pKa Of Acid Research Articles

Dependence of Shell Thickness on Core Compression in Acrylic Acid Modified Poly(N-isopropylacrylamide) Core/Shell Microgels

The swelling properties of poly(N-isopropylacrylamide) (pNIPAm)-based core/shell microgels are investigated as a function of shell thickness. Core particles composed of cross-linked pNIPAm-co-acrylic acid serve as nuclei for subsequent polymerization of a cross-linked pNIPAm shell. The thickness of the shell component is varied by changing the amount of monomer present during the shell addition polymerization. Photon correlation spectroscopy results indicate that the thickness of the shell greatly impacts the swelling properties of the core as a function of polymer network density, solution pH, and temperature. Previously reported results on this core/shell polymer combination show that the core is restricted from swelling to its native volume in the presence of the shell below the polymer phase transition temperature of 31 °C. The shell also compresses the core above the polymer phase transition temperature in pH solutions above the acid pKa by inducing a volume change, despite the fact that the core is ...

New syntheses and chemistry of hexafluorotropone.

Two new routes to hexafluorotropone have been developed, one from hexachlorotropone and a superior synthesis from hexafluorobenzene. Hexafluorotropone was found to be a very weak base, with a conjugate acid pK(a) of -6.2 +/- 0.5. The tropone adds in [6 + 4] fashion to cyclopentadiene and photocyclizes to hexafluorobicyclo[3.2.0]hepta-3,6-dien-2-one. Lithium hydroxide in benzene transforms the tropone into pentafluorotropolone, which functions as a bidentate ligand.

Shell-Restricted Swelling and Core Compression in Poly(N-isopropylacrylamide) Core−Shell Microgels

We report on an investigation of the structural relationship between the core and shell components in stimuli-sensitive core/shell microgels. Photon correlation spectroscopy measurements indicate that the presence of the shell alters the extent of core swelling. Core particles composed of poly(N-isopropylacrylamide-co-acrylic acid) (pNIPAm-co-AAc) undergo volume changes as a function of temperature and pH, where deprotonation of the acidic sites results in a volume increase (particle swelling). The addition of a poly(N-isopropylacrylamide) (pNIPAm) shell restricts the core from swelling to its native volume both above and below the pKa of acrylic acid. Furthermore, the pH responsive core undergoes only small temperature-induced volume changes above the characteristic lower critical solution temperature (LCST) of pNIPAm (31 °C) at pH values where the acid groups are fully deprotonated. The addition of a pNIPAm shell results in compression of the core and induces a large volume change at the pNIPAm LCST. Th...

Effect of Premicellar Aggregation on the pKa of Fatty Acid Soap Solutions

Associative interactions of the various species found in the premicellar concentration region of aqueous fatty acid solutions have been investigated using acid−base titration. In previous studies, aqueous films of fatty acid salts were investigated at various bulk solution pH values. It was found that there exists a pH where minimum evaporation of water, maximum foamability, maximum foam stability, minimum contact angle on PMMA surface, maximum single-bubble stability, and maximum surface viscosity are observed. It was also found that this optimum pH value is near the measured pKa of the fatty acid, which in turn depends on the length of the fatty acid chains. Titration of the homologous series of C8−C12 fatty acids to determine the solution pKa has shown an increase in apparent pKa with concentration. The increase in pKa is maintained at concentrations well below the critical micelle concentration (cmc). Thus, similar to micelle formation, the submicellar aggregates must be responsible for the increase i...

Significance of Charge Regulation in the Analysis of Protein Charge Ladders

Analysis of protein charge ladders using capillary electrophoresis (CE) provides a method of determining charges of proteins. This method has disregarded the effect of charge compensationa response of the protein and its environment to a change in electrostatic potential on the surface of the protein. This work examines the difference in charge, ΔZ, between the first two rungs of the ladder of bovine carbonic anhydrase II (BCAII) as a function of pH and ionic strength using CE. These data were analyzed in three ways: using models based on Hückel theory and on charge regulation, and using linear regression. These analyses were in only qualitative agreement, and the differences between them suggest that simple theoretical models for the behavior of colloidal particles cannot establish the value of ΔZ accurately in proteins. Linear regression of mobilities of the rungs of charge laddersa method proposed in earlier workcontinues to be a computationally convenient method of estimating the charge Z0 of native proteins, but the accuracy of this method depends on the value of ΔZ. The absolute value of ΔZ cannot presently be established accurately. In the case of BCAII, we suggest ΔZ = −0.93 for the difference in charge between the first two rungs of the charge ladder at pH = 8.4 and 10 mM ionic strength. An estimate of the uncertainty in this value for BCAII due to uncertainties in the values of pKa of amino acids and of the hydrodynamic radius is ±0.02. Other uncertainties not considered in this analysis will make this value larger.

