Fig. 2: AIMD studies of the TYR-catalyzed azide-alkyne cycloaddition reaction.

a Radial distribution function of atoms between Cu-N, Cu-C and Cu-Cu atoms. Atoms are color-coded: carbon in brown, copper in blue, nitrogen in white, and oxygen in red. Charge density difference of azido (b) and ethynyl (c) binding vertically on two Cu activation sites representing the coordinative bonding interaction, respectively. d Scheme of catalytic transformation from the initial state to the intermediate to the final product. e Energy variation of TYR-catalyzed two individual azido and ethynyl molecules to an intermediate. Simulation condition: one-dimensional free energy surface from a metadynamics simulation at 298 K for 16 ps. f Energy change of reaction from intermediate to final product. Simulation condition: one-dimensional free energy surface from a metadynamics simulation at 298 K for 12 ps. Insert in (e, f) is the Lewis structure of azido and ethynyl binding to TYR at different transition states.