Parametrization of calcium binding site in proteins and molecular dynamics simulation on phospholipase A2

The empirical energy parameters for a calcium ion and its ligands in proteins were determined within a pairwise additive framework. The interaction energies of Ca²⁺-water, Ca²⁺-peptide group and Ca²⁺-carboxyl group systems were calculated using the ab initio molecular orbital method with basis sets of double zeta quality including polarization or diffuse functions. The resulting potential energy surfaces served as references for the determination of the nonbonded parameters in the empirical energy function. The nonadditive corrections for the Ca²⁺-ligand pair potentials are incorporated implicitly in the nonbonded paremeters by treating three-body (1:2 complex) or seven-body (1:6 complex) systems in reference calculations. Ligand polarizations induced by Ca²⁺ are estimated from the partial atomic charges of two-body (1:1 complex) systems. The charge sets were determined by scaling so as to reproduce the reference potential energy surfaces. The newly determined parameter set was used in a stochastic boundary molecular dynamics simulation of phospholipase A₂. The solvated structure of the Ca²⁺-binding site obtained from an X-ray crystallographic study is well reproduced by the parameter set.     

Radiative melting of a horizontal clear ice layer

In this paper the horizontal layer of clear ice sticking to the substrate is melted by comparatively short wave radiation similar to solar radiation for the purpose of removing ice from the surface of the material subject to atmospheric icing. The radiating source used for melting is 300 wattages halogen lamps whose color temperature is 3200K at 100 voltages. From the present investigation, a typical phenomenon of backmelting is observed clearly and it can be found that the predicted results including the melting rate of upper and lower layers which are melted by radiant energy impinged on or penetrated the ice layer are in good agreement with the experimental results.

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Aufschmelzen einer waagerechten Klareisschicht durch Strahlung

Zusammenfassung Eine waagerechte Klareisschicht, die auf einer Unterlage aufgefroren war, wurde durch kurzwellige Strahlung, Ähnlich der Sonnenstrahlung, zum Schmelzen gebracht, um die Entfernung von Eis nach atmosphÄrischer Vereisung zu untersuchen. Die Strahlungsquelle war eine 300 Watt-Halogenlampe mit einer Farbtemperatur von 3200 Kelvin bei 100 Volt. Als typische Erscheinung wurde ein Rückseiten-Schmelzen gefunden, im übrigen sind die vorausberechneten Schmelzraten an der Ober- und der Unterseite durch aufgenommene oder durchgelassene Strahlungsenergie in guter übereinstimmung mit den Messungen.

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Nomenclature a_v monochromatic absorption coefficient - A transmission (= q _r ⁺ {h_i}/q_ro) - c_p specific heat - E_bv monochromatic emissive power - h_D mass transfer coefficient - h_i initial thickness of ice layer - h_m thickness of substrate - L_i latent heat of melting - L_w latent heat of evaporation or condensation - heat flux absorbed at surface of substrate - q_r0 radiant heat flux impinged onto ice or free surface - q _r ⁺ {y} forward radiant heat flux - q _r ^– {y} backward radiant heat flux - S₁ thickness of upper melt layer - S₂ thickness of lower melt layer - S'₂ distance from free surface to bottom surface of ice layer - t time - T temperature - T₁ temperature of air-water or air-ice interface - T₂ temperature of substrate surface - T₃ temperature of back side surface of substrate - T_b temperature of radiating source - T_i temperature in ice layer - T_w1 temperature in upper melt layer - T_w2 temperature in lower melt layer - T environmental temperature - W_w saturated vapor concentration at free surface - W_t8 vapor concentration at environment - y distance from free or ice surface - y grid size of water or ice - y_m grid size of substrate Greek symbols heat transfer coefficient - spectral absorptivity - _t total absorptivity - _i thermal diffusivity of ice - _m thermal diffusivity of substrate - _w thermal diffusivity of water - _i thermal conductivity of ice - _m thermal conductivity of substrate - _w thermal conductivity of water - wavelength - _av densitiy of air-vapor mixture - _i density of ice - Stefan-Boltzman constant     

