Browse
Submit Data
Databases
API
Help

Dataset Information

24 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Molecular recognition and self-assembly special feature: Dynamic combinatorial synthesis of a catenane based on donor-acceptor interactions in water.

ABSTRACT: A new type of neutral donor-acceptor [2]-catenane, containing both complementary units in the same ring was synthesized from a dynamic combinatorial library in water. The yield of the water soluble [2]-catenane is enhanced by increasing either building-block concentrations or ionic strength, or by the addition of an electron-rich template. NMR spectroscopy demonstrates that the template is intercalated between the 2 electron-deficient naphthalenediimide units of the catenane.

SUBMITTER: Au-Yeung HY

PROVIDER: S-EPMC2705551 | biostudies-literature | 2009 Jun

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Molecular recognition and self-assembly special feature: Dynamic combinatorial synthesis of a catenane based on donor-acceptor interactions in water.

Au-Yeung Ho Yu HY Pantos G Dan GD Sanders Jeremy K M JK

Proceedings of the National Academy of Sciences of the United States of America 20090126 26

A new type of neutral donor-acceptor [2]-catenane, containing both complementary units in the same ring was synthesized from a dynamic combinatorial library in water. The yield of the water soluble [2]-catenane is enhanced by increasing either building-block concentrations or ionic strength, or by the addition of an electron-rich template. NMR spectroscopy demonstrates that the template is intercalated between the 2 electron-deficient naphthalenediimide units of the catenane. ...[more]

PMID: 19171892

Similar Datasets

Molecular recognition and self-assembly special feature: Squaring cooperative binding circles.

Project description:The cooperative binding effects of viologens and pyridines to a synthetic bivalent porphyrin receptor are used as a model system to study how the magnitudes of these effects relate to the experimentally obtained values. The full thermodynamic and kinetic circles concerning both activation and inhibition of the cage of the receptor for the binding of viologens were measured and evaluated. The results strongly emphasize the apparent character of measured binding and rate constants, in which the fractional saturation of receptors with other guests is linearly expressed in these constants. The presented method can be used as a simple tool to better analyze and comprehend the experimentally observed kinetics and thermodynamics of natural and artificial cooperative systems.

| S-EPMC2705591 | biostudies-other

Dynamic donor-acceptor [2]catenanes.

Project description:Donor-acceptor [2]catenanes based on cyclobis(paraquat-p-phenylene) as the pi-acceptor ring have been used prominently in the construction of functional molecular devices. We report here their thermodynamically controlled synthesis from isolated pi-donor and pi-acceptor rings under the catalytic influence of tetra butylammonium iodide. The initial nucleophilic attack of iodide ion, which opens up the pi-acceptor ring, is followed by complexation to the pi-donor ring and the subsequent catenation of the pi-donor ring by the pi-acceptor ring [2]catenane. The reaction is general in scope and proceeds in high yields, without giving rise to side-products.

| S-EPMC1941822 | biostudies-other

Isolation by crystallization of translational isomers of a bistable donor-acceptor [2]catenane.

Project description:The template-directed synthesis of a bistable donor-acceptor [2]catenane wherein both translational isomers--one in which a tetrathiafulvalene unit in a mechanically interlocked crown ether occupies the cavity of a cyclobis(paraquat-p-phenylene) ring and the other in which a 1,5-dioxynaphthalene unit in the crown ether resides inside the cavity of the tetracationic cyclophane--exist in equilibrium in solution, has led to the isolation and separation by hand picking of single crystals colored red and green, respectively. These two crystalline co-conformations have been characterized separately at both the molecular and supramolecular levels, and also by dynamic NMR spectroscopy in solution where there is compelling evidence that the mechanically interlocked molecules are present as a complex mixture of translational, configurational, and conformational isomers wherein the isomerization is best described as being a highly dynamic and adaptable phenomenon.

| S-EPMC2922539 | biostudies-literature

Molecular recognition and self-assembly special feature: Assembly and organization processes in DNA-directed colloidal crystallization.

Project description:We present an analysis of the key steps involved in the DNA-directed assembly of nanoparticles into crystallites and polycrystalline aggregates. Additionally, the rate of crystal growth as a function of increased DNA linker length, solution temperature, and self-complementary versus non-self-complementary DNA linker strands (1- versus 2-component systems) has been studied. The data show that the crystals grow via a 3-step process: an initial "random binding" phase resulting in disordered DNA-AuNP aggregates, followed by localized reorganization and subsequent growth of crystalline domain size, where the resulting crystals are well-ordered at all subsequent stages of growth.

| S-EPMC2705589 | biostudies-literature

Molecular recognition and self-assembly special feature: Self-assembly of dimeric tetraurea calix[4]pyrrole capsules.

Project description:Calix[4]pyrroles having extended aromatic cavities have been functionalized with 4 ureas in the para position of their meso phenyl substituents. This elaboration of the upper rim was completed in 2 synthetic steps starting from the alpha,alpha,alpha,alpha-tetranitro isomer of the calix[4]pyrrole obtained in the acid catalyzed condensation of p-nitrophenyl methyl ketone and pyrrole. In dichloromethane solution and in the presence of 4,4'-bipyridine N-N'-dioxide the tetraurea calix[4]pyrrole dimerizes reversibly forming a cyclic array of 16 hydrogen bonds and encapsulating 1 molecule of bis-N-oxide. The encapsulated guest is bound in the cavity by hydrogen bonding to the 2 endohedral calix[4]pyrrole centers. Further evidence for dimerization of the tetraurea calix[4]pyrroles is provided by (1)H-NMR experiments and by the formation of mixed capsules.

| S-EPMC2705570 | biostudies-literature

Molecular recognition and self-assembly special feature: Supramolecular polymer formed by reversible self-assembly of tetrakisporphyrin.

