Growth mechanism of a gas clathrate hydrate from a dilute aqueous gas solution: a molecular dynamics simulation of a three-phase system

A molecular dynamics simulation of a three-phase system including a gas clathrate, liquid water, and a gas was carried out at 298 K and high pressure in order to investigate the growth mechanism of the clathrate from a dilute aqueous gas solution. The simulation indicated that the clathrate grew on interfaces between the clathrate and the liquid water, after transfer of the gas molecules from the gas phase to the interfaces. The results suggest a two-step process for growth: first, gas molecules are arranged at cage sites, and second, H(2)O molecules are ordered near the gas molecules. The results also suggest that only the H(2)O molecules, which are surrounded or sandwiched by the gas molecules, form the stable polygons that constitute the cages of the clathrate. In addition, the growth of the clathrate from a concentrated aqueous gas solution was also simulated, and the results suggested a growth mechanism in which many H(2)O and gas molecules correctively form the structure of the clathrate. The clathrate grown from the concentrated solution contained some empty cages, whereas the formation of empty cages was not observed during the growth from the dilute solution. The results obtained by both simulations are compared with the results of an experimental study, and the growth mechanism of the clathrate in a real system is discussed.     

Monodictyquinone A: a new antimicrobial anthraquinone from a sea urchin-derived fungus Monodictys sp

A new antimicrobial anthraquinone, 1,8-dihydroxy-2-methoxy-6-methylanthraquinone, monodictyquinone A (1), was isolated from a culture of a marine-derived fungus of the genus Monodictys which was isolated from the sea urchin, Anthocidaris crassispina, along with three known compounds, pachybasin (2), chrysophanol (3), and emodin (4).     

Formation of a two-dimensionally well-ordered monolayer of a peptide oligomer by a simple spin-coating process

Oligo(N(6)-carbobenzyloxy-L-lysine) (OCBL) with n = 8 (n is the number-average degree of polymerization) was synthesized by the n-propylamine-catalyzed ring-opening polymerization of N(6)-carbobenzyloxy-L-lysine N-carboxylic anhydride, which was derived from N(6)-carbobenzyloxy-L-lysine. The formation of two-dimensionally well-ordered strip array monolayer films of the OBCL oligopeptide on graphite substrates was first succeeded by a conventional solution spin-coating process. The ordered strip array monolayer structure was characterized in detail by atomic force microscopy, and its assembly mechanism was examined.     

Photocatalytic decomposition of an alkylammonium cation in a Langmuir-Blodgett film of a titania nanosheet

The formation of inorganic-organic hybrid films of a titania nanosheet and an amphiphilic alkylammonium cation has been investigated, and the photocatalytic decomposition of the alkylammonium cation in the film has been pursued. When a solution of the amphiphilic alkylammonium salt (octadecylammonium chloride: ODAH+ Cl-) was spread on an interface between the air and a titania nanosheet suspension, the negatively charged nanosheets were adsorbed onto the floating monolayer of ODAH+ to form a hybrid monolayer. The hybridization was confirmed by pi-A isotherm measurements, atomic force microscopy, and X-ray photoelectron spectroscopy. Multilayered films were fabricated in a layer-by-layer way by transferring the hybrid monolayers onto glass plates. Areas per ODAH+ cation in the films were estimated from the infrared (IR) spectra of the films, but these areas were smaller than those estimated from the pi-A isotherm curves. The orientation of the alkyl chain of ODAH+ in the hybrid film was determined by means of polarized IR spectroscopy. The alkyl chains were tilted 41 +/- 1 degrees and 47 +/- 1 degrees from the surface normal for the films prepared from the 8 and 20 ppm (ppm = mg dm(-3)) suspensions, respectively. Together with X-ray diffraction data of the films, the structure of the hybrid film was discussed. When the films were illuminated with a UV light, the absorption intensities due to the alkyl chain of ODAH+ decreased exponentially, indicating the photocatalytic decomposition of ODAH+ by the titania nanosheets in the films. Deviation from the exponential trend in the decomposition rate was observed in the initial period for the hybrid films prepared from the suspensions at low concentrations. Interestingly, the layered structure of the hybrid film was disturbed significantly after the ODAH+ cations were decomposed.     

