
Communication: Biological applications of coupledcluster frozendensity embedding J. Chem. Phys. (IF 2.965) Pub Date : 20180409
Johannes Heuser, Sebastian HöfenerWe report the implementation of the Laplacetransform scaled oppositespin (LTSOS) resolutionoftheidentity secondorder approximate coupledcluster singles and doubles (RICC2) combined with frozendensity embedding for excitation energies and molecular properties. In the present work, we furthermore employ the HartreeFock 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 coupledcluster 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 LTSOSRICC2 and densityfunctional 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.

Communication: Photoinduced carbon dioxide binding with surfacefunctionalized silicon quantum dots J. Chem. Phys. (IF 2.965) Pub Date : 20180411
Oscar A. DouglasGallardo, Cristián Gabriel Sánchez, Esteban VöhringerMartinezNowadays, 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 surfacefunctionalized silicon quantum dots (sfSiQDs) 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 TightBinding (DFTB) approach along with a timedependent 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 sfSiQDs for photochemically activated carbon dioxide fixation.

Communication: A coilstretch transition in planar elongational flow of an entangled polymeric melt J. Chem. Phys. (IF 2.965) Pub Date : 20180413
Mohammad H. Nafar Sefiddashti, Brian J. Edwards, Bamin KhomamiVirtual 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 coilstretch 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 doublewell conformational free energy potential with an activation barrier between the two configurational minima.

Communication: Adaptive boundaries in multiscale simulations J. Chem. Phys. (IF 2.965) Pub Date : 20180413
Jason A. Wagoner, Vijay S. PandeCombinedresolution 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 highresolution 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.

Mesoscopic electrohydrodynamic simulations of binary colloidal suspensions J. Chem. Phys. (IF 2.965) Pub Date : 20180409
Nicolas Rivas, Stefan Frijters, Ignacio Pagonabarraga, Jens HartingA model is presented for the solution of electrokinetic phenomena of colloidal suspensions in fluid mixtures. We solve the discrete Boltzmann equation with a BhatnagarGrossKrook collision operator using the lattice Boltzmann method to simulate binary fluid flows. Solventsolvent and solventsolute interactions are implemented using a pseudopotential model. The NernstPlanck equation, describing the kinetics of dissolved ion species, is solved using a finite difference discretization based on the linkflux 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.

Clustering methods for the optimization of atomic cluster structure J. Chem. Phys. (IF 2.965) Pub Date : 20180410
Francesco Bagattini, Fabio Schoen, Luca TigliIn this paper, we propose a revised global optimization method and apply it to large scale cluster conformation problems. In the 1990s, the socalled 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 LennardJones 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, stateoftheart 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.

Lowlying excited states by constrained DFT J. Chem. Phys. (IF 2.965) Pub Date : 20180410
Pablo Ramos, Michele PavanelloExploiting the machinery of Constrained Density Functional Theory (CDFT), we propose a variational method for calculating lowlying excited states of molecular systems. We dub this method eXcited CDFT (XCDFT). Excited states are obtained by selfconsistently constraining a userdefined 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 linearresponse timedependent 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 condensedphase 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 singlereference methods for computations of excited states in terms of time to solution, rate of convergence, and accuracy of the result.

Using reweighting and free energy surface interpolation to predict solidsolid phase diagrams J. Chem. Phys. (IF 2.965) Pub Date : 20180410
Natalie P. Schieber, Eric C. Dybeck, Michael R. ShirtsMany 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 solidsolid 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.

Improving accuracy of electrochemical capacitance and solvation energetics in firstprinciples calculations J. Chem. Phys. (IF 2.965) Pub Date : 20180411
Ravishankar Sundararaman, Kendra LetchworthWeaver, Kathleen A. SchwarzReliable firstprinciples 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 nonadsorbing, 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 firstprinciples electrochemistry of metal surfaces in nonadsorbing, aqueous electrolytes: dielectric and ionic nonlinearity, and a dielectriconly 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 softsphere solvation model which both captures the capacitance features observed experimentally and serves as a generalpurpose continuum solvation model.

