Using single molecule imaging to explore intracellular heterogeneity.

Despite more than 100 years of study, it is unclear if the movement of proteins inside the cell is best described as a mosh pit or an exquisitely choreographed dance. Recent studies suggest the latter. Local interactions induce molecular condensates such as liquid-liquid phase separations (LLPSs) or non-liquid, functionally significant molecular aggregates, including synaptic densities, nucleoli, and Amyloid fibrils. Molecular condensates trigger intracellular signaling and drive processes ranging from gene expression to cell division. However, the descriptions of condensates tend to be qualitative and correlative. Here, we indicate how single-molecule imaging and analyses can be applied to quantify condensates. We discuss the pros and cons of different techniques for measuring differences between transient molecular behaviors inside and outside condensates. Finally, we offer suggestions for how imaging and analyses from different time and space regimes can be combined to identify molecular behaviors indicative of condensates within the dynamic high-density intracellular environment.

Humidity-Controlled Molecular Assembly and Photoisomerization Behavior with a Bubble-Assisted Patterning Approach.

Precise control of molecular assembly is of great significance in the application of functional molecules. This work has systematically investigated the humidity effect in bubble-assisted molecular assembly. This work finds humidity is critical in the evolution of the soft confined space, leading to the formation of microscale liquid confined space under high humidity, and nanoscale liquid confined space under low humidity. It is also revealed that the differences in surface wettability and adhesion play the key role. Consequently, a flat pattern with thermodynamically favorable ordered structure and a sharp pattern with dynamically favorable disordered structure are achieved, which show different solid-state photoisomerization behaviors and photoresponsiveness. Interestingly, conductivity of sharp pattern with disordered structure is higher than that of flat pattern with layered ordered structure due to electronic transport mechanism of different spatial dimensions. This work opens a new way for manipulating the molecular self-assembly to control the morphology and function of molecular patterns.

Modeling Excited States of Molecular Organic Aggregates for Optoelectronics.

Light-driven phenomena in organic molecular aggregates underpin several mechanisms relevant to optoelectronic applications. Modeling these processes is essential for aiding the design of new materials and optimizing optoelectronic devices. In this review, we cover the use of different atomistic models, excited-state dynamics, and transport approaches for understanding light-activated phenomena in molecular aggregates, including radiative and nonradiative decay pathways. We consider both intra- and intermolecular mechanisms and focus on the role of conical intersections as facilitators of internal conversion. We explore the use of the exciton models for Frenkel and charge transfer states and the electronic structure methods and algorithms commonly applied for excited-state dynamics. Throughout the review, we analyze the approximations employed for the simulation of internal conversion, intersystem crossing, and reverse intersystem crossing rates and analyze the molecular processes behind single fission, triplet-triplet annihilation, Dexter energy transfer, and Förster energy transfer.

Efficient, Color-Stable, and Long-Lived White Organic Light-Emitting Diodes Utilizing Phosphorescent Molecular Aggregates.

Highly efficient and stable single-stack hybrid white organic light-emitting diode (WOLED) devices are developed using two emissive layers: one with amber-colored phosphorescent molecular-aggregate emission from the Pd(II) complex, Pd(II) 7-(3-(pyridine-2-yl-κN)phenoxy-κC)(benzo-κC)([c]benzo[4,5]imidazo-κN)[1,2-a][1,5]naphthyridine, Pd3O8-Py5, and the other with blue fluorescence emission. An optimized device structure achieves high color stability under various current densities, an external quantum efficiency (EQE) of 45.5%, a power efficiency of 97.4 Lm W-1 , and an estimated LT95 (operational time to 95% of the initial luminance) of 50 744 h at an initial luminance of 1000 cd m-2 .

Thermally activated delayed fluorescence (TADF) emitters: sensing and boosting spin-flipping by aggregation.

Metal-free organic emitters with thermally activated delayed fluorescence (TADF) characteristics are emerging due to the potential applications in optoelectronic devices, time-resolved luminescence imaging, and solid-phase sensing. Herein, we synthesized two (4-bromobenzoyl)pyridine (BPy)-based donor-acceptor (D-A) compounds with varying donor size and strength: the emitter BPy-pTC with tert-butylcarbazole (TC) as the donor and BPy-p3C with bulky tricarbazole (3C) as the donor unit. Both BPy-pTC and BPy-p3C exhibited prominent emission with TADF properties in solution and in the solid phase. The stronger excited-state charge transfer was obtained for BPy-p3C due to the bulkier donor, leading to a more twisted D-A geometry than that of BPy-pTC. Hence, BPy-p3C exhibited aggregation-induced enhanced emission (AIEE) in a THF/water mixture. Interestingly, the singlet-triplet energy gap (ΔE ST) was reduced for both compounds in the aggregated state as compared to toluene solution. Consequently, a faster reverse intersystem crossing rate (k RISC) was obtained in the aggregated state, facilitating photon upconversion, leading to enhanced delayed fluorescence. Further, the lone-pair electrons of the pyridinyl nitrogen atom were found to be sensitive to acidic protons. Hence, the exposure to acid and base vapors using trifluoroacetic acid (TFA) and triethylamine (TEA) led to solid-phase fluorescence switching with fatigue resistance. The current study demonstrates the role of the donor strength and size in tuning ΔE ST in the aggregated state as well as the relevance for fluorescence-based acid-base sensing.

