Protonation Equilibria Research Articles

Model-based analysis for kinetic complexation study of Pizda and Cu(II)

In the present work, the multivariate kinetic complexation of a new synthesized ligand, 1-(2″-hydroxyl cyclohexyl)-3′-[aminopropyl]-4-[3′-aminopropyl]piperazine (Pizda) and Cu 2+ in 50% ethanol–water solution is investigated using the UV–vis stopped-flow technique and state-of-the-art multi-wavelength numerical analysis. Model-based least squares fitting analysis or hard modeling is a specific part of chemometrics which is based on mathematical relationships for describing the measurements. Some recent developments include the incorporation of the effects of non-ideal experimental conditions into the fitting algorithm so it can substantially simplify experimental procedures. In this study no buffers are required because pH changes are taken into computations. Some 21 multi-wavelength kinetic measurements, taken at various initial concentrations of [H +] were analyzed globally, i.e. simultaneously applying an all inclusive reaction mechanism and a common set of species spectra. Using numerical analysis, the pH of the experimental solutions was allowed to vary as a consequence of the proceeding reactions. This enabled the complete kinetic analysis of the formation and dissociation of Cu(Pizda) n+ . Here protonation equilibria have been directly incorporated into the rate law, so thus variable pH values have been allowed during each measurement. Using the independently estimated stability constants (from spectrophotometric and potentiometric measurements) for the Cu(Pizda) n+ complexes, a total of six rate constants and one protonation constant could be elucidated. The results of the analysis include the concentration distribution and spectra of all chemical species involved in the reaction. A low standard deviation and residual profiles obtained validate the results.

Synthesis and properties of novel HMS-based sulfonated poly(arylene ether sulfone)/silica nano-composite membranes for DMFC applications

Novel 4,4′-dihydroxy-α-methylstilbene (HMS)-based sulfonated poly(arylene ether sulfone) with sulfonic acid composition ranging from 10 to 40 mol% was synthesized via nucleophilic step polymerization of 4,4′-dihydroxy-α-methylstilbene, 4,4′-dichloro-3,3′-disulfonic acid diphenylsulfone and 4,4′-dichlorodiphenylsulfone and blended with silica sol to form organic/inorganic nano-composite membranes. The organic/inorganic nano-composite copolymers produced show a high glass transition temperature and thermal decomposition temperatures from 318 to 451 °C. The copolymers present appropriate toughness during the membrane process. The equilibrium water uptake and proton conductivity of the obtained organic/inorganic nano-composite membranes were measured as functions of temperature, degree of sulfonation and silica content. In general, the water uptake increased from 8 to 37 wt.%, and the proton conductivity of the organic/inorganic nano-composite membranes increased from 0.003 to 0.110 S cm −1 as the degree of sulfonation increased from 10 to 40 mol%, the silica content increased from 3 to 10 wt.%, and the temperature increased from 30 to 80 °C. The single cell performance of the 40 mol% organic/inorganic nano-composite membrane with various silica contents ranged from 11 to 13 mW cm −2 at 80 °C, and the power density was higher than Nafion ® 117. Including the thermal properties, swelling, conductivity and single cell performance, the nano-composite membranes are able to satisfy the requirements of proton exchange membranes for direct methanol fuel cells (DMFC).

Structure and Medium Effects on the Photochemical Behavior of Nonfluorinated Quinolone Antibiotics†

The photophysical behavior of the quinolone antibiotics, oxolinic (OX), cinoxacin (CNX) and pipemidic (PM) acids was studied as a function of pH and solvent properties. The ground state of these compounds exhibits different protonated forms, which also exist in the first excited states. Theoretical calculations of the Fukui indexes allowed to assigning the different protonation equilibria. The pK values indicate that the acidity of the 3-carboxylic and 4-carbonyl groups increases with the N-atom at position 2 in CNX. It has been found that fluorescence properties are strongly affected by pH, the more fluorescent species is that with protonated carboxylic acid, protonated species at the carbonyl group and the totally deprotonated form present very low fluorescence. The fluorescence behavior also depends on the chemical structure of the quinolone and on the solvent properties. The analysis of the solvent effect on the maximum and the width of the fluorescence band of OX, using the linear solvent-energy relation solvatochromic equation, indicates that the polarizability and hydrogen bond donor ability are the parameters that condition the spectral changes. The hydrogen bond acceptor ability of the solvents also contributes to the spectral shifts of CNX. The compound bearing the piperazinyl group at the position 7, PM only is fluorescent in high protic solvents. These results are discussed in terms of the competition between the intra- and intermolecular hydrogen bonds. The irradiation of OX, CNX and PM using 300 nm UV light led to a very low photodecomposition rate. Under the same conditions the nalidixic acid (NA), a structurally related quinolone, photodecomposes two orders of magnitude faster.

