Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Crystallographic observation of 'induced fit' in a cryptophane host-guest model system.

ABSTRACT: Cryptophane-A, comprised of two cyclotriguaiacylenes joined by three ethylene linkers, is a prototypal organic host molecule that binds reversibly to neutral small molecules via London forces. Of note are trifunctionalized, water-soluble cryptophane-A derivatives, which exhibit exceptional affinity for xenon in aqueous solution. In this paper, we report high-resolution X-ray structures of cryptophane-A and trifunctionalized derivatives in crown-crown and crown-saddle conformations, as well as in complexes with water, methanol, xenon or chloroform. Cryptophane internal volume varied by more than 20% across this series, which exemplifies 'induced fit' in a model host-guest system.

SUBMITTER: Taratula O

PROVIDER: S-EPMC3105606 | biostudies-literature | 2010

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Crystallographic observation of 'induced fit' in a cryptophane host-guest model system.

Taratula Olena O Hill P Aru PA Khan Najat S NS Carroll Patrick J PJ Dmochowski Ivan J IJ

Nature communications 20101221

Cryptophane-A, comprised of two cyclotriguaiacylenes joined by three ethylene linkers, is a prototypal organic host molecule that binds reversibly to neutral small molecules via London forces. Of note are trifunctionalized, water-soluble cryptophane-A derivatives, which exhibit exceptional affinity for xenon in aqueous solution. In this paper, we report high-resolution X-ray structures of cryptophane-A and trifunctionalized derivatives in crown-crown and crown-saddle conformations, as well as in ...[more]

PMID: 21266998

Similar Datasets

Host-guest complexes between cryptophane-C and chloromethanes revisited.

Project description:Cryptophane-C is composed of two nonequivalent cyclotribenzylene caps, one of which contains methoxy group substituents on the phenyl rings. The two caps are connected by three OCH(2)CH(2)O linkers in an anti arrangement. Host-guest complexes of cryptophane-C with dichloromethane and chloroform in solution were investigated in detail by nuclear magnetic resonance techniques and density functional theory (DFT) calculations. Variable temperature proton and carbon-13 spectra show a variety of dynamic processes, such as guest exchange and host conformational transitions. The guest exchange was studied quantitatively by exchange spectroscopy measurements or by line-shape analysis. The conformational preferences of the guest-containing host were interpreted through cross-relaxation measurements, providing evidence of the gauche+2 and gauche-2 conformations of the linkers. In addition, the mobility of the chloroform guest inside the cavity was studied by carbon-13 relaxation experiments. Combining different types of evidence led to a detailed picture of molecular recognition, interpreted in terms of conformational selection.

| S-EPMC3568900 | biostudies-other

Thermodynamic Contribution of Water in Cryptophane Host-Guest Binding Reaction.

Project description:A detailed examination of binding thermodynamics is undertaken for the interaction between rubidium ion and a water-soluble cryptophane molecule using isothermal titration calorimetry. The equilibrium-binding quotient for this host-guest pair decreases with increasing product formation. When analyzed with a thermodynamic framework that considers water explicitly in the governing equation, the shift in equilibrium is ascribed to an unfavorable change in the free energy of solvation upon formation of the inclusion complex. A van't Hoff analysis of the binding data, as well as an observation of aggregation between inclusion complexes, suggests that charge-charge interactions between rubidium ion and the phenolate groups of the cryptophane host provide the driving force for association in water that overcomes a large and unfavorable change in solvent enthalpy.

| S-EPMC10479154 | biostudies-literature

"Lock and Key" and "Induced-Fit" Host-Guest Models in Two Digold(I)-Based Metallotweezers.