Radiative melting of ice layer adhering to a vertical surface

This paper is concerned with melting of a vertical ice layer adhering to the substrate by using radiating heat source of halogen lamps having a large fraction of short wave beam or nichrome heater having a comparatively large fraction of long wave one. From the present experimental results, it can be seen that the heating of short wave radiation produces a peculiar melting behavior of strongly rough melting-surface due to the internal melting at the grain boundary of ice-surface. On the other hand, for the case of long wave radiation the melting-surface becomes very smooth. The melting rate of clear ice layer by short wave radiation obtained from halogen lamps is smaller than that of cloudy ice layer due to the good penetration of short wave fraction through the clear ice layer. Moreover, the raising of temperature of ice-substrate interface could offer a feasibility of removing ice layer from the structure subject to atmospheric icing. Concludingly, it is clarified that the melting rate of ice layer could be predicted numerically by using the band model of extinction coefficient or absorption coefficient presented in this study.

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Schmelzen einer Eisschicht an einer senkrechten Wand durch Strahlung

Zusammenfassung Diese Arbeit behandelt das Schmelzen einer senkrechten Eisschicht auf einer Unterlage mit Hilfe von Halogen-Lampen mit einem hohen Anteil an kurzen Wellen und Nichromheizern mit einem hohen Anteil an langen Wellen. Aus diesen Versuchen läßt sich ableiten, daß die Heizung durch kurzwellige Strahlung ein eigentümliches Schmelzverhalten mit sehr rauher Oberfläche hervorruft, verursacht durch Schmelzen an den Korngrenzen der Eisoberfläche. Bei langwelliger Heizung wird die Oberfläche sehr glatt. Die Abschmelzrate einer Klareisschicht bei kurzwelliger Heizung durch Halogen-Lampen ist geringer als die einer Opaleisschicht wegen des besseren Eindringens der kurzen Wellen in das klare Eis. Der Temperaturanstieg an der Grenze Eis — Unterlage bietet die Möglichkeit der Enteisung von Bauteilen, die der atmosphärischen Vereisung ausgesetzt sind. Es folgt, daß die Abschmelzrate einer Eisschicht, numerisch vorausberechnet werden kann, indem man das Bandmodell des Extinktions- und des Absorptionskoeffizienten dieser Arbeit verwendet.

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Nomenclature A transmission, defined in equation (4) - a monochromatic absorption coefficient of clear ice - C constant - E_b monochromatic emissive power - h_i thickness of ice layer - h_in initial thickness of ice layer - h_m thickness of substrate - k₀ extinction coefficient for h₀ 0 - k_s modified extinction coefficient - k monochromatic extinction coefficient - L_i latent heat of melting - n index number, defined in equation (2) - heat flux absorbed at surface of substrate - q_r0 radiant heat flux impinged onto ices-urface - q_ri{y} radiant heat flux in ice layer - S distance from initial ice-surface to transient melting-surface - T_b temperature of radiating heat source - T_i temperature in ice layer - T_m temperature in substrate - T environmental temperature - T₁ temperature of surface of ice layer - T₂ temperature of substrate-surface - T₃ temperature of back side surface of substrate - t time - y distance from initial ice-surface - Z ratio of backward radiative heat flux to forward one for cloudy ice Greek Symbols heat transfer coefficient - _i thermal diffusivity of ice - _m thermal diffusivity of substrate - _i thermal conductivity of ice - _m thermal conductivity of substrate - wavelength - _c critical wavelength - _i density of ice - Stefan-Boltzmann constant     

Freezing limit of water in a closed circular tube

This paper is concerned with the freezing of water in a closed metal tube by regarding the effect of volumetric change of water which is closely related with solidification. The pressure of unfrozen water in the tube increases gradually with increasing frozen layer, consequently the freezing temperature of the water decreases monotonically. It is found from the present results that the freezing limit of water corresponding to the cease of freezing caused by no temperature difference between environmental temperature and freezing point would exist. This remarkable phenomena are mainly attributed to the combined effect of environmental temperature and inner diameter of the tube.     