Transient Spectroscopy of Ninhydrin¶

The photochemistry of ninhydrin in benzene and water was studied by laser flash photolysis and electron paramagnetic resonance. Its photochemistry was shown to be dependent on the solvent. In benzene, a triplet excited state was observed, which underwent hydrogen abstraction reactions or reduction to the radical anion. In water, the radical anion of ninhydrin was formed within the laser pulse (15 ns) at neutral pH, whereas the neutral ketyl radical was formed by protonation of the radical anion at low pH. A pKa of 0.77 was determined for the protonation equilibrium. The formation of hydrindantin is proposed to occur through the dimerization of the ketyl radical or the radical anion (or both). In addition, ninhydrin was shown to be a poor precursor for the photogeneration of hydroxyl radicals.

YinYang Atom: A Simple Combined ab Initio Quantum Mechanical Molecular Mechanical Model

A simple interface is proposed for combined quantum mechanical (QM) molecular mechanical (MM) calculations for the systems where the QM and MM regions are connected through covalent bonds. Within this model, the atom that connects the two regions, called YinYang atom here, serves as an ordinary MM atom to other MM atoms and as a hydrogen-like atom to other QM atoms. Only one new empirical parameter is introduced to adjust the length of the connecting bond and is calibrated with the molecule propanol. This model is tested with the computation of equilibrium geometries and protonation energies for dozens of molecules. Special attention is paid on the influence of MM point charges on optimized geometry and protonation energy, and it is found that it is important to maintain local charge-neutrality in the MM region in order for the accurate calculation of the protonation and deprotonation energies. Overall the simple YinYang atom model yields comparable results to some other QM/MM models.

Dynamic Protonation Equilibrium of Solvated Acetic Acid

Taking the long way home: The dynamic protonation equilibrium between acetic acid and a water box is studied by molecular dynamics simulations. Two types of motion are found: 1) the proton is swapped rapidly between acetic acid and a hydrogen-bonded water molecule (see picture); 2) the proton escapes into the bulk volume and rebinds to acetic acid only at a separation of roughly 5 Å.

Proton Activity in Nafion Films: Probing Exchangeable Protons with Methylene Blue

A simple approach to monitor the H(+) activity of a proton-exchange membrane (Nafion) is introduced by incorporating methylene blue as an indicator dye. The dye exhibits characteristics absorption maxima at 665 and 745 nm corresponding to its singly and doubly protonated forms, respectively. The apparent proton activity of Nafion as monitored from the appearance of doubly protonated methylene blue absorption is equivalent to 1.2 M H2SO4. By monitoring the spectral changes associated with the protonation equilibrium of the dye, it is possible to probe the rate and the exchangeable proton sites within the Nafion film. For the Nafion 117 film, we estimate the total exchangeable proton sites to be 2.5 x 10(19) sites/cm(2) or 4.2 x 10(-5) mols/cm(2). The equilibrium constant for the H(+)/Na(+) exchange for the bound sites is determined to be 2.2. The feasibility of methylene blue as a probe to monitor proton activity during the operation of a direct methanol fuel cell has been explored.

The Missing Link in COS Metabolism: A Model Study on the Reactivation of Carbonic Anhydrase from its Hydrosulfide Analogue

