Fluorescence Quenching in BODIPY Dyes: The Role of Intramolecular Interactions and Charge Transfer

Evidence for a transfer-to-trap mechanism of fluorophore concentration quenching in lipid bilayers

It is important to understand the behaviors of fluorescent molecules because, firstly, they are often utilized as probes in biophysical experiments and, secondly, they are crucial cofactors in biological processes such as photosynthesis. A phenomenon called "fluorescence quenching" occurs when fluorophores are present at high concentrations, but the mechanisms for quenching are debated. Here, we used a technique called "in-membrane electrophoresis" to generate concentration gradients of fluorophores within a supported lipid bilayer, across which quenching was expected to occur. Fluorescence lifetime imaging microscopy (FLIM) provides images where the fluorescence intensity in each pixel is correlated to fluorescence lifetime: the intensity provides information about the location and concentration of fluorophores and the lifetime reveals the occurrence of energy-dissipative processes. FLIM was used to compare the quenching behavior of three commonly used fluorophores: Texas Red (TR), nitrobenzoaxadiazole (NBD), and 4,4-difluoro-4-bora-3a,4a-diaza-s-indacene (BODIPY). FLIM images provided evidence of quenching in regions where the fluorophores accumulated, but the degree of quenching varied between the different fluorophores. The relationship between quenching and concentration was quantified and the "critical radius for trap formation," representing the relative quenching strength, was calculated as 2.70, 2.02, and 1.14 nm, for BODIPY, TR, and NBD, respectively. The experimental data support the theory that quenching takes place via a "transfer-to-trap" mechanism which proposes, firstly, that excitation energy is transferred between fluorophores and may reach a "trap site," resulting in immediate energy dissipation, and, secondly, that trap sites are formed in a concentration-dependent manner. Some previous work suggested that quenching occurs only when fluorophores aggregate, or form long-lived dimers, but our data and this theory argue that traps may be "statistical pairs" of fluorophores that exist only transiently. Our findings should inspire future work to assess whether these traps can be charge-transfer states, excited-state dimers, or something else.

First-Principles Calculations of Excited-State Decay Rate Constants in Organic Fluorophores

In this Perspective, we discuss recent advances made to evaluate from first-principles the excited-state decay rate constants of organic fluorophores, focusing on the so-called static strategy. In this strategy, one essentially takes advantage of Fermi's golden rule (FGR) to evaluate rate constants at key points of the potential energy surfaces, a procedure that can be refined in a variety of ways. In this way, the radiative rate constant can be straightforwardly obtained by integrating the fluorescence line shape, itself determined from vibronic calculations. Likewise, FGR allows for a consistent calculation of the internal conversion (related to the non-adiabatic couplings) in the weak-coupling regime and intersystem crossing rates, therefore giving access to estimates of the emission yields when no complex photophysical phenomenon is at play. Beyond outlining the underlying theories, we summarize here the results of benchmarks performed for various types of rates, highlighting that both the quality of the vibronic calculations and the accuracy of the relative energies are crucial to reaching semiquantitative estimates. Finally, we illustrate the successes and challenges in determining the fluorescence quantum yields using a series of organic fluorophores.

Extensive Analysis of the Parameters Influencing Radiative Rates Obtained through Vibronic Calculations

Defining a theoretical model systematically delivering accurate ab initio predictions of the fluorescence quantum yields of organic dyes is highly desirable for designing improved fluorophores in a systematic rather than trial-and-error way. To this end, the first required step is to obtain reliable radiative rates (kr), as low kr typically precludes effective emission. In the present contribution, using a series of 10 substituted phenyls with known experimental kr, we analyze the impact of the computational protocol on the kr determined through the thermal vibration correlation function (TVCF) approach on the basis of time-dependent density functional theory (TD-DFT) calculations of the energies, structures, and vibrational parameters. Both the electronic structure (selected exchange-correlation functional, application or not of the Tamm-Dancoff approximation) and the vibronic parameters (line-shape formalism, coordinate system, potential energy surface model, and dipole expansion) are tackled. Considering all possible combinations yields more than 3500 cases, allowing to extract statistically-relevant information regarding the impact of each computational parameter on the magnitude of the estimated kr. It turns out that the selected vibronic model can have a significant impact on the computed kr, especially the potential energy surface model. This effect is of the same order of magnitude as the difference noted between B3LYP and CAM-B3LYP estimates. For the treated compounds, all evaluated functionals do deliver reasonable trends, fitting the experimental values.

