The pH inside a swollen polyelectrolyte gel: poly(N-vinylimidazole)

The pH inside a dissolved polyelectrolyte coil or a swollen ionic polymer network is not accessible to direct measurement. It is here calculated through a simple model, based on Donnan equilibrium, counterion condensation (for charge density exceeding the critical value), and balance of mobile ions, without any assumption on the pKa of the ionizable groups. The data needed for the calculation with this model are polymer concentration, pH value in the initial solution, and pH value in the bath at equilibrium. All three can be determined experimentally by a batch method where the polymer is immersed in a different pot for each starting pH. The model is applied to a sample system, namely, chemically cross-linked poly(N-vinylimidazole) immersed in acidic baths of different pH values. The imidazole units are basic and become protonated by the acid, thus changing the pH of the initial bath. The model shows how the pH developed inside the swollen gel is several units higher than the pH of the bath at equilibrium, both with or without the correction for counterion condensation. Consequently, when the pKa of the polyelectrolyte is determined in the usual way (with the pH measured in the external bath), it gives an apparent value that is several units below the pKa determined from the actual pH inside the swollen gel at equilibrium. The inclusion of the counterion condensation decreases very slightly the polymer basicity. Surface effects and intramolecular association between protonated and unprotonated imidazole rings are discussed to explain the pKa behavior in the limit of low degree of ionization.     

Investigation of proton transport tautomerism in clusters of protonated nucleic acid bases (cytosine, uracil, thymine, and adenine) and ammonia by high-pressure mass spectrometry and ab initio calculations

The energetics of the ion-molecule interactions and structures of the clusters formed between protonated nucleic acid bases (cytosine, uracil, thymine, and adenine) and ammonia have been studied by pulsed ionization high-pressure mass spectrometry (HPMS) and ab initio calculations. For protonated cytosine, uracil, thymine, and adenine with ammonia, the measured enthalpies of association with ammonia are -21.7, -27.9, -22.1, and -17.5 kcal mol-1, respectively. Different isomers of the neutral and protonated nucleic acid bases as well as their clusters with ammonia have been investigated at the B3LYP/6-31+G(d,p) level of theory, and the corresponding binding energetics have also been obtained. The potential energy surfaces for proton transfer and interconversion of the clusters of protonated thymine and uracil with ammonia have been constructed. For cytosine, the experimental binding energy is in agreement with the computed binding energy for the most stable isomer, CN01-01, which is derived from the enol form of protonated cytosine, CH01, and ammonia. Although adenine has a proton affinity similar to that of cytosine, the binding energy of protonated adenine to ammonia is much lower than that for protonated cytosine. This is shown to be due to the differing types of hydrogen bonds being formed. Similarly, although uracil and thymine have similar structures and proton affinities, the binding energies between the protonated species and ammonia are different. Strikingly, the addition of a single methyl group, in going from uracil to thymine, results in a significant structural change for the most stable isomers, UN01-01 and TN03-01, respectively. This then leads to the difference in their measured binding energies with ammonia. Because thymine is found only in DNA while uracil is found in RNA, this provides some potential insight into the difference between uracil and thymine, especially their interactions with other molecules.     

The models of proton assisted and the unassisted formation of CGC base triplets

The triple helix is formed by combining a double and a single strand DNAs in low pH and dissociates in high pH. Under such conditions, protonation of cytosine in the single strand is necessary for triplex formation where cytosine-guanine-cytosine (CGC+) base triplet stabilizes the triple helix. The mechanism of CGC+ triplet formation from guanine-cytosine (GC) and a protonated cytosine (C+) shows the importance of N3 proton. Similarly in the case of CGC (unprotonated) triplet, the donor acceptor H-bond at N3 hydrogen of the cytosine analog (C) initiates the interaction with GC. The correspondence between the two models of triplets, CGC+ and CGC, unambiguously assigned that protonation at N3 cytosine in low pH to be the first step in triplet formation, but a donor acceptor triplet (CGC) can be designed without involving a proton in the Hoogsteen H-bond. Further, the bases of cytosine analogue also show the capability of forming Watson Crick (WC) H-bonds with guanine.     

