The anomalous halogen bonding interactions between chlorine and bromine with water in clathrate hydrates.

Clathrate hydrate phases of Cl2 and Br2 guest molecules have been known for about 200 years. The crystal structure of these phases was recently re-determined with high accuracy by single crystal X-ray diffraction. In these structures, the water oxygen-halogen atom distances are determined to be shorter than the sum of the van der Waals radii, which indicates the action of some type of non-covalent interaction between the dihalogens and water molecules. Given that in the hydrate phases both lone pairs of each water oxygen atom are engaged in hydrogen bonding with other water molecules of the lattice, the nature of the oxygen-halogen interactions may not be the standard halogen bonds characterized recently in the solid state materials and enzyme-substrate compounds. The nature of the halogen-water interactions for the Cl2 and Br2 molecules in two isolated clathrate hydrate cages has recently been studied with ab initio calculations and Natural Bond Order analysis (Ochoa-Resendiz et al. J. Chem. Phys. 2016, 145, 161104). Here we present the results of ab initio calculations and natural localized molecular orbital analysis for Cl2 and Br2 guests in all cage types observed in the cubic structure I and tetragonal structure I clathrate hydrates to characterize the orbital interactions between the dihalogen guests and water. Calculations with isolated cages and cages with one shell of coordinating molecules are considered. The computational analysis is used to understand the nature of the halogen bonding in these materials and to interpret the guest positions in the hydrate cages obtained from the X-ray crystal structures.

Disorder of Hydrofluorocarbon Molecules Entrapped in the Water Cages of Structure†I Clathrate Hydrate.

Water versus fluorine: Clathrate hydrates encaging hydrofluorocarbons as guests show both isotropic and anisotropic distributions within host water cages, depending on the number of fluorine atoms in the guest molecule; this is caused by changes in intermolecular interactions to host water molecules in the hydrates.

Selective occupancy of methane by cage symmetry in TBAB ionic clathrate hydrate.

Methane trapped in the two distinct dodecahedral cages of the ionic clathrate hydrate of TBAB was studied by single crystal XRD and MD simulation. The relative CH4 occupancies over the cage types were opposite to those of CO2, which illustrates the interplay between the cage symmetry and guest shape and dynamics, and thus the gas selectivity.

Facilitating guest transport in clathrate hydrates by tuning guest-host interactions.

The understanding and eventual control of guest molecule transport in gas hydrates is of central importance for the efficient synthesis and processing of these materials for applications in the storage, separation, and sequestration of gases and natural gas production. Previously, some links have been established between dynamics of the host water molecules and guest-host hydrogen bonding interactions, but direct observation of transport in the form of cage-to-cage guest diffusion is still lacking. Recent calculations have suggested that pairs of different guest molecules in neighboring cages can affect guest-host hydrogen bonding and, therefore, defect injection and water lattice motions. We have chosen two sets of hydrate guest pairs, tetrahydrofuran (THF)-CO2 and isobutane-CO2, that are predicted to enhance or to diminish guest-host hydrogen bonding interactions as compared to those in pure CO2 hydrate and we have studied guest dynamics in each using (13)C nuclear magnetic resonance (NMR) methods. In addition, we have obtained the crystal structure of the THF-CO2 sII hydrate using the combined single crystal X-ray diffraction and (13)C NMR powder pattern data and have performed molecular dynamics-simulation of the CO2 dynamics. The NMR powder line shape studies confirm the enhanced and delayed dynamics for the THF and isobutane containing hydrates, respectively, as compared to those in the CO2 hydrate. In addition, from line shape studies and 2D exchange spectroscopy NMR, we observe cage-to-cage exchange of CO2 molecules in the THF-CO2 hydrate, but not in the other hydrates studied. We conclude that the relatively rapid intercage guest dynamics are the result of synergistic guest A-host water-guest B interactions, thus allowing tuning of the guest transport properties in the hydrates by choice of the appropriate guest molecules. Our experimental value for inter-cage hopping is slower by a factor of 10(6) than a published calculated value.

Methanol incorporation in clathrate hydrates and the implications for oil and gas pipeline flow assurance and icy planetary bodies.

