CHAPTER OUTLINE
7.2 Nature of the Carbonyl Group
7.3 Relative Reactivity of Carbonyl-Containing Functional Groups
7.4 Hydration of Aldehydes and Ketones
7.5 Reactions of Aldehydes and Ketones with Alcohols
Box 7.1—Glucuronidation in the metabolism of drugs
Box 7.2—Imines in drug-protein conjugates
7.8 Chemical Hydrolysis of Ester and Amide Bonds
7.9 Enzymatic Hydrolysis of Peptide Bonds by Proteases
Box 7.3—Drugs designed to inhibit proteases
7.1 Introduction
In this chapter we explore the structure and reactivity of the carbonyl (C=O) bond and related carbon–heteroatom (C=X) double bonds. These functional groups are ubiquitous in both biological molecules and in the structures of drugs. A prominent example in biological molecules is the amide bond (peptide bond), which serves as the structural backbone of proteins and also helps determine how proteins fold into the specific three-dimensional shapes that lead to function. Other biological molecules containing ketone or thioester functions are involved in cellular metabolism and in sterol biosynthesis in animals and terpene biosynthesis in plants.
Carbonyl-containing functional groups are also found in the structures of many drugs. Often these groups play a structural role, linking and helping to properly orient other functionality for interaction with the drug’s target. These groups can also make direct contact with the target, forming hydrogen bonds and other intermolecular interactions as we have seen in Chapter 2. The chemical reactivity of carbonyl functional groups can also be important in drug action, as is the case for the cyclic amide (β-lactam) present in penicillins and related β-lactam antibiotics. This chapter examines many important classes of carbonyl-containing functional groups and reviews the biologically relevant chemistry of the carbonyl.
7.2 Nature of the Carbonyl Group
Carbonyl-containing functional groups are those possessing a double bond between a carbon and oxygen atom (C=O). The molecular orbital description of a carbonyl involves a σ bond between sp2 hybrid orbitals on carbon and oxygen atoms and a π bond involving the 2p orbitals on the bonded atoms. It is the interacting p orbitals of the π bond that prevents rotation about the C=O bond. The two remaining sp2 hybrid orbitals on carbon form σ bonds with additional substituents that lie in the plane of the carbonyl bond, and separated by ~120o (Figure 7.1). Two electron lone pairs on oxygen project out at a ~120o angle and can accept hydrogen bonds or be protonated under acidic conditions.
Figure 7.1 Structures and stick models of carbonyl groups in formaldehyde, acetaldehyde, and acetone. (Reproduced, with permission, from Carey FA, Giuliano RM. Organic Chemistry. 9th ed. New York: McGraw-Hill Education; 2014.)
The bonding between carbon and oxygen in a carbonyl is analogous to that between the carbon atoms of ethylene. The greater electronegativity of oxygen as compared to carbon, however, means that electron density in the carbonyl function is polarized. This polarization can also be understood in resonance terms, the resonance forms shown below implying partial positive character at carbon and partial negative character at oxygen. These partial charges can be indicated as a dipole or using the δ+ and δ- nomenclature we have used previously (Figure 7.2).
Figure 7.2 Shown at top is a molecular orbital view of formaldehyde showing the π bond formed by overlap of p orbitals on carbon and oxygen. Polarization of the carbonyl bond can be illustrated using resonance structures, as partial charges, or as a dipole. (Reproduced, with permission, from Carey FA, Giuliano RM. Organic Chemistry. 9th ed. New York: McGraw-Hill Education; 2014.)
This polarization is an important contributor to the reactivity of the carbonyl group as it makes the carbon atom electrophilic and thus reactive with nucleophiles. Substituents that reduce polarization of the C=O bond make the carbonyl less reactive while substituents that increase polarization make the carbonyl more reactive. Hydrogen bonding to (or protonation of) the lone pair electrons of a carbonyl increases its polarization and thus enhances its reactivity with nucleophiles.
