Large-cage occupation and quantum dynamics of hydrogen molecules in sII clathrate hydrates.

Hydrogen clathrate hydrates are ice-like crystalline substances in which hydrogen molecules are trapped inside polyhedral cages formed by the water molecules. Small cages can host only a single H2 molecule, while each large cage can be occupied by up to four H2 molecules. Here, we present a neutron scattering study on the structure of the sII hydrogen clathrate hydrate and on the low-temperature dynamics of the hydrogen molecules trapped in its large cages, as a function of the gas content in the samples. We observe spectral features at low energy transfer (between 1 and 3 meV), and we show that they can be successfully assigned to the rattling motion of a single hydrogen molecule occupying a large water cage. These inelastic bands remarkably lose their intensity with increasing the hydrogen filling, consistently with the fact that the probability of single occupation (as opposed to multiple occupation) increases as the hydrogen content in the sample gets lower. The spectral intensity of the H2 rattling bands is studied as a function of the momentum transfer for partially emptied samples and compared with three distinct quantum models for a single H2 molecule in a large cage: (i) the exact solution of the Schrödinger equation for a well-assessed semiempirical force field, (ii) a particle trapped in a rigid sphere, and (iii) an isotropic three-dimensional harmonic oscillator. The first model provides good agreement between calculations and experimental data, while the last two only reproduce their qualitative trend. Finally, the radial wavefunctions of the three aforementioned models, as well as their potential surfaces, are presented and discussed.

Soft Phonon Mode Triggering Fast Ag Diffusion in Superionic Argyrodite Ag8 GeSe6.

The structural coexistence of dual rigid and mobile sublattices in superionic Argyrodites yields ultralow lattice thermal conductivity along with decent electrical and ionic conductivities and therefore attracts intense interest for batteries, fuel cells, and thermoelectric applications. However, a comprehensive understanding of their underlying lattice and diffusive dynamics in terms of the interplay between phonons and mobile ions is missing. Herein, inelastic neutron scattering is employed to unravel that phonon softening on heating to Tc ≈ 350 K triggers fast Ag diffusion in the canonical superionic Argyrodite Ag8 GeSe6 . Ab initio molecular dynamics simulations reproduce the experimental neutron scattering signals and identify the partially ultrafast Ag diffusion with a large diffusion coefficient of 10-4 cm-2 s-1 . The study illustrates the microscopic interconnection between soft phonons and mobile ions and provides a paradigm for an intertwined interaction of the lattice and diffusive dynamics in superionic materials.

Thermoelectric properties and lattice dynamics of tetragonal topological semimetal Ba3Si4.

We report the lattice dynamics and thermoelectric properties of topological semimetal Ba3Si4. The lattice dynamics has been studied by Raman and inelastic neutron scattering experiments. Good agreement has been found with first-principles calculations. The presence of low-energy optical modes at about 7 meV mainly due to the heavy mass of the Ba atoms suggests a propensity to low thermal conductivity, which is favorable for thermoelectric applications. Our density functional theory calculations indicate that the semimetallic nature of Ba3Si4 is the origin for the rather large thermopower. Ba3Si4 shows high potential for a thermoelectric material with a Seebeck coefficient as large as -120 µV K-1 for 0.2 electrons/formula units through the substitution of Ba by appropriate cations, such as Y.

Magnetoelastic hybrid excitations in CeAuAl3.

Nearly a century of research has established the Born-Oppenheimer approximation as a cornerstone of condensed-matter systems, stating that the motion of the atomic nuclei and electrons may be treated separately. Interactions beyond the Born-Oppenheimer approximation are at the heart of magneto-elastic functionalities and instabilities. We report comprehensive neutron spectroscopy and ab initio phonon calculations of the coupling between phonons, CEF-split localized 4f electron states, and conduction electrons in the paramagnetic regime of [Formula: see text], an archetypal Kondo lattice compound. We identify two distinct magneto-elastic hybrid excitations that form even though all coupling constants are small. First, we find a CEF-phonon bound state reminiscent of the vibronic bound state (VBS) observed in other materials. However, in contrast to an abundance of optical phonons, so far believed to be essential for a VBS, the VBS in [Formula: see text] arises from a comparatively low density of states of acoustic phonons. Second, we find a pronounced anticrossing of the CEF excitations with acoustic phonons at zero magnetic field not observed before. Remarkably, both magneto-elastic excitations are well developed despite considerable damping of the CEFs that arises dominantly by the conduction electrons. Taking together the weak coupling with the simultaneous existence of a distinct VBS and anticrossing in the same material in the presence of damping suggests strongly that similarly well-developed magneto-elastic hybrid excitations must be abundant in a wide range of materials. In turn, our study of the excitation spectra of [Formula: see text] identifies a tractable point of reference in the search for magneto-elastic functionalities and instabilities.