One of the best-known uses of methanol is as antifreeze. Methanol is used in large quantities in industrial applications to prevent methane clathrate hydrate blockages from forming in oil and gas pipelines. Methanol is also assigned a major role as antifreeze in giving icy planetary bodies (e.g., Titan) a liquid subsurface ocean and/or an atmosphere containing significant quantities of methane. In this work, we reveal a previously unverified role for methanol as a guest in clathrate hydrate cages. X-ray diffraction (XRD) and NMR experiments showed that at temperatures near 273 K, methanol is incorporated in the hydrate lattice along with other guest molecules. The amount of included methanol depends on the preparative method used. For instance, single-crystal XRD shows that at low temperatures, the methanol molecules are hydrogen-bonded in 4.4% of the small cages of tetrahydrofuran cubic structure II hydrate. At higher temperatures, NMR spectroscopy reveals a number of methanol species incorporated in hydrocarbon hydrate lattices. At temperatures characteristic of icy planetary bodies, vapor deposits of methanol, water, and methane or xenon show that the presence of methanol accelerates hydrate formation on annealing and that there is unusually complex phase behavior as revealed by powder XRD and NMR spectroscopy. The presence of cubic structure I hydrate was confirmed and a unique hydrate phase was postulated to account for the data. Molecular dynamics calculations confirmed the possibility of methanol incorporation into the hydrate lattice and show that methanol can favorably replace a number of methane guests.

Rearrangements and addition reactions of biarylazacyclooctynones and the implications to copper-free click chemistry.

Highly strained biarylazacyclooctynone (BARAC) and analogous bioconjugation reagents were shown to undergo novel rearrangement and addition reactions leading to tetracyclic products. This may limit their practical applicability as bioorthogonal reporters for imaging biomolecules within living systems.

Ammonia clathrate hydrates as new solid phases for Titan, Enceladus, and other planetary systems.

There is interest in the role of ammonia on Saturn's moons Titan and Enceladus as the presence of water, methane, and ammonia under temperature and pressure conditions of the surface and interior make these moons rich environments for the study of phases formed by these materials. Ammonia is known to form solid hemi-, mono-, and dihydrate crystal phases under conditions consistent with the surface of Titan and Enceladus, but has also been assigned a role as water-ice antifreeze and methane hydrate inhibitor which is thought to contribute to the outgassing of methane clathrate hydrates into these moons' atmospheres. Here we show, through direct synthesis from solution and vapor deposition experiments under conditions consistent with extraterrestrial planetary atmospheres, that ammonia forms clathrate hydrates and participates synergistically in clathrate hydrate formation in the presence of methane gas at low temperatures. The binary structure II tetrahydrofuran + ammonia, structure I ammonia, and binary structure I ammonia + methane clathrate hydrate phases synthesized have been characterized by X-ray diffraction, molecular dynamics simulation, and Raman spectroscopy methods.

C-Methyl-calix[4]resorcinarene-1,4-bis-(pyridin-3-yl)-2,3-diaza-1,3-butadiene (1/2).

In the title compound, 2C(12)H(10)N(4)·C(32)H(32)O(8), the calixarene adopts a rctt conformation with dihedral angles of 138.40 (1) and 9.10 (1)° between the opposite rings. The dihedral angles between the rings of the pyridine derivative are 8.80 (1) and 9.20 (1)°. In the crystal, adjacent C-methylcalix[4]resorcinarene molecules are connected into columns parallel to [010] by O-H⋯O hydrogen bonds. O-H⋯N hydrogen bonds between the axial phenoxyl groups and bipyridine molecules link the columns into sheets parallel to (011), which are connected by O-H⋯N hydrogen bonds. Further O-H⋯N hydrogen bonds link the bipyridine and C-methylcalix[4]resorcinarene molecules, giving rise to a three-dimensional network.

Bis(guanidinium) cyananilate.

The asymmetric unit of the title compound, 2CH(6)N(3) (+)·C(8)N(2)O(4) (2-), contains one half of a centrosymmetric 2,5-di-cyano-3,6-dioxocyclo-hexa-1,4-diene-1,4-diolate (cyananil-ate) anion and one guanidinium cation, which are connected by N-H⋯O and N-H⋯N hydrogen bonds into a three-dimensional network.

