Encaged Molecules Research Articles

C60 in a peptidic cage: a case of symmetry mismatch studied by crystallography and solid-state NMR.

A supramolecular complex, formed by encapsulation of C60 fullerene in a molecular container built from two resorcin[4]arene rims zipped together by peptidic arms hydrogen bonded into a cylindrical β-sheet, was studied by X-ray crystallography, solid-state and solution NMR, EPR spectroscopy and differential scanning calorimetry (DSC). The crystal structure, determined at 100 K, reveals that the complex occupies 422 site symmetry, which is compatible with the molecular symmetry of the container but not of the fullerene molecule, which has only 222 symmetry. The additional crystallographic symmetry leads to a complicated but discrete disorder, which could be resolved and modelled using advanced features of the existing refinement software. Solid-state NMR measurements at 184-333 K indicate that the thermal motion of C60 in this temperature range is fast but has different activation energies at different temperatures, which was attributed to a phase transition, which was confirmed by DSC. Intriguingly, the activation energy for reorientations of C60 in the solid state is very similar for the free and encaged molecules. Also, the rotational diffusion coefficients seem to be very similar or even slightly higher for the encaged fullerene compared to the free molecule. We also found that chemical shift anisotropy (CSA) is not the main relaxation mechanism for the 13C spins of C60 in the studied complex.

Deep-Sea Field Test of the CH4 Hydrate to CO2 Hydrate Spontaneous Conversion Hypothesis

We have carried out a small-scale deep-sea field test of the hypothesis that CH4 gas can be spontaneously produced from CH4 hydrate by injection of a CO2/N2 gas mixture, thereby inducing release of the encaged molecules with sequestration of the injected gas. Pressure cell studies have shown that, under some pressure and temperature conditions, this gas mixture can induce formation of a solid N2/CO2 hydrate with no associated liquid water production. We transported a cylinder of pure CH4 hydrate, contained within a pressure vessel, to the sea floor at 690 m depth off shore Monterey, CA, using the remotely operated vehicle (ROV) Ventana. Upon opening the pressure vessel with the vehicle robotic arm, we emplaced the hydrate specimen on a metal stand and covered this with a glass cylinder full of a 25% CO2/75% N2 gas mixture, thereby fully displacing the surrounding seawater (T = 4.92 °C). We observed complete and rapid dissociation of the CH4 hydrate with release of liquid water and creation of a mixed gas ...

Effects of clay minerals and biosurfactants on isotopic and molecular characteristics of methane encaged in pressure vessel gas hydrates

The stable isotope values of carbon (δ13Cmethane) and hydrogen (δ2Hmethane) from methane molecules trapped in gas hydrates are useful for differentiation of methane from microbial and thermal origins, providing valuable information during hydrocarbon exploration. Recent studies have reported catalysis of methane hydrates when smectite clays and biosurfactants are present in hydrate-hosting sediments, but catalytic influences on the values of δ13Cmethane and δ2Hmethane are not well documented. In this study, pressure vessel methane hydrates were formed from solutions in contact with smectite clays (montmorillonite and nontronite) and biosurfactants (rhamnolipids and surfactin). Experiments show less than 1‰ differences in values of δ13Cmethane between free and encaged molecules and up to 10‰ variations in values of δ2Hmethane between free and encaged molecules. Notably, methane consumption increased in methane hydrates formed from solutions containing biosurfactants and biosurfactant–smectite mixtures. Results presented here indicate that a hydrate formed in the presence of smectite clays and biosurfactants are characterized by small shifts in free and encaged values of δ13Cmethane and δ2Hmethane and do not complicate interpretation of gas origin. In contrast, methane consumption in hydrates formed under the catalytic effect of smectite clays and biosurfactants modifies gas wetness, obscures gas origin and complicates interpretation of thermal maturity.

