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Verification of structural and electrostatic properties obtained by the use of different pseudoatom databases

Verification of structural and electrostatic properties obtained by the use of different... The existing pseudoatom databases (ELMAM, Invariom, UBDB and ELMAM2) enable structure refinement to be performed with the use of aspherical scattering factors computed from the transferable aspherical atom model (TAAM) as an alternative to independent atom model refinement. In addition, electrostatic properties can be estimated with the help of the databases. The quality of the structural and electrostatic properties obtained from the individual databases was tested. On the basis of a 100 K high‐resolution single‐crystal X‐ray diffraction experiment on l‐His–l‐Ala dihydrate and 23 K high‐resolution data for l‐Ala [Destro & Marsh (1988). J. Phys. Chem.92, 966–973], the structural properties, electron‐density distributions and molecular electrostatic potentials obtained from different TAAMs were compared to each other and to reference models. Experimental multipolar models and theoretical models refined against theoretical structure factors computed from periodic density functional theory (DFT) calculations were compared to the TAAMs in order to determine which model best describes the crystal‐field effect. Unperturbed wavefunctions based on the MP2 and DFT calculations and properties obtained directly from these were used as a reference to judge how properly the databases reproduce the properties of isolated molecules. For Gly–l‐His dihydrate, d,l‐His and the above‐mentioned two crystal structures, deviations of the molecular dipole moments and Coulombic intermolecular interaction energies from the reference values were examined. Root‐mean‐square deviations (RMSDs) and correlation coefficients were used as a quantitative measure of the quality of the analysed properties. TAAM refinements reproduce X—H bond lengths optimized in theoretical periodic calculations. Structural properties obtained from different database models are similar to each other. The anisotropic displacement parameters from TAAMs are similar to the results of experimental multipolar refinement; differences are about 0.5 and 2.5% for high‐resolution and low‐resolution data, respectively. Differences in dipole‐moment magnitudes calculated from database models are about 5%, and directions differ by up to 30°. The values of electrostatic interaction energies estimated from the individual TAAMs differ greatly from each other and from the reference values. RMSDs are about 9–15 and 22–33 kJ mol−1 for UBDB and the other database models, respectively. http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Acta Crystallographica Section A Foundations of Crystallography Wiley

Verification of structural and electrostatic properties obtained by the use of different pseudoatom databases

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References (72)

Publisher
Wiley
Copyright
Copyright © 2011 Wiley Subscription Services, Inc., A Wiley Company
ISSN
0108-7673
eISSN
1600-5724
DOI
10.1107/S0108767310049731
pmid
21325717
Publisher site
See Article on Publisher Site

Abstract

The existing pseudoatom databases (ELMAM, Invariom, UBDB and ELMAM2) enable structure refinement to be performed with the use of aspherical scattering factors computed from the transferable aspherical atom model (TAAM) as an alternative to independent atom model refinement. In addition, electrostatic properties can be estimated with the help of the databases. The quality of the structural and electrostatic properties obtained from the individual databases was tested. On the basis of a 100 K high‐resolution single‐crystal X‐ray diffraction experiment on l‐His–l‐Ala dihydrate and 23 K high‐resolution data for l‐Ala [Destro & Marsh (1988). J. Phys. Chem.92, 966–973], the structural properties, electron‐density distributions and molecular electrostatic potentials obtained from different TAAMs were compared to each other and to reference models. Experimental multipolar models and theoretical models refined against theoretical structure factors computed from periodic density functional theory (DFT) calculations were compared to the TAAMs in order to determine which model best describes the crystal‐field effect. Unperturbed wavefunctions based on the MP2 and DFT calculations and properties obtained directly from these were used as a reference to judge how properly the databases reproduce the properties of isolated molecules. For Gly–l‐His dihydrate, d,l‐His and the above‐mentioned two crystal structures, deviations of the molecular dipole moments and Coulombic intermolecular interaction energies from the reference values were examined. Root‐mean‐square deviations (RMSDs) and correlation coefficients were used as a quantitative measure of the quality of the analysed properties. TAAM refinements reproduce X—H bond lengths optimized in theoretical periodic calculations. Structural properties obtained from different database models are similar to each other. The anisotropic displacement parameters from TAAMs are similar to the results of experimental multipolar refinement; differences are about 0.5 and 2.5% for high‐resolution and low‐resolution data, respectively. Differences in dipole‐moment magnitudes calculated from database models are about 5%, and directions differ by up to 30°. The values of electrostatic interaction energies estimated from the individual TAAMs differ greatly from each other and from the reference values. RMSDs are about 9–15 and 22–33 kJ mol−1 for UBDB and the other database models, respectively.

Journal

Acta Crystallographica Section A Foundations of CrystallographyWiley

Published: Jan 1, 2011

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