A molecular dynamics study of ethanol-water hydrogen bonding in binary structure I clathrate hydrate with CO2

Guest-host hydrogen bonding in clathrate hydrates occurs when in addition to the hydrophilic moiety which causes the molecule to form hydrates under high pressure-low temperature conditions, the guests contain a hydrophilic, hydrogen bonding functional group. In the presence of carbon dioxide, ethanol clathrate hydrate has been synthesized with 10% of large structure I (sI) cages occupied by ethanol. In this work, we use molecular dynamics simulations to study hydrogen bonding structure and dynamics in this binary sI clathrate hydrate in the temperature range of 100-250 K. We observe that ethanol forms long-lived (>500 ps) proton-donating and accepting hydrogen bonds with cage water molecules from both hexagonal and pentagonal faces of the large cages while maintaining the general cage integrity of the sI clathrate hydrate. The presence of the nondipolar CO(2) molecules stabilizes the hydrate phase, despite the strong and prevalent alcohol-water hydrogen bonding. The distortions of the large cages from the ideal form, the radial distribution functions of the guest-host interactions, and the ethanol guest dynamics are characterized in this study. In previous work through dielectric and NMR relaxation time studies, single crystal x-ray diffraction, and molecular dynamics simulations we have observed guest-water hydrogen bonding in structure II and structure H clathrate hydrates. The present work extends the observation of hydrogen bonding to structure I hydrates.     

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.     

Effect of small cage guests on hydrogen bonding of tetrahydrofuran in binary structure II clathrate hydrates

Molecular dynamics simulations of the pure structure II tetrahydrofuran clathrate hydrate and binary structure II tetrahydrofuran clathrate hydrate with CO(2), CH(4), H(2)S, and Xe small cage guests are performed to study the effect of the shape, size, and intermolecular forces of the small cages guests on the structure and dynamics of the hydrate. The simulations show that the number and nature of the guest in the small cage affects the probability of hydrogen bonding of the tetrahydrofuran guest with the large cage water molecules. The effect on hydrogen bonding of tetrahydrofuran occurs despite the fact that the guests in the small cage do not themselves form hydrogen bonds with water. These results indicate that nearest neighbour guest-guest interactions (mediated through the water lattice framework) can affect the clathrate structure and stability. The implications of these subtle small guest effects on clathrate hydrate stability are discussed.     

Single crystal vibrational studies of hydrogen bonding in ethylenediammonium chloride

Ethylenediammonium chloride (EDC) single crystal vibrational studies have been performed at room and low temperature as well. The results allowed to get further insight as to the nature of the unusual profile of the NH stretching spectral region. A careful analysis of the infrared spectra in polarized light of the ab and ac crystal faces using the oriented gas model approximation has shown that the absorption profile of the higher frequency region is due mainly to an anharmonic interaction between NH stretching modes and those combination tones which develop parallel transition moments. Single crystal Raman spectra at room and low temperatures (≈10 K) have allowed to localize the peaks of the NH stretching modes. The Raman active lattice mode frequencies were measured at 10 K and 300 K as well. Finally, an almost complete assignment of the internal modes has been reported.     

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.     

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.     

One and two hydrogen molecules in the large cage of the structure II clathrate hydrate: quantum translation-rotation dynamics close to the cage wall

We have performed a rigorous theoretical study of the quantum translation-rotation (T-R) dynamics of one and two H2 and D2 molecules confined inside the large hexakaidecahedral (5(12)6(4)) cage of the sII clathrate hydrate. For a single encapsulated H2 and D2 molecule, accurate quantum five-dimensional calculations of the T-R energy levels and wave functions are performed that include explicitly, as fully coupled, all three translational and the two rotational degrees of freedom of the hydrogen molecule, while the cage is taken to be rigid. In addition, the ground-state properties, energetics, and spatial distribution of one and two p-H2 and o-D2 molecules in the large cage are calculated rigorously using the diffusion Monte Carlo method. These calculations reveal that the low-energy T-R dynamics of hydrogen molecules in the large cage are qualitatively different from that inside the small cage, studied by us recently. This is caused by the following: (i) The large cage has a cavity whose diameter is about twice that of the small cage for the hydrogen molecule. (ii) In the small cage, the potential energy surface (PES) for H2 is essentially flat in the central region, while in the large cage the PES has a prominent maximum at the cage center, whose height exceeds the T-R zero-point energy of H2/D2. As a result, the guest molecule is excluded from the central part of the large cage, its wave function localized around the off-center global minimum. Peculiar quantum dynamics of the hydrogen molecule squeezed between the central maximum and the cage wall manifests in the excited T-R states whose energies and wave functions differ greatly from those for the small cage. Moreover, they are sensitive to the variations in the hydrogen-bonding topology, which modulate the corrugation of the cage wall.     

