Browse
Submit Data
Databases
API
Help

Dataset Information

12 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

π-Stacking Stopper-Macrocycle Stabilized Dynamically Interlocked [2]Rotaxanes.

ABSTRACT: The synthesis of mechanically interlocked molecules is valuable due to their unique topologies. With π-stacking intercomponent interaction, e.g., phenanthroline and anthracene, novel [2]rotaxanes have been synthesized by dynamic imine clipping reaction. Their X-ray crystal structures indicate the π-stackings between the anthracene moiety (stopper) on the thread and the (hetero)aromatic rings at the macrocycle of the rotaxanes. Moreover, the length of glycol chains affects the extra π-stacking intercomponent interactions between the phenyl groups and the dimethoxy phenyl groups on the thread. Dynamic combinatorial library has shown at best 84% distribution of anthracene-threaded phenanthroline-based rotaxane, coinciding with the crystallography in that the additional π-stacking intercomponent interactions could increase the thermodynamic stability and selectivity of the rotaxanes.

SUBMITTER: Chan SM

PROVIDER: S-EPMC8347712 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Daisy Chain Rotaxanes Made from Interlocked DNA Nanostructures.

Project description:We report the stepwise assembly of supramolecular daisy chain rotaxanes (DCR) made of double-stranded DNA: Small dsDNA macrocycles bearing an axle assemble into a pseudo-DCR precursor that was connected to rigid DNA stoppers to form DCR with the macrocycles hybridized to the axles. In presence of release oligodeoxynucleotides (rODNs), the macrocycles are released from their respective hybridization sites on the axles, leading to stable mechanically interlocked DCRs. Besides the expected threaded DCRs, certain amounts of externally hybridized structures were observed, which dissociate into dumbbell structures in presence of rODNs. We show that the genuine DCRs have significantly higher degrees of freedom in their movement along the thread axle than the hybridized DCR precursors. Interlocking of DNA in DCRs might serve as a versatile principle for constructing functional DNA nanostructures where the movement of the subunits is restricted within precisely confined tolerance ranges.

| S-EPMC4850751 | biostudies-literature

Complete Regression of Xenograft Tumors upon Targeted Delivery of Paclitaxel via Π-Π Stacking Stabilized Polymeric Micelles.

Project description:Treatment of cancer patients with taxane-based chemotherapeutics, such as paclitaxel (PTX), is complicated by their narrow therapeutic index. Polymeric micelles are attractive nanocarriers for tumor-targeted delivery of PTX, as they can be tailored to encapsulate large amounts of hydrophobic drugs and achiv prolonged circulation kinetics. As a result, PTX deposition in tumors is increased, while drug exposure to healthy tissues is reduced. However, many PTX-loaded micelle formulations suffer from low stability and fast drug release in the circulation, limiting their suitability for systemic drug targeting. To overcome these limitations, we have developed PTX-loaded micelles which are stable without chemical cross-linking and covalent drug attachment. These micelles are characterized by excellent loading capacity and strong drug retention, attributed to π-π stacking interaction between PTX and the aromatic groups of the polymer chains in the micellar core. The micelles are based on methoxy poly(ethylene glycol)-b-(N-(2-benzoyloxypropyl)methacrylamide) (mPEG-b-p(HPMAm-Bz)) block copolymers, which improved the pharmacokinetics and the biodistribution of PTX, and substantially increased PTX tumor accumulation (by more than 2000%; as compared to Taxol or control micellar formulations). Improved biodistribution and tumor accumulation were confirmed by hybrid μCT-FMT imaging using near-infrared labeled micelles and payload. The PTX-loaded micelles were well tolerated at different doses, while they induced complete tumor regression in two different xenograft models (i.e., A431 and MDA-MB-468). Our findings consequently indicate that π-π stacking-stabilized polymeric micelles are promising carriers to improve the delivery of highly hydrophobic drugs to tumors and to increase their therapeutic index.

| S-EPMC4523313 | biostudies-literature

Metastable doubly threaded [3]rotaxanes with a large macrocycle.

Project description:Ring size is a critically important parameter in many interlocked molecules as it directly impacts many of the unique molecular motions that they exhibit. Reported herein are studies using one of the largest macrocycles reported to date to synthesize doubly threaded [3]rotaxanes. A large ditopic 46 atom macrocycle containing two 2,6-bis(N-alkyl-benzimidazolyl)pyridine ligands has been used to synthesize several metastable doubly threaded [3]rotaxanes in high yield (65-75% isolated) via metal templating. Macrocycle and linear thread components were synthesized and self-assembled upon addition of iron(ii) ions to form the doubly threaded pseudo[3]rotaxanes that could be subsequently stoppered using azide-alkyne cycloaddition chemistry. Following demetallation with base, these doubly threaded [3]rotaxanes were fully characterized utilizing a variety of NMR spectroscopy, mass spectrometry, size-exclusion chromatography, and all-atom simulation techniques. Critical to the success of accessing a metastable [3]rotaxane with such a large macrocycle was the nature of the stopper group employed. By varying the size of the stopper group it was possible to access metastable [3]rotaxanes with stabilities in deuterated chloroform ranging from a half-life of <1 minute to ca. 6 months at room temperature potentially opening the door to interlocked materials with controllable degradation rates.

| S-EPMC9093191 | biostudies-literature

Diversity Oriented Preparation of Pillar[5]arene-Containing [2]Rotaxanes by a Stopper Exchange Strategy.

Project description:Rotaxane building blocks bearing 3,5-bis(trifluoromethyl) benzenesulfonate (BTBS) stoppers have been efficiently prepared from a pillar[5]arene derivative, 3,5-bis(trifluoromethyl) benzenesulfonyl chloride (BTBSCl) and different diols, namely 1,10-decanediol and 1,12-dodecanediol. The BTBS moieties of these compounds are good leaving groups and stopper exchange reactions could be achieved by treatment with different nucleophiles thus affording rotaxanes with ester, thioether or ether stoppers.

| S-EPMC7110104 | biostudies-literature

Intermolecular π-π Stacking Interactions Made Visible.

