Total publications: 610
481. Validated predictive QSAR modeling of N-aryl-oxazolidinone-5-carboxamides for anti-HIV protease activity
in Bioorganic and Medicinal Chemistry Letters, 2010, ISSN: 0960-894X, Volume: 20,
Article, Indexed in: crossref, scopus
Validated predictive QSAR modeling was done on some N-aryl-oxazolidinone-5- carboxamides for higher anti-HIV protease activities. Stepwise regression developed significant models showing importance of atom based descriptors like RTSA indices, Wang-Ford charges and different whole molecular descriptors. The true predictabilities of QSAR models were justified by challenging these against an external dataset. A representative high active compound was predicted by this modeling. It showed that internal and external validations may lead to the same conclusion.
482. Water adsorption and dissociation on the Au(321) stepped surface
in JOURNAL OF MOLECULAR STRUCTURE-THEOCHEM, 2010, ISSN: 0166-1280, Volume: 946,
Article, Indexed in: crossref, scopus, wos
The H(2)O adsorption and dissociation on the zigzag stepped Au(3 2 1) surface was investigated using density functional theory and a periodic supercell approach. The water molecule interacts directly with the lowest coordinated gold atoms on the surface with one of its hydrogen atoms pointing towards the (1 1 1) terraces below. The adsorption energy with respect to the separated H(2)O and metal clean slab is -0.23 eV. The co-adsorption of the OH and H species is also more favorable with the fragments adsorbed nearby the step (bridge sites). The calculated interaction energy, with respect to gaseous water and to the clean slab, is 0.96 eV. The dissociation of water is endothermic by 1.19 eV and the barrier of the reaction is 1.33 eV. Finally, the rate constant for this reaction was determined for two different temperatures from transition state theory. The reaction rate constants are 1 x 10(-4) s(-1) and 2 x 10(0) s(-1) at 150 and 300 degrees C evidencing that the reaction of water dissociation is slow on the Au(3 2 1) surface. Importantly, these results suggest that the high performance of some Au-based catalysts in the water gas shift reaction (WGSR) is not related only with the presence of low-coordinated atoms, and that the support nature and structure, and support-gold interaction must have also an important role in the catalytic activity.
483. 3D entropy and moments prediction of enzyme classes and experimental-theoretic study of peptide fingerprints in <i>Leishmania</i> parasites
in BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS, 2009, ISSN: 1570-9639, Volume: 1794,
Article, Indexed in: crossref, wos
484. A TOPological Sub-structural Molecular Design (TOPS-MODE)-QSAR approach for modeling the antiproliferative activity against murine leukemia tumor cell line (L1210)
in BIOORGANIC & MEDICINAL CHEMISTRY, 2009, ISSN: 0968-0896, Volume: 17,
Article, Indexed in: crossref, scopus, wos
Lately, Quantitative Structure-Activity Relationship (QSAR) studies have been afar used to predict anticancer activity taking into account different molecular descriptors, statistical techniques, cell lines and data set of congeneric and non-congeneric compounds. Herein we report a QSAR study based on a TOPological Sub-structural Molecular Design (TOPS-MODE) approach, aiming at predicting the anticancer leukemia activity of a diverse data set of indolocarbazoles derivatives. Finally, several aspects of the structural activity relationships are discussed in terms of the contribution of different bonds to the anticancer activity, thereby making the relationship between structure and biological activity more transparent.
485. Comparative QSAR modelling of 2-phenylindole-3-carbaldehyde derivatives as potential antimitotic agents
in Bioorganic and Medicinal Chemistry Letters, 2009, ISSN: 0960-894X, Volume: 19,
Article, Indexed in: crossref, scopus
QSAR modelling was done on some 2-phenylindole-3-carbaldehyde derivatives to find out structural requirements for more active antimitotic agents. Four statistical methods were used to develop models. The results show the importance of ETSA indices, RTSA indices, IC1, SIC4, Jhetv and MSD on the activity. Electrostatic potential charges of atoms, increased surface area, and presence of bulky group along Y-axis and chlorine substitution were also found to be important.
486. Computational chemistry study of 3D-structure-function relationships for enzymes based on Markov models for protein electrostatic, HINT, and van der Waals potentials
in Journal of Computational Chemistry, 2009, ISSN: 0192-8651, Volume: 30,
Article, Indexed in: crossref
487. Convenient QSAR model for predicting the complexation of structurally diverse compounds with beta-cyclodextrins
in BIOORGANIC & MEDICINAL CHEMISTRY, 2009, ISSN: 0968-0896, Volume: 17,
Article, Indexed in: crossref, scopus, wos
This paper reports a QSAR study for predicting the complexation of a large and heterogeneous variety of substances (233 organic compounds) with beta-cyclodextrins (beta-CDs). Several different theoretical molecular descriptors, calculated solely from the molecular structure of the compounds under investigation, and an efficient variable selection procedure, like the Genetic Algorithm, led to models with satisfactory global accuracy and predictivity. But the best-final QSAR model is based on Topological descriptors meanwhile offering a reasonable interpretation. This QSAR model was able to explain ca. 84% of the variance in the experimental activity, and displayed very good internal cross-validation statistics and predictivity on external data. It shows that the driving forces for CD complexation are mainly hydrophobic and steric (van der Waals) interactions. Thus, the results of our study provide a valuable tool for future screening and priority testing of beta-CDs guest molecules.
488. Effect of the exchange-correlation potential and of surface relaxation on the description of the H2O dissociation on Cu(111)
in JOURNAL OF CHEMICAL PHYSICS, 2009, ISSN: 0021-9606, Volume: 130,
Article, Indexed in: crossref, scopus, wos
The role of the exchange-correlation density functional (PBE, PW91, RevPBE) and of surface relaxation in the determination of the adsorption energies, reaction energy barriers, and reaction rate constants has been analyzed taking water dissociation on Cu(111) surface as a test case. The PBE and PW91 functionals yield similar adsorption geometries and, adsorption and activation energies, but differ significantly from RevPBE results. For each of the functionals tested, surface relaxation was found to have only a minor effect on the calculated (co)adsorption geometries and (co)adsorption energies. The calculated energy barriers for water dissociation are more affected by the functional used, especially in the case of the RevPBE, with obvious implications on the calculated energy barriers and derived reaction rate constants. (C) 2009 American Institute of Physics. [DOI: 10.1063/1.3149851]