Carbonic anhydrase (CA) is known to react with carbonyl sulfide, an atmospheric trace gas, whereby H(2)S is formed. It has been shown that, in the course of this reaction, the active catalyst, the His(3)ZnOH structural motif, is converted to its hydrosulfide form: His(3)ZnOH+COS-->His(3)ZnSH+CO(2). In this study, we elucidate the mechanism of reactivation of carbonic anhydrase (CA) from its hydrosulfide analogue by using density functional calculations, a model reaction and in vivo experimental investigation. The desulfuration occurs according to the overall equation His(3)ZnSH+H(2)O right harpoon over left harpoon His(3)ZnOH+H(2)S. The initial step is a protonation equilibrium at the zinc-bound hydrosulfide. The hydrogen sulfide ligand thus formed is then replaced by a water molecule, which is subsequently deprotonated to yield the reactivated catalytic centre of CA. Such a mechanism is thought to enable a plant cell to expel H(2)S or rapidly metabolise it to cysteine via the cysteine synthase complex. The proposed mechanism of desulfuration of the hydrosulfide analogue of CA can thus be regarded as the missing link between COS consumption of plants and their sulfur metabolism.

Spectroscopic, Computational, and Kinetic Studies of the μ4-Sulfide-Bridged Tetranuclear CuZ Cluster in N2O Reductase: pH Effect on the Edge Ligand and Its Contribution to Reactivity

A combination of spectroscopy and density functional theory (DFT) calculations has been used to evaluate the pH effect at the CuZ site in Pseudomonas nautica (Pn) nitrous oxide reductase (N2OR) and Achromobacter cycloclastes (Ac) N2OR and its relevance to catalysis. Absorption, magnetic circular dichroism, and electron paramagnetic resonance with sulfur K-edge X-ray absorption spectra of the enzymes at high and low pH show minor changes. However, resonance Raman (rR) spectroscopy of PnN2OR at high pH shows that the 415 cm-1 Cu-S vibration (observed at low pH) shifts to higher frequency, loses intensity, and obtains a 9 cm-1 18O shift, implying significant Cu-O character, demonstrating the presence of a OH- ligand at the CuICuIV edge. From DFT calculations, protonation of either the OH- to H2O or the mu4-S2- to mu4-SH- would produce large spectral changes which are not observed. Alternatively, DFT calculations including a lysine residue at an H-bonding distance from the CuICuIV edge ligand show that the position of the OH- ligand depends on the protonation state of the lysine. This would change the coupling of the Cu-(OH) stretch with the Cu-S stretch, as observed in the rR spectrum. Thus, the observed pH effect (pKa approximately 9.2) likely reflects protonation equilibrium of the lysine residue, which would both raise E degrees and provide a proton for lowering the barrier for the N-O cleavage and for reduction of the [Cu4S(im)7OH]2+ to the fully reduced 4CuI active form for turnover.

A simple NMR analysis of the protonation equilibrium that accompanies aminoglycoside recognition: Dramatic alterations in the neomycin-B protonation state upon binding to a 23-mer RNA aptamer

A complete characterisation of the protonation equilibrium that accompanies the molecular recognition of neomycin-B by a specific RNA receptor has been achieved by employing simple NMR measurements.

Studies on protonation and Th(IV) complexation behaviour of dihydroxybenzenes in aqueous 1 M NaClO4 medium

Complexing behaviour of three dihydroxybenzenes (DHB) namely, hydroquinone, resorcinol and catechol with Th(IV) along with their protonation constants were studied in 1 M NaClO4 medium at 23 ± 0.5 °C, using pH titration technique. Both protonation and metal-ligand equilibrium constants of dihydroxybenzenes were computed using advance software suite of program HYPERQUAD. Logarithmic values of overall protonation constants (log β1H and log β2H) were found to be 11.47 ± 0.05 and 21.45 ± 0.06, for hydroquinone, 11.76 ± 0.04 and 20.98 ± 0.04 for resorcinol and 12.58 ± 0.03 and 21.87 ± 0.08 for catechol respectively. Complex formation has been investigated in the pH range 2 to 4. The logarithmic values of metal-ligand equilibrium constants obtained in the present work were β13-1=48.51 ± 0.67 and β14-1=64.86 ± 1.25 for hydroquinone, β110=16.98 ± 0.16, β13-1=46.46 ± 0.18 and β14-2=59.65 ± 0.20 for resorcinol and β11-1=14.06 ± 0.10 for catechol. The literature values were reviewed.

