Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

A mutually stabilized host-guest pair.

ABSTRACT: By using click chemistry, a hexacationic cage was synthesized. The cage contains two triscationic π-electron-deficient trispyridiniumtriazine (TPZ3+) platforms that are bridged in a face-to-face manner by three ethylene-triazole-ethylene linkers. A diversity of π-electron-rich guests can be recognized within the pocket of the cage, driven by host-guest π-π interactions. The cage cavity acts as a protecting group, preventing an anthracene guest from undergoing Diels-Alder reaction. Under ultraviolet (UV) light, the pyridinium C─N bonds in TPZ3+ platforms are polarized and weakened, resulting in the occurrence of cage decomposition via β-elimination. Guest recognition could help to prevent this UV-stimulated cage decomposition by suppressing the excitation of the TPZ3+ units.

SUBMITTER: Zhang C

PROVIDER: S-EPMC6957241 | biostudies-literature | 2019 Nov

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

A mutually stabilized host-guest pair.

Zhang Chi C Wang Hongye H Zhong Jie J Lei Ye Y Du Renfeng R Zhang Yang Y Shen Libo L Jiao Tianyu T Zhu Yulu Y Zhu Haiming H Li Haoran H Li Hao H

Science advances 20191101 11

By using click chemistry, a hexacationic cage was synthesized. The cage contains two triscationic π-electron-deficient trispyridiniumtriazine (TPZ<sup>3+</sup>) platforms that are bridged in a face-to-face manner by three ethylene-triazole-ethylene linkers. A diversity of π-electron-rich guests can be recognized within the pocket of the cage, driven by host-guest π-π interactions. The cage cavity acts as a protecting group, preventing an anthracene guest from undergoing Diels-Alder reaction. Und ...[more]

PMID: 31976368

Similar Datasets

Binding enthalpy calculations for a neutral host-guest pair yield widely divergent salt effects across water models.

Project description:Dissolved salts are a part of the physiological milieu and can significantly influence the kinetics and thermodynamics of various biomolecular processes, such as binding and catalysis; thus, it is important for molecular simulations to reliably describe their effects. The present study uses a simple, nonionized host-guest model system to study the sensitivity of computed binding enthalpies to the choice of water and salt models. Molecular dynamics simulations of a cucurbit[7]uril host with a neutral guest molecule show striking differences in the salt dependency of the binding enthalpy across four water models, TIP3P, SPC/E, TIP4P-Ew, and OPC, with additional sensitivity to the choice of parameters for sodium and chloride. In particular, although all of the models predict that binding will be less exothermic with increasing NaCl concentration, the strength of this effect varies by 7 kcal/mol across models. The differences appear to result primarily from differences in the number of sodium ions displaced from the host upon binding the guest rather than from differences in the enthalpy associated with this displacement, and it is the electrostatic energy that contributes most to the changes in enthalpy with increasing salt concentration. That a high sensitivity of salt affecting the choice of water model, as observed for the present host-guest system despite it being nonionized, raises issues regarding the selection and adjustment of water models for use with biological macromolecules, especially as these typically possess multiple ionized groups that can interact relatively strongly with ions in solution.

| S-EPMC4668924 | biostudies-literature

Dual-action host-guest chemistry suppresses virulence in Pseudomonas aeruginosa

Project description:This study describes the influence of selected synthetic macrocycle on the gene expression in Pseudomonas aeruginosa PAO1. In this work, we propose two distinct functionalities responsible for a dual mechanism of action. We identified a water-soluble pillararene whose inner cavity tightly binds to specific homoserine lactones (HSLs) thereby interfering with interbacterial signalling, leading to effective synchronized suppression of exotoxins and biofilms in P. aeruginosa. An additional concerted mechanism of action is suggested that involves the cationic functional side groups on the pillararene that disrupt both the bacterial outer membrane and biofilms, to increase the penetration and efficacy of intracellular antibiotics.

2023-02-27 | GSE182853 | GEO

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

Host-guest chemistry of the peptidoglycan.

