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Atomic Properties (atomic + property)
Selected AbstractsAtomic Properties of Amino Acids: Computed Atom Types as a Guide for Future Force-Field DesignCHEMPHYSCHEM, Issue 8 2003Paul L. A. Popelier Dr. Abstract The quantum chemical topology (QCT) is able to propose atom types by direct computation rather than by chemical intuition. In previous work, molecular electron densities of 20 amino acids and smaller derived molecules were partitioned into a set of 760 topological atoms. Each atom was characterised by seven atomic properties and subjected to cluster analysis element by element, that is, C, H, O, N, and S. From the respective dendrograms, 21 carbon atom types were distinguished, 7 hydrogen, 2 nitrogen, 6 oxygen, and 6 sulfur atom types. Herein, we contrast the QCT atom types with those of the assisted model building with energy refinement (AMBER) force field. We conclude that in spite of fair agreement between QCT and AMBER atom types, the latter are sometimes underdifferentiated and sometimes overdifferentiated. In summary, we suggest that QCT is a useful guide in designing new force fields or improving existing ones. The computational origin of QCT atom types makes their determination unbiased compared to atom type determination by chemical intuition and a priori assumptions. We provide a list of specific recommendations. [source] An efficient grid-based scheme to compute QTAIM atomic properties without explicit calculation of zero-flux surfacesJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 7 2009Juan I. Rodríguez Abstract We introduce a method to compute atomic properties according to the "quantum theory of atoms in molecules." An integration grid in real space is partitioned into subsets, ,i. The subset, ,i, is composed of all grid points contained in the atomic basin, ,i, so that integration over ,i is reduced to simple quadrature over the points in ,i. The partition is constructed from deMon2k's atomic center grids by following the steepest ascent path of the density starting from each point in the grid. We also introduce a technique that exploits the cellular nature of the grid to make the algorithm faster. The performance of the method is tested by computing properties of atoms and nonnuclear attractors (energies, charges, dipole, and quadrupole moments) for a set of representative molecules. © 2008 Wiley Periodicals, Inc. J Comput Chem 2009 [source] Newly developed basis sets for density functional calculationsJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 2 2005S. Chiodo Abstract Optimized contracted Gaussian basis sets of double-zeta valence polarized (DZVP) quality for first-row transition metals are presented. The DZVP functions were optimized using the PWP86 generalized gradient approximation (GGA) functional and the B3LYP hybrid functional. For a careful analysis of the basis sets performance the transition metal atoms and cations excitation energies were calculated and compared with the experimental ones. The calculated values were also compared with those obtained using the previously available DZVP basis sets developed at the local-density functional level. Because the new basis sets work better than the previous ones, possible reasons of this behavior are analyzed. The newly developed basis sets also provide a good estimation of other atomic properties such as ionization energies. © 2004 Wiley Periodicals, Inc. J Comput Chem 26: 175,183, 2005 [source] Intramolecular interactions and intramolecular hydrogen bonding in conformers of gaseous glycineJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 7 2001L. F. Pacios Abstract Ab initio calculations at the MP2/6-311++G** level of theory led recently to the identification of 13 stable conformers of gaseous glycine with relative energies within 11 kcal/mol. The stability of every structure depends on subtle intramolecular effects arising from conformational changes. These intramolecular interactions are examined with the tools provided by the Atoms In Molecules (AIM) theory, which allows obtaining a wealth of quantum mechanics information from the molecular electron density ,(r). The analysis of the topological features of ,(r) on one side and the atomic properties integrated in the basins defined by the gradient vector field of the density on the other side makes possible to explore the different intramolecular effects in every conformer. The existence of intramolecular hydrogen bonds on some conformers is demonstrated, while the presence of other stabilizing interactions arising from favorable conformations is shown to explain the stability of other structures in the potential energy surface of glycine. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 702,716, 2001 [source] Validation of experimental charge densities: refinement of the macrolide antibiotic roxithromycinACTA CRYSTALLOGRAPHICA SECTION B, Issue 5 2010J. J. Holstein Multipole refinements of larger organic molecules have so far been limited to a few exceptional cases. We report an investigation of the detailed experimental electron-density distribution (EDD) of roxithromycin, a macrolide antibiotic consisting of 134 atoms. Although the experimental multipole refinement on high-resolution synchrotron data converged smoothly, validation of the electron density by calculation of an `experiment minus invariom' difference density revealed conformational disorder of the H atoms. Hydrogen disorder is shown to affect the EDD, the electrostatic potential and atomic properties as defined by Bader's quantum theory of atoms in molecules. A procedure to obtain the electron density distribution in the presence of disorder is proposed. [source] Atomic Properties of Amino Acids: Computed Atom Types as a Guide for Future Force-Field DesignCHEMPHYSCHEM, Issue 8 2003Paul L. A. Popelier Dr. Abstract The quantum chemical topology (QCT) is able to propose atom types by direct computation rather than by chemical intuition. In previous work, molecular electron densities of 20 amino acids and smaller derived molecules were partitioned into a set of 760 topological atoms. Each atom was characterised by seven atomic properties and subjected to cluster analysis element by element, that is, C, H, O, N, and S. From the respective dendrograms, 21 carbon atom types were distinguished, 7 hydrogen, 2 nitrogen, 6 oxygen, and 6 sulfur atom types. Herein, we contrast the QCT atom types with those of the assisted model building with energy refinement (AMBER) force field. We conclude that in spite of fair agreement between QCT and AMBER atom types, the latter are sometimes underdifferentiated and sometimes overdifferentiated. In summary, we suggest that QCT is a useful guide in designing new force fields or improving existing ones. The computational origin of QCT atom types makes their determination unbiased compared to atom type determination by chemical intuition and a priori assumptions. We provide a list of specific recommendations. [source] | ||||||||||