Reaction mechanisms

What is the mechanism of a chemical reaction?

The reaction mechanism is the detailed step-by-step description of the transformation of reactants into the corresponding products in a chemical reaction.

The description should include the movement of electrons that takes place by means of curved arrows, the formal charge associated with the atoms involved in the process, the breaking and formation of bonds, the description of the reaction intermediates, etc. In some cases, it is convenient to consider the spatial orientation of atoms during the transformation.

The following considerations must be made before writing a reaction mechanism:

  • Reactions commonly encountered in organic chemistry involve the interaction of an electronophile (Lewis acid) and a nucleophile (Lewis base).
  • For better localization of the electronophile and nucleophile, Lewis structures should be drawn with unshared electron pairs, especially in the functional groups between which the reaction takes place. Also, the formal charge on the atoms involved in the reaction is indicated. This must be the same in the reactants as in the products.
  • Identification of the reagent (or functional group) acting as nucleophile and the one acting as electronophile. In general the reagent acting as a nucleophile has an electron pair, negative charge, or multiple bond that can be shared. While the one acting as electronophile is electron deficient, positively charged, or partially positively charged (δ+), and with empty orbitals susceptible to accommodate electrons.
  • Use of curly arrows to indicate the movement of electrons. These arrows have their origin in the free electron pair, or bonding electrons, and their destination is the electron-deficient atom. These arrows also indicate the breaking and formation of bonds.

The following figure indicates the reagent acting as nucleophile and as electophile, the formal charge, as well as the electron flow in the following examples:


Historical background

Another area in which the current activity of organic chemistry is developed is the study of organic processes in general and of reaction mechanisms in particular. The purpose of this knowledge is twofold. On the one hand, the understanding of how a chemical process takes place by scrutinizing its details. On the other hand, the use of this knowledge to achieve a better control of the process in order to be able to modify it and thus obtain specific goals such as the improvement of yield and/or selectivity.

The main advances in this field come from the development of new techniques for kinetic determinations, the elaboration of theoretical models and the consolidation of Computational Organic Chemistry. In addition, the knowledge of reaction mechanisms has a didactic aspect, consisting in the generalization of the different reactions of organic chemistry.

A classic example of how a good mechanistic study can open new fields of activity in the field of synthesis is the contribution of G.A. Olah in directly identifying and characterizing organic carbocations, their formation and transpositions, through the development of superacid media combined with NMR. This discovery had an impact not only on research in this area, but also on the automotive fuel production industry through the development of new catalysts.

Part of the mechanisms of polar reactions is explained in organic chemistry with the participation of carbocationic intermediates. But not only NMR, but also UV/vis and IR spectroscopy have been used for the detection of highly reactive intermediates following the technique of inert matrix treatment at low temperature, allowing great advances in the field of photochemistry.

On the other hand, one of the most novel contributions in the field of ultrafast detection is offered by so-called femtosecond kinetics or spectroscopy. Since the mid-1980s, physicists have been making progress towards the long-held dream of filming the events governing molecular transformations in real time.

Using photon pulse lasers of durations of less than 10-12 seconds, it has been possible to obtain information on the initial stages of simple organic reactions. These studies include the direct study of transition states.