Hydrodynamic force on a microparticle approaching a wall in a nanoparticle dispersion: observation of a separation-dependent effective viscosity

Colloid probe atomic force microscopy was used to measure the hydrodynamic force exerted on a 30-μm-diameter silica particle being moved toward or away from a silica plate in aqueous dispersions of 22-nm-diameter silica nanoparticles (6 or 8 vol %). Upon comparing the measured force to predictions made using the well-known expression of Cox and Brenner (Cox, R. G.; Brenner, H. Chem. Eng. Sci.1967, 22, 1753-1777) assuming a constant viscosity equal to that of the bulk dispersion, the measured drag force was found to become significantly less than that predicted at smaller particle-plate separation distances (e.g., <500 nm). A recent theoretical paper by Bhattacharya and Blawzdziewicz (Bhattacharya, S.; Blawzdziewicz, J. J. Chem. Phys.2008, 128, 214704) predicted that in a solution of dispersed nanoparticles the effective viscosity characterizing the hydrodynamic force on the particle should vary from that of the solvent at contact to that of the bulk dispersion at large separations. By adjusting the viscosity in the Cox and Brenner expression to make the predicted hydrodynamic force match that measured (i.e., the effective viscosity), a curve showing these exact characteristics was obtained. The effective viscosity profile was not a function of particle speed, and changes in the effective viscosity extended to separation distances of as large as 2 μm (nearly 100 times the hard diameter of the nanoparticles). These results suggest that in the range of typical colloidal forces (on the order of 100 nm), the dynamics of particle motion in such systems are determined by the viscosity of the solvent and not that of the bulk dispersion.     

Penimethavone A,a flavone from a gorgonian-derived fungus Penicillium chrysogenum

A novel flavone, penimethavone A (1), possessing a rare unique methyl group at ring-B, was isolated from the fungus Penicillium chrysogenum cultured from a gorgonian Carijoa sp. collected from the South China Sea. The structure was elucidated by extensive spectroscopic analysis and by comparison with related known compound. Compound 1 showed selective and moderate cytotoxicity against cervical cancer (HeLa) and rhabdomyosarcoma cell lines with IC₅₀ values of 8.41 and 8.18 μM, respectively.     

Identification of a potent peptide deformylase inhibitor from a rationally designed combinatorial library

Peptide deformylase catalyzes the removal of the N-terminal formyl group from nascent polypeptides during prokaryotic protein synthesis and maturation and is essential for bacterial survival. Its apparent absence from mammalian organisms makes it an attractive target for designing novel antibacterial agents. Based on the substrate specificity of peptide deformylase from Escherichia coli, a focused library of peptide thiols was synthesized on TentaGel resin using a disulfide linkage. Screening of the library against the purified deformylase was carried out in solution phase after the inhibitors were released from the resin with a reducing agent. A potent deformylase inhibitor was obtained from a 750-member library and was further optimized through rational modification into a low nanomolar inhibitor (KI = 15 nM against E. coli deformylase).     

Characterization of TrdL as a 10-hydroxy dehydrogenase and generation of new analogues from a tirandamycin biosynthetic pathway

TrdL, encoding a flavin-dependent oxidoreductase in the tirandamycin gene cluster, was inactivated to afford a ΔtrdL mutant, the fermentation of which yielded a new intermediate, tirandamycin E (5), and an additional early intermediate, tirandamycin F (6), if XAD-16 resin was introduced. TrdL was overexpressed in E. coli, and the protein was shown to efficiently catalyze the transformations from 5 to tirandamycin A (1) and from 6 to tirandamycin D (4), demonstrating its function as a 10-hydroxy dehydrogenase.     

Separation of strontium ions from a simulated highly active liquid waste using a composite of silica-crown ether in a polymer

To partition Sr(II) from highly active liquid waste (HLW), a macroporous silica-based 4,4',(5')-di(t-butylcyclohexano)-18-crown-6 (DtBuCH18C6)-tri-n-butyl phosphate (TBP) polymeric composite, (DtBuCH18C6+TBP)/SiO(2)-P, was synthesized. It was done by impregnation and immobilization of DtBuCH18C6 and TBP into the pores of the SiO(2)-P particles, where DtBuCH18C6 was modified with TBP. The sorption of Sr(II) and some co-existent elements contained in a simulated HLW onto (DtBuCH18C6+TBP)/SiO(2)-P was investigated at 323 K. It was found that in 2.0 M HNO(3), Sr(II) exhibited strong sorption ability and high selectivity over all the tested metals except Ba(II). Chromatographic partitioning of Sr(II) from 2.0 M HNO(3) containing 5 mM of the tested elements was performed by (DtBuCH18C6+TBP)/SiO(2)-P packed column. La(III), Y(III), Na(I), K(I), Cs(I), Ru(III), Mo(VI), and Pd(II) had almost no sorption and flowed into effluent along with 2.0 M HNO(3). Sr(II) adsorbed strongly by (DtBuCH18C6+TBP)/SiO(2)-P was then eluted effectively by water, while Ba(II) flowed into effluent along with Sr(II) due to the similar chemical properties. In addition, the bleeding of total organic carbon in aqueous phase was evaluated. The results demonstrated that in 2.0 M HNO(3), application of the macroporous silica-based DtBuCH18C6 polymeric composite in chromatographic partitioning of Sr(II) from the simulated HLW is feasible.     

