Chapter 3. Quantum mechanical treatment of enzyme reactions

Náray‐Szabó, Gábor; Menyhárd, Dóra K.

doi:10.1039/pc094049

Cited by 1 publication

(4 citation statements)

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“…It is an old hypothesis that enzymes should be capable of efficiently catalyzing reactions with unfavorable entropies of activation by acting as "entropy traps;" this means that the binding energy of the enzyme is used to freeze out rotational and translational degrees of freedom by converting them to confined vibrations in the process of forming the activated complex. These effects may be smaller than previously thought since enzyme molecules are quite flexible, e.g., an examination of the entropic contribution to the rate acceleration of serine proteases indicate that this is a small effect (7).…”

Section: Transition State Theorymentioning

confidence: 98%

“…Enzymes, like other catalysts, usually work by stabilizing the corresponding transition states (7). Nevertheless, enzymatic reactions, like other types of catalysis, have their unique features.…”

Section: Catalytic Systemsmentioning

confidence: 99%

“…It is certainly not enough to obtain an accurate quantum mechanical description of the isolated substrate. In principle, one can model enzymatic reactions by QM/MM approaches using ab initio or semiempirical Hamiltonians, including the empirical valence bond (EVB) Hamiltonian (7). The EVB method is also called molecular-mechanics/valence-bond (MMVB); it involves creating a n x n configuration interaction matrix (where n is the number of configurations, typically 2 to 6, but in some cases as large as 14) with MM diabatic energies on the diagonal and a semiempirical expression for the nonzero couplings.…”

Section: Catalytic Systemsmentioning

confidence: 99%

“…Owing to their relative mathematical simplicity molecular mechanics and classical trajectory studies may be applied with explicit consideration of all components; however full models of practically important systems are beyond the scope of quantum mechanical methods. A more and more popular approach to quantum mechanical modeling is partitioning of the catalytic system (substrate interactions with an enzyme, zeolite pore, solid surface, or solvent) into various regions (1)(2)(3)(4)(5)(6)(7)(8). The active site or central machinery (C) is surrounded by a polarizable environment (P) which is embedded in a non-polarizable region (N) and solvent (S).…”

mentioning

confidence: 99%

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Quantum Catalysis: The Modeling of Catalytic Transition States

Hall

Margl

Náray‐Szabó

et al. 1999

ACS Symposium Series

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We present an introduction to the computational modeling of transition states for catalytic reactions. We consider both homogeneous catalysis and heterogeneous catalysis, including organometallic catalysts, enzymes, zeolites and metal oxides, and metal surfaces. We summarize successes, promising approaches, and problems. We attempt to delineate the key issues and summarize the current status of our understanding of these issues. Topics covered include basis sets, classical trajectories, cluster calculations, combined quantum -mechanical/molecular-mechanical (QM/MM) methods, density functional theory, electrostatics, empirical valence bond theory, free energies of activation, frictional effects and nonequilibrium solvation, kinetic isotope effects, localized orbitals at surfaces, the reliability of correlated electronic structure calculations, the role of d orbitals in transition metals, transition state geometries, and tunneling.Computational chemistry has achieved great strides in recent years, and it has become a strong partner with experimental methods, displacing purely analytic theory almost completely. The essential element in computational chemistry is the use of very general theoretical frameworks that can be applied broadly across a number of fields. Examples are molecular orbital theory, molecular mechanics, transition state theory, 2

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Section: Transition State Theorymentioning

confidence: 98%

Section: Catalytic Systemsmentioning

confidence: 99%