Epimerization of Alanyl-Alanine Induced by γ-Rays Irradiation in Aqueous Solutions

Living organisms have homochiral L-amino acids in proteins and homochiral D-mononucleotides in nucleic acids. The chemical evolutionary process to protein homochirality has been discussed for many years. Although many scenarios have been proposed for homochirality in the monomeric compounds, homochirality in amino acids and mononucleotides does not always guarantee homochirality in polypeptides and polynucleotides. Integrated scenarios containing the pathways from monomer to polymer should be proposed because in the pathways oligomers and polymers as well as monomers racemize (or epimerize), degrade, and condense. This research addresses epimerization and degradation of dipeptides under γ-rays irradiation by a cobalt-60 (⁶⁰Co) radiation source. The different rate constants of epimerization between diastereomeric dipeptides in the research suggest that the potential pathway toward homochirality could be much more complex.     

Does Dimeric Melittin Occur in Aqueous Solutions?

Melittin, a peptide from bee venom, is known to undergo a monomer / tetramer conversion in aqueous solutions. We have studied the possible participation of dimers in the association equilibrium of melittin by sedimentation equilibrium experiments in the analytical ultracentrifuge and subsequent mathematical analysis of the concentration distributions obtained. It was found that the dimeric state is not significantly populated, the contribution of dimer to the total peptide weight probably being below 0.5%.     

Structure of microbial communities performing the simultaneous reduction of Fe(II)EDTA.NO2−and Fe(III)EDTA−

BioDeNOx is a combined physicochemical and biological process for the removal of nitrogen oxides (NOx) from flue gas. In the present study, two anaerobic bioreactors performing BioDeNOx were run consecutively (RUN-1 and RUN-2) at a dilution rate of 0.01 h⁻¹ with Fe(II)EDTA.NO²⁻ and Fe(III)EDTA⁻ as electron acceptors and ethanol as electron donor. The measured protein concentration of the reactor biomass of both runs was 120 mg/l. Different molecular methods were used to determine the identity and abundance of the bacterial populations in both bioreactors. Bacillus azotoformans strain KT-1 was recognized as a key player in Fe(II)EDTA.NO²⁻ reduction. PCR-denaturing gradient gel electrophoresis analysis of the reactor biomass showed a greater diversity in RUN-2 than in RUN-1. Enrichments of Fe(II)EDTA.NO²⁻ and Fe(III)EDTA⁻ reducers and activity assays were conducted using the biomass from RUN-2 as an inoculum. The results on substrate turnover, overall microbial diversity, and enrichments and finally activity assays confirmed that ethanol was used as electron donor for Fe(II)EDTA.NO²⁻ reduction. In addition, the Fe(III)EDTA⁻ reduction rate of the microbial community proved to be feasible enough to run the bioreactors, ruling out the chemical reduction of Fe(III)EDTA⁻ with sulfide as was proposed by other researchers.     

Relative Reactivity of Ribosyl 2′-OH vs. 3′-OH in Concentrated Aqueous Solutions of Phosphoimidazolide Activated Nucleotides

Phosphoimidazolide activated ribomononucleotides (*pN, see structure) are useful substrates for the non-enzymatic synthesis of oligonucleotides. In the presence of metal ions, aqueous solutions of *pN yield primarily the two internucleotide-linked (pN^2'pN and pN^3'pN) and the pyrophosphate-linked (N^5'ppN) dimers. Small amounts of cyclic dimers and higher oligomers are also produced. In this study the relative reactivity of 2-OH vs. 3-OH was determined from the ratio of the yields of pN^2'pN vs. pN^3'pN. Experiments were performed at 23 °C in the range 7.2 pH 8.4 with substrates that differ in nucleobase (guanosine (G), cytidine (C), uridine (U), and adenosine (A)) and leaving group (imidazole (Im), 2-methylimidazole (2-MeIm) and 2,4-dimethylimidazole (2,4-diMeIm)). Two metal ions (Mg²⁺ or Mn²⁺) were employed as catalysts. The conditions used here, i.e. a substrate concentration in the range 0.1 M to 1.0 M and metal ion concentration in the range 0.05 M to 0.2 M, favor base-stacking interactions. The ratio pN^2'pN: pN^3'pN = 2-5: 3-5 was found independent of nucleobase and typically varied between 2 to 3 indicating that the 2-OH is about 2 to 3 times more reactive than the 3-OH. *pN with Im, compared to 2-MeIm and 2,4-diMeIm leaving group, produce lower yields of internucleotide linked dimers, and a higher pN^2'pN: pN^3'pN ratio. Trends in the data, observed with all three leaving groups, suggest an increase in pN^2'pN: pN^3'pN ratio with decreasing substrate concentration (up to 5.47 with 0.051 M ImpG). The observations are in accord with earlier studies reporting a relative reactivity 2'-5': 3'-5'= 6 to 9 obtained with Im as the leaving group, in dilute nucleotide solutions and under conditions that disfavor stacking. It is speculated that the concentration induced change in the relative reactivity is the result of self-association via base-stacking that enhances selectively the proximity of the 3-OH of one molecule to the reactive P-N bond of an other molecule. The implication of these conclusions for oligomerization/ligation reactions is discussed.     

