Trimethylamine-N-oxide depletes urea in a peptide solvation shell.

Trimethylamine-N-oxide (TMAO) and urea are metabolites that are used by some marine animals to maintain their cell volume in a saline environment. Urea is a well-known denaturant, and TMAO is a protective osmolyte that counteracts urea-induced protein denaturation. TMAO also has a general protein-protective effect, for example, it counters pressure-induced protein denaturation in deep-sea fish. These opposing effects on protein stability have been linked to the spatial relationship of TMAO, urea, and protein molecules. It is generally accepted that urea-induced denaturation proceeds through the accumulation of urea at the protein surface and their subsequent interaction. In contrast, it has been suggested that TMAO's protein-stabilizing effects stem from its exclusion from the protein surface, and its ability to deplete urea from protein surfaces; however, these spatial relationships are uncertain. We used neutron diffraction, coupled with structural refinement modeling, to study the spatial associations of TMAO and urea with the tripeptide derivative glycine-proline-glycinamide in aqueous urea, aqueous TMAO, and aqueous urea-TMAO (in the mole ratio 1:2 TMAO:urea). We found that TMAO depleted urea from the peptide's surface and that while TMAO was not excluded from the tripeptide's surface, strong atomic interactions between the peptide and TMAO were limited to hydrogen bond donating peptide groups. We found that the repartition of urea, by TMAO, was associated with preferential TMAO-urea bonding and enhanced urea-water hydrogen bonding, thereby anchoring urea in the bulk solution and depleting urea from the peptide surface.

Hydrophobic hydration of the hydrocarbon adamantane in amorphous ice.

Hydrophobic molecules are by definition difficult to hydrate. Previous studies in the area of hydrophobic hydration have therefore often relied on using amphiphilic molecules where the hydrophilic part of a molecule enabled the solubility in liquid water. Here, we show that the hydrophobic adamantane (C10H16) molecule can be fully hydrated through vapour codeposition with water onto a cryogenic substrate at 80 K resulting in the matrix isolation of adamantane in amorphous ice. Using neutron diffraction in combination with the isotopic substitution method and the empirical potential structure refinement technique, we find that the first hydration shell of adamantane is well structured consisting of a hydrogen-bonded cage of 28 water molecules that is also found in cubic structure II clathrate hydrates. The four hexagonal faces of the 51264 cage are situated above the four methine (CH) groups of adamantane whereas the methylene (CH2) groups are positioned below the edges of two adjoining pentagonal faces. The oxygen atoms of the 28 water molecules can be categorised on the basis of symmetry equivalences as twelve A, twelve B and four C oxygens. The water molecules of the first hydration shell display orientations consistent with those expected for a clathrate-hydrate-type cage, but also unfavourable ones with respect to the hydrogen bonding between the water molecules. Annealing the samples at 140 K, which is just below the crystallisation temperature of the matrix, removes the unfavourable orientations and leads to a slight increase in the structural order of the first hydration shell. The very closest water molecules display a tendency for their dipole moments to point towards the adamantane which is attributed to steric effects. Other than this, no significant polarisation effects are observed which is consistent with weak interactions between adamantane and the amorphous ice matrix. FT-IR spectroscopy shows that the incorporation of adamantane into amorphous ice leads to a weakening of the hydrogen bonds. In summary, the matrix-isolation of the highly symmetric adamantane in amorphous ice provides an interesting test case for hydrophobic hydration. Studying the structure and spectroscopic properties of water at the interface with hydrophobic hydrocarbons is also relevant for astrophysical environments, such as comets or the interstellar medium, where amorphous ice and hydrocarbons have been shown to coexist in large quantities.

Visualization of Self-Assembly and Hydration of a ß-Hairpin through Integrated Small and Wide-Angle Neutron Scattering.

