Molecular mechanics description

T. K. Firman, C. R. Landis, J. Am. Chem. Soc. 123, 11728 (2001). Valence Bond Concepts Applied to the Molecular Mechanics Description of Molecular Shapes. 4. Transition Metals with rr-Bonds. 

D.M. Root, C.R. Landis, T. Cleveland, Valence bond concepts applied to the molecular mechanics description of molecular shapes. 1. Application to nonhypervalent molecules of the P-block, J. Am. Chem. Soc.,1993 (115) 4201 - 4209. 

Quantum chemical methods aim to treat the fundamental quantum mechanics of electronic structure, and so can be used to model chemical reactions. Such quantum chemical methods are more flexible and more generally applicable than molecular mechanics methods, and so are often preferable and can be easier to apply. The major problem with electronic structure calculations on enzymes is presented by the very large computational resources required, which significantly limits the size of the system that can be treated. To overcome this problem, small models of enzyme active sites can be studied in isolation (and perhaps with an approximate model of solvation). Alternatively, a quantum chemical treatment of the enzyme active site can be combined with a molecular mechanics description of the protein and solvent environment the QM/MM approach. Both will be described below. 

Also, metal ion directed stereoselective syntheses often involve organometallic complexes. While, in terms of a molecular-mechanics description of the structures, there is no fundamental difference between metal-carbon and metal-heteroatom bonds, modeling rc-bonded ligands is not trivial. Given a known reaction mechanism (which is not possible for many catalytic reactions) the main problem is the parameterization of the potential energy functions for the intermediates and transition states. The problem is that force field parameters are generally carefully... 

This method uses quantum mechanical and molecular mechanics descriptions for different parts of the system, and it has proven to be successful in the quantification of steric effects in a munber of organometaUic applications... 

Relating Structures and Energies A Molecular Mechanics Description of Proteins... 

The most important computational models in use today for proteins are based on a molecular mechanics description. They represent the protein as a collection of spherical particles (the atoms), approximately incompressible, connected together by springs, each one bearing a small electric charge [30, 44]. Solvent molecules can be described in the same way. To parameterize such a model for a large class of molecules like proteins takes several decades of researcher-years. Once in place, and despite its simplicity, a molecular mechanics model is a powerful tool to study the structure and stability of biomolecules. 

It should be noted that these embedding schemes are closely related to the QM/MM approaches (quantum mechanical description of the active site and molecular mechanics description of the environment) [54] which are currently widely used in the treatment of homogeneous catalysis and in particular biocatalysis [55]. It should also be mentioned that many different schemes have been proposed for embedding quantum clusters into metallic substrates... 

As particular implementations of these principles we have demonstrated how the effective electronic Hamiltonian approach can be applied to the purpose of junction construction. It has required the use of a quantum chemical description underlying the molecular mechanics description. The APSLG-type trial wave function was used for this description. 

Applied to Molecular Mechanics Description of Molecular Shapes. 4. Transition Metals... 

In this paper we present an overview of the various strategies developed to insert a quantum computation on the chemically active part of a large system into a molecular mechanical description, leading to the so-called QM/MM approaches, with a particular emphasis on the Local Self Consistent Field method developed in our group. 

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