Entangled trajectories Hamiltonian dynamics for treating quantum nuclear effects J. Chem. Phys. (IF 2.965) Pub Date : 20180411
Brendan Smith, Alexey V. AkimovA simple and robust methodology, dubbed Entangled Trajectories Hamiltonian Dynamics (ETHD), is developed to capture quantum nuclear effects such as tunneling and zeropoint energy through the coupling of multiple classical trajectories. The approach reformulates the classically mapped secondorder Quantized Hamiltonian Dynamics (QHD2) 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 QHD2. 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.

Five and sixelectron harmonium atoms: Highly accurate electronic properties and their application to benchmarking of approximate 1matrix functionals J. Chem. Phys. (IF 2.965) Pub Date : 20180411
Jerzy Cioslowski, Krzysztof StrasburgerElectronic properties of several states of the five and sixelectron harmonium atoms are obtained from largescale 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 fiveelectron 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 electronelectron repulsion energy in terms of the 1matrix that are at heart of the density matrix functional theory (DMFT). On the other hand, the properties of the three lowlying states of the sixelectron harmonium atom, computed at ω = 500 and ω = 1000, uncover deficiencies of the 1matrix 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.

An atomic meanfield spinorbit approach within exact twocomponent theory for a nonperturbative treatment of spinorbit coupling J. Chem. Phys. (IF 2.965) Pub Date : 20180412
Junzi Liu, Lan ChengAn atomic meanfield (AMF) spinorbit (SO) approach within exact twocomponent theory (X2C) is reported, thereby exploiting the exact decoupling scheme of X2C, the oneelectron approximation for the scalarrelativistic contributions, the meanfield approximation for the treatment of the twoelectron SO contribution, and the local nature of the SO interactions. The Hamiltonian of the proposed SOX2CAMF scheme comprises the oneelectron X2C Hamiltonian, the instantaneous twoelectron Coulomb interaction, and an AMF SO term derived from spherically averaged DiracCoulomb HartreeFock calculations of atoms; no molecular relativistic twoelectron integrals are required. Benchmark calculations for bond lengths, harmonic frequencies, dipole moments, and electricfield 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 scalarrelativistic effects and appears to be a promising candidate for applications to heavyelement containing systems. SOX2CAMF coupledcluster 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.

Forcedetected nanoscale absorption spectroscopy in water at room temperature using an optical trap J. Chem. Phys. (IF 2.965) Pub Date : 20180409
Alexander Parobek, Jacob W. Black, Maria Kamenetska, Ziad GanimMeasuring absorption spectra of single molecules presents a fundamental challenge for standard transmissionbased 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 400800 nm range. These measurements provide proofofprinciple experiments for forcedetected nanoscale spectroscopies that operate under ambient chemical conditions.

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 : 20180409
S. Fuchs, J. Fischer, A. Slenczka, M. Karra, B. FriedrichWe 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 Pchelium complex.

Heliuminduced electronic transitions in photoexcited Ba+–Hen exciplexes J. Chem. Phys. (IF 2.965) Pub Date : 20180409
Patricia Vindel Zandbergen, Manuel Barranco, Fausto Cargnoni, Marcel Drabbels, Martí Pi, Nadine HalberstadtThe possibility for heliuminduced electronic transitions in a photoexcited 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 noninteracting 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 ringshaped 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 heliuminduced nonadiabatic transitions observed in other systems.

Highresolution infrared spectroscopy of O2H+ in a cryogenic ion trap J. Chem. Phys. (IF 2.965) Pub Date : 20180409
Hiroshi Kohguchi, Pavol Jusko, Koichi M. T. Yamada, Stephan Schlemmer, Oskar AsvanyThe protonated oxygen molecule, O2H+, and its helium complex, HeO2H+, have been investigated by vibrational action spectroscopy in a cryogenic 22pole ion trap. For the HeO2H+ complex, the frequencies of three vibrational bands have been determined by predissociation spectroscopy. The elusive O2H+ has been characterized for the first time by highresolution rovibrational spectroscopy via its ν1 OHstretching band. Thirtyeight 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.

