Showing papers on "Path integral molecular dynamics published in 2018"

The Quest for Accurate Liquid Water Properties from First Principles.

Abstract: Developing accurate ab initio molecular dynamics (AIMD) models that capture both electronic reorganization and nuclear quantum effects associated with hydrogen bonding is key to quantitative understanding of bulk water and its anomalies as well as its role as a universal solvent. For condensed phase simulations, AIMD has typically relied on the generalized gradient approximation (GGA) of density functional theory (DFT) as the underlying model chemistry for the potential energy surface, with nuclear quantum effects (NQEs) sometimes modeled by performing classical molecular dynamics simulations at elevated temperatures. Here we show that the properties of liquid water obtained from the meta-GGA B97M-rV functional, when evaluated using accelerated path integral molecular dynamics simulations, display accuracy comparable to a computationally expensive dispersion-corrected hybrid functional, revPBE0-D3. We show that the meta-GGA DFT functional reproduces bulk water properties including radial distribution functions, self-diffusion coefficients, and infrared spectra with comparable accuracy of a much more expensive hybrid functional. This work demonstrates that the underlying quality of a good DFT functional requires evaluation with quantum nuclei and that high-temperature simulations are a poor proxy for properly treating NQEs.

Decisive role of nuclear quantum effects on surface mediated water dissociation at finite temperature.

Abstract: Water molecules adsorbed on inorganic substrates play an important role in several technological applications. In the presence of light atoms in adsorbates, nuclear quantum effects (NQEs) influence the structural stability and the dynamical properties of these systems. In this work, we explore the impact of NQEs on the dissociation of water wires on stepped Pt(221) surfaces. By performing ab initio molecular dynamics simulations with van der Waals corrected density functional theory, we note that several competing minima for both intact and dissociated structures are accessible at finite temperatures, making it important to assess whether harmonic estimates of the quantum free energy are sufficient to determine the relative stability of the different states. We thus perform ab initio path integral molecular dynamics (PIMD) in order to calculate these contributions taking into account the conformational entropy and anharmonicities at finite temperatures. We propose that when adsorption is weak and NQEs on the substrate are negligible, PIMD simulations can be performed through a simple partition of the system, resulting in considerable computational savings. We then calculate the full contribution of NQEs to the free energies, including also anharmonic terms. We find that they result in an increase of up to 20% of the quantum contribution to the dissociation free energy compared with the harmonic estimates. We also find that the dissociation process has a negligible contribution from tunneling but is dominated by zero point energies, which can enhance the rate of dissociation by three orders of magnitude. Finally we highlight how both temperature and NQEs indirectly impact dipoles and the redistribution of electron density, causing work function changes of up to 0.4 eV with respect to static estimates. This quantitative determination of the change in the work function provides a possible approach to determine experimentally the most stable configurations of water oligomers on the stepped surfaces.

Coupled electron-ion Monte Carlo simulation of hydrogen molecular crystals

Abstract: We performed simulations for solid molecular hydrogen at high pressures (250 GPa ≤ P ≤ 500 GPa) along two isotherms at T = 200 K (phase III) and at T = 414 K (phase IV). At T = 200 K, we considered likely candidates for phase III, the C2c and Cmca12 structures, while at T = 414 K in phase IV, we studied the Pc48 structure. We employed both Coupled Electron-Ion Monte Carlo (CEIMC) and Path Integral Molecular Dynamics (PIMD). The latter is based on Density Functional Theory (DFT) with the van der Waals approximation (vdW-DF). The comparison between the two methods allows us to address the question of the accuracy of the exchange-correlation approximation of DFT for thermal and quantum protons without recurring to perturbation theories. In general, we find that atomic and molecular fluctuations in PIMD are larger than in CEIMC which suggests that the potential energy surface from vdW-DF is less structured than the one from quantum Monte Carlo. We find qualitatively different behaviors for systems prepared in the C2c structure for increasing pressure. Within PIMD, the C2c structure is dynamically partially stable for P ≤ 250 GPa only: it retains the symmetry of the molecular centers but not the molecular orientation; at intermediate pressures, it develops layered structures like Pbcn or Ibam and transforms to the metallic Cmca-4 structure at P ≥ 450 GPa. Instead, within CEIMC, the C2c structure is found to be dynamically stable at least up to 450 GPa; at increasing pressure, the molecular bond length increases and the nuclear correlation decreases. For the other two structures, the two methods are in qualitative agreement although quantitative differences remain. We discuss various structural properties and the electrical conductivity. We find that these structures become conducting around 350 GPa but the metallic Drude-like behavior is reached only at around 500 GPa, consistent with recent experimental claims.

