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The Skaggs Institute for Chemical Biology
Scientific Report 1999-2000

Molecules Inside Molecules

J. Rebek, Jr., M. Brody, R. Castellano, Y.-L. Cho, S. Craig, G. Haberhauer, T. Haino, F. Hof, P. Iovine, S. Körner, U. Lücking, S. Mecozzi, C. Nemes, C. Nuckolls, A. Rafai Far, A. Renslo, J. Rivera-Ortiz, D. Rudkevich, S. Saito, L. Sébo, L. Somogyi, S. Starnes, N. Svenstrup, F. Tucci, P. Wash

Chiral Microenvironments For Molecular Recognition

Chirality is defined as the lack of mirror-image symmetry. Any object that is chiral exists as a pair of mirror-image isomers, or enantiomers, that are not superimposible on each other. Nucleic acids, carbohydrates, proteins, and most drugs are chiral and are present as only a single enantiomer. The chemical reactions that fuel life are carried out when chiral macromolecules (enzymes) recognize and bind smaller chiral molecules (substrates) within pockets or cavities. We have undertaken studies of chiral assembly and recognition to better understand how biological molecules recognize and discriminate between pairs of enantiomers.

We synthesized a chiral molecule that is curved and has self-complementary hydrogen-bonding sites. When 4 copies of the molecule come together, they self-organize in a head-to-tail manner to form a molecular capsule that encloses a pseudospherical cavity. The result is a capsule that is itself chiral. The self-assembled capsule binds small molecules of appropriate size and shape within its cavity. The relatively weak forces that the individual molecules can exert on their surroundings are amplified through the assembly process. The capsule can discriminate between mirror-image isomers of guest molecules and successfully mimics the ability of biological macromolecules to recognize and bind single enantiomers of chiral molecules (Fig. 1).

Changing Partners

Much of our research has been concerned with designing, synthesizing, and characterizing molecules that self-assemble into molecular capsules. In the course of our investigations, we created heterodimers, versions of these molecules that form capsules composed of 2 different pieces. We continue to develop new types of heterodimeric capsules so that we can move closer to realizing one of our ultimate goals: incorporating the capsules into informational polymers reminiscent of DNA.

Calixarenes provide a bowl-shaped molecular scaffold that is easily changed on the rim by substituting parts with hydrogen-bonding functionality. We showed several years ago that aryl urea-derived calixarenes form dimers through a directional, hydrogen-bonding seam at the capsule equator (Fig. 2). By synthesizing and analyzing a host of different calixarenes that differed in their urea substituents, we discovered that amino acid-derived ureas with ß-branched side chains, such as isoleucine and valine, exclusively heterodimerize with aryl-derived ureas.

The point chirality, or the handedness, of the amino acids in these assemblies is smoothly transferred to the hydrogen-bonding seam, giving rise to a chiral capsule with only a single direction to its head-to-tail arrangement of ureas. These chiral capsules act as hosts that can discriminate between mirror-image forms of guests in solution. The compounds described here illustrate the consequences, both chemical and stereochemical, of a well-positioned, yet remote, chiral center on molecular assembly.

Nanoscale Self-Folding Cavities

One of the ultimate goals of molecular recognition is to construct molecular hosts that completely surround their guests. A "scaggs" molecule (semicapsule allowing giant guest seizure) is the most recent development in this field. The new structure (Fig. 3) consists of 2 deepened, bowl-shaped molecules connected by an extended aromatic spacer. The structure is among the largest of synthetic unimolecular hosts, with cavity dimensions of approximately 23 x 10 Å and an internal volume of approximately 800 Å3. In addition to covalent bonding, intramolecular hydrogen bonding holds the internal cavity in place. These hydrogen bonds also control the reversible seizing and release of the guest and make access to the cavity easy under mild conditions.

Of particular importance, the molecule accommodates guests of nanoscale dimensions (up to 18 Å). The direct observation of encapsulated species and their orientation within the cavity and the determination of the stoichiometry of the complexes can be accomplished by using nuclear magnetic resonance spectroscopy. The most immediate applications of scaggs molecules are as sensors for chemical analysis and as delivery vehicles. They can also be used as reaction vessels; the internal space can accommodate more than a single guest, and the constant flow of guests into and products out of the cavity is visible. The synthesis of water-soluble scaggs versions for molecular recognition in aqueous solution is under way.

Avoiding Vacuums

A unique and useful feature of our molecular hosts is that guests enter and leave in convenient lengths of time. For example, it takes approximately 1 hour for a single guest to displace another guest from the "softball" (Fig. 4). We established that guest exchange occurs in 2 steps. First, solvent molecules rinse out the resident guest, leaving a capsule filled temporarily with the less desirable solvent. The solvent is then rapidly displaced, either by one of the original guest molecules or by one of the preferred, incoming guests.

The host remains intact during the exchange but is not static. The ring of atoms in the box in Figure 4A acts as a hinge, and windows are constantly opening and closing in the softball casing. When 2 windows open at once, solvent and guest molecules have enough room to sluice through the exposed interior (Fig. 4C).

At no point is the host completely empty: one molecule enters as another molecule exits. The guests and solvent, therefore, must pass simultaneously through passageways of a size comparable to the size of the molecules themselves. Here, as in the capsule interior, molecular recognition plays a role; guests move in and out at rates that depend on their size, shape, and functionality. The windows and the interior are selective for different attributes, and we have observed relatively poor guests that outrace their preferred counterparts for the capsule interior. Our understanding of these processes has contributed to new uses for encapsulation complexes, including molecular imprinting and the kinetic control of reactions in solution. Brody, M.S., Schalley, C.A., Rudkevich, D.M., Rebek, J., Jr. Synthesis and characterization of an intramolecularly self-assembled capsule. Angew. Chem. Int. Ed. 38:1640, 1999.

Castellano, R.K., Nuckolls, C., Rebek, J., Jr. Transfer of chiral information through molecular assembly. J. Am. Chem. Soc. 121:11156, 1999.

Lützen, A., Renslo, A.R., Schalley, C.A., O'Leary, B.M., Rebek, J., Jr. Encapsulation of ion-molecule complexes: Second-sphere supramolecular chemistry. J. Am. Chem. Soc. 121:7455, 1999.

Ma, S., Rudkevich, D.M., Rebek, J., Jr. Supramolecular isomerism in caviplexes. Angew. Chem. Int. Ed. 38:2600, 1999.

Nuckolls, C., Hof, F., Martin, T., Rebek, J., Jr. Chiral microenvironments in self-assembled capsules. J. Am. Chem. Soc. 121:10281, 1999.

Renslo, A.R., Rudkevich, D.M., Rebek, J., Jr. Self-complementary cavitands. J. Am. Chem. Soc. 121:7459, 1999.

Renslo, A.R., Tucci, F.C., Rudkevich, D.M., Rebek, J., Jr. Synthesis and assembly of self-complementary cavitands. J. Am. Chem. Soc., in press.

Rudkevich, D.M., Rebek, J., Jr. Deepening cavitands. Eur. J. Org. Chem. 9:1991, 1999.

Santamaria, J., Martin, T., Hilmersson, G., Craig, S.L., Rebek, J., Jr. Guest exchange in an encapsulation complex: A supramolecular substitution reaction. Proc. Natl. Acad. Sci. U. S. A. 96:8344, 1999.

Tucci, F.C., Renslo, A., Rudkevich, D.M., Rebek, J., Jr. Nanoscale container structures and their host-guest properties. Angew. Chem. Int. Ed. 39:1076, 2000.



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