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  • Communication: Biological applications of coupled-cluster frozen-density embedding
    J. Chem. Phys. (IF 2.965) Pub Date : 2018-04-09
    Johannes Heuser, Sebastian Höfener

    We report the implementation of the Laplace-transform scaled opposite-spin (LT-SOS) resolution-of-the-identity second-order approximate coupled-cluster singles and doubles (RICC2) combined with frozen-density embedding for excitation energies and molecular properties. In the present work, we furthermore employ the Hartree-Fock density for the interaction energy leading to a simplified Lagrangian which is linear in the Lagrangian multipliers. This approximation has the key advantage of a decoupling of the coupled-cluster amplitude and multipliers, leading also to a significant reduction in computation time. Using the new simplified Lagrangian in combination with efficient wavefunction models such as RICC2 or LT-SOS-RICC2 and density-functional theory (DFT) for the environment molecules (CC2–in–DFT) enables the efficient study of biological applications such as the rhodopsin and visual cone pigments using ab initio methods as routine applications.

    更新日期:2018-04-14
  • Communication: Photoinduced carbon dioxide binding with surface-functionalized silicon quantum dots
    J. Chem. Phys. (IF 2.965) Pub Date : 2018-04-11
    Oscar A. Douglas-Gallardo, Cristián Gabriel Sánchez, Esteban Vöhringer-Martinez

    Nowadays, the search for efficient methods able to reduce the high atmospheric carbon dioxide concentration has turned into a very dynamic research area. Several environmental problems have been closely associated with the high atmospheric level of this greenhouse gas. Here, a novel system based on the use of surface-functionalized silicon quantum dots (sf-SiQDs) is theoretically proposed as a versatile device to bind carbon dioxide. Within this approach, carbon dioxide trapping is modulated by a photoinduced charge redistribution between the capping molecule and the silicon quantum dots (SiQDs). The chemical and electronic properties of the proposed SiQDs have been studied with a Density Functional Theory and Density Functional Tight-Binding (DFTB) approach along with a time-dependent model based on the DFTB framework. To the best of our knowledge, this is the first report that proposes and explores the potential application of a versatile and friendly device based on the use of sf-SiQDs for photochemically activated carbon dioxide fixation.

    更新日期:2018-04-14
  • Communication: A coil-stretch transition in planar elongational flow of an entangled polymeric melt
    J. Chem. Phys. (IF 2.965) Pub Date : 2018-04-13
    Mohammad H. Nafar Sefiddashti, Brian J. Edwards, Bamin Khomami

    Virtual experimentation of atomistic entangled polyethylene melts undergoing planar elongational flow revealed an amazingly detailed depiction of individual macromolecular dynamics and the resulting effect on bistable configurational states. A clear coil-stretch transition was evident, in much the same form as first envisioned by de Gennes for dilute solutions of high polymers, resulting in an associated hysteresis in the configurational flow profile over the range of strain rates predicted by theory. Simulations conducted at steady state revealed bimodal distribution functions, in which equilibrium configurational states were simultaneously populated by relatively coiled and stretched molecules which could transition from one conformational mode to the other over a relatively long time scale at critical values of strain rates. The implication of such behavior points to a double-well conformational free energy potential with an activation barrier between the two configurational minima.

    更新日期:2018-04-14
  • Communication: Adaptive boundaries in multiscale simulations
    J. Chem. Phys. (IF 2.965) Pub Date : 2018-04-13
    Jason A. Wagoner, Vijay S. Pande

    Combined-resolution simulations are an effective way to study molecular properties across a range of length and time scales. These simulations can benefit from adaptive boundaries that allow the high-resolution region to adapt (change size and/or shape) as the simulation progresses. The number of degrees of freedom required to accurately represent even a simple molecular process can vary by several orders of magnitude throughout the course of a simulation, and adaptive boundaries react to these changes to include an appropriate but not excessive amount of detail. Here, we derive the Hamiltonian and distribution function for such a molecular simulation. We also design an algorithm that can efficiently sample the boundary as a new coordinate of the system. We apply this framework to a mixed explicit/continuum simulation of a peptide in solvent. We use this example to discuss the conditions necessary for a successful implementation of adaptive boundaries that is both efficient and accurate in reproducing molecular properties.

    更新日期:2018-04-14
  • Mesoscopic electrohydrodynamic simulations of binary colloidal suspensions
    J. Chem. Phys. (IF 2.965) Pub Date : 2018-04-09
    Nicolas Rivas, Stefan Frijters, Ignacio Pagonabarraga, Jens Harting

    A model is presented for the solution of electrokinetic phenomena of colloidal suspensions in fluid mixtures. We solve the discrete Boltzmann equation with a Bhatnagar-Gross-Krook collision operator using the lattice Boltzmann method to simulate binary fluid flows. Solvent-solvent and solvent-solute interactions are implemented using a pseudopotential model. The Nernst-Planck equation, describing the kinetics of dissolved ion species, is solved using a finite difference discretization based on the link-flux method. The colloids are resolved on the lattice and coupled to the hydrodynamics and electrokinetics through appropriate boundary conditions. We present the first full integration of these three elements. The model is validated by comparing with known analytic solutions of ionic distributions at fluid interfaces, dielectric droplet deformations, and the electrophoretic mobility of colloidal suspensions. Its possibilities are explored by considering various physical systems, such as breakup of charged and neutral droplets and colloidal dynamics at either planar or spherical fluid interfaces.

    更新日期:2018-04-14
  • Clustering methods for the optimization of atomic cluster structure
    J. Chem. Phys. (IF 2.965) Pub Date : 2018-04-10
    Francesco Bagattini, Fabio Schoen, Luca Tigli

    In this paper, we propose a revised global optimization method and apply it to large scale cluster conformation problems. In the 1990s, the so-called clustering methods were considered among the most efficient general purpose global optimization techniques; however, their usage has quickly declined in recent years, mainly due to the inherent difficulties of clustering approaches in large dimensional spaces. Inspired from the machine learning literature, we redesigned clustering methods in order to deal with molecular structures in a reduced feature space. Our aim is to show that by suitably choosing a good set of geometrical features coupled with a very efficient descent method, an effective optimization tool is obtained which is capable of finding, with a very high success rate, all known putative optima for medium size clusters without any prior information, both for Lennard-Jones and Morse potentials. The main result is that, beyond being a reliable approach, the proposed method, based on the idea of starting a computationally expensive deep local search only when it seems worth doing so, is capable of saving a huge amount of searches with respect to an analogous algorithm which does not employ a clustering phase. In this paper, we are not claiming the superiority of the proposed method compared to specific, refined, state-of-the-art procedures, but rather indicating a quite straightforward way to save local searches by means of a clustering scheme working in a reduced variable space, which might prove useful when included in many modern methods.

    更新日期:2018-04-14
  • Low-lying excited states by constrained DFT
    J. Chem. Phys. (IF 2.965) Pub Date : 2018-04-10
    Pablo Ramos, Michele Pavanello

    Exploiting the machinery of Constrained Density Functional Theory (CDFT), we propose a variational method for calculating low-lying excited states of molecular systems. We dub this method eXcited CDFT (XCDFT). Excited states are obtained by self-consistently constraining a user-defined population of electrons, Nc, in the virtual space of a reference set of occupied orbitals. By imposing this population to be Nc = 1.0, we computed the first excited state of 15 molecules from a test set. Our results show that XCDFT achieves an accuracy in the predicted excitation energy only slightly worse than linear-response time-dependent DFT (TDDFT), but without incurring into problems of variational collapse typical of the more commonly adopted ΔSCF method. In addition, we selected a few challenging processes to test the limits of applicability of XCDFT. We find that in contrast to TDDFT, XCDFT is capable of reproducing energy surfaces featuring conical intersections (azobenzene and H3) with correct topology and correct overall energetics also away from the intersection. Venturing to condensed-phase systems, XCDFT reproduces the TDDFT solvatochromic shift of benzaldehyde when it is embedded by a cluster of water molecules. Thus, we find XCDFT to be a competitive method among single-reference methods for computations of excited states in terms of time to solution, rate of convergence, and accuracy of the result.

    更新日期:2018-04-14
  • Using reweighting and free energy surface interpolation to predict solid-solid phase diagrams
    J. Chem. Phys. (IF 2.965) Pub Date : 2018-04-10
    Natalie P. Schieber, Eric C. Dybeck, Michael R. Shirts

    Many physical properties of small organic molecules are dependent on the current crystal packing, or polymorph, of the material, including bioavailability of pharmaceuticals, optical properties of dyes, and charge transport properties of semiconductors. Predicting the most stable crystalline form at a given temperature and pressure requires determining the crystalline form with the lowest relative Gibbs free energy. Effective computational prediction of the most stable polymorph could save significant time and effort in the design of novel molecular crystalline solids or predict their behavior under new conditions. In this study, we introduce a new approach using multistate reweighting to address the problem of determining solid-solid phase diagrams and apply this approach to the phase diagram of solid benzene. For this approach, we perform sampling at a selection of temperature and pressure states in the region of interest. We use multistate reweighting methods to determine the reduced free energy differences between T and P states within a given polymorph and validate this phase diagram using several measures. The relative stability of the polymorphs at the sampled states can be successively interpolated from these points to create the phase diagram by combining these reduced free energy differences with a reference Gibbs free energy difference between polymorphs. The method also allows for straightforward estimation of uncertainties in the phase boundary. We also find that when properly implemented, multistate reweighting for phase diagram determination scales better with the size of the system than previously estimated.

