A mathematical model of the synthon is suggested. The term synthon is used to denote one or several molecules or their part(s) with free valences. The notion of isomeric synthons on a set of atoms A and that of the Family of Isomeric Synthons FIS(A) are introduced. Matrix operators are defined for modelling the elementary steps of reorganization of electrons during reactions. A new notion of the reaction distance of isomeric synthons is introduced as the smallest number of elementary steps of reorganization of electrons during the reaction transforming one synthon into another.