Probing structural transition and guest dynamics of hydroquinone clathrates by temperature-dependent terahertz time-domain spectroscopy

The structural transition from hydroquinone clathrates to crystalline α-form hydroquinone was observed up to the range of 3 THz frequency as a function of temperatures. We found that all three hydroquinone clathrates, CO(2)-, CH(4)-, and CO(2)/CH(4)-loaded hydroquinone clathrates, transform into the α-form hydroquinone at around 102 ± 7 °C. The resonance peak of the CO(2)-loaded hydroquinone clathrate at 2.15 THz decreases with increasing temperature, indicating that CO(2) guest molecules are readily released from the host framework prior to the structural transformation. This reveals that the hydroquinone clathrates may transform into the stable α-form hydroquinone via the metastable form of guest-free clathrate, which depends on guest molecules enclathrated in the cages of the host frameworks. A strong resonance of the α-form hydroquinone at 1.18 THz gradually shifts to the low frequency with increasing temperature and shifts back to the high frequency with decreasing temperature.     

Computational study of methyl group dynamics in the hydroquinone clathrate of acetonitrile

We report molecular dynamics simulations of the acetonitrile clathrate of hydroquinone, with a focus on the dynamics of acetonitrile methyl groups. There are three inequivalent acetonitrile molecules in the unit cell, one with its dipole parallel to the c-axis, and the other two antiparallel. Although these three guest molecules have previously been found to exhibit two slightly different frequencies of rotation over a wide range of temperatures, the frequencies could not be assigned to specific methyl groups. Perhaps counterintuitively, our simulations suggest that the molecule with the lower frequency is one of the two molecules oriented the same way, the different dynamical behaviour being due to subtle differences in the environments of the molecules.     

Molecular dynamics study of structure H clathrate hydrates of methane and large guest molecules

Methane storage in structure H (sH) clathrate hydrates is attractive due to the relatively higher stability of sH as compared to structure I methane hydrate. The additional stability is gained without losing a significant amount of gas storage density as happens in the case of structure II (sII) methane clathrate. Our previous work has showed that the selection of a specific large molecule guest substance (LMGS) as the sH hydrate former is critical in obtaining the optimum conditions for crystallization kinetics, hydrate stability, and methane content. In this work, molecular dynamics simulations are employed to provide further insight regarding the dependence of methane occupancy on the type of the LMGS and pressure. Moreover, the preference of methane molecules to occupy the small (5(12)) or medium (4(3)5(6)6(3)) cages and the minimum cage occupancy required to maintain sH clathrate mechanical stability are examined. We found that thermodynamically, methane occupancy depends on pressure but not on the nature of the LMGS. The experimentally observed differences in methane occupancy for different LMGS may be attributed to the differences in crystallization kinetics and/or the nonequilibrium conditions during the formation. It is also predicted that full methane occupancies in both small and medium clathrate cages are preferred at higher pressures but these cages are not fully occupied at lower pressures. It was found that both small and medium cages are equally favored for occupancy by methane guests and at the same methane content, the system suffers a free energy penalty if only one type of cage is occupied. The simulations confirm the instability of the hydrate when the small and medium cages are empty. Hydrate decomposition was observed when less than 40% of the small and medium cages are occupied.     

Structural analysis of lignin by resonance Raman spectroscopy

Resonance Raman (RR) spectroscopy, combined with Kerr gated fluorescence rejection in the time domain, has recently elucidated lignin structure with unique sensitivity and selectivity. This promises structural studies of fluorescent natural macromolecules, such as lignin, which were previously not possible. Such studies rely on an improved understanding of the RR spectral behavior of lignin, which is today scarcely understood. We explain for the first time this behavior by a semi-empirical theory, and observe its pertinent features for lignin in vascular plants. We have used well-defined oxidative treatments as means of probing lignin structural elements, and show that RR sensitivity and selectivity depend crucially on excitation wavelength. Through the theory we relate these results to basic structural aspects of lignin. Spectra obtained by blue light laser excitation (400 nm) are dominated by low redox potential syringyl lignin groups, whereas lower photon energy (500 nm) decreases the selectivity markedly. RR bands depend on molecular structure but also on molecular environment. Thus charge transfer donor-acceptor interactions within lignin reduce the intensity of bands associated with electron rich moieties. New possibilities for basic and selective structural information on fluorescent natural materials, such as lignin, have thus appeared.     

