Basic sites, protonation

Studies on simple nickel-thiolate complexes are pertinent to discussions on the mechanisms of action of hydrogenases. Consider the pathway for reduction of protons. Initial protonation of metal-thiolate species will always occur at the lone pair of electrons on sulfur (most basic site). Protonation at the metal is thermodynamically less favourable, and usually kinetically slower than protonation of a stereochemical lone pair of electrons [48-50]. 

The mechanism for acid-catalyzed hydrolysis of amides involves attack by water on the protonated amide. An inqjortant feature of the chemistry of amides is that the most basic site in an amide is the carbonyl oxygen. Very little of the N-protonated form is present. The major factor that contributes to the stability of the O-protonated form is the... 

When a Br nsted plot includes acids or bases with different numbers of acidic or basic sites, statistical corrections are sometimes applied in effect, the rate and equilibrium constants are corrected to a per functional group basis. If an acid has p equivalent dissociable protons and its conjugate base has q equivalent sites for proton addition, the statistically corrected forms of the Br insted relationships are... 

Amino acid zwitterions are internal salts and therefore have many of the physical properties associated with salts. They have large dipole moments, are soluble in water but insoluble in hydrocarbons, and are crystalline substances with relatively high melting points. In addition, amino acids are amphiprotic they can react either as acids or as bases, depending on the circumstances. In aqueous acid solution, an amino acid zwitterion is a base that accepts a proton to yield a cation in aqueous base solution, the zwitterion is an add that loses a proton to form an anion. Note that it is the carboxylate, -C02-, that acts as the basic site and accepts a proton in acid solution, and it is the ammonium cation, -NH3+, that acts as the acidic site and donates a proton in base solution. 

If p is the number of equivalent acidic protons in BH+, and q the number of equivalent basic sites in its conjugate base B, then a more precise form for the Brpnsted relation is... 

The most important multiply charged polyatomic positive ions are compounds with two or more basic groups which when protonated lead to doubly or poly-charged ions. Typical examples are diamines such as the double protonated a, to alkyldiamines, H3N(CH2)pNH2+, and the most important class, the polyprotonated peptides and proteins, which have multiple basic residues. Charge reduction for these systems occurs through proton transfer from one of the protonated basic sites to a solvent molecule. Such a reaction is shown below for the monohydrate of a doubly protonated diamine ... 

The dendrimer-type tetranuclear Ru(II)-Os(II)3 complex (22, protonated form) shows an interesting electrochemical behavior due to the presence of free basic sites in its bridging ligands [41]. The protonated form shows a 3-1 oxidation pattern due to the simultaneous oxidation of the three Os-based units, followed by the one-electron oxidation of the Ru-based unit. On addition of base, the six chelating moieties (three on the Ru center and one on each Os center) undergo deprotonation. This causes changes in the oxidation potential of the metal ions, with a consequent switching from 3-1 to 1-3 in the oxidation pattern. 

The charges of the molecule are important for binding. When the amidine group accepts a proton and becomes an amidinium ion, noformycin and amidinomycin become biscationic and bind strongly to AT sequences. These two molecules have large pKa values at both basic sites and, as such, are biscationic at physiological pH. 

The possibility of intervention of a solvent bridge between the proton and the basic site, where the solvent molecule acts simultaneously as a proton donor and proton acceptor, should always be considered. Here as elsewhere, the operational recognition of what Hammett (1970) calls the stoichiometric involvement of solvent is not a simple task. 

The most dramatic rate retardations of proton transfers have been observed when the acidic or basic site is contained within a molecular cavity. The first kinetic and equilibrium studies of the protonation of such a basic site were made with large ring bicyclic diamines [72] (Simmons and Park, 1968 Park and Simmons, 1968a). It was also observed (Park and Simmons, 1968b) that chloride ion could be trapped inside the diprotonated amines. The binding of metal ions and small molecules by macrocyclic compounds is now a well-known phenomenon (Pedersen, 1967, 1978 Lehn, 1978). In the first studies of proton encapsulation, equilibrium and kinetic measurements were made with several macrobicyclic diamines [72] using an nmr technique. 

