Computational chemistry molecular mechanics methods

Despite the availability of fast computers and efficient codes for accurate quantum chemistry calculations, it is not likely in the near future that we will be able to study chemical reactions in proteins taking all the proteins atoms into quantum mechanical calculations. Hybrid methods in which different parts of large molecular systems are treated by different theoretical levels of methods are likely to play a key role in such studies for the coming decade or more. The ONIOM method we have developed is a versatile hybrid method that allows combining different quantum mechanical methods as well as molecular mechanics method in multiple layers, some features of... 

There are many computational chemistry software packages available that enable students to make and study the properties of molecules, by quantum mechanics and molecular mechanics methods. These include Gaussian, HyperChem, Spartan, and Biosym. The first four homework problems assume that the student has one of... 

The credit load for die computational chemistry laboratory course requires that the average student should be able to complete almost all of the work required for the course within die time constraint of one four-hour laboratory period per week. This constraint limits the material covered in the course. Four principal computational methods have been identified as being of primary importance in the practice of chemistry and thus in the education of chemistry students (1) Monte Carlo Methods, (2) Molecular Mechanics Methods, (3) Molecular Dynamics Simulations, and (4) Quantum Chemical Calculations. Clearly, other important topics could be added when time permits. These four methods are developed as separate units, in each case beginning with die fundamental principles including simple programming and visualization, and building to the sophisticated application of the technique to a chemical problem. 

Chapter 1 outlined the tools that computational chemists have at their disposal, Chapter 2 set the stage for the application of these tools to the exploration of potential energy surfaces, and Chapter 3 introduced one of these tools, molecular mechanics. In this chapter you will be introduced to quantum mechanics, and to quantum chemistry, the application of quantum mechanics to chemistry. Molecular mechanics is based on classical physics, physics before modern physics one of the cornerstones of modem physics is quantum mechanics, and ab initio (Chapter 5), semiempirical (Chapter 6), and density functional (Chapter 7) methods belong to quantum chemistry. This chapter is designed to ease the way to an understanding of... 

EVA descriptors were recently proposed by Ferguson et al. [Ferguson et al, 1997 Turner et al., 1997] as a new approach to extract chemical structural information from mid- and near-infrared spectra. The approach is to use, as a multivariate descriptor, the vibrational frequencies of a molecule, a fundamental molecular property characterized reliably and easily from the potential energy function. The EigenVAIue (EVA) descriptor is a function of the eigenvalues obtained from the normal coordinate matrix they correspond to the fundamental vibrational frequencies of the molecule, which can be calculated using standard quantum or molecular mechanical methods from -> computational chemistry. 

Thus it was not only the ab initio methods, but also less exacting procedures—model-based—such as the semiempirical molecular orbital and empirical molecular mechanics methods that developed, as outlined above, that contributed to today s computational chemistry. 

Smgh U C and P A Kollman 1986. A Combined Ab Initio Quantum Mechamcal and Molecular Mechanical Method for Carrying out Simulations on Complex Molecular Systems Applications to the CHsQ + Q Exchange Reachon and Gas Phase Protonation of Polyethers. Journal of Computational Chemistry 7-718-730... 

Initially computational chemistry mainly referred to the more applied aspects of quantum chemistry. Computational chemistry now encompasses a wide variety of areas, which include quantum chemistry, molecular mechanics, molecular dynamics, Monte Carlo methods. Brownian dynamics, continuum electrostatics, reaction dynamics, numerical analysis methods, artificial intelligence, chemometrics and others. This chapter deals mainly with the first three of these areas. We focus on these areas for reasons of space, personal interest, and expertise, and because two of these (quantum mechanics and molecular mechanics) are areas that have received attention in the Journal of Chemical Education. We do not cover aspects related to computational polymer chemistry or computational materials science. 

Molecular mechanics has become a standard method in computational chemistry and is extensively used to solve problems in organic chemistry, in medicinal chemistry, and in many other areas of chemistry. Today, sophisticated computer graphics interfaces are generally used in connection with molecular mechanics calculations. The molecule to be studied may conveniently be constructed on the computer screen and the setup for the calculation may be done simply by choosing one or several computational options displayed by the graphics interface. In addition, various molecular mechanics methods are implemented on personal desktop computers or small workstations. This technological advance has drastically increased access to molecular mechanics calcu-... 

There is a lot of confusion over the meaning of the terms theoretical chemistry, computational chemistry and molecular modelling. Indeed, many practitioners use all three labels to describe aspects of their research, as the occasion demands "Theoretical chemistry is often considered synonymous with quantum mechanics, whereas computational chemistry encompasses not only quantum mechanics but also molecular mechaiucs, minimisation, simulations, conformational analysis and other computer-based methods for understanding and predicting the behaviour of molecular systems. Molecular modellers use all of these methods and so we shall not concern ourselves with semantics but rather shall consider any theoretical or computational tecluiique that provides insight into the behaviour of molecular systems to be an example of molecular modelling. If a distinction has to be... 

Gao J 1995. Methods and Applications of Combined Quantum Mechanical and Molecular Mechanical Potentials. In Lipkowitz K B and D B Boyd (Editors) Reviews in Computational Chemistry Volume 7. New York, VCH Publishers, pp. 119-185. 

Tripos a molecular mechanics force field, also the name of a company that sells computational chemistry software TST (transition state theory) method for computing rate constants UHF (unrestricted Hartree-Fock)... 

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