How Computational Chemistry Is Used

It has recently been shown that computational chemistry methods can provide the accuracy required to reliably solve complex environmental problems but accuracy significantly increases the computational demands. Examples of how computational chemistry is being used to impact environmental science include the following ... 

Quantum mechanics gives a mathematical description of the behavior of electrons that has never been found to be wrong. However, the quantum mechanical equations have never been solved exactly for any chemical system other than the hydrogen atom. Thus, the entire held of computational chemistry is built around approximate solutions. Some of these solutions are very crude and others are expected to be more accurate than any experiment that has yet been conducted. There are several implications of this situation. First, computational chemists require a knowledge of each approximation being used and how accurate the results are expected to be. Second, obtaining very accurate results requires extremely powerful computers. Third, if the equations can be solved analytically, much of the work now done on supercomputers could be performed faster and more accurately on a PC. 

This chapter describes an area of research that is finding new uses every day. The tools of computational chemistry—computers and software—have become so ubiquitous that there are few chemists left today who have not heard of them or used them. However, the reader may reasonably ask Why is there a chapter on computational chemistry in a book on stress testing of pharmaceutically interesting compounds The reason does not lie in a vast number of papers crying for review. Indeed, relatively little work has been published in this area thus far. So what is the reason The objective of this chapter is to increase awareness of how computational chemistry can be used by pharmaceutical chemists to help confront some of the research problems they face in stress testing research. Hence, the nature of this chapter is intended to be primarily tutorial... and perhaps with a little proselytizing for increased use of the powerful techniques of computational chemistry now available. 

In making the selections for Table 1, we used the broad w orking definitions of computational chemistry given elsewhere.The quantitative modeling of chemical phenomena by computer-implemented techniques is how we view the scope of the field, so it includes practically all aspects of chemical research that are expedited or rendered practical by computers. The scope of computational chemistry is thus set very wide. 

About 100 articles have been published in the chemical literature that describe the use of some variant of the GA, most of which have appeared in the last few years. A GA has been used in just about ever imaginable subfield of computational chemistry where optimization is called for, so a complete review of the use of GAs in the chemistry literature would entail something of a survey of all of computational chemistry. That is a bigger task than is undertaken here, so only some representative uses of the GA have been chosen, with an emphasis on how the GA is useful or on novel twists on the GA that are required in different contexts. For more information on the chemistry behind the applications, the original papers cited should provide good starting points. 

In this review, we have shown how computational chemistry can be used to successfully predict the important effects the environment has on properties and processes of (supra)molecular systems. The overview of the theoretical methods and the computational tools available is necessarily not exhaustive. However, those selected exemplify the most reliable and accurate protocols available for a correct comparison with the experiments. All of them are based on a multiscale strategy, where the whole system is partitioned into distinct but interacting parts, described at different levels of accuracy. Here, in particular, we have mostly focused on those multiscale strategies which combine a quantum chemical description with classical models. These strategies have shown to be extremely effective both in terms of the ratio of computational cost to accuracy, and their extensibility to systems of increasing complexity. We believe that these hybrid QM/classical approaches will continue to play a dominant role, even if the incredibly fast developments in the QM methods on one side and in the computational tools on the other side are rapidly extending the dimension of the QM part of the systems towards a reahsm which has never been reached before. 

This discussion may well leave one wondering what role reality plays in computation chemistry. Only some things are known exactly. For example, the quantum mechanical description of the hydrogen atom matches the observed spectrum as accurately as any experiment ever done. If an approximation is used, one must ask how accurate an answer should be. Computations of the energetics of molecules and reactions often attempt to attain what is called chemical accuracy, meaning an error of less than about 1 kcal/mol. This is suf-hcient to describe van der Waals interactions, the weakest interaction considered to affect most chemistry. Most chemists have no use for answers more accurate than this. 

When using computational chemistry to answer a chemical question, the obvious problem is that the researcher needs to know how to use the software. The difficulty sometimes overlooked is that one must estimate how accurate the answer will be in advance. The sections below provide a checklist to follow. 

Software tools for computational chemistry are often based on empirical information. To use these tools, you need to understand how the technique is implemented and the nature of the database used to parameterize the method. You use this knowledge to determine the most appropriate tools for specific investigations and to define the limits of confidence in results. 

This part describes the essentials of HyperChem s theoretical and computational chemistry or how HyperChem performs chemical calculations that you request from the Setup and Compute menus. While it has pedagogical value, it is not a textbook of computational chemistry the discussions are restricted to topics of immediate relevance to HyperChem only. Nevertheless, you can learn much about computational chemistry by reading this manual while using HyperChem. 

It is interesting to consider the meanings of the terms of ab initio calculations as well as the closely related term first principles calculations . How are these terms currently used by the computational chemistry community Do these terms mean the same thing ... 

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