Conformational analysis problems involving

This section illustrates several interesting applications of molecular mechanics to problems involving areas other than conformational analysis and reaction mechanisms. 

Mention must be made of the use of an internal standard to monitor a reaction by g.l.c. analysis, and also to calculate the g.l.c. yield. Here, a known weight of the standard, inert to the reaction conditions and conforming to the other criteria of selection noted above, is added initially to the reaction mixture. In the case where samples of the mixture can be removed and loaded directly on to the column, the subsequent analysis presents no problem and may be deduced from the discussion above. In the case of samples which require evaporation of solvent prior to chromatographic examination, it is only necessary to ensure that the standard, and indeed the components to be analysed, do not volatilise under the conditions of concentration. If the samples require more involved solvent extraction procedures, then further experimentation is required to establish that... 

There is a general problem in defining a structural change into a strained state. Such a structural change may only involve changes in the position of a small number of residues by a few tenths of an angstrom and will therefore remain undetected by current structural analysis. Alternatively, the strained state may represent a quasi-equilibrium between two or more conformations, none of which is stable under the conditions discussed here. In the absence of load, the transition between the states can... 

Development of time-dependent DFS studies have to await further technological challenges in AFM where the lag phase of a mechanical contraption like a tip of AFM probe riding on a cantilever hovering over the rugged surface of a protein anchored on a platform by its very nature is slow compared to time-scales involved in the conformational dynamics from one peak to another in the energy landscape of a protein. As we encountered similar problems in molecular dynamics (MD), density functional studies (DFT), and 3D multi-nuclear NMR studies, analysis of voluminous data is very tedious. 

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