    更新日期:2018-04-14
  • Improving accuracy of electrochemical capacitance and solvation energetics in first-principles calculations
    J. Chem. Phys. (IF 2.965) Pub Date : 2018-04-11
    Ravishankar Sundararaman, Kendra Letchworth-Weaver, Kathleen A. Schwarz

    Reliable first-principles calculations of electrochemical processes require accurate prediction of the interfacial capacitance, a challenge for current computationally efficient continuum solvation methodologies. We develop a model for the double layer of a metallic electrode that reproduces the features of the experimental capacitance of Ag(100) in a non-adsorbing, aqueous electrolyte, including a broad hump in the capacitance near the potential of zero charge and a dip in the capacitance under conditions of low ionic strength. Using this model, we identify the necessary characteristics of a solvation model suitable for first-principles electrochemistry of metal surfaces in non-adsorbing, aqueous electrolytes: dielectric and ionic nonlinearity, and a dielectric-only region at the interface. The dielectric nonlinearity, caused by the saturation of dipole rotational response in water, creates the capacitance hump, while ionic nonlinearity, caused by the compactness of the diffuse layer, generates the capacitance dip seen at low ionic strength. We show that none of the previously developed solvation models simultaneously meet all these criteria. We design the nonlinear electrochemical soft-sphere solvation model which both captures the capacitance features observed experimentally and serves as a general-purpose continuum solvation model.

    更新日期:2018-04-14
  • Entangled trajectories Hamiltonian dynamics for treating quantum nuclear effects
    J. Chem. Phys. (IF 2.965) Pub Date : 2018-04-11
    Brendan Smith, Alexey V. Akimov

    A simple and robust methodology, dubbed Entangled Trajectories Hamiltonian Dynamics (ETHD), is developed to capture quantum nuclear effects such as tunneling and zero-point energy through the coupling of multiple classical trajectories. The approach reformulates the classically mapped second-order Quantized Hamiltonian Dynamics (QHD-2) in terms of coupled classical trajectories. The method partially enforces the uncertainty principle and facilitates tunneling. The applicability of the method is demonstrated by studying the dynamics in symmetric double well and cubic metastable state potentials. The methodology is validated using exact quantum simulations and is compared to QHD-2. We illustrate its relationship to the rigorous Bohmian quantum potential approach, from which ETHD can be derived. Our simulations show a remarkable agreement of the ETHD calculation with the quantum results, suggesting that ETHD may be a simple and inexpensive way of including quantum nuclear effects in molecular dynamics simulations.

    更新日期:2018-04-14
  • Five- and six-electron harmonium atoms: Highly accurate electronic properties and their application to benchmarking of approximate 1-matrix functionals
    J. Chem. Phys. (IF 2.965) Pub Date : 2018-04-11
    Jerzy Cioslowski, Krzysztof Strasburger

    Electronic properties of several states of the five- and six-electron harmonium atoms are obtained from large-scale calculations employing explicitly correlated basis functions. The high accuracy of the computed energies (including their components), natural spinorbitals, and their occupation numbers makes them suitable for testing, calibration, and benchmarking of approximate formalisms of quantum chemistry and solid state physics. In the case of the five-electron species, the availability of the new data for a wide range of the confinement strengths ω allows for confirmation and generalization of the previously reached conclusions concerning the performance of the presently known approximations for the electron-electron repulsion energy in terms of the 1-matrix that are at heart of the density matrix functional theory (DMFT). On the other hand, the properties of the three low-lying states of the six-electron harmonium atom, computed at ω = 500 and ω = 1000, uncover deficiencies of the 1-matrix functionals not revealed by previous studies. In general, the previously published assessment of the present implementations of DMFT being of poor accuracy is found to hold. Extending the present work to harmonically confined systems with even more electrons is most likely counterproductive as the steep increase in computational cost required to maintain sufficient accuracy of the calculated properties is not expected to be matched by the benefits of additional information gathered from the resulting benchmarks.

    更新日期:2018-04-14
  • An atomic mean-field spin-orbit approach within exact two-component theory for a non-perturbative treatment of spin-orbit coupling
    J. Chem. Phys. (IF 2.965) Pub Date : 2018-04-12
    Junzi Liu, Lan Cheng

    An atomic mean-field (AMF) spin-orbit (SO) approach within exact two-component theory (X2C) is reported, thereby exploiting the exact decoupling scheme of X2C, the one-electron approximation for the scalar-relativistic contributions, the mean-field approximation for the treatment of the two-electron SO contribution, and the local nature of the SO interactions. The Hamiltonian of the proposed SOX2CAMF scheme comprises the one-electron X2C Hamiltonian, the instantaneous two-electron Coulomb interaction, and an AMF SO term derived from spherically averaged Dirac-Coulomb Hartree-Fock calculations of atoms; no molecular relativistic two-electron integrals are required. Benchmark calculations for bond lengths, harmonic frequencies, dipole moments, and electric-field gradients for a set of diatomic molecules containing elements across the periodic table show that the SOX2CAMF scheme offers a balanced treatment for SO and scalar-relativistic effects and appears to be a promising candidate for applications to heavy-element containing systems. SOX2CAMF coupled-cluster calculations of molecular properties for bismuth compounds (BiN, BiP, BiF, BiCl, and BiI) are also presented and compared with experimental results to further demonstrate the accuracy and applicability of the SOX2CAMF scheme.

    更新日期:2018-04-14
  • Force-detected nanoscale absorption spectroscopy in water at room temperature using an optical trap
    J. Chem. Phys. (IF 2.965) Pub Date : 2018-04-09
    Alexander Parobek, Jacob W. Black, Maria Kamenetska, Ziad Ganim

    Measuring absorption spectra of single molecules presents a fundamental challenge for standard transmission-based instruments because of the inherently low signal relative to the large background of the excitation source. Here we demonstrate a new approach for performing absorption spectroscopy in solution using a force measurement to read out optical excitation at the nanoscale. The photoinduced force between model chromophores and an optically trapped gold nanoshell has been measured in water at room temperature. This photoinduced force is characterized as a function of wavelength to yield the force spectrum, which is shown to be correlated to the absorption spectrum for four model systems. The instrument constructed for these measurements combines an optical tweezer with frequency domain absorption spectroscopy over the 400-800 nm range. These measurements provide proof-of-principle experiments for force-detected nanoscale spectroscopies that operate under ambient chemical conditions.

    更新日期:2018-04-14
  • Microsolvation of phthalocyanine molecules in superfluid helium nanodroplets as revealed by the optical line shape at electronic origin
    J. Chem. Phys. (IF 2.965) Pub Date : 2018-04-09
    S. Fuchs, J. Fischer, A. Slenczka, M. Karra, B. Friedrich

    We investigate the solvent shift of phthalocyanine (Pc) doped into superfluid helium droplets and probed by optical spectroscopy at the electronic origin. Our present work complements extant studies and provides results that in part contradict previous conclusions. In particular, the solvent shift does not increase monotonously with droplet radius all the way up to the bulk limit, but exhibits just the reverse dependence instead. Moreover, a substructure is resolved, whose characteristics depend on the droplet size. This behavior can hardly be reconciled with that of a freely rotating Pc-helium complex.

    更新日期:2018-04-14
  • Helium-induced electronic transitions in photo-excited Ba+–Hen exciplexes
    J. Chem. Phys. (IF 2.965) Pub Date : 2018-04-09
    Patricia Vindel Zandbergen, Manuel Barranco, Fausto Cargnoni, Marcel Drabbels, Martí Pi, Nadine Halberstadt

    The possibility for helium-induced electronic transitions in a photo-excited atom is investigated using Ba+ excited to the 6p 2P state as a prototypical example. A diabatization scheme has been designed to obtain the necessary potential energy surfaces and couplings for complexes of Ba+ with an arbitrary number of helium atoms. It involves computing new He–Ba+ electronic wave functions and expanding them in determinants of the non-interacting complex. The 6p 2P ← 6s 2S photodissociation spectrum of He⋯Ba+ calculated with this model shows very weak coupling for a single He atom. However, several electronic relaxation mechanisms are identified, which could potentially explain the expulsion of barium ions from helium nanodroplets observed experimentally upon Ba+ photoexcitation. For instance, an avoided crossing in the ring-shaped He7Ba+ structure is shown to provide an efficient pathway for fine structure relaxation. Symmetry breaking by either helium density fluctuations or vibrations can also induce efficient relaxation in these systems, e.g., bending vibrations in the linear He2Ba+ excimer. The identified relaxation mechanisms can provide insight into helium-induced non-adiabatic transitions observed in other systems.

    更新日期:2018-04-14
  • High-resolution infrared spectroscopy of O2H+ in a cryogenic ion trap
    J. Chem. Phys. (IF 2.965) Pub Date : 2018-04-09
    Hiroshi Kohguchi, Pavol Jusko, Koichi M. T. Yamada, Stephan Schlemmer, Oskar Asvany

    The protonated oxygen molecule, O2H+, and its helium complex, He-O2H+, have been investigated by vibrational action spectroscopy in a cryogenic 22-pole ion trap. For the He-O2H+ complex, the frequencies of three vibrational bands have been determined by predissociation spectroscopy. The elusive O2H+ has been characterized for the first time by high-resolution rovibrational spectroscopy via its ν1 OH-stretching band. Thirty-eight rovibrational fine structure transitions with partly resolved hyperfine satellites were measured (56 resolved lines in total). Spectroscopic parameters were determined by fitting the observed lines with an effective Hamiltonian for an asymmetric rotor in a triplet electronic ground state, X̃3A′′, yielding a band origin at 3016.73 cm−1. Based on these spectroscopic parameters, the rotational spectrum is predicted, but not yet detected.

