Browse
Submit Data
Databases
API
Help

Dataset Information

21 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Ordering, flexibility and frustration in arrays of porphyrin nanorings.

ABSTRACT: 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.

SUBMITTER: Summerfield A

PROVIDER: S-EPMC6610075 | biostudies-literature | 2019 Jul

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Ordering, flexibility and frustration in arrays of porphyrin nanorings.

Summerfield Alex A Baldoni Matteo M Kondratuk Dmitry V DV Anderson Harry L HL Whitelam Stephen S Garrahan Juan P JP Besley Elena E Beton Peter H PH

Nature communications 20190703 1

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- ...[more]

PMID: 31270343

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

Self-Assembly of Russian Doll Concentric Porphyrin Nanorings.

Project description: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.

| S-EPMC4655919 | 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

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

Aromaticity and Antiaromaticity in the Excited States of Porphyrin Nanorings.

Project description:Aromaticity can be a useful concept for predicting the behavior of excited states. Here we show that π-conjugated porphyrin nanorings exhibit size-dependent excited-state global aromaticity and antiaromaticity for rings containing up to eight porphyrin subunits, although they have no significant global aromaticity in their neutral singlet ground states. Applying Baird's rule, even rings ([4 n] π-electrons) are aromatic in their lowest excited states, whereas the lowest excited states of odd rings ([4 n + 2] π-electrons) are antiaromatic. These predictions are borne out by density functional theory (DFT) studies of the nucleus-independent chemical shift (NICS) in the T1 triplet state of each ring, which reveal the critical importance of the triplet delocalization to the emergence of excited-state aromaticity. The singlet excited states (S1) are explored by measurements of the radiative rate and fluorescence peak wavelength, revealing a subtle odd-even alternation as a function of ring size, consistent with symmetry breaking in antiaromatic excited states.

| S-EPMC6488184 | biostudies-literature

Current-Density Calculations on Zn-Porphyrin<sub>40</sub> Nanorings.

Project description:Two porphyrinoid nanorings have been studied computationally. They were built by linking 40 Zn-porphyrin units with butadiyne bridges. The molecular structures belonging to the D40h point group were fully optimized with the Turbomole program at the density functional theory (DFT) level using the B3LYP functional and the def2-SVP basis sets. The aromatic character was studied at the DFT level by calculating the magnetically induced current-density (MICD) susceptibility using the GIMIC program. The neutral molecules are globally non-aromatic with aromatic Zn-porphyrin units. Charged nanorings could not be studied because almost degenerate frontier orbitals led to vanishing optical gaps for the cations. Since DFT calculations of the MICD are computationally expensive, we also calculated the MICD using three pseudo-π models. Appropriate pseudo-π models were constructed by removing the outer hydrogen atoms and replacing all carbon and nitrogen atoms with hydrogen atoms. The central Zn atom was either replaced with a beryllium atom or with two inner hydrogen atoms. Calculations with the computationally inexpensive pseudo-π models yielded qualitatively the same magnetic response as obtained in the all-electron calculations.

| S-EPMC10510378 | biostudies-literature

Synthesis of Five-Porphyrin Nanorings by Using Ferrocene and Corannulene Templates.

Project description:The smallest and most strained member of a family of ?-conjugated cyclic porphyrin oligomers was synthesized by using pentapyridyl templates based on ferrocene and corannulene. Both templates are effective for directing the synthesis of the butadiyne-linked cyclic pentamer, despite the fact that the radii of their N5 donor sets are too small by 0.5?Å and 0.9?Å, respectively (from DFT calculations). The five-porphyrin nanoring exhibits a structured absorption spectrum and its fluorescence extends to 1200?nm, reflecting strong ??conjugation and Herzberg-Teller vibronic coupling.

| S-EPMC5089564 | biostudies-literature

How Aromatic Are Molecular Nanorings? The Case of a Six-Porphyrin Nanoring*.

Project description:Large conjugated rings with persistent currents are novel promising structures in molecular-scale electronics. A six-porphyrin nanoring structure that allegedly sustained an aromatic ring current involving 78π electrons was recently synthesized. We provide here compelling evidence that this molecule is not aromatic, contrary to what was inferred from the analysis of 1 H-NMR data and computational calculations that suffer from large delocalization errors. The main reason behind the absence of an aromatic ring current in these nanorings is the low delocalization in the transition from the porphyrins to the bridging butadiyne linkers, which disrupts the overall conjugated circuit. These results highlight the importance of choosing a suitable computational method to study large conjugated molecules and the appropriate aromaticity descriptors to identify the part of the molecule responsible for the loss of aromaticity.

| S-EPMC8596448 | 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