Polymerization of β-amino Acids in Aqueous Solution

We have compared carbonyl diimidazole (CDI) and 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide (EDAC) as activating agents for the oligomerization of negatively-charged - and -amino acids in homogeneous aqueous solution. -Amino acids can be oligomerized efficiently using CDI, but not by EDAC. -Amino acids can be oligomerized efficiently using EDAC, but not by CDI. Aspartic acid, an - and -dicarboxylic acid is oligomerized efficiently by both reagents. These results are explained in terms of the mechanisms of the reactions, and their relevance to prebiotic chemistry is discussed.     

Solid–Liquid Equilibrium of Maltitol Aqueous Solutions—Implications on the Crystallization Behavior and Process

The solubility of maltitol in pure water and industrial syrup was measured in a temperature range from 10 to 90 °C. Maltitol is highly soluble in water, and this yields high viscosity values for the saturated aqueous solutions at different temperatures. In addition, solubility of maltitol in ethanol/water mixtures was followed at 30, 35, 45, and 55 °C. Results show that maltitol solubility is highly dependent on water content in the solvent mixture. Moreover, it increases monotonically with temperature. The logarithm of viscosity changes linearly against the mole fraction of maltitol in the aqueous solutions up to saturation. The saturated solutions showed a Newtonian behavior in a temperature range from 20 to 90 °C. Maltitol is also characterized in supersaturated solutions by a narrow metastable zone, which slightly increases as temperature is raised. The density of aqueous solutions of maltitol was measured as a function of molality up to saturation at 20 °C, and results show that density can be correlated with concentration according to a linear relation. The obtained results were used to explain maltitol crystallization, which exhibits a high nucleation rate and a slow growth leading to small size crystals.     

Radiation-induced Ring Cleavage of β-Cyclodextrin in Oxygen-free Aqueous Solution

The degraded products of β-cyclodextrin (β-CD) by γ-irradiation in aqueous solution were identified as six oligosaccharides, such as glucose, maltose, maltotriose, maltotetraose, malto-pentaose and maltohexaose, by the gel-filtration method on Biogel P-2 at 60°C. Analysis of the hyperfine structure of the ESR spectrum observed in the oxidation of β-CD with Ti³⁺-hydrogen peroxide system indicated that a radical was formed mainly by hydrogen abstraction at C-5 of a glucose residue. A mechanism of the ring cleavage of β-CD by γ-irradiation in oxygen-free aqueous solution was proposed.     

Decomposition Pathways of p-Bromophenol on γ-Irradiation in Aqueous Systems

In order to elucidate the radiolysis mechanism of p-bromophenol, quantitative determination of the radiolysis products was carried out by gas chromatography and polarography. G(?p · BP) and G(Br^?) were 3.86 and 2.58 at neutral pH, and 1.09 and 0.26 at pH 1.0, respectively, This, together with the radical scavenger effects indicated that hydrated electrons contribute principally to the degradation of p-bromophenol through debromination, followed by the formation of dimer and trimer products by phenylation of the resulting p-hydroxyphenyl radical. This chain-like reaction may cause the difference (G-value = 1.28) between G(?p· BP) and G(Br^?). The contribution of OH radicals to G(?p· BP) is known to be small as compared with other aromatic compounds, because of the poor yield of hydroxylated products such as hydroquinone, 4-bromocatechol and 4-bromoresorcinol.     

Hydration of Cytidine, 2′-Deoxycytidine and their Phosphate Salts in the Aqueous Solutions. A Molecular Dynamics Computer Simulation Study

Abstract

To compare the hydration pattern of the cytidine (Cyd) and 2′-deoxycytidine (dCyd) in the aqueous solutions at the level of microscopic interactions, Molecular Dynamics (MD) computer simulations have been undertaken. The results indicate that the hydration of the heterocyclic base moiety in cytidine and 2′-deoxycytidine has a hydrophobic character. None of the three potential Watson—;Crick base pair centres hydrogen bonds with the water molecules and the formation of something akin to a clathrate cage structure of water around base moieties of nucleosides in the aqueous solution is suggested. In contrast, the hydration of Cyd and dCyd sugar moieties shows a hydrophilic character and the three-dimensional networks of H-bonds involving all hydrophilic centres are formed differently around the ribose and 2′-deoxyribose. The sugar hydroxyl groups participate in the hydrogen bonding with water both as H-donor and as H-acceptor. Their donor-acceptor abilities have been evaluated and compared. The coordination numbers, the geometrical data of the first hydration shell, and the number of hydrogen bonds have been calculated. The changes in the pattern of hydration with the increased concentration of nucleosides and upon nucleoside protonation are discussed. The analysis of the pairwise interaction energies are also presented.     