A Triphenylamine with Two Phenoxy Radicals Having Unusual Bonding Patterns and a Closed‐Shell Electronic State

Reported herein is the structure and the electronic properties of a novel triphenylamine derivative having two phenoxy radicals appended to the amino nitrogen atom. X‐ray single crystal analysis and the magnetic resonance measurements demonstrates the unexpected closed‐shell electronic structure, even at room temperature, of the molecule and two unusual C? N bonds with multiple‐bond character. The theoretical calculations support the experimentally determined molecular geometry with the closed‐shell electronic structure, and predicted a small HOMO–LUMO gap originating from the nonbonding character of the HOMO. The optical and electrochemical measurements show that the molecule has a remarkably small HOMO–LUMO gap compared with its triphenylamine precursor.     

Thermally Tunable Hydrogels Displaying Angle‐Independent Structural Colors

We report the preparation of thermally tunable hydrogels displaying angle‐independent structural colors. The porous structures were formed with short‐range order using colloidal amorphous array templates and a small amount of carbon black (CB). The resultant porous hydrogels prepared using colloidal amorphous arrays without CB appeared white, whereas the hydrogels with CB revealed bright structural colors. The brightly colored hydrogels rapidly changed hues in a reversible manner, and the hues varied widely depending on the water temperature. Moreover, the structural colors were angle‐independent under diffusive lighting because of the isotropic nanostructure generated from the colloidal amorphous arrays.     

Heat transfer from the heated concave wall of a return bend with rectangular cross section

The characteristics of the turbulent heat transfer along the heated concave walls of return bends which have rectangular cross sections with large aspect ratio have been examined for various clearances of the ducts in detail. The experiments are carried out under the condition that the concave walls are heated at constant heat flux while the convex walls are insulated. Water as the working fluid is utilized. Using three kinds of clearance of 9, 34, and 55 mm, the Reynolds number in the turbulent range are varied from 5×10³ to 8×10⁴ with the Prandtl numbers ranging from 4 to 13. As a result it is elucidated that both the mean and the local Nusselt numbers are always greater than those for the straight parallel plates or for the straight duct, respectively. This is attributed to Görtier vortices, which are visualized here. It is also found that the more the clearance increases, the more both the local and the mean Nusselt numbers increase. Correlation equations for the mean and the local Nusselt numbers are determined in the range of parameters covered. Introducing the Richardson number, it appears that the local Nusselt number,Nu _x , may be described as the following equation:Nu _x =447.745 ·Re _x ^1.497 ·De _x ^?1.596 ·F ^0.960 ·Pr ^0.412     

Metabolomic investigation of cholestasis in a rat model using ultra-performance liquid chromatography/tandem mass spectrometry

Metabolomics follows the changes in concentrations of endogenous metabolites, which may reflect various disease states as well as systemic responses to environmental, therapeutic, or genetic interventions. In this study, we applied metabolomic approaches to monitor dynamic changes in plasma and urine metabolites, and compared these metabolite profiles in Eisai hyperbilirubinemic rats (EHBR, an animal model of cholestasis) with those in the parent strain of EHBR - Sprague-Dawley (SD) rats - in order to characterize cholestasis pathophysiologically. Ultra-performance liquid chromatography/tandem mass spectrometry-based analytical methods were used to assay metabolite levels. More than 250 metabolites were detected in both plasma and urine, and metabolite profiles of EHBR differed from those of SD rats. The levels of antioxidative and cytoprotective metabolites, taurine and hypotaurine, were markedly increased in urine of EHBR. The levels of many bile acids were also elevated in plasma and urine of EHBR, but the extent of elevation depended on the particular bile acid. The levels of cytoprotective ursodeoxycholic acid and its conjugates were markedly elevated, while that of cytotoxic chenodeoxycholic acid remained unchanged, suggesting the balance of bile acids had shifted resulting in decreased toxicity. In EHBR, reduced biliary excretion leads to increased systemic exposure to harmful compounds including some endogenous metabolites. Our metabolomic data suggest that mechanisms exist in EHBR that compensate for cholestasis-related damage.     

