Solution pK Research Articles

Proton transfer facilitated by ligand binding. An energetic analysis of the catalytic mechanism of Trypanosoma cruzi trans-sialidase.

Trans-sialidase is a crucial enzyme for the infection of Trypanosoma cruzi, the protozoa responsible for Chagas' disease in humans. This enzyme catalyzes the transfer of sialic acids from mammalian host cells to parasitic cell surfaces in order to mask the infection from the host's immune system. It represents a promising target for the development of therapeutics to treat the disease and has been subject of extensive structural studies. Elaborate experiments suggested formation of a long-lived covalent intermediate in the catalytic mechanism and identified a Tyr/Glu pair as an unusual catalytic couple. This requires that the tyrosine hydroxyl proton is transferred to the carboxylate group of glutamate before the nucleophilic attack. Since the solution pK(a)s of tyrosine and glutamate are very different, this transfer can only be accomplished if the reaction environment selectively stabilizes the product state. We compute the free energy profile for the proton transfer in different environments, and our results indicate that it can take place in the active site of trans-sialidase, but only after substrate binding. By means of the energy decomposition method, we explain the influence that the active site residues exert on the reaction and how the pattern is changed when the substrate is present. This study represents an initial step that can shed light on our understanding of the catalytic mechanism of this reaction.

Hydrogen Bonding in the Active Site of Ketosteroid Isomerase: Electronic Inductive Effects and Hydrogen Bond Coupling

Computational studies are performed to analyze the physical properties of hydrogen bonds donated by Tyr16 and Asp103 to a series of substituted phenolate inhibitors bound in the active site of ketosteroid isomerase (KSI). As the solution pK(a) of the phenolate increases, these hydrogen bond distances decrease, the associated nuclear magnetic resonance (NMR) chemical shifts increase, and the fraction of protonated inhibitor increases, in agreement with prior experiments. The quantum mechanical/molecular mechanical calculations provide insight into the electronic inductive effects along the hydrogen bonding network that includes Tyr16, Tyr57, and Tyr32, as well as insight into hydrogen bond coupling in the active site. The calculations predict that the most-downfield NMR chemical shift observed experimentally corresponds to the Tyr16-phenolate hydrogen bond and that Tyr16 is the proton donor when a bound naphtholate inhibitor is observed to be protonated in electronic absorption experiments. According to these calculations, the electronic inductive effects along the hydrogen bonding network of tyrosines cause the Tyr16 hydroxyl to be more acidic than the Asp103 carboxylic acid moiety, which is immersed in a relatively nonpolar environment. When one of the distal tyrosine residues in the network is mutated to phenylalanine, thereby diminishing this inductive effect, the Tyr16-phenolate hydrogen bond becomes longer and the Asp103-phenolate hydrogen bond shorter, as observed in NMR experiments. Furthermore, the calculations suggest that the differences in the experimental NMR data and electronic absorption spectra for pKSI and tKSI, two homologous bacterial forms of the enzyme, are due predominantly to the third tyrosine that is present in the hydrogen bonding network of pKSI but not tKSI. These studies also provide experimentally testable predictions about the impact of mutating the distal tyrosine residues in this hydrogen bonding network on the NMR chemical shifts and electronic absorption spectra.

Elucidating the Nature of theStreptomyces plicatusβ-Hexosaminidase-Bound Intermediate Using ab initio Molecular Dynamics Simulations

By using all-atom ab initio molecular dynamics simulations, the solution pK(a) of the oxazolinium ion intermediate formed during the Streptomyces plicatus beta-hexosaminidase (SpHex)-catalyzed hydrolysis of beta-D-N-acetylglucosaminides is estimated as pK(a) = 7.7. The structure and protonation state of the enzyme-bound intermediate have also been investigated, using hybrid QM/MM methods. The protonation state and conformational properties of the enzyme bound intermediate are found to be sensitive to the protonation state of a number of ionisable residues (other than the aspartate-glutamate catalytic dyad) suggesting that the microscopic electrostatic environment of SpHex not only perturbs the relative magnitudes of the pK(a) values of the Asp side chain carboxylate and oxazolinium ion but also that SpHex binds its intermediate in a distorted conformation with respect to its ground-state conformation in solution.

