Valence bonds molecular system simulations

In this article, we present an ab initio approach, suitable for condensed phase simulations, that combines Hartree-Fock molecular orbital theory and modem valence bond theory which is termed as MOVB to describe the potential energy surface (PES) for reactive systems. We first provide a briefreview of the block-localized wave function (BLW) method that is used to define diabatic electronic states. Then, the MOVB model is presented in association with combined QM/MM simulations. The method is demonstrated by model proton transfer reactions in the gas phase and solution as well as a model Sn2 reaction in water. 

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... 

Solvent effects can significantly influence the function and reactivity of organic molecules.1 Because of the complexity and size of the molecular system, it presents a great challenge in theoretical chemistry to accurately calculate the rates for complex reactions in solution. Although continuum solvation models that treat the solvent as a structureless medium with a characteristic dielectric constant have been successfully used for studying solvent effects,2,3 these methods do not provide detailed information on specific intermolecular interactions. An alternative approach is to use statistical mechanical Monte Carlo and molecular dynamics simulation to model solute-solvent interactions explicitly.4 8 In this article, we review a combined quantum mechanical and molecular mechanical (QM/MM) method that couples molecular orbital and valence bond theories, called the MOVB method, to determine the free energy reaction profiles, or potentials of mean force (PMF), for chemical reactions in solution. We apply the combined QM-MOVB/MM method to... 

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. 

In order to obtain more insight into the dynamics, molecular dynamics (MD) simulations of similar slit systems have been performed [62-64], Since ab initio MD methods are not applicable, an effort was made to incorporate the Grotthus mechanism into the MD simulations via a simplified empirical valence bond (EVB) model [65],... 

In early applications of the molecular mechanics method, an evident difficulty was that when the simple expression 2.6a was used, force constants were not transferable even among closely related systems. It was soon realized that the influence of some interaction between atoms not bound together but bound to the same atom (the geminal or 1-3 interactions) or, more generally, also between all other non-bonded atoms, had to be somehow considered. These supplementary non-bonded terms were to represent the change in chemical environment that could not be accounted for when using completely transferable force constants. The Urey-Bradley force field adds these interactions to a valence force field that includes only diagonal terms [4]. For application to molecular mechanics calculations, these non-bonded interactions were simulated by some function of the interatomic distance ... 

To address these questions, molecular dynamics simulations were carried out for a simple benchmark symmetric S 2 reaction. Cl -I- CH3 Cl - CH3CI-I-CI, at different locations of the water/chloroform interface. The reaction was modeled using the Empirical Valence Bond (EVB) approach. Briefly, EVB assumes the electronic state of the reactive system can be described using two orthonormal valence states, y/-[ = C1 CH3-C1 and y/2 = Cl-CHjClr... 

Computational methodology has been used to accompany or to anticipate experimental results for many classes of compounds. Such results are particularly helpful for transient species, for rationalization of physical and structural properties, and for simulation of reaction pathways and transition states. Semiempirical valence electron (CNDO/MNDO), ab initio, and nonquantum mechanical force field (molecular mechanics) calculations have mainly been used for the examination of structure and stability of moderately strained olefins, whereas many-electron quantum-chemical methods have been used for detailed discussion of electronic aspects. Excellent reviews of molecular mechanics calculations, the principal method used to describe geometrical and energy features in distorted double bond systems, have been written by Osawa and Musso (61). 

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