[show abstract][hide abstract] ABSTRACT: An ab initio density functional theory study is reported of the conformational energy map of acetylcholine, with respect to the two central dihedral angles of the molecule. The acetylcholine molecule pays a central role in neurotransmission and has been studied widely using semi-empirical computational modelling. The ab initio results are compared with a number of previous investigations and with experiment. The ab initio data indicate that the most stable conformation of acetylcholine is the trans, gauche arrangement of the central dihedral angles. Furthermore, Mulliken population analysis of the electronic structure of the molecule in this conformation indicates that the positive charge of the molecule is spread over the exterior of the cationic head of the molecule.
Molecular Physics 12/2010; February 20(1998):365-370. · 1.67 Impact Factor
[show abstract][hide abstract] ABSTRACT: Ab initio calculations are presented of the cohesive energies of aluminium in a number of diverse hypothetical structures which span a wide range of the coordination number, C, from C = 0 to C = 12. The calculations have been performed to investigate the nature of multi-atom bonding, its dependence on C and to form a database for testing and developing empirical and semi-empirical models. The results support the saturation of cohesive energy for large C predicted by several simple theoretical models. Calculations on the same structures using semi-empirical schemes suggest that these methods might have a greater degree of accuracy than had previously been believed.
[show abstract][hide abstract] ABSTRACT: An overview is presented of the method used to parallelize a set of total energy pseudopotential codes on a 64-node i860 Meiko Computing Surface and a 32-node Intel iPSC/860 Hypercube. These codes have been used to calculate the surface energies and relaxed structures of the 3 × 3, 5 × 5 and 7 × 7 Takayanagi reconstructions of the (111) surface of silicon. It is found that the 7 × 7 reconstruction has the lowest energy and that structural trends across the series of reconstructions can be related to the degree of charge transfer from the adatoms to the rest atoms.
Physica Scripta 01/2007; 1992(T45):265. · 1.03 Impact Factor
[show abstract][hide abstract] ABSTRACT: The CASTEP code for first principles electronic
structure calculations will be described. A brief, nontechnical overview will be given and some of the features
and capabilities highlighted. Some features which are unique
to CASTEP will be described and near-future development
[show abstract][hide abstract] ABSTRACT: We present a systematic methodology for the accurate calculation of defect structures in supercells which we illustrate with a study of the neutral vacancy in silicon. This is a prototypical defect which has been studied extensively using ab initio methods, yet remarkably there is still no consensus about the energy or structure of this defect, or even whether the nearest neighbour atoms relax inwards or outwards. In this paper we show that the differences between previous calculations can be attributed to supercell convergence errors, and we demonstrate how to systematically reduce each such source of error. The various sources of scatter in previous theoretical studies are discussed and a new effect, that of supercell symmetry, is identified. It is shown that a consistent treatment of this effect is crucial to understanding the systematic effects of increasing the supercell size. This work therefore also presents the best converged ab initio study of the neutral silicon vacancy to date. Comment: 18 pages, 5 figures, requires RevTex4
[show abstract][hide abstract] ABSTRACT: First-principles simulation, meaning density-functional theory calculations with plane waves and pseudopotentials, has become a prized technique in condensed-matter theory. Here I look at the basics of the suject, give a brief review of the theory, examining the strengths and weaknesses of its implementation, and illustrating some of the ways simulators approach problems through a small case study. I also discuss why and how modern software design methods have been used in writing a completely new modular version of the CASTEP code.
[show abstract][hide abstract] ABSTRACT: A comparison between experimental and theoretical electron energy loss near edge structure (ELNES) of B and N K edges in cubic boron nitride is presented. The electron energy loss spectra of cubic boron nitride particles were measured using a scanning transmission electron microscope. The theoretical calculation of the ELNES was performed within the framework of density functional theory including single particle core-hole effects. The results suggest that core-hole effects can be adequately incorporated into the plane-wave pseudopotential method to produce striking agreement with the best available experimental spectra.
[show abstract][hide abstract] ABSTRACT: We present a theoretical study of the formation of the first intermediate, dimethyl ether, in the methanol to gasoline conversion within the framework of an ab initio molecular dynamics approach. The study is performed under conditions that closely resemble the reaction conditions in the zeolite catalyst including the full topology of the framework. The use of the method of thermodynamic integration allows us to extract the free-energy profile along the reaction coordinate. We find that the entropic contribution qualitatively alters the free-energy profile relative to the total energy profile. Different transition states are found from the internal and free energy profiles. The entropy contribution varies significantly along the reaction coordinate and is responsible for stabilizing the products and for lowering the energy barrier. The hugely inhomogeneous variation of the entropy can be understood in terms of elementary processes that take place during the chemical reaction. Our simulations provide new insights into the complex nature of this chemical reaction.
[show abstract][hide abstract] ABSTRACT: Atomic force microscopy operating in the contact mode is studied using total-energy pseudopotential calculations. It is shown that, in the case of a diamond tip and a diamond surface, it is possible for a tip terminated by a single atom to sustain forces in excess of 30 nN. It is also shown that imaging at atomic resolution may be limited by blunting of the tip during lateral scanning.
[show abstract][hide abstract] ABSTRACT: We show that plane wave ultrasoft pseudopotential methods readily extend to the calculation of the structural properties of lanthanide and actinide containing compounds. This is demonstrated through a series of calculations performed on UO, UO2, UO3, U3O8, UC2, alpha-CeC2, CeB6, CeSe, CeO2, NdB6, TmOI, LaBi, LaTiO3, YbO, and elemental Lu.
