Ab initio molecular dynamics simulation of liquid hydrogen fluoride

Hidden Halogen-Bonding Ability of Fluorine Manifesting in the Hydrogen-Bond Configurations of Hydrogen Fluoride

Elucidating how the intermolecular interactions of a covalently bonded fluorine atom are similar to and different from those of the other halogen atoms will be helpful for a better unified understanding of them. In the present study, the case of hydrogen fluoride is theoretically studied from this viewpoint by using the techniques of electron density analysis, molecular dynamics of liquid, and others. It is shown that the extra-point model, which locates an additional charge site on the line extended from (not within) the covalent bond and has been adopted for halogen-bonding systems as a key to the generation of proper stability and directionality, works well also in this case. A significantly bent hydrogen-bond configuration, which is characteristic of the intermolecular interactions of hydrogen fluoride, is reasonably well reproduced, meaning that it is a manifestation of the latent halogen-bonding ability, which is hidden by the strongly electronegative nature.

New Molecular-Mechanics Model for Simulations of Hydrogen Fluoride in Chemistry and Biology

Hydrogen fluoride (HF) is the most polar diatomic molecule and one of the simplest molecules capable of hydrogen-bonding. HF deviates from ideality both in the gas phase and in solution and is thus of great interest from a fundamental standpoint. Pure and aqueous HF solutions are broadly used in chemical and industrial processes, despite their high toxicity. HF is a stable species also in some biological conditions, because it does not readily dissociate in water unlike other hydrogen halides; yet, little is known about how HF interacts with biomolecules. Here, we set out to develop a molecular-mechanics model to enable computer simulations of HF in chemical and biological applications. This model is based on a comprehensive high-level ab initio quantum chemical investigation of the structure and energetics of the HF monomer and dimer; (HF)_n clusters, for n = 3-7; various clusters of HF and H₂O; and complexes of HF with analogs of all 20 amino acids and of several commonly occurring lipids, both neutral and ionized. This systematic analysis explains the unique properties of this molecule: for example, that interacting HF molecules favor nonlinear geometries despite being diatomic and that HF is a strong H-bond donor but a poor acceptor. The ab initio data also enables us to calibrate a three-site molecular-mechanics model, with which we investigate the structure and thermodynamic properties of gaseous, liquid, and supercritical HF in a wide range of temperatures and pressures; the solvation structure of HF in water and of H₂O in liquid HF; and the free diffusion of HF across a lipid bilayer, a key process underlying the high cytotoxicity of HF. Despite its inherent simplifications, the model presented significantly improves upon previous efforts to capture the properties of pure and aqueous HF fluids by molecular-mechanics methods and to our knowledge constitutes the first parameter set calibrated for biomolecular simulations.

Quantum mechanical force field for hydrogen fluoride with explicit electronic polarization

The explicit polarization (X-Pol) theory is a fragment-based quantum chemical method that explicitly models the internal electronic polarization and intermolecular interactions of a chemical system. X-Pol theory provides a framework to construct a quantum mechanical force field, which we have extended to liquid hydrogen fluoride (HF) in this work. The parameterization, called XPHF, is built upon the same formalism introduced for the XP3P model of liquid water, which is based on the polarized molecular orbital (PMO) semiempirical quantum chemistry method and the dipole-preserving polarization consistent point charge model. We introduce a fluorine parameter set for PMO, and find good agreement for various gas-phase results of small HF clusters compared to experiments and ab initio calculations at the M06-2X/MG3S level of theory. In addition, the XPHF model shows reasonable agreement with experiments for a variety of structural and thermodynamic properties in the liquid state, including radial distribution functions, interaction energies, diffusion coefficients, and densities at various state points.

Aqueous solutions: state of the art in ab initio molecular dynamics

The simulation of liquids by ab initio molecular dynamics (AIMD) has been a subject of intense activity over the last two decades. The significant increase in computational resources as well as the development of new and efficient algorithms has elevated this method to the status of a standard quantum mechanical tool that is used by both experimentalists and theoreticians. As AIMD computes the electronic structure from first principles, it is free of ad hoc parametrizations and has thus been applied to a large variety of physical and chemical problems. In particular, AIMD has provided microscopic insight into the structural and dynamical properties of aqueous solutions which are often challenging to probe experimentally. In this review, after a brief theoretical description of the Born-Oppenheimer and Car-Parrinello molecular dynamics formalisms, we show how AIMD has enhanced our understanding of the properties of liquid water and its constituent ions: the proton and the hydroxide ion. Thereafter, a broad overview of the application of AIMD to other aqueous systems, such as solvated organic molecules and inorganic ions, is presented. We also briefly describe the latest theoretical developments made in AIMD, such as methods for enhanced sampling and the inclusion of nuclear quantum effects.

