The ideas of resonance can be extended to understanding the structures of the related carbonyl containing groups, carboxylic acids and esters. For esters and carboxylic acids, the appropriate resonance structures are shown in Figure 2.12. Note that the structures having C=O+R or C=O+H double bond character also place formal positive charges at O atoms. Recall that oxygen is the secondmost electronegative group in the periodic table. Hence we expect that resonance structures with a formal positive charge on O will be less important than those with a formal charge on N.

Figure 2.12. Resonance structures for esters and carboxylic acids (carboxylic acid, R₂ = H; ester, R₂ = alkyl, aryl, etc).

As in the case of the resonance structure with the C=N+HR linkage for amides, the resonance structure with the C=O+R linkage (R=H in carboxylic acids and R=alkyl, aryl, etc. in esters) is expected to be the minor contributor in esters and carboxylic acids due to the formal positive charge on the highly electronegative O atom. In carboxylic acids, it is found that the O-H bond lies in the plane of the groups attached to the carbonyl carbon. If partial double bond character accounts for this geometric arrangement, then we expect a barrier to rotation about the C=O+H bond. We also expect the possiblity of two distinct isomers for the syn and anti configurations as was seen for amides. Both experiment and computational results confirm these expectations. In the simple carboxylic acid, formic acid, all atoms lie in the same plane. In general, the syn conformer is more stable than the anti by about 20 kJ/mol. Barriers to rotation about the C-OH bond are estimated to be 40 kJ/mol, signifcantly less than the 72 kJ/mol for rotation about an amide C=N double bond but significant nonetheless.

Figure 2.13. Energy profile and structures of syn and anti conformers of carboxylic acids

When the hydroxyl group of a carboxylic acid is replaced with an alkoxy group, an ester is generated. Like the carboxylic acid and the amide groups, the ester group is planar with bond angles about the carbonyl C tending to ca. 120^o. The O-C bond (blue in Figure 2.??) of esters also lies in the plane of the carbonyl group. Like carboxylic acids and amides, both syn and anti conformations are possible with the syn conformation preferred by around 15-20 kJ/mol. The barrier to rotation of the ester C-OR bond is approximately 45 kJ/mol (Figure 2.14). Again, such a barrier is suggestive of some double bond character in the C-O. Such double bond character can be rationalized by consideration of the dipolar resonance structure shown with the usual Lewis structure for esters in Figure 2.12.

Figure 2.14. Energy profile and structures of syn and anti conformers of esters.

2.5 Carbonyls Have Distinctive Spectroscopic Properties

The effect of resonance on the structure and the planarity of the amide bond have been described in the above sections. These explanations seem reasonable, believable, valid. But what if you don't believe what you've been told? What if you didn't even have access to the above information and wanted to learn for yourself about the properties of carbonyl-containing compounds? What would you do?

What researchers working with HIV Protease (and in fact with a wide variety of other chemistry projects) do to study compounds is to use spectroscopic methods of instrumental analysis. For example, suppose you are given a sample of HIV Protease or some other protein or peptide and asked to determine its structure. The first things that you would be likely to do would be to obtain an Infrared (IR) spectrum and Nuclear Magnetic Resonance spectra of your compound. These spectra are shown in Figure 2.15.

Figure 2.15. a) IR, b) ¹³C, and c) ¹H NMR of a peptide.

a)

b)

c)

Although upon a first inspection these spectra look impossibly complicated, they are in fact quite useful. Focus first on the different areas of absorptions in the IR spectrum. Spectroscopic features of carbonyl groups are a distinctive characteristic of compounds containing this functionality, and almost all carbonyl groups exhibit very strong IR absorptions in the range of 1600-1800cm^-1. These absorptions are very useful in identifying carbonyls because this region of the IR spectrum contains very few other bands. Note from the example shown in Figure 2.?? that the C=O molar absorptivities are much stronger than those of simple C=C bonds. This in not unexpected as stretching and compressing the highly polarized C=O leads to a large oscillating dipole moment, hence the strong absorption of IR light. Table 2.4 compares the stretching frequencies of compounds containing C=C with those containing a carbonyl group. Using the information in Table 2.4, what can you say about the types of carbonyl compounds (if any) that are present in the IR spectrum given in Figure 2.15 above?

