Spectroscopic observation of critical guest concentration appearing in tert-butyl alcohol clathrate hydrate

The tert-butyl alcohol (TBA) is the most hydrophobic of the simple alcohol and by itself does not form a clathrate hydrate with water. A genuine clathrate hydrate is synthesized by exposing a gaseous guest to solid TBA + H2O powders. Here, we examine three consecutive spectroscopic approaches of (1) the occurrence of a "free" OH stretching band (nu(OH)) signal of TBA molecules representing an absence of hydrogen bonding between the host water and guest TBA, (2) a tuning effect for creating fresh cages via the rearrangement of the host-water lattice, and finally (3) the existence of a critical guest concentration (CGC) that appears only when the TBA concentration is dilute. The present findings from this simple three-step approach can be extended to other alcoholic guest species with the specific modifications to provide the new insights into inclusion chemistry.     

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.     

Spectroscopic methods in gas hydrate research

Gas hydrates are crystalline structures comprising a guest molecule surrounded by a water cage, and are particularly relevant due to their natural occurrence in the deep sea and in permafrost areas. Low molecular weight molecules such as methane and carbon dioxide can be sequestered into that cage at suitable temperatures and pressures, facilitating the transition to the solid phase. While the composition and structure of gas hydrates appear to be well understood, their formation and dissociation mechanisms, along with the dynamics and kinetics associated with those processes, remain ambiguous. In order to take advantage of gas hydrates as an energy resource (e.g., methane hydrate), as a sequestration matrix in (for example) CO₂ storage, or for chemical energy conservation/storage, a more detailed molecular level understanding of their formation and dissociation processes, as well as the chemical, physical, and biological parameters that affect these processes, is required. Spectroscopic techniques appear to be most suitable for analyzing the structures of gas hydrates (sometimes in situ), thus providing access to such information across the electromagnetic spectrum. A variety of spectroscopic methods are currently used in gas hydrate research to determine the composition, structure, cage occupancy, guest molecule position, and binding/formation/dissociation mechanisms of the hydrate. To date, the most commonly applied techniques are Raman spectroscopy and solid-state nuclear magnetic resonance (NMR) spectroscopy. Diffraction methods such as neutron and X-ray diffraction are used to determine gas hydrate structures, and to study lattice expansions. Furthermore, UV-vis spectroscopic techniques and scanning electron microscopy (SEM) have assisted in structural studies of gas hydrates. Most recently, waveguide-coupled mid-infrared spectroscopy in the 3–20 μm spectral range has demonstrated its value for in situ studies on the formation and dissociation of gas hydrates. This comprehensive review summarizes the importance of spectroscopic analytical techniques to our understanding of the structure and dynamics of gas hydrate systems, and highlights selected examples that illustrate the utility of these individual methods.     

Spectroscopic properties of tyrosyl radicals in dipeptides

Redox-active tyrosine residues play important roles in long-distance electron reactions in enzymes, including prostaglandin H synthase, galactose oxidase, ribonucleotide reductase, and photosystem II. Magnetic resonance and vibrational spectroscopy provide methods with which to study the structures of redox-active amino acids in proteins. In this report, ultraviolet photolysis was used to generate tyrosyl radicals from polycrystalline tyrosinate or dipeptides, and the structure of the radical was investigated with EPR and reaction-induced FT-IR spectroscopy at 77 K. Photolysis at 77 K is expected to generate a neutral tyrosyl radical through oxidation of the aromatic ring. EPR and FT-IR results obtained from (13)C-labeled tyrosine were consistent with that expectation. Surprisingly, labeling of the tyrosyl amino group with (15)N also resulted in isotope-shifted bands in the photolysis spectrum. The force constant of a NH deformation mode increased when the tyrosyl radical was generated. These data suggest an interaction between the pi system of the tyrosyl radical and the amino group. In spectra acquired from the dipeptides, evidence for a sequence-dependent interaction between the tyrosyl radical and the amide bond of the dipeptide was also obtained. We postulate that perturbation of the amino or the amide/imide groups may occur through a spin polarization mechanism, which is indirectly detected as a change in NH force constant. This conclusion is supported by density functional calculations, which suggest a conformationally sensitive delocalization of spin density onto the amino and carboxylate groups of the tyrosyl radical. These experiments provide a step toward a detailed spectral interpretation for protein-based tyrosyl radicals.     

