Diastereomeric Xe chemical shifts in tethered cryptophane cages

Cryptophane cages serve as host molecules to a Xe atom. Functionalization of cryptophane-A has permitted the development of Xe as a biosensor. Synthetic routes used to prepare cryptophanes result in racemic mixtures of the chiral cages. In the preparation of a tethered cryptophane-A cage for biosensor applications, some achiral and chiral substituents such as left-handed amino acids have been used. When the substituent is achiral, the NMR signal of the Xe atom in the functionalized cage in solution is a single isotropic peak, since the Xe shielding tensor components in the R and L cages differ by no more than the signs of the off-diagonal elements. Chiral substituents can split the cage-encapsulated Xe NMR signal into one or more sets of doublets, depending on the number of asymmetric centers in the substituent. We carry out quantum mechanical calculations of Xe nuclear magnetic shielding for the Xe atom at the same strategic position within an L cryptophane-A cage, under the influence of chiral potentials that represent r or l substituents outside the cage. Calculations of the Xe shielding response in the Lr and Ll diastereomeric pairs permit the prediction of the relative order of the Xe chemical shifts in solutions containing the Rl and Ll diastereomers. Where the substituent itself possesses two chiral centers, comparison of the calculated isotropic shielding responses in the Llr, Lrl, Rll, and Lrr systems, respectively, permits the prediction of the Xe spectrum of diastereomeric systems in solutions containing Llr, Rlr, Lll, and Rll systems. Assignment of the peaks observed in the experimental Xe NMR spectra is therefore possible, without having to undertake the difficult synthetic route that produces a single optically pure enantiomer.     

13C chemical shifts of propane molecules encaged in structure II clathrate hydrate

Experimental NMR measurements for (13)C chemical shifts of propane molecules encaged in 16-hedral cages of structure II clathrate hydrate were conducted to investigate the effects of guest-host interaction of pure propane clathrate on the (13)C chemical shifts of propane guests. Experimental (13)C NMR measurements revealed that the clathrate hydration of propane reverses the (13)C chemical shifts of methyl and methylene carbons in propane guests to gaseous propane at room temperature and atmospheric pressure or isolated propane, suggesting a change in magnetic environment around the propane guest by the clathrate hydration. Inversion of the (13)C chemical shifts of propane clathrate suggests that the deshielding effect of the water cage on the methyl carbons of the propane molecule encaged in the 16-hedral cage is greater than that on its methylene carbon.     

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.     

Spectroscopic signatures of halogens in clathrate hydrate cages. 1. Bromine

We report the first UV-vis spectroscopic study of bromine molecules confined in clathrate hydrate cages. Bromine in its natural hydrate occupies 51262 and 51263 lattice cavities. Bromine also can be encapsulated into the larger 51264 cages of a type II hydrate formed mainly from tetrahydrofuran or dichloromethane and water. The visible spectra of the enclathrated halogen molecule retain the spectral envelope of the gas-phase spectra while shifting to the blue. In contrast, spectra of bromine in liquid water or amorphous ice are broadened and significantly more blue-shifted. The absorption bands shift by about 360 cm-1 for bromine in large 51264 cages of type II clathrate, by about 900 cm-1 for bromine in a combination of 51262 and 51263 cages of pure bromine hydrate, and by more than 1700 cm-1 for bromine in liquid water or amorphous ice. The dramatic shift and broadening in water and ice is due to the strong interaction of the water lone-pair orbitals with the halogen sigma* orbital. In the clathrate hydrates, the oxygen lone-pair orbitals are all involved in the hydrogen-bonded water lattice and are thus unavailable to interact with the halogen guest molecule. The blue shifts observed in the clathrate hydrate cages are related to the spatial constraints on the halogen excited states by the cage walls.     