Fundamental understanding of the structure and assembly of nanoscale building blocks is crucial for the development of novel biomaterials with defined architectures and function. However, accessing self-consistent structural information across multiple length scales is challenging. This limits opportunities to exploit atomic scale interactions to achieve emergent macroscale properties. In this work we present an integrative small- and wide-angle neutron scattering approach coupled with computational modeling to reveal the multiscale structure of hierarchically self-assembled ß hairpins in aqueous solution across 4 orders of magnitude in length scale from 0.1 Å to 300 nm. Our results demonstrate the power of this self-consistent cross-length scale approach and allows us to model both the large-scale self-assembly and small-scale hairpin hydration of the model ß hairpin CLN025. Using this combination of techniques, we map the hydrophobic/hydrophilic character of this model self-assembled biomolecular surface with atomic resolution. These results have important implications for the multiscale investigation of aqueous peptides and proteins, for the prediction of ligand binding and molecular associations for drug design, and for understanding the self-assembly of peptides and proteins for functional biomaterials.

The structure of liquid thiophene from total neutron scattering.

The structure of pure liquid thiophene is revealed by using a combination of total neutron scattering experiments with isotopic substitution and molecular simulations via the next generation empirical potential refinement software, Dissolve. In the liquid, thiophene presents three principle local structural motifs within the first solvation shell, in plane and out of the plane of the thiophene ring. Firstly, above/below the ring plane thiophenes present a single H towards the π cloud, due to a combination of electrostatic and dispersion interactions. Secondly, around the ring plane, perpendicular thiophene molecules find 5 preferred sites driven by bifurcated C-H⋯S interactions, showing that hydrogen-sulfur bonding prevails over the charge asymmetry created by the heteroatom. Finally, parallel thiophenes sit above and below the ring, excluded from directly above the ring center and above the sulfur.

Strong structuring arising from weak cooperative O-H···π and C-H···O hydrogen bonding in benzene-methanol solution.

Weak hydrogen bonds, such as O-H···π and C-H···O, are thought to direct biochemical assembly, molecular recognition, and chemical selectivity but are seldom observed in solution. We have used neutron diffraction combined with H/D isotopic substitution to obtain a detailed spatial and orientational picture of the structure of benzene-methanol mixtures. Our analysis reveals that methanol fully solvates and surrounds each benzene molecule. The expected O-H···π interaction is highly localised and directional, with the methanol hydroxyl bond aligned normal to the aromatic plane and the hydrogen at a distance of 2.30 Å from the ring centroid. Simultaneously, the tendency of methanol to form chain and cyclic motifs in the bulk liquid is manifest in a highly templated solvation structure in the plane of the ring. The methanol molecules surround the benzene so that the O-H bonds are coplanar with the aromatic ring while the oxygens interact with C-H groups through simultaneous bifurcated hydrogen bonds. This demonstrates that weak hydrogen bonding can modulate existing stronger interactions to give rise to highly ordered cooperative structural motifs that persist in the liquid phase.

The local ordering of polar solvents around crystalline carbon nitride nanosheets in solution.

The crystalline graphitic carbon nitride, poly-triazine imide (PTI) is highly unusual among layered materials since it is spontaneously soluble in aprotic, polar solvents including dimethylformamide (DMF). The PTI material consists of layers of carbon nitride intercalated with LiBr. When dissolved, the resulting solutions consist of dissolved, luminescent single to multilayer nanosheets of around 60-125 nm in diameter and Li+ and Br- ions originating from the intercalating salt. To understand this unique solubility, the structure of these solutions has been investigated by high-energy X-ray and neutron diffraction. Although the diffraction patterns are dominated by inter-solvent correlations there are clear differences between the X-ray diffraction data of the PTI solution and the solvent in the 4-6 Å-1 range, with real space differences persisting to at least 10 Å. Structural modelling using both neutron and X-ray datasets as a constraint reveal the formation of distinct, dense solvation shells surrounding the nanoparticles with a layer of Br-close to the PTI-solvent interface. This solvent ordering provides a configuration that is energetically favourable underpinning thermodynamically driven PTI dissolution. This article is part of the theme issue 'Exploring the length scales, timescales and chemistry of challenging materials (Part 2)'.