Direct measurement of a pK(a) near neutrality for the catalytic cytosine in the genomic HDV ribozyme using Raman crystallography

The hepatitis delta virus (HDV) ribozyme uses a cytosine to facilitate general acid-base catalysis. Biochemical studies suggest that C75 has a pKa perturbed to near neutrality. To measure this pKa directly, Raman spectra were recorded on single ribozyme crystals using a Raman microscope. A spectral feature arising from a single neutral cytosine was identified at 1528 cm(-1). At low pH, this mode was replaced with a new spectral feature. Monitoring these features as a function of pH revealed pKa values for the cytosine that couple anticooperatively with Mg2+ binding, with values of 6.15 and 6.40 in the presence of 20 and 2 mM Mg2+, respectively. These pKa values agree well with those obtained from ribozyme activity experiments in solution. To correlate the observed pKa with a specific nucleotide, crystals of C75U, which is catalytically inactive, were examined. The Raman difference spectra show that this mutation does not affect the conformation of the ribozyme. However, crystals of C75U did not produce a signal from a protonatable cytosine, providing strong evidence that protonation of C75 is being monitored in the wild-type ribozyme. These studies provide the first direct physical measurement of a pKa near neutrality for a catalytic residue in a ribozyme and show that ribozymes, like their protein enzyme counterparts, can optimize the pKa of their side chains for proton transfer.     

Evaluation of the interaction of propranolol with 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) liposomes: the Langmuir model

The interaction of the amine containing beta-receptor blocking agent propranolol (Ppn) with dimyristoylphosphatidylcholine (DMPC) vesicles was studied. Using a centrifugation assay, the protonated as well as unprotonated amount of the drug sorbed was verified, whereas the binding of the protonated Ppn was deduced from the surface charge density of the vesicles as calculated from electrophoretic mobility measurements. Assuming a 1:1 binding, a Langmuir model with only two parameters was found to be sufficient to fit all experimental data. Sensitivity analysis revealed that the estimated values of these parameters were reliable and independent from each other. These parameters were truly intrinsic, as electrostatic interactions were accounted for in the model. It was found that the pKa of Ppn shifted from 9.24, when dissolved in water, downward by 1.34 units upon sorption, indicating that the intrinsic partition coefficient of the unprotonated Ppn was about 22 times higher than that of the protonated analog. In addition, a significant increase in the affinity of both Ppn analogs with increasing salt concentration was found. Theoretical analysis revealed that the Langmuir sorption model may be considered as a partitioning model with decreasing partition coefficient as the sorbed amount increases. Thus, the Langmuir model provides a better fit than a simple partition model at conditions that induce a substantial amount of propranolol sorbed, such as high pH and high propranolol concentrations.     

Determination of acid-base dissociation constants of amino- and guanidinopurine nucleotide analogs and related compounds by capillary zone electrophoresis

CZE has been applied for determination of acid-base dissociation constants (pKa) of ionogenic groups of newly synthesized amino- and (amino)guanidinopurine nucleotide analogs, such as acyclic nucleoside phosphonate, acyclic nucleoside phosphonate diesters and other related compounds. These compounds bear characteristic pharmacophores contained in various important biologically active substances, such as cytostatics and antivirals. The pKa values of ionogenic groups of the above compounds were determined by nonlinear regression analysis of the experimentally measured pH dependence of their effective electrophoretic mobilities. The effective mobilities were measured by CZE performed in series of BGEs in a broad pH range (3.50-11.25), at constant ionic strength (25 mM) and temperature (25 degrees C). pKa values were determined for the protonated guanidinyl group in (amino)guanidino 9-alkylpurines and in (amino)guanidinopurine nucleotide analogs, such as acyclic nucleoside phosphonates and acyclic nucleoside phosphonate diesters, for phosphonic acid to the second dissociation degree (-2) in acyclic nucleoside phosphonates of amino and (amino)guanidino 9-alkylpurines, and for protonated nitrogen in position 1 (N1) of purine moiety in acyclic nucleoside phosphonates of amino 9-alkylpurines. Thermodynamic pKa of protonated guanidinyl group was estimated to be in the range of 7.75-10.32, pKa of phosphonic acid to the second dissociation degree achieved values of 6.64-7.46, and pKa of protonated nitrogen in position 1 of purine was in the range of 4.13-4.89, depending on the structure of the analyzed compounds.     

