Clathrate Cages Research Articles

A theoretical investigation into the trapping of noble gases by clathrates on Titan

In this paper, we use a statistical thermodynamic approach to quantify the efficiency with which clathrates on the surface of Titan trap noble gases. We consider different values of the Ar, Kr, Xe, CH 4, C 2H 6 and N 2 abundances in the gas phase that may be representative of Titan's early atmosphere. We discuss the effect of the various parameters that are chosen to represent the interactions between the guest species and the ice cage in our calculations. We also discuss the results of varying the size of the clathrate cages. We show that the trapping efficiency of clathrates is high enough to significantly decrease the atmospheric concentrations of Xe and, to a lesser extent, of Kr, irrespective of the initial gas phase composition, provided that these clathrates are abundant enough on the surface of Titan. In contrast, we find that Ar is poorly trapped in clathrates and, as a consequence, that the atmospheric abundance of argon should remain almost constant. We conclude that the mechanism of trapping noble gases via clathration can explain the deficiency in primordial Xe and Kr observed in Titan's atmosphere by Huygens, but that this mechanism is not sufficient to explain the deficiency in Ar.

Ice mixtures formed by simultaneous condensation of formaldehyde and water: an in situ study by micro-Raman scattering

Thin films of formaldehyde-water mixtures are co-deposited at 88 K and 10(-1) Torr from gas collected above formaldehyde aqueous solutions of different concentrations (5, 10, 15, 20, 30 mol%). They are analyzed in situ by micro-Raman scattering in the 2700-3800 cm(-1) spectral range. The spectral characteristic of H2CO distributed molecularly in amorphous solid water is obtained under vacuum conditions. As temperature is increased formaldehyde is released during the crystallization of ice between 118 and 138 K. On the other hand, under controlled nitrogen atmosphere, the deposits crystallize in hydrate phases (or solid H2CO(s)) during annealing. A new phase (metastable FOR-A) of H2CO(s) (or a low hydrate after rejection by crystallizing ice) can be spectroscopically identified at 138 K before transformation into a hydrate (with molecular H2CO distributed within the cages of the clathrate FOR-B) takes place at 148 K. This latter phase decomposes between ca. 180 and 200 K. The significant spectral differences between these hydrates and those formed in frozen formaldehyde aqueous solutions reflect the existence of H2CO-clusters of distinctive structural nature relative to those resulting from important oligomerization process in the liquid. Moreover, the structure, the gas distribution and relative gas population in the formaldehyde clathrate cages are influenced by the relative amount of trapped nitrogen at the surface, which moreover depends on the ice film morphology. The dependence on the crystallization temperature of the deposits is explained by the relative amounts of occluded H2CO/N2 and the external pressure conditions. The distinct behavior observed between vacuum and N2-atmosphere conditions certainly reflects a complex mechanism of surface mediated nucleation in which the transport of the reactants to the hydrate reaction zone is facilitated by the presence of a polar dopant.

Effect of surface hydrophilicity on the confined water film

The effect of surface hydrophilicity on the water film confined within a nanogap between a smooth plate and a highly polished steel ball has been investigated. It was found that the confined water film formed the thicker lubricate film than the prediction of elastic-isoviscous lubrication theory. Experimental results indicated that the hydrophobic surface induced the thicker water film than the hydrophilic one. It is thought that the “structured” interfacial water layer is formed between the solid surfaces and the hydrophobic group induces the more ordered hydrogen-bonding network of clathrate cages which forms the thicker water film than hydrophilic one.

Spectroscopic identification, thermodynamic stability and molecular composition of hydrogen and 1,4-dioxane binary clathrate hydrate

We present the spectroscopic identification of the binary hydrogen and 1,4-dioxane clathrate hydrates in which H 2 molecules are encapsulated in small cages of the structure II hydrate framework. X-ray diffraction, solid-state NMR and Raman spectroscopy were used to confirm the mixed hydrate structure and more importantly the occupancy pattern of hydrogen in clathrate cages. The corresponding pressure–temperature behavior and direct gas release measurements were also determined to support the spectroscopic results. The direct volumetric measurements revealed that the favorable confinement of hydrogen molecules over 0.4 wt% could be obtained by the compositional tuning of the binary products.

