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.

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.

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.

Comprehensive Synthesis of Monohydroxy-Cucurbit[n]urils (n = 5, 6, 7, 8): High Purity and High Conversions.

We describe a photochemical method to introduce a single alcohol function directly on cucurbit[n]urils (n = 5, 6, 7, 8) with conversions of the order 95-100% using hydrogen peroxide and UV light. The reaction was easily scaled up to 1 g for CB[6] and CB[7]. Spin trapping of cucurbituril radicals combined with MS experiments allowed us to get insights about the reaction mechanism and characterize CB[5], CB[6], CB[7], and CB[8] monofunctional compounds. Experiments involving (18)O isotopically labeled water indicated that the mechanism was complex and showed signs of both radical and ionic intermediates. DFT calculations allowed estimating the Bond Dissociation Energies (BDEs) of each hydrogen atom type in the CB series, providing an explanation of the higher reactivity of the "equatorial" C-H position of CB[n] compounds. These results also showed that, for CB[8], direct functionalization on the cucurbituril skeleton is more difficult because one of the methylene hydrogen atoms (Hb) has its BDE lowering within the series and coming close to that of Hc, thus opening the way to other types of free radicals generated on the CB[8] skeleton leading to several side products. Yet CB[5]-(OH)1 and CB[8]-(OH)1, the first CB[8] derivative, were obtained in excellent yields thanks to the soft method presented here.

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) 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.

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.

Communication: Single crystal x-ray diffraction observation of hydrogen bonding between 1-propanol and water in a structure II clathrate hydrate.

Single crystal x-ray crystallography is used to detect guest-host hydrogen bonding in structure II (sII) binary clathrate hydrate of 1-propanol and methane. X-ray structural analysis shows that the 1-propanol oxygen atom is at a distance of 2.749 and 2.788 Å from the closest clathrate hydrate water oxygen atoms from a hexagonal face of the large sII cage. The 1-propanol hydroxyl hydrogen atom is disordered and at distances of 1.956 and 2.035 Å from the closest cage water oxygen atoms. These distances are compatible with guest-water hydrogen bonding. The C-C-C-O torsional angle in 1-propanol in the cage is 91.47° which corresponds to a staggered conformation for the guest. Molecular dynamics studies of this system demonstrated guest-water hydrogen bonding in this hydrate. The molecular dynamics simulations predict most probable distances for the 1-propanol-water oxygen atoms to be 2.725 Å, and the average C-C-C-O torsional angle to be ~59° consistent with a gauche conformation. The individual cage distortions resulting from guest-host hydrogen bonding from the simulations are rather large, but due to the random nature of the hydrogen bonding of the guest with the 24 water molecules making up the hexagonal faces of the large sII cages, these distortions are not observed in the x-ray structure.

Solid-state 137Ba NMR spectroscopy: an experimental and theoretical investigation of 137Ba electric field gradient tensors and their relation to structure and symmetry.

Ultrawideline (137)Ba SSNMR spectra of several barium-containing systems (barium nitrate, barium carbonate, barium chlorate monohydrate, barium chloride dihydrate, anhydrous barium chloride, and barium hydrogen phosphate) were acquired at two different magnetic field strengths (9.4 and 21.1 T) using frequency-stepped techniques. The recently reported WURST-QCPMG pulse sequence (O'Dell et al. Chem. Phys. Lett. 2008, 464, 97-102) is shown to be very useful for rapidly acquiring high signal-to-noise (137)Ba SSNMR spectra. The breadths of the second-order quadrupolar-dominated spectra and experimental times are notably reduced for experiments conducted at 21.1 T. Analytical simulations of the (137)Ba SSNMR spectra at both fields yield the quadrupolar parameters, and in select cases the barium chemical shift anisotropies (CSAs). Quadrupolar interactions dominate the (137)Ba powder patterns, with quadrupolar coupling constants, C(Q)((137)Ba), ranging from 7.0 to 28.8 MHz. The (137)Ba electric field gradient (EFG) parameters extracted from these spectra are correlated to the local environments at the barium sites, via consideration of molecular symmetry and structure, and first principles calculations of (137)Ba EFG tensors performed using CASTEP software. The rapidity with which (137)Ba SSNMR spectra can be acquired using the WURST pulse sequence and/or at ultrahigh magnetic fields and the sensitivity of the (137)Ba EFG tensor parameters to the changes in the barium environment suggest that (137)Ba SSNMR has great potential for structural characterization of a variety of barium-containing materials.

Effect of guest-host hydrogen bonding on the structures and properties of clathrate hydrates.

To provide improved understanding of guest-host interactions in clathrate hydrates, we present some correlations between guest chemical structures and observations on the corresponding hydrate properties. From these correlations it is clear that directional interactions such as hydrogen bonding between guest and host are likely, although these have been ignored to greater or lesser degrees because there has been no direct structural evidence for such interactions. For the first time, single-crystal X-ray crystallography has been used to detect guest-host hydrogen bonding in structure II (sII) and structure H (sH) clathrate hydrates. The clathrates studied are the tert-butylamine (tBA) sII clathrate with H(2)S/Xe help gases and the pinacolone + H(2)S binary sH clathrate. X-ray structural analysis shows that the tBA nitrogen atom lies at a distance of 2.64 A from the closest clathrate hydrate water oxygen atom, whereas the pinacolone oxygen atom is determined to lie at a distance of 2.96 A from the closest water oxygen atom. These distances are compatible with guest-water hydrogen bonding. Results of molecular dynamics simulations on these systems are consistent with the X-ray crystallographic observations. The tBA guest shows long-lived guest-host hydrogen bonding with the nitrogen atom tethered to a water HO group that rotates towards the cage center to face the guest nitrogen atom. Pinacolone forms thermally activated guest-host hydrogen bonds with the lattice water molecules; these have been studied for temperatures in the range of 100-250 K. Guest-host hydrogen bonding leads to the formation of Bjerrum L-defects in the clathrate water lattice between two adjacent water molecules, and these are implicated in the stabilities of the hydrate lattices, the water dynamics, and the dielectric properties. The reported stable hydrogen-bonded guest-host structures also tend to blur the longstanding distinction between true clathrates and semiclathrates.

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.

Probing cucurbituril assemblies in water with TEMPO-like nitroxides: a trinitroxide supraradical with spin-spin interactions.

Nitroxide free radicals are demonstrated to be useful guests for probing cucurbit[n]uril (CB[n]) assemblies in water by EPR spectroscopy. CB[7] and CB[8] significantly aggregate either in solution or in the solid state (as evidenced by a single-crystal X-ray structure in which CB[8] forms supramolecular triangles with 4-methoxy-TEMPO). The included nitroxides show a striking resistance to biologically relevant reduction, benefiting from the carcerand effect of CB[7] and CB[8] solutions.

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.