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Concept: Equilibrium constant

170

The comparison of volumes of cells and subcellular structures with the pH values reported for them leads to a conflict with the definition of the pH scale. The pH scale is based on the ionic product of water, K(w) = [H(+)]×[OH(-)].We used K(w) [in a reversed way] to calculate the number of undissociated H(2)O molecules required by this equilibrium constant to yield at least one of its daughter ions, H(+) or OH(-) at a given pH. In this way we obtained a formula that relates pH to the minimal volume V(pH) required to provide a physical meaning to K(w), [Formula: see text] (where N(A) is Avogadro’s number). For example, at pH 7 (neutral at 25°C) V(pH) = 16.6 aL. Any deviation from neutral pH results in a larger V(pH) value. Our results indicate that many subcellular structures, including coated vesicles and lysosomes, are too small to contain free H(+) ions at equilibrium, thus the definition of pH based on K(w) is no longer valid. Larger subcellular structures, such as mitochondria, apparently contain only a few free H(+) ions. These results indicate that pH fails to describe intracellular conditions, and that water appears to be dissociated too weakly to provide free H(+) ions as a general source for biochemical reactions. Consequences of this finding are discussed.

Concepts: Acid, Chemistry, Atom, Acid dissociation constant, PH, Activity, PH indicator, Equilibrium constant

14

The interaction of silica-titania xerogel with triphenylmethane dyes (pyrocatechol violet, chrome azurol S, eriochrome cyanine R) has been investigated to create a new sensor material for solid phase spectrophotometric determination of food oxalates. The complex forming reaction between xerogel incorporated titanium(IV) and triphenylmethane dyes has been studied; half-reaction periods, complex composition, equilibrium constants, and xerogel sorption capacity have been calculated for each dye. Eriochrome cyanine R (ECR) is characterized by the shortest half-reaction period, the smallest equilibrium constant, and the greatest capacity; it has been chosen for the sensor material construction because titanium(IV)-ECR complex is formed faster and can be destroyed easier than other studied complexes. The interaction of this sensor material with oxalates has been described: the presence of oxalates causes sensor material discoloration and the absorbance is used as analytical signal. The analytical range is 35-900 mg/L (LOD 10.5 mg/L,n= 7). High concentrations of interfering inorganic anions, organic acids, and sucrose did not affect oxalate determination. Proposed solid phase spectrophotometric procedure has been successfully applied for the determination of oxalates in food samples (sorrel, spinach, parsley, ginger, and black pepper) and the results are in good agreement with HPLC oxalate determination.

Concepts: Condensed matter physics, Chemical equilibrium, Acid dissociation constant, PH, Dye, Phase diagram, Equilibrium constant, Spinach

4

H2 turnover at the [FeFe]-hydrogenase cofactor (H-cluster) is assumed to follow a reversible heterolytic mechanism, first yielding a proton and a hydrido-species which again is double-oxidized to release another proton. Three of the four presumed catalytic intermediates (Hox, Hred/Hred and Hsred) were characterized, using various spectroscopic techniques. However, in catalytically active enzyme, the state containing the hydrido-species, which is eponymous for the proposed heterolytic mechanism, has yet only been speculated about. We use different strategies to trap and spectroscopically characterize this transient hydride state (Hhyd) for three wild-type [FeFe]-hydrogenases. Applying a novel set-up for real-time attenuated total-reflection Fourier-transform infrared spectroscopy, we monitor compositional changes in the state-specific infrared signatures of [FeFe]-hydrogenases, varying buffer pH and gas composition. We selectively enrich the equilibrium concentration of Hhyd, applying Le Chatelier’s principle by simultaneously increasing substrate and product concentrations (H2/H(+)). Site-directed manipulation, targeting either the proton-transfer pathway or the adt ligand, significantly enhances Hhyd accumulation independent of pH.

Concepts: Spectroscopy, Enzyme, Chemical equilibrium, Le Chatelier's principle, Infrared spectroscopy, Fourier transform spectroscopy, Near infrared spectroscopy, Equilibrium constant

4

DNA hybridization thermodynamics is critical for accurate design of oligonucleotides for biotechnology and nanotechnology applications, but parameters currently in use are inaccurately extrapolated based on limited quantitative understanding of thermal behaviours. Here, we present a method to measure the ΔG° of DNA motifs at temperatures and buffer conditions of interest, with significantly better accuracy (6- to 14-fold lower s.e.) than prior methods. The equilibrium constant of a reaction with thermodynamics closely approximating that of a desired motif is numerically calculated from directly observed reactant and product equilibrium concentrations; a DNA catalyst is designed to accelerate equilibration. We measured the ΔG° of terminal fluorophores, single-nucleotide dangles and multinucleotide dangles, in temperatures ranging from 10 to 45 °C.

