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  • Perspective: Identification of collective variables and metastable states of protein dynamics
    J. Chem. Phys. (IF 2.843) Pub Date : 2018-10-15
    Florian Sittel, Gerhard Stock

    The statistical analysis of molecular dynamics simulations requires dimensionality reduction techniques, which yield a low-dimensional set of collective variables (CVs) {xi} = x that in some sense describe the essential dynamics of the system. Considering the distribution P(x) of the CVs, the primal goal of a statistical analysis is to detect the characteristic features of P(x), in particular, its maxima and their connection paths. This is because these features characterize the low-energy regions and the energy barriers of the corresponding free energy landscape ΔG(x) = −kBT ln P(x), and therefore amount to the metastable states and transition regions of the system. In this perspective, we outline a systematic strategy to identify CVs and metastable states, which subsequently can be employed to construct a Langevin or a Markov state model of the dynamics. In particular, we account for the still limited sampling typically achieved by molecular dynamics simulations, which in practice seriously limits the applicability of theories (e.g., assuming ergodicity) and black-box software tools (e.g., using redundant input coordinates). We show that it is essential to use internal (rather than Cartesian) input coordinates, employ dimensionality reduction methods that avoid rescaling errors (such as principal component analysis), and perform density based (rather than k-means-type) clustering. Finally, we briefly discuss a machine learning approach to dimensionality reduction, which highlights the essential internal coordinates of a system and may reveal hidden reaction mechanisms.

    更新日期:2018-10-19
  • Communication: Approaching exact quantum chemistry by cluster analysis of full configuration interaction quantum Monte Carlo wave functions
    J. Chem. Phys. (IF 2.843) Pub Date : 2018-10-18
    J. Emiliano Deustua, Ilias Magoulas, Jun Shen, Piotr Piecuch

    We propose to accelerate convergence toward full configuration interaction (FCI) energetics by using the coupled-cluster approach, in which singly and doubly excited clusters, needed to determine the energy, are iterated in the presence of their three- and four-body counterparts extracted from FCI quantum Monte Carlo (FCIQMC) propagations. Preliminary calculations for the water molecule at the equilibrium and stretched geometries show that we can accurately extrapolate the FCI energetics based on the early stages of FCIQMC propagations.

    更新日期:2018-10-19
  • Stability of velocity-Verlet- and Liouville-operator-derived algorithms to integrate non-Hamiltonian systems
    J. Chem. Phys. (IF 2.843) Pub Date : 2018-10-15
    Hiroshi Watanabe

    We investigate the difference between the velocity Verlet and the Liouville-operator-derived (LOD) algorithms by studying two non-Hamiltonian systems, one dissipative and the other conservative, for which the Jacobian of the transformation can be determined exactly. For the two systems, we demonstrate that (1) the velocity Verlet scheme fails to integrate the former system while the first- and second-order LOD schemes succeed and (2) some first-order LOD fails to integrate the latter system while the velocity Verlet and the other first- and second-order schemes succeed. We have shown that the LOD schemes are stable for the former system by determining the explicit forms of the shadow Hamiltonians which are exactly conserved by the schemes. We have shown that the Jacobian of the velocity Verlet scheme for the former system and that of the first-order LOD scheme for the latter system are always smaller than the exact values, and therefore, the schemes are unstable. The decomposition-order dependence of LOD schemes is also considered.

    更新日期:2018-10-19
  • Angle-resolved photoemission spectroscopy from first-principles quantum Monte Carlo
    J. Chem. Phys. (IF 2.843) Pub Date : 2018-10-15
    Matteo Barborini, Sandro Sorella, Massimo Rontani, Stefano Corni

    Angle-resolved photoemission spectroscopy allows one to visualize in momentum space the probability weight maps of electrons subtracted from molecules deposited on a substrate. The interpretation of these maps usually relies on the plane wave approximation through the Fourier transform of single particle orbitals obtained from density functional theory. Here we propose a first-principle many-body approach based on quantum Monte Carlo (QMC) to directly calculate the quasi-particle wave functions (also known as Dyson orbitals) of molecules in momentum space. The comparison between these correlated QMC images and their single particle counterpart highlights features that arise from many-body effects. We test the QMC approach on the linear C2H2, CO2, and N2 molecules, for which only small amplitude remodulations are visible. Then, we consider the case of the pentacene molecule, focusing on the relationship between the momentum space features and the real space quasi-particle orbital. Eventually, we verify the correlation effects present in the metal CuCl42− planar complex.

    更新日期:2018-10-19
  • Data-driven computation of molecular reaction coordinates
    J. Chem. Phys. (IF 2.843) Pub Date : 2018-10-15
    Andreas Bittracher, Ralf Banisch, Christof Schütte

    The identification of meaningful reaction coordinates plays a key role in the study of complex molecular systems whose essential dynamics are characterized by rare or slow transition events. In a recent publication, precise defining characteristics of such reaction coordinates were identified and linked to the existence of a so-called transition manifold. This theory gives rise to a novel numerical method for the pointwise computation of reaction coordinates that relies on short parallel MD simulations only, but yields accurate approximation of the long time behavior of the system under consideration. This article presents an extension of the method towards practical applicability in computational chemistry. It links the newly defined reaction coordinates to concepts from transition path theory and Markov state model building. The main result is an alternative computational scheme that allows for a global computation of reaction coordinates based on commonly available types of simulation data, such as single long molecular trajectories or the push-forward of arbitrary canonically distributed point clouds. It is based on a Galerkin approximation of the transition manifold reaction coordinates that can be tuned to individual requirements by the choice of the Galerkin ansatz functions. Moreover, we propose a ready-to-implement variant of the new scheme, which computes data-fitted, mesh-free ansatz functions directly from the available simulation data. The efficacy of the new method is demonstrated on a small protein system.

    更新日期:2018-10-19
  • Momentum-resolved TDDFT algorithm in atomic basis for real time tracking of electronic excitation
    J. Chem. Phys. (IF 2.843) Pub Date : 2018-10-15
    Chao Lian, Shi-Qi Hu, Meng-Xue Guan, Sheng Meng

    Ultrafast electronic dynamics in solids lies at the core of modern condensed matter and materials physics. To build up a practical ab initio method for studying solids under photoexcitation, we develop a momentum-resolved real-time time dependent density functional theory (rt-TDDFT) algorithm using numerical atomic basis, together with the implementation of both the length and vector gauge of the electromagnetic field. When applied to simulate elementary excitations in two-dimensional materials such as graphene, different excitation modes, only distinguishable in momentum space, are observed. The momentum-resolved rt-TDDFT is important and computationally efficient for the study of ultrafast dynamics in extended systems.

    更新日期:2018-10-19
  • Accurate calculations of weakly bound state energy and scattering length near magnetically tuned Feshbach resonance using the separable potential method
    J. Chem. Phys. (IF 2.843) Pub Date : 2018-10-17
    Jing-Lun Li, Shu-Lin Cong

    We present a theoretical model for investigating the magnetically tuned Feshbach resonance (MTFR) of alkali metal atoms using the separable potential method (SPM). We discuss the relationship and difference between the SPM and the asymptotic bound state model. To demonstrate the validity of the SPM, we use it to calculate the weakly bound state energy and magnetically tuned scattering length for the 6Li–40K, 7Li2, and 6Li2 systems with narrow and broad Feshbach resonances. The results of the SPM calculations are in good agreement with those of coupled channel calculations and with experimental measurements for all three systems. The SPM, by simplifying the calculation of the two-body MTFR, is expected to simplify numerical computations for three-atom collisions in a magnetic field and the Feshbach-optimized photoassociation process.

    更新日期:2018-10-19
  • Gauge invariance and origin independence of electronic charge density and current density induced by optical fields
    J. Chem. Phys. (IF 2.843) Pub Date : 2018-10-17
    Paolo Lazzeretti

    Expressions for the first-order polarization charge density ρ(1) and current density J(1) induced in a molecule by a monochromatic plane wave, obtained by time-dependent quantum mechanical perturbation theory, have been investigated to assess their gauge invariance and independence of the coordinate system in passive and active translations. The conditions arrived at show that, within the (long wavelengths) dipole approximation, only the electric contributions to these densities are needed to rationalize the phenomenology. To the next higher quadrupole approximation, assuming that the magnetic field and the electric field gradient are uniform over the molecular dimensions, corresponding contributions to ρ(1) and J(1) are considered. It has been found that total densities are independent of the origin, whereas the contributions from electric and magnetic fields are not separately invariant. A magnetic contribution to J(1), which is by itself origin independent, can be defined by means of an approach based on continuous translation of the origin of the coordinate system.

    更新日期:2018-10-19
  • Adaptive coupling of a deep neural network potential to a classical force field
    J. Chem. Phys. (IF 2.843) Pub Date : 2018-10-17
    Linfeng Zhang, Han Wang, Weinan E

    An adaptive modeling method (AMM) that couples a deep neural network potential and a classical force field is introduced to address the accuracy-efficiency dilemma faced by the molecular simulation community. The AMM simulated system is decomposed into three types of regions. The first type captures the important phenomena in the system and requires high accuracy, for which we use the Deep Potential Molecular Dynamics (DeePMD) model in this work. The DeePMD model is trained to accurately reproduce the statistical properties of the ab initio molecular dynamics. The second type does not require high accuracy, and a classical force field is used to describe it in an efficient way. The third type is used for a smooth transition between the first and the second types of regions. By using a force interpolation scheme and imposing a thermodynamics force in the transition region, we make the DeePMD region embedded in the AMM simulated system as if it were embedded in a system that is fully described by the accurate potential. A representative example of the liquid water system is used to show the feasibility and promise of this method.

