Adsorption of simple gases into the porous glass MCM-41.

The porous glass MCM-41 is an important adsorbent to study the process of adsorption of gases onto a cylindrical surface. In this work, we study the adsorption of oxygen, nitrogen, deuterium, and deuteriated methane gases into MCM-41 using a combination of neutron diffraction analysis and atomistic computer modeling to interpret the measured data. Adsorption is achieved by immersing a sample of MCM-41 in a bath of the relevant gas, keeping the gas pressure constant (0.1 MPa), and lowering the temperature in steps toward the corresponding bulk liquid boiling point. All four gases have closely analogous behaviors, with an initial layering of liquid on the inside surface of the pores, followed by a relatively sharp capillary condensation (CC) when the pore becomes filled with dense fluid, signaled by a sharp decrease in the intensity of (100) Bragg diffraction reflection. At the temperature of CC, there is a marked distortion of the hexagonal lattice of pores, as others have seen, which relaxes close to the original structure after CC, and this appears to be accompanied by notable excess heterogeneity along the pore compared to when CC is complete. In none of the four gases studied does the final density of fluid in the pore fully attain the value of the bulk liquid at its boiling point at this pressure, although it does approach that limit closely near the center of the pore, and in all cases, the pronounced layering near the silica interface seen in previous studies is observed here as well.

Trimethylamine N-oxide (TMAO) resists the compression of water structure by magnesium perchlorate: terrestrial kosmotrope vs. Martian chaotrope.

The presence of magnesium perchlorate (Mg(ClO4)2) as the dominant ionic compound in the Martian regolith and the recent discovery of a subsurface lake on Mars suggests that beneath the Martian surface may lie an aqueous environment suitable for life, rich in chaotropic ions. Closer to Earth, terrestrial organisms use osmolytes, such as trimethylamine N-oxide (TMAO), to overcome the biologically damaging effects of pressure. While previous studies have revealed that Mg(ClO4)2 acts to modify water structure as if it has been pressurized, little is known about the competing effects of chaotropes and kosmotropes. Here we ask whether TMAO can help to preserve the hydrogen bond network of water against the pressurising effect of Mg(ClO4)2? We address this question using neutron scattering, computational modelling using Empirical Potential Structure Refinement (EPSR) analysis, and a new approach to quantifying hydrogen bond conformations and energies. We find that the addition of 1.0 M TMAO to 0.2 M Mg(ClO4)2 or to 2.7 M Mg(ClO4)2 is capable of partially restoring the hydrogen bond network of water, and the fraction of water molecules in energetically unfavourable conformations. This suggests that terrestrial protecting osmolytes could provide a protective mechanism to the extremes found in Martian environments for biological systems.

Formation of Methane Hydrate in the Presence of Natural and Synthetic Nanoparticles.

Natural gas hydrates occur widely on the ocean-bed and in permafrost regions, and have potential as an untapped energy resource. Their formation and growth, however, poses major problems for the energy sector due to their tendency to block oil and gas pipelines, whereas their melting is viewed as a potential contributor to climate change. Although recent advances have been made in understanding bulk methane hydrate formation, the effect of impurity particles, which are always present under conditions relevant to industry and the environment, remains an open question. Here we present results from neutron scattering experiments and molecular dynamics simulations that show that the formation of methane hydrate is insensitive to the addition of a wide range of impurity particles. Our analysis shows that this is due to the different chemical natures of methane and water, with methane generally excluded from the volume surrounding the nanoparticles. This has important consequences for our understanding of the mechanism of hydrate nucleation and the design of new inhibitor molecules.

Structural evidence for solvent-stabilisation by aspartic acid as a mechanism for halophilic protein stability in high salt concentrations.

Halophilic organisms have adapted to survive in high salt environments, where mesophilic organisms would perish. One of the biggest challenges faced by halophilic proteins is the ability to maintain both the structure and function at molar concentrations of salt. A distinct adaptation of halophilic proteins, compared to mesophilic homologues, is the abundance of aspartic acid on the protein surface. Mutagenesis and crystallographic studies of halophilic proteins suggest an important role for solvent interactions with the surface aspartic acid residues. This interaction, between the regions of the acidic protein surface and the solvent, is thought to maintain a hydration layer around the protein at molar salt concentrations thereby allowing halophilic proteins to retain their functional state. Here we present neutron diffraction data of the monomeric zwitterionic form of aspartic acid solutions at physiological pH in 0.25 M and 2.5 M concentration of potassium chloride, to mimic mesophilic and halophilic-like environmental conditions. We have used isotopic substitution in combination with empirical potential structure refinement to extract atomic-scale information from the data. Our study provides structural insights that support the hypothesis that carboxyl groups on acidic residues bind water more tightly under high salt conditions, in support of the residue-ion interaction model of halophilic protein stabilisation. Furthermore our data show that in the presence of high salt the self-association between the zwitterionic form of aspartic acid molecules is reduced, suggesting a possible mechanism through which protein aggregation is prevented.

