Appendix. Software Packages

This appendix is not intended to provide a comprehensive listing of computational chemistry software packages. Some of the software packages listed here are included because they are very widely used. Others are included because they pertained to topics discussed in this book. A few relevant pieces of software were omitted because we were not able to obtain an evaluation copy prior to publication. 

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There are numerous articles and references on computational research studies. If none exist for the task at hand, the researcher may have to guess which method to use based on its assumptions. It is then prudent to perform a short study to verify the method s accuracy before applying it to an unknown. When an expert predicts an error or best method without the benefit of prior related research, he or she should have a fair amount of knowledge about available options A savvy researcher must know the merits and drawbacks of various methods and software packages in order to make an informed choice. The bibliography at the end of this chapter lists sources for reviewing accuracy data. Appendix A of this book provides short reviews of many software packages. 

Some of these software packages also have semiempirical or molecular mechanics functionality. However, the primary strength of each is ah initio calculation. There are also ah initio programs bundled with the Unichem, Spartan, and Hyperchem products discussed previously in this appendix. 

We conclude this chapter with a few illustrative color plates. Simple B W graphics are sufficient for viewing CA only in the special case when sites take on one of two values. In all other cases, color is indispensable for visualizing the behavior of the system. The plates were produced using the freely available CA software packages MCell, Cellab and WinCA. See Appendix A CA Research Tools for a description of these programs and links to web sites from which they can be HnwnlnnHpH... 

Conventional SEC calculations were performed with the SEC software package GPCl (Chromatix). As described below a universal calibration was carried out to obtain the peak position molecular weight at each V a modified version of GPCl then was used to calculate weight-and number-average molecular weights for the sample fraction at V (Appendix). 

We have attempted to collect in appendix B a list of the most used thermochemical databases. Each one has been built with a particular class of substances and a specific set of properties in mind. We can find compilations of thermochemical values for gas-phase ions, for condensed and gas-phase pure organic compounds, for organometallic molecules, for gas-phase organic free radicals, for inorganic substances, and so on. Most are available in printed form, some are distributed in a software package, and a few can be used online, through the World Wide Web. 

A widely used mathematical tool for PCA is SVD which is a standard method implemented in many mathematical software packages (see also Appendix A.2.7). According to SVD, any matrix X (size nxm) can be decomposed into a product of three matrices (Figure 3.11). 

Use SPARTAN (see Appendix J) or some other software package to answer the following ... 

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