    更新日期:2018-10-19
  • Determining whether diabolical singularities limit the accuracy of molecular property based diabatic representations: The 1,21A states of methylamine
    J. Chem. Phys. (IF 2.843) Pub Date : 2018-10-17
    Yuchen Wang, David R. Yarkony

    An efficient, easily implemented method for locating singularities attributable to the failure of the defining equations in a molecular property based diabatization, termed diabolical singular points, is reported. For two state diabatizations, the singular points form a seam of dimension Nint − 2, where Nint is the number of internal degrees of freedom. The dynamical outcomes of nuclear trajectories that reach the region of this seam are flawed. The algorithm easily identifies these otherwise hard to anticipate regions of fallaciously large derivative coupling. The fact that the algorithm is easily incorporated into a two state diabatization code based on molecular properties makes it a practical tool for determining whether the existence of diabolical singularities is relevant to the problem being considered. The algorithm is illustrated using a multireference single and double excitation configuration interaction description of the 1,21A states of CH3NH2.

    更新日期:2018-10-19
  • Do CCSD and approximate CCSD-F12 variants converge to the same basis set limits? The case of atomization energies
    J. Chem. Phys. (IF 2.843) Pub Date : 2018-10-18
    Manoj K. Kesharwani, Nitai Sylvetsky, Andreas Köhn, David P. Tew, Jan M. L. Martin

    While the title question is a clear “yes” from purely theoretical arguments, the case is less clear for practical calculations with finite (one-particle) basis sets. To shed further light on this issue, the convergence to the basis set limit of CCSD (coupled cluster theory with all single and double excitations) and of different approximate implementations of CCSD-F12 (explicitly correlated CCSD) has been investigated in detail for the W4-17 thermochemical benchmark. Near the CBS ([1-particle] complete basis set) limit, CCSD and CCSD(F12*) agree to within their respective uncertainties (about ±0.04 kcal/mol) due to residual basis set incompleteness error, but a nontrivial difference remains between CCSD-F12b and CCSD(F12*), which is roughly proportional to the degree of static correlation. The observed basis set convergence behavior results from the superposition of a rapidly converging, attractive, CCSD[F12]–CCSD-F12b difference (consisting mostly of third-order terms) and a more slowly converging, repulsive, fourth-order difference between CCSD(F12*) and CCSD[F12]. For accurate thermochemistry, we recommend CCSD(F12*) over CCSD-F12b if at all possible. There are some indications that the nZaPa family of basis sets exhibits somewhat smoother convergence than the correlation consistent family.

    更新日期:2018-10-19
  • Bayesian calibration of force-fields from experimental data: TIP4P water
    J. Chem. Phys. (IF 2.843) Pub Date : 2018-10-18
    Ritabrata Dutta, Zacharias Faidon Brotzakis, Antonietta Mira

    Molecular dynamics (MD) simulations give access to equilibrium structures and dynamic properties given an ergodic sampling and an accurate force-field. The force-field parameters are calibrated to reproduce properties measured by experiments or simulations. The main contribution of this paper is an approximate Bayesian framework for the calibration and uncertainty quantification of the force-field parameters, without assuming parameter uncertainty to be Gaussian. To this aim, since the likelihood function of the MD simulation models is intractable in the absence of Gaussianity assumption, we use a likelihood-free inference scheme known as approximate Bayesian computation (ABC) and propose an adaptive population Monte Carlo ABC algorithm, which is illustrated to converge faster and scales better than the previously used ABCsubsim algorithm for the calibration of the force-field of a helium system. The second contribution is the adaptation of ABC algorithms for High Performance Computing to MD simulations within the Python ecosystem ABCpy. This adaptation includes a novel use of a dynamic allocation scheme for Message Passing Interface (MPI). We illustrate the performance of the developed methodology to learn posterior distribution and Bayesian estimates of Lennard-Jones force-field parameters of helium and the TIP4P system of water implemented for both simulated and experimental datasets collected using neutron and X-ray diffraction. For simulated data, the Bayesian estimate is in close agreement with the true parameter value used to generate the dataset. For experimental as well as for simulated data, the Bayesian posterior distribution shows a strong correlation pattern between the force-field parameters. Providing an estimate of the entire posterior distribution, our methodology also allows us to perform the uncertainty quantification of model prediction. This research opens up the possibility to rigorously calibrate force-fields from available experimental datasets of any structural and dynamic property.

    更新日期:2018-10-19
  • A general approach for the calculation and characterization of x-ray absorption spectra
    J. Chem. Phys. (IF 2.843) Pub Date : 2018-10-19
    Simon P. Neville, Michael S. Schuurman

    We present a general approach for the calculation and assignment of X-ray absorption spectra based on electronic wavepacket propagations performed using explicitly time-dependent electronic structure calculations. Such calculations have the appeal of yielding the entire absorption spectrum for the cost of a single set of electronic wavepacket propagations, obviating the need to explicitly calculate large numbers of core-excited states. The spectrum can either be calculated from the Fourier transform of the time-dependent dipole moment or from the Fourier transform of the wavepacket autocorrelation function. We propose that calculating the absorption spectrum using the latter approach will generally be the preferred option. This method has two important advantages. First, the autocorrelation functions can be obtained for twice the propagation time, resulting in a halving of the computational effort required to calculate the spectrum relative to the time-dependent dipole moment approach. Second, using the tools of filter diagonalisation, the autocorrelation functions may be used to determine the time-independent final core-excited states underlying the peaks of interest in the spectrum. The proposed scheme is validated by calculating and characterizing the X-ray absorption spectra of benzene and trifluoroacetonitrile at the time-dependent second-order algebraic diagrammatic construction level of theory.

    更新日期:2018-10-19
  • Beyond Marcus theory and the Landauer-Büttiker approach in molecular junctions: A unified framework
    J. Chem. Phys. (IF 2.843) Pub Date : 2018-10-19
    Jakub K. Sowa, Jan A. Mol, G. Andrew D. Briggs, Erik M. Gauger

    Charge transport through molecular junctions is often described either as a purely coherent or a purely classical phenomenon, and described using the Landauer–Büttiker formalism or Marcus theory (MT), respectively. Using a generalised quantum master equation, we here derive an expression for current through a molecular junction modelled as a single electronic level coupled with a collection of thermalised vibrational modes. We demonstrate that the aforementioned theoretical approaches can be viewed as two limiting cases of this more general expression and present a series of approximations of this result valid at higher temperatures. We find that MT is often insufficient in describing the molecular charge transport characteristics and gives rise to a number of artefacts, especially at lower temperatures. Alternative expressions, retaining its mathematical simplicity, but rectifying those shortcomings, are suggested. In particular, we show how lifetime broadening can be consistently incorporated into MT, and we derive a low-temperature correction to the semi-classical Marcus hopping rates. Our results are applied to examples building on phenomenological as well as microscopically motivated electron-vibrational coupling. We expect them to be particularly useful in experimental studies of charge transport through single-molecule junctions as well as self-assembled monolayers.

    更新日期:2018-10-19
  • Feed-forward comb-assisted coherence transfer to a widely tunable DFB diode laser
    J. Chem. Phys. (IF 2.843) Pub Date : 2018-10-15
    Riccardo Gotti, Tommaso Sala, Marco Prevedelli, Samir Kassi, Marco Marangoni, Daniele Romanini

    The transfer of phase coherence from an ultrastable master laser to a distributed feedback diode laser, using an optical comb as a transfer oscillator, is obtained via a new scheme allowing continuous scanning across the whole tuning range of the slave laser together with absolute frequency determination. This is accomplished without phase lock loops, through a robust high-bandwidth feed-forward control acting directly on the slave laser output radiation. The correction is obtained by means of a dual-parallel Mach–Zehnder interferometer used as an optical single-sideband modulator. Coherence transfer across a master–slave frequency gap of 14 THz yields an ∼10 kHz linewidth providing high injection efficiency of an optical cavity with finesse 250 000. This allows demonstrating a cavity ring-down absorption spectrum of low-pressure ambient air over a 300 GHz spectral window.

    更新日期:2018-10-19
  • Large-scale ab initio simulations of MAS DNP enhancements using a Monte Carlo optimization strategy
    J. Chem. Phys. (IF 2.843) Pub Date : 2018-10-19
    Frédéric A. Perras, Marek Pruski

    Magic-angle-spinning (MAS) dynamic nuclear polarization (DNP) has recently emerged as a powerful technology enabling otherwise unrealistic solid-state NMR experiments. The simulation of DNP processes which might, for example, aid in refining the experimental conditions or the design of better performing polarizing agents, is, however, plagued with significant challenges, often limiting the system size to only 3 spins. Here, we present the first approach to fully ab initio large-scale simulations of MAS DNP enhancements. The Landau-Zener equation is used to treat all interactions concerning electron spins, and the low-order correlations in the Liouville space method is used to accurately treat the spin diffusion, as well as its MAS speed dependence. As the propagator cannot be stored, a Monte Carlo optimization method is used to determine the steady-state enhancement factors. This new software is employed to investigate the MAS speed dependence of the enhancement factors in large spin systems where spin diffusion is of importance, as well as to investigate the impacts of solvent and polarizing agent deuteration on the performance of MAS DNP.

