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arXiv2018

Even-handed subsystem selection in projection-based embedding

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

physics.chem-ph↗

arXiv2018

Matrix product state formulation of the multiconfiguration time-dependent Hartree theory

A matrix product state formulation of the multiconfiguration time-dependent Hartree (MPS-MCTDH) theory is presented. The Hilbert space that is spanned by the direct products of the phonon degree of freedoms, which is linearly parameterized in the MCTDH ansatz and thus results in an exponential increase of the computational cost, is parametrized by the MPS form. Equations of motion based on the Dirac-Frenkel time-dependent variational principle is derived by using the tangent space projection and the projector-splitting technique for the MPS, which have been recently developed. The mean-field operators, which appears in the equation of motion of the MCTDH single particle functions, are written in terms of the MPS form and efficiently evaluated by a sweep algorithm that is similar to the DMRG sweep. The efficiency and convergence of the MPS formulation to the MCTDH are demonstrated by quantum dynamics simulations of extended excitonic molecular systems.

physics.chem-ph↗

arXiv2018

Curing basis-set convergence of wave-function theory using density-functional theory: a systematically improvable approach

The present work proposes to use density-functional theory (DFT) to correct for the basis-set error of wave-function theory (WFT). One of the key ideas developed here is to define a range-separation parameter which automatically adapts to a given basis set. The derivation of the exact equations are based on the Levy-Lieb formulation of DFT, which helps us to define a complementary functional which corrects uniquely for the basis-set error of WFT. The coupling of DFT and WFT is done through the definition of a real-space representation of the electron-electron Coulomb operator projected in a one-particle basis set. Such an effective interaction has the particularity to coincide with the exact electron-electron interaction in the limit of a complete basis set, and to be finite at the electron-electron coalescence point when the basis set is incomplete. The non-diverging character of the effective interaction allows one to define a mapping with the long-range interaction used in the context of range-separated DFT and to design practical approximations for the unknown complementary functional. Here, a local-density approximation is proposed for both full-configuration-interaction (FCI) and selected configuration-interaction approaches. Our theory is numerically tested to compute total energies and ionization potentials for a series of atomic systems. The results clearly show that the DFT correction drastically improves the basis-set convergence of both the total energies and the energy differences. For instance, a sub kcal/mol accuracy is obtained from the aug-cc-pVTZ basis set with the method proposed here when an aug-cc-pV5Z basis set barely reaches such a level of accuracy at the near FCI level.

physics.chem-ph↗

arXiv2018

Equation-of-Motion Coupled-Cluster Theory based on the 4-component Dirac-Coulomb(-Gaunt) Hamiltonian. Energies for single electron detachment, attachment and electronically excited states

We report in this paper an implementation of 4-component relativistic Hamiltonian based Equation-of-Motion Coupled-Cluster with singles and doubles (EOM-CCSD) theory for the calculation of ionization potential (IP), electron affinity (EA) and excitation energy (EE). In this work we utilize previously developed double group symmetry-based generalized tensor contraction scheme, and also extend it in order to carry out tensor contractions involving non-totally symmetric and odd-ranked tensors. Several approximated spin-free and two-component Hamiltonians can also be accessed in this implementation. We have applied this method to the halogen monoxide (XO, X= Cl, Br, I, At, Ts) species, in order to assess the quality of a few other recent EOMCC implementations, where spin-orbit coupling contribution has been approximated in different degree. Besides, we also have studied various excited states of CH$_2$IBr, CH$_2$I$_2$ and I$_2^-$(as well as single electron attachment and detachment electronic states of the same species) where comparison has been made with a closely related multi-reference coupled-cluster method, namely Intermediate Hamiltonian Fock Space Coupled-Cluster singles and doubles (IHFS-CCSD) theory.