Spectroscopic signatures of halogens in clathrate hydrate cages. 2. Iodine

UV-vis and Raman spectroscopy were used to study iodine molecules trapped in sII clathrate hydrate structures stabilized by THF, CH(2)Cl(2), or CHCl(3). The spectra show that the environment for iodine inside the water cage is significantly less perturbed than either in aqueous solution or in amorphous water-ice. The resonance Raman progression of I(2) in THF clathrate hydrate can be observed up to v = 6 when excited at 532 nm. The extracted vibrational frequency omega e = 214 +/- 1 cm(-1) is the same as that of the free molecule to within experimental error. At the same time, the UV-vis absorption spectrum of I(2) in the sII hydrate exhibits a relatively large, 1440 cm(-1), blue-shift. This is mainly ascribed to the differential solvation of the I(2) electronic states. We conclude that iodine in sII hydrate resides in a 5(12)6(4) cavity, in which the ground-state I(2) potential is not significantly perturbed by the hydrate lattice. In contrast, in water and in ice, the valence absorption band of I(2) is dramatically broadened and blue-shifted by 3000 cm(-1), and the resonance Raman scattering is effectively quenched. These observations are shown to be consistent with a strong interaction between water molecule and iodine through the lone pair of electrons on water as in the case of bromine in the same media. The results presented here, and the stability of other halogen hydrates, were used to test the predictions of simple models and force-field calculations of the host cage-guest association energy.     

Multiple H2 occupancy of cages of clathrate hydrate under mild conditions

Experiments were carried out by reacting H(2) gas with N(2) hydrate at a temperature of 243 K and a pressure of 15 MPa. The characterizations of the reaction products indicated that multiple H(2) molecules can be loaded into both large and small cages of structure II clathrate hydrates. The realization of multiple H(2) occupancy of hydrate cages under moderate conditions not only brings new insights into hydrogen clathrates but also refreshes the perspective of clathrate hydrates as hydrogen storage media.     

Molecular dynamics averaging of Xe chemical shifts in liquids

The Xe nuclear magnetic resonance chemical shift differences that afford the discrimination between various biological environments are of current interest for biosensor applications and medical diagnostic purposes. In many such environments the Xe signal appears close to that in water. We calculate average Xe chemical shifts (relative to the free Xe atom) in solution in eleven liquids: water, isobutane, perfluoro-isobutane, n-butane, n-pentane, neopentane, perfluoroneopentane, n-hexane, n-octane, n-perfluorooctane, and perfluorooctyl bromide. The latter is a liquid used for intravenous Xe delivery. We calculate quantum mechanically the Xe shielding response in Xe-molecule van der Waals complexes, from which calculations we develop Xe (atomic site) interpolating functions that reproduce the ab initio Xe shielding response in the complex. By assuming additivity, these Xe-site shielding functions can be used to calculate the shielding for any configuration of such molecules around Xe. The averaging over configurations is done via molecular dynamics (MD). The simulations were carried out using a MD technique that one of us had developed previously for the simulation of Henry's constants of gases dissolved in liquids. It is based on separating a gaseous compartment in the MD system from the solvent using a semipermeable membrane that is permeable only to the gas molecules. We reproduce the experimental trends in the Xe chemical shifts in n-alkanes with increasing number of carbons and the large chemical shift difference between Xe in water and in perfluorooctyl bromide. We also reproduce the trend for a given solvent of decreasing Xe chemical shift with increasing temperature. We predict chemical shift differences between Xe in alkanes vs their perfluoro counterparts.     

On the pressure-induced phase transformation in the structure II clathrate hydrate of tetrahydrofuran

A high-pressure phase of the clathrate hydrate of tetrahydrofuran was prepared by freezing a liquid phase of overall composition THF · 7 H₂O under a pressure of 3.0 kbar, or by pressurizing the solid structure II THF hydrate of 255K to 3.4 kbar. Unfortunately, the products recovered at 77K were always mixed phase materials as shown by X-ray powder diffraction. A number of diffraction lines could be indexed in terms of the cubic structure I hydrate with a slightly expanded lattice parameter, 12.08 Å, giving some support to Dyadin's idea that the high pressure phase transition involves a conversion of Structure II to Structure I. Other phases observed in the recovered product include Ice IX and amorphous materials. The reversion of the high pressure sample to the structure II hydrate was followed by differential scanning calorimetry. At ambient pressure, the high pressure sample converts slowly back to Structure II hydrate event at 77K.NRCC No. 35786.     

