Give or Take: Effects of Electron-Accepting/-Withdrawing Groups in Red-Fluorescent BODIPY Molecular Rotors

Mapping microviscosity, temperature, and polarity in biosystems is an important capability that can aid in disease detection. This can be achieved using fluorescent sensors based on a green-emitting BODIPY group. However, red fluorescent sensors are desired for convenient imaging of biological samples. It is known that phenyl substituents in the β position of the BODIPY core can shift the fluorescence spectra to longer wavelengths. In this research, we report how electron-withdrawing (EWG) and -donating (EDG) groups can change the spectral and sensory properties of β-phenyl-substituted BODIPYs. We present a trifluoromethyl-substituted (EWG) conjugate with moderate temperature sensing properties and a methoxy-substituted (EDG) molecule that could be used as a lifetime-based polarity probe. In this study, we utilise experimental results of steady-state and time-resolved fluorescence, as well as quantum chemical calculations using density functional theory (DFT). We also explain how the energy barrier height (Ea) for non-radiative relaxation affects the probe’s sensitivity to temperature and viscosity and provide appropriate Ea ranges for the best possible sensitivity to viscosity and temperature.     

Mapping Live Cell Viscosity with an Aggregation‐Induced Emission Fluorogen by Means of Two‐Photon Fluorescence Lifetime Imaging

Intracellular viscosity is a crucial parameter that indicates the functioning of cells. In this work, we demonstrate the utility of TPE‐Cy, a cell‐permeable dye with aggregation‐induced emission (AIE) property, in mapping the viscosity inside live cells. Owing to the AIE characteristics, both the fluorescence intensity and lifetime of this dye are increased along with an increase in viscosity. Fluorescence lifetime imaging of live cells stained with TPE‐Cy reveals that the lifetime in lipid droplets is much shorter than that from the general cytoplasmic region. The loose packing of the lipids in a lipid droplet results in low viscosity and thus shorter lifetime of TPE‐Cy in this region. It demonstrates that the AIE dye could provide good resolution in intracellular viscosity sensing. This is also the first work in which AIE molecules are applied in fluorescence lifetime imaging and intracellular viscosity sensing.     

Mechanism and Nature of the Different Viscosity Sensitivities of Hemicyanine Dyes with Various Heterocycles

A series of hemicyanine derivatives are excellent fluorescent viscosity sensors in live cells and in imaging of living tissues due to their low quantum yields in solution but large fluorescence enhancements in viscous environments. Herein, three carbazole‐based hemicyanine dyes with different heterocycles are studied. They have different background quantum yields, and hence different sensitivities to viscosity detection, large Stokes shifts, and high sensitivity. Better understanding of the structure–property relationships for viscosity sensitivity could benefit the design of improved dyes. Computational studies on these dyes reveal the mechanism of viscosity sensitivity of fluorescent molecular rotors and the nature of the difference in viscosity sensitivity of the three dyes. The results show that the greatly raised HOMO and greatly lowered LUMO in the S₁ state compared with the S₀ state are responsible for the large Stokes shift of the three dyes. The heterocyclic moieties have the primary influence on the LUMO levels of the three hemicyanine dyes. Rotation about the C? C bond adjacent to the carbazole moiety of the three dyes drives the molecule toward a small energy gap between the ground state and the first excited state, which causes mainly nonradiative deactivation. The oscillator strengths in the lowest singlet excited state drop rapidly with increasing rotation between 0 and 95°, which leads to a dark state for these dyes when fully twisted at 95°. We draw a mechanistic picture at the molecular level to illustrate how these dyes work as viscosity‐sensitive fluorescent probes. The activation barriers and energy gaps of C? C bond rotation strongly depend on the choice of heterocycle, which plays a major role in reducing fluorescence quantum yield in the free state and provides high sensitivity to viscosity detection in viscous environments for the carbazole‐based hemicyanine dyes.     