Dense and Acidic Organelle-Targeted Visualization in Living Cells: Application of Viscosity-Responsive Fluorescence Utilizing Restricted Access to Minimum Energy Conical Intersection

Cell-imaging methods with functional fluorescent probes are an indispensable technique to evaluate physical parameters in cellular microenvironments. In particular, molecular rotors, which take advantage of the twisted intramolecular charge transfer (TICT) process, have helped evaluate microviscosity. However, the involvement of charge-separated species in the fluorescence process potentially limits the quantitative evaluation of viscosity. Herein, we developed viscosity-responsive fluorescent probes for cell imaging that are not dependent on the TICT process. We synthesized AnP₂-H and AnP₂-OEG, both of which contain 9,10-di(piperazinyl)anthracene, based on 9,10-bis(N,N-dialkylamino)anthracene that adopts a nonflat geometry at minimum energy conical intersection. AnP₂-H and AnP₂-OEG exhibited enhanced fluorescence as the viscosity increased, with sensitivities comparable to those of conventional molecular rotors. In living cell systems, AnP₂-OEG showed low cytotoxicity and, reflecting its viscosity-responsive property, allowed specific visualization of dense and acidic organelles such as lysosomes, secretory granules, and melanosomes under washout-free conditions. These results provide a new direction for developing functional fluorescent probes targeting dense organelles.

BODIPY-Ethynylestradiol molecular rotors as fluorescent viscosity probes in endoplasmic reticulum

Due to their capability for sensing changes in viscosity, fluorescent molecular rotors (FMRs) have emerged as potential tools to develop several promising viscosity probes; most of them, however, localize non-selectively within cells, precluding changes in the viscosity of specific cellular microdomains to be studied by these means. Following previous reports on enhanced fluorophore uptake efficiency and selectivity by incorporation of biological submolecular fragments, here we report two potential BODIPY FMRs based on an ethynylestradiol spindle, a non-cytotoxic semisynthetic estrogen well recognized by human cells. A critical evaluation of the potential of these fluorophores for being employed as FMRs is presented, including the photophysical characterization of the probes, SXRD studies and TD-DFT computations, as well as confocal microscopy imaging in MCF-7 (breast cancer) cells.

Controlling the fluorescence quantum yields of benzothiazole-difluoroborates by optimal substitution

Precise tuning of the fluorescence quantum yield, vital for countless applications of fluorophores, remains exceptionally challenging due to numerous factors affecting energy dissipation phenomena often leading to its counterintuitive behavior. In contrast to the absorption and emission wavelength which can be precisely shifted to the desired range by simple structural changes, no general strategy exists for controllable modification of the fluorescence quantum yield. The rigidification of the molecular skeleton is known to usually enhance the emission and can be practically realized via the limiting molecular vibrations by aggregation. However, the subtle balance between the abundant possible radiative and non-radiative decay pathways makes the final picture exceptionally sophisticated. In the present study, a series of nine fluorophores obtained by peripheral substitution with two relatively mild electron donating and electron withdrawing groups are reported. The obtained fluorescence quantum yields range from dark to ultra-bright and the extreme values are obtained for the isomeric molecules. These severe changes in emission efficiency have been shown to arise from the complex relationship between the Franck-Condon excited state and conical intersection position. The experimental findings are rationalized by the advanced quantum chemical calculations delivering good correlation between the measured emission parameters and theoretical radiative and internal conversion rate constants. Therefore, the described substituent exchange provides a method to rigorously adjust the properties of molecular probes structurally similar to thioflavin T.