Rapid determination of fumagillin residues in honey by liquid chromatography-tandem mass spectrometry using the QuEChERS method

A new, rapid, and efficient method for determining the fumagillin residues in honey was developed. The samples extracted were analyzed using LC/MS/MS. Chromatographic separation of fumagillin was performed in gradient mode on a C8 column (100 x 2.0 mm, 5 microm) at 40 degrees C. The mobile phase consisted of a mixture of 2 mM ammonium formate-0.01% formic acid solution and methanol; the flow rate was set to 0.2 mL/min. Under these conditions, it was possible to measure fumagillin and its isomers as a single peak. The sample preparation procedure used is based on the QuEChERS (quick, easy, cheap, effective, rugged, and safe) method, which is fast (approximately 30 min) and uses less organic solvent. The fumagillin was extracted with acetonitrile containing 0.1% formic acid, then purified using a solid-phase extraction method with an Oasis mixed-mode weak anion-exchange cartridge. The overall recovery of fumagillin ranged from 88.1 to 99.4%; the intra- and interassay CVs were <4.5% and <4.9%, respectively. The LOQ was 0.1 microg/kg. LC/MS/MS coupled with the QuEChERS method showed strong potential as a method for determining fumagillin residues in honey.     

Synthesis and structure of dawson polyoxometalate-based, multifunctional, inorganic-organic hybrid compounds: organogermyl complexes with one terminal functional group and organosilyl analogues with two terminal functional groups

Four novel multifunctional polyoxometalate (POM)-based inorganic-organic hybrid compounds, [α(2)-P(2)W(17)O(61){(RGe)}](7-) (Ge-1, R(1) = HOOC(CH(2))(2(-)) and Ge-2, R(2) = H(2)C═CHCH(2(-))) and [α(2)-P(2)W(17)O(61){(RSi)(2)O}](6-) (Si-1, R(1) and Si-2, R(2)), were prepared by incorporating organic chains having terminal functional groups (carboxylic acid and allyl groups) into monolacunary site of Dawson polyoxoanion [α(2)-P(2)W(17)O(61)](10-). In these POMs, new modification of the terminal functional groups was attained by introducing organogermyl and organosilyl groups. Dimethylammonium salts of the organogermyl complexes, (Me(2)NH(2))(7)[α(2)-P(2)W(17)O(61)(R(1)Ge)]·H(2)O MeN-Ge-1 and (Me(2)NH(2))(7)[α(2)-P(2)W(17)O(61)(R(2)Ge)]·4H(2)O MeN-Ge-2, were obtained as analytically pure crystals, in 22.8% and 55.3% yields, respectively, by stoichiometric reactions of [α(2)-P(2)W(17)O(61)](10-) with separately prepared Cl(3)GeC(2)H(4)COOH in water, and H(2)C═CHCH(2)GeCl(3) in a solvent mixture of water/acetonitrile. Synthesis and X-ray structure analysis of the Dawson POM-based organogermyl complexes were first successful. Dimethylammonium salts of the corresponding organosilyl complexes, (Me(2)NH(2))(6)[α(2)-P(2)W(17)O(61){(R(1)Si)(2)O}]·4H(2)O MeN-Si-1 and (Me(2)NH(2))(6)[α(2)-P(2)W(17)O(61){(R(2)Si)(2)O}]·6H(2)O MeN-Si-2, were also obtained as analytically pure crystalline crystals, in 17.1% and 63.5% yields, respectively, by stoichiometric reactions of [α(2)-P(2)W(17)O(61)](10-) with NaOOC(CH(2))(2)Si(OH)(2)(ONa) and H(2)C═CHCH(2)Si(OEt)(3). These complexes were characterized by elemental analysis, thermogravimetric and differential thermal analyses (TG/DTA), FTIR, solid-state ((31)P) and solution ((31)P, (1)H, and (13)C) NMR, and X-ray crystallography.