Chemical evolution molecular level

Ideally, MD or MC gives a complete description of the equilibrium states of liquids and crystals, and a molecular-level picture of any chemical process occurring within the system, including phase transitions. The limitations are obvious. The calculation is heavy, with some 5,000 molecules at most, and times or time-equivalents of the order of at most milliseconds. Force fields are by necessity restricted to atom-atom empirical ones. One gets at best a blurred and very short glimpse of the simulated process. And yet, appropriately designed molecular simulation is, for example, the only access to molecular aspects of chemical evolution involved in crystal nucleation and growth. 

Although empirical solubility rules and A//SO[n values show some degree of correlation with polarity or other attributes of solute and solvent, the situation at the molecular level can be rather complex (Sidebar 3.11). Heat evolution or absorption is thus a deep clue to the microscopic nature of solution formation, indicating its possible relationship to chemical reaction phenomena... 

Reaction characterisation by calorimetry generally involves construction of a model complete with kinetic and thermodynamic parameters (e.g. rate constants and reaction enthalpies) for the steps which together comprise the overall process. Experimental calorimetric measurements are then compared with those simulated on the basis of the reaction model and particular values for the various parameters. The measurements could be of heat evolution measured as a function of time for the reaction carried out isothermally under specified conditions. Congruence between the experimental measurements and simulated values is taken as the support for the model and the reliability of the parameters, which may then be used for the design of a manufacturing process, for example. A reaction modelin this sense should not be confused with a mechanism in the sense used by most organic chemists-they are different but equally valid descriptions of the reaction. The model is empirical and comprises a set of chemical equations and associated kinetic and thermodynamic parameters. The mechanism comprises a description of how at the molecular level reactants become products. Whilst there is no necessary connection between a useful model and the mechanism (known or otherwise), the application of sound mechanistic principles is likely to provide the most effective route to a good model. 

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