Gas-phase conjugation to arginine residues in polypeptide ions via N-hydroxysuccinimide ester-based reagent ions

Gas-phase conjugation to unprotonated arginine side-chains via N-hydroxysuccinimide (NHS) esters is demonstrated through both charge reduction and charge inversion ion/ion reactions. The unprotonated guanidino group of arginine can serve as a strong nucleophile, resulting in the facile displacement of NHS from NHS esters with concomitant covalent modification of the arginine residue. This reactivity is analogous to that observed with unprotonated primary amines such as the N-terminus or ε-amino group of lysine. In solution, however, the arginine residues tend to be protonated at pH values low enough to prevent hydrolysis of NHS esters, which would render them relatively unreactive with NHS esters. This work demonstrates novel means for gas-phase conjugation to arginine side chains in polypeptide ions.     

Computational determination of aqueous pKa values of protonated benzimidazoles (part 1)

Benzimidazoles are the organic compounds investigated in this work. The experimental determination of the pKa values of protonated benzimidazoles in water is a challenge because of their low solubility. In addition, some derivatives are involved in tautomeric equilibria which increase the complexity of the theoretical pKa determinations. In the present study, different approaches are considered to develop a methodology for the accurate prediction of aqueous pKa values of protonated benzimidazoles at 298.15 K. We have considered different reaction schemes for approximating the acid dissociation equilibrium; two distinct equations are used for the calculation of pKa values, and a number of levels of theory and empirical corrections are applied in the process of working toward this aim. The best correlations between the experimental and calculated data are obtained at the B3LYP/6-31+G(d,p)-PCM(opt) level of theory. The predictive capabilities of the methodologies attempted are tested with two compounds that were not included in the set of benzimidazoles initially investigated. The direct calculations differ significantly from the expected values, but the pKa values calculated using the correlation equations are very similar and in reasonable agreement with the expected pKa values.     

COMPLEXING OF RIBOFLAVIN AND ITS 2-SUBSTITUTED ANALOGS WITH ADENOSINE AND OTHER 6-SUBSTITUTED PURINE DERIVATIVES*

Abstract Fluorescence properties of riboflavin and its 2-substituted analogs and the quenching of fluorescence which occurs upon complexing with adenosine and other 6-substituted purine derivatives have been examined at different concentrations of interactants and hydrogen ion. The 6-substituted purines and their ribosides show varying degrees of association with riboflavin. Successive N-alkylation of the 6-amino group of purine ribosides leads to more stable complexing in the order ethyl > methyl > propyl with riboflavin and its analog. These results suggest that such groups, including the 6-amino group of adenine or adenine moiety of FAD, do not directly interact with flavins by hydrophobic or hydrogen bonding. Lowering the pH to above that required to protonate the isoalloxazine system disrupts the intermolecular complexes. Hence, only the unprotonated bases can form such complexes. The 2-substituted aminoriboflavins, as well as FAD, exhibit fluorescence optima upon changing pH. The species involved appear to be a non-fluorescent form with protonated isoalloxazine and amine or adenine portions at low pH, a fluorescent form with only the amine or adenine portions protonated at moderately acid pH, and a non-fluorescent form which is intramolecularly quenched at higher pH. The general electron donating properties of the amines may be the common reason for their quenching of fluorescence in inter- and intramolecular complexes with flavins.     

