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arXiv2018

Viscosity and self-diffusion of supercooled and stretched water from molecular dynamics simulations

Among the numerous anomalies of water, the acceleration of dynamics under pressure is particularly puzzling. Whereas the diffusivity anomaly observed in experiments has been reproduced in several computer studies, the parallel viscosity anomaly has received less attention. Here we simulate viscosity and self-diffusion coefficient of the TIP4P/2005 water model over a broad temperature and pressure range. We reproduce the experimental behavior, and find additional anomalies at negative pressure. The anomalous effect of pressure on dynamic properties becomes more pronounced upon cooling, reaching two orders of magnitude for viscosity at 220 K. We analyze our results with a dynamic extension of a thermodynamic two-state model, an approach which has proved successful in describing experimental data. Water is regarded as a mixture of interconverting species with contrasting dynamic behaviors, one being strong (Arrhenius), and the other fragile (non-Arrhenius). The dynamic parameters of the two-state models are remarkably close between experiment and simulations. The larger pressure range accessible to simulations suggests a modification of the dynamic two-state model, which in turn also improves the agreement with experimental data. Furthermore, our simulations demonstrate the decoupling between viscosity $η$ and self-diffusion coefficient $D$ as a function of temperature $T$. The Stokes-Einstein relation, which predicts a constant $D η/T$, is violated when $T$ is lowered, in connection with the Widom line defined by an equal fraction of the two interconverting species. These results provide a unifying picture of thermodynamics and dynamics in water, and call for experiments at negative pressure.

physics.chem-ph↗
arXiv2018

Multiphoton Photoelectron Circular Dichroism of Limonene with Independent Polarization State Control of the Bound-Bound and Bound-Continuum Transitions

Photoionization of randomly oriented chiral molecules with circularly polarized light leads to a strong forward/backward asymmetry in the photoelectron angular distribution. This chiroptical effect, referred to as Photoelectron Circular Dichroism (PECD), was shown to take place in all ionization regimes, from single photon to tunnel ionization. In the Resonance Enhanced Multiphoton Ionisation (REMPI) regime, where most of the table-top PECD experiments have been performed, understanding the role of the intermediate resonances is currently the subject of experimental and theoretical investigations. In an attempt to decouple the role of bound-bound and bound-continuum transitions in REMPI-PECD, we photoionized the (+)-limonene enantiomer using two-color laser fields in [1+1'] and [2+2'] ionization schemes, where the polarization state of each color can be controlled independently. We demonstrate that the main effect of the bound-bound transition is to break the sample isotropy by orientation-dependent photoexcitation, in agreement with recent theoretical pre- dictions. We show that the angular distribution of PECD strongly depends on the anisotropy of photoexcitation to the intermediate state, which is different for circularly and linearly polarized laser pulses. On the contrary, the helicity of the pulse that drives the bound-bound transition is shown to have a negligible effect on the PECD.

physics.chem-ph↗
arXiv2018

Fluctuating Hydrodynamics of Reactive Liquid Mixtures

Fluctuating hydrodynamics (FHD) provides a framework for modeling microscopic fluctuations in a manner consistent with statistical mechanics and nonequilibrium thermodynamics. This paper presents an FHD formulation for isothermal reactive incompressible liquid mixtures with stochastic chemistry. Fluctuating multispecies mass diffusion is formulated using a Maxwell-Stefan description without assuming a dilute solution, and momentum dynamics is described by a stochastic Navier-Stokes equation for the fluid velocity. We consider a thermodynamically consistent generalization for the law of mass action for non-dilute mixtures and use it in the chemical master equation (CME) to model reactions as a Poisson process. The FHD approach provides remarkable computational efficiency over traditional reaction-diffusion master equation methods when the number of reactive molecules is large, while also retaining accuracy even when there are as few as ten reactive molecules per hydrodynamic cell. We present a numerical algorithm to solve the coupled FHD and CME equations and validate it on both equilibrium and nonequilibrium problems. We simulate a diffusively-driven gravitational instability in the presence of an acid-base neutralization reaction, starting from a perfectly flat interface. We demonstrate that the coupling between velocity and concentration fluctuations dominate the initial growth of the instability.