    更新日期:2018-10-19
  • Collisional dissipation of the laser-induced alignment of ethane gas: A requantized classical model
    J. Chem. Phys. (IF 2.843) Pub Date : 2018-10-17
    J.-M. Hartmann, C. Boulet, H. Zhang, F. Billard, O. Faucher, B. Lavorel

    We present the first theoretical study of collisional dissipation of the alignment of a symmetric-top molecule (ethane gas) impulsively induced by a linearly polarized non-resonant laser field. For this, Classical Molecular Dynamics Simulations (CMDSs) are carried out for an ensemble of C2H6 molecules based on knowledge of the laser-pulse characteristics and on an input intermolecular potential. These provide, for a given gas pressure and initial temperature, the orientations of all molecules at all times from which the alignment factor is directly obtained. Comparisons with measurements show that these CMDSs well predict the permanent alignment induced by the laser pulse and its decay with time but, as expected, fail in generating alignment revivals. However, it is shown that introducing a simple requantization procedure in the CMDS “creates” these revivals and that their predicted dissipation decay agrees very well with measured values. The calculations also confirm that, as for linear molecules, the permanent alignment of ethane decays more slowly than the transient revivals. The influence of the intermolecular potential is studied as well as that of the degree of freedom associated with the molecular rotation around the symmetry axis. This reveals that ethane practically behaves as a linear molecule because the intermolecular potential is only weakly sensitive to rotation around the C–C axis.

    更新日期:2018-10-19
  • Fundamental vibration frequency and rotational structure of the first excited vibrational level of the molecular helium ion (He2+)
    J. Chem. Phys. (IF 2.843) Pub Date : 2018-10-17
    Paul Jansen, Luca Semeria, Frédéric Merkt

    The term values of the rotational levels of the first excited vibrational state of the electronic ground state of He2+ with a rotational quantum number N+ ≤ 13 have been determined with an accuracy of 1.2 × 10−3 cm−1 (∼35 MHz) by multichannel-quantum-defect-theory-assisted Rydberg spectroscopy of metastable He2. Comparison of the experimental term values with the most accurate ab initio results for He2+ available in the literature [W.-C. Tung, M. Pavanello, and L. Adamowicz, J. Chem. Phys. 136, 104309 (2012)] reveals inconsistencies between the theoretical and experimental results that increase with increasing rotational quantum numbers. The fundamental vibrational wavenumber of He2+ was determined to be 1628.3832(12) cm−1 by fitting effective molecular constants to the obtained term values.

    更新日期:2018-10-19
  • Accurate potential energy surface of H2S+(X2A″) via extrapolation to the complete basis set limit and its use in dynamics study of S+(D2)+H2(X1Σg+) reaction
    J. Chem. Phys. (IF 2.843) Pub Date : 2018-10-18
    Lulu Zhang, Shoubao Gao, Qingtian Meng, Jie Pan, Yuzhi Song

    The single-sheeted potential energy surface (PES) of H2S+(X 2A′′) is developed based on the ab initio energies calculated by the multi-reference configuration interaction method including the Davidson correction. All the ab initio energies are first calculated using aug-cc-pVQdZ and aug-cc-pV5dZ basis sets, which are then extrapolated to the complete basis set (CBS) limit. A switching function is developed to model the transition of S+D2 to S+S4. The many-body expansion formalism is employed to obtain the H2S+(X 2A′′) PES by fitting such CBS energies and the root-mean square derivation is 0.0367 eV. The topographical features of the present PES are examined in detail, which are well consistent with previous studies. The quasiclassical trajectory method is subsequently utilized to study the S+D2+H2(X1Σg+) → SH+(X 3Σ−)+H(S2) reaction. The capture time, integral cross sections, and rovibrational distributions are calculated. By examining the capture time, it can be concluded that the title reaction is mainly controlled by the indirect mechanism for lower collision energies, while the direct and indirect mechanisms coexist and the latter plays a dominant role for higher collision energies.

    更新日期:2018-10-19
  • High-order harmonic generation from 2D periodic potentials in circularly and bichromatic circularly polarized laser fields
    J. Chem. Phys. (IF 2.843) Pub Date : 2018-10-18
    Guang-Rui Jia, Xin-Qiang Wang, Tao-Yuan Du, Xiao-Huan Huang, Xue-Bin Bian

    We studied the high-order harmonic generation (HHG) from 2D solid materials in circularly and bichromatic circularly polarized laser fields numerically by simulating the dynamics of single-active-electron processes in 2D periodic potentials. Contrary to the absence of HHG in the atomic case, circular HHGs below the bandgap with different helicities are produced from intraband transitions in solids with C4 symmetry driven by circularly polarized lasers. Harmonics above the bandgap are elliptically polarized due to the interband transitions. High-order elliptically polarized harmonics can be generated efficiently by both co-rotating and counter-rotating bicircular mid-infrared lasers. The cutoff energy, ellipticity, phase, and intensity of the harmonics can be tuned by the control of the relative phase difference between the 1ω and 2ω fields in bicircularly polarized lasers, which can be utilized as an ultrafast optical tool to image the structure of solids.

    更新日期:2018-10-19
  • Fundamental understanding of chemical processes in extreme ultraviolet resist materials
    J. Chem. Phys. (IF 2.843) Pub Date : 2018-10-19
    Oleg Kostko, Bo Xu, Musahid Ahmed, Daniel S. Slaughter, D. Frank Ogletree, Kristina D. Closser, David G. Prendergast, Patrick Naulleau, Deirdre L. Olynick, Paul D. Ashby, Yi Liu, William D. Hinsberg, Gregory M. Wallraff

    New photoresists are needed to advance extreme ultraviolet (EUV) lithography. The tailored design of efficient photoresists is enabled by a fundamental understanding of EUV induced chemistry. Processes that occur in the resist film after absorption of an EUV photon are discussed, and a new approach to study these processes on a fundamental level is described. The processes of photoabsorption, electron emission, and molecular fragmentation were studied experimentally in the gas-phase on analogs of the monomer units employed in chemically amplified EUV resists. To demonstrate the dependence of the EUV absorption cross section on selective light harvesting substituents, halogenated methylphenols were characterized employing the following techniques. Photoelectron spectroscopy was utilized to investigate kinetic energies and yield of electrons emitted by a molecule. The emission of Auger electrons was detected following photoionization in the case of iodo-methylphenol. Mass-spectrometry was used to deduce the molecular fragmentation pathways following electron emission and atomic relaxation. To gain insight on the interaction of emitted electrons with neutral molecules in a condensed film, the fragmentation pattern of neutral gas-phase molecules, interacting with an electron beam, was studied and observed to be similar to EUV photon fragmentation. Below the ionization threshold, electrons were confirmed to dissociate iodo-methylphenol by resonant electron attachment.

    更新日期:2018-10-19
  • Femtosecond laser induced Coulomb explosion imaging of aligned OCS oligomers inside helium nanodroplets
    J. Chem. Phys. (IF 2.843) Pub Date : 2018-10-19
    James D. Pickering, Benjamin Shepperson, Lars Christiansen, Henrik Stapelfeldt

    Dimers and trimers of carbonyl sulfide (OCS) molecules embedded in helium nanodroplets are aligned by a linearly polarized 160 ps long moderately intense laser pulse and Coulomb exploded with an intense 40 fs long probe pulse in order to determine their structures. For the dimer, recording of 2D images of OCS+ and S+ ions and covariance analysis of the emission directions of the ions allow us to conclude that the structure is a slipped-parallel shape similar to the structure found for gas phase dimers. For the trimer, the OCS+ ion images and the corresponding covariance maps reveal the presence of a barrel-shaped structure (as in the gas phase) but also other structures not present in the gas phase, most notably a linear chain structure.

    更新日期:2018-10-19
  • Halogen bond in the water adduct of chloropentafluoroethane revealed by rotational spectroscopy
    J. Chem. Phys. (IF 2.843) Pub Date : 2018-10-19

    The rotational spectrum of the chloropentafluoroethane-water complex has been investigated by pulsed jet Fourier transform microwave spectroscopy. Experimental rotational and quadrupole coupling constants of five isotopologues imply that the two subunits are held together by an almost linear C–Cl⋯O halogen bond. Water lies effectively in the symmetric plane of C2F5Cl and undergoes a plausible free internal rotation. The experimental structure and dissociation energies of the complex are also deduced.

    更新日期:2018-10-19
  • Frequency measurements and self-broadening of sub-Doppler transitions in the v1 + v3 band of C2H2
    J. Chem. Phys. (IF 2.843) Pub Date : 2018-10-19
    Sylvestre Twagirayezu, Gregory E. Hall, Trevor J. Sears

    Frequency comb-referenced measurements of sub-Doppler laser saturation dip absorption lines in the v1 + v3 band of acetylene near 1.5 μm are reported. These measurements include transitions involving higher rotational levels than previously frequency measured in this band. The accuracy of the measured frequencies is typically better than 10 kHz. Measurements of the observed sub-Doppler line widths as a function of pressure showed that the self-pressure-broadening coefficients are about 3.5 times larger than those derived from conventional pressure broadening of unsaturated Doppler-limited spectra. This is attributed to the contribution of velocity-changing collisions to the total dephasing rate in the low pressure sub-Doppler measurements. At higher pressures, when the homogeneous broadening becomes comparable to the typical Doppler shift per elastic collision, the velocity changing collisions cease to contribute significantly to the incremental pressure broadening. A time-dependent soft collision model is developed to illustrate the transition between low and high pressure regimes of sub-Doppler pressure-broadening.

