Changes in dynamics of SRE-RNA on binding to the VTS1p-SAM domain studied by 13C NMR relaxation

RNA recognition by proteins is often accompanied by significant changes in RNA dynamics in addition to conformational changes. However, there are very few studies which characterize the changes in molecular motions in RNA on protein binding. We present a quantitative (13)C NMR relaxation study of the changes in RNA dynamics in the pico-nanosecond time scale and micro-millisecond time scale resulting from interaction of the stem-loop SRE-RNA with the VTS1p-SAM domain. (13)C relaxation rates of the protonated carbons of the nucleotide base and anomeric carbons have been analyzed by employing the model-free formalism, for a fully (13)C/(15)N-labeled sample of the SRE-RNA in the free and protein-bound forms. In the free RNA, the nature of molecular motions are found to be distinctly different in the stem and the loop region. On binding to the protein, the nature of motions becomes more homogeneous throughout the RNA, with many residues showing increased flexibility at the aromatic carbon sites, while the anomeric carbon sites become more rigid. Surprisingly, we also observe indications of a slow collective motion of the RNA in the binding pocket of the protein. The observation of increased motions on binding is interesting in the context of growing evidence that binding does not always lead to motional restrictions and the resulting entropy gain could favor the free energy of association.     

Cover Picture: Supramolecular Self-Assembly as a Tool To Preserve the Electronic Purity of Perylene Diimide Chromophores (Angew. Chem. Int. Ed. 12/2023)

Organic semiconductors are promising for efficient, printable optoelectronics. However, strong excited-state quenching due to uncontrolled aggregation limits their use in devices. We report on the self-assembly of a supramolecular pseudo-cube formed from six perylene diimides (PDIs). The rigid, shape-persistent cage sets the distance and orientation of the PDIs and suppresses intramolecular rotations and vibrations, leading to non-aggregated, monomer-like properties in solution and the solid state, in contrast to the fast fluorescence quenching in the free ligand. The stabilized excited state and electronic purity in the cage enables the observation of delayed fluorescence due to a bright excited multimer, acting as excited-state reservoir in a rare case of benign inter-chromophore interactions in the cage. We show that self-assembly provides a powerful tool for retaining and controlling the electronic properties of chromophores, and to bring molecular electronics devices within reach.     

Visible-Light-Induced Control over Reversible Single-Chain Nanoparticle Folding

We introduce a class of single-chain nanoparticles (SCNPs) that respond to visible light (λ_max=415 nm) with complete unfolding from their compact structure into linear chain analogues. The initial folding is achieved by a simple esterification reaction of the polymer backbone constituted of acrylic acid and polyethylene glycol carrying monomer units, introducing bimane moieties, which allow for the photochemical unfolding, reversing the ester-bond formation. The compaction and the light driven unfolding proceed cleanly and are readily followed by size exclusion chromatography (SEC) and diffusion ordered NMR spectroscopy (DOSY), monitoring the change in the hydrodynamic radius (R_H). Importantly, the folding reaction and the light-induced unfolding are reversible, supported by the high conversion of the photo cleavage. As the unfolding reaction occurs in aqueous systems, the system holds promise for controlling the unfolding of SCNPs in biological environments.     

Molecular dynamics simulations of heptyl phosphonic acid: a potential polymer component for fuel cell polymer membrane

Atomistic molecular dynamics simulations have been performed on heptyl phosphonic acid (HPA) to understand the dynamic hydrogen bonding network in the liquid phase. HPA is a phosphonic-acid functionalized alkane (heptane) and a model compound for one of the promising polymers for high temperature (>100 degrees C) fuel cell polymer electrolyte membranes. For the simulation, a force field for this molecule has been generated with the help of quantum chemical calculations and optimized by simplex algorithm. The force field has been validated against experimentally measured properties, for example, density and self-diffusion constant. From molecular dynamics simulations conducted at different temperatures, we have confirmed the hypothesis of dynamic hydrogen bond network formation in this material.     

Ultrafast ring-closure reaction of photochromic indolylfulgimides studied with UV-pump-IR-probe spectroscopy

The ring-opening and ring-closure reactions of a photochromic indolylfulgimide are investigated with femtosecond vibrational spectroscopy. Spectral signatures due to excited-state decay and vibrational cooling are seen in the mid-IR region. For the ring-opening reaction triggered with visible pulses, a lifetime of the excited electronic state of 4 ps was obtained in polar solution. In a nonpolar solvent, this time constant is reduced to 2 ps. The ring-closure reaction induced with UV pulses displays an excited-state lifetime and thus a building of the photoproduct of roughly 0.5 ps. For all processes, the subsequent cooling occurs on a 15-ps time scale lasting up to approximately 50 ps. The time-resolved IR measurements do not support the existence of any long-living intermediate states.     

Chemoenzymatic approaches toward dechloroansamitocin P-3

[reaction: see text] The enantioselective total synthesis of proansamitocin, a key biosynthetic intermediate of the highly potent antitumor agent ansamitocin P-3, is described which bears a diene-ene RCM as the key macrocyclization step. Feeding of proansamitocin to an AHBA block mutant Actinosynnema pretiosum (HGF073) yielded ansamitocin P-3 as well as dechloroansamitocin P-3, the latter also being formed upon fermentation in the presence of 3-amino-5-methoxybenzoic acid.     

