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.     

Simulations of structure II H2 and D2 clathrates: potentials incorporating quantum corrections

Molecular dynamics simulations are used to study the stability of structure II H(2) and D(2) clathrates with different large and small guest occupancies at 160 and 250 K and 2.0 kbars. Simulations are performed with the recently proposed anisotropic site-site potentials of Wang for H2 and D2 [J. Quant. Spectrosc. Radiat. Transf. 76, 23 (2003)] which are parameterized to account for quantum corrections of order variant Planck's over 2pi(2) in the second virial coefficient. Occupancies of 0-2 in the small cages and 2-5 in the large cages are considered. Thermodynamic integration is used to determine the most stable guest occupancy at each temperature. Since lattice free energy and configurational energy differences are small for a number of different combinations of cage occupancies, one must expect that in bulk samples various combinations will indeed be observed. Special attention is given to the differences between H(2) and D(2) guests and implications on the hydrogen storage capacity of the clathrates are discussed.     

Molecular Engineering of Conjugated Polybenzothiadiazoles for Enhanced Hydrogen Production by Photosynthesis

The search for metal‐free organic photocatalysts for H₂ production from water using visible light remains a key challenge. Reported herein is a molecular structural design of pure organic photocatalysts, derived from conjugated polybenzothiadiazoles, for photocatalytic H₂ evolution using visible light. By alternating the substitution position of the electron‐withdrawing benzothiadizole unit on the phenyl unit as a comonomer, various polymers with either one‐ or three‐dimensional structures were synthesized and the effect of the molecular structure on their catalytic activity was investigated. Photocatalytic H₂ evolution efficiencies up to 116 μmol h^?1 were observed by employing the linear polymer based on a phenyl‐benzothiadiazole alternating main chain, with an apparent quantum yield (AQY) of 4.01 % at 420 nm using triethanolamine as the sacrificial agent.     

How much carbon dioxide can be stored in the structure H clathrate hydrates?: a molecular dynamics study

The stability of structure H (sH) carbon dioxide clathrate hydrates at three temperature-pressure conditions are determined by molecular dynamics simulations on a 3x3x3 sH unit cell replica. Simulations are performed at 100 K at ambient pressure, 273 K at 100 bars and also 300 K and 5.0 kbars. The small and medium cages of the sH unit cell are occupied by a single carbon dioxide guest and large cage guest occupancies of 1-5 are considered. Radial distribution functions are given for guests in the large cages and unit cell volumes and configurational energies are studied as a function of large cage CO(2) occupancy. Free energy calculations are carried out to determine the stability of clathrates for large cage occupancies at three temperature/pressure conditions stated above. At the low temperature, large cage occupancy of 5 is the most stable while at the higher temperature, the occupancy of 3 is the most favored. Calculations are also performed to show that the CO(2) sH clathrate is more stable than the methane clathrate analog. Implications on CO(2) sequestration by clathrate formation are discussed.     

Numerical simulations of a Cu–water nanofluid-based parabolic-trough solar collector

Journal of Thermal Analysis and Calorimetry - In this study, the thermal and flow characteristics of a parabolic-trough solar collector have been numerically investigated. The turbulent flow inside...     

An Optimal Extension of the Polak–Ribière–Polyak Conjugate Gradient Method

Based on a singular value analysis on an extension of the Polak–Ribière–Polyak method, a nonlinear conjugate gradient method with the following two optimal features is proposed: the condition number of its search direction matrix is minimum and also, the distance of its search direction from the search direction of a descent nonlinear conjugate gradient method proposed by Zhang et al. is minimum. Under proper conditions, global convergence of the method can be achieved. To enhance e?ciency of the proposed method, Powell’s truncation of the conjugate gradient parameters is used. The method is computationally compared with the nonlinear conjugate gradient method proposed by Zhang et al. and a modified Polak–Ribière–Polyak method proposed by Yuan. Results of numerical comparisons show e?ciency of the proposed method in the sense of the Dolan–Moré performance profile.     

Design,Synthesis, and Biological Evaluation of Quercetagetin Analogues as JNK1 Inhibitors

The recent discovery of c‐Jun NH₂‐terminal kinase JNK1 suppression by natural quercetagetin ( 1 ) is a promising lead for the development of novel anticancer agents. Using both X‐ray structure and docking analyses we predicted that 5′‐hydroxy‐ ( 2 ) and 5′‐hydroxymethyl‐quercetagetin ( 3 ) would inhibit JNK1 more actively than the parent compound 1 . Notably, our drug design was based on the active enzyme–ligand complex as opposed to the enzyme’s relatively open apo structure. In this paper we test our theoretical predictions, aided by docking‐model experiments, and report the first synthesis and biological evaluation of quercetagetin analogues 2 and 3 . As calculated, both compounds strongly suppress JNK1 activity. The IC₅₀ values were determined to be 3.4 μM and 12.2 μM , respectively, which shows that 2 surpasses the potency of the parent compound 1 (IC₅₀=4.6 μM ). Compound 2 was also shown to suppress matrix metalloproteinase‐1 expression with high specificity after UV irradiation.     

Effects of Sucrose and Trehalose on Stability,Kinetic Properties,and Thermal Aggregation of Firefly Luciferase

In this study, we used sugars as stabilizing additives to improve the thermostability and to inhibit aggregation of firefly luciferase. The combination of sucrose and trehalose has a strong stabilizing effect on firefly luciferase activity and prevents its thermoinactivation. These additives can also increase optimum temperature. It has been shown that the presence of both sucrose and trehalose can inhibit thermal aggregation of firefly luciferase and decrease bioluminescence decay rate. In order to understand the molecular mechanism of thermostabilization, we investigated the effects of sucrose and trehalose combination on the secondary structure of luciferase by Fourier transform infrared spectroscopy. Minor changes in content of secondary structure of firefly luciferase are observed upon treatment with additives.     

Design of a coupled bioluminescent assay for a recombinant pyruvate kinase from a thermophilic Geobacillus

A simple and rapid method using coupled bioluminescent assay was developed to determine level of ADP. ADP is involved in many biological reactions and ADP assay can be used for assaying some reactions universally by monitoring ADP formation or depletion. ADP analysis involves incubation of ADP or extracts containing ADP with pyruvate kinase (PK) and PEP. The ATP formed by this reaction is determined by measuring the intensity of the initial light flash produced when luciferin-luciferase preparation injected into the reaction mixture. In regard to the main role of the PK in this assay, the gene of PK from a Geobacillus species has been cloned in expression vector pET28a (+), sequenced and overexpressed in Escherichia coli. Recombinant protein was purified using Ni-NTA column and then the purified PK was used in a coupled bioluminescent assay for ADP measurement. Kinetic properties of PK are determined according to a bioluminescent assay using firefly luciferase.