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Molecular Surface Area (molecular + surface_area)
Selected AbstractsInvestigation of the molecular surface area and volume: Defined and calculated by the molecular face theoryJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 11 2010Li-Dong Gong Abstract Based on the molecular face (MF) theory, the molecular face surface area (MFSA) and molecular face volume (MFV) are defined. For a variety of organic molecules and several inorganic molecules, the MFSA and MFV have been studied and calculated in terms of an algorithm of our own via the Matlab package. The MFV shows a very good linear relationship with the experimentally measured critical molar volume. It is also found that the MFSA and MFV have significant linear correlations with those of the commonly used hard-sphere model and the electron density isosurface. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010 [source] Estimation of Aqueous-Phase Reaction Rate Constants of Hydroxyl Radical with Phenols, Alkanes and AlcoholsMOLECULAR INFORMATICS, Issue 11-12 2009Ya-nan Wang Abstract A quantitative structure activity relationship (QSAR) model was developed for the aqueous-phase hydroxyl radical reaction rate constants (kOH) employing quantum chemical descriptors and multiple linear regressions (MLR). The QSAR development followed the OECD guidelines, with special attention to validation, applicability domain (AD) and mechanistic interpretation. The established model yielded satisfactory performance: the correlation coefficient square (R2) was 0.905, the root mean squared error (RMSE) was 0.139, the leave-many-out cross-validated QLMO2 was 0.806, and the external validated QEXT2 was 0.922 log units. The AD of the model covering compounds of phenols, alkanes and alcohols, was analyzed by Williams plot. The main molecular structural factors governing kOH are the energy of the highest occupied molecular orbital (EHOMO), average net atomic charges on hydrogen atoms (), molecular surface area (MSA) and dipole moment (,). It was concluded that kOH increased with increasing EHOMO and MSA, while decreased with increasing and ,. [source] Osmolyte controlled fibrillation kinetics of insulin: New insight into fibrillation using the preferential exclusion principleBIOTECHNOLOGY PROGRESS, Issue 5 2009Arpan Nayak Abstract Amyloid proteins are converted from their native-fold to long ,-sheet-rich fibrils in a typical sigmoidal time-dependent protein aggregation curve. This reaction process from monomer or dimer to oligomer to nuclei and then to fibrils is the subject of intense study. The main results of this work are based on the use of a well-studied model amyloid protein, insulin, which has been used in vitro by others. Nine osmolyte molecules, added during the protein aggregation process for the production of amyloid fibrils, slow-down or speed up the process depending on the molecular structure of each osmolyte. Of these, all stabilizing osmolytes (sugars) slow down the aggregation process in the following order: tri > di > monosaccharides, whereas destabilizing osmolytes (urea, guanidium hydrochloride) speed up the aggregation process in a predictable way that fits the trend of all osmolytes. With respect to kinetics, we illustrate, by adapting our earlier reaction model to the insulin system, that the intermediates (trimers, tetramers, pentamers, etc.) are at very low concentrations and that nucleation is orders of magnitude slower than fibril growth. The results are then collated into a cogent explanation using the preferential exclusion and accumulation of osmolytes away from and at the protein surface during nucleation, respectively. Both the heat of solution and the neutral molecular surface area of the osmolytes correlate linearly with two fitting parameters of the kinetic rate model, that is, the lag time and the nucleation rate prior to fibril formation. These kinetic and thermodynamic results support the preferential exclusion model and the existence of oligomers including nuclei and larger structures that could induce toxicity. © 2009 American Institute of Chemical Engineers Biotechnol. Prog., 2009 [source] Novel computer program for fast exact calculation of accessible and molecular surface areas and average surface curvatureJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 6 2002Oleg V. Tsodikov Abstract New computer programs, SurfRace and FastSurf, perform fast calculations of the solvent accessible and molecular (solvent excluded) surface areas of macromolecules. Program SurfRace also calculates the areas of cavities inaccessible from the outside. We introduce the definition of average curvature of molecular surface and calculate average molecular surface curvatures for each atom in a structure. All surface area and curvature calculations are analytic and therefore yield exact values of these quantities. High calculation speed of this software is achieved primarily by avoiding computationally expensive mathematical procedures wherever possible and by efficient handling of surface data structures. The programs are written initially in the language C for PCs running Windows 2000/98/NT, but their code is portable to other platforms with only minor changes in input-output procedures. The algorithm is robust and does not ignore either multiplicity or degeneracy of atomic overlaps. Fast, memory-efficient and robust execution make this software attractive for applications both in computationally expensive energy minimization algorithms, such as docking or molecular dynamics simulations, and in stand-alone surface area and curvature calculations. © 2002 Wiley Periodicals, Inc. J Comput Chem 23: 600,609, 2002 [source] | ||||||||||