Now showing 1 - 2 of 2
  • Publication
    Comparative studies for evaluation of CO2 fixation in the cavity of the Rubisco enzyme using QM, QM/MM and linear-scaling DFT methods
    We evaluate the minimum energy configuration (MM) and binding free energy (QM/MM and QM) of CO2 to Rubisco, of fundamental importance to the carboxylation step of the reaction. Two structural motifs have been used to achieve this goal, one of which starts from the initial X-ray Protein Data Bank structure of Rubisco's active centre (671 atoms), and the other is a simplified, smaller model (77 atoms) which has been used most successfully, thus far, for study. The small model is subjected to quantum chemical density functional theory (DFT) studies, both in vacuo and using implicit solvation. The effects of the protein environment are also included by means of a hybrid quantum mechanical/molecular mechanical (QM/MM) approach, using PM6/AMBER and B3LYP/AMBER schemes. Finally, linear-scaling DFT methods have also been applied to evaluate energetic features of the large motif, and the result obtained for the binding free energy of the CO2 underlines the importance of the accurate modelling of the surrounding protein milieu using a full DFT description.
    Scopus© Citations 12  566
  • Publication
    Mechanism of Atmospheric CO2 Fixation in the Cavities of a Dinuclear Cryptate
    Using density functional theory (DFT) methods, we have investigated two possible mechanisms for atmospheric CO2 fixation in the cavity of the dinuclear zinc (II) octaazacryptate, and the subsequent reaction with methanol whereby this latter reaction transforms the (essentially) chemically inert CO2 into useful products. The first mechanism (I) was proposed by Chen et al. [Chem. Asian J. 2007, 2, 710], and involves the attachment of one CO2 molecule onto the hydroxyl-cryptate form, resulting in the formation of a bicarbonate-cryptate species and subsequent reaction with one methanol molecule. In addition, we suggest another mechanism that is initiated via the attachment of a methanol molecule onto one of the Zn-centres, yielding a methoxy-cryptate species. The product is used to activate a CO2 molecule and generate a methoxycarbonate-cryptate. The energy profiles of both mechanisms were determined and we conclude that, while both mechanisms are energetically feasible, free energy profiles suggest that the scheme proposed by Chen et al. is most likely.
    Scopus© Citations 22  1124