physics.chem-ph↗

arXiv2019

Simulated XUV Photoelectron Spectra of THz-pumped Liquid Water

Highly intense, sub-picosecond terahertz (THz) pulses can be used to induce ultrafast temperature jumps (T-jumps) in liquid water. A supercritical state of gas-like water with liquid density is established, and the accompanying structural changes are expected to give rise to time-dependent chemical shifts. We investigate the possibility of using extreme ultraviolet (XUV) photoelectron spectroscopy as a probe for ultrafast dynamics induced by sub-picosecond THz pulses of varying intensities and frequencies. To this end, we use ab initio methods to calculate photoionization cross sections and photoelectron energies of (H2O)$_{20}$ clusters embedded in an aqueous environment represented by point charges. The cluster geometries are sampled from ab initio molecular dynamics simulations modeling the THz-water interactions. We find that the peaks in the valence photoelectron spectrum are shifted by up to 0.4 eV after the pump pulse, and that they are broadened with respect to unheated water. The shifts can be connected to structural changes caused by the heating, but due to saturation effects they are not sensitive enough to serve as a thermometer for T-jumped water.

physics.chem-ph↗

arXiv2018

A quantum mechanical insight into SN2 reactions: Semiclassical initial value representation calculations of vibrational features of the Cl$^-$--CH$_3$Cl pre-reaction complex with the VENUS suite of codes

The role of vibrational excitation of reactants in driving reactions involving polyatomic species has been often studied by means of classical or quasi-classical trajectory simulations. We propose a different approach based on investigation of vibrational features of the Cl$^-$--CH$_3$Cl pre-reaction complex for the Cl$^-$ + CH$_3$Cl SN$_2$ reaction. We present vibrational power spectra and frequency estimates for the title pre-reaction complex calculated at the level of classical, semiclassical, and second-order vibrational perturbation theory on a pre-existing analytical potential energy surface. The main goals of the paper are the study of anharmonic effects and understanding of vibrational couplings that permit energy transfer between the collisional kinetic energy and the internal vibrations of the reactants. We provide both classical and quantum pictures of intermode couplings and show that the SN2 mechanism is favored by the coupling of a C--Cl bend involving the Cl$^-$ projectile with the CH$_3$ rocking motion of the target molecule. We also illustrate how the routines needed for semiclassical vibrational spectroscopy simulations can be interfaced in a user-friendly way to pre-existing molecular dynamics software. In particular, we present an implementation of semiclassical spectroscopy into the VENUS suite of codes, thus providing a useful computational tool for users who are not experts of semiclassical dynamics.

physics.chem-ph↗

arXiv2018

Nucleation instability in super-cooled Cu-Zr-Al glass-forming liquids

Special role in computer simulations of supercooled liquid and glasses is played by few general models representing certain classes of real glass-forming systems. Recently, it was shown that one of the most widely used model glassformers -- Kob-Andersen binary Lennard-Jones mixture -- crystalizes in quite lengthy molecular dynamics simulations and, moreover, it is in fact a very poor glassformer at large system sizes. Thus, our understanding of crystallization stability of model glassformers is far from complete due to the fact that relatively small system sizes and short timescales have been considered so far. Here we address this issue for two embedded atom models intensively used last years in numerical studies of Cu-Zr-(Al) bulk metallic glasses. We consider ${\rm Cu_{64.5}Zr_{35.5}}$ and ${\rm Cu_{46}Zr_{46}Al_{8}}$ alloys as those having high glass-forming ability. Exploring their structural evolution at continuous cooling and isothermal annealing, we observe that both systems nucleate in sufficiently lengthy simulations, though ${\rm Cu_{46}Zr_{46}Al_{8}}$ demonstrate order of magnitude higher critical nucleation time. Moreover, ${\rm Cu_{64.5}Zr_{35.5}}$ is actually unstable to crystallization for large system sizes ($N > 20,000$). Both systems crystallize with the formation of tetrahedrally close packed Laves phases of different types. We reveal that structure of both systems in liquid and glassy state contains comparable amount of polytetrahedral clusters. We argue that nucleation instability of simulated ${\rm Cu_{64.5}Zr_{35.5}}$ alloy is due to the fact that its composition is very close to that for stable ${\rm Cu_2 Zr}$ compound with C15 Laves phase structure.

cond-mat.mtrl-sci↗

arXiv2019

Nanoscale domains in ionic liquids: A statistical mechanics definition for molecular dynamics studies

