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Electronic Structure Benchmark Calculations of CO2 Fixing Elementary Chemical Steps in RuBisCO Using the Projector-Based Embedding Approach

preprint
submitted on 16.04.2020 and posted on 20.04.2020 by Oscar A. Douglas-Gallardo, Ian J. Shepherd, Simon Bennie, Kara Ranaghan, Adrian Mulholland, Esteban Vöhringer-Martinez
Ribulose 1,5-bisphosphate carboxylase-oxygenase (RuBisCO) is the main enzyme involved in atmospheric carbon dioxide (CO2) fixation in the biosphere. This enzyme catalyses a set of five chemical steps that take place in the same active-site within magnesium (II) coordination sphere. Here, a set of electronic structure benchmark calculations have been carried out on a reaction path proposed by Gready et al. by means of the projector-based embedding approach. Activation and reaction energies for all main steps catalyzed by RuBisCO have been calculated at the MP2, SCS-MP2, CCSD and CCSD(T)/aug-cc-pVDZ and cc-pVDZ levels of theory.

The treatment of the magnesium cation with post-HF methods is explored to determine the nature of its involvement in the mechanism. With the high-level ab initio values as a reference, we tested the performance of a set of density functional theory (DFT) exchange-correlation (xc) functionals in reproducing the reaction energetics of RuBisCO carboxylase activity on a set of model fragments. Different DFT xc-functionals show large variation in activation and reaction energies. Activation and reaction energies computed at the B3LYP level are close to the reference SCS-MP2 results for carboxylation, hydration and protonation reactions.

However, for the carbon-carbon bond dissociation reaction, B3LYP and other functionals give results that differ significantly from the ab initio reference values. The results show the applicability of the projector-based embedding approach to metalloenzymes. This technique removes the uncertainty associated with the selection of different DFT xc-functionals and so can overcome some of inherent limitations of DFT calculations, complementing and potentially adding to modelling of enzyme reaction mechanisms with DFT methods.

Funding

Max-Planck Society , FONDECYT 1160193, FONDECYT 3170029, EMBO short-term fellowship STF 8022 ,

History

Email Address of Submitting Author

evohringer@udec.cl

Institution

Facultad de Ciencias Químicas, Universidad de Concepción

Country

Chile

ORCID For Submitting Author

0000-0003-1785-4558

Declaration of Conflict of Interest

no

Exports