Computational chemistry caveat

This section provides a brief discussion of technical issues pertaining to modeling organic molecules. The bibliography focuses on pertinent review literature. Many computational chemistry methods can be applied to organic molecules. However, there are a few caveats to note as discussed here. 

For this and other caveats regarding the multistep methods see Cramer CJ (2004) Essentials of computational chemistry, 2nd edn. Wiley, Chichester, UK, pp 241-244... 

In today s world of ever-increasing importance and penetration of computational chemistry, it is instructive to quote Gay-Lussac [77] We are perhaps not far removed from the time when we shall be able to submit the bulk of chemical phenomena to calculation. This statement is not only remarkable for its prescience but to us it is also a caveat. Today we are closer to Gay-Lussac s target by more than a century but it is still far away for many purposes. 

Before going further, we offer some important caveats about the results obtainable. First, this chapter does not encompass every conceivable computational chemistry program. Thousands of programs are now in use, and it is impractical to track every one. An attempt is made to cover programs many readers would find of most interest. In the future, additional programs of interest can be covered. 

On the subject of how much impact computational chemists have on the scientific community, a quantifiable measure of a person s contribution to a scientific field, besides the physical mass of one s publications, is the number of citations to a person s papers. It is usually assumed that the more popular a new method, or the more valuable new data, the more the work will be used and cited by subsequent authors. Thus, the number of citations has become one of many measures of the scientific community s assessment of the merits of a person s work. However, critics point to various faults with citation frequency data. For example, some scientists can have a profound and lasting influence on a field of research and still not be the most highly cited. Some scientists can be highly cited and not have much influence beyond their own sphere of interest. Self citation can inflate numbers. Another caveat about citation rankings arises from how the ISI database stores a person s identity. If two or more people share the same last name and initial(s), then they could be miscounted as the same person. Conversely, if an author uses two initials in some papers and only one initial in other papers, then that person could be counted as two different individuals. Furthermore, if a person s name changes or if a person s name is misspelled or spelled inconsistently in citations, that person s citations could look misleadingly low. Fortunately, most of the well-known computational chemists have individualistic names. Further discussion of the issues associated with citation analysis can be found elsewhere. Citation frequency in the field of computational chemistry was earlier analyzed in this book series. ... 

The majority of studies aimed at understanding the mechanisms of ethylene epoxidation rely on either experimental physical chemistry studies of single crystal-silver surfaces or computational studies looking at enthalpies of different reaction states. One unfortunate caveat of the experimental studies lies in the fact that the binding of ethylene to the silver surface is too weak for ultrahigh vacuum (UHV) studies to be of any use. Therefore, the majority of silver surface epoxidation reactions use olefins that stick to the surface better both before and after epoxidation (e.g., butadiene or styrene). 

Contemporary Boron Chemistry contains 80 reports in nine chapters. Clearly, since much research is interdisciplinary in nature, our decision to include a report in one particular section rather than another was sometimes an arbitrary one. With this caveat in mind, the sections are as follows Applications to Polyolefin Catalysis Materials and Polymers Medicinal Applications Cluster Synthesis Carboranes Metallaboranes Metallaheteroboranes Organic and Inorganic Chemistry of Mono- and Di-boron Systems and Theoretical and Computational Studies. 

This chapter outlines the premises for attempting a 3D-QSAR model, illustrating some of the difficulties and biases related to obtaining high-quality target property values, as well as some of the caveats related to 3D-QSAR models in the context of computational medicinal chemistry. Introductions to the 3D-QSAR procedures are available for CoMFA [26-28], while 3D-QSAR models and techniques have been recently reviewed critically [29-34]. The reader is kindly referred to those texts for further detail. 

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