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14 Dec 2010

Volume 133, Issue 22, Articles (22xxxx)

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J. Chem. Phys. 133, 221101 (2010); http://dx.doi.org/10.1063/1.3522773 (4 pages)

Bradley P. Lambeth, Jr., Christoph Junghans, Kurt Kremer, Cecilia Clementi, and Luigi Delle Site
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Communication: On the locality of Hydrogen bond networks at hydrophobic interfaces

Bradley P. Lambeth, Jr., Christoph Junghans, Kurt Kremer, Cecilia Clementi, and Luigi Delle Site

J. Chem. Phys. 133, 221101 (2010); http://dx.doi.org/10.1063/1.3522773 (4 pages) | Cited 2 times

Online Publication Date: 9 December 2010

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The formation of structured hydrogen bond networks in the solvation shells immediate to hydrophobic solutes is crucial for a large number of water mediated processes. A long lasting debate in this context regards the mutual influence of the hydrophobic solute into the bulk water and the role of the hydrogen bond network of the bulk in supporting the solvation structure around a hydrophobic molecule. In this context we present a molecular dynamics study of the solvation of various hydrophobic molecules where the effect of different regions around the solvent can be analyzed by employing an adaptive resolution method, which can systematically separate local and nonlocal factors in the structure of water around a hydrophobic molecule. A number of hydrophobic solutes of different sizes and two different model potential interactions between the water and the solute are investigated.
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82.30.Nr Association, addition, insertion, cluster formation
82.20.Bc State selected dynamics and product distribution
82.20.Yn Solvent effects on reactivity
82.20.Wt Computational modeling; simulation
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Communication: Experimental proof of symmetry breaking in tilted smectics composed of molecules with axial chirality

Milada Glogarová, František Hampl, Lubor Lejček, Vladimíra Novotná, Jiří Svoboda, and Martin Cigl

J. Chem. Phys. 133, 221102 (2010); http://dx.doi.org/10.1063/1.3525644 (4 pages)

Online Publication Date: 14 December 2010

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For the first time, domains with twisted structures have been established in planar samples of achiral compounds in tilted smectic C phase. This evidences separation of molecular conformers differing in the sense of axial chirality and confirms polar C2 symmetry of these domains. A simple model considering polar surface anchoring energy and bulk energy of the twist can account for this finding. Conditions for coexistence of twisted and homogeneous domains are discussed.
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61.30.-v Liquid crystals
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back to top Theoretical Methods and Algorithms

Steepest descent reaction path integration using a first-order predictor–corrector method

Hrant P. Hratchian, Michael J. Frisch, and H. Bernhard Schlegel

J. Chem. Phys. 133, 224101 (2010); http://dx.doi.org/10.1063/1.3514202 (8 pages) | Cited 1 time

Online Publication Date: 8 December 2010

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The theoretical treatment of chemical reactions inevitably includes the integration of reaction pathways. After reactant, transition structure, and product stationary points on the potential energy surface are located, steepest descent reaction path following provides a means for verifying reaction mechanisms. Accurately integrated paths are also needed when evaluating reaction rates using variational transition state theory or reaction path Hamiltonian models. In this work an Euler-based predictor–corrector integrator is presented and tested using one analytic model surface and five chemical reactions. The use of Hessian updating, as a means for reducing the overall computational cost of the reaction path calculation, is also discussed.
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82.20.Hf Product distribution
82.20.Db Transition state theory and statistical theories of rate constants

Phase behavior of polydisperse spheres: Simulation strategies and an application to the freezing transition

Nigel B. Wilding and Peter Sollich

J. Chem. Phys. 133, 224102 (2010); http://dx.doi.org/10.1063/1.3510534 (12 pages) | Cited 2 times

Online Publication Date: 9 December 2010

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The statistical mechanics of phase transitions in dense systems of polydisperse particles presents distinctive challenges to computer simulation and analytical theory alike. The core difficulty, namely, dealing correctly with particle size fractionation between coexisting phases, is set out in the context of a critique of previous simulation work on such systems. Specialized Monte Carlo simulation techniques and moment free energy method calculations, capable of treating fractionation exactly, are then described and deployed to study the fluid–solid transition of an assembly of repulsive spherical particles described by a top-hat “parent” distribution of particle sizes. The cloud curve delineating the solid–fluid coexistence region is mapped as a function of the degree of polydispersity δ, and the properties of the incipient “shadow” phases are presented. The coexistence region is found to shift to higher densities as δ increases, but does not exhibit the sharp narrowing predicted by many theories and some simulations.
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61.20.Ja Computer simulation of liquid structure
82.70.-y Disperse systems; complex fluids
64.70.D- Solid-liquid transitions