Project description: Not available

| S-EPMC2908483 | biostudies-literature

Metallacycles Capabilities in Host-Guest Chemistry.

Project description: Not available

| S-EPMC4608535 | biostudies-literature

Host-Guest Carbon Dots for Enhanced Optical Properties and Beyond.

Project description:Carbon dots, generally small carbon nanoparticles with various forms of surface passivation, have achieved the performance level of semiconductor quantum dots in the green spectral region, but their absorption and fluorescence in red/near-IR are relatively weaker. Conceptually similar to endofullerenes, host-guest carbon dots were designed and prepared with red/near-IR dyes encapsulated as guest in the carbon nanoparticle core. Beyond the desired enhancement in optical properties, the host-guest configuration may significantly broaden the field of carbon dots.

| S-EPMC4508828 | biostudies-other

Host Spin-Crossover Thermodynamics Indicate Guest Fit.

Project description:Spin-crossover (SCO) metal-organic cages capable of switching between high-spin and low-spin states have the potential to be used as magnetic sensors and switches. Variation of the donor strength of heterocyclic aldehyde subcomponents in imine-based ligands can tune the ligand field for a FeII center, which results in both homoleptic and heteroleptic cages with diverse SCO behaviors. The tetrahedral SCO cage built from 1-methyl-1H-imidazole-2-carbaldehyde is capable of encapsulating various guests, which stabilize different cage spin states depending on guest size. Conversely, the SCO tetrahedron exhibits different affinities for guests in different spin states, which is inferred to result from subtle structural differences of the cavity caused by the change in metal center spin state. Examination of SCO thermodynamics across a series of host-guest complexes enabled sensitive probing of guest fit to the host cavity, providing information complementary to binding-constant determination.

| S-EPMC10098494 | biostudies-literature

Exploring pH Dependent Host/Guest Binding Affinities.

Project description:When the electrostatic environment surrounding binding partners changes between unbound and bound states, the net uptake or release of a proton is possible by either binding partner. This process is pH-dependent in that the free energy required to uptake or release the proton varies with pH. This pH-dependence is typically not considered in conventional free energy methods where the use of fixed protonation states is the norm. In the present paper, we apply a simple two-step approach to calculate the pH-dependent binding free energy of a model cucubit[7]uril host/guest system. By use of λ-dynamics with an enhanced sampling protocol, adaptive landscape flattening, pKa shifts and reference binding free energies upon complexation were determined. This information enables the construction of pH-dependent binding profiles that accurately capture the pKa shifts and reproduce binding free energies at the different pH conditions that were observed experimentally. Our calculations illustrate a general framework for computing pH-dependent binding free energies but also point to some issues in modeling the molecular charge distributions within this series of molecules with CGenFF. However, by introducing some minor charge modifications to the CGenFF force field, we saw significant improvement in accuracy of the calculated pKa shifts.

| S-EPMC7442968 | 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

Unveiling host-guest-solvent interactions in solution by identifying highly unstable host-guest configurations in thermal non-equilibrium gas phase.

Project description:We propose a novel scheme of examining the host-guest-solvent interactions in solution from their gas phase structures. By adopting the permethylated β-cyclodextrin (perm β-CD)-protonated L-Lysine non-covalent complex as a prototypical system, we present the infrared multiple photon dissociation (IRMPD) spectrum of the gas phase complex produced by electrospray ionization technique. In order to elucidate the structure of perm β-CD)/LysH+ complex in the gas phase, we carry out quantum chemical calculations to assign the two strong peaks at 3,340 and 3,560 cm-1 in the IRMPD spectrum, finding that the carboxyl forms loose hydrogen bonding with the perm β-CD, whereas the ammonium group of L-Lysine is away from the perm β-CD unit. By simulating the structures of perm β-CD/H+/L-Lysine complex in solution using the supramolecule/continuum model, we find that the extremely unstable gas phase structure corresponds to the most stable conformer in solution.

| S-EPMC9114120 | 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