Showing papers by "Roberto Car published in 2005"

Carbon phase diagram from ab initio molecular dynamics.

Abstract: We compute the free energy of solid and liquid diamond from first-principles electronic structure theory using efficient thermodynamic integration techniques. Our calculated melting curve is in excellent agreement with the experimental estimate of the graphite-diamond-liquid triple point and is consistent with shock wave experiments. We predict the phase diagram of diamond at pressures and temperatures that are difficult to access experimentally. We confirm early speculations on the presence of a reentrant point in the diamond melting line but find no evidence for a first order liquid-liquid phase transition near the reentrant point.

Oxygen Diffusion in Yttria-Stabilized Zirconia: A New Simulation Model

Abstract: We present a multiscale modeling approach to study oxygen diffusion in cubic yttria-stabilized zirconia. In this approach, we employ density functional theory methods to calculate activation energies for oxygen migration in different cation environments. These are used in a kinetic Monte Carlo framework to calculate long-time oxygen diffusivities. Simulation results show that the oxygen diffusivity attains a maximum value at around 0.1 mole fraction yttria. This variation in the oxygen diffusivity with yttria mole fraction and the calculated values for the diffusivity agree well with experiment. The competing effects of increased oxygen vacancy concentration and increasing activation energy and correlation effects for oxygen diffusion with increasing yttria mole fraction are responsible for the observed dopant content dependence of the oxygen diffusivity. We provide a detailed analysis of cation-dopant-induced correlation effects in support of the above explanation.

Intermolecular dynamical charge fluctuations in water: a signature of the H-bond network.

Abstract: We report a simulation of deuterated water using a Car-Parrinello approach based on maximally localized Wannier functions. This provides local information on the dynamics of the hydrogen-bond network and on the origin of the low-frequency infrared activity. The oscillator strength of the translational modes, peaked around $\ensuremath{\sim}200\text{ }\text{ }{\mathrm{cm}}^{\ensuremath{-}1}$, is anisotropic and originates from intermolecular---not intramolecular---charge fluctuations. These fluctuations are a signature of a tetrahedral hydrogen-bonding environment.

Density Functional Theory of the Electrical Conductivity of Molecular Devices

Abstract: Time-dependent density functional theory is extended to include dissipative systems evolving under a master equation, providing a Hamiltonian treatment for molecular electronics. For weak electric fields, the isothermal conductivity is shown to match the adiabatic conductivity, thereby recovering the Landauer result.

Use of dielectric functions in the theory of dispersion forces

Abstract: The modern theory of dispersion forces uses macroscopic dielectric functions $ϵ(\ensuremath{\omega})$ as a central ingredient. We reexamined the formalism and found that at separation distance $l2\phantom{\rule{0.3em}{0ex}}\mathrm{nm}$ the full dielectric function $ϵ(\ensuremath{\omega},\mathbf{k})$ is needed. The use of $ϵ(\ensuremath{\omega},\mathbf{k})$ results in as much as 30% reduction of the calculated Hamaker constants reported in the current literature. At larger distances, the theory reduces to the traditional method, which uses dielectric functions in the long-wavelength limit. We illustrate the formalism using the example of interaction between two graphite slabs. This example is of importance for intercalation and exfoliation of graphite and for the use of exfoliated graphite in composite materials. The formalism can also be extended to study anisotropic van der Waals interactions.

Quantum chemical evaluation of protein control over heme ligation: CO/O2 discrimination in myoglobin.

Abstract: Control of O 2 versus CO binding in myoglobin (Mb) is tuned by a distal histidine residue through steric and H-bonding interactions. These interactions have been evaluated via Car-Parrinello DFT calculations, whose efficiency allows full quantum mechanical treatment of the 13 closest residues surrounding the heme. The small (8°) deviation of the Fe-C-O bond angle from linearity results from the steric influence of a distal valine residue and not the distal histidine. H-bond energies were evaluated by replacing the distal histidine with the non-H-bonding residue isoleucine. Binding energies for CO and O 2 decreased by 0.8 and 4.1 kcal/ mol for MbCO and MbO 2 , in good agreement with experimental H-bond estimates. Ligand discrimination is dominated by distal histidine H-bonding, which is also found to stabilize a metastable side-on isomer of MbO 2 that may play a key role in MbO 2 photodynamics.

