Microscopic structure of low temperature liquid ammonia: A neutron diffraction experiment

Quantum cluster equilibrium theory applied to liquid ammonia

Through this paper, the authors propose using the quantum cluster equilibrium (QCE) theory to reinvestigate ammonia clusters in the liquid phase. The ammonia clusters from size monomer to hexadecamer were considered to simulate the liquid ammonia in this approach. The clusterset used to model the liquid ammonia is an ensemble of different structures of ammonia clusters. After studious research of the representative configurations of ammonia clusters through the cluster research program ABCluster, the configurations have been optimized at the MN15/6-31++G(d,p) level of theory. These optimizations lead to geometries and frequencies as inputs for the Peacemaker code. The QCE study of this molecular system permits us to get the liquid phase populations in a temperature range of 190-260 K, covering the temperatures from the melting point to the boiling point. The results show that the population of liquid ammonia comprises mainly the ammonia hexadecamer followed by pentadecamer, tetradecamer, and tridecamer. We noted that the small-sized ammonia clusters do not contribute to the population of liquid ammonia. In addition, the thermodynamic properties, such as heat of vaporization, heat capacity, entropy, enthalpy, and free energies, obtained by the QCE theory have been compared to the experiment given some relatively good agreements in the gas phase and show considerable discrepancies in liquid phase except the density. Finally, based on the predicted population, we calculated the infrared spectrum of liquid ammonia at 215 K temperature. It comes out that the calculated infrared spectrum qualitatively agrees with the experiment.

Neutron scattering and neural-network quantum molecular dynamics investigation of the vibrations of ammonia along the solid-to-liquid transition

Vibrational spectroscopy allows us to understand complex physical and chemical interactions of molecular crystals and liquids such as ammonia, which has recently emerged as a strong hydrogen fuel candidate to support a sustainable society. We report inelastic neutron scattering measurement of vibrational properties of ammonia along the solid-to-liquid phase transition with high enough resolution for direct comparisons to ab-initio simulations. Theoretical analysis reveals the essential role of nuclear quantum effects (NQEs) for correctly describing the intermolecular spectrum as well as high energy intramolecular N-H stretching modes. This is achieved by training neural network models using ab-initio path-integral molecular dynamics (PIMD) simulations, thereby encompassing large spatiotemporal trajectories required to resolve low energy dynamics while retaining NQEs. Our results not only establish the role of NQEs in ammonia but also provide general computational frameworks to study complex molecular systems with NQEs.

Hydrogen Bonding in Liquid Ammonia

The nature of hydrogen bonding in condensed ammonia phases, liquid and crystalline ammonia has been a topic of much investigation. Here, we use quantum molecular dynamics simulations to investigate hydrogen bond structure and lifetimes in two ammonia phases: liquid ammonia and crystalline ammonia-I. Unlike liquid water, which has two covalently bonded hydrogen and two hydrogen bonds per oxygen atom, each nitrogen atom in liquid ammonia is found to have only one hydrogen bond at 2.24 Å. The computed lifetime of the hydrogen bond is t ≅ 0.1 ps. In contrast to crystalline water-ice, we find that hydrogen bonding is practically nonexistent in crystalline ammonia-I.

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.

MB-Fit: Software infrastructure for data-driven many-body potential energy functions

Many-body potential energy functions (MB-PEFs), which integrate data-driven representations of many-body short-range quantum mechanical interactions with physics-based representations of many-body polarization and long-range interactions, have recently been shown to provide high accuracy in the description of molecular interactions from the gas to the condensed phase. Here, we present MB-Fit, a software infrastructure for the automated development of MB-PEFs for generic molecules within the TTM-nrg (Thole-type model energy) and MB-nrg (many-body energy) theoretical frameworks. Besides providing all the necessary computational tools for generating TTM-nrg and MB-nrg PEFs, MB-Fit provides a seamless interface with the MBX software, a many-body energy and force calculator for computer simulations. Given the demonstrated accuracy of the MB-PEFs, particularly within the MB-nrg framework, we believe that MB-Fit will enable routine predictive computer simulations of generic (small) molecules in the gas, liquid, and solid phases, including, but not limited to, the modeling of quantum isomeric equilibria in molecular clusters, solvation processes, molecular crystals, and phase diagrams.

