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21 Jun 2013

Volume 138, Issue 23 (partial)

Issue Cover Spotlight Figure

J. Chem. Phys. 138, 234901 (2013); http://dx.doi.org/10.1063/1.4809993 (16 pages)

Antonio Raudino, Siewert J. Marrink, and Martina Pannuzzo
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back to top Theoretical Methods and Algorithms

Features in chemical kinetics. I. Signatures of self-emerging dimensional reduction from a general format of the evolution law

Paolo Nicolini and Diego Frezzato

J. Chem. Phys. 138, 234101 (2013); http://dx.doi.org/10.1063/1.4809592 (16 pages)

Online Publication Date: 17 June 2013

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Simplification of chemical kinetics description through dimensional reduction is particularly important to achieve an accurate numerical treatment of complex reacting systems, especially when stiff kinetics are considered and a comprehensive picture of the evolving system is required. To this aim several tools have been proposed in the past decades, such as sensitivity analysis, lumping approaches, and exploitation of time scales separation. In addition, there are methods based on the existence of the so-called slow manifolds, which are hyper-surfaces of lower dimension than the one of the whole phase-space and in whose neighborhood the slow evolution occurs after an initial fast transient. On the other hand, all tools contain to some extent a degree of subjectivity which seems to be irremovable. With reference to macroscopic and spatially homogeneous reacting systems under isothermal conditions, in this work we shall adopt a phenomenological approach to let self-emerge the dimensional reduction from the mathematical structure of the evolution law. By transforming the original system of polynomial differential equations, which describes the chemical evolution, into a universal quadratic format, and making a direct inspection of the high-order time-derivatives of the new dynamic variables, we then formulate a conjecture which leads to the concept of an “attractiveness” region in the phase-space where a well-defined state-dependent rate function ω has the simple evolution math = −ω2 along any trajectory up to the stationary state. This constitutes, by itself, a drastic dimensional reduction from a system of N-dimensional equations (being N the number of chemical species) to a one-dimensional and universal evolution law for such a characteristic rate. Step-by-step numerical inspections on model kinetic schemes are presented. In the companion paper [P. Nicolini and D. Frezzato, J. Chem. Phys. 138, 234102 (2013)]10.1063/1.4809593 this outcome will be naturally related to the appearance (and hence, to the definition) of the slow manifolds.
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82.20.Fd Collision theories; trajectory models
82.20.Wt Computational modeling; simulation

Features in chemical kinetics. II. A self-emerging definition of slow manifolds

Paolo Nicolini and Diego Frezzato

J. Chem. Phys. 138, 234102 (2013); http://dx.doi.org/10.1063/1.4809593 (14 pages)

Online Publication Date: 17 June 2013

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In the preceding paper of this series (Part I [P. Nicolini and D. Frezzato, J. Chem. Phys. 138, 234101 (2013)]10.1063/1.4809592) we have unveiled some ubiquitous features encoded in the systems of polynomial differential equations normally applied in the description of homogeneous and isothermal chemical kinetics (mass-action law). Here we proceed by investigating a deeply related feature: the appearance of so-called slow manifolds (SMs) which are low-dimensional hyper-surfaces in the neighborhood of which the slow evolution of the reacting system occurs after an initial fast transient. Indeed a geometrical definition of SM, devoid of subjectivity, “naturally” follows in terms of a specific sub-dimensional domain embedded in the peculiar region of the concentrations phase-space that in Part I we termed as “attractiveness region.” Numerical inspections on simple low-dimensional model cases are presented, including the benchmark case of Davis and Skodje [J. Chem. Phys. 111, 859 (1999)]10.1063/1.479372 and the preliminary analysis of a simplified model mechanism of hydrogen combustion.
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82.20.Db Transition state theory and statistical theories of rate constants
82.33.Vx Reactions in flames, combustion, and explosions

On the analytical representation of free energy profiles with a Morse/long-range model: Application to the water dimer

Yalina Tritzant-Martinez, Tao Zeng, Aron Broom, Elizabeth Meiering, Robert J. Le Roy, and Pierre-Nicholas Roy

J. Chem. Phys. 138, 234103 (2013); http://dx.doi.org/10.1063/1.4810006 (12 pages)

Online Publication Date: 18 June 2013

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We investigate the analytical representation of potentials of mean force (pmf) using the Morse/long-range (MLR) potential approach. The MLR method had previously been used to represent potential energy surfaces, and we assess its validity for representing free-energies. The advantage of the approach is that the potential of mean force data only needs to be calculated in the short to medium range region of the reaction coordinate while the long range can be handled analytically. This can result in significant savings in terms of computational effort since one does not need to cover the whole range of the reaction coordinate during simulations. The water dimer with rigid monomers whose interactions are described by the commonly used TIP4P model [W. Jorgensen and J. Madura, Mol. Phys. 56, 1381 (1985)]10.1080/00268978500103111 is used as a test case. We first calculate an “exact” pmf using direct Monte Carlo (MC) integration and term such a calculation as our gold standard (GS). Second, we compare this GS with several MLR fits to the GS to test the validity of the fitting procedure. We then obtain the water dimer pmf using metadynamics simulations in a limited range of the reaction coordinate and show how the MLR treatment allows the accurate generation of the full pmf. We finally calculate the transition state theory rate constant for the water dimer dissociation process using the GS, the GS MLR fits, and the metadynamics MLR fits. Our approach can yield a compact, smooth, and accurate analytical representation of pmf data with reduced computational cost.
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82.30.Lp Decomposition reactions (pyrolysis, dissociation, and fragmentation)
82.20.Kh Potential energy surfaces for chemical reactions
82.20.Pm Rate constants, reaction cross sections, and activation energies
82.20.Db Transition state theory and statistical theories of rate constants