Project description:S-shaped tetrakisporphyrin 2 forms supramolecular polymeric assemblies via a complementary affinity of its bisporphyrin units in solution. The self-association constant determined by applying the isodesmic model is >10(6) L mol(-1), which suggests that a sizable polymer forms at millimolar concentrations at room temperature. The electron deficient aromatic guest (TNF) binds within the molecular clefts provided by the bisporphyrin units via a charge-transfer interaction. This guest complexation completely disrupts supramolecular polymeric assembly. The long, fibrous fragments of the polymeric assemblies were characterized by atomic-force microscopy imaging of a film cast on a mica surface. The polymeric assemblies have lengths of >1mum and show a coiled structure with a higher level of organization. The approach discussed in this report concerning the quick preparation of supramolecular polymeric assemblies driven by noncovalent forces sets the stage for the preparation of a previously undescribed class of macromolecular porphyrin architectures.

| S-EPMC2705564 | biostudies-other

Molecular recognition and self-assembly special feature: Multipoint molecular recognition within a calix[6]arene funnel complex.

Project description:A multipoint recognition system based on a calix[6]arene is described. The calixarene core is decorated on alternating aromatic subunits by 3 imidazole arms at the small rim and 3 aniline groups at the large rim. This substitution pattern projects the aniline nitrogens toward each other when Zn(II) binds at the Tris-imidazole site or when a proton binds at an aniline. The XRD structure of the monoprotonated complex having an acetonitrile molecule bound to Zn(II) in the cavity revealed a constrained geometry at the metal center reminiscent of an entatic state. Computer modeling suggests that the aniline groups behave as a tritopic monobasic site in which only 1 aniline unit is protonated and interacts with the other 2 through strong hydrogen bonding. The metal complex selectively binds a monoprotonated diamine vs. a monoamine through multipoint recognition: coordination to the metal ion at the small rim, hydrogen bonding to the calix-oxygen core, CH/pi interaction within the cavity's aromatic walls, and H-bonding to the anilines at the large rim.

| S-EPMC2705605 | biostudies-literature

Molecular recognition and self-assembly special feature: Disproportionation and self-sorting in molecular encapsulation.

Project description:Self-assembled capsules are nanoscale structures made up of multiple synthetic subunits held together by weak intermolecular forces. They act as host structures that can completely surround small molecule guests of the appropriate size, shape and chemical surface. Like their biological counterparts, multimeric enzymes and receptors, the subunits of the capsules are generally identical, and lead to homomeric assemblies of high symmetry. In both biological and synthetic systems small variations in structures are tolerated and lead to heteromeric assemblies with slightly different recognition properties. The synthetic capsules are dynamic, with lifetimes from milliseconds to hours, and allow the direct spectroscopic observation of smaller molecules inside, under ambient conditions at equilibrium in solution. We report here the assembly of hybrid capsules made up of 2 very different structures, both capable of forming their own homomeric capsules through hydrogen bonding. These hybrids exhibit host properties that differ markedly from the parent capsules, and suggest that other capsules may emerge from seemingly unrelated modules that have curved surfaces and are rich in hydrogen bonding capabilities.

| S-EPMC2705539 | biostudies-literature

A dynamic combinatorial library for biomimetic recognition of dipeptides in water.

Project description:Small peptides are involved in countless biological processes. Hence selective binding motifs for peptides can be powerful tools for labeling or inhibition. Finding those binding motifs, especially in water which competes for intermolecular H-bonds, poses an enormous challenge. A dynamic combinatorial library can be a powerful method to overcome this issue. We previously reported artificial receptors emerging form a dynamic combinatorial library of peptide building blocks. In this study we aimed to broaden this scope towards recognition of small peptides. Employing CXC peptide building blocks, we found that cyclic dimers of oxidized CFC bind to the aromatic peptides FF and YY (K ≈ 229-702 M-1), while AA binds significantly weaker (K ≈ 65-71 M-1).

| S-EPMC7356556 | biostudies-literature

Molecular recognition and self-assembly special feature: Encapsulation and characterization of proton-bound amine homodimers in a water-soluble, self-assembled supramolecular host.

Project description:Cyclic amines can be encapsulated in a water-soluble self-assembled supramolecular host upon protonation. The hydrogen-bonding ability of the cyclic amines, as well as the reduced degrees of rotational freedom, allows for the formation of proton-bound homodimers inside of the assembly that are otherwise not observable in aqueous solution. The generality of homodimer formation was explored with small N-alkyl aziridines, azetidines, pyrrolidines, and piperidines. Proton-bound homodimer formation is observed for N-alkylaziridines (R = methyl, isopropyl, tert-butyl), N-alkylazetidines (R = isopropyl, tert-butyl), and N-methylpyrrolidine. At high concentration, formation of a proton-bound homotrimer is observed in the case of N-methylaziridine. The homodimers stay intact inside the assembly over a large concentration range, thereby suggesting cooperative encapsulation. Both G3(MP2)B3 and G3B3 calculations of the proton-bound homodimers were used to investigate the enthalpy of the hydrogen bond in the proton-bound homodimers and suggest that the enthalpic gain upon formation of the proton-bound homodimers may drive guest encapsulation.

| S-EPMC2705522 | 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