    更新日期:2018-04-14
  • The effect of the condensed-phase environment on the vibrational frequency shift of a hydrogen molecule inside clathrate hydrates
    J. Chem. Phys. (IF 2.965) Pub Date : 2018-04-09
    Anna Powers, Yohann Scribano, David Lauvergnat, Elsy Mebe, David M. Benoit, Zlatko Bačić

    We report a theoretical study of the frequency shift (redshift) of the stretching fundamental transition of an H2 molecule confined inside the small dodecahedral cage of the structure II clathrate hydrate and its dependence on the condensed-phase environment. In order to determine how much the hydrate water molecules beyond the confining small cage contribute to the vibrational frequency shift, quantum five-dimensional (5D) calculations of the coupled translation-rotation eigenstates are performed for H2 in the v=0 and v=1 vibrational states inside spherical clathrate hydrate domains of increasing radius and a growing number of water molecules, ranging from 20 for the isolated small cage to over 1900. In these calculations, both H2 and the water domains are treated as rigid. The 5D intermolecular potential energy surface (PES) of H2 inside a hydrate domain is assumed to be pairwise additive. The H2–H2O pair interaction, represented by the 5D (rigid monomer) PES that depends on the vibrational state of H2, v=0 or v=1, is derived from the high-quality ab initio full-dimensional (9D) PES of the H2–H2O complex [P. Valiron et al., J. Chem. Phys. 129, 134306 (2008)]. The H2 vibrational frequency shift calculated for the largest clathrate domain considered, which mimics the condensed-phase environment, is about 10% larger in magnitude than that obtained by taking into account only the small cage. The calculated splittings of the translational fundamental of H2 change very little with the domain size, unlike the H2 j = 1 rotational splittings that decrease significantly as the domain size increases. The changes in both the vibrational frequency shift and the j = 1 rotational splitting due to the condensed-phase effects arise predominantly from the H2O molecules in the first three complete hydration shells around H2.

    更新日期:2018-04-14
  • Dissociation cross section for high energy O2–O2 collisions
    J. Chem. Phys. (IF 2.965) Pub Date : 2018-04-09
    T. K. Mankodi, U. V. Bhandarkar, B. P. Puranik

    Collision-induced dissociation cross section database for high energy O2–O2 collisions (up to 30 eV) is generated and published using the quasiclassical trajectory method on the singlet, triplet, and quintet spin ground state O4 potential energy surfaces. At equilibrium conditions, these cross sections predict reaction rate coefficients that match those obtained experimentally. The main advantage of the cross section database based on ab initio computations is in the study of complex flows with high degree of non-equilibrium. Direct simulation Monte Carlo simulations using the reactive cross section databases are carried out for high enthalpy hypersonic oxygen flow over a cylinder at rarefied ambient conditions. A comparative study with the phenomenological total collision energy chemical model is also undertaken to point out the difference and advantage of the reported ab initio reaction model.

    更新日期:2018-04-14
  • The control of electron quantum trajectories on the high-order harmonic generation of CO and N2 molecules in the presence of a low frequency field
    J. Chem. Phys. (IF 2.965) Pub Date : 2018-04-09
    A. M. Koushki, R. Sadighi-Bonabi, M. Mohsen-Nia, E. Irani

    In the present work, an efficient method is theoretically investigated for extending high-order harmonics and ultrashort attosecond pulse generation in N2 and CO molecules by using the time-dependent density functional theory approach. Our results show that by utilizing chirped laser field in the presence of a low frequency field, not only is the harmonic cutoff extended remarkably but also the single short quantum trajectory is selected to contribute to the harmonic spectra. When a low frequency field is added to the two-color chirped laser field, the long quantum trajectories are suppressed and only the short quantum trajectories contribute to the higher harmonic emission mechanism. As a result, the spectral modulation is significantly decreased and an intense ultrashort pulse can be generated from the supercontinuum region of high harmonics. With such a scheme, the isolated ultrashort attosecond pulses can be generated in length, velocity, and acceleration gauges. Furthermore, these results are explained by using the classical and quantum time-frequency analyses.

    更新日期:2018-04-14
  • Aqueous solvation of Mg(ii) and Ca(ii): A Born-Oppenheimer molecular dynamics study of microhydrated gas phase clusters
    J. Chem. Phys. (IF 2.965) Pub Date : 2018-04-09
    C. I. León-Pimentel, J. I. Amaro-Estrada, J. Hernández-Cobos, H. Saint-Martin, A. Ramírez-Solís

    The hydration features of [Mg(H2O)n]2+ and [Ca(H2O)n]2+ clusters with n = 3-6, 8, 18, and 27 were studied by means of Born-Oppenheimer molecular dynamics simulations at the B3LYP/6-31+G** level of theory. For both ions, it is energetically more favorable to have all water molecules in the first hydration shell when n ≤ 6, but stable lower coordination average structures with one water molecule not directly interacting with the ion were found for Mg2+ at room temperature, showing signatures of proton transfer events for the smaller cation but not for the larger one. A more rigid octahedral-type structure for Mg2+ than for Ca2+ was observed in all simulations, with no exchange of water molecules to the second hydration shell. Significant thermal effects on the average structure of clusters were found: while static optimizations lead to compact, spherically symmetric hydration geometries, the effects introduced by finite-temperature dynamics yield more prolate configurations. The calculated vibrational spectra are in agreement with infrared spectroscopy results. Previous studies proposed an increase in the coordination number (CN) from six to eight water molecules for [Ca(H2O)n]2+ clusters when n ≥ 12; however, in agreement with recent measurements of binding energies, no transition to a larger CN was found when n > 8. Moreover, the excellent agreement found between the calculated extended X-ray absorption fine structure spectroscopy spectra for the larger cluster and the experimental data of the aqueous solution supports a CN of six for Ca2+.

    更新日期:2018-04-14
  • Positron scattering from pyridine
    J. Chem. Phys. (IF 2.965) Pub Date : 2018-04-11
    D. Stevens, T. J. Babij, J. R. Machacek, S. J. Buckman, M. J. Brunger, R. D. White, G. García, F. Blanco, L. Ellis-Gibbings, J. P. Sullivan

    We present a range of cross section measurements for the low-energy scattering of positrons from pyridine, for incident positron energies of less than 20 eV, as well as the independent atom model with the screening corrected additivity rule including interference effects calculation, of positron scattering from pyridine, with dipole rotational excitations accounted for using the Born approximation. Comparisons are made between the experimental measurements and theoretical calculations. For the positronium formation cross section, we also compare with results from a recent empirical model. In general, quite good agreement is seen between the calculations and measurements although some discrepancies remain which may require further investigation. It is hoped that the present study will stimulate development of ab initio level theoretical methods to be applied to this important scattering system.

    更新日期:2018-04-14
  • “Trampoline” ejection of organic molecules from graphene and graphite via keV cluster ions impacts
    J. Chem. Phys. (IF 2.965) Pub Date : 2018-04-12
    Stanislav V. Verkhoturov, Mikołaj Gołuński, Dmitriy S. Verkhoturov, Sheng Geng, Zbigniew Postawa, Emile A. Schweikert

    We present the data on ejection of molecules and emission of molecular ions caused by single impacts of 50 keV C602+ on a molecular layer of deuterated phenylalanine (D8Phe) deposited on free standing, 2-layer graphene. The projectile impacts on the graphene side stimulate the abundant ejection of intact molecules and the emission of molecular ions in the transmission direction. To gain insight into the mechanism of ejection, Molecular Dynamic simulations were performed. It was found that the projectile penetrates the thin layer of graphene, partially depositing the projectile’s kinetic energy, and molecules are ejected from the hot area around the hole that is made by the projectile. The yield, Y, of negative ions of deprotonated phenylalanine, (D8Phe-H)−, emitted in the transmission direction is 0.1 ions per projectile impact. To characterize the ejection and ionization of molecules, we have performed the experiments on emission of (D8Phe-H)− from the surface of bulk D8Phe (Y = 0.13) and from the single molecular layer of D8Phe deposited on bulk pyrolytic graphite (Y = 0.15). We show that, despite the similar yields of molecular ions, the scenario of the energy deposition and ejection of molecules is different for the case of graphene due to the confined volume of projectile-analyte interaction. The projectile impact on the graphene-D8Phe sample stimulates the collective radial movement of analyte atoms, which compresses the D8Phe layer radially from the hole. At the same time, this compression bends and stretches the graphene membrane around the hole thus accumulating potential energy. The accumulated potential energy is transformed into the kinetic energy of correlated movement upward for membrane atoms, thus the membrane acts as a trampoline for the molecules. The ejected molecules are effectively ionized; the ionization probability is ∼30× higher compared to that obtained for the bulk D8Phe target. The proposed mechanism of ionization involves tunneling of electrons from the vibrationally excited area around the hole to the molecules. Another proposed mechanism is a direct proton transfer exchange, which is suitable for a bulk target: ions of molecular fragments (i.e., CN−) generated in the impact area interact with intact molecules from the rim of this area. There is a direct proton exchange process for the system D8Phe molecule + CN−.

