Overcoming the Limitations of a Connection Table Description: A Universal Representation of Chemical Species

The following paper describes a new model for the representation of chemical structures in information processing. This representation overcomes the limitations of connection tables designed to only represent chemical structures with bonds localized between two atoms. The representation introduced is based on the separation of the σ- and π-electrons of bonds and the delocalization of electrons also across more than two atoms. It also allows the description of chemical compounds containing multicenter or coordinative bonds. The representation was implemented using object-oriented programming techniques. The important classes of the developed class library are introduced.

[1]  Johann Gasteiger,et al.  The Coding of the Three-Dimensional Structure of Molecules by Molecular Transforms and Its Application to Structure-Spectra Correlations and Studies of Biological Activity , 1996, J. Chem. Inf. Comput. Sci..

[2]  Mary Ellen Switzer,et al.  ON THE ELECTRONIC GROUND STATES OF MANGANOCENE AND 1,1′-DIMETHYLMANGANOCENE , 1975 .

[3]  Johann Gasteiger,et al.  Prediction of Mass Spectra from Structural Information , 1992 .

[4]  K. Klabunde,et al.  Synthesis employing oxidative insertion of palladium atoms into aryl, alkyl, and acyl carbon-halogen bonds. Properties of and phosphine trapping of the nonligand stabilizer RPdX and PCOPdX intermediates , 1974 .

[5]  Ivar Ugi,et al.  Beschreibung chemischer Systeme und ihrer Umwandlungen durch be-Matrizen und ihre Transformations-Eigenschaften , 1971 .

[6]  Konstantin S. Lebedev,et al.  Computer-aided molecular formula determination from mass, proton and carbon-13 NMR spectra , 1992, J. Chem. Inf. Comput. Sci..

[7]  Andreas Dietz,et al.  Yet Another Representation of Molecular Structure , 1995, Journal of chemical information and computer sciences.

[8]  Natalie Stein New Perspectives in Computer-Assisted Formal Synthesis Design-Treatment of Delocalized Electrons , 1995, J. Chem. Inf. Comput. Sci..

[9]  Ivar Ugi,et al.  New elements in the representation of the logical structure of chemistry by qualitative mathematical models and corresponding data structures , 1993 .

[10]  Ivar Ugi,et al.  Matter Preserving Synthetic Pathways and Semi‐Empirical Computer Assisted Planning of Syntheses , 1971 .

[11]  Johann Gasteiger A Representation of p Systems for Efficient Computer Manipulation , 1979, J. Chem. Inf. Comput. Sci..

[12]  Robert E. Stobaugh,et al.  The Chemical Abstracts Service Chemical Registry System. VII. Tautomerism and Alternating Bonds , 1980, J. Chem. Inf. Comput. Sci..

[13]  Johann Gasteiger,et al.  Hash codes for the identification and classification of molecular structure elements , 1994, J. Comput. Chem..

[14]  Johann Gasteiger,et al.  Automated derivation of reaction rules for the EROS 6.0 system for reaction prediction , 1991 .

[15]  Johann Gasteiger Automatische Erzeugung pericyclischer Reaktionen/Automatic Generation of Pericyclic Reactions , 1979 .

[16]  James Dugundji,et al.  An algebraic model of constitutional chemistry as a basis for chemical computer programs , 1973 .

[17]  Arthur Dalby,et al.  Description of several chemical structure file formats used by computer programs developed at Molecular Design Limited , 1992, J. Chem. Inf. Comput. Sci..

[18]  I. Ugi,et al.  Representation of Chemical Systems and Interconversions by be Matrices and Their Transformation Properties , 1971 .