Structural transition in the surfactant layer that surrounds gold nanorods as observed by analytical surface-enhanced Raman spectroscopy

Surface-enhanced Raman spectroscopy (SERS) of gold nanorods in cetyltrimethylammonium bromide solution has been used to analyze the interfacial surfactant structure based on the distance-dependent electromagnetic enhancement. The spectra were consistent with a surfactant bilayer oriented normal to the surface. As the surfactant concentration was reduced, a structural transition in the surfactant layer was observed through a sudden increase in the signal from the alkane chains. The structural transition was shown to influence the displacement of the surfactant layer by thiolated poly(ethylene glycol). The monodisperse and thoroughly characterized gold nanorod samples yield consistent enhancement factors that were compared to electromagnetic simulations.     

Structural transformation due to Co-host inclusion in ionic clathrate hydrates

The present findings on the co-host role in restructuring the host water framework might provide important information on tuning the cage dimensions via lattice distortion and promoting the total number of cages via structural transformation. This co-host-induced structural modification can improve the physicochemical properties of ionized clathrate hydrates, particularly given that the host framework is able to function as a pathway to deliver protons or electrons.     

Molecular vibrations at a liquid-liquid interface observed by fourth-order Raman spectroscopy

Interface-selective, Raman-based observation of molecular vibrations is demonstrated at a liquid-liquid interface. An aqueous solution of oxazine 170 dye interfaced with hexadecane is irradiated with pump and probe light pulses of 630-nm wavelengths in 17-fs width. The ultrashort pulses are broadened due to group velocity dispersion when traveling through the hexadecane layer. The dispersion is optically corrected to give an optimized instrumental response. The pump pulse induces a vibrational coherence of the dye via impulsive stimulated Raman scattering. The probe pulse generates second-harmonic light at the interface. The efficiency of the generation is modulated as a function of the pump-probe delay by the coherently excited molecules. Fourier transformation of the modulated efficiency presents the frequency spectrum of the vibrations. Five bands are recognized at 534, 557, 593, 619, and 683 cm(-1). The pump-and-probe process induces a fourth-order optical response that is forbidden in a centrosymmetric media. The contribution of an undesired, cascaded optical process is quantitatively considered and excluded.     

Molecular motion and phase transition in hydroquinone clathrate compounds

Distinction between the host-guest and guest-guest interaction in the roles they play in determining the physical properties of the clathrate compounds is discussed. It is shown that the latter causes cooperative effects and phase transitions. Experimental data on the phase transitions and molecular motion in the hydroquinone clathrate compounds are reviewed. Dipole interaction between the guest molecules is shown to have a correct magnitude of energy to explain the experimentally found transition temperatures. Possibility of quantum effects in the clathrate property is discussed in relation to the free rotation and ortho-para conversion of the hydrogen sulphide and other guest molecules.Contribution No. 80 from Chemical Thermodynamics Laboratory     

Structure transition and swapping pattern of clathrate hydrates driven by external guest molecules

We first report here that under strong surrounding gas of external CH4 guest molecules the sII and sH methane hydrates are structurally transformed to the crystalline framework of sI, leading to a favorable change of the lattice dimension of the host-guest networks. The high power decoupling 13C NMR and Raman spectroscopies were used to identify structure transitions of the mixed CH4 + C2H6 hydrates (sII) and hydrocarbons (methylcyclohexane, isopentane) + CH4 hydrates (sH). The present findings might be expected to provide rational evidences regarding the preponderant occurrence of naturally occurring sI methane hydrates in marine sediments. More importantly, we note that the unique and cage-specific swapping pattern of multiguests is expected to provide a new insight for better understanding the inclusion phenomena of clathrate materials.     