Tetracaine-Membrane Interactions: Effects of Lipid Composition and Phase on Drug Partitioning, Location, and Ionization

Interactions of the local anesthetic tetracaine with unilamellar vesicles made of dimyristoyl or dipalmitoyl phosphatidylcholine (DMPC or DPPC), the latter without or with cholesterol, were examined by following changes in the drug's fluorescent properties. Tetracaine's location within the membrane (as indicated by the equivalent dielectric constant around the aromatic fluorophore), its membrane:buffer partition coefficients for protonated and base forms, and its apparent pK a when adsorbed to the membrane were determined by measuring, respectively, the saturating blue shifts of fluorescence emission at high lipid:tetracaine, the corresponding increases in fluorescence intensity at this lower wavelength with increasing lipid, and the dependence of fluorescence intensity of membrane-bound tetracaine (TTC) on solution pH. Results show that partition coefficients were greater for liquid-crystalline than solid-gel phase membranes, whether the phase was set by temperature or lipid composition, and were decreased by cholesterol; neutral TTC partitioned into membranes more strongly than the protonated species (TTCH +). Tetracaine's location in the membrane placed the drug's tertiary amine near the phosphate of the headgroup, its ester bond in the region of the lipids’ ester bonds, and associated dipole field and the aromatic moiety near fatty acyl carbons 2–5; importantly, this location was unaffected by cholesterol and was the same for neutral and protonated tetracaine, showing that the dipole-dipole and hydrophobic interactions are the critical determinants of tetracaine's location. Tetracaine's effective pK a was reduced by 0.3–0.4 pH units from the solution pK a upon adsorption to these neutral bilayers, regardless of physical state or composition. We propose that the partitioning of tetracaine into solid-gel membranes is determined primarily by its steric accommodation between lipids, whereas in the liquid-crystalline membrane, in which the distance between lipid molecules is larger and steric hindrance is less important, hydrophobic and ionic interactions between tetracaine and lipid molecules predominate.

Estimation of Adsorption Capacity for Dissociating and Non Dissociating Aromatic Compounds on Activated Carbon with Different Models

The process of adsorption of two dissociating and two non-dissociating aromatic compounds from dilute aqueous solutions on an untreated commercially available activated carbon (B.D.H.) was investigated systematically. All adsorption experiments were carried out in pH controlled aqueous solutions. The experimental isotherms were fitted into four different models (Langmuir homogenous Models, Langmuir binary Model, Langmuir-Freundlich single model and Langmuir-Freundlich double model). Variation of the model parameters with the solution pH was studied and used to gain further insight into the adsorption process. The relationship between the model parameters and the solution pH and pK(a) was used to predict the adsorption capacity in molecular and ionic form of solutes in other solution. A relationship was sought to predict the effect of pH on the adsorption systems and for estimating the maximum adsorption capacity of carbon at any pH where the solute is ionized reasonably well. N-2 and CO2 adsorption were used to characterize the carbon. X-ray Photoelectron Spectroscopy (XPS) measurement was used for surface elemental analysis of the activated carbon.

The structure and stability of biological metaphosphate, phosphate, and phosphorane compounds in the gas phase and in solution.

Density functional calculations of a series of metaphosphates, acyclic and cyclic phosphates and phosphoranes relevant to RNA catalysis are presented. Solvent effects calculated with three well-established solvation models are analyzed and compared. The structure and stability of the compounds are characterized in terms of thermodynamic quantities for isomerization and ligand substitution reactions, gas-phase proton affinities, and microscopic solution pK(a)() values. The large dataset of compounds allows the estimation of bond energies to determine the relative strengths of axial and equatorial P-O phosphorane single bonds and P-O single and double bonds in metaphosphates and phosphates. The relative apicophilicty of hydroxyl and methoxy ligands in phosphoranes are characterized. The results presented here provide quantitative insight into RNA catalysis and serve as a first step toward the construction of a high-level quantum database for development of new semiempirical Hamiltonian models for biological reactions

