PfCa-value

The 5 2 TEAF reagent is acidic, with the extent of the acidity depending upon the solvent in which the reagent is used. Variations of triethylamine and formic acid pfCa-values with solvent are listed in Table 35.2. The pfCa of formic acid in many of the common solvents used is much higher than water, so there would appear to be little free formate in the reaction thus, it becomes difficult to explain the reaction in such conditions (e.g., those in Table 35.1). 

Gruber, C. and Buh, V. (1989) Quantum mechanically calculated properties for the development of quantitative structure-activity relationships (QSARs). pfCa values of phenols and aromatic and aliphatic carboxylic acids. Chemosphere, 19, 1595-1609. 

Final adjustment with HC1 may be needed if the pH is more than one unit away from a pfCa value. When two buffering materials are present, the composition should be calculated independently for each. The measurement of pH should always be done with great care because it is easy to make errors. Everything depends upon the reliability of the standard buffers used to calibrate the pH meter.7 Often, especially during isolation of small compounds, it is desirable to work in the neutral pH region with volatile buffers, e.g., trimethylamine and C02 or ammonium bicarbonate,... 

Exactly 0.01-mol portions of glycine were placed in several 100-ml volumetric flasks. The following exact amounts of HC1 or NaOH were added to the flasks, the solutions were made to volume with water, mixed, and the pH measured. Calculate the pfCa values for the carboxyl and amino groups from the following, making as many independent calculations of each pKa as the data permit. At low pH values you must correct for the free hydrogen ion concentration (see question 2c).581... 

The dissociation constants fC — Kn for a multi-protic acid HrA are defined as stepwise or macroscopic constants (also called molecular constants). For some compounds, e.g. alanine, the pfCa values are far apart (pfC and pK2 are 2.4 and 9.8, respectively). The macroscopic constants can be assigned specifically, fCj to the carboxyl group and K2 to the protonated amino group. At the isoelectric pH of 6.1 the alanine exists almost entirely as the dipolar ion. However, for compounds in which the macroscopic pfCa values are closer together, they cannot be assigned to specific groups. We will consider some specific examples in the next section. 

For example, the following give good approximations of pfCa values.d... 

Acid-base titration gave the following three pKa values for cysteine 1.70,8.36, and 10.53. Spectro-photometric data allowed H. B. F. Dixon and K. F Tipton (1973, Biochem. 133,837-842) to estimate the following ratio of tautomeric species at pH 9.4 [ -OOC - C(NH3+)- CH2S] / [OOC - C(NH2) -CH2SH] = 2.12, as is also shown in Fig. 6-5. Verify and assign the four microscopic pfCa values. 

Studies of the pH dependence of Vmax //ccat(Eq.9-57) reveal a bell-shaped dependence on pH with pfCa values301 302 of 4 and 9. However, the ion pair is formed at a pH below four with apparent pfCa values of 2.5,2.9, and 3.3 for ficin, caricain, and papain, respectively.302 These low values can be assigned principally to Cys 25 with only very small contributions from His 159 (see Eq. 6-75). A third pKa, perhaps of a nearby carboxylate from Glu 50, affects the rate. For caricain the nearby Asp 158 (Fig. 12-15) has been implicated.303 304... 

The pH dependence of the action of fumarate hydratase indicates participation of both an acidic and a basic group with pfCa values of 5.8 and 7.1.56 See Chapter 9 for additional information. However, either anion or carbocation mechanisms might be possible. That the cleavage of the C-H bond is not rate limiting is suggested by the observation that malate containing 2H in the pro-R position is dehydrated at the same rate as ordinary malate. If the anion mechanism (Eq. 13-13) is correct, the 2H from the pro-R position of specifically labeled malate might be removed rapidly, while the loss of OH could be slower. If so, the 2H would be "washed out" of L-malate faster than could happen by conversion to fumarate followed by rehydration to malate. In fact, the opposite was observed. 

The active sites of aldo-keto reductases contain an essential tyrosine (Tyr 48) with a low pfCa value. 

The variation of fluorescence intensity with pH can provide direct information about the pfCa in the excited state. Forster suggested the following indirect procedure for estimating excited-state pfCa values for phenols. Let Ei represent the energy of the 0-0 transition (preferably measured as the mean of the observed 0-0 transition energies in absorption and fluorescent emission spectra) let E2 represent the energy of the... 