Reductive Coupling of Aldehydes by H2S in Aqueous Solutions,a C?C Bond Forming Reaction of Prebiotic Interest

We report here a novel reductive coupling reaction of conjugated, non‐ or poorly enolizable aldehydes induced by H₂S and operative in aqueous solutions under prebiotically relevant conditions. This reaction leads from retinal to β‐carotene, and from benzylic aldehydes to the corresponding diarylethylenes. This novel reaction also opens a new potentially prebiotic pathway leading from glyoxylic acid to various compounds that are involved in the reductive tricarboxylic acid cycle. This C? C bond forming reaction of prebiotic interest might have been operative, notably, in the sulfide‐rich environments of hydrothermal vents, which have been postulated as possible sites for the first steps of organic chemical evolution.     

System X c − Antiporter Inhibitors: Azo-Linked Amino-Naphthyl-Sulfonate Analogues of Sulfasalazine

Neurochemical Research - The cystine/glutamate antiporter system x c ? (Sx c ? ) mediates the exchange of intracellular l-glutamate (l-Glu) with extracellular l-cystine (l-Cys2). Both...     

Recovery of β-Galactosidase from E. Coli Double Lysogen Using Aqueous Two Phase System

An aqueous two phase system (ATPS) was employed to recover -galactosidase from the lytic broth of the phage double lysogen system, where production of an intracellular product and cell disruption are carried out sequentially in a container. Partition of -galactosidase was more favorable to PEG phase comparing to total proteins, which was enhanced with Na₂SO₄. Recovery of -galactosidase was more than 90% in most cases, which was much more the recovery of total proteins.     

Secretion of HCO 3 − /OH− in cortical distal tubule of the rat

Secretion of bicarbonate has been described for distal nephron epithelium and attributed to apical Cl^–/HCO ₃ ^– exchange in beta-intercalated cells. We investigated the presence of this mechanism in cortical distal tubules by perfusing these segments with acid (pH 6) 10 mm phosphate Ringer. The kinetics of luminal alkalinization was studied in stationary microperfusion experiments by double-barreled pH (ion-exchange resin)/1 m KCl reference microelectrodes. Luminal alkalinization may be due to influx (into the lumen) of HCO ₃ ^– or OH^–, or efflux of H⁺. The magnitude of the Cl^–/ HCO ₃ ^– exchange component was measured by perfusing the lumen with solutions with or without chloride, which was substituted by gluconate. This component was not different from zero in control and alkalotic (chronic plus acute) Wistar rats. Homozygous Brattleboro rats (BRB), genetically devoid of antidiuretic hormone, were used since this hormone has been shown to stimulate H⁺ secretion, which could mask bicarbonate secretion. In these rats, no evidence for Cl^–/HCO ₃ ^– exchange was found in control BRB and in early distal segments of alkalotic animals, but in late distal tubule a significant component of 0.14±0.033 nmol/cm² · sec was observed, which, however, is small when compared to the reabsorptive flow found in control Wistar rats, of 0.95±0.10 nmol/cm² · sec. In addition, 5×10^–4 m SITS had no effect on distal bicarbonate reabsorption in controls as well as on secretion in alkalotic Wistar and Brattleboro rats, which is compatible with the absence of effect of this drug on the apical Cl^–/HCO ₃ ^– exchange in other tissues. It is concluded that most distal alkalinization is not Cl^– dependent, and that Cl^–/HCO ₃ ^– exchange may be found in cortical distal tubule, but its magnitude is, even in alkalosis, markedly smaller than the reabsorptive flux, which predominates in the rats studied in this paper, keeping luminal pH lower than that of blood.     

Guest-Host Chemistry with Dendrimers—Binding of Carboxylates in Aqueous Solution

Recognition and binding of anions in water is difficult due to the ability of water molecules to form strong hydrogen bonds and to solvate the anions. The complexation of two different carboxylates with 1-(4-carbomethoxypyrrolidone)-terminated PAMAM dendrimers was studied in aqueous solution using NMR and ITC binding models. Sodium 2-naphthoate and sodium 3-hydroxy-2-naphthoate were chosen as carboxylate model compounds, since they carry structural similarities to many non-steroidal anti-inflammatory drugs and they possess only a limited number of functional groups, making them ideal to study the carboxylate-dendrimer interaction selectively. The binding stoichiometry for 3-hydroxy-2-naphthoate was found to be two strongly bound guest molecules per dendrimer and an additional 40 molecules with weak binding affinity. The NOESY NMR showed a clear binding correlation of sodium 3-hydroxy-2-naphthoate with the lyophilic dendrimer core, possibly with the two high affinity guest molecules. In comparison, sodium 2-naphthoate showed a weaker binding strength and had a stoichiometry of two guests per dendrimer with no additional weakly bound guests. This stronger dendrimer interaction with sodium 3-hydroxy-2-naphthoate is possibly a result of the additional interactions of the dendrimer with the extra hydroxyl group and an internal stabilization of the negative charge due to the hydroxyl group. These findings illustrate the potential of the G4 1-(4-carbomethoxy) pyrrolidone dendrimer to complex carboxylate guests in water and act as a possible carrier of such molecules.