Normal coordinate analysis and spectroscopic constants of formic acid and its isotopes

A normal coordinate analysis has been performed for the molecule formic acid and its isotopes. The force constants have been computed assuming the GVFF. Using the force constants other spectroscopic constants such as mean square amplitudes of vibration, generalized mean square ampli¬ tudes of vibration, Coriolis coupling coefficients, centrifugal distortion constants have been calculated and presented here. With the aid of vibrational frequencies and the structural parameters, the thermodynamics functions such as heat content, heat capacity, free energy and entropy have also been evaluated.Natarajan A., Kolandaivel P. Normal coordinate analysis and spectroscopic constants of formic acid and its isotopes. In: Bulletin de la Classe des sciences, tome 70, 1984. pp. 538-549

Molecular constants of methylene chloride and its isotope

A complete vibrational analysis was made for the molecules methylenechloride and its isotope. The reasonable set of force constants have been evaluated using the general valence force field. The mean square amplitudes, generalised mean square amplitudes, Coriolis coupling constants, shrinkage constants and centrifugal distortion constants have been calculated using the revised vibrational frequencies and the structural parameters. The thermodynamic functions have been computed for the ideal gaseous state using a rigid rotor harmonic oscillator approximation. A comparison is made between the values obtained in the present investigation and the values available in the literature.Natarajan A., Kolandaivel P. Molecular constants of methylene chloride and its isotope. In: Bulletin de la Classe des sciences, tome 69, 1983. pp. 295-303

Structure, Stability and Interaction Studies on Schiff Base Analogue Systems

Abstract: Ab initio and density functional theory methods have been applied to study the molecular structure and interaction of water with N-methyl-2-propenylidenimine and Nmethyl- 2-butenylidenimine molecules. The most possible reactive sites of the above molecules have been identified for the water interactions. The strength of the hydrogen bond is discussed using the atomic charges, which were calculated using the Mulliken population analysis and Natural population analysis schemes at MP2/6-31G* level of theory. The electron density (ÃÂ) and laplacian of electron density (∇2ÃÂ) have been calculated for the possible existence of the hydrogen bonds with CH and CH3 groups of molecules using the “Atoms in molecules†approach. The chemical hardness and chemical potential for these complexes have been calculated at HF/6-31G* level of theory and discussed for the conformational stability of these molecules

Structure, Stability and Interaction Studies on Nucleotide Analogue Systems

Abstract: Most of the biological molecules have a good interaction with water molecules. The hydrogen bonding interactions with the structural analogues of nucleic acid phosphate group namely dimethyl phosphate anion (DMP) and diethyl phosphate anion (DEP) are studied employing the ab initio and density functional theory methods. Inspections have been made to locate the reactive sites for the interactions of isomeric forms of mono, di and tri hydrates of alkyl phosphate anion using the above theories. It reveals, water molecules have a very strong interaction with the phosphate group in both the molecules and their interactions induce the changes in the structural parameters of the PO4 group for both the DMP and DEP anions. The optimized structural parameters, total energy, dipole moment and rotational constants are calculated and are compared with the available experimental values. The chemical hardness and chemical potential for these complexes have been calculated at HF/6-31G* level of theory and discussed the conformational stability of these complexes

Computational studies of pandemic 1918 and 2009 H1N1 hemagglutinins bound to avian and human receptor analogs

<div><p>The purpose of this work was to study the binding properties of two pandemic influenza A virus 1918 H1N1 (SC1918) and 2009 H1N1 (CA09) hemagglutinin (HA) with avian and human receptors. The quantum chemical calculations have been performed to analyze the interactions of 130 loop, 190 helix, 220 loop region, and conserved residues 95,145,153–155, of pandemic viruses’ HA with sialo-trisaccharide receptor of avian and human using density functional theory. The HA’s residues Tyr 95, Ala 138, Gln 191, Arg 220, and Asp 225 from the above regions have stronger interaction with avian receptor. The residues Thr 136, Trp 153, His 183, and Asp 190 of HA are important and play a significant role to bind with human receptor. The residues Tyr 95, Ala 138, Lys 145, Trp 153, Gln 192, and Gln 226 of HA of CA09 virus have found more interaction energies with human than avian receptors. Due to mutations in the active residues of HA of CA09 virus comparing with SC1918, the binding capabilities of HA with human have been increased. The molecular dynamics simulation was made to understand the different dynamical properties of HA and molecular interactions between HA of these two viruses with sialo-trisaccharide receptors of avian and human receptors. The interaction energy of HA of CA09 virus with human receptor decreases due to the human receptor far away from conserved residue region of HA protein. This reveals that the conserved residues particularly Lys 145 play major contribution to interaction with human receptor in HA of CA09 virus.</p></div