Convergence behaviour of solvation shells in simulated liquids

A convenient way to analyse solvent structure around a solute is to use solvation shells, whereby solvent position around the solute is discretised by the size of a solvent molecule, leading to multiple shells around the solute. The two main ways to define multiple shells around a solute are either directly with respect to the solute, called solute-centric, or locally for both solute and solvent molecules alike. It might be assumed that both methods lead to solvation shells with similar properties. However, our analysis suggests otherwise. Solvation shells are analysed in a series of simulations of five pure liquids of differing polarity. Shells are defined locally working outwards from each molecule treated as a reference molecule using two methods: the cutoff at the first minimum in the radial distribution function and the parameter-free Relative Angular Distance method (RAD). The molecular properties studied are potential energy, coordination number and coordination radius. Rather than converging to bulk values, as might be expected for pure solvents, properties are found to deviate as a function of shell index. This behaviour occurs because molecules with larger coordination numbers and radius have more neighbours, which make them more likely to be connected to the reference molecule via fewer shells. The effect is amplified for RAD because of its more variable coordination radii and for water with its more open structure and stronger interactions. These findings indicate that locally defined shells should not be thought of as directly comparable to solute-centric shells or to distance. As well as showing how box size and cutoff affect the non-convergence, to restore convergence we propose a hybrid method by defining a new set of shells with boundaries at the uppermost distance of each locally derived shell.

Dihydrogen vs. hydrogen bonding in the solvation of ammonia borane by tetrahydrofuran and liquid ammonia

The solvation structures of two systems rich in hydrogen and dihydrogen bonding interactions have been studied in detail experimentally through neutron diffraction with hydrogen/deuterium isotopic substitution.

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.

Influence of Solvation and Dynamics on the Mechanism and Kinetics of Nucleophilic Aromatic Substitution Reactions in Liquid Ammonia

The role of the solvent and the influence of dynamics on the kinetics and mechanism of the SNAr reaction of several halonitrobenzenes in liquid ammonia, using both static calculations and dynamic ab initio molecular dynamics simulations, are investigated. A combination of metadynamics and committor analysis methods reveals how this reaction can change from a concerted, one-step mechanism in gas phase to a stepwise pathway, involving a metastable Meisenheimer complex, in liquid ammonia. This clearly establishes, among others, the important role of the solvent and highlights the fact that accurately treating solvation is of crucial importance to correctly unravel the reaction mechanism. It is indeed shown that H-bond formation of the reacting NH3 with the solvent drastically reduces the barrier of NH3 addition. The halide elimination step, however, is greatly facilitated by proton transfer from the reacting NH3 to the solvent. Furthermore, the free energy surface strongly depends on the halide substituent and the number of electron-withdrawing nitro substituents.

Topological analyses and small-world patterns of hydrogen bond networks in water + t-butanol, water + n-butanol and water + ammonia mixtures

H-bond networks in aqueous mixtures obtained by Monte Carlo simulations and analyzed by statistical mechanics based tools revealed small-word patterns.

Polarizable Atomic Multipole-based Molecular Mechanics for Organic Molecules

An empirical potential based on permanent atomic multipoles and atomic induced dipoles is reported for alkanes, alcohols, amines, sulfides, aldehydes, carboxylic acids, amides, aromatics and other small organic molecules. Permanent atomic multipole moments through quadrupole moments have been derived from gas phase ab initio molecular orbital calculations. The van der Waals parameters are obtained by fitting to gas phase homodimer QM energies and structures, as well as experimental densities and heats of vaporization of neat liquids. As a validation, the hydrogen bonding energies and structures of gas phase heterodimers with water are evaluated using the resulting potential. For 32 homo- and heterodimers, the association energy agrees with ab initio results to within 0.4 kcal/mol. The RMS deviation of hydrogen bond distance from QM optimized geometry is less than 0.06 Å. In addition, liquid self-diffusion and static dielectric constants computed from molecular dynamics simulation are consistent with experimental values. The force field is also used to compute the solvation free energy of 27 compounds not included in the parameterization process, with a RMS error of 0.69 kcal/mol. The results obtained in this study suggest the AMOEBA force field performs well across different environments and phases. The key algorithms involved in the electrostatic model and a protocol for developing parameters are detailed to facilitate extension to additional molecular systems.