Stereoselective degradation of aqueous endosulfan in modular estuarine mesocosms: formation of endosulfan gamma-hydroxycarboxylate.

Solutions of alpha-endosulfan, beta-endosulfan, and technical grade endosulfan (70alpha:30beta) were added to modular estuarine mesocosms; the kinetics and degradation products from each mesocosm are reported. The persistent product endosulfan sulfate was generated in all cases; however, its yield was approximately a factor of three higher from alpha-endosulfan relative to beta-endosulfan. Beta-endosulfan hydrolyzed faster than alpha-endosulfan to endosulfan diol, which then rapidly degraded to endosulfan ether, endosulfan alpha-hydroxyether (major product), and endosulfan lactone. The ring-opened form of the lactone, endosulfan gamma-hydroxycarboxylate, is reported for the first time; it appears to be a terminal product, at least over the timescale of the experiment. The equilibrium between endosulfan gamma-hydroxycarboxylate and endosulfan lactone is dependent on pH, as only the protonated form of the gamma-hydroxy acid undergoes ring-closure. The pKa of the gamma-hydroxy acid was determined to be 5.7, implying that the lactone will quickly open and deprontonate under environmentally relevant conditions.

Determination of proton transfer rates by chemical rescue: application to bacterial reaction centers.

The bacterial reaction center (RC) converts light into chemical energy through the reduction of an internal quinone molecule Q(B) to Q(B)H(2). In the native RC, proton transfer is coupled to electron transfer and is not rate-controlling. Consequently, proton transfer is not directly observable, and its rate was unknown. In this work, we present a method for making proton transfer rate-controlling, which enabled us to determine its rate. The imidazole groups of the His-H126 and His-H128 proton donors, located at the entrance of the transfer pathways, were removed by site-directed mutagenesis (His --> Ala). This resulted in a reduction in the observed proton-coupled electron transfer rate [(Q(A)(-)(*)Q(B))Glu(-) + H(+) --> (Q(A)Q(B)(-)(*))GluH], which became rate-controlled by proton uptake to Glu-L212 [Adelroth, P., et al. (2001) Biochemistry 40, 14538-14546]. The proton uptake rate was enhanced (rescued) in a controlled fashion by the addition of imidazole or other amine-containing acids. From the dependence of the observed rate on acid concentration, an apparent second-order rate constant k((2)) for the "rescue" of the rate was determined. k((2)) is a function of the proton transfer rate and the binding of the acid. The dependence of k((2)) on the acid pK(a) (i.e., the proton driving force) was measured over 9 pK(a) units, resulting in a Brönsted plot that was characteristic of general acid catalysis. The results were fitted to a model that includes the binding (facilitated by electrostatic attraction) of the cationic acid to the RC surface, proton transfer to an intermediate proton acceptor group, and subsequent proton transfer to Glu-L212. A proton transfer rate constant of approximately 10(5) s(-)(1) was determined for transfer from the bound imidazole group to Glu-L212 (over a distance of approximately 20 A). The same method was used to determine a proton transfer rate constant of 2 x 10(4) s(-)(1) for transfer to Q(B)(-)(*). The relatively fast proton transfer rates are explained by the presence of an intermediate acceptor group that breaks the process into sequential proton transfer steps over shorter distances. This study illustrates an approach that could be generally applied to obtain information about the individual rates and energies for proton transfer processes, as well as the pK(a)s of transfer components, in a variety of proton translocating systems.

Adenovirus Type 37 Binds to Cell Surface Sialic Acid Through a Charge-Dependent Interaction

Most adenoviruses use the coxsackie-adenovirus receptor (CAR) as a major cellular receptor. We have shown recently that adenovirus types 8, 19a, and 37, which are the major causes of epidemic keratoconjunctivitis, use sialic acid rather than CAR as a major cellular receptor. The predicted isoelectric point of the receptor-interacting knob domain in the adenovirus fiber protein is unusually high (9.0–9.1) in type 8, 19a, and 37. The pKa of sialic acid is low, 2.6, implying a possible involvement of charge in fiber knob–sialic acid interactions. Here we show that (i) positively charged adenovirus knobs require sialic acid for efficient cell membrane interactions; (ii) viral and knob interactions with immobilized sialic acid or cell-surface sialic acid are sensitive to increased ionic strength; (iii) negatively charged molecules such as sulfated glycosaminoglycans inhibit the binding of virions to target cells in a nonspecific, charge-dependent manner; and that (iv) the ability of adenovirus knobs to interact with sialic acid correlates with the overall charge on the top surface of the respective knobs as predicted by homology modeling. Taken together, the results presented provide strong evidence for a charge mechanism during the interaction between the Ad37 fiber knob and sialic acid.

