Now showing 1 - 6 of 6
  • 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
    A theoretical thermodynamic investigation of cascade reactions in dinuclear octa-azacryptates involving carbon dioxide
    This paper investigates the thermodynamics of gas-phase CO2 cascade uptake-reactions in the form of carbonate or methoxycarbonate anions in the host cavity of various dinuclear octa-azacryptates of m-CH2C6H4CH2 and 2,5-furano-spaced hosts, L1 and L2 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 are also investigated to determine the parameters which affect the stability of the complexes. Natural bond orbital (NBO) analysis has been used to investigate the interactions between the trapped anion and its host. The ion selectivity has been studied in terms of the formation of dinuclear crypate complexes, while the basicity and nucleophilicity of cryptands towards Lewis acids have also been studied, and good agreement was found vis-à-vis available experimental data.
    Scopus© Citations 5  848
  • Publication
    Monomer diffusion rates in photopolymer material : Part II High-frequency gratings and bulk diffusion
    (Optical Society of America, 2011-04-01) ; ; ;
    Photosensitive polymers are of practical importance, and mass transport within such materials plays a critical role in their behavior. Building on the work in Part I [J. Opt. Soc. Am. B doc. ID 136413 (posted 5 January 2011, in press)], the diffusion constants of a number of materials (i.e., acrylamide, polyacrylamide, water, propanol, and acetone) within a photosensitive layer are measured. A combination of optical and physical chemistry techniques is applied under different conditions. Determining the rates of diffusion is beneficial as it: (i) indicates material stability over time and (ii) supports material characterization, modeling, and performance optimization
      948Scopus© Citations 30
  • Publication
    Electrophoretic deposition of poly(3-decylthiophene) onto gold-mounted cadmium selenide nanorods
    Molecular mechanisms of electrophoretic deposition (EPD) of poly(3-decylthiophene) (P3DT) molecules onto vertically aligned cadmium selenide arrays have been studied using large-scale, nonequilibrium molecular dynamics (MD), in the absence and presence of static external electric fields. The field application and larger polymer charges accelerated EPD. Placement of multiple polymers at the same lateral displacement from the surface reduced average deposition times due to “crowding”, giving monolayer coverage. These findings were used to develop and validate Brownian dynamics simulations of multilayer polymer EPD in scaled-up systems with larger inter-rod spacings, presenting a generalized picture in qualitative agreement with random sequential adsorption.
    Scopus© Citations 6  660
  • 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
  • Publication
    Electronic structures of N- and C-doped NiO from first-principles calculations
    The large intrinsic band gap of NiO has hindered severely its potential application under visible-light irradiation. In this study, we have performed first-principles calculations on the electronic properties of N- and C-doped NiO to ascertain if its band gap may be narrowed theoretically. It was found that impurity bands driven by N 2p or C 2p states appear in the band gap of NiO and that some of these locate at the conduction band minimum, which leads to a significant band gap narrowing. Our results show that N-doped NiO may serve as a potential photocatalyst relative to C-doped NiO, due to the presence of some recombination centres in C-doped NiO.
      974Scopus© Citations 30