Molecular Modelling Personal Computer

New chapter on computational chemistry and computer-assisted drug design, exploring techniques of molecular modeling and computational chemistiy in response to the growth ot powerful personal computers on the desks of today s medicinal chemists... 

California), Sibyl (Tripos, Missouri), ChemX (Chemical Design, UK), BioGraf (Molecular Simulations, California), Charmm/Quanta (Polygen Corp., Massachusetts), PC Model (Serena Software, Indiana), ChemLab (ChemLab Inc., Illinois), and a large number of personal computer-based packages. 

With the introduction of Gear s algorithm (25) for integration of stiff differential equations, the complete set of continuity equations describing the evolution of radical and molecular species can be solved even with a personal computer. Many models incorporating radical reactions have been pubHshed. 

This workbook contains over 200 problems that will allow you to build and refine your understanding of chemistry from the molecule s eye view . This is achieved by basing every problem on a set of molecular models that you view and manipulate on your own personal computer. We believe that this combination of problems-i-models will improve your understanding of molecular structure and the relationship between molecular structure and other properties. More importantly, we believe that when you do the problems in this workbook you will gain a much better grasp of the conceptual basis of organic chemistry, and that this will make the rest of your study of organic chemistry more satisfactory and ultimately more successful. 

My main goal, as outlined in the Preface to the First Edition, which appears herein, is the same as before to help you see the logical thread that connects those mysterious diffraction patterns to the lovely molecular models you can display and play with on your personal computer. An equally important aim is to inform you that not all crystallographic models are perfect and that cartoon models do not exhaust the usefulness of crystallographic analysis. Often there is both less and more than meets the eye in a crystallographic model. 

Molecular mechanics is an interpolative method. It thus follows that the strain energy and the structure of a very strained species may not be reliably computed on the basis of a parameterization scheme fitted with a set of experimental data obtained from unstrained molecules, since this amounts to extrapolation. Therefore, to obtain a generally reliable force field, extreme cases have to be included in the fitting procedure of the force field. The speed with which structure optimizations are produced (minutes of CPU time on a simple personal computer for molecules with around 100 atoms) does not place any restriction on the size of a data base for the parameterization of a class of compounds - the limit is usually given by the amount of experimental data available. The major appeal of molecular mechanics is the fact that unknown compounds may be modeled in much the same way as model kits are used, with the important difference that quantitative information becomes available, enabling an effective design of new compounds. 

Yoneo Yamamoto and Masanao Miyata, NEC PC-9800 Series Exercises in Molecular Modeling for Personal Computer, Kodansha, Tokyo, 1989. 

Many of the aforementioned features are combined in integrated molecular modeling software such as SYBYL, Chem-X, COSMIC,80 Quanta and CHARMm, BIOGRAF, Insight and Discover, Chemlab, and MOLIDEA. These packages are available on a variety of hardware platforms ranging from personal computers (PCs) to mainframe computers. 

An updated, greatly enlarged compendium of software for molecular modeling appears as the Appendix. Programs that run on personal computers, minicomputers, workstations, mainframes, and supercomputers are listed together with some of their features. Telephone numbers and addresses of the vendors and/or developers are provided. To our knowledge, this is the most complete listing of sources of software for computational chemistry anywhere. 

---