physics.flu-dyn↗
arXiv2018

The Saturated and Supercritical Stirling Cycle Thermodynamic Heat Engine Cycle

On the assumption that experimentally validated tabulated thermodynamic properties of saturated fluids published by the National Institute of Standards and Technology are accurate, a theoretical thermodynamic cycle can be demonstrated that produces a net-negative entropy generation to the universe. The experimental data on the internal energy can also be used to obtain a simple, empirical equation for the change in internal energy of a real fluid undergoing isothermal expansion and compression. This demonstration provides experimental evidence to the theory that temperature-dependent intermolecular attractive forces can be an entropic force that can enhance the thermodynamic efficiency of a real-fluid macroscopic heat engine to exceed that of the Carnot efficiency.

physics.chem-ph↗
arXiv2018

Selected configuration interaction dressed by perturbation

Selected configuration interaction (sCI) methods including second-order perturbative corrections provide near full CI (FCI) quality energies with only a small fraction of the determinants of the FCI space. Here, we introduce both a state-specific and a multi-state sCI method based on the CIPSI (Configuration Interaction using a Perturbative Selection made Iteratively) algorithm. The present method revises the reference (internal) space under the effect of its interaction with the outer space via the construction of an effective Hamiltonian, following the shifted-Bk philosophy of Davidson and coworkers. In particular, the multi-state algorithm removes the storage bottleneck of the effective Hamiltonian via a low-rank factorization of the dressing matrix.

physics.chem-ph↗
arXiv2018

Ultrafast extreme ultraviolet photoemission without space charge

Time- and Angle-resolved photoelectron spectroscopy from surfaces can be used to record the dynamics of electrons and holes in condensed matter on ultrafast time scales. However, ultrafast photoemission experiments using extreme-ultraviolet (XUV) light have previously been limited by either space-charge effects, low photon flux, or limited tuning range. In this article, we describe space-charge-free XUV photoelectron spectroscopy experiments with up to 5 nA of average sample current using a tunable cavity-enhanced high-harmonic source operating at 88 MHz repetition rate. The source delivers $ > 10^{11}$ photons/s in isolated harmonics to the sample over a broad photon energy range from 18 to 37 eV with a spot size of $58 \times 100 \; μ$m$^2$. From photoelectron spectroscopy data, we place conservative upper limits on the XUV pulse duration and photon energy bandwidth of 93 fs and 65 meV, respectively. The high photocurrent, lack of space charge distortions of the photoelectron spectra, and excellent isolation of individual harmonic orders allow us to observe the laser-assisted photoelectric effect with sideband amplitudes as low as $6 \times 10^{-4}$, enabling time-resolved XUV photoemission experiments in a qualitatively new regime.

physics.optics↗
arXiv2018

Using Fluorescence Detected Two-Dimensional Spectroscopy to Investigate Initial Exciton Delocalization Between Coupled Chromophores

Förster theory describes electronic exciton energy migration in molecular assemblies as an incoherent hopping process between donor and acceptor molecules. The rate is expressed in terms of the overlap integral between donor fluorescence and acceptor absorption spectra. Typical time scales for systems like photosynthetic antennae are on the order of a few picoseconds. Prior to transfer it is assumed that the initially excited donor molecule has equilibrated with respect to the local environment. However, upon excitation and during the equilibration phase the state of the system needs to be described by the full density matrix, including coherences between donor and acceptor states. While being intuitively clear, addressing this regime experimentally has been a challenge until the recently reported advances in Fluorescence Detected Two-Dimensional Spectroscopy (FD2DS). Here, we demonstrate using fourth order perturbation theory, the conditions for the presence of donor-acceptor coherence induced cross-peaks at zero waiting time between the first and the second pair of pulses. The approach is illustrated for a heterodimer model which facilitates an analytical solution.

physics.chem-ph↗
arXiv2019

Invariance of experimental observables with respect to coarse-graining in standard and many-body dissipative particle dynamics

Dissipative particle dynamics (DPD) is a well-established mesoscale simulation method. However, there have been long-standing ambiguities regarding the dependence of its (purely repulsive) force field parameter on temperature as well as the variation of the resulting experimental observables, such as diffusivity or surface tension, with coarse-graining (CG) degree. Here, we revisit the role of the CG degree and rederive the temperature dependence in standard DPD simulations. Consequently, we derive a scaling of the input variables that renders the system properties invariant with respect to CG degree, and illustrate the versatility of the method by computing the surface tensions of binary solvent mixtures. We then extend this procedure to many-body dissipative particle dynamics (MDPD) and, by computing surface tensions of the same mixtures at a range of CG degrees, demonstrate that this newer method, which has not been widely applied so far, is also capable of simulating complex fluids of practical interest.