Activation Energy of Organic Cation Rotation in CH3NH3PbI3 and CD3NH3PbI3: Quasi-Elastic Neutron Scattering Measurements and First-Principles Analysis Including Nuclear Quantum Effects.

Abstract: The motion of CH3NH3+ cations in the low-temperature phase of the promising photovoltaic material methylammonium lead triiodide (CH3NH3PbI3) is investigated experimentally as well as theoretically, with a particular focus on the activation energy. Inelastic and quasi-elastic neutron scattering measurements reveal an activation energy of ∼48 meV. Through a combination of experiments and first-principles calculations, we attribute this activation energy to the relative rotation of CH3 against an NH3 group that stays bound to the inorganic cage. The inclusion of nuclear quantum effects through path integral molecular dynamics gives an activation energy of ∼42 meV, in good agreement with the neutron scattering experiments. For deuterated samples (CD3NH3PbI3), both theory and experiment observe a higher activation energy for the rotation of CD3 against NH3, which results from the smaller nuclear quantum effects in CD3. The rotation of the NH3 group, which is bound to the inorganic cage via strong hydrogen bond...

On the importance of accounting for nuclear quantum effects in ab initio calibrated force fields in biological simulations.

Abstract: In many important processes in chemistry, physics, and biology the nuclear degrees of freedom cannot be described using the laws of classical mechanics. At the same time, the vast majority of molecular simulations that employ wide-coverage force fields treat atomic motion classically. In light of the increasing desire for and accelerated development of quantum mechanics (QM)-parameterized interaction models, we reexamine whether the classical treatment is sufficient for a simple but crucial chemical species: alkanes. We show that when using an interaction model or force field in excellent agreement with the “gold standard” QM data, even very basic simulated properties of liquid alkanes, such as densities and heats of vaporization, deviate significantly from experimental values. Inclusion of nuclear quantum effects via techniques that treat nuclear degrees of freedom using the laws of classical mechanics brings the simulated properties much closer to reality.

Tunneling splittings from path-integral molecular dynamics using a Langevin thermostat.

Abstract: We report an improved method for the calculation of tunneling splittings between degenerate configurations in molecules and clusters using path-integral molecular dynamics (PIMD). Starting from an expression involving a ratio of thermodynamic density matrices at the bottom of the symmetric wells, we use thermodynamic integration with molecular dynamics simulations and a Langevin thermostat to compute the splittings stochastically. The thermodynamic integration is performed by sampling along the semiclassical instanton path, which provides an efficient reaction coordinate as well as being physically well-motivated. This approach allows us to carry out PIMD calculations of the multi-well tunneling splitting pattern in the water dimer and to refine previous PIMD calculations for one-dimensional models and malonaldehyde. The large (acceptor) splitting in the water dimer agrees to within 20% of benchmark variational results, and the smaller splittings agree to within 10%.

Unraveling electronic absorption spectra using nuclear quantum effects: Photoactive yellow protein and green fluorescent protein chromophores in water.

Abstract: Many physical phenomena must be accounted for to accurately model solution-phase optical spectral line shapes, from the sampling of chromophore-solvent configurations to the electronic-vibrational transitions leading to vibronic fine structure. Here we thoroughly explore the role of nuclear quantum effects, direct and indirect solvent effects, and vibronic effects in the computation of the optical spectrum of the aqueously solvated anionic chromophores of green fluorescent protein and photoactive yellow protein. By analyzing the chromophore and solvent configurations, the distributions of vertical excitation energies, the absorption spectra computed within the ensemble approach, and the absorption spectra computed within the ensemble plus zero-temperature Franck-Condon approach, we show how solvent, nuclear quantum effects, and vibronic transitions alter the optical absorption spectra. We find that including nuclear quantum effects in the sampling of chromophore-solvent configurations using ab initio path integral molecular dynamics simulations leads to improved spectral shapes through three mechanisms. The three mechanisms that lead to line shape broadening and a better description of the high-energy tail are softening of heavy atom bonds in the chromophore that couple to the optically bright state, widening the distribution of vertical excitation energies from more diverse solvation environments, and redistributing spectral weight from the 0-0 vibronic transition to higher energy vibronic transitions when computing the Franck-Condon spectrum in a frozen solvent pocket. The absorption spectra computed using the combined ensemble plus zero-temperature Franck-Condon approach yield significant improvements in spectral shape and width compared to the spectra computed with the ensemble approach. Using the combined approach with configurations sampled from path integral molecular dynamics trajectories presents a significant step forward in accurately modeling the absorption spectra of aqueously solvated chromophores.