Monosaccharides and the VO(IV) metal ion: Equilibrium, thermal studies and hypoglycemic effect

Protonation and complexation equilibriums of monosaccharides and the VO(IV) metal ion in aqueous solution were studied as well as their effect on the hyperglycemia of diabetic rats. The complexes formed were characterized by potentiometric titrations, paramagnetic resonance spectroscopy (EPR) and thermogravimetric–differential scanning calorimetry (TGA–DSC). The system involving d-gluconic acid (HGlu) and oxovanadium(IV) (VO 2+) was chosen to study the serum glucose levels in alloxan-induced diabetic rats. A binuclear species was detected in small quantities, which was formed by coordination of two HGlu molecules and two VO 2+ ions through a hydroxide bridge. The mononuclear species formed by HGlu and VO 2+ were confirmed by EPR. The anisotropic spectra obtained from aqueous frozen solutions (77 K) are characteristic of mononuclear VO-hexoses. The cyclic sugars d-ribone-1,4-lactone (Riblac), d-galactone-1,4-lactone (Galac) and 2-deoxy- d-glucopyranose (dGlu) showed weak interactions with the metal ion and they are not able to hold the metal in solution above pH 4.6 resulting in hydrolysis of the metal ion. Also, the acute treatment with sugar complexes of HGlu–VO led to a significant hypoglycemic effect (23% and 18% by intraperitoneal or oral gavage treatment, respectively) in diabetic rats. These results show the potential effectiveness of VO–HGlu complexes as anti-hyperglycemic agents through intraperitoneal injection in alloxan-induced diabetic rats.

Oxidation of the thiosulfate ion by some iron(III) complexes with phenolate - amide-amine coordination: A comparative kinetic study

The redox reactions of thiosulfate with four iron(III) complexes having phenolate-amide-amine coordination, FeIII(L){L = 1,2-bis(2-hydroxybenzamido)ethane, L1; 1,3-bis(2-hydroxybenzamido)propane, L2; 1,5-bis(2-hydroxybenzamido)3-azapentane, L3; and 1,8-bis(2-hydroxybenzamido)3,6-diazaoctane, L4} have been investigated in 10% v/v MeOH + H2O and I = 0.3 mol dm−3. At constant pH (~ 4.8) and under pseudo-first order conditions of [S2O32−] the reaction obeyed the rate law : − d[FeIII(L)]/dt = kobs [FeIII(L)] + kobs′ where kobs′ denotes the observed rate constant of thiosulfate decomposition; kobs = a[S2O32−] + b[S2O32−]T2 is valid for all the complexes, particularly at pH < 6, while kobs′ = [H+][S2O32−]T2 is consistent with the rate law for thiosulfate decomposition proposed earlier. The rate data (kobs) were analysed on the basis of the reactivities of various species of FeIII(L) generated by the equilibrium protonation of the sec-NH of dien and trien spacer units resulting in the ring opening (for [FeIII(L3/L4)]), and acid base equilibrium of the aqua ligand bound to the iron(III) centre ([FeIII(L)(OH2)n]). The redox activities, both for second and third order paths, show the ligand dependencies : L4<L3<L1<L2 conforming to the fact that the complexes tend to be less susceptible to electron transfer from S2O32− with (i) the increase of the number of chelate rings, (ii) the decrease of overall charge, and (iii) the decrease of ring size offered by the amine moiety (from six membered to five membered one as for [FeIII(L1/L2)(OH2)2]+. There was no evidence for the formation of inner sphere thiosulfato complex, the possibility of the formation of the outer sphere ion-pairs, [Fe(L/HL)(OH2)n+/2+, S2O32−] with low equilibrium constant value may not be excluded. In view of this, the outer sphere electron transfer (ET) mechanism is the most likely possibility.

DNA Cleavage by UVA Irradiation of NADH with Dioxygen via Radical Chain Processes

Efficient DNA cleaving-activity is observed by UVA irradiation of an O(2)-saturated aqueous solution of NADH (beta-nicotinamide adenine dinucleotide, reduced form). No DNA cleavage has been observed without NADH under otherwise the same experimental conditions. In the presence of NADH, energy transfer from the triplet excited state of NADH ((3)NADH*) to O(2) occurs to produce singlet oxygen ((1)O(2)) that is detected by the phosphorescence emission at 1270 nm. No quenching of (1)O(2) by NADH was observed as indicated by no change in the intensity of phosphorescence emission of (1)O(2) at 1270 nm in the presence of various concentrations of NADH. In addition to the energy transfer, photoinduced electron transfer from (3)NADH* to O(2) occurs to produce NADH(*+) and O(2)(*-), both of which was observed by ESR. The quantum yield of the photochemical oxidation of NADH with O(2) increases linearly with increasing concentration of NADH but decreases with increasing the light intensity absorbed by NADH. Such unusual dependence of the quantum yield on concentration of NADH and the light intensity absorbed by NADH indicates that the photochemical oxidation of NADH with O(2) proceeds via radical chain processes. The O(2)(*-) produced in the photoinduced electron transfer is in the protonation equilibrium with HO(2)(*), which acts as a chain carrier for the radical chain oxidation of NADH with O(2) to produce NAD(+) and H(2)O(2), leading to the DNA cleavage.