Non-Born–Oppenheimer approximation for very weakly bound states of molecular anions

W. R. Garrett

J. Chem. Phys. 133, 224103 (2010); http://dx.doi.org/10.1063/1.3511638 (6 pages)

Online Publication Date: 9 December 2010

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The influence of nuclear rotation on weak electron binding in the long range field of a linear polar molecule is treated in a way that leads ultimately, with suitable approximation, to the familiar equations for close coupling of electron-nuclear-rotational motions. Subsequently, a conventional pseudopotential approximation is invoked to examine the rotational spectra of HCN and DCN anions. It is shown that the number of rotationally excited anion states cannot be reliably predicted by assuming that zero binding occurs when the rotational energy equals the electron affinity obtained in the Born–Oppenheimer approximation. A method is suggested for combining accurate molecular orbital and parameterized pseudopotential methods to provide accurate electron affinities for very weakly bound anionic states.
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33.20.Sn Rotational analysis
33.15.Ry Ionization potentials, electron affinities, molecular core binding energy
31.15.-p Calculations and mathematical techniques in atomic and molecular physics

Crystal structure prediction using the minima hopping method

Maximilian Amsler and Stefan Goedecker

J. Chem. Phys. 133, 224104 (2010); http://dx.doi.org/10.1063/1.3512900 (8 pages) | Cited 1 time

Online Publication Date: 10 December 2010

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A structure prediction method is presented based on the minima hopping method. To escape local minima, moves on the configurational enthalpy surface are performed by variable cell shape molecular dynamics. To optimize the escape steps the initial atomic and cell velocities are aligned to low curvature directions of the current local minimum. The method is applied to both silicon crystals and well-studied binary Lennard-Jones mixtures. For the latter new putative ground state structures are presented. It is shown that a high success rate is achieved and a reliable prediction of unknown ground state structures is possible.
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81.05.Cy Elemental semiconductors
61.20.Ja Computer simulation of liquid structure
65.20.De General theory of thermodynamic properties of liquids, including computer simulation
65.40.G- Other thermodynamical quantities
61.66.Bi Elemental solids

Scalable free energy calculation of proteins via multiscale essential sampling

Kei Moritsugu, Tohru Terada, and Akinori Kidera

J. Chem. Phys. 133, 224105 (2010); http://dx.doi.org/10.1063/1.3510519 (6 pages)

Online Publication Date: 14 December 2010

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A multiscale simulation method, “multiscale essential sampling (MSES),” is proposed for calculating free energy surface of proteins in a sizable dimensional space with good scalability. In MSES, the configurational sampling of a full-dimensional model is enhanced by coupling with the accelerated dynamics of the essential degrees of freedom. Applying the Hamiltonian exchange method to MSES can remove the biasing potential from the coupling term, deriving the free energy surface of the essential degrees of freedom. The form of the coupling term ensures good scalability in the Hamiltonian exchange. As a test application, the free energy surface of the folding process of a miniprotein, chignolin, was calculated in the continuum solvent model. Results agreed with the free energy surface derived from the multicanonical simulation. Significantly improved scalability with the MSES method was clearly shown in the free energy calculation of chignolin in explicit solvent, which was achieved without increasing the number of replicas in the Hamiltonian exchange.
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87.15.Cc Folding: thermodynamics, statistical mechanics, models, and pathways
87.15.hm Folding dynamics
87.14.E- Proteins
87.15.A- Theory, modeling, and computer simulation
87.15.R- Reactions and kinetics