Figure 2.16. IR spectrum of 3-penten-2-one.

Table 2.3. Comparison of IR stretching frequencies of compounds containing C=O and C=C functional groups. The given frequency is for the carbonyl carbon (column one) or the equivalent C=C carbon (column two).

carbonyl compound	alkene

Along with ¹³C NMR, ¹H NMR spectra of carbonyl-containing compounds are often distinct. The acidic proton of carboxylic acids is found between 10 and 13 ppm, and the aldehyde CHO proton is usually found between 9 and 10.5 ppm. These and other ¹H NMR chemical shifts are shown in Table 2.6. Use the ¹³C and ¹H NMR information given in the tables to interpret the spectra in Figure 2.15. Are carbonyl groups present? If they are, can you identify any specific types of carbonyl groups?

Table 2.5. ¹H NMR chemical shifts for carbonyl compounds. The given d value is for the H shown in blue.The given d value is for the carbonyl carbon.

Type of carbonyl compound	Range of ppms	Examples
aldehyde	190-205 ppm
ketone	195-220 ppm
carboxylic acid	170-185 ppm
ester	165-180 ppm (-5 to -10 ppm shift from the carboxylic acid)
amide	165-180 ppm

Along with ¹³C NMR, ¹H NMR spectra of carbonyl-containing compounds are often distinct. The acidic proton of carboxylic acids is found between 10 and 13 ppm, and the aldehyde CHO proton is usually found between 9 and 10.5 ppm. These and other ¹H NMR chemical shifts are shown in Table 2.6. Use the ¹³C and ¹H NMR information given in the tables to interpret the spectra in Figure 2.15. Are carbonyl groups present? If they are, can you identify any specific types of carbonyl groups?

Table 2.6. ¹H NMR chemical shifts for carbonyl compounds. The given d value is for the H shown in blue.

Type of carbonyl compound	Range of ppms	Examples
aldehyde	9-10.5 ppm
ketone	2-3.6 ppm
carboxylic acid	10-13 ppm
ester	3.5-4 ppm
amide	5-10 ppm (often broad)

2.6. Carboxylic Acids, Esters, and Amides Are Found in Many Common Materials

So far we have considered the occurrence of carboxylic acids, esters, and amides only in the context of protein structures. Consider the common products shown in Figure 2.17. Aspirin and ibuprofen both contain aromatic groups and carboxylic acids (aspirin also has an ester group), the non-nutritive sweetener apartame contains both amide and ester groups, morphine also contains an amide group, the anti-Parkinsonian drug L-DOPA is a carboxylic acid, the ester isopentyl acetate largely is responsible for the odor of bananas, and the chief organic component of vinegar is the carboxylic acid, acetic acid.

Figure 2.17. Common compounds which contain various types of carbonyl groups.

Let's return to the ribbon structure of HIV Protease (Figure 2.1). You will notice that molecule is folded around on itself to form a well defined shape. What makes HIV Protease fold in this way? To address this critical issue we need to take a closer look at the protein and its functional groups. As the figure below depicts, many carboxylic acid side groups from amino acids such aspartic acid lie near the amine side groups of amino acids such as lysine. Closer inspection reveals that the carboxylic acid groups have transferred a proton to an amine group, in the process forming negatively charged carboxylate (R-COO^-) group and a posititvely charged ammonium group (R-NH₃⁺). Not surprisingly, the carboxylic acid group acts as a Br¿nsted acid and the amine group acts as a Br¿nsted base. We might expect that the oppositely charged ammonium and carboxylate groups have a substantial attraction. We will soon see that this formation of "salt bridges" plays a critical role in determining the protein shape. But first we must ask why carboxylic acids are acidic whereas alcohols are not.