Relative efficacy of vibrational vs. translational excitation in promoting atom-diatom reactivity: Rigorous examination of Polanyi's rules and proposition of sudden vector projection (SVP) model

Bin Jiang and Hua Guo

J. Chem. Phys. 138, 234104 (2013); http://dx.doi.org/10.1063/1.4810007 (10 pages)

Online Publication Date: 18 June 2013

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To provide a systematic and rigorous re-examination of the well-known Polanyi's rules, excitation functions of several A + BC(v = 0, 1) reactions are determined using the Chebyshev real wave packet method on accurate potential energy surfaces. Reactions with early (F + H2 and F + HCl), late (Cl + H2), and central (H/D/Mu + H2, where Mu is a short-lived light isotope of H) barriers are represented. Although Polanyi's rules are in general consistent with the quantum dynamical results, their predictions are strictly valid only in certain energy ranges divided by a cross-over point. In particular, vibrational excitation of the diatomic reactant typically enhances reactivity more effectively than translational excitation at high energies, while reverse is true at low energies. This feature persists irrespective of the barrier location. A sudden vector projection model is proposed as an alternative to Polanyi's rules. It is found to give similar, but more quantitative, predictions about mode selectivity in these reactions, and has the advantage to be extendible to reactions involving polyatomic molecules.
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33.20.Tp Vibrational analysis
31.15.vj Electron correlation calculations for atoms and ions: excited states
31.50.Df Potential energy surfaces for excited electronic states
32.10.Bi Atomic masses, mass spectra, abundances, and isotopes

Multiscale modeling with smoothed dissipative particle dynamics

Pandurang M. Kulkarni, Chia-Chun Fu, M. Scott Shell, and L. Gary Leal

J. Chem. Phys. 138, 234105 (2013); http://dx.doi.org/10.1063/1.4810754 (14 pages)

Online Publication Date: 18 June 2013

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In this work, we consider two issues related to the use of Smoothed Dissipative Particle Dynamics (SDPD) as an intermediate mesoscale model in a multiscale scheme for solution of flow problems when there are local parts of a macroscopic domain that require molecular resolution. The first is to demonstrate that SDPD with different levels of resolution can accurately represent the fluid properties from the continuum scale all the way to the molecular scale. Specifically, while the thermodynamic quantities such as temperature, pressure, and average density remain scale-invariant, we demonstrate that the dynamic properties are quantitatively consistent with an all-atom Lennard-Jones reference system when the SDPD resolution approaches the atomistic scale. This supports the idea that SDPD can serve as a natural bridge between molecular and continuum descriptions. In the second part, a simple multiscale methodology is proposed within the SDPD framework that allows several levels of resolution within a single domain. Each particle is characterized by a unique physical length scale called the smoothing length, which is inversely related to the local number density and can change on-the-fly. This multiscale methodology is shown to accurately reproduce fluid properties for the simple problem of steady and transient shear flow.
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47.55.Kf Particle-laden flows
47.11.St Multi-scale methods
back to top Atoms, Molecules, and Clusters

Ab initio potential energy surface and vibration-rotation energy levels of lithium monohydroxide

Jacek Koput

J. Chem. Phys. 138, 234301 (2013); http://dx.doi.org/10.1063/1.4810864 (8 pages)

Online Publication Date: 18 June 2013

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The accurate ground-state potential energy surface of lithium monohydroxide (LiOH) has been determined from ab initio calculations using the coupled-cluster approach in conjunction with the correlation-consistent core-valence basis sets up to septuple-zeta quality. Results obtained with the conventional and explicitly correlated coupled-cluster methods were compared. The higher-order electron correlation, scalar relativistic, and adiabatic effects were taken into account. The vibration-rotation energy levels of the LiOH, LiOD, Li18OH, and 6LiOH isotopologues were predicted to near “spectroscopic” accuracy.
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31.50.Bc Potential energy surfaces for ground electronic states
33.20.Sn Rotational analysis
33.20.Tp Vibrational analysis
31.15.aj Relativistic corrections, spin-orbit effects, fine structure; hyperfine structure
31.15.bw Coupled-cluster theory
31.30.Gs Hyperfine interactions and isotope effects

Gyroscopic destabilisation in polyatomic molecules: Rotational structure of the low-frequency bending vibrational states ν23 and ν11 of dimethylsulfoxide