First principles study of density, viscosity, and diffusion coefficients of liquid MgSiO3 at conditions of the Earth's deep mantle

Abstract: Constant-pressure constant-temperature {\it ab initio} molecular dynamics simulations at high temperatures have been used to study MgSiO$_3$ liquid, the major constituent of the Earth's lower mantle to conditions of the Earth's core-mantle boundary (CMB). We have performed variable-cell {\it ab initio} molecular dynamic simulations at relevant thermodynamic conditions across one of the measured melting curves. The calculated equilibrium volumes and densities are compared with the simulations using an orthorhombic perovskite configuration under the same conditions. For molten MgSiO$_3$, we have determined the diffusion coefficients and shear viscosities at different thermodynamic conditions. Our results provide new constraints on the properties of molten MgSiO$_3$ at conditions near the core-mantle boundary. The volume change on fusion is positive throughout the pressure-temperature conditions examined and ranges from 5% at 88 GPa and 3500 K to 2.9% at 120 GPa and 5000 K. Nevertheless, neutral or negatively buoyant melts from (Mg,Fe)SiO$_3$ perovskite compositions at deep lower mantle conditions are consistent with existing experimental constraints on solid-liquid partition coefficients for Fe. Our simulations indicate that MgSiO$_3$ is liquid at 120 GPa and 4500 K, consistent with the lower range of experimental melting curves for this material. Linear extrapolation of our results indicates that the densities of liquid and solid perovskite MgSiO$_3$ will become equal near 180 GPa.

Point defect dynamics in bcc metals

Abstract: We present an analysis of the time evolution of self-interstitial atom and vacancy (point defect) populations in pure bcc metals under constant irradiation flux conditions. Mean-field rate equations are developed in parallel to a kinetic Monte Carlo (kMC) model. When only considering the elementary processes of defect production, defect migration, recombination and absorption at sinks, the kMC model and rate equations are shown to be equivalent and the time evolution of the point defect populations is analyzed using simple scaling arguments. We show that the typically large mismatch of the rates of interstitial and vacancy migration in bcc metals can lead to a vacancy population that grows as the square root of time. The vacancy cluster size distribution under both irreversible and reversible attachment can be described by a simple exponential function. We also consider the effect of highly mobile interstitial clusters and apply the model with parameters appropriate for vanadium and $\ensuremath{\alpha}$-iron.

Quantum collision current in electronic circuits.

Abstract: and not as well-known quantum feature of electronic circuits. When a circuit of length L is described within classical or semiclassical approximations, the power needed for the circulation of a dc current I is given by W = LI in terms of the applied dc electromotive force . We will argue below that a larger power W > LI is required to circulate a current I in a quantum device. The reason for the inequality is that, in addition to the power needed to circulate the current I, some dc power is also needed to maintain a stationary charge distribution in the circuit. This is a genuine quantum effect. In circuits governed by the laws of classical physics, some power is needed to displace charges in the initial transient, but no dc power is required to maintain a stationary charge distribution when a dc current is flowing.

Longitudinal polarizability of long polymeric chains: Quasi-one-dimensional electrostatics as the origin of slow convergence

Abstract: The longitudinal linear polarizability alpha(N) of a stereoregular oligomer of size N is proportional to N in the large-N limit, provided the system is nonconducting in that limit. It has long been known that the convergence of alpha(N)/N to the asymptotic alpha(infinity) value is slow. We show that the leading term in the difference between alpha(N)/N and alpha(infinity) is of the order of 1/N. The difference [alpha(N)-alpha(N-1)], as well as alpha(center)(N) (when computationally accessible), also converge to alpha(infinity), but faster, the leading term being of the order of 1/N(2). We also present evidence that in these cases the power law convergence behavior is due to quasi-one-dimensional electrostatics, with one exception. Specifically, in molecular systems the difference between alpha(N)/N and alpha(infinity) has not just one but two sources of the O(1/N) term, with one being due to the aforementioned Coulomb interactions, and the second due to the short ranged exponentially decaying perturbations on chain ends. The major role of electrostatics in the convergence of the remainders is demonstrated by means of a Clausius-Mossotti-type classical model. The conclusions derived from the model are also shown to be applicable in molecular systems, by means of test-case ab initio calculations on linear stacks of H(2) molecules, and on polyacetylene chains. The implications of the modern theory of polarization for extended systems are also discussed.

