Browse
Submit Data
Databases
API
Help

Dataset Information

24 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Self-Assembly of Russian Doll Concentric Porphyrin Nanorings.

ABSTRACT: Electronic communication between concentric macrocycles with wave functions that extend around their circumferences can lead to remarkable behavior, as illustrated by multiwalled carbon nanotubes and photosynthetic chlorophyll arrays. However, it is difficult to hold one π-conjugated molecular ring inside another. Here, we show that ring-in-ring complexes, consisting of a 6-porphyrin ring locked inside a 12-porphyrin ring, can be assembled by placing different metals in the two rings (zinc and aluminum). A bridging ligand with carboxylate and imidazole binding sites forms spokes between the two rings, resulting in a highly cooperative supramolecular self-assembly process. Excitation is transferred from the inner 6-ring to the outer 12-ring of this Russian doll complex within 40 ps. These complexes lead to a form of template-directed synthesis in which one nanoring promotes formation of a larger concentric homologous ring; here, the effective template is an eight-component noncovalent assembly. Russian doll templating provides a new approach to amplifying the size of a covalent nanostructure.

SUBMITTER: Rousseaux SA

PROVIDER: S-EPMC4655919 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Cyclodextrin-templated porphyrin nanorings.

Project description:?- and ?-cyclodextrins have been used as scaffolds for the synthesis of six- and seven-legged templates by functionalizing every primary CH2OH with a 4-pyridyl moiety. Although these templates are flexible, they are very effective for directing the synthesis of macrocyclic porphyrin oligomers consisting of six or seven porphyrin units. The transfer of chirality from the cyclodextrin templates to their nanoring hosts is evident from NMR and circular dichroism spectroscopy. Surprisingly, the mean effective molarity for binding the flexible ?-cyclodextrin-based template within the six-porphyrin nanoring (74?M) is almost as high as for the previously studied rigid hexadentate template (180?M). The discovery that flexible templates are effective in this system, and the availability of a template with a prime number of binding sites, open up many possibilities for the template-directed synthesis of larger macrocycles.

| S-EPMC4298808 | biostudies-literature

Single-Acetylene Linked Porphyrin Nanorings.

Project description:The synthesis of ethyne-linked porphyrin nanorings has been achieved by template-directed Sonogashira coupling. The cyclic hexamer and octamer are predicted by density functional theory to adopt low symmetry conformations, due to dihedral twists between neighboring porphyrin units, but their symmetries are effectively D6h and D8h, respectively, in solution by 1H NMR. The fluorescence spectra indicate that the singlet excited states of these nanorings are highly delocalized.

| S-EPMC5719470 | biostudies-literature

Tuning the Circumference of Six-Porphyrin Nanorings.

Project description:Most macrocycles are made from a simple repeat unit, resulting in high symmetry. Breaking this symmetry allows fine-tuning of the circumference, providing better control of the host-guest behavior and electronic structure. Here, we present the template-directed synthesis of two unsymmetrical cyclic porphyrin hexamers with both ethyne (C2) and butadiyne (C4) links, and we compare these nanorings with the symmetrical analogues with six ethyne or six butadiyne links. Inserting two extra carbon atoms into the smaller nanoring causes a spectacular change in binding behavior: the template affinity increases by a factor of 3 × 109, to a value of ca. 1038 M-1, and the mean effective molarity is ca. 830 M. In contrast, removing two carbon atoms from the largest nanoring results in almost no change in its template-affinity. The strain in these nanorings is 90-130 kJ mol-1, as estimated both from DFT calculation of homodesmotic reactions and from comparing template affinities of linear and cyclic oligomers. Breaking the symmetry has little effect on the absorption and fluorescence behavior of the nanorings: the low radiative rates that are characteristic of a circular delocalized S1 excited state are preserved in the low-symmetry macrocycles.

| S-EPMC6523998 | biostudies-literature

Russian Doll Genes and Complex Chromosome Rearrangements in Oxytricha trifallax.