Development of the trappe force field for ammonia

The transferable potentials for phase equilibria (TraPPE) force field is extended through the development of a non-polarizable five-site ammonia model. In this model, the electrostatic interactions are represented by three positive partial charges placed at the hydrogen position and a compensating partial charge placed on an M site that is located on the C3 molecular axis and displaced from the nitrogen atom toward the hydrogen atoms. The repulsive and dispersive interactions are represented by placing a single Lennard–Jones site at the position of the nitrogen atom. Starting from the five-site model by Impey and Klein (Chem. Phys. Lett. 1984, 104, 579), this work optimizes the Lennard–Jones parameters and the magnitude of the partial charges for three values of the M site displacement. This parameterization is done by fitting to the vapor–liquid coexistence curve of neat ammonia. The accuracy of the three resulting models (differing in the displacement of the M site) is assessed through computation of the binary vapor–liquid equilibria with methane, the structure and the dielectric constant of liquid ammonia. The five-site model with an intermediate displacement of 0.08 Å for the M site yields a much better value for the dielectric constant, whereas differences in the other properties are quite small.

Charge delocalization dynamics of ammonia in different hydrogen bonding environments: free clusters and in liquid water solution

Valence and core level photoelectron spectra and Auger electron spectra of ammonia in pure clusters have been measured. The Auger electron spectra of gas-phase ammonia, pure ammonia clusters and ammonia in aqueous solution are compared and interpreted via ab initio calculations of the Auger spectrum of the ammonia monomer and dimer. The calculations reveal that the final two-hole valence states can be delocalized over both ammonia molecules. Features at energies pertaining to delocalized states involving one, or more, hydrogen bonding orbitals can be found in both the ammonia cluster Auger electron spectrum and in that of the liquid solvated molecule. The lower Coulombic repulsion between two delocalized valence final state holes gives higher kinetic energy of the Auger electrons which is also observed in the spectra. This decay path--specific to the condensed phase--is responsible for more than 5% of the total cluster Auger intensity. Moreover, this interpretation is also applicable to the solid phase since the same features have been observed, but not assigned, in the Auger spectrum of solid ammonia.

High frequency dynamics and structural relaxation process in liquid ammonia

The dynamic structure factor S(Q,omega) of liquid ammonia has been measured by inelastic x-ray scattering in the terahertz frequency region as a function of the temperature in the range of 220-298 K at a pressure P=85 bars. The data have been analyzed using the generalized hydrodynamic formalism with a three term memory function to take into account the thermal, the structural, (alpha) and the microscopic (mu) relaxation processes affecting the dynamics of the liquid. This allows to extract the temperature dependence of the structural relaxation time (tau(alpha)) and strength (Delta(alpha)). The former quantity follows an Arrhenius behavior with an activation energy E(a)=2.6+/-0.2 kcal/mol, while the latter is temperature independent suggesting that there are no changes in the interparticle potential and arrangement with T. The obtained results, compared with those already existing in liquid water and liquid hydrogen fluoride, suggest the strong influence of the connectivity of the molecular network on the structural relaxation.

Simulations of Liquid Ammonia Based on the Combined Quantum Mechanical/Molecular Mechanical (QM/MM) Approach

Two combined quantum mechanics/molecular mechanics (QM/MM) molecular dynamics simulations, namely, HF/MM and B3LYP/MM, have been performed to investigate the local structure and dynamics of liquid ammonia. The most interesting region, a sphere containing a central reference molecule and all its nearest surrounding molecules (first coordination shell), was treated by the Hartree-Fock (HF) and hybrid density functional B3LYP methods, whereas the rest of the system was described by the classical pair potentials. On the basis of both HF and B3LYP methods, it is observed that the hydrogen bonding in this peculiar liquid is weak. The structure and dynamics of this liquid are suggested to be determined by the steric packing effects, rather than by the directional hydrogen bonding interactions. Compared to previous empirical as well as Car-Parrinello (CP) molecular dynamics studies, our QM/MM simulations provide detailed information that is in better agreement with experimental data.