Suppressing non-radiative decay of photochromic organic molecular systems in the strong coupling regime

The lifetimes of electronic excited states have a strong influence on the efficiency of organic solar cells. However, in some molecular systems a given excited state lifetime is reduced due to the non-radiative decay through conical intersections. Several strategies may be used to suppress this decay channel. The use of the strong light-matter coupling provided in optical nano-cavities is the focus of this paper. Here, we consider the meso-tert-butyl-4,4-difluoro-4-bora-3a,4a-diaza-s-indacene molecule (meso-tert-butyl-BODIPY) as a showcase of how strong and ultrastrong coupling might help in the development of organic solar cells. The meso-tert-butyl-BODIPY is known for its low fluorescence yield caused by the non-radiative decay through a conical intersection. However, we show here that, by considering this system within a cavity, the strong coupling can lead to significant changes in the multidimensional landscape of the potential energy surfaces of meso-tert-butyl-BODIPY, suppressing almost completely the decay of the excited state wave packet back to the ground state. By means of multi configuration electronic structure calculations and nuclear wave packet dynamics, the coupling with the cavity is analyzed in-depth to provide further insight of the interaction. By fine-tuning the cavity field strength and resonance frequency, we show that one can change the nuclear dynamics in the excited state, and control the non-radiative decay. This may lead to a faster and more efficient population transfer or the suppression of it.

A Computational-Experimental Approach to Unravel the Excited State Landscape in Heavy-Atom Free BODIPY-Related Dyes

We performed a time-gated laser-spectroscopy study in a set of heavy-atom free single BODIPY fluorophores, supported by accurate, excited-state computational simulations of the key low-lying excited states in these chromophores. Despite the strong fluorescence of these emitters, we observed a significant fraction of time-delayed (microseconds scale) emission associated with processes that involved passage through the triplet manifold. The accuracy of the predictions of the energy arrangement and electronic nature of the low-lying singlet and triplet excited states meant that an unambiguous assignment of the main deactivation pathways, including thermally activated delayed fluorescence and/or room temperature phosphorescence, was possible. The observation of triplet state formation indicates a breakthrough in the "classic" interpretation of the photophysical properties of the renowned BODIPY and its derivatives.

Phototoxicity of BODIPY in long-term imaging can be reduced by intramolecular motion

For long-term live-cell fluorescence imaging and biosensing, it is crucial to work with a dye that has high fluorescence quantum yield and photostability without being detrimental to the cells. In this paper, we demonstrate that neutral boron-dipyrromethene (BODIPY)-based molecular rotors have great properties for high-light-dosage demanding live-cell fluorescence imaging applications that require repetitive illuminations. In molecular rotors, an intramolecular rotation (IMR) allows an alternative route for the decay of the singlet excited state (S₁) via the formation of an intramolecular charge transfer state (CT). The occurrence of IMR reduces the probability of the formation of a triplet state (T₁) which could further react with molecular oxygen (³O₂) to form cytotoxic reactive oxygen species, e.g., singlet oxygen (¹O₂). We demonstrate that the oxygen-related nature of the phototoxicity for BODIPY derivatives can be significantly reduced if a neutral molecular rotor is used as a probe. The studied neutral molecular rotor probe shows remarkably lower phototoxicity when compared with both the non-rotating BODIPY derivative and the cationic BODIPY-based molecular rotor in different light dosages and dye concentrations. It is also evident that the charge and localization of the fluorescent probe are as significant as the IMR in terms of the phototoxicity in a long-term live-cell imaging.

Transforming Dyes into Fluorophores: Exciton-Induced Emission with Chain-like Oligo-BODIPY Superstructures

Herein we present a systematic study demonstrating to which extent exciton formation can amplify fluorescence based on a series of ethylene-bridged oligo-BODIPYs. A set of non- and weakly fluorescent BODIPY motifs was selected and transformed into discrete, chain-like oligomers by linkage via a flexible ethylene tether. The prepared superstructures constitute excitonically active entities with non-conjugated, Coulomb-coupled oscillators. The non-radiative deactivation channels of Internal Conversion (IC), also combined with an upstream reductive Photoelectron Transfer (rPET) and Intersystem Crossing (ISC) were addressed at the monomeric state and the evolution of fluorescence and (non-)radiative decay rates studied along the oligomeric series. We demonstrate that a "masked" fluorescence can be fully reactivated irrespective of the imposed conformational rigidity. This work challenges the paradigm that a collective fluorescence enhancement is limited to sterically induced motional restrictions.

