Phase Transition of a Structure II Cubic Clathrate Hydrate to a Tetragonal Form

The crystal structure and phase transition of cubic structure II (sII) binary clathrate hydrates of methane (CH₄) and propanol are reported from powder X‐ray diffraction measurements. The deformation of host water cages at the cubic–tetragonal phase transition of 2‐propanol+CH₄ hydrate, but not 1‐propanol+CH₄ hydrate, was observed below about 110 K. It is shown that the deformation of the host water cages of 2‐propanol+CH₄ hydrate can be explained by the restriction of the motion of 2‐propanol within the 5¹²6⁴ host water cages. This result provides a low‐temperature structure due to a temperature‐induced symmetry‐lowering transition of clathrate hydrate. This is the first example of a cubic structure of the common clathrate hydrate families at a fixed composition.     

On optimality of two adaptive choices for the parameter of Dai–Liao method

Orthonormal matrices are a class of well-conditioned matrices with the least spectral condition number. Here, at first it is shown that a recently proposed choice for parameter of the Dai–Liao nonlinear conjugate gradient method makes the search direction matrix as close as possible to an orthonormal matrix in the Frobenius norm. Then, conducting a brief singular value analysis, it is shown that another recently proposed choice for the Dai–Liao parameter improves spectral condition number of the search direction matrix. Thus, theoretical justifications of the two choices for the Dai–Liao parameter are enhanced. Finally, some comparative numerical results are reported.     

Pore Aperture Control Toward Size-Exclusion-Based Hydrocarbon Separations

Metal–organic frameworks (MOFs) have been proposed as a promising material for non-thermal chemical separations owing to their high structural diversity and tunability. Here, we report the synthesis of a zinc-based MOF containing a three-dimensional (3D) linker, bicyclo[2.2.2]octane-1,4-dicarboxylic acid, with high thermal stability towards the separation of hexane isomers. The incorporation of the 3D linker enhances the structural stability and provides well-defined pore apertures/channels with sub-Ångstrom precision. This precision allowed for the separation of similarly sized hexane isomers based on subtle differences in their kinetic diameters. Multi-component liquid phase batch experiments confirmed the separation of hexanes mixture into linear, monobranched, and dibranched isomers. This work represents a significant milestone in the construction of stable Zn-based MOFs and the incorporation of 3D linkers as a potential solution to challenging separations.     

Surface Arginine Saturation Effect on Unfolding Reaction of Firefly Luciferase: A Thermodynamic and Kinetic Perspective

Replacement of some hydrophobic solvent‐exposed residues in Lampyris turkestanicus luciferase with arginine increases thermostability of this enzyme. Herein, thermodynamic and kinetic of unfolding reactions of wild type (WT), E354R/356R, E354R/356R‐I232R and E354R/356R‐Q35R/L182R/I232R variants, has been investigated. Fluorescence and Far‐UV circular dichroism measurements using urea as a chemical denaturant indicated that the value of for all variants is greater than that of WT enzyme. Analysis of m‐values, as a measure of difference in the solvent accessible surface area between the native and denatured states of protein, revealed that higher stability of mutants is related to their higher degree of compactness in the folded state. Results of unfolding kinetic experiments showed that all variants have three‐exponential behavior in which they unfolded with three rate constants and corresponding amplitudes. Increasing the rate constants of fast unfolding phase in mutants relative to WT protein may be attributed to more compactness and more kinetic sensitivity of their folded state to urea. However, more population of WT protein was unfolded from fast unfolding phase. Results of this investigation highlight kinetic stability of luciferase via a slow rate of unfolding.     

A molecular dynamics study of ethanol-water hydrogen bonding in binary structure I clathrate hydrate with CO2

Guest-host hydrogen bonding in clathrate hydrates occurs when in addition to the hydrophilic moiety which causes the molecule to form hydrates under high pressure-low temperature conditions, the guests contain a hydrophilic, hydrogen bonding functional group. In the presence of carbon dioxide, ethanol clathrate hydrate has been synthesized with 10% of large structure I (sI) cages occupied by ethanol. In this work, we use molecular dynamics simulations to study hydrogen bonding structure and dynamics in this binary sI clathrate hydrate in the temperature range of 100-250 K. We observe that ethanol forms long-lived (>500 ps) proton-donating and accepting hydrogen bonds with cage water molecules from both hexagonal and pentagonal faces of the large cages while maintaining the general cage integrity of the sI clathrate hydrate. The presence of the nondipolar CO(2) molecules stabilizes the hydrate phase, despite the strong and prevalent alcohol-water hydrogen bonding. The distortions of the large cages from the ideal form, the radial distribution functions of the guest-host interactions, and the ethanol guest dynamics are characterized in this study. In previous work through dielectric and NMR relaxation time studies, single crystal x-ray diffraction, and molecular dynamics simulations we have observed guest-water hydrogen bonding in structure II and structure H clathrate hydrates. The present work extends the observation of hydrogen bonding to structure I hydrates.     