Project description:Two different metallotweezers, each with two pyrene-imidazolylidene-gold(I) arms, were used as hosts for a series of planar aromatic guests. The metallotweezer with a dibenzoacridinebis(alkynyl) spacer (1) orients the two pyrene-imidazolylidene-gold(I) arms in a parallel disposition, with an interpanel distance of about 7 Å. The second metallotweezer (2) contains a carbazolylbis(alkynyl) spacer that directs the two pyrene panels in a diverging orientation. Determination of the association constants via 1H NMR titrations demonstrates that the binding strength shown by 1 is significantly larger than that found by 2, with binding affinities as large as 104 M-1 (in CDCl3), for the encapsulation of N,N'-dimethylnaphthalenetetracarboxydiimide with 1. The differences in the binding affinities are due to binding models associated with formation of the related host-guest complexes. While 1 operates via a "lock and key" model, in which the host does not suffer distortions upon formation of the inclusion complex, 2 operates via a guest-induced fit model. The large association constants shown by 1 with two planar guests were used for promotion of the template-directed synthesis of 1, which in the absence of an external template is produced in an equimolecular mixture with its self-aggregated congener, clippane [12]. This observation strongly suggests that the mechanically interlocked clippane is formed through a self-template-directed mechanism, while bonds are broken/formed during the synthetic protocol.

| S-EPMC9974064 | biostudies-literature

Multivalency in a Dendritic Host-Guest System.

Project description:Multivalency is an important instrument in the supramolecular chemistry toolkit for the creation of strong specific interactions. In this paper we investigate the multivalency effect in a dendritic host-guest system using molecular dynamics simulations. Specifically, we consider urea-adamantyl decorated poly(propyleneimine) dendrimers that together with compatible mono-, bi-, and tetravalent ureidoacetic acid guests can form dynamic patchy nanoparticles. First, we simulate the self-assembly of these particles into macromolecular nanostructures, showing guest-controlled reduction of dendrimer aggregation. Subsequently, we systematically study guest concentration dependent multivalent binding. At low guest concentrations multivalency of the guests clearly increases relative binding as tethered headgroups bind more often than free guests' headgroups. We find that despite an abundance of binding sites, most of the tethered headgroups bind in close proximity, irrespective of the spacer length; nevertheless, longer spacers do increase binding. At high guest concentrations the dendrimer becomes saturated with bound headgroups, independent of guest valency. However, in direct competition the tetravalent guests prevail over the monovalent ones. This demonstrates the benefit of multivalency at high as well as low concentrations.

| S-EPMC6458993 | biostudies-literature

Dual-action host-guest chemistry suppresses PAO1 virulence in A549 cell line model

Project description:Our study showed that selected pillararene was able to decrease the level of cell death and demage caused to human A549 epithelial cells by Pseudomonas aeruginosa PAO1 infection. To further understand the protective effects of pillararene during bacterial infections, we analyzed total mRNA isolated from the A549 epithelial cells. Our study showed that pillararene alone had minimal effect on A549 epithelial cells. The addition of PAO1 to A549 cells greatly altered expression levels. The addition of pillararene to infected A549 epithelial cells displayed a concentration-dependent reduction in the inflammatory response.

2023-02-27 | GSE182847 | GEO

A stimuli-responsive nanopore based on a photoresponsive host-guest system.

Project description:The open-close states of the ion channels in a living system are regulated by multiple stimuli such as ligand, pH, potential and light. Functionalizing natural channels by using synthetic chemistry would provide biological nanopores with novel properties and applications. Here we use para-sulfonato-calix[4]arene-based host-guest supramolecular system to develop artificial gating mechanisms aiming at regulating wild-type ?-HL commanded by both ligand and light stimuli. Using the gating property of ?-hemolysin, we studied the host-guest interactions between para-sulfonato-calix[4]arene and 4, 4'-dipyridinium-azobenzene at the single-molecule level. Subsequently, we have extended the application of this gating system to the real-time study of light-induced molecular shuttle based on para-sulfonato-calix[4]arene and 4, 4'-dipyridinium-azobenzene at the single-molecule level. These experiments provide a more efficient method to develop a general tool to analyze the individual motions of supramolecular systems by using commercially available ?-HL nanopores.

| S-EPMC3627192 | biostudies-literature

Symmetry-breaking host-guest assembly in a hydrogen-bonded supramolecular system.