Hydrogen Encapsulation in a Silicon Clathrate Type I Structure: Na5.5(H2)2.15Si46: Synthesis and Characterization

A hydrogen-encapsulated inorganic clathrate, which is stable at ambient temperature and pressure, has been prepared in high yield. Na5.5(H2)2.15Si46 is a sodium-deficient, hydrogen-encapsulated, type I silicon clathrate. It was prepared by the reaction between NaSi and NH4Br under dynamic vacuum at 300 degrees C. The Rietveld refinement of the powder X-ray diffraction data is consistent with the clathrate type I structure. The type I clathrate structure has two types of cages where the guest species, in this case Na and H2, can reside: a large cage composed of 24 Si, in which the guest resides in the 6d crystallographic position, and a smaller one composed of 20 Si, in which the guest occupies the 2a position. Solid-state 23Na, 1H, and 29Si MAS NMR confirmed the presence of both sodium and hydrogen in the clathrate cages. 23Na NMR shows that sodium completely fills the small cage and is deficient in the larger cage. The 1H NMR spectrum shows a pattern consistent with mobile hydrogen in the large cage. 29Si NMR spectrum is consistent with phase pure type I clathrate framework. Elemental analysis is consistent with the stoichiometry Na5.5(H2.15)2Si46. The sodium occupancy was also examined using spherical aberration (Cs) corrected scanning transmission electron microscopy (STEM). The high-angle annular dark-field (HAADF) STEM experimental and simulated images indicated that the Na occupancy of the large cage, 6d sites, is less than 2/3, consistent with the NMR and elemental analysis.

Host Structure Engineering in Thermoelectric Clathrates

Three Ba8Al16Ge30 clathrate type I samples have been prepared using three different synthesis methods; flux growth, Czochralski growth, and stoichiometric mixing. The samples were characterized by X-ray powder diffraction, multi-temperature single-crystal X-ray diffraction, high-resolution low-temperature (20 K) single-crystal neutron diffraction, and measurement of transport properties. The samples show a remarkable variation in the aluminum/germanium occupancies on the host-structure sites and minor variation in the total aluminum content. The observed occupancy variation forms the basis for the formulation of a set of simple rules for the maximum site occupancy factors of trivalent elements in the host structure. The rules provide an explanation for why the overwhelming majority of clathrate samples containing trivalent elements are n-type rather than p-type. The nuclear density of the barium guest atom in the large cage is calculated from the neutron diffraction data, and it is found to be strongly dependent on the host structure and the exact aluminum siting. Thus, the sample with low aluminum content has a prolate-shaped barium nuclear density, whereas a higher aluminum content leads to the well-known torus shape observed in other clathrates. This demonstrates that the host−guest interactions are not merely ionic and that they significantly influence the guest-atom structure and dynamics. Comparison of derived Einstein temperatures and bond distances for the three samples reveals that the compound with the highest aluminum content (flux growth) has the strongest host−guest interaction, even though it also has the largest unit cell. Again, the specific properties of the guest atoms are not only determined by the clathrate cage size but also by the subtle chemical interactions between the host structure and the guest. The thermal conductivity is about 3 times smaller for the stoichiometric sample than for the Czochralski-pulled sample. Thus, control of the host-structure chemistry is not only a key to manipulating the electrical properties of clathrates but also the thermal conductivity.

Interactions of anionic polysaccharides with carbon nanotubes

Agarose, i-, k-, and l-carrageenans, and xanthan gum in aqueous solutions interacted with single-walled carbon nanotubes (SWCNTs) as proven by their wetting in solution and by the microRaman spectroscopy, rheological studies, and differential scanning calorimetry. The investigations provided evidence that the effect of complexation of polysaccharides was independent of the possibility of the formation of helical complexes. Complexation involved, to a certain extent, interactions between hydrophobic surface of nanotubes and hydrophobic sides of the saccharide units of polysaccharides. However, clathration of nanotubes in the polysaccharide matrices was also essential. Formation of the clathrate cages involved intra- and intermolecular hydrogen bonds within polysaccharides.