Steric effects between carbon substituents represent another important contributor to carbonyl reactivity. Reaction of a carbonyl with a nucleophile results in a change from planar sp2 hybridization to tetrahedral sp3 hybridization. The introduction of a new substituent (from the nucleophile) combined with the smaller 109.5o bond angle associated with sp3 hybridization leads to greater steric strain in the tetrahedral product (Figure 7.3). This steric effect will be greatest when the transition state for the addition reaction is “late” (i.e., when it resembles the tetrahedral product). As we discuss the reactivity of various functional groups in the sections that follow it will be helpful to keep in mind the two main contributors to carbonyl reactivity—polarization of the carbonyl bond and the size of the carbonyl substituents.
Figure 7.3 Nucleophilic addition to a carbonyl results in a change from sp2 to sp3 hybridization and a reduction in bond angle from ~120o to ~109.5o at carbon. The smaller bond angle results in greater steric strain in the product of the reaction.
7.3 Relative Reactivity of Carbonyl-Containing Functional Groups
The simplest carbonyl-containing functional group is the aldehyde and the simplest aldehyde is formaldehyde. The hydrogen atoms in formaldehyde can do little to stabilize the positive character of the carbonyl carbon and hence this carbonyl is quite polarized. Add to this the very small size of the carbonyl substituents (hydrogen atoms) and we might expect that formaldehyde should be quite reactive with nucleophiles. Indeed, the reaction of formaldehyde with even a weak nucleophile such as water is very favorable, and in aqueous solution >99.9% of formaldehyde exists in the “hydrated” form (Table 7.1). Acetaldehyde, with methyl and hydrogen substituents, is less reactive than formaldehyde for both electronic and steric reasons and only about 50% hydrated in aqueous solution. Addition of a second methyl group on carbon leads to a ketone (acetone) that is only ~0.14% hydrated in aqueous solution.
Table 7.1 Hydration Reaction for Selected Aldehydes and Ketones.
Electronic effects on carbonyl reactivity can be mediated through both inductive and resonance effects. A striking example of carbonyl activaton by an inductive effect is evident in comparing the hydration equilibrium constants for acetaldehyde and trifluoroacetaldehyde. The trifluoromethyl group is significantly bulkier than methyl, yet the highly electron-withdrawing nature of this substituent results in a hydration equilibrium constant even greater than that of formaldehyde (Table 7.1). Resonance effects can also have a dramatic effect on the reactivity of aldehydes and ketones. In the case of benzaldehyde, for example, the carbonyl π bond is delocalized into the π system of the aromatic ring, thereby reducing the degree of carbonyl polarization. As a result, benzaldehyde is much less electrophilic than acetaldehyde or even pivaldehyde with its very bulky tert-butyl group. When a C=O bond is immediately adjacent to a C=C bond, the effect is to reduce polarization of the C=O bond while increasing polarization of the C=C. These effects in the molecule acrolein are illustrated using resonance structures and partial charge nomenclature (Figure 7.4).
Figure 7.4 The carbonyl in acrolein is depolarized by delocalization of the carbonyl and alkene π systems. The alkene bond, however, is more polarized than in a simple unsubstituted alkene.
Inductive and resonance effects also help determine the reactivity of C=O bonds substituted with non-carbon atoms like oxygen, sulfur, nitrogen, or chlorine (Figure 7.5). Acid chlorides have highly reactive carbonyls because of the strong inductive electron-withdrawing effect of the chlorine atom and also because chloride (Cl−) is a good leaving group (it is the conjugate base of hydrochloric acid, a strong acid). Acid anyhydrides are nearly as reactive as acid chlorides, having a leaving group (acetate) in which negative charge is shared between two electronegative oxygen atoms. Next in order of reactivity are aldehydes and ketones, followed by esters, which are generally less reactive than ketones or aldehydes because the −OR substituent donates significant electron density by a resonance effect. Thioesters are more reactive than esters since the lone pair electrons on sulfur are in d orbitals that have poor overlap with the carbonyl π bond and thus provide less resonance stabilization than in an ester. Amides are significantly less electrophilic than esters because of the reduced electronegativity of nitrogen compared to oxygen combined with a stronger electron-donating resonance effect. We generally consider carboxylic acids to be non-electrophilic since under physiological conditions these groups exist in the carboxylate form with the negative charge fully delocalized into the carbonyl bond. This leaves no significant electrophilic character at carbon in a carboxylate.
