Quantum and molecular mechanical QM/MM

Ranganathan S, Gready JE. Hybrid quantum and molecular mechanical (QM/MM) studies of the pyruvate to L-lactate interconversion in L-lactate dehydrogenase. J Phys Chem B 1997 101 5614-5618. 

Cummins PL, Gready JE. Combined quantum and molecular mechanics (QM/MM) study of the ionization state of 8-methylpteridin substrate bound to dihydrofolate reductase. J Phys Chem B 2000 104 4503-4510. 

Acevedo O, Jorgensen WL (2010) Advances in quantum and molecular mechanical (QM/ MM) simulations for organic and enzymatic reactions. Acc Chem Res 43 142-151... 

Numerous theoretical studies on both early and late transition metal SSCs have appeared in recent years covering nearly all aspects of the olefin polymerization process (for reviews, see Refs. 282 and 283). The employed methodologies include molecular mechanics (284-291), ah initio electronic structure methods (292-297), density functional studies (298-303), as well as various hybrid techniques (304-308), such as the combination of quantum and molecular mechanics (QM/MM). A detailed description of these studies is outside the scope of this article nevertheless, these theoretical investigations have played a major role in elucidating the elementary steps of olefin complexation, chain propagation, and chain termination as well as the mechanisms of stereocontrol in catalytic olefin polymerization. 

Acevedo O, Jorgensen WL (2010) Advances in quantum and molecular mechanical (QM/ MM) simulations for organic and enzymatic reactions. Acc Chem Res 43 142-151 Bands P, Jurecka P, Walter NG, Sponer J, Otyepka M (2009) Theoretical studies of RNA catalysis hybrid QM/MM methods and their comparison with MD and QM. Methods 49 202... 

Quantum mechanics is essential for studying enzymatic processes [1-3]. Depending on the specific problem of interest, there are different requirements on the level of theory used and the scale of treatment involved. This ranges from the simplest cluster representation of the active site, modeled by the most accurate quantum chemical methods, to a hybrid description of the biomacromolecular catalyst by quantum mechanics and molecular mechanics (QM/MM) [1], to the full treatment of the entire enzyme-solvent system by a fully quantum-mechanical force field [4-8], In addition, the time-evolution of the macromolecular system can be modeled purely by classical mechanics in molecular dynamicssimulations, whereas the explicit incorporation... 

In order to examine the nature of the unusual geometric distortions observed in the X-ray structures of complexes 3 and 4, we have performed a series of density functional theory (DFT) and combined quantum mechanics and molecular mechanics (QM/MM) calculations [22-27], Although the computational resources to wholly treat both 3 and 4 at the DFT level are available, we have employed the combined QM/MM method to unravel the... 

In this and subsequent sections, we investigate the reaction mechanism of the palladium catalyzed hydrosilylation of styrene via ah initio molecular dynamics and combined quantum mechanics and molecular mechanics (QM/MM) techniques. Both methodologies constitute powerful approaches for the study of the catalytic activity and selectivity of transition metal... 

Abstract A mixed molecular orbital and valence bond (MOVB) method has been developed and applied to chemical reactions. In the MOVB method, a diabatic or valence bond (VB) state is defined with a block-localized wave function (BLW). 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 (EVB) approach for defining solvent reaction coordinate in the combined quantum mechanical and molecular mechanical (QM/MM) simulations employing explicit molecular orbital methods. 

A very promising methodology bridging quantum mechanics and molecular mechanics (QM/MM), allowing the mechanisms of enzymatic reactions to be analyzed in detail, has been reviewed in the fifth chapter by Mulholland and Grant. 

The atomic radii may be further refined to improve the agreement between experimental and theoretical solvation free energies. Work on this direction has been done by Luque and Orozco (see [66] and references cited therein) while Barone et al. [67] defined a set of rules to estimate atomic radii. Further discussion on this point can be found in the review by Tomasi and co-workers [15], It must be noted that the parameterization of atomic radii on the basis of a good experiment-theory agreement of solvation energies is problematic because of the difficulty to separate electrostatic and non-electrostatic terms. The comparison of continuum calculations with statistical simulations provides another way to check the validity of cavity definition. A comparison between continuum and classical Monte Carlo simulations was reported by Costa-Cabral et al. [68] in the early 1980s and more recently, molecular dynamics simulations using combined quantum mechanics and molecular mechanics (QM/MM) force-fields have been carried out to analyze the case of water molecule in liquid water [69],... 

Addressing large molecular systems is the aim of Chapter 3, which reviews a recently developed model based on the combined use of quantum mechanics and molecular mechanics (QM/MM). This approach uses a fully self-consistent polarizable embedding (PE) scheme described in the paper. The PE model is generally compatible with any quantum chemical method, but this review is focused on its combination with density functional theory (DFT) and time-dependent density functional theory (TD-DFT). The PE method is based on the use of an electrostatic embedding potential resulting from the permanent charge distribution of the classically treated part of... 

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... 

Bioinformatic tools are of increasing importance for the characterization of flavoenzymes. This finding holds for protein sequence and protein structural analysis as well as for gaining insight into the reactivity of the flavin cofactor by combined quantum mechanical and molecular mechanical (QM/MM) simulations (12). 

A widely used type of multiscale simulation combines quantum mechanical and molecular mechanical (QM/MM) simulations. In this approach, the functional core of the molecular system, for example, the catalytic sites of an enzyme, is described at the electronic level (QM region), whereas the surrounding macromolecular system is treated using a classical description (MM region). Some of the biological applications for which QM/MM calculations have been widely utilized are chemical reactions in enzymes, proton transfer in proteins and optical excitations. In QM/MM... 

Diels-Alder reactionsJ Using a combined quantum-mechanical and molecular-mechanical (QM/MM) potential, Gao carried out Monte Carlo simulations to investigate the hydrophobic and hydrogenbonding effects on Diels-Alder reactions in aqueous solution. Enhanced hydrogen-bonding interaction and the hydrophobic effect were found to contribute to the transition-state stabilization. The number of hydrogen bonds was found to cause strong Coulomb interaction and discriminate heats of formation of transition states for exo/endo products. 

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