Turn-on Fluorescent Biosensors for Imaging Hypoxia-like Conditions in Living Cells

We present the synthesis, photophysical properties, and biological application of nontoxic 3-azo-conjugated BODIPY dyes as masked fluorescent biosensors of hypoxia-like conditions. The synthetic methodology is based on an operationally simple N=N bond-forming protocol, followed by a Suzuki coupling, that allows for a direct access to simple and underexplored 3-azo-substituted BODIPY. These dyes can turn on their emission properties under both chemical and biological reductive conditions, including bacterial and human azoreductases, which trigger the azo bond cleavage, leading to fluorescent 3-amino-BODIPY. We have also developed a practical enzymatic protocol, using an immobilized bacterial azoreductase that allows for the evaluation of these azo-based probes and can be used as a model for the less accessible and expensive human reductase NQO1. Quantum mechanical calculations uncover the restructuration of the topography of the S₁ potential energy surface following the reduction of the azo moiety and rationalize the fluorescent quenching event through the mapping of an unprecedented pathway. Fluorescent microscopy experiments show that these azos can be used to visualize hypoxia-like conditions within living cells.

Rationales Design von Phe-BODIPY-Aminosäuren als fluorogene Bausteine für den peptidbasierten Nachweis von Candida-Infektionen im Harntrakt

Pilzinfektionen, die durch Candida‐Arten verursacht werden, gehören zu den häufigsten Infektionen bei Krankenhauspatienten. Die derzeitigen Methoden zum Nachweis von Candida‐Pilzzellen in klinischen Proben beruhen jedoch auf zeitaufwändigen Analysen, die eine schnelle und zuverlässige Diagnose erschweren. In diesem Beitrag beschreiben wir die rationale Entwicklung neuer Phe‐BODIPY‐Aminosäuren als kleine fluorogene Bausteine und ihre Anwendung zur Erzeugung fluoreszierender antimikrobieller Peptide für die schnelle Markierung von Candida‐Zellen im Urin. Mit Hilfe von computergestützten Berechnungen haben wir das fluorogene Verhalten von BODIPY‐substituierten aromatischen Aminosäuren analysiert und Bioaktivitäts‐ und konfokale Mikroskopieexperimente bei verschiedenen Stämmen durchgeführt, um den Nutzen und die Vielseitigkeit von Peptiden mit Phe‐BODIPYs zu bestätigen. Schließlich haben wir einen einfachen und sensitiven fluoreszensbasierten Test zum Nachweis von Candida albicans in menschlichen Urinproben entwickelt.

Rational Design of Phe-BODIPY Amino Acids as Fluorogenic Building Blocks for Peptide-Based Detection of Urinary Tract Candida Infections

Fungal infections caused by Candida species are among the most prevalent in hospitalized patients. However, current methods for the detection of Candida fungal cells in clinical samples rely on time-consuming assays that hamper rapid and reliable diagnosis. Herein, we describe the rational development of new Phe-BODIPY amino acids as small fluorogenic building blocks and their application to generate fluorescent antimicrobial peptides for rapid labelling of Candida cells in urine. We have used computational methods to analyse the fluorogenic behaviour of BODIPY-substituted aromatic amino acids and performed bioactivity and confocal microscopy experiments in different strains to confirm the utility and versatility of peptides incorporating Phe-BODIPYs. Finally, we have designed a simple and sensitive fluorescence-based assay for the detection of Candida albicans in human urine samples.

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.