One of the many open questions concerning Ionic Liquids (ILs) is the existence of nanoscale supramolecular domains which characterize the bulk. The hypothesis of their existence does not meet a general consensus since their definition seems to be based on ad hoc arbitrary criteria rather than on general and solid first principles of physics. In this work, we propose a suitable definition of supramolecular domains based on first principles of statistical mechanics. Such principles can be realized through the application of a recently developed computational tool which employs adaptive molecular resolution. The method can identify the smallest region of a liquid for which the atomistic details are strictly required, while the exterior plays the role of a generic structureless thermodynamic reservoir. We consider four different imidazolium-based ILs and show that indeed one can quantitatively represent the liquid as a collection of atomistically self-contained nanodroplets embedded in a generic thermodynamic bath. Such nanodroplets express a characteristic length scale for heterogeneity in ILs.

physics.chem-ph↗

arXiv2018

Fast Semistochastic Heat-Bath Configuration Interaction

This paper presents in detail our fast semistochastic heat-bath configuration interaction (SHCI) method for solving the many-body Schrodinger equation. We identify and eliminate computational bottlenecks in both the variational and perturbative steps of the SHCI algorithm. We also describe the parallelization and the key data structures in our implementation, such as the distributed hash table. The improved SHCI algorithm enables us to include in our variational wavefunction two orders of magnitude more determinants than has been reported previously with other selected configuration interaction methods. We use our algorithm to calculate an accurate benchmark energy for the chromium dimer with the X2C relativistic Hamiltonian in the cc-pVDZ-DK basis, correlating 28 electrons in 76 spatial orbitals. Our largest calculation uses two billion Slater determinants in the variational space, and semistochastically includes perturbative contributions from at least trillions of additional determinants with better than 10 microhartree statistical uncertainty.

physics.chem-ph↗

arXiv2018

Ehrenfest+R Dynamics II: A Semiclassical QED Framework for Raman Scattering

In a previous paper, we introduced Ehrenfest+R dynamics for a two-level system and showed how spontaneous emission can be heuristically included such that, after averaging over an ensemble of Ehrenfest+R trajectories, one can recover both coherent and incoherent electromagnetic fields. In the present paper, we now show that Ehrenfest+R dynamics can also correctly describe Raman scattering, whose features are completely absent from standard Ehrenfest dynamics. Ehrenfest+R dynamics appear to be quantitatively accurate both for resonant and off-resonant Raman signals, as compared with Kramers-Heisenberg-Dirac (KHD) theory.

physics.chem-ph↗

arXiv2019

Predictive Collective Variable Discovery with Deep Bayesian Models

Extending spatio-temporal scale limitations of models for complex atomistic systems considered in biochemistry and materials science necessitates the development of enhanced sampling methods. The potential acceleration in exploring the configurational space by enhanced sampling methods depends on the choice of collective variables (CVs). In this work, we formulate the discovery of CVs as a Bayesian inference problem and consider the CVs as hidden generators of the full-atomistic trajectory. The ability to generate samples of the fine-scale atomistic configurations using limited training data allows us to compute estimates of observables as well as our probabilistic confidence on them. The methodology is based on emerging methodological advances in machine learning and variational inference. The discovered CVs are related to physicochemical properties which are essential for understanding mechanisms especially in unexplored complex systems. We provide a quantitative assessment of the CVs in terms of their predictive ability for alanine dipeptide (ALA-2) and ALA-15 peptide.

stat.ML↗

arXiv2018

Time-resolved double-resonance spectroscopy: Lifetime measurement of the $6\,^1Σ_g^+(7,31)$ electronic state of molecular sodium

