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Molecular Volume (molecular + volume)
Selected AbstractsPrediction of octanol,water partition coefficients of organic compounds by multiple linear regression, partial least squares, and artificial neural networkJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 15 2009Hassan Golmohammadi Abstract A quantitative structure,property relationship (QSPR) study was performed to develop models those relate the structure of 141 organic compounds to their octanol,water partition coefficients (log Po/w). A genetic algorithm was applied as a variable selection tool. Modeling of log Po/w of these compounds as a function of theoretically derived descriptors was established by multiple linear regression (MLR), partial least squares (PLS), and artificial neural network (ANN). The best selected descriptors that appear in the models are: atomic charge weighted partial positively charged surface area (PPSA-3), fractional atomic charge weighted partial positive surface area (FPSA-3), minimum atomic partial charge (Qmin), molecular volume (MV), total dipole moment of molecule (,), maximum antibonding contribution of a molecule orbital in the molecule (MAC), and maximum free valency of a C atom in the molecule (MFV). The result obtained showed the ability of developed artificial neural network to prediction of partition coefficients of organic compounds. Also, the results revealed the superiority of ANN over the MLR and PLS models. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2009 [source] Building cavities in a fluid of spherical or rod-like particles: A contribution to the solvation free energy in isotropic and anisotropic polarizable continuum modelJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 11 2005Caterina Benzi Abstract A general formalism for the calculation of cavitation energies in the framework of the scaled particle theory has been implemented in the Polarizable Continuum Model (PCM), contributing to the nonelectrostatic part of the molecular free energy in solution. The solute cavity and the solvent molecules are described as hard spherocylinders, whose radius and length are related to the actual molecular shape, while the solvent density is estimated from experimental data, or from the solvent molecular volume, suitably scaled. The present model can describe isotropic solutions of spherical and rod-like molecules in spherical or rod-like solvents, and also anisotropic solutions in which the solvent molecules are oriented in space: in this case, the cavitation energy also depends on the relative orientation of solute and solvent molecules. Test calculations have been performed on simple systems to evaluate the accuracy of the present approach, in comparison with other methods and with the available experimental estimates of the cavitation energy, giving encouraging results. © 2005 Wiley Periodicals, Inc. J Comput Chem 26: 1096,1105, 2005 [source] New analytic approximation to the standard molecular volume definition and its application to generalized Born calculationsJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 11 2003Michael S. Lee Abstract In a recent article (Lee, M. S.; Salsbury, F. R. Jr.; Brooks, C. L., III. J Chem Phys 2002, 116, 10606), we demonstrated that generalized Born (GB) theory provides a good approximation to Poisson electrostatic solvation energy calculations if one uses the same definitions of molecular volume for each. In this work, we present a new and improved analytic method for reproducing the Lee,Richards molecular volume, which is the most common volume definition for Poisson calculations. Overall, 1% errors are achieved for absolute solvation energies of a large set of proteins and relative solvation energies of protein conformations. We also introduce an accurate SASA approximation that uses the same machinery employed by our GB method and requires a small addition of computational cost. The combined methodology is shown to yield an efficient and accurate implicit solvent representation for simulations of biopolymers. