Reaction Mechanisms

FIELDS OF STUDY: Organic Chemistry; Inorganic Chemistry; Biochemistry

ABSTRACT

The concept of reaction mechanisms and its importance in chemistry-related fields is elaborated. A reaction mechanism is the process by which a reaction theoretically takes place and describes the reorganization of electrons and orbitals in the reactants as they interact to form the products.

Visualizing Chemical Processes

A reaction mechanism is the hypothetical description of how a reaction occurs. It is based on observation and the logical application of the principles of modern atomic theory and molecular orbital theory. All reaction mechanisms begin with the observation of an overall reaction process, which is shown to occur between two reactants and to produce certain products. The purpose of a proposed reaction mechanism is to describe a logical means of transforming the reactants into the products that agrees with the theoretical principles governing molecular structures and their substituent functional groups as well as the characteristic behavior of atoms.

The purpose of a reaction mechanism is to describe the transformation of one compound into another by identifying individual electron movements and molecular orbital rearrangements that account for the observed changes that take place in the reaction. Reaction mechanisms consist of a sequence of elementary reactions, which in this context form individual reaction steps. Each individual reaction step must also be in agreement with the electron movements and orbital rearrangements that are allowed in theory.

Theory can be modified when empirical results call the existing theoretical principles into question, however. It has often been the case historically that a reaction that is expected to produce a certain product by a certain mechanism instead produces a compound with the correct components but in an unexpected arrangement. In such cases, the observation provides new information about the actual reaction mechanism that has taken place, allowing the theoretical mechanism to be modified. The modified theoretical mechanism can then be more successfully applied to other reactions. For example, the reaction of triphenylmethyl halides with silver metal forms a particular dimer, which is a compound made from two similar monomers. For nearly seventy years after this reaction was identified, the product was assumed to be hexaphenylethane, but the compound did not behave the way hexaphenylethane should behave. Newer methods of analysis demonstrated that the structure of that particular dimer is not that of hexaphenylethane, and therefore the proposed mechanism for its formation in the reaction was wrong.

Reactions and Reaction Mechanisms

In any chemical reaction, atoms and molecules interact in certain ways, and any mechanism that describes the reaction is only one means of visualizing how their interaction may have transpired. Because reaction mechanisms are theoretical in nature, a given reaction mechanism can rarely if ever be proved to be the way in which the atoms and molecules have actually reacted. Even if a proposed mechanism accounts perfectly for the results of a reaction, it can only be said that those results were obtained because it is as though the atoms and molecules had interacted in that way.

Chemists visualize reaction mechanisms by drawing molecular structure diagrams and annotating them with standardized arrows that indicate the movement of electrons and orbitals. There are two main conventions used in drawing a proposed mechanism. The first is that the movement of two electrons from one orbital to another is shown by a curved arrow with a full, double-barbed arrowhead. The second is that the movement of individual electrons from one orbital to another is shown by a curved arrow with a half arrowhead. Thus, the formation of a bond between a chloride ion (Cl⁻) and the tert-butyl carbonium ion, producing tert-butyl chloride, would be drawn as

and the movement of the electrons in the diene and dienophile in a Diels-Alder reaction would be drawn as

With these two simple conventions, a great deal of information about a particular reaction can be communicated in a very compact form.

An overall reaction equation can be written as follows:

This equation represents a Robinson annulation reaction, which is a reaction that produces organic ring-shaped molecules. It identifies the initial reactants and the product but gives no information about the reaction conditions or any intermediary stages in the process. A mechanistic representation of just the first elementary reaction in the overall process would be drawn as

with several other elementary reactions following. For someone familiar with the conventions and the theoretical bases of the interactions, such diagrams very clearly communicate in a relatively small space concepts that would require several pages to describe in words.

When synthesizing complex molecules, such multistep procedures are the rule rather than the exception. The goal of each step in a multistep synthesis is to have complete control of the formation of the molecular structure of the product. A mechanistic reaction equation readily identifies all of the components of the reaction process, including transition states, reactive intermediates, catalysts (if present), and the activated complexes that may be involved in the overall reaction process.

Mechanisms and Kinetics

"Reaction kinetics" refers to the study of how reactions occur over time in relation to the amounts of reactants and products that are present in the reaction mixture. The amounts are expressed in terms of concentration, that is, the amount of a material that is present in a specific volume of the reaction mixture. The probable mechanism by which a reaction proceeds can often be discerned from the kinetic behavior of the reaction. Of particular interest in determining a reaction mechanism is the reaction step known as the rate-determining step. The overall rate of the reaction cannot be faster than the slowest reaction step in the mechanism. In cases where more than one mechanism can be reasonably proposed for a reaction, identification of the rate-determining step from the reaction kinetics can help identify which mechanism, if any, is more likely than the others to be accurate.

The presence of a catalyst alters the reaction kinetics by reducing the activation energy of the overall reaction, which is the energy that a chemical system must acquire in order for a reaction to proceed. It also changes the reaction mechanism because the catalyst is intimately involved in the reaction process along with the reactants, though it is not itself consumed in the reaction.

Reaction Mechanisms in Biological Systems

All biochemical reactions are mediated by enzymes. Due to the large size and complicated structures of enzymes, the mechanisms of enzyme-mediated reactions have a high level of complexity that is only found in biochemical environments. Essentially, the enzyme’s active site encloses the substrate (reactant) in such a way that it forms a closed system in which the substrate interacts with its environment to effect a chemical change. Various functional groups in the enzyme’s active site coordinate to both the substrate and any other molecule involved in the reaction. The individual steps of the overall reaction mechanism are therefore difficult to differentiate, since all steps take place in the same enzyme-substrate combination. Enzyme-mediated reactions exhibit characteristic kinetic behavior because of this intimate relationship.

PRINCIPAL TERMS

• activated complex: the various intermediate molecular structures that exist during a chemical reaction while the original chemical bonds are being broken and new bonds are being formed.
• elementary reaction: a chemical reaction that is completed in a single reaction step with only one transition state; often part of a multistep sequence of reactions that constitutes a mechanism.
• reaction step:a stage in a multistep reaction in which an elementary reaction converts either the reactants or a previously formed intermediate structure into either a new intermediate structure or the final products.
• reactive intermediate: a short-lived, highly reactive chemical species that is formed during an intermediate reaction step in a multistep reaction and typically cannot be isolated.
• transition state: an unstable structure formed during a chemical reaction at the peak of its potential energy that cannot be isolated and ultimately breaks down, either forming the products of the reaction or reverting back to the original reactants.

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