A total scattering study of prenucleation structures in saturated aqueous magnesium sulfate - observation of extended clusters.

Through a combination of X-ray and neutron total scattering and Empirical Potential Structure Refinement (EPSR) we explore the prenucleation structures of saturated aqueous magnesium sulfate. The atomistic model we present reveals a system characterised by isolated octahedral aquo magnesium species Mg(H2O)6, magnesium sulfate pairs (Mg(H2O)5SO4) and extended clusters built from corner-sharing MgO6 and SO4 polyhedra. Many of these features are directly observed in the crystal structures of the known solid form hydrates, including isolated polyhedra, corner sharing chains and rings, and it is only for the extended 3D polyhedral networks of the lower hydrates (mono- & di-) that no proto structures are observed in 2M solution. Looking at the average first solvation shell of the sulfate anion we see a complex and flexible environment that commonly includes water molecules brought into proximity by a coordinated hydrated magnesium. What emerges is a high probability that 10 water molecules will be observed in a combined tetrahedral/octahedral arrangement with a further 7 taking up more dispersed positions giving an average coordination of 17. The tendency for ions to aggregate into clusters allows areas of bulk water to exist that exhibit subtle differences in structure to that of pure water.

Weak Interactions in Dimethyl Sulfoxide (DMSO)-Tertiary Amide Solutions: The Versatility of DMSO as a Solvent.

The structures of equimolar mixtures of the commonly used polar aprotic solvents dimethylformamide (DMF) and dimethylacetamide (DMAc) in dimethyl sulfoxide (DMSO) have been investigated via neutron diffraction augmented by extensive hydrogen/deuterium isotopic substitution. Detailed 3-dimensional structural models of these solutions have been derived from the neutron data via Empirical Potential Structure Refinement (EPSR). The intermolecular center-of-mass (CoM) distributions show that the first coordination shell of the amides comprises ∼13-14 neighbors, of which approximately half are DMSO. In spite of this near ideal coordination shell mixing, the changes to the amide-amide structure are found to be relatively subtle when compared to the pure liquids. Analysis of specific intermolecular atom-atom correlations allows quantitative interpretation of the competition between weak interactions in the solution. We find a hierarchy of formic and methyl C-H···O hydrogen bonds forms the dominant local motifs, with peak positions in the range of 2.5-3.0 Å. We also observe a rich variety of steric and dispersion interactions, including those involving the O═C-N amide π-backbones. This detailed insight into the structural landscape of these important liquids demonstrates the versatility of DMSO as a solvent and the remarkable sensitivity of neutron diffraction, which is critical for understanding weak intermolecular interactions at the nanoscale and thereby tailoring solvent properties to specific applications.

The structure of protic ionic liquids based on sulfuric acid, doped with excess of sulfuric acid or with water.

Neutron scattering with isotopic substitution was used to study the structure of concentrated sulfuric acid, and two protic ionic liquids (PILs): a Brønsted-acidic PIL, synthesised using pyridine and excess of sulfuric acid, [Hpy][HSO4]·H2SO4, and a hydrated PIL, in which an equimolar mixture of sulfuric acid and pyridine has been doped with water, [Hpy][HSO4]·2H2O. Brønsted acidic PILs are excellent solvents/catalysts for esterifications, driving reaction to completion by phase-separating water and ester products. Water-doped PILs are efficient solvents/antisolvents in biomass fractionation. This study was carried out to provide an insight into the relationship between the performance of PILs in the two respective processes and their liquid structure. It was found that a persistent sulfate/sulfuric acid/water network structure was retained through the transition from sulfuric acid to PILs, even in the presence of 2 moles (∼17 wt%) of water. Hydrogen sulfate PILs have the propensity to incorporate water into hydrogen-bonded anionic chains, with strong and directional hydrogen bonds, which essentially form a new water-in-salt solvent system, with its own distinct structure and physico-chemical properties. It is the properties of this hydrated PIL that can be credited both for the good performance in esterification and beneficial solvent/antisolvent behaviour in biomass fractionation.

