Localized and long-range diffusion in condensed matter: state of the art of QENS studies and future prospects

Effects of Crowding and Cosolutes on Biomolecular Function at Extreme Environmental Conditions

The extent of the effect of cellular crowding and cosolutes on the functioning of proteins and cells is manifold and includes the stabilization of the biomolecular systems, the excluded volume effect, and the modulation of molecular dynamics. Simultaneously, it is becoming increasingly clear how important it is to take the environment into account if we are to shed light on biological function under various external conditions. Many biosystems thrive under extreme conditions, including the deep sea and subseafloor crust, and can take advantage of some of the effects of crowding. These relationships have been studied in recent years using various biophysical techniques, including neutron and X-ray scattering, calorimetry, FTIR, UV-vis and fluorescence spectroscopies. Combining knowledge of the structure and conformational dynamics of biomolecules under extreme conditions, such as temperature, high hydrostatic pressure, and high salinity, we highlight the importance of considering all results in the context of the environment. Here we discuss crowding and cosolute effects on proteins, nucleic acids, membranes, and live cells and explain how it is possible to experimentally separate crowding-induced effects from other influences. Such findings will contribute to a better understanding of the homeoviscous adaptation of organisms and the limits of life in general.

Decoupling Ion Transport and Matrix Dynamics to Make High Performance Solid Polymer Electrolytes

Transport of ions through solid polymeric electrolytes (SPEs) involves a complicated interplay of ion solvation, ion-ion interactions, ion-polymer interactions, and free volume. Nonetheless, prevailing viewpoints on the subject promote a significantly simplified picture, likening ion transport in a polymer to that in an unstructured fluid at low solute concentrations. Although this idealized liquid transport model has been successful in guiding the design of homogeneous electrolytes, structured electrolytes provide a promising alternate route to achieve high ionic conductivity and selectivity. In this perspective, we begin by describing the physical origins of the idealized liquid transport mechanism and then proceed to examine known cases of decoupling between the matrix dynamics and ionic transport in SPEs. Specifically we discuss conditions for "decoupled" mobility that include a highly polar electrolyte environment, a percolated path of free volume elements (either through structured or unstructured channels), high ion concentrations, and labile ion-electrolyte interactions. Finally, we proceed to reflect on the potential of these mechanisms to promote multivalent ion conductivity and the need for research into the interfacial properties of solid polymer electrolytes as well as their performance at elevated potentials.

The Impact of Surface Charges of Carboxylated Cellulose Nanofibrils on the Water Motions in Hydrated Films

Cellulose nanofibrils (CNFs) with carboxylated surface ligands are a class of materials with tunable surface functionality, good mechanical properties, and bio-/environmental friendliness. They have been used in many applications as scaffold, reinforcing, or functional materials, where the interaction between adsorbed moisture and the CNF could lead to different properties and structures and become critical to the performance of the materials. In this work, we exploited multiple experimental methods to study the water movement in hydrated films made of carboxylated CNFs prepared by TEMPO oxidation with two different surface charges of 600 and 1550 μmol·g^-1. A combination of quartz crystal microbalance with dissipation (QCM-D) and small-angle X-ray scattering (SAXS) shows that both the surface charge of a single fibril and the films' network structure contribute to the moisture uptake. The films with 1550 μmol·g^-1 surface charges take up twice the amount of moisture per unit mass, leading to the formation of nanostructures with an average radius of gyration of 2.1 nm. Via the nondestructive quasi-elastic neutron scattering (QENS), a faster motion is explained as a localized movement of water molecules inside confined spheres, and a slow diffusive motion is found with the diffusion coefficient close to bulk water at room temperature via a random jump diffusion model and regardless of the surface charge in films made from CNFs.

MOFs in the time domain

Many of the proposed applications of metal-organic framework (MOF) materials may fail to materialize if the community does not fully address the difficult fundamental work needed to map out the 'time gap' in the literature - that is, the lack of investigation into the time-dependent behaviours of MOFs as opposed to equilibrium or steady-state properties. Although there are a range of excellent investigations into MOF dynamics and time-dependent phenomena, these works represent only a tiny fraction of the vast number of MOF studies. This Review provides an overview of current research into the temporal evolution of MOF structures and properties by analysing the time-resolved experimental techniques that can be used to monitor such behaviours. We focus on innovative techniques, while also discussing older methods often used in other chemical systems. Four areas are examined: MOF formation, guest motion, electron motion and framework motion. In each area, we highlight the disparity between the relatively small amount of (published) research on key time-dependent phenomena and the enormous scope for acquiring the wider and deeper understanding that is essential for the future of the field.