Arnaud Cuisset and Dmitrií A. Sadovskií

J. Chem. Phys. 138, 234302 (2013); http://dx.doi.org/10.1063/1.4809738 (17 pages)

Online Publication Date: 18 June 2013

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We give details of the spectroscopic observation of the gyroscopic destabilisation in the ν23 vibrational state of dimethylsulfoxide (DMSO) announced by Cuisset, Pirali, and Sadovskií [Phys. Rev. Lett. 109, 094101 (2012)]10.1103/PhysRevLett.109.094101 . Following the first successful high-resolution spectroscopic study of the rotational structure of the “perpendicular” band of DMSO at 324 cm−1 associated with the ν23 bending vibrational mode, the rare subsystem of ν23 rotational levels consisting of a series of fourfold quasidegenerate levels (4-clusters) was identified. Our complete analysis of the underlying rotational dynamics uncovered a bifurcation leading to the gyroscopic destabilisation of one of the two stable principal axes of inertia, a phenomenon known previously only in a few triatomic molecules.
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33.20.Ea Infrared spectra
31.15.-p Calculations and mathematical techniques in atomic and molecular physics
33.20.Sn Rotational analysis
33.15.Mt Rotation, vibration, and vibration-rotation constants
33.15.Bh General molecular conformation and symmetry; stereochemistry
36.40.Mr Spectroscopy and geometrical structure of clusters

Accurate structure, thermodynamics, and spectroscopy of medium-sized radicals by hybrid coupled cluster/density functional theory approaches: The case of phenyl radical

Vincenzo Barone, Malgorzata Biczysko, Julien Bloino, Franco Egidi, and Cristina Puzzarini

J. Chem. Phys. 138, 234303 (2013); http://dx.doi.org/10.1063/1.4810863 (14 pages)

Online Publication Date: 19 June 2013

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The coupled-cluster singles doubles model with perturbative treatment of triples (CCSD(T)) coupled with extrapolation to the complete basis-set limit and additive approaches represent the “golden standard” for the structural and spectroscopic characterization of building blocks of biomolecules and nanosystems. However, when open-shell systems are considered, additional problems related to both specific computational difficulties and the need of obtaining spin-dependent properties appear. In this contribution, we present a comprehensive study of the molecular structure and spectroscopic (IR, Raman, EPR) properties of the phenyl radical with the aim of validating an accurate computational protocol able to deal with conjugated open-shell species. We succeeded in obtaining reliable and accurate results, thus confirming and, partly, extending the available experimental data. The main issue to be pointed out is the need of going beyond the CCSD(T) level by including a full treatment of triple excitations in order to fulfil the accuracy requirements. On the other hand, the reliability of density functional theory in properly treating open-shell systems has been further confirmed.
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33.20.Ea Infrared spectra
33.20.Fb Raman and Rayleigh spectra (including optical scattering)
33.35.+r Electron resonance and relaxation
31.15.bw Coupled-cluster theory
31.15.E- Density-functional theory
33.15.Bh General molecular conformation and symmetry; stereochemistry

Negative ions of p-nitroaniline: Photodetachment, collisions, and ab initio calculations

Byron H. Smith, Angela Buonaugurio, Jing Chen, Evan Collins, Kit H. Bowen, Robert N. Compton, and Thomas Sommerfeld

J. Chem. Phys. 138, 234304 (2013); http://dx.doi.org/10.1063/1.4810869 (8 pages)

Online Publication Date: 19 June 2013

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The structures of parent anion, M−, and deprotonated molecule, [M−H]−, anions of the highly polar p-nitroaniline (pNA) molecule are studied experimentally and theoretically. Photoelectron spectroscopy (PES) of the parent anion is employed to estimate the adiabatic electron affinity (EAa = 0.75 ± 0.1 eV) and vertical detachment energy (VDE = 1.1 eV). These measured energies are in good agreement with computed values of 0.73 eV for the EAa and the range of 0.85 to 1.0 eV for the VDE at the EOM-CCSD/Aug-cc-pVTZ level. Collision induced dissociation (CID) of deprotonated pNA, [pNA − H]−, with argon yielded [pNA − H − NO]− (i.e., rearrangement to give loss of NO) with a threshold energy of 2.36 eV. Calculations of the energy difference between [pNA − H]− and [pNA − H − NO]− give 1.64 eV, allowing an estimate of a 0.72 eV activation barrier for the rearrangement reaction. Direct dissociation of [pNA − H]− yielding NO 2− occurs at a threshold energy of 3.80 eV, in good agreement with theory (between 3.39 eV and 4.30 eV). As a result of the exceedingly large dipole moment for pNA (6.2 Debye measured in acetone), we predict two dipole-bound states, one at ∼110 meV and an excited state at 2 meV. No dipole-bound states are observed in the photodetachment experiments due the pronounced mixing between states with dipole-bound and valence character similar to what has been observed in other nitro systems. For the same reason, dipole-bound states are expected to provide highly efficient “doorway states” for the formation of the pNA− valence anion, and these states should be observable as resonances in the reverse process, that is, in the photodetachment spectrum of pNA− near the photodetachment threshold.
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33.80.Eh Autoionization, photoionization, and photodetachment
33.80.Gj Diffuse spectra; predissociation, photodissociation
31.15.ap Polarizabilities and other atomic and molecular properties
31.15.bw Coupled-cluster theory
33.15.Bh General molecular conformation and symmetry; stereochemistry
33.15.Ry Ionization potentials, electron affinities, molecular core binding energy