Direct observation of atomic hydrogen generated from the water framework of clathrate hydrates

We demonstrate that the N(2)-induced ionic hydrate system can be a solution to produce the hydrogen radical from water without direct energy sources such as H(2) and CH(4).     

Spectroscopic analysis of asymmetric top free radicals

Several key problems involved in the analyses of spectra of asymmetric top molecules, i.e., the effective Hamiltonian, the representation and basis vector, identification of energy levels, the selection rules, the relative intensity, and Zeeman tuning rate, were elucidated systematically. Introducing the high-order centrifugal distortion terms into the effective Hamiltonian, the precision for calculation has been improved substantially, which allows us to analyze the high-lying rotational transitions. A global analysis of all available spectra of¹⁴N¹⁶O₂ in the ground vibronic state has been made to obtain a set of molecular constants of¹⁴N¹⁶O₂ in the ground vibronic state which is the most precise and extensive so far. Using the improved parameters, some FIR LMR lines left unassigned hitherto have been identified successfully.     

Mechanisms for thermal conduction in hydrogen hydrate

Extensive equilibrium molecular dynamics simulations have been performed to investigate thermal conduction mechanisms via the Green-Kubo approach for (type II) hydrogen hydrate, at 0.05 kbar and between 30 and 250 K, for both lightly filled H(2) hydrates (1s4l) and for more densely filled H(2) systems (2s4l), in which four H(2) molecules are present in the large cavities, with respective single- and double-occupation of the small cages. The TIP4P water model was used in conjunction with a fully atomistic hydrogen potential along with long-range Ewald electrostatics. It was found that substantially less damping in guest-host energy transfer is present in hydrogen hydrate as is observed in common type I clathrates (e.g., methane hydrate), but more akin in to previous results for type II and H methane hydrate polymorphs. This gives rise to larger thermal conductivities relative to common type I hydrates, and also larger than type II and H methane hydrate polymorphs, and a more crystal-like temperature dependence of the thermal conductivity.     

Multiple functionalization of benzophenones inside polyphenylene dendrimers--toward entrapped ions and radicals

Polyphenylene dendrimers possessing a defined number of keto groups in the dendritic scaffold have been synthesized by using a benzophenone-functionalized tetraphenylcyclopentadienone branching unit. A postsynthetic functionalization of the polyphenylene backbone was achieved by reacting the entrapped keto groups with organolithium reagents yielding monodisperse alcohol products. To investigate the accessibility and reactivity of the embedded groups, many functions of different size and nature, for example, the chromophore pyrene, were introduced. Moreover, suitable precursors for the synthesis of dendrimer entrapped species, trityl cations, trityl radicals, and ketyl radical anions, were obtained. To gain insight into the structure of these newly functionalized dendrimers, UV/vis, EPR, and NMR measurements have been performed. They showed a delocalization of the charge/spin into the polyphenylene dendritic arms leading to a stabilization of the ions/radicals. Remarkably, for the ketyl radicals, EPR measurements indicated the occurrence of intermolecular metal-bridged biradicals. They suggest the existence of a dendritic radical network of the dendrimers themselves.     

Spectroscopic study of hydrogen bonding in aminoanthrapyridones

By an analysis of the IR spectra of solutions of aminoanthrapyridones in chloroform it was demonstrated that the primary and secondary amino groups in the 1 and 6 positions form an intermolecular hydrogen bond with the CO groups; the amino groups in the 6 position form a stronger hydrogen bond. An anomalous form of the absorption band of the stretching vibrations of the NH group was detected in the IR spectrum of 6-n-hexylamino-3-ethylanthrapyridone. The long-wave band in the electronic spectra of aminoanthrapyridone is related to the band of charge transfer of the unshared pair of electrons of the amino nitrogen atom to the π system of the rings.     

Reaction of methyl radicals with atomic oxygen

The reaction of hydrogen atoms with diazomethane was used as a source of methyl radicals to study the reaction of oxygen atoms with methyl radicals. This investigation verifies directly the earlier results that formaldehyde is a major product and that the rate constant is greater than 3×10^?11cm³ molecule^?1 sec^?1.     

