Molecular-dynamics simulations of pyronine 6G and rhodamine 6G dimers in aqueous solution

We have carried out molecular-dynamics (MD) simulations on dimers of the positively charged laser dyes pyronine 6G (P6G) and rhodamine 6G (R6G) in aqueous solution, generating trajectories of 2.5 ns for various computational protocols. We discuss how the choice of atomic partial charges and the length of the trajectories affect the predicted structures of the dimers and compare our results to those of earlier MD-simulations, which were restricted to only 0.7 ns. Our results confirm that monomers of P6G easily undergo relative rotations within the dimer, but we found new conformations of the R6G dimer at longer simulation times. In addition, we analyzed in detail the energy change during the formation of dimers. With suitable corrections, the electrostatic energy from an Ewald treatment agrees with the results from an approach relying on a residue-based cutoff. For P6G, we show that the strong solvent-mediated electrostatic attraction between the monomers is counteracted by an almost equally large solvent-induced entropy contribution to yield a small driving force to dimer formation, in very good agreement with the free-energy change from a thermodynamic-integration procedure. Thus, earlier rationalizations of the dimer formation, based only on energy arguments, yield a qualitatively wrong picture.Electronic Supplementary Material Supplementary material is available for this article at and is accessible for authorized users.     

Removal of rhodamine B from aqueous solution by sorption on Turbinaria conoides (Phaeophyta)

The ability of the brown seaweed, Turbinaria conoides to absorb rhodamine B (RB) from aqueous solution was investigated in a batch system. The effects of various experimental parameters (e.g., morphology, initial dye concentration, temperature, and pH) were investigated and optimal experimental condition was ascertained. The results revealed that sorption capacity of T. conoides increased with increasing temperature, and decreasing initial dye concentration and pH. Sorption equilibrium studies using Langmuir and Freundlich models demonstrated that RB biosorption fitted well to the Langmuir isotherm. This study suggested that T. conoides can be used as a potential biosorbent for the removal of RB from wastewater.     

Feulgen type staining of mammalian tissues with Dahlia-SO2.

The use of the basic dye, Dahlia, which belongs to triphenylmethane group but without a primary amino group in its molecule has been described as useful in the staining of aldehyde groups of acid hydrolysed DNA in tissue sections following the conventional Feulgen procedure. Dahlia-SO2 prepared with sodium hydrosulphite is highly suitable when used at pH 4-0 to 5-0. The absorption characteristics of the stained nuclei indicate on the peak of maximum absorption at 560 nm, whereas, that of the aqueous dye solution is at 590 nm.     

Presence of a protein methylesterase in mammalian tissues.

Using enzymatically methylated protein-³H methyl esters as substrates, a protein methylesterase activity was observed in mammalian tissues. The product of hydrolysis was identified as radioactive methanol by microdistillation under reduced pressure and formation of a 3,5-dinitrobenzoate derivative. The enzyme was active over a broad range of pH and appeared in all tissues investigated. Since protein carboxyl-methylation is involved in chemotaxis of leukocytes and exocytotic secretion, this protein methylesterase probably participates in the regulation of these processes.     

Ozonolytic depolymerization of polysaccharides in aqueous solution.

The selective oxidation of beta-D-glycosidic linkages of polysaccharides by ozone has great utility as a general method for depolymerization of polysaccharides. Here we describe a 'one-step' method whereby polysaccharides dissolved in water or basic solutions are depolymerized by ozonolysis. The oxidation of glycosidic linkages of unprotected carbohydrates by ozone is complicated by several side reactions. We describe here optimized conditions for carrying out ozonolysis degradation. We also characterize the major pathways for unwanted degradation by various side reactions. In the preferred oxidation pathway, the aldosidic linkage is oxidized to an aldonic ester function that hydrolyzes under the basic conditions employed to give a free aldonate, with cleavage of the polysaccharide chain. Nonselective degradation pathways include oxidative degradation by radical species that oxidize glycosyl residues to formic, acetic, and oxalic acids. The nonselective degradation caused by acids is minimized by basic buffers. The products of polysaccharide depolymerization form a size distribution around a nominal molecular weight, and the average molecular weight of the products can be controlled by the rate or amount of ozone passed through the reaction mixture. The ozonolysis method described herein provides a convenient, inexpensive, and controllable means for generating small polysaccharides or large oligosaccharide fragments.     

The interaction of calcium ions with glycocholate micelles in aqueous solution.

The formation of soluble complexes of Ca2+ ions and glycocholate has been demonstrated. The dissociation constant is 26 nmol/litre and a maximum of 2 Ca2+ ions are bound to each glycocholate micelle. The formation of this complex is shown to be reversible. Binding is increased by the introduction of phosphatidylcholine into the micelle; it is decreased by a decrease in pH and by increased counter-ion concentration. The biological significance of these effects is discussed.     

Electron paramagnetic resonance spectra of catalase in mammalian tissues.