Effects of Lanthanide Dopants on Oxygen Diffusion in Yttria‐Stabilized Zirconia

Abstract: The effects of lanthanide co-dopants on oxygen diffusion in yttria-stabilized zirconia (YSZ) are studied using a combined first principles density functional theory (DFT)/kinetic Monte Carlo (kMC) modeling approach. DFT methods are used to calculate barrier energies for oxygen migration in different local cation environments, which are then input into kMC simulations to obtain long-time oxygen diffusivities and activation energies. Simulation results show a substantial increase in the maximum value of the oxygen diffusivity upon co-doping and in the dopant content at which this value is obtained for Lu-co-doped YSZ; while relatively little change is seen for Gd-co-doped YSZ. Examination of the DFT barrier energies reveals a linear scaling of barrier heights with the size of cations at the diffusion transition state. Using this strong correlation, oxygen diffusivity is examined in YSZ co-doped with several lanthanide elements. The oxygen diffusivity decreases with dopant atomic number (and decreasing dopant ion size) for co-dopants smaller than Y, and changes relatively little when Y is replaced by co-dopants larger than it. These results are broadly consistent with experiment, and are explained in terms of cation-dopant and vacancy concentration-dependent correlation effects, with the aid of a simple analytical model.

First-Principles Molecular Dynamics

Abstract: Ab initio or first-principles methods have emerged in the last two decades as a powerful tool to probe the properties of matter at the microscopic scale. These approaches are used to derive macroscopic observables under the controlled condition of a “computational experiment,” and with a predictive power rooted in the quantum-mechanical description of interacting atoms and electrons. Density-functional theory (DFT) has become de facto the method of choice for most applications, due to its combination of reasonable scaling with system size and good accuracy in reproducing most ground state properties. Such an electronic-structure approach can then be combined with classical molecular dynamics to provide an accurate description of thermodynamic properties and phase stability, atomic dynamics, and chemical reactions, or as a tool to sample the features of a potential energy surface.

Protonation-induced stereoisomerism in nicotine: conformational studies using classical (AMBER) and ab initio (Car-Parrinello) molecular dynamics.

Abstract: A variety of biologically active small molecules contain prochiral tertiary amines, which become chiral centers upon protonation. S-nicotine, the prototypical nicotinic acetylcholine receptor agonist, produces two diastereomers on protonation. Results, using both classical (AMBER) and ab initio (Car–Parrinello) molecular dynamical studies, illustrate the significant differences in conformational space explored by each diastereomer. As is expected, this phenomenon has an appreciable effect on nicotine’s energy hypersurface and leads to differentiation in molecular shape and divergent sampling. Thus, protonation induced isomerism can produce dynamic effects that may influence the behavior of a molecule in its interaction with a target protein. We also examine differences in the conformational dynamics for each diastereomer as quantified by both molecular dynamics methods.

Molecular and solid-state (8-hydroxy-quinoline)aluminum interaction with magnesium: A first-principles study

Abstract: The interaction between Mg and (8-hydroxyquinoline)aluminum, Alq3, is investigated via ab initio molecular dynamics based on density-functional theory. We model the Alq3 thin film both with a single Alq3 molecule in vacuo (as is usually done in the literature) and with an Alq3 crystalline structure. Comparing the results from these two models, we show that bulk calculations provide a better description of the chemical processes involved, allowing the Mg atom to react with two neighboring Alq3 molecules, as was alluded to in a previous publication [S. Meloni, A. Palma, A. Kahn, J. Schwartz, and R. Car, J. Am. Chem. Soc. 125, 7808 (2003)]. Moreover, core-level shift calculations are in good agreement with experimental measurements only when using the solid phase approach. We also propose a different interpretation of the Al(2p) experimental core level presented in a previous work [C. Shen, A. Kahn, and J. Schwartz, J. Appl. Phys. 89, 449 (2001)].

