Now showing 1 - 10 of 40
  • Publication
    Implicit and explicit solvent models for modelling a bifunctional arene ruthenium hydrogen-storage catalyst: a classical and ab initio molecular simulation study
    Classical and ab initio, density functional theory- and semiempirical-based molecular simulation, including molecular dynamics, have been carried out to compare and contrast the effect of explicit and implicit solvation representation of tetrahydrofuran (THF) solvent on the structural, energetic, and dynamical properties of a novel bifunctional arene ruthenium catalyst embedded therein. Particular scrutiny was afforded to hydrogen-bonding and energetic interactions with the THF liquid. It was found that the presence of explicit THF solvent molecules is required to capture an accurate picture of the catalyst's structural properties, particularly in view of the importance of hydrogen bonding with the surrounding THF molecules. This has implications for accurate modeling of the reactivity of the catalyst.
    Scopus© Citations 6  393
  • Publication
    First-principles calculation of nitrogen-tungsten codoping effects on the band structure of anatase-titania
    (American Institute of Physics, 2009-04-02) ;
    The electronic properties and photocatalytic activity of nitrogen (N) and/or tungsten (W)-doped anatase are calculated using density functional theory. For N-doping, isolated N 2p states above the top of the valence band are responsible for experimentally observed redshifts in the optical absorption edge. For W-doping, W 5d states below the conduction band lead to band gap narrowing; the transition energy is reduced by 0.2 eV. Addition of W to the N-doped system yields significant band gap narrowing gap by 0.5 eV. This rationalizes recent experimental data which showed that N/W-doped titania exhibits higher visible-light photocatalytic efficiency than either N- or W-doping alone.
    Scopus© Citations 121  1534
  • 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  572
  • Publication
    Diffusive hydrogen inter-cage migration in hydrogen and hydrogen-tetrahydrofuran clathrate hydrates
    (American Institute of Physics, 2013-03-07) ; ;
    Classical equilibrium molecular dynamics (MD) simulations have been performed to investigate the diffusive properties of inter-cage hydrogen migration in both pure hydrogen and mixed hydrogen-tetrahydrofuran sII hydrates at 0.05 kbar from 200 K and up to 250-260 K. For mixed H2- THF systems in which there is single H2 occupation of the small cage (labelled ‘1SC 1LC’), we found that no H2 migration occurs. However, for more densely-filled H2-THF and pure- H2 systems, in which there is more than single H2 occupation in the small cage, there is an onset of inter-cage H2 migration events from the small cages to neighbouring cavities at around 200 K. The mean square displacements of the hydrogen molecules were fitted to a mathematical model consisting of an anomalous term and a Fickian component, and non-linear regression fitting was conducted to estimate long-time (inter-cage) diffusivities. An approximate Arrhenius temperature relationship for the diffusion coefficient was examined and a rough estimation of the hydrogen hopping energy barrier was calculated for each system.
    Scopus© Citations 48  443
  • Publication
    Energetic and electronic properties of P Doping at the rutile TiO2 (110) Surface from First Principles
    (ACS Publications, 2009-04-20) ;
    The energetic and electronic properties of various P doping configurations at the rutile TiO2 (110) surface are investigated by first-principles density functional theory (DFT) calculations. Several substitution and adsorption configurations for P impurities at the surface and the subsurface are considered. The stability of the P-doped systems is compared on the basis of the calculated formation energy and adsorption energy. Our calculated results indicate that the P impurities replace surface Ti atoms preferentially under O-rich growth conditions,and surface O atoms under Ti-rich conditions. In addition, it was found that the creation of oxygen vacancies favors P incorporation at substitution sites but not at adsorption sites. Doping with a single P atom into an O site may lead to either anionic or cationic states in the dopant. This causes either band-to-band transitions or introduces gap states to band transitions, with the former corresponding to a small band gap narrowing or broadening and the latter resulting in obvious reductions of photon transition energy. Substitutional replacement of Ti atoms by P atoms and adsorption on the surface (P-cation doping) results in either a small band reduction or a slight band gap enlargement, depending on the doping sites. It is speculated that the interaction between P impurities and surface oxygen vacancies will lead to further enhanced photocatalytic activity in the visible light region.