Experimental Study on Phenol-Formaldehyde Resin Aggregates as In-Depth Conformance Control Agents Stabilized by Polymer.

To improve the dispersion stability of phenol-formaldehyde resin (PFR) particles in simulated oilfield injection water and their propagation ability in petroleum reservoir, a hydrophobically associating polymer (HAP) was employed as a stabilizer in this paper. The dispersion stability of PFR in the injection water was studied by measuring turbidity as a function of time. In addition, the migration property of the PFR/HAP dispersion was evaluated by both cellulose membrane filtration and sand packs-flooding experiments. The results show that HAP can stabilize the PFR dispersion prepared with the simulated injection water by forming PFR/HAP complex molecular aggregates. These aggregates can migrate in sand packs with strong flow resistance due to deformation or disaggregation of the aggregates when passing through the pore throat. Oil recovery was improved by up to 21.1% on the basis of water flooding, and the higher the concentration of PFR/HAP dispersion system, the better the oil recovery effect. Moreover, the cycle of log-jamming/dispersion of the aggregates leads to their penetrations through the bigger pores in the sand packs with a higher flow resistance than water. This process can improve the conformance of water in high permeability sand packs on a micro/macro scale and thus divert more water into low permeability sand packs. Therefore, more oil could be recovered from the low permeability sand packs. Moreover, the bigger the sand pack's permeability ratio, the lower the oil recovery rate by waterflood, and the more the incremental oil can be recovered by the PFR/HAP flood.

Discriminating Chiral Supramolecular Motions by Circularly Polarized Luminescence.

Molecular motions are closely associated with the behaviors and properties of organic materials. However, monitoring molecular motions is challenging. Herein, a chiral supramolecular system consisting of L-/D-phenylalanine (LPF/DPF) as a chiral inducer and an achiral tetraphenylethene derivative (TPEF) as a molecular rotor has been proposed and explored for real-time discriminating the supramolecular motions by the visualization of circularly polarized luminescence (CPL) signal variations. Derived from the ordered molecular motions of TPEF induced by LPF/DPF, highly organized aggregates have been progressively assembled in a controlled manner with differentiated morphologies, including spherical particles, one-dimensional fibers, and floor-shaped supercrystals. Notably, increasing level of ordered aggregates, in turn, led to quenching emissions, while the CPL signals have been dramatically amplified accompanying by a sharp enhancement of luminescence dissymmetry factors (glum ) from nearly 0 to -0.1. The significant amplification of CPL is attributed to the ordered aggregates of supramolecules, leading to the decrease of electric transition dipole moments in supramolecular system. As a result of the chiral supramolecular motions powered by supramolecular crystallization, the supramolecular motions are conveniently discriminated by visual CPL signal variation with an enhancement of glum value from 0 to -0.1 in real time.

Exciton Transfer at Heterointerfaces of MoS2 Monolayers and Fluorescent Molecular Aggregates.

Integration of distinct materials to form heterostructures enables the proposal of new functional devices based on emergent physical phenomena beyond the properties of the constituent materials. The optical responses and electrical transport characteristics of heterostructures depend on the charge and exciton transfer (CT and ET) at the interfaces, determined by the interfacial energy level alignment. In this work, heterostructures consisting of aggregates of fluorescent molecules (DY1) and 2D semiconductor MoS2 monolayers are fabricated. Photoluminescence spectra of DY1/MoS2 show quenching of the DY1 emission and enhancement of the MoS2 emission, indicating a strong electronic interaction between these two materials. Nanoscopic mappings of the light-induced contact potential difference changes rule out the CT process at the interface. Using femtosecond transient absorption spectroscopy, the rapid interfacial ET process from DY1 aggregates to MoS2 and a fourfold extension of the exciton lifetime in MoS2 are elucidated. These results suggest that the integration of 2D inorganic semiconductors with fluorescent molecules can provide versatile approaches to engineer the physical characteristics of materials for both fundamental studies and novel optoelectronic device applications.

