Pitfalls, Interpretation, and Communication

There are two outcomes of a single molecular mechanics calculation the stmctural geometry of a local or the global energy minimum and the energy value of that 

Structures determined by spectroscopic means are generally underdetermined in that the number of variables is similar to or greater than the number of observations. In such a case, the energy-minimized stmctures can be used to aid in the refinement of the stmcture or as a check of the stmcture [217]. Applications of molecular mechanics modeling to the determination of solution stmctures are described in 

Where the structure has not been determined or carniot be determined experimentally, by diffraction techniques or spectroscopy, molecular mechanics can be used as a predictive tool. This is of particular value when the structure of a compound is the main target, such as in modeling associated with rational drug design (see Chapter 13). 

When the goal is visualization rather than quantitative analysis, somewhat less well-refined molecular mechanics models have a valid role to play. For example, the force fields for proteins and nucleic acids and for their metal complexes are in general less rigorous than those for small molecules. Despite this, much useful information has been obtained from structures produced using these force fields. However, it is important not to overinterpret the results in such cases. In particular, the minimized strain energies obtained from such models should be considered to be qualitative estimates at best. 

Instead, the comparison of strain energies should be limited to sets of isomers. When the atom connectivities are the same, electronic factors and other omissions and errors in the force field can be assumed to be constant and therefore will cancel when differences between strain energies are considered. The values of the strain energies reveal which isomer is the most stable (has the lowest strain energy) and what percentage of each isomer should be observed in an equilibrated system [95]. The methods for calculating these percentages are described in Chapter 8. 

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It is clear to those who regularly perform knee wear testing, and especially those who try hard to do testing well, that the devil is in the detail . With the exception of some specialist workshops (e.g., by ASTM) even scientific conferences appear lately to be more focused on results they leave little room for detailed discussion, especially on methodological detail where most of the variability in results emanate, in the author s view. Nevertheless, this chapter is still not a detailed how-to manual. International standards (where available) are cited instead. Published international standards typically describe such methods in sufficient detail. Nor is this text a review of the results of TKR tests from the literature, as useful as that may be. The results are too many and varied only some are cited here to illustrate specific points. The main emphasis here is on matters of rationale and know-how to avoid pitfalls in the choice of test methods, in their implementation, and in the interpretation of results. This emphasis should help engineers in the orthopedic industry and in the research community who hunger for the type of detail they cannot usually find in published research papers, usually for lack of space in such result-oriented research articles. 

This edited volume provides the cement science community with a state-of-the-art overview of analytical techniques used in cement chemistry to study the hydration and microstructure of cements. Each chapter focusses on a specific technique, not only describing the basic principles behind the technique, but also providing essential, practical details on its application to the study of cement hydration. Each chapter sets out present best practice, and draws attention to the limitations and potential experimental pitfalls of the technique. Databases that supply examples and that support the analysis and interpretation of the experimental results strengthen a very valuable ready reference. 

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