Ultrafast dynamics in C 1s core-excited CF4 revealed by two-dimensional resonant Auger spectroscopy

M. N. Piancastelli, R. Guillemin, M. Simon, H. Iwayama, and E. Shigemasa

J. Chem. Phys. 138, 234305 (2013); http://dx.doi.org/10.1063/1.4810871 (5 pages)

Online Publication Date: 19 June 2013

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Following core excitation in an isolated molecule, ultrafast dissociation of one particular chemical bond can occur, where “ultrafast” is defined as taking place during the lifetime of the core hole, of the order of few femtoseconds. The signature of such phenomenon can be observed in resonant Auger spectra following core excitation. We present here an investigation of ultrafast dissociation following C 1s-to-σ* core excitation in CF4, with high-resolution resonant Auger spectroscopy. We are able to characterize final states of both the molecular ion and the CF 3+ fragment. We use two-dimensional (2D) maps to record resonant Auger spectra across the resonance as a function of photon energy and to characterize ultrafast dynamics. This method provides immediate visual evidence of one of the important characteristics of the study of spectral features related to molecular versus fragment ionic final states, and namely their dispersion law. In the 2D maps we are also able to identify the dissociation limit for one of the molecular final states.
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33.80.Gj Diffuse spectra; predissociation, photodissociation
33.80.Eh Autoionization, photoionization, and photodetachment

The photoelectron angular distribution of water clusters

Chaofan Zhang, Tomas Andersson, Marko Förstel, Melanie Mucke, Tiberiu Arion, Maxim Tchaplyguine, Olle Björneholm, and Uwe Hergenhahn

J. Chem. Phys. 138, 234306 (2013); http://dx.doi.org/10.1063/1.4809748 (7 pages)

Online Publication Date: 19 June 2013

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The angular distribution of photoelectrons emitted from water clusters has been measured by linearly polarized synchrotron radiation of 40 and 60 eV photon energy. Results are given for the three outermost valence orbitals. The emission patterns are found more isotropic than for isolated molecules. While a simple scattering model is able to explain most of the deviation from molecular behavior, some of our data also suggest an intrinsic change of the angular distribution parameter. The angular distribution function was mapped by rotating the axis of linear polarization of the synchrotron radiation.
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36.40.Mr Spectroscopy and geometrical structure of clusters

Theoretical explanation of the low-lying ν6 vibrational fundamental of the FSO3 radical by the linear vibronic coupling approach

Tereza Uhlíková and Štěpán Urban

J. Chem. Phys. 138, 234307 (2013); http://dx.doi.org/10.1063/1.4810800 (7 pages)

Online Publication Date: 19 June 2013

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The first attempt for a theoretical explanation of the ν6 fundamental energy levels of the fluorosulfate radical (FSO3) electronic ground state has been made. The vibronic interaction of the two lowest electronic states of the radical (math 2A2 and math 2E) has been taken into consideration in the basis of the linear vibronic coupling (LVC) approximation. The strengths of the intrastate and interstate vibronic couplings have been calculated within the framework of the Köppel, Domcke, and Cederbaum (KDC) model Hamiltonian. Already this simple KDC-LVC model provides the ν6 fundamental energy, which is in very good agreement with the experimental results. From the inclusion of vibronic interactions such as the pseudo-Jahn-Teller and Jahn-Teller effects into the calculation of the fundamental energy of the ν6 mode, it can be said that mainly the interstate coupling with the electronic excited state E causes the unexpectedly low fundamental energy ν6 of the FSO3 radical.
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33.20.Wr Vibronic, rovibronic, and rotation-electron-spin interactions
31.15.-p Calculations and mathematical techniques in atomic and molecular physics
31.30.-i Corrections to electronic structure
31.50.Df Potential energy surfaces for excited electronic states
33.15.Mt Rotation, vibration, and vibration-rotation constants

Quantum decoherence of I2 in liquid xenon: A classical Wigner approach

Yossi Elran and Paul Brumer

J. Chem. Phys. 138, 234308 (2013); http://dx.doi.org/10.1063/1.4810009 (11 pages)

Online Publication Date: 19 June 2013

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Vibrational decoherence of a “breathing sphere” oscillator in a thermal Lennard-Jones bath is examined using a classical analog approach. The equivalence between this approach and the linearized semiclassical initial value representation (IVR) is established and the method is exploited to produce a useful computational strategy that can efficiently evaluate the time dependence of the decoherence in these systems. A comparison between Harmonic and Morse “breathing sphere” models is presented and the rate of decoherence is found to depend on the choice of model, the initial state of the oscillator, the initial conditions of the bath (temperature, density), and the choice of quantity measuring the decoherence rate. The results are used to examine the utility of the Caldeira-Leggett model in this realistic system.
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61.20.-p Structure of liquids
63.20.-e Phonons in crystal lattices
04.20.Ex Initial value problem, existence and uniqueness of solutions
03.65.-w Quantum mechanics
back to top Liquids, Glasses, and Crystals