The effect of the condensedphase environment on the vibrational frequency shift of a hydrogen molecule inside clathrate hydrates J. Chem. Phys. (IF 2.965) Pub Date : 20180409
Anna Powers, Yohann Scribano, David Lauvergnat, Elsy Mebe, David M. Benoit, Zlatko BačićWe 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 condensedphase environment. In order to determine how much the hydrate water molecules beyond the confining small cage contribute to the vibrational frequency shift, quantum fivedimensional (5D) calculations of the coupled translationrotation 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 highquality ab initio fulldimensional (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 condensedphase 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 condensedphase effects arise predominantly from the H2O molecules in the first three complete hydration shells around H2.

Dissociation cross section for high energy O2–O2 collisions J. Chem. Phys. (IF 2.965) Pub Date : 20180409
T. K. Mankodi, U. V. Bhandarkar, B. P. PuranikCollisioninduced 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 nonequilibrium. 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.

The control of electron quantum trajectories on the highorder harmonic generation of CO and N2 molecules in the presence of a low frequency field J. Chem. Phys. (IF 2.965) Pub Date : 20180409
A. M. Koushki, R. SadighiBonabi, M. MohsenNia, E. IraniIn the present work, an efficient method is theoretically investigated for extending highorder harmonics and ultrashort attosecond pulse generation in N2 and CO molecules by using the timedependent 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 twocolor 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 timefrequency analyses.

Aqueous solvation of Mg(ii) and Ca(ii): A BornOppenheimer molecular dynamics study of microhydrated gas phase clusters J. Chem. Phys. (IF 2.965) Pub Date : 20180409
C. I. LeónPimentel, J. I. AmaroEstrada, J. HernándezCobos, H. SaintMartin, A. RamírezSolísThe hydration features of [Mg(H2O)n]2+ and [Ca(H2O)n]2+ clusters with n = 36, 8, 18, and 27 were studied by means of BornOppenheimer molecular dynamics simulations at the B3LYP/631+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 octahedraltype 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 finitetemperature 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 Xray absorption fine structure spectroscopy spectra for the larger cluster and the experimental data of the aqueous solution supports a CN of six for Ca2+.

Positron scattering from pyridine J. Chem. Phys. (IF 2.965) Pub Date : 20180411
D. Stevens, T. J. Babij, J. R. Machacek, S. J. Buckman, M. J. Brunger, R. D. White, G. García, F. Blanco, L. EllisGibbings, J. P. SullivanWe present a range of cross section measurements for the lowenergy 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.

“Trampoline” ejection of organic molecules from graphene and graphite via keV cluster ions impacts J. Chem. Phys. (IF 2.965) Pub Date : 20180412
Stanislav V. Verkhoturov, Mikołaj Gołuński, Dmitriy S. Verkhoturov, Sheng Geng, Zbigniew Postawa, Emile A. SchweikertWe 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, 2layer 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, (D8PheH)−, 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 (D8PheH)− 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 projectileanalyte interaction. The projectile impact on the grapheneD8Phe 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−.

High pressure synthesis and stability of cobalt hydrides J. Chem. Phys. (IF 2.965) Pub Date : 20180413
Mengnan Wang, Jack Binns, MaryEllen Donnelly, Miriam PeñaAlvarez, Philip DalladaySimpson, Ross T. HowieIn situ highpressure hightemperature Xray powder diffraction studies of the cobalthydrogen 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 firstrow transition metal, cobalt has a relatively lower mass than other hydrideforming 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.

Unraveling the electronic relaxation dynamics in photoexcited 2,4difluoroaniline via femtosecond timeresolved photoelectron imaging J. Chem. Phys. (IF 2.965) Pub Date : 20180413
Fengzi Ling, Shuai Li, Jie Wei, Kai Liu, Yanmei Wang, Bing ZhangTimeresolved photoelectron imaging is employed to investigate the relaxation dynamics of the lowest two excited electronic states S1(ππ*) and S2(π3s/πσ*) in 2,4difluoroaniline (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.

Vapor phase nucleation of the shortchain nalkanes (npentane, nhexane and nheptane): Experiments and Monte Carlo simulations J. Chem. Phys. (IF 2.965) Pub Date : 20180413
Kehinde E. Ogunronbi, Aliasghar Sepehri, Bin Chen, Barbara E. WyslouzilWe measured the nucleation rates of npentane through nheptane in a supersonic nozzle at temperatures ranging from ca. 109 K to 168 K. For npentane and nhexane, 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 equilibriaunited atom potentials, suggest that despite the high degree of supercooling, the critical clusters remain liquid like under experimental conditions for npentane through nheptane, but adopt more ordered structures for noctane and nnonane. 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.

