Chapter 1
Click Chemistry: Mechanistic and Synthetic Perspectives

Ramesh Ramapanicker and Poonam Chauhan

Search for reactions that can be used to link two or more diversely functionalized molecules with minimum effort and without the formation of side products has become increasingly important in the past 15 years. As organic molecules started to find their place as easily tunable and functional materials, the requirement of new conjugation reactions that can be used effectively by nonsynthetic organic chemists became unavoidable. Such a reaction should be easier to carry out, yield high selectivity, should be compatible with water and other protic solvents, and should lead to quantitative conversions. Click chemistry is a collection of such reactions that has evolved as an efficient tool for ligation, which gained quick acceptance in biotechnology, material and polymer science, medicinal chemistry, and so on. Among all the click reactions, copper-catalyzed 1,3-dipolar Huisgen cycloaddition (HDC) between a terminal alkyne and an azide is the jewel in the crown. Owing to its remarkable functional group tolerance, researchers can fearlessly introduce easily functionalizable groups such as hydroxyl, carboxyl, and amino groups into conjugate molecules using this reaction.

The concept of click chemistry was first introduced by Sharpless and coworkers in 2001 at the Scripps Research Institute [1]. Click chemistry is not limited to a set of organic reactions, but is a synthetic philosophy inspired by nature in terms of their efficiency, selectivity, and simplicity. Any reaction that can produce conjugate molecules efficiently from smaller units under simpler reaction conditions can be considered as a click reaction. The catchy term click refers to reactions that are modular in approach, efficient, selective, versatile in nature, give single product (high yielding), and can be performed in benign and easily removable solvents without the need for chromatographic purification. There are various reactions with different mechanisms that can be considered as click reactions, provided they follow a simple common reaction trajectory [1].

Sharpless first introduced the concept of click chemistry to provide an effective conjugation technique in drug discovery [2], but the concept and methodology were widely accepted, and click chemistry found its applications in almost all facets of research and technology, which employ organic molecules, such as polymer science [3], nanoscience [4], bioconjugation [5], and development of sensors [6] .

In this chapter, we have provided a detailed account of various click reactions with emphasis on their mechanisms and synthetic details. The discussions are based on the following classification of click reactions.

1.1 Cycloaddition Click Reactions

1.1.1 Azide-Alkyne Huisgen 1,3-Dipolar Cycloaddition

The classical HDC reaction between an alkyne and an azide is the most discussed among click reactions. Both alkynes and azides are unreactive under physiological conditions and undergo a cycloaddition reaction only at elevated temperatures (Scheme 1.1) [7, 8]. Although both alkynes and azide functions can easily be introduced on to the substrates, the cycloaddition reaction is highly exothermic (?H0 is between -50 and -65 kcal/mol) and has a high activation barrier of 25-26 kcal/mol (for methyl azide and propyne). Hence, the uncatalyzed reaction is generally slow and is not regioselective [9]. The difference between HOMO-LUMO energy levels of both azide and alkyne are comparable, thus both dipole HOMO and dipole LUMO pathways can operate in this reaction leading to a mixture of 1,4 and 1,5-triazole regioisomers. It is, however, observed that the use of electron-deficient terminal alkynes can impart 1,4-regioselectivity to a reasonable extent. These factors limit the use of uncatalyzed Huisgen cycloaddition as an effective conjugation technique.

Scheme 1.1 Huisgen 1,3-dipolar cycloaddition between alkynes and azides.

1.1.2 Copper-Catalyzed Azide-Alkyne Cycloaddition (CuAAC) Click Reaction

Sharpless [9] and Meldal [10] independently reported a Cu(I)-catalyzed version of the cycloaddition reaction between azides and terminal alkynes, which is 107 times faster than the uncatalyzed reaction. The interaction between Cu(I) and terminal alkynes makes the latter a better 1,3-dipolarophile, enhancing its reaction with azides. The Cu(I)-catalyzed reaction is highly regioselective and only the 1,4-adducts are formed. The Cu(I)-catalyzed reactions can be carried out at room temperature and at a much faster rate.