Project description:Mixing the liquids hexafluorobenzene (1) and 1,3,5-trimethylbenzene (mesitylene, 2) results in a crystalline solid with a melting point of 34 °C. The solid consists of alternating π-π stacked pillars of both aromatics. This simple experiment can be used to visually demonstrate the existence and the effect of noncovalent intermolecular π-π stacking interactions. Both benzene derivatives are relatively benign and widely available, and the experiment can be performed within minutes for less than $15 when done on a 22 mL scale (total volume). The demonstration is very robust, as 1:2 mixtures in volume ratios between 2/3 and 3/2 all give a visually similar result (molar ratios of 1.8-0.8). Substituting 2 with the liquid aromatics o-xylene, p-xylene, and aniline also resulted in the formation of a crystalline solid, while using many other liquid aromatics did not.

| S-EPMC7876799 | biostudies-literature

Dynamically stabilized magnetic skyrmions.

Project description:Magnetic skyrmions are topologically non-trivial spin textures that manifest themselves as quasiparticles in ferromagnetic thin films or noncentrosymmetric bulk materials. So far attention has focused on skyrmions stabilized either by the Dzyaloshinskii-Moriya interaction (DMI) or by dipolar interaction, where in the latter case the excitations are known as bubble skyrmions. Here we demonstrate the existence of a dynamically stabilized skyrmion, which exists even when dipolar interactions and DMI are absent. We establish how such dynamic skyrmions can be nucleated, sustained and manipulated in an effectively lossless medium under a nanocontact. As quasiparticles, they can be transported between two nanocontacts in a nanowire, even in complete absence of DMI. Conversely, in the presence of DMI, we observe that the dynamical skyrmion experiences strong breathing. All of this points towards a wide range of skyrmion manipulation, which can be studied in a much wider class of materials than considered so far.

| S-EPMC4579603 | biostudies-literature

Pi-pi stacking tackled with density functional theory.

Project description:Through comparison with ab initio reference data, we have evaluated the performance of various density functionals for describing pi-pi interactions as a function of the geometry between two stacked benzenes or benzene analogs, between two stacked DNA bases, and between two stacked Watson-Crick pairs. Our main purpose is to find a robust and computationally efficient density functional to be used specifically and only for describing pi-pi stacking interactions in DNA and other biological molecules in the framework of our recently developed QM/QM approach "QUILD". In line with previous studies, most standard density functionals recover, at best, only part of the favorable stacking interactions. An exception is the new KT1 functional, which correctly yields bound pi-stacked structures. Surprisingly, a similarly good performance is achieved with the computationally very robust and efficient local density approximation (LDA). Furthermore, we show that classical electrostatic interactions determine the shape and depth of the pi-pi stacking potential energy surface.

| S-EPMC2039870 | biostudies-literature

One-, two- and three-dimensional interlocked polymers based on hybrid inorganic-organic rotaxanes.

Project description:We report three new polymers, based on mechanically interlocked inorganic-organic rotaxanes. They are made in very mild conditions and involve pyrimidine head groups binding to copper(ii) linking units. A two-dimensional 6,3 net and a three-dimensional 10,3b net are found depending on the solvent used in the reaction.

| S-EPMC11348830 | biostudies-literature

Amplification of integrated microscopic motions of high-density [2]rotaxanes in mechanically interlocked networks.

Project description:Integrating individual microscopic motion to perform tasks in macroscopic sale is common in living organisms. However, developing artificial materials in which molecular-level motions could be amplified to behave macroscopically is still challenging. Herein, we present a class of mechanically interlocked networks (MINs) carrying densely rotaxanated backbones as a model system to understand macroscopic mechanical properties stemmed from the integration and amplification of intramolecular motion of the embedded [2]rotaxane motifs. On the one hand, the motion of mechanical bonds introduces the original dangling chains into the network, and the synergy of numerous such microscopic motions leads to an expansion of entire network, imparting good stretchability and puncture resistance to the MINs. On the other hand, the dissociation of host-guest recognition and subsequent sliding motion represent a peculiar energy dissipation pathway, whose integration and amplification result in the bulk materials with favorable toughness and damping capacity. Thereinto, we develop a continuous stress-relaxation method to elucidate the microscopic motion of [2]rotaxane units, which contributes to the understanding of the relationship between cumulative microscopic motions and amplified macroscopic mechanical performance.

| S-EPMC9636211 | biostudies-literature

Structure-guided development of YEATS domain inhibitors by targeting π-π-π stacking.

Project description:Chemical probes of epigenetic 'readers' of histone post-translational modifications (PTMs) have become powerful tools for mechanistic and functional studies of their target proteins in normal physiology and disease pathogenesis. Here we report the development of the first class of chemical probes of YEATS domains, newly identified 'readers' of histone lysine acetylation (Kac) and crotonylation (Kcr). Guided by the structural analysis of a YEATS-Kcr complex, we developed a series of peptide-based inhibitors of YEATS domains by targeting a unique π-π-π stacking interaction at the proteins' Kcr recognition site. Further structure optimization resulted in the selective inhibitors preferentially binding to individual YEATS-containing proteins including AF9 and ENL with submicromolar affinities. We demonstrate that one of the ENL YEATS-selective inhibitors, XL-13m, engages with endogenous ENL, perturbs the recruitment of ENL onto chromatin, and synergizes the BET and DOT1L inhibition-induced downregulation of oncogenes in MLL-rearranged acute leukemia.

| S-EPMC6503841 | 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