Browse
Submit Data
Databases
API
Help

Dataset Information

29 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Breaking the Symmetry in Molecular Nanorings.

ABSTRACT: Because of their unique electronic properties, cyclic molecular structures ranging from benzene to natural light-harvesting complexes have received much attention. Rigid ?-conjugated templated porphyrin nanorings serve as excellent model systems here because they possess well-defined structures that can readily be controlled and because they support highly delocalized excitations. In this study, we have deliberately modified a series of six-porphyrin nanorings to examine the impact of lowering the rotational symmetry on their photophysical properties. We reveal that as symmetry distortions increase in severity along the series of structures, spectral changes and an enhancement of radiative emission strength occur, which derive from a transfer of oscillator strength into the lowest (k = 0) state. We find that concomitantly, the degeneracy of the dipole-allowed first excited (k = ±1) state is lifted, leading to an ultrafast polarization switching effect in the emission from strongly symmetry-broken nanorings.

SUBMITTER: Gong JQ

PROVIDER: S-EPMC4745607 | biostudies-literature | 2016 Jan

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Breaking the Symmetry in Molecular Nanorings.

Gong Juliane Q JQ Favereau Ludovic L Anderson Harry L HL Herz Laura M LM

The journal of physical chemistry letters 20160108 2

Because of their unique electronic properties, cyclic molecular structures ranging from benzene to natural light-harvesting complexes have received much attention. Rigid π-conjugated templated porphyrin nanorings serve as excellent model systems here because they possess well-defined structures that can readily be controlled and because they support highly delocalized excitations. In this study, we have deliberately modified a series of six-porphyrin nanorings to examine the impact of lowering t ...[more]

PMID: 26735906

Similar Datasets

Carbon nanorings with inserted acenes: breaking symmetry in excited state dynamics.

Project description:Conjugated cycloparaphenylene rings have unique electronic properties being the smallest segments of carbon nanotubes. Their conjugated backbones support delocalized electronic excitations, which dynamics is strongly influenced by cyclic geometry. Here we present a comparative theoretical study of the electronic and vibrational energy relaxation and redistribution in photoexcited cycloparaphenylene carbon nanorings with inserted naphthalene, anthracene, and tetracene units using non-adiabatic excited-state molecular dynamics simulations. Calculated excited state structures reflect modifications of optical selection rules and appearance of low-energy electronic states localized on the acenes due to gradual departure from a perfect circular symmetry. After photoexcitation, an ultrafast electronic energy relaxation to the lowest excited state is observed on the time scale of hundreds of femtoseconds in all molecules studied. Concomitantly, the efficiency of the exciton trapping in the acene raises when moving from naphthalene to anthracene and to tetracene, being negligible in naphthalene, and ~60% and 70% in anthracene and tetracene within the first 500 fs after photoexcitation. Observed photoinduced dynamics is further analyzed in details using induced molecular distortions, delocatization properties of participating electronic states and non-adiabatic coupling strengths. Our results provide a number of insights into design of cyclic molecular systems for electronic and light-harvesting applications.

| S-EPMC4978956 | biostudies-literature

Symmetry breaking in gastruloid development

Project description:We use single cell RNA sequencing to describe the transcriptional changes during gastruloid development from 24 to 84 hours with 12 hours intervals.

2021-09-04 | GSE183255 | GEO

Symmetry breaking in gastruloid development

Project description:We use single cell RNA sequencing to describe the transcriptional changes during gastruloid development from 0 to 120h hours.

2023-04-29 | GSE229513 | GEO

A molecular mechanism of symmetry breaking in the early chick embryo.

Project description:The first obvious sign of bilateral symmetry in mammalian and avian embryos is the appearance of the primitive streak in the future posterior region of a radially symmetric disc. The primitive streak marks the midline of the future embryo. The mechanisms responsible for positioning the primitive streak remain largely unknown. Here we combine experimental embryology and mathematical modelling to analyse the role of the TGF?-related molecules BMP4 and Vg1/GDF1 in positioning the primitive streak. Bmp4 and Vg1 are first expressed throughout the embryo, and then become localised to the future anterior and posterior regions of the embryo, where they will, respectively, inhibit or induce formation of the primitive streak. We propose a model based on paracrine signalling to account for the separation of the two domains starting from a homogeneous array of cells, and thus for the topological transformation of a radially symmetric disc to a bilaterally symmetric embryo.

| S-EPMC5694015 | biostudies-literature

Unidirectional molecular assembly alignment on graphene enabled by nanomechanical symmetry breaking.

Project description:Precise fabrication of molecular assemblies on a solid surface has long been of central interest in surface science. Their perfectly oriented growth only along a desired in-plane direction, however, remains a challenge, because of the thermodynamical equivalence of multiple axis directions on a solid-surface lattice. Here we demonstrate the successful fabrication of an in-plane, unidirectional molecular assembly on graphene. Our methodology relies on nanomechanical symmetry breaking effects under atomic force microscopy tip scanning, which has never been used in molecular alignment. Individual one-dimensional (1D) molecular assemblies were aligned along a selected symmetry axis of the graphene lattice under finely-tuned scanning conditions after removing initially-adsorbed molecules. Experimental statistics and computational simulations suggest that the anisotropic tip scanning locally breaks the directional equivalence of the graphene surface, which enables nucleation of the unidirectional 1D assemblies. Our findings will open new opportunities in the molecular alignment control on various atomically flat surfaces.

| S-EPMC5799215 | biostudies-literature

Ultrafast imaging of spontaneous symmetry breaking in a photoionized molecular system.

