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28 Mar 2013

Volume 138, Issue 12, Articles (12xxxx)

Issue Cover Spotlight Figure

J. Chem. Phys. 138, 124701 (2013); http://dx.doi.org/10.1063/1.4794685 (9 pages)

Luying Wang, Randall S. Dumont, and James M. Dickson
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back to top Atoms, Molecules, and Clusters

Resonance Regge poles and the state-to-state F + H2 reaction: QP decomposition, parametrized S matrix, and semiclassical complex angular momentum analysis of the angular scattering

J. N. L. Connor

J. Chem. Phys. 138, 124310 (2013); http://dx.doi.org/10.1063/1.4794859 (21 pages)

Online Publication Date: 28 March 2013

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Three new contributions to the complex angular momentum (CAM) theory of differential cross sections (DCSs) for chemical reactions are reported. They exploit recent advances in the Padé reconstruction of a scattering (S) matrix in a region surrounding the Re J axis, where J is the total angular momentum quantum variable, starting from the discrete values, J = 0, 1, 2, …. In particular, use is made of Padé continuations obtained by Sokolovski, Castillo, and Tully [Chem. Phys. Lett. 313, 225 (1999)10.1016/S0009-2614(99)01016-7] for the S matrix of the benchmark F + H2(vi = 0, ji = 0, mi = 0) → FH(vf = 3, jf = 3, mf = 0) + H reaction. Here vi, ji, mi and vf, jf, mf are the initial and final vibrational, rotational, and helicity quantum numbers, respectively. The three contributions are: (1) A new exact decomposition of the partial wave (PW) S matrix is introduced, which is called the QP decomposition. The P part contains information on the Regge poles. The Q part is then constructed exactly by subtracting a rapidly oscillating phase and the PW P matrix from the input PW S matrix. After a simple modification, it is found that the corresponding scattering subamplitudes provide insight into the angular-scattering dynamics using simple partial wave series (PWS) computations. It is shown that the leading n = 0 Regge pole contributes to the small-angle scattering in the centre-of-mass frame. (2) The Q matrix part of the QP decomposition has simpler properties than the input S matrix. This fact is exploited to deduce a parametrized (analytic) formula for the PW S matrix in which all terms have a direct physical interpretation. This is a long sort-after goal in reaction dynamics, and in particular for the state-to-state F + H2 reaction. (3) The first definitive test is reported for the accuracy of a uniform semiclassical (asymptotic) CAM theory for a DCS based on the Watson transformation. The parametrized S matrix obtained in contribution (2) is used in both the PW and semiclassical parts of the calculation. Powerful uniform asymptotic approximations are employed for the background integral; they allow for the proximity of a Regge pole and a saddle point. The CAM DCS agrees well with the PWS DCS, across the whole angular range, except close to the forward and backward directions, where, as expected, the CAM theory becomes non-uniform. At small angles, θR ≲ 40°, the PWS DCS can be reproduced using a nearside semiclassical subamplitude, which allows for a pole being close to a saddle point, plus the farside surface wave of the n = 0 pole sub-subamplitude, with the oscillations in the DCS arising from nearside-farside interference. This proves that the n = 0 Regge resonance pole contributes to the small-angle scattering.
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82.30.Lp Decomposition reactions (pyrolysis, dissociation, and fragmentation)
82.30.Cf Atom and radical reactions; chain reactions; molecule-molecule reactions
82.20.Ln Semiclassical theory of reactions and/or energy transfer
33.20.Tp Vibrational analysis
33.20.Sn Rotational analysis

Carbon X-ray absorption spectra of fluoroethenes and acetone: A study at the coupled cluster, density functional, and static-exchange levels of theory

Thomas Fransson, Sonia Coriani, Ove Christiansen, and Patrick Norman

J. Chem. Phys. 138, 124311 (2013); http://dx.doi.org/10.1063/1.4795835 (12 pages)

Online Publication Date: 29 March 2013

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Near carbon K-edge X-ray absorption fine structure spectra of a series of fluorine-substituted ethenes and acetone have been studied using coupled cluster and density functional theory (DFT) polarization propagator methods, as well as the static-exchange (STEX) approach. With the complex polarization propagator (CPP) implemented in coupled cluster theory, relaxation effects following the excitation of core electrons are accounted for in terms of electron correlation, enabling a systematic convergence of these effects with respect to electron excitations in the cluster operator. Coupled cluster results have been used as benchmarks for the assessment of propagator methods in DFT as well as the state-specific static-exchange approach. Calculations on ethene and 1,1-difluoroethene illustrate the possibility of using nonrelativistic coupled cluster singles and doubles (CCSD) with additional effects of electron correlation and relativity added as scalar shifts in energetics. It has been demonstrated that CPP spectra obtained with coupled cluster singles and approximate doubles (CC2), CCSD, and DFT (with a Coulomb attenuated exchange-correlation functional) yield excellent predictions of chemical shifts for vinylfluoride, 1,1-difluoroethene, trifluoroethene, as well as good spectral features for acetone in the case of CCSD and DFT. Following this, CPP-DFT is considered to be a viable option for the calculation of X-ray absorption spectra of larger π-conjugated systems, and CC2 is deemed applicable for chemical shifts but not for studies of fine structure features. The CCSD method as well as the more approximate CC2 method are shown to yield spectral features relating to π*-resonances in good agreement with experiment, not only for the aforementioned molecules but also for ethene, cis-1,2-difluoroethene, and tetrafluoroethene. The STEX approach is shown to underestimate π*-peak separations due to spectral compressions, a characteristic which is inherent to this method.
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33.20.Rm X-ray spectra
31.15.E- Density-functional theory
31.15.bw Coupled-cluster theory
31.15.eg Exchange-correlation functionals (in current density functional theory)