Figure 7.5 Carbonyl-containing functional groups in order of decreasing reactivity from left to right.
7.4 Hydration of Aldehydes and Ketones
Water serves as solvent for the chemistry of life and so the reactions of water, whether acting as a nucleophile or serving as an acid or base, are of significant interest. In this section, we explore in depth the mechanism of the hydration of aldehydes and ketones under different reaction conditions. In the previous section we have seen how the types of substituents on a carbonyl function can greatly impact the equilibrium constant (Khydr) of the hydration reaction (Table 7.1). While equilibrium constants can tell us about the thermodynamics of a hydration reaction, studying the kinetics of these reactions can shed light on the reaction mechanism. In the mechanistic discussions that follow, it will be helpful to remember two general points. The first is that C–O bond forming reactions, such as in the addition of water to a carbonyl, are usually much slower processes than proton transfer (acid-base) reactions. The second point is that chemical species (reactants, intermediates, or products) in which opposing charges are separated in space will generally be higher in energy than neutral species with more evenly distributed charge.
If we study the hydration of a ketone in 18O-labeled water, we find that the rate of 18O incorporation in the product is slowest around pH 7 and more rapid at either acidic or basic pH. To understand why this is so, we must consider the protonation states of the reactants at different pH values. At neutral pH where the reaction rate is slowest, both the water nucleophile and the electrophilic carbonyl species are neutral and unprotonated (Figure 7.6). The rate-determining step of the reaction is the C–O bond forming reaction—the addition of water to the carbonyl (step 1, Figure 7.6). This addition reaction involves neutral reactants and produces an intermediate in which positive and negative charges are separated in space. The significant energy difference between the neutral reactants and the charged intermediate corresponds to a high activation energy and this is what accounts for the slow reaction rate. Once formed, the charged intermediate will either revert back to the neutral reactants or undergo a rapid proton transfer reaction (step 2, Figure 7.6) to afford the product.
Figure 7.6 Hydration of an aldehyde or ketone under neutral conditions (pH ~7).
Next, let us consider the mechanism of the same reaction when carried out under acidic conditions (Figure 7.7). Under acidic conditions where hydronium ion (H3O+) concentrations are significant, the carbonyl species can become protonated on oxygen. This has the effect of further polarizing the carbonyl bond and increasing its reactivity as an electrophile. The reactivity of the water nucleophile, by contrast, has not changed significantly when compared to the reaction under neutral conditions. Following the nucleophilic addition step, a single proton transfer to water produces the neutral product and regenerates the hydronium ion catalyst. Since hydronium ion is present on both sides of the reaction equation, the equilibrium constant is not affected—acid catalysis simply accelerates the rate of the reaction.
Figure 7.7 Hydration of an aldehyde or ketone under acidic conditions. (Reproduced, with permission, from Carey FA, Giuliano RM. Organic Chemistry. 9th ed. New York: McGraw-Hill Education; 2014.)
Finally, consider the hydration reaction under basic conditions (Figure 7.8). At higher pH values, hydroxide ion (OH−) is present at significant concentrations. Hydroxide is a much stronger nucleophile than neutral water and thus reacts more rapidly with the carbonyl electrophile (which is no more reactive than at neutral pH). A proton transfer with water then produces the diol product and regenerates hydroxide ion catalyst. As with acid catalysis, basic catalysis affects the rate of the reaction but does not impact the equilibrium constant. To summarize, the hydration of aldehydes and ketones is accelerated under acidic conditions due to activation of the carbonyl electrophile and is accelerated under basic conditions due to a more reactive nucleophile.