Converged Colored Noise Path Integral Molecular Dynamics Study of the Zundel Cation Down to Ultralow Temperatures at Coupled Cluster Accuracy

Abstract: For a long time, performing converged path integral simulations at ultralow but finite temperatures of a few Kelvin has been a nearly impossible task However, recent developments in advanced colored noise thermostatting schemes for path integral simulations, namely, the Path Integral Generalized Langevin Equation Thermostat (PIGLET) and the Path Integral Quantum Thermal Bath (PIQTB), have been able to greatly reduce the computational cost of these simulations, thus making the ultralow temperature regime accessible in practice In this work, we investigate the influence of these two thermostatting schemes on the description of hydrogen-bonded systems at temperatures down to a few Kelvin as encountered, for example, in helium nanodroplet isolation or tagging photodissociation spectroscopy experiments For this purpose, we analyze the prototypical hydrogen bond in the Zundel cation (H5O2+) as a function of both oxygen–oxygen distance and temperature in order to elucidate how the anisotropic quantum delocali

Proton transfer in guanine–cytosine base pair analogues studied by NMR spectroscopy and PIMD simulations

Abstract: It has been hypothesised that proton tunnelling between paired nucleobases significantly enhances the formation of rare tautomeric forms and hence leads to errors in DNA replication. Here, we study nuclear quantum effects (NQEs) using deuterium isotope-induced changes of nitrogen NMR chemical shifts in a model base pair consisting of two tautomers of isocytosine, which form hydrogen-bonded dimers in the same way as the guanine–cytosine base pair. Isotope effects in NMR are consequences of NQEs, because ro-vibrational averaging of different isotopologues gives rise to different magnetic shielding of the nuclei. The experimental deuterium-induced chemical shift changes are compared with those calculated by a combination of path integral molecular dynamics (PIMD) simulations with DFT calculations of nuclear shielding. These calculations can directly link the observable isotope-induced shifts with NQEs. A comparison of the deuterium-induced changes of 15N chemical shifts with those predicted by PIMD simulations shows that inter-base proton transfer reactions do not take place in this system. We demonstrate, however, that NMR isotope shifts provide a unique possibility to study NQEs and to evaluate the accuracy of the computational methods used for modelling quantum effects in molecules. Calculations based on the PBE functional from the general-gradient-approximation family provided significantly worse predictions of deuterium isotope shifts than those with the hybrid B3LYP functional.

Path integral molecular dynamic simulation of flexible molecular systems in their ground state: Application to the water dimer.

Abstract: We extend the Langevin equation Path Integral Ground State (LePIGS), a ground state quantum molecular dynamics method, to simulate flexible molecular systems and calculate both energetic and structural properties. We test the approach with the H2O and D2O monomers and dimers. We systematically optimize all simulation parameters and use a unity trial wavefunction. We report ground state energies, dissociation energies, and structural properties using three different water models, two of which are empirically based, q-TIP4P/F and q-SPC/Fw, and one which is ab initio, MB-pol. We demonstrate that our energies calculated from LePIGS can be merged seamlessly with low temperature path integral molecular dynamics calculations and note the similarities between the two methods. We also benchmark our energies against previous diffusion Monte Carlo calculations using the same potentials and compare to experimental results. We further demonstrate that accurate vibrational energies of the H2O and D2O monomer can be calculated from imaginary time correlation functions generated from the LePIGS simulations using solely the unity trial wavefunction.

Path integral molecular dynamics for exact quantum statistics of multi-electronic-state systems.

Abstract: An exact approach to compute physical properties for general multi-electronic-state (MES) systems in thermal equilibrium is presented. The approach is extended from our recent progress on path integral molecular dynamics (PIMD), Liu et al. [J. Chem. Phys. 145, 024103 (2016)] and Zhang et al. [J. Chem. Phys. 147, 034109 (2017)], for quantum statistical mechanics when a single potential energy surface is involved. We first define an effective potential function that is numerically favorable for MES-PIMD and then derive corresponding estimators in MES-PIMD for evaluating various physical properties. Its application to several representative one-dimensional and multi-dimensional models demonstrates that MES-PIMD in principle offers a practical tool in either of the diabatic and adiabatic representations for studying exact quantum statistics of complex/large MES systems when the Born-Oppenheimer approximation, Condon approximation, and harmonic bath approximation are broken.

Nuclear quantum effects induce metallization of dense solid molecular hydrogen.