Unravelling the Adaptation Mechanisms to High Pressure in Proteins.

Life is thought to have appeared in the depth of the sea under high hydrostatic pressure. Nowadays, it is known that the deep biosphere hosts a myriad of life forms thriving under high-pressure conditions. However, the evolutionary mechanisms leading to their adaptation are still not known. Here, we show the molecular bases of these mechanisms through a joint structural and dynamical study of two orthologous proteins. We observed that pressure adaptation involves the decoupling of protein-water dynamics and the elimination of cavities in the protein core. This is achieved by rearranging the charged residues on the protein surface and using bulkier hydrophobic residues in the core. These findings will be the starting point in the search for a complete genomic model explaining high-pressure adaptation.

Water Mobility in the Interfacial Liquid Layer of Ice/Clay Nanocomposites.

At solid/ice interfaces, a premelting layer is formed at temperatures below the melting point of bulk water. However, the structural and dynamic properties within the premelting layer have been a topic of intense debate. Herein, we determined the translational diffusion coefficient Dt of water in ice/clay nanocomposites serving as model systems for permafrost by quasi-elastic neutron scattering. Below the bulk melting point, a rapid decrease of Dt is found for charged hydrophilic vermiculite, uncharged hydrophilic kaolin, and more hydrophobic talc, reaching plateau values below -4 °C. At this temperature, Dt in the premelting layer is reduced up to a factor of two compared to supercooled bulk water. Adjacent to charged vermiculite the lowest water mobility was observed, followed by kaolin and the more hydrophobic talc. Results are explained by the intermolecular water interactions with different clay surfaces and interfacial segregation of the low-density liquid water (LDL) component.

Inelastic neutron scattering study of the lattice dynamics of the homologous compounds (PbSe)5(Bi2Se3)3m (m = 1, 2 and 3).

We report on the inelastic response of the homologous compounds (PbSe)5(Bi2Se3)3m for m = 1, 2 and 3 followed in a broad temperature range (50-500 K) using high-resolution powder inelastic neutron scattering experiments. These results are complemented by low-temperature measurements of the specific heat (2-300 K). The evolution of the anisotropic crystal structure of these compounds with varying m, built from alternate Pb-Se and mBi-Se layers, only weakly influences the generalized phonon density of states. In all the three compounds, intense inelastic signals, likely mainly associated with the dynamics of the Pb atoms, are observed in the 4.5-6 meV low-energy range. The response of these low-energy modes to temperature variations indicates a conventional quasi-harmonic behavior over the whole temperature range investigated. The modes located above 8 meV show a minor temperature effect regardless of the value of m. The low-energy excess of vibrational modes manifests itself in the low-temperature specific heat as a pronounced peak in the Cp(T)/T3 data near 10 K. The lack of significant anharmonicity beyond that associated with the thermal expansion of the lattice suggests that the inherent disorder in the monoclinic unit cell and scattering at interlayer interfaces are the most important ingredients that limit the heat transport in this series of compounds.

Diffusion of Carbon Dioxide and Nitrogen in the Small-Pore Titanium Bis(phosphonate) Metal-Organic Framework MIL-91 (Ti): A Combination of Quasielastic Neutron Scattering Measurements and Molecular Dynamics Simulations.

The diffusivity of CO2 and N2 in the small-pore titanium-based bis(phosphonate) metal-organic framework MIL-91(Ti) was explored by using a combination of quasielastic neutron scattering measurements and molecular dynamics simulations. These two techniques were used to determine the loading dependence of the self-diffusivity, corrected and transport diffusivities of these two gases to complement our previously reported thermodynamics study, which revealed that this material was a promising candidate for CO2 /N2 separation. The calculated and measured diffusivities of both gases were shown to be of an order of magnitude sufficiently high, from 10-9 to 10-10  m2 s-1 , and N2 diffused faster than CO2 through the small channel of MIL-91(Ti). Consequently, the separation process does not involve any kinetic-driven limitations. This study further revealed that the global diffusion mechanism involves motions of gases along the channels by a jump sequence, and the residence times for CO2 in the region close to the specific PO⋅⋅⋅H⋅⋅⋅N zwitterionic sites are much higher than those for N2 , which explains the faster diffusivity observed for N2 .