A two-dimensional type I superionic conductor

Superionic conductors possess liquid-like ionic diffusivity in the solid state, finding wide applicability from electrolytes in energy storage to materials for thermoelectric energy conversion. Type I superionic conductors (for example, AgI, Ag₂Se and so on) are defined by a first-order transition to the superionic state and have so far been found exclusively in three-dimensional crystal structures. Here, we reveal a two-dimensional type I superionic conductor, α-KAg₃Se₂, by scattering techniques and complementary simulations. Quasi-elastic neutron scattering and ab initio molecular dynamics simulations confirm that the superionic Ag⁺ ions are confined to subnanometre sheets, with the simulated local structure validated by experimental X-ray powder pair-distribution-function analysis. Finally, we demonstrate that the phase transition temperature can be controlled by chemical substitution of the alkali metal ions that compose the immobile charge-balancing layers. Our work thus extends the known classes of superionic conductors and will facilitate the design of new materials with tailored ionic conductivities and phase transitions.

Ion transport in small-molecule and polymer electrolytes

Solid-state polymer electrolytes and high-concentration liquid electrolytes, such as water-in-salt electrolytes and ionic liquids, are emerging materials to replace the flammable organic electrolytes widely used in industrial lithium-ion batteries. Extensive efforts have been made to understand the ion transport mechanisms and optimize the ion transport properties. This perspective reviews the current understanding of the ion transport and polymer dynamics in liquid and polymer electrolytes, comparing the similarities and differences in the two types of electrolytes. Combining recent experimental and theoretical findings, we attempt to connect and explain ion transport mechanisms in different types of small-molecule and polymer electrolytes from a theoretical perspective, linking the macroscopic transport coefficients to the microscopic, molecular properties such as the solvation environment of the ions, salt concentration, solvent/polymer molecular weight, ion pairing, and correlated ion motion. We emphasize universal features in the ion transport and polymer dynamics by highlighting the relevant time and length scales. Several outstanding questions and anticipated developments for electrolyte design are discussed, including the negative transference number, control of ion transport through precision synthesis, and development of predictive multiscale modeling approaches.

Protein and RNA dynamical fingerprinting

Protein structural vibrations impact biology by steering the structure to functional intermediate states; enhancing tunneling events; and optimizing energy transfer. Strong water absorption and a broad continuous vibrational density of states have prevented optical identification of these vibrations. Recently spectroscopic signatures that change with functional state were measured using anisotropic terahertz microscopy. The technique however has complex sample positioning requirements and long measurement times, limiting access for the biomolecular community. Here we demonstrate that a simplified system increases spectroscopic structure to dynamically fingerprint biomacromolecules with a factor of 6 reduction in data acquisition time. Using this technique, polarization varying anisotropy terahertz microscopy, we show sensitivity to inhibitor binding and unique vibrational spectra for several proteins and an RNA G-quadruplex. The technique’s sensitivity to anisotropic absorbance and birefringence provides rapid assessment of macromolecular dynamics that impact biology.

The characterization of biomacromolecule structural vibrations has been impeded by a broad continuous vibrational density of states obscuring molecule specific vibrations. A terahertz microscopy system using polarization control produces signatures to dynamically fingerprint proteins and a RNA G-quadruplex.

Relationship between Segmental Dynamics Measured by Quasi-Elastic Neutron Scattering and Conductivity in Polymer Electrolytes

Quasi-elastic neutron scattering experiments on mixtures of poly(ethylene oxide) and lithium bis(trifluoromethane)sulfonimide salt, a standard polymer electrolyte, led to the quantification of the effect of salt on segmental dynamics in the 1-10 Å length scale. The monomeric friction coefficient characterizing segmental dynamics on these length scales increases exponentially with salt concentration. More importantly, we find that this change in monomeric friction alone is responsible for all of the observed nonlinearity in the dependence of ionic conductivity on salt concentration. Our analysis leads to a surprisingly simple relationship between macroscopic ion transport in polymers and dynamics at monomeric length scales.