Project description:Bio-inspired self-assembly is invaluable to create well-defined giant structures from small molecular units. Owing to a large entropy loss in the self-assembly process, highly symmetric structures are typically obtained as thermodynamic products while formation of low symmetric assemblies is still challenging. In this study, we report the symmetry-breaking self-assembly of a defined C1-symmetric supramolecular structure from an Oh-symmetric hydrogen-bonded resorcin[4]arene capsule and C2-symmetric cationic bis-cyclometalated Ir complexes, carrying sterically demanding tertiary butyl (tBu) groups, on the basis of synergistic effects of weak binding forces. The flexible capsule framework shows a large structural change upon guest binding to form a distorted resorcin[4]arene hexameric capsule, providing an asymmetric cavity. Location of the chiral guest inside the anisotropic environment leads to modulation of its Electric Dipole (ED) and Magnetic Dipole (MD) transition moments in the excited state, causing an increased emission quantum yield, longer emission lifetime, and enhancement of the dissymmetry factor (glum) in the circularly polarized luminescence.

| S-EPMC9834293 | biostudies-literature

Host-Guest Induced Peptide Folding with Sequence-Specific Structural Chirality.

Project description:Controlling the spatial and temporal behavior of peptide segments is essential in the fabrication of functional peptide-based materials and nanostructures. To achieve a desired structure, complex sequence design is often required, coupled with the inclusion of unnatural amino acids or synthetic modifications. Herein, we investigate the structural properties of 1:1 inclusion complexes between specific oligopeptides and cucurbit[8]uril (CB[8]), inducing the formation of turns, and by alteration of the peptide sequence, tunable structural chirality. We also explore extended peptide sequence binding with CB[8], demonstrating a simple approach to construct a peptide hairpin.

| S-EPMC8154536 | biostudies-literature

A light-regulated host-guest-based nanochannel system inspired by channelrhodopsins protein.

Project description:The light-controlled gating of ion transport across membranes is central to nature (e.g., in protein channels). Herein, inspired by channelrhodopsins, we introduce a facile non-covalent approach towards light-responsive biomimetic channelrhodopsin nanochannels using host-guest interactions between a negative pillararene host and a positive azobenzene guest. By switching between threading and dethreading states with alternating visible and UV light irradiation, the functional channels can be flexible to regulate the inner surface charge of the channels, which in turn was exploited to achieve different forms of ion transport, for instance, cation-selective transport and anion-selective transport. Additionally, the pillararene-azobenzene-based nanochannel system could be used to construct a light-activated valve for molecular transport. Given these promising results, we suggest that this system could not only provide a better understanding of some biological processes, but also be applied for drug delivery and various biotechnological applications.Light-controlled gating of ion transport across membranes occurs in nature via channelrhodopsin nanochannels. Here, the authors show facile non-covalent approach towards light-responsive biomimetic nanochannels using host-guest interactions between a negative pillararene host and a positive azobenzene guest.

| S-EPMC5558008 | biostudies-literature

Gelation Based on Host-Guest Interactions Induced by Multi-Functionalized Nanosheets.

Project description:Host-guest interaction, being reversible and stimuli-responsive, is ideal to be applied to the design of hydrogels. We created a gelation system based on the host-guest interactions between the adamantyl groups and β-cyclodextrin (β-CD) polymer. N,N,N-trimethyl-1-adamantylammonium hydroxide (TriMAA) cations were attached to the pre-exfoliated α-zirconium phosphate (α-ZrP) nanosheets by ionic bonding through a displacement reaction with the exfoliating agents. The exfoliated α-ZrP nanosheets with adamantyl groups directly or indirectly attached to the surface act as reversible high-functionality crosslinkers within the β-CD polymer. The gelation occurred at a host-to-guest ratio of 1:10 or 1:5 at room temperature within minutes. The agents used to exfoliate α-ZrP can tailor the surface of the resultant α-ZrP nanosheets and the ionic strength of the system, which directly affects the further gelation results. Plus, the exfoliating agent cations may generate a host-and-guest interaction with the β-CD polymer as well. This gelation process without covalent bonding formation should help fellow researchers to better understand the gelation system and host-guest interactions.

| S-EPMC8396050 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data