Scientific Report 2007

The Skaggs Institute for Chemical Biology

The Behavior of Surrounded Molecules

J. Rebek, Jr., D. Ajami, E. Barrett, T.J. Dale, N. Gombosuren, R.J. Hooley, J.-L. Hou, T. Iwasawa, E. Mann, L. Moisan, S. Odermatt, F.R. Pinacho Crisotomo, P. Restorp, M. Schramm, S. Shenoy, C. Turner, H. Van Anda

Stabilization and Observation of Transient Reaction Intermediates

Cavitands are synthetic receptors that more or less surround small-molecule targets. The cavitand provides a means to isolate molecules from the bulk medium, and the labile tetrahedral intermediates in the reaction of primary amines with aldehydes to give imines can be observed (Fig. 1). The reaction proceeds through an intermediate hemiaminal, which, except in special cases, does not occur in free solution. The receptor recognizes and surrounds amines of appropriate size and shape and then presents them with a covalently attached aldehyde group. The small volume of the receptor amplifies the concentration of amine reactant, and the bound hemiaminal intermediates can be detected at ambient temperatures by using conventional nuclear magnetic resonance spectroscopy. Extra stabilization is provided by hydrogen-bonding interactions. Depending on the amine added, these hemiaminals can have half-lives of up to 100 hours; in equivalent reactions in free solution, no hemiaminals occur. The receptor has all the hallmarks of an enzyme: it presents the intermediate with complementary hydrogen-bonding groups and isolates the intermediate in a well-defined limited space, leading to selective stabilization. The synthetic receptor provides a window into an enzymelike reaction chamber.

Fig. 1. Top, Illustration of the reaction taking place inside the cavity. Bottom, Structure (left) and energy-minimized representation (right) of the reactive intermediate hemiaminal. Some groups have been removed for clarity.

Cavitands in Micelles

Other cavitands have served as small-molecule hosts with guest selectivity, guest exchange, reaction acceleration, and even catalysis. The deepened hydrophobic interiors facilitate sequestration of both neutral and charged organic molecules from bulk solution, most commonly via the hydrophobic effect. To develop a general cavitand for guest recognition in aqueous micelles, we prepared a hydrophobic cavitand (Fig. 2). We found that the cavitand is incorporated in aqueous phosphocholine micelles, folds into the vase shape, and functions as a small-molecule host. Hydrophobic guest "anchors" are held deep in its interior. These anchors include cycloalkanes, adamantanes, and nitrogen heterocycles that compete favorably with the large excess of phosphocholine alkyl side chains that make up the micelle interior. The adamantyl anchor shown in Figure 2 was further functionalized with fluorophores and dipeptides, and both guests retained their recognition properties.

Fig. 2 The vase-shaped cavitand (1) acts as a selective small-molecule receptor for the adamantyl "anchor" with a fluorescent label (green). The assembly is formed while immersed in aqueous micelles (red).

These small-molecule cavitand hosts are themselves guests within the hydrophobic interior of the micelle and are thus simple biomimetic receptors. The next steps of this research program will be to transport fluorophores and druglike molecules into more complicated lipid bilayer and cellular systems.

Energy Transfer

Another aspect of our research involves modeling natural photosynthesis by using knowledge of noncovalent interacting systems. The photosynthetic pathway involves the absorption of light, a series of electron-transfer events, and, finally, conversion of the light energy into chemical work. These electron-transfer reactions occur between a series of electron donors and electron acceptors, ultimately producing a charge- separated state. By attaching suitable electron-transfer donors and acceptors noncovalently, the desired charge-separated state from the electron-transfer event has a longer lifetime than do similar systems in which covalent attachments are used. The long charge-separated lifetime is desirable because it facilitates conversion of the absorbed light energy into chemical work.

We have attached a porphyrin to the outside of a cylindrical capsule to act as both the light absorber and the electron acceptor (Fig. 3). When a suitable electron donor is encapsulated inside the capsule, the absorption of light by the porphyrin induces a transfer of electrons across the capsular boundary to the porphyrin and produces the desired charge-separated state. We are studying this system in an attempt to harness the captured light energy as an energy source.

Fig. 3 Electron transfer from an encapsulated molecule to an appended porphyrin.

Capsule Dynamics

We showed that 2 capsules of vastly different sizes, shapes, and hydrogen-bonding patterns formed not only their respective host-guest assemblies in solution but also a hybrid assembly (Fig. 4). We used fluorescence resonance energy transfer to study the formation of the hybrid assembly. Fluorescence resonance energy transfer, although common in the study of dynamic processes in biology, is rarely used in synthetic supramolecular systems. It allows study of subunit exchange and guest exchange at nanomolar concentrations, providing information unattainable from experiments done at millimolar concentrations. The modules that make up the capsules were synthesized with either a donor or an acceptor fluorophore. Fluorescence resonance energy transfer occurs only when the hybrid capsule is assembled, a process that takes several days to complete.

Fig. 4. Representation of the donor-labeled cylindrical capsule and the acceptor-labeled hexameric capsule in equilibrium with a hybrid capsule. Fluorescence resonance energy transfer occurs only when donor and acceptor are parts of the same assembly. ET = electron transfer.

Publications

Ajami, D., Schramm, M.P., Volonterio, A., Rebek, J., Jr. Assembly of hybrid synthetic structures. Angew. Chem. Int. Ed. 46:242, 2007.

Barrett, E.S., Dale, T.J., Rebek, J., Jr. Assembly and exchange of resorcinarene capsules monitored by fluorescence resonance energy transfer. J. Am. Chem. Soc. 129:3818, 2007.

Barrett, E.S., Dale, T.J., Rebek, J., Jr. Self-assembly dynamics of a cylindrical capsule monitored by fluorescence resonance energy transfer. J. Am. Chem. Soc. 129:8818, 2007.

Butterfield, S., Rebek, J., Jr. A cavitand stabilizes the Meisenheimer complex of SNAr reactions. Chem. Commun. (Camb.) 1605, 2007, Issue 16.

Hooley, R.J., Rebek, Jr., J. Self-complexed deep cavitands: alkyl chains coil into a nearby cavity. Org. Lett. 9:1179, 2007.

Iwasawa, T., Hooley, R.J., Rebek, J., Jr. Stabilization of labile carbonyl addition intermediates by a synthetic receptor. Science 317:493. 2007.

Iwasawa, T., Wash, P., Gibson, C., Rebek, J., Jr. Reaction of an introverted carboxylic acid with carbodiimide. Tetrahedron 63:6506, 2007.

Schramm, M.P., Hooley, R.J., Rebek, J., Jr. Guest recognition with micelle-bound cavitands. J. Am. Chem. Soc. 129:9773, 2007.

Van Anda, H., Myles, A.J., Rebek, J., Jr. Charge transfer and encapsulation in a synthetic, self-assembled receptor. N. J. Chem. 31:631, 2007.