Molecular cloning, expression and sequence analysis of DNA polymerase I from an Iranian thermophilic bacterium, Bacillus sp. G (2006)

Thermostable DNA polymerases are widely used in DNA amplification reactions such as the Polymerase Chain Reaction (PCR), requiring the activity of the enzymes at high temperatures. The aim of the present study was to assess the potential biotechnological capabilities of Iranian thermostable DNA polymerases. To this end, we cloned the gene encoding a DNA polymerase from a novel thermophilic eubacterium, Bacillus sp. G (2006). Phylogentic analysis of this gene revealed that the new isolate belongs to the genera Bacillus. Sequence analysis of the fragment produced by degenerate primers also showed that it consists of 2,631 bp encoding an 876 amino acid protein, and subsequent amino acid sequence analysis of this DNA polymerase showed that it belongs to family A-type DNA polymerases. The expression vector pET28a (+) was chosen for expression of the gene fragment in the mesophilic host bacterium E. coli BL21. This expression vector has some advantages such as attachment of a Poly-His tag to the N-terminus of the protein for the ease of purification and a powerful promoter of lac-Z induced by IPTG. The band corresponding to the protein product was observed in the molecular weight range of about 100KDa on the SDS-PAGE gel after heat and Ni⁺²-NTA column chromatography. Using the dot blot technique, the polymerase activity of the enzyme was qualitatively confirmed at 70 °C. Therefore, it is suggested that optimizations of this activity could make this enzyme appropriate for PCR processes in future.     

A note on the global convergence theorem of the scaled conjugate gradient algorithms proposed by Andrei

In (Andrei, Comput. Optim. Appl. 38:402?C416, 2007), the efficient scaled conjugate gradient algorithm SCALCG is proposed for solving unconstrained optimization problems. However, due to a wrong inequality used in (Andrei, Comput. Optim. Appl. 38:402?C416, 2007) to show the sufficient descent property for the search directions of SCALCG, the proof of Theorem?2, the global convergence theorem of SCALCG, is incorrect. Here, in order to complete the proof of Theorem?2 in (Andrei, Comput. Optim. Appl. 38:402?C416, 2007), we show that the search directions of SCALCG satisfy the sufficient descent condition. It is remarkable that the convergence analyses in (Andrei, Optim. Methods Softw. 22:561?C571, 2007; Eur. J. Oper. Res. 204:410?C420, 2010) should be revised similarly.     

On the sufficient descent property of the Shanno’s conjugate gradient method

Satisfying in the sufficient descent condition is a strength of a conjugate gradient method. Here, it is shown that under the Wolfe line search conditions the search directions generated by the memoryless BFGS conjugate gradient algorithm proposed by Shanno satisfy the sufficient descent condition for uniformly convex functions.     

Molecular-dynamics simulations of binary structure II hydrogen and tetrahydrofurane clathrates

The binary structure II hydrogen and tetrahydrofurane (THF) clathrates are studied with molecular-dynamics simulations. Simulations are done at pressures of 120 and 1.013 bars for temperatures ranging from 100 to 273 K. For the small cages of the structure II unit cell, H2 guest molecule occupancies of 0, 16 (single occupancy), and 32 (double occupancy) are considered. THF occupancies of 0-8 in the large cages are studied. For cases in which THF does not occupy all large cages in a unit cell, the remaining large cages can be occupied with sets of four H2 guest molecules. The unit-cell volumes and configurational energies are compared in the different occupancy cases. Increasing the small cage occupancy leads to an increase in the unit-cell volume and thermal-expansion coefficient. Among simulations with the same small cage occupancy, those with the large cages containing 4H2 guests have the largest volumes. The THF guest molecules have a stabilizing effect on the clathrate and the configurational energy of the unit cell decreases linearly as the THF content increases. For binary THF + H2 clathrates, the substitution of the THF molecules in the large cages with sets of 4H2 molecules increases the configurational energy. For the binary clathrates, various combinations of THF and H2 occupancies have similar configurational energies.