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Abstract
In the frame of a promolecular representation of a molecule or a crystal, a chemical structure is considered to be the superposition of independent spherical atomic contributions. Promolecular models have often been shown as reasonable or even very good approximation levels to model electron density (ED) distributions, for example in chemical bond analysis or molecular similarity applications [19] even if the ED topology may differ between experimental and theoretical models especially at covalent bonds [9]. Analytical descriptions of promolecular ED distributions are either based on atomic or ionic wavefunctions [1,2,5,9], exponential functions [4], or fitted Gaussian functions [3,5,8], and are thus especially adapted to fast calculations of approximated molecular ED and their properties.
The present work is focussed on the use of PASA (Promolecular Atomic Shell Approximation) ED distributions [10] at various levels of smoothing in molecular superposition applications. Different similarity measures (overlap, Coulomb, and kinetictype integrals, electrostatic attraction energy) are considered to generate various similarity evaluators, such as the wellknown Carbó, HodgkinRichards, Shape Tanimoto, and Kulczynski indices.
First superpositions, applied to rigid endothiapepsin ligands, were achieved using a basic MonteCarlo/Simulated Annealing algorithm. They showed that smoothing increases the speed of the convergence to acceptable solutions. Also, distancedependent similarity measures, such as Coulomb integrals and electrostatic energy, could lead to acceptable solutions, even when smoothing was not considered. The best results were obtained when using kinetictype integrals and the Shape Tanimoto index, especially for the superposition of molecules with different sizes.
References:
[1] A.C. Good, and W.G.J. Richards, Chem. Inf. Comput. Sci., 33, 112 (1993)
[2] V.G. Tsirelson et al., Acta Cryst. B, 54, 8 (1998)
[3] X. Gironés et al., J. Mol. Graphics Modell., 16, 190 (1998)
[4] V. Botella, and L.F. Pacios, J. Mol. Struct. (Theochem), 426, 75 (1998)
[5] A.S. Mitchell, and M.A. Spackman, J. Comput. Chem., 21, 933 (2000)
[6] X. Gironés et al., J. Mol. Graphics Modell.,19, 343 (2001)
[7] R.T. Downs et al., Phys. Chem. Miner., 29, 369 (2002)
[8] P. Bultinck et al., J. Chem. Inf. Comput. Sci., 43, 1208 (2003)
[9] E. Aubert et al., Acta Cryst. B, 59, 687 (2003)
[10] L. Amat, and R. CarbóDorca, J. Comput. Chem., 18, 2023 (1997)
The present work is focussed on the use of PASA (Promolecular Atomic Shell Approximation) ED distributions [10] at various levels of smoothing in molecular superposition applications. Different similarity measures (overlap, Coulomb, and kinetictype integrals, electrostatic attraction energy) are considered to generate various similarity evaluators, such as the wellknown Carbó, HodgkinRichards, Shape Tanimoto, and Kulczynski indices.
First superpositions, applied to rigid endothiapepsin ligands, were achieved using a basic MonteCarlo/Simulated Annealing algorithm. They showed that smoothing increases the speed of the convergence to acceptable solutions. Also, distancedependent similarity measures, such as Coulomb integrals and electrostatic energy, could lead to acceptable solutions, even when smoothing was not considered. The best results were obtained when using kinetictype integrals and the Shape Tanimoto index, especially for the superposition of molecules with different sizes.
References:
[1] A.C. Good, and W.G.J. Richards, Chem. Inf. Comput. Sci., 33, 112 (1993)
[2] V.G. Tsirelson et al., Acta Cryst. B, 54, 8 (1998)
[3] X. Gironés et al., J. Mol. Graphics Modell., 16, 190 (1998)
[4] V. Botella, and L.F. Pacios, J. Mol. Struct. (Theochem), 426, 75 (1998)
[5] A.S. Mitchell, and M.A. Spackman, J. Comput. Chem., 21, 933 (2000)
[6] X. Gironés et al., J. Mol. Graphics Modell.,19, 343 (2001)
[7] R.T. Downs et al., Phys. Chem. Miner., 29, 369 (2002)
[8] P. Bultinck et al., J. Chem. Inf. Comput. Sci., 43, 1208 (2003)
[9] E. Aubert et al., Acta Cryst. B, 59, 687 (2003)
[10] L. Amat, and R. CarbóDorca, J. Comput. Chem., 18, 2023 (1997)
Original language  English 

Publication status  Published  27 Jan 2006 
Event  Quantum Chemistry in Belgium : VIIth meeting  Universite de MonsHainaut, Belgium Duration: 27 Jan 2006 → … 
Symposium
Symposium  Quantum Chemistry in Belgium : VIIth meeting 

Country/Territory  Belgium 
City  Universite de MonsHainaut 
Period  27/01/06 → … 
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Multiresolution analysis of electron density maps
Leherte, L., Vercauteren, D. & Meurice, N.
1/09/95 → …
Project: Research