The relatively small number of paramagnetic species and the high concentration of catalase in mammalian liver and blood make it possible to directly study this enzyme in frozen whole tissue. The EPR spectra of catalase are dependent on the heme environment and in human blood only catalase A, gxy = 6.48, 5.36 is observed whereas in liver a second spectrum, catalase B, gxy = 6.80, 5.07 can also be seen. Using rapid freeze techniques it has been shown that in rat liver catalase A corresponds to the in vivo steady state and that after death this is largely converted into catalase B. Data from the perfusion of rat livers with oxygenated and deoxygenated blood and dextran solutions together with results from in vitro studies of catalase are interpreted as indicating that catalase B results from the interaction of catalase with an organic acid, most probably formic acid, that the acid is a peroxidative substrate for catalase in vivo and that peroxidation of the acid is not the major role for catalase in rat liver. Catalase binding with other small molecules in intact liver has been demonstrated by perfusion with nitrite-containing dextrans and by intraperitoneal injection of 3-amino-1,2,4-triazole.     

Changes in sulfated mucopolysaccharide composition of mammalian tissues during growth and in cancer tissues.

The distribution of sulfated mucopolysaccharides in different tissues during growth and in cancer tissues is reported. It is shown that most of the tissues of 1 day-old rats and rabbits contain chondroitin sulfate A/C, chondroitin sulfate B and heparan sulfate in about the same proportions, whereas in adult animals chondroitin sulfate A/C decreases in concentration or disappears. Changes in the relative proportions of chondroitin sulfate B and heparan sulfate were also observed in most of the tissues. In rats, these changes occur in the first 25 days of extrauterine development. A great increase of chondroitin sulfate A/C was observed in human tumors of different origins when compared with the normal adjacent tissues. Changes in the relative proportions of chondroitin sulfate B and heparan sulfate were also observed in most of the tumors analysed. The possible role of chondroitin sulfate A/C in cell division is discussed in view of the present findings.     

Species-specific differences in the toxicity of rhodamine 123 towards cultured mammalian cells

The toxicity of cationic fluorescent dye, rhodamine 123, towards a number of independently established cell lines from three different species, namely human, mouse, and Chinese hamster, has been examined. All of the cell lines from any one species that were examined were found to exhibit similar sensitivities towards rhodamine 123 and no appreciable differences were observed between the normal and transformed cell types. However, in comparison to the cells of human origin, mouse and Chinese hamster cell lines exhibited about 10-fold and 70-fold higher resistance, respectively, and these differences appeared to be species related. In contrast to rhodamine 123, no differences in relative toxicities for these cell lines were observed for the structurally related neutral dye, rhodamine B. Fluorescence studies with rhodamine 123 show that in comparison to mouse and Chinese hamster cells, the more sensitive human cells show much higher uptake/binding of the drug, and a good correlation was seen in these studies between the extent of dye uptake/binding and the relative sensitivities of cell lines to rhodamine 123. These results provide evidence that the observed species-related differences in cellular toxicities are due to differences in the cellular uptake/binding of the dye.     

Multiple forms of protein phosphatase inhibitors in mammalian tissues.

The heat-stable inhibitors of phosphorylase phosphatase from rat skeletal muscle, rat liver, beef heart, and beef adrenal cortex were studied. Two major types of inhibitors can be separated from all these tissues by chromatography on DEAE-cellulose. The two types of inhibitors from rat muscle are the same as those reported for rabbit muscle. The type-1 inhibitor, but not the type-2, is regulated by phosphorylation and dephosphorylation reactions. There is also a phosphorylatable inhibitor in beef heart and adrenal cortex, but such an inhibitor could not be demonstrated in liver.     

Spatial configuration of deoxyribotrinucleoside diphosphates in aqueous solution.

The detailed conformational features and dynamics of the naturally occurring deoxyribotrinucleoside diphosphates d-TpTpT and d-TpTpC have been investigated at 20 degrees C and 80 degrees C in aqueous solution by nuclear magnetic resonance spectroscopy. The observed NMR parameters indicate that the conformational properties of the trimers are very similar to those of the constituent dimers and monomers, i.e., the monomers and dimers conserve their intrinsic conformational features when they become incorporated into oligomers. Model building indicate that the distant shieldings can originate from spatial configurations in which the central nucleotidyl unit is bulged out and the w'1w1, w'2w2 occupy /g+g+, g+g+/ domains.     

Gamma-radiolysis of D-glucose in aerated, aqueous solution.

Gamma-Radiolysis of D-glucose in aerated, aqueous solution gives mainly D-glucono-1,5-lactone, D-arabino-hexosulose, and D-ribo-hexos-3-ulose, together with D-xylo-hexos-4-ulose, D-xylo-hexos-5-ulose, and other pentose, tetrose, and triose derivatives as minor products, which were estimated by mass spectrometry of their alditol-d acetates. These hexose derivatives appear to be produced by the decomposition of D-glucose peroxy-radicals which are formed by the reaction of the primary radicals of D-glucose with oxygen. Bond scission of the peroxy-radicals yields triose, tetrose, and pentose. A radiolysis mechanism for the degradation of D-glucose in aerated, aqueous solution is proposed, based on the reaction of several kinds of D-glucose radical with oxygen.     

Photochemical properties of Yt base in aqueous solution.

Photoreactivity of Yt base [I] has been studied in aqueous solution [pH approximately 6] saturated with oxygen. Two photoproducts (II,III], resulting from irradiation at lambda = 253.7 nm and lambda greater than or equal to 290 nm, were isolated and their structures determined. The quantum yield for Yt base disappearance [zeta dis] is 0.002 [lambda = 313 nm]. It was shown that dye-sensitized photooxidation of Yt base in aqueous solution occurs according to a Type I mechanism, as well as with participation of singlet state oxygen. Quantum yields, fluorescence decay times and phosphorescence of Yt base have been also determined.