Protonation/deprotonation reactions

Eq. (18)]. Similar protonation-deprotonation reactions are known in other systems (46, 146). 

Figure 3 Ligand exchange and protonation/deprotonation reactions at [Re02(CN)4]. ...

Surface protonation/deprotonation reactions at the edge of the silanol and aluminol sites (>SOH) of montmorillonite, which can be exemplified by the following reactions ... 

The foregoing considerations can also be applied to the electrochemistry of a number of organic compounds in contact with aqueous buffers [107, 119-125]. Here, protonation/deprotonation reactions are coupled with electron transfer processes, as described for the case of indigoid-, anthraquinonic-, and flavonoid-type pigments, among others. In contact with aqueous electrolytes, the electrochemical processes can generally be described as ... 

Numerous processes may be linked to proton transfer and protonation/deprotonation reactions (for general descriptions of proton transfer see, for instance, [8.214-8.217]). Proton-triggered yes/no or +/- switching is contained in the ability of polyamine receptors and carriers to bind and transport cations when unproton-ated and anions when protonated also, zwitterions such as amino acids may change from bound to unbound or vice versa, when they undergo charge inversion as a function of pH. 

The time required to reach equilibrium very much depends on the pKd value of the acid. An acid with a pKa value of 4, for example, deprotonates with a rate of 106 s Thus, the equilibrium is established within a few microseconds. On the other hand, an acid with a pKa value of 7 dissociates with a rate of ca. 103 s"1, and the equilibrium becomes established only on the millisecond time range. In a pulse radiolytic experiment, a large part of the radicals will thus have disappeared in bimolecular termination reactions, before an equilibrium is reached. Buffers speed-up the protonation/deprotonation reactions, and their addition can overcome this problem. Yet, they deprotonate acids and protonate their corresponding anions typically two to three orders of magnitude more slowly than OH and H+ (for a DNA-related example, see Chap. 10.4 for potential artifacts in the determination of pKa values using too low buffer concentrations, see, e.g., von Sonntag et al. 2002). 

It has been mentioned above that the pyrimidine radical cations are reasonably strong acids and rapidly deprotonate at a heteroatom. As all protonation/ deprotonation reactions at heteroatoms are reversible [e.g., equilibrium (22)], the radical cations are regenerated upon reprotonation. Deprotonation at carbon or reaction with water yield the final free-radical products. For the l,3Me2Thy system, where the deprotonation/reprotonation equilibria such as reaction (22) fall away, reactions (25)-(28) have been postulated to account for the fact that in the presence of 02 l,3Me25HOMeUra and l,3Me25(CHO)Ura [reaction (29)] are formed in a combined yield of 80% of primary S04 radicals (Rashid et al. 1991). The formation of these products has been taken as evidence that a free radical cation must be an intermediate. It is, however, also possible that the allylic radical is formed in a concerted reaction HS04 elimination. For such a process, a six-membered transition state can be written. 

When covalently attached to electron transfer active subunits, the DHA-VHF couple can facilitate chemical and physical switching of electronic properties, as a result of photochemically induced rearrangement accompanied by a change in the redox potential. An interesting example of such a switching system is the compound containing a dihydroazulene component and a covalently attached anthraquinone moiety.1311 This system is able to act as a multimode switch, assisted by various processes such as photochromism, reversible electron transfer, and protonation-deprotonation reactions (Scheme 8). 

FETs that can transduce other than simple protonation/deprotonation reactions have been reported in the literature. In 1975 Moss et al (20) described an ISFET that has a PVC membrane physically attached to the gate oxide of an SiOj FET in which valinomycin was introduced to obtain a K+ sensitive device. Although a response to variations in K+ concentrations was observed there are some serious drawbacks that until now have prevented that such devices can compete with or even replace conventional Ion Sensitive Electrodes. Firstly, the physical... 

Morphological switching between nanotube, hexameric receptor and monomers is readily achieved by simple protonation-deprotonation reactions. This system can be described as a library of dynamic, size selective fullerene receptors whose structure... 

Complexation/decomplexation of metal ions or of neutral organic molecules, protonation/deprotonation reactions, and oxidation/reduction processes can all be exploited to alter reversibly the stereoelectronic properties of one of the two recognition sites, thus affecting its ability to sustain noncovalent bonds [30-34, 41]. These kinds of switchable [2 catenanes can be prepared following the template-directed synthetic strategy illustrated in Figure 5, wherein one of the two macrocyclic components is preformed and then the other one is clipped around it with the help of noncovalent bonding interactions. 

Protonation/deprotonation reactions are included in SCM s to describe the amphoteric behavior of oxide surfaces ... 

Often there is more than one basic or acidic site in a molecule. Remember that protonation-deprotonation reactions are very rapid and reversible reactions, so just because a substrate has an acidic or basic site, it doesn t mean that protonation or deprotonation of that site is the first step in your mechanism. It s up to you to figure out which site must be deprotonated for the reaction in question to proceed. 

At a high ApKa only one of two consecutive protonation/deprotonation reactions (5.32) and (5.33) can occur to significant degree in normally studied pH range (3 11), and the other reaction has negligible effect on the overall surface... 

We usually think of protonation-deprotonation reactions occurring in solution where protons can move with solvent molecules. In an enzyme active-site, there is no "solvent", so there must be another mechanism for movement of protons. Often, conformational changes in the protein will move atoms closer or farther. Histidine serves the function of moving a proton toward or away from a particular site by using its different nitrogens in concert as a proton acceptor and a proton donor. 

Protonation/deprotonation reactions are among the fastest reactions in solution, and it is believed that surface protonation/deprotonation reactions are also fast. Therefore, the experimentally observed kinetics in surface protonation experiments is transport-controlled. Different models of kinetics of ion exchange with intraparticle rate control are discussed in [165]. Kinetic models based on a series of consecutive and/or branched reactions and experimental setups for kinetic measurements are reviewed in [166]. 

Order-of-magnitude generalizations concerning reactivity are often useful in developing models and making predictions about transformation and fate. Some reactions can be classified as fast relative to other pertinent physical and chemical processes, and can be treated as being instantaneous. Many protonation-deprotonation reactions, for example, occur at time scales significantly below one second, and can therefore be treated as pseudoequilibrium reaction steps. 

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