Dynamics of human acetylcholinesterase bound to non-covalent and covalent inhibitors shedding light on changes to the water network structure.

We investigated the effects of non-covalent reversible and covalent irreversible inhibitors on human acetylcholinesterase and human butyrylcholinesterase. Remarkably a non-covalent inhibitor, Huperzine A, has almost no effect on the molecular dynamics of the protein, whereas the covalently binding nerve agent soman renders the molecular structure stiffer in its aged form. The modified movements were studied by incoherent neutron scattering on different time scales and they indicate a stabilization and stiffening of aged human acetylcholinesterase. It is not straightforward to understand the forces leading to this strong effect. In addition to the specific interactions of the adduct within the protein, some indications point towards an extensive water structure change for the aged conjugate as water Bragg peaks appeared at cryogenic temperature despite an identical initial hydration state for all samples. Such a change associated to an apparent increase in free water volume upon aging suggests higher ordering of the hydration shell that leads to the stiffening of protein. Thus, several additive contributions seem responsible for the improved flexibility or stiffening effect of the inhibitors rather than a single interaction.

Picosecond dynamics in haemoglobin from different species: a quasielastic neutron scattering study.

BACKGROUND: Dynamics in haemoglobin from platypus (Ornithorhynchus anatinus), chicken (Gallus gallus domesticus) and saltwater crocodile (Crocodylus porosus) were measured to investigate response of conformational motions on the picosecond time scale to naturally occurring variations in the amino acid sequence of structurally identical proteins. METHODS: Protein dynamics was measured using incoherent quasielastic neutron scattering. The quasielastic broadening was interpreted first with a simple single Lorentzian approach and then by using the Kneller-Volino Brownian dynamics model. RESULTS: Mean square displacements of conformational motions, diffusion coefficients of internal dynamics and residence times for jump-diffusion between sites and corresponding effective force constants (resilience) and activation energies were determined from the data. CONCLUSIONS: Modifications of the physicochemical properties caused by mutations of the amino acids were found to have a significant impact on protein dynamics. Activation energies of local side chain dynamics were found to be similar between the different proteins being close to the energy, which is required for the rupture of single hydrogen bond in a protein. GENERAL SIGNIFICANCE: The measured dynamic quantities showed significant and systematic variations between the investigated species, suggesting that they are the signature of an evolutionary adaptation process stimulated by the different physiological environments of the respective protein.

On the microscopic dynamics of the 'Einstein solids' AlV2Al20 and GaV2Al20, and of YV2Al20: a benchmark system for 'rattling' excitations.

The inelastic response of AV2Al20 (with A = Al, Ga and Y) was probed by high-resolution inelastic neutron scattering experiments and density functional theory (DFT) based lattice dynamics calculations (LDC). Features characteristic of the dynamics of Al, Ga and Y are established experimentally in the low-energy range of the compounds. In the stereotype 'Einstein-solid' compound AlV2Al20 we identify a unique spectral density extending up to 10 meV at 1.6 K. Its dominating feature is a peak centred at 2 meV at the base temperature. A very similar spectral distribution is established in GaV2Al20 albeit the strong peak is located at 1 meV at 1.6 K. In YV2Al20 signals characteristic of Y dynamics are located above 8 meV. The spectral distributions are reproduced by the DFT-based LDC and identified as a set of phonons. The response to temperature changes between 1.6 and ∼300 K is studied experimentally and the exceptionally vivid renormalization of the A characteristic modes in AlV2Al20 and GaV2Al20 is quantified by following the energy of the strong peak. At about 300 K it is shifted to higher energies by 300% for A = Al and 450% for A = Ga. The dynamics of A = Y in YV2Al20 show a minor temperature effect. This holds in general for modes located above 10 meV in any of the compounds. They are associated with vibrations of the V2Al20 matrix. Atomic potentials derived through DFT calculations indicate the propensity of A = Al and Ga to a strong positive energy shift upon temperature increase by a high quartic component. The effect of the strong phonon renormalization on thermodynamic observables is computed on grounds of the LDC results. It is shown that through the hybridization of A = Al and Ga with the V2Al20 dynamics the matrix vibrations in the low-energy range follow this renormalization.

Effect of the electropositive elements A = Sc, La, and Ce on the microscopic dynamics of AV2Al20.