Calculating the acidity of silanols and related oxyacids in aqueous solution

Ab initio molecular orbital theory was used to calculate deprotonation energies and enthalpies (ΔE d, ΔH d) of oxyacid monomers and oligomers. Results were interpreted with reference to current phenomenological models for estimating metal-oxide surface acidities. The ultimate goal is to predict surface acidities using the ab initio method. We evaluated contributions to ΔE d and ΔH d from the electrostatic potential at the proton, electronic relaxation, geometric relaxation, solvation, and polymerization for the neutral-charge gas-phase molecules H 2O, CH 3OH, HCOOH, SiH 3OH, Si(OH) 4, Si 2O 7H 6, H 3PO 4, P 2O 7H 4, H 2SO 3, H 2SO 4, HOCl, HClO 4, Ge(OH) 4, As(OH) 3, and AsO(OH) 3. ΔE d, gas calculated at the modest 6-31G∗ HF of theory level correlates well with experimental pK a in solution, because hydration enthalpies for the acid anions (ΔH hyd, A−) are closely proportional to ΔE d, gas. That is, anion interaction energies with water in aqueous solution and with H + in the gas phase are closely correlated. Correction for differential hydration between an acid and its conjugate base permits generalization of the ΔE d, gas – pK a correlation to deprotonation reactions involving charged acids. Thus, stable protonated, neutral, and deprotonated species Si(OH) 3(OH 2) 1+, Si(OH) 4 0, Si(OH) 3O 1−, and Si(OH) 2O 2 2− have been characterized, and solution pK a’s for Si(OH) 3(OH 2) 1+ and Si(OH) 3O 1− were estimated, assuming that the charged species (Si(OH) 3(OH 2) 1+, Si(OH) 3O −1) fit into the same ΔE d, gas – pK a correlation as do the neutral acids. The correlation yields a negative pK a (∼ −5) for Si(OH) 3(OH 2) +1. Calculated ΔE d, gas also correlates well with the degree of O under-bonding evaluated using Brown’s bond-length based approach. ΔE d, gas increases along the series HClO 4 – Si(OH) 4 mainly because of increasingly negative potential at the site of the proton, not because of differing electronic or geometric relaxation energies. Thus, pK a can be correlated with underbondings or local electrostatic energies for the monomers, partially explaining the success of phenomenological models in correlating surface pK a of oxides with bond-strengths. Accurate evaluation of ΔH d, gas requires calculations with larger basis sets, inclusion of electron correlation effects, and corrections for vibrational, rotational, and translational contributions. Density functional and 2nd-order Moller-Plesset results for deprotonation enthalpies match well against higher-level G2(MP2) calculations. Direct calculation of solution pK a without resorting to correlations is presently impossible by ab initio methods because of inaccurate methods to account for solvation. Inclusion of explicit water molecules around the monomer immersed in a self-consistent reaction field (SCRF) provides the most accurate absolute hydration enthalpy (ΔH hyd) values, but IPCM values for the bare acid (HA) and anion (A −) give reasonable values of ΔH hyd, A − – ΔH hyd, HA values with much smaller computational expense. Polymers of silicate are used as model systems that begin to approach solid silica, known to be much more acidic than its monomer, Si(OH) 4. Polymerization of silicate or phosphate reduces their gas-phase ΔE d, gas relative to the monomers; differences in the electrostatic potential at H +, electronic relaxation and geometric relaxation energies all contribute to the effect. Internal H-bonding in the dimers results in unusually small ΔE d,gas which is partially counteracted by a reduced ΔH hyd. Accurate representation of hydration for oligomers persists as a fundamental problem in determining their solution pK a, because of the prohibitive cost involved in directly modeling interactions between many water molecules and the species of interest. Fortunately, though, the local contribution to the difference in hydration energy between the neutral polymeric acid and its anion seems to stabilize for a small number of explicit water molecules.

Role of D1-His190 in the proton-coupled oxidation of tyrosine YZ in manganese-depleted photosystem II.

To further characterize the role of D1-His190 in the oxidation of tyrosine Y(Z) in photosystem II, the pH dependence of P(680)(*)()(+) reduction was measured in H190A and Mn-depleted wild-type PSII particles isolated from the cyanobacterium, Synechocystis sp. PCC 6803. Measurements were conducted in the presence and absence of imidazole and other small organic bases. In H190A PSII particles, rapid reduction of P(680)(*)()(+) attributed to electron transfer from Y(Z) increased dramatically above pH 9, with an apparent pK(A) of approximately 10.3. In the presence of ethanolamine and imidazole, this dramatic increase occurred at lower pH values, with the efficiency of Y(Z) oxidation correlating with the solution pK(A) value of the added base. We conclude that the pK(A) of Y(Z) is approximately 10.3 in D1-H190A PSII particles. In Mn-depleted wild-type PSII particles, P(680)(*)()(+) reduction was accelerated by all exogenous bases examined (substituted imidazoles, histidine, Tris, and 1,4-diazabicyclo[2.2.2]octane). We conclude that Y(Z) is solvent accessible in Mn-depleted wild-type PSII particles and that its pK(A) is near that of tyrosine in solution. In Mn-depleted wild-type PSII particles, over 80% of the kinetics of P(680)(*)()(+) reduction after a flash could be described by three kinetic components. The individual rate constants of these components varied slightly with pH, but their relative proportions varied dramatically with pH, showing apparent pK(A) values of 7.5 and 6.25 (6.9 and 5.8 in the presence of Ca(2+) and Mg(2+) ions). An additional pK(A) value (pK(A) < 4.5) may also be present. To describe these data, we propose (1) the pK(A) of His190 is 6.9-7.5, depending on buffer ions, (2) the deprotonation of Y(Z) is facilitated by the transient formation of a either a hydrogen bond or a hydrogen-bonded water bridge between Y(Z) and D1-His190, and (3) when protonated, D1-His190 interacts with nearby residues having pK(A) values near 6 and 4. Because Y(Z) and D1-His190 are located near the Mn cluster, these residues may interact with the Mn cluster in the intact system.

