Computational Chemistry and Organic Synthesis

Computational Chemistry and Organic Synthesis

A course to introduce computational chemistry to synthetic-organic chemists, who would like to understand why they got the product they got and not (always) the compound they wanted. With emphasis on the Transition State (TS): how to construct it, characterize it, and compare it to other alternatives. Starting with conformational changes, and ending with 'real' reactions.

(AMPAC5.0 GUI graphics)


At the CAOS/CAMM Center we noticed an increasing interest, from synthetic chemists, for molecular modelling as a tool, next to spectroscopic and other physical techniques.
Mostly what they are after is an explanation for experimental product ratios.

This observation inspired us to compose a course on this subject, with emphasis on a practical approach and a minimum of mathematics or theory.

Molecular modelling is interpreted here as the interactive combination of visualization and computational techniques, with emphasis on the former. These days computational chemistry is more or less the same, but with emphasis on the latter. Visualization has become an integral part of almost all computational methods.

As a technique computational chemistry has the advantage of producing answers cheaply and quickly (compared to e.g. thermodynamic measurements), and for hypothetical structures, like transition states.

This is a point of concern at the same time: it is easy to make errors that remain undetected; it is often difficult to judge the significance of a result. Just by clicking a few buttons one can create scores of huge files filled with numbers, which may turn out to be irrelevant on closer inspection.
Literature research and comparison to known systems and data are mandatory to benefit from computational techniques.


The aim of this course is to lower the threshold a bit, throw some light on (if not in) the black boxes and to encourage the dialogue between synthetic chemists and their more theoretical colleagues.
Through this course one is encouraged to:


The course material is organized in five main areas:
  1. Chapter 1, Types of coordinates, z-matrices, input files
  2. Chapter 2, How to locate a Transition State
  3. Chapter 3, More theory
  4. Chapter 4, Programs used, file formats and conversion
  5. Chapter 5, Literature and pointers to WWW sites

There is also a navigator in the form of a table.

Last update: July 15, 1996 (!) by Hens Borkent
This tutorial is a more or less finished product, and technically dated.
A new approach has been followed in our Chime-based mopac input and output file interface: Mol4D. From there you can prepare input files, submit the job, and view the result, all within web pages. This includes grid calculations!

For remarks, questions, corrections, you can send mail to me at

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