyzed using the valence and peptide deformation angles applying B3LYP/6–311G** level of theory. The conformational preference of the backbone of all-trans and all-cis cyclo[(1R,3S)-γ-Acc-Gly]3 hexapeptides is found to depend on the puckering of cyclohexane rings. The non-uniform distribution of water inside the cavity is observed, where sometimes water molecules formed a chain like conformation through hydrogen bond networks while traversing the pore of all-cis cyclo[(1R,3S)-γ-Acc-Gly]3 peptide. Larger relaxation times of the order of a hundred to two hundred pico seconds for active site…water hydrogen bond interactions were noticed. The hydrophobic nature of the cavity of all-trans cyclo[(1R,3S)-γ-Acc-Gly]3 due to the presence of cyclohexane moiety has been analyzed. Further this investigation emphasized on the non-transport of molecules through the pore of all-trans cyclo[(1R,3S)-γ-Acc-Gly]3 peptide due to the obstruction produced by cyclohexane groups.
STRUCTURAL AND INTERACTION PROPERTIES OF PORPHYRIN LAYERS — A QUANTUM CHEMICAL STUDY
(IOP Science, 2015) G, Praveena; A, Abiram
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.
STRUCTURAL PROPERTIES AND ANION BINDING AFFINITY OF CYCLO[(1R,3S)-Γ-ACC-GLY]3 HEXAPEPTIDE
(Taylor & Francis group, 2009-08-01) G, Praveena; P, Kolandaivel
The structural and anion binding properties of all-trans cyclo[(1R,3S)-γ-Acc-Gly]3 hexapeptide[named as (TAG)3] were explored via quantum chemical studies. The (TAG)3 form complexes with F-, Cl-, and Br- ions inside the cavity exhibiting receptor like conformation. The structural arrangement of (TAG)3 upon ionic enclosure coincides well with the experimentally obtained -γ cyclic peptide anionic complexes. A good consistency is noted between geometrical parameters and electronic effects. The concentrated LUMO sites in (TAG)3 are useful in deciding the selectivity of N-H group for strong hydrogen bond interaction with anion. This study emphasize that the minimal structural distortions would have pronounced effect over anion binding affinity. The overall structure of (TAG)3 is found to be highly rigid upon Cl- and Br- ionic enclosures. The strong association of (TAG)3 towards inorganic anions with large binding energies, in general shows the hybrid α-γ cyclic peptides as promising anion receptors.
STUDY OF ATOMIC AND CONDENSED ATOMIC INDICES FOR REACTIVE SITES OF MOLECULES
(Springer, 2005-09) P, Kolandaivel; G, Praveena; P, Selvarengen
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)αk 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.
TAMARIND SEED SKIN-DERIVED FIBER-LIKE CARBON NANOSTRUCTURES AS NOVEL ANODE MATERIAL FOR LITHIUM-ION BATTERY
(Springer Berlin Heidelberg, 2018-11-01) Sumit Ranjan Sahu; D, Parimala Devi; V V N, Phanikumar; T, Ramesh; N, Rajalakshmi; G, Praveena; R, Prakash; Bijoy Das; R, Gopalan
THERAPEUTIC MANAGEMENT OF POSTPARTURIENT HAEMOGLOBINURIA IN A BUFFALO
(Indian Journals, 2014) Reddy B, Sudhakara; S, Sivajothi; G, Praveena; R, Venkatasivakumar
A buffalo was presented with history of calving four weeks prior, passing of reddish and frothy urine from previous evening. On clinical examination, buffalo had dullness, pale mucous membranes, tachycardia and abnormal vital parameters. Laboratory examination revealed lowered RBC, Haemoglobin, PCV, serum phosphorus, total protein, albumin and glucose levels. Buffalo was treated with parenteral phosphorous and supportive therapy. Animal recovered four days after therapy.