Bis(guanidinium) chloranilate.

The asymmetric unit of the title co-crystal, 2CH(6)N(3) (+)·C(6)Cl(2)O(4) (2-), contains one half of a chloranilate anion and one guanidinium cation, which are connected by strong N-H⋯O hydrogen bonds into a two-dimensional network.

Direct space methods for powder X-ray diffraction for guest-host materials: applications to cage occupancies and guest distributions in clathrate hydrates.

Structural determination of crystalline powders, especially those of complex materials, is not a trivial task. For non-stoichiometric guest-host materials, the difficulty lies in how to determine dynamical disorder and partial cage occupancies of the guest molecules without other supporting information or constraints. Here, we show how direct space methods combined with Rietveld analysis can be applied to a class of host-guest materials, in this case the clathrate hydrates. We report crystal structures in the three important hydrate crystal classes, sI, sII, and sH, for the guests CO(2), C(2)H(6), C(3)H(8), and methylcyclohexane + CH(4). The results obtained for powder samples are found to be in good agreement with the experimental data from single crystal X-ray diffraction and (13)C solid-state NMR spectroscopy. This method is also used to determine the guest disorder and cage occupancies of neohexane and tert-butyl methyl ether binary hydrates with CH(4) in the structure H clathrate hydrates. The results are found to be in good agreement with the results from the (13)C solid-state NMR and molecular dynamics simulations. It is demonstrated that the ab initio crystal structure determination methodology reported here is able to determine absolute cage occupancies and the dynamical disorder of guest molecules in clathrate hydrates from powdered crystalline samples.

Inclusion complexes of coumarin in cucurbiturils.

Coumarin was found to form stable inclusion complexes with cucurbiturils. In the presence of cucurbit[7]uril (CB[7]), 1 : 1 inclusion complexes were observed in aqueous solution, as monitored by (1)H NMR and UV-visible absorption spectroscopies, and further supported by ab initio calculations, whereas with cucurbit[8]uril (CB[8]) a solid phase 1 : 2 host : guest complex was found in a single crystal X-ray diffraction structure determination.

Single-crystal to single-crystal phase transition of cucurbit[5]uril hydrochloride hydrates: large water-filled channels transforming to layers of unusual stability.

Cucurbit[5]uril hydrochloride hydrate crystals with large water-filled channels transform to a highly stable layer structure via a single-crystal to single-crystal mechanism; (129)Xe NMR showed that porosity in CB[5] samples depends critically on the method of preparation.

Inclusion of 4-methoxy-2,2,6,6-tetramethylpiperidine-N-oxyl in a calixarene nanocapsule in the solid state.

We present an X-ray diffraction (XRD) and multi frequency electron spin resonance (ESR) study of the structure and dynamics of an inclusion complex of p-hexanoyl calix[4]arene (C6OH) with 4-methoxy-2,2,6,6-tetramethylpiperidine-N-oxyl (MT). The single crystal XRD experiments reveal that MT along with ethanol (solvent) molecules are entrapped in a capsular type crystalline lattice of the host C6OH material. ESR measurements were performed at 9.2 GHz/0.33 T (X-band) and at 360 GHz/14 T. In order to avoid ESR line broadening resulting from electron dipole-dipole interaction between nitroxides occupying neighbouring capsules in the crystal lattice, the capsules containing nitroxides were separated from each other by capsules containing diamagnetic dibenzylketone (DBK). Due to the extremely high g-tensor resolution of ESR at 360 GHz, we were able to distinguish, by shifts of their gxx component, between encapsulated nitroxide molecules forming a hydrogen bond between their O-(N) group and the OH group of an ethanol molecule occupying the same capsule and nitroxides missing this interaction. Temperature dependent ESR measurements revealed an orientational anisotropy in the motion of MT encapsulated in C6OH. Solid lipid nanoparticles (SLN) prepared from C6OH and loaded with the nitroxide retained the microcrystalline capsular structure of the pertinent inclusion complex. We found that encapsulated MT in SLNs becomes inaccessible to reducing agents such as sodium ascorbate.