Clathrate Hydrates of Oxidants in the Ice Shell of Europa

Europa's icy surface is radiolytically modified by high-energy electrons and ions, and photolytically modified by solar ultraviolet photons. Observations from the Galileo Near Infrared Mapping Spectrometer, ground-based telescopes, the International Ultraviolet Explorer, and the Hubble Space Telescope, along with laboratory experiment results, indicate that the production of oxidants, such as H2O2, O2, CO2, and SO2, is a consequence of the surface radiolytic chemistry. Once created, some of the products may be entrained deeper into the ice shell through impact gardening or other resurfacing processes. The temperature and pressure environments of regions within the europan hydrosphere are expected to permit the formation of mixed clathrate compounds. The formation of carbon dioxide and sulfur dioxide clathrates has been examined in some detail. Here we add to this analysis by considering oxidants produced radiolytically on the surface of Europa. Our results indicate that the bulk ice shell could have a approximately 1.7-7.6% by number contamination of oxidants resulting from radiolysis at the surface. Oxidant-hosting clathrates would consequently make up approximately 12-53% of the ice shell by number relative to ice, if oxidants were entrained throughout. We examine, in brief, the consequences of such contamination on bulk ice shell thickness and find that clathrate formation could lead to substantially thinner ice shells on Europa than otherwise expected. Finally, we propose that double occupancy of clathrate cages by O2 molecules could serve as an explanation for the observation of condensed-phase O2 on Europa. Clathrate-sealed, gas-filled bubbles in the near surface ice could also provide an effective trapping mechanism, though they cannot explain the 5771 A (O2)2 absorption.

Anharmonic motions of Kr in the clathrate hydrate

The anomalous glass-like thermal conductivity of crystalline clathrates has been suggested to be the result of the scattering of thermal phonons of the framework by 'rattling' motions of the guests in the clathrate cages. Using the site-specific (83)Kr nuclear resonant inelastic scattering spectroscopy in combination with conventional incoherent inelastic neutron scattering and molecular-dynamics simulations, we provide unambiguous evidence and characterization of the effects on these guest-host interactions in a structure-II Kr clathrate hydrate. The resonant scattering of phonons led to unprecedented large anharmonic motions of the guest atoms. The anharmonic interaction underlies the anomalous thermal transport in this system. Clathrates are prototypical models for a class of crystalline framework materials with glass-like thermal conductivity. The explanation of the unusual molecular dynamics has a wide implication for the understanding of the thermal properties of disordered solids and structural glasses.

Probing adsorption sites in a cubic II water clathrate cage by methyl group rotation of CH3I guest molecules

Methyl iodide enclosed in the 51264 cage of cubic II water clathrate is investigated by neutron spectroscopy in the temperature regime from 1.8 to 145 K. The three tunnelling bands observed at the lowest temperature at 497, 372 and 243 μeV of relative intensities 2 : 3 : 5 represent three distinct adsorption sites of CH3I. Sites of occurrence probabilities corresponding closely to the observed line intensities are related to the three types of hydrogen bonds of the cage. The band at 372 μeV shows fast spin conversion compared to the two others. The corresponding site is facing the shortest O–H..O hydrogen bond with the fastest proton dynamics. Spin conversion may thus reflect hydrogen jumps within the H-bond network of host molecules. Jump rates of the order of 10−4 s−1 can be estimated. Above a temperature T ∼ 45 K the methyl dynamics become classical and can be described by rotational diffusion on a circle. A second quasielastic process becomes visible at a higher temperature and is identified as head-to-tail flips of the whole molecule with a characteristic jump distance of about 5 Å. Above T ∼ 90 K translational freedom of the CH3I leads to a rattling mode appearing at ∼0.95 meV.

Structure, thermal, and transport properties of the clathratesSr8Zn8Ge38,Sr8Ga16Ge30, andBa8Ga16Si30

The structural parameters, thermal properties, and transport properties of three type I clathrates, namely ${\mathrm{Sr}}_{8}{\mathrm{Zn}}_{8}{\mathrm{Ge}}_{38}$, ${\mathrm{Sr}}_{8}{\mathrm{Ga}}_{16}{\mathrm{Ge}}_{30}$, and ${\mathrm{Ba}}_{8}{\mathrm{Ga}}_{16}{\mathrm{Si}}_{30}$, have been determined at or below room temperature. The structural parameters of these clathrates were determined by powder neutron diffraction. Their lattice thermal expansion is two to four times greater than that of the diamond phases of silicon and germanium, consistent with more anharmonic lattice vibrations. From the temperature dependence of the isotropic atomic displacement parameters, the estimated rattling frequencies of guests in the large cages of these clathrates are in the range $50--60\phantom{\rule{0.3em}{0ex}}{\mathrm{cm}}^{\ensuremath{-}1}$. The heat capacities of these three clathrate materials increase smoothly with increasing temperatures and approach the Dulong--Petit value around room temperature. The Gr\"uneisen parameter of these materials is constant between $100$ and $300\phantom{\rule{0.3em}{0ex}}\mathrm{K}$ but increases below $100\phantom{\rule{0.3em}{0ex}}\mathrm{K}$, due to the dominance of the low-frequency guest-rattling modes. The room-temperature electrical resistivity and the Seebeck coefficient show that these materials are metallic. The temperature profile of the thermal conductivities and calculated phonon mean free paths of these materials show glasslike behavior, although they are crystalline materials, indicating strong resonant scattering of heat-carrying acoustic phonons via the rattling of the guests in the clathrate cages.