Investigations of the valenceshell excitations of molecular ethane by highenergy electron scattering J. Chem. Phys. (IF 2.965) Pub Date : 20180413
WeiQing Xu, LongQuan Xu, DeGuang Qi, Tao Chen, YaWei Liu, LinFan ZhuThe differential cross sections and generalized oscillator strengths for the lowlying excitations of the valenceshell 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 BEscaling (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.

Performance of exchangecorrelation functionals in density functional theory calculations for liquid metal: A benchmark test for sodium J. Chem. Phys. (IF 2.965) Pub Date : 20180409
JeongHwan Han, Takuji OdaThe performance of exchangecorrelation functionals in densityfunctional theory (DFT) calculations for liquid metal has not been sufficiently examined. In the present study, benchmark tests of PerdewBurkeErnzerhof (PBE), ArmientoMattsson 2005 (AM05), PBE reparameterized 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 exchangecorrelation functional and that the DFT functional performance in solid simulations can be used to roughly estimate the performance in liquid simulations.

Instability and thermal conductivity of pressuredensified and elastically altered orientational glass of Buckminsterfullerene J. Chem. Phys. (IF 2.965) Pub Date : 20180409
G. P. Johari, Ove Andersson, Bertil SundqvistWe report on the temperature, pressure, and time (T, p, and t)dependent features of thermal conductivity, κ, of partially ordered, nonequilibrium state of C60OG, the orientational glass of Buckminsterfullerene (at T below the orientational freezing temperature Tog) made more unstable (i) by partially depressurizing its highp formed state to elastically expand it and (ii) by further pressurizing that state to elastically contract it. The subTog effects observed on heating of C60OG differ from those of glasses because phonon propagation depends on the ratio of two welldefined orientational states of C60 molecules and the density of the solid. A broad peaklike feature appears at T near Tog in the κT plots of C60OG formed at 0.7 GPa, depressurized to 0.2 GPa and heated at 0.2 GPa, which we attribute to partial overlap of the subTog and Tog features. A subTog local minimum appears in the κT plots at T well below Tog of C60OG 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 JohariGoldstein relaxation. All seem to affect the phenomenology of its glasslike transition.

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 : 20180409
KaiYang Leong, Feng WangThe surface tension of nanoscale droplets of water was studied with molecular dynamics simulations using the BLYPSP4F 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 YoungLaplace 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 bulklike interior.

A comparative computational study of coarsegrained and allatom water models in shock Hugoniot states J. Chem. Phys. (IF 2.965) Pub Date : 20180409
Sa Hoon Min, Max L. BerkowitzWe 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 oftenused allatom TIP4P/2005 model, while the other two were coarsegrained models used with the MARTINI force field: nonpolarizable and polarizable MARTINI water. The allatom 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 coarsegrained 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 nonpolarizable 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 coarsegrained models predicted much higher temperatures. These high temperatures for MARTINI water can be explained by the loss of degrees of freedom due to coarsegraining procedure.

Persistent optical holeburning spectroscopy of nanoconfined dye molecules in liquid at room temperature: Spectral narrowing due to a glassy state and extraordinary relaxation in a nanocage J. Chem. Phys. (IF 2.965) Pub Date : 20180410
Hiroshi MurakamiPersistent optical holeburning 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 siteselective 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 holeburning spectra exhibit large shifts from excitation frequencies, and their positions are almost independent of excitation frequencies. The holeburning 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 holeburning efficiencies of vibronic to electronicband 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 holeburning spectra measured for the dyecontaining 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.

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 : 20180410
Daisman P. B. Aji, G. P. JohariThe effect of structural relaxation on electrical resistivity, ρglass, of strainfree 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 nonexponentially with the aging time. The activation energy of aging kinetics is 189 kJ mol−1, which is higher than the activation energy of the JohariGoldstein (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 ZimanNagel 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.