Figure 7.8 Hydration of an aldehyde or ketone under acidic conditions. (Reproduced, with permission, from Carey FA, Giuliano RM. Organic Chemistry. 9th ed. New York: McGraw-Hill Education; 2014.)
7.5 Reactions of Aldehydes and Ketones with Alcohols
The reaction of a carbonyl species with an alcohol as nucleophile is similar in many ways to the hydration reaction, but with some interesting additional features. Addition of an alcohol to an aldehyde or ketone results in the formation of a hemi-acetal or hemi-ketal, tetrahedral species that are analogous to the diol product of the hydration reaction. These reactions are slow and reversible at neutral pH, with the equilibrium generally favoring the carbonyl starting material over the hemi-acetal or hemi-ketal. If, however, the reaction is carried out under acidic conditions, a second equivalent of the alcohol nucleophile can be incorporated, producing stable acetal or ketal products. The mechanism of this reaction reveals two important roles for the acid catalyst and also reveals why acetal formation does not occur under basic conditions (Figure 7.9).
Figure 7.9 Acetal formation in the reaction of benzaldehyde with ethanol. (Reproduced, with permission, from Carey FA, Giuliano RM. Organic Chemistry. 9th ed. New York: McGraw-Hill Education; 2014.)
The initial role of the acid catalyst is to protonate and thereby activate the carbonyl electrophile (benzaldehyde in the example shown in Figure 7.9). Reaction with nucleophile (Et–OH in this example) then leads ultimately to a hemi-acetal intermediate (steps 1–3). Next, the hemi-acetal can be protonated on the hydroxyl function and the C–O bond cleaved with loss of water, a good leaving group (steps 4 and 5). The loss of water results in formation of an oxygen-stabilized carbocation, which can be drawn in different resonance forms but is most often shown with a C=O double bond. This cationic species is of course an excellent electrophile and will react readily with an available nucleophile (water or Et–OH). Reaction with water leads back to the hemi-acetal, while reaction with alcohol generates the acetal product (had the carbonyl reactant been a ketone, the product would be a ketal). Because each step in this process is reversible, the reaction can be driven in either direction depending on the reaction conditions. For example, acetal formation is favored if the alcohol nucleophile is used as solvent and so is in large excess. Conversely, acetals can be converted back to aldehydes by reaction with aqueous acid. Acetals do not form under basic conditions because there is no means to produce the requisite oxygen-stabilized carbocation intermediate.
Earlier in this section we have noted that hemi-acetals and hemi-ketals are generally not stable and prefer to decompose to their component carbonyl and alcohol species. An exception to this rule is the case of cyclic hemi-acetals, which are often more stable than the corresponding acyclic hydroxy-aldehyde form. For example, the common sugars D-glucose and D-fructose exist chiefly in the form of a cyclic hemi-acetal and cyclic hemi-ketal, respectively (Figure 7.10). Whereas glucose exists primarily as a six-membered “pyranose” ring, fructose exists as a mixture of pyranose and five-membered “furanose” forms (the furanose form is shown in Figure 7.10). The hemi-acetal function of a sugar molecule (or monosaccharide) can react with an alcohol function of a second sugar to produce a disaccharide in which the two sugars are linked by an oxygen atom. In the context of carbohydrate chemistry, these acetal linkages are known as glycosidic bonds. Glycosidic bonds can be found in a wide variety of biologically important macromolecules, including in polysaccharides, that play important structural and energy-storage roles in biology. An example of a glycosidic bond relevant to drug metabolism is that formed between glucuronic acid and nucleophilic drugs or drug metabolites (Box 7.1).
Figure 7.10 Structures of D-glucose in D-fructose it their cyclic forms. The hemi-acetal and hemi-ketal bonds are highlighted in blue. Sucrose (table sugar) is a disaccharide formed by joining D-glucose and D-fructose via a glycosidic bond (also shown in blue).