Vibrational and vibronic spectra of tryptamine conformers

Nitzan Mayorkas, Amir Bernat, Shay Izbitski, and Ilana Bar

J. Chem. Phys. 138, 124312 (2013); http://dx.doi.org/10.1063/1.4798218 (12 pages)

Online Publication Date: 29 March 2013

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Conformation-specific ionization-detected stimulated Raman spectra, including both Raman loss and Raman gain lines, along with visible-visible-ultraviolet hole-burning spectra of tryptamine (TRA) conformers have been measured simultaneously, with the aim of obtaining new data for identifying them. The slightly different orientations of the ethylamine side chain relative to the indole lead to unique spectral signatures, pointing to the presence of seven TRA conformers in the molecular beam. Comparison of ionization-loss stimulated Raman spectra to computationally scaled harmonic Raman spectra, especially in the alkyl C–H and amine N–H stretch regions together with the retrieved information on the stabilities of the TRA conformers assisted their characterization and structural identification. The prospects and limitations of using these spectroscopic methods as potential conformational probes of flexible molecules are discussed.
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33.20.Fb Raman and Rayleigh spectra (including optical scattering)
33.20.Tp Vibrational analysis
33.20.Wr Vibronic, rovibronic, and rotation-electron-spin interactions
33.80.Rv Multiphoton ionization and excitation to highly excited states (e.g., Rydberg states)
33.15.Bh General molecular conformation and symmetry; stereochemistry
33.15.Mt Rotation, vibration, and vibration-rotation constants

The molecular frame electric dipole moment and hyperfine interactions in hafnium fluoride, HfF

Anh Le, Timothy C. Steimle, Leonid Skripnikov, and Anatoly V. Titov

J. Chem. Phys. 138, 124313 (2013); http://dx.doi.org/10.1063/1.4794049 (9 pages)

Online Publication Date: 29 March 2013

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The (1,0) [17.9]2.5−X2Δ3/2 band of hafnium monofluoride (HfF) has been recorded using high-resolution laser-induced fluorescence spectroscopy both field-free and in the presence of a static electric field. The field-free spectra of 177HfF, 179HfF, and 180HfF were modeled to generate a set of fine and hyperfine parameter for the X2Δ3/2(v = 0) and [17.9]2.5 (v = 1) states. The observed optical Stark shifts for the 180HfF isotopologue were analyzed to produce the molecular frame electric dipole moments of 1.66(1) D and 0.419(7) D for the X2Δ3/2 and [17.9]2.5 state, respectively. Both the generalized effective core potential and all-electron four component approaches were used in ab initio calculations to predict the properties of ground state HfF including equilibrium distance, dipole moments, quadrupole coupling, and magnetic hyperfine constants.
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31.30.Gs Hyperfine interactions and isotope effects
33.15.Kr Electric and magnetic moments (and derivatives), polarizability, and magnetic susceptibility
33.15.Pw Fine and hyperfine structure
33.50.Dq Fluorescence and phosphorescence spectra
33.70.Jg Line and band widths, shapes, and shifts
31.15.aj Relativistic corrections, spin-orbit effects, fine structure; hyperfine structure
back to top Liquids, Glasses, and Crystals

Global sampling of the photochemical reaction paths of bromoform by ultrafast deep-UV through near-IR transient absorption and ab initio multiconfigurational calculations