Designing a Red-Emitting Viscosity-Sensitive BODIPY Fluorophore for Intracellular Viscosity Imaging

Viscosity imaging at a microscopic scale can provide important information about biosystems, including the development of serious illnesses. Microviscosity imaging is achievable with viscosity-sensitive fluorophores, the most popular of which are based on the BODIPY group. However, most of the BODIPY probes fluoresce green light, whereas the red luminescence is desired for the imaging of biological samples. Designing a new viscosity probe with suitable spectroscopic properties is a challenging task because it is difficult to preserve viscosity sensitivity after modifying the molecular structure. Here we describe how we developed a new red-emitting, viscosity-sensitive, BODIPY fluorophore BP-PH-2M-NO₂ that is suitable for reliable intracellular viscosity imaging of lipid droplets in MCF-7 breast cancer cells. The design of BP-PH-2M-NO₂ was aided by DFT calculations that allowed a successful prediction of the viscosity sensitivity of fluorophores before synthesis. In summary, we report a new red viscosity probe possessing monoexponential fluorescence decay that makes it attractive for lifetime-based viscosity imaging.

Oxidative C-H/C-H Coupling of Dipyrromethanes with Azines by TiO2-Based Photocatalytic System. Synthesis of New BODIPY Dyes and Their Photophysical and Electrochemical Properties

Oxidative C-H/C-H coupling reactions of dipyrromethanes with azines in the presence of a heterophase oxidative photocatalytic system (O₂/TiO₂/visible light irradiation) were carried out. As a result of cyclization of obtained compounds with boron trifluoride etherate, new hetaryl-containing derivatives of 4,4-difluoro-4-boron-3a,4a-diaza-s-indacene were synthesized. For the obtained compounds, absorption and luminescence spectra, quantum yields of luminescence as well as cyclic volt-amperograms were measured.

Cyclopropyl Substituents Transform the Viscosity-Sensitive BODIPY Molecular Rotor into a Temperature Sensor

A quantitative fluorescent probe that responds to changes in temperature is highly desirable for studies of biological environments, particularly in cellulo. Here, we report new cell-permeable fluorescence probes based on the BODIPY moiety that respond to environmental temperature. The new probes were developed on the basis of a well-established BODIPY-based viscosity probe by functionalization with cyclopropyl substituents at α and β positions of the BODIPY core. In contrast to the parent BODIPY fluorophore, α-cyclopropyl-substituted fluorophore displays temperature-dependent time-resolved fluorescence decays showing greatly diminished viscosity dependence, making it an attractive sensor to be used with fluorescence lifetime imaging microscopy (FLIM). We performed theoretical calculations that help rationalize the effect of the cyclopropyl substituents on the photophysical behavior of the new BODIPYs. In summary, we designed an attractive new quantitative FLIM-based temperature probe that can be used for temperature sensing in live cells.

Caveat when using ADC(2) for studying the photochemistry of carbonyl-containing molecules

Several electronic-structure methods are available to study the photochemistry and photophysics of organic molecules. Among them, ADC(2) stands as a sweet spot between computational efficiency and accuracy. As a result, ADC(2) has recently seen its number of applications booming, in particular to unravel the deactivation pathways and photodynamics of organic molecules. Despite this growing success, we demonstrate here that care has to be taken when studying the nonradiative pathways of carbonyl-containing molecules, as ADC(2) appears to suffer from a systematic flaw.

BODIPY dimers: structure, interaction, and absorption spectrum

The object of the present study are BODIPY molecules obtained previously by Piskorz et al. (Dyes Pigm. 178:108322, 2020) for their antimicrobial activity. Structural analysis of the BODIPY dimers is presented in context of the aggregation influence on the photophysical properties. The thorough investigation of the nature of intermolecular interaction in the representative BODIPY dimers is provided together with the decomposition of the interaction energy into the components of well-defined origin according to SAPT procedure. For the model BODIPY systems the careful examination of the interaction nature for the dimer structure based on experimental crystal study as well as fully optimized is given. The tendencies observed in the model dimers are further on investigated for two pairs of BODIPY systems designed for biomedical application. The analyzed molecules are shown to maximize the mutual interaction by the optimization of the stacking dispersion contacts between the aromatic rings of the molecules, therefore producing stable dimers. The estimation of SAPT0 interaction energy components confirms the dominating dispersion character arising from mutual BODIPY core contacts. The influence of the dimerization process on the photophysical properties of the systems studied theoretically depends to the high extend on the dimerization mode and is significant for parallel and antiparallel dispersion-governed dimers.