Activity-Based Sensing of Ascorbate by Using Copper-Mediated Oxidative Bond Cleavage

Ascorbate is an important biological reductant and enzyme cofactor. Although direct detection through ascorbate-mediated reduction is possible, this approach suffers from poor selectivity due to the wide range of cellular reducing agents. To overcome this limitation, we leverage reduction potential of ascorbate to mediate a copper-mediated oxidative bond cleavage of ether-caged fluorophores. The copper(II) complexes supported by a {bis(2-pyridylmethyl)}benzylamine or a {bis(2-pyridylmethyl)}(2-methoxybenzyl)amine ligand were identified as an ascorbate responsive unit and their reaction with ascorbate yields a copper-based oxidant that enables rapid benzylic oxidation and the release of an ether-caged dye (coumarin or fluorescein). The copper-mediated bond cleavage is specific to ascorbate and the trigger can be readily derivatized for tuning photophysical properties of the probes. The probes were successfully applied for the fluorometric detection of ascorbate in commercial food samples, human plasma, and serum, and within live cells by using confocal microscopy and flow cytometry.     

Determining the Local Shear Viscosity of a Lipid Bilayer System by Reverse Non‐Equilibrium Molecular Dynamics Simulations

The parallel shear viscosity of a dipalmitoylphosphatidylcholine (DPPC) bilayer system is studied by reverse non‐equilibrium molecular dynamics simulations (RNEMD) with two different united‐atom force fields. The results are related to diffusion coefficients and structural distributions obtained by equilibrium molecular simulations. We investigate technical issues of the algorithm in the bilayer setup, namely, the dependence of the velocity profiles on the imposed flux and the influence of the thermostat on the calculated shear viscosity. We introduce the concept of local shear viscosity and investigate its dependence on the slip velocity of the monolayers and the particle density at the headgroup–water interface and the tail–tail interface. With this we demonstrate that the lipid bilayer is more viscous than the surrounding water phase, and that slip takes place near the headgroup region and in the centre of the bilayer where the alkyl tails meet. We also quantify the apparent increase in viscosity of the water molecules entangled at the water–headgroup interface.     

Storage of CO2 into Porous Coordination Polymer Controlled by Molecular Rotor Dynamics

Design to store gas molecules, such as CO₂, H₂, and CH₄, under low pressure is one of the most important challenges in chemistry and materials science. Herein, we describe the storage of CO₂ in the cavities of a porous coordination polymer (PCP) using molecular rotor dynamics. Owing to the narrow pore windows of PCP, CO₂ was not adsorbed at 195 K. As the temperature increased, the rotors exhibited rotational modes; such rotations dynamically expanded the size of the windows, leading to CO₂ adsorption. The rotational frequencies of the rotors (k≈10^?6 s) and correlation times of adsorbed CO₂ (τ≈10^?8 s) were elucidated via solid‐state NMR studies, which suggest that the slow rotation of the rotors sterically restricts CO₂ diffusion in the pores. This restriction results in an unusually slow CO₂ mobility close to solid state (τ≥10^?8 s). Once adsorbed at room temperature, CO₂ is robustly stored in the PCP under vacuum at 195–233 K because of the steric hindrance of the rotors. We also demonstrate that this mechanism can be applied to the storage of CH₄.     

Enhancing the Viscosity-Sensitive Range of a BODIPY Molecular Rotor by Two Orders of Magnitude

Molecular rotors are a class of fluorophores that enable convenient imaging of viscosity inside microscopic samples such as lipid vesicles or live cells. Currently, rotor compounds containing a boron-dipyrromethene (BODIPY) group are among the most promising viscosity probes. In this work, it is reported that by adding heavy-electron-withdrawing −NO₂ groups, the viscosity-sensitive range of a BODIPY probe is drastically expanded from 5–1500 cP to 0.5–50 000 cP. The improved range makes it, to our knowledge, the first hydrophobic molecular rotor applicable not only at moderate viscosities but also for viscosity measurements in highly viscous samples. Furthermore, the photophysical mechanism of the BODIPY molecular rotors under study has been determined by performing quantum chemical calculations and transient absorption experiments. This mechanism demonstrates how BODIPY molecular rotors work in general, why the −NO₂ group causes such an improvement, and why BODIPY molecular rotors suffer from undesirable sensitivity to temperature. Overall, besides reporting a viscosity probe with remarkable properties, the results obtained expand the general understanding of molecular rotors and show a way to use the knowledge of their molecular action mechanism for augmenting their viscosity-sensing properties.     