Ultrafast dynamics of myoglobin probed by time-resolved resonance Raman spectroscopy

Recent experimental work carried out in this laboratory on the ultrafast dynamics of myoglobin (Mb) is summarized with a stress on structural and vibrational energy relaxation. Studies on the structural relaxation of Mb following CO photolysis revealed that the structural change of heme itself, caused by CO photodissociation, is completed within the instrumental response time of the time-resolved resonance Raman apparatus used (approximately 2 ps). In contrast, changes in the intensity and frequency of the iron-histidine (Fe-His) stretching mode upon dissociation of the trans ligand were found to occur in the picosecond regime. The Fe-His band is absent for the CO-bound form, and its appearance upon photodissociation was not instantaneous, in contrast with that observed in the vibrational modes of heme, suggesting appreciable time evolution of the Fe displacement from the heme plane. The band position of the Fe-His stretching mode changed with a time constant of about 100 ps, indicating that tertiary structural changes of the protein occurred in a 100-ps range. Temporal changes of the anti-Stokes Raman intensity of the v4 and v7 bands demonstrated immediate generation of vibrationally excited heme upon the photodissociation and decay of the excited populations, whose time constants were 1.1 +/- 0.6 and 1.9 +/- 0.6 ps, respectively. In addition, the development of the time-resolved resonance Raman apparatus and prospects in this research field are described.     

Structural study of tungstate fluorophosphate glasses by Raman and X-ray absorption spectroscopy

Transparent glasses were synthesized in the NaPO₃-BaF₂-WO₃ ternary system and several structural characterizations were performed by X-ray absorption spectroscopy (XANES) at the tungsten L_I and L_III absorption edges and by Raman spectroscopy. Special attention was paid to the coordination state of tungsten atoms in the vitreous network.XANES investigations showed that tungsten atoms are only six-fold coordinated (octahedra WO₆) and that these glasses are free of tungstate tetrahedra (WO₄).In addition, Raman spectroscopy allowed to identify a break in the linear phosphate chains as the amount of WO₃ increases and the formation of P-O-W bonds in the vitreous network indicating the modifier behavior of WO₆ octahedra in the glass network. Based on XANES data, we suggested a new attribution of several Raman absorption bands which allowed to identify the presence of W-O⁻ and WO terminal bonds and a progressive apparition of W-O-W bridging bonds for the most WO₃ concentrated samples (?30% molar) due to the formation of WO₆ clusters.     

Laser Raman spectroscopy of THF clathrate hydrate in the temperature range 90-300 K

In situ Raman and Fourier transform infrared (FTIR-NIR) spectroscopic studies on tetrahydrofuran (THF-C(4)H(8)O) clathrate hydrate (CH) were reported. The Raman results in lattice (64 cm(-1)), ring breathing and C-H stretching mode regions are in conformity with earlier reports, while the FTIR (NIR) studies in second order mode region were reported for the first time. Comparison of the results indicate that the band assigned to ring breathing mode around 922 cm(-1) (in Raman) and corresponding second order mode in NIR around 4295 cm(-1) broadens and shifts in enclathrated THF. The ring breathing mode at lower temperatures (T<120 K) is highly asymmetric and splits into two and are due to different host-guest interactions at lower temperatures.     

Vibrational spectroscopy and dynamics in the CH-stretch region of fluorene by IVR-assisted, ionization-gain stimulated Raman spectroscopy

We report stimulated Raman spectra at 0.2 and 0.03 cm(-1) resolution in the CH-stretching region of jet-cooled fluorene. The results were obtained by a version of ionization-gain stimulated Raman spectroscopy in which resonant two-photon ionization probing of the state-population changes arising from stimulated Raman transitions is assisted by the process of intramolecular vibrational redistribution (IVR) in the Raman-excited molecule. The fluorene spectra reveal extensive vibrational coupling interactions involving both the aliphatic and aromatic CH-stretching first excited states with nearby background states. Results pertaining to the symmetric aliphatic CH-stretching fundamental are consistent with a tier model of IVR and point to vibrational energy flow out of the CH stretch on a approximately 1 ps time scale with subsequent redistribution on a approximately 5 ps time scale.     