S. K. Pal, A. S. Mereshchenko, E. V. Butaeva, P. Z. El-Khoury, and A. N. Tarnovsky

J. Chem. Phys. 138, 124501 (2013); http://dx.doi.org/10.1063/1.4789268 (19 pages)

Online Publication Date: 22 March 2013

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Ultrafast deep-ultraviolet through near infrared (210–950 nm) transient absorption spectroscopy complemented by ab initio multiconfigurational calculations offers a global description of the photochemical reaction pathways of bromoform following 255-nm excitation in methylcyclohexane and acetonitrile solutions. Photoexcitation of CHBr3 leads to the ground-state iso-CHBr3 product in a large quantum yield (∼35%), formed through two different mechanisms: concerted excited-state isomerization and cage-induced isomerization through the recombination of the nascent radical pair. These two processes take place on different time scales of tens of femtoseconds and several picoseconds, respectively. The novel ultrafast direct isomerization pathway proposed herein is consistent with the occurrence of a conical intersection between the first excited singlet state of CHBr3 and the ground electronic state of iso-CHBr3. Complete active space self-consistent field calculations characterize this singularity in the vicinity of a second order saddle point on the ground state which connects the two isomer forms. For cage-induced isomerization, both the formation of the nascent radical pair and its subsequent collapse into ground-state iso-CHBr3 are directly monitored through the deep-ultraviolet absorption signatures of the radical species. In both mechanisms, the optically active (i.e., those with largest Franck-Condon factors) C−Br−Br bending and Br−Br stretching modes of ground-state iso-CHBr3 have the largest projection on the reaction coordinate, enabling us to trace the structural changes accompanying vibrational relaxation of the non-equilibrated isomers through transient absorption dynamics. The iso-CHBr3 photoproduct is stable in methylcyclohexane, but undergoes either facile thermal isomerization to the parent CHBr3 structure through a cyclic transition state stabilized by the polar acetonitrile medium (∼300-ps lifetime), and hydrolysis in the presence of water.
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33.20.Lg Ultraviolet spectra
33.70.Ca Oscillator and band strengths, lifetimes, transition moments, and Franck-Condon factors
82.30.Qt Isomerization and rearrangement
31.15.ae Electronic structure and bonding characteristics
31.15.xr Self-consistent-field methods
33.20.Ea Infrared spectra

A thermodynamic derivation of the reciprocal relations

N. Kocherginsky and M. Gruebele

J. Chem. Phys. 138, 124502 (2013); http://dx.doi.org/10.1063/1.4793258 (6 pages)

Online Publication Date: 25 March 2013

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Starting with the continuity and Smoluchowski equations, we write the mass flux for a system out of equilibrium in terms of the physicochemical potential μg. μg is a coarse-grained analog of the chemical potential in the presence of forces that drive the system out of equilibrium. The expression for flux in terms of μg allows for a macroscopic derivation of the Onsager reciprocal relations for the case of transport by diffusion and drift in single or multi-component systems, without recourse to microscopic fluctuations or equations of motion. Transport coefficients for any time reversal-invariant properties now are expressed in terms of only partial molar derivatives and mobilities (diffusion coefficients). The thermodynamic derivation cannot treat time reversal.
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05.60.-k Transport processes
05.70.-a Thermodynamics

Hyperfine coupling of the hydrogen atom in high temperature water

Kirill Nuzhdin and David M. Bartels

J. Chem. Phys. 138, 124503 (2013); http://dx.doi.org/10.1063/1.4795005 (8 pages)

Online Publication Date: 26 March 2013

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The hyperfine coupling constant of the hydrogen atom has been measured in pressurized liquid water up to 300 °C. The reduced constant Awater/Avacuum is 0.9939 at room temperature, and decreases to a minimum of 0.9918 at 240 °C. The reduced constant then increases at higher temperature. The g-factor is 2.002244(10) at room temperature and decreases to 2.00221(1) at 240 °C. The change in g-factor is proportional to the change in hyperfine coupling. The behavior below 110 °C is in excellent agreement with a previously proposed model in which the H atom is confined to a harmonic solvent cage, and vibrations within the cage mix “p-type” character into the wavefunction, resulting in Awater/Avacuum < 1. The harmonic model breaks down above 130 °C. We demonstrate that a classical binary collision model using approximate partial molar volume information can recover the observed minima near 240 °C.
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31.30.Gs Hyperfine interactions and isotope effects
31.70.Dk Environmental and solvent effects
32.10.Fn Fine and hyperfine structure

Water proton configurations in structures I, II, and H clathrate hydrate unit cells

Fumihito Takeuchi, Masaki Hiratsuka, Ryo Ohmura, Saman Alavi, Amadeu K. Sum, and Kenji Yasuoka

J. Chem. Phys. 138, 124504 (2013); http://dx.doi.org/10.1063/1.4795499 (12 pages)

Online Publication Date: 27 March 2013

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Position and orientation of water protons need to be specified when the molecular simulation studies are performed for clathrate hydrates. Positions of oxygen atoms in water are experimentally determined by X-ray diffraction analysis of clathrate hydrate structures, but positions of water hydrogen atoms in the lattice are disordered. This study reports a determination of the water proton coordinates in unit cell of structure I (sI), II (sII), and H (sH) clathrate hydrates that satisfy the ice rules, have the lowest potential energy configuration for the protons, and give a net zero dipole moment. Possible proton coordinates in the unit cell were chosen by analyzing the symmetry of protons on the hexagonal or pentagonal faces in the hydrate cages and generating all possible proton distributions which satisfy the ice rules. We found that in the sI and sII unit cells, proton distributions with small net dipole moments have fairly narrow potential energy spreads of about 1 kJ/mol. The total Coulomb potential on a test unit charge placed in the cage center for the minimum energy/minimum dipole unit cell configurations was calculated. In the sI small cages, the Coulomb potential energy spread in each class of cage is less than 0.1 kJ/mol, while the potential energy spread increases to values up to 6 kJ/mol in sH and 15 kJ/mol in the sII cages. The guest environments inside the cages can therefore be substantially different in the sII case. Cartesian coordinates for oxygen and hydrogen atoms in the sI, sII, and sH unit cells are reported for reference.
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34.20.Gj Intermolecular and atom-molecule potentials and forces
31.50.-x Potential energy surfaces
33.15.Bh General molecular conformation and symmetry; stereochemistry

Non-monotonic size dependence of diffusion and levitation effect: A mode-coupling theory analysis