A linked electron pair functional

Peter J. Knowles and Bridgette Cooper

J. Chem. Phys. 133, 224106 (2010); http://dx.doi.org/10.1063/1.3507876 (5 pages) | Cited 4 times

Online Publication Date: 14 December 2010

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A modification of the variational configuration interaction functional in the first-order interacting space for molecular electronic structure is presented. The modified functional is a fully linked expression that by construction is extensive and invariant to transformations of the underlying orbital basis and is exact for an ensemble of separated two-electron subsystems. In addition, an approximation to variational coupled cluster is generated through truncation of the exponential cluster operator. When combined, these methods demonstrate accuracy that exceeds that of the standard coupled-cluster method, in particular in situations where the reference Slater determinant is not a good approximation.
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31.15.V- Electron correlation calculations for atoms, ions and molecules
31.15.xt Variational techniques
31.15.bw Coupled-cluster theory
back to top Gas Phase Dynamics and Structure: Spectroscopy, Molecular Interactions, Scattering, and Photochemistry

Equation of state and liquid-vapor equilibrium of polarizable Stockmayer fluids

Adrián Rocha-Ichante, Fernando del Río, and Edgar Ávalos

J. Chem. Phys. 133, 224301 (2010); http://dx.doi.org/10.1063/1.3517867 (12 pages)

Online Publication Date: 8 December 2010

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In this work we develop the concept of an effective potential to obtain the equation of state of polarizable Stockmayer (PSM) fluids. This potential consists of a Lennard-Jones function with appropriate energy and distance parameters that depend on the reduced dipolar moment μ* and polarizability α*. The approach deals accurately with polarizable SM fluids with μ* ≤ 2.0 and α* ≤ 0.1. However, prediction of second virial coefficients is reliable up to μ* ≤ 4.0. When the low-density sphericalized potential is used at moderate and large densities, the effect of the dipole–dipole attraction is overestimated in agreement with an effect previously found in the literature. This effect can be traced back to a frustration mechanism due to the interaction between three and more dipoles. We propose a model to account for this frustration effect and are able to reproduce the vapor-liquid equilibrium of polarizable SM fluids in agreement with simulated results from the literature. Molecular dynamics simulations were carried out to show that the effective SM fluid has a radial distribution function very close to that of the true SM system.
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61.20.Ja Computer simulation of liquid structure
64.30.-t Equations of state of specific substances
05.20.Jj Statistical mechanics of classical fluids
05.70.Ce Thermodynamic functions and equations of state

Structures of tin cluster cations Sn 3+ to Sn 15+

Nedko Drebov, Esther Oger, Thomas Rapps, Rebecca Kelting, Detlef Schooss, Patrick Weis, Manfred M. Kappes, and Reinhart Ahlrichs

J. Chem. Phys. 133, 224302 (2010); http://dx.doi.org/10.1063/1.3514907 (9 pages) | Cited 4 times

Online Publication Date: 10 December 2010

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We employ a combination of ion mobility measurements and an unbiased systematic structure search with density functional theory methods to study structure and energetics of gas phase tin cluster cations, Sn n+, in the range of n = 3–15. For Sn 13+ we also carry out trapped ion electron diffraction measurements to ascertain the results obtained by the other procedures. The structures for the smaller systems are most easily described by idealized point group symmetries, although they are all Jahn–Teller distorted: D3h (trigonal bipyramid), D4h (octahedron), D5h (pentagonal bipyramid) for n = 5, 6, and 7. For the larger systems we find capped D5h for Sn 8+ and Sn 9+, D3h (tricapped trigonal prism) and D4d (bicapped squared antiprism) plus adatoms for n = 10, 11, 14, and 15. A centered icosahedron with a peripheral atom removed is the dominant motif in Sn 12+. For Sn 13+ the calculations predict a family of virtually isoenergetic isomers, an icosahedron and slightly distorted icosahedra, which are about 0.25 eV below two C1 structures. The experiments indicate the presence of two structures, one from the Ih family and a prolate C1 isomer based on fused deltahedral moieties.
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36.40.Mr Spectroscopy and geometrical structure of clusters
33.15.Ta Mass spectra
31.30.-i Corrections to electronic structure
33.15.Bh General molecular conformation and symmetry; stereochemistry
31.15.es Applications of density-functional theory (e.g., to electronic structure and stability; defect formation; dielectric properties, susceptibilities; viscoelastic coefficients; Rydberg transition frequencies)
36.40.Cg Electronic and magnetic properties of clusters
back to top Condensed Phase Dynamics, Structure, and Thermodynamics: Spectroscopy, Reactions, and Relaxation