Concepts: DNA, Chemical reaction, Measurement, Temperature, Chemical equilibrium, Acid dissociation constant, PH, Equilibrium constant

2

Microbial sulfate reduction (SR) is a dominant process of organic matter mineralization in sulfate-rich anoxic environments at neutral pH. Recent studies have demonstrated SR in low pH environments, but investigations on the microbial activity at variable pH and CO2 partial pressure are still lacking. In this study, the effect of pH and pCO2 on microbial activity was investigated by incubation experiments with radioactive (35)S targeting SR in sediments from the shallow-sea hydrothermal vent system of Milos, Greece, where pH is naturally decreased by CO2 release. Sediments differed in their physicochemical characteristics with distance from the main site of fluid discharge. Adjacent to the vent site (T ~40-75°C, pH ~5), maximal sulfate reduction rates (SRR) were observed between pH 5 and 6. SR in hydrothermally influenced sediments decreased at neutral pH. Sediments unaffected by hydrothermal venting (T ~26°C, pH ~8) expressed the highest SRR between pH 6 and 7. Further experiments investigating the effect of pCO2 on SR revealed a steep decrease in activity when the partial pressure increased from 2 to 3 bar. Findings suggest that sulfate reducing microbial communities associated with hydrothermal vent system are adapted to low pH and high CO2, while communities at control sites required a higher pH for optimal activity.

Concepts: Photosynthesis, Carbon dioxide, Redox, Nitrogen, PH, Hydrothermal vent, Greece, Equilibrium constant

1

A microfluidic system combined with substrate-integrated hollow waveguide (iHWG) vapor phase infrared spectroscopy has been developed for evaluating the chemical activity of volatile compounds dissolved in complex fluids. Chemical activity is an im-portant yet rarely exploited parameter in process analysis and control. Access to chemical activity parameters enables systematic studies on phase diagrams of complex fluids, the detection of aggregation processes, etc.. The instrumental approach developed herein uniquely enables controlled evaporation/permeation from a sample solution into a hollow waveguide structure, and analyz-ing the partial pressures of volatile constituents. For the example of a binary system, it was shown that the chemical activity may be deduced from partial pressure measurements at thermodynamic equilibrium conditions. The combined microfluidic-iHWG mid-infrared sensor system (µFLUID-IR) allows realizing such studies in absence of any perturbations provoked by sampling opera-tions, which is unavoidable using state-of-the-art analytical techniques such as headspace gas chromatography. For demonstration purposes, a water-ethanol mixture was investigated, and the derived data was cross-validated with established literature values at different mixture ratios. Next to perturbation-free measurements, a response time of the sensor <150 seconds (t90) at a recovery time <300 seconds (tr) has been achieved, which substantiates the utility of µFLUID-IR for future process analysis-and-control applica-tions.

Concepts: Chemical equilibrium, Thermodynamics, Pressure, Vapor pressure, Infrared, Partial pressure, Vapor, Equilibrium constant

1

A new click bioorthogonal reaction system was devised to enable the fast ligation (kON ≈340 m(-1)  s(-1) ) of conjugatable derivatives of a rigid cyclic diol (nopoldiol) and a carefully optimized boronic acid partner, 2-methyl-5-carboxymethylphenylboronic acid. Using NMR and fluorescence spectroscopy studies, the corresponding boronates were found to form reversibly within minutes at low micromolar concentration in water, providing submicromolar equilibrium constant (Keq ≈10(5) -10(6)  m(-1) ). Efficient protein conjugation under physiological conditions was demonstrated with model proteins thioredoxin and albumin, and characterized by mass spectrometry and gel electrophoresis.

