Tripodal BODIPY-Tagged and Functional Molecular Probes: Synthesis, Computational Investigations and Explorations by Multiphoton Fluorescence Lifetime Imaging Microscopy

A range of novel BODIPY derivatives with a tripodal aromatic core was synthesized and characterized spectroscopically. These new fluorophores showed promising features as probes for in vitro assays in live cells and offer strategic routes for further functionalization towards hybrid nanomaterials. Incorporation of biotin tags facilitated proof-of-concept access to targeted bioconjugates as molecular probes. Computational explorations using DFT and TD-DFT calculations identified the most stable tripodal linker conformations and predicted their absorption and emission behavior. The uptake and speciation of these molecules in living prostate cancer cells was imaged by single- and two-photon excitation techniques coupled with two-photon fluorescence lifetime imaging (2P FLIM).

Tunable optical properties of isoreticular UiO-67 MOFs for photocatalysis: a theoretical study

A theoretical study of the reported photocatalytic systems based on Zr-based MOF (UiO-67) with biphenyl-4,4'-dicarboxylic acid (bpdc) and 2,2'-bipyridine-5,5'-dicarboxylic acid (bpydc) as linkers was performed. Quantum chemical calculations were carried out to understand the optical properties of the materials and to facilitate the rational design of new UiO-67 derivatives with potentially improved features as photocatalysts under ambient conditions. Hence, the effect of the structural modifications on the optical properties was studied considering different designs based on the nature of the linkers: in 1 only the bpdc linker was considered, or the mixture 1 : 1 between bpdc and bpydc linkers (labeled as 1A). Also, substituents R, -NH2, and -SH, were included in the 1A MOF only over the bpdc linker (labeled as 1A-bpdc-R) and on both bpdc and bpydc linkers (labeled as 1A-R). Thus a family of six isoreticular UiO-67 derivatives was theoretically characterized using Density Functional Theory (DFT) calculations on the ground singlet (S0) and first excited states (singlet and triplet) using Time-Dependent Density Functional Theory (TD-DFT), multiconfigurational post-Hartree-Fock method via Complete Active Space Self-Consistent Field (CASSCF). In addition, the use of periodic DFT calculations suggest that the energy transfer (ET) channel between bpdc and bpydc linkers might generate more luminescence quenching of 1A when compare to 1. Besides, the results suggest that the 1A-R (R: -SH and NH2) can be used under ambient conditions; however, the ET exhibited by 1A, cannot take place in the same magnitude in these systems. These ET can favor the photocatalytic reduction of a potential metal ion, that can coordinate with the bpydc ligand, via LMCT transition. Consequently, the MOF might be photocatalytically active against molecules of interest (such as H2, N2, CO2, among others) with photo-reduced metal ions. These theoretical results serve as a useful tool to guide experimental efforts in the design of new photocatalytic MOF-based systems.

A Practical and Modular Method for Direct C-H Functionalization of the BODIPY Core via Thianthrenium Salts

Direct structural modification of small-molecule fluorophores represents a straightforward and appealing strategy for accessing new fluorescent dyes with desired functionalities. We report herein a general and efficient visible-light-mediated method for the direct C-H functionalization of BODIPY, an important fluorescent chromophore, using readily accessible and bench-stable aryl and alkenylthianthrenium salts. This practical approach operates at room temperature with extraordinary site-selectivity, providing a step-economical means to construct various valuable aryl- and alkenyl-substituted BODIPY dyes. Remarkably, this protocol encompasses a broad substrate scope and excellent functional-group tolerance, and allows for the modular synthesis of sophisticated symmetrical and asymmetrical disubstituted BODIPYs by simply employing different combinations of thianthrenium salts. Moreover, the late-stage BODIPY modification of complex drug molecules further highlights the potential of this novel methodology in the synthesis of fluorophore-drug conjugates.

Solvatochromic Sensitivity of BODIPY Probes: A New Tool for Selecting Fluorophores and Polarity Mapping

This research work is devoted to collecting a high-quality dataset of BODIPYs in a series of 10-30 solvents. In total, 115 individual compounds in 71 solvents are represented by 1698 arrays of the spectral and photophysical properties of the fluorophore. Each dye for a series of solvents is characterized by a calculated value of solvatochromic sensitivity according to a semiempirical approach applied to a series of solvents. The whole dataset is classified into 6 and 24 clusters of solvatochromic sensitivity, from high negative to high positive solvatochromism. The results of the analysis are visualized by the polarity mapping plots depicting, in terms of wavenumbers, the absorption versus emission, stokes shift versus - (absorption maxima + emission maxima), and quantum yield versus stokes shift. An analysis of the clusters combining several dyes in an individual series of solvents shows that dyes of a high solvatochromic sensitivity demonstrate regular behaviour of the corresponding plots suitable for polarity and viscosity mapping. The fluorophores collected in this study represent a high quality dataset of pattern dyes for analytical and bioanalytical applications. The developed tools could be applied for the analysis of the applicability domain of the fluorescent sensors.