Numerical simulation of free evolution in solid-state nuclear magnetic resonance using low-order correlations in Liouville space

Jean-Nicolas Dumez, Mark C. Butler, and Lyndon Emsley

J. Chem. Phys. 133, 224501 (2010); http://dx.doi.org/10.1063/1.3505455 (11 pages) | Cited 3 times

Online Publication Date: 9 December 2010

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The design of simulations of free evolution in dipolar-coupled nuclear-spin systems using low-order correlations in Liouville space (LCL) is discussed, and a computational scheme relying on the Suzuki–Trotter algorithm and involving minimal memory requirements is described. The unusual nature of the approximation introduced by Liouville-space reduction in a spinning solid is highlighted by considering the accuracy of LCL simulations at different spinning frequencies, the quasiequilibria achieved by spin systems in LCL simulations, and the growth of high-order coherences in the exact dynamics. In particular, it is shown that accurate LCL simulations of proton spin diffusion occur in a regime where the reduced space excludes the coherences that make the dominant contribution to ∥σ∥2, the norm-squared of the density matrix.
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76.60.Cq Chemical and Knight shifts
75.30.Ds Spin waves
75.40.Gb Dynamic properties (dynamic susceptibility, spin waves, spin diffusion, dynamic scaling, etc.)

Chiral symmetry breaking in a microscopic model with asymmetric autocatalysis and inhibition

Harold W. Hatch, Frank H. Stillinger, and Pablo G. Debenedetti

J. Chem. Phys. 133, 224502 (2010); http://dx.doi.org/10.1063/1.3511715 (7 pages)

Online Publication Date: 9 December 2010

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Asymmetric autocatalysis and inhibition have been proposed as key processes in the spontaneous emergence of chiral symmetry breaking in a prebiotic world. An elementary lattice model is formulated to simulate the kinetics of chiral symmetry breaking via autocatalysis and inhibition in a mixture of prochiral reactants, chiral products, and inert solvent. Starting from a chirally unbiased initial state, spontaneous symmetry breaking occurs in spite of equal a priori probability for creating either product enantiomer, and the coupled reaction–diffusion processes subsequently amplify the random early-stage symmetry breaking. The processes of reaction and diffusion are kinetically intertwined in a way leading to competition in the appearance of enantiomeric excess. An effective transition temperature can be identified below which spontaneous symmetry breaking appears. In the absence of inhibition, reactions are predominantly autocatalytic under both reaction control (fast diffusion, slow reaction) or diffusion control (fast reaction, slow diffusion) conditions. In the presence of inhibition, simulations with different system sizes converge to the same transition temperature under reaction control conditions, and in this limit the reactions are predominantly nonautocatalytic.
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87.15.Vv Diffusion
87.15.hj Transport dynamics
87.10.Hk Lattice models
87.15.ap Molecular dynamics simulation
87.15.A- Theory, modeling, and computer simulation
87.15.B- Structure of biomolecules

Understanding mixing of Ni and Pt in the Ni/Pt(111) bimetallic catalyst via molecular simulation and experiments

Hangyao Wang, Michail Stamatakis, Danielle A. Hansgen, Stavros Caratzoulas, and Dionisios G. Vlachos

J. Chem. Phys. 133, 224503 (2010); http://dx.doi.org/10.1063/1.3512644 (11 pages)

Online Publication Date: 9 December 2010

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Molecular dynamics (MD) simulations employing embedded atom method potentials and ultrahigh vacuum (UHV) experiments were carried out to study the mixing process between the Ni and Pt atoms in the Ni/Pt(111) bimetallic system. The barrier for a Ni atom to diffuse from the top surface to the subsurface layer is rather high (around 1.7 eV) as calculated using the nudged elastic band (NEB) method. Analysis of the relaxation dynamics of the Ni atoms showed that they undergo diffusive motion through a mechanism of correlated hops. At 600 K, all Ni atoms remain trapped on the top surface due to large diffusion barriers. At 900 K, the majority of Ni atoms diffuse to the second layer and at 1200 K diffusion to the bulk is observed. We also find that smaller Ni coverages and the presence of Pt steps facilitate the Ni–Pt mixing. By simulated annealing simulations, we found that in the mixed state, the Ni fraction oscillates between layers, with the second layer being Ni-richer at equilibrium. The simulation results at multiple time scales are consistent with the experimental data.
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66.30.Ny Chemical interdiffusion; diffusion barriers
64.75.Ef Mixing

