Crystals, molecular mechanics applications

Molecular mechanics force fields have largely been parameterised using the best available data from the gas phase and (in some cases) from liquid phase or solution data. The question therefore arises as to how applicable molecular mechanics force fields are to predicting structures of molecules in the liquid crystal phase. There is now good evidence from NMR measurements that the structure of liquid crystal molecules change depending on the nature of their... 

Kokufuta, E Jinbo, E, A Hydrogel Capable of Facilitating Polymer Diffusion through the Gel Porosity and Its Application in Enzyme Immobilization, Macromolecules 25, 3549, 1992. Kresge, CT Leonowicz, ME Roth, WJ Vartuli, JC Beck, JS, Ordered Mesoporous Molecular Sieves Synthesized by a Liquid-Crystal Template Mechanism, Nature 359, 710, 1992. 

The theoretician uses these programs to predict structure, either of single molecules or of assemblages of molecules, using X-ray or NMR data, when available, to test his predictions (13-15). It has been known for a long time that even the earlier molecular mechanics programs can predict the structures of certain types of molecules with excellent reliability. For the cyclic alkanes, an accuracy comparable to that of the best X-ray crystal structure analysis can be obtained. In fact, the method is more widely applicable since neither compound nor crystals are necessary (1 . 

Phenylacetylene derivatives, (V), were prepared by Tang [2] and converted into the corresponding polyacetylenes, (VI), as illustrated below, containing a side-chain liquid crystal molecular architecture of backbone + spacer + mesogenic group. These products were subsequently used in electronic and mechanical applications. 

The exponential increase in computer power and the development of highly efficient algorithms has distinctly expanded the range of structures that can be treated on a first-principle level. Using parallel computers, AIMD simulations of systems with few hundred atoms can be performed nowadays. This range already starts to approach the one relevant in biochemistry. Indeed, some simulations of entire biomolecules in laboratory-realizable conditions (such as crystals or aqueous solutions) have been performed recently [25-28]. For most applications however, the systems are still too large to be treated fully at the AIMD level. By combining AIMD simulations with a classical MD force field in a mixed quantum mechanical/molecular mechanical fashion (Hybrid-AIMD) the effects of the protein environment can be explicitly taken into account and the system size can be extended. 

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