Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

In-Fjord Substitution in Expanded Helicenes: Effects of the Insert on the Inversion Barrier and Helical Pitch.

ABSTRACT: A series of expanded helicenes of different sizes and shapes incorporating phenyl- and biphenyl-substituents at the deepest part of their fjord have been synthesized via sequential Au-catalyzed hydroarylation of appropriately designed diynes, and their racemization barriers have been calculated employing electronic structure methods. These show that the overall profile of the inversions (energies, number of transition states and intermediates, and their relative position) is intensively affected by the interplay of steric and attractive London dispersion interactions. Hence, in-fjord substitution constitutes an additional tool to handle the mechanical properties in helicenes of uncommonly large diameter. The photochemical characterization of the newly prepared helical structures is also reported.

SUBMITTER: Suarez-Pantiga S

PROVIDER: S-EPMC8519012 | biostudies-literature | 2021 Sep

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

In-Fjord Substitution in Expanded Helicenes: Effects of the Insert on the Inversion Barrier and Helical Pitch.

Suárez-Pantiga Samuel S Redero Pablo P Aniban Xaiza X Simon Martin M Golz Christopher C Mata Ricardo A RA Alcarazo Manuel M

Chemistry (Weinheim an der Bergstrasse, Germany) 20210813 53

A series of expanded helicenes of different sizes and shapes incorporating phenyl- and biphenyl-substituents at the deepest part of their fjord have been synthesized via sequential Au-catalyzed hydroarylation of appropriately designed diynes, and their racemization barriers have been calculated employing electronic structure methods. These show that the overall profile of the inversions (energies, number of transition states and intermediates, and their relative position) is intensively affected ...[more]

PMID: 34288171

Similar Datasets

Dynamical barrier and isotope effects in the simplest substitution reaction via Walden inversion mechanism.

Project description:Reactions occurring at a carbon atom through the Walden inversion mechanism are one of the most important and useful classes of reactions in chemistry. Here we report an accurate theoretical study of the simplest reaction of that type: the H+CH4 substitution reaction and its isotope analogues. It is found that the reaction threshold versus collision energy is considerably higher than the barrier height. The reaction exhibits a strong normal secondary isotope effect on the cross-sections measured above the reaction threshold, and a small but reverse secondary kinetic isotope effect at room temperature. Detailed analysis reveals that the reaction proceeds along a path with a higher barrier height instead of the minimum-energy path because the umbrella angle of the non-reacting methyl group cannot change synchronously with the other reaction coordinates during the reaction due to insufficient energy transfer from the translational motion to the umbrella mode.

| S-EPMC5336572 | biostudies-literature

Ruthenium-Locked Helical Chirality: A Barrier of Inversion and Formation of an Asymmetric Macrocycle.

Project description:Upon coordination to metal centers, tetradentate ligands based on the 6,6'-bis(2″-aminopyridyl)-2,2'-bipyridine (bapbpy) structure form helical chiral complexes due to the steric clash between the terminal pyridines of the ligand. For octahedral ruthenium(II) complexes, the two additional axial ligands bound to the metal center, when different, generate diastereotopic aromatic protons that can be distinguished by NMR. Based on these geometrical features, the inversion barrier of helical [RuII(L)(RR'SO)Cl]+ complexes, where L is a sterically hindered bapbpy derivative and RR'SO is a chiral or achiral sulfoxide ligand, was studied by variable-temperature 1H NMR. The coalescence energies for the inversion of the helical chirality of [Ru(bapbpy)(DMSO)(Cl)]Cl and [Ru(bapbpy)(MTSO)(Cl)]Cl (where MTSO is (R)-methyl p-tolylsulfoxide) were found to be 43 and 44 kJ/mol, respectively. By contrast, in [Ru(biqbpy)(DMSO)(Cl)]Cl (biqbpy = 6,6'-bis(aminoquinolyl)-2,2'-bipyridine), increased strain caused by the larger terminal quinoline groups resulted in a coalescence temperature higher than 376 K, which pointed to an absence of helical chirality inversion at room temperature. Further increasing the steric strain by introducing methoxy groups ortho to the nitrogen atoms of the terminal pyridyl groups in bapbpy resulted in the serendipitous discovery of a ring-closing reaction that took place upon trying to make [Ru(OMe-bapbpy)(DMSO)Cl]+ (OMe-bapbpy = 6,6'-bis(6-methoxy-aminopyridyl)-2,2'-bipyridine). This reaction generated, in excellent yields, a chiral complex [Ru(L″)(DMSO)Cl]Cl, where L″ is an asymmetric tetrapyridyl macrocycle. This unexpected transformation appears to be specific to ruthenium(II) as macrocyclization did not occur upon coordination of the same ligand to palladium(II) or rhodium(III).

