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Chemical Modeling (chemical + modeling)
Selected AbstractsModeling based on subspace orthogonal projections for QSAR and QSPR researchJOURNAL OF CHEMOMETRICS, Issue 1 2008Yizeng Liang Abstract A novel projection modeling method for quantitative structure activity relationship (QSAR) and quantitative structure property relationship (QSPR) is developed in this paper. Orthogonalization of block variables is introduced to deal with the problem of variable selection. Projections based on least squares are used to construct the modeling space in order to search for the best regression directions for chemical modeling. A suitable prediction space for such a model is further defined to confine the usage range of the model. Three real data sets were analyzed to check the performance of the proposed modeling method. The results obtained from Monte-Carlo cross-validation (MCCV) showed that the proposed modeling method might provide better results for QSAR and QSPR modeling than PCR and PLS with respect to both fitting and prediction abilities. Copyright © 2007 John Wiley & Sons, Ltd. [source] Quantum chemical modeling of enzymatic reactions: The case of histone lysine methyltransferaseJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 8 2010Polina Georgieva Abstract Quantum chemical cluster models of enzyme active sites are today an important and powerful tool in the study of various aspects of enzymatic reactivity. This methodology has been applied to a wide spectrum of reactions and many important mechanistic problems have been solved. Herein, we report a systematic study of the reaction mechanism of the histone lysine methyltransferase (HKMT) SET7/9 enzyme, which catalyzes the methylation of the N-terminal histone tail of the chromatin structure. In this study, HKMT SET7/9 serves as a representative case to examine the modeling approach for the important class of methyl transfer enzymes. Active site models of different sizes are used to evaluate the methodology. In particular, the dependence of the calculated energies on the model size, the influence of the dielectric medium, and the particular choice of the dielectric constant are discussed. In addition, we examine the validity of some technical aspects, such as geometry optimization in solvent or with a large basis set, and the use of different density functional methods. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010 [source] Quantum chemical modeling of the reduction of cis -diammineplatinum(IV) tetrachloride [Pt(NH3)2Cl4] by methyl thiolate anionJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 9 2005Ia. I. Dobrogorskaia, Méreau Abstract We present here both an ab initio and quantum mechanical/molecular mechanical (QM/MM) study of the cis -[Pt(NH3)2Cl4] complex reduction by methyl thiolate anion, SCH, which is used as a model of glutathione. Geometry and electronic structure of cis -[Pt(NH3)2Cl4] are determined without and in aqueous medium. The mechanism of the reaction of reduction is characterized. The calculated activation energy of the reaction compares remarkably well with the experimental value. © 2005 Wiley Periodicals, Inc. J Comput Chem 26: 865,870, 2005 [source] Self-initiation of the UV photopolymerization of brominated acrylatesJOURNAL OF POLYMER SCIENCE (IN TWO SECTIONS), Issue 14 2008Tom Scherzer Abstract Brominated aromatic acrylates were found to polymerize rapidly upon exposure to UV light. Moreover, they are able to initiate the UV-induced polymerization of acrylic formulations that do not contain a conventional photoinitiator. In contrast, the corresponding unbrominated homologues are not effective as initiators. Investigations by real-time FTIR spectroscopy have shown that the addition of only 1 wt % of a brominated acrylate is sufficient for an efficient initiation. Fast photopolymerization is achieved even if irradiation is carried out at , > 300 nm where most acrylates do not absorb. Short-lived transients were studied by laser flash photolysis. The triplet was found to show low sensitivity to oxygen which is because of its very short lifetime. Bromine radicals split of from the acrylates were trapped with bromine ions from tetraethyl ammonium bromide and detected as Br. The resulting quantum yields for the formation of bromine radicals are in the range of up to 0.3. Quantum chemical modeling was carried out to establish a mechanism for the release of bromine radicals. Both bromine and bromophenyl radicals are able to initiate the polymerization reaction. © 2008 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 46: 4905,4916, 2008 [source] | ||||||||||