Browse
Submit Data
Databases
API
Help

Dataset Information

20 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

All-Thiophene-Based Double Helix: Synthesis, Crystal Structure, Chiroptical Property and Arylation.

ABSTRACT: The all-thiophene-based double helix DH-1 was designed and prepared originally from the selective deprotonation of cyclooctatetrathiophene (tetra[3,4]thienylene, COTh) and following the Negishi coupling reaction with 3,3'-bithiophene. The X-ray crystallographic studies revealed that DH-1 has a double-helical scaffold. The arylations including tetraphenylation and tetrathienylation were efficiently employed to replace the four ?-protons of the central COTh of DH-1 with phenyl and thiophenyl groups via cross-coupling reactions. The chiral resolution of rac-DH-1 was fulfilled via chiral high-performance liquid chromatography, and the chiroptical properties were characterized by circular dichroism spectra and optical rotation. Ultraviolet-visible absorption and fluorescence behaviors of DH-1 and its arylation products were also characterized to describe the extended conjugated scaffold.

SUBMITTER: Li B

PROVIDER: S-EPMC6644213 | biostudies-literature | 2018 Nov

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

All-Thiophene-Based Double Helix: Synthesis, Crystal Structure, Chiroptical Property and Arylation.

Li Bingbing B Zhang Sheng S Li Lu L Ma Zhiying Z Li Chunli C Xu Li L Wang Hua H

ACS omega 20181127 11

The all-thiophene-based double helix DH-1 was designed and prepared originally from the selective deprotonation of cyclooctatetrathiophene (tetra[3,4]thienylene, COTh) and following the Negishi coupling reaction with 3,3'-bithiophene. The X-ray crystallographic studies revealed that DH-1 has a double-helical scaffold. The arylations including tetraphenylation and tetrathienylation were efficiently employed to replace the four α-protons of the central COTh of DH-1</ ...[more]

PMID: 31458239

Similar Datasets

Thiophene/selenophene-based S-shaped double helicenes: regioselective synthesis and structures.

Project description:2,5-Di(trimethylsilanyl)dithieno[2,3-b:3',2'-d]thiophene ((TMS)2-bb-DTT), 2,5-di(trimethylsilanyl)diseleno[2,3-b:3',2'-d]thiophene ((TMS)2-bb-DST), and 2,5-di(trimethylsilanyl)diseleno[2,3-b:3',2'-d] selenophene ((TMS)2-bb-DSS) were used as starting materials to synthesize three S-shaped double helicenes (i.e., DH-1, DH-2, and DH-3) through monobromination, formylation, the Wittig reaction, and double oxidative photocyclization. The photocyclization was a highly regioselective process. The molecular structures of DH-1 and DH-2 were confirmed by X-ray single-crystal analysis. Multiple intermolecular interactions, such as C-S, C-Se, S-S, S-Se, and Se-Se, were observed in the crystal packing structures of these compounds. Spectroscopic results and our previous work showed that the combination of molecular structure change and heteroatom replacement from S to Se could precisely modulate molecular energy levels.

| S-EPMC9273980 | biostudies-literature

A'-form RNA double helix in the single crystal structure of r(UGAGCUUCGGCUC).

Project description:Here we demonstrate the presence of the A'-RNA conformation using the single crystal structure of a tridecamer: r(UGAGCUUCGGCUC). The average A'-RNA conformation deduced from X-ray fiber diffraction data had only been available previously, but now the presence of the A'-RNA conformation has been found in a single crystal structure for the first time. Statistical analysis showed that the A'-RNA conformation is distinguishable from the A-RNA conformation in a plot of the major groove width against the base pair inclination angle. The major groove of the A'-RNA conformation is wide enough to accommodate a protein or peptide while that of the A-RNA conformation is too narrow to do so. The presence of the A'-RNA conformation is significant for protein-RNA interaction.

| S-EPMC148272 | biostudies-other

9-Vinylanthracene Based Fluorogens: Synthesis, Structure-Property Relationships and Applications.

