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.

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.

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.

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.

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.

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.

Impact of Sucrose as Osmolyte on Molecular Dynamics of Mouse Acetylcholinesterase.

The enzyme model, mouse acetylcholinesterase, which exhibits its active site at the bottom of a narrow gorge, was investigated in the presence of different concentrations of sucrose to shed light on the protein and water dynamics in cholinesterases. The study was conducted by incoherent neutron scattering, giving access to molecular dynamics within the time scale of sub-nano to nanoseconds, in comparison with molecular dynamics simulations. With increasing sucrose concentration, we found non-linear effects, e.g., first a decrease in the dynamics at 5 wt% followed by a gain at 10 wt% sucrose. Direct comparisons with simulations permitted us to understand the following findings: at 5 wt%, sugar molecules interact with the protein surface through water molecules and damp the motions to reduce the overall protein mobility, although the motions inside the gorge are enhanced due to water depletion. When going to 10 wt% of sucrose, some water molecules at the protein surface are replaced by sugar molecules. By penetrating the protein surface, they disrupt some of the intra-protein contacts, and induce new ones, creating new pathways for correlated motions, and therefore, increasing the dynamics. This exhaustive study allowed for an explanation of the detail interactions leading to the observed non-linear behavior.

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.

A Quasielastic Neutron Scattering Investigation on the Molecular Self-Dynamics of Human Myelin Protein P2.

The human myelin protein P2 is a membrane binding protein believed to maintain correct lipid composition and organization in peripheral nerve myelin. Its function is related to its ability to stack membranes, and this function can be enhanced by the P38G mutation, whereby the overall protein structure does not change but the molecular dynamics increase. Mutations in P2 are linked to human peripheral neuropathy. Here, the dynamics of wild-type P2 and the P38G variant were studied using quasielastic neutron scattering on time scales from 10 ps to 1 ns at 300 K. The results suggest that the mutant protein dynamics are increased on both the fastest and the slowest measured time scales, by increasing the dynamics amplitude and/or the portion of atoms participating in the movement.

In Vivo Water Dynamics in Shewanella oneidensis Bacteria at High Pressure.

Following observations of survival of microbes and other life forms in deep subsurface environments it is necessary to understand their biological functioning under high pressure conditions. Key aspects of biochemical reactions and transport processes within cells are determined by the intracellular water dynamics. We studied water diffusion and rotational relaxation in live Shewanella oneidensis bacteria at pressures up to 500 MPa using quasi-elastic neutron scattering (QENS). The intracellular diffusion exhibits a significantly greater slowdown (by -10-30%) and an increase in rotational relaxation times (+10-40%) compared with water dynamics in the aqueous solutions used to resuspend the bacterial samples. Those results indicate both a pressure-induced viscosity increase and slowdown in ionic/macromolecular transport properties within the cells affecting the rates of metabolic and other biological processes. Our new data support emerging models for intracellular organisation with nanoscale water channels threading between macromolecular regions within a dynamically organized structure rather than a homogenous gel-like cytoplasm.

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.

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.

Fast methane diffusion at the interface of two clathrate structures.

Methane hydrates naturally form on Earth and in the interiors of some icy bodies of the Universe, and are also expected to play a paramount role in future energy and environmental technologies. Here we report experimental observation of an extremely fast methane diffusion at the interface of the two most common clathrate hydrate structures, namely clathrate structures I and II. Methane translational diffusion-measured by quasielastic neutron scattering at 0.8 GPa-is faster than that expected in pure supercritical methane at comparable pressure and temperature. This phenomenon could be an effect of strong confinement or of methane aggregation in the form of micro-nanobubbles at the interface of the two structures. Our results could have implications for understanding the replacement kinetics during sI-sII conversion in gas exchange experiments and for establishing the methane mobility in methane hydrates embedded in the cryosphere of large icy bodies in the Universe.

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 .

Probing the dynamics of complexed local anesthetics via neutron scattering spectroscopy and DFT calculations.

Since potential changes in the dynamics and mobility of drugs upon complexation for delivery may affect their ultimate efficacy, we have investigated the dynamics of two local anesthetic molecules, bupivacaine (BVC, C18H28N2O) and ropivacaine (RVC, C17H26N2O), in both their crystalline forms and complexed with water-soluble oligosaccharide 2-hydroxypropyl-ß-cyclodextrin (HP-ß-CD). The study was carried out by neutron scattering spectroscopy, along with thermal analysis, and density functional theory computation. Mean square displacements suggest that RVC may be less flexible in crystalline form than BVC, but both molecules exhibit very similar dynamics when confined in HP-ß-CD. The use of vibrational analysis by density functional theory (DFT) made possible the identification of molecular modes that are most affected in both molecules by insertion into HP-ß-CD, namely those of the piperidine rings and methyl groups. Nonetheless, the somewhat greater structure in the vibrational spectrum at room temperature of complexed RVC than that of BVC, suggests that the effects of complexation are more severe for the latter. This unique approach to the molecular level study of encapsulated drugs should lead to deeper understanding of their mobility and the respective release dynamics.

Dynamical Crossover in Hot Dense Water: The Hydrogen Bond Role.

We investigate the terahertz dynamics of liquid H2O as a function of pressure along the 450 K isotherm, by coupled quasielastic neutron scattering and inelastic X-ray scattering experiments. The pressure dependence of the single-molecule dynamics is anomalous in terms of both microscopic translation and rotation. In particular, the Stokes-Einstein-Debye equations are shown to be violated in hot water compressed to the GPa regime. The dynamics of the hydrogen bond network is only weakly affected by the pressure variation. The time scale of the structural relaxation driving the collective dynamics increases by a mere factor of 2 along the investigated isotherm, and the structural relaxation strength turns out to be almost pressure independent. Our results point at the persistence of the hydrogen bond network in hot dense water up to ice VII crystallization, thus questioning the long-standing perception that hydrogen bonds are broken in liquid water under the effect of compression.

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.

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.