Influences of salinity and temperature on the stable isotopic composition of methane and hydrogen sulfide trapped in pressure-vessel hydrates

The stable isotopic composition of carbon (δ13CCH4) and hydrogen (δ2HCH4) in methane and sulfur (δ34SH2S) in hydrogen sulfide can be used to infer the source of volatile molecules encaged in gas hydrates. Differentiation of methane and hydrogen sulfide from microbial and thermal origins provides valuable information for hydrocarbon exploration and for climatic models assessing the role of gas hydrates during climate change. In astrobiological studies, δ13CCH4, δ2HCH4, and δ34SH2S values will be critical in deciphering the origin of methane and hydrogen sulfide molecules if gas hydrates are detected within the cryosphere of Mars or associated with ice-covered oceans on Europa or Enceladus. It is challenging, however, to apply isotope systematics to hydrate-forming systems due to complex influences on nucleation and decomposition under varying conditions of salinity, pressure, and temperature. Few laboratory studies have evaluated the effect of hydrate formation, on isotopic composition of free, encaged, and dissolved gas molecules. In this study, pressure-vessel hydrates were nucleated under conditions inferred for marine continental margins and terrestrial permafrost: low temperatures, moderate pressures, saturation of methane and/or hydrogen sulfide saturation, and varying concentration of sodium chloride (NaCl) and magnesium sulfate heptahydrate (MgSO4·7H2O). Methane experiments show less than 1‰ differences in values of δ13CCH4 between free and encaged molecules and up to 6.5‰ variations in values of δ2HCH4 between free and encaged molecules. In hydrogen-sulfide hydrates, δ34SH2S values show less than 4‰ differences between free and encaged molecules, but up to 14‰ differences between dissolved and free molecules and between dissolved and encaged molecules. Results presented here indicate that shifts found for free and encaged values of δ13CCH4 and δ2HCH4 are small and do not complicate interpretation of gas provenance. Conversely, in hydrate systems containing H2S molecules values of δ34SH2S need to be interpreted with caution. Although isotopic fractionation between free- and encaged-sulfur molecules is mild during hydrate formation, values of dissolved δ34SH2S are substantially fractionated and necessitate careful examination of sulfur isotopic values. Because dissolved H2S could potentially be recycled by oxidation and reduction processes during hydrate formation events, use of δ34SH2S values might complicate assessment of biosignatures for other planetary bodies.

Controlling the Stereospecificity of a Volume-Conserving Adiabatic Photoisomerization within a Nanotubular Self-Assembled Cage: A Reversible Light–Heat Torque Converter

We present herein a host-guest supramolecular system by which we were able to obtain precise control of the stereospecificity of a new and unusual adiabatic photoisomerization reaction capable of restoring reversibly the original configuration. The host-guest system is composed of (a) a naphthalene ring linked centrosymmetrically-via sp(2) hybridized oxygen atoms-with methoxytriethyleneglycol chains (1) and (b) a nanotubular cage formed by four self-assembled face-to-face β-cyclodextrins threaded onto the long "axle" of 1. The compound 1 can exist in distinct cis,cis, cis,trans, and trans,trans conformations that are spectrally distinguishable (see Scheme 1 ). Spectroscopic and kinetic manifestations of the torsional isomerization of 1 in the lowest excited singlet state both in solution and within the tubular cage were investigated. The results provide clear evidence that the compact cavity completely blocks the photoisomerization pathway manifested in common solution (cis,cis* → cis,trans*), allowing observation of stereospecific, volume-conserving turning of the naphthalene ring about the two "quasidouble" bonds C(Naph)-O by φ ≈ 180° (cis,cis* → trans,trans*). The photoisomerization is purely adiabatic, and the encaged molecule restores its original configuration by generating torque thermally, when relaxing to the ground state.

Methane clathrate hydrate infrared spectrum

Context. Recently, we recorded the infrared spectrum of the methane clathrate hydrate stretching mode at low temperature, a caged compound of possible interest for solar system studies as well as interstellar ice mantles.Aims. We provide a practical infrared spectroscopic identification for methane clathrate hydrate to examine its astrophysical presence or absence. We investigate the crystal field induced shifts, and assign the different transitions to the different encaged molecules environments in this clathrate hydrate.Methods. A methane clathrate crystal is produced in an infrared transmitting moderate-pressure closed cell. Using Fourier transform infrared (FTIR) spectroscopy, the overtones (3ν 4 , 2ν 3 ) and combination modes (ν 2 +2ν 4 , ν 1 +ν 4 , ν 3 +ν 4 , ν 2 +ν 3 , ν 3 +2ν 4 , 2ν 2 +2ν 4 , ν 2 +ν 3 +ν 4 ) falling in the 6000–3000 cm-1 (~1.65–3.4 μ m) and their temperature behaviour are investigated. In addition, non-astrophysical CH4 /CF4 gas mixtures are used to build clathrates with different methane large and small cage occupancies to help in assignments.Results. Combination modes show the two distinct cages and the quasi-free rotor low temperature ro-vibrational structure expected for methane clathrate hydrates. A comparison with the pure phase I is performed. Implications for methane clathrate hydrate detection are clearly identified.Conclusions. Solid methane actual remote observations of solar system objects surfaces do not display the clathrate hydrates' specific shift and occupancy signatures. Observationnally, a search for their infrared spectroscopic specific signatures should be performed, focusing on thermodynamically favourable objects like trans- neptunian objects (TNOs) or recently exposed (e.g. fresh impact) planet (or their satellites) surfaces. On the modeling side, efforts must be undertaken to progressively implement clathrate formation kinetics.