Thermodynamic scaling of dynamics in polymer melts: Predictions from the generalized entropy theory

Wen-Sheng Xu and Karl F. Freed

J. Chem. Phys. 138, 234501 (2013); http://dx.doi.org/10.1063/1.4809991 (10 pages)

Online Publication Date: 17 June 2013

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Many glass-forming fluids exhibit a remarkable thermodynamic scaling in which dynamic properties, such as the viscosity, the relaxation time, and the diffusion constant, can be described under different thermodynamic conditions in terms of a unique scaling function of the ratio ργ/T, where ρ is the density, T is the temperature, and γ is a material dependent constant. Interest in the scaling is also heightened because the exponent γ enters prominently into considerations of the relative contributions to the dynamics from pressure effects (e.g., activation barriers) vs. volume effects (e.g., free volume). Although this scaling is clearly of great practical use, a molecular understanding of the scaling remains elusive. Providing this molecular understanding would greatly enhance the utility of the empirically observed scaling in assisting the rational design of materials by describing how controllable molecular factors, such as monomer structures, interactions, flexibility, etc., influence the scaling exponent γ and, hence, the dynamics. Given the successes of the generalized entropy theory in elucidating the influence of molecular details on the universal properties of glass-forming polymers, this theory is extended here to investigate the thermodynamic scaling in polymer melts. The predictions of theory are in accord with the appearance of thermodynamic scaling for pressures not in excess of ∼50 MPa. (The failure at higher pressures arises due to inherent limitations of a lattice model.) In line with arguments relating the magnitude of γ to the steepness of the repulsive part of the intermolecular potential, the abrupt, square-well nature of the lattice model interactions lead, as expected, to much larger values of the scaling exponent. Nevertheless, the theory is employed to study how individual molecular parameters affect the scaling exponent in order to extract a molecular understanding of the information content contained in the exponent. The chain rigidity, cohesive energy, chain length, and the side group length are all found to significantly affect the magnitude of the scaling exponent, and the computed trends agree well with available experiments. The variations of γ with these molecular parameters are explained by establishing a correlation between the computed molecular dependence of the scaling exponent and the fragility. Thus, the efficiency of packing the polymers is established as the universal physical mechanism determining both the fragility and the scaling exponent γ.
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61.25.hk Polymer melts and blends
65.40.gd Entropy
61.43.Fs Glasses
64.70.P- Glass transitions of specific systems
66.30.Ny Chemical interdiffusion; diffusion barriers
62.20.de Elastic moduli

Critical asymmetry in renormalization group theory for fluids

Wei Zhao, Liang Wu, Long Wang, Liyan Li, and Jun Cai

J. Chem. Phys. 138, 234502 (2013); http://dx.doi.org/10.1063/1.4810809 (12 pages)

Online Publication Date: 19 June 2013

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The renormalization-group (RG) approaches for fluids are employed to investigate critical asymmetry of vapour-liquid equilibrium (VLE) of fluids. Three different approaches based on RG theory for fluids are reviewed and compared. RG approaches are applied to various fluid systems: hard-core square-well fluids of variable ranges, hard-core Yukawa fluids, and square-well dimer fluids and modelling VLE of n-alkane molecules. Phase diagrams of simple model fluids and alkanes described by RG approaches are analyzed to assess the capability of describing the VLE critical asymmetry which is suggested in complete scaling theory. Results of thermodynamic properties obtained by RG theory for fluids agree with the simulation and experimental data. Coexistence diameters, which are smaller than the critical densities, are found in the RG descriptions of critical asymmetries of several fluids. Our calculation and analysis show that the approach coupling local free energy with White's RG iteration which aims to incorporate density fluctuations into free energy is not adequate for VLE critical asymmetry due to the inadequate order parameter and the local free energy functional used in the partition function.
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81.30.Dz Phase diagrams of other materials
65.20.Jk Studies of thermodynamic properties of specific liquids
back to top Surfaces, Interfaces, and Materials

Experimental and theoretical study of electronic structure of lutetium bi-phthalocyanine

I. Bidermane, J. Lüder, S. Boudet, T. Zhang, S. Ahmadi, C. Grazioli, M. Bouvet, J. Rusz, B. Sanyal, O. Eriksson, B. Brena, C. Puglia, and N. Witkowski