A multicomponent reaction platform towards multimodal near-infrared BODIPY dyes for STED and fluorescence lifetime imaging

We report a platform combining multicomponent reaction synthesis and automated cell-based screening to develop biocompatible NIR-BODIPY fluorophores. From a library of over 60 fluorophores, we optimised compound NIRBD-62c as a multimodal probe with suitable properties for STED super-resolution and fluorescence lifetime imaging. Furthermore, we employed NIRBD-62c for imaging trafficking inside cells and to examine how pharmacological inhibitors can alter the vesicular traffic between intracellular compartments and the plasma membrane.

Microwave-assisted direct synthesis of BODIPY dyes and derivatives

A microwave-assisted one-pot synthesis of BODIPY dyes from pyrroles and acyl chlorides is reported. This protocol features short reaction times, low temperatures, minimum amount of solvent, scalability, versatility, and good yields of the products. These simple, efficient and sustainable conditions can be also applied to the synthesis of derivatives such as BOPHY, BOAHY and BOPAHY.

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.

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.

Quantum Chemical Characterization and Design of Quantum Dots for Sensing Applications

The ability to tune the optoelectronic properties of quantum dots (QDs) makes them ideally suited for the use as fluorescence sensing probes. The vast structural diversity in terms of the composition and size of QDs can make designing a QD for a specific sensing application a challenging process. Quantum chemical calculations have the potential to aid this process through the characterization of the properties of QDs, leading to their in silico design. This is explored in the context of QDs for the fluorescence sensing of dopamine based upon density functional theory and time-dependent density functional theory (TDDFT) calculations. The excited states of hydrogenated carbon, silicon, and germanium QDs are characterized through TDDFT calculations. Analysis of the molecular orbital diagrams for the isolated molecules and calculations of the excited states of the dopamine-functionalized quantum dots establish the possibility of a photoinduced electron-transfer process by determining the relative energies of the electronic states formed from a local excitation on the QD and the lowest QD → dopamine electron-transfer state. The results suggest that the Si₁₆₅H₁₀₀ and Ge₈₄H₆₄ QDs have the potential to act as fluorescent markers that could distinguish between the oxidized and reduced forms of dopamine, where the fluorescence would be quenched for the oxidized form. The work contributes to a better understanding of the optical and electronic behavior of QD-based sensors and illustrates how quantum chemical calculations can be used to inform the design of QDs for specific fluorescent sensing applications.

Computational development of a phase-sensitive membrane raft probe

Derivatives of the widely used 1,6-diphenyl-1,3,5-hexatriene molecular probe have been considered using a multiscale approach involving spin-flip time-dependent density functional theory, classical molecular dynamics and hybrid quantum mechanics/molecular mechanics. We identify a potential probe of membrane phase (i.e. to preferentially detect liquid-ordered regions of lipid bilayers), which exhibits restricted access to a conical intersection in the liquid-ordered phase but is freely accessible in less ordered molecular environments. The characteristics of this probe also mark it as a candidate for an aggregation induced emission fluorophore.

Rationalizing the effect of benzo-fusion at [a] and [b] positions of BODIPY on fluorescence yields

The origin of the large difference of fluorescence yields between benzo[a] and benzo[b] BODIPY derivatives was investigated. The benzo[a]-BODIPY chromophore shows high fluorescence yields while the totally quenched fluorescence of benzo[b]-BODIPYs is observed. Quantum calculations indicated that larger spin-orbit coupling (SOC) and smaller singlet-triplet energy gaps result in non-fluorescence for benzo[b]-BODIPY. Benzo[b]-fusion makes a partial contribution to the HOMO but a full contribution to the HOMO-1, and thus the S₁→ S₀ and T₂→ S₀ transitions, involved in HOMO-LUMO and HOMO-1-LUMO, have different characteristics, which leads to spin flipping for intersystem crossing (ISC) and increases the SOC to 1.70 cm^-1. However, benzo[a] contributes to HOMO and HOMO-1 equally, and minimizes the SOC between S₁ and T₂, leading to slow ISC from S₁, thus possessing strong fluorescence. These results are useful for the rational design of heavy-atom-free triplet organic chromophores.