Ordered equilibrium structures of soft particles in thin layers

Mario Kahn, Jean-Jacques Weis, and Gerhard Kahl

J. Chem. Phys. 133, 224504 (2010); http://dx.doi.org/10.1063/1.3509380 (12 pages)

Online Publication Date: 10 December 2010

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Considering a system of Gaussian particles confined between two hard, parallel plates, we investigate at T = 0, ordered equilibrium configurations that the system forms as the distance D between the plates gradually increases. Using a very sensitive and reliable optimization technique that is based on ideas of genetic algorithms, we are able to identify the emerging sequences of the energetically most favorable structures. Although the resulting phase diagram is rather complex, its essential features can be reduced to the discussion of two archetypes of structural transitions: (i) a continuous transformation at a fixed number of layers, leading from a square to a centered rectangular and then to a hexagonal lattice; (ii) a discontinuous transition, transforming a hexagonal to a square lattice via complex intermediate structures, i.e., the so-called buckling transition, which is encountered as the system forms a new layer. Detailed Monte Carlo simulations are able to confirm the theoretical predictions on a semiquantitative level but are not able to grasp the tiny energetic differences between competing structures.
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81.30.Hd Constant-composition solid-solid phase transformations: polymorphic, massive, and order-disorder
64.70.K- Solid-solid transitions
81.30.Dz Phase diagrams of other materials

The van Hove distribution function for Brownian hard spheres: Dynamical test particle theory and computer simulations for bulk dynamics

Paul Hopkins, Andrea Fortini, Andrew J. Archer, and Matthias Schmidt

J. Chem. Phys. 133, 224505 (2010); http://dx.doi.org/10.1063/1.3511719 (18 pages)

Online Publication Date: 13 December 2010

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We describe a test particle approach based on dynamical density functional theory (DDFT) for studying the correlated time evolution of the particles that constitute a fluid. Our theory provides a means of calculating the van Hove distribution function by treating its self and distinct parts as the two components of a binary fluid mixture, with the “self ” component having only one particle, the “distinct” component consisting of all the other particles, and using DDFT to calculate the time evolution of the density profiles for the two components. We apply this approach to a bulk fluid of Brownian hard spheres and compare to results for the van Hove function and the intermediate scattering function from Brownian dynamics computer simulations. We find good agreement at low and intermediate densities using the very simple Ramakrishnan–Yussouff [Phys. Rev. B 19, 2775 (1979)] approximation for the excess free energy functional. Since the DDFT is based on the equilibrium Helmholtz free energy functional, we can probe a free energy landscape that underlies the dynamics. Within the mean-field approximation we find that as the particle density increases, this landscape develops a minimum, while an exact treatment of a model confined situation shows that for an ergodic fluid this landscape should be monotonic. We discuss possible implications for slow, glassy, and arrested dynamics at high densities.
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61.20.Ja Computer simulation of liquid structure
61.20.Gy Theory and models of liquid structure
65.20.De General theory of thermodynamic properties of liquids, including computer simulation
back to top Surfaces, Interfaces, and Materials

Low O2 dissociation barrier on Pt(111) due to adsorbate–adsorbate interactions

D. J. Miller, H. Öberg, L.-Å. Näslund, T. Anniyev, H. Ogasawara, L. G. M. Pettersson, and A. Nilsson

J. Chem. Phys. 133, 224701 (2010); http://dx.doi.org/10.1063/1.3512618 (7 pages)

Online Publication Date: 10 December 2010

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O2 dissociation on Pt(111) has been followed at low and saturation coverage using temperature-programmed x-ray photoelectron spectroscopy and simulated with mean-field kinetic modeling, yielding dissociation (Ea) and desorption (Ed) barriers of 0.32 and 0.36 eV, respectively. Density functional theory calculations show that Ea is strongly influenced by the O–O interatomic potential in the atomic final state: of the supercells considered, that which maximizes attractive third-nearest-neighbor interactions in the atomic final state yields both the lowest computed dissociation barrier (0.24 eV) and the best agreement with experiment. It is proposed that the effect of adsorbate–adsorbate interactions must be considered when modeling catalytic processes involving dissociative steps.
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82.30.Lp Decomposition reactions (pyrolysis, dissociation, and fragmentation)
82.65.+r Surface and interface chemistry; heterogeneous catalysis at surfaces
82.80.Pv Electron spectroscopy (X-ray photoelectron (XPS), Auger electron spectroscopy (AES), etc.)
82.20.Db Transition state theory and statistical theories of rate constants
68.43.Mn Adsorption kinetics
68.43.Vx Thermal desorption