Ordering of guest-molecule dipoles in the structure I clathrate hydrate of trimethylene oxides

The rotational mobility of encaged trimethylene oxide (TMO) molecules was studied down to 1.8°K by sub-MHz dielectric measurements of the structure I H₂O clathrate and by proton magnetic resonance measurements of the corresponding D₂O clathrate. The results indicate that below a transitional temperature range about 105°K most TMO dipoles assume parallel alignment along the $\text{4}$ axes of the cages. Below the transition the proton second moment suggests the presence of hindered rotation of TMO about its polar axis until the rigid-lattice condition is reached below 5°K. Some residual very broad dielectric absorption (activation energy 2.1 kcal/mole) persists to very low temperatures. Guest-guest and guest-host interaction energies are calculated for simple models     

Theoretical nitrogen NMR chemical shifts in octahedral boron nitride cages

We have calculated the geometrical structure, relative stability, and nitrogen chemical shifts of five boron nitride hollow octahedral cages using density functional theory. Our results show three typical ranges for nitrogen chemical shifts corresponding to each of the nonequivalent magnetic sites of the N atoms. The principal component of the electric field gradient tensor at each 14N site in boron nitride cages is predicted to be much smaller than the corresponding value in borazine, which should reflect in sharper spectral lines and much better resolution.     

Pressure-amorphized cubic structure II clathrate hydrate: crystallization in slow motion

A range of techniques has so far been employed for producing amorphous aqueous solutions. In case of aqueous tetrahydrofuran (THF) this comprises hyperquenching of liquid droplets, vapour co-deposition and pressure-induced amorphization of the crystalline cubic structure II clathrate. All of these samples are thermally labile and crystallize at temperatures above 110 K. We here outline a variant of the pressure-amorphization protocol developed by Suzuki [Phys. Rev. B, 2004, 70, 172108], which results in a highly crystallization resistant amorphous THF hydrate. The hydrate produced according to our protocol (annealing to 180 K at 1.8 GPa rather than to 150 K at 1.5 GPa) does not transform to the cubic structure II THF clathrate even at 150 K. We track the reason for this higher stability to the presence of crystalline remnants when following the Suzuki protocol, which are removed when using our protocol involving higher pressures and an annealing step. These crystalline remnants later serve as crystallization seeds lowering the thermal stability of the amorphous sample. Our protocol thus makes a purely amorphous THF hydrate available to the research community. We use powder X-ray diffraction to study the process of nucleation and slow crystal growth in the temperature range 160-200 K and find that the local cage structure and periodicity of the fully crystalline hydrate develops even at the earliest stages of crystallization, when the "clathrate crystal" has a size of about two unit cells.     

Hyperfine structure of some near-infrared Xe I and Xe II lines

This work reports on the experimental determination of the hyperfine splitting of the Xe I lines at 828.01 nm and 834.68 nm and the Xe II line at 834.72 nm. Measurements were performed by means of Doppler-free saturation spectroscopy in a low-pressure radio-frequency discharge. The absolute wavelength of all hyperfine components is obtained by way of a high-precision wavemeter backed-up with the absorption spectrum of the NO₂ molecule. We provide an accurate estimate of hyperfine constants for the lower level of the Xe II transition at 834.72 nm. The two Xe I transition outcomes of our experimental study are compared with data available in the literature.     

Translation-rotation energy levels of one H2 molecule inside the small, medium and large cages of the structure H clathrate hydrate

We report quantum dynamics calculations of the translation-rotation energy levels of one hydrogen molecule inside the small, medium and large cages of the structure H clathrate hydrate. The calculations are performed using the multiconfiguration time-dependent Hartree (MCTDH) method. Some low-lying states are computed for para-H(2), ortho-H(2), para-D(2), ortho-D(2) and HD, by block improved relaxation.     

