NBO analysis, hybrid density functional theory (B3LYP/6-311+G**) and ab initio molecular orbital (HF/6-311+G**) based methods were used to study the anomeric effects (AE), electrostatic interactions, dipole-dipole interactions and steric repulsion effects on the conformational properties of 2-methoxy- (1), 2-methylthio- (2), 2-methylseleno- (3), 2-fluoro- (4), 2-chloro- (5) and 2-bromocyclohexa...

This paper presents a new algorithm for generating the conformational statistics of lattice polymer models. The inputs to the algorithm are the distributions of poses (positions and orientations) of reference frames attached to sequentially proximal bonds in the chain as it undergoes all possible torsional motions in the lattice. If z denotes the number of discrete torsional motions allowable a...

Based on equilibrium molecular simulations, it is usually difficult to efficiently visit the whole conformational space of complex systems, which are separated into some metastable regions by high free energy barriers. Nonequilibrium simulations could enhance transitions among these metastable regions and then be applied to sample equilibrium distributions in complex systems, since the associat...

human immunodeficiency virus infection / acquired immunodeficiency syndrome (hiv/aids) is a disease pertained to the human immune system. given its crucial role in viral replication, hiv-1 protease (hiv-1 pr) is a prime therapeutic target in aids therapy. in this regard, the dynamic aspects of ligand-enzyme interactions may indicate an important role of conformational variability in hiv-1 pr in...

cystic fibrosis (cf) is the most common inherited disorder in caucasian populations, with over 1400 cystic fibrosis transmembrane conductance regulator (cftr) mutations. the type of mutations and their distributions varies widely between different countries and/or ethnic groups. seventy iranian cystic fibrosis patients were screened for the cftr gene mutation using arms/pcr (amplification refra...

ab initio calculations at hf/6-31g* level of theory for geometry optimization and mp2/6-31g*//hf/6-31g* for a single point total energy calculation are reported for the importantenergy-minimum conformations and transition-state geometries of 1, 3-diazacyclohepta-1, 2-diene (2) and 1, 3-diazacycloocta-1, 2-diene (3). the c2 symmetric twist-chair (2-tc)conformation of 2 is calculated to be 7.4 kj...

ab initio calculation at hf/6-31g* level of theory for geometry optimization and mp2/6-31g*//hf/6-31g* for a single point total energy calculation are reported for the important energyminimumconformations and transition-state geometries of of cyclodeca-1,2,3-triene (1). the mostfavorable conformation of 1 is a unsymmetrical twist-chair (1-tc) structure. degenerateinterconversion of 1-tc with it...

the effects of electromagnetic fields (emfs) radiation at the frequency of 940 mhz on the structure and function of human adult and fetal hemoglobin (hba and hbf) were studied. after extraction and purification of hba and hbf, the oxygen absorption values for exposed and unexposed hba and hbf to emf were compared. the slope of oxygen absorption curve for exposed hba was increased while that for...

Cellular functions are regulated by molecules that interact with proteins and alter their activities. To enable such control, protein activity, and therefore protein conformational distributions, must be susceptible to alteration by molecular interactions at functional sites. Here we investigate whether interactions at functional sites cause a large change in the protein conformational distribu...