Intensification of methane and hydrogen storage in clathrate hydrate and future prospect

Gas hydrate is a new technology for energy gas (methane/hydrogen) storage due to its large capacity of gas storage and safe. But industrial application of hydrate storage process was hindered by some problems. For methane, the main problems are low formation rate and storage capacity, which can be solved by strengthening mass and heat transfer, such as adding additives, stirring, bubbling, etc. One kind of additives can change the equilibrium curve to reduce the formation pressure of methane hydrate, and the other kind of additives is surfactant, which can form micelle with water and increase the interface of water-gas. Dry water has the similar effects on the methane hydrate as surfactant. Additionally, stirring, bubbling, and spraying can increase formation rate and storage capacity due to mass transfer strengthened. Inserting internal or external heat exchange also can improve formation rate because of good heat transfer. For hydrogen, the main difficulties are very high pressure for hydrate formed. Tetrahydrofuran (THF), tetrabutylammonium bromide (TBAB) and tetrabutylammonium fluoride (TBAF) have been proved to be able to decrease the hydrogen hydrate formation pressure significantly.     

Double-bridge bonding of aluminium and hydrogen in the crystal structure of gamma-AlH3

Aluminum trihydride (alane) is one of the most promising among the prospective solid hydrogen-storage materials, with a high gravimetric and volumetric density of hydrogen. In the present work, the alane, crystallizing in the gamma-AlH3 polymorphic modification, was synthesized and then structurally characterized by means of synchrotron X-ray powder diffraction. This study revealed that gamma-AlH3 crystallizes with an orthorhombic unit cell (space group Pnnm, a = 5.3806(1) A, b = 7.3555(2) A, c = 5.77509(5) A). The crystal structure of gamma-AlH3 contains two types of AlH6 octahedra as the building blocks. The Al-H bond distances in the structure vary in the range of 1.66-1.79 A. A prominent feature of the crystal structure is the formation of the bifurcated double-bridge bonds, Al-2H-Al, in addition to the normal bridge bonds, Al-H-Al. This former feature has not been previously reported for Al-containing hydrides so far. The geometry of the double-bridge bond shows formation of short Al-Al (2.606 A) and Al-H (1.68-1.70 A) bonds compared to the Al-Al distances in Al metal (2.86 A) and Al-H distances for Al atoms involved in the formation of normal bridge bonds (1.769-1.784 A). The crystal structure of gamma-AlH3 contains large cavities between the AlH6 octahedra. As a consequence, the density is 11% less than for alpha-AlH3.     

Chemical bonding in the crystal structure of 1-hydrosilatrane

A study has been made of the crystal and molecular structure of 1-hydrosilatrane HSi(OCH_2CH₂)₃N. The quantum chemical calculations of its crystal structure have been carried out. According to an estimate of the energy, the coordination bond N→Si is by 5 kcal mol^?1 stronger than that in the crystal of 1-methylsilatrane. The charge values calculated within the framework of the topological analysis of the electron density demonstrate that the electron density of the coordination bond N→Si is primarily transferred to the region of the equatorial bonds Si—O and, to a lesser extent, to the bond Si—H. On going from the isolated molecule of 1-hydrosilatrane to its crystal, the interatomic distance N—Si decreases, mainly owing to the weak intermolecular interaction C—H...O.     

1-Phosphinodiazaphosphene: Synthesis,crystal structure,and bonding properties

The iminophosphane, tBu₂P PN NR₂ (RSiMe₃), produced by base-catalyzed elimination of ClSiMe₃ from the corresponding phosphane, possesses an unusually long PN bond (162 pm), which is in accord with quantum chemical calculations.     