Differential SERS activity of gold and silver nanostructures enabled by adsorbed poly(vinylpyrrolidone)

We report that poly(vinylpyrrolidone) (PVP), a common stabilizer of colloidal dispersions of noble metal nanostructures, has a dramatic effect on their surface-enhanced Raman scattering (SERS) activity and enables highly selective SERS detection of analytes of various type and charge. Nanostructures studied include PVP-stabilized Au-Ag nanoshells synthesized by galvanic exchange reaction of citrate-reduced Ag nanoparticles (NPs), as well as solid citrate-reduced Ag and Au NPs, both before and after stabilization with PVP. All nanostructures were characterized in terms of their size, surface plasmon resonance wavelength, surface charge, and chemical composition. While the SERS activities of the parent citrate-reduced Ag and Au NPs are similar for rhodamine 6G (R6G) and 1,2-bis(4-pyridyl)ethylene (BPE) at various pH values, PVP-stabilized nanostructures demonstrate large differences in SERS enhancement factors (EFs) between these analytes depending on their chemical nature and protonation state. At pH values higher than BPE's pK(a2) of 5.65, where the analyte is largely unprotonated, the PVP-coated Au-Ag nanoshells showed a high SERS EF of >10(8). In contrast, SERS EFs were 10(3)- to 10(5)-fold lower for the protonated form of BPE at lower pH values, or for the usually highly SERS-active cationic R6G. The differential SERS activity of PVP-stabilized nanostructures is a result of discriminatory binding of analytes within-adsorbed PVP monolayer and a subsequent increase of analyte concentration at the nanostructure surface. Our experimental and theoretical quantum chemical calculations show that BPE binding with PVP-stabilized Au-Ag nanoshells is stronger when the analyte is in its unprotonated form as compared to its cationic, protonated form at a lower pH.     

核酸水解产物嘌呤、嘧啶碱基在BDS柱上的分离及测定

 用高效液相色谱法测定了核酸水解的中间产物及最终产物 6种嘌呤、嘧啶碱基 ,探讨了色谱柱、流动相等对其分离的影响 ,确定了最佳色谱条件为 :HypersilBDS C18柱 ,乙腈 0 1mol/LKH2 PO4 (H3 PO4 调节 pH至4 0 5 ) (体积比为 2∶98)作流动相 ,紫外检测器在 2 6 0nm波长下检测。方法的精密度在 3%以内 ,回收率在 82 %～ 114%。方法应用于酵母核酸样品的测定中 ,取得了很好的结果。     

Probing pH-dependent dissociation of HdeA dimers

HdeA protein is a small, ATP-independent, acid stress chaperone that undergoes a dimer-to-monomer transition in acidic environments. The HdeA monomer binds a broad range of proteins to prevent their acid-induced aggregation. To understand better HdeA's function and mechanism, we perform constant-pH molecular dynamics simulations (CPHMD) to elucidate the details of the HdeA dimer dissociation process. First the pK(a) values of all the acidic titratable groups in HdeA are obtained and reveal a large pK(a) shift only for Glu(37). However, the pH-dependent monomer charge exhibits a large shift from -4 at pH > 6 to +6 at pH = 2.5, suggesting that the dramatic change in charge on each monomer may drive dissociation. By combining the CPHMD approach with umbrella sampling, we demonstrate a significant stability decrease of the HdeA dimer when the environmental pH changes from 4.0 to 3.5 and identify the key acidic residue-lysine interactions responsible for the observed pH sensing in HdeA chaperon activity function.     

Complexation of Amino Acid Methylesters and Amino Alcohols by 18-Crown-6 and Benzo-18-crown-6 in Methanol

The complexation of protonated amino acid methylesters and amino alcohols bythe ligands 18-crown-6 (18C6) and benzo-18-crown-6 (B18C6) has been studiedin methanol using calorimetric titrations. No influence of the anions upon thestability constants and thermodynamic data for the reaction of protonated aminoacid methylesters with both ligands has been noticed, which indicates the completedissociation of the salts employed. A similar effect has been observed for thecomplexation of protonated and unprotonated amino alcohols with 18C6 andB18C6. The values obtained of the reaction enthalpies for the complexation ofprotonated amino acid methylesters with 18C6 are larger than those correspondingto the complexation with B18C6. The results demonstrate that the complex formationof unprotonated amino alcohols is favored by entropic contributions, while thecomplexation of protonated amino alcohols is favored by enthalpic contributionswith both ligands. The influence of various substituents on the complexation behaviorof amino acid and amino alcohol has also been investigated.     