Computer-simulation studies of β-quinol clathrate with various gases. Molecular interactions and crystal structure

The crystal structure of β-quinol clathrate was investigated by empirical force-field calculations using two sets of potential functions—AMBER and CVFF. The crystal was approximated by the fragments containing 3402 and 15 750 quinol atoms. It was shown that the AMBER potentials are more precise when describing the experimental data on structure of β-quinol clathrate. The bond stretching, valence angle and out-of-plane bendings, dihedral torsion, van der Waals and electrostatic interactions, and hydrogen bonding were taken into account in the potential energy U. The contribution of each of these energies to the formation of structure was estimated. The energy U was minimized with respect to the independent coordinates of the lattice, unit-cell parameters, and both translation and orientation parameters of included molecules. The equilibrium states of encaged guest molecules, β-quinol lattice structure, and energy of clathrate formation were determined for 27 encaged guest molecules. It was shown that the β-quinol lattice can contract as well as expand depending on the type of an encaged molecule. The distribution of charges around the cage favors the positively charged atoms of the molecule to be located in the center of a cage, in contrast with those negatively charged which occupy the sites in the vicinity of peripheral hydroxyl hexagons. The electrostatic component of guest–guest interaction strongly affects the equilibrium position of guest molecules with large dipole moment. Quantitative estimates of various structural and energetic characteristics for β-quinol clathrate prove to be in good agreement with experimental data.

Brownian motion with superimposed interaction: cosine potential and molecular dynamics simulation

A molecular dynamics simulation of 108 C 2v triatomics is used to evaluate a model of the molecular liquid based on the Evans and Calderwood/Coffey itinerant oscillator concepts. Several weaknesses of the original models are investigated using P n Legendre a.c.f.'s of orientation and the related angular momentum a.c.f. The harmonic binding between cage and encaged molecule is clearly shown to be an oversimplification. Replacement by a cosine potential gives a better result after a numerical analysis due to Ferrario.

NMR behavior of the clathrate hydrate of tetrahydrofuran. II. Deuterium measurements

Deuterium NMR lineshapes, spin-echo signal shapes, and spin-lattice and spin-spin relaxation times of the hydrate of perdeuterated tetrahydrofuran (THF-d8·17H2O) were measured between 6 and 277 K. Below about 20 K the D quadrupole coupling constant for encaged THF-d8 is 173 kHz. At higher temperatures guest-molecule reorientation occurs with an effective activation energy of 0.92 kcal/mole, in agreement with previous proton NMR and dielectric results. The D measurements clearly show a degree of inequivalence among the preferred orientations of the encaged molecules up to about 200 K. This anisotropy disappears at higher temperatures, where reorientation of water molecules leads to an averaging of the 16-hedral cage coufigurations to the tetrahedral symmetry shown by X-ray studies. The D quadrupole coupling constant and asymmetry parameter of THF·17D2O are 215 kHz and 0.11, respectively, at 37 K. An activation energy of 7.2 kcal/mole for reorientation of D2O molecules is derived from T1 measurements.

Spectres d'absorption dans l'infrarouge lointain des clathrates de l'hydroquinone β avec H2S, H2Se; D2S et D2Se

Abstract The introduction of H 2 S, D 2 S, H 2 Se and D 2 Se in β quinol leads to three new absorption lines around the 65 cm −1 absorption band of pure hydroquinone β. They are located at 57, 75 and 79 cm −1 , and are explained as induced absorption by impurities revealing phonons at the Brillouin zone boundaries. Nevertheless the 57 cm −1 band is specially strong for H 2 S and D 2 S and most of its intensity shifts to 44 cm −1 with H 2 Se and D 2 Se. This could be explained as a resonance of the 57 cm −1 phonon peak with the rattling motion of the encaged molecule located at 57 cm −1 for H 2 S and D 2 S and decreasing down to 44 cm −1 for H 2 Se and D 2 Se. A broad band is observed at 20 cm −1 for H 2 S and D 2 S and shifts to 10 cm −1 for H 2 Se and D 2 Se at 10 K. It is a proof of nearly free rotation of the encaged molecule. A group theory analysis of the external vibrations leads to 4 infrared active vibrations. One is sufficiently strong to be observed at 65 cm −1 .

