Showing papers by "Roberto Car published in 2003"

Oxygen adsorption on graphite and nanotubes

Abstract: We study the binding of molecular oxygen to a graphene sheet and to a (8,0) single walled carbon nanotube, by means of spin-unrestricted density-functional calculations. We find that triplet oxygen retains its spin-polarized state when interacting with graphene or the nanotube. This leads to the formation of a weak bond with essentially no charge transfer between the molecule and the sheet or tube, as one would expect for a physisorptive bond. This result is independent on the approximation used for the exchange-correlation functional. The binding strength, however, depends strongly on the functional, reflecting the inability of current approximation functionals to deal correctly with dispersion forces. Gradient-corrected functionals yield very weak binding at distances around 4 A, whereas local density functional results yield substantially stronger binding for both graphene and the nanotube at distances of less than 3 A. The picture of oxygen physisorption is not substantially altered by the presence of topological defects such as 5–7 Stone–Wales pairs.

Photoinduced oxidation of carbon nanotubes

Abstract: Photoinduced phenomena are of general interest for new materials. Recently, photoinduced molecular desorption of oxygen has been reported in carbon nanotubes. Here we present, using thermopower measurements, that carbon nanotubes when exposed simultaneously to UV light and oxygen exhibit photoinduced oxidation of the nanotubes. At least two plausible mechanisms for the experimentally observed photoinduced oxidation are proposed: (i) a lower energy barrier for the adsorption of photo-generated singlet oxygen, or (ii) due to the presence of defects in carbon nanotubes that may facilitate the formation of locally electron-deficient and electron-rich regions on the nanotubes which facilitate the adsorption of oxygen molecules on the nanotubes.

First-principle molecular dynamics with ultrasoft pseudopotentials: parallel implementation and application to extended bio-inorganic system

Abstract: We present a plane-wave ultrasoft pseudopotential implementation of first-principle molecular dynamics, which is well suited to model large molecular systems containing transition metal centers. We describe an efficient strategy for parallelization that includes special features to deal with the augmented charge in the contest of Vanderbilt's ultrasoft pseudopotentials. We also discuss a simple approach to model molecular systems with a net charge and/or large dipole/quadrupole moments. We present test applications to manganese and iron porphyrins representative of a large class of biologically relevant metallorganic systems. Our results show that accurate Density-Functional Theory calculations on systems with several hundred atoms are feasible with access to moderate computational resources.

Interatomic potential for vanadium suitable for radiation damage simulations

Abstract: The ability to predict the behavior of point defects in metals, particularly interstitial defects, is central to accurate modeling of the microstructural evolution in environments with high radiation fluxes. Existing interatomic potentials of embedded atom method type predict disparate stable interstitial defect configurations in vanadium. This is not surprising since accurate first-principles interstitial data were not available when these potentials were fitted. In order to provide the input information required to fit a vanadium potential appropriate for radiation damage studies, we perform a series of first-principles calculations on six different interstitial geometries and vacancies. These calculations identify the 〈111〉 dumbbell as the most stable interstitial with a formation energy of approximately 3.1 eV, at variance with predictions based upon existing potentials. Our potential is of Finnis–Sinclair type and is fitted exactly to the experimental equilibrium lattice parameter, cohesive energy, elastic constants and a calculated unrelaxed vacancy formation energy. Two additional potential parameters were used to obtain the best fit to the set of interstitial formation energies determined from the first-principles calculations. The resulting potential was found to accurately predict both the magnitude and ordering of the formation energies of six interstitial configurations and the unrelaxed vacancy ground state, in addition to accurately describing the migration characteristics of the stable interstitial and vacancy. This vanadium potential is capable of describing the point defect properties appropriate for radiation damage simulations as well as for simulations of more common crystal and simple defect properties.

Electronic properties of metal-molecule-metal systems at zero bias: A periodic density functional study

Abstract: We have studied the electronic properties of conjugated and saturated dithiol molecules sandwiched between two Au(111) electrodes using first principles density functional calculations with a slab geometry. Relaxation of the molecule/surface adsorption geometry as well as the extended character of the metal electrode states are fully taken into account by our approach. Investigated quantities include the alignment of molecular energy levels with the Fermi energy (EF) of the metal, the charge transfer and electrostatic potential profile, and the local density of electronic states (LDOS) at EF. The behavior of the LDOS for benzene–, dibenzene–, and xylyl–dithiol molecules is analyzed and compared with that of alkane–dithiols of various lengths.

