Noncovalent interactions hold the key to understanding many chemical, biological, and technological problems. Describing these noncovalent interactions accurately, including their positions in real space, constitutes a first step in the process of decoupling the complex balance of forces that define noncovalent interactions. Because of the size of macromolecules, the most common approach has been to assign van der Waals interactions (vdW), steric clashes (SC), and hydrogen bonds (HBs) based on pairwise distances between atoms according to their vdW radii. We recently developed an alternative perspective, derived from the electronic density: the non-covalent interactions (NCI) index [J. Am. Chem. Soc. 2010, 132, 6498]. This index has the dual advantages of being generally transferable to diverse chemical applications and being very fast to compute, since it can be calculated from promolecular densities. Thus, NCI analysis is applicable to large systems, including proteins and DNA, where analysis of noncova...

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NCIPLOT: A Program for Plotting Noncovalent Interaction Regions

In 1981, the macrocyclic methylene-bridged glycoluril hexamer (CB[6]) was dubbed "cucurbituril" by Mock and co-workers because of its resemblance to the most prominent member of the cucurbitaceae family of plants--the pumpkin. In the intervening years, the fundamental binding properties of CB[6]-high affinity, highly selective, and constrictive binding interactions--have been delineated by the pioneering work of the research groups of Mock, Kim, and Buschmann, and has led to their applications in waste-water remediation, as artificial enzymes, and as molecular switches. More recently, the cucurbit[n]uril family has grown to include homologues (CB[5]-CB[10]), derivatives, congeners, and analogues whose sizes span and exceed the range available with the alpha-, beta-, and gamma-cyclodextrins. Their shapes, solubility, and chemical functionality may now be tailored by synthetic chemistry to play a central role in molecular recognition, self-assembly, and nanotechnology. This Review focuses on the synthesis, recognition properties, and applications of these unique macrocycles.

The cucurbit[n]uril family

Dynamic combinatorial chemistry.

Condensation of 1,4-dimethoxybenzene (DMB) with paraformaldehyde in the presence of BF3·O(C2H5)2 gave novel para-bridged pentacyclic pillar DMB (DMpillar[5]arene). Moreover, para-bridged pentacyclic hydroquinone (pillar[5]arene) was prepared. Pillar[5]arene formed 1:1 host–guest complexes with dialkyl viologen and alkyl pyridinium derivatives. However, pillar[5]arene did not form complexes with the diadamantyl viologen derivative since a bulky adamantyl group was unable to thread the cavity of pillar[5]arene.

para-Bridged symmetrical pillar[5]arenes: their Lewis acid catalyzed synthesis and host-guest property.

Functional π-Gelators and Their Applications

We determined the values of Ka for a wide range of host−guest complexes of cucurbit[n]uril (CB[n]), where n = 6−8, using 1H NMR competition experiments referenced to absolute binding constants measured by UV/vis titration. We find that the larger homologuesCB[7] and CB[8]individually maintain the size, shape, and functional group selectivity that typifies the recognition behavior of CB[6]. The cavity of CB[7] is found to effectively host trimethylsilyl groups. Remarkably, the values of Ka for the interaction of CB[7] with adamantane derivatives 22−24 exceeds 1012 M-1! The high levels of selectivity observed for each CB[n] individually is also observed for the CB[n] family collectively. That is, the selectivities of CB[6], CB[7], and CB[8] toward a common guest can be remarkably large. For example, guests 1, 3, and 11 prefer CB[8] relative to CB[7] by factors greater than 107, 106, and 3000, respectively. Conversely, guests 23 and 24 prefer CB[7] relative to CB[8] by factors greater than 5100 and 990, resp...

The Cucurbit[n]uril Family: Prime Components for Self-Sorting Systems

Im Jahre 1981 tauften Mock und Mitarbeiter das makrocyclische methylenverbruckte Glycoluril-Hexamer (CB[6]) auf den Namen “Cucurbituril” – da ihre Form einem Kurbis ahnelt, dem bekanntesten Mitglied der Cucurbitaceae-Familie in der Pflanzenwelt. In den folgenden Jahren wurden die grundlegenden Bindungseigenschaften von CB[6] – die hohe Affinitat und Selektivitat sowie der Einschluss von Gasten – in bahnbrechenden Arbeiten der Gruppen von Mock, Kim und Buschmann aufgezeigt; es folgten Anwendungen in der Wasseraufarbeitung, kunstlichen Enzymen und molekularen Schaltern. Erst vor kurzem wuchs die Cucurbit[n]uril-Familie um Homologe (CB[5]–CB[10]), Derivate, Verwandte und Analoga, sodass sie nun die Molekulgrosen von α-, β- und γ-Cyclodextrinen umfasst und ubersteigt. Auch die Formen, Loslichkeiten und chemischen Funktionalitaten konnen inzwischen durch spezielle Synthesen den Erfordernissen angepasst werden. Durch diese Eigenschaften sind die Cucurbiturile pradestiniert fur eine zentrale Rolle in molekularer Erkennung, Selbstorganisation und Nanotechnologie. Dieser Aufsatz stellt Synthesen, Erkennungseigenschaften und Anwendungen dieser einzigartigen Makrocyclen vor.

Die Cucurbit[n]uril-Familie

Spontaneous Colorimetric Sensing of the Positional Isomers of Dihydroxynaphthalene in a 1D Organogel Matrix

The molecular recognition platforms of natural systems often possess multiple binding epitopes, each of which has programmed functional consequences. We report the dynamic behavior of a system comprising CB[6], CB[7], and guests cyclohexanediammonium (1) and adamantanealkylammonium (2) that we refer to as a two-faced guest because it contains two distinct binding epitopes. We find that the presence of the two-faced guestjust as is observed for protein targeting in vivodictates the kinetic pathway that the system follows toward equilibrium. The influence of two-faced guest structure, cation concentration, cation identity, and individual rate and equilibrium constants on the behavior of the system was explored by a combination of experiment and simulation. Deconstruction of this system led to the discovery of an anomalous host−guest complex (CB[6]·1) whose dissociation rate constant (kout = 8.5 × 10-10 s-1) is ≈100-fold slower than the widely used avidin·biotin affinity pair. This result, in combination wit...

Pritam Mukhopadhyay

Papers

The cucurbit[n]uril family

The Cucurbit[n]uril Family: Prime Components for Self-Sorting Systems

Die Cucurbit[n]uril-Familie

Spontaneous Colorimetric Sensing of the Positional Isomers of Dihydroxynaphthalene in a 1D Organogel Matrix

High Fidelity Kinetic Self-Sorting in Multi-Component Systems Based on Guests with Multiple Binding Epitopes