A fast stable finite difference Poisson-Boltzmann (FDPB) model for implicit solvation in molecular dynamics simulations was developed using the smooth permittivity FDPB method implemented in the OpenEye ZAP libraries. This was interfaced with two widely used molecular dynamics packages, AMBER and CHARMM. Using the CHARMM-ZAP software combination, the implicit solvent model was tested on eight p...

In this research, Quantum-mechanical calculations were performed at the HF method with the 6-31+G*basis set and at the B3LYP method with the 6-31+G* basis set in the gas phase and five solvents such as water, DMSO, methanol, ethanol and dichloromethane at six temperatures. According to these theoretical results of IR, we extracted thermo chemical parameters such as enthalpy (∆H Kcal/mol), Gibbs...

Computer simulations of reaction processes in solution in general rely on the definition of a reaction coordinate and the determination of the thermodynamic changes of the system along the reaction coordinate. The reaction coordinate often is constituted of characteristic geometrical properties of the reactive solute species, while the contributions of solvent molecules are implicitly included ...

Based on Gibbs-Duhem law and using UNIFAC-FV computer algorithm, the activity of polymer component in polymer-solvent systems is determined. The variation of activity of components with concentration at different temperatures are used to find the equilibrium concentration, UCST, and LCST for the systems. Also by generalization of the method, Gel-Liquid equilibrium is studied in some three c...

Two dimensional thin layer chromatography on polyamide sheets is a useful method for identification of PTH-amino acids which have very close Rf-values. The solvent systems described here are particularly effective and have an edge over other solvent systems used for the separation of PTH-amino acids. The solvent systems provide a clear separation of all PTH-amono acids except lle / Leu in a...

We present Gibbs ensemble Monte Carlo simulations of monomer–solvent and polymer–solvent mixtures with soft interaction potentials, that are used in dissipative particle dynamics simulations. From the simulated phase behavior of the monomer–solvent mixtures one can derive an effective Flory–Huggins x-parameter as a function of the particle interaction potential. We show that this x-parameter ag...