Abstract: We present an accurate computational study of the electronic structure and lattice dynamics of solid molecular hydrogen at high pressure. The band-gap energies of the C2/c, Pc, and P63/m structures at pressures of 250, 300, and 350 GPa are calculated using the diffusion quantum Monte Carlo (DMC) method. The atomic configurations are obtained from ab initio path-integral molecular dynamics (PIMD) simulations at 300 K and 300 GPa to investigate the impact of zero-point energy and temperature-induced motion of the protons including anharmonic effects. We find that finite temperature and nuclear quantum effects reduce the band-gaps substantially, leading to metallization of the C2/c and Pc phases via band overlap; the effect on the band-gap of the P63/m structure is less pronounced. Our combined DMC-PIMD simulations predict that there are no excitonic or quasiparticle energy gaps for the C2/c and Pc phases at 300 GPa and 300 K. Our results also indicate a strong correlation between the band-gap energy and vibron modes. This strong coupling induces a band-gap reduction of more than 2.46 eV in high-pressure solid molecular hydrogen. Comparing our DMC-PIMD with experimental results available, we conclude that none of the structures proposed is a good candidate for phases III and IV of solid hydrogen. © 2017 Wiley Periodicals, Inc.

Quantum mechanical free energy profiles with post-quantization restraints: Binding free energy of the water dimer over a broad range of temperatures

Abstract: Free energy calculations are a crucial part of understanding chemical systems but are often computationally expensive for all but the simplest of systems. Various enhanced sampling techniques have been developed to improve the efficiency of these calculations in numerical simulations. However, the majority of these approaches have been applied using classical molecular dynamics. There are many situations where nuclear quantum effects impact the system of interest and a classical description fails to capture these details. In this work, path integral molecular dynamics has been used in conjunction with umbrella sampling, and it has been observed that correct results are only obtained when the umbrella sampling potential is applied to a single path integral bead post quantization. This method has been validated against a Lennard-Jones benchmark system before being applied to the more complicated water dimer system over a broad range of temperatures. Free energy profiles are obtained, and these are utilized in the calculation of the second virial coefficient as well as the change in free energy from the separated water monomers to the dimer. Comparisons to experimental and ground state calculation values from the literature are made for the second virial coefficient at higher temperature and the dissociation energy of the dimer in the ground state.

Tunneling-splittings from path-integral molecular dynamics using a Langevin thermostat

Abstract: We report an improved method for the calculation of tunneling splittings between degenerate configurations in molecules and clusters using path-integral molecular dynamics (PIMD). Starting from an expression involving a ratio of thermodynamic density matrices at the bottom of the symmetric wells, we use thermodynamic integration with molecular dynamics simulations and a Langevin thermostat to compute the splittings stochastically. The thermodynamic integration is performed by sampling along the semiclassical instanton path, which provides an efficient reaction coordinate as well as being physically well-motivated. This approach allows us to carry out PIMD calculations of the multi-well tunnelling splitting pattern in water dimer, and to refine previous PIMD calculations for one-dimensional models and malonaldehyde. The large (acceptor) splitting in water dimer agrees to within 20% of benchmark variational results, and the smaller splittings are within 10%.

Accurate Calculation of Equilibrium Reduced Density Matrix for the System-Bath Model: a Multilayer Multiconfiguration Time-Dependent Hartree Approach and its Comparison to a Multi-Electronic-State Path Integral Molecular Dynamics Approach †

Abstract: An efficient and accurate method for computing the equilibrium reduced density matrix is presented for treating open quantum systems characterized by the system-bath model. The method employs the multilayer multiconfiguration time-dependent Hartree theory for imaginary time propagation and an importance sampling procedure for calculating the quantum mechanical trace. The method is applied to the spin-boson Hamiltonian, which leads to accurate results in agreement with those produced by the multi-electronic-state path integral molecular dynamics method.

Continuum limit and preconditioned Langevin sampling of the path integral molecular dynamics

Abstract: We investigate the continuum limit that the number of beads goes to infinity in the ring polymer representation of thermal averages. Studying the continuum limit of the trajectory sampling equation sheds light on possible preconditioning techniques for sampling ring polymer configurations with large number of beads. We propose two preconditioned Langevin sampling dynamics, which are shown to have improved stability and sampling accuracy. We present a careful mode analysis of the preconditioned dynamics and show their connections to the normal mode, the staging coordinate and the Matsubara mode representation for ring polymers. In the case where the potential is quadratic, we show that the continuum limit of the preconditioned mass modified Langevin dynamics converges to its equilibrium exponentially fast, which suggests that the finite-dimensional counterpart has a dimension-independent convergence rate. In addition, the preconditioning techniques can be naturally applied to the multi-level quantum systems in the nonadiabatic regime, which are compatible with various numerical approaches.

Car-Parrinello and Path Integral Molecular Dynamics Study of the Proton Transfer in the Intramolecular Hydrogen Bonds in the Ketohydrazone-Azoenol System.

