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...

13 Proteins must move between different conformations of their native ensemble to perform their 14 functions. Crystal structures obtained from high-resolution X-ray diffraction data reflect this 15 heterogeneity as a spatial and temporal conformational average. Although movement between natively 16 populated alternative conformations can be critical for characterizing molecular mechanisms, it i...

The quantum-chemical calculations on the conformational properties of 2-flouro-2-oxo- 1,3,2-dioxaphosphorinane (1), 2-choloro-2-oxo-1,3,2-dioxaphosphorinane (2) and 2-bromo- 2-oxo-1,3,2-dioxaphosphorinane (3) have been investigated by means of ab initio molecular orbital (HF/6-311+G**) and hybrid density functional theory (B3LYP/6-311+G**) based methods and Natural Bond Orbital (NBO) interpreta...

Hybrid-density functional theory (B3LYP/Def2-TZVPP) based method and NBOinterpretation were used to investigate the conformational behavior of 1,2-dihalodisilanes[halo=F (1), Cl (2), Br (3), I (4)]. The B3LYP/Def2-TZVPP results showed that the anticonformations of compounds 1-4 are more stable than their corresponding gaucheconformations. The stability of the anti conformation compared to the g...

Bacteriophage T4 Lysozyme (T4L) catalyzes the hydrolysis of the peptidoglycan layer of the bacterial cell wall late in the infection cycle. It has long been postulated that equilibrium dynamics enable substrate access to the active site located at the interface between the N- and C-terminal domains. Crystal structures of WT-T4L and point mutants captured a range of conformations that differ by ...

Conformations of bovine pancreatic trypsin inhibitor were calculated by assuming that the final structure as well as properly chosen overlapping segments thereof are simultaneously in low-energy (not necessarily the lowest-energy) conformational states. Therefore, the whole chain can be built up from building blocks whose conformations are determined primarily by short-range interactions. Our e...

Macrocycles constitute superior ligands for targets that have flat binding sites but often require long synthetic routes, emphasizing the need property prediction prior to synthesis. We investigated scope and limitations of machine learning classification models regression predicting cell permeability a set de novo-designed, drug-like macrocycles. 2D-Based models, which are fast calculate, disc...

The role of crystal packing in determining the observed conformations of amino acid side-chains in protein crystals is investigated by (1) analysis of a database of proteins that have been crystallized in different unit cells (space group or unit cell dimensions) and (2) theoretical predictions of side-chain conformations with the crystal environment explicitly represented. Both of these approa...