Organic computational chemistry

The organic computational chemistry that so dazzled our allegorical eyes-wide-open chemist is based on the combined efforts of a large number of theoretical and experimental chemists over the last few decades. This combined experience has resulted, only... 

So then, what is the role of these, sometimes discouraging, always ponderous, calculations Does it make sense to expend so much time, effort, and money in return for these hard-earned results Yes Already the impact of these calculations on inorganic, or organometallic chemistry has been sizeable. How will, or should, this field evolve If one looks to the history of organic computational chemistry then at least some partial answers to such questions can be formulated. The theory, the methodology, and the computer programs that implement both, will evolve, and... 

I. Pettersson, T. Liljefors, Molecular mechanics calculated conformational energies of organic molecules a comparison of force fields, in Reviews in Computational Chemistry, Vbl. 9,... 

Price S L 2000. Towards More Accurate Model Intermolecular Potentials for Organic Molecules. Ii Lipkowitz K B and D B Boyd (Editors). Reviews in Computational Chemistry Volume 14. Nev York, VCH Publishers, pp. 225-289. 

Karfunkel H R and R J Gdanitz 1992. Ah initio Prediction of Possible Crystal Structures for General Organic Molecules. Journal of Computational Chemistry 13 1171-1183. 

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. 

Organic molecule calculations can be done routinely to good accuracy on workstation-class hardware. It is advisable to examine tabulations of results in order to choose a method with acceptable accuracy and computational time for the property of interest. The trend toward having microcomputer versions of computational chemistry codes is making calculations on small organic molecules even more readily accessible. 

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. ... 

Three different types of chemical mechanisms have evolved as attempts to simplify organic atmospheric chemistry surrogate (58,59), lumped (60—63), and carbon bond (64—66). These mechanisms were developed primarily to study the formation of and NO2 in photochemical smog, but can be extended to compute the concentrations of other pollutants, such as those leading to acid deposition (40,42). 

The methods of organic synthesis have continued to advance rapidly and we have made an effort to reflect those advances in this Fifth Edition. Among the broad areas that have seen major developments are enantioselective reactions and transition metal catalysis. Computational chemistry is having an expanding impact on synthetic chemistry by evaluating the energy profiles of mechanisms and providing structural representation of unobservable intermediates and transition states. 

Wiest, O., 1998, Transition States in Organic Chemistry Ab Initio in Encyclopedia of Computational Chemistry, Schleyer, P. v. R. (Editor-in-Chief), Wiley, Chichester. 

Robb MA, Garavelli M, Olivucci M, Bernardi F (2000) A computational strategy for organic photochemistry. In Lipkowitz KB Boyd DB (eds) Reviews in computational chemistry, vol. 15 Wiley-VCH, New York pp 87-146... 

The use of computational methods for the calculation of molecular properties has been a perennial goal of chemists. In recent years, the field of computational chemistry has become a firmly established discipline. Computational chemists have made impressive contributions to almost every aspect of chemistry, ranging from structural organic and inorganic chemistry to the prediction of polymer properties and the design of medicinally important therapeutic agents. While many computer-based methods are robust and widely utilized, the continued development and refinement of software and the underlying theory remains an active area of research.1,2... 

J. M. Blaney, V. Nienaber and S. K. Burley, Fragment-based lead discovery and optimization using X-ray crystallography, computational chemistry, and high throughput organic synthesis, in... 

The size of the atoms and the rigidity of the bonds, bond angles, torsions, etc. are determined empirically, that is, they are chosen to reproduce experimental data. Electrons are not part of the MM description, and as a result, several key chemical phenomena cannot be reproduced by this method. Nevertheless, MM methods are orders of magnitude cheaper from a computational point of view than quantum mechanical (QM) methods, and because of this, they have found a preferential position in a number of areas of computational chemistry, like conformational analysis of organic compounds or molecular dynamics. 

In fact, Chemoinformatics is a generic term that encompasses the design, creation, organization, management, retrieval, analysis, dissemination, visualization and use of chemical information. Related terms of chemoinformatics are cheminformatics, chemi-informatics, chemometrics, computational chemistry, chemical informatics, and chemical information management/science. 

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