Effects of Substituents on Photophysical and CO-Photoreleasing Properties of 2,6-Substituted meso-Carboxy BODIPY Derivatives

Carbon monoxide (CO) is an endogenously produced signaling molecule involved in the control of a vast array of physiological processes. One of the strategies to administer therapeutic amounts of CO is the precise spatial and temporal control over its release from photoactivatable CO-releasing molecules (photoCORMs). Here we present the synthesis and photophysical and photochemical properties of a small library of meso-carboxy BODIPY derivatives bearing different substituents at positions 2 and 6. We show that the nature of substituents has a major impact on both their photophysics and the efficiency of CO photorelease. CO was found to be efficiently released from π-extended 2,6-arylethynyl BODIPY derivatives possessing absorption spectra shifted to a more biologically desirable wavelength range. Selected photoCORMs were subjected to in vitro experiments that did not reveal any serious toxic effects, suggesting their potential for further biological research.

Toward Quantitative Prediction of Fluorescence Quantum Efficiency by Combining Direct Vibrational Conversion and Surface Crossing: BODIPYs as an Example

Accurate theoretical description of the electronic structure of boron dipyrromethene (BODIPY) molecules has been a challenge, let alone the prediction of fluorescence quantum efficiency. In this Letter, we show that the electronic structures of BODIPYs can be accurately evaluated via the spin-flip time-dependent density functional theory with the B3LYP functional. With the resulting electronic structures, the experimental spectral line shapes of representative BODIPYs are successfully reproduced by our previously developed thermal vibration correlation function method. Most importantly, a two-channel scheme is proposed to describe the internal conversion of S₁ to S₀ in BODIPYs: channel I via direct vibrational relaxation within the harmonic region and channel II via a distorted S₀/S₁ minimum energy crossing point well away from the harmonic region. The fluorescence quantum yields are accurately predicted within this two-channel scheme, which can therefore serve as a generalized method for predicting the photophysical parameters of organic fluorescent compounds.

Temperature- and Structure-Dependent Optical Properties and Photophysics of BODIPY Dyes

We report on the temperature- and structural-dependent optical properties and photophysics of a set of boron dipyrromethene (BODIPY) dyes with different substitution patterns of their meso-aryl subunit. Single-crystal X-ray diffraction analysis of the compounds enabled a classification of the dyes into a sterically hindered and a unhindered group. The steric hindrance refers to a blocked rotational motion of the aryl subunit around the bond connecting this moiety to the meso-position of the BODIPY core. The energy barriers related to this rotation were simulated by DFT calculations. As follows from the relatively low rotational barrier calculated to about 17 kcal/mol, a free rotation is only possible for sterically unhindered compounds. Rotational barriers of more than 40 kcal/mol determined for the sterically hindered compounds suggest an effective freezing of the rotational motion in these molecules. With the aid of temperature-dependent spectroscopic measurements, we could show that the ability to rotate directly affects the optical properties of our set of BODIPY dyes. This accounts for the strong temperature dependence of the fluorescence of the sterically unhindered compounds which show a drastic decrease in fluorescence quantum yield and a significant shortening in fluorescence lifetime upon heating. The optical properties of the sterically hindered compounds, however, are barely affected by temperature. Our results suggest a nonradiative deactivation of the first excited singlet state of the sterically unhindered compounds caused by a conical intersection of the potential energy surfaces of the ground and first excited state which is accessible by rotation of the meso-subunit. This is in good agreement with previously reported deactivation mechanisms. In addition, our results suggest the presence of a second nonradiative depopulation pathway of the first excited singlet state which is particularly relevant for the sterically hindered compounds.

Ready Access to Molecular Rotors Based on Boron Dipyrromethene Dyes-Coumarin Dyads Featuring Broadband Absorption

Herein we report on a straightforward access method for boron dipyrromethene dyes (BODIPYs)-coumarin hybrids linked through their respective 8- and 6- positions, with wide functionalization of the coumarin fragment, using salicylaldehyde as a versatile building block. The computationally-assisted photophysical study unveils broadband absorption upon proper functionalization of the coumarin, as well as the key role of the conformational freedom of the coumarin appended at the meso position of the BODIPY. Such free motion almost suppresses the fluorescence signal, but enables us to apply these dyads as molecular rotors to monitor the surrounding microviscosity.