Observation of interstitial molecular hydrogen in clathrate hydrates.

The current knowledge and description of guest molecules within clathrate hydrates only accounts for occupancy within regular polyhedral water cages. Experimental measurements and simulations, examining the tert-butylamine + H2 + H2O hydrate system, now suggest that H2 can also be incorporated within hydrate crystal structures by occupying interstitial sites, that is, locations other than the interior of regular polyhedral water cages. Specifically, H2 is found within the shared heptagonal faces of the large (4(3)5(9)6(2)7(3)) cage and in cavities formed from the disruption of smaller (4(4)5(4)) water cages. The ability of H2 to occupy these interstitial sites and fluctuate position in the crystal lattice demonstrates the dynamic behavior of H2 in solids and reveals new insight into guest-guest and guest-host interactions in clathrate hydrates, with potential implications in increasing overall energy storage properties.

Radical re-appraisal of water structure in hydrophilic confinement.

The structure of water confined in MCM41 silica cylindrical pores is studied to determine whether confined water is simply a version of the bulk liquid which can be substantially supercooled without crystallisation. A combination of total neutron scattering from the porous silica, both wet and dry, and computer simulation using a realistic model of the scattering substrate is used. The water in the pore is divided into three regions: core, interfacial and overlap. The average local densities of water in these simulations are found to be about 20% lower than bulk water density, while the density in the core region is below, but closer to, the bulk density. There is a decrease in both local and core densities when the temperature is lowered from 298 K to 210 K. The radical proposal is made here that water in hydrophilic confinement is under significant tension, around -100 MPa, inside the pore.

A hybrid neutron diffraction and computer simulation study on the solvation of N-methylformamide in dimethylsulfoxide.

The solvation of N-methylformamide (NMF) by dimethylsulfoxide (DMSO) in a 20% NMF/DMSO liquid mixture is investigated using a combination of neutron diffraction augmented with isotopic substitution and Monte Carlo simulations. The aim is to investigate the solute-solvent interactions and the structure of the solution. The results point to the formation of a hydrogen bond (H-bond) between the H bonded to the N of the amine group of NMF and the O of DMSO particularly strong when compared with other H-bonded liquids. Moreover, a second cooperative H-bond is identified with the S atom of DMSO. As a consequence of these H-bonds, molecules of NMF and DMSO are rather rigidly connected, establishing very stable dimmers in the mixture and very well organized first and second solvation shells.

Small-angle scattering and the structure of ambient liquid water.

Structural polyamorphism has been promoted as a means for understanding the anomalous thermodynamics and dynamics of water in the experimentally inaccessible supercooled region. In the metastable liquid region, theory has hypothesized the existence of a liquid-liquid critical point from which a dividing line separates two water species of high and low density. A recent small-angle X-ray scattering study has claimed that the two structural species postulated in the supercooled state are seen to exist in bulk water at ambient conditions. We analyze new small-angle X-ray scattering data on ambient liquid water taken at third generation synchrotron sources, and large 32,000 water molecule simulations using the TIP4P-Ew model of water, to show that the small-angle region measures standard number density fluctuations consistent with water's isothermal compressibility temperature trends. Our study shows that there is no support or need for heterogeneities in water structure at room temperature to explain the small-angle scattering data, as it is consistent with a unimodal density of the tetrahedral liquid at ambient conditions.

Axial structure of the Pd(II) aqua ion in solution.