Exceptional ideal strength of carbon clathrates.

We study by means of ab initio calculations the ideal tensile and shear strengths of the C-46 clathrate phase. While its bulk modulus and elastic constants are smaller than in diamond, its strength is found to be in all directions larger than the critical stresses associated with the diamond [111] planes of easy slip. This can be related to the frustration by the clathrate cage structure of the diamond to graphite instability under nonhydrostatic stress conditions [corrected] The criteria for designing strong materials are discussed.

Werner‐type metal complexes of potato starch

SummaryIt was shown that potato starch formed Werner‐type complexes. In these complexes a metal atom is ligated by the lone electron pairs of hydroxyl groups from d‐glucose units and phosphate groups in starch. Acetate, chloride and nitrate were counter‐ions to the transition metal atoms. The metal cations bound preferentially to the phosphoric acid moiety of amylopectin, but secondarily they were co‐ordinated by the hydroxyl groups of the d‐glucose units. This resulted in the formation of clathrate cages in which a significant number of the water molecules were trapped. Such structures were able to co‐ordinate further metal cations. Only Mn(II) and Co(II) ions, with acetate counter‐ions, neither formed clathrate cages nor were co‐ordinated by the hydroxyl groups of the d‐glucose of starch.

The nuclear magnetic resonance line shapes of Xe in the cages of clathrate hydrates.

We report, for the first time, a prediction of the line shapes that would be observed in the (129)Xe nuclear magnetic resonance (NMR) spectrum of xenon in the cages of clathrate hydrates. We use the dimer tensor model to represent pairwise contributions to the intermolecular magnetic shielding tensor for Xe at a specific location in a clathrate cage. The individual tensor components from quantum mechanical calculations in clathrate hydrate structure I are represented by contributions from parallel and perpendicular tensor components of Xe-O and Xe-H dimers. Subsequently these dimer tensor components are used to reconstruct the full magnetic shielding tensor for Xe at an arbitrary location in a clathrate cage. The reconstructed tensors are employed in canonical Monte Carlo simulations to find the Xe shielding tensor component along a particular magnetic field direction. The shielding tensor component weighted according to the probability of finding a crystal fragment oriented along this direction in a polycrystalline sample leads to a predicted line shape. Using the same set of Xe-O and Xe-H shielding functions and the same Xe-O and Xe-H potential functions we calculate the Xe NMR spectra of Xe atom in 12 distinct cage types in clathrate hydrates structures I, II, H, and bromine hydrate. Agreement with experimental spectra in terms of the number of unique tensor components and their relative magnitudes is excellent. Agreement with absolute magnitudes of chemical shifts relative to free Xe atom is very good. We predict the Xe line shapes in two cages in which Xe has not yet been observed.

Theoretical Study of Clathrate Hydrates with Multiple Occupation

In this work, the electronic, structural, dynamic andthermodynamic properties of structure II, H and tetragonalAr clathrate hydrates have been calculated and the effectof multiple occupancy on their stability has been examinedusing first-principles and lattice dynamics calculations.The dynamic properties of these clathrates have beeninvestigated depending on the number of guest moleculesin a clathrate cage. It has been found that selectedhydrate structures are dynamically stable. The calculatedcell parameters are in agreement with experimental data.We also report the results of a systematic investigationof cage-like water structures using first-principles calculations. Ithas been observed that Ar clusters can be stabilized indifferent water cages and the stability is strongly dependenton the number of argon atoms inside the cages.

The chemical shifts of Xe in the cages of clathrate hydrate Structures I and II.