In the transition metal-catalyzed reactions described above, the addition of a small quantity of base dramatically increases the reaction rate [17-21]. A more elegant approach is to include a basic site into the catalysts, as is depicted in Scheme 20.13. Noyori and others proposed a mechanism for reactions catalyzed with these 16-electron ruthenium complexes (30) that involves a six-membered transition state (31) [48-50]. The basic nitrogen atom of the ligand abstracts the hydroxyl proton from the hydrogen donor (16) and, in a concerted manner, a hydride shift takes place from the a-position of the alcohol to ruthenium (a), re-... 

Isonicotinamide, 5. This compound was sufficiently soluble to allow SERS spectra to be obtained at the 50 mM level in 0.10 M KC1 and 0.10 M KC1 + 0.10 M HC1 at -0.20 V. The spectra resembled those seen with other pyridines. In particular, an intense band at 1600 cm-1 was seen with the neutral electrolyte and it was replaced by a band at 1640 cm-1 in the acidic electrolyte. Of the two basic sites, only the ring nitrogen will be protonated in 0.10 M HC1 (22) so, with this compound also, the 1640 cm-1 band appears to be due to the protonated pyridine. No carbonyl band was seen in either spectrum. 

Cyclobutane has not been polymerised cationically (or by any other mechanism). Thermochemistry tells us that the reason is not thermodynamic it is attributable to the fact that the compound does not possess a point of attack for the initiating species, the ring being too big for the formation of a non-classical carbonium ion analogous to the cyclopropyl ion, so that there is no reaction path for initiation. The oxetans in which the oxygen atom provides a basic site for protonation, are readily polymerizable. Methylenecyclobutane polymerises without opening of the cyclobutane ring [72, 73]. 

Oximes are another solute type having nitrogen and oxygen as basic sites. From the one available example (24), the primary and secondary interactions appear to be at oxygen and nitrogen, respectively. Nonequivalence shown by the three methyl resonances of the oxime derived from This example suggests a... 

The rich variety of active sites that can be present in zeolites (i) protonic acidic sites, which catalyze acid reactions (ii) Lewis-acid sites, which often act in association with basic sites (acid-base catalysis) (iii) basic sites (iv) redox sites, incorporated either in the zeolite framework (e.g., Ti of titanosHicates) or in the channels or cages (e.g., Pt clusters, metal complexes). Moreover, redox and acidic or basic sites can act in a concerted way for catalyzing bifunctional processes. 

Example The cleavage of disulfide bonds by reduction with 1,4-dithiothreitol causes the unfolding of the protein. This exposes additional basic sites to protonation, and therefore results in higher average charge states in the corresponding ESI spectrum (Fig. 11.14). [88]... 

More recent work revealed the importance of gas phase proton transfer reactions. [91-94] This implies that multiply charged peptide ions do not exist as preformed ions in solution, but are generated by gas phase ion-ion reactions (Chap. 11.4.4). The proton exchange is driven by the difference in proton affinities (PA, Chap. 2.11) of the species encountered, e.g., a protonated solvent molecule of low PA will protonate a peptide ion with some basic sites left. Under equilibrium conditions, the process would continue until the peptide ion is saturated with protons, a state that also marks its maximum number of charges. 

The reasons for the reluctance of the diamines to undergo protonation is due to the inaccessibility of the basic sites. The high thermodynamic basicity is probably due to a combination of the formation of a strong intramolecular hydrogen bond and to unfavourable lone pair interactions in the diamines that cannot be relieved by solvation. 

The dehydration of neopentyl alcohol can best be explained by a concerted mechanism involving the removal of the proton from the y-carbon atom by the basic sites and of the hydroxyl group by the acid sites of the alumina, with migration of the methyl group ... 

There is a strong parallel between elimination reactions in solution and the dehydration of alcohols over alumina. The trans elimination reactions and the anchimeric assistance of alcohols over aluminas suggest that the dehydration must occur within either the submicroscopical pores, or crevices, or channels of the aluminas. The aluminas therefore must surround the alcohol molecules providing acid sites to act as proton donors or electron acceptors and basic sites to act as proton acceptors or electron donors. For that reason the aluminas seem to act as solvating agents and therefore may be considered as a pseudosolvents for dehydration reactions. 

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