Characterization of Ester Hydrolysis in Terms of Microscopic Rate Constants

Hydroxide-catalyzed ester hydrolysis for molecules of coexisting species is quantitated in terms of microscopic rate constants, a new, species-specific physicochemical parameter. Relationships between the overall and component reactions, as well as the macroscopic and microscopic rate constants are deduced. Experimental techniques, evaluation methods, and feasibility are discussed. Species-specific, pH-independent rate constants of four coexisting, differently hydrolyzing microspecies are determined for the first time. Protonation of an alpha-amino and beta-imidazolyl site in amino acid esters has been found to accelerate the hydroxide-catalyzed hydrolysis by factors of 120 and 7.5, respectively, whereas they jointly exert a nearly 3000-fold acceleration. A total of 20 microscopic protonation equilibrium constants, as component parameters in the rate equations, have also been determined. The species-specific rate constants have been found to correlate with the site- and species-specific basicity of the leaving group and the NMR chemical shift of an adjacent proton. Individual contributions of the various microforms to the overall hydrolysis rate are depicted in microscopic reaction fraction diagrams.

Oxidation of hydroxyurea with oxovanadium(V) ions in acidic aqueous solution

Hydroxyurea (HU) effectively reduces vanadium(V) into vanadium(IV) species (hereafter V V and V IV species, respectively) in acidic aqueous solution via the formation of a transient complex followed by an electron transfer process that includes the formation and subsequent fading out of a free radical, U (U ≡ H 2N–C(=O)N(H)O ). The electron paramagnetic resonance (EPR) spectra of U in H 2O/D 2O solutions suggest that the unpaired electron is located predominantly on the hydroxamate hydroxyl-oxygen atom. Visible and V IV–EPR spectroscopic data reveal HU as a two-electron donor, whereas formation of U , which reduces a second V V, indicates that electron transfer occurs in two successive one-electron steps. At the molarity ratio [V V]/[HU] = 2, the studied reaction can be formulated as: 2 V V + HU → 2 V IV + 0.98 CO 2 + 0.44 N 2O + 1.1 NH 3 + 0.1 NH 2OH. Lack of evidence for the formation of NO is suggested to be a consequence of the slow oxidation of HNO due to the too low reduction potential of the V V/V IV couple under the experimental conditions used. The nuclear magnetic resonance ( 51V-NMR) spectral data indicate protonation of ( H 2 O ) 4 V V O 2 + , and the protonation equilibrium constant was determined to be K = 0.7 M −1. Spectrophotometric titration data for the V V–HU system reveal formation of (H 2O) 2V VO(OH)U + and (H 2O) 3V VOU 2+. Their stability constants were calculated as K 110 = 5 M −1 and K 111 = 22 M −2, where the subscript digits refer to ( H 2 O ) 4 V V O 2 + , HU and H +, respectively.

Solvent-dependent regioselectivity of hydrogen chloride-mediated ring opening of alkylidenecyclopropanone acetal

Ring opening reactions of 2-cyclohexylidene-3,3-dimethylcyclopropanone acetal ( 1) are readily induced by treatment of hydrogen chloride in various solvents. Bond cleavage takes place at the C1–C2 or C2–C3 bond, and the ratio of C1–C2/C2–C3 cleavages changes from >99/1 to <1/99 depending on the solvent. The two modes of bond cleavage must be initiated by protonations at the carbon–carbon double bond and the acetal oxygen, respectively. The regioselectivity can be rationalized by the rate-determining protonation at carbon and the equilibrium protonation at oxygen.