J. Chem. Phys. 138, 234701 (2013); http://dx.doi.org/10.1063/1.4809725 (8 pages)

Online Publication Date: 17 June 2013

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Using Near Edge X-Ray Absorption Fine Structure (NEXAFS) Spectroscopy, the thickness dependent formation of Lutetium Phthalocyanine (LuPc2) films on a stepped passivated Si(100)2×1 reconstructed surface was studied. Density functional theory (DFT) calculations were employed to gain detailed insights into the electronic structure. Photoelectron spectroscopy measurements have not revealed any noticeable interaction of LuPc2 with the H-passivated Si surface. The presented study can be considered to give a comprehensive description of the LuPc2 molecular electronic structure. The DFT calculations reveal the interaction of the two molecular rings with each other and with the metallic center forming new kinds of orbitals in between the phthalocyanine rings, which allows to better understand the experimentally obtained NEXAFS results.
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78.70.Dm X-ray absorption spectra
71.15.Mb Density functional theory, local density approximation, gradient and other corrections
81.65.Rv Passivation

Comparison of density functionals for nitrogen impurities in ZnO

Sung Sakong, Johann Gutjahr, and Peter Kratzer

J. Chem. Phys. 138, 234702 (2013); http://dx.doi.org/10.1063/1.4810862 (8 pages)

Online Publication Date: 18 June 2013

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Hybrid functionals and empirical correction schemes are compared to conventional semi-local density functional theory (DFT) calculations in order to assess the predictive power of these methods concerning the formation energy and the charge transfer level of impurities in the wide-gap semiconductor ZnO. While the generalized gradient approximation fails to describe the electronic structure of the N impurity in ZnO correctly, methods that widen the band gap of ZnO by introducing additional non-local potentials yield the formation energy and charge transfer level of the impurity in reasonable agreement with hybrid functional calculations. Summarizing the results obtained with different methods, we corroborate earlier findings that the formation of substitutional N impurities at the oxygen site in ZnO from N atoms is most likely slightly endothermic under oxygen-rich preparation conditions, and introduces a deep level more than 1 eV above the valence band edge of ZnO. Moreover, the comparison of methods elucidates subtle differences in the predicted electronic structure, e.g., concerning the orientation of unoccupied orbitals in the crystal field and the stability of the charged triplet state of the N impurity. Further experimental or theoretical analysis of these features could provide useful tests for validating the performance of DFT methods in their application to defects in wide-gap materials.
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71.55.Gs II-VI semiconductors
71.70.Ch Crystal and ligand fields
71.15.Mb Density functional theory, local density approximation, gradient and other corrections
71.20.Nr Semiconductor compounds

Dependence between velocity slip and temperature jump in shear flows

Jie Sun, Wen Wang, and Hua Sheng Wang

J. Chem. Phys. 138, 234703 (2013); http://dx.doi.org/10.1063/1.4810810 (8 pages)

Online Publication Date: 19 June 2013

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In this paper, we investigate the dependence of coupled velocity slip (quantified by the slip length) and temperature jump (quantified by the Kapitza length) on solid-liquid bonding strength and shear rate in shear flows. We find that the interfacial behaviors of nano-confined liquid are distinctly different in the weak and strong solid-liquid interaction regimes identified by a threshold of β = 2 (β being the proportional factor of solid-liquid bonding strength). In the weak solid-liquid interaction regime, the liquid molecules adjacent to the surface of the wall are randomly distributed and are free to slip. The variations of the slip and Kapitza lengths against solid-liquid bonding strength and shear rate are regular and monotonic. In the strong solid-liquid interaction regime, the liquid molecules in the vicinity of the wall are in multi-layered ordering and are largely restricted. The slip length becomes multivalued with increasing solid-liquid bonding strength and shear rate, while the Kapitza length seems insensitive to these two parameters. Furthermore, we find that (1) the temperature jump monotonically increases with velocity slip in the weak solid-liquid interaction regime, while it varies non-monotonically with a minimum value in the strong solid-liquid interaction regime; (2) the Kapitza length grows as a power function of the slip length in the weak solid-liquid interaction regime, while it keeps constant in the strong solid-liquid interaction regime.
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47.45.Gx Slip flows and accommodation
47.55.Hd Stratified flows

Phase transition in porous electrodes. III. For the case of a two component electrolyte

Kenji Kiyohara, Hiroshi Shioyama, Takushi Sugino, Kinji Asaka, Yasushi Soneda, Kiyoaki Imoto, and Masaya Kodama

J. Chem. Phys. 138, 234704 (2013); http://dx.doi.org/10.1063/1.4809743 (8 pages)

Online Publication Date: 19 June 2013

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The electrochemical thermodynamics of electrolytes in porous electrodes is qualitatively different from that in the bulk with planar electrodes when the pore size is comparable to the size of the electrolyte ions. In this paper, we discuss the thermodynamics of a two component electrolyte in a porous electrode by using Monte Carlo simulation. We show that electrolyte ions are selectively adsorbed in porous electrodes and the relative concentration of the two components significantly changes as a function of the applied voltage and the pore size. This selectivity is observed not only for the counterions but also for the coions.
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82.45.Fk Electrodes
82.45.Gj Electrolytes
61.43.Gt Powders, porous materials
65.60.+a Thermal properties of amorphous solids and glasses: heat capacity, thermal expansion, etc.
61.43.Bn Structural modeling: serial-addition models, computer simulation
68.43.Mn Adsorption kinetics

