Conformational analysis of siloxane-based enzyme-mimic precursors[1]

The conformational flexibility of six hybrid organodisiloxane oligomers were studied using the Low Mode-Monte Carlo conformational search method with the MM2* force field and the Generalized Born/Surface Area continuum solvent model for water. These systems have enzyme-like properties as synthetic acyltransferases and contain aminopyridine groups in various states of protonation. An ensemble of low energy structures was generated and used to investigate the dependence of molecular shape and flexibility on protonation, which plays an important role in catalyst solubility and self-association. The results as measured by the number of unique conformations, end-to-end or longest intramolecular distance and radius of gyration of the conformational point cloud indicate that the number of protonated pyridines plays a significant role in the overall molecular shape. A similar study was also carried out on various POSS-substitutive organodisiloxane oligomers.