[show abstract][hide abstract] ABSTRACT: First principles calculations have significantly advanced the understanding of the first stages of the methanol to gasoline conversion process in zeolite acid catalysts. The theoretical techniques used in first principles total energy pseudopotential calculations are described in this paper and the application of these calculations to investigate the first stages of the reaction of methanol in acid zeolites is described. First principles total energy pseudopotential calculations have shown that finite temperature effects are particularly important in this system. A fully ab initio calculation of the free energy barrier to the formation of dimethyl ether (DME) from methanol has been performed. It is found that the entropy of the system varies considerably along the reaction path and that the conversion of methanol to DME is entropically driven.
Microporous and Mesoporous Materials - MICROPOROUS MESOPOROUS MAT. 01/2001; 48(1):375-381.
[show abstract][hide abstract] ABSTRACT: The theoretical strength of diamond has been calculated for the <100>, <110>, and <111> directions using a first principles approach and is found to be strongly dependent on crystallographic direction. This elastic anisotropy, found at large strains, and particularly the pronounced minimum in cohesion in the <111> direction, is believed to be the reason for the remarkable dominance of the 111 cleavage plane when diamond is fractured. The extra energy required to cleave a crystal on planes other than 111 is discussed with reference to simple surface energy calculations and also the introduction of bond-bending terms.
[show abstract][hide abstract] ABSTRACT: Gallium impurities affect the atomic processes and material properties of aluminum metal to a high degree. Various ab initio calculations have been performed on a Σ=11 (113) symmetric tilt boundary in aluminum with and without some gallium substitutions. A simple interpretation of the results emerges, which can be applied to grain boundaries in general. The calculations relate to the energetics of gallium substitution on various sites, local relaxation effects, vibrational frequencies and a barrier to grain boundary migration.
[show abstract][hide abstract] ABSTRACT: The k.p expressions for the gradient and curvature (and hence effective masses) of electronic energy bands in reciprocal space are presented for calculations involving nonlocal and non-normconserving Vanderbilt ultrasoft pseudopotentials [D. Vanderbilt, Phys. Rev. B 41, 7892 (1990)]. The expressions have been implemented, and comparison with numerically calculated gradients and curvatures show that they are practical, accurate, and useful in the calculation of electronic densities-of-states.
Physical Review B - PHYS REV B. 01/2000; 62(7):4383-4388.
[show abstract][hide abstract] ABSTRACT: 1. The application of novel ab initio quantum mechanical methods to the states in the catalytic cycle of cytochrome P450 following the first reduction step is described. 2. A good correlation was found between the calculated energy of reduction and the experimentally determined redox potential for a range of substrate- and substrate analogue-bound systems. 3. On reduction of the haem system, the ground state of Fe remains Fe3+. On binding of a CO molecule, Fe adopts a low-spin Fe2+ state, in agreement with experiment. However, on binding of an O2 molecule, calculations indicate that the system adopts a ferric superoxide ground state, in which the Fe is in a low-spin Fe3+ state.
[show abstract][hide abstract] ABSTRACT: We present an extensive study of the initial stages of the methanol to gasoline conversion in the framework of the ab initio molecular dynamics approach. We investigate the effect of different zeolite environments, methanol loading, and temperature and show that, for understanding the initial adsorption and activation of the adsorbed species, all three factors need to be considered simultaneously. The results allow us to develop a simple model for the activation of the methanol molecule, which elucidates the role of both the zeolite framework and the methanol solvent. The zeolite framework plays an active role in methanol protonation. The solvent significantly softens the C−O bond of the methoxonium, rendering it very anharmonic. High mobility of the methoxonium cation, promoted by some zeolite frameworks, prevents it from forming hydrogen bonds with the active sites and the solvent leading to the activation of the methoxonium species. This picture is shown to be consistent with the experimental infrared spectra.
Journal of The American Chemical Society - J AM CHEM SOC. 03/1999; 121(14).
[show abstract][hide abstract] ABSTRACT: Al(110) has been studied for temperatures up to 900 K via ensemble density-functional molecular dynamics. The strong anharmonicity displayed by this surface results in a negative coefficient of thermal expansion, where the first interlayer distance decreases with increasing temperature. Very shallow channels of oscillation for the second-layer atoms in the direction perpendicular to the surface support this anomalous contraction, and provide a novel mechanism for the formation of adatom-vacancy pairs, preliminary to the disordering and premelting transition. Such characteristic behavior originates in the free-electron-gas bonding at a loosely packed surface. Comment: 4 pages, two-column style with 5 PostScript figures embedded. Uses RevTeX and epsf macros. To appear in Phys. Rev. Lett. Also available at http://www.physics.rutgers.edu/~marzari/preprints/index.html#al110
[show abstract][hide abstract] ABSTRACT: A highly efficient extrapolative Brillouin-zone integration scheme is presented that requires a very low k-point sampling density for spectral integrations. It is important to use an extrapolative approach, since at low sampling densities interpolative schemes are hindered by problems associated with band crossing, which introduce spurious singularities in the density of states (DOS). The information for the extrapolation is obtained using second-order k⋅p perturbation theory within a set of subcells of the Brillouin zone, which can be chosen to make full use of symmetry. The resulting piecewise quadratic representation of the band structure is converted directly to a DOS using an analytic approach. It is also shown that this method can be successfully applied even in the linear extrapolative case.