We report on the lifetime measurement of the $6\,^1Σ_g^+ (7,31)$ state of Na$_2$ molecules, produced in a heat-pipe oven, using a time-resolved spectroscopic technique. The $6\,^1Σ_g^+ (7,31)$ level was populated by two-step two-color double resonance excitation via the intermediate $A\,^1Σ_u^+ (8,30)$ state. The excitation scheme was done using two synchronized pulsed dye lasers pumped by a Nd:YAG laser operating at the second harmonics. The fluorescence emitted upon decay to the final state was measured using a time-correlated photon counting technique, as a function of argon pressure. From this the radiative lifetime was extracted by extrapolating the plot to collision-free zero pressure. We also report calculated radiative lifetimes of the Na$_2$ $6\,^1Σ_g^+$ ro-vibrational levels in the range of $v=0-200$ with $J=1$ and $J=31$ using the LEVEL program for bound-bound and the BCONT program for bound-free transitions. Our calculations reveal the importance of the bound-free transitions on the lifetime calculations and a large difference of about a factor of three between the $J=1$ and $J=31$ for the $v=40$ and $v=100$, due to the wavefunction alternating between having predominantly inner and outer well amplitude.

physics.chem-ph↗

arXiv2018

The electronic complexity of the ground-state of the FeMo cofactor of nitrogenase as relevant to quantum simulations

We report that a recent active space model of the nitrogenase FeMo cofactor, proposed in the context of quantum simulations, is not representative of the electronic structure of the FeMo cofactor ground-state. Although quantum resource estimates, outside of the cost of adiabatic state preparation, will not be much affected, conclusions should not be drawn from the complexity of classical simulations of the electronic structure of this system in this active space. We provide a different model active space for the FeMo cofactor that contains the basic open-shell qualitative character, which may be useful as a benchmark system for making classical and quantum resource estimates.

physics.chem-ph↗

arXiv2018

Pair and Many-body Interactions Between Ligated Au Nanoparticles

We report the results of molecular dynamics simulations of the properties of a pseudo-atom model of dodecane thiol ligated 5-nm diameter gold nanoparticles (AuNP) in vacuum as a function of ligand coverage and particle separation in three state of aggregation: the isolated AuNP, an isolated pair of AuNPs and a square assembly of AuNPs. Our calculations show that for all values of the coverage the ligand density along a radius emanating from the core of an isolated AuNP oscillates along the chain up to the fourth pseudo-atom, then smoothly decays to zero. We examine the ligand envelope as a function of the coverage and demonstrate that the deformation of that envelope generated by interaction between the NPs is coverage-dependent, so that the shape, depth and position of the minimum of the potential of mean force displays a systematic dependence on the coverage. We propose an accurate analytical description of the calculated potential of mean force with parameters that scale linearly with the ligand coverage. We define and calculate an effective pair potential of mean force for a square configuration of particles; our definition contains, implicitly, both the three- and four-particle contributions to deviation from additivity. We find that the effective pair potential of mean force in this configuration has a different minimum and a different well depth than the isolated pair potential of mean force. Previous work has found that the three-particle contribution to deviation from additivity is monotone repulsive, whereas we find that the combined three- and four-particle contributions have an attractive well, implying that the three- and four-particle contributions are of comparable magnitude but opposite sign, thereby suggesting that even higher order correction terms likely play a significant role in the behavior of assemblies of many nanoparticles.

physics.chem-ph↗

arXiv2018

Automated detection of many-particle solvation states for accurate characterizations of diffusion kinetics

Discrete-space kinetic models, i.e., Markov state models, have emerged as powerful tools for reducing the complexity of trajectories generated from molecular dynamics simulations. These models require configuration-space representations that accurately characterize the relevant dynamics. Well-established, low-dimensional order parameters for constructing this representation have led to widespread application of Markov state models to study conformational dynamics in biomolecular systems. On the contrary, applications to characterize single-molecule diffusion processes have been scarce and typically employ system-specific, higher-dimensional order parameters to characterize the local solvation state of the molecule. In this work, we propose an automated method for generating a coarse configuration-space representation, using generic features of solvation structure---the coordination numbers about each particle. To overcome the inherent noisy behavior of these low-dimensional observables, we treat the features as indicators of an underlying, latent Markov process. The resulting hidden Markov models filter the trajectories of each feature into the most likely latent solvation state at each time step. The filtered trajectories are then used to construct a configuration-space discretization, which accurately describes the diffusion kinetics. The method is validated on a standard model for glassy liquids, where particle jumps between local cages determine the diffusion properties of the system. Not only do the resulting models provide quantitatively accurate characterizations of the diffusion constant, but they also reveal a mechanistic description of diffusive jumps, quantifying the heterogeneity of local diffusion.

