Various ab initio calculations using the density-functional (DFT), the second order Möller-Plesset perturbation (MP2) and self-consistent reaction field (SCRF) theories were performed on thirteen theoretically possible inositol stereoisomers. Gas phase calculations reveal that the myo- and neo-isomers of inositol (bearing one and two axial hydroxyl groups, respectively) are marginally more stab...

A systematic density functional theory based study of hydrogen bond energies of 2465 single hydrogen bonds has been performed. In order to be closer to liquid phase conditions, different from the usual reference state of individual donor and acceptor molecules in vacuum, the reference state of donors and acceptors embedded in a perfect conductor as simulated by the COSMO solvation model has bee...

The hairpin ribozyme, a small catalytic RNA consisting of two helix-loop-helix motifs, serves as a paradigm for RNA folding. In the active conformer, the ribozyme is docked into a compact structure via loop-loop interactions. The crystal structure of the docked hairpin ribozyme shows an intricate network of hydrogen bonding interactions at the docking interface, mediated by the base, sugar, and...

in this work, a molecular dynamics simulation of the transport of water - methanol mixture through the single wall carbon nanotube (swcnt) is reported. methanol and water are selected as fluid molecules since water represents a strongly polar molecule while methanol is as an intermediate between polar and strongly polar molecules. some physical properties of the methanol-water mixture such as r...

Heterogeneous catalytic hydrogenation of cyclohexene, catalyzed by Pt/A1203, was carried out in thirteenvarious solvents (four alcoholic solvents, six aprotic polar solvents and three non polar solvents) at 25 °C.Single-parameter correlations of logk vs. normalized polarity parameter (ETN), hydrogen-bond acceptorbasicity (p), hydrogen-bond donor acidity (a) and dipolarity/polarizibility (it*) d...

The program HBexplore is a new tool for identifying and analyzing hydrogen bonding patterns in biological macromolecules. It selects all potential hydrogen bonds according to geometrical criteria. The hydrogen bond table can then be subjected to further automatic or interactive analysis tools. These tools include the calculation of mean values and distributions of geometrical hydrogen bond para...

heterogeneous catalytic hydrogenation of cyclohexene, catalyzed by pt/a1203, was carried out in thirteenvarious solvents (four alcoholic solvents, six aprotic polar solvents and three non polar solvents) at 25 °c.single-parameter correlations of logk vs. normalized polarity parameter (etn), hydrogen-bond acceptorbasicity (p), hydrogen-bond donor acidity (a) and dipolarity/polarizibility (it*) d...