Spectroscopic observation of nitrous oxide pentamers

Two new infrared bands in the ν(1) fundamental region of N(2)O are observed in a supersonic jet expansion and assigned to nitrous oxide pentamers. Each band is measured using both (14)N(2)(16)O and (15)N(2)(16)O. Although they are similar in appearance, the bands have slightly different lower state rotational parameters, and are thus assigned to distinct structural isomers of the pentamer. Cluster calculations using two N(2)O intermolecular potentials give results in good agreement with the observed spectra, and indicate that the two isomers probably have the same basic structure (which is unsymmetrical), but differ in the alignment (N-N-O or O-N-N) of one or two of the constituent monomers. Calculations using a resonant dipole interaction model also support the proposed assignment and structure. These are the first reported high-resolution spectra for N(2)O pentamers.     

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.     

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 properties of anion radicals studied using pulse radiolysis

The anion radicals of benzophenone, amino derivatives of benzophenone, fluorenone, furil and antharcene have been generated by pulse radiolysis in acetonitrile solution and their spectroscopic and kinetic properties have been characterized. The G-value for generation of anion radicals in acetonitrile has been measured to be 1.01 ± 0.1 per 100 eV. We have also investigated the electron-transfer reactions from anion radicals of one kind of solutes to the ground state of another solute. This study has demonstrated that pulse radiolysis can be a useful technique for generation and characterization of anion radicals and for studying electron-transfer reactions using acetonitrile as solvent.     

Reactions of atomic nitrogen and atomic hydrogen with methylacetylene

The reaction of nitrogen atoms with methylacetylene has been studied using a fast-flow low-pressure reactor coupled to a mass spctrometer by a nozzle-beam sampling system. Hydrogen atom concentrations were measured by ESR analysis. Experimental second-order rate constants for the consumption of N atoms, of C₃H₄, and for the formation of N₂ were determined in the temperature range of 283° to 485°K. Product profiles of all stable species and of hydrogen atoms and methyl radicals were obtained for different initial concentrations of the reactants. Two different reaction pathways can be distinguished: one provides for recombination of N atoms, and the second leads to the formation of cyano compounds and other hydrocarbons. Only the latter process is influenced by the addition of hydrogen atoms. Mechanisms for the two pathways are discussed.     

Reaction of pentafluoroethyl radicals with hydrogen cyanide

The reaction of C₂F₅ radicals with HCN has been studied over the range of 533–673 K using the pyrolysis of pentafluoroethyl iodide as the free-radical source. Arrhenius parameters for the reaction relative to C₄F₁₀ recombination are given by where θ = 2.303RT kJ/mol and k_H/k is in cm^3/2/mol^1/2·s^1/2.     

Intramolecular hydrogen bond in the hydroxycyclohexadienyl peroxy radicals

The hydroxycyclohexadienyl peroxy radicals (HO? C₆H₆? O₂) produced from the reaction of OH‐benzene adduct with O₂ were studied with density functional theory (DFT) calculations to determine their characteristics. The optimized geometries, vibrational frequencies, and total energies of 2‐hydroxycyclohexadienyl peroxy radical II_s and 4‐hydroxycyclohexadienyl peroxy radical III_s were calculated at the following theoretical levels, B3LYP/6‐31G(d), B3LYP/6‐311G(d,p), and B3LYP/6‐311+G(d,p). Both were shown to contain a red‐shifted intramolecular hydrogen bond (O? H … O? H bond). According to atoms‐in‐molecules (AIM) analysis, the intramolecular hydrogen bond in the 2‐hydroxycyclohexadienyl peroxy radical II_s is stronger than that one in 4‐hydroxycyclohexadienyl peroxy radical III_s, and the former is the most stable conformation among its isomers. Generally speaking, hydrogen bonding in these radicals plays an important role to make them more stable. Based on natural bond orbital (NBO) analysis, the stabilization energy between orbitals is the main factor to produce red‐shifted intramolecular hydrogen bond within these peroxy radicals. The hyperconjugative interactions can promote the transfer of some electron density to the O? H antibonding orbital, while the increased electron density in the O? H antibonding orbital leads to the elongation of the O? H bond and the red shift of the O? H stretching frequency. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

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 ? 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 ? 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 ?, 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.