Quantum and molecular mechanical

Csjmhined Quantum and Molecular Mechanics Methods J. Gao, M. Thompson, Eds., American Chemical Society, Washington (1998). 

The setup of these calculations is very similar for both quantum and molecular mechanics. In practice, molecular dynamics calculation s using the nl) initio and semi-empirical quantum mechanical SCFmethods are limited to relatively small systems. Each time step requires a complete calculation of the wave function and the forces. 

Combined Quantum and Molecular Mechanical Simulations. A recentiy developed technique is one wherein a molecular dynamics simulation includes the treatment of some part of the system with a quantum mechanical technique. This approach, QM/MM, is similar to the coupled quantum and molecular mechanical methods introduced by Warshel and Karplus (45) and at the heart of the MMI, MMP2, and MM3 programs by AUinger (60). These latter programs use quantum mechanical methods to treat the TT-systems of the stmctures in question separately from the sigma framework. 

S. Piofeta, Ji., Conformational Analysis of Aliphatic Amines by Quantum and Molecular Mechanical Methods, Pb.D. Dissertation, University of Georgia, 1978, available from University Microfilms International, Arm Arbor, Mich. 

Tab. 12.2 Combined ab initio quantum and molecular mechanical simulations of solvation of acetate and methylammonium ions in aqueous solution.

P. L. Cummins and J. E. Gready, Combined quantum and molecular mechanics... 

Bash, P. A., Field, M. J. and Karplus, M. Free energy perturbation method for chemical reactions in the condensed phase a dynamical approach based on a combined quantum and molecular mechanics potential,... 

Quantitative XPS, 24 92-94 Quantum and molecular mechanical simulations, combined, 76 750-751 Quantum condition equation, 23 803 Quantum cellular automata (QCA),... 

Simulations, combined quantum and molecular mechanical, 16 750-751 Simultaneous proportioning, 26 249-251 Simvastatin, 2 821-822, 5 143... 

Ryde, U. 2003. Combined Quantum and Molecular Mechanics Calculations on Metalloproteins Curr. Opin. Chem. Biol., 7, 136. 

There has been a decisive evolution in the treatment of steric effects in heteroaromatic chemistry. The quantitative estimation of the role of steric strain in reactivity was first made mostly with the help of linear free energy relationships. This method remains easy and helpful, but the basic observation is that the description of a substituent by only one parameter, whatever its empirical or geometrical origin, will describe the total bulk of the substituent and not its conformationally dependent shape. A better knowledge of static and dynamic stereochemistry has helped greatly in understanding not only intramolecular but also intermolecular steric effects associated with rates and equilibria. Quantum and molecular mechanics calculations will certainly be used in the future to a greater extent. 

Bash, P.A., Field M.J. and Karplus M., Free Energy Perturbation Method for Chemical Reactions in the Condensed Phase A Dynamical Approach Based on a Combined Quantum and Molecular Mechanics Potential. J. Am. Chem.Soc. (1987) 109 8092-8094. 

Gao, J., Hybrid Quantum and Molecular Mechanical Simulations An Alternative Avenue to Solvent Effects in Organic Chemistry. Accounts of Chemcal Research (1996) 29 298-305. 

Eurenius, K. R Chatfleld, D. C. Brooks, B. R. Hodoscek, M. Enzyme mechanisms with hybrid quantum and molecular mechanical potentials. I. Theoretical considerations, Int. J. Quant. Chem. 1996, 60, 1189-1200. 

Deerfield, D. W., Nicholas, H. B. J., Hiskey, R. G., and Pedersen, L. G., Salt or ion bridges in biological systems A study employing quantum and molecular mechanics. Proteins Struct. Func. Genetics 6,168-192(1989). 

Simulations Using Combined Quantum and Molecular Mechanical Potentials. J. Gao, in Reviews in Computational Chemistry, Vol. 7, in press. 

Molecular modeling is a term used to describe a series of techniques that employ both quantum and molecular mechanics in conjunction with computer simulations to study the chemical and physical properties of a material (1). This approach offers a wide range of benefits to industry shortens product develojHnent cycles, reduces production costs, improves product properties and key solid-state structures, and properties that cannot be examined by experimental techniques may be predicted and studied by computer. Following is a brief review of the fundamentals of modeling crystalline systems. 

There arc fundamental dil fcrcnees between the quantum and molecular mechanics approaches. They illustrate the dilemma that cun confront the medicinal chemist. Quantum mechanics is derived from basic theoretical principles at the atomic level. The model itself is exact, but the equations used in the technique are only approximate. The molecular properties are derived from the electronic structure of the molecule. The assumption is made that the distribution of electrons within a molecule can be described by a linear. sum of functions that represent an atomic orbital. (For carbon, this would be s./>,./>,. etc.) Quantum mechanics i.s computation intensive, with the calculation time for obtaining an approximate solution increasing by approximately N time.s. where N i.s the number of such functions. Until the advent of the high-.speed supercomputers, quantum mechanics in its pure form was re.stricted to small molecules. In other words, it was not practical to conduct a quantum mechanical analysis of a drug molecule. 

Gao, J. (1996). Hybrid quantum and molecular mechanical simulations an alternative avenue to solvent effects in organic chemistry. Acc. Chem. Res. 29, 298-305... 

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