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Int. J. Mol. Sci., Volume 4, Issue 8 (August-September 2003), Pages 486-536

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Research

Open AccessArticle Structure, Stability and Interaction Studies on Nucleotide Analogue Systems
Int. J. Mol. Sci. 2003, 4(8), 486-502; doi:10.3390/i4080486
Received: 27 January 2003 / Accepted: 25 August 2003 / Published: 30 August 2003
Cited by 5 | PDF Full-text (532 KB) | HTML Full-text | XML Full-text
Abstract
Most of the biological molecules have a good interaction with water molecules. The hydrogen bonding interactions with the structural analogues of nucleic acid phosphate group namely dimethyl phosphate anion (DMP) and diethyl phosphate anion (DEP) are studied employing the ab initio and density
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Most of the biological molecules have a good interaction with water molecules. The hydrogen bonding interactions with the structural analogues of nucleic acid phosphate group namely dimethyl phosphate anion (DMP) and diethyl phosphate anion (DEP) are studied employing the ab initio and density functional theory methods. Inspections have been made to locate the reactive sites for the interactions of isomeric forms of mono, di and tri hydrates of alkyl phosphate anion using the above theories. It reveals, water molecules have a very strong interaction with the phosphate group in both the molecules and their interactions induce the changes in the structural parameters of the PO4 group for both the DMP and DEP anions. The optimized structural parameters, total energy, dipole moment and rotational constants are calculated and are compared with the available experimental values. The chemical hardness and chemical potential for these complexes have been calculated at HF/6-31G* level of theory and discussed the conformational stability of these complexes. Full article
Open AccessArticle Modelling of Octahedral Manganese II Complexes with Inorganic Ligands: A Problem with Spin-States
Int. J. Mol. Sci. 2003, 4(8), 503-511; doi:10.3390/i4080503
Received: 10 April 2003 / Accepted: 18 June 2003 / Published: 30 August 2003
Cited by 6 | PDF Full-text (183 KB) | HTML Full-text | XML Full-text
Abstract
Quantum mechanical ab initio UHF, MP2, MC-SCF and DFT calculations with moderate Gaussian basis sets were performed for MnX6, X = H2O, F-, CN-, manganese octahedral complexes. The correct spin-state of the complexes was obtained only when the counter
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Quantum mechanical ab initio UHF, MP2, MC-SCF and DFT calculations with moderate Gaussian basis sets were performed for MnX6, X = H2O, F-, CN-, manganese octahedral complexes. The correct spin-state of the complexes was obtained only when the counter ions neutralizing the entire complexes were used in the modelling at the B3LYP level of theory. Full article
Open AccessArticle Total and Local Quadratic Indices of the “Molecular Pseudograph’s Atom Adjacency Matrix”. Application to Prediction of Caco-2 Permeability of Drugs
Int. J. Mol. Sci. 2003, 4(8), 512-536; doi:10.3390/i4080512
Received: 16 May 2003 / Accepted: 17 June 2003 / Published: 30 August 2003
Cited by 36 | PDF Full-text (302 KB) | HTML Full-text | XML Full-text
Abstract
The high interest in the prediction of the intestinal absorption for New Chemical Entities (NCEs) is generated by the increasing rate in the synthesis of compounds by combinatorial chemistry and the extensive cost of the traditional evaluation methods. Quantitative Structure–Permeability Relationships (QSPerR) of
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The high interest in the prediction of the intestinal absorption for New Chemical Entities (NCEs) is generated by the increasing rate in the synthesis of compounds by combinatorial chemistry and the extensive cost of the traditional evaluation methods. Quantitative Structure–Permeability Relationships (QSPerR) of the intestinal permeability across the Caco-2 cells monolayer (PCaco-2) could be obtained by the application of new molecular descriptors. In this sense, quadratic indices of the “molecular pseudograph’s atom adjacency matrix” and multiple linear regression analysis were used to obtain good quantitative models to determine the PCaco-2. QSPerR models found are significant from a statistical point of view. The total and local quadratic indices were calculated with the TOMO-COMD software. A leave-one-out cross-validation procedure (internal validation) and the evaluation of external test set of 20 drugs (external validation) revealed that regression models had a good predictive power. A comparison with results derived from other theoretical studies shown a quite satisfactory behavior of the present method. The descriptors included in the prediction models permitted the interpretation in structural terms of the permeability process, evidencing the main role of H-bonding and size properties. The models found were used in virtual screening of drug intestinal permeability and a relationship between PCaco-2 calculated and percentage of human intestinal absorption for the 72 compounds was established. These results suggest that the proposed method is able to predict PCaco-2, being a good tool for screening of PCaco-2 for large sets of NCEs synthesized via combinatorial chemistry approach. Full article

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