Evidence for basic ferryls in cytochromes P450

Using a combination of M?ssbauer spectroscopy and density functional calculations, we have determined that the ferryl forms of P450(BM3) and P450cam are protonated at physiological pH. Density functional calculations were performed on large active-site models of these enzymes to determine the theoretical M?ssbauer parameters for the ferryl and protonated ferryl (Fe(IV)OH) species. These calculations revealed a significant enlargement of the quadrupole splitting parameter upon protonation of the ferryl unit. The calculated quadrupole splittings for the protonated and unprotonated ferryl forms of P450(BM3) are DeltaE(Q) = 2.17 mm/s and DeltaE(Q) = 1.05 mm/s, respectively. For P450cam, they are DeltaE(Q) = 1.84 mm/s and DeltaE(Q) = 0.66 mm/s, respectively. The experimentally determined quadrupole splittings (P450(BM3), DeltaE(Q) = 2.16 mm/s; P450cam, DeltaE(Q) = 2.06 mm/s) are in good agreement with the values calculated for the protonated forms of the enzymes. Our results suggest that basic ferryls are a natural consequence of thiolate-ligated hemes.     

Effects of protonation on proton transfer processes in Watson–Crick adenine–thymine base pair

Intermolecular proton transfer processes in the Watson and Crick adenine–thymine neutral and protonated base pairs have been studied using the density functional theory (DFT) with the non-local hybrid B3LYP density functional. Protonated systems subject to study are those resulting from protonation at the main basic sites of the base pair model, namely N₇ and N₃ of adenine and O₂^′ and O₄^′ of thymine. Protonation of adenine induces a strengthening by about 4–5 kcal/mol of the base pair and does not significantly modify the double proton transfer energy profile obtained for the unprotonated system. On the other hand, protonation at the O₄^′ and O₂^′ thymine moiety causes thymine’s N₃ proton to spontaneously transfer to adenine while non-transferred minima disappear at this level of theory. The different behaviour between protonated adenine– thymine and protonated guanine–cytosine is discussed. Electronic Supplementary Material The online version of this article (doi:) contains supplementary material, which is available to authorized users. Contribution to the Fernando Bernardi Memorial Issue.     

Ab initio calculations and mass spectrometric determination of the gas-phase proton affinities of 4,4'-disubstituted 2,2'-bipyridines

The gas-phase proton affinities of 4,4'-di(R)-2,2'-bipyridines (R: H, Br, Cl, NO(2), Me) were determined by mass spectrometric measurements and by ab initio calculations at the HF/6-31G and MP2/6-31G levels of theory. The energy barriers for rotation about the central C-C bond were also studied computationally. Two minima were found for both unprotonated and protonated species, the global minima being at the trans planar and cis planar conformations, respectively. Local minima for the unprotonated compounds were at the cis nonplanar conformation and for the protonated compounds at the trans nonplanar. Two different proton affinity values were calculated for each compound by employing different conformations for the protonated species. The computational values were in good agreement with the experimental proton affinities. Substituents affect the proton affinity according to their ability to withdraw or to donate electrons, halogen and nitro-substituted bipyridines having a lower proton affinity and methyl-substituted bipyridine having a higher proton affinity than 2,2'-bipyridine itself.     