Ab initio molecular dynamics with maximally localized Wannier functions

Abstract: We present a novel formulation of ab initio molecular dynamics that should be useful to simulate insulating systems. In this scheme maximally localized Wannier functions instead of delocalized Bloch states evolve on the fly during nuclear dynamics. Localized Wannier orbitals offer several advantages over orbitals that are delocalized in the entire simulation cell. In fact, at variance with the latter, they provide a picture of the electronic bonds consistent with simple chemical intuition. In addition, by taking advantage of their exponential localization it should be possible to develop ab initio molecular dynamics schemes having a computational cost that scales linearly rather than cubically with system size. We show that maximally localized Wannier functions can be calculated efficiently within Car–Parrinello dynamics and use water in gas and liquid phase as a test system to demonstrate our scheme and illustrate its usefulness. © 2003 Wiley Periodicals, Inc. Int J Quantum Chem, 2003

Closing of the nucleotide pocket of kinesin-family motors upon binding to microtubules.

Abstract: We have used adenosine diphosphate analogs containing electron paramagnetic resonance (EPR) spin moieties and EPR spectroscopy to show that the nucleotide-binding site of kinesin-family motors closes when the motor.diphosphate complex binds to microtubules. Structural analyses demonstrate that a domain movement in the switch 1 region at the nucleotide site, homologous to domain movements in the switch 1 region in the G proteins [heterotrimeric guanine nucleotide-binding proteins], explains the EPR data. The switch movement primes the motor both for the free energy-yielding nucleotide hydrolysis reaction and for subsequent conformational changes that are crucial for the generation of force and directed motion along the microtubule.

Role of ligand bending in the photodissociation of O2 vs CO-heme: a time-dependent density functional study.

Abstract: Time-dependent DFT calculations reveal a strong dependence of low-lying excited states on the

Molecular dynamics study of the threshold displacement energy in vanadium

Abstract: The threshold displacement energy (TDE) is calculated for vanadium as a function of temperature and orientation by molecular dynamics simulations. The TDE varies from 13 to 51 eV, depending on orientation and is nearly temperature independent between 100 and 900 K. The lowest TDE is in the 〈100〉 direction. We characterize the defects associated with the displacement simulations and found that they consist of vacancies and 〈111〉-split dumbbells.

PbTiO3 at Finite Temperature: An Ab‐initio Molecular Dynamics Study

Abstract: PbTiO3 is a prototypical ferroelectric material that exhibits a single structural phase transition (cubic to tetragonal): it is a soft mode driven, predominantly displacive, transition. In this paper, we study the behavior of PbTiO3 at finite temperature by ab‐initio molecular dynamics simulations. In this approach classical mechanics is used to describe nuclear dynamics, while the interatomic potential is generated on the fly from the ground state of the electrons within density functional theory. Fluctuations of volume and shape of the simulation cell are included by means of Parrinello‐Rahman constant pressure scheme. Extensive convergence studies based on static calculations indicate that a 3×3×3 supercell containing 135 atoms, with a single k‐point sampling, is sufficient to represent accurately the T = 0 energetics of this material. Although computationally demanding, ab‐initio molecular dynamics simulations for PbTiO3 using a 3×3×3 cell are feasible with current computational methodologies. Here we report preliminary results of simulations that are both below and above the phase‐transition temperature. We discuss, in particular, how phonon softening occurs with temperature and how thermal expansion affects the results.

On the Mechanism of the Hydrogen/Platinum (111) Fuel Cell

Abstract: We discuss our recently proposed mechanism for the electro-oxidation/reduction on Pt(111) surfaces[J. of Electroanal. Chemistry, 537 (2002) 7] in the presence of sulfuric acid.The bisulfate ion has a large dipole moment and is strongly adsorbed on the positive electrode. Due to the large field gradients, the oxygen atoms of the adsorbed water molecules ( and the dipoles) point down and bind to the on-top positions of the platinum substrate. As the electrode becomes more negative the field gradient changes direction and the water dipoles gradually reverse their orientation. At a certain critical value of the orientational parameter, ( which depends also on the bisulfate surface concentration) a two dimensional honeycomb array of hydrogen bonded water molecules is formed. This is a new form of solid water, a true two dimensional ’ice’. For these negative potentials the stable structure has one of the hydrogen atoms of the water pointing down, and this means that it is adsorbed by the hollow site of the Pt lattice. In order to satisfy the stoichiometry of the hydrogen bonds, we need to adsorb 1/3 of the surface sites of H ions. The following reversible reaction occurs(1)For the (111) surface of Platinum, and because of the geometrical match-up (the Pt-Pt distance is 2.77 ˚ A,andthe waterdiameteris2.76 ˚ A) this reaction occurs as a first order transition, visible in the voltammogram as a sharp peak. From the [H] concentration dependence of this sharp spike we get an effective charge of 1.02±0.02 for the adsorbed moiety. High accuracy quantum calculations on a 5 layer platinum metal slab show that this compound is stable in the absence of bisulfate ions.The quantum calculations show also that the hydrogen atoms in the hollow positions are neutralized. Since there are 2/3 of the Pt sites in the hollow positions, our model gives a natural explanation to the well known fact that the hydrogen yield is 2/3 on this surface.We have revised our theory to shift the turning point of the water molecules to the transition potential where the HER honeycomb phase is formed. The turning point is in general agreement with the recent laser induced measurements of the potential of zero charge.