The structure of calcium–ammonia solutions by neutron diffraction

The microscopic structures of calcium-ammonia solutions have been established by using neutron diffraction. Total structure factors measured at 230 K reveal immediately the evolution of an uncommonly intense diffraction prepeak in the metallic solutions. As concentration is increased from 4 mole percent metal to 10 mole percent metal (i.e., saturation), this feature intensifies and shifts from 0.6 to 0.9 A(-1). It is therefore evidence of well developed intermediate-range ordering among the solvated cations, and is a microstructural signature of the observed strong phase separation of metallic (concentrated) and nonmetallic (dilute) solutions. The technique of isotopic labelling of *N by 15N was then used in conjunction with difference analysis to focus on the solvent structure in metallic solutions at 4 and 10 mole percent metal. These nitrogen-centered functions are analyzed in conjunction with classical Monte Carlo computer simulation techniques, to provide us with detailed insight into the calcium solvation and the extent of hydrogen bonding. We find that calcium is solvated by approximately 6-7 ammonia molecules, with a Ca-N distance of around 2.45 A. There is evidence of hydrogen bonding among the solvent molecules, even in the saturated 10 mole percent metal solution.

Structural studies of ammonia and metallic lithium-ammonia solutions

The technique of hydrogen/deuterium isotopic substitution has been used to extract detailed information concerning the solvent structure in pure ammonia and metallic lithium-ammonia solutions. In pure ammonia we find evidence for approximately 2.0 hydrogen bonds around each central nitrogen atom, with an average N-H distance of 2.4 A. On addition of alkali metal, we observe directly significant disruption of this hydrogen bonding. At 8 mol % metal there remains only around 0.7 hydrogen bond per nitrogen atom. This value decreases to 0.0 for the saturated solution of 21 mol % metal, as all ammonia molecules have then become incorporated into the tetrahedral first solvation spheres of the lithium cations. In conjunction with a classical three-dimensional computer modeling technique, we are now able to identify a well-defined second cationic solvation shell. In this secondary shell the nitrogen atoms tend to reside above the faces and edges of the primary tetrahedral shell. Furthermore, the computer-generated models reveal that on addition of alkali metal the solvent molecules form voids of approximate radius 2.5-3.0 A. Our data therefore provide new insight into the structure of the polaronic cavities and tunnels, which have been theoretically predicted for lithium-ammonia solutions.

Combined ab initio/empirical approach for optimization of Lennard-Jones parameters for polar-neutral compounds

The study of small functionalized organic molecules in aqueous solution is a useful step toward gaining a basic understanding of the behavior of biomolecular systems in their native aqueous environment. Interest in studying amines and fluorine-substituted compounds has risen from their intrinsic physicochemical properties and their prevalence in biological and pharmaceutical compounds. In the present study, a previously developed approach which optimizes Lennard-Jones (LJ) parameters via the use of rare gas atoms combined with the reproduction of experimental condensed phase properties was extended to polar-neutral compounds. Compounds studied included four amines (ammonia, methylamine, dimethylamine, and trimethylamine) and three fluoroethanes (1-fluoroethane, 1,1-difluoroethane, and 1,1,1-trifluoroethane). The resulting force field yielded heats of vaporization and molecular volumes in excellent agreement with the experiment, with average differences less than 1%. The current amine CHARMM parameters successfully reproduced experimental aqueous solvation data where methylamine is more hydrophilic than ammonia, with hydrophobicity increasing with additional methylation on the nitrogen. For both the amines and fluoroethanes the parabolic relationship of the extent of methylation or fluorination, respectively, to the heats of vaporization were reproduced by the new parameters. The present results are also discussed with respect to the impact of parameterization approach to molecular details obtained from computer simulations and to the unique biological properties of fluorine in pharmaceutical compounds.