Microscopic Structure of Liquid Nitric Oxide.

The microscopic structure of nitric oxide is investigated using neutron scattering experiments. The measurements are performed at various temperatures between 120 and 144 K and at pressures between 1.1 and 9 bar. Using the technique of empirical potential structure refinement (EPSR), our results show that the dimer is the main form, around 80%, of nitric oxide in the liquid phase at 120 K, but the degree of dissociation to monomers increases with increasing temperature. The reported degree of dissociation of dimers, and its trend with increasing temperature, is consistent with earlier measurements and studies. It is also shown that nonplanar dimers are not inconsistent with the diffraction data and that the possibility of nitric oxide molecules forming longer oligomers, consisting of bonded nitrogen atoms along the backbone, cannot be ruled out in the liquid. A molecular dynamics simulation is used to compare the present EPSR simulations with an earlier proposed intermolecular potential for the liquid.

The ability of trimethylamine N-oxide to resist pressure induced perturbations to water structure.

Trimethylamine N-oxide (TMAO) protects organisms from the damaging effects of high pressure. At the molecular level both TMAO and pressure perturb water structure but it is not understood how they act in combination. Here, we use neutron scattering coupled with computational modelling to provide atomistic insight into the structure of water under pressure at 4 kbar in the presence and absence of TMAO. The data reveal that TMAO resists pressure-induced perturbation to water structure, particularly in retaining a clear second solvation shell, enhanced hydrogen bonding between water molecules and strong TMAO - water hydrogen bonds. We calculate an 'osmolyte protection' ratio at which pressure and TMAO-induced energy changes effectively cancel out. Remarkably this ratio translates across scales to the organism level, matching the observed concentration dependence of TMAO in the muscle tissue of organisms as a function of depth. Osmolyte protection may therefore offer a molecular mechanism for the macroscale survival of life in extreme environments.

Intermediate Range Order in Metal-Ammonia Solutions: Pure and Na-Doped Ca-NH3.

The local and intermediate range ordering in Ca-NH3 solutions in their metallic phase is determined through H/D isotopically differenced neutron diffraction in combination with empirical potential structure refinements. For both low and high relative Ca concentrations, the Ca ions are found to be octahedrally coordinated by the NH3 solvent, and these hexammine units are spatially correlated out to lengthscales of ∼7.4-10.3 Šdepending on the concentration, leading to pronounced ordering in the bulk liquid. We further demonstrate that this liquid order can be progressively disrupted by the substitution of Ca for Na, whereby a distortion of the average ion primary solvation occurs and the intermediate range ion-ion correlations are disrupted.

Neutron total scattering investigation on the dissolution mechanism of trehalose in NaOH/urea aqueous solution.

Trehalose is chosen as a model molecule to investigate the dissolution mechanism of cellulose in NaOH/urea aqueous solution. The combination of neutron total scattering and empirical potential structure refinement yields the most probable all-atom positions in the complex fluid and reveals the cooperative dynamic effects of NaOH, urea, and water molecules in the dissolution process. NaOH directly interacts with glucose rings by breaking the inter- and intra-molecular hydrogen bonding. Na+, thus, accumulates around electronegative oxygen atoms in the hydration shell of trehalose. Its local concentration is thereby 2-9 times higher than that in the bulk fluid. Urea molecules are too large to interpenetrate into trehalose and too complex to form hydrogen bonds with trehalose. They can only participate in the formation of the hydration shell around trehalose via Na+ bridging. As the main component in the complex fluid, water molecules have a disturbed tetrahedral structure in the presence of NaOH and urea. The structure of the mixed solvent does not change when it is cooled to -12 °C. This indicates that the dissolution may be a dynamic process, i.e., a competition between hydration shell formation and inter-molecule hydrogen bonding determines its dissolution. We, therefore, predict that alkali with smaller ions, such as LiOH, has better solubility for cellulose.