    更新日期:2018-10-19
  • Configurational entropy of polydisperse supercooled liquids
    J. Chem. Phys. (IF 2.843) Pub Date : 2018-10-15
    Misaki Ozawa, Giorgio Parisi, Ludovic Berthier

    We propose a computational method to measure the configurational entropy in generic polydisperse glass-formers. In particular, our method resolves issues related to the diverging mixing entropy term due to a continuous polydispersity. The configurational entropy is measured as the difference between the well-defined fluid entropy and a more problematic glass entropy. We show that the glass entropy can be computed by a simple generalisation of the Frenkel-Ladd thermodynamic integration method, which takes into account permutations of the particle diameters. This approach automatically provides a physically meaningful mixing entropy for the glass entropy and includes contributions that are not purely vibrational. The proposed configurational entropy is thus devoid of conceptual and technical difficulties due to continuous polydispersity, while being conceptually closer, but technically simpler, than alternative free energy approaches.

    更新日期:2018-10-19
  • Hidden order in amorphous structures: Extraction of nearest neighbor networks of amorphous Nd–Fe alloys with Gabriel graph analyses
    J. Chem. Phys. (IF 2.843) Pub Date : 2018-10-19
    Asako Terasawa, Yoshihiro Gohda

    Using the scheme of Delaunay and Gabriel graphs, we analyzed the amorphous structures of computationally created Nd–Fe alloys for several composition ratios based on melt quench simulations with finite temperature first-principles molecular dynamics. By the comparison of the radial distribution functions of the whole system and those derived from the Delaunay and Gabriel graphs, it was shown that the Gabriel graphs represent the first nearest neighbor networks well in the examined amorphous systems. From the Gabriel graph analyses, we examined the coordination structures of amorphous Nd–Fe alloys statistically. We found that the ranges of distributions of coordination numbers are wider at the lower Nd composition ratios. The angular distributions among three adjacent atoms were also analyzed, and it was found that the steeper the angular distributions become the higher the Nd composition ratios are. These features mean that the orders in the amorphous system become stronger as the Nd ratio increases, which corresponds to the appearance of crystalline grain boundary phases at high Nd composition ratios [T. T. Sasaki et al., Acta Mater. 115, 269–277 (2016)].

    更新日期:2018-10-19
  • Experimental densities of subcooled deuterium oxide at pressures up to 160 MPa
    J. Chem. Phys. (IF 2.843) Pub Date : 2018-10-19
    Raffaella Romeo, Simona Lago, P. Alberto Giuliano Albo

    In this work, the experimental results of deuterium oxide density at high pressure and in a wide range of temperatures, by means of the pseudo-isochoric method, are presented. A specific stainless steel cell was devised to be used as a pycnometer and filled with variable mass of heavy water. The latter was measured by weighing with an analytical balance and using the substitution method. The volume of the pycnometric cell was measured by the gravimetric method and corrected for the effect of temperature and pressure. Each measurement cycle was performed at constant mass, measuring pressure as a function of temperature at equilibrium. From the mass and volume values, density was calculated according to its definition. Heavy water density was measured for temperatures down to 253 K and for pressures up to 163 MPa, thus both in stable and supercooled metastable states. All terms contributing to the uncertainty in determining the volume and the mass were considered, obtaining an expanded relative uncertainty of deuterium oxide density of 0.04%.

    更新日期:2018-10-19
  • Nonlinear optical response of a gold surface in the visible range: A study by two-color sum-frequency generation spectroscopy. III. Simulations of the experimental SFG intensities
    J. Chem. Phys. (IF 2.843) Pub Date : 2018-10-15
    B. Busson, L. Dalstein

    We model the amplitude line shape and absolute phase of the infrared-visible sum-frequency signals produced by a thiolated polycrystalline gold surface as a function of the visible wavelength. We follow two hypotheses: in the interband scenario, the resonant features are attributed to interband transitions, whereas in the effective surface state scenario, they stem mostly from the excitation of surface transitions. We find that both scenarios lead to a satisfactory account of the experimental data and that only free electrons may spill out of the gold bulk, as expected. For the interband scenario, the balance between free and bound electron contributions to sum-frequency generation has to be adjusted to fit the data. The surface transitions are shown to take their origin inside gold and we investigate the surface states involved in such transitions, with a comparison to the silver surfaces. We finally provide a work program dedicated to discriminate between the two scenarios.

    更新日期:2018-10-19
  • Photoluminescence, infrared, and Raman spectra of co-doped Si nanoparticles from first principles
    J. Chem. Phys. (IF 2.843) Pub Date : 2018-10-18
    Bálint Somogyi, Emilie Bruyer, Adam Gali

    Co-doped silicon nanoparticles (NPs) are promising for the realization of novel biological and optoelectronic applications. Despite the scientific and technological interest, the structure of heavily co-doped Si NPs is still not very well understood. By means of first principles simulations, various spectroscopic quantities can be computed and compared to the corresponding experimental data. In this paper, we demonstrate that the calculated infrared spectra, photoluminescence spectra, and Raman spectra can provide valuable insights into the atomistic structure of co-doped Si NPs.

    更新日期:2018-10-19
  • Perspective: Crossing the Widom line in no man’s land: Experiments, simulations, and the location of the liquid-liquid critical point in supercooled water
    J. Chem. Phys. (IF 2.843) Pub Date : 2018-10-08
    Nicholas J. Hestand, J. L. Skinner

    The origin of liquid water’s anomalous behavior continues to be a subject of interest and debate. One possible explanation is the liquid-liquid critical point hypothesis, which proposes that supercooled water separates into two distinct liquids at low temperatures and high pressures. According to this hypothesis, liquid water’s anomalies can be traced back to the critical point associated with this phase separation. If such a critical point actually exists, it is located in a region of the phase diagram known as No Man’s Land (NML), where it is difficult to characterize the liquid using conventional experimental techniques due to rapid crystallization. Recently, however, experimentalists have managed to explore NML near the proposed location of the Widom line (i.e., the Kanno-Angell line), thereby providing valuable information concerning the liquid-liquid critical point hypothesis. In this perspective, we analyze these experimental results, in conjunction with molecular dynamics simulations based on the E3B3 water model and discuss their implications for the validity of the liquid-liquid critical point hypothesis and the possible location of water’s second critical point.

    更新日期:2018-10-14
  • Communication: The pole structure of the dynamical polarizability tensor in equation-of-motion coupled-cluster theory
    J. Chem. Phys. (IF 2.843) Pub Date : 2018-10-08
    Kaushik D. Nanda, Anna I. Krylov, Jürgen Gauss

    In this letter, we investigate the pole structure of dynamical polarizabilities computed within the equation-of-motion coupled-cluster (EOM-CC) theory. We show, both theoretically and numerically, that approximate EOM-CC schemes such as, for example, the EOM-CC singles and doubles model exhibit an incorrect pole structure in which the poles that reflect the excitations from the target state (i.e., the EOM-CC state) are supplemented by artificial poles due to excitations from the CC reference state. These artificial poles can be avoided by skipping the amplitude response and reverting to a sum-over-states formulation. While numerical results are generally in favor of such a solution, its major drawback is that this scheme violates size extensivity.

    更新日期:2018-10-14
  • Communication: Nucleation rates of supersaturated aqueous NaCl using a polarizable force field
    J. Chem. Phys. (IF 2.843) Pub Date : 2018-10-08
    Hao Jiang, Pablo G. Debenedetti, Athanassios Z. Panagiotopoulos

    In this work, we use molecular dynamics simulations with a polarizable force field, namely, the modified AH/BK3 model [J. Kolafa, J. Chem. Phys. 145, 204509 (2016)], in combination with the forward flux sampling technique, to calculate the rates of homogeneous nucleation of NaCl from supersaturated aqueous solutions at 298 K and 1 bar. A non-polarizable model that reproduces the experimental equilibrium solubility {AH/TIP4P-2005 of Benavides et al. [J. Chem. Phys. 147, 104501 (2017)]} is also used for comparison. Nucleation rates calculated from the polarizable force field are found to be in good agreement with experimental measurements, while the non-polarizable model severely underestimates the nucleation rates. These results, in combination with our earlier study of a different non-polarizable force field [H. Jiang et al., J. Chem. Phys. 148, 044505 (2018)], lead to the conclusion that nucleation rates are sensitive to the details of force fields, and a good representation of nucleation rates may not be feasible using available non-polarizable force fields, even if these reproduce the equilibrium salt solubility. Inclusion of polarization could be important for an accurate prediction of nucleation rates in salt solutions.

    更新日期:2018-10-14
  • Communication: Nickel hydroxide as an exceptional deviation from the quantum size effect
    J. Chem. Phys. (IF 2.843) Pub Date : 2018-10-11
    Michael Nagli, Maytal Caspary Toroker

    The quantum size effect is a well-known fundamental scientific phenomenon. Due to quantum confinement, downscaling a system to small sizes should increase the bandgap of a solid state material. However, in this work, we present an exception: monolayers of nickel hydroxide have smaller bandgaps than their bulk analogues, due to the surface states appearing at energies within the bandgap region. Our findings are obtained by several state-of-the-art first principles calculations.

