Premium
Random Computer Generation of 3D Molecular Structures: Theoretical and Statistical Analysis
Author(s) -
Porquet Alain,
Duval Jérôme F. L.,
Buffle Jacques
Publication year - 2006
Publication title -
macromolecular theory and simulations
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.37
H-Index - 56
eISSN - 1521-3919
pISSN - 1022-1344
DOI - 10.1002/mats.200500049
Subject(s) - formalism (music) , fragment (logic) , molecule , chemistry , algorithm , electronic structure , computer science , statistical physics , chemical physics , computational chemistry , physics , art , musical , organic chemistry , visual arts
Summary: A computer program has been developed to generate three‐dimensional molecular structures randomly from a given collection of elementary chemical functional groups: the so‐called fragment database. The gradual assembly of the various fragments present in the database is performed according to a “self‐generation algorithm” (SGA). The latter is based on the covalent binding, step by step, between the unoccupied electronic valencies associated with the fragments of the database, and those of the growing molecular structure. When the number of electronic valencies of the molecular structure is zero, the growth process for this particular molecule is completed. It is shown that SGA is able to reproduce the asymmetric mass distributions of some natural colloids, like humic substances. In this article, particular attention is given to the analysis of the relationship existing between the fragment composition of the database and that of the collection of molecules generated. Mathematical expressions are derived and discussed, to understand the relationship between the proportions of the different types of fragments and the final composition of the generated molecular ensembles. For that purpose, a “pathway” formalism is proposed to describe exhaustively the whole set of generated molecules by specifying the distribution function of all of the fragments therein integrated. A statistical analysis that satisfactorily reproduces the predictions of the pathway model is extensively discussed.Example of a three‐dimensional structure obtained with the “self‐generation algorithm” (SGA).