physics.chem-ph↗
arXiv2018

Simulating vibronic spectra via Matsubara dynamics: coping with the sign problem

Measuring the vibronic spectrum probes dynamical processes in molecular systems. When interpreted via suitable theoretical tools, the experimental data provides comprehensive information about the system in question. For complex many-body problems, such an approach usually requires the formulation of proper classical-like approximations, which is particularly challenging if multiple electronic states are involved. In this manuscript, we express the imaginary-time shifted time correlation function (TCF) and, thus, the vibronic spectrum in terms of the so-called Matsubara dynamics, which combines quantum statistics and classical-like dynamics. In contrast to the existing literature, we invoke a local harmonic approximation to the potential allowing an analytical evaluation of integrals. By subsequently applying the Matsubara approximation, we derive a generalization of the existing Matsubara method to multiple potential energy surfaces (PESs), which, however, suffers from the sign problem as its single-PES counterpart does. The mathematical analysis for two shifted harmonic oscillators suggests a new modified method to simulate the standard correlation function via classical-like dynamics. Importantly, this modified method samples the thermal Wigner function without suffering from the sign problem and it yields an accurate approximation to the vibronic absorption spectrum, not only for the harmonic system, but also for an anharmonic one.

physics.chem-ph↗
arXiv2018

Towards Hybrid Density Functional Calculations of Molecular Crystals via Fragment-Based Methods

We introduce and employ two QM:QM schemes (a quantum mechanical method embedded into another quantum mechanical method) and report their performance for the X23 set of molecular crystals. We furthermore present the theory to calculate the stress tensors necessary for the computation of optimized cell volumes of molecular crystals and compare all results to those obtained with various density functionals and more approximate methods. Our QM:QM calculations with PBE0:PBE+D3, PBE0:PBE+MBD, and B3LYP:BLYP+D3 yield at a reduced computational cost lattice energy errors close to the ones of the parent hybrid density functional method, whereas for cell volumes, the errors of the QM:QM scheme methods are in between the GGA and hybrid functionals.

physics.chem-ph↗
arXiv2019

Performance Evaluation of the Symmetrical Quasi-Classical Dynamics Method based on Meyer-Miller Mapping Hamiltonian in the Treatment of Site-Exciton Models

The symmetrical quasi-classical dynamics method based on the Meyer-Miller mapping Hamiltonian (MM-SQC) shows the great potential in the treatment of the nonadiabatic dynamics of complex systems. We performed the comprehensive benchmark calculations to evaluate the performance of the MM-SQC method in various site-exciton models with respect to the accurate results of quantum dynamics method multilayer multiconfigurational time-dependent Hartree (ML-MCTDH). The parameters of the site-exciton models are chosen to represent a few of prototypes used in the description of photoinduced excitonic dynamics processes in photoharvesting systems and organic solar cells, which include the rather board situations with the fast or slow bath and different system-bath couplings. When the characteristic frequency of the bath is low, the MM-SQC method performs extremely well, and it gives almost the identical results to those of ML-MCTDH. When the fast bath is considered, the deviations exist between the MM-SQC and ML-MCTDH results if the high-frequency bath modes are improperly treated by the classical manner. When the so-called adiabatic renormalization was employed to construct the reduced Hamiltonian by freezing high-frequency modes, the MM-SQC dynamics can give the results comparable to the ML-MCTDH ones. Thus, the MM-SQC method itself provide reasonable results in all test site-exciton models, while the proper treatments of the bath modes must be employed. The possible dependence of the MM-SQC dynamics on the different initial sampling methods for the nuclear degrees of freedom is also discussed.

physics.chem-ph↗
arXiv2018

Differential capacitance of ionic liquids according to lattice-gas mean-field model with nearest-neighbor interactions

