Organic Mechanisms. Xiaoping Sun

uncatalyzed tautomerization and acid‐ and base‐catalyzed tautomerization is demonstrated in Figure 1.21d.

Very often, enzymatic catalysis can also be achieved by splitting an uncatalyzed mechanistic step with a high activation energy into multiple catalyzed microscopic steps with lower activation energies. This way of catalysis can be demonstrated by using carbonic anhydrase, the enzyme that catalyzes the reaction of carbon dioxide (CO₂) with water (H₂O) giving bicarbonate (HCO₃⁻) in human blood [8]. When CO₂ produced from respiration is transferred into the venous blood, it combines with water in the blood and this reaction happens. By virtue, the reaction of CO₂ with H₂O is a simple inorganic chemical reaction. When it happens in the venous blood and is catalyzed by carbonic anhydrase, it becomes a biochemical reaction.

FIGURE 1.21 Acid–base catalysis for enzymatic reactions. (a) Uncatalyzed concerted keto–enol tautomerization; (b) The acid‐catalyzed mechanism for the keto–enol tautomerization; (c) The base‐catalyzed mechanism for the keto–enol tautomerization; and (d) Comparison of energetics for uncatalyzed and acid‐ or base‐catalyzed keto–enol tautomerization.

The catalytic center of carbonic anhydrase is a sp³‐hybridized zinc ion (Zn²⁺) connecting to three imidazole rings (Im) of histidine residues in the enzyme's polypeptide chain [8]. The unoccupied (vacant) sp³ orbital in Zn²⁺ is strongly electrophilic. The transition state (TS) of the uncatalyzed reaction of CO₂ with H₂O is highly destabilized (with a high level of free energy) due to the formation of partial electric charges (Fig. 1.22a). In the presence of carbonic anhydrase, the reaction pathway is altered such that the first step of the reaction is that H₂O (hydrogen bonded to the enzyme) coordinates to the electrophilic Zn²⁺ center in the enzyme to lead to the formation of a nucleophilic hydroxide (OH⁻) attached to Zn²⁺ (Fig. 1.22b) [8]. The transition state (TS1) is substantially stabilized, relative to that (TS) of the uncatalyzed reaction, by the partially formed O…Zn²⁺ coordination bond. Then the strongly nucleophilic OH⁻ in the Zn²⁺ center attacks CO₂ to bring about a nucleophilic addition with a low‐level transition state (TS2), giving HCO₃⁻ and regenerating a free enzyme (Fig. 1.22b) [8]. In the in vivo reaction, the proton by‐product combines with hemoglobin in the blood. The comparison of energetics and mechanisms for the uncatalyzed and enzyme catalyzed reactions of CO₂ with H₂O is demonstrated in Figure 1.23.

FIGURE 1.22 (a) Mechanism for the concerted reaction of H₂O and CO₂ giving HCO₃⁻ and (b) Mechanism for the enzyme (carbonic anhydrase) catalyzed stepwise reaction of H₂O and CO₂ giving HCO₃⁻.

      Many biochemical reactions follow some fundamental organic reaction mechanisms demonstrated in this book. Various biological applications of the mechanisms are discussed in all the individual chapters.

      

1.12 THE GREEN CHEMISTRY METHODOLOGY

Traditionally, synthesis of organic compounds has been performed very commonly in various organic solvents to make homogeneous reactions occur because many organic reactants are hydrophobic (water insoluble), but lipophilic (soluble in “oil”—the organic media). Organic solvents are in general hazardous substances. Utilization of large amounts of toxic organic solvents in synthetic reactions has created a big burden to the environment. The ideal green synthesis of organic compounds should avoid utilization of any solvents or only include environmentally benign solvents in the reactions, among which the most convenient, most natural, and cheapest is water. Conducting organic reactions in (or on) water will minimize the difficulty in the waste disposal, greatly reduce the pollution of the environment with hazardous materials, and ease the product work‐up and separation. This protocol has received much attention from organic chemists in the past 15 years [9, 10]. Many synthetic reactions performed in water heterogeneously have been found substantially faster than the reactions traditionally carried out in organic solvents [9–12]. Effective and efficient organic synthesis in water represents a major aspect of methodology in the current green chemistry.

FIGURE 1.23 Comparison of energetics for the concerted and the enzyme (carbonic anhydrase) catalyzed stepwise reactions of H₂O and CO₂ giving HCO₃⁻.

Research by vibrational sum frequency (VSF) spectroscopy has shown that on the hydrophobic interface between water and an organic layer, such as CCl₄ and hexane, the intermolecular hydrogen bonding between water molecules is substantially weaker than the hydrogen bonds of water in the liquid–vapor interface and inside the liquid phase of water. This is indicated by a blue shift of the vibrational bands for hydrogen bonded water in H₂O/CCl₄ and H₂O/hexane interfaces relative to that for the water in the liquid–vapor interface [13]. This weakening in hydrogen bonding allows water molecules in the interface to move more freely and gives rise to strong orientation effects of water on the hydrophobic interface, such that the O─H bond in some water molecules (1 in 4 H₂O molecules) on the hydrophobic interface penetrates into the organic layer [9, 14]. In the cases of the heterogeneous organic reactions performed in water, if a reactant molecule can act as a hydrogen bond acceptor, the OH bond in water which penetrates into the organic layer can form a strong hydrogen bond with the reactant molecule and more importantly, form a strong hydrogen bond with the transition state of the reaction to stabilize the transition state and lower the activation energy [9, 14]. In addition, upon vigorous agitation of the reaction mixtures in water, the bulk organic phase can be separated into aggregates (droplets) by water. Formation of aggregates increases surface area of the reactants and therefore, enhances their energy to lower the activation energy as well [9]. As a result, the reactions that take place on the hydrophobic interface (heterogeneous reactions) become much faster than the homogenous reactions occurring in organic solvents or in neat reactants [9, 14]. The hydrophobic effects are summarized in Figure 1.24. This way water is not only used as a green solvent, but it also acts as an effective “catalyst” to speed up the reactions.

Figure 1.24a illustrates that a free OH bond in a water molecule of the hydrophobic interface partially penetrates into the organic layer and is hydrogen bonded to the transition state (via a hydrogen bond acceptor) of a reaction taking place