A Chiral Recognition System Orchestrated by Self‐Assembly: Molecular Chirality,Self‐Assembly Morphology,and Fluorescence Response

The newly developed oligophenylenevinylene (OPV)‐based fluorescent (FL) chiral chemosensor (OPV‐Me) for the representative enantiomeric guest, 1,2‐cyclohexanedicarboxylic acid (1,2‐CHDA: RR ‐ and SS ‐form) showed the high chiral discrimination ability, resulting in the different aggregation modes of OPV‐Me self‐assembly: RR ‐CHDA directed the fibrous supramolecular aggregate, whereas SS ‐CHDA directed the finite aggregate. The consequent FL intensity toward RR ‐CHDA was up to 30 times larger than that toward SS ‐CHDA. Accordingly, highly enantioselective recognition was achieved. Application to the chirality sensing was also possible: OPV‐Me exhibited a linear relationship between the FL intensity and the enantiomeric excess through the morphological development of stereocomplex aggregates. These results clearly show that the chiral recognition ability is manifested by the amplification cascade of the chirality difference through self‐assembly.     

Dissociation of the Signaling Protein K-Ras4B from Lipid Membranes Induced by a Molecular Tweezer

Oncogenic Ras mutations occur in more than 30 % of human cancers. K-Ras4B is the most frequently mutated isoform of Ras proteins. Development of effective K-Ras4B inhibitors has been challenging, hence new approaches to inhibit this oncogenic protein are urgently required. The polybasic domain of K-Ras4B with its stretch of lysine residues is essential for its plasma membrane targeting and localization. Employing CD and fluorescence spectroscopy, confocal fluorescence, and atomic force microscopy we show that the molecular tweezer CLR01 is able to efficiently bind to the lysine stretch in the polybasic domain of K-Ras4B, resulting in dissociation of the K-Ras4B protein from the lipid membrane and disintegration of K-Ras4B nanoclusters in the lipid bilayer. These results suggest that targeting of the polybasic domain of K-Ras4B by properly designed tweezers might represent an effective strategy for inactivation of K-Ras4B signaling.     

用GPC研究壳聚糖氧化降解过程中的分子量及其分布

用凝胶渗透色谱法跟踪研究了过氧化氢对壳聚糖氧化降解过程中壳聚糖的分子量及其分布的影响,结果表明,反应温度、时间和过氧化氢用量对壳聚糖的降解程度及降解产品质量均有影响。     

Inspection on the Mechanism of SARS-CoV-2 Inhibition by Penciclovir: A Molecular Dynamic Study

In recent years, humanity has had to face a critical pandemic due to SARS-CoV-2. In the rapid search for effective drugs against this RNA-positive virus, the repurposing of already existing nucleotide/nucleoside analogs able to stop RNA replication by inhibiting the RNA-dependent RNA polymerase enzyme has been evaluated. In this process, a valid contribution has been the use of in silico experiments, which allow for a rapid evaluation of the possible effectiveness of the proposed drugs. Here we propose a molecular dynamic study to provide insight into the inhibition mechanism of Penciclovir, a nucleotide analog on the RNA-dependent RNA polymerase enzyme. Besides the presented results, in this article, for the first time, molecular dynamic simulations have been performed considering not only the RNA-dependent RNA polymerase protein, but also its cofactors (fundamental for RNA replication) and double-strand RNA.