| S-EPMC9554910 | biostudies-literature

Impacts of heteroatom substitution on the excited state dynamics of π-extended helicenes.

Project description:Benzo-annulated aza[9]helicene ([9]AH) and thia[9]helicene ([9]TH) were prepared as novel π-extended heterohelicenes. [9]TH showed a quite short fluorescence lifetime of ∼0.3 ns and intense phosphorescence at low temperature that were attributed to its larger spin-orbit coupling and faster intersystem crossing between pseudo-degenerate S1/2 and triplet states.

| S-EPMC11320297 | biostudies-literature

Substitution rates in alpha-helical transmembrane proteins.

Project description:It has been shown previously that some membrane proteins have a conserved core of amino acid residues. This idea not only serves to orient helices during model building exercises but may also provide insight into the structural role of residues mediating helix-helix interactions. Using experimentally determined high-resolution structures of alpha-helical transmembrane proteins we show that, of the residues within the hydrophobic transmembrane spans, the residues at lipid and subunit interfaces are more evolutionarily variable than those within the lipid-inaccessible core of a polypeptide's transmembrane domain. This supports the idea that helix-helix interactions within the same polypeptide chain and those at the interface between different polypeptide chains may arise in distinct ways. To show this, we use a new method to estimate the substitution rate of an amino acid residue given an alignment and phylogenetic tree of closely related proteins. This method gives better sensitivity in the otherwise-conserved transmembrane domains than a conventional similarity analysis and is relatively insensitive to the sequences used.

| S-EPMC2374033 | biostudies-literature

Light-activated helical inversion in cholesteric liquid crystal microdroplets.

Project description:Cholesteric liquid crystal (CLC) droplets exhibit nontrivial topological features, which are controlled by the ratio between the cholesteric pitch and the droplet radius. The radial spherical structure (RSS) is of particular interest, as it reveals an onion-like concentric organization of the cholesteric helices, leading to the expression of spherical Bragg microcavities. Using an overcrowded alkene-based unidirectional molecular motor as a dopant, we show that the topological defect structure in the droplet can be activated by illumination. By using appropriate molecular motor concentrations, light can either break the symmetry of topological defects (as observed for the bent-twisted bipolar structure), or it can induce inversion of handedness in an onion-like organization (in the case of RSS). This latter feature may pave the way toward alternative activation modes of lasers based on cholesteric droplets. By also studying CLC droplets once they have reached full photoconversion at photostationary state (PSS), we highlight that the strong influence of confinement on the droplets structure occurs to the same extent after the helix inversion event. Our results are interpreted in terms of numerical simulations of the droplets' structure, which shed light on the major role played by curvature close to the droplets' center, this latter one becoming dominant when the droplet radius is small.

| S-EPMC5924914 | biostudies-literature

The effects of thioamide backbone substitution on protein stability: a study in α-helical, β-sheet, and polyproline II helical contexts.

Project description:Thioamides are single atom substitutions of the peptide bond that serve as versatile probes of protein structure. Effective use of thioamides requires a robust understanding of the impact that the substitution has on a protein of interest. However, the thermodynamic effects of thioamide incorporation have only been studied in small structural motifs, and their influence on secondary structure in the context of full-length proteins is not known. Here we describe a comprehensive survey of thioamide substitutions in three benchmark protein systems (calmodulin, the B1 domain of protein G, and collagen) featuring the most prevalent secondary structure motifs: α-helix, β-sheet, and polyproline type II helix. We find that in most cases, effects on thermostability can be understood in terms of the positioning and local environment of the thioamide relative to proximal structural elements and hydrogen bonding networks. These observations set the stage for the rational design of thioamide substituted proteins with predictable stabilities.

| S-EPMC5428018 | biostudies-literature

Establishment of expanded and streamlined pipeline of PITCh knock-in - a web-based design tool for MMEJ-mediated gene knock-in, PITCh designer, and the variations of PITCh, PITCh-TG and PITCh-KIKO.