Manoj Kumar Nandi, Atreyee Banerjee, and Sarika Maitra Bhattacharyya

J. Chem. Phys. 138, 124505 (2013); http://dx.doi.org/10.1063/1.4796232 (8 pages)

Online Publication Date: 28 March 2013

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We present a study of diffusion of small tagged particles in a solvent, using mode coupling theory (MCT) analysis and computer simulations. The study is carried out for various interaction potentials. For the first time, using MCT, it is shown that only for strongly attractive interaction potential with allowing interpenetration between the solute-solvent pair the diffusion exhibits a non-monotonic solute size dependence which has earlier been reported in simulation studies [P. K. Ghorai and S. Yashonath, J. Phys. Chem. B 109, 5824–5835 (2005)10.1021/jp046312w]. For weak attractive and repulsive potential the solute size dependence of diffusion shows monotonic behaviour. It is also found that for systems where the interaction potential does not allow solute-solvent interpenetration, the solute cannot explore the neck of the solvent cage. Thus these systems even with strong attractive interaction will never show any non-monotonic size dependence of diffusion. This non-monotonic size dependence of diffusion has earlier been connected to levitation effect [S. Yashonath and P. Santikary, J. Phys. Chem. 98, 6368 (1994)10.1021/j100076a022]. We also show that although levitation is a dynamic phenomena, the effect of levitation can be obtained in the static radial distribution function.
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66.10.C- Diffusion and thermal diffusion
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1H relaxation dispersion in solutions of nitroxide radicals: Influence of electron spin relaxation

D. Kruk, A. Korpała, A. Kubica, J. Kowalewski, E. A. Rössler, and J. Moscicki

J. Chem. Phys. 138, 124506 (2013); http://dx.doi.org/10.1063/1.4795006 (15 pages)

Online Publication Date: 29 March 2013

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The work presents a theory of nuclear (1H) spin-lattice relaxation dispersion for solutions of 15N and 14N radicals, including electron spin relaxation effects. The theory is a generalization of the approach presented by Kruk et al. [J. Chem. Phys. 137, 044512 (2012)]10.1063/1.4736854. The electron spin relaxation is attributed to the anisotropic part of the electron spin–nitrogen spin hyperfine interaction modulated by rotational dynamics of the paramagnetic molecule, and described by means of Redfield relaxation theory. The 1H relaxation is caused by electron spin–proton spin dipole-dipole interactions which are modulated by relative translational motion of the solvent and solute molecules. The spectral density characterizing the translational dynamics is described by the force-free-hard-sphere model. The electronic relaxation influences the 1H relaxation by contributing to the fluctuations of the inter-molecular dipolar interactions. The developed theory is tested against 1H spin-lattice relaxation dispersion data for glycerol solutions of 4-oxo-TEMPO-d16-15N and 4-oxo-TEMPO-d16-14N covering the frequency range of 10 kHz–20 MHz. The studies are carried out as a function of temperature starting at 328 K and going down to 290 K. The theory gives a consistent overall interpretation of the experimental data for both 14N and 15N systems and explains the features of 1H relaxation dispersion resulting from the electron spin relaxation.
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33.35.+r Electron resonance and relaxation
34.20.Gj Intermolecular and atom-molecule potentials and forces
33.15.Mt Rotation, vibration, and vibration-rotation constants
33.15.Pw Fine and hyperfine structure
33.20.Sn Rotational analysis
33.25.+k Nuclear resonance and relaxation
back to top Surfaces, Interfaces, and Materials
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Nonequilibrium molecular dynamics simulation of pressure-driven water transport through modified CNT membranes

Luying Wang, Randall S. Dumont, and James M. Dickson

J. Chem. Phys. 138, 124701 (2013); http://dx.doi.org/10.1063/1.4794685 (9 pages)

Online Publication Date: 22 March 2013

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Nonequilibrium molecular dynamics (NEMD) simulations are presented to investigate the effect of water-membrane interactions on the transport properties of pressure-driven water flow passing through carbon nanotube (CNT) membranes. The CNT membrane is modified with different physical properties to alter the van der Waals interactions or the electrostatic interactions between water molecules and the CNT membranes. The unmodified and modified CNT membranes are models of simplified nanofiltration (NF) membranes at operating conditions consistent with real NF systems. All NEMD simulations are run with constant pressure difference (8.0 MPa) temperature (300 K), constant pore size (0.643 nm radius for CNT (12, 12)), and membrane thickness (6.0 nm). The water flow rate, density, and velocity (in flow direction) distributions are obtained by analyzing the NEMD simulation results to compare transport through the modified and unmodified CNT membranes. The pressure-driven water flow through CNT membranes is from 11 to 21 times faster than predicted by the Navier-Stokes equations. For water passing through the modified membrane with stronger van der Waals or electrostatic interactions, the fast flow is reduced giving lower flow rates and velocities. These investigations show the effect of water-CNT membrane interactions on water transport under NF operating conditions. This work can help provide and improve the understanding of how these membrane characteristics affect membrane performance for real NF processes.
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47.60.Dx Flows in ducts and channels
02.70.Ns Molecular dynamics and particle methods
47.10.ad Navier-Stokes equations
47.11.Mn Molecular dynamics methods
47.56.+r Flows through porous media

