Monte Carlo study of sI hydrogen hydrates

In this study, we perform grand canonical Monte Carlo simulations to evaluate the hydrogen storage capacity of structure I (sI) hydrogen hydrates at pressures up to 500 MPa. Initially, we calculate the upper limit of H₂ content of sI hydrates by studying the hypothetical sI hydrate, where H₂ is the single guest component. It is found that the storage capacity of the hypothetical pure H₂ sI hydrate could reach 3.5 wt% at 500 MPa and 274 K. Depending on pressure, the large cavities of the pure H₂ hydrate can accommodate up to three H₂ molecules while the small ones are singly occupied at most, even at pressures as high as 500 MPa, without any double occupancy being observed. Subsequently, the binary H₂–ethylene oxide (EO) hydrate is examined. In this case, the large cavities are occupied by a single EO molecule while the small cavities can accommodate at most a single H₂ molecule. Such configuration results in a maximum H₂ content of only 0.37 wt%. The hydrogen storage capacity does not improve significantly even in case when EO is replaced by a component with smaller molecular weight.     

Molecular simulation of cage occupancy and selectivity of binary THF–H2 sII hydrate

The hydrogen capacity of the binary THF–H₂ sII hydrate is determined by the cage occupancy and by the selectivity of guest molecules. Grand canonical Monte Carlo (GCMC) simulation is used to study the cage occupancy and selectivity of guest molecules from the equilibrium configuration of the binary sII hydrate. The cage framework is regarded as a rigid body and the number of guest molecules is varied to preserve the grand canonical ensemble. The occupancy and selectivity were investigated at a temperature of 270 K for pressures ranging from 0.1 to 200 MPa. It was found that most large cages select THF as guest molecules while small cages include only hydrogen molecules. Multiple occupancy of hydrogen, up to four molecules in large cages and two molecules in small cages, was found as the pressure increases. GCMC results show that the hydrogen capacity is approximately 1.1 wt% at 200 MPa.     

Molecular dynamics simulation on the decomposition of type SII hydrogen hydrate and the performance of tetrahydrofuran as a stabiliser

Molecular dynamics simulation is used to study the decomposition and stability of SII hydrogen and hydrogen/tetrahydrofuran (THF) hydrates at 150 K, 220 K and 100 bar. The modelling of the microscopic decomposition process of hydrogen hydrate indicates that the decomposition of hydrogen hydrate is led by the diffusive behaviour of H₂ molecules. The hydrogen/THF hydrate presents higher stability, by comparing the distributions of the tetrahedral angle of H₂O molecules, radial distribution functions of H₂O molecules and mean square displacements or diffusion coefficients of H₂O and H₂ molecules in hydrogen hydrate with those in hydrogen/THF hydrate. It is also found that the resistance of the diffusion behaviour of H₂O and H₂ molecules can be enhanced by encaging THF molecules in the (5¹²6⁴) cavities. Additionally, the motion of THF molecules is restricted due to its high interaction energy barrier. Accordingly, THF, as a stabiliser, is helpful in increasing the stability of hydrogen hydrate.     

The thermal properties of binary structure sI clathrate hydrate from molecular dynamics simulation

In this work, we present temperature dependence of lattice parameter and normalised lattice parameter in the atmospheric pressure and 120 bar and also pressure dependence of unit cell volume and normalised unit cell volume at 150 and 250?K for variety guests with different size, polarity and guest–host hydrogen bonding capability such as trimethylene oxide (TMO), ethylene oxide (EO), formaldehyde (FA), cyclobutane (CB), cyclopropane (CP) and ethane (Et) in the large cages with CH₄ in small cages of sI clathrate hydrates by molecular dynamics simulations. The obtained values of lattice parameters for the guest species are compatible with the experimental values. These clathrate hydrates are simulated with TIP4P/ice four-site water potential. Herein, isobaric thermal expansivity and isothermal compressibility are calculated at a temperature range of 50–250?K and a wide pressure range. These structural properties have been compared for guests which they are isoelectronic and have similar masses but with different size and polarity. We use molecular dynamics simulations to relate microscopic guest properties, like guest–host hydrogen bonding to macroscopic sI clathrate hydrate properties. The temperature dependence of thermodynamic properties such as constant-volume and constant-pressure heat capacity is presented in the atmospheric pressure for these guest species.     