Moving in the Right Direction: Protein Vibrations Steering Function

Nearly all protein functions require structural change, such as enzymes clamping onto substrates, and ion channels opening and closing. These motions are a target for possible new therapies; however, the control mechanisms are under debate. Calculations have indicated protein vibrations enable structural change. However, previous measurements found these vibrations only weakly depend on the functional state. By using the novel technique of anisotropic terahertz microscopy, we find that there is a dramatic change to the vibrational directionality with inhibitor binding to lysozyme, whereas the vibrational energy distribution, as measured by neutron inelastic scattering, is only slightly altered. The anisotropic terahertz measurements provide unique access to the directionality of the intramolecular vibrations, and immediately resolve the inconsistency between calculations and previous measurements, which were only sensitive to the energy distribution. The biological importance of the vibrational directions versus the energy distribution is revealed by our calculations comparing wild-type lysozyme with a higher catalytic rate double deletion mutant. The vibrational energy distribution is identical, but the more efficient mutant shows an obvious reorientation of motions. These results show that it is essential to characterize the directionality of motion to understand and control protein dynamics to optimize or inhibit function.

Molecular Dynamics of POPC Phospholipid Bilayers through the Gel to Fluid Phase Transition: An Incoherent Quasi-Elastic Neutron Scattering Study

The microscopic dynamics for the gel and liquid-crystalline phase of highly aligned D2O-hydrated bilayers of 1-palmitoyl-oleoyl-sn-glycero-phosphocholine (POPC) were investigated in the temperature range from 248 to 273 K by using incoherent quasi-elastic neutrons scattering (QENS). We develop a model for describing the molecular motions of the liquid phase occurring in the 0.3 to 350 ps time range. Accordingly, the complex dynamics of hydrogen are described in terms of simple dynamical processes involving different parts of the phospholipid chain. The analysis of the data evidences the existence of three different motions: the fast motion of hydrogen vibrating around the carbon atoms, the intermediate motion of carbon atoms in the acyl chains, and the slower translational motion of the entire phospholipid molecule. The influence of the temperature on these dynamical processes is investigated. In particular, by going from gel to liquid-crystalline phase, we reveal an increase of the segmental motion mainly affecting the terminal part of the acyl chains and a change of the diffusional dynamics from a localized rattling-like motion to a confined diffusion.

Multi-component modeling of quasielastic neutron scattering from phospholipid membranes

We investigated molecular motions in the 0.3-350 ps time range of D2O-hydrated bilayers of 1-palmitoyl-oleoyl-sn-glycero-phosphocholine and 1,2-dimyristoyl-sn-glycero-phosphocholine in the liquid phase by quasielastic neutron scattering. Model analysis of sets of spectra covering scale lengths from 4.8 to 30 Å revealed the presence of three types of motion taking place on well-separated time scales: (i) slow diffusion of the whole phospholipid molecules in a confined cylindrical region; (ii) conformational motion of the phospholipid chains; and (iii) fast uniaxial rotation of the hydrogen atoms around their carbon atoms. Based on theoretical models for the hydrogen dynamics in phospholipids, the spatial extent of these motions was analysed in detail and the results were compared with existing literature data. The complex dynamics of protons was described in terms of elemental dynamical processes involving different parts of the phospholipid chain on whose motions the hydrogen atoms ride.

Incoherent Neutron Spin-Echo Spectroscopy as an Option to Study Long-Range Lipid Diffusion

Diffusion is the fundamental mechanism for lipids and other molecules to move in a membrane. It is an important process to consider in modelling the formation of membrane structures, such as rafts. Lipid diffusion is mainly studied by two different techniques: incoherent neutron scattering and fluorescence microscopy. Both techniques access distinctly different length scales. While neutron scattering measures diffusion over about 3 lipid diameters, microscopic techniques access motions of lipids over micrometer distances. The diffusion constants which are determined by these two methods often differ by about an order of magnitude, with the neutrons usually seeing a faster lipid diffusion. Different theories are used to describe lipid diffusion in the two experiments. In order to close the “gap” between these two techniques, we propose to study lipid diffusion at mesoscopic length scales using a neutron spin-echo (NSE) spectrometer. We have conducted an experiment in highly oriented, solid supported lipid bilayers to prove the feasibility of performing incoherent NSE on biological samples. Lateral lipid diffusion was measured in a fluid phase model membrane system at a length scale of 12 Å. Using the high-energy resolution of the NSE technique, we find evidence for two dynamic processes.