Project description:Ciliates have two different types of nuclei per cell, with one acting as a somatic, transcriptionally active nucleus (macronucleus; abbr. MAC) and another serving as a germline nucleus (micronucleus; abbr. MIC). Furthermore, Oxytricha trifallax undergoes extensive genome rearrangements during sexual conjugation and post-zygotic development of daughter cells. These rearrangements are necessary because the precursor MIC loci are often both fragmented and scrambled, with respect to the corresponding MAC loci. Such genome architectures are remarkably tolerant of encrypted MIC loci, because RNA-guided processes during MAC development reorganize the gene fragments in the correct order to resemble the parental MAC sequence. Here, we describe the germline organization of several nested and highly scrambled genes in Oxytricha trifallax These include cases with multiple layers of nesting, plus highly interleaved or tangled precursor loci that appear to deviate from previously described patterns. We present mathematical methods to measure the degree of nesting between precursor MIC loci, and revisit a method for a mathematical description of scrambling. After applying these methods to the chromosome rearrangement maps of O. trifallax we describe cases of nested arrangements with up to five layers of embedded genes, as well as the most scrambled loci in O. trifallax.

| S-EPMC5940158 | biostudies-literature

Monitoring Hierarchical Assembly of Ring-in-Ring and Russian Doll Complexes Based on Carbon Nanoring by Forster Resonance Energy Transfer.

Project description:We presented the construction of the ring-in-ring and Russian doll complexes on the basis of triptycene-derived carbon nanoring (TP-[12]CPP), which not only acts as a host for pillar[5]arene (P5A) but also serves as an energy donor for building Förster resonance energy transfer (FRET) systems. We also demonstrated that their hierarchical assembly processes could be efficiently monitored in real time using FRET. NMR, UV-vis and fluorescence, and mass spectroscopy analyses confirmed the successful encapsulation of the guests P5A/P5A-An by TP-[12]CPP, facilitated by C-H···π and ···π interactions, resulting in the formation of a distinct ring-in-ring complex with a binding constant of Ka = 2.23 × 104 M-1. The encapsulated P5A/P5A-An can further reverse its role to be a host for binding energy acceptors to form Russian doll complexes, as evidenced by the occurrence of FRET and mass spectroscopy analyses. The apparent binding constant of the Russian doll complexes was up to 3.6 × 104 M-1, thereby suggesting an enhanced synergistic effect. Importantly, the Russian doll complexes exhibited both intriguing one-step and sequential FRET dependent on the subcomponent P5A/P5A-An during hierarchical assembly, reminiscent of the structure and energy transfer of the light-harvesting system presented in purple bacteria.

| S-EPMC10900207 | biostudies-literature

Mechanical stiffening of porphyrin nanorings through supramolecular columnar stacking.

Project description:Solvent-induced aggregates of nanoring cyclic polymers may be transferred by electrospray deposition to a surface where they adsorb as three-dimensional columnar stacks. The observed stack height varies from single rings to four stacked rings with a layer spacing of 0.32 ± 0.04 nm as measured using scanning tunneling microscopy. The flexibility of the nanorings results in distortions from a circular shape, and we show, through a comparison with Monte Carlo simulations, that the bending stiffness increases linearly with the stack height. Our results show that noncovalent interactions may be used to control the shape and mechanical properties of artificial macromolecular aggregates offering a new route to solvent-induced control of two-dimensional supramolecular organization.

| S-EPMC3709264 | biostudies-literature

Ordering, flexibility and frustration in arrays of porphyrin nanorings.

Project description:The regular packing of atoms, molecules and nanoparticles provides the basis for the understanding of structural order within condensed phases of matter. Typically the constituent particles are considered to be rigid with a fixed shape. Here we show, through a combined experimental and numerical study of the adsorption of cyclic porphyrin polymers, nanorings, on a graphite surface, that flexible molecules can exhibit a rich and complex packing behaviour. Depending on the number of porphyrin sub-units within the nanoring we observe either a highly ordered hexagonal phase or frustrated packing driven by directional interactions which for some arrangements is combined with the internal deformation of the cyclic polymer. Frustration and deformation occur in arrays of polymers with ten sub-units since close packing and co-alignment of neighbouring groups cannot be simultaneously realised for nanorings with this internal symmetry.

| S-EPMC6610075 | biostudies-literature

Russian Doll-like 3d-4f Cluster Wheels with Slow Relaxation of Magnetization.

