Transition structures stabilization

A structural anomaly in subtilisin has functional consequences Transition-state stabilization in subtilisin is dissected by protein engineering Catalysis occurs without a catalytic triad Substrate molecules provide catalytic groups in substrate-assisted catalysis Conclusion Selected readings... 

Calculations at several levels of theory (AMI, 6-31G, and MP2/6-31G ) find lower activation energies for the transition state leading to the observed product. The transition-state calculations presumably reflect the same structural features as the frontier orbital approach. The greatest transition-state stabilization should arise from the most favorable orbital interactions. As discussed earlier for Diels-Alder reactions, the-HSAB theory can also be applied to interpretation of the regiochemistry of 1,3-dipolar cycloaddi-... 

To summarize we have reproduced the intricate structural properties of the Fe-Co, Fe-Ni and the Fe-Cu alloys by means of LMTO-ASA-CPA theory. We conclude that the phase diagram of especially the Fe-Ni alloys is heavily influenced by short range order effects. The general trend of a bcc-fcc phase transition at lower Fe concentrations is in accordance with simple band Ailing effects from canonical band theory. Due to this the structural stability of the Fe-Co alloys may be understood from VGA and canonical band calculations, since the common band model is appropriate below the Fermi energy for this system. However, for the Fe-Ni and the Fe-Cu system this simple picture breaks down. 

S. Papadia, B. Piveteau, D. Spanjaard and M. C. Desjonqudres, Structural Stability of Adislands on FCC(lll) Transition Metal Surfaces, submitted... 

Figure 6.16 The hypothetical structure of a transition state for alkene protonalion. The transition slate is closer in both energy and structure to the carbocation than to the alkene. Thus, an increase in carbocation stability (lower AG°) also causes an increase in transition-state stability (lower AG >, thereby increasing the rate of its formation.

The rate acceleration achieved by enzymes is due to several factors. Particularly important is the ability of the enzyme to stabilize and thus lower the energy of the transition state(s). That is, it s not the ability of the enzyme to bind the substrate that matters but rather its ability to bind and thereby stabilize the transition state. Often, in fact, the enzyme binds the transition structure as much as 1012 times more tightly than it binds the substrate or products. As a result, the transition state is substantially lowered in energy. An energy diagram for an enzyme-catalyzed process might look like that in Figure 26.8. 

The Structural Stability of Transition Metal Oxide Insertion Electrodes for Lithium Batteries... 

This review focuses on the structural stability of transition metal oxides to lithium insertion/extraction rather than on their electrochemical performance. The reader should refer to cited publications to access relevant electrochemical data. Because of the vast number of papers on lithium metal oxides that have been published since the 1970s, only a selected list of references has been provided. 

Stamenkovic V, Mun BS, Blizanac BB, Mayrhofer KJJ, Ross PN Jr, Markovic NM. 2006a. The effect of surface composition on electronic structure, stability and electrocehmical properties of Pt-transition metal alloys Pt-skin vs. Pt-skeleton surfaces. J Am Chem Soc 137 1. 

The differences in the rate constant for the water reaction and the catalyzed reactions reside in the mole fraction of substrate present as near attack conformers (NACs).171 These results and knowledge of the importance of transition-state stabilization in other cases support a proposal that enzymes utilize both NAC and transition-state stabilization in the mix required for the most efficient catalysis. Using a combined QM/MM Monte Carlo/free-energy perturbation (MC/FEP) method, 82%, 57%, and 1% of chorismate conformers were found to be NAC structures (NACs) in water, methanol, and the gas phase, respectively.172 The fact that the reaction occurred faster in water than in methanol was attributed to greater stabilization of the TS in water by specific interactions with first-shell solvent molecules. The Claisen rearrangements of chorismate in water and at the active site of E. coli chorismate mutase have been compared.173 It follows that the efficiency of formation of NAC (7.8 kcal/mol) at the active site provides approximately 90% of the kinetic advantage of the enzymatic reaction as compared with the water reaction. 

The structural and chemical mechanisms used by enzymes to achieve transition state stabilization have been reviewed in detail elsewhere (e.g., see Jencks, 1969, Warshel, 1998, Cannon and Benkovic, 1998, Copeland, 2000, Copeland and Anderson, 2002 and Kraut et al., 2003). Four of the most common strategies used by enzymes for transition state stabilization—approximation, covalent catalysis, acid/base catalysis, and conformational distortion—are discussed below. 

In this chapter we have seen that enzymatic catalysis is initiated by the reversible interactions of a substrate molecule with the active site of the enzyme to form a non-covalent binary complex. The chemical transformation of the substrate to the product molecule occurs within the context of the enzyme active site subsequent to initial complex formation. We saw that the enormous rate enhancements for enzyme-catalyzed reactions are the result of specific mechanisms that enzymes use to achieve large reductions in the energy of activation associated with attainment of the reaction transition state structure. Stabilization of the reaction transition state in the context of the enzymatic reaction is the key contributor to both enzymatic rate enhancement and substrate specificity. We described several chemical strategies by which enzymes achieve this transition state stabilization. We also saw in this chapter that enzyme reactions are most commonly studied by following the kinetics of these reactions under steady state conditions. We defined three kinetic constants—kai KM, and kcJKM—that can be used to define the efficiency of enzymatic catalysis, and each reports on different portions of the enzymatic reaction pathway. Perturbations... 

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