    更新日期:2018-04-14
  • High pressure synthesis and stability of cobalt hydrides
    J. Chem. Phys. (IF 2.965) Pub Date : 2018-04-13
    Mengnan Wang, Jack Binns, Mary-Ellen Donnelly, Miriam Peña-Alvarez, Philip Dalladay-Simpson, Ross T. Howie

    In situ high-pressure high-temperature X-ray powder diffraction studies of the cobalt-hydrogen system reveal the direct synthesis of both the binary cobalt hydride (CoH) and a novel cobalt dihydride (CoH2). We observe the formation of fcc CoH at pressures of 4 GPa, which persists to pressures of 45 GPa. At this pressure, we see the emergence with time of a further expanded fcc lattice, which we identify as CoH2, where the hydrogen atoms occupy the tetrahedral vacancies. We have explored alternative synthesis routes of CoH2 and can lower the synthesis pressure to 35 GPa by the application of high temperature. CoH2 is stable to at least 55 GPa and decomposes into CoH below 10 GPa, releasing molecular hydrogen before further decomposing completely into its constituent elements below 3 GPa. As a first-row transition metal, cobalt has a relatively lower mass than other hydride-forming transition metals, and as a result, CoH2 has a high hydrogen content of 3.3 wt. % and a volumetric hydrogen density of 214 g/l.

    更新日期:2018-04-14
  • Unraveling the electronic relaxation dynamics in photoexcited 2,4-difluoroaniline via femtosecond time-resolved photoelectron imaging
    J. Chem. Phys. (IF 2.965) Pub Date : 2018-04-13
    Fengzi Ling, Shuai Li, Jie Wei, Kai Liu, Yanmei Wang, Bing Zhang

    Time-resolved photoelectron imaging is employed to investigate the relaxation dynamics of the lowest two excited electronic states S1(ππ*) and S2(π3s/πσ*) in 2,4-difluoroaniline (24DFA). As the S1(ππ*) state is populated directly following 289 nm excitation, the population undergoes ultrafast intramolecular vibrational redistribution on a 540 fs time scale, followed by efficient intersystem crossing from S1(ππ*) to the triplet state within 379 ps, and the subsequent slower deactivation process of the triplet state. For excitation to the S2(π3s/πσ*) state at 238 nm, the population probably bifurcates into two decay channels. The dominant channel with 84 fs involves ultrafast internal conversion to the S1(ππ*) state, from which it relaxes to the electronic ground state on a 116 ps time scale. The other appears to involve motion along the S2(π3s/πσ*) potential energy surface. Our data also determine experimentally the electronic energies of S2(π3s/πσ*), S3(ππ*), and several Rydberg states in 24DFA.

    更新日期:2018-04-14
  • Vapor phase nucleation of the short-chain n-alkanes (n-pentane, n-hexane and n-heptane): Experiments and Monte Carlo simulations
    J. Chem. Phys. (IF 2.965) Pub Date : 2018-04-13
    Kehinde E. Ogunronbi, Aliasghar Sepehri, Bin Chen, Barbara E. Wyslouzil

    We measured the nucleation rates of n-pentane through n-heptane in a supersonic nozzle at temperatures ranging from ca. 109 K to 168 K. For n-pentane and n-hexane, these are the first nucleation rate measurements that have been made, and the trends in the current data agree well with those in the earlier work of Ghosh et al. [J. Chem. Phys. 132, 024307 (2010)] for longer chain alkanes. Complementary Monte Carlo simulations, using the transferable potentials for phase equilibria-united atom potentials, suggest that despite the high degree of supercooling, the critical clusters remain liquid like under experimental conditions for n-pentane through n-heptane, but adopt more ordered structures for n-octane and n-nonane. For all three alkanes, the experimental and simulated nucleation rates are offset by ∼3 orders of magnitude when plotted as a function of ln S/(Tc/T − 1)1.5. Explicitly accounting for the surface tension difference between the real and model substances, or alternatively using the Hale [Phys. Rev. A 33, 4156 (1986); Metall. Mater. Trans. A 23, 1863 (1992)] scaling parameter, Ω, consistent with the model potential, increases the offset to ∼6 orders of magnitude.

    更新日期:2018-04-14
  • Investigations of the valence-shell excitations of molecular ethane by high-energy electron scattering
    J. Chem. Phys. (IF 2.965) Pub Date : 2018-04-13
    Wei-Qing Xu, Long-Quan Xu, De-Guang Qi, Tao Chen, Ya-Wei Liu, Lin-Fan Zhu

    The differential cross sections and generalized oscillator strengths for the low-lying excitations of the valence-shell 1eg orbital electron in ethane have been measured for the first time at a high incident electron energy of 1500 eV and a scattering angular range of 1.5°–10°. A weak feature, termed X here, with a band center of about 7.5 eV has been observed, which was also announced by the previous experimental and theoretical studies. The dynamic behaviors of the generalized oscillator strengths for the 3s (8.7 eV), 3s+3p (9.31 eV, 9.41 eV), and X (∼7.5 eV) transitions on the momentum transfer squared have been obtained. The integral cross sections of these transitions from their thresholds to 5000 eV have been obtained with the aid of the BE-scaling (B is the binding energy and E is the excitation energy) method. The optical oscillator strengths of the above transitions determined by extrapolating their generalized oscillator strengths to the limit of the squared momentum transfer K2 → 0 are in good agreement with the ones from the photoabsorption spectrum [J. W. Au et al., Chem. Phys. 173, 209 (1993)], which indicates that the present differential cross sections, generalized oscillator strengths, and integral cross sections can serve as benchmark data.

    更新日期:2018-04-14
  • Performance of exchange-correlation functionals in density functional theory calculations for liquid metal: A benchmark test for sodium
    J. Chem. Phys. (IF 2.965) Pub Date : 2018-04-09
    Jeong-Hwan Han, Takuji Oda

    The performance of exchange-correlation functionals in density-functional theory (DFT) calculations for liquid metal has not been sufficiently examined. In the present study, benchmark tests of Perdew-Burke-Ernzerhof (PBE), Armiento-Mattsson 2005 (AM05), PBE re-parameterized for solids, and local density approximation (LDA) functionals are conducted for liquid sodium. The pair correlation function, equilibrium atomic volume, bulk modulus, and relative enthalpy are evaluated at 600 K and 1000 K. Compared with the available experimental data, the errors range from −11.2% to 0.0% for the atomic volume, from −5.2% to 22.0% for the bulk modulus, and from −3.5% to 2.5% for the relative enthalpy depending on the DFT functional. The generalized gradient approximation functionals are superior to the LDA functional, and the PBE and AM05 functionals exhibit the best performance. In addition, we assess whether the error tendency in liquid simulations is comparable to that in solid simulations, which would suggest that the atomic volume and relative enthalpy performances are comparable between solid and liquid states but that the bulk modulus performance is not. These benchmark test results indicate that the results of liquid simulations are significantly dependent on the exchange-correlation functional and that the DFT functional performance in solid simulations can be used to roughly estimate the performance in liquid simulations.

    更新日期:2018-04-14
  • Instability and thermal conductivity of pressure-densified and elastically altered orientational glass of Buckminsterfullerene
    J. Chem. Phys. (IF 2.965) Pub Date : 2018-04-09
    G. P. Johari, Ove Andersson, Bertil Sundqvist

    We report on the temperature, pressure, and time (T, p, and t)-dependent features of thermal conductivity, κ, of partially ordered, non-equilibrium state of C60-OG, the orientational glass of Buckminsterfullerene (at T below the orientational freezing temperature Tog) made more unstable (i) by partially depressurizing its high-p formed state to elastically expand it and (ii) by further pressurizing that state to elastically contract it. The sub-Tog effects observed on heating of C60-OG differ from those of glasses because phonon propagation depends on the ratio of two well-defined orientational states of C60 molecules and the density of the solid. A broad peak-like feature appears at T near Tog in the κ-T plots of C60-OG formed at 0.7 GPa, depressurized to 0.2 GPa and heated at 0.2 GPa, which we attribute to partial overlap of the sub-Tog and Tog features. A sub-Tog local minimum appears in the κ-T plots at T well below Tog of C60-OG formed at 0.1 GPa, pressurized to 0.5 GPa and heated at 0.5 GPa and it corresponds to the state of maximum disorder. Although Buckminsterfullerene is regarded as an orientationally disordered crystal, variation of its properties with T and p is qualitatively different from other such crystals. We discuss the findings in terms of the nature of its disorder, sensitivity of its rotational dynamics to temperature, and the absence of the Johari-Goldstein relaxation. All seem to affect the phenomenology of its glass-like transition.

    更新日期:2018-04-14
  • A molecular dynamics investigation of the surface tension of water nanodroplets and a new technique for local pressure determination through density correlation
    J. Chem. Phys. (IF 2.965) Pub Date : 2018-04-09
    Kai-Yang Leong, Feng Wang

    The surface tension of nanoscale droplets of water was studied with molecular dynamics simulations using the BLYPSP-4F water potential. The internal pressure of the droplet was measured using an empirical correlation between the pressure and density, established through a series of bulk simulations performed at pressures from 1 to 1000 bars. Such a procedure allows for reliable determination of internal pressure without the need to calculate the local virial. The surface tension, estimated with the Young-Laplace relation, shows good agreement with the Tolman equation with a Tolman length of −0.48 Å. The interface of a liquid water droplet is shown to be around 1.1–1.3 nm thick depending on radii. The fairly thick interface region puts a lower limit on the size of droplets that still have a bulk-like interior.