Solution chemistry of Pd(II) and Pt(II) complexes is relevant to many fields of chemistry given the widespread applications of their compounds in homogeneous and heterogeneous catalysis, intermediate reaction synthesis, and antitumoral drugs. The well-defined square-planar arrangement of their complexes contrasts with the rather diffuse axial environment in solution. A theoretical proposal for a characteristic hydration shell in this axial region, called the meso-shell, stimulated further experimental and theoretical studies which have led to different pictures. The present work characterizes the structure of the axial region of the Pd(II) aqua ion in solution using a combination of neutron and X-ray diffraction and extended X-ray absorption fine structure (EXAFS) spectroscopy, with empirical potential structure refinement (EPSR). The results confirm the existence of the axial region and structurally characterize the water molecules within it. An important finding not previously reported is that the counterion, in this case the perchlorate anion, competes with water molecules for the meso-shell occupancy. The important role played by the axial region in many ligand substitution reactions is therefore intimately connected with the presence of the counterion and not just hydration water. This must call the attention of the experimental community to the important role that the counterion of the precursor salt must play in the synthesis.

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.

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 nano- and meso-scale structure of amorphous calcium carbonate.

Understanding the underlying processes of biomineralization is crucial to a range of disciplines allowing us to quantify the effects of climate change on marine organisms, decipher the details of paleoclimate records and advance the development of biomimetic materials. Many biological minerals form via intermediate amorphous phases, which are hard to characterize due to their transient nature and a lack of long-range order. Here, using Monte Carlo simulations constrained by X-ray and neutron scattering data together with model building, we demonstrate a method for determining the structure of these intermediates with a study of amorphous calcium carbonate (ACC) which is a precursor in the bio-formation of crystalline calcium carbonates. We find that ACC consists of highly ordered anhydrous nano-domains of approx. 2 nm that can be described as nanocrystalline. These nano-domains are held together by an interstitial net-like matrix of water molecules which generate, on the mesoscale, a heterogeneous and gel-like structure of ACC. We probed the structural stability and dynamics of our model on the nanosecond timescale by molecular dynamics simulations. These simulations revealed a gel-like and glassy nature of ACC due to the water molecules and carbonate ions in the interstitial matrix featuring pronounced orientational and translational flexibility. This allows for viscous mobility with diffusion constants four to five orders of magnitude lower than those observed in solutions. Small and ultra-small angle neutron scattering indicates a hierarchically-ordered organization of ACC across length scales that allow us, based on our nano-domain model, to build a comprehensive picture of ACC formation by cluster assembly from solution. This contribution provides a new atomic-scale understanding of ACC and provides a framework for the general exploration of biomineralization and biomimetic processes.

An X-ray and neutron scattering study of the equilibrium between trimethylamine N-oxide and urea in aqueous solution.

The interaction of the osmolytes trimethylamine N-oxide (TMAO) and urea in aqueous solutions at 40 °C was investigated by isotopic substitution neutron scattering at a TMAO mole fraction of 0.05 and TMAO/urea concentration ratios of 1 : 2 and 1 : 4. The partial pair distribution functions obtained by the empirical potential structure refinement method are consistent with those obtained previously for similar pure TMAO and 1 : 1 TMAO-urea solutions and indicate that urea progressively replaces the water molecules in the first coordination shell of the TMAO oxygen atom. The apparent association constant for the TMAO : urea complex (K(1)) was calculated to be 0.14 M(-1), which is of the same order as the experimental urea-protein binding constants per site reported in the literature. This confirms that the two osmolytes act independently at least in the physiological range.

Bridging Structure, Dynamics, and Thermodynamics: An Example Study on Aqueous Potassium Halides.

Aqueous salt systems are ubiquitous in all areas of life. The ions in these solutions impose important structural and dynamic perturbations to water. In this study, we employ a combined neutron scattering, nuclear magnetic resonance, and computational modeling approach to deconstruct ion-specific perturbations to water structure and dynamics and shed light on the molecular origins of bulk thermodynamic properties of the solutions. Our approach uses the atomistic scale resolution offered to us by neutron scattering and computational modeling to investigate how the properties of particular short-ranged microenvironments within aqueous systems can be related to bulk properties of the system. We find that by considering only the water molecules in the first hydration shell of the ions that the enthalpy of hydration can be determined. We also quantify the range over which ions perturb water structure by calculating the average enthalpic interaction between a central halide anion and the surrounding water molecules as a function of distance and find that the favorable anion-water enthalpic interactions only extend to ∼4 Å. We further validate this by showing that ions induce structure in their solvating water molecules by examining the distribution of dipole angles in the first hydration shell of the ions but that this perturbation does not extend into the bulk water. We then use these structural findings to justify mathematical models that allow us to examine perturbations to rotational and diffusive dynamics in the first hydration shell around the potassium halide ions from NMR measurements. This shows that as one moves down the halide series from fluorine to iodine, and ionic charge density is therefore reduced, that the enthalpy of hydration becomes less negative. The first hydration shell also becomes less well structured, and rotational and diffusive motions of the hydrating water molecules are increased. This reduction in structure and increase in dynamics are likely the origin of the previously observed increased entropy of hydration as one moves down the halide series. These results also suggest that simple monovalent potassium halide ions induce mostly local perturbations to water structure and dynamics.