C-H-acidität—XI : Nddo-berechnungen zur c-h-acidität polycyclischer methylacene und -azaacene

The deprotonization energies of a number of polycyclic benzenoid methylarenes and methylazaarenes are calculated using the NDDO method and compared with the experimental solution pK s values. In agreement with corresponding CNDO/2 results for the methylarenes a splitting into structure-depending correlation lines (α-methylnaphthyl type and β-methylnaphthyl) type occurs. The methylazaarenes deviate systematically from these lines. The inclusion of the specific solvation (hydrogen-bonds) using a simple model leads to a significant improvement of the correlation within the two structure types. Our results show the general applicability of the NDDO method for the description of the reactivity of heterocyclic systems.

Ferric oxyhydroxide microparticles in water.

Mineralogy and specific surface area are major controls on the stabilities of ferric oxyhydroxide microparticles in natural waters. The thermodynamic stabilities of ferric oxyhydroxides, as described by the activity product in solution pK = -log [Fe(3+)] [OH(-)](3) range from pK = 37.1 for freshly precipitated amorphous oxyhydroxide to pK = 44.2 for well crystallized goethite. The sizes of suspended oxyhydroxide particles in natural waters range from less than 0.01 mum to greater than 5 mum. Oxyhydroxides precipitated in the laboratory from solutions simulating high-iron natural waters are needlelike or lathlike in shape and have mean thicknesses as small as 60 A. Large specific surface areas resulting from the small sizes of ferric oxyhydroxide particles cause increased solubilities and thus decreased pK values. Specific surface areas of 40-170 m(2)/g determined for laboratory precipitates gave computed decreases in pK of 0.4 to 1.6 units.

Ferric Oxyhydroxide Microparticles in Water

Mineralogy and specific surface area are major controls on the stabilities of ferric oxyhydroxide microparticles in natural waters. The thermodynamic stabilities of ferric oxyhydroxides, as described by the activity product in solution pK = -log [Fe(3+)] [OH(-)](3) range from pK = 37.1 for freshly precipitated amorphous oxyhydroxide to pK = 44.2 for well crystallized goethite. The sizes of suspended oxyhydroxide particles in natural waters range from less than 0.01 mum to greater than 5 mum. Oxyhydroxides precipitated in the laboratory from solutions simulating high-iron natural waters are needlelike or lathlike in shape and have mean thicknesses as small as 60 A. Large specific surface areas resulting from the small sizes of ferric oxyhydroxide particles cause increased solubilities and thus decreased pK values. Specific surface areas of 40-170 m(2)/g determined for laboratory precipitates gave computed decreases in pK of 0.4 to 1.6 units.

Der Einfluss von Substituenten in Stellung 4 auf das n‐Ionisationspotential des Chinuclidins

AbstractThe vertical ‘lone‐pair’ ionization potentials Iv(n) of fifteen 4‐substituted quinuclidines, of aza‐adamantane and of aza‐twistane have been determined by photoelectron spectroscopy. It is shown that the dependence of Iv(n) on the nature of the substituent S can be rationalized in terms of the contribution to the local potential at the ionization site (i.e. the nitrogen centre) by the dipole of S. Both the solution pK's and Iv(n) correlate with classical substituent parameters (e. g. σ* or F) and with each other. However, no conclusions can be drawn from such regressions concerning a close relationship between the electronic mechanisms responsible for the observed changes in pK or Iv(n).

Thiohydantoins. XI Kinetic Studies of the Alkaline Hydrolysis of 1-Acyl-2-thiohydantoins

1-Acyl-2-thiohydantoins ionize in alkaline solution (pK ∼ 7). In solutions more alkaline than pH &gt; 11 they are rapidly hydrolyzed to 2-thiohydantoin and a carboxylic acid, by attack of a hydroxide ion on the conjugate base of the 1-acyl-2-thiohydantoin. Possible mechanisms to accord with the entropy of activation, which is less negative than usual for base-catalyzed amide hydrolyses, are discussed. 1-Benzoyl-2-thiohydantoin hydrolyzes more rapidly than 1-acetyl-2-thiohydantoin, possibly because the ground state of the former molecule is destabilized by steric effects.

Basicity, visible spectra, and electron spin resonance of flavosemiquinone anions.

The dependence on pH of the disproportionation of the flavosemiquinone has been investigated by ESR. For 3-alkylated lumiflavin [R(3)=CH2COO−] in aqueous solution pK (for the dissociation of the neutral flavosemiquinone) is 8.4; pKred is 6.3. Hydrolytic ring cleavage in position 2, 8,8′-dimerization, and 10-dealkylation interfere with the formation of the flavosemiquinone anion. However, in non-aqueous dimethylformamide and with stoichiometric amounts of strong base (t-BuOK), 100% flavosemiquinone anion is formed without interfering side reactions. Its light absorption spectrum is practically identical to that of the “red flavoprotein radical”. From the ESR spectra the individual isotropic hyperfine coupling constants have been determined.