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Query: UNIPROT:Q86TM3 (cage)
 29,987 document(s) hit in 31,850,051 MEDLINE articles (0.00 seconds)

Deuteron spin-lattice relaxation was applied to study translational and rotational mobility of CD(4) molecules trapped in the cages of zeolites. Tetrahedral methane molecules are treated as quantum rotators. Relaxation rates related to the intraquadrupole interaction are derived for the T and A+E symmetry species in the presence of large tunneling splittings, consistently with the assumption that A and E species molecules relax at the same rate. An exchange model is presented, which describes the effect on relaxation of CD(4) jumping between two positions characterized by different potentials. While staying at either position bonded to an atom or ion at the cage wall, the molecule has some freedom to move in the vicinity. This causes a time-dependent external electric field gradient, which contributes to the deuteron relaxation rate via the electric quadrupole interaction. Spin conversion transitions couple the relaxation of magnetizations M(T) and M(AE), which is taken into account by reapplying the presented model under somewhat different conditions. Such a two-step procedure leads to successful fits with the experimental results obtained in the range of temperatures roughly 20-200 K for zeolites HY, NaA, and NaMordenite. At higher temperatures CD(4) molecules fly freely across zeolite cages and relaxation changes accordingly, while incoherent tunneling dominates for immobile molecules below 20 K.
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PMID:Translation and reorientation of CD4 molecules in nanoscale cages of zeolites as studied by deuteron spin-lattice relaxation. 1805 53

Classical molecular dynamics simulations were used to study low-density beta(0)-phase p-tert-butylcalix[4]arene inclusion compounds with multiple calix occupancies of xenon, carbon dioxide, methane, and hydrogen guest molecules with guest-host ratios ranging from 1:4 to 4:1. Custom parameterized force fields were used for the guests and the AMBER force field for the calixarene units was validated in our previous work (Chem. Eur. J. 2006, 12, 5231). The inclusion energy and unit cell volume of the calixarene inclusion compound were determined for various guest occupancies and for occupancies greater than 1:1, strong guest-guest interaction effects are observed. The structure and energetics of the 2:1 CO(2)/beta(0)-phase inclusion compound were compared to those of the low-temperature 2:1 CO(2)/calixarene in which the guest molecules occupy both cage and interstitial sites.
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PMID:Simulations of p-tert-butylcalix[4]arene with multiple occupancies of small guest molecules. 1805 85

Livestock and poultry producers face a number of challenges including pressure from the public to be good environmental stewards and adopt welfare-friendly practices. In response, producers often implement practices beyond those required for regulatory compliance to meet consumer demands. However, environmental stewardship and animal welfare may have conflicting objectives. Examples include pasture-based dairy and beef cattle production where high-fiber diets increase methane emissions compared with grain feeding practices in confinement. Grazing systems can contribute to nitrate contamination of surface and groundwater in some areas of the world where grazing is the predominant land use. Similarly, hoop housing for sows, an alternative to indoor gestation crates, can increase the risk of nutrient leaching into soil and groundwater. Direct air emissions may also increase with unconfined animal production as a result of less opportunity to trap and treat emissions, as well as the result of increased cage space and greater surface area per mass of excreta. Coupling welfare-friendly and organic production practices may require greater nutrient inputs to reach the same production end point, resulting in less efficient nutrient use and greater losses to the environment. Dual systems might additionally increase environmental contamination by pathogens. When swine are housed in welfare-friendly huts, Salmonella may cycle more freely between swine and their environment; however, population numbers of pathogenic bacteria may not be different between the indoor and outdoor systems evaluated. Alternatively, these dual purpose systems may reduce antibiotic and hormonal releases to the environment. Finally, intensity of resource use may be different under welfare-friendly and organic practices. In most situations, welfare-friendly production will require more land area per animal or per unit of product. Energy inputs into such systems, from feed production to rearing to product distribution, may also differ from prevalent industrial production practices. Clearly, consumers and producers considering the benefits and costs of ethical animal production practices need to understand the system-wide environmental impacts of these approaches to meeting demand for animal products.
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PMID:Environmental aspects of ethical animal production. 1821 85

This paper presents a systematic molecular simulation study of the heterogeneous crystal growth of methane hydrate sII from supersaturated aqueous methane solutions. The growth of sII hydrate on the [001] crystallographic face is achieved through utilization of a recently proposed methodology, and rates of crystal growth of 1 A/ns were sustained for the molecular models and specific conditions employed in this work. Characteristics of the crystals grown as well as properties and structure of the interface are examined. Water cages with a 5(12)6(3) arrangement, which are improper to both sI and sII structures, are identified during the heterogeneous growth of sII methane hydrate. We show that the growth of a [001] face of sII hydrate can produce an sI crystalline structure, confirming that cross-nucleation of methane hydrate structures is possible. Defects consisting of two methane molecules trapped in large 5(12)6(4) cages and water molecules trapped in small and large cages are observed, where in one instance we have found a large 5(12)6(4) cage containing three water molecules.
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PMID:Heterogeneous crystal growth of methane hydrate on its sII [001] crystallographic face. 1824 98