Gaussian process regression for absorption spectra analysis of molecular dimers.

A common task is the determination of system parameters from spectroscopy, where one compares the experimental spectrum with calculated spectra, that depend on the desired parameters. Here we discuss an approach based on a machine learning technique, where the parameters for the numerical calculations are chosen from Gaussian Process Regression (GPR). This approach does not only quickly converge to an optimal parameter set, but in addition provides information about the complete parameter space, which allows for example to identify extended parameter regions where numerical spectra are consistent with the experimental one. We consider as example dimers of organic molecules and aim at extracting in particular the interaction between the monomers, and their mutual orientation. We find that indeed the GPR gives reliable results which are in agreement with direct calculations of these parameters using quantum chemical methods.

Plasmon-Enhanced Exciton Delocalization in Squaraine-Type Molecular Aggregates.

Enlarging exciton coherence lengths in molecular aggregates is critical for enhancing the collective optical and transport properties of molecular thin film nanostructures or devices. We demonstrate that the exciton coherence length of squaraine aggregates can be increased from 10 to 24 molecular units at room temperature when preparing the aggregated thin film on a metallic rather than a dielectric substrate. Two-dimensional electronic spectroscopy measurements reveal a much lower degree of inhomogeneous line broadening for aggregates on a gold film, pointing to a reduced disorder. The result is corroborated by simulations based on a Frenkel exciton model including exciton-plasmon coupling effects. The simulation shows that localized, energetically nearly resonant excitons on spatially well separated segments can be radiatively coupled via delocalized surface plasmon polariton modes at a planar molecule-gold interface. Such plasmon-enhanced delocalization of the exciton wave function is of high importance for improving the coherent transport properties of molecular aggregates on the nanoscale. Additionally, it may help tailor the collective optical response of organic materials for quantum optical applications.

The Role of Pectobacterium atrosepticum Exopolysaccharides in Plant-Pathogen Interactions.

The phytopathogenic bacterium Pectobacterium atrosepticum (Pba), one of the members of the soft rot Pectobacteriaceae, forms biofilm-like structures known as bacterial emboli when colonizing the primary xylem vessels of the host plants. The initial extracellular matrix of the bacterial emboli is composed of the host plant's pectic polysaccharides, which are gradually substituted by the Pba-produced exopolysaccharides (Pba EPS) as the bacterial emboli "mature". No information about the properties of Pba EPS and their possible roles in Pba-plant interactions has so far been obtained. We have shown that Pba EPS possess physical properties that can promote the maintenance of the structural integrity of bacterial emboli. These polymers increase the viscosity of liquids and form large supramolecular aggregates. The formation of Pba EPS aggregates is provided (at least partly) by the acetyl groups of the Pba EPS molecules. Besides, Pba EPS scavenge reactive oxygen species (ROS), the accumulation of which is known to be associated with the formation of bacterial emboli. In addition, Pba EPS act as suppressors of the quantitative immunity of plants, repressing PAMP-induced reactions; this property is partly lost in the deacetylated form of Pba EPS. Overall, our study shows that Pba EPS play structural, protective, and immunosuppressive roles during Pba-plant interactions and thus should be considered as virulence factors of these bacteria.

Efficient and Stable Molecular-Aggregate-Based Organic Light-Emitting Diodes with Judicious Ligand Design.

Phosphorescent molecular aggregates show promise in realizing efficient and stable organic light-emitting diodes (OLEDs) operating at high brightness level, which is highly desired for future lighting and display applications. Herein, four tetradentate Pd(II) complexes are prepared with judicious ligand design, and their electrochemical and photophysical properties are thoroughly examined. The studies indicate that slight structural changes of ligands can modify the hole and electron transporting capabilities, and alter the horizontal emitting dipole ratios of aggregates in amorphous film, the latter of which are sensitive to the thin-film deposition conditions including the deposition rate and the choice of the templating layer. An optimized OLED device using Pd3O8-Py5 aggregates exhibits a peak external quantum efficiency (EQE) of 37.3% and a reduced efficiency roll-off with high EQEs of 36.0% and 32.5% at 1000 and 10 000 cd m-2 , respectively. Moreover, such an efficient device demonstrates a long measured LT95 (time to 95% of the initial luminance) lifetime of over 500 h with an initial brightness of 17 304 cd m-2 corresponding to an estimated LT95 lifetime of 48 246 h at 1000 cd m-2 .

Limitations of Linear Dichroism Spectroscopy for Elucidating Structural Issues of Light-Harvesting Aggregates in Chlorosomes.