Structure of pi-pi interactions in aromatic liquids.

High-resolution neutron diffraction has been used in conjunction with hydrogen/deuterium isotopic labeling to determine with unprecedented detail the structure of two archetypal aromatic liquids: benzene and toluene. We discover the nature of aromatic pi-pi interactions in the liquid state by constructing for the first time a full six-dimensional spatial and orientational picture of these systems. We find that in each case the nearest neighbor coordination shell contains approximately 12 molecules. Benzene is the more structured of the two liquids, showing, for example, a sharper nearest neighbor coordination peak in the radial distribution function. Superficially the first neighbor shells appear isotropic, but our multidimensional analysis shows that the local orientational order in these liquids is much more complex. At small molecular separations (<5 A) there is a preference for parallel pi-pi contacts in which the molecules are offset to mimic the interlayer structure of graphite. At larger separations (>5 A) the neighboring aromatic rings are predominantly perpendicular, with two H atoms per molecule directed toward the acceptor's pi orbitals. The so-called "anti-hydrogen-bond" configuration, proposed as the global minimum for the benzene dimer, occurs only as a saddle point in our data. The observed liquid structures are therefore fundamentally different than those deduced from the molecular dimer energy surfaces.

Structure and properties of an amorphous metal-organic framework.

ZIF-4, a metal-organic framework (MOF) with a zeolitic structure, undergoes a crystal-amorphous transition on heating to 300 degrees C. The amorphous form, which we term a-ZIF, is recoverable to ambient conditions or may be converted to a dense crystalline phase of the same composition by heating to 400 degrees C. Neutron and x-ray total scattering data collected during the amorphization process are used as a basis for reverse Monte Carlo refinement of an atomistic model of the structure of a-ZIF. The structure is best understood in terms of a continuous random network analogous to that of a-SiO2. Optical microscopy, electron diffraction and nanoindentation measurements reveal a-ZIF to be an isotropic glasslike phase capable of plastic flow on its formation. Our results suggest an avenue for designing broad new families of amorphous and glasslike materials that exploit the chemical and structural diversity of MOFs.

Molecular self-assembly in a model amphiphile system.

The physical origin of the large and negative excess entropy of mixing of alcohols and water remains controversial. In contrast to standard explanations that evoke concepts of water structuring, recent work has shown that, at ambient conditions, it can be quantitatively explained in terms of molecular scale partial demixing of the two components. Here, we estimate the negative excess entropy (DeltaS(E)) of aqueous methanol at low temperature and high pressure using experimentally-derived structural data and a recently introduced cluster model. On cooling to 190 K the cluster sizes increase, but the change in DeltaS(E), which according to this method of calculation depends on the surface area to volume ratio of the clusters, is not significant, suggesting that the topology of the clusters must change with decreased temperature. On compression the cluster sizes also increase, and DeltaS(E) is now positive, suggesting an even more pronounced change in cluster topology with increased pressure. This work suggests that it is the amphiphilic nature of a molecule that determines aggregation and self-assembly processes in aqueous solution. The results therefore give useful insight into the processes of cold and pressure denaturation of proteins.

Structure and water dynamics of aqueous peptide solutions in the presence of co-solvents.

We perform neutron diffraction and quasi-elastic neutron scattering (QENS) to probe hydration water structure, and dynamics down to supercooled temperatures, of a concentrated amphiphilic peptide system with the co-solvents glycerol and dimethyl sulfoxide. We find that the kosmotropic co-solvent glycerol preserves the hydration structure near the peptide that is observed in the water solvent alone, that in turn preserves the dynamical temperature trends of two water relaxation processes--one corresponding to a localized relaxation process of the peptide bound surface water and a second relaxation process of the outer hydration layers. By contrast the chaotropic co-solvent, by disrupting the hydration layer near the peptide surface, eliminates the inner hydration layer relaxation process induced by the peptide, to show a single time scale for translational water dynamics.