    更新日期:2018-04-14
  • A comparative computational study of coarse-grained and all-atom water models in shock Hugoniot states
    J. Chem. Phys. (IF 2.965) Pub Date : 2018-04-09
    Sa Hoon Min, Max L. Berkowitz

    We performed molecular dynamics simulations to study how well some of the water models used in simulations describe shocked states. Water in our simulations was described using three different models. One was an often-used all-atom TIP4P/2005 model, while the other two were coarse-grained models used with the MARTINI force field: non-polarizable and polarizable MARTINI water. The all-atom model provided results in good agreement with Hugoniot curves (for data on pressure versus specific volume or, equivalently, on shock wave velocity versus “piston” velocity) describing shocked states in the whole range of pressures (up to 11 GPa) under study. If simulations of shocked states of water using coarse-grained models were performed for short time periods, we observed that data obtained for shocked states at low pressure were fairly accurate compared to experimental Hugoniot curves. Polarizable MARTINI water still provided a good description of Hugoniot curves for pressures up to 11 GPa, while the results for the non-polarizable MARTINI water substantially deviated from the Hugoniot curves. We also calculated the temperature of the Hugoniot states and observed that for TIP4P/2005 water, they were consistent with those from theoretical calculations, while both coarse-grained models predicted much higher temperatures. These high temperatures for MARTINI water can be explained by the loss of degrees of freedom due to coarse-graining procedure.

    更新日期:2018-04-14
  • Persistent optical hole-burning spectroscopy of nano-confined dye molecules in liquid at room temperature: Spectral narrowing due to a glassy state and extraordinary relaxation in a nano-cage
    J. Chem. Phys. (IF 2.965) Pub Date : 2018-04-10
    Hiroshi Murakami

    Persistent optical hole-burning spectroscopy has been conducted for a dye molecule within a very small (∼1 nm) reverse micelle at room temperature. The spectra show a spectral narrowing due to site-selective excitation. This definitely demonstrates that the surroundings of the dye molecule are in a glassy state regardless of a solution at room temperature. On the other hand, the hole-burning spectra exhibit large shifts from excitation frequencies, and their positions are almost independent of excitation frequencies. The hole-burning spectra have been theoretically calculated by taking account of a vibronic absorption band of the dye molecule under the assumption that the surroundings of the dye molecule are in a glassy state. The calculated results agree with the experimental ones that were obtained for the dye molecule in a polymer glass for comparison, where it has been found that the ratio of hole-burning efficiencies of vibronic- to electronic-band excitations is quite high. On the other hand, the theoretical results do not explain the large spectral shift from the excitation frequency and small spectral narrowing observed in the hole-burning spectra measured for the dye-containing reverse micelle. It is thought that the spectral shift and broadening occur within the measurement time owing to the relaxation process of the surroundings that are hot with the thermal energy deposited by the dye molecule optically excited. Furthermore, the relaxation should be temporary because the cooling of the inside of the reverse micelle takes place with the dissipation of the excess thermal energy to the outer oil solvent, and so the surroundings of the dye molecule return to the glassy state and do not attain the thermal equilibrium. These results suggest that a very small reverse micelle provides a unique reaction field in which the diffusional motion can be controlled by light in a glassy state.

    更新日期:2018-04-14
  • Decrease in electrical resistivity on depletion of islands of mobility during aging of a bulk metal glass
    J. Chem. Phys. (IF 2.965) Pub Date : 2018-04-10
    Daisman P. B. Aji, G. P. Johari

    The effect of structural relaxation on electrical resistivity, ρglass, of strain-free Zr46.75Ti8.25Cu7.5Ni10Be27.5 bulk metallic glass was studied during isothermal aging at several temperatures, Tas. Since cooling of a liquid metal increases its resistivity ρliq, one expects ρglass to increase on aging toward ρliq at T = Ta. Instead, ρglass decreased non-exponentially with the aging time. The activation energy of aging kinetics is 189 kJ mol−1, which is higher than the activation energy of the Johari-Goldstein (JG) relaxation. After considering the sample’s contraction, phase separation, and crystallization as possible causes of the decrease in ρglass, we attribute the decrease to depletion of islands of atomic mobility, soft spots, or static heterogeneity. Vibrations of the atoms in these local (loosely packed) regions and in the region’s interfacial area contribute to electron scattering. As these deplete on aging, the contribution decreases and ρglass decreases, with a concomitant decrease in macroscopic volume, enthalpy, and entropy (V, H, and S). Local regions of faster mobility also decrease on cooling as V, H, and S of a liquid decrease, but structure fluctuations dominate electron scattering of a liquid metal and ρliq increases effectively according to the Ziman-Nagel theory for a homogenously disordered structure. Whether depletion of such local regions initiates the structural relaxation of a glass, or vice versa, may be resolved by finding a glass that physically ages but shows no JG relaxation.

    更新日期:2018-04-14
  • Relationship between x-ray emission and absorption spectroscopy and the local H-bond environment in water
    J. Chem. Phys. (IF 2.965) Pub Date : 2018-04-10
    Iurii Zhovtobriukh, Nicholas A. Besley, Thomas Fransson, Anders Nilsson, Lars G. M. Pettersson

    The connection between specific features in the water X-ray absorption spectrum and X-ray emission spectrum (XES) and the local H-bond coordination is studied based on structures obtained from path-integral molecular dynamics simulations using either the opt-PBE-vdW density functional or the MB-pol force field. Computing the XES spectrum using all molecules in a snapshot results in only one peak in the lone-pair (1b1) region, while the experiment shows two peaks separated by 0.8-0.9 eV. Different H-bond configurations were classified based on the local structure index (LSI) and a geometrical H-bond cone criterion. We find that tetrahedrally coordinated molecules characterized by high LSI values and two strong donated and two strong accepted H-bonds contribute to the low energy 1b1 emission peak and to the post-edge region in absorption. Molecules with the asymmetric H-bond environment with one strong accepted H-bond and one strong donated H-bond and low LSI values give rise to the high energy 1b1 peak in the emission spectrum and mainly contribute to the pre-edge and main-edge in the absorption spectrum. The 1b1 peak splitting can be increased to 0.62 eV by imposing constraints on the H-bond length, i.e., for very tetrahedral structures short H-bonds (less than 2.68 Å) and for very asymmetric structures elongated H-bonds (longer than 2.8 Å). Such structures are present, but underrepresented, in the simulations which give more of an average of the two extremes.

    更新日期:2018-04-14
  • Anomalous surface behavior of hydrated guanidinium ions due to ion pairing
    J. Chem. Phys. (IF 2.965) Pub Date : 2018-04-13
    Victor Ekholm, Mario Vazdar, Philip E. Mason, Erik Bialik, Marie-Madeleine Walz, Gunnar Öhrwall, Josephina Werner, Jan-Erik Rubensson, Pavel Jungwirth, Olle Björneholm

    Surface affinity of aqueous guanidinium chloride (GdmCl) is compared to that of aqueous tetrapropylammonium chloride (TPACl) upon addition of sodium chloride (NaCl) or disodium sulfate (Na2SO4). The experimental results have been acquired using the surface sensitive technique X-ray photoelectron spectroscopy on a liquid jet. Molecular dynamics simulations have been used to produce radial distribution functions and surface density plots. The surface affinities of both TPA+ and Gdm+ increase upon adding NaCl to the solution. With the addition of Na2SO4, the surface affinity of TPA+ increases, while that of Gdm+ decreases. From the results of MD simulations it is seen that Gdm+ and SO42− ions form pairs. This finding can be used to explain the decreased surface affinity of Gdm+ when co-dissolved with SO42− ions. Since SO42− ions avoid the surface due to the double charge and strong water interaction, the Gdm+-SO42− ion pair resides deeper in the solutions’ bulk than the Gdm+ ions. Since TPA+ does not form ion pairs with SO42−, the TPA+ ions are instead enriched at the surface.

    更新日期:2018-04-14
  • The dependency of adhesion and friction on electrostatic attraction
    J. Chem. Phys. (IF 2.965) Pub Date : 2018-04-09
    B. N. J. Persson

    I develop a general mean-field theory for the influence of electrostatic attraction between two solids on the contact mechanics. I assume elastic solids with random surface roughness. I consider two cases, namely, with and without an electrically insulating layer between the conducting solids. The former case is important for, e.g., the finger–touch screen interaction. I study how the electrostatic attraction influences the adhesion and friction. For the case of an insulating layer, I find that when the applied nominal contact pressure is relatively small, as the applied voltage increases, there is a sharp increase in the contact area, and hence in the friction, at a critical voltage.

    更新日期:2018-04-14
  • Kinetic effects on the morphology and stability of the pressure-induced extended-solid of carbon monoxide
    J. Chem. Phys. (IF 2.965) Pub Date : 2018-04-09
    Nhan C. Dang, Jennifer A. Ciezak-Jenkins

    In this work, the dependence of the morphology and stability of the extended solid of carbon monoxide (CO) is correlated to the rate of transformation from the molecular CO to extended solid of CO using optical imaging, photoluminescence, Raman spectroscopy, and X-ray diffraction. The analyses show the rate and pressure of the transformation to be strongly controlled by catalytic effects, both chemical and optical. In a larger volume per reaction area, the transformation was found to require either a longer time at an elevated pressure or a higher pressure compared to a sample synthesized in a smaller volume per reaction area, leading to the conclusion that the transformation rate is slower for a sample in a larger volume per reaction area. A faster rate of transformation was also noted when the reaction area of a CO sample was catalyzed with H2SO4. Through variation of the volume per reaction area, pressure or the addition of catalysts, it was possible to control the rate of the phase transition and therefore the morphology. In general, the extended solid of CO synthesized with a faster rate showed a more ordered structure and increased metastability relative to the material formed with a slower compression rate.