Project description:Fluorescent dyes with aggregation-induced emission (AIE) properties exhibit intensified emission upon aggregation. They are promising candidates to study biomolecules and cellular changes in aqueous environments when aggregation formation occurs. Here, we report a group of 9-position functionalized anthracene derivatives that were conveniently synthesized by the palladium-catalyzed Heck reaction. Using fluorometric analyses, these dyes were confirmed to show AIE behavior upon forming aggregates at high concentrations, in viscous solvents, and when poorly solubilized. Their photophysical properties were then further correlated with their structural features, using density functional theory (DFT) calculation. Finally, we demonstrated their potential applications in monitoring pH changes, quantifying globular proteins, as well as cell imaging with confocal microscopy.

| S-EPMC6149741 | biostudies-literature

A Sr2+-metal-organic framework with high chemical stability: synthesis, crystal structure and photoluminescence property.

Project description:Metal-organic frameworks (MOFs) are typically built by assembly of metal centres and organic linkers, and have emerged as promising crystalline materials in a variety of fields. However, the stability of MOFs is a key limitation for their practical applications. Herein, we report a novel Sr 2+: -MOF [Sr4(Tdada)2(H2O)3(DMF)2] (denoted as NKU- 105: , NKU = Nankai University; H4Tdada = 5,5'-((thiophene-2,5-dicar bonyl)bis(azanediyl))diisophthalic acid; DMF = N,N-dimethylformamide) featuring an open square channel of about 6 Å along the c-axis. Notably, NKU- 105: exhibits much outstanding chemical stability against common organic solvents, boiling water, acids and bases, relative to most MOF materials. Furthermore, NKU- 105: is an environment-friendly luminescent material with a bright cyan emission.This article is part of the themed issue 'Coordination polymers and metal-organic frameworks: materials by design'.

| S-EPMC5179931 | biostudies-literature

Thiophene-fused polyaromatics: synthesis, columnar liquid crystal, fluorescence and electrochemical properties.

Project description:Efficient syntheses that incorporate thiophene units into different extended conjugation systems are of interest as a result of the prevalence of sulfur-rich aromatics in organic electronics. Self-organization by using liquid crystal properties is also desirable for optimal processing of organic electronics and optical devices. In this article, we describe a two-step process to access extended regioisomers of polyaromatics with different shapes. This method involves an efficient single or double benzannulation from an alkyne precursor followed by Scholl cyclization. In spite of their unconventional nondiscoid shape, these materials display stable columnar liquid crystal phases. We examine the photophysical and electrochemical properties and find that structurally very similar thiophene-fused polyaromatics display significant differences in their properties.

| S-EPMC8159230 | biostudies-literature

A new Bi-based visible-light-sensitive photocatalyst BiLa1.4Ca0.6O4.2: crystal structure, optical property and photocatalytic activity.

Project description:A new compound of BiLa1.4Ca0.6O4.2 is synthesized through solid state reaction, where the Ca substitutes, in part, the La site in a stable BiLa2O4.5 phase. The structure of the BiLa1.4Ca0.6O4.2 crystallizes in space group R3mH with a hexagonal lattice constants of a = 3.893(1) Å, c = 9.891(1) Å. Its optical absorption edge is about 2.05 eV, which just spans the visible light region. The photocatalytic activity of the BiLa1.4Ca0.6O4.2 powder to degradation of RhB under visible light irradiation is measured and improved more than 7 times by annealing in nitrogen ambient, indicating that annealing in nitrogen can effectively improve the photocatalytic activity by producing oxygen vacancy. Although the absolute photocatalytic activity obtained is low, there is great potential for enhancing the activity such as nanoscaling, doping, and coupling with other compounds.

| S-EPMC4794645 | biostudies-other

5-Formylcytosine alters the structure of the DNA double helix.

