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R Car

Publications and source records attributed to R Car.

At least 19 recordsLinked to original sources
PubMed2006

Orientational order of molecular assemblies on inorganic crystals.

Surfactant micelles form oriented arrays on crystalline substrates although registration is unexpected since the template unit cell is small compared to the size of a rodlike micelle. Interaction energy calculations based on molecular simulations reveal that orientational energy differences on a molecular scale are too small to explain matters. With atomic force microscopy, we show that orientational ordering is a dynamic, multimolecule process. Treating the cooperative processes as a balance between van der Waals torque on a large, rodlike micellar assembly and Brownian motion shows that orientation is favored.

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PubMed2004

First-principles string molecular dynamics: an efficient approach for finding chemical reaction pathways.

A recently proposed approach, called "string method," allows us to find minimum energy pathways connecting two metastable states of a system [W. E et al., Phys. Rev. B 66, 052301 (2002)]. So far this approach has been only used with empirical force field parametrizations of the atomic potential energy surface or in the context of macroscopic continuum models. Here we show that the string method can be efficiently combined with first-principles molecular dynamics to provide an accurate description of chemical reaction pathways and barriers. We illustrate the first-principles string molecular dynamics by applying it to the study of a surface chemical reaction, for which extensive experimental and theoretical works are available, namely, the adsorption of H(2) on the reconstructed Si(100) surface.

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PubMed2004

First-principle molecular dynamics with ultrasoft pseudopotentials: parallel implementation and application to extended bioinorganic systems.

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 metalorganic systems. Our results show that accurate density-functional theory calculations on systems with several hundred atoms are feasible with access to moderate computational resources.

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PubMed2001

First solvation shell of the Cu(II) aqua ion: evidence for fivefold coordination.

We determined the structure of the hydrated Cu(II) complex by both neutron diffraction and first-principles molecular dynamics. In contrast with the generally accepted picture, which assumes an octahedrally solvated Cu(II) ion, our experimental and theoretical results favor fivefold coordination. The simulation reveals that the solvated complex undergoes frequent transformations between square pyramidal and trigonal bipyramidal configurations. We argue that this picture is also consistent with experimental data obtained previously by visible near-infrared absorption, x-ray absorption near-edge structure, and nuclear magnetic resonance methods. The preference of the Cu(II) ion for fivefold instead of sixfold coordination, which occurs for other cations of comparable charge and size, results from a Jahn-Teller destabilization of the octahedral complex.

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PubMed2000

Dangling bond defects at Si-SiO2 interfaces: atomic structure of the P(b1) center

Using a first-principles approach, we characterize dangling bond defects at Si-SiO2 interfaces by calculating hyperfine parameters for several relaxed structures. Interface models, in which defect Si atoms remain close to crystalline sites of the substrate upon relaxation, successfully describe P(b) and P(b0) defects at (111) and (100) interfaces, respectively. On the basis of calculated hyperfine parameters, we discard models of the P(b1) defect containing a first neighbor shell with an O atom or a strained bond. A novel model consisting of an asymmetrically oxidized dimer yields hyperfine parameters in excellent agreement with experiment and is proposed as the structure of the P(b1) center.

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PubMed1997

Origin of the High-Frequency Doublet in the Vibrational Spectrum of Vitreous SiO2

The vibrational properties of amorphous SiO2 were studied within first-principles density functional theory. The calculated spectrum is in good agreement with neutron data, showing, in particular, a double peak in the high-frequency region. This doublet results from different local modes of the tetrahedral subunits and cannot be ascribed to a longitudinal-optic-transverse-optic (LO-TO) effect. This solves a long-standing controversy about the origin of the doublet in neutron spectra. A LO-TO splitting is recovered only when the long-wavelength limit is probed, as in optical experiments. These findings should be a general feature of tetrahedral AX2 amorphous networks.

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PubMed1997

Microscopic Growth Mechanisms for Carbon Nanotubes

The uncatalyzed edge growth of carbon nanotubes was investigated by first-principles molecular dynamics simulations. At experimental temperatures the open end of single-walled nanotubes closed spontaneously into a graphitic dome, which may explain why these nanotubes do not grow in the absence of transition metal catalysts. On the other hand, chemical bonding between the edges of adjacent coaxial tubes ("lip-lip" interactions) trapped the end of a double-walled nanotube in a metastable energy minimum, thus preventing dome closure. These calculations show that this end geometry exhibits a high degree of chemical activity and easily accommodates incoming carbon fragments, supporting a model of growth by chemisorption from the vapor phase.

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