Monoxide carbon frequency shift as a tool for the characterization of TiO2 surfaces: Insights from first principles spectroscopy

Pablo G. Lustemberg and Damián A. Scherlis

J. Chem. Phys. 138, 124702 (2013); http://dx.doi.org/10.1063/1.4796199 (8 pages)

Online Publication Date: 26 March 2013

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The adsorption and vibrational frequency of CO on defective and undefective titanium dioxide surfaces is examined applying first-principles molecular dynamics simulations. In particular, the vibrational frequencies are obtained beyond the harmonic approximation, through the time correlation functions of the atomic trajectories. In agreement with experiments, at low CO coverages we find an upshift in the vibration frequency with respect to the free CO molecule, of 45 and 35 cm−1 on the stoichiometric rutile (110) and anatase (101) faces, respectively. A band falling 8 cm−1 below the frequency corresponding to the perfect face is observed for the reduced rutile (110) surface in the low vacancy concentration limit, where the adsorption is favored on Ti4 + sites. At a higher density of defects, adsorption on Ti3 + sites becomes more stable, accompanied by a downshift in the stretching band. In the case of anatase (101), we analyze the effect of subsurface oxygen vacancies, which have been shown to be predominant in this material. Interestingly, we find that the adsorption of CO on five coordinate Ti atoms placed over subsurface vacancies is favored with respect to other Ti4 + sites (7.25 against 6.95 kcal/mol), exhibiting a vibrational redshift of 20 cm−1. These results provide the basis to quantitatively assess the degree of reduction of rutile and anatase surfaces via IR spectroscopy, and at the same time allow for the assignment of characteristic bands in the CO spectra on TiO2 whose origin has remained ambiguous.
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68.43.Mn Adsorption kinetics
61.66.Bi Elemental solids
61.66.Dk Alloys
71.55.Ht Other nonmetals
61.72.jd Vacancies
78.30.Hv Other nonmetallic inorganics

Structure and chemical reactivity of the polar three-fold surfaces of GaPd: A density-functional study

M. Krajčí and J. Hafner

J. Chem. Phys. 138, 124703 (2013); http://dx.doi.org/10.1063/1.4795435 (20 pages)

Online Publication Date: 26 March 2013

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The polar threefold surfaces of the GaPd compound crystallizing in the B20 (FeSi-type) structure (space group P213) have been investigated using density-functional methods. Because of the lack of inversion symmetry the B20 structure exists in two enantiomorphic forms denoted as A and B. The threefold {111} surfaces have polar character. In both nonequivalent (111) and (mathmathmath) directions several surface terminations differing in structure and chemical composition are possible. The formation of the threefold surfaces has been studied by simulated cleavage experiments and by calculations of the surface energies. Because of the polar character of the threefold surfaces calculations for stoichiometric slabs permit only the determination of the average energy of the surfaces exposed on both sides of the slab. Calculations for nonstoichiometric slabs performed in the grand canonical ensemble yield differences of the surface energies for the possible terminations as a function of the chemical potential in the reactive atmosphere above the surface and predict a transition between Ga- and Pd-terminated surfaces as a function of the chemical potential. The {100} surfaces are stoichiometric and uniquely defined. The calculated surface energies are identical to the average energies of the {100} surfaces of the pure metals. The {210} surfaces are also stoichiometric, with an energy very close to that of the {100} surfaces. Assuming that for the {111} surfaces the energies of different possible terminations are in a proportion equal to that of the concentration-weighted energies of the {111} surfaces of the pure metals, surface energies for all possible {111} terminations may be calculated. The preferable termination perpendicular to the A⟨111⟩ direction consists of a bilayer with three Ga atoms in the upper and three Pd atoms in the lower part. The surface energy of this termination further decreases if the Pd triplet is covered by additional Ga atom. Perpendicular to the A〈mathmathmath〉 direction the lowest energy has been found for a bilayer with three Ga atoms per surface cell in the upper layer and one Ga and one Pd in the lower part. The calculated surface energies are in agreement with a simulated cleavage experiment. However, cleavage does not result in the formation of the lowest-energy surfaces, because all possible {111} cleavage planes expose a low-energy surface on one, and a high-energy surface on the other side. The prediction of Ga-terminated surfaces has been tested against the available experimental information. The calculated surface electronic density of states is in very good agreement with photo-emission spectroscopy. Calculated STM images of the most stable surfaces agree with all details of the available experimental images. The chemical reactivity of the most stable surfaces has been studied by the adsorption of CO molecules. The adsorption energies and maximum coverages calculated for the Ga-terminated surfaces permit a reasonable interpretation of the observed thermal desorption spectra, whereas for the Pd-terminated surfaces the calculated adsorption energies are far too high.
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61.66.Fn Inorganic compounds
68.03.Fg Evaporation and condensation of liquids
73.21.-b Electron states and collective excitations in multilayers, quantum wells, mesoscopic, and nanoscale systems
64.70.dg Crystallization of specific substances
65.40.gp Surface energy
61.50.Ah Theory of crystal structure, crystal symmetry; calculations and modeling