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1348,1356, 2003 [source] HYDROTHERMALLY FLUORITIZED ORDOVICIAN CARBONATES AS RESERVOIR ROCKS IN THE TAZHONG AREA, CENTRALTARIM BASIN, NW CHINAJOURNAL OF PETROLEUM GEOLOGY, Issue 1 2006Zhijun Jin Reservoir rocks at the Tazhong 45 oil pool, central Tarim Basin, consist of fluoritized carbonate strata of Middle - Late Ordovician age. Petrological observations indicate that the fluorite replaces calcite. Several other hydrothermal minerals including pyrite, quartz, sphalerite and chlorite accompany the fluorite. Two generations of fluid inclusions are present in the fluorite. Homogenization temperatures (Th) for primary inclusions are mostly between 260°C and 310°C and represent the temperature of the hydrothermal fluid responsible for fluorite precipitation. Th for secondary inclusions range from 100°C to 130°C, and represent the hydrocarbon charging temperature as shown by the presence of hydrocarbons trapped in some secondary inclusions. The mineral assemblage and the homogenization temperatures of the primary fluid inclusions indicate that the precipitation of fluorite is related to hydrothermal activity in the Tazhong area. Strontium isotope analyses imply that the hydrothermal fluids responsible for fluorite precipitation are related to late-stage magmatic activity, and felsic magmas were generated by mixing of mafic magma and crustal materials during the Permian. Theoretical calculations show that the molecular volume of a carbonate rock decreases by 33.5% when calcite is replaced by fluorite, and the volume shrinkage can greatly enhance reservoir porosity by the formation of abundant intercrystalline pores. Fluoritization has thus greatly enhanced the reservoir quality of Ordovician carbonates in the Tazhong 45 area, so that the fluorite and limestone host rocks have become an efficient hydrocarbon reservoir. According to the modelled burial and thermal history of the Tazhong 45 well, and the homogenization temperatures of secondary fluid inclusions in the fluorite, hydrocarbon charging at the Tazhong 45 reservoir took place in the Tertiary. [source] Extent and mechanism of solvation and partitioning of isomers of substituted benzoic acids: A thermodynamic study in the solid state and in solutionJOURNAL OF PHARMACEUTICAL SCIENCES, Issue 9 2008German L. Perlovich Abstract Temperature dependency of saturated vapour pressure and thermochemical characteristics of fusion processes for 2-, 3- and 4-methoxybenzoic acids (anisic acids) were measured and thermodynamic functions of sublimation, fusion, and evaporation calculated. A new approach to split specific and nonspecific energetic terms in the crystal lattice was developed. For methoxybenzoic acid isomers as well as for a number of analogous molecules, a parameter describing molecular packing density by the ratio of free volume of the molecules in the crystal lattice and van der Waals molecular volume is defined. Its relationship to Gibbs energy of sublimation and to the respective melting points was analysed. Temperature dependencies of solubility in buffers with pH 2.0 and 7.4, n -octanol and n -hexane were measured. The thermodynamic functions of solubility, solvation and transfer processes were deduced. Concentration dependence of partition coefficients for the outlined isomers was measured. Specific and nonspecific solvation terms were distinguished using the transfer from the ,inert' n -hexane to the other solvents. Comparison analysis of specific and nonspecific interactions in the solid state and in solution was carried out. A diagram enabling analysis of the mechanism of the partitioning process was applied. It was found that position of substituents essentially affects the mechanism of partitioning in buffer pH 2.0, however, at pH 7.4, the mechanism is independent of the position of the substituent. © 2007 Wiley-Liss, Inc. and the American Pharmacists Association J Pharm Sci 97:3883,3896, 2008 [source] General linearized biexponential model for QSAR data showing bilinear-type distributionJOURNAL OF PHARMACEUTICAL SCIENCES, Issue 11 2005Peter Buchwald Abstract A major impediment of many QSAR-type analyses is that the data show a maximum or minimum and can no longer be adequately described by linear functions that provide unrivaled simplicity and usually give good description over more restricted ranges. Here, a general linearized biexponential (LinBiExp) model is proposed that can adequately describe data showing bilinear-type distribution as a function of not just often-employed lipophilicity descriptors (e.g., log P) but as a function of any descriptor (e.g., molecular volume). Contrary to Hansch-type parabolic models, LinBiExp allows the natural extension of linear models and fitting of asymmetrical data. It is also more general and intuitive than Kubinyi's model as it has a more natural functional form. It was obtained by a differential equation-based approach starting from very general assumptions that cover both static equilibriums and first-order kinetic processes and that involve abstract processes through which the concentration of the compound of interest in an assumed "effect" compartment is connected to its "external" concentration. Physicochemical aspects placing LinBiExp within the framework of linear free energy relationship (LFER) approaches are presented together with illustrative applications in various fields such as toxicity, antimicrobial activity, anticholinergic activity, and glucocorticoid receptor binding. © 2005 Wiley-Liss, Inc. and the American Pharmacists Association J Pharm Sci 94:2355-2379, 2005 [source] Characterization of the complex formation of 1,6-anhydro-,-maltotriose with potassium using 1H and 39K NMR spectroscopyMAGNETIC RESONANCE IN CHEMISTRY, Issue 11 2009Takayuki Kato Abstract The 1H and 39K longitudinal relaxation times (T1) and 1H diffusion coefficients were measured to investigate the complex formation of 1,6-anhydro-,-maltotriose and potassium ions. Although the 1H- T1 values of H3,, H5,, H1, and H4, decreased in the presence of potassium ions, 1H chemical shifts and 1H diffusion coefficients did not show significant changes. The long-range coupling constants of 3JC,H around the glycosyl bonds did not show significant changes either. In the measurements of 39K spectra, the 39K signal obviously broadened and the 39K- T1 values decreased in the presence of 1,6-anhydro-,-maltotriose, indicating the complex formation of 1,6-anhydro-,-maltotriose and potassium ions. These results indicate that the conformation and molecular volume were unaffected in the complex formation. Copyright © 2009 John Wiley & Sons, Ltd. [source] Designing for topical delivery: Prodrugs can make the differenceMEDICINAL RESEARCH REVIEWS, Issue 6 2003Kenneth B. Sloan Abstract It has been shown for homologous series of prodrugs that those members who were the more water soluble ones gave the greatest enhancement in topical delivery of the parent drug and not the more lipophilic ones. However, until recently models for topical delivery and equations to predict topical delivery focused only on lipid solubility (SLIPID) or partition coefficient (KOCT:AQ) and molecular volume (or molecular weight, MW) as parameters. Now several equations (transformed Potts,Guy or Series/Parallel) have been developed which include aqueous solubility (SAQ) as a parameter for predicting flux through skin. Experimental fluxes, solubilities, and MW from seven series of prodrugs have been fit to the transformed Potts,Guy equation to give coefficients for log solubility in isopropyl myristate (log SIPM) and log solubility in water (log SAQ) (0.53 and 0.47, respectively) which show, for parent drugs delivered by prodrugs from IPM in vitro through hairless mouse skin, that water solubility is almost as important as lipid solubility. When the transformed Potts,Guy equation was fit to data for the delivery of NSAID from mineral oil (MO) in vivo through human skin, the coefficients were 0.72 log SMO and 0.28 log SAQ. When the transformed Potts,Guy equation was fit to data for the delivery of their parent drugs by three series of prodrugs from water in vitro through hairless mouse skin the coefficients were 0.66 log SIPM and 0.34 log SAQ. Numerous recent examples are also given where more water-soluble members of homologous series of prodrugs give higher flux values from water vehicles in vitro through human skin than the more lipid soluble ones. © 2003 Wiley Periodicals, Inc. Med Res Rev, 23 No. 6, 763,793, 2003 [source] Predicting Anti-HIV-1 Activities of HEPT-analog Compounds by Using Support Vector ClassificationMOLECULAR INFORMATICS, Issue 9 2005Wencong Lu Abstract The support vector classification (SVC), as a novel approach, was employed to make a distinction within a class of non-nucleoside reverse transcriptase inhibitors. 1-[(2-hydroxyethoxy) methyl]-6-(phenyl thio)-thymine (HEPT) derivatives with high anti-HIV-1 activities and those with low anti-HIV-1 activities were compared on the basis of the following molecular descriptors: net atomic charge on atom 4, molecular volume, partition coefficient, molecular refractivity, molecular polarisability and molecular weight. By using the SVC, a mathematical model was constructed, which can predict the anti-HIV-1 activities of the HEPT-analogue compounds, with an accuracy of 100% as calculated on the basis of the leave-one-out cross-validation (LOOCV) test. The results indicate that the performance of the SVC model exceeds that of the stepwise discriminant analysis (SDA) model, for which a prediction accuracy of 94% was reported. [source] BINOL-3,3,-Triflone N,N -Dimethyl Phosphoramidites: Through-Space 19F,31P Spin,Spin Coupling with a Remarkable Dependency on Temperature and Solvent Internal