Figure 2.18 Salt Bridges in HIV Protease with a close-up of a salt bridge

2.8. Acidity is Promoted by Resonance Stabilization

Place acetic acid (CH₃C(=O)OH)in water (i.e., make distilled white vinegar) and measure the solution pH with a meter or litmus paper. You will find that the solution is acidic by virtue of the following equilibrium:

The equilibrium constant for this reaction, called K_a, has the following value at 25^oC:

corresponding to a pK_a of 4.74. This means that at pH=4.74, half of the acetic acid is in the protonated or free acid form and half is in the deprotonated or acetate ion form. Because the pK_a of acetic acid is low, acetic acid is essentially entirely deprotonated at physiological pH (around pH=7.0).

The pK_a of acetic acid is not remarkable in and of itself; for a 0.1 M concentration in water the acetic acid is only 1.3% dissociated. Certainly other oxyacids such as H₂SO₄ (pK_a= -3), H₃PO₄ (pK_a=2.14), and HClO₄ (pK_a= -3) are far stronger acids. The unusual acidity of carboxylic acids is revealed only in comparison with the closely related functional group, the alcohol. Alcohols are weak acids; the pK_a of ethanol is only about 16. In fact, ethanol is a weaker acid than water. The differences of the pK_a's for ethanol and acetic acid are about 11, and this corresponds to equilibrium constants that differ by eleven orders of magnitude.

Why is acetic acid so much more acidic than ethanol? To rationalize this effect we must consider both the reactants and products of the acid dissociation reaction. Let us begin with the products and consider the relative stabilities of the two anions formed by loss of a proton, the ethoxide and acetate anions. In the acetate anion, the negative charge is distributed over both oxygen atoms of the carboxyl group, whereas the charge of ethoxide is mostly localized on the oxygen. The two oxygens of carboxylate groups are identical in all respects: for example, the two C-O bond lengths determined by X-ray crystallograpy are the same (1.26). This contrasts with the C-O bond lengths of the carboxylic acid, for which the two C-O bond lengths are significantly different (1.21 for C=O and 1.36 for C-O of acetic acid).

A single Lewis structure does not adequately describe the acetate ion. To rationalize the observed structure of the acetate ion we must consider two Lewis structures in resonance with one another (Figure 2.19). Alternatively, we may represent the net effect of the resonance structures as the sum of the two individual representations (Figure 2.20).

Figure 2.19. Lewis structures describing the acetate anion.

Figure 2.20. Single structure describing the acetate anion.

The effect of spreading the charge of the acetate anion over two oxygen atoms is to stabilize the the anion with respect to the ethoxide anion. This energetic effect, which is similar to the stabilization of benzene relative to non-conjugated alkenes, is referred to as resonance stabilization. We can view the energy lowering as resulting from spreading of the electron density over more atoms.

The above explanation focused on relative stabilities of the products of proton loss. We must be careful; the energetics of a chemical reaction depend on the differences between reactant and product energies. Therefore, it is not sufficient to examine the effects of resonance on the products, only. Let us consider now the reactants, ethanol and carboxylic acids. We can propose three resonance structures for acetic acid as shown below. Note that stabilization may be afforded by the resonance structure involving a formal positive charge on the O bonded to H; by electronegativity considerations we expect that this structure will be a minor contributor. Nonetheless we have already seen evidence for the participation of the third resonance structure shown below (recall the restriction of rotation about the C-OH bond).

Figure 2.21. Three resonance structures for acetic acid.

Even a small contribution of a resonance structure with a formal positive charge on the O of the O-H group will increase the acidity. By electrostatic-based reasoning, diminished negative charge on the O of the OH group will increase the tendency of the O-H bond to dissociate H⁺. An alcohol has no equivalent possibilities for resonance enhanced acidities. In conclusion, resonance provides a rationale for understanding the far higher stabilities of carboxylic acids relative to alcohols. We can view the influence of resonance either as Coulombic destabilization of the acid or as stabilization of the acetate anion via charge delocalization.