Molecular Modeling

Blandon, Peter, Gorton, John, and Hammond, Robert B.  Molecular Modeling: Computational Chemistry Demystified; RSC Publishing: Cambridge, UK.  ₤69.99 (softcover)  310 pp.  ISBN:  978-1-84973-352-6.

I have been intrigued by molecular models ever since I first saw them demonstrated in undergraduate chemistry classes.  The fascination continued in graduate school, and, although carefully-guarded model sets were available in some research groups, my concentration on heterocyclic and aromatic chemistry made the expensive Dreiding models less attractive to a “starving student.”  I eventually acquired various modeling sets, through purchase or discards, but I left the lab before I could justify any work with the embryonic modeling programs (although several models still adorn my bookshelves).

When JCIM (and JCICS) still published book and program reviews, most of the reviews of modeling programs and books understandably went to practitioners in the field.  Although usually left out of this group of experts, I am a visual species of chemist, and I am still fascinated with molecular modeling and have felt left out for decades.  When RSC approached me about reviewing this book for CIB, I jumped at the chance.

This review will be “static,” focusing on the content and presentation of the book, since at this time I choose not to load all of the necessary programs onto my aging tower PC for a full scale demo.  Therefore, a “dynamic,” hands-on work-through will, for now, be left to the reader.

This book provides an excellent, well documented introduction to molecular models and modeling, including a terse and sometimes humorous history.  On the assumption that students at a “well endowed university” taking computational chemistry would find all of the necessary resources, the book is aimed at molecular modelers who, for whatever reason, work alone.  CDs of Interprobe (INTERCHEM, PRESTO, 3D databases, etc.) open source software are included, and links are provided for additional free resources.  Problems and questions appear at the end of three of the chapters.

The introduction outlines chemical structure and structure representation, including SMILES strings. Chapter 2 describes the necessary computer resources to use the programs, plus a synopsis of operating systems and other computational processes.  Chapter 3 begins a primer on bonding and other molecular phenomena and on data as a basis for modeling.  Chapter 4 enables the user to “get down and dirty” by using INTERCHEM for molecular modeling.  Modeling of proteins, nucleic acids, and the solid state, as well as the basics and applications of stereochemistry and conformation analysis, are discussed and demonstrated in Chapters 5-7.  3D structures and modeling in medicinal chemistry and for drug discovery are described in Chapters 8-10. 

Appendices cover additional data and program information.  The text is well illustrated with structure line drawings, screen shots, and ball and stick computer drawn models.  Two errors were noted.  In ref. 1 on p. vii, the lead author is P. Gund.  Ref. 19, noted in the list on p. 11, is not cited in the text (the publisher has been informed).

The book is recommended for use in collegiate and graduate student molecular modeling courses, as well as by post graduate professionals.

 

Robert E. Buntrock
Buntrock Associates
Orono, ME
buntrock16@myfairpoint.net