Project description:The emerging genome editing technology has enabled the creation of gene knock-in cells easily, efficiently, and rapidly, which has dramatically accelerated research in the field of mammalian functional genomics, including in humans. We recently developed a microhomology-mediated end-joining-based gene knock-in method, termed the PITCh system, and presented various examples of its application. Since the PITCh system only requires very short microhomologies (up to 40 bp) and single-guide RNA target sites on the donor vector, the targeting construct can be rapidly prepared compared with the conventional targeting vector for homologous recombination-based knock-in. Here, we established a streamlined pipeline to design and perform PITCh knock-in to further expand the availability of this method by creating web-based design software, PITCh designer ( http://www.mls.sci.hiroshima-u.ac.jp/smg/PITChdesigner/index.html ), as well as presenting an experimental example of versatile gene cassette knock-in. PITCh designer can automatically design not only the appropriate microhomologies but also the primers to construct locus-specific donor vectors for PITCh knock-in. By using our newly established pipeline, a reporter cell line for monitoring endogenous gene expression, and transgenesis (TG) or knock-in/knockout (KIKO) cell line can be produced systematically. Using these new variations of PITCh, an exogenous promoter-driven gene cassette expressing fluorescent protein gene and drug resistance gene can be integrated into a safe harbor or a specific gene locus to create transgenic reporter cells (PITCh-TG) or knockout cells with reporter knock-in (PITCh-KIKO), respectively.

| S-EPMC5470537 | biostudies-literature

Tripyrrin-armed isosmaragdyrins: synthesis, heterodinuclear coordination, and protonation-triggered helical inversion.

Project description:Oxidative ring closure of linear oligopyrroles is one of the synthetic approaches to novel porphyrinoids with dinuclear coordination sites and helical chirality. The spatial arrangement of the pyrrolic groups of octapyrrole (P8) affected the position of the intramolecular oxidative coupling of the pyrrolic units; tripyrrin-armed isosmaragdyrin analogue (1) containing a β,β-linked bipyrrole moiety was synthesized regioselectively in a high yield by using FeCl3. NiII-coordination at the armed tripyrrin site of 1 allowed the formation of diastereomeric helical twisted complexes (2A and 2B) and succeeding CuII-coordination at the macrocyclic core afforded heterodinuclear NiII/CuII-complexes (3A and 3B). Each of them comprised a pair of separable enantiomers, exhibiting P- and M-helices, respectively. Notably, diastereomeric interconversion from 2A to 2B was quantitatively achieved as a consequence of helical transformation under acidic conditions.

| S-EPMC8157612 | biostudies-literature

Transient chirality inversion during racemization of a helical cobalt(III) complex.

Project description:SignificanceWe first observed a transient chirality inversion on a simple unimolecular platform during the racemization of a chiral helical complex [LCo3A6]3+, i.e., the helicity changed from P-rich (right-handed) to M-rich (left-handed), which then racemized to a P/M equimolar mixture in spite of the absence of a reagent that could induce the M helix. This transient chirality inversion was observed only in the forward reaction, whereas the reverse reaction showed a simple monotonic change with an induction time. Consequently, the M helicity appeared only in the forward reaction. These forward and reverse reactions constitute a hysteretic cycle. Compounds showing such unique time responses would be useful for developing time-programmable switchable materials that can control the physical/chemical properties in a time-dependent manner.

| S-EPMC8931221 | biostudies-literature

Optically Reconfigurable Chiral Microspheres of Self-Organized Helical Superstructures with Handedness Inversion.

Project description:Optically reconfigurable monodisperse chiral microspheres of self-organized helical superstructures with dynamic chirality were fabricated via a capillary-based microfluidic technique. Light-driven handedness-invertible transformations between different configurations of microspheres were vividly observed and optically tunable RGB photonic cross-communications among the microspheres were demonstrated.

| S-EPMC5796552 | 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