Relationship between xray emission and absorption spectroscopy and the local Hbond environment in water J. Chem. Phys. (IF 2.965) Pub Date : 20180410
Iurii Zhovtobriukh, Nicholas A. Besley, Thomas Fransson, Anders Nilsson, Lars G. M. PetterssonThe connection between specific features in the water Xray absorption spectrum and Xray emission spectrum (XES) and the local Hbond coordination is studied based on structures obtained from pathintegral molecular dynamics simulations using either the optPBEvdW density functional or the MBpol force field. Computing the XES spectrum using all molecules in a snapshot results in only one peak in the lonepair (1b1) region, while the experiment shows two peaks separated by 0.80.9 eV. Different Hbond configurations were classified based on the local structure index (LSI) and a geometrical Hbond cone criterion. We find that tetrahedrally coordinated molecules characterized by high LSI values and two strong donated and two strong accepted Hbonds contribute to the low energy 1b1 emission peak and to the postedge region in absorption. Molecules with the asymmetric Hbond environment with one strong accepted Hbond and one strong donated Hbond and low LSI values give rise to the high energy 1b1 peak in the emission spectrum and mainly contribute to the preedge and mainedge in the absorption spectrum. The 1b1 peak splitting can be increased to 0.62 eV by imposing constraints on the Hbond length, i.e., for very tetrahedral structures short Hbonds (less than 2.68 Å) and for very asymmetric structures elongated Hbonds (longer than 2.8 Å). Such structures are present, but underrepresented, in the simulations which give more of an average of the two extremes.

Anomalous surface behavior of hydrated guanidinium ions due to ion pairing J. Chem. Phys. (IF 2.965) Pub Date : 20180413
Victor Ekholm, Mario Vazdar, Philip E. Mason, Erik Bialik, MarieMadeleine Walz, Gunnar Öhrwall, Josephina Werner, JanErik Rubensson, Pavel Jungwirth, Olle BjörneholmSurface 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 Xray 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 codissolved 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.

The dependency of adhesion and friction on electrostatic attraction J. Chem. Phys. (IF 2.965) Pub Date : 20180409
B. N. J. PerssonI develop a general meanfield 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.

Kinetic effects on the morphology and stability of the pressureinduced extendedsolid of carbon monoxide J. Chem. Phys. (IF 2.965) Pub Date : 20180409
Nhan C. Dang, Jennifer A. CiezakJenkinsIn 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 Xray 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.

The structure of PbCl2 on the {100} surface of NaCl and its consequences for crystal growth J. Chem. Phys. (IF 2.965) Pub Date : 20180409
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 VliegThe 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 xray 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}.

Simulations of submonolayer Xe on Pt(111): The case for a chaotic low temperature phase J. Chem. Phys. (IF 2.965) Pub Date : 20180410
Anthony D. Novaco, Jessica BavarescoMolecular 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 twodimensional molecular dynamics simulation, the model takes into consideration the thermal excitation of quantum states associated with surfacenormal 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 lowtemperature 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 chaoticlike nature, exhibiting longlived metastable 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.

Water dissociating on rigid Ni(100): A quantum dynamics study on a fulldimensional potential energy surface J. Chem. Phys. (IF 2.965) Pub Date : 20180410
Tianhui Liu, Jun Chen, Zhaojun Zhang, Xiangjian Shen, Bina Fu, Dong H. ZhangWe constructed a ninedimensional (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 sitespecific results from the sevendimensional (7D) calculations, indicating the importance of fulldimensional quantum dynamics to quantitatively characterize this gassurface reaction. It is found that the validity of the siteaveraging approximation with exact potential holds well, where the siteaveraging 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.

Soft phonon modes driven huge difference on lattice thermal conductivity between topological semimetal WC and WN J. Chem. Phys. (IF 2.965) Pub Date : 20180411
SanDong Guo, Peng ChenTopological semimetals are currently attracting increasing interest due to their potential applications in topological qubits and lowpower 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 angleresolved photoemission spectroscopy. In this work, by solving the Boltzmann transport equation based on firstprinciples calculations, we systematically investigate the phonon transport properties of topological semimetals WC and WN. The predicted roomtemperature 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 acousticoptical (ao) 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 ao 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.

