Chemical graph theory

The graph theory (chemistry) or even chemical graph theory deals with the formalization and application of graph theoretical principles in the field of chemistry, especially the chemo computer science. Object of graph theory, the processing of molecular structures.

Important applications include the identification of substructures, for example, group contribution methods, topological indices, the Kekulisierung of molecular structures and the calculation of Characteristic polynomials.

Typical molecular representations as a graph

Molecular structures are usually stored in a matrix form, typical forms of presentation are the

• Adjacency matrix, which has and recorded the presence of the compound of atoms as much rows and columns as there are atoms
• Distance matrix having columns and rows as much as the distance between the atoms two atoms listed. The distance may be the number of bonds in the shortest path or the spatial distance.
• Incidence matrix, and having recorded the atoms connecting the respective columns, such as binding to one another as much atoms and lines like bonds.
• Binding matrix, which is a variant of the adjacency matrix, but with lists the bond order.

An alternative representation is the binding list that is mostly used by graphics programs and provides space for more information. The binding list is usually a list of atoms, including, for example, the coordinates, atom types, charges etc. and then a list of the bonds with the specification of the connected atoms, including the bond order and further geometric information.