PressureCHEMISTRY - A EUROPEAN JOURNAL, Issue 26 2008Matthias Kruck Abstract A combined computational and experimental study of the effects of solvent, temperature and stereochemistry on the magnitude of the through-space spin,spin coupling between 31P and 19F nuclei which are six-bonds apart is described. The reaction of 3-trifluoromethylsulfonyl-2,,2-dihydroxy-1,1,-binaphthalene (3-SO2CF3 -BINOL) with hexamethylphosphorous triamide (P(NMe2)3) generates a pair of N,N -dimethylphosphoramidites which are diastereomeric due to their differing relative configurations at the stereogenic phosphorous centre and the axially chiral (atropisomeric) BINOL unit. Through-space NMR coupling of the 31P and 19F nuclei of the phosphoramidite and sulfone is detected in one diastereomer only. In the analogous N,N -dimethylphosphoramidite generated from 3,3,-(SO2CF3)2 -BINOL only one of the diastereotopic trifluoromethylsulfone moieties couples with the 31P of the phosphoramidite. In both cases, the magnitude of the coupling is strongly modulated (up to 400,%) by solvent and temperature. A detailed DFT analysis of the response of the coupling to the orientation of the CF3 moiety with respect to the P-lone pair facilitates a confident assignment of the stereochemical identity of the pair of diastereomers. The analysis shows that the intriguing effects of environment on the magnitude of the coupling can be rationalised by a complex interplay of solvent internal pressure, molecular volume and thermal access to a wider conformational space. These phenomena suggest the possibility for the design of sensitive molecular probes for local environment that can be addressed via through-space NMR coupling. [source] Enhanced Stabilization of Reverse Micelles by Compressed CO2CHEMISTRY - A EUROPEAN JOURNAL, Issue 4 2005Dong Shen Dr. Abstract The effect of compressed CO2 on the solubilization capacity of water in reverse micelles of sodium bis(2-ethylhexyl) sulfosuccinate (AOT) in longer chain n -alkanes was studied at different temperatures and pressures. It was found that the amount of solubilized water is increased considerably by CO2 in a suitable pressure range. The suitable CO2 pressure range in which the solubilization capacity of water could be enhanced decreased with increasing W0 (water-to-AOT molar ratio). The microenvironments in the CO2 -stabilized reverse micelles were investigated by UV/Vis adsorption spectroscopy with methyl orange (MO) as probe. The mechanism by which the reverse micelles are stabilized by CO2 is discussed in detail. The main reason is likely to be that CO2 has a much smaller molecular volume than the n -alkane solvents studied in this work. Therefore, it can penetrate the interfacial film of the reverse micelles and stabilize them by increasing the rigidity of the micellar interface and thus reducing the attractive interaction between the droplets. However, if the CO2 pressure is too high, the solvent strength of the solvents is reduced markedly, and this induces phase separation in the micellar solution. [source] Computational screening of biomolecular adsorption and self-assembly on nanoscale surfacesJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 7 2010Hendrik Heinz Abstract The quantification of binding properties of ions, surfactants, biopolymers, and other macromolecules to nanometer-scale surfaces is often difficult experimentally and a recurring challenge in molecular simulation. A simple and computationally efficient method is introduced to compute quantitatively the energy of adsorption of solute molecules on a given surface. Highly accurate summation of Coulomb energies as well as precise control of temperature and pressure is required to extract the small energy differences in complex environments characterized by a large total energy. The method involves the simulation of four systems, the surface-solute,solvent system, the solute,solvent system, the solvent system, and the surface-solvent system under consideration of equal molecular volumes of each component under NVT conditions using standard molecular dynamics or Monte Carlo algorithms. Particularly in chemically detailed systems including thousands of explicit solvent molecules and specific concentrations of ions and organic solutes, the method takes into account the effect of complex nonbond interactions and rotational isomeric states on the adsorption behavior on surfaces. As a numerical example, the adsorption of a dodecapeptide on the Au {111} and mica {001} surfaces is described in aqueous solution. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010 [source] | ||||||||||