Negative ionizable groups

A vast class of instabilities in enzymatic systems arises from the pH dependence of enzymatic activity. In general, protein molecules contain a number of ionizing groups, such as (—COOH), which can be ionized to give the negatively charged (—COO") ion, and (—NH2), which can add on a proton to give (—NH ). The active enzyme may be represented as in Fig. 4 then addition of acid or base to the active enzyme may be depicted as in Fig. 5, or schematically... 

C-2 Substitution. In solvents that support the complete ionization of an ionic group at C-6, C-2 substitution has a relatively small effect on the spectrum. Thus the /max of C-2 esters is shifted only 5-7 nm to the red relative to that of dianion, and this relative shift is essentially the same regardless of the solvent. This is probably the consequence of interaction of the negative carboxylate group with C-9, a center of relatively low electron density in the ion. There is little difference in the extinction coefficients of Rose Bengal C-2 esters and the disodium salt (Figure 10). 

When you build a model structure, consider the experimental conditions relevant to the system you want to study. If the molecule s environment is acidic and it contains a basic nitrogen, the nitrogen can be protonated and a positive charge must be added to the model. If the molecule s environment is basic and it contains a carboxyl or other ionizable group, then the model can have the acidic hydrogen removed and a negative charge must be added to the model. On the other hand, if you are just interested in the shape of the MOs, then a calculation on a neutral model may be adequate. 

Catalyst models (hypotheses) consist of sets of abstract chemical features arranged at certain positions in the three-dimensional space. The feature definitions are designed to cover different types of interactions between ligand and target, e.g. hydrophobic, H-bond donor, H-bond acceptor, positive ionizable, negative ionizable. Except in some special cases, different chemical groups that lead to the same type of interaction, and thus to the same type of biological effect,... 

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