Free energy profile along a discretized reaction path via the hyperplane constraint force and torque

Abstract: By employing mechanical work analogies, we derive a convenient computational approach for evaluation of the free energy profile (FEP) along some discretized path defined as a sequence of hyperplanes. A hyperplane is fully specified by any of its point and a tangent vector. The FEP is obtained as an integral of two components. The translational component of the free energy is computed by integrating the hyperplane constraint force. The rotational component is evaluated via the hyperplane torque. Both ingredients—the constraint force and the hyperplane torque—are evaluated on each hyperplane independently. The integration procedure utilizes a set of reference points defining a point of rotation on each hyperplane, and these points can be chosen before or after the sampling takes place. A shift in the reference points redistributes the FEP contributions between the translational and rotational components. For systems where the FEP is dominated by the potential energy differences, reference points residing on the minimum energy path present a natural choice. We demonstrate the validity of our approach on two examples, a simple two-dimensional (2D) potential, and a seven-atom Lennard-Jones cluster. In each case, we compare the numerical FEP with the harmonic approximation estimates. Our results for the 2D potential are also verified by the data available in the literature. In both cases, the rotational component of the FEP represents a sizable contribution to the total FEP, so ignoring it would yield clearly incorrect results.

Electron transport with dissipation: A quantum kinetic approach

Abstract: We present a method for calculating electronic transport properties at the nanoscale. In this approach we describe the electron kinetics in the presence of an external field and of a heat bath. While the electric field accelerates the electrons, energy is dissipated as a result of interaction with the heat bath, allowing the system to reach steady state. The method is based on a Liouville master equation that constitutes a fully quantum generalization of the Boltzmann kinetic equation. As an example we report an application to transport through a double-barrier resonant tunneling structure. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2005

1.4 first-principles molecular dynamics

Abstract: Ab initio or first-principles methods have emerged in the last two decades as a powerful tool to probe the properties of matter at the microscopic scale. These approaches are used to derive macroscopic observables under the controlled condition of a “computational experiment,” and with a predictive power rooted in the quantum-mechanical description of interacting atoms and electrons. Density-functional theory (DFT) has become de facto the method of choice for most applications, due to its combination of reasonable scaling with system size and good accuracy in reproducing most ground state properties. Such an electronic-structure approach can then be combined with classical molecular dynamics to provide an accurate description of thermodynamic properties and phase stability, atomic dynamics, and chemical reactions, or as a tool to sample the features of a potential energy surface. In a molecular-dynamics (MD) simulation the microscopic trajectory of each individual atom in the system is determined by integration of Newton’s equations of motion. In classical MD, the system is considered composed of massive, point-like nuclei, with forces acting between them derived from empirical effective potentials. Ab initio MD maintains the same assumption of treating atomic nuclei as classical particles; however, the forces acting on them are considered quantum mechanical in nature, and are derived from an electronic-structure calculation. The approximation of treating quantummechanically only the electronic subsystem is usually perfectly appropriate, due to the large difference in mass between electrons and nuclei. Nevertheless, nuclear quantum effects can be sometimes relevant, especially for light

Electron transport in molecular devices

Abstract: Submitted for the MAR06 Meeting of The American Physical Society Electron transport in molecular devices SIMONE PICCININ, Princeton Univeristy Department of Chemistry, RALPH GEBAUER, ICTP Trieste (Italy), ROBERTO CAR, Princeton University Department of Chemistry — We present an application of a recently proposed quantum-kinetic scheme for non equilibrium transport properties in nanoscale systems, based on a Liouville-master equation for the reduced density operator and combined with a Density Functional Theory description of the electronic structure [1,2]. The systems studied are the well known benzene-dithiol sandwiched between two gold electrodes and the gold quantum point contact. The results we obtain are in general agreement with previous theoretical works and with recent experimental measurements. We analyze the spatial distribution of the current density and the effect of geometrical distortions on the transport properties. Simone Piccinin Princeton Univeristy Department of Chemistry Date submitted: 30 Nov 2005 Electronic form version 1.4