A restrained molecular dynamics simulation approach that explicitly includes the effect of the surrounding solvent molecules is applied to the NMR determination of the conformations of the B-loop fragments of human transforming growth factor alpha and epidermal growth factor. Backbone interproton distance restraints are obtained by using two-dimensional rotating frame nuclear Overhauser effect ...

the present study aimed to use a method for the synthesis of some 3, 4-dihydropyrimidin-2-(1h) - ones/thiones. the study tried to answer the question whether this reaction can be performed without solvent and with new catalyst or not. to find answer to the question, we described a novel protocol for the efficient synthesis of 3, 4-dihydropyrimidin-2-(1h)-one derivatives using aromatic aldehyde,...

Alamethicin is a 20-amino acid antibiotic peptide that forms voltage-gated ion channels in lipid bilayers. Here we report calculations of its association free energy with membranes. The calculations take into account the various free-energy terms that contribute to the transfer of the peptide from the aqueous phase into bilayers of different widths. The electrostatic and nonpolar contributions ...

A comprehensive conformational analysis of both 2,3-difluorobutane diastereomers is presented based on density functional theory calculations in vacuum and in solution, as well as NMR experiments in solution. While for 1,2-difluoroethane the fluorine gauche effect is clearly the dominant effect determining its conformation, it was found that for 2,3-difluorobutane there is a complex interplay o...

The reaction of 2-naphthol and also para-substituted phenols with glyoxal in presence of choline chloride: 2 ZnCl2 [ChCl: 2ZnCl2], a deep eutectic solvent (DES), as a green catalyst was studied. The amount of catalyst, solvent type, temperature, and time on the yield of reaction were investigated. It was found that the optimal condition included 10% mol ratio of catalyst (mol percentage of DES ...

The binding affinity between a probe hydrophobic particle and model hydrophobic plates with different charge (or dipole) densities in water was investigated through molecular dynamics simulation free-energy perturbation calculations. We observed a reduced binding affinity when the plates are charged, in agreement with previous findings. With increased charge density, the plates can change from ...

In the present work, at first, DFT calculations were carried out to study molecular structure of tenofovir B3LYP/MidiX level theory and in water as solvent. The HOMO/LUMO orbitals, excitation energies oscillator strengths investigated drug also calculated presented. NBO analysis was performed illustrate intramolecular rehybridization electron density delocalization. following, a docking for scr...

glycine, alanine and valine are taken as amino acids with an equal polar head and with thedifference in the length of hydrocarbon chains. the structural optimizations show the results of theisolated glycine, alanine and valine in the gases phase, at the hartree-fock level by means ofsto-3g,3-21g, 6-31g and 6-31+g basis sets. the calculations were performed for the ten (1-10)solvents using pcm m...

Identifying stable speciation in multi-component liquid solutions is fundamentally important to areas from electrochemistry organic chemistry and biomolecular systems. Here we introduce a fully automated, high-throughput computational framework for the accurate prediction of species by computing nuclear magnetic resonance (NMR) chemical shifts. The automatically extracts categorizes hundreds th...