Linear dichroism (LD) spectroscopy is a widely used technique for studying the mutual orientation of the transition-dipole moments of the electronically excited states of molecular aggregates. Often the method is applied to aggregates where detailed information about the geometrical arrangement of the monomers is lacking. However, for complex molecular assemblies where the monomers are assembled hierarchically in tiers of supramolecular structural elements, the method cannot extract well-founded information about the monomer arrangement. Here we discuss this difficulty on the example of chlorosomes, which are the light-harvesting aggregates of photosynthetic green-(non) sulfur bacteria. Chlorosomes consist of hundreds of thousands of bacteriochlorophyll molecules that self-assemble into secondary structural elements of curved lamellar or cylindrical morphology. We exploit data from polarization-resolved fluorescence-excitation spectroscopy performed on single chlorosomes for reconstructing the corresponding LD spectra. This reveals that LD spectroscopy is not suited for benchmarking structural models in particular for complex hierarchically organized molecular supramolecular assemblies.

Capture of enzyme aggregates by covalent immobilization on solid supports. Relevant stabilization of enzymes by aggregation.

In this paper, a novel procedure for the immobilization and stabilization of enzymes is proposed: the multipoint covalent attachment of bi-molecular enzyme aggregates. This immobilization protocol allows the "capture" and fixation of the enzyme aggregate on the support surface. In addition to stabilization by multipoint attachment, enzyme aggregation promotes very interesting stabilizing effects. In the presence of low concentrations of polyethylene glycol (30 %) the dimeric amine oxidase from Pisum sativum forms soluble bi-molecular aggregates. Enzyme aggregates were analyzed by Dynamic Light Scattering and by full chemical loading of a mesoporous support (10 % agarose gels activated with glyoxyl groups). The soluble aggregate was immobilized by multipoint attachment on glyoxyl- agarose at pH 8.5 though the four amino termini of the two dimeric molecules (Lys residues are not reactive at this pH). The immobilized aggregated structure cannot undergo any movement (translational or rotational) after multipoint attachment and the aggregate is "fixed" on the support surface even after the removal of PEG. The immobilized aggregate was further incubated at pH 10 in order to allow the Lys residues to react with the glyoxyl groups on the support. Enzyme aggregation has an important effect on enzyme stabilization: the aggregated derivative was 40 fold more stable than a similar derivative of the isolated enzyme and 200 fold more than native enzymes in experiments of thermal inactivation.

Template Assisted Generation of Chiral Luminescence in Organic Fluorophores.

Development of efficient ways of fabricating chiral light emitting materials is an active area of research due to the vast potential offered by these materials in the field of optoelectronic devices, data storage, and asymmetric synthesis. Among the various methods employed, template assisted generation of chiral luminescence is gaining enormous attention due to its simplicity, applicability over a wide range of fluorescent molecules/dyes, and the display of high anisotropic values.

Extreme and Topological Dissipative Solitons with Structured Matter and Structured Light.

Structuring of matter with nanoobjects allows one to generate soliton-like light bundles with extreme characteristics-temporal duration and spatial dimensions. On the other hand, structuring of light gives the possibility to form light bundles with complicated internal structure; their topology could be used for information coding similar to that in self-replicating RNA molecules carrying genetic code. Here we review the both variants of structuring. In the first variant, we consider a linear molecular chain and organic film interacting resonantly with laser radiation. Demonstrated are optical bistability, switching waves, and dissipative solitons, whose sizes for molecular J-aggregates can reach the nanometer range. We also discuss some theoretical approaches to take into account multi-particle interaction and correlations between molecules. In the second variant, light structuring in large-size laser medium with saturable amplification and absorption is achieved by preparation of the initial field distribution with a number of closed and unclosed vortex lines where the field vanishes. Various types of topological solitons, parameter domains of their stability, and transformation of the solitons with slow variation of the scheme parameters are presented.

Nature of the optical band shapes in polymethine dyes and H-aggregates: dozy chaos and excitons. Comparison with dimers, H*- and J-aggregates.