Vibrational spectra of deuterated methane and water molecules in structure I clathrate hydrate from ab initio MD simulation

The deuteration of the lattice molecules in clathrate hydrates is a widely used experimental technique to clearly separate the vibrational modes. However, the effect of the deuteration on the vibrational spectra and molecular motions is not fully understood. Since the guest–host coupling may change the vibrational spectra, a detailed analysis of the vibrational spectra of deuterated clathrate hydrate is significant in the understanding of the mechanism of the vibrational shift. In this study, the vibrational spectra of the deuterated methane hydrates were calculated by ab initio molecular dynamics simulation. The intramolecular vibrational frequency of the methane in D₂O lattice and deuterated methane in H₂O lattice was calculated and compared with the pure methane hydrate. The bending, rocking and overtone of the bending mode was also reported. The effect of coupling of the rattling motions of guest and host molecules on the vibrational spectra was revealed.     

Comparison of the structures and electronic properties of sodalites containing alkali metals and alkali-earth metals and their hydrates

The effects of different alkali and alkali-earth metal ions on the electronic structures and properties of sodalite M_n[AlSiO₄]₆ (M-SOD) and their hydrates M_n[AlSiO₄]₆?8H₂O (M=Li, Na, K, n = 6; M=Ca, n = 3) were studied using density functional theory method. Theoretical calculations predicted that the Al–O–Si bond angle and cation-framework oxide distance in sodalites with alkali metal cations are correlated with cell volumes. The reduced bandwidths in M-SOD (M=Li, Na and K) show that the inter-atomic orbital overlap in sodalites is weaker than those in the hydrate phases. Frontier molecular orbital analysis indicated that oxygen atoms in the frameworks and most metal ions of SOD and their corresponding hydrates exhibit high reactivity. The interactions existing in sodalites and hydrates were qualitative described. The calculated combination energies of metal ions with framework of sodalites are in the order of K⁺< Na⁺< Li⁺< Ca²⁺. This finding confirms the experimental observation for ion exchange.     

Stability analysis for binary sII hydrogen–promoter hydrates by molecular dynamics simulation

Molecular dynamics simulation was applied for the binary sII hydrogen–promoter hydrates to search the potential promoters to stabilise the hydrogen hydrates. The simulations were performed at 10.1 MPa. The simulation temperature was maintained at 260 K for 100 ps, and then it was increased at the rate of 0.1 TK/s. The cell volumes of the hydrates slowly increased with increasing temperature, and then the cell volumes rapidly increased. The temperature at which the cell volumes rapidly increased is identified as the simulated collapse temperature. The promoter which gives high simulated collapse temperature is judged to stabilise the hydrates. The simulated collapse temperature of the hydrate filled with cyclobutane is the highest among the promoters studied in this work.     

Dissociation mechanism of gas hydrates (I,II, H) of alkane molecules: a comparative molecular dynamics simulation

Employing NPT molecular dynamics method with consistent valence force field, the dissociation processes of sI, sII and sH gas hydrates are simulated at different temperatures and at a constant pressure of 100 MPa. The dissociation mechanisms of gas hydrates are revealed by analysing the structural snapshots, radial distribution functions and diffusion coefficients at different temperatures. As temperature increases, the diffusion rates of water molecules and guest molecules increase; thus the clathrate skeleton formed by water molecules with hydrogen bonds distorts and breaks down; meanwhile the guest molecules encapsulated in the water cavities are released. The size of guest molecules affects the dissociation behaviour of gas hydrate. In addition, the dissociation behaviour also relies on the structural phase of gas hydrates.     