Abstract: Car-Parrinello (CPMD) and path integral molecular dynamics (PIMD) simulations were carried out for 1-(phenylazo)-2-naphthol (I) and 1-(4-F-phenylazo)-2-naphthol (II) (Sudan I) in vacuo and in the solid state at 298 K. The fast proton transfer (FPT) and tautomerism in the ketohydrazone-azoenol systems have been analyzed on the basis of CPMD and PIMD methods level. The two-dimensional free-energy landscape of reaction coordinate δ-parameter and RN···O distances shows the NH tautomer to be more favorable in the gas phase as well as in the solid state according to the CP and PI results, respectively. The hydrogen between the nitrogen and the oxygen atoms adopts a starkly asymmetrical position in the double potential well. The molecular geometry and energy barrier for the intramolecular proton transference were calculated, and the value found suggested a strong hydrogen bond with low barrier for FPT mechanism. These studies and the two-dimensional average index of π-delocalization ⟨λ⟩ landscape of time evolutions of RN1···O1 and RC1═O1 distances for both the crystals indicate that the hydrogen bonds in the crystals of 1-(phenylazo)-2-naphthol (I) and 1-(4-F-phenylazo)-2-naphthol (II) have characteristic properties for the type of bonding model: resonance-assisted hydrogen bonds and low-barrier hydrogen bonds, without the existence of equilibrium in the two tautomers. The infrared spectrum has been calculated, and a comparative vibrational analysis has been performed. The CPMD vibrational results appear to qualitatively agree with the experimental ones.

Accelerated sampling by infinite swapping of path integral molecular dynamics with surface hopping

Abstract: To accelerate the thermal equilibrium sampling of multi-level quantum systems, the infinite swapping limit of a recently proposed multi-level ring polymer representation is investigated. In the infinite swapping limit, the ring polymer evolves according to an averaged Hamiltonian with respect to all possible surface index configurations of the ring polymer and thus connects the surface hopping approach to the mean-field path-integral molecular dynamics. A multiscale integrator for the infinite swapping limit is also proposed to enable efficient sampling based on the limiting dynamics. Numerical results demonstrate the huge improvement of sampling efficiency of the infinite swapping compared with the direct simulation of path-integral molecular dynamics with surface hopping.

Formation of rubidium dimers on the surface of helium clusters: a first step through quantum molecular dynamics simulations

Abstract: Starting with separated atoms on the surface of helium clusters 4HeN, and as a first step to assess the formation of rubidium dimers Rb2 in the triplet state, we perform Path Integral Molecular Dynamics simulations in the NVT canonical ensemble. Based on an accurate potential energy surface (PES) for the He–Rb2(3Σ u +) interaction [Guillon et al., J. Chem. Phys. 136, 174307 (2012)], the total PES is analytically described as the addition of pair interactions. The i-PI code [Ceriotti et al., Comput. Phys. Commun. 185, 1019 (2014)] was used to perform the simulations. At a temperature of 2 K, clusters containing up to N = 70 helium atoms, with a number up to 200 beads per particle to describe quantum effects, were considered.

A Molecular Perspective on Ion Hydration

Abstract: Author(s): Bajaj, Pushp | Advisor(s): Paesani, Francesco | Abstract: Hydration of anions, particularly halide ions, presents a particularly challenging problem where due to strong intermolecular interactions the ion can significantly alter the hydrogen bonding network of water. The extent to which varies greatly depending on the nature of ion-water interactions. An accurate description of the interplay between ion-water and water-water interactions is necessary to achieve a molecular level understanding of ion hydration. In this work, we present a bottom-up analysis of the structure, energetics, vibrational spectroscopy and hydrogen bond arrangement of small halide-water clusters (X-(H2O)n, X- = F-, Cl-, Br-, I-) using state-of-the-art computational chemistry tools. We begin by developing ab initio based many-body potential energy functions PEFs, called MB-nrg, for describing halide-water intermolecular interactions that include many-body effects for all system sizes by taking into account explicitly the two-body and three-body interactions, and all higher order interactions implicitly through a mean field approximation. To directly probe the strength of halide-water intermolecular interactions, full dimensional vibrational spectra are calculated for both X-(H2O) and X-(D2O) dimers at the quantum-mechanical level. Followed by an analysis of the structure, hydrogen bond arrangement and temperature dependent dynamics of the I-(H2O)2 and I-(D2O)2 through quantum path integral molecular dynamics simulations. Tunneling pathways leading hydrogen bond rearrangement were identified and the corresponding tunneling splitting patterns were calculated using the ring polymer instanton method. Finally, we studied the structural, thermodynamic and spectroscopic properties of small X-(H2O)n clusters where X- = F-, Cl-, Br-, I-), n=3-6, using replica exchange molecular dynamics simulations. Across all sizes, fluoride-water clusters exhibit qualitatively different structures and properties compared to the chloride-, bromide- and iodide-water clusters which, on the other hand, are found to be similar to each other. This is a direct consequence of the exceptionally strong fluoride-water intermolecular interactions, which significantly affect the water-water hydrogen bonding strength and arrangement in the vicinity. Through extensive comparisons between the MB-nrg PEFs and classical polarizable force fields and approximate ab initio methods like density functional theory and MP2, our results emphasize the importance of an accurate description of the quantum mechanical many-body intermolecular interactions for a robust molecular level understanding of halide ion hydration. Follow-up studies of larger cluster sizes will focus on the evolution of the hydration shells in a systematic way.