Adsorption configuration effects on the surface diffusion of large organic molecules: The case of Violet Lander

F. Sato, S. B. Legoas, R. Otero, F. Hümmelink, P. Thostrup, E. Lægsgaard, I. Stensgaard, F. Besenbacher, and D. S. Galvão

J. Chem. Phys. 133, 224702 (2010); http://dx.doi.org/10.1063/1.3512623 (6 pages)

Online Publication Date: 10 December 2010

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Violet Lander (C108H104) is a large organic molecule that when deposited on Cu(110) surface exhibits lock-and-key like behavior [Otero et al., Nature Mater. 3, 779 (2004)]. In this work, we report a detailed fully atomistic molecular mechanics and molecular dynamics study of this phenomenon. Our results show that it has its physical basis on the interplay of the molecular hydrogens and the Cu(110) atomic spacing, which is a direct consequence of the matching between molecule and surface dimensions. This information could be used to find new molecules capable of displaying lock-and-key behavior with new potential applications in nanotechnology.
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68.43.Jk Diffusion of adsorbates, kinetics of coarsening and aggregation
68.43.Mn Adsorption kinetics

Structure and adsorption of water in nonuniform cylindrical nanopores

G. M. Torrie, G. Lakatos, and G. N. Patey

J. Chem. Phys. 133, 224703 (2010); http://dx.doi.org/10.1063/1.3505453 (6 pages)

Online Publication Date: 13 December 2010

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Grand canonical Monte Carlo simulations are used to examine the adsorption and structure of water in the interior of cylindrical nanopores in which the axial symmetry is broken either by varying the radius as a function of position along the pore axis or by introducing regions where the characteristic strength of the water–nanopore interaction is reduced. Using the extended simple point charge (SPC/E) model for water, nanopores with a uniform radius of 6.0 Å are found to fill with water at chemical potentials approximately 0.5 kJ/mol higher than the chemical potential of the saturated vapor. The water in these filled pores exists in either a weakly structured fluidlike state or a highly structured uniformly polarized state composed of a series of stacked water clusters with pentagonal cross sections. This highly structured state can be disrupted by creating hydrophobic regions on the surface of the nanopore, and the degree of disruption can be systematically controlled by adjusting the size of the hydrophobic regions. In particular, hydrophobic banded regions with lengths larger than 9.2 Å result in a complete loss of structure and the formation of a liquid–vapor coexistence in the tube interior. Similarly, the introduction of spatial variation in the nanopore radius can produce two condensation transitions at distinct points along the filling isotherm.
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61.46.Bc Structure of clusters (e.g., metcars; not fragments of crystals; free or loosely aggregated or loosely attached to a substrate)
68.43.Mn Adsorption kinetics
68.03.Fg Evaporation and condensation of liquids
68.08.Bc Wetting
65.80.-g Thermal properties of small particles, nanocrystals, nanotubes, and other related systems

Adsorption geometry, molecular interaction, and charge transfer of triphenylamine-based dye on rutile TiO2(110)

Shun Yu, Sareh Ahmadi, Marcelo Zuleta, Haining Tian, Karina Schulte, Annette Pietzsch, Franz Hennies, Jonas Weissenrieder, Xichuan Yang, and Mats Göthelid