Localized translational motions in semicrystalline poly(ethylene terephthalate) studied by incoherent quasielastic neutron scattering

One of the simplest ways to confine polymeric materials is by self-assembling during the crystallization process. The remaining amorphous phase is then constrained by the lamellar crystals. In this manuscript, we aim to shed additional light in the understanding of the amorphous chains dynamics of semicrystalline polymers above the Tg by using incoherent quasielastic neutron scattering QENS in a nanoscopic time scale (10(-9)-10(-10)s) on poly(ethylene terephthalate). The observed dynamics is satisfactorily described by a theoretical model that considers that the proton mobility follows a random jump-diffusion in a restricted environment. We demonstrate that the combination of macroscopic with nanoscopic dynamic tools allows a complete description of the confined dynamics on a paradigmatic semicrystalline polymer like poly(ethylene terephthalate).

Protein diffusion in crowded electrolyte solutions

We report on a combined cold neutron backscattering and spin-echo study of the short-range and long-range nanosecond diffusion of the model globular protein bovine serum albumin (BSA) in aqueous solution as a function of protein concentration and NaCl salt concentration. Complementary small angle X-ray scattering data are used to obtain information on the correlations of the proteins in solution. Particular emphasis is put on the effect of crowding, i.e. conditions under which the proteins cannot be considered as objects independent of each other. We thus address the question at which concentration this crowding starts to influence the static and in particular also the dynamical behaviour. We also briefly discuss qualitatively which charge effects, i.e. effects due to the interplay of charged molecules in an electrolyte solution, may be anticipated. Both the issue of crowding as well as that of charge effects are particularly relevant for proteins and their function under physiological conditions, where the protein volume fraction can be up to approximately 40% and salt ions are ubiquitous. The interpretation of the data is put in the context of existing studies on related systems and of existing theoretical models.

Dynamics of well-folded and natively disordered proteins in solution: a time-of-flight neutron scattering study

Casein proteins belong to the class of natively disordered proteins. The existence of disordered biologically active proteins questions the assumption that a well-folded structure is required for function. A hypothesis generally put forward is that the unstructured nature of these proteins results from the functional need of a higher flexibility. This interplay between structure and dynamics was investigated in a series of time-of-flight neutron scattering experiments, performed on casein proteins, as well as on three well-folded proteins with distinct secondary structures, namely, myoglobin (alpha), lysozyme (alpha/beta) and concanavalin A (beta). To illustrate the subtraction of the solvent contribution from the scattering spectra, we used the dynamic susceptibility spectra emphasizing the high frequency part of the spectrum, where the solvent dominates. The quality of the procedure is checked by comparing the corrected spectra to those of the dry and hydrated protein with negligible solvent contamination. Results of spectra analysis reveal differences in motional amplitudes of well-folded proteins, where beta-sheet structures appear to be more rigid than a cluster of alpha-helices. The disordered caseins display the largest conformational displacements. Moreover their global diffusion rates deviate from the expected dependence, suggesting further large-scale conformational motions.

Relationship Between Structure, Dynamics and Function of Hydrated Purple Membrane Investigated by Neutron Scattering and Dielectric Spectroscopy

We investigated the influence of hydration water on the relationship between structure, dynamics and function in a biological membrane system. For the example of the purple membrane (PM) with its protein bacteriorhodopsin (BR), a light-driven proton pump, complementary information from neutron diffraction, quasi-elastic neutron scattering (QENS) and dielectric spectroscopy will form a comprehensive picture of the structural and dynamic behavior of the PM in the temperature range between 150 and 290 K. Temperature- and humidity-dependent changes in the membrane system influence the accessibility of the different photocycle intermediates of BR. The melting of the 'freezing bound water' between 220 and 250 K could be related to the transition from the M1 to the M2 intermediate, which represents the key step in the photocycle. The dynamic transition in the vicinity of 180 K was shown to be necessary to ensure that the M1 intermediate can be populated and that the melting of crystallized bulk water above 255 K enables the completion of the photocycle.

