Catalysis quantum dynamics

Quantum dynamics effects for hydride transfer in enzyme catalysis have been analyzed by Alhambra et. al., 2000. This process is simulated using canonically variational transition-states for overbarrier dynamics and optimized multidimensional paths for tunneling. A system is divided into a primary zone (substrate-enzyme-coenzyme), which is embedded in a secondary zone (substrate-enzyme-coenzyme-solvent). The potential energy surface of the first zone is treated by quantum mechanical electronic structure methods, and protein, coenzyme, and solvent atoms by molecular mechanical force fields. The theory allows the calculation of Schaad-Swain exponents for primary (aprim) and secondary (asec) KIE... 

D. J. (2000) Quantum dynamics of hydride transfer in enzyme catalysis,... 

Elementary Molecule-Surface Scattering Processes Relevant to Heterogeneous Catalysis Insights from Quantum Dynamics Calculations... 

The important criterion thus becomes the ability of the enzyme to distort and thereby reduce barrier width, and not stabilisation of the transition state with concomitant reduction in barrier height (activation energy). We now describe theoretical approaches to enzymatic catalysis that have led to the development of dynamic barrier (width) tunneUing theories for hydrogen transfer. Indeed, enzymatic hydrogen tunnelling can be treated conceptually in a similar way to the well-established quantum theories for electron transfer in proteins. 

Wang S, Hu P, Zhang Y (2007) Ab initio quantum mechanical/molecular mechanical molecular dynamics simulation of enzyme catalysis the case of histone lysine methyltransferase set7/9. J Phys Chem B ASAP... 

A reaction looked at earlier simulates borate inhibition of serine proteinases.33 Resorufin acetate (234) is proposed as an attractive substrate to use with chymotrypsin since the absorbance of the product is several times more intense than that formed when the more usual p-nitrophcnyl acetate is used as a substrate. The steady-state values are the same for the two substrates, which is expected if the slow deacylation step involves a common intermediate. Experiments show that the acetate can bind to chymotrypsin other than at the active site.210 Brownian dynamics simulations of the encounter kinetics between the active site of an acetylcholinesterase and a charged substrate together with ah initio quantum chemical calculations using the 3-21G set to probe the transformation of the Michaelis complex into a covalently bound tetrahedral intermediate have been carried out.211 The Glu 199 residue located near the enzyme active triad boosts acetylcholinesterase activity by increasing the encounter rate due to the favourable modification of the electric field inside the enzyme and by stabilization of the TS for the first chemical step of catalysis.211... 

Multinuclear (isocyanide)gold complexes, reactivity, 2, 287 Multi-phase organometallic catalysis, in ionic liquids, 1, 856 Multiple-quantum MAS, half-integer spin quadrupolar nuclei central transition NMR studies, 1, 466 Multistate magnetization transfer, in dynamic NMR magnetization, 1, 410 Multistep catalytic cycles... 

From its inception, the combined Quantum Mechanics/Molecular Mechanics (QM/MM) method [1-3] has played an important roll in the explicit modeling of solvent [4], Whereas Molecular Mechanics (MM) methods on their own are generally only able to describe the effect of solvent on classical properties, QM/MM methods allow one to examine the effect of the solvent on solute properties that require a quantum mechanical (QM) description. In most cases, the solute, sometimes together with a few solvent molecules, is treated at the QM level of theory. The solvent molecules, except for those included in the QM region, are then treated with an MM force field. The resulting potential can be explored using Monte Carlo (MC) or Molecular Dynamics (MD) simulations. Besides the modeling of solvent, QM/MM methods have been particularly successful in the study of biochemical systems [5] and catalysis [6],... 

Bavykin, Dmitry V. is a Ph.D. researcher in the Laboratory of photocatalysis on semiconductors at the Boreskov Institute of Catalysis, Novosibirsk, Russia. The title of his PhD thesis (1998) Luminescent and photocatalytic properties of CdS nanocolloids . Area of his interests is the photophysical-photochemical properties of nanosized sulfide semiconductors, including synthesis of particles with definite size and surface properties, their characterisation the study of the photoexcited states dynamics, relaxation in quantum dots by the luminescence and flash photolysis measurements studies of the interfacial charge transfer from colloidal semiconductor particles by the steady state photolysis, luminescence quenching method. 

O. Tapia, Beyond standard quantum chemical semi-classic approaches Towards a quantum theory of enzyme catalysis, in P. Paneth, A. Dybala-Defratyka (Eds.), Kinetics and Dynamics, From nano- to bio-scale, Challenges and advances in computational chemistry and physics 12, Springer Science, Dordrecht, 2010, p. 267-298. 

The next section gives a brief overview of the main computational techniques currently applied to catalytic problems. These techniques include ab initio electronic structure calculations, (ab initio) molecular dynamics, and Monte Carlo methods. The next three sections are devoted to particular applications of these techniques to catalytic and electrocatalytic issues. We focus on the interaction of CO and hydrogen with metal and alloy surfaces, both from quantum-chemical and statistical-mechanical points of view, as these processes play an important role in fuel-cell catalysis. We also demonstrate the role of the solvent in electrocatalytic bondbreaking reactions, using molecular dynamics simulations as well as extensive electronic structure and ab initio molecular dynamics calculations. Monte Carlo simulations illustrate the importance of lateral interactions, mixing, and surface diffusion in obtaining a correct kinetic description of catalytic processes. Finally, we summarize the main conclusions and give an outlook of the role of computational chemistry in catalysis and electrocatalysis. 

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