A Convenient Approach to meso-Uracil–4,4-Difluoro-4-bora-3a, 4a-diaza-s-indacene Derivatives

An effective and convenient protocol for the synthesis of 1-substituted uracil-6-carbaldehyde derivatives has been developed. A three-step sequence permits the preparation of uracil-6-carbaldehydes with various substituents at the N-1 in large quantities by using low-cost precursors. The aldehyde-functionalized uracils served as useful precursors for the preparation of meso-(1-substituted 6-uracil)-derivatives of 4,4-difluoro-4-bora-3a,4a-diaza-s-indacene (BODIPY). In this way, regioselectively functionalized BODIPYs with a direct connection to a nucleobase were prepared in yields of 30–45%. MALDI-TOF mass spectrometry, NMR, UV/vis absorption, and steady-state and time-­resolved fluorescence spectroscopies were used to characterize the structures and the spectroscopic/photophysical properties of the resultant dyes.

New insights into quantifying the solvatochromism of BODIPY based fluorescent probes

A simple semiempiric phenomenological approach is developed for quantifying the solvent effect on the absorption and emission properties of BODIPYs. It is based on a new rule describing the linear relationship between the difference (Stokes shift) and the sum (double Gibbs free energy of electron transfer) for absorption and emission wavenumbers derived from a combination of solvent functions of Liptay theory. This rule is correspondent to changes of dipole moments in the ground and excited states. High reliability and advantages of the developed approach in comparison with traditional methods of the analysis of the solvatochromism based on Dimroth-Reichard and Lippert-Mataga solvent scales are illustrated for selected BODIPYs exhibiting positive, negative, and near-zero solvatochromism.

Aggregation-Induced Emission: From Small Molecules to Polymers-Historical Background, Mechanisms and Photophysics

The enhancement of photoluminescence through formation of molecular aggregates in organic oligomers and conjugated organic polymers is reviewed. A historical contextualization of aggregation-induced emission (AIE) phenomena is presented. This includes the loose bolt or free rotor effect and J-aggregation phenomena, and discusses their characteristic features, including structures and mechanisms. The basis of both effects is examined in key molecules, with a particular emphasis on the AIE effect occurring in conjugated organic polymers with a polythiophene (PT) skeleton with triphenylethylene (TPE) units. Rigidification of the excited state structure is one of the defining conditions required to obtain AIE, and thus, by changing from a flexible ground state to rigid (quinoidal-like) structures, oligo and PTs are among the most promising emerging molecules alongside with the more extensively used TPE derivatives. Molecular structures moving away from the domination of aggregation-caused quenching to AIE are presented. Future perspectives for the rational design of AIEgen structures are discussed.

Chimeric Drug Design with a Noncharged Carrier for Mitochondrial Delivery

Recently, it was proposed that the thiophene ring is capable of promoting mitochondrial accumulation when linked to fluorescent markers. As a noncharged group, thiophene presents several advantages from a synthetic point of view, making it easier to incorporate such a side moiety into different molecules. Herein, we confirm the general applicability of the thiophene group as a mitochondrial carrier for drugs and fluorescent markers based on a new concept of nonprotonable, noncharged transporter. We implemented this concept in a medicinal chemistry application by developing an antitumor, metabolic chimeric drug based on the pyruvate dehydrogenase kinase (PDHK) inhibitor dichloroacetate (DCA). The promising features of the thiophene moiety as a noncharged carrier for targeting mitochondria may represent a starting point for the design of new metabolism-targeting drugs.

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.

Studying the reactivity of alkyl substituted BODIPYs: first enantioselective addition of BODIPY to MBH carbonates

The first enantioselective addition of alkyl BODIPYs to Morita-Baylis-Hillman (MBH) carbonates is reported. This is the first reported enantioselective methodology using the methylene position of BODIPYs as a nucleophile. The reaction is efficiently catalyzed by cinchona alkaloids, achieving high enantioselectivities and total diastereoselectivity. The use of cinchona alkaloid pseudo enantiomers (chinine/cinchonine) allows us to obtain both pairs of enantiomers in similar yields and enantioselectivities, a common issue in this type of reaction. The photophysical study of these dyes (absorption and fluorescence) has been performed in order to determine their parameters and explore future possible application in bioimaging. In addition, electronic circular dichroism (ECD) studies supported by time-dependent density functional theory (TD-DFT) calculations were also performed.

Entropic Mixing Allows Monomeric-Like Absorption in Neat BODIPY Films

Intermolecular interactions play a crucial role in materials chemistry because they govern thin film morphology. The photophysical properties of films of organic dyes are highly sensitive to the local environment, and a considerable effort has therefore been dedicated to engineering the morphology of organic thin films. Solubilizing side chains can successfully spatially separate chromophores, reducing detrimental intermolecular interactions. However, this strategy is also significantly decreasing achievable dye concentration. Here, five BODIPY derivatives containing small alkyl chains in the α-position were synthesized and photophysically characterized. By blending two or more derivatives, the increase in entropy reduces aggregation and therefore produces films with extreme dye concentration and, at the same time almost solution like absorption properties. Such a film was placed inside an optical cavity and the achieved system was demonstrated to reach the strong exciton-photon coupling regime by virtue of the achieved dye concentration and sharp absorption features of the film.