Sharpless reported the possibility of using in situ generated copper(I), obtained through the reduction of copper sulfate pentahydrate (CuSO4·5H2O) with ascorbic acid, as an efficient catalyst for carrying out azide-alkyne conjugation reactions in solutions [9]. The reactions worked well when a mixture of water and an alcohol is used as the solvent. The solvent mixture allowed effective dissolution of the metal salt and the organic components needed to be conjugated. Meldal and coworkers reported a very practical application of azide-alkyne cycloaddition catalyzed with cuprous iodide in conjugating peptides through side chains or the backbone in solid phase [10]. Both reactions were selective for the formation of 1,4-disubstituted 1,2,3-triazoles and together revolutionized the concept of click reactions (Scheme 1.2).

Scheme 1.2 CuAAC click reaction.

In addition to being a stable linker, the triazole group has certain other advantages. On comparison with an amide bond, which was otherwise the most common linkage used, a triazole group exhibits certain interesting and unique properties. Unlike an amide bond, triazoles are not susceptible to hydrolytic cleavage. They cannot be reduced or oxidized under normal conditions. A triazole linkage, with an extra atom in its backbone, places the carbon atoms linked to 1- and 4-positions at a distance of 5.0 Å, while an amide linkage places the carbon atoms only at 3.8 Å apart from each other. The nitrogen atoms at 2- and 3-positions of the triazole have weak hydrogen-bond-accepting properties. The inherent dipole moment in a triazole ring leads to polarization of the C5-H bonds, making them hydrogen bond donors and enabling C-H?X hydrogen bonds, similarly to an amide bond [11]. These properties also enabled Cu(I)-catalyzed triazole formation to gain attention as an effective conjugation method.

Conjugation of functional molecules through triazoles received immediate attention especially in drug discovery. Linhardt et al. synthesized some sialic acid conjugates using copper catalyzed azide-alkyne cycloaddition (CuAAC), which are potential neuraminidase inhibitors with good IC50 values (Figure 1.1) [12]. There are a large number of such examples of CuAAC being used effectively for assembling small molecular units to obtain more functional and useful molecules. An interesting example is the synthesis of the rigid macrocycle C (Figure 1.2) by Flood et al., in which triazole units function as rigid structural units and provide acidic hydrogens to interact and detect chloride ions in organic solvents [13]. In a similar attempt, Beer et al. have reported a ferrocene-containing bis(triazole) macrocycle D (Figure 1.2), in which they have increased the anion binding tendency of the C-H of triazole by converting triazole units to cationic triazolium moieties. Alkylation of a triazole increases its binding capability with anions such as chloride and benzoate ions even in polar organic solvents [14].

Figure 1.1 Sialic-acid-based neuraminidase inhibitors; a disaccharide mimic A and a dendrimer B.

Figure 1.2 Triazole-containing macrocycles used for the detection of anions.

1.1.2.1 Mechanism of CuAAC Click Reactions

A detailed mechanistic analysis of CuAAC was reported by Jan H. van Maarseveen and coworkers in 2006 [15]. The report was based on comprehensive kinetic studies and DFT calculations. Studies showed that the Cu-catalyzed cycloaddition reaction proceeds through a stepwise mechanism and the activation energy is 11 kcal/mol less than that of the uncatalyzed reaction, which has an activation energy of 26 kcal/mol. However, a concerted mechanism involving Cu-acetylene p-complex and the azide was calculated to have a higher activation energy of 27.8 kcal/mol. The reaction begins with the formation of a Cu-alkyne p complex, which then forms a copper acetylide after deprotonation of the alkyne proton. Coordination of copper with the alkyne makes the acetylenic proton more acidic, increasing its acidity by up to 9.7 pH units, which allows the deprotonation to occur in aqueous media even in the absence of a base. The copper acetylide exists in equilibrium between a monomer and a dimer. One of the Cu ions in the dimer coordinates with the azide nitrogen and activates it. This complex then cyclizes to give a metallacycle via a nucleophilic attack of the terminal nitrogen of the azide group on the internal carbon of the alkyne. The metallacycle then undergoes a ring contraction through a transannular interaction between the lone pair of electrons on the substituted nitrogen of the azide and the CCu bond. This relatively faster step yields a Cu triazolide, which undergoes protonation to liberate the 1,4-disubstituted triazole and regenerates...