A new type of liquid crystal involving hydrogen bonding: single crystal X-ray structure characterization and properties of the liquid crystal

A new liquid crystal involving hydrogen bonding between 4-hexyloxybenzoic acid and 4-octyloxylphenylethynylpyridine has been investigated by DSC, polarizing optical microscopy and X-ray diffraction. The mesogen shows a nematic phase and an unknown liquid crystalline phase. The liquid crystal crystallizes with a triclinic space group P-1 with the parameters: a = 8.879(2)Å, b = 10.137(2)Å, c = 17.629(4)Å; α = 104.16(3)°, β = 95.47(3)°, γ = 101.48(3)°; V = 1490.3(6)ų; Z = 2; F(000) = 572; μ = 0.076 mm^?1; λ(MoK_α) = 0.71073 Å; final R ₁ = 0.0435. The complex is formed by strong intermolecular hydrogen bonding.     

Sr(II) in water: A labile hydrate with a highly mobile structure

Despite the large number of experimental as well as theoretical investigations available in the literature, some properties of the hydration structure of Sr(II), for example, the coordination number, are still ambiguous. The presented molecular dynamics study based on a most suitable ab initio QM/MM protocol allowed a detailed investigation of structural and dynamical properties of this hydrate, which shows a considerable degree of internal flexebility as well as ligand mobility within the first shell. Despite the high computational effort an exceptionally long QM/MM simulation had to be carried out to obtain sufficient information to investigate first shell ligand exchange reactions.     

Synthesis and x-ray crystal structure of a tripeptidic cyclol

Properties, spectral data and X-ray crystallographic analysis of a tetracyclic tripeptidic aza-cyclol, obtained by cyclization of CF₃COOH·Pro-Phe-Pro-CNp in aqueous medium, are reported.     

Two new phosphinic amides: Synthesis,crystal structure,and theoretical study of hydrogen bonding

Two novel phosphinic amides, (C₆H₅)₂P(O)(NH?cyclo?C₇H₁₃) (I) and (C₆H₅)₂P(O)(NH?cyclo?C₆H₁₁) (II) were synthesized and characterized by spectroscopic methods and X-ray crystallography. Both compounds crystallize in the orthorhombic chiral space group P2₁2₁2₁ and in both structures, the N—H···O hydrogen bonds lead to one-dimensional arrangements along the a axis. The molecular geometries and vibrational frequencies of I and II were investigated with quantum chemical calculations at the B3LYP/6–311G^** level of theory. Furthermore, the hydrogen bonds were studied by means of the Bader theory of atoms in molecules (AIM) and natural bond orbital (NBO) analysis.     

Molecular structure of the CH-acid and C-H...O hydrogen bonding in the chloronitroacetanilide crystal

Conclusions An x-ray diffraction study has shown that the acidic hydrogen in chloronitroacetanilide forms weak, forked intermolecular hydrogen bonds with the oxygen atoms of the NO₂ and CO groups.Translated from Izvestiya Akademii Nauk SSSR, Seriya Khimicheskaya, No, 6, pp. 1300–1304, June, 1987.     

Poly(hexamethylene terephthalate)—II. The crystal structure of forms I and II,from electron and x-ray diffraction,and packing analyses

Form I of poly(hexamethylene terephthalate), poly(6GT), has been shown, through electron diffraction of micro-single crystals, and fibre X-ray diffraction to belong to the triclinic system. The unit cell containing only one chain has dimensions $\text{a = 5.217(8), b = 5.284(12), c = 15.738(16)}\text{A}\text{?}\text{(}\text{fibre axis}\text{), α = 129.4(2), β = 97.6(2)}\text{and}\text{γ = 95.6(2)°}$. The space group is PT. The crystal structure of poly(6GT) form I has been established by the model compound approach and confirmed using 19 independent electron diffraction intensities. Upon refinement of the scale and temperature factors, the agreement index R reaches 0.172, with an overall isotropic temperature factor $\text{B = 3.0}\text{A}\text{?}{}_2$. Calculation of dynamical amplitudes, and also of structure amplitudes which allow for crystal bending, confirms that the electron diffraction data are suitable for a conventional structure analysis. The chain of the polyester has the same fully extended conformation as its related model compound hexamethylene glycol dibenzoate. The planar chain in the single cell is at 35° to the α-axis. The unit-cell dimensions of poly(6GT) form II differ from those of form I by the doubling of the b-dimension. The two chains in the double unit-cell are at 31 and 39° respectively from the a-axis. The agreement index R is 0.161 for the 19 reflections of the single cell and R = 0.196 when the 10 reflections causing the doubling of b are included.