Fragment model representing the active centre of Rubsico. The structure corresponds to the coordination sphere of the Mg ion with enediolate-bound CO2. The fragment involves a hydrogen bond network, represented by green lines. The Mg···O bonds of the first coordination sphere are displayed in the top left.
Initial placement of (a) CO2 and (b) O2 molecules at the Rubisco active site. Carbon atoms are displayed in grey, oxygen in red, and magnesium in green.
Two representative examples of the evolution of distance of the three atoms of the CO2 molecule vis-à-vis the (essentially stationary) Mg ion, and also of the carbon with respect to its initial position. The substantial variation in “induction time” prior to moving appreciably away from the Mg ion is evident, i.e., 0.2 ns in (a) versus 3.3 ns in (b). In addition, the “flipping” mechanism depicted in Fig. 3 is evident at the end of the induction time, with both of the oxygen atoms becoming equidistant from the Mg ion; a short-lived flip is evident for the (b) case at 1.25 ns, prior to eventual movement at 3.3 ns. Arrows are shown for indicative purposes of the induction time.
Snapshots of the “flipping” mechanism of the CO2 in the vicinity of Mg: (a) initial placement, wherein the Coulombic interaction dominates, and due to random thermal motion, wherein the van der Waals component competes with the electrostatic component, flipping occurs as in (b) minimisation of interaction energy primarily via the van der Waals energy and essential decoupling, or weakening, of the interaction, resulting in CO2 self-diffusion away from the centre of the active site.
Normalised autocorrelation functions of O2 (dotted line) CO2 (dashed line) orientations along their bond vectors. Also shown (solid lines) are the exp(−t/τ) fits to the respective curves. Because of the differences in relaxation times, the top x-axis corresponds to O2, while the bottom x-axis corresponds to relaxation times for CO2.
Plot of averaged (a) O2-Mg and (b) CO2-Mg van der Waals and electrostatic interaction energies against distance from the Mg to centres-of-mass of the gas molecules.
Plot of averaged interaction energies between the gas molecules and the complex versus distance from the Mg to the centres-of-mass of the gas molecules.
Schematic showing multi-step reactions for both carboxylation and oxygenation.
The optimised geometries of the transition state of the carboxylation (TSCO2) and the oxygenation (TSO2) steps at B3LYP/6-31+G(d,p). Various distances and angles are indicated on the molecular skeleton.
Energy profiles for the carboxylation and oxygenation steps at the B3LYP/6-31+G(d,p) level in vacuo.
The difference in polarisation of the fragments (ΔPL), net charge transfer between the fragments ΔCT (e−), intramolecular CO2 angle, and O-O length in O2, as well as EDA results tabulated as a function of the distance between the centre-of-mass of the either CO2 or O2 (X) and the C2 carbon.
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