Evolution molecular level

All the four essential features of the active site of chymotrypsin are thus also present in subtilisin. Furthermore, these features are spatially arranged in the same way in the two enzymes, even though different framework structures bring different loop regions into position in the active site. This is a classical example of convergent evolution at the molecular level. 

The present theory can be placed in some sort of perspective by dividing the nonequilibrium field into thermodynamics and statistical mechanics. As will become clearer later, the division between the two is fuzzy, but for the present purposes nonequilibrium thermodynamics will be considered that phenomenological theory that takes the existence of the transport coefficients and laws as axiomatic. Nonequilibrium statistical mechanics will be taken to be that field that deals with molecular-level (i.e., phase space) quantities such as probabilities and time correlation functions. The probability, fluctuations, and evolution of macrostates belong to the overlap of the two fields. 

The reaction of tetraalkyltin complexes with oxide surfaces was studied244,245 but no description at the molecular level has been reported. The low-temperature reactivity of tetraalkyltin (SnR4, where R=Me, Et, i-Pr, Bu) complexes toward the surface of silica was studied in detail.246 At room temperature, the complex is physisorbed. Above 100°C, the adsorbed molecules react with the OH groups and the evolution of alkanes is observed (Scheme 7.15). 

T. S. Whittam (Eds), Evolution at the Molecular Level, Sinauer Associates, Sunderland, MA, pp. 77-95. 

Note that even evolutionary studies have moved to the molecular level over the last generation (mainly because this is the level at which genetics is now practiced). Using these studies to understand phenotypic evolution will require a molecular or, at least, a physical account of development. 

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. 

Successful molecular evolution that puts strict demands on accurate transfer of molecular information executed by highly precise control of size, shape, topology, flexibility, and surface chemistry at the molecular level. The latter five features have been dubbed critical molecular design parameters. 

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... 

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