Concepts: Protein, Spectroscopy, Oxygen, Molecular biology, Gel electrophoresis, Chemical equilibrium, Acid dissociation constant, Equilibrium constant

0

Supramolecular assembly is shown to provide control over excited-state chloride release. Two dicationic chromophores were designed with a ligand that recognizes halide ions in CH2Cl2 and a luminescent excited state whose dipole was directed toward, 12+, or away, 22+, from an associated chloride ion. The dipole orientation had little influence on the ground-state equilibrium constant, Keq ∼ 4 × 106 M-1, but induced a profound change in the excited-state equilibrium. Light excitation of [12+,Cl-]+ resulted in time-dependent shifts in the photoluminescence spectra with the appearance of biexponential kinetics consistent with the photorelease of Cl-. Remarkably, the excited-state equilibrium constant was lowered by a factor of 20 and resulted in nearly 45% dissociation of chloride. In contrast, light excitation of [22+,Cl-]+ revealed a 45-fold increase in the excited-state equilibrium constant. The data show that rational design and supramolecular assembly enables the detection and photorelease of chloride ions with the potential for future applications in biology and chemistry.

Concepts: Chemistry, Atom, Chemical equilibrium, Sodium chloride, Ion, Chlorine, Chloride, Equilibrium constant

0

Haptoglobin (Hp) sequesters hemoglobin (Hb) preventing the Hb-based damage occurring upon its physiological release into plasma. Here, reductive nitrosylation of ferric human hemoglobin [Hb(III)] bound to human haptoglobin (Hp) 1-1 and 2-2 [Hp1-1:Hb(III) and Hp2-2:Hb(III), respectively] has been investigated between pH 7.5 and 9.5, at T=20.0 °C. Over the whole pH range explored, only one process is detected reflecting NO binding to Hp1-1:Hb(III) and Hp2-2:Hb(III). Values of the pseudo-first-order rate constant for Hp1-1:Hb(III) and Hp2-2:Hb(III) nitrosylation (k) do not depend linearly on the ligand concentration but tend to level off. The conversion of Hp1-1:Hb(III)-NO to Hp1-1:Hb(II)-NO and of Hp2-2:Hb(III)-NO to Hp2-2:Hb(II)-NO is limited by the OH– and H2O-based catalysis. In fact, bimolecular NO binding to Hp1-1:Hb(III), Hp2-2:Hb(III), Hp1-1:Hb(II), and Hp2-2:Hb(II) proceeds very rapidly. The analysis of data allowed to determine the values of the dissociation equilibrium constant for Hp1-1:Hb(III) and Hp2-2:Hb(III) nitrosylation [K = (1.2 ± 0.1) × 10-4M], which is pH-independent, and of the first-order rate constant for Hp1-1:Hb(III) and Hp2-2:Hb(III) conversion to Hp1-1:Hb(II)-NO and Hp2-2:Hb(II)-NO, respectively (k'). From the dependence of k' on [OH-], values of hOH-[(4.9 ± 0.6) × 103 M-1 s-1and (6.79 ± 0.7) × 103 M-1 s-1, respectively] and of [Formula: see text] [(2.6 ± 0.3) × 10-3 s-1] were determined. Values of kinetic and thermodynamic parameters for Hp1-1:Hb(III) and Hp2-2:Hb(III) reductive nitrosylation match well with those of the Hb R-state, which is typical of the αβ dimers of Hb bound to Hp.

Concepts: Hemoglobin, Thermodynamics, Acid dissociation constant, PH, Rate equation, Reaction rate, Equilibrium chemistry, Equilibrium constant

0

Sodium nonatitanate powder is a layered material containing some potential exchangeable sodium ions between layers. In this work, sorption mechanism of this material has been studied and modeled at the solid-liquid interface. In particular, the ion-exchange mechanism is up to now not entirely known and especially the role of the pH on sorption properties. To investigate this latter, the solid is first equilibrated with inert acidic and base (nitric acid and triethylamine) for which the co-ions nitrate and triethylammonium do not penetrate the solid. The exchange between proton or divalent ions (strontium or calcium), and the sodium initially located in the sodium nonatitanate, is characterized through capillary ionic chromatography and conductivity experiments. To understand and explain the sorption properties, we modeled the equilibrium constant of different exchange reactions as a function of the solution pH. The equilibrium constants of the strontium/sodium and the calcium/sodium exchange have been obtained. We have shown the important role of the pH on the sorption rate of the strontium and moreover the hydrolysis rate of the sodium nonatitanate is calculated. We found that one eighth of sodium is spontaneously hydrolysed in aqueous phase whereas seven-eighths are exchanged by different divalent cations (strontium or calcium). Strontium and calcium exhibit similar exchange curves and competition with the proton adsorbed is modeled with global equilibrium constant. The prediction is in agreement with the conductivity experiments and the global extraction isotherms.

Concepts: Acid, Chemistry, Acid dissociation constant, PH, Ion, Sodium, Sodium hydroxide, Equilibrium constant