Monosaccharides as silicon chelators: pentacoordinate bis(diolato)(phenyl)silicates with the cis-furanose isomers of common pentoses and hexoses

Five-coordinate phenylsilicates are formed from the reaction of trimethoxy(phenyl)silane with monosaccharides in methanol in the presence of a stoichiometric amount of base. Five complexes have been isolated and characterized with two ketoses and three aldopentoses. The silicon central atom in [K([18]crown-6)][PhSi(beta-D-Fruf 2,3H-2)2].MeOH (1, Fru=fructose) is part of two chelate rings, with the ligands being beta-D-fructofuranose-O2,O3 dianions. The beta-furanose isomer is best suited for silicon ligation because it exhibits a torsion angle close to 0 degrees for the most acidic diol function, thus assuring a flat chelate ring. The same structural principles are also found in [K([18]crown-6)][PhSi(beta-D-Araf1,2H-2)2].2 MeOH (2, Ara=arabinose), [K([18]crown-6)][PhSi(alpha-D-Ribf1,2H-2)2] (3, Rib=ribose), [K([18]crown-6)][PhSi(alpha-D-Xylf1,2H-2)2]. acetone (4, Xyl=xylose), and [K([18]crown-6)][PhSi(alpha-D-Rulf2,3H-2)2] (5, Rul=ribulose).     

Differentiation between Shallow and Deep Charge Trap States on Single Poly(3‐hexylthiophene) Chains through Fluorescence Photon Statistics

Blinking of the photoluminescence (PL) emitted from individual conjugated polymer chains is one of the central observations made by single‐molecule spectroscopy (SMS). Important information, for example regarding excitation energy transfer, can be extracted by evaluating dynamic quenching. However, the nature of trap states, which are responsible for PL quenching, often remains obscured. We present a detailed investigation of the photon statistics of single poly(3‐hexylthiophene) (P3HT) chains obtained by SMS. The photon statistics provide a measure of the number and brightness of independently emitting areas on a single chain. These observables can be followed during blinking. A decrease in PL intensity is shown to be correlated with either 1) a decrease in the average brightness of the emitting sites; or 2) a decrease in the number of emitting regions. We attribute these phenomena to the formation of 1) shallow charge traps, which can weakly affect all emitting areas of a single chain at once; and 2) deep traps, which have a strong effect on small regions within the single chains.     

Pre-organization of the core structure of E-selectin antagonists

A new class of N-acetyl-D-glucosamine (GlcNAc) mimics for E-selectin antagonists was designed and synthesized. The mimic consists of a cyclohexane ring substituted with alkyl substituents adjacent to the linking position of the fucose moiety. Incorporation into E-selectin antagonists led to the test compounds 8 and the 2'-benzoylated analogues 21, which exhibit affinities in the low micromolar range. By using saturation transfer difference (STD)-NMR it could be shown that the increase in affinity does not result from an additional hydrophobic contact of the alkyl substituent with the target protein E-selectin, but rather from a steric effect stabilizing the antagonist in its bioactive conformation. The loss of affinity found for antagonists 10 and 35 containing a methyl substituent in a remote position (and therefore unable to support to the stabilization of the core) further supports this hypothesis. Finally, when a GlcNAc mimetic containing two methyl substituents (52 and 53) was used, in which one methyl was positioned adjacent to the fucose linking position and the other was in a remote position, the affinity was regained.     

Acid-induced degradation of phosphorescent dopants for OLEDs and its application to the synthesis of tris-heteroleptic iridium(III) bis-cyclometalated complexes

Investigations of blue phosphorescent organic light emitting diodes (OLEDs) based on [Ir(2-(2,4-difluorophenyl)pyridine)(2)(picolinate)] (FIrPic) have pointed to the cleavage of the picolinate as a possible reason for device instability. We reproduced the loss of picolinate and acetylacetonate ancillary ligands in solution by the addition of Br?nsted or Lewis acids. When hydrochloric acid is added to a solution of a [Ir(C^N)(2)(X^O)] complex (C^N = 2-phenylpyridine (ppy) or 2-(2,4-difluorophenyl)pyridine (diFppy) and X^O = picolinate (pic) or acetylacetonate (acac)), the cleavage of the ancillary ligand results in the direct formation of the chloro-bridged iridium(III) dimer [{Ir(C^N)(2)(μ-Cl)}(2)]. When triflic acid or boron trifluoride are used, a source of chloride (here tetrabutylammonium chloride) is added to obtain the same chloro-bridged iridium(III) dimer. Then, we advantageously used this degradation reaction for the efficient synthesis of tris-heteroleptic cyclometalated iridium(III) complexes [Ir(C^N(1))(C^N(2))(L)], a family of cyclometalated complexes otherwise challenging to prepare. We used an iridium(I) complex, [{Ir(COD)(μ-Cl)}(2)], and a stoichiometric amount of two different C^N ligands (C^N(1) = ppy; C^N(2) = diFppy) as starting materials for the swift preparation of the chloro-bridged iridium(III) dimers. After reacting the mixture with acetylacetonate and subsequent purification, the tris-heteroleptic complex [Ir(ppy)(diFppy)(acac)] could be isolated with good yield from the crude containing as well the bis-heteroleptic complexes [Ir(ppy)(2)(acac)] and [Ir(diFppy)(2)(acac)]. Reaction of the tris-heteroleptic acac complex with hydrochloric acid gives pure heteroleptic chloro-bridged iridium dimer [{Ir(ppy)(diFppy)(μ-Cl)}(2)], which can be used as starting material for the preparation of a new tris-heteroleptic iridium(III) complex based on these two C^N ligands. Finally, we use DFT/LR-TDDFT to rationalize the impact of the two different C^N ligands on the observed photophysical and electrochemical properties.