NMR/MRI study of clathrate hydrate mechanisms

Clathrate hydrates are of great importance in many aspects. However, hydrate formation and dissociation mechanisms, essential to all hydrate applications, are still not well understood due to the limitations of experimental techniques capable of providing dynamic and structural information on a molecular level. NMR has been shown to be a powerful tool to noninvasively measure molecular level dynamic information. In this work, we measured nuclear magnetic resonance (NMR) spin lattice relaxation times (T1's) of tetrahydrofuran (THF) in liquid deuterium oxide (D2O) during THF hydrate formation and dissociation. At the same time, we also used magnetic resonance imaging (MRI) to monitor hydrate formation and dissociation patterns. The results showed that solid hydrate significantly influences coexisting fluid structure. Molecular evidence of residual structure was identified. Hydrate formation and dissociation mechanisms were proposed based on the NMR/MRI observations.     

Interfacial mechanisms governing cyclopentane clathrate hydrate adhesion/cohesion

The present work uses a micromechanical force apparatus to directly measure cyclopentane clathrate hydrate cohesive force and hydrate-steel adhesive force, as a function of contact time, contact force and temperature. We present a hydrate interparticle force model, which includes capillary and sintering contributions and is based on fundamental interparticle force theories. In this process, we estimate the cyclopentane hydrate tensile strength to be approximately 0.91 MPa. This hydrate interparticle force model also predicts the effect of temperature on hydrate particle cohesion force. Finally, we present the first direct measurements of hydrate cohesive force in the gas phase to be 9.1 ± 2.1 mN/m at approximately 3 °C (as opposed to 4.3 ± 0.4 mN/m in liquid cyclopentane).     

Molecular motion and phase transitions of clathrate hydrates**

Abstract

Heat capacities and complex dielectric permittivities of three clathrate hydrates of type II, encaging tetrahydrofuran (THF), acetone (Ac), and trimethylene oxide (TMO), were measured at low temperatures. The heat capacity measurement was done in the temperature range 13–300 K by using an adiabatic calorimeter with a built-in cryorefrigerator. The permittivities were measured in the temperature range 20–260 K and in the frequency range 20 Hz-1 MHz. For pure samples, with a glass transition due to freezing out of water, reorientational motion of the host lattice was observed calorimetrically at 85 K for THF and at 90 K for Ac hydrates, respectively. Spontaneous temperature drift rates of the calorimetric cell were measured under adiabatic conditions to derive the characteristic time for enthalpy relaxation. The enthalpy relaxation times thus derived were well correlated in an Arrhenius plot with the dielectric relaxation times derived from the dielectric relaxation of orientation polarization. The situation is the same as hexagonal ice which has a similar four co-ordinated hydrogen-bonded network.     

Molecular hydrogen storage in binary THF-H2 clathrate hydrates

The hydrogen storage capacity of binary THF-H(2) clathrate hydrate has been determined as a function of formation pressure, THF composition, and time. The amount of hydrogen stored in the stoichiometric hydrate increases with pressure and exhibits asymptotic (Langmuir) behavior to approximately 1.0 wt % H(2). This hydrogen concentration corresponds to one hydrogen molecule occupying each of the small 5(12) cavities and one THF molecule in each large 5(12)6(4) cavity in the hydrate framework. Contrary to previous reports, hydrogen storage was not increased upon decreasing the THF concentration below the stoichiometric 5.6 mol % solution to 0.5 mol %, at constant pressure, even after one week. This provides strong evidence that THF preferentially occupies the large 5(12)6(4) cavity over hydrogen, for the range of experimental conditions tested. The maximum amount of hydrogen stored in this binary hydrate was about 1.0 wt % at moderate pressure (<60 MPa) and is independent of the initial THF concentration over the range of conditions tested.     