We report, for the first time, a calculation of the isotropic NMR chemical shift of 129Xe in the cages of clathrate hydrates Structures I and II. We generate a shielding surface for Xe in the clathrate cages by quantum mechanical calculations. Subsequently this shielding surface is employed in canonical Monte Carlo simulations to find the average isotropic Xe shielding values in the various cages. For the two types of cages in clathrate hydrate Structure I, we find the intermolecular shielding values [sigma(Xe@5(12) cage)-sigma(Xe atom)]=-214.0 ppm, and [sigma(Xe@5(12)6(2) cage)-sigma(Xe atom)]=-146.9 ppm, in reasonable agreement with the values -242 and -152 ppm, respectively, observed experimentally by Ripmeester and co-workers between 263 and 293 K. For the 5(12) and 5(12)6(4) cages of Structure II we find [sigma(Xe@5(12) cage)-sigma(Xe atom)]=-206.7 ppm, and [sigma(Xe@5(12)6(4) cage)-sigma(Xe atom)]=-104.7 ppm, also in reasonable agreement with the values -225 and -80 ppm, respectively, measured in a Xe-propane type II mixed clathrate hydrate at 77 and 220-240 K by Ripmeester et al.

Thermodynamic stability of hydrogen clathrates.

The stability of the recently characterized type II hydrogen clathrate [Mao, W. L., Mao, H.-K., Goncharov, A. F., Struzhkin, V. V., Guo, Q., et al. (2002) Science 297, 2247-2249] with respect to hydrogen occupancy is examined with a statistical mechanical model in conjunction with first-principles quantum chemistry calculations. It is found that the stability of the clathrate is mainly caused by dispersive interactions between H2 molecules and the water forming the cage walls. Theoretical analysis shows that both individual hydrogen molecules and nH2 guest clusters undergo essentially free rotations inside the clathrate cages. Calculations at the experimental conditions--2,000 bar (1 bar = 100 kPa) and 250 K confirm multiple occupancy of the clathrate cages with average occupations of 2.00 and 3.96 H2 molecules per D-5(12) (small) and H-5(12)6(4) (large) cage, respectively. The H2-H2O interactions also are responsible for the experimentally observed softening of the H[bond]H stretching modes. The clathrate is found to be thermodynamically stable at 25 bar and 150 K.

Low-energy excitations of guest molecules in clathrates and the Boson peak

The heat capacity, Cp, of seven ice clathrates, four β-quinol clathrates and one squarate clathrate containing rare gas atoms or molecules as guests in their cage-like structures at T<30 K has been analysed, and compared against that of empty β-quinol-clathrate, two channel-type thiourea clathrates containing polar molecules and four canonical glasses. Ethylene oxide–ice clathrate shows a peak in Cp/T3 at ca. 7.5 K, and argon–β-quinol clathrate at ca. 16 K. Other clathrates show an approach toward a Cp/T3 peak at 5<T<12 K. On the basis of their (i) Cp, (ii) Raman scattering, (iii) far infra-red absorption, and (iv) density of vibrational states data, it is shown that low-energy (2–8 meV) excitations are intrinsic to clathrates. Their features are remarkably similar to those of the Boson peak, which has been interpreted in terms of translational vibrations of 20–100 atoms group or of strongly cohesive nanometer size zones separated by softer zones in the heterogeneous glass structures. Since only translational (rattling) and/or rotational (torsional oscillations or librations) motions of atoms or molecules can occur in clathrate cages and channels, and nanometer size clusters cannot form, the similarity noted above indicates that the microstructural origin of the Boson peak in glasses may need reconsideration. Interaction between the guest and cage molecules explains satisfactorily neither the low-energy (2–8 meV) features of clathrates, nor its low-thermal conductivity relative to ice.

Fast anomalous diffusion of small hydrophobic species in water.

Using Car-Parrinello molecular dynamics a structural diffusion mechanism for the simplest hydrophobic species in water, an H atom, is proposed. The hydrophobic solvation cavity is a highly dynamical aggregate that actually drives, by its own hydrogen-bond fluctuations, the diffusion of the enclosed solute. This makes possible an anomalously fast diffusion that falls only short of that of "Grotthuss structural diffusion" of H+ in water. Here, the picture of a static, i.e., "iceberglike," clathrate cage is a misleading concept. The uncovered scenario is similar to the "dynamical hole mechanism" found in a very different context, that is, large molecules moving in hot polymeric melts.

Hydrogen clusters in clathrate hydrate.

High-pressure Raman, infrared, x-ray, and neutron studies show that H2 and H2O mixtures crystallize into the sII clathrate structure with an approximate H2/H2O molar ratio of 1:2. The clathrate cages are multiply occupied, with a cluster of two H2 molecules in the small cage and four in the large cage. Substantial softening and splitting of hydrogen vibrons indicate increased intermolecular interactions. The quenched clathrate is stable up to 145 kelvin at ambient pressure. Retention of hydrogen at such high temperatures could help its condensation in planetary nebulae and may play a key role in the evolution of icy bodies.