An important application of distance geometry to biochemistry studies the embeddings of the vertices of a weighted graph in the three-dimensional Euclidean space such that the edge weights are equal to the Euclidean distances between corresponding point pairs. When the graph represents the backbone of a protein, one can exploit the natural vertex order to show that the search space for feasible...

In this paper we propose a VNS-based algorithm for the solution of the Molecular Distance Geometry Problem. First, we use VNS to solve a smoothed version of the problem to identify the most promising zone in the solution space. We then use VNS again to solve the original problem restricted to the promising zone. This algorithm often manages to find a solutions having higher accuracy than other ...

Molecular replacement (MR) is a well established computational method for phasing in macromolecular crystallography. In MR searches, spaces of motions are explored for determining the appropriate placement of rigid models of macromolecules in crystallographic asymmetric units. In the first paper of this series, it was shown that this space of motions, when endowed with an appropriate compositio...

Molecular Mechanics describes molecules as particle configurations interacting via classical potentials. These configurational energies usually consist of the sum of different phenomenological terms which are tailored to the description of specific bonding geometries. This approach is followed here to model the fullerene C60, an allotrope of carbon corresponding to a specific hollow spherical s...

Detailed kinetic models to aid the understanding of complex chemical systems require many thousands of reaction rate coefficients, most of which are estimated, some quite approximately and with unknown uncertainties. This motivates the development of high-throughput methods to determine rate coefficients via transition state theory calculations, which requires the automatic prediction of transi...

The molecular structure of the stable conformation of phosphonic acid in gas phase has beencomputed by employing complete geometry optimization in Density Functional Theory(DFT) methods. The methods used for calculations are B3LYP, BP86 and B3PW91 that havebeen studied in two series of basis sets: D95** and 6-31+G(d,p) for hydrogen and oxygenatoms; LANL2DZ for phosphorus. Bond lengths and angle...

Antioxidants are made for the struggle and reconstruction of the damaged cells, because of their ability in destroying the free radicals. On account of their importance, a theoretical procedure was applied for the study of the molecular structure and radical scavenging activity of six hydroxyphenols which have been introduced as antioxidant compounds. All geometry structures were optimized by M...

As a continuous research for discovery of new COX-2 inhibitors, chemical synthesis, in vitro biological activity and molecular docking study of anew group of 1,4-dihydropyridine (DHP) derivatives were presented. Novel synthesized compounds possessing a COX-2 SO2Me pharmacophore at the para position of C-4 phenyl ring, different hydrophobic groups (R1) at C-2 position and alkoxycarbonyl groups (...

Molecular structure, isomerism, conformational stability and intramolecular hydrogen bonding (IHB) of cis-enol forms of 1-(n-pyridyl)butane-1,3-diones (nPBD) (n = 2, 3, or 4) have been investigated by means of density functional theory (DFT) calculations. Energy differences for all possible nPBD cis-enol forms of isomers with respect to the most stable form of the correspondin...

Some new coordination compounds of tin(IV) having general formula [SnBu2 (L)2 ] (where L = carbohydrazone ligand) have been synthesized by the reaction of dibutyltin oxide with carbohydrazone ligands with the ratio of 1:2 (metal- ligand) using dry benzene as a reaction medium. The newly synthesized complexes were characterized by elemental analysis, molecular weight determinations, conductivity...