Siting quantum mechanical approach

Quantum mechanical approaches have been successfully used to predict hydrogen abstraction potentials and likely sites of metabolism of drug molecules [78-81]. AMI, Fukui functions, and density functional theory calculations could identify potential sites of metabolism. Activation energies for hydrogen abstraction were calculated by Olsen et al. [81] to be below 80 kj/mol, suggesting most CH groups can be metabolized which particular one depends on steric accessibility and intrinsic reactivities. 

In one quantum mechanical approach based on the diabatic approximation , the electron is assumed to be confined initially at one of the reactant sites and electron transfer is treated as a transition between the vibrational levels of the reactants to those of the products. The quantum mechanical treatment begins with the time dependent Schrodinger equation, Hip = -ihSiplSt, where the wavefunction tj/ is written as a sum of the initial (reactant) and final (product) states. In the limit that the Bom-Oppenheimer approximation for the separation of electronic and nuclear motion is valid, the time dependent Schrodinger equation eventually leads to the Golden Rule result in equation (25). 

Overall, the quantum mechanical approach to uncovering the sources of enzyme catalysis is one of building up understanding by incrementally adding on models of portions of the enzyme environment (for example, a reaction field or an explicit model of an active site residue) in order to discover how they affect the activation parameters and detailed mechanism of the reaction in question, and whether these components of the enzymatic surroundings produce additive or synergistic effects when combined. 

Abstract The chemical activation of light alkanes by acidic zeolites was studied by a combined Classical Mechanics/Quantum Mechanics approach. The diffusion and adsorption steps were investigated by Molecular Mechanics, Molecular Dynamics and Monte Carlo simulations. The chemical reactions step was studied at the DPT (B3LYP) level with 6-31IG basis sets and 3T and 5T clusters to represent the acid site ofthe zeolite. 

Given recent developments in computer modeling of chemical reactions, there is considerable interest in attempting to develop a mathematical understanding of enzyme catalysis. The sheer complexity of enzymes means that at present, it is possible to apply a strict quantum mechanical approach to only a limited region, such as the active site, and classical molecular mechanics are used to describe the remainder of the molecule. This combined approach had some success in modeling some aspects of enzyme-catalyzed reactions, such as the importance of particular side chains in the catalytic process.However, a complete mathematical description of enzyme catalysis remains a considerable way off. 

The first quantum mechanical approach to the problem of siting of Fe in FAU was performed by Beran et al. [186]. They have modeled a FAU with Fe, Fe and Fe(OH)+ ions localized in Sn and Sf extra-framework positions or with Fe in the framework sites, using the CNDO/2 method on a cluster representing the six-membered ring opening. No difference was found for the framework properties when replacing Al with Fe and the framework Fe was predicted to be quite stable also in the presence of a reduction to Fe +. 

The MM approach contrasts with the quantum mechanical (QM) part of the modeling which is restricted to the immediate area of the active site and considers either all electrons (or sometimes just outer shell electrons) explicitly in arriving at a first principle evaluation by solving the Schrodinger equation to deduce the local potential energy surface for the active site. 

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