    更新日期:2018-10-14
  • Even-handed subsystem selection in projection-based embedding
    J. Chem. Phys. (IF 2.843) Pub Date : 2018-10-08
    Matthew Welborn, Frederick R. Manby, Thomas F. MillerIII

    Projection-based embedding offers a simple framework for embedding correlated wavefunction methods in density functional theory. Partitioning between the correlated wavefunction and density functional subsystems is performed in the space of localized molecular orbitals. However, during a large geometry change—such as a chemical reaction—the nature of these localized molecular orbitals, as well as their partitioning into the two subsystems, can change dramatically. This can lead to unphysical cusps and even discontinuities in the potential energy surface. In this work, we present an even-handed framework for localized orbital partitioning that ensures consistent subsystems across a set of molecular geometries. We illustrate this problem and the even-handed solution with a simple example of an SN2 reaction. Applications to a nitrogen umbrella flip in a cobalt-based CO2 reduction catalyst and to the binding of CO to Cu clusters are presented. In both cases, we find that even-handed partitioning enables chemically accurate embedding with modestly sized embedded regions for systems in which previous partitioning strategies are problematic.

    更新日期:2018-10-14
  • Anharmonic vibrational spectroscopy of polycyclic aromatic hydrocarbons (PAHs)
    J. Chem. Phys. (IF 2.843) Pub Date : 2018-10-08
    Giacomo Mulas, Cyril Falvo, Patrick Cassam-Chenaï, Christine Joblin

    While powerful techniques exist to accurately account for anharmonicity in vibrational molecular spectroscopy, they are computationally very expensive and cannot be routinely employed for large species and/or at non-zero vibrational temperatures. Motivated by the study of Polycyclic Aromatic Hydrocarbon (PAH) emission in space, we developed a new code, which takes into account all modes and can describe all infrared transitions including bands becoming active due to resonances as well as overtone, combination, and difference bands. In this article, we describe the methodology that was implemented and discuss how the main difficulties were overcome, so as to keep the problem tractable. Benchmarking with high-level calculations was performed on a small molecule. We carried out specific convergence tests on two prototypical PAHs, pyrene (C16H10) and coronene (C24H12), aiming at optimising tunable parameters to achieve both acceptable accuracy and computational costs for this class of molecules. We then report the results obtained at 0 K for pyrene and coronene, comparing the calculated spectra with available experimental data. The theoretical band positions were found to be significantly improved compared to harmonic density functional theory calculations. The band intensities are in reasonable agreement with experiments, the main limitation being the accuracy of the underlying calculations of the quartic force field. This is a first step toward calculating moderately high-temperature spectra of PAHs and other similarly rigid molecules using Monte Carlo sampling.

    更新日期:2018-10-14
  • Independent amplitude approximations in coupled cluster valence bond theory: Incorporation of 3-electron-pair correlation and application to spin frustration in the low-lying excited states of a ferredoxin-type tetrametallic iron-sulfur cluster
    J. Chem. Phys. (IF 2.843) Pub Date : 2018-10-08
    David W. Small, Martin Head-Gordon

    Coupled cluster valence bond (CCVB) is a simple electronic structure method based on a perfect pairing (PP) reference with 2-pair recouplings for strong electron correlation problems. CCVB is spin-pure, size-consistent, and can exactly (in its active space) separate any molecule into atoms for which unrestricted Hartree-Fock (UHF) at dissociation is the sum of the ground state UHF energies of the atoms. However CCVB is far from a complete description of strong correlations. Its first failure to exactly describe spin-recouplings arises at the level of 3 electron pairs, such as the recoupling of 3 triplet oxygen atoms in the dissociation of singlet ozone. Such situations are often associated with spin frustration. To address this limitation, an extension of CCVB, termed CCVB+i3, is reported here that includes an independent (i) amplitude approximation to the 3-pair recouplings. CCVB+i3 thereby has the same basic computational requirements as those of CCVB, which has previously been shown to be an efficient method. CCVB+i3 correctly separates molecules that CCVB cannot. As a by-product, an independent 2-pair amplitude approximation to CCVB, called PP+i2, is also defined. Remarkably, PP+i2 can also correctly separate systems that CCVB cannot. CCVB+i3 is validated on the symmetric dissociation of D3h ozone. CCVB+i3 is then used to explore the role of 3-pair recouplings in an [Fe4S4(SCH3)4]2− cluster that has been used to model the iron-sulfur core of [Fe4S4] ferredoxins. Using localized PP orbitals, such recouplings are demonstrated to be large in some low-lying singlet excited states of the cluster. Significant 3 pair recoupling amplitudes include the usual triangular motif associated with spin frustration and other geometric arrangements of the 3 entangled pairs across the 4 iron centers.

    更新日期:2018-10-14
  • Dynamic correlation for non-orthogonal reference states: Improved perturbational and variational methods
    J. Chem. Phys. (IF 2.843) Pub Date : 2018-10-08
    Sven Kähler, Jeppe Olsen

    The use of non-orthogonal orbitals allows the construction and use of more compact wave functions than offered by standard methods using orthogonal molecular orbitals; in particular, for molecules containing partly occupied atomic orbitals as present, for example, in transition metal complexes. With the purpose of developing efficient dynamic correlation methods, we discuss several new internal correlation methods employing a reference state containing non-orthogonal active orbitals. The non-orthogonal internally contracted perturbation theory approach is improved in several directions. The major improvements are the use of the Dyall Hamiltonian including two-electron interactions within the active space as the zero-order operator, the calculation of third-order energy-corrections, and the inclusion of excitations in the space of active orbitals. The latter improvement corrects for the use of an incomplete reference state. The improvements are tested for the nitrogen molecule and the challenging chromium dimer. The combined use of the improved zero-order Hamiltonian and the inclusion of active space excitations allow us to obtain potential curves for the chromium dimer that are close to those obtained using the larger complete active space reference wave function.

    更新日期:2018-10-14
  • Orbital-free approximations to the kinetic-energy density in exchange-correlation MGGA functionals: Tests on solids
    J. Chem. Phys. (IF 2.843) Pub Date : 2018-10-08
    Fabien Tran, Péter Kovács, Leila Kalantari, Georg K. H. Madsen, Peter Blaha

    A recent study of Mejia-Rodriguez and Trickey [Phys. Rev. A 96, 052512 (2017)] showed that the deorbitalization procedure (replacing the exact Kohn-Sham kinetic-energy density by an approximate orbital-free expression) applied to exchange-correlation functionals of the meta-generalized gradient approximation (MGGA) can lead to important changes in the results for molecular properties. For the present work, the deorbitalization of MGGA functionals is further investigated by considering various properties of solids. It is shown that depending on the MGGA, common orbital-free approximations to the kinetic-energy density can be sufficiently accurate for the lattice constant, bulk modulus, and cohesive energy. For the bandgap, calculated with the modified Becke-Johnson MGGA potential, the deorbitalization has a larger impact on the results.

    更新日期:2018-10-14
  • Bethe–Salpeter correlation energies of atoms and molecules
    J. Chem. Phys. (IF 2.843) Pub Date : 2018-10-09
    Christof Holzer, Xin Gui, Michael E. Harding, Georg Kresse, Trygve Helgaker, Wim Klopper

    A variety of approaches are presented for the computation of atomic and molecular correlation energies based on the Bethe–Salpeter equation in the framework of the adiabatic-connection fluctuation–dissipation theorem. The performance of the approaches is assessed by computing the total energies of the atoms H—Ne and the atomization energies of the high-accuracy extrapolated ab initio thermochemistry set of small molecules as well as by determining the bond lengths and harmonic vibrational frequencies of the metal monoxides MO with M=Ca—Zn.

    更新日期:2018-10-14
  • Permutation invariant polynomial neural network approach to fitting potential energy surfaces. IV. Coupled diabatic potential energy matrices
    J. Chem. Phys. (IF 2.843) Pub Date : 2018-10-09
    Changjian Xie, Xiaolei Zhu, David R. Yarkony, Hua Guo

    A machine learning method is proposed for representing the elements of diabatic potential energy matrices (PEMs) with high fidelity. This is an extension of the so-called permutation invariant polynomial-neural network (PIP-NN) method for representing adiabatic potential energy surfaces. While for one-dimensional irreducible representations the diagonal elements of a diabatic PEM are invariant under exchange of identical nuclei in a molecular system, the off-diagonal elements require special symmetry consideration, particularly in the presence of a conical intersection. A multiplicative factor is introduced to take into consideration the particular symmetry properties while maintaining the PIP-NN framework. We demonstrate here that the extended PIP-NN approach is accurate in representing diabatic PEMs, as evidenced by small fitting errors and by the reproduction of absorption spectra and product branching ratios in both H2O(X̃/B̃) and NH3(X̃/Ã) non-adiabatic photodissociation.

    更新日期:2018-10-14
  • Semiclassical tunneling splittings for arbitrary vibrational states in multidimensional double wells
    J. Chem. Phys. (IF 2.843) Pub Date : 2018-10-09
    Kenneth G. Kay

    A semiclassical theory developed in a previous paper [K. G. Kay, Phys. Rev. A 96, 042116 (2017)] is applied to calculate tunneling splittings for arbitrary vibrational states of model two-dimensional double-well systems. Cases in which the classical dynamics for the wells is chaotic, mixed, and regular are considered. A perturbative treatment, based on the condition of small tunneling amplitudes, is found to be sufficiently accurate for the cases studied and is applied for most of the calculations. Treatments that approximate certain imaginary-time trajectories in the classically forbidden region by linearization about a variety of judiciously selected reference trajectories yield good results for all systems treated. These calculations can be greatly simplified by approximating all imaginary-time trajectories as linearizations about a single reference trajectory. A simple way to determine optimal reference trajectories for this purpose is presented. It is found that their use yields splittings of satisfactory accuracy for the cases studied.

