(1) 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. The first and the third books are concerned with Fujita's unit-subduced-cycle-index (USCI) method for symmetry-itemized enumeration of 3D structures as well as graphs.
(2) 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), access-free).
This account deals with combinatorical enumeration of three-dimensional trees,
where trees as graphs are extended to 3D trees having 3D structures.
(3) Another book on interdisciplinary topics between mathematics and chemistry:
Combinatorial Enumeration of Graphs, Three-Dimensional Structures, and
(University of Kragujevac, Kragujevac, 2013),
has published to introduce Fujita's proligand method (Chapter 7), which provides us with a powerful tool for gross enumeration of 3D structures. This is a substantial extension of Polya's theorem, which aims at gross enumeration of graphs.
The landmark article on Polya's theorem appeared originally in 1937 and was translated into English in 1987 (after 50 years!):
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), access-free).
(4) A further book on interdisciplinary topics between mathematics and chemistry has appeared recently:
Mathematical Stereochemistry (De Gruyter, Berlin, 2015). xviii + 437pp
This book deals with Fujita's stereoisogram approach, where RS-stereoisomers as new concepts are represented by stereoisograms diagrammatically.