Transition structure computational approaches

Investigations of enzyme-catalyzed direct electron transfer introduce the basis for a future generation of electrocatalysts based on enzyme mimics. This avenue could offer new methods of synthesis for nonprecious metal electrocatalysts, based on nano-structured (for example, sol—gel-derived) molecular imprints from a biological catalyst (enzyme) with pronounced and, in some cases, unique electrocatalytic properties. Computational approaches to the study of transition state stabilization by biocatalysts has led to the concept of theozymes . " ... 

The excellent agreement with the experimental and calculated isotope effect (calculated for formaldehyde, 3.22, and for acetaldehyde, 3.3 experimental value 2.9) supports the computational approach. This suggests that the computed transition structure for hydride transfer in the reaction of the lithium enolate of acetone with acetaldehyde (Figure 30) is realistic. 

Calculations of time-dependent electromagnetic properties of molecules at the correlated electronic structure level are conveniently carried out by the utilization of modern response theory [43-51], The transition of modern response theory for gas phase molecular systems to solvated molecules has been established [1-6] and these methods include the use of correlated electronic wavefunctions. These methods, reviewed here, have given rise a large number of computational approaches for calculating electric and magnetic molecular properties of solvated molecules. 

In one approach, the free energies of binding, out of water into the enzyme active site, of the reactant(s) and transition structure are computed, in order to see if rate acceleration can be explained by selective binding of the transition structure. However, there are several caveats associated with such an approach. First, it must be decided whether to use the same reactant and transition state structures in solution and in the enzyme. If the same structures are used, then the potential for catalysis specifically by selective transition state binding can be quantified. Of course, the actual enzyme-bound structures may be different than those in aqueous solution, and... 

In the ideal case, both of these approaches are applied to the same reaction. The reaction coordinate in the enzyme is computed directly, and then the binding energies of the reactant(s) and transition structure(s) obtained from these calculations are themselves computed. 

The physical chemical properties of proteins inform their function and as such have been the object of intense investigation for over 50 years. Indeed, major progress in the understanding of protein structure, dynamics and thermodynamics, as well as their inter-relationships has been made thanks to advances in experimental and computational approaches. Despite this gain in fundamental understanding, a complete description of the factors that control these properties has not been achieved. In particular, the characterization of the role of solvent in controlling protein conformational transitions and stability remains to be accomplished [1]. 

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