Nucleophilic and Acid Catalysis in Phosphoramidite Alcoholysis

Numerous triflates, mesylates, chlorides, trifluoroacetates and tetrazolides of trialkylammonium, pyridinium and azolium ions have been studied as activators for the reaction of N,N,O,O′-tetraisopropylphosphoramidite with propan-2-ol in acetonitrile. The progress of the reactions was followed by 31P NMR spectroscopy, and the pKa values of the activators were determined by a 13C NMR spectroscopic method based on competing simultaneous protonation of two bases. The salts promoted the reaction both as acids and nucleophiles, the acidity playing a more important role than the nucleophilicity. The Bronsted α value for the general acid catalysis was observed to range from 0.6 to 0.9 and the βnucl value to be 0.2 (pKa of the conjugate acid used as the measure of nucleophilicity). Mixtures of neutral azoles or pyridines and weakly acidic ammonium salts were also shown to be useful activators that allow the acidity and nucleophilicity to be tuned independently of each other.

Saccharide-accelerated hydrolysis of boronic acid imines

Twenty substituted N-benzylidineaniline derivatives have been synthesised and their kinetic behaviour investigated. The rate of hydrolysis of the boronic acid imines was found to be accelerated by added saccharide. Catalytic activity was only observed below the pKa of the boronic acid. Altering the concentration or type of saccharide revealed a Brønsted-like linear free energy relationship, indicating that intramolecular general acid catalysis was operating. Structure–activity relationship studies demonstrated that the system's electronic demands were independent of the boronic acid moiety.

Formation and stability of peptide enolates in aqueous solution.

Second-order rate constants k(DO) (M(-1) s(-1)) were determined in D(2)O for deprotonation of the N-terminal alpha-amino carbon of glycylglycine and glycylglycylglycine zwitterions, the internal alpha-amino carbon of the glycylglycylglycine anion, and the acetyl methyl group and the alpha-amino carbon of the N-acetylglycine anion and N-acetylglycinamide by deuterioxide ion. The data were used to estimate values of k(HO) (M(-1) s(-1)) for proton transfer from these carbon acids to hydroxide ion in H(2)O. Values of the pK(a) for these carbon acids ranging from 23.9 to 30.8 were obtained by interpolation or extrapolation of good linear correlations between log k(HO) and carbon acid pK(a) established in earlier work for deprotonation of related neutral and cationic alpha-carbonyl carbon acids. The alpha-amino carbon at a N-protonated N-terminus of a peptide or protein is estimated to undergo deprotonation about 130-fold faster than the alpha-amino carbon at the corresponding internal amino acid residue. The value of k(HO) for deprotonation of the N-terminal alpha-amino carbon of the glycylglycylglycine zwitterion (pK(a) = 25.1) is similar to that for deprotonation of the more acidic ketone acetone (pK(a) = 19.3), as a result of a lower Marcus intrinsic barrier to deprotonation of cationic alpha-carbonyl carbon acids. The cationic NH(3)(+) group is generally more strongly electron-withdrawing than the neutral NHAc group, but the alpha-NH(3)(+) and the alpha-NHAc substituents result in very similar decreases in the pK(a) of several alpha-carbonyl carbon acids.

RNA-sensitive N-isopropylacrylamide/vinylphenylboronic acid random copolymer

Random copolymers of N-isopropylacrylamide (NIPA) and 4-vinylphenylboronic acid (VPBA) were obtained by solution polymerization using 2,2′-azobisizobutyronitrile as the initiator in ethanol at 65 °C. NIPA-co-VPBA copolymer exhibited both temperature- and pH-sensitivity. Thermally reversible phase transitions were observed both in the acidic and alkaline pH region for the copolymers produced with different VPBA/NIPA feed ratios. The pH dependency of the lower critical solution temperature (LCST) was stronger for the copolymers produced with higher VPBA feed concentrations. RNA was selected as a model biomolecule having vicinal-diol and amino groups that were potentially reactive with the boronic acid groups of NIPA-co-VPBA copolymer. The effect of RNA concentration on the LCST of NIPA-co-VPBA copolymer was investigated in aqueous media at different pHs. Although no significant effect was observed at pH 4, 7 or 10.5, the LCST decreased linearly with increasing RNA concentration at a pH approximately equal to the pKa of boronic acid. This behavior was explained by considering the binding of RNA onto the copolymer chains to occur via two types of complex formation. For the formation of these complexes, the amino and vicinal-diol groups of RNA should react with the boronic acid groups of the copolymer in the tetrahedral anionic form. The results indicated that NIPA-co-VPBA copolymer could be utilized as a new reagent for the determination of RNA concentration in aqueous media. The proposed method was valid for the RNA concentration range of 0–4 g · mL−1. The schematical representation of the possible interactions between NIPA-co-VPBA copolymer and RNA. (A) A typical structure of single-stranded RNA. (B) Tetrahedral anionic form of boronic acid groups. (C) The interaction between the amino groups of the unpaired bases of RNA and the boronic acid groups of the copolymer. (D) Cyclic borate ester formation by the interaction between vicinal diol groups located at the 3′-end of RNA and boronic acid groups of the copolymer.