The Bragg-Williams free energy is used to incorporate nearest-neighbor interactions into the lattice gas model of a solvent-free ionic liquid near a planar electrode. We calculate the differential capacitance from solutions of the mean-field consistency relation, arriving at an explicit expression in the limit of a weakly charged electrode. The two additional material parameters that appear in the theory -- the degree of nonideality and the resistance to concentration changes of each ion type -- give rise to different regimes that we identify and discuss. As the nonideality parameter, which becomes more positive for stronger nearest-neighbor attraction between like-charged ions, increases and the electrode is weakly charged, the differential capacitance is predicted to transition through a divergence and subsequently adopt negative values just before the ionic liquid becomes structurally unstable. This is associated with the spontaneous charging of an electrode at vanishing potential. The physical origin of the divergence and the negative sign of the differential capacitance is a nonmonotonic relationship between surface potential and surface charge density, which reflects the formation of layered domains alternatingly enriched in counterions and coions near the electrode. The decay length of this layered domain pattern, which can be many times larger than the ion size, is reminiscent of the recently introduced concept of "underscreening".

physics.chem-ph↗
arXiv2018

Analysis of Trajectory Similarity and Configuration Similarity in On-the-Fly Surface-Hopping Simulation on Multi-Channel Nonadiabatic Photoisomerization Dynamics

We propose an 'automatic' approach to analyze the results of the on-the-fly trajectory surface hopping simulation on the multi-channel nonadiabatic photoisomerization dynamics by considering the trajectory similarity and the configuration similarity. We choose a representative system phytochromobilin chromophore model to illustrate the analysis protocol. After a large number of trajectories are obtained, it is possible to define the similarity of different trajectories by the Fréchet distance and to employ the trajectory clustering analysis to divide all trajectories into several clusters. Each cluster in principle represents a photoinduced isomerization reaction channel. This idea provides an effective approach to understand the branching ratio of the multi-channel photoisomerization dynamics. For each cluster the dimensionality reduction is employed to understand the configuration similarity in the trajectory propagation, which provides the understanding of the major geometry evolution features in each reaction channel. The results show that this analysis protocol not only assigns all trajectories into different photoisomerization reaction channels, but also extracts the major molecular motion without the requirement of the pre-known knowledge of the active photoisomerization site. As a side product of this analysis tool, we can also easily to find the so-called 'typical' or 'representative' trajectory for each reaction channel.

physics.chem-ph↗
arXiv2018

Temperature dependence of the solid-liquid interface free energy of Ni and Al from molecular dynamics simulation of nucleation

The temperature dependence of the solid-liquid interfacial free energy, γ, is investigated for Al and Ni at the undercooled temperature regime based on a recently developed persistent-embryo method. The atomistic description of the nucleus shape is obtained from molecular dynamics simulations. The computed γ shows a linear dependence on the temperature. The values of γ extrapolated to the melting temperature agree well with previous data obtained by the capillary fluctuation method. Using the temperature dependence of γ, we estimate the nucleation free energy barrier in a wide temperature range from the classical nucleation theory. The obtained data agree very well with the results from the brute-force molecular dynamics simulations.

physics.chem-ph↗
arXiv2018

Beyond Marcus theory and the Landauer-Büttiker approach in molecular junctions: A unified framework

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, 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 to 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 Marcus theory 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 Marcus theory, 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.

cond-mat.mes-hall↗
arXiv2018

Four-component relativistic range-separated density-functional theory: Short-range exchange local-density approximation

We lay out the extension of range-separated density-functional theory to a four-component relativistic frame-work using a Dirac-Coulomb-Breit Hamiltonian in the no-pair approximation. This formalism combines a wave-function method for the long-range part of the electron-electron interaction with a density(-current) functionalfor the short-range part of the interaction. We construct for this formalism a short-range exchange local-densityapproximation based on calculations on a relativistic homogeneous electron gas with a modified Coulomb-Breitelectron-electron interaction. More specifically, we provide the relativistic short-range Coulomb and Breit ex-change energies per particle of the relativistic homogeneous electron gas in the form of Pad e approximantswhich are systematically improvable to arbitrary accuracy. These quantities, as well as the associated effectiveCoulomb-Breit exchange hole, show the important impact of relativity on short-range exchange effects for highdensities.

physics.chem-ph↗
arXiv2018

Anharmonic vibrational spectroscopy of Polycyclic Aromatic Hydrocarbons (PAHs)

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 IR transitions including bands becoming active due to resonances as well as overtones, 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 (C$_{16}$H$_{10}$) and coronene (C$_{24}$H$_{12}$), 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 (DFT) 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 towards calculating moderately high-temperature spectra of PAHs and other similarly rigid molecules using Monte Carlo sampling.

physics.chem-ph↗