Tetrahedron Computer Methodology最新文献

The extension of a previously described method for the evaluation of atomic charges in organic structures is presented. The application to conjugated and aromatic systems is considered. The identification of the atoms involved in the conjugation and their conjugative distances is afforded by a novel and straightforward method. Merging of the two algorithms for charge calculation is accomplished. The method is tested through calculation of several molecules and results are discussed.

“Dietz” response factors (RF) have been measured under standard conditions for 100 substituted benzenes and pyridines. The data have been treated by the partial least squares (PLS) method, using as explanatory variables the molecular weight together with structural features such as the numbers of atoms of each element and of multiple bonds, functional groups, etc. The “Dietz” RF are explained to 84% of the variance by three PLS components. It is shown that Dietz RF can be predicted from the structural formulae for many classes of compounds with an average deviation of 0.05 within the model and 0.09 out of the model. This should be of considerable utility in the quantitative analysis of complex product mixtures by GC/MS, especially for those cases where some or all of the products are unavailable. The PREDICT.EXE program for the PC and Fortran code, PREDICT.FOR, as well as the raw data set used to derive the model are included on disk.

A fast algorithm for the evaluation of residual charges in organic structures is presented. Its validity extends over single and isolated multiple bonds. The model considers only atom connectivities as the topological basis and atom electronegativities and covalent radii as physical characteristics; the use of an iterative procedure and well-defined computational rules ensures self consistency for the method which is tested through the calculation of atomic charges in several molecules and through a comparison of results obtained with other methods. The Fortran 77 source code RESCHA.FOR the PC executable RESCHA.EXE, sample input PROST.MOL, and resulting output PROST.OUT are included on disk.

A new maximal common subgraph search algorithm (MCS-1) is described and applied to selection of starting materials for synthesis of a target molecule. This algorithm achieves parallelism of up to 20-fold with a single processor by using a unique storage tree. The storage tree requires only 79% of the storage required by a sequential organization and the storage tree requires only 28% of the bonds to be represented. The algorithm continues to improve relative to the sequential organization as the number of compounds in the library increases. The efficiency of the algorithm was evaluated with four queries for ten different sized libraries, ordered in various ways. An execution trace of MCS-1 is included.

Mathematical analysis of bioassay-directed fractionations results of crude extracts can help isolation of active compounds. From the values of weights and activities of the different fractions, it is possible to calculate purification indices related to the increase of concentration of the active compound in each fraction, and relative recovered quantities related to the amounts of active compound present in each fraction. SESAME is a program based on this method. It calculates the different values useful for the interpretation of a fractionation, and analyses the efficiency of the purification and the preservation of the active compound, and gives evidence of the possible presence of several active compounds.

A method is presented to depict the interaction possibilities of a molecule by projecting the van der Waals envelope and the electrostatic potential onto a cylinder surface. Unfolding of the cylinder allows the viewing of the molecule from all sides simultaneously, thus rendering unnecessary multiple representations from different viewing angles. The comparison of similar molecules, e.g. mimics, is thus greatly simplified. Qualitative representations and quantitative expressions for differences between molecules are easily derived from the procedure. The method should be especially useful in cases where the entire van der Waals surface is expected to be in contact with a complexation site, i.e. where interacting molecules are surrounded entirely by their binding site, e.g. in enzymes, cyclodextrins or polymer matrices. Molecule structure files are included on disk.

CLUSMOL is designed to conceptualize the chemist's understanding of a group of molecules, by creating taxonomic trees, in which structurally similar molecules are placed in the close leaf nodes, while the intermediary nodes represent the maximal common substructures for the leaf structures under the node. The system is tested on some antibiotics and shown to be useful for lead structure recognition in drug design.