Catalysis computational studies

A variety of techniques have been applied to investigate enzyme reaction mechanisms. Kinetic and X-ray crystallographic studies have made major contributions to the elucidation of enzyme mechanisms. Valuable information has been gained from chanical, spectroscopic and biochemical studies of the transition-state structures and intermediates of enzyme catalysis. Computational studies provide necessary refinement toward our understanding of enzyme mechanisms. The ability of an enzyme to accelerate the rate of a chemical reaction derives from the complementarity of the enzyme s active site structure to the activated complex. The transition state by definition has a very short lifetime ( 10 s). Stabilization of the transition state alone is necessary but not sufficient to give catalysis, which requires differential binding of substrate and transition state. Thus a detailed enzyme reaction mechanism can be proposed only when kinetic, chemical and structural components have been studied. The online enzyme catalytic mechanism database is accessible at EzCatDB (http //mbs.cbrc.jp/EzCatDB/). 

D.A. Rudd, L.A. Apuvicio, J.E. Bekoske and A.A. Trevino, The Microkinetics of Heterogeneous Catalysis (1993), American Chemical Society, Washington DC]. Ideally, as many parameters as can be determined by surface science studies of adsorption and of elementary steps, as well as results from computational studies, are used as the input in a kinetic model, so that fitting of parameters, as employed in Section 7.2, can be avoided. We shall use the synthesis of ammonia as a worked example [P. Stoltze and J.K. Norskov, Phys. Rev. Lett. 55 (1985) 2502 J. Catal. 110 (1988) Ij. 

MD simulations can aid in the understanding of enzymic reactions by providing new insights into the structures and intermolecular interactions fundamental to the chemical catalysis. By studying the structures from the simulation of the lysozyme-(GlcNAc)g complex, we have proposed an alternative to the accepted mechanism which accounts for the available experimental observations. The proposal of this lysozyme mechanism illustrates one way in which simulations can serve to generate new ideas which can be explored by experiment and computation. 

Although Echavarren et al. reported similar conversions by platinum catalysis, lower selectivity was observed [165-167]. Computational studies then suggested the initial formation of a cyclopropyl carbenoid intermediate 213, as shown in Scheme 8.28. 

For a recent computational study to elucidate the catalytic function of cucurbit [6]uril in the 1,3-dipolar cycloaddition between an azide and an alkyne see Carlqvist, P. and Maseras, F. (2007) A theoretical analysis of a classic example of supramolecular catalysis. Chem. Commun., 748-750. 

DFT/MM methods currently seem to offer the best balance between computational cost and accuracy for the computational study of many of the systems of experimental interest to homogeneous catalysis. This does not mean that the theoretical work is always easy. In fact, the results summarized in this contribution show a varying degree of progress in the understanding of the different reactions, usually associated with the amount of ef-... 

As indicated from computational studies, the catalyst-activated iminium ion MM3-2 was expected to form with only the (E)-conformation to avoid nonbonding interactions between the substrate double bond and the gem-dimethyl substituents on the catalyst framework. In addition, the benzyl group of the imidazolidinone moiety should effectively shield the iminium-ion Si-face, leaving the Re-face exposed for enantioselective bond formation. The efficiency of chiral amine 1 in iminium catalysis was demonstrated by its successful application in several transformations such as enantioselective Diels-Alder reactions [6], nitrone additions [12], and Friedel-Crafts alkylations of pyrrole nucleophiles [13]. However, diminished reactivity was observed when indole and furan heteroaromatics where used for similar conjugate additions, causing the MacMillan group to embark upon studies to identify a more reactive and versatile amine catalyst. This led ultimately to the discovery of the second-generation imidazolidinone catalyst 3 (Fig. 3.1, bottom) [14],... 

Lim D, C Jenson, MP Repasky, WL Jorgenson (1999) Solvent as Catalyst Computational Studies of Organic Reactions in Solution. In Transition State Modeling for Catalysis, edited by D. G. Truhlar and K. Morokuma. Washington, DC American Chemical Society. 

A particularly thoughtful computational study of chain transfer mechanisms in olefin polymerization catalysis suggests that two distinct pathways exist for (1-hydrogen of a hydrogen from the growing chain to a second olefin, the classical path involving aM-H interaction and a direct transfer in which the metal does not participate directly. Whether a catalyst will display one or the other mechanism is determined by subtle effects that are discussed in detail in the paper.91... 

In a very recent computational study, Diggle et al. have calculated the activation barriers for C(aryl)-X activation (X = H, F, OH, NH, CH3) as 0 (H), 9 (F), 12 (OH), 20 (NH ) and 21.3 kcal mol (CH3), respectively [155]. In comparison, the activation barrier for C(sp3)-H is 6.6 kcal moF [156]. C-X activation occurs under reaction conditions relevant for homogenous catalysis [157], but does not always result in decomposition as C-H activation is often reversible and can be exploited in catalytic transfer hydrogenations involving alcohols [156]. 

One computational study see Molecular Orbital Theory) has appeared using RhCl(PH3)2 to model the rhodium-catalyzed hydroboration of ethylene see Hydroboration Catalysis). Both associative and dissociative pathways were examined (equation 47). In the associative path, three possible... 

Contemporary Boron Chemistry contains 80 reports in nine chapters. Clearly, since much research is interdisciplinary in nature, our decision to include a report in one particular section rather than another was sometimes an arbitrary one. With this caveat in mind, the sections are as follows Applications to Polyolefin Catalysis Materials and Polymers Medicinal Applications Cluster Synthesis Carboranes Metallaboranes Metallaheteroboranes Organic and Inorganic Chemistry of Mono- and Di-boron Systems and Theoretical and Computational Studies. 

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