Molecular simulation of shale gas adsorption and diffusion in inorganic nanopores

We studied the structural and dynamical properties of methane and ethane in montmorillonite (MMT) slit pore of sizes 10, 20 and 30 Å using grand canonical Monte Carlo and classical molecular dynamics (MD) simulations. The isotherm, at 298.15 K, is generated for pressures up to 60 bar. The molecules preferentially adsorb at the surface as indicated by the density profile. In case of methane, we observe only a single layer, at the pore wall, whose density increases with increasing pressure. However, ethane also displays a second layer, though of low density in case of pore widths 20 and 30 Å. In-plane self-diffusion coefficient, D_‖, of methane and ethane is of the order of 10^? 6 m²/s. At low pressure, D_‖ increases significantly with the pore size. However, D_‖ decreases rapidly with increasing pressure. Furthermore, the effect of pore size on D_‖ diminishes at high pressure. Ideal adsorbed solution theory is used to understand the adsorption behaviour of the binary mixture of methane (80%) and ethane (20%) at 298.15 K. Furthermore, we calculate the selectivity of the gases at various pressures of the mixture, and found high selectivity for ethane in MMT pores. However, selectivity of ethane decreases with increase in pressure or pore size.     

Analysis of dissociation process for gas hydrates by molecular dynamics simulation

The dissociation processes of methane and carbon dioxide hydrates were investigated by molecular dynamics simulation. The simulations were performed with 368 water molecules and 64 gas molecules using NPT ensembles. The TraPPE (single-site) and 5-site models were adopted for methane molecules. The EPM2 (3-site) and SPC/E models were used for carbon dioxide and water molecules, respectively. The simulations were carried out at 270 K and 5.0 MPa for hydrate stabilisation. Then, temperature was increased up to 370 K. The temperature increasing rates were 0.1–20 TK/s. The gas hydrates dissociated during increasing temperature or at 370 K. The potential models of methane molecule did not much influence the dissociation process of methane hydrate. The mechanisms of dissociation process were analysed with the coordination numbers and mean square displacements. It was found that the water cages break down first, then the gas molecules escape from the water cages. The methane hydrate was more stable than the carbon dioxide hydrate at the calculated conditions.     

Probing the Combined Effect of Flunitrazepam and Lidocaine on the Stability and Organization of Bilayer Lipid Membranes. A Differential Scanning Calorimetry and Dynamic Light Scattering Study

Combined effects of flunitrazepam (FNZ) and lidocaine (LDC) were studied on the thermotropic equilibrium of dipalmitoyl phosphatidylcholine (dpPC) bilayers. This adds a thermodynamic dimension to previously reported geometric analysis in the erythrocyte model. LDC decreased the enthalpy and temperature for dpPC pre- and main-transitions (ΔH _p, ΔH _m, T _p, T _m) and decreased the cooperativity of the main-transition (ΔT _1/2,_m). FNZ decreased ΔH _m and, at least up to 59 μM, also decreased ΔH _p. In conjunction with LDC, FNZ induced a recovery of ?T _1/2,m control values and increased ΔH _m even above the control level. The deconvolution of the main-transition peak at high LDC concentrations revealed three components possibly represented by: a self-segregated fraction of pure dpPC, a dpPC–LDC mixture and a phase with a lipid structure of intermediate stability associated with LDC self-aggregation within the lipid phase. Some LDC effects on thermodynamic parameters were reverted at proper LDC/FNZ molar ratios, suggesting that FNZ restricts the maximal availability of the LDC partitioned into the lipid phase. Thus, beyond its complexity, the lipid–LDC mixture can be rationalized as an equilibrium of coexisting phases which gains homogeneity in the presence of FNZ. This work stresses the relevance of nonspecific drug–membrane binding on LDC–FNZ pharmacological interactions and would have pharmaceutical applications in liposomal multidrug-delivery.     

Age-related changes and circadian variations in peripheral levels of thyroid hormones in Murrah buffaloes