Real-world predictions from ab initio molecular dynamics simulations

In this review we present the techniques of ab initio molecular dynamics simulation improved to its current stage where the analysis of existing processes and the prediction of further chemical features and real-world processes are feasible. For this reason we describe the relevant developments in ab initio molecular dynamics leading to this stage. Among them, parallel implementations, different basis set functions, density functionals, and van der Waals corrections are reported. The chemical features accessible through AIMD are discussed. These are IR, NMR, as well as EXAFS spectra, sampling methods like metadynamics and others, Wannier functions, dipole moments of molecules in condensed phase, and many other properties. Electrochemical reactions investigated by ab initio molecular dynamics methods in solution, on surfaces as well as complex interfaces, are also presented.

Collective High Frequency Motions in Liquid Deuterium Fluoride

The collective motions in liquid deuterium fluoride (DF) have been investigated by neutron scattering motivated by a MD simulation, which predicted an optic-type mode at small momentum transfers. Spectra of the measured longitudinal current correlation function show two modes. The lower frequency one originates from acoustic-type movements. The intensity of the higher frequency excitation can be attributed to an out of phase motion of neighboring DF molecules, an optic-type mode. Both, the frequencies and the intensity distribution in momentum space agree well with the MD simulation. The widths of the experimental spectra exceed the widths from the MD simulation and indicate missing relaxation processes in the simulation.

Correlated atomic motions in liquid deuterium fluoride studied by coherent quasielastic neutron scattering

The collective dynamics of liquid deuterium fluoride are studied by means of high-resolution quasielastic and inelastic neutron scattering over a range of four decades in energy transfer. The spectra show a low-energy coherent quasielastic component which arises from correlated stochastic motions as well as a broad inelastic feature originating from overdamped density oscillations. While these results are at variance with previous works which report on the presence of propagating collective modes, they are fully consistent with neutron diffraction, nuclear magnetic resonance, and infrared/Raman experiments on this prototypical hydrogen-bonded fluid.

Effective force field for liquid hydrogen fluoride from ab initio molecular dynamics simulation using the force-matching method

A recently developed force-matching method for obtaining effective force fields for condensed matter systems from ab initio molecular dynamics (MD) simulations has been applied to fit a simple nonpolarizable two-site pairwise force field for liquid hydrogen fluoride. The ab initio MD in this case was a Car-Parrinello (CP) MD simulation of 64 HF molecules at nearly ambient conditions within the Becke-Lee-Yang-Parr approximation to the electronic density functional theory. The force-matching procedure included a fit of short-ranged nonbonded forces, bonded forces, and atomic partial charges. The performance of the force-match potential was examined for the gas-phase dimer and for the liquid phase at various temperatures. The model was able to reproduce correctly the bent structure and energetics of the gas-phase dimer, while the results for the structural properties, self-diffusion, vibrational spectra, density, and thermodynamic properties of liquid HF were compared to both experiment and the CP MD simulation. The force-matching model performs well in reproducing nearly all of the liquid properties as well as the aggregation behavior at different temperatures. The model is computationally cheap and compares favorably to many more computationally expensive potential energy functions for liquid HF.

Observation of fractional Stokes-Einstein behavior in the simplest hydrogen-bonded liquid

Quasielastic neutron scattering has been used to investigate the single-particle dynamics of hydrogen fluoride across its entire liquid range at ambient pressure. For T>230 K, translational diffusion obeys the celebrated Stokes-Einstein relation, in agreement with nuclear magnetic resonance studies. At lower temperatures, we find significant deviations from the above behavior in the form of a power law with exponent xi=-0.71+/-0.05. More striking than the above is a complete breakdown of the Debye-Stokes-Einstein relation for rotational diffusion. Our findings provide the first experimental verification of fractional Stokes-Einstein behavior in a hydrogen-bonded liquid, in agreement with recent computer simulations [S. R. Becker, Phys. Rev. Lett. 97, 055901 (2006)10.1103/PhysRevLett.97.055901].

On the variation of the structure of liquid deuterium fluoride with temperature

The structure of liquid deuterium fluoride has been measured using pulsed neutron diffraction and high energy x-ray diffraction techniques as a function of temperature. The neutron experiments were performed at T=296+/-2 K, 246+/-2 K, and 193+/-2 K and the x-ray measurements carried out at 296+/-2 K and 195+/-2 K. The x-ray pair correlation functions, which are dominated by fluorine-fluorine interactions, show the first peak at approximately 2.53+/-0.05 A remains very nearly invariant with decreasing temperature. Peaks around 4.5 and 5.0 A also appear at both temperatures in the x-ray data. In contrast, the intermolecular peaks in the total neutron pair correlation function show that significant systematic local structural changes occur as the temperature is lowered. The first intermolecular peak position shortens from 1.64+/-0.05 A at 296 K to 1.56+/-0.05 A at 195 K. Although there are overlapping contributions from the intermolecular hydrogen-fluorine and hydrogen-hydrogen correlations, it is clear that the temperature dependent structural changes are largely due to a rearrangement of the deuterium atom positions in the fluid. By comparison with partial structure factor data the hydrogen bonds appear to become more linear at lower temperatures.

