Valence bond, empirical

For this reason, there has been much work on empirical potentials suitable for use on a wide range of systems. These take a sensible functional form with parameters fitted to reproduce available data. Many different potentials, known as molecular mechanics (MM) potentials, have been developed for ground-state organic and biochemical systems [58-60], They have the advantages of simplicity, and are transferable between systems, but do suffer firom inaccuracies and rigidity—no reactions are possible. Schemes have been developed to correct for these deficiencies. The empirical valence bond (EVB) method of Warshel [61,62], and the molecular mechanics-valence bond (MMVB) of Bemardi et al. [63,64] try to extend MM to include excited-state effects and reactions. The MMVB Hamiltonian is parameterized against CASSCF calculations, and is thus particularly suited to photochemistry. 

This chapter presents the implementaiton and applicable of a QM-MM method for studying enzyme-catalyzed reactions. The application of QM-MM methods to study solution-phase reactions has been reviewed elsewhere [44]. Similiarly, empirical valence bond methods, which have been successfully applied to studying enzymatic reactions by Warshel and coworkers [19,45], are not covered in this chapter. 

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... 

Empirical Valence Bond (EVB) [163,164] simulations as an alternative to Molecular Orbital based methods. 

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. ... 

In 1976 Warshel and Levitt introduced the idea of a hybrid QM/MM method [23] that treated a small part of a system (e.g., the solute) using a quantum mechanical representation, while the rest of the system, which did not need such a detailed description (e.g., the solvent) was represented by an empirical force field. These hybrid methods, in particular the empirical valence bond approach, were then used to study a wide variety of reactions in solution. The combined QM/MM methods use the MM method with the potential calculated ab initio [24]. 

These results can be interpreted successfully in terms of Pauling s valence bond order concept. In the framework of this model, a chemical bond between X and H in diatomic molecule XH or between H and B in a HB molecule can be characterized by empirical valence bond orders Pxh and Phb decreasing exponentially with bond distance ... 

A second important application of CMD has been to study the dynamics of the hydrated proton. This study involved extensive CMD simulations to determine the proton transport rate in on our Multi-State Empirical Valence Bond (MS-EVB) model for the hydrated proton. = Shown in Fig. 4 are results for the population correlation function, (n(t)n(O)), for the Eigen cation, HsO, in liquid water. Also shown is the correlation function for D3O+ in heavy water. It should be noted that the population correlation function is expected to decay exponentially at long times, the rate of which reflects the excess proton transport rate. The straight line fits (dotted lines) to the semi-log plots of the correlation functions give this rate. For the normal water case, the CMD simulation using the MS-EVB model yields excellent agreement with the experimental proton hopping... 

Abstract A mixed molecular orbital and valence bond (MOVE) method has been developed and applied to chemical reactions. In the MOVE method, a diabatic or valence bond (VE) state is defined with a block-localized wave function (ELW). Consequently, the adiabatic state can be described by the superposition of a set of critical adiabatic states. Test cases indicate the method is a viable alternative to the empirical valence bond (EVE) approach for defining solvent reaction coordinate in the combined qnantum mechanical and molecnlar mechanical (QM/MM) simulations employing exphcit molecular orbital methods. 

A method that has certain connections with QM/MM techniques even if it does not usually involve simultaneous evaluation of QM and MM operators during a particular calculation is the empirical valence bond method (EVB Warshel and Weiss 1980). At the heart of the EVB method is the notion diat arbitrarily complex reactions may be modeled as the influence of a surrounding environment on a fundamental process that may be represented by some combination of valence bond resonance structures. For example, tlie proton transfer from one water molecule to another may, at any point along the reaction path, be envisaged as involving some admixture of tlie two VB wave functions corresponding formally to... 

Advancement of MD Methods 2.4.1. Empirical Valence Bond Models... 

Valence bond (VB) theories or empirical valence bond (EVB) methods have been developed in order to solve this problem with bond potential functions that (i) allow the change of the valence bond network over time and (ii) are simple enough to be used efficiently in an otherwise classical MD simulation code. In an EVB scheme, the chemical bond in a dissociating molecule is described as the superposition of two states a less-polar bonded state and an ionic dissociated state. One of the descriptions is given by Walbran and Kornyshev in modeling of the water dissociation process.4,5 As... 

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