The effect of solvent polarity and macromolecular crowding on the viscosity sensitivity of a molecular rotor BODIPY-C10

Viscosity is the key parameter of many biological systems such as live cells. It can be conveniently measured with ‘molecular rotors’ – fluorescent sensors of microviscosity. Here, we investigate one of the most applied molecular rotors BODIPY-C₁₀.

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.

Molecular design of near-infrared fluorescent Pdots for tumor targeting: aggregation-induced emission versus anti-aggregation-caused quenching

Semiconducting polymer dots (Pdots) have recently emerged as a new type of ultrabright fluorescent probe that has been proved to be very useful for biomedical imaging. However, Pdots often suffer from serious fluorescence aggregation-caused quenching (ACQ) especially for near-infrared (NIR) fluorescent Pdots. This article compared two strategies to overcome the ACQ effect in near-infrared emissive Pdot systems: aggregation-induced emission (AIE) and anti-aggregation-caused quenching (anti-ACQ). The results show that the anti-ACQ platform outperforms the AIE system. The fluorescence quantum yield of anti-ACQ-based Pdots can be over 50% and the average per-particle brightness of the Pdots is about 5 times higher than that of the commercially available quantum dots. To help understand why the monomer conformations could greatly affect the optical properties of Pdots, molecular dynamics simulations were performed for the first time in such complicated Pdot systems. To demonstrate applications for in vivo fluorescence imaging, both microangiography imaging on living zebrafish embryos and specific tumor targeting on mice were performed. We anticipate that these studies will pave the way for the design of new highly fluorescent Pdot systems.

Mechanisms of fluorescence quenching in prototypical aggregation-induced emission systems: excited state dynamics with TD-DFTB

A recent implementation of time-dependent tight-binding density functional theory is employed in excited state molecular dynamics for the investigation of the fluorescence quenching mechanism in 3 prototypical aggregation-induced emission systems.

Synthesis, Photophysical Study, and Biological Application Analysis of Complex Borondipyrromethene Dyes

A series of complex boronic acids were prepared through multicomponent reactions (MCRs). Both Passerini and Ugi MCRs were carried out in which one component was an arylboronic acid. The resulting highly functionalized boronic acids participated efficiently in the Liebeskind-Srogl cross-coupling reaction with meso-methylthioBODIPY derivatives to yield complex borondipyrromethene (BODIPY) dyes in good yields. The joined spectroscopic and computational study points out the deep impact of the arylated chromophoric position on the photophysical signatures. Thus, unconstrained aryls grafted at the meso position did not sway the spectral band positions but switched on new nonradiative relaxation channels, whereas additional arylation at the opposite α-pyrrolic position softened such fluorescence quenching and shifted the emission to the red-edge of the visible spectrum. The conducted biological analysis revealed that peripheral blood mononuclear cells incubated with these new compounds showed reduced cytotoxicity and retained their normal activities. Additionally, the dyes remained stable inside the cells after 24 h of incubation. These results demonstrated that these novel fluorescent probes based on BODIPY can be applied for cell imaging and analysis, expanding their applications.

Analyzing Fluxional Molecules Using DORI

The Density Overlap Region Indicator (DORI) is a density-based scalar field that reveals covalent bonding patterns and noncovalent interactions in the same value range. This work goes beyond the traditional static quantum chemistry use of scalar fields and illustrates the suitability of DORI for analyzing geometrical and electronic signatures in highly fluxional molecular systems. Examples include a dithiocyclophane, which possesses multiple local minima with differing extents of π-stacking interactions and a temperature dependent rotation of a molecular rotor, where the descriptor is employed to capture fingerprints of CH-π and π-π interactions. Finally, DORI serves to examine the fluctuating π-conjugation pathway of a photochromic torsional switch (PTS). Attention is also placed on postprocessing the large amount of generated data and juxtaposing DORI with a data-driven low-dimensional representation of the structural landscape.