A simple hierarchical data structure (Mathematica expression) has been developed to represent the constitution (topology) of organic chemical structures. This representation also supports the notions of chemical valence and stereochemistry. Mathematica expression patterns and built-in functions can be used to perform chemically meaningful transformations on instances of this data structure. The important aspects of the implementation will be presented, and as well as its strengths and weaknesses. Application of this methodology to chemical constitution optimization (inverse QSAR and average molecular structure generation) and chemical reactivity will be described or demonstrated.