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.

Physicochemical and computational insight of 19F NMR and emission properties of meso-(o-aryl)-BODIPYs

Magnetic differentiation of the fluorine atoms was observed. The trends were explained in terms of their rotational energy barriers, group electronegativity and σ-Hammett.

PyrrolylBODIPYs: Syntheses, Properties, and Application as Environment-Sensitive Fluorescence Probes

Four pyrrole B-ring-functionalized pyrrolylBODIPYs and their B-ring unsubstituted analogues were synthesized from easily accessible starting 5-halo-2-formylpyrroles and were characterized by nuclear magnetic resonance, high-resolution mass spectrometry, X-ray analysis, and optical/electronic properties. In great contrast to the substitution(s) at the other two pyrrolic units, electron-donating substituent(s) at pyrrole B-ring bring significant blue shift of the absorption and emission bands. Cyclic voltammetry and density functional theory calculations indicate that this blue shift may be attributed to the increased highest occupied molecular orbital and the lowest unoccupied molecular orbital energy levels and the overall increase in the energy band gaps. These pyrrolylBODIPYs generally show intense absorption (centered at 570-624 nm) and fluorescence emission (582-654 nm) in nonpolar solvents. A gradual decrease in the fluorescence intensity was observed for these dyes with the increase in solvent dipolar moment, which combines with the red to far-red absorption/emission, rendering these pyrrolylBODIPYs potential applications as environment-sensitive fluorescence probes as demonstrated in this work for bovine serum albumin.

Calculations of BODIPY dyes in the ground and excited states using the M06-2X and PBE0 functionals

A number of fluorescent dyes based on BODIPY (4,4'-difluoro-4-bora-3a,4a-diaza-s-indacene) have been studied theoretically. This paper presents the results of calculations of these BODIPY dyes in their ground and excited states, performed using DFT and TD-DFT methods, respectively. The influences of N,N-dimethylaminobenzyl, ortho-fluorophenol, and methyl substituents as well as the solvent polarity on the positions of the absorption and emission bands of the dyes were analyzed. The computational data obtained in this work were compared to the corresponding experimental data. The trends in the experimental data were found to agree with those shown by the computational data. Differences between the potential curves obtained when using linear-response (LR) and state-specific (SS) approaches for the ground and excited states are also reported. Graphical Abstract The article shows that the trends of the experimental dependencies λabs = f(Δf) and λem = f(Δf) well described by PBE0 (LR approach) and M06-2X (SS approach) calculations, respectively. The influence of substituents on the spectral characteristics of the BODIPY chromophore are analysed.

Exploring the Application of the Negishi Reaction of HaloBODIPYs: Generality, Regioselectivity, and Synthetic Utility in the Development of BODIPY Laser Dyes

The generality of the palladium-catalyzed C-C coupling Negishi reaction when applied to haloBODIPYs is demonstrated on the basis of selected starting BODIPYs, including polyhalogenated and/or asymmetrical systems, and organozinc reagents. This reaction is an interesting synthetic tool in BODIPY chemistry, mainly because it allows a valuable regioselective postfunctionalization of BODIPY chromophores with different functional groups. In this way, functional patterns that are difficult to obtain by other procedures (e.g., asymmetrically functionalized BODIPYs involving halogenated positions) can now be made. The regioselectivity is achieved by controlling the reaction conditions and is based on almost-general reactivity preferences, and the nature of the involved halogens and their positions. This ability is exemplified by the preparation of a series of new BODIPY dyes with unprecedented substitution patterns allowing noticeable lasing properties.

Regioisomeric donor–acceptor–donor triads based on benzodithiophene and BODIPY with distinct optical properties and mobilities

Two regioisomeric donor–acceptor–donor triads composed of benzodithiophene and BODIPY exhibit distinct optical and charge transfer properties, and mobilities of ∼10⁻⁴ cm² V⁻¹ s⁻¹.

Synthesis, structure and properties of thiophene-fused BODIPYs and azaBODIPYs as near-infrared agents

Annulation of thiophene to the BODIPY/aza-BODIPY core showed a significant impact on the spectral properties of the resulting scaffolds.

Effect of the substitution position (2, 3 or 8) on the spectroscopic and photophysical properties of BODIPY dyes with a phenyl, styryl or phenylethynyl group

Understanding the spectroscopic properties of BODIPY dyes for a rational design of tailored fluorescent probes.

A ratiometric, fluorescent BODIPY-based probe for transition and heavy metal ions

A BODIPY-based fluorescent sensor for heavy and transition metal ions has been synthesized and spectroscopically characterized.