First principles simulation of a superionic phase of hydrogen fluoride (HF) at high pressures and temperatures

We have conducted ab initio molecular dynamics simulations of hydrogen fluoride (HF) at pressures of 5-66 GPa along the 900 K isotherm. We predict a superionic phase at 33 GPa, where the fluorine atoms are fixed in a bcc lattice while the hydrogen atoms diffuse rapidly with a diffusion constant between 2 x 10(-5) and 5 x 10(-5)cm(2)s. We find that a transformation from asymmetric to symmetric hydrogen bonding occurs in HF at 66 GPa and 900 K. With superionic HF we have discovered a model system where symmetric hydrogen bonding occurs at experimentally achievable conditions. Given previous results on superionic H(2)O [Goldman et al., Phys. Rev. Lett. 94, 217801 (2005)] and NH(3) [Cavazzoni et al., Science 283, 44 (1999)], we conclude that high P, T superionic phases of electronegative element hydrides could be common.

Evidence of the presence of opticlike collective modes in a liquid from neutron scattering experiments

Inelastic neutron scattering data from liquid DF close to the melting point show, in addition to spectra comprising quasielastic and heavily damped acoustic motions, an intense, nondispersive band centered at about 27 meV along with a broader higher energy feature. Observation of the former band provides the first direct verification of the existence within the liquid state of collective opticlike excitations as predicted by molecular dynamics simulations. The latter corresponds to mainly reorientational motions assigned from mode eigenvector analysis carried out by computer simulations.

Development of a new polarizable potential model of hydrogen fluoride and comparison with other effective models in liquid and supercritical states

Development of a new polarizable potential of hydrogen fluoride through the reparametrization of the JV-P model is presented: The length of the H-F bond has been shortened and the other parameters of the model have been readjusted accordingly. The structural, thermodynamic, and liquid-vapor equilibrium properties of the new model are compared with those of other effective potential models of HF as well as with experimental data in a broad range of thermodynamic states, from near-freezing to supercritical conditions. It is found that although the reparametrization does not change the structural properties of the HF model noticeably at the level of the pair correlations, it improves the reproduction of the thermodynamic properties of hydrogen fluoride over the entire range of existence of a thermodynamically stable liquid phase and also that of the vapor-liquid coexistence curve. However, the new model, which still overestimates the close-contact separation of the HF molecules, underestimates the density of the coexisting liquid phase and overestimates the saturation pressure, probably due to the too steep repulsion of the potential function.

How Does Ammonium Dynamically Interact with Benzene in Aqueous Media? A First Principle Study Using the Car−Parrinello Molecular Dynamics Method

The Car-Parrinello molecular dynamics (CPMD) method was used to study the dynamic characteristics of the cation-pi interaction between ammonium and benzene in gaseous and aqueous media. The results obtained from the CPMD calculation on the cation-pi complex in the gaseous state were very similar to those calculated from the Gaussian98 program with DFT and MP2 algorithms, demonstrating that CPMD is a valid approach for studying this system. Unlike the interaction in the gaseous state, our 12-ps CPMD simulation showed that the geometry of the complex in aqueous solution changes frequently in terms of the interaction angles and distances. Furthermore, the simulation revealed that the ammonium is constantly oscillating above the benzene plane in an aqueous environment and interacts with benzene mostly through three of its hydrogen atoms. In contrast, the interaction of the cation with the aromatic molecule in the gaseous state involves two hydrogen atoms. In addition, the free energy profile in aqueous solution was studied using constrained CPMD simulations, resulting in a calculated binding free energy of -5.75 kcal/mol at an optimum interaction distance of approximately 3.25 A, indicating that the cation-pi interaction between ammonium and benzene is stable even in aqueous solution. Thus, this CPMD study suggested that the cation-pi interaction between an ammonium (group) and an aromatic structure could take place even on surfaces of protein or nucleic acids in solution.