The cages, dynamics, and structuring of incipient methane clathrate hydrates

Interest in describing clathrate hydrate formation mechanisms spans multiple fields of science and technical applications. Here, we report findings from multiple molecular dynamics simulations of spontaneous methane clathrate hydrate nucleation and growth from fully demixed and disordered two-phase fluid systems of methane and water. Across a range of thermodynamic conditions and simulation geometries and sizes, a set of seven cage types comprises approximately 95% of all cages formed in the nucleated solids. This set includes the ubiquitous 5(12) cage, the 5(12)6(n) subset (where n ranges from 2-4), and the 4(1)5(10)6(n) subset (where n also ranges from 2-4). Transformations among these cages occur via water pair insertions/removals and rotations, and may elucidate the mechanisms of solid-solid structural rearrangements observed experimentally. Some consistency is observed in the relative abundance of cages among all nucleation trajectories. 5(12) cages are always among the two most abundant cage types in the nucleated solids and are usually the most abundant cage type. In all simulations, the 5(12)6(n) cages outnumber their 4(1)5(10)6(n) counterparts with the same number of water molecules. Within these consistent features, some stochasticity is observed in certain cage ratios and in the long-range ordering of the nucleated solids. Even when comparing simulations performed at the same conditions, some trajectories yield swaths of multiple adjacent sI unit cells and long-range order over 5 nm, while others yield only isolated sI unit cells and little long-range order. The nucleated solids containing long-range order have higher 5(12)6(2)/5(12) and 5(12)6(3)/4(1)5(10)6(2) cage ratios when compared to systems that nucleate with little long-range order. The formation of multiple adjacent unit cells of sI hydrate at high driving forces suggests an alternative or addition to the prevailing hydrate nucleation hypotheses which involve formation through amorphous intermediates.     

Molecular vibrations of methane molecules in the structure I clathrate hydrate from ab initio molecular dynamics simulation

Vibrational frequencies of guest molecules in clathrate hydrates reflect the molecular environment and dynamical behavior of molecules. A detailed understanding of the mechanism for the vibrational frequency changes of the guest molecules in the clathrate hydrate cages is still incomplete. In this study, molecular vibrations of methane molecules in a structure I clathrate hydrate are calculated from ab initio molecular dynamics simulation. The vibrational spectra of methane are computed by Fourier transform of autocorrelation functions, which reveal distinct separation of each vibrational mode. Calculated symmetric and asymmetric stretching vibrational frequencies of methane molecules are lower in the large cages than in the small cages (8 and 16 cm(-1) for symmetric and asymmetric stretching, respectively). These changes are closely linked with the C-H bond length. The vibrational frequencies for the bending and rocking vibrational modes nearly overlap in each of the cages.     

The thermodynamic stability of clathrate hydrate. Encaging non-spherical propane molecules

The thermodynamic stability of a clathrate hydrate encaging non-spherical molecules has been investigated by examining the free energy of cage occupancy. In the present study, a generalized van der Waals and Platteeuw theory is extended to treat the rotational motion of guest molecules in clathrate hydrate cages. The vibrational free energy of both guest and host molecules is divided into harmonic and anharmonic contributions. The anharmonic free energy associated with the non-spherical nature of the guest molecules is evaluated as a perturbation from the spherical guest. Predicted thermodynamic properties are compared with measured values. It is shown that this anharmonic contribution is important in the free energy of the hindered rotation of the guests.     

Spectroscopic identification of the mixed hydrogen and carbon dioxide clathrate hydrate

In this contribution, we first found the novel clathrate hydrate containing two gaseous guests of hydrogen and carbon dioxide by spectroscopic analysis. X-ray powder diffraction and NMR spectroscopy were used to identify structure and guest distribution of the mixed H2 + CO2 hydrate. X-ray diffraction result confirmed that the unit cell parameter was 11.8602 +/- 0.0010 A, and the formed hydrate was identified as structure I hydrate. 1H magic angle spinning (MAS) NMR and 13C cross-polarization (CP) NMR spectroscopy were used to examine the distribution of hydrogen and carbon dioxide molecules in the cages of structure I, respectively. These NMR spectra showed that carbon dioxide molecules occupied both small 512 cages and large 51262 cages, and hydrogen molecules only were occluded in small 512 cages of structure I. The new finding of the mixed hydrogen hydrate is expected to contribute toward the development of hydrogen production technology and, particularly, inclusion chemistry.     

Heat capacity and glass transition of ethylene oxide clathrate hydrate

The heat capacity of structure I ethylene oxide clathrate hydrate EO-6.86 H₂O was measured in the temperature range 6–300 K with an adiabatic calorimeter. The temperature and enthalpy of congruent melting were determined to be (284.11 ± 0.02) K and 48.26 kJ mol^–1, respectively. A glass transition related to the proton configurational mode in the hydrogen-bonded host was observed around 90 K. This glass transition was similar to the one observed previously for the structure II tetrahydrofuran hydrate but showed a wider distribution of relaxation times. The anomalous heat capacity and activation enthalpy associated with the glass transition were almost the same as those for THF-hydrate.Dedicated to Dr D. W. Davidson in honor of his great contributions to the sciences of inclusion phenomena.Author for correspondence.