    更新日期:2018-10-14
  • A local tensor that unifies kinetic energy density and vorticity in density functional theory
    J. Chem. Phys. (IF 2.843) Pub Date : 2018-10-10
    Sangita Sen, Erik I. Tellgren

    We present a kinetic energy tensor that unifies a scalar kinetic energy density commonly used in meta-generalized gradient approximation functionals and the vorticity density that appears in paramagnetic current-density-functional theory. Both types of functionals can thus be subsumed as special cases of a novel functional form that is naturally placed on the third rung of Jacob’s ladder. Moreover, the kinetic energy tensor is related to the exchange hole curvature, is gauge invariant, and has very clearcut N-representability conditions. The latter conditions enable the definition of an effective number of non-negligible orbitals. Whereas quantities such as the electron localization function can discriminate effective one-orbital regions from other regions, the present kinetic energy tensor can discriminate between one-, two-, three-, and four-or-more orbital regions.

    更新日期:2018-10-14
  • Ewald sum for hydrodynamic interactions of rigid spherical microswimmers
    J. Chem. Phys. (IF 2.843) Pub Date : 2018-10-11
    Tapan Chandra Adhyapak, Sara Jabbari-Farouji

    We derive the Ewald sum decomposition of the grand mobility tensor which captures the hydrodynamic interactions in an infinite suspension of rigid spherical microswimmers. The grand mobility tensor connects the motion of an individual swimmer to the active and passive forces and torques acting on all the swimmers, and it is calculated based on a minimal microswimmer model incorporating the swimmers’ finite body size. Our results have direct applications to the Stokesian dynamics simulations of an infinite suspension of rigid-bodied microswimmers. They also provide a platform to develop more advanced methods such as particle-mesh-Ewald-sum and accelerated Stokesian dynamics simulations.

    更新日期:2018-10-14
  • Statistical efficiency of methods for computing free energy of hydration
    J. Chem. Phys. (IF 2.843) Pub Date : 2018-10-11
    Ahmet Yildirim, Tsjerk A. Wassenaar, David van der Spoel

    The hydration free energy (HFE) is a critical property for predicting and understanding chemical and biological processes in aqueous solution. There are a number of computational methods to derive HFE, generally classified into the equilibrium or non-equilibrium methods, based on the type of calculations used. In the present study, we compute the hydration free energies of 34 small, neutral, organic molecules with experimental HFE between +2 and −16 kcal/mol. The one-sided non-equilibrium methods Jarzynski Forward (JF) and Backward (JB), the two-sided non-equilibrium methods Jarzynski mean based on the average of JF and JB, Crooks Gaussian Intersection (CGI), and the Bennett Acceptance Ratio (BAR) are compared to the estimates from the two-sided equilibrium method Multistate Bennett Acceptance Ratio (MBAR), which is considered as the reference method for HFE calculations, and experimental data from the literature. Our results show that the estimated hydration free energies from all the methods are consistent with MBAR results, and all methods provide a mean absolute error of ∼0.8 kcal/mol and root mean square error of ∼1 kcal for the 34 organic molecules studied. In addition, the results show that one-sided methods JF and JB result in systematic deviations that cannot be corrected entirely. The statistical efficiency ε of the different methods can be expressed as the one over the simulation time times the average variance in the HFE. From such an analysis, we conclude that ε(MBAR) > ε(BAR) ≈ ε(CGI) > ε(JX), where JX is any of the Jarzynski methods. In other words, the non-equilibrium methods tested here for the prediction of HFE have lower computational efficiency than the MBAR method.

    更新日期:2018-10-14
  • An efficient first principles method for molecular pump-probe NEXAFS spectra: Application to thymine and azobenzene
    J. Chem. Phys. (IF 2.843) Pub Date : 2018-10-11
    Christopher Ehlert, Markus Gühr, Peter Saalfrank

    Pump-probe near edge X-ray absorption fine structure (PP-NEXAFS) spectra of molecules offer insight into valence-excited states, even if optically dark. In PP-NEXAFS spectroscopy, the molecule is “pumped” by UV or visible light enforcing a valence excitation, followed by an X-ray “probe” exciting core electrons into (now) partially empty valence orbitals. Calculations of PP-NEXAFS have so far been done by costly, correlated wavefunction methods which are not easily applicable to medium-sized or large molecules. Here we propose an efficient, first principles method based on density functional theory in combination with the transition potential and ΔSCF methodology (TP-DFT/ΔSCF) to compute molecular ground state and PP-NEXAFS spectra. We apply the method to n → π* pump/O-K-edge NEXAFS probe spectroscopy of thymine (for which both experimental and other theoretical data exist) and to n → π* or π → π* pump/N-K-edge NEXAFS probe spectroscopies of trans- and cis-azobenzene.

    更新日期:2018-10-14
  • Enhanced sampling and free energy calculations with hybrid functionals and plane waves for chemical reactions
    J. Chem. Phys. (IF 2.843) Pub Date : 2018-10-12
    Sagarmoy Mandal, Jayashrita Debnath, Bernd Meyer, Nisanth N. Nair

    Plane wave basis sets offer many advantages in ab initio molecular dynamics due to their efficiency and simplicity. In combination with hybrid density functionals, they become computationally expensive due to the evaluation of the Hartree-Fock exchange energy. The computational cost can be significantly reduced by screening the Kohn-Sham orbital products after localizing the orbitals in real space. However, such a procedure introduces apparent errors in the wavefunctions and nuclear forces resulting in unstable dynamics. It is shown here that a noise-stabilized dynamics approach can overcome this problem and at the same time permits using insufficiently converged wavefunctions for evaluating atomic forces. In this way, we achieve significant speed up even for a small system containing about 100 atoms. After benchmarking the accuracy and efficiency of this approach, we use it in combination with well-sliced metadynamics to compute the free energy barrier of formamide hydrolysis in alkaline aqueous medium. These results provide insight into the error of the Perdew-Burke-Ernzerhof functional in predicting the free energy barrier for hydrolysis reactions in water.

    更新日期:2018-10-14
  • Hydration of CH3HgOH and CH3HgCl compared to HgCl2, HgClOH, and Hg(OH)2: A DFT microsolvation cluster approach
    J. Chem. Phys. (IF 2.843) Pub Date : 2018-10-08
    Jorge I. Amaro-Estrada, Jorge Hernández-Cobos, Humberto Saint-Martin, Laurent Maron, Alejandro Ramírez-Solís

    We address the aqueous microsolvation of the CH3HgCl and CH3HgOH molecules using a stepwise hydration scheme including up to 33 water molecules and compare our results with the previously studied HgCl2, HgClOH, and Hg(OH)2 complexes. Optimized geometries and Gibbs free energies were obtained at the B3PW91/aug-RECP(Hg)-6-31G(d,p) level. At least 33 water molecules were required to build the first solvation shell around both methylmercury compounds. Optimized geometries were found having favorable interactions of water molecules with Hg, Cl, and the OH moiety. Born-Oppenheimer molecular dynamics simulations were performed on the largest CH3HgX(X = Cl, OH)–(H2O)33 clusters at the same level of theory. Born-Oppenheimer molecular dynamics simulations at T = 300 K (ca. 0.62 kcal/mol) revealed the presence of configurations with hydrogen-bonded networks that include the OH moiety in CH3HgOH and exclude both the Hg and Cl in CH3HgCl, favoring a clathrate-type structure around the methyl moiety. The comparison to the microsolvated HgClOH, Hg(OH)2, and HgCl2 molecules showed that, in all cases, the water molecules easily move away from Cl, thus supporting the idea that HgCl2 behaves as a non-polar solute. The theoretical (LIII edge) X-ray absorption near edge structure spectra are obtained and found in good agreement with experimental data, especially for the CH3HgCl species.

    更新日期:2018-10-14
  • Photoionization of the iodine 3d, 4s, and 4p orbitals in methyl iodide
    J. Chem. Phys. (IF 2.843) Pub Date : 2018-10-08
    Ruaridh Forbes, Alberto De Fanis, Cédric Bomme, Daniel Rolles, Stephen T. Pratt, Ivan Powis, Nicholas A. Besley, Marc Simon, Saikat Nandi, Aleksandar R. Milosavljević, Christophe Nicolas, John D. Bozek, Jonathan G. Underwood, David M. P. Holland

    Ionization of the I 3d, 4s, and 4p orbitals in methyl iodide (CH3I) has been studied by using synchrotron radiation to measure the total ion yield and by recording photoelectron spectra with linearly polarized radiation in two polarization orientations. The complete photoelectron spectrum of CH3I has been recorded at several photon energies, and bands due to the C 1s, I 3d, 4s, 4p, and 4d atomic-like orbitals, as well as the molecular orbitals, have been observed and assigned. In the vicinity of the I 3d5/2 and 3d3/2 ionization thresholds at 626.8 and 638.3 eV, respectively, the ion yield displays weak structure in the pre-edge region due to transitions into valence or Rydberg states, and, at higher energies, a shoulder and a broad maximum attributed to the I 3d5/2 → εf and the I 3d3/2 → εf shape resonances, respectively. The absorption spectrum calculated using time-dependent density functional theory, within the Tamm-Dancoff approximation, has allowed assignments to be proposed for the valence and Rydberg states. The Stieltjes imaging technique has been used to simulate the absorption spectrum above the ionization threshold and indicates that transitions into the f(l = 3) continuum channel dominate. This conclusion has been corroborated by a Continuum Multiple Scattering–Xα (CMS–Xα) calculation. The asymmetric broadening of the photoelectron bands associated with the I 3d orbital, due to post collision interaction, is taken into account in our experimental analysis. Experimentally derived photoelectron anisotropy parameters for the I 3d orbital are in good agreement with the theoretical predictions obtained with the CMS–Xα approach. The I 3d shake-up/shake-off photoelectron spectrum has been recorded, and assignments have been proposed for several of the satellites. The M4N45N45 and M5N45N45 Auger electron yields have been measured, and that for the M5N45N45 decay exhibits a maximum due to interchannel coupling between the 3d5/2 and 3d3/2 continua. The photoelectron band associated with the I 4p orbital has an unusual appearance. Based upon previous theoretical work for the analogous Xe 4p orbital, it appears that the initial I 4p−1 hole state decays rapidly through Coster-Kronig and super-Coster-Kronig transitions. This leads to a redistribution of the spectral intensity associated with the I 4p orbital and results in a photoelectron spectrum containing a single structured band together with an extended continuum. Another continuum is observed on the high binding energy side of the peak due to the 4s orbital, and we assign this to super-Coster-Kronig transitions into the 4p-14d−1 continuum.

