Because my monograph:
S. Fujita, Symmetry and Combinatorial Enumeration in Chemistry (Springer 1991)
has been referred to as an endeavor of dealing with topics of
organic chemistry on the basis of mathematics,
I would like to add two monographs aiming at
organic reactions and stereochemistry coupled with mathematics (group theory):
Computer-Oriented Representation of Organic Reactions
(Yoshioka Shoten, Kyoto, 2001)
Diagrammatical Approach to Molecular Symmetry and Enumeration of Stereoisomers
(University of Kragujevac, Kragujevac, 2007)
which have appeared more recently.
PS (Feb. 13, 2013)
For a more recent publication (not a book) on interdisciplinary topics between
mathematics and chemistry, I would like to introduce an account article,
which is freely available:
"Numbers of Alkanes and Monosubstituted Alkanes. A Long-Standing Interdisciplinary Problem over 130 Years"
(Bull. Chem. Soc. Japan, 83, 1--18 (2010)).
This account deals with combinatorical enumeration of three-dimensional trees,
where trees as graphs are extended to 3D trees having 3D structures.
PS (July 17, 2013)
I have published another book on interdisciplinary topics between
mathematics and chemistry:
Combinatorial Enumeration of Graphs, Three-Dimensional Structures, and
(University of Kragujevac, Kragujevac, 2013).
Chapter 7 (Proligand Method) of this book is concerned with a substantial extension
of Polya's theorem. The landmark article on Polya's theorem appeared originally in 1937
and was translated into English in 1987:
G. Polya and R. C. Read,
Combinatorial Enumeration of Groups, Graphs, and Chemical Compounds
As found in their book titles, chemical compounds are regarded as three-dimensional structures
in Fujita's book, while they are regarded as graphs in Polya-Read's book.
This difference is critical to discuss stereochemistry:
Sphericities of Cycles. What Polya's Theorem is Deficient in for Stereoisomer Enumeration
(Croat. Chem. Acta, 79, 411--427 (2006)).