The Isobutylene−Isobutane Alkylation Process in Liquid HF Revisited

Details on the mechanism of HF catalyzed isobutylene-isobutane alkylation were investigated. On the basis of available experimental data and high-level quantum chemical calculations, a detailed reaction mechanism is proposed taking into account solvation effects of the medium. On the basis of our computational results, we explain why the density of the liquid media and stirring rates are the most important parameters to achieve maximum yield of alkylate, in agreement with experimental findings. The ab initio Car-Parrinello molecular dynamics calculations show that isobutylene is irreversibly protonated in the liquid HF medium at higher densities, leading to the ion pair formation, which is shown to be a minimum on the potential energy surface after optimization using periodic boundary conditions. The HF medium solvates preferentially the fluoride anion, which is found as solvated [FHF](-) or solvated F(-.)(HF)(3). On the other hand, the tert-butyl cation is weakly solvated, where the closest HF molecules appear at a distance of about 2.9 Angstrom with the fluorine termination of an HF chain.

Structure of dense hydrogen fluoride gas from neutron diffraction and molecular dynamics simulations

The gas phase of hydrogen fluoride has been investigated by neutron diffraction experiments at three different particle densities. All investigated states are within the liquid-gas coexistence region of hydrogen fluoride. From the obtained diffraction data we deduced information about the local structure of the gas phase, which consists of small agglomerates. This has been expected as liquid hydrogen fluoride forms the strongest hydrogen bonds known. Molecular dynamics simulations with a modified potential have been carried out for all experimentally investigated states. The results confirmed that the size of the formed agglomerates in the gas phase is growing with increasing density of the gas phase.

On the Quantum Nature of an Excess Proton in Liquid Hydrogen Fluoride

Liquid hydrogen fluoride consists of chains of hydrogen-bonded molecules. The nature of an excess proton in liquid HF, which is of interest not only for its own sake, but also in relation to super-acid chemistry and to its behavior in water, has been studied using computer simulations. The methodology employed is the density-functional-theory-based path-integral Car-Parrinello ab initio molecular dynamics. The excess proton, which formally exists as a H2F+ or a H2F2+ defect in an HF chain, is found to strongly perturb the chain to which it is attached. Moreover, due to large zero-point energy, the charge defect is largely delocalized over several HF molecules.

Ab initiomolecular-dynamics study of liquid formamide

Properties of neat liquid formamide (HCONH2) have been studied by the combination of gradient-corrected density-functional theory, norm-conserving pseudopotentials, and the adaptive finite-element method. The structural and dynamical quantities have been calculated through molecular dynamics simulations under the Born-Oppenheimer approximation. Satisfactory agreement with experimental data was obtained for both intramolecular and intermolecular properties. Our results are also compared with those of the empirical potential functions to clarify their accuracies.

Nuclear Quantum Effects and Hydrogen Bonding in Liquids

We have employed ab initio path integral molecular dynamics simulations to investigate the role of nuclear quantum effects on the strength of hydrogen bonds in liquid hydrogen fluoride. Nuclear quantum effects are shown to be responsible for a stronger hydrogen bond and an enhanced dipole-dipole interaction, which lead, in turn, to a shortening of the H...F intrachain distance. The simulation results are analyzed in terms of the electronic density shifts with respect to a purely classical treatment of the nuclei. The observed enhanced hydrogen-bond interaction, which arises from a coupling of intra- and intermolecular effects, should be a general phenomenon occurring in all hydrogen-bonded systems.

Ab initio molecular dynamics with density functional theory

Recent applications of density functional theory base ab initio molecular dynamics in chemical relevant systems are reviewed. The emphasis is on the dynamical aspect in the study of structures, reaction mechanisms, and electronic properties in both the molecular and condensed phases. Examples were chosen from fluxional molecules, solution reactions, and biological systems to illustrate the broad potential applications and unique information that can be obtained from ab initio molecular dynamics calculations. Recent advances in the development of efficient numerical algorithms for the prediction of spectroscopic properties are highlighted.

Solvated CH5+ in liquid superacid

The transition states for methane activation in liquid superacid have been studied by experimentally determined secondary kinetic deuterium isotope effects (SKIEs) and computational chemistry. For the first time, the SKIEs on hydrogen/deuterium exchange of methane have been measured by using the methane isotopologues in homogeneous liquid superacid (2HF/SbF5). To achieve high accuracy of the SKIEs, the rate constants for pairs of methane isotopologues were simultaneously measured in the same superacid solution by using NMR spectroscopy. Density functional theory (DFT) and high-level ab initio methods have been employed to model possible intermediates and transition states, assuming that the superacids involved in the exchange reactions are H2F+ ions solvated by HF. Only the unsolvated superacid H2F+ is found to be strong enough to protonate methane, yielding the methonium ion solvated by HF as a potential energy minimum. In contrast, the (HF)x-solvated H2F+ superacids (x = 1-4) do not appear to be strong enough to yield stable solvated methonium ions. However, such ions show up as parts of the transition states of the exchange in which the methonium ions are solvated by (HF)x. The calculated DFT activation barrier is in good agreement with that experimentally observed.