Finding, optimization, and verification of transition state structures with semi-empirical and ab-initio computational methods Branko S. Jursic Department of Chemistry, University of New Orleans, New Orleans, LA 70148, USA Received 10 July 1998; accepted 26 July 1998 Abstract With a goal of introducing transition state optimization and estimating reaction barriers into an undergraduate organic curriculum, a simple step by step computational study for three isomerization reactions with MOPAC computational package was described. The procedures for finding optimization, and verification of the transition state structure is quite straightforward and concise. The introductory procedure was further extended to ab-initio and density functional theory computational method. This simple procedure can easily be integrated into most current organic chemistry curriculums.  1999 Elsevier Science B.V. All rights reserved. Keywords: Transition state structures; Semi-empirical; Ab-initio computational methods 1. Introduction Nowadays, teaching chemistry at undergraduate and graduate levels benefits enormously from compu- ter advances. Desktop computers are becoming affordable, not only for colleges but also for their students. Many computational packages that can adequately illustrate chemical structures in three dimensions are within the range of most students’ budgets. These programs for organic chemistry provide undergraduates with a three-dimensional approach in which they can better visualize and under- stand organic structures. Organic chemistry combines many chemical transformations that students are forced to memorize, but few understand the causality or mechanisms of the chemical transformations. It is even more critical for students to understand the nature of chemical transformations when the selectiv- ity of chemical reactions is discussed. As teachers, we explain the selectivity of chemical reactions as the effect of stability of certain reaction intermediates of product formation, although the majority of the time chemical reactions are determined by which reaction has the highest activation barrier. The task of edifying and emphasizing to undergraduate and even graduate students the importance of understanding causality is not an easy task. Here, we present a very simple procedure by which it is possible to compute transi- tion state structures and determine activation barriers for simple organic transformations by using computa- tional packages that are affordable or available from public domains. This can be included as a part of the organic chemistry laboratory experience. When the procedure for finding and optimizing of transition state structures of simple structures presented in this paper is learned, it can be applied to any problem (reaction) currently being taught in curriculums of organic chemistry for undergraduate and graduate students. Fascination with structural arrangements that are Journal of Molecular Structure (Theochem) 465 (1999) 173–182 0166-1280/99/$ - see front matter  1999 Elsevier Science B.V. All rights reserved. PII: S0166-1280(98)00328-5