Project description:The modified base 5-formylcytosine (5fC) was recently identified in mammalian DNA and might be considered to be the 'seventh' base of the genome. This nucleotide has been implicated in active demethylation mediated by the base excision repair enzyme thymine DNA glycosylase. Genomics and proteomics studies have suggested an additional role for 5fC in transcription regulation through chromatin remodeling. Here we propose that 5fC might affect these processes through its effect on DNA conformation. Biophysical and structural analysis revealed that 5fC alters the structure of the DNA double helix and leads to a conformation unique among known DNA structures including those comprising other cytosine modifications. The 1.4-Å-resolution X-ray crystal structure of a DNA dodecamer comprising three 5fCpG sites shows how 5fC changes the geometry of the grooves and base pairs associated with the modified base, leading to helical underwinding.

| S-EPMC4287393 | biostudies-literature

Direct insight into the structure-property relation of interfaces from constrained crystal structure prediction.

Project description:A major issue that prevents a full understanding of heterogeneous materials is the lack of systematic first-principles methods to consistently predict energetics and electronic properties of reconstructed interfaces. In this work we address this problem with an efficient and accurate computational scheme. We extend the minima-hopping method implementing constraints crafted for two-dimensional atomic relaxation and enabling variations of the atomic density close to the interface. A combination of density-functional and accurate density-functional tight-binding calculations supply energy and forces to structure prediction. We demonstrate the power of this method by applying it to extract structure-property relations for a large and varied family of symmetric and asymmetric tilt boundaries in polycrystalline silicon. We find a rich polymorphism in the interface reconstructions, with recurring bonding patterns that we classify in increasing energetic order. Finally, a clear relation between bonding patterns and electrically active grain boundary states is unveiled and discussed.

| S-EPMC7864966 | biostudies-literature

Crystal structure of a poly(rA) staggered zipper at acidic pH: evidence that adenine N1 protonation mediates parallel double helix formation.

Project description:We have solved at 1. 07: Å resolution the X-ray crystal structure of a polyriboadenylic acid (poly(rA)) parallel and continuous double helix. Fifty-nine years ago, double helices of poly(rA) were first proposed to form at acidic pH. Here, we show that 7-mer oligo(rA), i.e. rA7, hybridizes and overlaps in all registers at pH 3.5 to form stacked double helices that span the crystal. Under these conditions, rA7 forms well-ordered crystals, whereas rA6 forms fragile crystalline-like structures, and rA5, rA8 and rA11 fail to crystallize. Our findings support studies from ?50 years ago: one showed using spectroscopic methods that duplex formation at pH 4.5 largely starts with rA7 and begins to plateau with rA8; another proposed a so-called 'staggered zipper' model in which oligo(rA) strands overlap in multiple registers to extend the helical duplex. While never shown, protonation of adenines at position N1 has been hypothesized to be critical for helix formation. Bond angles in our structure suggest that N1 is protonated on the adenines of every other rAMP-rAMP helix base pair. Our data offer new insights into poly(rA) duplex formation that may be useful in developing a pH sensor.

| S-EPMC5041459 | biostudies-literature

Thiophene-Based Double Helices: Radical Cations with SOMO-HOMO Energy Level Inversion.

Project description:We report relatively persistent, open-shell thiophene-based double helices, radical cations 1•+ -TMS12 and 2•+ -TMS8 . Closed-shell neutral double helices, 1-TMS12 and 2-TMS8 , have nearly identical first oxidation potentials, E +/0 ≈ +1.33 V, corresponding to reversible oxidation to their radical cations. The radical cations are generated, using tungsten hexachloride in dichloromethane (DCM) as an oxidant, E +/0 ≈ +1.56 V. EPR spectra consist of a relatively sharp singlet peak with an unusually low g-value of 2.001-2.002, thus suggesting exclusive delocalization of spin density over π-conjugated system consisting of carbon atoms only. DFT computations confirm these findings, as only negligible fraction of spin density is found on sulfur and silicon atoms and the spin density is delocalized over a single tetrathiophene moiety. For radical cation, 1•+ -TMS12 , energy level of the singly occupied molecular orbital (SOMO) lies below the four highest occupied molecular orbitals (HOMOs), thus indicating the SOMO-HOMO inversion (SHI) and therefore, violating the Aufbau principle. 1•+ -TMS12 has a half-life of the order of only 5 min at room temperature. EPR peak intensity of 2•+ -TMS8 , which does not show SHI, is practically unchanged over at least 2 h.

| S-EPMC8688166 | 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