Project description:The Jahn-Teller effect is an essential mechanism of spontaneous symmetry breaking in molecular and solid state systems, and has far-reaching consequences in many fields. Up to now, to directly image the onset of Jahn-Teller symmetry breaking remains unreached. Here we employ ultrafast ion-coincidence Coulomb explosion imaging with sub-10 fs resolution and unambiguously image the ultrafast dynamics of Jahn-Teller deformations of [Formula: see text] cation in symmetry space. It is unraveled that the Jahn-Teller deformation from C3v to C2v geometries takes a characteristic time of 20 ± 7 fs for this system. Classical and quantum molecular dynamics simulations agree well with the measurement, and reveal dynamics for the build-up of the C2v structure involving complex revival process of multiple vibrational pathways of the [Formula: see text] cation.

| S-EPMC8270947 | biostudies-literature

Breaking translational symmetry via polymer chain overcrowding in molecular bottlebrush crystallization.

Project description:One of the fundamental laws in crystallization is translational symmetry, which accounts for the profound shapes observed in natural mineral crystals and snowflakes. Herein, we report on the spontaneous formation of spherical hollow crystals with broken translational symmetry in crystalline molecular bottlebrush (mBB) polymers. The unique structure is named as mBB crystalsome (mBBC), highlighting its similarity to the classical molecular vesicles. Fluorescence resonance energy transfer (FRET) experiments show that the mBBC formation is driven by local chain overcrowding-induced asymmetric lamella bending, which is further confirmed by correlating crystalsome size with crystallization temperature and mBB's side chain grafting density. Our study unravels a new principle of spontaneous translational symmetry breaking, providing a general route towards designing versatile nanostructures.

| S-EPMC7195396 | biostudies-literature

Symmetry breaking meets multisite modification.

Project description:Multisite modification is a basic way of conferring functionality to proteins and a key component of post-translational modification networks. Additional interest in multisite modification stems from its capability of acting as complex information processors. In this paper, we connect two seemingly disparate themes: symmetry and multisite modification. We examine different classes of random modification networks of substrates involving separate or common enzymes. We demonstrate that under different instances of symmetry of the modification network (invoked explicitly or implicitly and discussed in the literature), the biochemistry of multisite modification can lead to the symmetry being broken. This is shown computationally and consolidated analytically, revealing parameter regions where this can (and in fact does) happen, and characteristics of the symmetry-broken state. We discuss the relevance of these results in situations where exact symmetry is not present. Overall, through our study we show how symmetry breaking (i) can confer new capabilities to protein networks, including concentration robustness of different combinations of species (in conjunction with multiple steady states); (ii) could have been the basis for ordering of multisite modification, which is widely observed in cells; (iii) can significantly impact information processing in multisite modification and in cell signalling networks/pathways where multisite modification is present; and (iv) can be a fruitful new angle for engineering in synthetic biology and chemistry. All in all, the emerging conceptual synthesis provides a new vantage point for the elucidation and the engineering of molecular systems at the junction of chemical and biological systems.

| S-EPMC8439660 | biostudies-literature

Mechanochemical symmetry breaking in Hydra aggregates.

Project description:Tissue morphogenesis comprises the self-organized creation of various patterns and shapes. Although detailed underlying mechanisms are still elusive in many cases, an increasing amount of experimental data suggests that chemical morphogen and mechanical processes are strongly coupled. Here, we develop and test a minimal model of the axis-defining step (i.e., symmetry breaking) in aggregates of the Hydra polyp. Based on previous findings, we combine osmotically driven shape oscillations with tissue mechanics and morphogen dynamics. We show that the model incorporating a simple feedback loop between morphogen patterning and tissue stretch reproduces a wide range of experimental data. Finally, we compare different hypothetical morphogen patterning mechanisms (Turing, tissue-curvature, and self-organized criticality). Our results suggest the experimental investigation of bigger (i.e., multiple head) aggregates as a key step for a deeper understanding of mechanochemical symmetry breaking in Hydra.

| S-EPMC4423050 | biostudies-literature

Spontaneous symmetry breaking in genome evolution.

Project description:The quest for evolutionary mechanisms providing separation between the coding (exons) and noncoding (introns) parts of genomic DNA remains an important focus of genetics. This work combines an analysis of the most recent achievements of genomics and fundamental concepts of random processes to provide a novel point of view on genome evolution. Exon sizes in sequenced genomes show a lognormal distribution typical of a random Kolmogoroff fractioning process. This implies that the process of intron incretion may be independent of exon size, and therefore could be dependent on intron-exon boundaries. All genomes examined have two distinctive classes of exons, each with different evolutionary histories. In the framework proposed in this article, these two classes of exons can be derived from a hypothetical ancestral genome by (spontaneous) symmetry breaking. We note that one of these exon classes comprises mostly alternatively spliced exons.

| S-EPMC2377439 | 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