Loading-dependent structures of CO2 in the flexible molecular van der Waals host p-tert-butylcalix[4]arene with 1 : 1 and 2 : 1 guest-host stoichiometries.

The adsorption of CO(2) into the low density form of p-tert-butylcalix[4]arene (tBC) has been studied by (13)C solid state NMR, single crystal X-ray diffraction and volumetric adsorption measurements. The experimental results indicate that tBC and carbon dioxide can form two distinct inclusion compounds. At low loadings the structure of the empty low-density form of the tBC framework (space group P2(1)/n) is preserved with the included CO(2) molecules located within the conical cavities of the tBC molecules. The ideal composition of this form is therefore 1 : 1 (CO(2) : tBC). With higher applied CO(2) pressures the guest loading increases and the structure of the tBC framework transforms to a well studied tetragonal (space group P4/n) form. In this form an additional CO(2) molecule is located on an interstitial site resulting in an ideal composition 2 : 1 (CO(2) : tBC). In agreement with SCXRD and the gas adsorption measurements, (13)C NMR measurements show the change in structure that takes place as a function of sample loading. Inclusion of CO(2) is a rather slow activated process that can be accelerated by increasing the temperature and the transition between crystal forms is inhomogeneous over a bulk sample. After gas release, the empty (or near empty) P4/n structure survives, thus providing another low density phase of tBC. The magnitude and temperature variation of the (13)C chemical shift anisotropy of CO(2) in both low and high occupancy complexes with tBC indicates restricted motion of the CO(2) molecules. The location and dynamics of CO(2) molecules inside the tBC structure are discussed and a motional model for CO(2) is proposed. The CO(2) molecules in the highly loaded compound are shown to exchange rapidly as a single resonance is observed for the two distinct CO(2) molecules.

Mechanical gas capture and release in a network solid via multiple single-crystalline transformations.

Metal-organic frameworks have demonstrated functionality stemming from both robustness and pliancy and as such, offer promise for a broad range of new materials. The flexible aspect of some of these solids is intriguing for so-called 'smart' materials in that they could structurally respond to an external stimulus. Herein, we present an open-channel metal-organic framework that, on dehydration, shifts structure to form closed pores in the solid. This occurs through multiple single-crystal-to-single-crystal transformations such that snapshots of the mechanism of solid-state conversion can be obtained. Notably, the gas composing the atmosphere during dehydration becomes trapped in the closed pores. On rehydration, the pores open to release the trapped gas. Thus, this new material represents a thermally robust and porous material that is also capable of dynamically capturing and releasing gas in a controlled manner.

Structure, dynamics and ordering in structure i ether clathrate hydrates from single-crystal X-ray diffraction and 2H NMR spectroscopy.

The structure and dynamics of trimethylene oxide (TMO) and ethylene oxide (EO) structure I (sI) hydrates are reported from single-crystal X-ray diffraction and 2H NMR spectroscopic measurements. The guest molecule positions in the large cage were determined with considerable improvement over previous diffraction work so that a dynamic model that was consistent with these orientations could be developed to explain the 2H NMR data. Reorientations are shown to take place among both symmetry-related and symmetry-independent sites, 16 positions in all. Because of the prochiral nature of the molecules, both guests show 2H NMR line shapes with large asymmetry parameters, rather unusual for guest molecules in the sI hydrate large cage. The results also show that the dipolar axis of the TMO molecule lies close to the 4 bar axis of the cage on average, whereas for EO, this is not the case. For TMO, progressive alignment of the polar axis with decrease of temperature then allows the dipoles to interact more strongly until dipole reversal is quenched at the ordering transition. The lack of ordering of EO is consistent with the much weaker alignment of the molecular dipoles along the 4 bar axis. With the new complementary information on the structure and dynamics from crystallography and NMR, it is possible to understand why the large cage guests order in the large cage of sI hydrate for TMO hydrate but not for EO hydrate.

A molecular turnstile in para-octanoyl calix[4]arene nanocapsules.

The thermal treatment of different inclusion complexes of para-octanoyl calix[4]arene leads to the formation of a guest-free van der Waals nanocapsular structure possessing a remarkable stability caused by the high mobility of alkanoyl arms.