We report on the inelastic response of AV2Al20 (with A = Sc, La and Ce) probed by high-resolution inelastic neutron scattering experiments. Intense signals associated with the dynamics of Sc, La and Ce are identified in the low-energy range at 6-14 meV in ScV2Al20 and at 8-16 meV in LaV2Al20 and CeV2Al20. Their response to temperature changes between 2 and 300 K reveals a very weak softening of the modes upon heating in LaV2Al20 and CeV2Al20 and a distinguished blue shift by about 2 meV in ScV2Al20. By means of density functional theory (DFT) and lattice dynamics calculations (LDC) we show that the unusual anharmonicity of the Sc-dominated modes is due to the local potential of Sc featured by a strong quartic term. The vibrational dynamics of ScV2Al20 as well as of LaV2Al20 and CeV2Al20 is reproduced by a set of eigenmodes. To screen the validity of the DFT and LDC results they are confronted with data from X-ray diffraction measurements. The effect of the strong phonon renormalization in ScV2Al20 on thermodynamic observables is computed on grounds of the LDC derived inelastic response. To set the data in a general context of AV2Al20 compounds and their physical properties we report in addition computer and experimental results of the binary V2Al20 compound.

Nanocrystalline silicon: lattice dynamics and enhanced thermoelectric properties.

Silicon has several advantages when compared to other thermoelectric materials, but until recently it was not used for thermoelectric applications due to its high thermal conductivity, 156 W K(-1) m(-1) at room temperature. Nanostructuration as means to decrease thermal transport through enhanced phonon scattering has been a subject of many studies. In this work we have evaluated the effects of nanostructuration on the lattice dynamics of bulk nanocrystalline doped silicon. The samples were prepared by gas phase synthesis, followed by current and pressure assisted sintering. The heat capacity, density of phonons states, and elastic constants were measured, which all reveal a significant, ≈25%, reduction in the speed of sound. The samples present a significantly decreased lattice thermal conductivity, ≈25 W K(-1) m(-1), which, combined with a very high carrier mobility, results in a dimensionless figure of merit with a competitive value that peaks at ZT≈ 0.57 at 973 °C. Due to its easily scalable and extremely low-cost production process, nanocrystalline Si prepared by gas phase synthesis followed by sintering could become the material of choice for high temperature thermoelectric generators.

Crossover from gas-like to liquid-like molecular diffusion in a simple supercritical fluid.

According to textbooks, no physical observable can be discerned allowing to distinguish a liquid from a gas beyond the critical point. Yet, several proposals have been put forward challenging this view and various transition boundaries between a gas-like and a liquid-like behaviour, including the so-called Widom and Frenkel lines, and percolation line, have been suggested to delineate the supercritical state space. Here we report observation of a crossover from gas-like (Gaussian) to liquid-like (Lorentzian) self-dynamic structure factor by incoherent quasi-elastic neutron scattering measurements on supercritical fluid methane as a function of pressure, along the 200 K isotherm. The molecular self-diffusion coefficient was derived from the best Gaussian (at low pressures) or Lorentzian (at high pressures) fits to the neutron spectra. The Gaussian-to-Lorentzian crossover is progressive and takes place at about the Widom line intercept (59 bar). At considerably higher pressures, a liquid-like jump diffusion mechanism properly describes the supercritical fluid on both sides of the Frenkel line. The present observation of a gas-like to liquid-like crossover in the self dynamics of a simple supercritical fluid confirms emerging views on the unexpectedly complex physics of the supercritical state, and could have planet-wide implications and possible industrial applications in green chemistry.

Application of incoherent inelastic neutron scattering in pharmaceutical analysis: relaxation dynamics in phenacetin.

This study centers on the use of inelastic neutron scattering as an alternative tool for physical characterization of solid pharmaceutical drugs. On the basis of such approach, relaxation processes in the pharmaceutical compound phenacetin (p-ethoxyacetanilide, C(10)H(13)NO(2)) were evidenced on heating between 2 and 300 K. By evaluating the mean-square displacement obtained from the elastic fixed window approach, using the neutron backscattering technique, a crossover of the molecular fluctuations between harmonic and nonharmonic dynamical regimes around 75 K was observed. From the temperature dependence of the quasi-elastic line-width, summed over the total Q range explored by the time-of-flight technique, it was possible to attribute the onset of this anharmonicity to methyl group rotations. Finally, using density functional theory-based methods, we were able to calculate the lattice vibrations in the harmonic approximation. The overall spectral profile of the calculated partial contributions to the generalized density of states compares satisfactorily to the experimental spectra in the region of the lattice modes where the intermolecular interactions are expected to play an important role. This study contributes to understanding the relationships between intermolecular hydrogen bonds, intramolecular dynamics, and conformational flexibility in pharmaceuticals on a molecular level, which can help in evaluating phase stability with respect to temperature variations on processing or on storage, and is related to control of polymorphism and pseudopolymorphism.