Two model systems of methane hydrate are constructed. One has a small cage surrounded by 12 large cages. The other has a large cage surrounded by four small cages and ten large cages. Three different H-bonding network patterns between waters are formed, and three random configurations of methane in each cage are chosen. A new method called the surface water fixed model is presented in which the energy minimum conformations for both model systems are preserved close to the X-ray crystallized structure. With normal mode analysis, we calculated frequencies of 2916.6 cm(-1) for a small cage at a centre, 2915.9 cm(-1) not at a centre, and 2911.7 cm(-1) for a large cage at a centre, and 2911.3 cm(-1) not at a centre. These frequencies are in moderate agreement with the corresponding Raman spectra, though not adequate. With our new method, however, it should be possible to improve agreement with the Raman spectra, if a model system vastly larger than the present model systems were constructed.
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PMID:Application of the independent molecule model to elucidate the dynamics of structure I methane hydrate: a second report. 1833 35

By performing a large scale of molecular dynamics simulations, we analyze 60 x 10(6) hydration shells of methane to examine whether the dodecahedral water cluster (DWC) can naturally form in methane aqueous solutions--a fundamental question relevant to the nucleation mechanisms of methane hydrate. The analyzing method is based on identifying the incomplete cages (ICs) from the hydration shells and quantifying their cagelike degrees (zetaC=0-1). Here, the zetaC is calculated according to the H-bond topological network of IC and reflects how the IC resembles the complete polyhedral cage. In this study, we obtain the zetaC distributions of ICs in methane solutions and find the occurrence probabilities of ICs reduce with zetaC very rapidly. The ICs with zetaC>or=0.65 are studied, which can be regarded as the acceptable cagelike structures in appearance. Both increasing the methane concentration and lowering the temperature can increase their occurrence probabilities through slowing down the water molecules. Their shapes, cage-maker numbers, and average radii are also discussed. About 13-14 of these ICs are face saturated, meaning that every edges are shared by two faces. The face-saturated ICs have the potential to act as precursors of hydrate nucleus because they can prevent the encaged methane from directly contacting other dissolved methane when an event of methane aggregation occurs. The complete cages, i.e., the ICs with zetaC=1, form only in the solutions with high methane concentration, and their occurrence probabilities are about 10(-6). Most of their shapes are different from the known hydrate cages, but we indeed observe a standard 5(12)6(2) hydrate cage. We do not find the expected DWC, and its occurrence probability is estimated to be far less than 10(-7). Additionally, the IC analysis proposed in this work is also very useful in other studies not only on the formation, dissociation, and structural transition of hydrates but also on the hydrophobic hydration of apolar solutes.
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PMID:Can the dodecahedral water cluster naturally form in methane aqueous solutions? A molecular dynamics study on the hydrate nucleation mechanisms. 1850 Aug 77

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.
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PMID:Molecular dynamics study of structure H clathrate hydrates of methane and large guest molecules. 1850 Aug 78

Molecular dynamics simulations were used to determine the influence of a methane-water interface on the position and stability of methane hydrate cages. A potential of mean force was calculated as a function of the separation of a methane hydrate cage and a methane-water interface. The hydrate cages are found to be strongly repelled from the methane gas into the water phase. At low enough temperatures, however, the most favorable location for the hydrate cage is at the interface on the water side. Cage lifetime simulations were performed in bulk water and near a methane-water interface. The methane-water interface increases the cage lifetime by almost a factor of 2 compared to cage lifetimes of cages in bulk water. The potential of mean force and the cage lifetime results give additional explanations for the proposed nucleation of gas hydrates at gas-water interfaces.
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PMID:The effect of the water/methane interface on methane hydrate cages: the potential of mean force and cage lifetimes. 1864 32

Classical molecular dynamics simulations have been performed to investigate the interface between liquid water and methane gas under methane hydrate forming conditions. The local environments of the water molecules were studied using order parameters which distinguish between liquid water, ice and methane hydrate phases. Bulk water and water/air interfaces were also studied to allow comparisons to be made between water molecules in the different environments and to determine the effects of the different methane densities studied. Good agreement between experimental and calculated surface tensions is obtained if long range corrections are included. The water surface is found to have a structure which is very similar to that of bulk water, but more tetrahedral, and more clathrate-like than ice-like. In these simulations the concentration of methane in water at the interface is shown to be appropriate for clathrates at higher gas densities (pressures). The orientation of water molecules around methane molecules in the interfacial region appears to depend only weakly on pressure and one of the difficulties in forming hydrate is the availability of water molecules tangential to the hydrate cage. At the interface, the water structure is more disordered than in the bulk water region with increased occurrence compared with the bulk of those angles and orientations found in the clathrate structure.
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PMID:The interface between water and a hydrophobic gas. 1866 11

Nucleation of gas hydrates remains a poorly understood phenomenon, despite its importance as a critical step in understanding the performance and mode of action of low dosage hydrate inhibitors. We present here a detailed analysis of the structural and mechanistic processes by which gas hydrates nucleate in a molecular dynamics simulation of dissolved methane at a methane/water interface. It was found that hydrate initially nucleates into a phase consistent with none of the common bulk crystal structures, but containing structural units of all of them. The process of water cage formation has been found to correlate strongly with the collective arrangement of methane molecules.
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PMID:Gas hydrate nucleation and cage formation at a water/methane interface. 1868 29


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