    更新日期:2018-10-14
  • Sub-Doppler slit jet infrared spectroscopy of astrochemically relevant cations: The NH stretching mode in ND3H+
    J. Chem. Phys. (IF 2.843) Pub Date : 2018-10-08
    Chih-Hsuan Chang, Preston G. Scrape, David J. Nesbitt

    High-resolution rotationally resolved spectra of the N–H stretch vibrational mode (ν1) of jet-cooled ND3H+ ions are collected and analyzed in a sub-Doppler slit-jet infrared spectrometer. The isotopomeric ammonium ions are generated by proton transfer from H3+ to ND3 in a discharge of an ND3/H2 gas mixture, whereby the slit jet expansion cools the nascent ND3H+ ions into lower rotational states. Rotational assignments are confirmed by four-line combination differences that agree to within the spectrometer precision (9 MHz). Based on precision two-line ground-state combination differences and a symmetric top Hamiltonian, the B, DJ, and DJK rotational constants for the ground vibrational state of ND3H+ are determined with high precision for the first time. Approximate rotational constants for the ν1 excited state are also determined, with a band origin at 3316.8425(19) cm−1 and in remarkable (∼0.1 cm−1) agreement with high level anharmonic theoretical predictions by Guo and co-workers [J. Phys. Chem. A, 120, 2185 (2016)]. Our results allow us to predict several low-J pure rotational transitions of ND3H+, which we hope will support future studies of this important ion in laboratory and astronomical rotational spectroscopy.

    更新日期:2018-10-14
  • Torsional splitting and the four-fold barrier to internal rotation: The rotational spectra of vinylsulfur pentafluoride
    J. Chem. Phys. (IF 2.843) Pub Date : 2018-10-08
    W. Orellana, Susanna L. Stephens, Wallace C. Pringle, Peter Groner, Stewart E. Novick, S. A. Cooke

    Vinylsulfur pentafluoride (VSPF), a molecule with a four-fold internal rotor, —SF4, has been studied with high resolution Fourier transform microwave spectroscopy. We believe that this is the first report of resolved four-fold internal rotation. As such, we have presented the tools needed to understand and analyze such a problem. These include debugging the ERHAM computer program necessary to fit the spectra and the free rotor to high barrier correlation diagram necessary to understand the torsional states of the four-fold rotor. The A, E, and B torsional state rotational transitions are well resolved and assigned. Spectroscopic transitions of four isotopologues of VSPF, H2C=CH—SF5, the normal isotopologue, and the singly substituted 34S and 13C isotopologues were measured and assigned. Contrary to expectation, the A torsional state could not be fit with only a semi-rigid Hamiltonian. The barrier to internal rotation, V4, is found to be 227 cm−1. Ab initio calculations at the MP2 aug-cc-pVQZ level of theory and basis set were performed and the results of this calculation are compared to our experimental results.

    更新日期:2018-10-14
  • Photoelectron velocity map imaging spectroscopic and theoretical study of heteronuclear vanadium-nickel carbonyl anions VNi(CO)n− (n = 2-6)
    J. Chem. Phys. (IF 2.843) Pub Date : 2018-10-09
    Qinqin Yuan, Jumei Zhang, Jinghan Zou, Hongjun Fan, Ling Jiang, Hua Xie

    Mass-selected heteronuclear vanadium-nickel carbonyl anions VNi(CO)n− (n = 2-6) were investigated by photoelectron velocity-map imaging spectroscopy and quantum chemical calculations to obtain their chemical bonding and intrinsic electronic structure in the gas phase. The calculated energies (adiabatic detachment energies)/vertical detachment energies (VDEs) match well with experimental values: 1.30/1.49, 1.66/1.95, 2.22/2.48, 2.70/2.89, and 2.95/3.15 eV. The VDE value of VNi(CO)n− increases with an increase of cluster size, implying that the negative electron is stabilized upon the bonding of CO molecules. VNi(CO)2− consists of one bridging carbonyl and one terminal carbonyl, whose feature is different from MNi(CO)2− (M = Sc, Y, La, and Ce) with the involvement of one side-on-bonded carbonyl and one terminal CO carbonyl. The building block composed of three bridging carbonyls is favored for VNi(CO)3−, the structure of which persists up to n = 6. The additional CO ligands are preferentially coordinated in the terminal mode to the Ni atom at n = 4 and then to the V atom at n = 5 and 6. The results obtained in this work would provide a molecular-level understanding about chemisorbed CO molecules on alloy surfaces/interfaces, which is important to understand CO molecule activation processes.

    更新日期:2018-10-14
  • Conformational effect on the almost free internal rotation in 4-hexyn-3-ol studied by microwave spectroscopy and quantum chemistry
    J. Chem. Phys. (IF 2.843) Pub Date : 2018-10-09
    Konrad Eibl, Wolfgang Stahl, Isabelle Kleiner, Ha Vinh Lam Nguyen

    The microwave spectrum of 4-hexyn-3-ol, CH3—C≡C—CH(OH)—CH2CH3, was recorded in the frequency range of 2–26.5 GHz by molecular jet Fourier transform microwave spectroscopy. The conformational analysis based on quantum chemical calculations yielded nine conformers exhibiting C1 symmetry, of which three could be assigned in the experimental spectrum. The propynyl methyl group CH3—C≡C— experiences internal rotation with a very low barrier due to the presence of the cylindrically symmetric —C≡C— group serving as a spacer to the rest of the molecule, which is 7.161 012(7) cm−1, 4.236 5(26) cm−1, and 7.901 6(39) cm−1 for the three assigned conformers, respectively. The spectrum was analyzed with the program XIAM using the combined axis method and the program BELGI-C1 using the rho axis method and a very flexible Hamiltonian which yields fits with root-mean-square deviations within the measurement accuracy.

    更新日期:2018-10-14
  • Probing the structures and bonding of auropolyynes, Au—(C≡C)n—Au− (n = 1–3), using high-resolution photoelectron imaging
    J. Chem. Phys. (IF 2.843) Pub Date : 2018-10-09
    Iker León, Fernando Ruipérez, Jesus M. Ugalde, Lai-Sheng Wang

    We report an investigation of a series of auropolyynes, Au—(C≡C)n—Au− (n = 1–3), using high-resolution photoelectron imaging and ab initio calculations. Vibrationally resolved photoelectron spectra are obtained, allowing the electron affinities of Au—(C≡C)n—Au to be accurately measured as 1.651(1), 1.715(1), and 1.873(1) eV for n = 1–3, respectively. Both the Au—C symmetric stretching and a bending vibrational frequency are observed for each neutral auropolyyne. Theoretical calculations find that the ground state of Au2C2− has a linear acetylenic Au—C≡C—Au− structure, whereas the asymmetric Au—Au—C≡C− structure is a low-lying isomer. However, for Au2C4− and Au2C6−, our calculations show that the asymmetric Au—Au—(C≡C)n− isomers are the global minima and the Au—(C≡C)n—Au− symmetric structures become low-lying isomers. All the asymmetric Au—Au—(C≡C)n− isomers are found computationally to have much higher electron binding energies and are not accessible at the detachment photon energies used in the current study. For neutral Au2C2n, the Au—(C≡C)n—Au auropolyyne structures are found to be the global minima for n = 1–3. The electronic structures and bonding for Au—(C≡C)n—Au (n = 1–3) are compared with the corresponding Au—(C≡C)n and Au—(C≡C)n—H species.