Direct measurements of forces between different charged colloidal particles and their prediction by the theory of Derjaguin, Landau, Verwey, and Overbeek (DLVO)

F. Javier Montes Ruiz-Cabello, Plinio Maroni, and Michal Borkovec

J. Chem. Phys. 138, 234705 (2013); http://dx.doi.org/10.1063/1.4810901 (10 pages)

Online Publication Date: 19 June 2013

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Force measurements between three types of latex particles of diameters down to 1 μm with sulfate and carboxyl surface functionalities were carried out with the multi-particle colloidal probe technique. The experiments were performed in monovalent electrolyte up to concentrations of about 5 mM. The force profiles could be quantified with the theory of Derjaguin, Landau, Verwey, and Overbeek (DLVO) by invoking non-retarded van der Waals forces and the Poisson-Boltzmann description of double layer forces within the constant regulation approximation. The forces measured in the symmetric systems were used to extract particle and surface properties, namely, the Hamaker constant, surface potentials, and regulation parameters. The regulation parameter is found to be independent of solution composition. With these values at hand, the DLVO theory is capable to accurately predict the measured forces in the asymmetric systems down to distances of 2–3 nm without adjustable parameters. This success indicates that DLVO theory is highly reliable to quantify interaction forces in such systems. However, charge regulation effects are found to be important, and they must be considered to obtain correct description of the forces. The use of the classical constant charge or constant potential boundary conditions may lead to erroneous results. To make reliable predictions of the force profiles, the surface potentials must be extracted from direct force measurements too. For highly charged surfaces, the commonly used electrophoresis techniques are found to yield incorrect estimates of this quantity.
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34.20.Cf Interatomic potentials and forces
82.70.Dd Colloids

Critical behavior of self-assembled rigid rods on two-dimensional lattices: Bethe-Peierls approximation and Monte Carlo simulations

L. G. López, D. H. Linares, A. J. Ramirez-Pastor, D. A. Stariolo, and S. A. Cannas

J. Chem. Phys. 138, 234706 (2013); http://dx.doi.org/10.1063/1.4809987 (12 pages)

Online Publication Date: 19 June 2013

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The critical behavior of adsorbed monomers that reversibly polymerize into linear chains with restricted orientations relative to the substrate has been studied. In the model considered here, which is known as self-assembled rigid rods (SARRs) model, the surface is represented by a two-dimensional lattice and a continuous orientational transition occurs as a function of temperature and coverage. The phase diagrams were obtained for the square, triangular, and honeycomb lattices by means of Monte Carlo simulations and finite-size scaling analysis. The numerical results were compared with Bethe-Peierls analytical predictions about the orientational transition for the square and triangular lattices. The analysis of the phase diagrams, along with the behavior of the critical average rod lengths, showed that the critical properties of the model do not depend on the structure of the lattice at low temperatures (coverage), revealing a quasi-one-dimensional behavior in this regime. Finally, the universality class of the SARRs model, which has been subject of controversy, has been revisited.
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81.16.Dn Self-assembly
61.43.Bn Structural modeling: serial-addition models, computer simulation
82.35.-x Polymers: properties; reactions; polymerization
81.30.Dz Phase diagrams of other materials
61.66.Hq Organic compounds
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Anomalous viscosity effect in the early stages of the ion-assisted adhesion/fusion event between lipid bilayers: A theoretical and computational study

Antonio Raudino, Siewert J. Marrink, and Martina Pannuzzo

J. Chem. Phys. 138, 234901 (2013); http://dx.doi.org/10.1063/1.4809993 (16 pages)

Online Publication Date: 17 June 2013

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The effect of viscosity on the encounter rate of two interacting membranes was investigated by combining a non-equilibrium Fokker-Planck model together with extensive Molecular Dynamics (MD) calculations. The encounter probability and stabilization of transient contact points represent the preliminary steps toward short-range adhesion and fusion of lipid leaflets. To strengthen our analytical model, we used a Coarse Grained MD method to follow the behavior of two charged palmitoyl oleoyl phosphatidylglycerol membranes embedded in a electrolyte-containing box at different viscosity regimes. Solvent friction was modulated by varying the concentration of a neutral, water-soluble polymer, polyethylene glycol, while contact points were stabilized by divalent ions that form bridges among juxtaposed membranes. While a naïve picture foresees a monotonous decrease of the membranes encounter rate with solvent viscosity, both the analytical model and MD simulations show a complex behavior. Under particular conditions, the encounter rate could exhibit a maximum at a critical viscosity value or for a critical concentration of bridging ions. These results seem to be confirmed by experimental observations taken from the literature.
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87.16.dm Mechanical properties and rheology
87.14.Cc Lipids
87.16.dj Dynamics and fluctuations
87.50.cj Electroporation/membrane effects
87.15.ap Molecular dynamics simulation

Nonlinear dynamics of spherical particles in Poiseuille flow under creeping-flow condition