Investigations of the hydrogen bond in the crystals of tropolone and thiotropolone via car‐parrinello and path integral molecular dynamics

Abstract: Car-Parrinello and path integrals molecular dynamics (CPMD and PIMD) simulations were carried out for the 10π-electron aromatic systems: 2-hydroxy-2,4,6-cycloheptatrien-1-one, commonly known as Tropolone (I) and 2-hydroxy-2,4,6-cycloheptatriene-1-thione, called Thiotropolone (II) in vacuo and in the solid state. The extremely fast proton transfer (FPT) and "prototropy" tautomerism in the keto-enol (thione-enethiol) systems have been analyzed on the basis of CPMD and PIMD methods level. Comparisons of two-dimensional (2D) free-energy landscapes of reaction coordinate δ-parameter and RO…O or RO…S distances shows that the OH… tautomer to be more favorable in the Thiotropolone. The hydrogen between the oxygen and the sulfur atoms adopts a starkly asymmetrical position in the double potential well. The values of the energy barriers for the FPT were calculated and suggested a strong hydrogen bond with low barrier for FPT mechanism. These studies and the 2D average index of π-delocalization 〈λ〉 landscape of time evolutions of RO1…O2 and RC7O2 or RC7S1 distances for the both crystals indicate that hydrogen bonds in the crystals of Tropolone (I) and Thiotropolone (II) have characteristic properties for the type of bonding model resonance-assisted hydrogen bonds and also low-barrier hydrogen bonds. In the crystal of the Thiotropolone (II), we found the hydrogen bond OH…S existing without the equilibrium of the two tautomers whereas in the crystal of the Tropolone (I) has been confirmed the hydrogen bond OH…O existing with the equilibrium of the two tautomers. It was also found the significant differences in frequency, speed, and the image of the FPT in the studied crystals. © 2018 Wiley Periodicals, Inc.

Quantum Simulation Verifies the Stability of an 18-Coordinated Actinium-Helium Complex.

Abstract: Structures of a trivalent actinium cation in helium clusters (Ac3+ ⋅Hen ) have been studied by quantum path integral molecular dynamics simulations with different cluster sizes, n=18-200. The nuclear quantum effect of helium atoms plays an important role in the vibrational amplitude of the Ac3+ -He complex at low temperatures (1-3 K) at which the complex is stable. We found that the coordination number of helium atoms comprising the first solvation shell can be as high as eighteen. In this case, the helium atoms are arranged in D4d symmetry. The Ac3+ -He18 complex becomes more rigid as the cluster increases in size, which implies that it becomes more stable. The simulation results are based on an accurate description of the Ac3+ -He interaction using relativistic ab initio calculations.

Quantum structural fluctuation in para-hydrogen clusters revealed by the variational path integral method

Abstract: In this paper, the ground state of para-hydrogen clusters for size regime N ≤ 40 has been studied by our variational path integral molecular dynamics method. Long molecular dynamics calculations have been performed to accurately evaluate ground state properties. The chemical potential of the hydrogen molecule is found to have a zigzag size dependence, indicating the magic number stability for the clusters of the size N = 13, 26, 29, 34, and 39. One-body density of the hydrogen molecule is demonstrated to have a structured profile, not a melted one. The observed magic number stability is examined using the inherent structure analysis. We also have developed a novel method combining our variational path integral hybrid Monte Carlo method with the replica exchange technique. We introduce replicas of the original system bridging from the structured to the melted cluster, which is realized by scaling the potential energy of the system. Using the enhanced sampling method, the clusters are demonstrated to have the structured density profile in the ground state.

Can Path Integral Molecular Dynamics Make a Good Approximation for Vapor Pressure Isotope Effects Prediction for Organic Solvents? A Comparison to ONIOM QM/MM and QM Cluster Calculation.

