Molecular mechanics—valence bond dynamics

Molecular mechanics-valence bond dynamics have been used to study the model 4 + 4-photocycloadditions of butadiene with butadiene. The photoirradiation of t-butyl 9-anthroate and furan produces a mixture of 4 + 4-cycloadduct and 4 - - 4-cyclodimers. 

Molecular mechanics-valence bond dynamics have been used to study the model 4 +... 

Eckart conditions, Renner-Teller effect, triatomic molecules, 610-615 Ehrenfest dynamics, direct molecular dynamics error sources, 403—404 Gaussian wavepacket propagation, 378-383 molecular mechanics valence bond (MMVB), 409-411... 

Molecular mechanics valence bond (MMVB) conical intersection location, 489—490 direct molecular dynamics ... 

Bearpark MJ et al (2006) Excited states of conjugated hydrocarbons using the molecular mechanics-valence bond (MMVB) method Conical intersections and dynamics. Theor Chem Acc 116 670-682... 

Equation (4-5) can be directly utilized in statistical mechanical Monte Carlo and molecular dynamics simulations by choosing an appropriate QM model, balancing computational efficiency and accuracy, and MM force fields for biomacromolecules and the solvent water. Our group has extensively explored various QM/MM methods using different quantum models, ranging from semiempirical methods to ab initio molecular orbital and valence bond theories to density functional theory, applied to a wide range of applications in chemistry and biology. Some of these studies have been discussed before and they are not emphasized in this article. We focus on developments that have not been often discussed. 

The rich metric structure of macroscopic thermodynamics also presents unusually stringent tests of theoretical models. Attempts to understand thermodynamic phenomena at a molecular level seem to demand improved dynamical and quantum statistical thermodynamic models that adequately incorporate the subtleties of quantum-mechanical valency and bonding interactions. Development of such models is an active area of modem physical chemistry research, but a more complete survey of the current molecular theory of gases and liquids is beyond the scope of the present work. 

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... 

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],... 

Another fairly new method, using the electrostatic molecular potential, will not be discussed here since it is the subject of another contribution to this volume 50>. I will now consider methods that have had the widest application in the theoretical study of chemical reactivity, in order of increasing complexity a) molecular mechanics b) extended Htickel method c), d) empirical self-consistent field methods such as CNDO and MINDO e) the simplest ab initio approach f) the different S.C.F. methods, possibly including configuration interaction g) valence bond methods, and h) the dynamical approach, including the calculation of trajectories 61>. 

Computer simulations of excess proton conductivity in water have reached a powerful level [8,92,93,102]. Importantly, simulations extend to quantum-mechanical proton dynamic features, so that proton motion can be coupled to details of the molecular environmental dynamics. A recent feature article explored an analytical theory in order to rationalize these complex processes that involve interconversion of proton-bearing clusters and proton transfers [103]. With a simple two-state empirical valence bond model (see below for details), which implements in a classical way the above-mentioned idea of two limiting protonated structures, namely the 11502 and the H30 cluster, it was indeed observed that the two alternative sequences are equivalent with similar life times for both clusters, and that conversions between the two clusters are purely fluctuative. 

In the course of these studies, it was realized that the rotation of, for example, a backbone C—C bond in n-alkane produces periodical variation in the C—C bond length as well as in the C—C—X (X = H, C) valence angles . These observations are the most striking evidence for the molecular mechanics principle, wherein the dynamics of molecules is assumed to respond to a mechanical modeP . 

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