S. Reddig and H. Stark

J. Chem. Phys. 138, 234902 (2013); http://dx.doi.org/10.1063/1.4809989 (10 pages)

Online Publication Date: 17 June 2013

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We study the nonlinear dynamics of spherical colloids under the influence of a pressure driven flow at vanishing Reynolds number. The colloids are confined between two parallel planar walls with a distance comparable to the particle diameter and they interact hydrodynamically via the solvent. We show that the bounded Poiseuille flow gives rise to new classes of trajectories resulting in cross-streamline migration. Two particles moving on these new trajectories exhibit either bound or unbound states. In the first case they oscillate on closed trajectories in the center-of-mass frame. In the second case, they exhibit cross-swapping trajectories in addition to swapping trajectories which were already observed in unbounded or bounded linear shear flow. The different classes of trajectories occur depending on the initial positions of the two particles and their size. We present state diagrams in the lateral positions, where we categorize the trajectories and color code the oscillation frequencies of the bound states. Finally we discuss how the results on the two-particle system help to understand the stability of particle trains composed of several particles.
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47.57.J- Colloidal systems
47.15.G- Low-Reynolds-number (creeping) flows
47.15.Cb Laminar boundary layers
47.55.Kf Particle-laden flows
47.60.-i Flow phenomena in quasi-one-dimensional systems
47.15.Rq Laminar flows in cavities, channels, ducts, and conduits

Wall-induced orientational order in athermal semidilute solutions of semiflexible polymers: Monte Carlo simulations of a lattice model

V. A. Ivanov, A. S. Rodionova, J. A. Martemyanova, M. R. Stukan, M. Müller, W. Paul, and K. Binder

J. Chem. Phys. 138, 234903 (2013); http://dx.doi.org/10.1063/1.4810745 (20 pages)

Online Publication Date: 18 June 2013

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An athermal solution of semiflexible macromolecules with excluded volume interactions has been studied at various concentrations (dilute, semidilute, and concentrated solutions) in a film of thickness D between two hard walls by grand canonical Monte Carlo simulations of the bond fluctuation lattice model. Analyzing profiles of orientational order parameters across the film, we find that for thick films two phase transitions occur at chemical potentials of the polymers (or polymer densities, respectively) where the bulk polymer solution still is in the disordered isotropic phase. At rather small polymer densities, polymers accumulate at the walls due to an entropic attraction and undergo a transition to two-dimensional nematic order. Due to the properties of the lattice model, this order has Ising character, and the simulation results seem to be compatible with a second-order transition. Increasing the polymer density, nematically ordered “wetting” layers form at both walls; the increase of thickness of these layers is compatible with a logarithmic divergence when the chemical potential of the isotropic–nematic transition in the bulk is approached. In a system of finite width, D, between the walls, this leads to capillary nematization, exhibiting a reduction of the transition chemical potential inversely proportional to D. This transition exists only if D exceeds some critical value Dc, while the transition from the isotropic phase to the two-dimensional nematic state is suggested to persist down to ultrathin films.
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61.25.he Polymer solutions
68.15.+e Liquid thin films
64.70.Ja Liquid-liquid transitions
61.20.Ja Computer simulation of liquid structure

Dynamics of two-dimensional and quasi-two-dimensional polymers

Bong June Sung and Arun Yethiraj

J. Chem. Phys. 138, 234904 (2013); http://dx.doi.org/10.1063/1.4810755 (6 pages)

Online Publication Date: 18 June 2013

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The dynamic properties of dense two-dimensional (2D) polymer melts are studied using discontinuous molecular dynamics simulations. Both strictly 2D and quasi-2D systems are investigated. The strictly 2D model system consists of a fluid of freely jointed tangent hard disc chains. The translational diffusion coefficient, D, is strongly system size dependent with D ∼ ln L where L is the linear dimension of the square simulation cell. The rotational correlation time, τrot, is, however, independent of system size. The dynamics is consistent with Rouse behavior with D/ln L ∼ N−1 and τrot ∼ N2 for all area fractions. Analysis of the intermediate scattering function, Fs(k, t), shows that the dynamics becomes slow for N = 256 and the area fraction of 0.454 and that there might be a glass transition for long polymers at sufficiently high area fractions. The polymer mobility is not correlated with the conformation of the molecules. In the quasi-2D system hard sphere chains are confined between corrugated surfaces so that chains cannot go over each other or into the surfaces. The conformational properties are identical to the 2D case, but D and τrot are independent of system size. The scaling of D and τrot with N is similar to that of strictly 2D systems. The simulations suggest that 2D polymers are never entangled and follow Rouse dynamics at all densities.
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61.25.hk Polymer melts and blends
64.70.P- Glass transitions of specific systems
61.43.Bn Structural modeling: serial-addition models, computer simulation
66.30.Ny Chemical interdiffusion; diffusion barriers
68.35.Fx Diffusion; interface formation
81.05.Lg Polymers and plastics; rubber; synthetic and natural fibers; organometallic and organic materials
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