Model organisms

Jorgenson W 1989 Free energy calculations a breakthrough in modeling organic chemistry in solution Accounts Chem. Res. 22 184... 

Dubois L FI and Nuzzo R G 1992 Synthesis, structure, and properties of model organic surfaces Annu. Rev. Phys. Chem. 43 437-63... 

Dubois L FI, Zegarski B R and Nuzzo R G 1990 Temperature induced reconstruction of model organic-surfaces J. Eiectron Spectrosc. Reiat. Phenom. 54/55 1143-52... 

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. 

Many semiempirical methods have been created for modeling organic compounds. These methods correctly predict many aspects of electronic structure, such as aromaticity. Furthermore, these orbital-based methods give additional information about the compounds, such as population analysis. There are also good techniques for including solvation elfects in some semiempirical calculations. Semiempirical methods are discussed further in Chapter 4. 

Modeling the elements discussed in this section is fairly similar to modeling organic compounds. This is primarily because d and/orbitals play a minor role in their chemistry. When d and/ orbitals do affect the chemistry, their effect is well defined and for the most part understood. 

Modeling the lighter main group inorganic compounds is similar to modeling organic compounds. Thus, the choice of method and basis set is nearly identical. The second-row compounds (i.e., sulfur) do have unfilled d orbitals, making it often necessary to use basis sets with d functions. 

A few of the methods available are applicable to inorganic compounds. These include the PM3/TM method. However, the program is most useful for modeling organic compounds due to a lack of technical features often needed to contend with spin contamination, convergence failure, and so forth. 

Gaussian has seen the widest use in modeling organic molecules. However, there are also options for handling many of the difficulties that can be encoun-... 

Littman, B. H., and Williams, S. A. (2005). The ultimate model organism Progress in experimental medicine. Nature Rev. Drug Disc. 4 631-638. 

Kielbasa W, Fung HL Pharmacokinetics of a model organic nitrite inhalant and its alcohol metabolite in rats. Drug Metab Dispos 28 386-391, 2000... 

Cobb JA, Bjergbaek L (2006) RecQ heUcases lessons from model organisms. Nucleic Acids Res 34 4106 114... 

Schaffner, K. F. (1998), Genes, behavior and developmental emergentism one process, indivisible Model organisms and behavioral genetics a rejoinder , Philos. Sci, 65, 209-252 276-288. 

Jorgensen, W. L. Free energy calculations, a breakthrough for modeling organic chemistry in solution. Acc. Chem. Res. 1989, 22, 184-189... 

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