Revision of the Model System Concept for the Prediction of pKa's in Proteins

An approach to modeling the protonation equilibria in molecular systems with conformational flexibility, applied to pKa prediction in proteins, is formulated. This approach is based on the widely used concept of model system, usually identified with a free amino acid (model compound). However, analysis of the influence of conformational variability on the observed pKa for the free amino acids points to the necessity of reducing the model system to only the set of atoms defining an the essentially nonflexible group (model group). A method for parametrizing the corresponding pKa(model), based on the hybrid Molecular Dynamics and Poisson−Boltzmann model, is presented. The results are tested on two proteins: hen egg white lysozyme and turkey ovomucoid third domain. Comparison between the predicted and experimental pKa values for these systems allows one to examine the problem of the magnitude of the dielectric constant to be used for the protein in this kind of modeling. The proposed methodology may be extended to any system involving proton exchange.

Regulation of catalase enzyme activity by cell signaling molecules.

Mitogenic cell proliferation requires a rapid and transient H2O2 generation, which is blocked by catalase or PKA activators. Previously, we observed that anemic HIV(+) individuals expressed acidic pIs of catalase in RBC with significantly high activities [Mol Cell Biochem 165: 77-81, 1996]. These findings led us to hypothesize that cell signaling molecules regulate catalase to control cell mitogenesis. To test the hypothesis, we determined (i) whether RBC counts correlate with their catalase activities, (ii) whether protein kinases and phosphatases alter catalase activity in vitro, and (iii) whether protein kinase activators increase catalase activity to suppress proliferation of cultured cells. The results indicated that RBC counts inversely correlated with RBC catalase activities in both HIV(+) (r: -0.6769, r2: 0.4582, n: 69 male, p < 0.0001) and HIV(-) (r: -0.3827, r2: 0.1464, n: 177 male, p < 0.0001) populations. Catalytic PKA, PKC and Casein Kinase II, but none of PKG, Ca2+/calmodulin kinase II and p34cdc/cyclinB, rapidly elevated catalase activity in vitro by up to 2-fold. Whereas a major CAT subunit (60 kDa) showed immunoreactive phosphoserine and phosphothreonine, the kinases- and gamma-32P-ATP-dependent phosphorylation occurred with a minor component (110 kDa). Among PKC isozymes examined, PKCzeta was the most effective modulator followed by PKCgamma, and protein phosphatase 1gamma and 2A decreased the catalase activity. PKA and PKCzeta activators of forskolin and okadaic acid increased catalase activity and 110 kDa expression in NIH3T3 cells up to 2.4-fold and suppressed the cell growth, showing an inverse correlation of the indices (r: -0.9286, r2: 0.8622, n: 18, p < 0.0001). Taken together, these results suggest for the first time that catalase is under the regulation of cell signaling molecules and capable of modulating mitogenic cell proliferation.

Synthesis and Acidity of 5-Phenyltetrazol-2-ylalkanoic Acids and the Corresponding 5-(5-Phenyltetrazol-2-ylalkyl)tetrazoles

We have obtained 5-phenyltetrazol-2-ylalkanoic acids and their derivatives containing terminal nitrile, amide, and tetrazol-5-yl groups. Tetrazolylalkanoic acids with two (pK a 4.93) and three (pK a 5.45) bridging methylene groups are weaker acids than the corresponding ditetrazoles pK a 4.68 and 5.29 respectively). However, the acidity of 5-phenyltetrazol-2-ylacetic acid (pK a 3.12), is higher than acidity of the corresponding ditetrazole (pK a 3.27).

