Polarizable Interaction Model for Liquid, Supercritical, and Aqueous Ammonia

Collective Proton Transfers in Cyclic Water-Ammonia Tetramers: A Path Integral Machine-Learning Study

We present results from machine-learning-based path integral molecular dynamics simulations that describe isomerization paths articulated via collective proton transfers along mixed, cyclic tetramers combining water and ammonia at cryogenic conditions. The net result of such isomerizations is a reverse of the chirality of the global hydrogen-bonding architecture along the different cyclic moieties. In monocomponent tetramers, the classical free energy profiles associated with these isomerizations present the usual symmetric double-well characteristics whereas the reactive paths exhibit full concertedness among the different intermolecular transfer processes. Contrastingly, in mixed water/ammonia tetramers, the incorporation of a second component introduces imbalances in the strengths of the different hydrogen bonds leading to a partial loss of concertedness, most notably at the vicinity of the transition state. As such, the highest and lowest degrees of progression are registered along OH···N and O···HN coordinations, respectively. These characteristics lead to polarized transition state scenarios akin to solvent-separated ion-pair configurations. The explicit incorporation of nuclear quantum effects promotes drastic depletions in the activation free energies and modifications in the overall shape of the profiles which include central plateau-like stages, indicating the prevalence of deep tunneling regimes. On the other hand, the quantum treatment of the nuclei partially restores the degree of concertedness among the evolutions of the individual transfers.

Equilibrium and Dynamical Characteristics of Hydrogen Bond Bifurcations in Water-Water and Water-Ammonia Dimers: A Path Integral Molecular Dynamics Study

We present path integral molecular dynamics results that describe the effects of nuclear quantum fluctuations on equilibrium and dynamical characteristics pertaining to bifurcation pathways in hydrogen bonded dimers combining water and ammonia, at cryogenic temperatures of the order of 20 K. Along these isomerizations, the hydrogen atoms in the molecules acting as hydrogen-bond donors interchange their original dangling/connective characters. Our results reveal that the resulting quantum transition paths comprise three stages: the initial and final ones involve overall rotations during which the two protons retain their classical-like characteristics. Effects from quantum fluctuation are clearly manifested in the changes operated at the intermediate passages over transition states, as the spatial extents of the protons stretch over typical lengths comparable to the distances between connective and dangling basins of attractions. Consequently, the classical over-the-hill path is replaced by a tunneling controlled mechanism which, within the path integral perspective, can be cast in terms of concerted inter-basin migrations of polymer beads from dangling-to-connective and from connective-to-dangling, at practically no energy costs. We also estimated the characteristic timescales describing such interconversions within the approximate ring polymer rate theory. Effects derived from full and partial deuteration are also discussed.

Observation of intermolecular Coulombic decay and shake-up satellites in liquid ammonia

We report the first nitrogen 1s Auger-Meitner electron spectrum from a liquid ammonia microjet at a temperature of ∼223 K (-50 °C) and compare it with the simultaneously measured spectrum for gas-phase ammonia. The spectra from both phases are interpreted with the assistance of high-level electronic structure and ab initio molecular dynamics calculations. In addition to the regular Auger-Meitner-electron features, we observe electron emission at kinetic energies of 374-388 eV, above the leading Auger-Meitner peak (3a₁ ²). Based on the electronic structure calculations, we assign this peak to a shake-up satellite in the gas phase, i.e., Auger-Meitner emission from an intermediate state with additional valence excitation present. The high-energy contribution is significantly enhanced in the liquid phase. We consider various mechanisms contributing to this feature. First, in analogy with other hydrogen-bonded liquids (noticeably water), the high-energy signal may be a signature for an ultrafast proton transfer taking place before the electronic decay (proton transfer mediated charge separation). The ab initio dynamical calculations show, however, that such a process is much slower than electronic decay and is, thus, very unlikely. Next, we consider a non-local version of the Auger-Meitner decay, the Intermolecular Coulombic Decay. The electronic structure calculations support an important contribution of this purely electronic mechanism. Finally, we discuss a non-local enhancement of the shake-up processes.

