The nuclear isotropic shielding constants sigma((17)O) and sigma((13)C) of the carbonyl bond of acetone in water at supercritical (P=340.2 atm and T=673 K) and normal water conditions have been studied theoretically using Monte Carlo simulation and quantum mechanics calculations based on the B3LYP6-311++G(2d,2p) method. Statistically uncorrelated configurations have been obtained from Monte Car...

Molecular dynamics simulations of triclinic hen egg white lysozyme in aqueous solution were performed to calculate the intrinsic pKas of 14 ionizable residues. An all-atom model was used for both solvent and solute, and a single 180 ps simulation in conjunction with a Gaussian fluctuation analysis method was used. An advantage of the Gaussian fluctuation method is that it only requires a single...

We study two designed and one natural zinc finger peptide each with the Cys(2)His(2) (CCHH) type of metal binding motif. In the approach we have developed, we describe the role of the protein and solvent outside the Zn(II)-CCHH metal-residue cluster by a molecular field represented by generalized harmonic restraints. The strength of the field is adjusted to reproduce the binding energy distribu...

A stochastic model for the dynamics of enzymatic catalysis in explicit, effective solvents under physiological conditions is presented. Analytically-computed first passage time densities of a diffusing particle in a spherical shell with absorbing boundaries are combined with densities obtained from explicit simulation to obtain the overall probability density for the total reaction cycle time o...

Probe mapping is a common approach for identifying potential binding sites in structure-based drug design; however, it typically relies on energy minimizations of probes in the gas phase and a static protein structure. The mixed-solvent molecular dynamics (MixMD) approach was recently developed to account for full protein flexibility and solvation effects in hot-spot mapping. Our first study us...

The classical STD NMR protocol to monitor solvent interactions in gels is strongly dependent on gelator and concentrations does not report the degree of structuration at particle/solvent interface. We hypothesised that, for suspensions large particles, could be characterised by when taking into account particle-to-solvent 1 H– H spin diffusion transfer using 1D equation. have carried out a syst...

Molecular simulations play important roles in computer-aided drug design (CADD). Especially, these calculations are useful for the analyses of 3D structures of biopolymers, such as proteins, nucleic acids or sugar chains, in structure-based drug design (SBDD) trials. The molecular dynamics (MD) simulation is most widely used for the molecular simulations of biopolymers, and it plays significant...

The production of anhydrous ethanol, due to the presence azeotrope, is difficult using conventional distillation, at pressure atmospheric, as a separation process. One methods used extractive consisting in addition third substance capable change vapor-liquid equilibrium system and obtaining dehydration ethanol. Therefore, ethanol process propylene glycol solvent was evaluated ProSimPlus softwar...