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Diffusion and interactions of carbon dioxide and oxygen in the vicinity of the active site of Rubisco: Molecular dynamics and quantum chemical studies
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Image of FIG. 1.
FIG. 1.

Fragment model representing the active centre of Rubsico. The structure corresponds to the coordination sphere of the Mg ion with enediolate-bound CO. 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.

Image of FIG. 2.
FIG. 2.

Initial placement of (a) CO and (b) O molecules at the Rubisco active site. Carbon atoms are displayed in grey, oxygen in red, and magnesium in green.

Image of FIG. 3.
FIG. 3.

Two representative examples of the evolution of distance of the three atoms of the CO 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.

Image of FIG. 4.
FIG. 4.

Snapshots of the “flipping” mechanism of the CO 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 CO self-diffusion away from the centre of the active site.

Image of FIG. 5.
FIG. 5.

Normalised autocorrelation functions of O (dotted line) CO (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 O, while the bottom x-axis corresponds to relaxation times for CO.

Image of FIG. 6.
FIG. 6.

Plot of averaged (a) O-Mg and (b) CO-Mg van der Waals and electrostatic interaction energies against distance from the Mg to centres-of-mass of the gas molecules.

Image of FIG. 7.
FIG. 7.

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.

Image of FIG. 8.
FIG. 8.

Schematic showing multi-step reactions for both carboxylation and oxygenation.

Image of FIG. 9.
FIG. 9.

The optimised geometries of the transition state of the carboxylation (TS) and the oxygenation (TS) steps at B3LYP/6-31+G(,). Various distances and angles are indicated on the molecular skeleton.

Image of FIG. 10.
FIG. 10.

Energy profiles for the carboxylation and oxygenation steps at the B3LYP/6-31+G(,) level .


Generic image for table
Table I.

The difference in polarisation of the fragments (ΔPL), net charge transfer between the fragments ΔCT (e), intramolecular CO angle, and O-O length in O, as well as EDA results tabulated as a function of the distance between the centre-of-mass of the either CO or O (X) and the C2 carbon.


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752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: Diffusion and interactions of carbon dioxide and oxygen in the vicinity of the active site of Rubisco: Molecular dynamics and quantum chemical studies