Biochemistry: The Chemical Reactions of Living Cells, Volume 2 - D. Metzler 1980

Types of reactions catalyzed by enzymes
Nucleophilic substitution reactions (Type 1 reactions)
Factors affecting the rates of substitution reactions

In the previous chapter (Section D), we discussed the Displacement of the iodide ion from methyl iodide by a hydroxyl ion. Can we similarly substitute the methyl group of ethane (CH₃—CH₃) by cleaving the C—C bond to yield CH₃OH? No, we cannot. Ethane is stable in alkali solutions and cannot be cleaved via simple substitution reactions within our body either. Similarly, the long hydrocarbon chains that make up Fatty acids cannot be degraded in this manner during fatty acid METABOLISM. Thus, Nucleophilic substitution reactions occur when displacement proceeds readily, yet they do not take place when substitution is severely hindered. Furthermore, not every anion or base B can replace another group.

One can rule out at least four factors that determine the likelihood of a substitution reaction: (1) the equilibrium position of the overall reaction, (2) the reactivity (nucleophilicity) of the incoming nucleophile, (3) the Chemical Nature of the leaving group displaced in the reaction, and (4) the specific Structural Features of the substrate.

The first factor is thermodynamic. As an example, let us consider Hydrolases, which catalyze the Cleavage of amide, ester, and phosphodiester bonds using Water as the incoming nucleophile. Since Enzymes typically operate in an environment with a high water content, the equilibrium is virtually always shifted toward Hydrolysis rather than the reverse synthesis reactions.

Nucleophilic reactivity (nucleophilicity) is determined in part by basicity: compounds classified as strong bases generally undergo non-enzymatic reactions faster than weaker bases. The hydroxyl ion (OH^-) serves as a better nucleophile than —COO^-. However, enzymes usually function at optimal rates near neutral pH. At pH 7, the —COO^- group exhibits higher reactivity than stronger basic groups such as —NH₂ or OH^-, because at neutral pH these groups are almost completely protonated, and the concentration of the active nucleophile must be very low.

The second factor influencing nucleophilicity is polarizability. By this term, we mean the ease with which the electron distribution around an atom or within a chemical group is distorted. High polarizability is promoted by a large atomic radius and the presence of double bonds in the group. In general, the more strongly a group is polarized, the faster it will react in a nucleophilic substitution reaction (evidently because a polarizable group can form partial bonds at a greater distance than a nonpolarizable group). Thus, the I^- anion is more reactive than Br^-, which in turn is more reactive than Cl^-. Polarizable bases, such as imidazole, are often much more reactive than nonpolarizable ones, such as —NH₂. Sulfur compounds exhibit high nucleophilicity, which may account for the essential role of SH groups in biochemical processes. Interestingly, in Substitution reactions at carbonyl groups (Table 7-1, reaction type 1.B), hard (low-polarizability) nucleophiles are more reactive than easily polarizable ones such as I^-.

Attempts are frequently made to express nucleophilicity in terms of basicity combined with some other property, such as polarizability [1].

Another phenomenon, which may not play a major role in Enzymatic Catalysis but helps explain the mode of Introduction/43.html">Action of Certain poisons, is termed the α-effect. This refers to the well-known fact that certain combinations of atoms (in which an atom with a lone pair of electrons is directly bonded to the nucleophilic center of an ongoing reaction) possess greater nucleophilicity than Other Compounds of comparable basicity. The high reactivity of certain toxic substances—such as hydroxylamine (NH₂OH) and the cyanide ion (CN^-)—can be explained precisely in this manner [4].

The chemical Nature of the leaving group strongly affects both The rate of nucleophilic substitution and the equilibrium position. A leaving group must possess a pair of electrons and often carries a negative charge. The methyl group split off from ethane or methane as CH^-₃ must be an extremely poor leaving group (the pK_a of methane as an acid is reported to be 47 [5]). The iodide ion is a good leaving group, whereas F^- is a significantly poorer one (by a factor of more than 10⁴) [5]. In an aqueous medium, the phosphate ion is a much better leaving group than OH^-, while pyrophosphate and tripolyphosphate are even better leaving groups.