Emergence of Landauer transport from quantum dynamics: A model Hamiltonian approach J. Chem. Phys. (IF 2.965) Pub Date : 20180412
Partha Pratim Pal, S. Ramakrishna, Tamar SeidemanThe Landauer expression for computing currentvoltage characteristics in nanoscale devices is efficient but not suited to transient phenomena and a timedependent 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 timedependent current in an electrodemoleculeelectrode 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 timedependent 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 timeindependent charge flow. Our generalized Landauer formula is valid at all times for models beyond the wideband limit, nonuniform electrode density of states and for time and energydependent 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 timedependent electronic coupling. Finally, we comment on the applicability of the Landauer formula to compute hotelectron current arising upon plasmon decoherence.

Spatially resolved proton momentum distributions in KDP from firstprinciples J. Chem. Phys. (IF 2.965) Pub Date : 20180412
Edgar A. EngelThe ferroelectric to paraelectric (PE) phase transition of KH2PO4 (KDP) is investigated as a stringent test of the firstprinciples, 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 pathintegral 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.

Empirical potential for molecular simulation of graphene nanoplatelets J. Chem. Phys. (IF 2.965) Pub Date : 20180413
Alexander J. Bourque, Gregory C. RutledgeA new empirical potential for layered graphitic materials is reported. Interatomic interactions within a single graphene sheet are modeled using a StillingerWeber potential. Interatomic interactions between atoms in different sheets of graphene in the nanoplatelet are modeled using a LennardJones 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 multilayer graphene nanoplatelets.

Polymer effects on Kármán vortex: Molecular dynamics study J. Chem. Phys. (IF 2.965) Pub Date : 20180409
Yuta Asano, Hiroshi Watanabe, Hiroshi NoguchiWe 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 shortpolymer 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 longpolymer 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.

Reaction kinetics in open reactors and serial transfers between closed reactors J. Chem. Phys. (IF 2.965) Pub Date : 20180413
Alex Blokhuis, David Lacoste, Pierre GaspardKinetic theory and thermodynamics of reaction networks are extended to the outofequilibrium dynamics of continuousflow 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 crosscatalytic 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.

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 : 20180409
Mert Gur, Elizabeth A. Blackburn, Jia Ning, Vikram Narayan, Kathryn L. Ball, Malcolm D. Walkinshaw, Burak ErmanCyclophilin 40 (Cyp40) is a member of the immunophilin family that acts as a peptidylprolylisomerase enzyme and binds to the heat shock protein 90 (Hsp90). Its structure comprises an Nterminal cyclophilin domain and a Cterminal tetratricopeptide (TPR) domain. Cyp40 is overexpressed in prostate cancer and certain Tcell 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 Cyp40Hsp90 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 allatom 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 cyclophilinTPR interdomain distances. The K308A mutant was only observed in the extended form which is observed in the Cyp40 Xray structure. The wildtype, 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.

Communication: Probing the interaction of infrared antenna arrays and molecular films with ultrafast quantum dynamics J. Chem. Phys. (IF 2.965) Pub Date : 20180404
Bar Cohn, Amit K. Prasad, Lev ChuntonovNarrowband vibrational molecular transitions interacting with the broadband resonance of infrared plasmonic antennas lead to Fano lineshapes observed in linear (FTIR) and thirdorder (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 nmthick polymer film spincoated on an array of infrared halfwavelength gold antennas. Despite the pronounced Fano lineshapes obtained for the molecular transitions, and up to a four order of magnitude enhancement of the thirdorder 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 μmthick 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.

Communication: Fast dynamics perspective on the breakdown of the StokesEinstein law in fragile glassformers J. Chem. Phys. (IF 2.965) Pub Date : 20180405
F. Puosi, A. Pasturel, N. Jakse, D. LeporiniThe breakdown of the StokesEinstein (SE) law in fragile glassformers is examined by MolecularDynamics simulations of atomic liquids and polymers and consideration of the experimental data concerning the archetypical orthoterphenyl glassformer. All the four systems comply with the universal scaling between the viscosity (or the structural relaxation) and the DebyeWaller 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.

QED effects on individual atomic orbital energies J. Chem. Phys. (IF 2.965) Pub Date : 20180402
Karol Kozioł, Gustavo A. AucarSeveral issues, concerning QED corrections, that are important in precise atomic calculations are presented. The leading QED corrections, selfenergy 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 Zdependence 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 nssubshell for group 1 and 11 atoms and discuss about the reliability of these numbers by comparing them with experimental first ionization potential data.

