Tetrahedron Computer Methodology最新文献

The program system RAIN for bilateral generation of reaction pathways requires a procedure that automatically represents each molecule to be entered into a reaction network in terms of all conceivable resonance and tautomeric structures. Thus ambiguities can be avoided, and substantially decreased numbers of required reaction steps for closing reaction pathways between starting materials and products of chemical reactions are achieved. It is shown how the formal reaction generator of RAIN can be guided by a set of constraints to produce only resonance or tautomeric structures of a considered molecule. The effects of these boundary conditions are shown in several illustrative examples.

The problem of computer-assisted generation of carbocationic rearrangements is considered. The formalized approach to the description of carbocationic transformations is presented and the ICAR program (Investigation of CArbocationic Rearrangements) is briefly described. The ICAR program combines the pure combinatorial methods of the generation of carbocationic transformations with a flexible system of empirical selection criteria. Main principles of constructive enumeration of rearranged pathways and examples of selection criteria are discussed. The results of the solution of several carbocationic problems are also briefly mentioned. For instance, it is shown that the well-known “adamantane-land” is incomplete and should be supplemented with new possible precursors of adamantane. The working PC-version of the ICAR program with user's manual is included on disk in this issue.

Neural network technology is finding new applications in chemical research. This paper briefly describes neural network technology, reviews recent applications in chemistry, and introduces the papers appearing in this special issue of Tetrahedron Computer Methodology.

This paper provides a detailed description of a database of protein structure implemented in the logic programming language PROLOG. The database allows flexible access to structural information at the atom, residue, secondary structure and topology levels of the protein structural hierarchy. An extended version of the Kabsch and Sander algorithm for secondary structure definition has been implemented in PROLOG, forming an integral part of the database. For protein structure analysis, the PROLOG system shows significant advantages in flexibility over conventional programming languages such as Fortran, and Relational Database Management Systems using SQL.

The MARK algorithm allows one to calculate the name of a compound by means of its structural data without using a data bank. On the basis of the described algorithm the ALKANES program makes it possible to name the branched acyclic alkanes according to the IUPAC rules. This program is available on disk.

An original graphical representation of relationships between acids and bases or between electrophiles and nucleophiles is proposed. It is based on the notion of an isoreferential plane of reactivity. An isoreferential plane of reactivity contains all the quantitative homologous measurements of a set of bases (nucleophiles) toward a given acid (electrophile). Symmetrically, the same representation applies to sets of acids (electrophiles) opposed to a given base (nucleophile). The relative spatial disposition of isoreferential planes associated with different acids (electrophiles) indicates immediately if inversions of ranking in reactivity of bases (nucleophiles) are expected to occur when one passes from one acid (electrophile) to another. A program (DBLSCALE on Disk 18) written in Basic and working on PC computers (IBM and IBM compatibles) allows the direct representation, on the screen, of sets of donors and acceptors, using the parameters derived from Drago's Double Scale approach.

A framework for analogical reasoning in chemistry is introduced to estimate unknown molecular properties from the structure. When some chemical properties are concerned, an anchor position can be defined in the molecular structure to designate the local component responsible for the property appearance. If two structures are compared matching their anchors, the partial order relationship can be judged between the structures. The molecules are ordered in a discrimination net using this partial order, so that the similarity search becomes possible on this net. Three analogical reasoning methods are discussed which utilizes the similar structures as well as their properties found on the net.

End-to-end diffusion-limited aggregation of an ideal, monodisperse pectin species with variable probability of interrmolecular crosslinking has been simulated on a lattice. The aggregate was fixed on the lattice as a structure of segmented rods. The growth of averages of size, length, width, and radius of gyration followed a power law dependence on time as measured by number of random lattice movements of diffusing monomer. The structures exhibited multifractal properties that arise from both the diffusion process and the random generation of crosslinking sites. The growth of the average length of the structures was independent of probability of crosslinking under the condition of constant presence of diffusing monomer. The growth of the average size of the structures was directly related to the growth of the average number of crosslinks. Average length, width, and radius of gyration were related to growth of average size by power laws. Macintosh and IBM PC source code and executables are included on disk in this issue.

The extension of a previously described method for the evaluation of atomic charges in organic structures is presented. The application to structures containing charged atoms is considered. A search for the atoms involved in the initial distribution of the charge is afforded extending a method previously described. Bond orders are changed according to the existence of canonical forms. The problem of backdonating atoms is analyzed and discussed and a possible solution is presented. The method is tested through calculation on several molecules and results are discussed. This program is included on disk in this issue.