physics.chem-ph↗

arXiv2018

Heat transfer statistics in mixed quantum-classical systems

The modelling of quantum heat transfer processes at the nanoscale is crucial for the development of energy harvesting and molecular electronics devices. Herein, we adopt a mixed quantum-classical description of a device, in which the open subsystem of interest is treated quantum mechanically and the surrounding heat baths are treated in a classical-like fashion. By introducing such a mixed quantum-classical description of the composite system, one is able to study the heat transfer between the subsystem and bath from a closed system point of view, thereby avoiding simplifying assumptions related to the bath time scale and subsystem-bath coupling strength. In particular, we adopt the full counting statistics approach to derive a general expression for the moment generating function of heat in systems whose dynamics are described by the quantum-classical Liouville equation (QCLE). From this expression, one can deduce expressions for the dynamics of the average heat and heat current, which may be evaluated using numerical simulations. Due to the approximate nature of the QCLE, we also find that the steady state fluctuation symmetry holds up to order $\hbar$ for systems whose subsystembath couplings and baths go beyond bilinear and harmonic, respectively. To demonstrate the approach, we consider the nonequilibrium spin boson model and simulate its time-dependent average heat and heat current under various conditions.

physics.chem-ph↗

arXiv2018

Phononic heat transport in molecular junctions: quantum effects and vibrational mismatch

Problems of heat transport are ubiquitous to various technologies such as power generation, cooling, electronics, and thermoelectrics. In this paper we advocate for the application of the quantum self-consistent reservoir method, which is based on the generalized quantum Langevin equation, to study phononic thermal conduction in molecular junctions. The method emulates phonon-phonon scattering processes while taking into account quantum effects and far-from-equilibrium (large temperature difference) conditions. We test the applicability of the method by simulating the thermal conductance of molecular junctions with one-dimensional molecules sandwiched between solid surfaces. Our results satisfy the expected behavior of the thermal conductance in anharmonic chains as a function of length, phonon scattering rate and temperature, thus validating the computational scheme. Moreover, we examine the effects of vibrational mismatch between the solids' phonon spectra on the heat transfer characteristics in molecular junctions. Here, we reveal the dual role of vibrational anharmonicity: It raises the resistance of the junction due to multiple scattering processes, yet it promotes energy transport across a vibrational mismatch by enabling phonon recombination and decay processes.

cond-mat.mes-hall↗

arXiv2018

Feynman Diagram Description of 2D-Raman-THz Spectroscopy Applied to Water

2D-Raman-THz spectroscopy of liquid water, which has been presented recently (Proc. Natl. Acad. Sci. USA 110, 20402 (2013)), directly probes the intermolecular degrees of freedom of the hydrogen-bond network. However, being a relatively new technique, its information content is not fully explored as to date. While the spectroscopic signal can be simulated based on molecular dynamics simulation in connection with a water force field, it is difficult to relate spectroscopic signatures to the underlying microscopic features of the force field. Here, a completely different approach is taken that starts from an as simple as possible model, i.e., a single vibrational mode with electrical and mechanical anharmonicity augmented with homogeneous and inhomogeneous broadening. An intuitive Feynman diagram picture is developed for all possible pulse sequences of hybrid 2D-Raman-THz spectroscopy. It is shown that the model can explain the experimental data essentially quantitatively with a very small set of parameters, and it is tentatively concluded that the experimental signal originates from the hydrogen-bond stretching vibration around 170 cm$^{-1}$. Furthermore, the echo observed in the experimental data can be quantified by fitting the model. A dominant fraction of its linewidth is attributed to quasi-inhomogeneous broadening in the slow-modulation limit with a correlation time of 370 fs, reflecting the lifetime of the hydrogen-bond networks giving rise the absorption band.

physics.chem-ph↗