The aim of this study was to investigate the variations in plasma triiodothyronine (T₃) and thyroxine (T₄) with the advancement of age and to determine their circadian patterns in prepubertal and pubertal Murrah buffaloes. The variations in plasma T₃ and T₄ with the advancement of age were observed from day 1 to 24 months of age. Significant higher levels of T₃ and T₄ were observed after birth and a gradual decrease in their concentrations occurred until 15 days of age. The mean plasma T₃ and T₄ ranged between 1.26–3.79 and 60.7–166 ng/ml, respectively, during 1–30 days of age. During 1–24 months of age, the variations in plasma T₃ did not differ (p > 0.05) with the advancement of age, whereas significant (p < 0.0001) changes were observed in plasma T₄. The circadian patterns of T₃ and T₄ were evaluated in prepubertal Murrah buffaloes (n = 8) aged between 14 and 16 months. The mean plasma T₃ and T₄ ranged between 1.04–1.85 and 43.0–76.1 ng/ml, respectively. Significant (p > 0.0001) changes in the secretory pattern of T₃ were observed, whereas the secretory pattern of T₄ did not differ significantly (p > 0.05). In addition, the circadian patterns of T₃ and T₄ in pubertal buffaloes (n = 4) aged between 28 and 30 months were observed and compared to that of prepubertal group (n = 4). The prepubertal group showed significant (p < 0.001) higher plasma T₃ concentrations over 24 h than the pubertal group.     

Use of salt hydrates for controlling activity of tyrosinase in organic solvents

Summary Three procedures were employed to identify salt hydrates which were efficient water donors to dry tyrosinase suspended in a substrate solution in chloroform or toluene. Three salts (Na₂SO₄·10H₂O, Na₂HPO₄·12H₂O and Na₂CO₃·10H₂O) were effective activators whereas eleven others were ineffective. It was concluded that the thermodynamic water activity (a_w) of the hydrate was the major determinant controlling enzyme activity.     

Synthesis and biological evaluation of a new dysprosium(III) complex containing 2,9-dimethyl 1,10-phenanthroline

The binding of [Dy(dmp)₂Cl₃(OH₂)], where dmp is 2,9-dimethyl 1,10-phenanthroline, with Fish salmon DNA (FS-DNA) is investigated by absorption and emission spectroscopy, quenching studies, salt dependent, and gel electrophoresis. The binding constant (K_b) of the interaction is calculated as (1.27 ± .05) × 10⁵ M^?1 from absorption spectral titration data. The Stern–Volmer constant (K_SV), thermodynamic parameters involves ΔG°, ?H°, and ?S° are calculated by fluorescent data and Van’t Hoff equation. The thermodynamic studies show that the reaction for the binding of the complex with FS-DNA is endothermic and entropically driven (ΔS° > 0, ΔH° > 0). The effect of the complex concentration on FS-DNA cleavage reactions is also investigated by gel electrophoresis. Furthermore, the Dy(III) complex has been screened for its antibacterial activity. The experimental results suggest that the Dy(III) complex binds significantly to FS-DNA by hydrophobic groove binding mode and the complex has more efficient antibacterial activity compared to its metal salt.     

Evaluation of DNA,BSA binding,and antimicrobial activity of new synthesized neodymium complex containing 29-dimethyl 110-phenanthroline

In order to evaluate biological potential of a novel synthesized complex [Nd(dmp)₂Cl₃.OH₂] where dmp is 29-dimethyl 110-phenanthroline, the DNA-binding, cleavage, BSA binding, and antimicrobial activity properties of the complex are investigated by multispectroscopic techniques study in physiological buffer (pH 7.2).The intrinsic binding constant (K_b) for interaction of Nd(III) complex and FS–DNA is calculated by UV–Vis (K_b = 2.7 ± 0.07 × 10⁵) and fluorescence spectroscopy (K_b = 1.13 ± 0.03 × 10⁵). The Stern–Volmer constant (K_SV), thermodynamic parameters including free energy change (ΔG°), enthalpy change (?H°), and entropy change (?S°), are calculated by fluorescent data and Vant’ Hoff equation. The experimental results show that the complex can bind to FS–DNA and the major binding mode is groove binding. Meanwhile, the interaction of Nd(III) complex with protein, bovine serum albumin (BSA), has also been studied by using absorption and emission spectroscopic tools. The experimental results show that the complex exhibits good binding propensity to BSA. The positive ΔH° and ?S° values indicate that the hydrophobic interaction is main force in the binding of the Nd(III) complex to BSA, and the complex can quench the intrinsic fluorescence of BSA remarkably through a static quenching process. Also, DNA cleavage was investigated by agarose gel electrophoresis that according to the results cleavage of DNA increased with increasing of concentration of the complex. Antimicrobial screening test gives good results in the presence of Nd(III) complex system.     