    Scopus© Citations 19  834
  • 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  1140
  • Publication
    Dynamical cage behaviour and hydrogen migration in hydrogen and hydrogen-tetrahydrofuran clathrate hydrates
    (American Institute of Physics, 2012-01-24) ; ;
    Classical equilibrium molecular dynamics(MD) simulations have been performed to investigate dynamical properties of cage radial breathing modes and intra- and inter-cage hydrogen migration in both pure hydrogen and mixed hydrogen-tetrahydrofuran sII hydrates at 0.05 kbar and up to 250K. For the mixed H2-THF system in which there is single H2 occupation of the small cage (labelled ‘1SC 1LC’), we find that no H2 migration occurs, and this is also the case for pure H2 hydrate with single small-cavity occupation and quadruple occupancy for large cages (dubbed ‘1SC 4LC’). However, for the more densely-filled H2-THF and pure- H2 systems, in which there is double H2 occupation in the small cage (dubbed ‘2SC 1LC’ and ‘2SC 4LC’, respectively), there is an onset of inter-cage H2 migration events from the small cages to neighbouring cavities at around 200 K, with an approximate Arrhenius temperature-dependence for the migration rate from 200 to 250 K. It was found that these ‘cage hopping’ events are facilitated by temporary openings of pentagonal small-cage faces with the relaxation and reformation of key stabilising hydrogen bonds during and following passage. The cages remain essentially intact up to 250 K, save for transient hydrogen bond weakening and reformation during and after inter-cage hydrogen diffusion events in the 200 to 250 K range. The ‘breathing modes’, or underlying frequencies governing the variation in the cavities’ radii, exhibit a certain overlap with THF rattling motion in the case of large cavities, while a there is some overlap of small cages’ radial breathing modes with lattice acoustic modes.
      593Scopus© Citations 34
  • Publication
    Towards the design of novel boron- and nitrogen-substituted ammonia-borane and bifunctional arene ruthenium catalysts for hydrogen storage
    Electronic-structure density functional theory calculations have been performed to construct the potential energy surface for H2 release from ammonia-borane, with a novel bifunctional cationic ruthenium catalyst based on the sterically bulky β-diketiminato ligand (Schreiber et al., ACS Catal. 2012, 2, 2505). The focus is on identifying both a suitable substitution pattern for ammonia-borane optimized for chemical hydrogen storage and allowing for low-energy dehydrogenation. The interaction of ammonia-borane, and related substituted ammonia-boranes, with a bifunctional η6-arene ruthenium catalyst and associated variants is investigated for dehydrogenation. Interestingly, in a number of cases, hydride-proton transfer from the substituted ammonia-borane to the catalyst undergoes a barrier-less process in the gas phase, with rapid formation of hydrogenated catalyst in the gas phase. Amongst the catalysts considered, N,N-difluoro ammonia-borane and N-phenyl ammonia-borane systems resulted in negative activation energy barriers. However, these types of ammonia-boranes are inherently thermodynamically unstable and undergo barrierless decay in the gas phase. Apart from N,N-difluoro ammonia-borane, the interaction between different types of catalyst and ammonia borane was modeled in the solvent phase, revealing free-energy barriers slightly higher than those in the gas phase. Amongst the various potential candidate Ru-complexes screened, few are found to differ in terms of efficiency for the dehydrogenation (rate-limiting) step. To model dehydrogenation more accurately, a selection of explicit protic solvent molecules was considered, with the goal of lowering energy barriers for H-H recombination. It was found that primary (1°), 2°, and 3° alcohols are the most suitable to enhance reaction rate. © 2014 Wiley Periodicals, Inc.
    Scopus© Citations 6  519
  • Publication
    Electronic properties of F/Zr co-doped anatase TiO2 photocatalysts from GGA + U calculations
    (Elsevier, 2010-10-08) ;
    The energetic and electronic properties of F and/or Zr-doped anatase TiO2 are investigated by first-principles calculations. For F-doping, reduced Ti3+ ions are formed and Ti orbitals lie slightly below the conduction band, leading to band gap narrowing. For Zr-doping, Zr 4d orbitals reside well into the conduction band, with essentially no band gap change. For F/Zr–codoping, the electronic structure is similar to that for F–monodoping, where Ti3+ gap states are induced by both the oxygen vacancy and F dopant. The influence of oxygen vacancies indicates that interplay between dopants and oxygen vacancies is key for improvement of photocatalytic activity. The theoretical findings present a reasonable explanation of recent experimental results.
      3719Scopus© Citations 27
  • Publication
    Magnetic properties of first-row element-doped ZnS semiconductors : a density functional theory investigation
    (American Physical Society, 2009-09-22) ;
    Based on first-principles calculations, we have investigated the magnetic properties of the first-row element-doped ZnS semiconductors. Calculations reveal that Be, B, and C dopants can induce magnetic, while N cannot lead to spin polarization in ZnS. A possible explanation was rationalized from the elements’ electronegativity and interaction between dopant atoms and host atoms. The total magnetic moments are 2.00, 3.16, and 2.38 μB per 2 x 2 x 2 supercell for Be, B, and C doping, respectively, and ferromagnetic coupling is generally observed in these cases. The ferromagnetism of Be-, B-, and C-doped ZnS can be explained by hole-mediated s-p or p-p interactions’ coupling mechanisms. However, the clustering effect was found to be in Be-, B-, and C-doped ZnS but the degree is more obvious in the former two cases than in latter case. Analysis revealed that C-doped ZnS displays better potential ferromagnetic behavior than Be- and B-doped ZnS due to its half-metallic characteristic.
      1167Scopus© Citations 78