J. Chem. Phys. 133, 224704 (2010); http://dx.doi.org/10.1063/1.3509389 (11 pages) | Cited 2 times

Online Publication Date: 13 December 2010

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The fast development of new organic sensitizers leads to the need for a better understanding of the complexity and significance of their adsorption processes on TiO2 surfaces. We have investigated a prototype of the triphenylamine−cyanoacrylic acid (donor-acceptor) on rutile TiO2 (110) surface with special attention on the monolayer region. This molecule belongs to the type of dye, some of which so far has delivered the record efficiency of 10%–10.3% for pure organic sensitizers [W. Zeng, Y. Cao, Y. Bai, Y. Wang, Y. Shi, M. Zhang, F. Wang, C. Pan, and P. Wang, Chem. Mater. 22, 1915 (2010)]. The molecular configuration of this dye on the TiO2 surface was found to vary with coverage and adopt gradually an upright geometry, as determined from near edge x-ray absorption fine structure spectroscopy. Due to the molecular interaction within the increasingly dense packed layer, the molecular electronic structure changes systematically: all energy levels shift to higher binding energies, as shown by photoelectron spectroscopy. Furthermore, the investigation of charge delocalization within the molecule was carried out by means of resonant photoelectron spectroscopy. A fast delocalization (∼1.8 fs) occurs at the donor part while a competing process between delocalization and localization takes place at the acceptor part. This depicts the “push−pull” concept in donor−acceptor molecular system in time scale.
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68.43.Mn Adsorption kinetics
73.20.Hb Impurity and defect levels; energy states of adsorbed species
71.15.Nc Total energy and cohesive energy calculations
82.30.Fi Ion-molecule, ion-ion, and charge-transfer reactions
79.60.Dp Adsorbed layers and thin films
78.70.Dm X-ray absorption spectra

Energy-gap opening and quenching in graphene under periodic external potentials

Aihua Zhang, Zhenxiang Dai, Lei Shi, Yuan Ping Feng, and Chun Zhang

J. Chem. Phys. 133, 224705 (2010); http://dx.doi.org/10.1063/1.3511782 (5 pages)

Online Publication Date: 13 December 2010

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We investigated the effects of periodic external potentials on properties of charge carriers in graphene using both the first-principles method based on density functional theory (DFT) and a theoretical approach based on a generalized effective spinor Hamiltonian. DFT calculations were done in a modified Kohn–Sham procedure that includes the effects of the periodic external potential. Unexpected energy band gap opening and quenching were predicted for the graphene superlattice with two symmetrical sublattices and those with two unsymmetrical sublattices, respectively. Theoretical analysis based on the spinor Hamiltonian showed that the correlations between pseudospins of Dirac fermions in graphene and the applied external potential, and the potential-induced intervalley scattering, play important roles in energy-gap opening and quenching.
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73.22.Pr Electronic structure of graphene
71.15.Mb Density functional theory, local density approximation, gradient and other corrections
73.21.Cd Superlattices

A comparative study of argon ion irradiated pristine and fluorinated single-wall carbon nanotubes

Yu. V. Fedoseeva, L. G. Bulusheva, A. V. Okotrub, D. V. Vyalikh, and A. Fonseca

J. Chem. Phys. 133, 224706 (2010); http://dx.doi.org/10.1063/1.3506579 (6 pages)

Online Publication Date: 14 December 2010

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Effect of Ar+ ion irradiation on the structure of pristine and fluorinated single-wall carbon nanotubes (SWCNTs) was examined using transmission electron microscopy (TEM), Raman, and x-ray photoelectron spectroscopy (XPS). The TEM analysis revealed retention of tubular structures in both irradiated samples while Raman spectroscopy and XPS data indicated a partial destruction of nanotubes and formation of oxygen-containing groups on the nanotube surface. From similarity of electronic states of carbon in the irradiated pristine and fluorinated SWCNTs observed by XPS, it was suggested that defluorination of nanotubes proceeded with breaking of C–F bonds.
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61.46.Fg Nanotubes
61.80.Jh Ion radiation effects
79.60.Jv Interfaces; heterostructures; nanostructures
78.30.Hv Other nonmetallic inorganics
back to top Polymers and Complex Systems

Structural and dynamical analysis of monodisperse and polydisperse colloidal systems