The dynamical Matryoshka model: 2. Modeling of local lipid dynamics at the sub-nanosecond timescale in phospholipid membranes.

Biological membranes are generally formed by lipids and proteins. Often, the membrane properties are studied through model membranes formed by phospholipids only. They are molecules composed by a hydrophilic head group and hydrophobic tails, which can present a panoply of various motions, including small localized movements of a few atoms up to the diffusion of the whole lipid or collective motions of many of them. In the past, efforts were made to measure these motions experimentally by incoherent neutron scattering and to quantify them, but with upcoming modern neutron sources and instruments, such models can now be improved. In the present work, we expose a quantitative and exhaustive study of lipid dynamics on DMPC and DMPG membranes, using the Matryoshka model recently developed by our group. The model is confronted here to experimental data collected on two different membrane samples, at three temperatures and two instruments. Despite such complexity, the model describes reliably the data and permits to extract a series of parameters. The results compare also very well to other values found in the literature.

The dynamical Matryoshka model: 3. Diffusive nature of the atomic motions contained in a new dynamical model for deciphering local lipid dynamics.

In accompanying papers [Bicout et al., BioRxiv https://doi.org/10.1101/2021.09.21.461198 (2021); Cissé et al., BioRxiv https://doi.org/10.1101/2022.03.30.486370 (2022)], a new model called Matryoshka model has been proposed to describe the geometry of atomic motions in phospholipid molecules in bilayers and multilamellar vesicles based on their quasielastic neutron scattering (QENS) spectra. Here, in order to characterize the relaxational aspects of this model, the energy widths of the QENS spectra of the samples were analyzed first in a model-free way. The spectra were decomposed into three Lorentzian functions, which are classified as slow, intermediate, and fast motions depending on their widths. The analysis provides the diffusion coefficients, residence times, and geometrical parameters for the three classes of motions. The results corroborate the parameter values such as the amplitudes and the mobile fractions of atomic motions obtained by the application of the Matryoshka model to the same samples. Since the current analysis was carried out independently of the development of the Matryoshka model, the present results enhance the validity of the model. The model will serve as a powerful tool to decipher the dynamics of lipid molecules not only in model systems, but also in more complex systems such as mixtures of different kinds of lipids or natural cell membranes.

Diffusion in dense supercritical methane from quasi-elastic neutron scattering measurements.

Methane, the principal component of natural gas, is an important energy source and raw material for chemical reactions. It also plays a significant role in planetary physics, being one of the major constituents of giant planets. Here, we report measurements of the molecular self-diffusion coefficient of dense supercritical CH4 reaching the freezing pressure. We find that the high-pressure behaviour of the self-diffusion coefficient measured by quasi-elastic neutron scattering at 300 K departs from that expected for a dense fluid of hard spheres and suggests a density-dependent molecular diameter. Breakdown of the Stokes-Einstein-Sutherland relation is observed and the experimental results suggest the existence of another scaling between self-diffusion coefficient D and shear viscosity η, in such a way that Dη/ρ=constant at constant temperature, with ρ the density. These findings underpin the lack of a simple model for dense fluids including the pressure dependence of their transport properties.

Dynamics of heparan sulfate explored by neutron scattering.

The temperature dependence of atomic fluctuations in heparan sulfate was measured for different time-scales between the picosecond and the nanosecond. The data established the role of hydration for the emergence of high-amplitude motions at 200-240 K, and the higher resilience of the polysaccharide compared to proteins measured under similar conditions.

A neutron scattering perspective on the structure, softness and dynamics of the ligand shell of PbS nanocrystals in solution.

Small-angle neutron and X-ray scattering, neutron backscattering and neutron time-of-flight spectroscopy are applied to reveal the structure of the ligand shell, the temperature-dependent diffusion properties and the phonon spectrum of PbS nanocrystals functionalized with oleic acid in deuterated hexane. The nanocrystals decorated with oleic acid as well as the desorbed ligand molecules exhibit simple Brownian diffusion with a Stokes-Einstein temperature-dependence and inhibited freezing. Ligand molecules desorbed from the surface show strong spatial confinement. The phonon spectrum of oleic acid adsorbed to the nanocrystal surface exhibits hybrid modes with a predominant Pb-character. Low-energy surface modes of the NCs are prominent and indicate a large mechanical softness in solution. This work provides comprehensive insights into the ligand-particle interaction of colloidal nanocrystals in solution and highlights its effect on the diffusion and vibrational properties as well as their mechanical softness.