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21 Jun 2013

Volume 138, Issue 23 (partial)

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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
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
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
back to top Polymers and Soft Matter
FREE

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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