Methanomethylovorans uponensis sp. nov., a methylotrophic methanogen isolated from wetland sediment

A novel mesophilic, methylotrophic, methanogenic archaeon, designated strain EK1^T, was enriched and isolated from wetland sediment. Phylogenetic analysis showed that strain EK1^T was affiliated with the genus Methanomethylovorans within the family Methanosarcinaceae, and shared the highest 16S rRNA and methyl-coenzyme M reductase alpha-subunit gene sequence similarity with the type strain of Methanomethylovorans hollandica (98.8 and 92.6 %, respectively). The cells of strain EK1^T were observed to be Gram-negative, non-motile and irregular cocci that did not lyse in 0.1 % (w/v) sodium dodecyl sulfate. Methanol, mono-, di- and trimethylamine, dimethyl sulfide and methanethiol were found to be used as catabolic and methanogenic substrates, whereas H₂/CO₂, formate, 2-propanol and acetate were not. Growth was observed at 25–40 °C (optimum, 37 °C), at pH 5.5–7.5 (optimum, pH 6.0–6.5) and in the presence of 0–0.1 M NaCl (optimum, 0 M). Growth and methane production rates were stimulated in the presence of H₂/CO₂ although methane production and growth yields were not significantly affected; acetate, formate, 2-propanol and CO/CO₂/N₂ did not affect methane production. CoCl₂ (0.6–2.0 μM) and FeCl₂ (25 mg/l) stimulated growth, while yeast extract and peptone did not. The DNA–DNA hybridization experiment revealed a relatedness of <20 % between EK1^T and the type strains of the genus Methanomethylovorans. The DNA G+C content of strain EK1^T was determined to be 39.2 mol%. Based on the polyphasic taxonomic study, strain EK1^T represents a novel species belonging to the genus Methanomethylovorans, for which the name Methanomethylovorans uponensis sp. nov. is proposed. The type strain is strain EK1^T(=NBRC 109636^T = KCTC 4119^T = JCM 19217^T).     

Molecular simulations of adsorption and separation of ethylene/ethane and propylene/propane mixtures on Ni2(dobdc) and Ni2(m-dobdc) metal-organic frameworks

Porous solid adsorbents have received considerable attention as a promising alternative to the traditional cryogenic distillation for separating olefin/paraffin mixtures. In this work, we studied pure components as well as ethylene/ethane and propylene/propane binary mixtures uptakes and selectivities at 318 K and 1 bar into metal-organic frameworks Ni₂(dobdc) and Ni₂(m-dobdc) using GCMC simulations. We used DFT method to modify the potential model of carbon–carbon double bond in unsaturated hydrocarbons. GCMC results show that ethylene and ethane uptakes on Ni₂(m-dobdc) are higher than that of Ni₂(dobdc) but propylene and propane uptakes are equal in Ni₂(m-dobdc) and Ni₂(dobdc). Also, Ni₂(m-dobdc) has higher selectivity than Ni₂(dobdc) for separation of ethylene/ethane and propylene/propane mixtures.     

Diurnal variation in repeated sprint performance cannot be offset when rectal and muscle temperatures are at optimal levels (38.5°C)

The present study investigated whether increasing morning rectal temperatures (T_rec) to evening levels, or increasing morning and evening T_rec to an “optimal” level (38.5°C), resulting in increased muscle temperatures (T_m), would offset diurnal variation in repeated sprint (RS) performance in a causal manner. Twelve trained males underwent five sessions [age (mean ± SD) 21.0 ± 2.3 years, maximal oxygen consumption (V?O₂max) 60.0 ± 4.4 mL.kg^–1 min^–1, height 1.79 ± 0.06 m, body mass 78.2 ± 11.8 kg]. These included control morning (M, 07:30 h) and evening (E, 17:30 h) sessions (5-min warm-up), and three further sessions consisting of a warm-up morning trial (M_E, in 39–40°C water) until T_rec reached evening levels; two “optimal” trials in the morning and evening (M_38.5 and E_38.5, in 39–40°C water) respectively, until T_rec reached 38.5°C. All sessions included 3 × 3-s task-specific warm-up sprints, thereafter 10 × 3-s RS with 30-s recoveries were performed a non-motorised treadmill. T_rec and T_m measurements were taken at the start of the protocol and following the warm-up periods. Values for T_rec and T_m at rest were higher in the evening compared to morning values (0.48°C and 0.69°C, p < 0.0005). RS performance was lower (7.8–8.3%) in the M for distance covered (DC; p = 0.002), average power (AP; p = 0.029) and average velocity (AV; p = 0.002). Increasing T_rec in the morning to evening values or optimal values (38.5°C) did not increase RS performance to evening levels (p = 1.000). However, increasing T_rec in the evening to “optimal” level through a passive warm-up significantly reduced DC (p = 0.008), AP (p < 0.0005) and AV (p = 0.007) to values found in the M condition (6.0–6.9%). Diurnal variation in T_rec and T_m is not wholly accountable for time-of-day oscillations in RS performance on a non-motorised treadmill; the exact mechanism(s) for a causal link between central temperature and human performance are still unclear and require more research.     

