Surface-simulation synthesis

It should be noted that the above strategy, although first employed In the delineation of protein antigenic sites. Is applicable, with appropriate adaptations, to the precise delineation and chemical synthesis of other types of protein binding sites. The Introduction of the concept of surface-simulation synthesis ( 4, ) has provided a methodology by which In principle any type of protein binding site can be mimicked synthetically after careful chemical characterization. 

Figure 4. Photograph of a lysozyme model showing the relative positions of the residues constituting antigenic sites 1 and 2. The side chains of the residues in the sites are outlined, those making up site 1 are speckled areas, while those constituting site 2 are shown as dotted areas to avoid confusion. The preferred direction of site 1 (at least by surface-simulation synthesis) is Arg-125 to Lys-13. Site 2 also had a preferred direction (Trp-62 to Asp-87) ...

Fig. 9,2. The antigenic sites of hen egg white lysozyme and the corresponding synthetic peptides used in the method of surface simulation synthesis (from Atassi and Lee, 1978b).

For a given pair of electrode reactions of known thermodynamic and kinetic characteristics, electrochemical engineering procedures must provide a reactor design in which these reactions can occur with high material and energy efficiencies. Simultaneously, appropriate provisions have to be made for the input of reactants and outflow of products and for the addition (or removal) of electric and thermal energy. The emphasis here is on the complete system and the inter-related surface reactions and transport processes. System analysis and design of electrochemical reactors require elaborate computer-implemented process simulation, synthesis, and optimization. 

Holm and Andersson have provided an up-to-date survey of simulation experiments on the synthesis under hydrothermal conditions of molecules important for biogenesis (Holm and Andersson, 2005). It is clear that several research groups have been able to show in the meantime, using simulation experiments, that the conditions present at deep sea vents appear suitable for the synthesis of very different groups of substances. However, it remains unclear how these compounds could have been stabilized and protected against rapid decomposition. At present, metal ions (as complexing agents) and mineral surfaces are the subject of discussion and experiment. 

Supercritical water (SCW) presents a unique combination of aqueous and non-aqueous character, thus being able to replace an organic solvent in certain kinds of chemical synthesis. In order to allow for a better understanding of the particular properties of SCW and of its influence on the rate of chemical reactions, molecular dynamics computer simulations were used to determine the free energy of the SN2 substitution reaction of Cl- and CH3C1 in SCW as a function of the reaction coordinate [216]. The free energy surface of this reaction was compared with that for the gas-phase and ambient water (AW) [248], In the gas phase, an ion-dipole complex and a symmetric transition... 

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