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 : 20180403
Marius S. Frank, Christof HättigWe present a pair natural orbital (PNO)based implementation of coupled cluster singles and doubles (CCSD) excitation energies that builds upon the previously proposed statespecific 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 densityfitting 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 costscaling for the CCSD iterations with the system size.

Flexible scheme to truncate the hierarchy of pure states J. Chem. Phys. (IF 2.965) Pub Date : 20180402
P.P. Zhang, C. D. B. Bentley, A. EisfeldThe hierarchy of pure states (HOPS) is a wavefunctionbased 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 “nparticle approximation” to HOPS. We also introduce a new approximation, which we call the “nmode 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.

Fluctuating chemohydrodynamics and the stochastic motion of selfdiffusiophoretic particles J. Chem. Phys. (IF 2.965) Pub Date : 20180402
Pierre Gaspard, Raymond KapralThe propulsion of active particles by selfdiffusiophoresis 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 OnsagerCasimir 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.

Expanding the calculation of activation volumes: Selfdiffusion in liquid water J. Chem. Phys. (IF 2.965) Pub Date : 20180402
Zeke A. Piskulich, Oluwaseun O. Mesele, Ward H. ThompsonA 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 selfdiffusion 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.

Assessment of interactionstrength interpolation formulas for gold and silver clusters J. Chem. Phys. (IF 2.965) Pub Date : 20180402
Sara Giarrusso, Paola GoriGiorgi, Fabio Della Sala, Eduardo FabianoThe performance of functionals based on the idea of interpolating between the weak and the stronginteraction limits the global adiabaticconnection integrand is carefully studied for the challenging case of noblemetal 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 HartreeFock, 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.

Committor of elementary reactions on multistate systems J. Chem. Phys. (IF 2.965) Pub Date : 20180402
Péter Király, Dóra Judit Kiss, Gergely TóthIn our study, we extend the committor concept on multiminima 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 threehole twodimensional model system explored by singleparticle 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 energycommittor 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 2chlorobutane, where an elementary reaction committor, the probability densities, the potential energy/committor, and the freeenergy/committor curves are presented.

Adaptive enhanced sampling by forcebiasing using neural networks J. Chem. Phys. (IF 2.965) Pub Date : 20180403
Ashley Z. Guo, Emre Sevgen, Hythem Sidky, Jonathan K. Whitmer, Jeffrey A. Hubbell, Juan J. de PabloA 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 selfregularizing 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.

Current density tensors J. Chem. Phys. (IF 2.965) Pub Date : 20180403
Paolo LazzerettiIt is shown that nonsymmetric secondrank 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 spinspin 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 secondrank 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 spinspin 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.

A walk through the approximations of ab initio multiple spawning J. Chem. Phys. (IF 2.965) Pub Date : 20180403
Benoit Mignolet, Basile F. E. CurchodFull multiple spawning offers an in principle exact framework for excitedstate 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 excitedstate 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 lowdimensional system, the qualitative excitedstate dynamics is adequately captured, and affordable corrections can further be applied to ameliorate the coupling between trajectory basis functions.

Transient dynamics of a quantumdot: From Kondo regime to mixed valence and to empty orbital regimes J. Chem. Phys. (IF 2.965) Pub Date : 20180403
YongXi Cheng, ZhenHua Li, JianHua Wei, YiHang Nie, YiJing YanBased on the hierarchical equations of motion approach, we study the timedependent 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 resonanttunneling.

Fate of the openshell singlet ground state in the experimentally accessible acenes: A quantum Monte Carlo study J. Chem. Phys. (IF 2.965) Pub Date : 20180403
Nicolas Dupuy, Michele CasulaBy 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 resonatingvalencebond (RVB) ansatz proposed by Pauling and Wheland to describe aromatic compounds. We show that the longranged RVB correlations built in the acenes’ ground state are detrimental for the occurrence of openshell diradical or polyradical instabilities, previously found by lowerlevel theories. We substantiate our outcome by a direct comparison with another wave function, tailored to be an openshell singlet (OSS) for longenough 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 multireference 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 spinspin 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 longrange decay of the chargecharge correlation functions is compatible with a quasimetallic behavior.
Some contents have been Reproduced by permission of The Royal Society of Chemistry.