Comparison of small molecules using promolecular electron density distribution functions

Research output: Contribution to conferencePoster

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 [1-9] 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 kinetic-type integrals, electrostatic attraction energy) are considered to generate various similarity evaluators, such as the well-known Carbó, Hodgkin-Richards, 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, distance-dependent 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 kinetic-type integrals, 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. Carbó-Dorca, J. Comput. Chem., 18, 2023 (1997)
Original languageEnglish
Publication statusPublished - 12 Oct 2006
EventAssemblée générale de la Société Royale de Chimie - Bruxelles, Belgium
Duration: 12 Oct 2006 → …

Meeting

MeetingAssemblée générale de la Société Royale de Chimie
CountryBelgium
CityBruxelles
Period12/10/06 → …

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    • 1 Participation in workshop, seminar, course

    Assemblée générale de la Société Royale de Chimie

    Christophe Meunier (Speaker)

    12 Oct 2006

    Activity: Participating in or organising an event typesParticipation in workshop, seminar, course

    Cite this

    Leherte, L., & Vercauteren, D. (2006). Comparison of small molecules using promolecular electron density distribution functions. Poster session presented at Assemblée générale de la Société Royale de Chimie, Bruxelles, Belgium.