Phonon thermal transport outside of local equilibrium in nanowires via molecular dynamics

Ya Zhou and Alejandro Strachan

J. Chem. Phys. 138, 124704 (2013); http://dx.doi.org/10.1063/1.4793530 (6 pages)

Online Publication Date: 27 March 2013

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We study thermal transport through Pt nanowires that bridge planar contacts as a function of wire length and vibrational frequency of the contacts. When phonons in the contacts have lower average frequencies than those in the wires thermal transport occurs under conditions away from local equilibrium with low-frequency phonons experiencing a higher thermal gradient than high-frequency ones. This results in a size-dependent increase in the effective thermal conductivity of the wire with decreasing vibrational frequencies of the contacts. The interfacial resistivity when heat flows from the wire to the contact is also size-dependent and has the same physical origin in the lack of full equilibration in short nanowires. We develop a model based on a 1D atomic chain that captures the salient physics of the MD results.
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81.05.Bx Metals, semimetals, and alloys
63.22.Gh Nanotubes and nanowires
81.07.Gf Nanowires
72.15.Eb Electrical and thermal conduction in crystalline metals and alloys

Knudsen layer formation in laser induced thermal desorption

Akihiko Ikeda, Masuaki Matsumoto, Shohei Ogura, Tatsuo Okano, and Katsuyuki Fukutani

J. Chem. Phys. 138, 124705 (2013); http://dx.doi.org/10.1063/1.4795827 (6 pages)

Online Publication Date: 27 March 2013

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Laser induced thermal desorption of Xe atoms into vacuum from a metal surface following the nano-second pulsed laser heating was investigated by the time-of-flight (TOF) measurement. The desorption flow was studied at a wide range of desorption flux by varying the initially prepared Xe coverage Θ (1 ML = 4.5 × 1018 atoms/m2). At Θ = 0.3 ML, the TOF of Xe was well represented by a Maxwell-Boltzmann velocity distribution, which is in good agreement with thermal desorption followed by collision-free flow. At Θ > 0.3 ML, the peak positions of the TOF spectra were shifted towards the smaller values and became constant at large Θ, which were well fitted with a shifted Maxwell-Boltzmann velocity distribution with a temperature TD and a stream velocity u. With TD fixed at 165 K, u was found to increase from 80 to 125 m/s with increasing Θ from 1.2 to 4 ML. At Θ > 4 ML, the value of u becomes constant at 125 m/s. The converging feature of u was found to be consistent with analytical predictions and simulated results based on the Knudsen layer formation theory. We found that the Knudsen layer formation in laser desorption is completed at Knudsen number Kn <0.39.
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68.43.Vx Thermal desorption
68.43.Nr Desorption kinetics
79.20.Ds Laser-beam impact phenomena

Electronic and optical properties of graphene and graphitic ZnO nanocomposite structures

Wei Hu, Zhenyu Li, and Jinlong Yang

J. Chem. Phys. 138, 124706 (2013); http://dx.doi.org/10.1063/1.4796602 (5 pages)

Online Publication Date: 28 March 2013

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Electronic and optical properties of graphene and graphitic ZnO (G/g-ZnO) nanocomposites have been investigated with density functional theory. Graphene interacts overall weakly with g-ZnO monolayer via van der Waals interaction. There is no charge transfer between the graphene and g-ZnO monolayer, while a charge redistribution does happen within the graphene layer itself, forming well-defined electron-hole puddles. When Al or Li is doped in the g-ZnO monolayer, substantial electron (n-type) and hole (p-type) doping can be induced in graphene, leading to well-separated electron-hole pairs at their interfaces. Improved optical properties in graphene/g-ZnO nanocomposite systems are also observed, with potential photocatalytic and photovoltaic applications.
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71.20.Nr Semiconductor compounds
72.20.Jv Charge carriers: generation, recombination, lifetime, and trapping
71.15.Mb Density functional theory, local density approximation, gradient and other corrections
61.72.up Other materials
78.40.Fy Semiconductors

Grain boundary melting in ice

E. S. Thomson, Hendrik Hansen-Goos, J. S. Wettlaufer, and L. A. Wilen

J. Chem. Phys. 138, 124707 (2013); http://dx.doi.org/10.1063/1.4797468 (5 pages) | Cited 1 time

Online Publication Date: 28 March 2013

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We describe an optical scattering study of grain boundary premelting in water ice. Ubiquitous long ranged attractive polarization forces act to suppress grain boundary melting whereas repulsive forces originating in screened Coulomb interactions and classical colligative effects enhance it. The liquid enhancing effects can be manipulated by adding dopant ions to the system. For all measured grain boundaries this leads to increasing premelted film thickness with increasing electrolyte concentration. Although we understand that the interfacial surface charge densities qs and solute concentrations can potentially dominate the film thickness, we cannot directly measure them within a given grain boundary. Therefore, as a framework for interpreting the data we consider two appropriate qs dependent limits; one is dominated by the colligative effect and other is dominated by electrostatic interactions.
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64.70.dj Melting of specific substances
61.72.Mm Grain and twin boundaries

Deposition of model chains on surfaces: Anomalous relation between flux and stability