NMR Dynamic Studies Suggest that Allosteric Activation Regulates Ligand Binding in Chicken Liver Bile Acid-binding Protein

Apo chicken liver bile acid-binding protein has been structurally characterized by NMR. The dynamic behavior of the protein in its apo- and holo-forms, complexed with chenodeoxycholate, has been determined via (15)N relaxation and steady state heteronuclear (15)N((1)H) nuclear Overhauser effect measurements. The dynamic parameters were obtained at two pH values (5.6 and 7.0) for the apoprotein and at pH 7.0 for the holoprotein, using the model free approach. Relaxation studies, performed at three different magnetic fields, revealed a substantial conformational flexibility on the microsecond to millisecond time scales, mainly localized in the C-terminal face of the beta-barrel. The observed dynamics are primarily caused by the protonation/deprotonation of a buried histidine residue, His(98), located on this flexible face. A network of polar buried side chains, defining a spine going from the E to J strand, is likely to provide the long range connectivity needed to communicate motion from His(98) to the EF loop region. NMR data are accompanied by molecular dynamics simulations, suggesting that His(98) protonation equilibrium is the triggering event for the modulation of a functionally important motion, i.e. the opening/closing at the protein open end, whereas ligand binding stabilizes one of the preexisting conformations (the open form). The results presented here, complemented with an analysis of proteins belonging to the intracellular lipid-binding protein family, are consistent with a model of allosteric activation governing the binding mechanism. The functional role of this mechanism is thoroughly discussed within the framework of the mechanism for the enterohepatic circulation of bile acids.

Simulation of the interface of (1 0 0) rutile with aqueous ionic solution

The interface of the rutile (1 0 0) surface with NaCl solutions has been simulated by classical molecular dynamics. In contrast to earlier simulations the protonation and hydroxylation equilibriums have been adjusted for different pH values (4, 7.4, and 9). The short range order close to the surface is described by two water layers with some orientational order and intermediate layers of positive or negative ions depending on the surface charge. A Stern model is confirmed with a dense layer of counterions on the charged TiO 2 surface and a diffuse layer, which only consists of few ions in our system. The increase of orientational order of the water molecules close to the surface is described by an exponential function with a decay parameter of 1.9 Å, superposed by a damped oscillation which is independent of the pH value. The diffusion is significantly slower than in the bulk within a range of 13 Å from the surface. We propose a common approach for describing the different z-dependences of orientational order and of the diffusion coefficients.

Molecular-Thermodynamic Theory of Micellization of pH-Sensitive Surfactants

A predictive, molecular-thermodynamic theory is developed to model the micellization of pH-sensitive surfactants. The theory combines a molecular-thermodynamic description of micellization in binary surfactant mixtures with the protonation equilibrium of the surfactant monomers. The thermodynamic component of the theory models the pH-mediated equilibrium between micelles, surfactant monomers, and counterions. These counterions may originate from the surfactant or from added salt, acid, or base. The molecular component of the theory models the various contributions to the free energy of micellization, which corresponds to the free-energy change associated with forming a mixed micelle from the protonated and deprotonated forms of the surfactant and from the bound counterions. The free energy of micellization includes hydrophobic, interfacial, packing, steric, electrostatic, and entropic contributions, which are all calculated molecularly. The theory also requires knowledge of the surfactant molecular structure and the solution conditions, including the temperature and the amount of any added salt, acid, or base. To account for the pH sensitivity of the surfactant, the theory requires knowledge of the surfactant monomer equilibrium deprotonation constant (pK1), which may be obtained from experimental titration data obtained below the critical micelle concentration (cmc). The theory can be utilized to predict the equilibrium micelle and solution properties, including the cmc, the micelle composition, the micelle shape and aggregation number, the solution pH, and the micelle deprotonation equilibrium constant (pKm). Theoretical predictions of the cmc, the micelle aggregation number, and the pKm compare favorably with the available experimental data for alkyldimethylamine oxide surfactants. This class of pH-sensitive surfactants exhibits a form of self-synergy, which has previously been attributed to hydrogen-bond formation at the micelle interface. Instead, we show that much of the observed synergy is related to the electrostatic contribution to the free energy of micellization. Although we do not explicitly include hydrogen bonding in the molecular model of micellization, we briefly discuss how it may be incorporated and its anticipated effect on the predicted micellization behavior.