Superalkali-Alkalide Interactions and Ion Pairing in Low-Polarity Solvents.

The nature of anionic alkali metals in solution is traditionally thought to be "gaslike" and unperturbed. In contrast to this noninteracting picture, we present experimental and computational data herein that support ion pairing in alkalide solutions. Concentration dependent ionic conductivity, dielectric spectroscopy, and neutron scattering results are consistent with the presence of superalkali-alkalide ion pairs in solution, whose stability and properties have been further investigated by DFT calculations. Our temperature dependent alkali metal NMR measurements reveal that the dynamics of the alkalide species is both reversible and thermally activated suggesting a complicated exchange process for the ion paired species. The results of this study go beyond a picture of alkalides being a "gaslike" anion in solution and highlight the significance of the interaction of the alkalide with its complex countercation (superalkali).

Subtle changes in hydrogen bond orientation result in glassification of carbon capture solvents.

Water-lean CO2 capture solvents show promise for more efficient and cost-effective CO2 capture, although their long-term behavior in operation has yet to be well studied. New observations of extended structure solvent behavior show that some solvent formulations transform into a glass-like phase upon aging at operating temperatures after contact with CO2. The glassification of a solvent would be detrimental to a carbon-capture process due to plugging of infrastructure, introducing a critical need to decipher the underlying principles of this phenomenon to prevent it from happening. We present the first integrated theoretical and experimental study to characterize the nano-structure of metastable and glassy states of an archetypal single-component alkanolguanidine carbon-capture solvent and assess how minute changes in atomic-level interactions convert the solvent between metastable and glass-like states. Small-angle neutron scattering and neutron diffraction coupled with small- and wide-angle X-ray scattering analysis demonstrate that minute structural changes in solution precipitae reversible aggregation of zwitterionic alkylcarbonate clusters in solution. Our findings indicate that our test system, an alkanolguanidine, exhibits a first-order phase transition, similar to a glass transition, at approximately 40 °C-close to the operating absorption temperature for post-combustion CO2 capture processes. We anticipate that these phenomena are not specific to this system, but are present in other classes of colvents as well. We discuss how molecular-level interactions can have vast implications for solvent-based carbon-capture technologies, concluding that fortunately in this case, glassification of water-lean solvents can be avoided as long as the solvent is run above its glass transition temperature.

Publisher Correction: Liquid phase blending of metal-organic frameworks.

The original version of this Article contained an error in Figure 1b, where the blue '(ZIF-4-Zn)0.5 (ZIF-62)0.5 blend' data curve was omitted from the enthalpy response plot. This has now been corrected in both the PDF and HTML versions of the Article.

Local Structure and Polar Order in Liquid N-Methyl-2-pyrrolidone (NMP).

N-Methyl-2-pyrrolidone (NMP) is an exceptional solvent, widely used in industry and for nanomaterials processing. Yet despite its ubiquity, its liquid structure, which ultimately dictates its solvation properties, is not fully known. Here, neutron scattering is used to determine NMP's structure in unprecedented detail. Two dominant nearest-neighbor arrangements are found, where rings are parallel or perpendicular. However, compared with related solvents, NMP has a relatively large population of parallel approaches, similar only to benzene, despite its nonaromaticity and the presence of the normally structure-reducing methyl group. This arrangement is underpinned by NMP's dipole moment, which has a profound effect on its structure: nearest-neighbor molecules arrange in an antiparallel but offset fashion. This polar-induced order extends beyond the first solvation shell, resulting in ordered trimers that reach the nanometer range. The degree of order and balance of interactions rationalize NMP's high boiling point and versatile capabilities to solvate both charged and uncharged species.

Liquid phase blending of metal-organic frameworks.

