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.     

Ultrasonic absorption in aqueous solution of lysozyme.

The titration curve of ultrasonic absorption at 2.82 MHz in aqueous solutions of lysozyme measured by Zana and Lang [J. Phys. Chem., 74 , 2734 (1970)] is theoretically analyzed. The maxima at pH 3 and pH 11 are describable with proton-transfer reactions of dissociable carboxyl and amino groups by assuming that volume changes due to the reactions are 2.3 and 5.2 cm³/mole, respectively, which are appreciably smaller than those of simple amino acids. The remaining, pH-independent excess absorption over solvent is measured at frequencies ranging from 3 to 150 MHz. The absorption is ascribed to the internal loss of protein. The complex compressibility β′_p ? iβ″_p of lysozyme molecule is evaluated as β′_p = 7.2 × 10^?12 cm²/dyne and β″_P = 4.3 × 10^?14 cm²/dyne from the increments over solvent in absorption as well as in sound velocity.     

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.     

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.     

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.     

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.