A FLUORESCENCE STUDY OF TRYPTOPHAN-HISTIDINE INTERACTIONS IN THE PEPTIDE ANANTIN AND IN SOLUTION

Abstract—Anantin is a heptadecapeptide in which the C-terminal peptide chain pierces the covalently cyclized peptide ring formed by an amide link between the α-NH₂ end group and the β-carboxyl group of Asp(8). It contains a tryptophan and a histidine at positions 5 and 12 , respectively. Des-Phe(17)-anantin lacks the C-terminal phenylalanine. Fluorescence emission intensity as a function of pH follows the ionization of a single residue. The pK_a amounts to 7.23 ± 0.03 for anantin and is attributed to His(12). At pH 9 the quantum yield is 0.12 ± 0.01 for anantin, whereas at pH 4.5 the quantum yield decreases more than two-fold (0.05 2 0.01). Practically identical parameters are observed for des-Phe(17)-anantin. This pH dependency reveals intramolecular quenching of the excited indole ring of Trp(5) by the imidazole of His(12), which results in a marked decrease of the tryptophan fluorescence at low pH. In a multifrequency phase fluorometric study the fluorescence lifetimes for both peptides at pH 4.5 and pH 9 are determined. At both, pH fluorescence decay is well described by a sum of two exponentials. For anantin at pH 4.5 the lifetimes are 0.72 ± 0.07 ns and 1.67 ± 0.07 ns. At pH 9 the lifetimes are 1.11 ±0.12 ns and 2.55 ± 0.03 ns. In methanol we find two lifetimes for anantin: 0.68 ± 0.01 ns and 2.57 ± 0.01 ns. The lifetimes are found to be slightly dependent upon emission wavelength. For des-Phe(17)-anantin practically the same values are observed. The quenching of tryptophan fluorescence by histidine is further studied in solution using N-acetyl-tryptophanamide in the presence of increasing concentrations of imidazole in the protonated (pH 4.5) and unprotonated (pH 9) state and in methanol. At both pH values and in methanol, a linear increase in both the inverse of the steady-state fluorescence F_o/F and the inverse of the lifetime 1/τ with increasing imidazole concentration indicates that a collisional mechanism is at the root of the observed quenching. The quenching efficiency values, γ, are calculated and amount to about 0.32 at pH 4. 5 , 0.02 at pH 9 and 0.002 in methanol, showing that protonated imidazole is a better quencher than the unprotonated form, and that the nature of the solvent is involved even in the quenching by unprotonated imidazole. Tryptophan-histidine interactions in solution and in the peptide are compared.     

15N nuclear magnetic resonance studies of acid-base properties of pyridoxal-5'-phosphate aldimines in aqueous solution

By use of 15N NMR spectroscopy, we have measured the pKa values of the aldimines 15N-(pyridoxyl-5'-phosphate-idine)-methylamine (2a), N-(pyridoxyl-5'-phosphate-15N-idine)-methylamine (2b), and 15N-(pyridoxyl-idine)-methylamine (3). These aldimines model the cofactor pyridoxal-5'-phosphate (PLP, 1) in a variety of PLP-dependent enzymes. The acid-base properties of the aldimines differ substantially from those of the free cofactor in the aldehyde form 1a or in the hydrated form 1b, which were also investigated using 15N NMR for comparison. All compounds contain three protonation sites, the pyridine ring, the phenol group, and the side chain phosphate (1, 2) or hydroxyl group (3). In agreement with the literature, 1a exhibits one of several pKas at 2.9 and 1b at 4.2. The 15N chemical shifts indicate that the corresponding deprotonation occurs partially in the pyridine and partially in the phenolic site, which compete for the remaining proton. The equilibrium constant of this ring-phenolate tautomerism was measured to be 0.40 for 1a and 0.06 for 1b. The tautomerism is essentially unaltered above pH 6.1, where the phosphate group is deprotonated to the dianion. This means that the pyridine ring is more basic than the phenolate group. Pyridine nitrogen deprotonation occurs at 8.2 for 1a and at 8.7 for 1b. By contrast, above pH 4 the phosphate site of 2 is deprotonated, while the pyridine ring pKa is 5.8. The Schiff base nitrogen does not deprotonate below pH 11.4. When the phosphate group is removed, the pKa of the Schiff base nitrogen decreases to 10.5. The phenol site cannot compete for the proton of the Schiff base nitrogen and is present in the entire pH range as a phenolate, preferentially hydrogen bonded to the solvent. The intrinsic 15N chemical shifts provide information about the hydrogen bond structures of the protonated and unprotonated species involved. Evidence is presented that the intramolecular OHN hydrogen bond of PLP aldimines is broken in aqueous solution. The coupling between the inter- and intramolecular OHN hydrogen bonds is also lost in this environment. The pyridine ring of the PLP aldimines is not protonated in aqueous solution near neutral pH. The basicity of the aldimine nitrogens would be even lower without the doubly negatively charged phosphate group. Protonation of both the Schiff base and pyridine nitrogens has been discussed as a prerequisite for catalytic activity, and the implications of the present findings for PLP catalysis are discussed.