Primary reaction dynamics of halorhodopsin,observed by sub-picosecond IR – vibrational spectroscopy

The primary all-trans to 13-cis chromophore isomerization of the light driven chloride pump halorhodopsin has been studied by means of transient absorption spectroscopy in the visible and mid-infrared regime at a time resolution of better than 100 and 220 fs, respectively. The picosecond vibrational dynamics are dominated by two time constants, i.e., 2 and 7.7 ps in accordance with the biphasic decay of the retinal excited electronic state and electronic ground state formation with 1.5 and 6.6 ps. The transient vibrational spectra of the participating electronic states strongly suggest the existence of two distinct S₁ populations as a result of an early branching reaction. It is shown that the 13-cis product is formed with the fast time constant, whereas the all-trans educt state is repopulated via both time constants. Concomitant protein dynamics are indicated by spectral changes on a similar time scale in the amide region.     

Structural changes from heating amber and copal as observed by nuclear magnetic resonance spectroscopy

Structural changes caused by heating of fossilized (amber) and semifossilized (copal) resins have been examined by nuclear magnetic resonance spectroscopy. A set of 28 samples was constituted to include different geographical sources, degrees of maturation, colors, and structural groupings. The onset of structural alterations was determined by observation of the lowest temperature at which spectral changes occurred. Both proton spectra in solution and carbon-13? spectra in the solid state then were recorded of cooled samples after heating for 12 hr at temperature increments, until liquification of the sample began. The spectra of both nuclides exhibit loss of a few peaks, broadening of most peaks, and enhancement of the unsaturated or aromatic region at the expense of saturated resonances. Such changes are irreversible and lead to a harder and less soluble material on cooling. The changes parallel those that occur with maturation of fossil resins or materials that lead to coal.     

Excited-state structural dynamics of cytosine from resonance Raman spectroscopy

Cytosine, a nucleobase found in both DNA and RNA, is known to form photoproducts upon UV irradiation, damaging the nucleic acids and leading to cancer and other diseases. To determine the molecular mechanism by which these photoproducts occur, we have measured the resonance Raman spectra of cytosine at wavelengths throughout its 267 nm absorption band. Self-consistent analysis of the resulting resonance Raman excitation profiles and absorption spectrum using a time-dependent wave packet formalism yields both the excited-state structural changes and electronic parameters. From this analysis, we have been able to determine that, at most, 31% of the reorganization energy upon excitation is directed along photochemically relevant modes.     

Molecular dynamics of liquid acetone determined by depolarized Rayleigh and low-frequency Raman scattering spectroscopy

Slow to ultrafast dynamics of liquid acetone at variable temperature was investigated by depolarized Rayleigh and low-frequency Raman scattering spectroscopy, in the region 0-200 cm(-1). A detailed analysis was performed on the spectra and corresponding time responses, and a consistent view of the molecular dynamics of this dipolar solvent was obtained. The effects of temperature on the spectra were interpreted, and distinct dynamical processes identified. At very low frequencies, or long time scales, acetone dynamics is characterized by a slow diffusive reorientation obeying the Stokes-Einstein-Debye hydrodynamic theory only in the limit of subslip boundary conditions. An alternative model based on the microviscosity concept proved to be able to reproduce this correlation time and its temperature dependence. A comparative analysis of collective and single-molecule reorientational times, these latter estimated from intramolecular Raman spectra, led to an orientational correlation parameter g(2) of unity, which denotes a statistical disorder of molecular polarizability tensors. A fast local restructuring process is putatively responsible for an additional contribution at subpicosecond time scales often referred to as intermediate response in other molecular liquids. The high frequency portion of the dynamical susceptibility showed the signature of librational intermolecular motions, giving rise to an ultrafast decay of the time correlation function of polarizability anisotropy. The overall approach, which provided valuable information on dynamics, structure and molecular interactions of neat acetone, will be applied to acetone electrolytic solutions.