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Equilibrium and non-equilibrium molecular dynamics (MD) simulations have been performed to investigate thermal-driven break-up of planar CO2 hydrate interfaces in liquid water at 300-320 K. Different guest compositions, at 85%, 95%, and 100% of maximum theoretical occupation, led to statistically-significant differences in the observed initial dissociation rates. The melting temperatures of each interface were estimated, and dissociation rates were observed to be strongly dependent on temperature, with higher dissociation rates at larger over-temperatures vis-à-vis melting. A simple coupled mass and heat transfer model developed previously was applied to fit the observed dissociation profiles, and this helps to identify clearly two distinct régimes of break-up; a second well-defined region is essentially independent of composition and temperature, in which the remaining nanoscale, de facto two-dimensional system's lattice framework is intrinsically unstable. From equilibrium MD of the two-phase systems at their melting point, the relaxation times of the auto-correlation functions of fluctuations in number of enclathrated guest molecules were used as a basis for comparison of the variation in the underlying, non-equilibrium, thermal-driven dissociation rates via Onsager's hypothesis, and statistically significant differences were found, confirming the value of a fluctuation-dissipation approach in this case.

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.

Molecular dynamics (MD) at the molecular mechanical level and geometry optimisation at the quantum mechanical level have been performed to investigate the transport and fixation of oxygen and carbon dioxide in the cavity of ribulose-1,5-bisphosphate carboxylase/oxygenase, or Rubisco. Multiple MD simulations have been carried out to study the diffusive behaviour of O(2) and CO(2) molecules from the Mg(2+) cation in Rubisco at 298 K and 1 bar, being one step in the overall process of carboxylation/oxygenation in Rubisco. In addition to this work, in order to gain additional perspective on the role of chemical reaction rates and thermodynamics, oxygen, and carbon dioxide uptake mechanisms have also been investigated by the aid of quantum chemical calculations. The results indicate that the activation barrier for carboxylation is slightly lower than that of oxygenation. This agrees qualitatively with experimental findings, and rationalises the observed competition between both catalytic processes in nature. Finally, the longer-lived persistence of CO(2) in the vicinity of the active centre (i.e., slower self-diffusion) may serve to explain, in part, why carboxylation is the more kinetically favoured on an overall basis compared to oxygenation.

Using density functional theory (DFT) methods, we have investigated two possible mechanisms for atmospheric CO(2) fixation in the cavity of the dinuclear zinc(II) octa-azacryptate, and the subsequent reaction with methanol whereby this latter reaction transforms the (essentially) chemically inert CO(2) 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 CO(2) 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-centers, yielding a methoxy-cryptate species. The product is used to activate a CO(2) 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.

This paper investigates the thermodynamics of gas-phase CO(2) cascade uptake-reactions in the form of carbonate or monomethylcarbonate anions in the host cavity of various dinuclear octa-azacryptates of m-CH(2)C(6)H(4)CH(2) and 2,5-furano-spaced hosts, L (1) and L (2) cryptands, using density functional theory (DFT). The cascade process involves two stages, namely the formation of dinuclear cryptate complexes, and the subsequent formation of either μ-carbonato cryptate complexes or μ-monomethylcarbonato cryptates. The geometric and electronic structures were also investigated to determine the parameters that affect the stability of the complexes. Natural bond orbital (NBO) analysis was used to investigate the interactions between the trapped anion and its host. Ion selectivity was studied in terms of the formation of dinuclear cryptate complexes, while the basicity and nucleophilicity of cryptands towards Lewis acids was also studied, and good agreement was found vis-à-vis available experimental data.