Structure generation problem description

Many types of energy calculations have been applied in CSP studies, starting from the simplest atom-atom descriptions of interactions. While fairly simple brute force (grid and random strncture generation) approaches are often suc-cessfnl at addressing the crystal structure generation problem, the assessment of relative energies requires the development of sophisticated methods to achieve the required accuracy for CSP. One approach has been the development of more elaborate, anisotropic (nonspherical) atom-atom models." Recently, the application of QM solid-state electronic strncture calculations has also been demonstrated to be very successful. " ... 

As already mentioned in Section 2.9, automatic 3D structure t eneration has a long tradition in th.c field of chcmoinformatics. Varions algorithms and approaches to addressing the problem of automatically generating 3D molecular models have been developed and published in the literature since the early 1980s, Some of the basic concepts and methods arc discussed in Section 2,9 and a more detailed description is given in Chapter II, Section 7.1 in the Handbook. 

When considering the stability of spin-delocalized radicals the use of isodesmic reaction Eq. 1 presents one further problem, which can be illustrated using the 1-methyl allyl radical 24. The description of this radical through resonance structures 24a and 24b indicates that 24 may formally be considered to either be a methyl-substituted allyl radical or a methylvinyl-substituted methyl radical. While this discussion is rather pointless for a delocalized, resonance-stabilized radical such as 24, there are indeed two options for the localized closed shell reference compound. When selecting 1-butene (25) as the closed shell parent, C - H abstraction at the C3 position leads to 24 with a radical stabilization energy of - 91.3 kj/mol, while C - H abstraction from the Cl position of trans-2-butene (26) generates the same radical with a RSE value of - 79.5 kj/mol (Scheme 6). The difference between these two values (12 kj/mol) reflects nothing else but the stability difference of the two parents 25 and 26. 

To develop the kinetic equations in condensed phases the master equation must be formulated. In Section 3 the master equation is used to generate the kinetic equations for local concentrations and pair correlation functions. The latter set of equations permits consideration of history of formation of the local solid structure as well as its influence on the subsequent elementary stages. The many-body problem and closing procedure for kinetic equations are discussed. The influence of fast and slow stages on a closed system of equations is demonstrated. The multistage character of the kinetic processes in condensed phase creates a problem of self-consistency in describing the dynamics of elementary stages and the equilibrium state of the condensed system. This problem is solved within the framework of a lattice-gas model description of the condensed phases. 

For the description of large numbers of molecules needed for selecting a BBL, however, 3D and other computational chemistry methods tend to be slow and cumbersome involving conformational problems. They need to be automated and connected to other software for the automatic generation of structural co-ordinates. The development of such systems is underway in several laboratories, but they are not yet routinely available. 

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