    更新日期:2018-04-14
  • The structure of PbCl2 on the {100} surface of NaCl and its consequences for crystal growth
    J. Chem. Phys. (IF 2.965) Pub Date : 2018-04-09
    Eleanor R. Townsend, Sander J. T. Brugman, Melian A. R. Blijlevens, Mireille M. H. Smets, Wester de Poel, Willem J. P. van Enckevort, Jan A. M. Meijer, Elias Vlieg

    The role that additives play in the growth of sodium chloride is a topic which has been widely researched but not always fully understood at an atomic level. Lead chloride (PbCl2) is one such additive which has been reported to have growth inhibition effects on NaCl {100} and {111}; however, no definitive evidence has been reported which details the mechanism of this interaction. In this investigation, we used the technique of surface x-ray diffraction to determine the interaction between PbCl2 and NaCl {100} and the structure at the surface. We find that Pb2+ replaces a surface Na+ ion, while a Cl− ion is located on top of the Pb2+. This leads to a charge mismatch in the bulk crystal, which, as energetically unfavourable, leads to a growth blocking effect. While this is a similar mechanism as in the anticaking agent ferrocyanide, the effect of PbCl2 is much weaker, most likely due to the fact that the Pb2+ ion can more easily desorb. Moreover, PbCl2 has an even stronger effect on NaCl {111}.

    更新日期:2018-04-14
  • Simulations of submonolayer Xe on Pt(111): The case for a chaotic low temperature phase
    J. Chem. Phys. (IF 2.965) Pub Date : 2018-04-10
    Anthony D. Novaco, Jessica Bavaresco

    Molecular dynamics simulations are reported for the structural and thermodynamic properties of submonolayer xenon adsorbed on the (111) surface of platinum for temperatures up to the (apparently incipient) triple point and beyond. While the motion of the atoms in the surface plane is treated with a standard two-dimensional molecular dynamics simulation, the model takes into consideration the thermal excitation of quantum states associated with surface-normal dynamics in an attempt to describe the apparent smoothing of the corrugation with increasing temperature. We examine the importance of this thermal smoothing to the relative stability of several observed and proposed low-temperature structures. Structure factor calculations are compared to experimental results in an attempt to determine the low temperature structure of this system. These calculations provide strong evidence that, at very low temperatures, the domain wall structure of a xenon monolayer adsorbed on a Pt(111) substrate possesses a chaotic-like nature, exhibiting long-lived meta-stable states with pinned domain walls, these walls having narrow widths and irregular shapes. This result is contrary to the standard wisdom regarding this system, namely, that the very low temperature phase of this system is a striped incommensurate phase. We present the case for further experimental investigation of this and similar systems as possible examples of chaotic low temperature phases in two dimensions.

    更新日期:2018-04-14
  • Water dissociating on rigid Ni(100): A quantum dynamics study on a full-dimensional potential energy surface
    J. Chem. Phys. (IF 2.965) Pub Date : 2018-04-10
    Tianhui Liu, Jun Chen, Zhaojun Zhang, Xiangjian Shen, Bina Fu, Dong H. Zhang

    We constructed a nine-dimensional (9D) potential energy surface (PES) for the dissociative chemisorption of H2O on a rigid Ni(100) surface using the neural network method based on roughly 110 000 energies obtained from extensive density functional theory (DFT) calculations. The resulting PES is accurate and smooth, based on the small fitting errors and the good agreement between the fitted PES and the direct DFT calculations. Time dependent wave packet calculations also showed that the PES is very well converged with respect to the fitting procedure. The dissociation probabilities of H2O initially in the ground rovibrational state from 9D quantum dynamics calculations are quite different from the site-specific results from the seven-dimensional (7D) calculations, indicating the importance of full-dimensional quantum dynamics to quantitatively characterize this gas-surface reaction. It is found that the validity of the site-averaging approximation with exact potential holds well, where the site-averaging dissociation probability over 15 fixed impact sites obtained from 7D quantum dynamics calculations can accurately approximate the 9D dissociation probability for H2O in the ground rovibrational state.

    更新日期:2018-04-14
  • Soft phonon modes driven huge difference on lattice thermal conductivity between topological semimetal WC and WN
    J. Chem. Phys. (IF 2.965) Pub Date : 2018-04-11
    San-Dong Guo, Peng Chen

    Topological semimetals are currently attracting increasing interest due to their potential applications in topological qubits and low-power electronics, which are closely related to their thermal transport properties. Recently, the triply degenerate nodal points near the Fermi level of WC are observed by using angle-resolved photoemission spectroscopy. In this work, by solving the Boltzmann transport equation based on first-principles calculations, we systematically investigate the phonon transport properties of topological semimetals WC and WN. The predicted room-temperature lattice thermal conductivities of WC (WN) along the a and c directions are 1140.64 (7.47) W m−1 K−1 and 1214.69 (5.39) W m−1 K−1. Considering the similar crystal structure of WC and WN, it is quite interesting to find that the thermal conductivity of WC is more than two orders of magnitude higher than that of WN. It is found that, different from WN, the large acoustic-optical (a-o) gap prohibits the acoustic+acoustic → optical (aao) scattering, which gives rise to very long phonon lifetimes, leading to ultrahigh lattice thermal conductivity in WC. For WN, the lack of an a-o gap is due to soft phonon modes in optical branches, which can provide more scattering channels for aao scattering, producing very short phonon lifetimes. Further deep insight can be attained from their different electronic structures. Distinctly different from that in WC, the density of states of WN at the Fermi level becomes very sharp, which leads to destabilization of WN, producing soft phonon modes. It is found that the small shear modulus G and C44 limit the stability of WN, compared with WC. Our studies provide valuable information for phonon transports in WC and WN, and motivate further experimental studies to study their lattice thermal conductivities.

    更新日期:2018-04-14
  • Emergence of Landauer transport from quantum dynamics: A model Hamiltonian approach
    J. Chem. Phys. (IF 2.965) Pub Date : 2018-04-12
    Partha Pratim Pal, S. Ramakrishna, Tamar Seideman

    The Landauer expression for computing current-voltage characteristics in nanoscale devices is efficient but not suited to transient phenomena and a time-dependent current because it is applicable only when the charge carriers transition into a steady flux after an external perturbation. In this article, we construct a very general expression for time-dependent current in an electrode-molecule-electrode arrangement. Utilizing a model Hamiltonian (consisting of the subsystem energy levels and their electronic coupling terms), we propagate the Schrödinger wave function equation to numerically compute the time-dependent population in the individual subsystems. The current in each electrode (defined in terms of the rate of change of the corresponding population) has two components, one due to the charges originating from the same electrode and the other due to the charges initially residing at the other electrode. We derive an analytical expression for the first component and illustrate that it agrees reasonably with its numerical counterpart at early times. Exploiting the unitary evolution of a wavefunction, we construct a more general Landauer style formula and illustrate the emergence of Landauer transport from our simulations without the assumption of time-independent charge flow. Our generalized Landauer formula is valid at all times for models beyond the wide-band limit, non-uniform electrode density of states and for time and energy-dependent electronic coupling between the subsystems. Subsequently, we investigate the ingredients in our model that regulate the onset time scale of this steady state. We compare the performance of our general current expression with the Landauer current for time-dependent electronic coupling. Finally, we comment on the applicability of the Landauer formula to compute hot-electron current arising upon plasmon decoherence.

    更新日期:2018-04-14
  • Spatially resolved proton momentum distributions in KDP from first-principles
    J. Chem. Phys. (IF 2.965) Pub Date : 2018-04-12
    Edgar A. Engel

    The ferroelectric to paraelectric (PE) phase transition of KH2PO4 (KDP) is investigated as a stringent test of the first-principles, normal modes framework proposed for calculating anharmonic quantum nuclear motion. Accurate spatially resolved momentum distribution functions (MDFs) are directly calculated from the nuclear wavefunction, overcoming the limitations of path-integral molecular dynamics methods. They indicate coherent, correlated tunneling of protons across hydrogen bonds in the PE phase in agreement with neutron Compton scattering data and reproduces the key features of the experimental MDF. It further highlights the role of Slater’s lateral configurations in the PE phase. The analysis in terms of normal modes demonstrates the importance of collective, correlated proton motion and underlines the value of the employed framework in interpreting experimental data. This also makes the framework very attractive for application to deuterated KDP to further elucidate the nature of the PE transition and to systems exhibiting strong quantum nuclear effects in general.

    更新日期:2018-04-14
  • Empirical potential for molecular simulation of graphene nanoplatelets
    J. Chem. Phys. (IF 2.965) Pub Date : 2018-04-13
    Alexander J. Bourque, Gregory C. Rutledge

    A new empirical potential for layered graphitic materials is reported. Interatomic interactions within a single graphene sheet are modeled using a Stillinger-Weber potential. Interatomic interactions between atoms in different sheets of graphene in the nanoplatelet are modeled using a Lennard-Jones interaction potential. The potential is validated by comparing molecular dynamics simulations of tensile deformation with the reported elastic constants for graphite. The graphite is found to fracture into graphene nanoplatelets when subjected to ∼15% tensile strain normal to the basal surface of the graphene stack, with an ultimate stress of 2.0 GPa and toughness of 0.33 GPa. This force field is useful to model molecular interactions in an important class of composite systems comprising 2D materials like graphene and multi-layer graphene nanoplatelets.