The pKa values of Thy and Ura are close to 9.5. Thus, near neutrality they are deprotonated by OH formed in the pulse. Due to the low pfCa values, the reprotonation of the anions by water is sufficiently slow ( 3 x 105 s 1) to allow the anions to build-up to higher than steady-state concentrations. Of the two anions that are formed upon deprotonation [e.g., reaction (1)] only the one deprotonated at N( ) absorbs at longer wavelengths than the neutral molecules (Morita et al. 1981). This explains, why with the nucleosides which have the same pfCa values as the nucleobases no such intermediates are formed, although deprotonation by OH occurs as well. 

Usually, radical cations have much lower pfCa values than their parent compounds. A typical examples is phenol, whose pfCa value is at 10 while that of its radical cation is at -2 (Dixon and Murphy 1976). Thus in this case, ionization causes an increase in acidity by 12 orders of magnitude. It is hence expected that also the nucleobase radical cations should be much stronger acids than their parents. This has indeed been found in all systems where equilibrium conditions are established, and the consequences for DNA base pairs have been discussed (Steenken 1992). 

This view is been confirmed by an electrochemical product study (Hatta et al. 2001) that is discussed below. The pfCa value of the Thy radical cation has been determined at 3.2 (Geimer and Beckert 1998). When the position at N( ) is substituted by a methyl group and deprotonation of the radical cation can no longer occur at this position, deprotonation occurs at N(3) (Geimer and Beckert 1999 for spin density calculations using density functional theory (DFT) see Naumov et al. 2000). This N(3) type radical is also produced upon biphotonic photoionization of N(l)-substituted Thy anions [reaction (7)] in basic 8 molar NaC104 D20 glasses which allowed to measure their EPR spectra under such conditions (Sevilla 1976). 

In basic solution, Ura and Thy undergo a series of reactions as depicted in reactions (72)—(76) for Ura as an example (Fujita and Steenken 1981). Ura dissociates athighpH [equilibrium (72) for pfCa values see Table 10.11], Its OH-adductscan also be deprotonated at nitrogen leading to an oxidizing heteroatom-centered radical [reaction (76)]. 

The other functional groups, especially the second carbonyl function, withdraws considerable electron density, and hence the pK3 values of these O-pro-tonated radical anions are much lower than those of the simple a-hydroxyalkyl radicals (Thy pKa = 6.9 (Hayon 1969) Ura pfCa = 7.2 (Shragge and Hunt 1974) the value of 4.3 reported for the pfCa for the protonated 5,6Me2Ura radical anion (Aravindakumar et al. 1998) is surprising low and difficult to explain on the basis of the effects of methyl substituents on the pfCa values of a-hydroxyalkyl radi-... 

The resulting neutral radical must have a pKa value > 11, as shown by conductance measurements in pulse radiolysis (Hissung and von Sonntag 1979). The absence of any noticeable changes in the absorption spectrum of the radical derived from Cyd in the pH range 6-13 suggests that its pfCa value is even >13 (Steenken et al. 1992). Like the situation in the corresponding Thy system, the heteroatom-protonated species is not thermodynamically favored and subsequent (irreversible) protonation seems to occur at carbon [reaction (175)], albeit with a rate constant (estimated at 2.5 x 103 s 1 Nese et al. 1992) too slow to be measured by pulse radiolysis. 

Biocatalysts do not operate by different scientific principles from organic catalysts. The existence of a multitude of enzyme models including oligopeptidic or polypeptidic catalysts proves that all enzyme action can be explained by rational chemical and physical principles. However, enzymes can create unusual and superior reaction conditions such as extremely low pfCa values or a high positive potential for a redox metal ion. Enzymes increasingly have been found to catalyze almost any reaction of organic chemistry. 

If Ke signifies the concentrations of enol and keto tautomers in a carboxylic acid, then pfCE is the difference between the pKa values of the a-protons of the keto tautomer and the hydroxyl group of the enol tautomer. pfCE, however, is also the difference in pfCa values between the a-protons and the proton of the carbonyl group of the carbonyl-protonated acid, that is deemed to be decisive (Gerlt, 1991) for the kinetics of abstraction of a proton, rather than the pfQ value of the substrate in solution. The pki of mandelic acid (15.4) links the pka of the a-proton of the keto tautomer (22.0) with the pK.d value of the enol tautomer (6.6). The pk, value also links the pka value of the a-proton with that of the carbonyl-bound proton of the protonated mandelic acid. If the pka value of the carbonyl-bound proton of the protonated mandelic acid is assumed to be about -8.0 then the pfQ value of the a-proton is about 7.4. This value matches well with the pka -values of Lys and His residues which have been assigned recently in the active center of mandelate race-mase, so electrophilic catalysis alone is able to explain the catalytic power of mandelate racemase. 

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