Interplay of water and a supramolecular capsule for catalysis of reductive elimination reaction from gold.

Supramolecular assemblies have gained tremendous attention due to their ability to catalyze reactions with the efficiencies of natural enzymes. Using ab initio molecular dynamics, we identify the origin of the catalysis by the supramolecular capsule Ga4L612- on the reductive elimination reaction from gold complexes and assess their similarity to natural enzymes. By comparing the free energies of the reactants and transition states for the catalyzed and uncatalyzed reactions, we determine that an encapsulated water molecule generates electric fields that contributes the most to the reduction in the activation free energy. Although this is unlike the biomimetic scenario of catalysis through direct host-guest interactions, the electric fields from the nanocage also supports the transition state to complete the reductive elimination reaction with greater catalytic efficiency. However it is also shown that the nanocage poorly organizes the interfacial water, which in turn creates electric fields that misalign with the breaking bonds of the substrate, thus identifying new opportunities for catalytic design improvements in nanocage assemblies

Electrostatics Generated by a Supramolecular Capsule Stabilizes the Transition State for Carbon-Carbon Reductive Elimination from Gold(III) Complex.

Tetrahedral assemblies of stoichiometry M4L6 have been proven to catalyze a range of chemical reactions including the carbon-carbon reductive elimination reaction from transition metals such as gold. Here, we perform quantum chemical calculations of Gold(III) transition metal complexes in vacuum, and encapsulated in Ga4L612- or Si4L68- assemblies within both a reaction field continuum solvent and in an aqueous molecular environment with counterions, to rationalize the rate enhancements observed experimentally for the reductive elimination reaction. We find that the Ga4L612- assembly lowers the energy barrier of the reaction compared to Si4L68-, which is consistent with kinetic trends observed experimentally. We have determined that the primary factor for catalytic rate acceleration stems from the electrostatic environment emanating from the Ga4L612- capsule as opposed to the water or counterions

Computational Design of Synthetic Enzymes.

We review the standard model for de novo computational design of enzymes, which primarily focuses on the development of an active-site geometry, composed of protein functional groups in orientations optimized to stabilize the transition state, for a novel chemical reaction not found in nature. Its emphasis is placed on the structure and energetics of the active site embedded in an accommodating protein that serves as a physical support that shields the reaction chemistry from solvent, which is typically improved upon by laboratory-directed evolution. We also provide a review of design strategies that move beyond the standard model, by placing more emphasis on the designed enzyme as a whole catalytic construct. Starting with complete de novo enzyme design examples, we consider additional design factors such as entropy of individual residues, correlated motion between side chains (mutual information), dynamical correlations of the enzyme motions that could aid the reaction, reorganization energy, and electric fields as ways to exploit the entire protein scaffold to improve upon the catalytic rate, thereby providing directed evolution with better starting sequences for increasing biocatalytic performance