The free energy of binding between avidin and seven biotin analogues has been calculated with the molecular mechanics Poisson-Boltzmann surface area (MM/PBSA) method. We have studied how the force field and the method to generate geometries affect the calculated binding free energies. Four different force fields were compared, but we saw no significant difference in the results. However, mixing the force fields used for the geometry generation and energy calculations is not recommended. In the molecular dynamics simulations, explicit water molecules must be used, but the size of the simulated system and the boundary conditions are less important. In fact, nonperiodic simulations with a fixed protein outside a relatively small simulated system (18 A) seem to be a proper approach. The mean absolute error was 9-19 kJ/mol, with a standard error of 5-15 kJ/mol, which arises mainly from the entropy term.

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[reaction: see text] Significant rate acceleration of metal-catalyzed Michael addition reactions in water was observed upon addition of small, dibasic ligands. Ytterbium triflate and TMEDA was the most effective combination leading to a nearly 20-fold faster reaction than in the absence of ligand.

Addition reactions O 0060Expanding the Scope of Lewis Acid Catalysis in Water: Remarkable Ligand Acceleration of Aqueous Ytterbium Triflate Catalyzed Michael Addition Reactions. -Addition of TMEDA to Yb(O-Tf)3 enables highly efficient Michael addition reaction in water. -(DING, R.; KATEBZADEH, K.; ROMAN, L.; BERGQUIST, K.-E.; LINDSTROEM*, U. M.; J. Org. Chem. 71 (2006) 1, 352-355; Dep. Org. Chem., Univ. Lund, S-221 00 Lund, Swed.; Eng.) -Jannicke 21-036