    更新日期:2018-04-14
  • Polymer effects on Kármán vortex: Molecular dynamics study
    J. Chem. Phys. (IF 2.965) Pub Date : 2018-04-09
    Yuta Asano, Hiroshi Watanabe, Hiroshi Noguchi

    We investigated the Kármán vortex behind a circular cylinder in a polymer solution by a molecular dynamics simulation. The vortex characteristics are distinctly different for short and long polymers. The solution with the long polymer exhibits a reduction in the vortex shedding frequency and broadening of the lift coefficient spectrum. On the other hand, the characteristics of the short-polymer solution are almost the same as those of the Newtonian fluid. These facts are consistent with the experiments. Because the distributions of the gyration radius and the orientational order of the long-polymer solution are highly inhomogeneous in the flow field, we conclude that the extensional property of the polymer plays an important role in changing the flow characteristics.

    更新日期:2018-04-14
  • Reaction kinetics in open reactors and serial transfers between closed reactors
    J. Chem. Phys. (IF 2.965) Pub Date : 2018-04-13
    Alex Blokhuis, David Lacoste, Pierre Gaspard

    Kinetic theory and thermodynamics of reaction networks are extended to the out-of-equilibrium dynamics of continuous-flow stirred tank reactors (CSTR) and serial transfers. On the basis of their stoichiometry matrix, the conservation laws and the cycles of the network are determined for both dynamics. It is shown that the CSTR and serial transfer dynamics are equivalent in the limit where the time interval between the transfers tends to zero proportionally to the ratio of the fractions of fresh to transferred solutions. These results are illustrated with a finite cross-catalytic reaction network and an infinite reaction network describing mass exchange between polymers. Serial transfer dynamics is typically used in molecular evolution experiments in the context of research on the origins of life. The present study is shedding a new light on the role played by serial transfer parameters in these experiments.

    更新日期:2018-04-14
  • Molecular dynamics simulations of site point mutations in the TPR domain of cyclophilin 40 identify conformational states with distinct dynamic and enzymatic properties
    J. Chem. Phys. (IF 2.965) Pub Date : 2018-04-09
    Mert Gur, Elizabeth A. Blackburn, Jia Ning, Vikram Narayan, Kathryn L. Ball, Malcolm D. Walkinshaw, Burak Erman

    Cyclophilin 40 (Cyp40) is a member of the immunophilin family that acts as a peptidyl-prolyl-isomerase enzyme and binds to the heat shock protein 90 (Hsp90). Its structure comprises an N-terminal cyclophilin domain and a C-terminal tetratricopeptide (TPR) domain. Cyp40 is overexpressed in prostate cancer and certain T-cell lymphomas. The groove for Hsp90 binding on the TPR domain includes residues Lys227 and Lys308, referred to as the carboxylate clamp, and is essential for Cyp40-Hsp90 binding. In this study, the effect of two mutations, K227A and K308A, and their combinative mutant was investigated by performing a total of 5.76 μs of all-atom molecular dynamics (MD) simulations in explicit solvent. All simulations, except the K308A mutant, were found to adopt two distinct (extended or compact) conformers defined by different cyclophilin-TPR interdomain distances. The K308A mutant was only observed in the extended form which is observed in the Cyp40 X-ray structure. The wild-type, K227A, and combined mutant also showed bimodal distributions. The experimental melting temperature, Tm, values of the mutants correlate with the degree of compactness with the K308A extended mutant having a marginally lower melting temperature. Another novel measure of compactness determined from the MD data, the “coordination shell volume,” also shows a direct correlation with Tm. In addition, the MD simulations show an allosteric effect with the mutations in the remote TPR domain having a pronounced effect on the molecular motions of the enzymatic cyclophilin domain which helps rationalise the experimentally observed increase in enzyme activity measured for all three mutations.

    更新日期:2018-04-14
  • Communication: Probing the interaction of infrared antenna arrays and molecular films with ultrafast quantum dynamics
    J. Chem. Phys. (IF 2.965) Pub Date : 2018-04-04
    Bar Cohn, Amit K. Prasad, Lev Chuntonov

    Narrowband vibrational molecular transitions interacting with the broadband resonance of infrared plasmonic antennas lead to Fano lineshapes observed in linear (FTIR) and third-order (transient absorption and 2DIR) spectroscopic experiments. Both molecular and plasmonic components are inherently dissipative, and the effects associated with their coupling can be observed, in principle, when measuring the corresponding ultrafast quantum dynamics. We used 2DIR spectroscopy to study the waiting time evolution of quantum coherence excited in the carbonyl stretching modes of rhodium (acetylacetonato) dicarbonyl molecules, which were embedded in an 80 nm-thick polymer film spin-coated on an array of infrared half-wavelength gold antennas. Despite the pronounced Fano lineshapes obtained for the molecular transitions, and up to a four order of magnitude enhancement of the third-order signals, which taken together, indicate the coupling between the plasmonic and molecular transitions, the dynamics of the quantum coherence were identical to that obtained with 3 μm-thick film without the interaction with the plamson mode. This suggests that the coupling rate between the molecular and plasmonic excitations is significantly smaller than the relaxation rates of the molecular excitations monitored in the experiment. Here, the Fano lineshape, observed at the frequency of the molecular transition, can result from the mutual radiation damping of the molecular and plasmon modes.

    更新日期:2018-04-07
  • Communication: Fast dynamics perspective on the breakdown of the Stokes-Einstein law in fragile glassformers
    J. Chem. Phys. (IF 2.965) Pub Date : 2018-04-05
    F. Puosi, A. Pasturel, N. Jakse, D. Leporini

    The breakdown of the Stokes-Einstein (SE) law in fragile glassformers is examined by Molecular-Dynamics simulations of atomic liquids and polymers and consideration of the experimental data concerning the archetypical ortho-terphenyl glassformer. All the four systems comply with the universal scaling between the viscosity (or the structural relaxation) and the Debye-Waller factor ⟨u2⟩, the mean square amplitude of the particle rattling in the cage formed by the surrounding neighbors. It is found that the SE breakdown is scaled in a master curve by a reduced ⟨u2⟩. Two approximated expressions of the latter, with no and one adjustable parameter, respectively, are derived.

    更新日期:2018-04-07
  • QED effects on individual atomic orbital energies
    J. Chem. Phys. (IF 2.965) Pub Date : 2018-04-02
    Karol Kozioł, Gustavo A. Aucar

    Several issues, concerning QED corrections, that are important in precise atomic calculations are presented. The leading QED corrections, self-energy and vacuum polarization, to the orbital energy for selected atoms with 30 ≤ Z ≤ 118 have been calculated. The sum of QED and Breit contributions to the orbital energy is analyzed. It has been found that for ns subshells the Breit and QED contributions are of comparative size, but for np and nd subshells the Breit contribution takes a major part of the QED+Breit sum. It has also, been found that the Breit to leading QED contributions ratio for ns subshells is almost independent of Z. The Z-dependence of QED and Breit+QED contributions per subshell is shown. The fitting coefficients may be used to estimate QED effects on inner molecular orbitals. We present results of our calculations for QED contributions to orbital energy of valence ns-subshell for group 1 and 11 atoms and discuss about the reliability of these numbers by comparing them with experimental first ionization potential data.

    更新日期:2018-04-07
  • A pair natural orbital based implementation of CCSD excitation energies within the framework of linear response theory
    J. Chem. Phys. (IF 2.965) Pub Date : 2018-04-03
    Marius S. Frank, Christof Hättig

    We present a pair natural orbital (PNO)-based implementation of coupled cluster singles and doubles (CCSD) excitation energies that builds upon the previously proposed state-specific PNO approach to the excited state eigenvalue problem. We construct the excited state PNOs for each state separately in a truncated orbital specific virtual basis and use a local density-fitting approximation to achieve an at most quadratic scaling of the computational costs for the PNO construction. The earlier reported excited state PNO construction is generalized such that a smooth convergence of the results for charge transfer states is ensured for general coupled cluster methods. We investigate the accuracy of our implementation by applying it to a large and diverse test set comprising 153 singlet excitations in organic molecules. Already moderate PNO thresholds yield mean absolute errors below 0.01 eV. The performance of the implementation is investigated through the calculations on alkene chains and reveals an at most cubic cost-scaling for the CCSD iterations with the system size.

    更新日期:2018-04-07
  • Flexible scheme to truncate the hierarchy of pure states
    J. Chem. Phys. (IF 2.965) Pub Date : 2018-04-02
    P.-P. Zhang, C. D. B. Bentley, A. Eisfeld

    The hierarchy of pure states (HOPS) is a wavefunction-based method that can be used for numerically modeling open quantum systems. Formally, HOPS recovers the exact system dynamics for an infinite depth of the hierarchy. However, truncation of the hierarchy is required to numerically implement HOPS. We want to choose a “good” truncation method, where by “good” we mean that it is numerically feasible to check convergence of the results. For the truncation approximation used in previous applications of HOPS, convergence checks are numerically challenging. In this work, we demonstrate the application of the “n-particle approximation” to HOPS. We also introduce a new approximation, which we call the “n-mode approximation.” We then explore the convergence of these truncation approximations with respect to the number of equations required in the hierarchy in two exemplary problems: absorption and energy transfer of molecular aggregates.