Project description:The solvothermal reactions of LnCl3·6H2O and MCl2·6H2O (M = Co, Ni) with 2,2'-diphenol (H2L1) and 5,7-dichloro-8-hydroxyquinoline (HL2) gave three 3d-4f heterometallic wheel-like nano-clusters [Ln7M6(L1)6(L2)6(µ3-OH)6(OCH3)6Cl(CH3CN)6]Cl2·xH2O (Ln = Dy, M = Co, x = 3 for 1; Ln = Dy, M = Ni, x = 0 for 2; Ln = Tb, M = Ni, x = 0 for 3) with similar cluster structure. The innermost Ln(III) ion is encapsulated in a planar Ln6 ring which is further embedded in a chair-conformation M6 ring, constructing a Russian doll-like 3d-4f cluster wheel Ln(III)⸦Ln6⸦M6. 2 and 3 show obvious slow magnetic relaxation behavior with negligible opening of the magnetic hysteresis loop. Such a Russian doll-like 3d-4f cluster wheel with the lanthanide disc isolated by transition metallo-ring is rarely reported.

| S-EPMC10421525 | biostudies-literature

Cooperativity in the self-assembly of porphyrin ladders.

Project description:Cooperativity is a general feature of intermolecular interactions in biomolecular systems, but there are many different facets of the phenomenon that are not well understood. Positive cooperativity stabilizes a system as progressively more interactions are added, and the origin of the beneficial free energy may be entropic or enthalpic in origin. An "enthalpic chelate effect" has been proposed to operate through structural tightening that improves all of the functional group interactions in a complex, when it is more strongly bound. Here, we present direct calorimetric evidence that no such enthalpic effects exist in the cooperative assembly of supramolecular ladder complexes composed of metalloporphyrin oligomers coordinated to bipyridine ligands. The enthalpic contributions of the individual coordination interactions are 35 kJ.mol(-1) and constant over a range of free energies of self-assembly of -35 to -111 kJ.mol(-1). In rigid well defined systems of this type, the enthalpies of individual interactions are additive, and no enthalpic cooperative effects are apparent. The implication is that in more flexible, less well defined systems such as biomolecular assemblies, the enthalpy contributions available from specific functional group interactions are well defined and constant parameters.

| S-EPMC1413879 | biostudies-literature

Exploring template-bound dinuclear copper porphyrin nanorings by EPR spectroscopy.

Project description:Electron paramagnetic resonance (EPR) spectroscopy has been used to study the molecular geometry as well as metal-ligand interactions in ten-membered porphyrin nanorings ( c-P10Cu2 ) containing two copper and eight zinc centers. The presence of copper in the structures allows intramolecular interactions, including dipolar interactions between electron spins and hyperfine interactions to be quantified. Results obtained for c-P10Cu2 samples bound to two molecular templates with four or five binding sites, respectively, are compared to those obtained for a sample of the porphyrin ring in the absence of any templates. It is shown that the observed lower binding affinity of the nitrogen ligand to copper as compared to zinc has a strong impact on the geometries of the respective template-bound c-P10Cu2 structures. The interaction between the central copper atom and nitrogen ligands is weak, but pulsed EPR hyperfine techniques such as ENDOR and HYSCORE are very sensitive to this interaction. Upon binding of a nitrogen ligand to copper, the hyperfine couplings of the in-plane nitrogen atoms of the porphyrin core are reduced by about 3 MHz. In addition, the copper hyperfine couplings as well as the g-factors are altered, as detected by continuous wave EPR. DFT calculations of the hyperfine coupling tensors support the assignment of the measured couplings to the nuclei within the structure and reproduce the experimentally observed trends. Finally, Double Electron Electron Resonance (DEER) is used to measure the distances between the copper centers in a range between 2.5 and 5 nm, revealing the preferred geometries of the template-bound nanorings.

| S-EPMC5363685 | 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