    更新日期:2018-10-14
  • A dinuclear Cu(i)-mediated complex: Theoretical studies of the G2Cu24+ cluster ion
    J. Chem. Phys. (IF 2.843) Pub Date : 2018-10-09
    Guo-Jin Cao

    Recently, the T–Hg(ii)2–A base pair containing two equivalents of Hg(ii) has been prepared and characterized experimentally, which implies that there might exist considerable stable metal-mediated base pairs holding two neighbouring metal centers. Here we report a quantum chemical study on geometries, electronic structures, and bonding of various G2Cu24+ (G = guanine) isomers including one di-copper(i) unit. Different density functional methods [Becke 3-parameter-Lee-Yang-Parr, Perdew−Becke−Ernzerhof, Becke−Perdew, Density Functional Theory with Dispersion Corrections (DFT-D)] assign ambiguous relative energies to these isomers with the singlet and triplet states. High-level ab initio [domain-based local pair natural orbital (DLPNO) coupled-cluster with single and double excitations and DLPNO-coupled-cluster with single, double, and perturbative triple excitations] calculations confirm that the lowest-lying isomer of the G2Cu24+ ion has C2h symmetry with the singlet state and is comparable to the singly and doubly charged homologues (G2Cu2+ and G2Cu22+). The extended transition state (ETS)-natural orbitals for the chemical valence (ETS-NOCV) calculations point out that it has larger instantaneous interaction energy and bond dissociation energy than the corresponding singly and doubly charged complexes due to its relatively stronger attractive energies and weaker Pauli repulsion. The orbital interactions in the quadruply charged cluster chiefly come from Cu24+ ← G⋯G π donations. The results may help the understanding of the bonding properties of other potential metal-base pair complexes with the electron transfer.

    更新日期:2018-10-14
  • A theoretical study of energy transfer in Ar(1S) + SO2(X̃1A′) collisions: Cross sections and rate coefficients for vibrational transitions
    J. Chem. Phys. (IF 2.843) Pub Date : 2018-10-09
    Ramon S. da Silva, Maikel Y. Ballester

    Vibrational transitions, induced by collisions between rare-gas atoms and molecules, play a key role in many problems of interest in physics and chemistry. A theoretical investigation of the translation-to-vibration (T-V) energy transfer process in argon atom and sulfur dioxide molecule collisions is presented here. For such a purpose, the framework of the quasi-classical trajectory (QCT) methodology was followed over the range of translational energies 2 ≤ Etr/kcal mol−1 ≤ 100. A new realistic potential energy surface (PES) for the ArSO2 system was developed using pairwise addition for the four-body energy term within the double many-body expansion. The topological features of the obtained function are compared with a previous one reported by Hippler et al. [J. Phys. Chem. 90, 6158 (1986)]. To test the accuracy of the PES, additional coupled cluster singles and doubles method with a perturbative contribution of connected triples calculations were carried out for the global minimum configuration. From dynamical calculations, the cross sections for the T-V excitation process indicate a barrier-type mechanism due to strong repulsive interactions between SO2 molecules and the Ar atom. Corrections to zero-point energy leakage in QCT were carried out using vibrational energy quantum mechanical threshold of the complex and variations. Rate coefficients and cross sections are calculated for some vibrational transitions using pseudo-quantization approaches of the vibrational energy of products. Main attributes of the title molecular collision are discussed and compared with available information in the literature.

    更新日期:2018-10-14
  • Vacuum ultraviolet excited state dynamics of the smallest ring, cyclopropane. I. A reinterpretation of the electronic spectrum and the effect of intensity borrowing
    J. Chem. Phys. (IF 2.843) Pub Date : 2018-10-12
    Simon P. Neville, Albert Stolow, Michael S. Schuurman

    Cyclopropane, the smallest organic ring compound, exhibits complex spectroscopy and excited state dynamics. In Paper I, we reinterpret the vacuum ultraviolet (VUV) electronic absorption spectrum of cyclopropane via ab initio computation. The first two bands in the VUV spectrum are simulated using wavepacket propagations employing the multiconfigurational time-dependent Hartee method and a newly parameterized linear vibronic coupling Hamiltonian. The parameters of the model Hamiltonian are obtained directly from high level multireference configuration interaction calculations. An analysis of the results, with an emphasis on previously neglected vibronic coupling effects, reveals that these vibronic coupling terms must be included in order to account for strong intensity borrowing effects. This treatment dramatically changes the assignment of much of the VUV spectrum, with intensity borrowing by the optically dark A2′(σ3px/3py) and A1′(σ3px/3py) states from the E′(σ3px/3py) state being found to give rise to almost all the spectral intensities below 8 eV. This is in stark contrast to previous studies, which attributed the first two bands to transitions to the E′(σ3px/3py) state. This highlights the limitations of assigning spectral features based solely on calculated electronic excitation energies and oscillator strengths. Furthermore, we address the significant but infrequently discussed difficulties involved in determining the electronic character of a wavepacket produced in the pump step of ultrafast pump-probe experiments for systems exhibiting strong vibronic coupling.

    更新日期:2018-10-14
  • Vacuum ultraviolet excited state dynamics of the smallest ring, cyclopropane. II. Time-resolved photoelectron spectroscopy and ab initio dynamics
    J. Chem. Phys. (IF 2.843) Pub Date : 2018-10-12
    Michael R. Coates, Martin A. B. Larsen, Ruaridh Forbes, Simon P. Neville, Andrey E. Boguslavskiy, Iain Wilkinson, Theis I. Sølling, Rune Lausten, Albert Stolow, Michael S. Schuurman

    The vacuum-ultraviolet photoinduced dynamics of cyclopropane (C3H6) were studied using time-resolved photoelectron spectroscopy (TRPES) in conjunction with ab initio quantum dynamics simulations. Following excitation at 160.8 nm, and subsequent probing via photoionization at 266.45 nm, the initially prepared wave packet is found to exhibit a fast decay (<100 fs) that is attributed to the rapid dissociation of C3H6 to ethylene (C2H4) and methylene (CH2). The photodissociation process proceeds via concerted ring opening and C–C bond cleavage in the excited state. Ab initio multiple spawning simulations indicate that ring-opening occurs prior to dissociation. The dynamics simulations were subsequently employed to simulate a TRPES spectrum, which was found to be in excellent agreement with the experimental result. On the basis of this agreement, the fitted time constants of 35 ± 20 and 57 ± 35 fs were assigned to prompt (i) dissociation on the lowest-lying excited state, prepared directly by the pump pulse, and (ii) non-adiabatic relaxation from higher-lying excited states that lead to delayed dissociation, respectively.

    更新日期:2018-10-14
  • Self-diffusion coefficient of the square-well fluid from molecular dynamics simulations within the constant force approach
    J. Chem. Phys. (IF 2.843) Pub Date : 2018-10-09
    Alexis Torres-Carbajal, Victor M. Trejos, Luz Adriana Nicasio-Collazo

    We present a systematic study of the self-diffusion coefficient for a fluid of particles interacting via the square-well pair potential by means of molecular dynamics simulations in the canonical (N, V, T) ensemble. The discrete nature of the interaction potential is modeled by the constant force approximation, and the self-diffusion coefficient is determined for several fluid densities at supercritical thermodynamic states. The dependence of the self-diffusion coefficient on the potential range λ is analyzed in the range of 1.1 ≤ λ ≤ 1.5. The obtained simulation results are in agreement with the self-diffusion coefficient predicted by the Enskog method. Additionally, we show that the diffusion coefficient is very sensitive to the potential range λ. Our results for the self-diffusion coefficient times density extrapolate well to the values in the zero-density limit obtained from the Chapman-Enskog theory for dilute gases. The constant force approximation used in this work to model the discrete pair potentials has shown to be an excellent scheme to compute the transport properties of square-well fluids using molecular dynamics simulations. Finally, the simulation results presented here are useful for improving theoretical approaches, such as the Enskog method.

    更新日期:2018-10-14
  • Superconductivity at 3.5 K and/or 7.2 K in potassium-doped triphenylbismuth
    J. Chem. Phys. (IF 2.843) Pub Date : 2018-10-11
    Ren-Shu Wang, Jia Cheng, Xiao-Lin Wu, Hui Yang, Xiao-Jia Chen, Yun Gao, Zhong-Bing Huang

    We develop a two-step synthesis method—ultrasound treatment and low temperature annealing to explore superconductivity in potassium-doped triphenylbismuth, which is composed of one bismuth atom and three phenyl rings. The combination of dc and ac magnetic measurements reveals that one hundred percent of synthesized samples exhibit superconductivity at 3.5 K and/or 7.2 K at ambient pressure. The magnetization hysteresis loops provide a strong piece of evidence of type-II superconductors. It is found that the doped materials crystallize into the triclinic P1 structure, with a mole ratio of 4:1 between potassium and triphenylbismuth. Both the calculated electronic structure and measured Raman spectra indicate that superconductivity is realized by transferring electrons from the K-4s to C-2p orbital. Our study opens an encouraging window for the search of organic superconductors in organometallic molecules.

    更新日期:2018-10-14
  • In an ionic liquid, high local friction is determined by the proximity to the charge network
    J. Chem. Phys. (IF 2.843) Pub Date : 2018-10-11
    Juan C. Araque, Claudio J. Margulis

    Structural heterogeneity in Ionic Liquids (ILs) is to a large extent defined by nanoscale apolar pockets that act as spacers between strings of positive and negative charges that alternate. In contrast to this, recent work from our group and that of others appear to indicate that dynamic, energetic, and mechanical heterogeneities are governed by the charged part of the liquid. In this article, we study the dynamics of methane, a small apolar solute, in the family of ILs 1-alkyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide (Im1,n+/NTf2−), with n = 2, 4, 8 at temperatures that make the viscosity for each liquid similar and around 8 cP. We do this in an attempt to equalize the effect of the solvent on the dynamics of the solute. In all cases, we find that solute proximity to charge-enhanced regions coincides with translationally caged regimes (high local friction) whereas the opposite is true in charge-depleted regions. In a way, these ILs behave like a liquid within a liquid where the charge network is the high friction component.

    更新日期:2018-10-14
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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