Ab Initio Cluster Approach for High Harmonic Generation in Liquids

High harmonic generation (HHG) takes place in all phases of matter. In gaseous atomic and molecular media, it has been extensively studied and is very well understood. In solids, research is ongoing, but a consensus is forming for the dominant microscopic HHG mechanisms. In liquids, on the other hand, no established theory yet exists, and approaches developed for gases and solids are generally inapplicable, hindering our current understanding. We develop here a powerful and reliable ab initio cluster-based approach for describing the nonlinear interactions between isotropic bulk liquids and intense laser pulses. The scheme is based on time-dependent density functional theory and utilizes several approximations that make it feasible yet accurate in realistic systems. We demonstrate our approach with HHG calculations in water, ammonia, and methane liquids and compare the characteristic response of polar and nonpolar liquids. We identify unique features in the HHG spectra of liquid methane that could be utilized for ultrafast spectroscopy of its chemical and physical properties, including a structural minimum at 15-17 eV that is associated solely with the liquid phase. Our results pave the way to accessible calculations of HHG in liquids and illustrate the unique nonlinear nature of liquid systems.

Modeling Shows that Rotation about the Peroxide O-O Bond Assists Protein and Lipid Functional Groups in Discriminating between H2O2 and H2O

Long associated with cell death, hydrogen peroxide (H₂O₂) is now known to perform many physiological roles. Unraveling its biological mechanisms of action requires atomic-level knowledge of its association with proteins and lipids, which we address here. High-level [MP2(full)/6-311++G(3df,3pd)] ab initio calculations reveal skew rotamers as the lowest-energy states of isolated H₂O₂ (ϕ_HOOH ∼ 112°) with minimum and maximum electrostatic potentials (kcal/mol) of -24.8 (V_s,min) and 36.5 (V_s,max), respectively. Transition-state, nonpolar trans rotamers (ϕ_HOOH ∼ 180°) at 1.2 kcal/mol higher in energy are poorer H-bond acceptors (V_s,min = -16.6) than the skew rotamers, while highly polar cis rotamers (ϕ_HOOH ∼ 0°) at 7.8 kcal/mol are much better H-bond donors (V_s,max = 52.7). Modeling H₂O₂ association with neutral and charged analogs of protein residues and lipid groups (e.g., ester, phosphate, choline) reveals that skew rotamers (ϕ_HOOH = 84-122°) are favored in the neutral and cationic complexes, which display gas-phase interaction energies (E^CP, kcal/mol) of -1.5 to -18. The neutral and cationic complexes of H₂O exhibit a similar range of stabilities (E^CP ∼ -1 to -18). However, considerably higher energies (E^CP ∼ -14 to -36) are found for the H₂O₂ complexes of the anionic ligands, which are stabilized by charge-assisted H-bond donation from cis and distorted cis rotamers (ϕ_HOOH = 0-60°). H₂O is a much poorer H-bond donor (V_s,max = 33.4) than cis-H₂O₂, so its anionic complexes are significantly weaker (E^CP ∼ -11 to -20). Thus, by dictating the rotamer preference of H₂O₂, functional groups in biomolecules can discriminate between H₂O₂ and H₂O. Finally, exploiting the present ab initio data, we calibrated and validated our published molecular mechanics model for H₂O₂ (Orabi, E. A.; English, A. M. J. Chem. Theory Comput. 2018, 14, 2808-2821) to provide an important tool for simulating H₂O₂ in biology.

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.

Applicability of Effective Fragment Potential Version 2-Molecular Dynamics (EFP2-MD) Simulations for Predicting Dynamic Liquid Properties Including the Supercritical Fluid Phase

Effective fragment potential version 2-molecular dynamics (EFP2-MD) simulations, where the EFP2 is a polarizable force field based on ab initio electronic structure calculations, were applied to predict the static and dynamic liquid properties of compressed liquid NH₃. By analyzing the temperature dependence of the radial distribution function, the autocorrelation functions of velocity ( C_v( t)) and reorientation ( C_r( t)), and the self-diffusion constant, we clarified that the ab initio EFP2 force field can effectively describe the properties of compressed liquids. These descriptions can be performed with at least semiquantitative accuracy and at a sufficiently low computational cost. In the EFP2-MD protocol, no force field training is required. This training is mandatory when simulating liquid properties with classical MD techniques (especially in extreme conditions with high pressures and temperatures). EFP2-MD is a promising technique for predicting the physicochemical properties of novel functional compressed liquids, including supercritical fluid phase properties.