Pritam Kumar Jana and Andreas Heuer

J. Chem. Phys. 138, 124708 (2013); http://dx.doi.org/10.1063/1.4795316 (7 pages)

Online Publication Date: 29 March 2013

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Model chains are studied via Monte Carlo simulations which are deposited with a fixed flux on a substrate. They may represent, e.g., stiff lipophilic chains with an head group and tail groups mimicking the alkyl chain. After some subsequent fixed simulation time we determine the final energy as a function of flux and temperature. Surprisingly, in some range of temperature and flux the final energy increases with decreasing flux. The physical origin of this counterintuitive observation is elucidated. In contrast, when performing equivalent cooling experiments no such anomaly is observed. Furthermore, it is elaborated whether flux experiments give rise to configurations with lower energies as compared to cooling experiments. These results are related to recent experiments by the Ediger group where very stable configurations of glass-forming systems have been generated via flux experiments.
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68.43.Mn Adsorption kinetics
64.70.P- Glass transitions of specific systems
65.40.gp Surface energy

Interaction of magnetic transition metal dimers with spin-polarized hydrogenated graphene

S. W. Ong, J. Wu, A. Z. H. Thong, E. S. Tok, and H. C. Kang

J. Chem. Phys. 138, 124709 (2013); http://dx.doi.org/10.1063/1.4795500 (12 pages)

Online Publication Date: 29 March 2013

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The coadsorption of hydrogen and transition metal dimers Fe2, Co2, Ni2, and FeCo on graphene is investigated using density functional theory calculations. Our work is motivated by observations that the magnetic moments of these transition metal dimers are large and that hydrogen adsorption partitions the graphene lattice into magnetic subdomains. Thus, we expect the magnetic dimers to interact strongly with the lattice. Our results show that the majority-spin direction of the lattice electronic states depends upon the dimer identity, the lattice spin polarization being in the same direction as the dimer spin polarization for Fe2 and FeCo, but opposite for Co2 and Ni2. We can understand this by examining the electronic density of states of the dimer and the lattice. We also show that coadsorption significantly increases the adsorption energies of both dimer and hydrogen leading to a more strongly-adsorbed dimer, while the bond length and magnetic moment of the upper dimer atom, the latter important for potential magnetic storage applications, are negligibly changed. Our work shows that the coadsorbed hydrogen and metal dimer interact over a long-range, this interaction being mediated by the hydrogen-induced spin-polarization of the graphene lattice. We obtain general insight into how the elemental identity of these magnetic dimers determines the spin-polarized states on the hydrogenated graphene lattice. These results could be important for potential applications of magnetic properties of decorated graphene lattices.
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68.43.Mn Adsorption kinetics
72.25.-b Spin polarized transport
73.20.Hb Impurity and defect levels; energy states of adsorbed species
75.30.Cr Saturation moments and magnetic susceptibilities
75.60.Ch Domain walls and domain structure
75.76.+j Spin transport effects
back to top Polymers and Soft Matter

Perturbation theory for non-spherical fluids based on discretization of the interactions

Francisco Gámez and Ana Laura Benavides

J. Chem. Phys. 138, 124901 (2013); http://dx.doi.org/10.1063/1.4794783 (7 pages)

Online Publication Date: 22 March 2013

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An extension of the discrete perturbation theory [A. L. Benavides and A. Gil-Villegas, Mol. Phys. 97(12), 1225 (1999)10.1080/00268979909482924] accounting for non-spherical interactions is presented. An analytical expression for the Helmholtz free energy for an equivalent discrete potential is given as a function of density, temperature, and intermolecular parameters with implicit shape dependence. The presented procedure is suitable for the description of the thermodynamics of general intermolecular potential models of arbitrary shape. The overlap and dispersion forces are represented by a discrete potential formed by a sequence of square-well and square-shoulders potentials of shape-dependent widths. By varying the intermolecular parameters through their geometrical dependence, some illustrative cases of square-well spherocylinders and Kihara fluids are considered, and their vapor-liquid phase diagrams are tested against available simulation data. It is found that this theoretical approach is able to reproduce qualitatively and quantitatively well the Monte Carlo data for the selected potentials, except near the critical region.
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65.20.De General theory of thermodynamic properties of liquids, including computer simulation
61.20.Ja Computer simulation of liquid structure

Comparing different coarse-grained potentials for star polymers

Roberto Menichetti and Andrea Pelissetto

J. Chem. Phys. 138, 124902 (2013); http://dx.doi.org/10.1063/1.4796143 (9 pages)

Online Publication Date: 25 March 2013

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We compare different coarse-grained single-blob models for star polymers. We find that phenomenological models inspired by the Daoud-Cotton theory reproduce quite poorly the thermodynamics of these systems, even if the potential is assumed to be density dependent, as done in the analysis of experimental results. Using the numerically determined coarse-grained potential, we also determine the minimum value fc of the functionality of the star polymer for which a fluid-solid transition occurs. By applying the Hansen-Verlet criterion we find 35 < fc ≲ 40. This result is confirmed by an analysis that uses the modified (reference) hypernetted chain method and is qualitatively consistent with previous work.
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61.25.he Polymer solutions
64.70.D- Solid-liquid transitions
65.20.De General theory of thermodynamic properties of liquids, including computer simulation

