Computational chemistry molecular mechanics

Computational Chemistry Molecular Mechanics and Quantum Mechanics... 

Over the span of two decades, molecular modeling has emerged as a viable and powerful approach to chemistry. Molecular mechanics calculations coupled with computer graphics are now widely used in lieu of tactile models to visualize molecular shape and quantify steric demands. Quantum chemical calculations, once a mere novelty, continue to play an ever increasing role in chemical research and teaching. They offer the real promise of being able to complement experiment as a means to uncover and explore new chemistry. 

The scope of computational chemistry can be inferred from the methodologies it encompasses. Some of the more common tools include computer graphics, molecular modeling, quantum chemistry, molecular mechanics (MM), statistical analysis of structure-property relationships, and data management (informatics). As with any dynamic field of research, computational... 

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... 

Fifth in rank in Figure 6 is molecular modeling . This is another general term with multiple meanings and can imply manipulating three-dimensional (3D) structures of molecules on a computer screen, molecular mechanics, and even QSAR and quantum chemistry, which are other ways to model chemical structures. 

The computations used molecular mechanical treatment of the mini-ciystal lattice for the preceding and various further reactions. As noted earlier, however, the weakness of molecular mechanics in dealing with such chemistry is that electronic effects are not included in the calculations. This is true for any open-shell reaction. 

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. 

The chapter is outlined as follows. First we present some curriculum issues related to molecular modeling and to quantum chemistry. Then we give a brief introduction to the fields of quantum chemistry, molecular mechanics, and molecular dynamics. Following this, we survey the use of molecular mechanics in the curriculum, particularly as it relates to articles that have appeared in the Journal of Chemical Education. Finally, we each present material that outlines our use of computers in the curriculum. This approach allows us to review the literature in each of the areas we cover. We each teach in an undergraduate institution, but many of the topics we discuss also can be included in a graduate course, albeit at a greater depth than at the undergraduate level. 

Before turning to specific applications at our institutions, we present a brief theoretical section on each of the three areas of quantum chemistry, molecular mechanics, and molecular dynamics. Our plan is that these theory sections will present the context in which our applications take place. This is to emphasize our contention that computational exercises should not take place without adequate background into the theory behind the exercise. Otherwise the user will treat the computer as a blackbox. At the least the user needs to appreciate what kinds of chemical questions can be answered by particular computational methodologies. 

At one point in the history of structural chemistry molecular mechanics calculations dominated the computational work for relatively large molecules. The origins of these calculations were intimately connected to another modeling approach that one of its initiators vividly described. Frank Westheimer (Fig. 1.2a) had participated in the American defense efforts during WWII and when the war had ended, he returned to the University of Chicago to resume his teaching and research. He had to start anew and had time to think about basic problems. This is how half a century later he remembered the birth of molecular mechanics [5] ... 

Key words computational chemistry, molecular dynamics, poly(ethylene oxide), Li mobility mechanism, perfluorosulphonic acid membranes. Nation, proton transport, battery, fuel cell. 

I. Pettersson, T. Liljefors, Molecular mechanics calculated conformational energies of organic molecules a comparison of force fields, in Reviews in Computational Chemistry, Vbl. 9,... 

M. Jalaie, K. B. Lipkowitz, Published force field parameters for molecular mechanics, molecular dynamics, and Monte Carlo simulations, in Reviews in Computational Chemistry, Vol. 14, K.B. Lipkowitz, D. B. Boyd (Eds.), Wiley-VCH, New York, 2000, pp. 441-486. 

Many of llic i(Jc isati(J insucs sii non rutin g ihc use of molecular mechanics (or force field technology) in computational chemistry are common to all force fields and in this section we describe many of Lli esc basic ideas. 

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... 

Bowen J P and N L Allinger 1991. Molecular Mechanics The Art and Science of Parameterisation. I Lipkowitz K B and D B Boyd (Editors). Reviews in Computational Chemistry Volume 2. New Yorl VCH Publishers, pp. 81-97. 

Amara P and M J Field 1998. Combined Quantum Mechanical and Molecular Mechanical Potentials. In Schleyer, P v R, N L Allinger, T Clark, J Gasteiger, P A Kolhnan H F Schaefer HI and P R Schreiner (Editors). The Encyclopedia of Computational Chemistry. Chichester, John Wiley Sons. 

Field M J, P A Bash and M Karplus 1990. A Combined Quantum Mechanical and Molecular Mechanical Potential for Molecular Dynamics Simulations. Journal of Computational Chemistry 11 700-733. 

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