Abstract: Isotopic fractionation of volatile organic compounds (VOCs), which are under strict measures of control because of their potential harm to the environment and humans, has an important ecological aspect, as the isotopic composition of compounds may depend on the conditions in which such compounds are distributed in Nature. Therefore, detailed knowledge on isotopic fractionation, not only experimental but also based on theoretical models, is crucial to follow conditions and pathways within which these contaminants are spread throughout the ecosystems. In this work, we present carbon and, for the first time, bromine vapor pressure isotope effect (VPIE) on the evaporation process from pure-phase systems—dibromomethane and bromobenzene, the representatives of aliphatic and aromatic brominated VOCs. We combine isotope effects measurements with their theoretical prediction using three computational techniques, namely path integral molecular dynamics, QM cluster, and hybrid ONIOM models. While evaporation of both...

First-Principles Molecular Dynamics and Computed Rate Constants for the Series of OH-HX Reactions (X = H or the Halogens): Non-Arrhenius Kinetics, Stereodynamics and Quantum Tunnel

Abstract: This paper is part of a series aiming at elucidating the mechanisms involved in the non-Arrhenius behavior of the four-body OH + HX (X = H, F,Cl, Br and I) reactions. These reactions are very important in atmospheric chemistry. Additionally, these four-body reactions are also of basic relevance for chemical kinetics. Their kinetics has manifested non-Arrhenius behavior: the experimental rate constants for the OH + HCl and OH + H2 reactions, when extended to low temperatures, show a concave curvature in the Arrhenius plot, a phenomenon designated as sub-Arrhenius behavior, while reactions with HBr and HI are considered as typical processes that exhibit negative temperature dependence of the rate constants (anti-Arrhenius behavior). From a theoretical point of view, these reactions have been studied in order to obtain the potential energy surface and to reproduce these complex rate constants using the Transition State Theory. Here, in order to understand the non-Arrhenius mechanism, we exploit recent information from ab initio molecular dynamics. For OH + HI and OH + HBr, the visualizations of rearrangements of bonds along trajectories has shown how molecular reorientation occurs in order that the reactants encounter a mutual angle of approach favorable for them to proceed to reaction. Besides the demonstration of the crucial role of stereodynamics, additional documentation was also provided on the interesting manifestation of the roaming phenomenon, both regarding the search for reactive configurations sterically favorable to reaction and the subsequent departure of products involving their vibrational excitation. Under moderate tunneling regime, the OH + H2 reaction was satisfactory described by deformed-Transition-State Theory. In the same reaction, the catalytic effect of water can be assessed by path integral molecular dynamics. For the OH + HCl reaction, the theoretical rate coefficients calculated with Bell tunneling correction were in good agreement with experimental data in the entire temperature range 200–2000 K, with minimal effort compared to much more elaborate treatments. Furthermore, the Born-Oppenheimer molecular dynamics simulation showed that the orientation process was less effective than for HBr and HI reactions, emphasizing the role of the quantum tunneling effect of penetration of an energy barrier in the reaction path along the potential energy surface. These results can shed light on the clarification of the different non-Arrhenius mechanisms involved in four-body reaction, providing rate constants and their temperature dependence of relevance for pure and applied chemical kinetics.

Nuclear quantum effects in the direct ionization process of pure helium clusters: path-integral and ring-polymer molecular dynamics simulations on the diatomics-in-molecule potential energy surfaces

Abstract: The direct photoionization of pure helium clusters, Hen (n = 100, 200 and 300), and its subsequent short-time process have been studied by path integral molecular dynamics (PIMD) and ring-polymer molecular dynamics (RPMD) simulations that can effectively describe the nuclear quantum effects in large systems. The modified diatomics-in-molecule (DIM) model [Calvo et al., J. Chem. Phys., 2011, 135, 124308] has been used to describe the electronic structures of Hen+ clusters. The PIMD simulations were able to reproduce the experimental ionization spectra having a broad and asymmetric nature, which can be ascribed to the inhomogeneity of the energy levels of He atoms in the inner and outer regions of the cluster. From the RPMD simulations, it is found that the ionized helium cluster in the higher excited state is followed by fast electronic state relaxation via nonadiabatic charge transfer including a small contribution of nuclear motions, and subsequently by slow relaxation of the cluster structure.