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     

Molecular dynamics study of the stability of methane structure H clathrate hydrates

Molecular dynamics simulations are used to study the stability of structure H (sH) methane clathrate hydrates in a 3 x 3 x 3 sH unit cell replica. Simulations are performed at experimental conditions of 300 K and 2 GPa for three methane intermolecular potentials. The five small cages of the sH unit cell are assigned methane guest occupancies of one and large cage guest occupancies of one to five are considered. Radial distribution functions, unit cell volumes, and configurational energies are studied as a function of large cage CH(4) occupancy. Free energy calculations are carried out to determine the stability of clathrates for large cage occupancies. Large cage occupancy of five is the most stable configuration for a Lennard-Jones united-atom potential and the Tse-Klein-McDonald potential parametrized for condensed methane phases and two for the most stable configuation for the Murad and Gubbins potential.     

Molecular dynamics simulations of binary structure H hydrogen and methyl-tert-butylether clathrate hydrates

Binary structure H (sH) hydrogen and methyl-tert-butylether (MTBE) clathrate hydrates are studied with molecular dynamics simulations. Simulations on a 3 x 3 x 3 sH unit cell with up to 4.7 mass % hydrogen gas are run at pressures of 100 bars and 2 kbars at 100 and 273 K. For the small and medium cages of the sH unit cell, H2 guest molecule occupancies of 0, 1 (single occupancy), and 2 (double occupancy) are considered with the MTBE molecule occupying all of the large cages. An increase of the small and medium cage occupancies from 1 to 2 leads to a jump in the unit cell volume and configurational energy. Calculations are also set up with 13, 23, and 89 of the MTBE molecules in the large cages replaced by sets of three to six H2 molecules, and the effects on the configurational energy and volume of the simulation cell are determined. As MTBE molecules are replaced with sets of H2 guests in the large cages, the configurational energy of the unit cell increases. At the lower temperature, the energy and volume of the clathrate are not sensitive to the number of hydrogen guests in the large cages; however, at higher temperatures the repulsions among the H2 guest molecules in the large cages cause an increase in the system energy and volume.     

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.     

Collisional deactivation mechanism of luminescence in hydrogen-loaded Ge-doped fibers

We report experimental results on the temperature and Ge-content dependencies of the decay times of the 3.1 eV emission of twofold-coordinated germaniums, excited at 3.51 eV, in both virgin and H2-loaded germanosilicate optical fibers. For T<110 K, the lifetimes are temperature invariant in the two kinds of fibers; at higher temperatures, they are progressively shortened in the H2-loaded fibers whereas they remain unaltered in the virgin fibers. On increasing the Ge content in the fiber core the lifetime decreases in the whole temperature range. We also found a direct correlation in H2-loaded samples between the dependencies on temperature of the emission lifetime and the diffusion lengths of H2 molecules in silica glass determined from earlier work. These experimental features are explained by assuming an elastic-collisional deactivation mechanism due to interaction with diffusing H2 molecules, described in terms of an Arrhenius law with activation energy approximately 64 meV that operates in competition with the normal radiative process.     

Molecular mechanisms of antibiotic resistance

Over the past decade, resistance to antibiotics has emerged as a crisis of global proportion. Microbes resistant to many and even all clinically approved antibiotics are increasingly common and easily spread across continents. At the same time there are fewer new antibiotic drugs coming to market. We are reaching a point where we are no longer able to confidently treat a growing number of bacterial infections. The molecular mechanisms of drug resistance provide the essential knowledge on new drug development and clinical use. These mechanisms include enzyme catalyzed antibiotic modifications, bypass of antibiotic targets and active efflux of drugs from the cell. Understanding the chemical rationale and underpinnings of resistance is an essential component of our response to this clinical challenge.     