Antimicrobial study on trivalent lighter rare-earth complexes of 2-pyrazinecarboxylate with hydrazinium cation

The hydrazinium lanthanide metal complexes of 2-pyrazinecarboxylic acid (HpyzCOO) of the formulae (N₂H₅)₂[Ln(pyzCOO)₅]·2H₂O, where Ln=La or Ce and (N₂H₅)₃[Ln(pyzCOO)₄(H₂O)]·2NO₃, where Ln=Pr, Nd, Sm or Dy have been synthesized by the addition of an aqueous solution of the corresponding metal nitrate hydrates to an aqueous mixture of the respective carboxylic acids and hydrazine hydrate. The in vitro antibacterial screening of the free acid and its metal complexes has been carried out against Escherichia coli, Salmonella typhi and Vibrio cholerae. Antifungal activities of all the synthesized compounds were screened for in vitro growth inhibitory activity against Aspergillus fumigatus and Aspergillus niger by using the disc diffusion method. The antimicrobial activities of the prepared metal complexes show more promising activity than the corresponding free acid, its hydrazinium salts, and the standard control antibiotics, Co-trimoxazole and Carbendazim.     

Assessment of the elastic properties of amorphous calcium silicates hydrates (I) and (II) structures by molecular dynamics simulation

Based on Hamid model of 11Å tobermorite, amorphous calcium silicates hydrates (or C-S-H) structures (Ca₄Si₆O₁₄(OH)₄?2H₂O as the C-S-H(I) and (CaO)_1.67(SiO₂)(H₂O)_1.75 as the C-S-H(II)) with the Ca/Si ratio of 0.67 and 1.7 are concerned. Then, as the representative ‘globule’ C-S-H, two amorphous C-S-H structures with the size of 5.352 × 4.434 × 4.556 nm³ during the stretch process are simulated at a certain strain rate of 10^?3 ps^?1 by LAMMPS program for molecular dynamics simulation, using ClayFF force field. The tensile stress–strain curves are obtained and analysed. Besides, elastic modulus of the ‘globule’ C-S-H is calculated to assess the elastic modulus of C-S-H phases (the low-density C-S-H – LD C-S-H – and the high-density C-S-H – HD C-S-H), where the porosity is a critical factor for explaining the relationship between ‘globule’ C-S-H at nanoscale and C-S-H phases at microscale. Results show that: (1) The C-S-H(I) structure has transformed from crystalline to amorphous during the annealing process, Young’s moduli in x, y and z directions are almost the same. Besides, the extent of aggregation and aggregation path for water molecules in the structure is different in three directions. (2) Young’s modulus of both amorphous C-S-H(I) and C-S-H(II) structures with a size of about 5 nm under strain rate of 10^?3 ps^?1 at 300 K in three directions is averaged to be equal, of which C-S-H(II) structure is about 60.95 GPa thus can be seen as the elastic modulus of the ‘globule’ C-S-H. (3) Based on the ‘globule’ C-S-H, the LD C-S-H and HD C-S-H can be assessed by using the Self-Consistent Scheme (separately 18.11 and 31.45 GPa) and using the Mori–Tanaka scheme (29.78 and 37.71 GPa), which are close to the nanoindentation experiments by Constantinides et al. (21.7 and 29.4 GPa).