Molecular dynamics simulations of vibrational spectra of hydrogen-bonded systems

Abstract: In this chapter, we present current studies on molecular dynamics (MD) simulations of hydrogen-bonded systems with emphasis on vibrational spectra analysis. One of the most informative experimental data are spectroscopic data (infrared and Raman spectroscopy), which give information important in diverse fields, e.g. protein folding, drug design, sensors, nanotechnology, separations, etc. Spectroscopic data are very sensitive on inter- and intramolecular interactions. The processes of melting, boiling, unfolding and strand separation involve disruption of molecular interactions, that engage attractive or repulsive forces between molecules. In this chapter, we focus on calculations of IR spectra of hydrogen-bonded complexes based on linear response theory, in which the spectral density is the Fourier transform of the autocorrelation function of the dipole moment operator involved in the IR transitions. Recently, Born–Oppenheimer molecular dynamics (BOMD), Car–Parrinello molecular dynamics (CPMD), path integral molecular dynamics (PIMD), hybrid molecular dynamics (QM/MM) and other methods which use trajectories from molecular dynamics have been employed to simulate IR spectra of hydrogen-bonded systems. Each of these methods has some advantages and disadvantages which will be discussed in this chapter presenting also recent applications of these methods.

Nuclear Quantum Effect and H/D Isotope Effect on Hydrogen-Bonded Systems with Path Integral Simulation

Abstract: In the past two decades, ab initio path integral (PI) simulation , in particular , ab initio path integral molecular dynamics simulation has reached its maturity and has been widely used to take account of nuclear quantum effects, such as zero-point vibrational energy and tunneling, in complex many-body systems. In particular, this method has significantly contributed to provide important insights into structures and fluctuation of the hydrogen-bonded systems as well as their isotopomers at finite temperature. In this chapter, we will review the recent advances in ab initio PI simulation. The development of an efficient algorithm for ab initio PI simulation and some applications will be featured. The efficient algorithm for path integral hybrid Monte Carlo method based on the second- and fourth-order Trotter expansion, which realizes large reduction of computational effort without loss of accuracy, will be described in detail. The applications focusing on the hydrogen-bonded systems, protonated and deprotonated water dimers (H5O2 + and H3O2 −), F−(H2O)n (n = 1–3) clusters, and hydrogen maleate anion demonstrate the ability and powerfulness of PI simulation.

Using a monomer potential energy surface to perform approximate path integral molecular dynamics simulation of ab-initio water with near-zero added cost

Abstract: It is now established that nuclear quantum motion plays an important role in determining water's hydrogen bonding, structure, and dynamics. Such effects are important to include in density functional theory (DFT) based molecular dynamics simulation of water. The standard way of treating nuclear quantum effects, path integral molecular dynamics (PIMD), multiplies the number of energy/force calculations by the number of beads required. In this work we introduce a method whereby PIMD can be incorporated into a DFT simulation with little extra cost and little loss in accuracy. The method is based on the many body expansion of the energy and has the benefit of including a monomer level correction to the DFT energy. Our method calculates intramolecular forces using the highly accurate monomer potential energy surface developed by Partridge-Schwenke, which is cheap to evaluate. Intermolecular forces and energies are calculated with DFT only once per timestep using the centroid positions. We show how our method may be used in conjunction with a multiple time step algorithm for an additional speedup and how it relates to ring polymer contraction and other schemes that have been introduced recently to speed up PIMD simulations. We show that our method, which we call "monomer PIMD", correctly captures changes in the structure of water found in a full PIMD simulation but at much lower computational cost.

Nuclear quantum effects in molecular dynamics simulations

Abstract: To take into account nuclear quantum effects on the dynamics of atoms, the path integral molecular dynamics (PIMD) method used since 1980s is based on the formalism developed by R. P. Feynman. However, the huge computation time required for the PIMD reduces its range of applicability. Another drawback is the requirement of additional techniques to access time correlation functions (ring polymer MD or centroid MD). We developed an alternative technique based on a quantum thermal bath (QTB) which reduces the computation time by a factor of ~20. The QTB approach consists in a classical Langevin dynamics in which the white noise random force is replaced by a Gaussian random force having the power spectral density given by the quantum fluctuation-dissipation theorem. The method has yielded satisfactory results for weakly anharmonic systems: the quantum harmonic oscillator, the heat capacity of a MgO crystal, and isotope effects in 7 LiH and 7 LiD. Unfortunately, the QTB is subject to the problem of zero-point energy leakage (ZPEL) in highly anharmonic systems, which is inherent in the use of classical mechanics. Indeed, a part of the energy of the high-frequency modes is transferred to the low-frequency modes leading to a wrong energy distribution. We have shown that in order to reduce or even eliminate ZPEL, it is sufficient to increase the value of the frictional coefficient. Another way to solve the ZPEL problem is to combine the QTB and PIMD techniques. It requires the modification of the power spectral density of the random force within the QTB. This combination can also be seen as a way to speed up the PIMD.