Marianna Yiannourakou, Ioannis G. Economou, and Ioannis A. Bitsanis

J. Chem. Phys. 133, 224901 (2010); http://dx.doi.org/10.1063/1.3506576 (10 pages)

Online Publication Date: 13 December 2010

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We present a semigrand ensemble Monte Carlo and Brownian dynamics simulation study of structural and dynamical properties of polydisperse soft spheres interacting via purely repulsive power-law potentials with a varying degree of “softness.” Comparisons focus on crystal and amorphous phases at their coexistence points. It is shown through detailed structural analysis that as potential interactions soften, the “quality of crystallinity” of both monodisperse and polydisperse systems deteriorates. In general, polydisperse crystalline phases are characterized by a more ordered structure than the corresponding monodisperse ones (i.e., for the same potential softness). This counter-intuitive feature originates partly from the fact that particles of different sizes may be accommodated more flexibly in a crystal structure and from the reality that coexistence (osmotic) pressure is substantially higher for polydisperse systems. These trends diminish for softer potentials. Potential softness eventually produces substitutionally disordered crystals. However, substitutional order is apparent for the hard-spherelike interactions. Diffusionwise, crystals appear quite robust with a slight difference in the vibrational amplitudes of small and large particles. This difference, again, diminishes with potential softness. Overcrowding in amorphous polydisperse suspensions causes “delayed” diffusion at intermediate times.
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82.70.Dd Colloids
83.80.Hj Suspensions, dispersions, pastes, slurries, colloids
83.10.Mj Molecular dynamics, Brownian dynamics
66.10.cg Mass diffusion, including self-diffusion, mutual diffusion, tracer diffusion, etc.
61.20.Ja Computer simulation of liquid structure

Slow dynamics of a colloidal lamellar phase

Doru Constantin, Patrick Davidson, Éric Freyssingeas, and Anders Madsen

J. Chem. Phys. 133, 224902 (2010); http://dx.doi.org/10.1063/1.3509399 (8 pages)

Online Publication Date: 14 December 2010

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We used x-ray photon correlation spectroscopy to study the dynamics in the lamellar phase of a platelet suspension as a function of the particle concentration. We measured the collective diffusion coefficient along the director of the phase, over length scales down to the interparticle distance, and quantified the hydrodynamic interaction between the particles. This interaction sets in with increasing concentration and can be described qualitatively by a simplified model. No change in the microscopic structure or dynamics is observed at the transition between the fluid and the gel-like lamellar phases.
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82.70.Dd Colloids
82.70.Kj Emulsions and suspensions
61.25.-f Studies of specific liquid structures
66.10.C- Diffusion and thermal diffusion
78.70.Ck X-ray scattering
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Atomistic theory of amyloid fibril nucleation

Raffaela Cabriolu, Dimo Kashchiev, and Stefan Auer

J. Chem. Phys. 133, 225101 (2010); http://dx.doi.org/10.1063/1.3512642 (12 pages) | Cited 1 time

Online Publication Date: 9 December 2010

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We consider the nucleation of amyloid fibrils at the molecular level when the process takes place by a direct polymerization of peptides or protein segments into β-sheets. Employing the atomistic nucleation theory (ANT), we derive a general expression for the work to form a nanosized amyloid fibril (protofilament) composed of successively layered β-sheets. The application of this expression to a recently studied peptide system allows us to determine the size of the fibril nucleus, the fibril nucleation work, and the fibril nucleation rate as functions of the supersaturation of the protein solution. Our analysis illustrates the unique feature of ANT that the size of the fibril nucleus is a constant integer in a given supersaturation range. We obtain the ANT nucleation rate and compare it with the rates determined previously in the scope of the classical nucleation theory (CNT) and the corrected classical nucleation theory (CCNT). We find that while the CNT nucleation rate is orders of magnitude greater than the ANT one, the CCNT and ANT nucleation rates are in very good quantitative agreement. The results obtained are applicable to homogeneous nucleation, which occurs when the protein solution is sufficiently pure and/or strongly supersaturated.
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87.15.rp Polymerization
87.15.N- Properties of solutions of macromolecules
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Erratum: “Observation of buried water molecules in phospholipid membranes by surface sum-frequency generation spectroscopy” [J. Chem. Phys. 131, 161107 (2009)]

M. Sovago, E. Vartiainen, and M. Bonn

J. Chem. Phys. 133, 229901 (2010); http://dx.doi.org/10.1063/1.3511705 (2 pages) | Cited 2 times

Online Publication Date: 8 December 2010

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87.16.dt Structure, static correlations, domains, and rafts
68.18.Fg Liquid thin film structure: measurements and simulations
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