Electrospray ionization from a droplet deposited on a surface-modified glass rod

This paper reports development of a non-mechanical electrospray ionization (ESI) method to generate electrospray from a droplet deposited on an optical fiber coated with a thin gold or Nafion film. Modification of the surface of the optical fiber in this manner increases its wettability, such that a droplet of the aqueous sample solution can adhere sufficiently strongly to the tip of the fiber. The aqueous sample solution was deposited near the tip of the fiber with a micropipette. When a high voltage (2,000 V) was applied to the fiber by electrical connection through the gold film, the sample solution moved and hung at the tip of the fiber. Simultaneously, ESI was generated from the sample droplet. Multiply charged peptide and protein ions were detected by connecting the ESI source to a quadrupole mass analyzer.     

Isotachophoresis of beta-blockers in a capillary and on a poly(methyl methacrylate) chip

Analysis of the beta-blockers oxprenolol, atenolol, timolol, propranolol, metoprolol, and acebutolol in human urine by a combination of isotachophoresis (ITP) and zone electrophoresis (ZE) was investigated. Methods were developed with a conventional capillary electrophoresis (CE) apparatus and a poly(methyl methacrylate) (PMMA) microchip system. With CE the separation of oxprenolol, atenolol, timolol, and acebutolol from a standard solution containing 5 microg/mL of each compound was accomplished by performing ZE with transient ITP. The electrolyte system consisted of 10 mM sodium morpholinoethane sulfonate (pH 5.5) and 0.1% methylhydroxyethylcellulose as the leading electrolyte and 30 mM ortho-phosphoric acid (pH 2.0) as both the terminating and the ZE background electrolyte. With the microchip system the separation of oxprenolol and acebutolol from a standard solution containing 10 microg/mL of each compound was accomplished by a coupled-channel ITP-ZE device using the same leading electrolyte solution as the CE system but 5 mM glutamic acid (pH 3.4) as terminating and background electrolytes. The systems were used for analyses of patient urine samples. Water-soluble hydrophilic matrix compounds were removed from the urine samples by solid-phase extraction (SPE). Limits of quantification below 5 microg/mL could be achieved. The PMMA ITP-ZE chip has not earlier been used for analyses of any drugs from urine samples.     

Synthesis of a core trisaccharide as a versatile building block for N-glycans and glycoconjugates

N-linked oligosaccharides from glycoproteins (N-glycans) can be conveniently assembled with a building block approach. A protected form of the core trisaccharide (beta-mannosyl chitobiose) was identified as a key building block. The chitobiose part of the core trisaccharide was built from a glycosyl fluoride, which served as a precursor for the reducing GlcNAc azide and the inner GlcNAc moiety. Beta-mannosylation was accomplished at the trisaccharide stage by intramolecular inversion of a beta-glucosyl chitobiose. The benzylidene protection of the beta-mannoside and the azido group at the reducing end of the core trisaccharide allow modular synthesis of N-glycans and their glycoconjugates.     

Assembly of a supramolecular capsule on a molecular printboard

A molecular capsule based on ionic interactions between two oppositely charged calix[4]arenes, 1 and 2, was assembled both in solution and on a surface. In solution, the formation of the equimolar assembly 1.2 was studied by (1)H NMR, ESI-MS, and isothermal titration calorimetry, giving an association constant (K(a)) of 7.5 x 10(5) M(-1). A beta-cyclodextrin self-assembled monolayer (beta-CD SAM) on gold was used as a molecular printboard to anchor the tetraguanidinium calix[4]arene (2). The binding of tetrasulfonate calix[4]arene 1 was monitored by surface plasmon resonance spectroscopy. Rinsing of the surface with a high ionic strength aqueous solution allows the removal of the tetrasulfonate calix[4]arene (1), while by rinsing with 2-propanol it is possible to achieve the complete desorption of the tetraguanidinium calix[4]arene (2) from the beta-CD SAM. The K(a) for the capsule formation on a surface is 3.5 x 10(6) M(-1), thus comparing well with the K(a) determined in solution.     

