Protonation and deprotonation

In these equilibria, A is the conjugate base of the acid HA, and BH+ is the conjugate acid of the base B. Even in the absence of added acids and bases, proton transfer occurs between water molecules, and the autoprotolysis equilibrium  

As will be familiar from introductory chemistry, the hydronium ion concentration is commonly expressed in terms of the pH, which is defined formally as 

If the molar concentration of H3O+ is 2.0 mmol dm (where 1 mmol = 10 mol), then 

If the molar concentration were 10 times less, at 0.20 mmol dm 3, then the pH would be 3.70. 

Notice that the higher the pH, the lower the concentration of hydronium ions in the solution and that a change in pH by 1 unit corresponds to a 10-fold change in their molar concentration. However, it should never be forgotten that the replacement of activities by molar concentration is invariably hazardous. Because ions interact over long distances, the replacement is unreliable for all but the most dilute solutions. 

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Conjugated dipyrrolic pigments, the dipyrromethenes, are synthesized by add-catalyzed condensation of an a-formyl pyrrole and an a-unsubstituted pyrrole. They are readily protonated and deprotonated and are difficult to purify by chromatography. 

Tile ID and 2D NMR experiments for 5-aza-7-deaza-2 -deoxyguanosine concluded that the oxo-amino tautomer 59a is preferable in DMSO-dg whereas the oxo-imino form 59b dominates in D2O (87JOC5136). Evidence for the hydroxy-imino tautomer 59c was not found. Poor solubility of the parent compound, 5-aza-7-deazaguanine (60) did not allow study of its tautomerism, but the pK values of protonation and deprotonation for 60 are identical with those for 59. 

Protonation and deprotonation reactions of corroles have already been mentioned (see Introduction). Attempts to achieve electrophilic substitution reactions, at the corrole, e.g. Friedel-Crafts acylation, have been unsuccessful.1 Heating corroles with acetic anhydride yields the corresponding 21-acetyl derivatives l.8a,b... 

The rates for protonation and deprotonation depend on the conformation and in some eases they are so small that no equilibrium constants could be measured properly. But in those cases where rate constants have been determined, some equilibrium constants have been calculated (Smith et al., 1981). 

Different orientations for the protonated and deprotonated species as well as a change of the surface coverage with the bulk aqueous pH can further complicate the problem. 

The rates of protonation and deprotonation reactions are sufficiently large in comparison with corresponding diffusion rates, so that it can be assumed that these reactions are at equilibrium even when current is flowing, that is, the following equations are valid everywhere at t > 0, t being the time ... 

One element of database generation that is a key consideration is whether to expand the representative compounds to include alternative tautomers, protonated and deprotonated forms of the molecule, and also to enumerate stereochemistry fully if not specified in the input. Depending on the molecules in question and the options considered, these can lead to a 10-fold increase in the size of the database to be explored. However, such an expansion is necessary if methods are used that are sensitive to such chemical precision (e.g., docking). For 3D similarity searching, it is sometimes more efficient to consider various modifications to the query, leading to multiple searches against a smaller database. 

Thus, the pKa value equals pH if the concentrations of protonated and deprotonated states are identical. For this reason, pKa is also called p/fi/2- Equation (10-4) can be rearranged and written in a generalized form in the presence of multiple titration sites,... 

Figure 10-4. The double- and single-site titration models for His and Asp groups [42]. (A) In the double site model, only one X is used for describing the equilibrium between the protonated and deprotonated forms, while the tautomer interversion process is represented by the variable x. (B) In the single-site model, protonation at different sites is represented by different X variables. HSP refers to the doubly protonated form of histidine. HSD and HSE refer to the singly protonated histidine with a proton on the h and e nitrogens, respectively. ASP1 and ASP2 refer to the protonated carboxylic acid with a proton on either of the carboxlate oxygens...

Cyanine and squaraine dyes with hydrogen substituents on the indolenine-nitrogen in one or both of the heterocyclic end-groups, the so-called norcyanines and norsquaraines, are useful as fluorescent pH-indicators due to the reversible equilibrium between their protonated and deprotonated forms ... 