Method of evaluating curvature-dependent elastic parameters for small unilamellar vesicles using molecular dynamics trajectory

Takenobu Nakamura and Wataru Shinoda

J. Chem. Phys. 138, 124903 (2013); http://dx.doi.org/10.1063/1.4795579 (7 pages)

Online Publication Date: 27 March 2013

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A numerical method is proposed for evaluating the curvature dependency of elastic parameters of a spherical vesicle based on a calculation of the pressure profile across the membrane. The proposed method is particularly useful for small unilamellar vesicles (SUVs), in which the internal structure of the membrane is asymmetric owing to the high curvature. In this case, the elastic energy is insufficiently described as a perturbation from a planar membrane. The calculated saddle-splay curvature modulus of SUVs, which is about 16 nm in diameter, is found to be much higher than that of a planar membrane. A comparison of the free energy change in the initial stage of vesicle-to-bicelle transformation with the Fromherz theory demonstrates that the elastic parameters estimated for SUVs provide better estimation of the free energy than those estimated for a planar membrane.
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87.16.dm Mechanical properties and rheology
87.16.-b Subcellular structure and processes
87.10.Tf Molecular dynamics simulation
87.16.D- Membranes, bilayers, and vesicles

Capacitance and optical studies of elastic and dielectric properties in an organosiloxane tetrapode exhibiting a NB phase

S. Polineni, J. L. Figueirinhas, C. Cruz, D. A. Wilson, and G. H. Mehl

J. Chem. Phys. 138, 124904 (2013); http://dx.doi.org/10.1063/1.4795582 (11 pages)

Online Publication Date: 28 March 2013

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Biaxial (NB) and uniaxial nematic (NU) phase behavior was detected and confirmed for an organosiloxane tetrapode material using capacitance and birefringence measurements. Elastic constants, permittivities at two distinct low frequencies, and birefringencies were determined as a function of temperature over both the NU and the NB phase ranges. The NU-NB transition is clearly observed in the birefringencies and conoscopy data. A temperature dependent cross-over frequency is also detected in this material for the permittivities, allowing the electrical switching of both planar and homeotropic aligned samples.
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77.22.Ch Permittivity (dielectric function)
77.84.Nh Liquids, emulsions, and suspensions; liquid crystals
78.20.Fm Birefringence
64.70.mj Experimental studies of liquid crystal transitions
61.30.Eb Experimental determinations of smectic, nematic, cholesteric, and other structures
62.10.+s Mechanical properties of liquids
back to top Biological Molecules and Networks

Near-IR laser generation of a high-energy conformer of L-alanine and the mechanism of its decay in a low-temperature nitrogen matrix

Cláudio M. Nunes, Leszek Lapinski, Rui Fausto, and Igor Reva

J. Chem. Phys. 138, 125101 (2013); http://dx.doi.org/10.1063/1.4795823 (12 pages)

Online Publication Date: 28 March 2013

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Monomers of L-alanine (ALA) were isolated in cryogenic nitrogen matrices at 14 K. Two conformers were identified for the compound trapped from the gas-phase into the solid nitrogen environment. The potential energy surface (PES) of ALA was theoretically calculated at the MP2 and QCISD levels. Twelve minima were located on this PES. Seven low-energy conformers fall within the 0–10 kJ mol−1 range and should be appreciably populated in the equilibrium gas phase prior to deposition. Observation of only two forms in the matrices is explained in terms of calculated barriers to conformational rearrangements. All conformers with the O=C−O−H moiety in the cis orientation are separated by low barriers and collapse to the most stable form I during deposition of the matrix onto the low-temperature substrate. The second observed form II has the O=C−O−H group in the trans orientation. The remaining trans forms have very high relative energies (between 24 and 30 kJ mol−1) and are not populated. The high-energy trans form VI, that differs from I only by rotation of the OH group, was found to be separated from other conformers by barriers that are high enough to open a perspective for its stabilization in a matrix. The form VI was photoproduced in situ by narrow-band near-infrared irradiation of the samples at 6935–6910 cm−1, where the first overtone of the OH stretching vibration in form I appears. The photogenerated form VI decays in N2 matrices back to conformer I with a characteristic decay time of ∼15 min. The mechanism of the VI → I relaxation is rationalized in terms of the proton tunneling.
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87.15.-v Biomolecules: structure and physical properties
31.15.bw Coupled-cluster theory
31.15.xp Perturbation theory
31.50.-x Potential energy surfaces
36.20.Hb Configuration (bonds, dimensions)
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Preface: Special Topic on the Glass Transition

Marsha I. Lester, Editor

J. Chem. Phys. 138, 12A101 (2013); http://dx.doi.org/10.1063/1.4796105 (1 page)

Online Publication Date: 26 March 2013

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This Special Topic on the Glass Transition contains a perspective article and a collection of original research articles that showcase recent experimental and theoretical advances in the field. This special issue provides a timely discussion of modern developments in our understanding of the behavior of supercooled liquids and amorphous materials, which have implications in diverse fields ranging from biology to materials science.
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64.70.P- Glass transitions of specific systems
61.43.-j Disordered solids
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