Energy empirical valence bond

The approach presented above is referred to as the empirical valence bond (EVB) method (Ref. 6). This approach exploits the simple physical picture of the VB model which allows for a convenient representation of the diagonal matrix elements by classical force fields and convenient incorporation of realistic solvent models in the solute Hamiltonian. A key point about the EVB method is its unique calibration using well-defined experimental information. That is, after evaluating the free-energy surface with the initial parameter a , we can use conveniently the fact that the free energy of the proton transfer reaction is given by... 

Electrostatic stabilization, 181, 195,225-228 Empirical valence bond model, see Valence bond model, empirical Energy minimization methods, 114-117 computer programs for, 128-132 convergence of, 115 local vr. overall minima, 116-117 use in protein structure determination,... 

Warshel is to utilize a formula identical to (11.22) in this chapter to compute the free energy change. They employed an empirical valence bond (EVB, below) approach to approximately model electronic effects, and the calculations included the full experimental structure of carbonic anhydrase. An H/D isotope effect of 3.9 1.0 was obtained in the calculation, which compared favorably with the experimental value of 3.8. This benchmark calculation gives optimism that quantum effects on free energies can be realistically modeled for complex biochemical systems. 

The empirical valence bond (EVB) method of Warshel [19] has features of both the structurally and thermodynamically coupled QM/MM method. In the EVB method the different states of the process studied are described in terms of relevant covalent and ionic resonance structures. The potential energy surface of the QM system is calibrated to reproduce the known experimental... 

The empirical valence bond (EVB) approach introduced by Warshel and co-workers is an effective way to incorporate environmental effects on breaking and making of chemical bonds in solution. It is based on parame-terizations of empirical interactions between reactant states, product states, and, where appropriate, a number of intermediate states. The interaction parameters, corresponding to off-diagonal matrix elements of the classical Hamiltonian, are calibrated by ab initio potential energy surfaces in solu-fion and relevant experimental data. This procedure significantly reduces the computational expenses of molecular level calculations in comparison to direct ab initio calculations. The EVB approach thus provides a powerful avenue for studying chemical reactions and proton transfer events in complex media, with a multitude of applications in catalysis, biochemistry, and PEMs. 

Molecular dynamics free-energy perturbation simulations utilizing the empirical valence bond model have been used to study the catalytic action of -cyclodextrin in ester hydrolysis. Reaction routes for nucleophilic attack on m-f-butylphenyl acetate (225) by the secondary alkoxide ions 0(2) and 0(3) of cyclodextrin giving the R and S stereoisomers of ester tetrahedral intermediate were examined. Only the reaction path leading to the S isomer at 0(2) shows an activation barrier that is lower (by about 3kcal mol ) than the barrier for the corresponding reference reaction in water. The calculated rate acceleration was in excellent agreement with experimental data. ... 

W. Wu, S. J. Zhong, S. Shaik, Chem. Phys. Lett. 292, 7 (1998). VBDFT(s) A Hiickel-Type Semi-empirical Valence Bond Method Scaled to Density Functional Energies. Application to Linear Polyenes. 

Marelius J, Kolmodin K, Feierberg I, Aqvist J (1998) Q a molecular dynamics program for free energy calculations and empirical valence bond simulations in biomolecular systems. J Mol Graph Model 16(4-6) 213-225, 261... 

The Knudsen effusion method In conjunction with mass spectrometrlc analysis has been used to determine the bond energies and appearance potentials of diatomic metals and small metallic clusters. The experimental bond energies are reported and Interpreted In terms of various empirical models of bonding, such as the Pauling model of a polar single bond, the empirical valence bond model for certain multiply-bonded dlatomlcs, the atomic cell model, and bond additivity concepts. The stability of positive Ions of metal molecules Is also discussed. 

The use of empirical models of bonding has been Invaluable for the interpretation of the experimental dissociation energies of diatomrLc Intermetallic molecules as well as for the prediction of the bond energies of new molecules. In the course of our work, conducted for over a decade, we have extended the applicability of the Pauling model of a polar single bond (31) and have developed new models such as the empirical valence bond model for certain multiple bonded transition metal molecules (32,33) and the atomic cell model (34). 

A comparison of experimental values for intermetallic diatomic molecules with gold with the corresponding value calculated by the Pauling model and by the atomic cell model has been given in Table 6 of Reference ( ). Table 7 of Reference ( ) shows a comparison between experimental dissociation energies with values calculated by the atomic cell model and the empirical valence bond model. Table 9 of Reference ( ) takes Mledema s refinements (43) of the atomic cell model into account In these comparisons. 

Warshel and collaborators (Warshel and Sussman, 1986 Warshel et al., 1988) developed the empirical valence bond method for obtaining free-energy differences and activation free energies. The effects of Gly-to-Ala mutations in trypsin were accurately simulated. This method was earlier applied to calculation of the potential surface for general acid catalysis of a disaccharide in solution and bound to lysozyme (Warshel and Weiss, 1980). 

Molecular dynamics simulations of enzyme reactions have been performed successfully with semiempirical QM/MM methods [54,57,64,72] (see section 6). The sampling provided by such QM/MM molecular dynamics simulations may be used to calculate activation free energies (and to address dynamical effects on the reaction). Thus, semiempirical QM/MM simulations have an important role to play. It has been suggested that a mapping procedure can be used to calculate ab initio QM/MM reaction free energies from empirical valence bond simulations [39,176]. This approach shows promise, but calculation of energies within the QM system (as opposed to its interaction with its surroundings) from such a simulation remains problematic. 

Chang, Y.-T. and Miller, W.H. (1990) An Empirical Valence Bond Model for Constructing Global Potential Energy Surfaces for Chemical Reactions of Polyatomic Molecular Systems, J. Phys. Chem. 94, 5884-5888. 

Sawaryn and Sokalski (1979) considered the MEP of a few amino-acid residues around the active site and suggested that the Zn24 and OH" ions stabilise the transition state of the reaction. Unfortunately, the mechanism studied involves an attack of water rather than hydroxyl on C02 and the calculation did not treat correctly the protein dielectrics. The crucial role of the Zn2f cation and its local environment was determined quantitatively by the Empirical Valence Bond/Free Energy Perturbation study ofAqvist and Warshel (1992) and Aqvist et al. (1993). This study demonstrated... 

Quantitative study of this system was reported by Yadav et al. (1991). This study performed a careful Empirical Valence Bond/Free Energy Perturbation calcula-... 

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