Revisiting the Kinetics and Mechanism of Bromate-Bromide Reaction

The bromate-bromide reaction was investigated in an acidity range not studied yet. The reaction was followed at the Br2/Br3- isosbestic point (lambda = 446 nm). It was observed a first-order behavior for bromate and bromide ions and a second-order behavior for H+ ion that results in the rate law nu = k[BrO3-][Br- ][H+]². This rate law suggests a mechanism involving two successive protonation of bromate followed by the interaction of the intermediate species H2BrO3+ with bromide. These results disagree with the obtained by other authors who observed a second-order behavior for the bromide and first-order for H+, and have proposed intermediate species like H2Br2O3 and HBr2O3-. The second-order for [H+] observed in the range 0.005 <= [H+] <= 2.77 mol L-1 sets down that the pKa of bromic acid, HBrO3, must be lower than -0.5 (T = 25 °C), different from all other values for this pKa proposed in the literature.

Nucleophilic and acid catalysis in phosphoramidite alcoholysis

Numerous triflates, mesylates, chlorides, trifluoroacetates and tetrazolides of trialkylammonium, pyridinium and azolium ions have been studied as activators for the reaction of N,N,O,O′-tetraisopropylphosphoramidite with propan-2-ol in acetonitrile. The progress of the reactions was followed by 31P NMR spectroscopy, and the pKa values of the activators were determined by a 13C NMR spectroscopic method based on competing simultaneous protonation of two bases. The salts promoted the reaction both as acids and nucleophiles, the acidity playing a more important role than the nucleophilicity. The Bronsted α value for the general acid catalysis was observed to range from 0.6 to 0.9 and the βnucl value to be 0.2 (pKa of the conjugate acid used as the measure of nucleophilicity). Mixtures of neutral azoles or pyridines and weakly acidic ammonium salts were also shown to be useful activators that allow the acidity and nucleophilicity to be tuned independently of each other.

Effect of Dissolved CO2 on Gran Plots

This paper discusses the determination of the pKa of a weak acid by the use of a Gran plot and the effect of CO2 dissolved in the titrant, a strong base solution. Experimental examples are shown for the titration of benzoic acid with "CO2-free" and CO2-containing KOH solutions. Dissolved CO2 does not cause a large error in the determination of pKa by the use of Gran plots, even when the amount of CO2 dissolved in the titrant is so high that the simulation of the titration curve gives a serious error in the pKa value. Owing to this advantage of Gran plots, the preparation and storage of strong base solutions used for Gran plots are simple, and hence the determination of the pKa value of a weak acid can be completed in a single 3-hour undergraduate laboratory.

Structural insights into the catalytic mechanism of a family 18 exo-chitinase.

Chitinase B (ChiB) from Serratia marcescens is a family 18 exo-chitinase whose catalytic domain has a TIM-barrel fold with a tunnel-shaped active site. We have solved structures of three ChiB complexes that reveal details of substrate binding, substrate-assisted catalysis, and product displacement. The structure of an inactive ChiB mutant (E144Q) complexed with a pentameric substrate (binding in subsites -2 to +3) shows closure of the "roof" of the active site tunnel. It also shows that the sugar in the -1 position is distorted to a boat conformation, thus providing structural evidence in support of a previously proposed catalytic mechanism. The structures of the active enzyme complexed to allosamidin (an analogue of a proposed reaction intermediate) and of the active enzyme soaked with pentameric substrate show events after cleavage of the glycosidic bond. The latter structure shows reopening of the roof of the active site tunnel and enzyme-assisted product displacement in the +1 and +2 sites, allowing a water molecule to approach the reaction center. Catalysis is accompanied by correlated structural changes in the core of the TIM barrel that involve conserved polar residues whose functions were hitherto unknown. These changes simultaneously contribute to stabilization of the reaction intermediate and alternation of the pKa of the catalytic acid during the catalytic cycle.

Solvolysis of 1-Decenyl(phenyl)iodonium Tetrafluoroborate: Mechanisms of Nucleophilic Substitution and Elimination

Abstract Solvolysis of (E)-1-decenyl(phenyl)iodonium tetrafluoroborate 1 was carried out in some alcohols, acetic acid, and mixed aqueous alcoholic solvents at 50–60 °C and the effects of added carboxylates and other salts were also examined in methanol. Reaction products include enol derivatives (substitution) and 1-decyne (elimination) as well as iodobenzene. Rates for the solvolysis increase with increasing nucleophilicity of the solvent but have no correlation with the solvent ionizing power. The substitution occurs mostly via inversion of configuration, and is concluded to follow the in-plane SN2 mechanism with a minor concomitant out-of-plane SN2 pathway. The reactions with the deuterated substrates show that stronger bases of pKa of the conjugate acid &amp;gt; 3 induce exclusively α-elimination of 1 in methanol. However, both α- and β-elimination occur in neutral methanol in a ratio of about 3/1 besides the substitution. Mechanisms for these reactions are proposed.