The inhibitory performance of flavonoid cyanidin-3-sambubiocide against H274Y mutation in H1N1 influenza virus

<p>Oseltamivir (Tamiflu) is the most accepted antiviral drug that targets the neuraminidase (NA) protein to inhibit the viral release from the host cell. Few H1N1 influenza strains with the H274Y mutation creates drug resistance to oseltamivir. In this study, we report that flavonoid cyanidin-3-sambubiocide (C3S) compound acts as a potential inhibitor against H274Y mutation. The drug resistance mechanism and inhibitory activity of C3S and oseltamivir against wild-type (WT) and H274Y mutant-type (MT) have been studied and compared based on the results of molecular docking, molecular dynamics, and quantum chemical methods. Oseltamivir has been found less binding affinity with MT. C3S has more binding affinity with WT and MT proteins. From the dynamical study, the 150th loop of the MT protein has found more deformation than WT. A single H274Y mutation induces the conformational changes in the 150th loop which leads to produce more resistance to oseltamivir. The 150th cavity is more attractive target for C3S to stop the conformational changes in the MT, than 430th cavity of NA protein. The C3S is stabilized with MT by more number of hydrogen bonds than oseltamivir. The electrostatic interaction energy shows a stronger C3S binding with MT and this compound may be more effective against oseltamivir-resistant virus strains.</p

Study of mutation and misfolding of Cu-Zn SOD1 protein

<div><p>The main objective of this work is to determine the mechanism for misfolding and aggregation as a result of mutations in Cu-Zn superoxide dismutase1. The quantum mechanical approach is beneficial for investigating the early stages of mutation, misfolding, and loss of protection of the native structures involved in the neuro-degeneration disease Amyotrophic Lateral Sclerosis. All the structures were optimized using density functional theory (B3LYP) with 6–31G* and LANL2DZ basis sets. The binding energies of the metal ions with their associated residues in the active site loop and metal binding loop have been investigated for native and metal-bound mutated structures. The metal ion affinity (MIA) was computed for all the structures. The binding energy and MIA in gas phase reveal the nature of interaction of active site residues with the metal cations. The electronic effect prevailing between the side chains of the residues in the active site governing the intermolecular interactions is given by the polarizability studies. The role of the bridging residue His 63 in the active site of the protein in the native and metal-bound mutated structures have been studied using ONIOM method to reveal the changes that takes place in the structural parameters during mutation. The molecular dynamics simulation is used to explore different dynamic properties of active site in native and metal-bound mutated structures. The structural information provided by the molecular dynamics simulation illustrates the structural consequences in the mutated structures.</p></div

A theoretical perspective of the nature of hydrogen-bond types – the atoms in molecules approach

<p>Hydrogen bonds and their strength were analysed based on their X–H proton–donor bond properties and the parameters of the H–Y distance (Y proton acceptor). Strong, moderate and weak interactions in hydrogen-bond types were verified through the proton affinities of bases (PA), deprotanation enthalpies of acids (DPE) and the chemical shift (σ). The aromaticity and anti-aromaticity were analysed by means of the NICS (0) (nucleus-independent chemical shift), NICS (1) and ΔNICS (0), ΔNICS (1) of hydrogen-bonded molecules. The strength of a hydrogen bond depends on the capacity of hydrogen atom engrossing into the electronegative acceptor atom. The correlation between the above parameters and their relations were discussed through curve fitting. Bader's theory of atoms in molecules has been applied to estimate the occurrence of hydrogen bonds through eight criteria reported by Popelier <i>et al</i>. The lengths and potential energy shifts have been found to have a strong negative linear correlation, whereas the lengths and Laplacian shifts have a strong positive linear correlation. This study illustrates the common factors responsible for strong, moderate and weak interactions in hydrogen-bond types.</p

Electron charge transfer in linear and cyclic structures of polypeptides

10.1166/jctn.2008.1131Journal of Computational and Theoretical Nanoscience5112264-226