Organic chemistry computer modelling

The widespread use of molecular modeling in the curriculum is both inevitable and desirable. Chemistry itself is one of the most symbolically based of the academic disciplines, and it is the organic chemistry course that develops spatial concepts that are the foundation of more sophisticated symbolic manipulation for advanced organic chemistry, computational chemistry, biology, biochemistry, and inorganic chemistry. Turro captured the many ways in which chemists utilize symbolic manipulation, as shown in Figure 1. 

Organic chemistry is a very visual science and computer modeling is making it even more so... 

In computational chemistry it can be very useful to have a generic model that you can apply to any situation. Even if less accurate, such a computational tool is very useful for comparing results between molecules and certainly lowers the level of pain in using a model from one that almost always fails. The MM+ force field is meant to apply to general organic chemistry more than the other force fields of HyperChem, which really focus on proteins and nucleic acids. HyperChem includes a default scheme such that when MM+ fails to find a force constant (more generally, force field parameter), HyperChem substitutes a default value. This occurs universally with the periodic table so all conceivable molecules will allow computations. Whether or not the results of such a calculation are realistic can only be determined by close examination of the default parameters and the particular molecular situation. ... 

Molecular modeling has evolved as a synthesis of techniques from a number of disciplines—organic chemistry, medicinal chemistry, physical chemistry, chemical physics, computer science, mathematics, and statistics. With the development of quantum mechanics (1,2) ia the early 1900s, the laws of physics necessary to relate molecular electronic stmcture to observable properties were defined. In a confluence of related developments, engineering and the national defense both played roles ia the development of computing machinery itself ia the United States (3). This evolution had a direct impact on computing ia chemistry, as the newly developed devices could be appHed to problems ia chemistry, permitting solutions to problems previously considered intractable. 

H. B. Schlegel and M. J. Frisch, Computational Bottlenecks in Molecular Orbital Calculations, in Theoretical and Computational Models for Organic Chemistry, ed. S. J. Formosinho et. al. (Kluwer Academic Pubs., NATO-ASI Series C 339, The Netherlands, 1991), 5-33. 

This workbook contains over 200 problems that will allow you to build and refine your understanding of chemistry from the molecule s eye view . This is achieved by basing every problem on a set of molecular models that you view and manipulate on your own personal computer. We believe that this combination of problems-i-models will improve your understanding of molecular structure and the relationship between molecular structure and other properties. More importantly, we believe that when you do the problems in this workbook you will gain a much better grasp of the conceptual basis of organic chemistry, and that this will make the rest of your study of organic chemistry more satisfactory and ultimately more successful. 

Mezey, P.G. (1991) New symmetry theorems and similarity rules for transition structures. In Theoretical and Computational Models for Organic Chemistry, Formosinho, SJ. Csizmadia, I.G. and Amaut, L.G. (Eds.), Kluwer Academic Publishers, Dordrecht. 

N. Allinger in S.J. Formoshino, I.G. Csizmadia and L.G. Arnaut (eds.), Theoretical and Computational Models for Organic Chemistry, 1991, Nato ASI Series C339, Kluwer, Dordrecht. 

Computer modeling of enzyme catalysis and its relationship to concepts in physical organic chemistry, 40, 201... 

The volume is organized in thirteen chapters. The first of them makes a brief overview of the computational methods available for this field of chemistry, and each of the other twelve chapters reviews the application of computational modeling to a particular catalytic process. Their authors are leading researchers in the field, and because of this, they give the reader a first hand knowledge on the state of the art. 

Chemists routinely manipulate physical models in an attempt to ascertain what actually occurs during a conformational change. A successful example of this is in showing first-time students of organic chemistry that interconversion between anti and gauche conformers of w-butane involves a simple rotation about the central carbon-carbon bond (see discussion in Chapter 1). Much less satisfactory is the attempt to show the interconversion of chair forms of cyclohexane. Here, computer animations provide a better alternative. 

Once a chemical submodel has been developed, it must be tested extensively prior to its application in comprehensive computer models of an air basin or region. This is done by testing the chemical submodel predictions against the results of environmental chamber experiments. While agreement with the chamber experiments is necessary to have some confidence in the model, such agreement is not sufficient to confirm that the chemistry is indeed correct and applicable to real-world air masses. Some of the uncertainties include those introduced by condensing the organic reactions, uncertainties in kinetics and mechanisms of key reactions (e.g., of aromatics), and how to take into account chamber-specific effects such as the unknown radical source. 

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