Studies of dynamic interactions between a pyrene-labeled polyelectrolyte and an oppositely charged rodlike micelle by a fluorescence quenching technique with use of a hydrophobic quencher

Electrostatic interactions of poly(sodium 2-(acrylamido)-2-methylpropanesulfonate) (PyPAMPS) labeled with pyrene and a rodlike micelle of dimethyloleylamine oxide (DMOAO), an amine oxide type surfactant, mixed with varying mole fractions (Y) of hexadecyltrimethylammonium chloride (CTAC), a cationic surfactant, were investigated by a fluorescence quenching technique using 3,4'-dimethylbenzophenone (DBP), a hydrophobic quencher, that can only reside in the micellar phase. Fluorescence measurements were performed under homogeneous conditions in the region 0Yc, the fluorescence was efficiently quenched by DBP-carrying DMOAO/CTAC mixed micelles, both steady-state and time-dependent fluorescence data indicating that the degree of the quenching and hence the extent of the complex formation increased significantly with increasing Y. Applying a kinetic model to the steady-state and time-dependent fluorescence data, the residence time for PyPAMPS in the polymer-micelle complex was calculated. The residence time was found to depend on both Y and mu, e.g., when Y was increased from 0.01 to 0.03, the residence time increased from 4 to 80 mus at mu=0.05 whereas little or no increase in the residence time was observed in this range of Y at mu=0.20. At this higher ionic strength, the residence time increased only moderately from 3 to 10 mus when Y was increased from 0.01 to 0.09.     

Structure of salvioccidentalin, a diterpenoid with a rearranged neo-clerodane skeleton from Salvia occidentalis

From the aerial parts of Salvia occidentalis (Labiatae) a new diterpenoid with a rearranged neo-clerodane skeleton was isolated. This new compound was named salvioccidentalin and its structure was established by spectroscopic means. A probable biogenetic relationship with salvigenolide from S. fulgens and salvileucalin A and spiroleucantholide from Salvia leucantha is proposed.     

Iriomoteolide-3a, a cytotoxic 15-membered macrolide from a marine dinoflagellate amphidinium species

A 15-membered macrolide, iriomoteolide-3a (1), with an allyl epoxide has been isolated from a marine benthic dinoflagellate Amphidinium sp. (strain HYA024), and the structure was assigned by detailed analyses of 2D NMR data. Relative and absolute configurations were elucidated on the basis of conformational studies of 1 and its acetonide (2) and modified Mosher's method of 1, respectively. Iriomoteolide-3a (1) and the acetonide (2) exhibited potently cytotoxic activity against antitumor cells.     

Molecular dynamics study on the interaction of a mithramycin dimer with a decanucleotide duplex

The complex of a minor groove binding drug mithramycin (MTR) and the self-complementary d(TAGCTAGCTA) 10-mer duplex was investigated by molecular dynamics (MD) simulations using the AMBER 7.0 suite of programs. There is one disaccharide and trisaccharide segment projecting from opposite ends of an aglycone chromophore of MTR. A MTR dimer complex (MTR)2Mg2+ is formed in the presence of a coordinated ion Mg2+. A NMR solution structure of two (MTR)2Mg2+ complexes bound with one DNA duplex, namely, the 2:1 duplex complex, was taken as the starting structure for the MD simulation. The partial charge on each atom was calculated using the multiple-RESP fitting procedure, and all of the missing parameters in the Parm99 force field used were adapted comparably from the literature. The length of the MD simulation was 5 ns, and the binding free energy for the formation of a 1:1 or 2:1 duplex complex was determined from the last 4 ns of the simulation. The binding free energies were decomposed to components of the contributions from different energy types, and the changes in the helical parameters of the bound DNA duplex plus the glycosidic linkages between sugar residues of the bound MTR dimer were determined. It was found that binding of the first (MTR)2Mg2+ complex with the DNA duplex to form a 1:1 duplex complex does not cause stiffening of the duplex especially in the unoccupied site of the duplex. However, the overall flexibility of the DNA duplex is reduced substantially once the second (MTR)2Mg2+ complex is bound with the unoccupied site to form the 2:1 duplex complex. The van der Waals interactions were found to be dominant in the central part of the DNA duplex where sugar residues from each bound (MTR)2Mg2+ complex were inwardly pointing and the corresponding minor groove was widened.     

Chemical fractionation of a fly ash sample by a sequential leaching method

A five-stage sequential leaching procedure was optimized for the analysis of the fly ash sample, CW6, as a candidate reference material. The distribution of particulate elements was achieved for Cd, Cr, Cu, Pb, Zn, and V into different fractions: (1) exchangeable, (2) bound to carbonate, (3) bound to Fe/Mn oxides, (4) bound to sulfide compounds, and (5) acid soluble, residual fraction. The leachability of the metals proved to be different, so various distribution patterns have been achieved. The results of the total elemental analysis and the sequential leaching method were compared and a good agreement was found. The uncertainty of the leaching method is reasonable, even when experimental parameters are strictly fixed and the analysis is quite tedious. The ratio of environmentally mobile fractions was compared to that from the conventional test method and a reasonable conformity has been found. This characterization method can be used to interpret the leaching behavior of element species and mode of binding to the matrix. Using the optimized sequential procedure, a new aspect can be interpreted to understand the behavior of toxic elements released from fly ashes into nature.