Square-650-pH having a pKa in the physiological pH range (pKa = 7.1 for free dye and the pKa 6.1 when labeled to an antibody) was recently introduced by SETA BioMedicals [119]. This dye is commercially available as a free carboxylic acid and a mono-NHS ester. Square-650-pH has spectral properties similar to those of the CypHer dyes but is fluorescent in both the protonated and deproto-nated forms. This dye displays reasonable molar absorptivities (135,000 and 48,000 M-1cm-1) and quantum yields (16% and 9%) for the protonated and deprotonated forms, an extremely large Stokes shift of more than 100 nm for the deprotonated form, and enables excitation and emission ratiometric measurement... 

The virial methods differ conceptually from other techniques in that they take little or no explicit account of the distribution of species in solution. In their simplest form, the equations recognize only free ions, as though each salt has fully dissociated in solution. The molality m/ of the Na+ ion, then, is taken to be the analytical concentration of sodium. All of the calcium in solution is represented by Ca++, the chlorine by Cl-, the sulfate by SO4-, and so on. In many chemical systems, however, it is desirable to include some complex species in the virial formulation. Species that protonate and deprotonate with pH, such as those in the series COg -HCOJ-C02(aq) and A1+++-A10H++-A1(0H), typically need to be included, and incorporating strong ion pairs such as CaSO aq) may improve the model s accuracy at high temperatures. Weare (1987, pp. 148-153) discusses the criteria for selecting complex species to include in a virial formulation. 

Label Aq represents each possible surface complex, including protonated and deprotonated sites (e.g., >(w)FeO- and >(w)FeOH ) and complexes with cations and anions (>(w)FeOZn+ and >(w)FeP04-, for example). The molalities of the uncomplexed and complexed sites, respectively, are mp and mq. 

The rate law is based on a surface complexation model Liger et al. (1999) developed for the hematite nanoparticles (see Chapter 10, Surface Complexation ). The >FeOH surface sites react by protonation and deprotonation to form >FeOII2h and >FeO-, by complexation with ferrous iron to form >FeOFe+ and >FeOFeOH, and to make a complex >Fe0U020H with uranyl. Table 28.1 shows the reactions and corresponding log K values. The nanoparticles are taken to have a specific surface area of 109 m2 g-1, and a site density of 0.06 per Fe2C>3. 

The mechanism for the addition of singlet carbenes to alcohols has been studied in some detail (Bethell et al, 1971 Kirmse et al, 1981). By and large, the evidence supports two routes. The first, more common, sequence features initial formation of an ylid. Under some circumstances this reaction is reversible (Zupancic et al., 1985 Liu and Subramanian, 1984 Warner and Chu, 1984). Next, proton transfer, either intramolecularly, which may be slowed by symmetry constraints, or by a pair of intermolecular protonation and deprotonation steps, gives the ether. These reactions are outlined in (7). 

The equilibrium constant for this reaction depends on the stability constants of the ionophore-M+ complexes and on the distribution of ions in aqueous test solution and organic membrane phases. For a membrane of fixed composition exposed to a test solution of a given pH, the optical absorption of the membrane depends on the ratio of the protonated and deprotonated indicator which is controlled by the activity of M+ in the test solution (H,tq, is fixed by buffer). By using a to represent the fraction of total indicator (Ct) in the deprotonated form ([C]), a can be related to the absorbance values at a given wavelength as... 

The triply protonated decavanadate, [H. VKI028l i, reaches its highest concentration at pH 2, but with a decrease in the pH it is rapidly converted to the relatively more stable [V02(H20)4]+ ion, which begins to dominate from pH <1.5 (Figs. 2 and 3). Protonation and deprotonation of the decavanadates are fast, but equilibria between decavana-... 

When a metal oxide surface is exposed to water, adsorption of water molecules takes place as shown in Equation 2.1. Cation sites can be considered as Lewis acids and interact with donor molecules like water through a combination of ion-dipole attraction and orbital overlap. Subsequent protonation and deprotonation of the surface hydroxyls produce charged oxide surfaces as shown in Equation 2.2 and Equation 2.3, respectively ... 

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