Graph representation of molecular structures is widely used in computational chemistry and theoretical chemical researches. Trinajstic noted that the roots of chemical graph theory may be found in the works by chemists of 18-19 centuries such as Higgins, Kopp, Crum Brown. They have used first chemical graphs for representing molecules. Molecular structures are represented by graphs where vertices correspond to atoms, and edges to chemical bonds. This kind of a graph, called now a molecular graph, is the object of study in the theory of ordinary graphs. However ordinary graphs do not adequately describe chemical compounds of nonclassical structure. A substantial drawback of the structure theory is the lack of a convenient representation for molecules with polycentric bonds. Most often polycentric bonds are encountered in organometallic (sandwich-type) compounds, polycyclic conjugated molecules, benzenoid systems in particular, etc.
In 1994 the concept of a molecular hypergraph, as a mathematical tool suitable for modeling the structure of molecules with polycentric bonds was introduced [46]. Main goal of this Lecture Notes is to demonstrate advantages of an application of hypergraph theory in chemical researches.