Spectres d'absorption dans l'infrarouge lointain des clathrates de l'hydroquinone β avec HCl, H2S, CH3CN et CH3OH à basses températures

The different molecules trapped in the β-quinol clathrate do not destroy the translational symmetry of the crystal and we have not seen at low temperatures any background absorption induced by the impurities molecules. However the characteristic band of the pure β-quinol at 60 cm −1 (for 300°K), is broader and its frequency is larger when an increasing number of cages are occupied with SO 2 , N 2 , HBr, HCl, H 2 S or CH 3 OH molecules. All these molecules show some possibilities of rotations either pure or hindered. With CH 3 CN which cannot rotate in the cage, the lattice band is not altered at 300°K. The α-quinol which does not possess the clathrate structure gives ten lines from 10 to 100 cm −1 as a consequence of a lower symmetry. The absorption band of both the α and β-quinol are sharp and lattice vibrations seem quasi-harmonic even at room temperature. The genuine degrees of freedom of the encaged molecule give three lines at 20, 57 and 76 cm −1 , for H 2 S at 18°K. They correspond to the lines of HCl at 25 and 52 cm −1 , respectively ascribed to the rotation and translation frequencies of the encaged molecule.

Physico-chemical phenomena in comets—II: Gas adsorption in the snows of the nucleus

Circumstantial evidence shows that water is likely to be abundant in the cometary nucleus. Therefore adsorption of gases on water snows must be taken into consideration. It is first shown that for an incoming comet the regulating mechanism in gas production is not the desorption process, but remains the sublimation rate of water snow. The equations describing plain adsorption on water snow and the formation of a clathrate hydrate of gas are shown to be alike. The formation of a clathrate hydrate can be formally described as a peculiar adsorption with a very large specific area of 500 m 2g −1, which means that the other adsorptions by and large remain negligible. However, clathrates cannot be assimilated to adsorption in all respects. In particular, the existence of cavities in clathrates stabilize the encaged molecules much more. Concentrations of radicals much larger than was previously believed possible may be stored in the snows. The only serious argument left against the direct ejection of some of the observed radicals cornes from the observed lifetimes in the inner coma, which have been attributed to hypothetical parent molecules. The identification of individual parent molecules has been unsuccessful so far. A model is proposed where some of the observed lifetimes are nothing else than lifetimes of ice grains in the evaporating halo, releasing molecules and radicals within an extended source. The likely existence of these ice grains has been experimentally established in paper I. A coma model is developed along these lines and applied to comet Burnham in a forthcoming paper III.

Spectroscopic study of the encaged molecule motion in some clathrates

The far infra-red spectra of seven different gases trapped in the cages of β-quinol clathrates have been studied. Data are provided for N2, CO2, CO, HCl, HBr, SO2 and HCN in the frequency range 10–100 cm–1. For the chosen systems it has been possible to indicate (i) the degree to which quantization of the rotational states is maintained by polar guests in the clathrate and what displacement can be seen relative to free gas molecules, (ii) some factors governing the translational (“rattling”) mode of the guest molecule. The frequencies and relative intensities of quantized rotation, hindered rotation and “rattling” mode absorptions have been studied over a temperature range 4.2–300 K.

Dielectric properties of the hydrates of argon and nitrogen

The dielectric relaxation of water in the structure I clathrate hydrates of argon and nitrogen was studied over a range of temperature and pressure. Hydrates were slowly grown at pressures of 1 to 2 kbar in a coaxial cell enclosed in a pressure vessel. The complex permittivity loci resemble circular arcs with static dielectric constants of ~56 at 0 °C and high-frequency dielectric constants of 2.85 ± 0.05. Relaxation near 0 °C is about as slow as in ice I, but activation energies and entropies are much smaller. Formation of Bjerrum defects probably takes place preferentially near the occasional sites at which argon and nitrogen molecules have replaced water molecules in the lattice. The much faster relaxations found previously in the isostructural hydrates of ethers arise from orientational defects induced in the water lattice by the encaged molecules, a small proportion of which may form hydrogen bonds with water. The effect of small gaps in series with samples showing circular-arc dispersion behavior was evaluated.