Cation-π Interactions between Quaternary Ammonium Ions and Amino Acid Aromatic Groups in Aqueous Solution

Cation-π interactions play important roles in the stabilization of protein structures and protein-ligand complexes. They contribute to the binding of quaternary ammonium ligands (mainly RNH₃⁺ and RN(CH₃)₃⁺) to various protein receptors and are likely involved in the blockage of potassium channels by tetramethylammonium (TMA⁺) and tetraethylammonium (TEA⁺). Polarizable molecular models are calibrated for NH₄⁺, TMA⁺, and TEA⁺ interacting with benzene, toluene, 4-methylphenol, and 3-methylindole (representing aromatic amino acid side chains) based on the ab initio MP2(full)/6-311++G(d,p) properties of the complexes. Whereas the gas-phase affinity of the ions with a given aromatic follows the trend NH₄⁺ > TMA⁺ > TEA⁺, molecular dynamics simulations using the polarizable models show a reverse trend in water, likely due to a contribution from the hydrophobic effect. This reversed trend follows the solubility of aromatic hydrocarbons in quaternary ammonium salt solutions, which suggests a role for cation-π interactions in the salting-in of aromatic compounds in solution. Simulations in water show that the complexes possess binding free energies ranging from -1.3 to -3.3 kcal/mol (compared to gas-phase binding energies between -8.5 and -25.0 kcal/mol). Interestingly, whereas the most stable complexes involve TEA⁺ (the largest ion), the most stable solvent-separated complexes involve TMA⁺ (the intermediate-size ion).

Aqueous Solvation of Ammonia and Ammonium: Probing Hydrogen Bond Motifs with FT-IR and Soft X-ray Spectroscopy

In a multifaceted investigation combining local soft X-ray and vibrational spectroscopic probes with ab initio molecular dynamics simulations, hydrogen-bonding interactions of two key principal amine compounds in aqueous solution, ammonia (NH₃) and ammonium ion (NH₄⁺), are quantitatively assessed in terms of electronic structure, solvation structure, and dynamics. From the X-ray measurements and complementary determination of the IR-active hydrogen stretching and bending modes of NH₃ and NH₄⁺ in aqueous solution, the picture emerges of a comparatively strongly hydrogen-bonded NH₄⁺ ion via N-H donating interactions, whereas NH₃ has a strongly accepting hydrogen bond with one water molecule at the nitrogen lone pair but only weakly N-H donating hydrogen bonds. In contrast to the case of hydrogen bonding among solvent water molecules, we find that energy mismatch between occupied orbitals of both the solutes NH₃ and NH₄⁺ and the surrounding water prevents strong mixing between orbitals upon hydrogen bonding and, thus, inhibits substantial charge transfer between solute and solvent. A close inspection of the calculated unoccupied molecular orbitals, in conjunction with experimentally measured N K-edge absorption spectra, reveals the different nature of the electronic structural effects of these two key principal amine compounds imposed by hydrogen bonding to water, where a pH-dependent excitation energy appears to be an intrinsic property. These results provide a benchmark for hydrogen bonding of other nitrogen-containing acids and bases.

Probing hydrogen bonding orbitals: resonant inelastic soft X-ray scattering of aqueous NH3

Resonant inelastic soft X-ray scattering was used to probe the hydrogen bonding orbitals in aqueous ammonia.

Is there a third order phase transition for supercritical fluids?

We prove that according to Molecular Dynamics (MD) simulations of liquid mixtures of Lennard-Jones (L-J) particles, there is no third order phase transition in the supercritical regime beyond Andrew's critical point. This result is in open contrast with recent theoretical studies and experiments which instead suggest not only its existence but also its universality regarding the chemical nature of the fluid. We argue that our results are solid enough to go beyond the limitations of MD and the generic character of L-J models, thus suggesting a rather smooth liquid-vapor thermodynamic behavior of fluids in supercritical regime.