Results on the theoretical explanation of the shape of optical bands in polymethine dyes, their dimers and aggregates are summarized. The theoretical dependence of the shape of optical bands for the dye monomers in the vinylogous series in line with a change in the solvent polarity is considered. A simple physical (analytical) model of the shape of optical absorption bands in H-aggregates of polymethine dyes is developed based on taking the dozy-chaos dynamics of the transient state and the Frenkel exciton effect in the theory of molecular quantum transitions into account. As an example, the details of the experimental shape of one of the known H-bands are well reproduced by this analytical model under the assumption that the main optical chromophore of H-aggregates is a tetramer resulting from the two most probable processes of inelastic binary collisions in sequence: first, monomers between themselves, and then, between the resulting dimers. The obtained results indicate that in contrast with the compact structure of J-aggregates (brickwork structure), the structure of H-aggregates is not the compact pack-of-cards structure, as stated in the literature, but a loose alternate structure. Based on this theoretical model, a simple general (analytical) method for treating the more complex shapes of optical bands in polymethine dyes in comparison with the H-band under consideration is proposed. This method mirrors the physical process of molecular aggregates forming in liquid solutions: aggregates are generated in the most probable processes of inelastic multiple binary collisions between polymethine species generally differing in complexity. The results obtained are given against a background of the theoretical results on the shape of optical bands in polymethine dyes and their aggregates (dimers, H*- and J-aggregates) previously obtained by V.V.E.

Interferon Beta: From Molecular Level to Therapeutic Effects.

Interferon beta (IFNß) is a cytokine that is naturally produced by the immune system in response to biological and chemical stimuli. It signals by binding to the heterodimeric type I IFN receptor composed of the IFNAR1 and IFNAR2 chains, and regulates the expression of a plethora of genes by means of the classical JAK/STAT and other pathways. IFNß is pleiotropic in that it elicits antiviral, antiproliferative, and immunomodulatory activities on numerous cell types. The biological activities underpin the mechanisms by which the protein is used to treat various diseases such as hepatitis C infection and multiple sclerosis. Despite the success of IFNß therapy, the drug may evoke the production of antidrug antibodies that may reduce treatment efficiency. Immunogenicity is related to many factors: among them, structural properties, particularly aggregation, and T-cell and B-cell epitopes in the structure of IFNß, appear to be important. Knowledge of the structural properties of IFNß and its relation to immunogenicity may help scientists to develop safer and more effective forms. Several methods have been used to predict and reduce the immunogenicity of certain IFNß drug products. In this chapter, we review the current knowledge on IFNß from its structure, dynamic conformation, signaling pathway, and mechanism of action to its therapeutic effects. Immunogenicity and its relation to structural properties of IFNß are also discussed.

Molecular clusters size of Puerariae thomsonii radix aqueous decoction and relevance to oral absorption.

The multi-component system of traditional Chinese medicine (TCM) is very complicated. The clusters are dynamic aggregates whose molecules are held together by hydrogen-bonded, Van der Waals forces or the opposite charges of particles attract each other. In this paper, field emission scanning electron microscopy proved that molecules form clusters in Pueraria thomsonii Benth (Fenge) water decoction. Four kinds of Fenge water decoction, 0.07 g∙mL-1 (F-1), 0.1 g∙mL-1 (F-2), 0.17 g∙mL-1 (F-3), 0.35 g∙mL-1 (F-4); F-1, average diameter of molecular was about 120 nm; F-2, 195 nm; F-3, 256 nm; and F-4, 480 nm. The molecular size was shown to depend on concentration. Rabbits were given equal does of 2.8 g∙kg-1, to perfuse F-1, F-2, F-3, F-4 in volume of 80 mL, 56 mL, 33 mL, 17 mL, respectively. At 0-180 min to collect 2 mL blood from the rabbit ears middle arteries for metabolism fingerprints, the results show the particle size of molecular is smaller, the absorption of drugs is better instead. The acute blood stasis model rats were treatment with Fenge decoction of 1.5 g∙kg-1 for 14 days, the concentrations of Ang II in plasma were significantly lower in F-1 and F-2 groups than those in model group (p < 0.01 or p < 0.05), but there were no significantly difference in F-3 and F-4 groups than those in model group (p > 0.05). Despite the molecular aggregation is a common physical phenomenon, it influence on the kind and amount of molecule per unit volume. Molecules morphology influence on the absorption behavior of drugs in vivo therefore is to have an impact on pharmacological function.

A dimension map for molecular aggregates.

A pair of gyradius ratios, defined from the principal radii of gyration, are used to generate a dimension map that describes the geometry of molecular aggregates in water and in organic solvents. Molecular dynamics simulations were performed on the aggregation of representative biomolecules and polyaromatic compounds to demonstrate application of the dimension map. It was shown that molecular aggregate data on the dimension map were bounded by two boundary curves, and that the map could be separated into three regions representing three groups of structures: one-dimensional rod-like structures; two-dimensional planar structures or short-cylinder-like structures; and three-dimensional sphere-like structures. Examining the location of the aggregates on the dimension map and how the location changes with solvent type and solute material parameter provides a simple yet effective way to infer the aggregation manner and to study solubility and mechanism of aggregation.