Crystallization software

Structure Solution Using Single Crystal Software... 

While overshadowed by dedicated powder diffraction based structure solution software, single crystal structure solution programs can still be used where a list of HKLs and intensities are available and can be usefully applied (Table 17.23). This allows not only the use of Direct Methods, but also Patterson and Patterson-based fragment searching. Armel Le Bail s Overlap program (listed in Table 17.16) can remove reflections that are excessively overlapped, sometimes aiding single crystal software based structure solution. 

While computer-based structure validation is integrated in single crystal software, it is somewhat lagging in the powder diffraction community. Ton Spek s... 

A clear and exhaustive description of the method is in Dovesi, R. Civalleri, B. Orlando, R. Roetti, C. Saunders, V. R. Ab initio quantum simulations in solid state chemistry. Revs. Comp. Chem. 2005, 21, 1-125. This review contains a discussion of all aspects of periodic calculations, including differences between conducting and non-conducting systems, Brillouin zone sampling, basis set dependence, etc., and a survey of available computer packages. For the CRYSTAL software package for periodic MO calculations in crystals, developed by the authors, see www.crystal.unito.it. 

This is the method used by the commercial software packages Crystal Ball and RISK . The method is ideally suited to computers as the description of the method will reveal. Suppose we are trying to combine two independent variables, say gross reservoir thickness and net-to-gross ratio (the ratio of the net sand thickness to the gross thickness of the reservoir section) which need to be multiplied to produce a net sand thickness. We have described the two variables as follows ... 

CRYSTAL98 Is the current version of the commercial HF program developed at the University of Torino and at Daresbury Laboratory (http //www.dl.ac.uk/TCS/Software/CRYSTAL/)... 

One way to model a solid is to use software designed for gas-phase molecular computations. A large enough piece of the solid can be modeled so that the region in the center for practical purposes describes the region at the center of an inhnite crystal. This is called a cluster calculation. 

Another recent database, still in evolution, is the Linus Pauling File (covering both metals and other inorganics) and, like the Cambridge Crystallographic Database, it has a "smart software part which allows derivative information, such as the statistical distribution of structures between symmetry types, to be obtained. Such uses are described in an article about the file (Villars et al. 1998). The Linus Pauling File incorporates other data besides crystal structures, such as melting temperature, and this feature allows numerous correlations to be displayed. 

In conclusion, it is likely that computational approaches for metabolism prediction will continue to be developed and integrated with other algorithms for pharmaceutical research and development, which may in turn ultimately aid in their more widespread use in both industry and academia. Such models may already be having some impact when integrated with bioanalytical approaches to narrow the search for possible metabolites that are experimentally observed. Software that can be updated by the user as new metabolism information becomes available would also be of further potential value. The held of metabolism prediction has therefore advanced rapidly over the past decade, and it will be important to maintain this momentum in the future as the hndings from crystal structures for many discrete metabolic enzymes are integrated with the diverse types of computational models already derived. 

Once a structure of the desired protein has been solved, it is a very rapid process to produce subsequent high-quality structures and, in fact, some groups have even linked various scripts together, or modified software tools to provide much more automated software aids to repeated crystal structure solution, such as when solving multiple ligand complexes of the same protein [7]. 

We have adapted a commercially available x-ray diffractometer normally used for structure determinations on single crystals to operate as a very flexible device for performing x-ray pole figure determinations and related studies on polymeric materials. Descriptions of crystallite orientations, as provided by pole figures, are useful in studying many aspects of the behavior of products made from semicrystalline polymers. This paper describes the software that we have written for our pole figure facility. Except for some vendor-provided routines to drive the hardware Interface all of our software is written in FORTRAN. Menu driven operation is provided to maximize user convenience. 

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