顺铂耐药的分子机制

顺铂被广泛用于多种类型的实体肿瘤的临床治疗.DNA是顺铂的主要靶点,顺铂结合会导致DNA损伤并诱发细胞凋亡.然而,顺铂化疗常常受到内在的和获得性的耐药性的限制.在过去30多年里,大量的研究致力于对顺铂耐药性的理解,并且提出了几种导致顺铂耐药性的分子机制.这些机制显示顺铂的耐药性具有多因素特征.本文系统描述和讨论了顺铂的耐药性机制,包括细胞内药物积累的减少,药物去活作用的增强,DNA修复作用,DNA损伤反应和凋亡通路的变化以及一些间接信号通路的调控影响.     

Molecular dynamics simulation of NMR powder lineshapes of linear guests in structure I clathrate hydrates

We perform molecular dynamics simulations (up to 6 ns) for the structure I clathrate hydrates of linear molecules CS, CS(2), OCS, and C(2)H(2) in large cages at different temperatures in the stability range to determine the angular distribution and dynamics of the guests in the large cages. The long axes of linear guest molecules in the oblate large structure I clathrate hydrate cages are primarily confined near the equatorial plane of the cage rather than axial regions. This non-uniform spatial distribution leads to well-known anisotropic lineshapes in the solid-state NMR spectra of the guest species. We use the dynamic distribution of guest orientations in the cages during the MD simulations at different temperatures to predict the (13)C NMR powder lineshapes of the guests in the large cages. The length of the guests and intermolecular interactions of the guests in the water cages determine the angular distribution and the mobility of the guests in the sI large cages at different temperatures. At low temperatures the range of motion of the guests in the cages are limited and this is reflected in the skew of the predicted (13)C lineshapes. As the guest molecules reach the fast motion limit at higher temperatures, the lineshapes for CS, OCS, and C(2)H(2) are predicted to have the "standard" powder lineshapes of guest molecules.     

Solid clathrate solutions

The classification of solid clathrate solutions may be subdivided into three types: interstitial solutions, those with the substitution of one guest by another and those with the substitution of the particles in a host framework is given. All these types of solutions are illustrated by experimental (or computed) state diagrams of binary and ternary systems of guest-host and host-guest1-guest2 kinds, where host components are water, urea, thiourea and hydroquinone.     

Molecular hydrogen occupancy in binary THF-H2 clathrate hydrates by high resolution neutron diffraction

We have determined the time-space average filling of hydrogen molecules in a binary tetrahydrofuran (THF)-d(8) + D(2) sII clathrate hydrate using high resolution neutron diffraction. The filling of hydrogen in the lattice of a THF-d(8) clathrate hydrate occurred upon pressurization. The hydrogen molecules were localized in the small dodecahedral cavities at 20 K, with nuclear density from the hydrogen approximately spherically distributed and centered in the small cavity. With a formation pressure of 70 MPa, molecular hydrogen was found to only singly occupy the sII small cavity. This result helps explain discrepancies about the hydrogen occupancy in the THF binary hydrate system.     

Molecular mechanisms characterizing cone photoresponses

In the vertebrate retina, rods mediate twilight vision and cones mediate daylight vision. Their photoresponse characteristics are different. The light-sensitivity of a cone is 10(2)-10(3) times lower than that of a rod. In addition, the photoresponse time course is much faster in cones. The mechanism characterizing cone photoresponses has not been known mainly because of the difficulty in isolating cones in large quantities to perform biochemistry. Recently, we developed a method to purify cones from carp retina using a density gradient, which made it possible to analyze the differences in the molecular mechanism of phototransduction between rods and cones. The results showed that signal amplification in cones is less effective, which explains the lower light-sensitivity of cones. The results also showed that visual pigment phosphorylation, a quenching mechanism of light-activated visual pigment, is much more rapid in cones than in rods. The rapid phosphorylation in cones is attributed to a very high total kinase activity in cones. Because of this high activity, cone pigment is readily phosphorylated even at very high bleaching levels, which probably explains why cone photoresponses recover quickly. Based on these findings, the molecular mechanisms of the differences in the photoresponse characteristics between rods and cones are outlined.