Molecules in silico: a graph description of chemical reactions.

A general mathematical description, mostly in terms of graph theory, is given for reactions of organic chemistry. The corresponding computer program generates all products that can result from a given set of starting materials interacting according to a given set of reaction schemes. Example reactions from combinatorial chemistry, synthetic organic chemistry, and mass spectroscopic structure elucidation are considered in detail.

QSPR using MOLGEN-QSPR: the challenge of fluoroalkane boiling points.

By means of the new software MOLGEN-QSPR, a multilinear regression model for the boiling points of lower fluoroalkanes is established. The model is based exclusively on simple descriptors derived directly from molecular structure and nevertheless describes a broader set of data more precisely than previous attempts that used either more demanding (quantum chemical) descriptors or more demanding (nonlinear) statistical methods such as neural networks. The model's internal consistency was confirmed by leave-one-out cross-validation.

QSPR using MOLGEN-QSPR: the example of haloalkane boiling points.

MOLGEN-QSPR is a software newly developed for use in quantitative structure property relationships (QSPR) work. It allows to import, to manually edit, or to generate chemical structures, to detect duplicate structures, to import or to manually input property values, to calculate the values of a broad pool of molecular descriptors, to establish QSPR equations (models), and using such models to predict unknown property values. In connection with the molecule generator MOLGEN, MOLGEN-QSPR is able to predict property values for all compounds in a predetermined structure space (inverse QSPR).

Manual construction and mathematics- and computer-aided counting of stereoisomers. The example of oligoinositols.

Two methods to obtain numbers of stereoisomers and of achiral stereoisomers of a given molecular structure are detailed on the example of di- and triinositols. The first method is manual exhaustive construction free of redundance of all stereoisomers, which is rendered feasible by symmetry considerations despite the large number of isomeric triinositols (82176). The second method is counting without constructing, made possible by use of a mathematical tool, the Cauchy-Frobenius lemma, which actually is a formalized manner of considering symmetry.

MOLGEN-CID--A canonizer for molecules and graphs accessible through the Internet.

The MOLGEN Chemical Identifier MOLGEN-CID is a software module freely accessible via the Internet. For a molecule or graph entered in molfile format (2D) it produces, by a canonical renumbering procedure, a canonical molfile and a unique character string that is easily compared by computer to a similar string. The mode of operation of MOLGEN-CID is detailed and visualized with examples.