Separable cooperative and localized translational motions of water confined by a chemically heterogeneous environment

We report quasi-elastic neutron scattering experiments at two resolutions that probe timescales of picoseconds to nanoseconds for the hydration dynamics of water, confined in a concentrated solution of N-acetyl-leucine-methylamide (NALMA) peptides in water over a temperature range of 248 K to 288 K. The two QENS resolutions used allow for a clean separation of two observable translational components, and ultimately two very different relaxation processes, that become evident when analyzed under a combination of the jump diffusion model and the relaxation cage model. The first translational motion is a localized beta-relaxation process of the bound surface water, and exhibits an Arrhenius temperature dependence and a large activation energy of approximately 8 kcal mol(-1). The second non-Arrhenius translational component is a dynamical signature of the alpha-relaxation of more fluid water, exhibiting a glass transition temperature of approximately 116 K when fit to the Volger Fulcher Tamman functional form. These peptide solutions provide a novel experimental system for examining confinement in order to understand the dynamical transition in bulk supercooled water by removing the unwanted interface of the confining material on water dynamics.

Molecular view of water dynamics near model peptides

Incoherent quasi-elastic neutron scattering (QENS) has been used to measure the dynamics of water molecules in solutions of a model protein backbone, N-acetyl-glycine-methylamide (NAGMA), as a function of concentration, for comparison with results for water dynamics in aqueous solutions of the N-acetyl-leucine-methylamide (NALMA) hydrophobic peptide at comparable concentrations. From the analysis of the elastic incoherent structure factor, we find significant fractions of elastic intensity at high and low concentrations for both solutes, which corresponds to a greater population of protons with rotational time scales outside the experimental resolution (>13 ps). The higher-concentration solutions show a component of the elastic fraction that we propose is due to water motions that are strongly coupled to the solute motions, while for low-concentration solutions an additional component is activated due to dynamic coupling between inner and outer hydration layers. An important difference between the solute types at the highest concentration studied is found from stretched exponential fits to their experimental intermediate scattering functions, showing more pronounced anomalous diffusion signatures for NALMA, including a smaller stretched exponent beta and a longer structural relaxation time tau than those found for NAGMA. The more normal water diffusion exhibited near the hydrophilic NAGMA provides experimental support for an explanation of the origin of the anomalous diffusion behavior of NALMA as arising from frustrated interactions between water molecules when a chemical interface is formed upon addition of a hydrophobic side chain, inducing spatial heterogeneity in the hydration dynamics in the two types of regions of the NALMA peptide. We place our QENS measurements on model biological solutes in the context of other spectroscopic techniques and provide both confirming as well as complementary dynamic information that attempts to give a unifying molecular view of hydration dynamics signatures near peptides and proteins.

Hydration dynamics near a model protein surface

The evolution of water dynamics from dilute to very high concentration solutions of a prototypical hydrophobic amino acid with its polar backbone, N-acetyl-leucine-methylamide (NALMA), is studied by quasi-elastic neutron scattering (QENS) and molecular dynamics (MD) simulation for both the completely deuterated and completely hydrogenated leucine monomer. The NALMA-water system and the QENS data together provide a unique study for characterizing the dynamics of different hydration layers near a prototypical hydrophobic side chain and the backbone of which it is attached. We observe several unexpected features in the dynamics of these biological solutions under ambient conditions. The NALMA dynamics shows evidence of de Gennes narrowing, an indication of coherent long timescale structural relaxation dynamics. The translational and rotational water dynamics at the highest solute concentrations are found to be highly suppressed as characterized by long residential time and slow diffusion coefficients. The analysis of the more dilute concentration solutions models the first hydration shell with the 2.0 M spectra. We find that for outer layer hydration dynamics that the translational diffusion dynamics is still suppressed, although the rotational relaxation time and residential time are converged to bulk-water values. Molecular dynamics analysis of the first hydration shell water dynamics shows spatially heterogeneous water dynamics, with fast water motions near the hydrophobic side chain, and much slower water motions near the hydrophilic backbone. We discuss the hydration dynamics results of this model protein system in the context of protein function and protein-protein recognition.