The liquid and glass states of metal-organic frameworks (MOFs) have recently become of interest due to the potential for liquid-phase separations and ion transport, alongside the fundamental nature of the latter as a new, fourth category of melt-quenched glass. Here we show that the MOF liquid state can be blended with another MOF component, resulting in a domain structured MOF glass with a single, tailorable glass transition. Intra-domain connectivity and short range order is confirmed by nuclear magnetic resonance spectroscopy and pair distribution function measurements. The interfacial binding between MOF domains in the glass state is evidenced by electron tomography, and the relationship between domain size and Tg investigated. Nanoindentation experiments are also performed to place this new class of MOF materials into context with organic blends and inorganic alloys.

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. The results were analysed by an atomistic Monte Carlo simulation employing refinement to the experimental scattering data. The systems studied were the hydrogen storage material ammonia borane (NH3BH3, AB) dissolved in tetrahydrofuran (THF), and liquid ammonia (NH3), the latter in which AB shows unusually high solubility (260 g AB per 100 g NH3) and potential regeneration properties. The full orientational and positional manner in which AB-AB, AB-THF and AB-NH3 pairs interact with each other were successfully deciphered from the wide Q-range total neutron scattering data. This provided an unprecedented level of detail into such highly (di)hydrogen bonding solute-solvent interactions. In particular this allowed insight into the way in which H-B acts as a hydrogen bond acceptor. The (di)hydrogen bonding was naturally determined to dictate the intermolecular interactions, at times negating the otherwise expected tendency for polar molecules to align themselves with anti-parallel dipole moments. Several causes for the extreme solubility of AB in ammonia were determined, including the ability of ammonia to (di)hydrogen bond to both ends of the AB molecule and the small size of the ammonia molecule relative to AB and THF. The AB B-H to ammonia H dihydrogen bond was found to dominate the intermolecular interactions, occurring almost three times more often than any other hydrogen or dihydrogen bond in the system. The favourability of this interaction was seen on the bulk scale by a large decrease in AB clustering in ammonia compared to in the dihydrogen bond-less THF.

Multi-scale simulation of asphaltene aggregation and deposition in capillary flow.

Asphaltenes are known as the 'cholesterol' of crude oil. They form nano-aggregates, precipitate, adhere to surfaces, block rock pores and may alter the wetting characteristics of mineral surfaces within the reservoir, hindering oil recovery efficiency. Despite a significant research effort, the structure, aggregation and deposition of asphaltenes under flowing conditions remain poorly understood. For this reason, we have investigated asphaltenes, their aggregation and their deposition in capillary flow using multi-scale simulations and experiments. At the colloid scale, we use a hybrid simulation approach: for the solvent, we used the stochastic rotation dynamics (also known as multi particle collision dynamics) simulation method, which provides both hydrodynamics and Brownian motion. This is coupled to a coarse-grained MD approach for the asphaltene colloids. The colloids interact through a screened Coulomb potential with varying well depth epsilon. We tune the flow rate to obtain Pe(flow) >> 1 (hydrodynamic interactions dominate) and Re << 1 (Stokes flow). Imposing a constant pressure drop over the capillary length, we observe that the transient solvent flow rate decreases with increasing well depth epsilon. The interactions between the mesoscopic asphaltene colloids can be related to atomistic MD simulations. Molecular structures for the atomistic calculations were obtained using the quantitative molecular representation approach. Using these structures, we calculate the potential of mean force (PMF) between pairs of asphaltene molecules in an explicit solvent. We obtain a reasonable fit using a -1/r2 attraction for the attractive tail of the PMF at intermediate distances. We speculate that this is due to the two-dimensional nature of the asphaltene molecules. Finally, we discuss how we can relate this interaction to the mesoscopic colloid aggregate interaction. We assume that the colloidal aggregates consist of nano-aggregates. Taking into account observed solvent entrainment effects, we deduct the presence of lubrication layers between the nano-aggregates, which leads to a significant screening of the direct asphaltene-asphaltene interactions.