Computational chemistry, small molecule

GAs or other methods from evolutionary computation are applied in various fields of chemistry Its tasks include the geometry optimization of conformations of small molecules, the elaboration of models for the prediction of properties or biological activities, the design of molecules de novo, the analysis of the interaction of proteins and their ligands, or the selection of descriptors [18]. The last application is explained briefly in Section 9.7.6. 

A R 1991, A Survey of Methods for Searching the Conformational Space of Small and Medium-iized Molecules. In Lipkowitz K B and D B Boyd (Editors) Reviews in Computational Chemistry /olume 2. New York, VCH Publishers, pp. 1-55. 

Judson R S, W P Jaeger, A M Treasurywala and M L Peterson 1993. Conformational Searching Methods for Small Molecules. 2. Genetic Algorithm Approach. Journal of Computational Chemistry 14 1407-1414. 

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. 

When addressing problems in computational chemistry, the choice of computational scheme depends on the applicability of the method (i.e. the types of atoms and/or molecules, and the type of property, that can be treated satisfactorily) and the size of the system to be investigated. In biochemical applications the method of choice - if we are interested in the dynamics and effects of temperature on an entire protein with, say, 10,000 atoms - will be to run a classical molecular dynamics (MD) simulation. The key problem then becomes that of choosing a relevant force field in which the different atomic interactions are described. If, on the other hand, we are interested in electronic and/or spectroscopic properties or explicit bond breaking and bond formation in an enzymatic active site, we must resort to a quantum chemical methodology in which electrons are treated explicitly. These phenomena are usually highly localized, and thus only involve a small number of chemical groups compared with the complete macromolecule. 

An understanding of the recognition of chirality at a molecular level has become of interest in many fields of chemistry and biology. In the past decade, many attempts to clarify the mechanism of chiral recognition on CSPs for liquid chromatography have been made by means of chromatography, NMR spectroscopy,199 202 X-ray analysis, and computational methods.203 - 206 The successful studies have been mostly carried out for the small-molecule CSPs, especially cyclodextrin-based CSPs and Pirkle-type (brush-type) CSPs. In contrast, only a few mechanistic studies on chiral discrimination at the molecular... 

Quantum chemistry aims to understand a large variety of chemical facts. In some systems an interesting feature was obtained whose study and whose application can help to reduce the computational effort considerably this is the transferability. Transfer-ability can be interpreted in several ways. The orbitals, on the one hand, may be considered transferable in the case when certain properties of these orbitals are close to each other to a certain extent (Rothenberg, 1971). The transferability of orbitals can be discussed directly on the other hand too. Orbitals of small molecules can be used for constructing the wave-function of related, larger molecules. This can be done with or without further optimizations. In this interpretation the orbitals are transferable if the molecular properties calculated with and without optimizations are close to each other (O Leary et al, 1975). The transferability of orbitals for cyclic hydrocarbons was discussed exhaustively (Edmiston et al., 1963). 

Leach, A.R.(1991)A survey of methods for searching the conformational space of small and medium-sized molecules. In Reviews in computational chemistry, Lipkowitz, K. B. and Boyd, D. B. (eds.), VCH Publishers, New York, Vol. 2, pp. 1-55. 

In the next two subsections, we describe collections of calculations that have been used to probe the physical accuracy of plane-wave DFT calculations. An important feature of plane-wave calculations is that they can be applied to bulk materials and other situations where the localized basis set approaches of molecular quantum chemistry are computationally impractical. To develop benchmarks for the performance of plane-wave methods for these properties, they must be compared with accurate experimental data. One of the reasons that benchmarking efforts for molecular quantum chemistry have been so successful is that very large collections of high-precision experimental data are available for small molecules. Data sets of similar size are not always available for the properties of interest in plane-wave DFT calculations, and this has limited the number of studies that have been performed with the aim of comparing predictions from plane-wave DFT with quantitative experimental information from a large number of materials. There are, of course, many hundreds of comparisons that have been made with individual experimental measurements. If you follow our advice and become familiar with the state-of-the-art literature in your particular area of interest, you will find examples of this kind. Below, we collect a number of examples where efforts have been made to compare the accuracy of plane-wave DFT calculations against systematic collections of experimental data. 

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