    更新日期:2018-04-07
  • Fluctuating chemohydrodynamics and the stochastic motion of self-diffusiophoretic particles
    J. Chem. Phys. (IF 2.965) Pub Date : 2018-04-02
    Pierre Gaspard, Raymond Kapral

    The propulsion of active particles by self-diffusiophoresis is driven by asymmetric catalytic reactions on the particle surface that generate a mechanochemical coupling between the fluid velocity and the concentration fields of fuel and product in the surrounding solution. Because of thermal and molecular fluctuations in the solution, the motion of micrometric or submicrometric active particles is stochastic. Coupled Langevin equations describing the translation, rotation, and reaction of such active particles are deduced from fluctuating chemohydrodynamics and fluctuating boundary conditions at the interface between the fluid and the particle. These equations are consistent with microreversibility and the Onsager-Casimir reciprocal relations between affinities and currents and provide a thermodynamically consistent basis for the investigation of the dynamics of active particles propelled by diffusiophoretic mechanisms.

    更新日期:2018-04-07
  • Expanding the calculation of activation volumes: Self-diffusion in liquid water
    J. Chem. Phys. (IF 2.965) Pub Date : 2018-04-02
    Zeke A. Piskulich, Oluwaseun O. Mesele, Ward H. Thompson

    A general method for calculating the dependence of dynamical time scales on macroscopic thermodynamic variables from a single set of simulations is presented. The approach is applied to the pressure dependence of the self-diffusion coefficient of liquid water as a particularly useful illustration. It is shown how the activation volume associated with diffusion can be obtained directly from simulations at a single pressure, avoiding approximations that are typically invoked.

    更新日期:2018-04-07
  • Assessment of interaction-strength interpolation formulas for gold and silver clusters
    J. Chem. Phys. (IF 2.965) Pub Date : 2018-04-02
    Sara Giarrusso, Paola Gori-Giorgi, Fabio Della Sala, Eduardo Fabiano

    The performance of functionals based on the idea of interpolating between the weak- and the strong-interaction limits the global adiabatic-connection integrand is carefully studied for the challenging case of noble-metal clusters. Different interpolation formulas are considered and various features of this approach are analyzed. It is found that these functionals, when used as a correlation correction to Hartree-Fock, are quite robust for the description of atomization energies, while performing less well for ionization potentials. Future directions that can be envisaged from this study and a previous one on main group chemistry are discussed.

    更新日期:2018-04-07
  • Committor of elementary reactions on multistate systems
    J. Chem. Phys. (IF 2.965) Pub Date : 2018-04-02
    Péter Király, Dóra Judit Kiss, Gergely Tóth

    In our study, we extend the committor concept on multi-minima systems, where more than one reaction may proceed, but the feasible data evaluation needs the projection onto partial reactions. The elementary reaction committor and the corresponding probability density of the reactive trajectories are defined and calculated on a three-hole two-dimensional model system explored by single-particle Langevin dynamics. We propose a method to visualize more elementary reaction committor functions or probability densities of reactive trajectories on a single plot that helps to identify the most important reaction channels and the nonreactive domains simultaneously. We suggest a weighting for the energy-committor plots that correctly shows the limits of both the minimal energy path and the average energy concepts. The methods also performed well on the analysis of molecular dynamics trajectories of 2-chlorobutane, where an elementary reaction committor, the probability densities, the potential energy/committor, and the free-energy/committor curves are presented.

    更新日期:2018-04-07
  • Adaptive enhanced sampling by force-biasing using neural networks
    J. Chem. Phys. (IF 2.965) Pub Date : 2018-04-03
    Ashley Z. Guo, Emre Sevgen, Hythem Sidky, Jonathan K. Whitmer, Jeffrey A. Hubbell, Juan J. de Pablo

    A machine learning assisted method is presented for molecular simulation of systems with rugged free energy landscapes. The method is general and can be combined with other advanced sampling techniques. In the particular implementation proposed here, it is illustrated in the context of an adaptive biasing force approach where, rather than relying on discrete force estimates, one can resort to a self-regularizing artificial neural network to generate continuous, estimated generalized forces. By doing so, the proposed approach addresses several shortcomings common to adaptive biasing force and other algorithms. Specifically, the neural network enables (1) smooth estimates of generalized forces in sparsely sampled regions, (2) force estimates in previously unexplored regions, and (3) continuous force estimates with which to bias the simulation, as opposed to biases generated at specific points of a discrete grid. The usefulness of the method is illustrated with three different examples, chosen to highlight the wide range of applicability of the underlying concepts. In all three cases, the new method is found to enhance considerably the underlying traditional adaptive biasing force approach. The method is also found to provide improvements over previous implementations of neural network assisted algorithms.

    更新日期:2018-04-07
  • Current density tensors
    J. Chem. Phys. (IF 2.965) Pub Date : 2018-04-03
    Paolo Lazzeretti

    It is shown that nonsymmetric second-rank current density tensors, related to the current densities induced by magnetic fields and nuclear magnetic dipole moments, are fundamental properties of a molecule. Together with magnetizability, nuclear magnetic shielding, and nuclear spin-spin coupling, they completely characterize its response to magnetic perturbations. Gauge invariance, resolution into isotropic, deviatoric, and antisymmetric parts, and contributions of current density tensors to magnetic properties are discussed. The components of the second-rank tensor properties are rationalized via relationships explicitly connecting them to the direction of the induced current density vectors and to the components of the current density tensors. The contribution of the deviatoric part to the average value of magnetizability, nuclear shielding, and nuclear spin-spin coupling, uniquely determined by the antisymmetric part of current density tensors, vanishes identically. The physical meaning of isotropic and anisotropic invariants of current density tensors has been investigated, and the connection between anisotropy magnitude and electron delocalization has been discussed.

    更新日期:2018-04-07
  • A walk through the approximations of ab initio multiple spawning
    J. Chem. Phys. (IF 2.965) Pub Date : 2018-04-03
    Benoit Mignolet, Basile F. E. Curchod

    Full multiple spawning offers an in principle exact framework for excited-state dynamics, where nuclear wavefunctions in different electronic states are represented by a set of coupled trajectory basis functions that follow classical trajectories. The couplings between trajectory basis functions can be approximated to treat molecular systems, leading to the ab initio multiple spawning method which has been successfully employed to study the photochemistry and photophysics of several molecules. However, a detailed investigation of its approximations and their consequences is currently missing in the literature. In this work, we simulate the explicit photoexcitation and subsequent excited-state dynamics of a simple system, LiH, and we analyze (i) the effect of the ab initio multiple spawning approximations on different observables and (ii) the convergence of the ab initio multiple spawning results towards numerically exact quantum dynamics upon a progressive relaxation of these approximations. We show that, despite the crude character of the approximations underlying ab initio multiple spawning for this low-dimensional system, the qualitative excited-state dynamics is adequately captured, and affordable corrections can further be applied to ameliorate the coupling between trajectory basis functions.

    更新日期:2018-04-07
  • Transient dynamics of a quantum-dot: From Kondo regime to mixed valence and to empty orbital regimes
    J. Chem. Phys. (IF 2.965) Pub Date : 2018-04-03
    YongXi Cheng, ZhenHua Li, JianHua Wei, YiHang Nie, YiJing Yan

    Based on the hierarchical equations of motion approach, we study the time-dependent transport properties of a strongly correlated quantum dot system in the Kondo regime (KR), mixed valence regime (MVR), and empty orbital regime (EOR). We find that the transient current in KR shows the strongest nonlinear response and the most distinct oscillation behaviors. Both behaviors become weaker in MVR and diminish in EOR. To understand the physical insight, we examine also the corresponding dot occupancies and the spectral functions, with their dependence on the Coulomb interaction, temperature, and applied step bias voltage. The above nonlinear and oscillation behaviors could be understood as the interplay between dynamical Kondo resonance and single electron resonant-tunneling.

    更新日期:2018-04-07
  • Fate of the open-shell singlet ground state in the experimentally accessible acenes: A quantum Monte Carlo study
    J. Chem. Phys. (IF 2.965) Pub Date : 2018-04-03
    Nicolas Dupuy, Michele Casula

    By means of the Jastrow correlated antisymmetrized geminal power (JAGP) wave function and quantum Monte Carlo (QMC) methods, we study the ground state properties of the oligoacene series, up to the nonacene. The JAGP is the accurate variational realization of the resonating-valence-bond (RVB) ansatz proposed by Pauling and Wheland to describe aromatic compounds. We show that the long-ranged RVB correlations built in the acenes’ ground state are detrimental for the occurrence of open-shell diradical or polyradical instabilities, previously found by lower-level theories. We substantiate our outcome by a direct comparison with another wave function, tailored to be an open-shell singlet (OSS) for long-enough acenes. By comparing on the same footing the RVB and OSS wave functions, both optimized at a variational QMC level and further projected by the lattice regularized diffusion Monte Carlo method, we prove that the RVB wave function has always a lower variational energy and better nodes than the OSS, for all molecular species considered in this work. The entangled multi-reference RVB state acts against the electron edge localization implied by the OSS wave function and weakens the diradical tendency for higher oligoacenes. These properties are reflected by several descriptors, including wave function parameters, bond length alternation, aromatic indices, and spin-spin correlation functions. In this context, we propose a new aromatic index estimator suitable for geminal wave functions. For the largest acenes taken into account, the long-range decay of the charge-charge correlation functions is compatible with a quasi-metallic behavior.

    更新日期:2018-04-07
Some contents have been Reproduced with permission of the American Chemical Society.
Some contents have been Reproduced by permission of The Royal Society of Chemistry.
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