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).

Cyclotriphosphazene: A Versatile Building Block for Diverse Functional Materials

Cyclotriphosphazene (CP) is a cyclic inorganic compound with the chemical formula N3P3. This unique molecule consists of a six-membered ring composed of alternating nitrogen and phosphorus atoms, each bonded to two chlorine atoms. CP exhibits remarkable versatility and significance in the realm of materials chemistry due to its easy functionalization via facile nucleophilic substitution reactions in mild conditions as well as intriguing properties of resultant final CP-based molecules or polymers. CP has been served as an important building block for numerous functional materials. This review provides a general and broad overview of the synthesis of CP-based small molecules through nucleophilic substitution of hexachlorocyclotriphosphazene (HCCP), and their applications, including flame retardants, liquid crystals (LC), chemosensors, electronics, biomedical materials, and lubricants, have been summarized and discussed. It would be expected that this review would offer a timely summary of various CP-based materials and hence give an insight into further exploration of CP-based molecules in the future.

Mechanistic Insight into the Thermal "Blueing" of Cyanine Dyes

In recent work to develop cyanine dyes with especially large Stokes shifts, we encountered a "blueing" reaction, in which the heptamethine cyanine dye Cy7 (IUPAC: 1,3,3-trimethyl-2-((1E,3E,5E)-7-((E)-1,3,3-trimethylindolin-2-ylidene)hepta-1,3,5-trien-1-yl)-3H-indol-1-ium) undergoes shortening in two-carbon steps to form the pentamethine (Cy5) and trimethine (Cy3) analogs. Each step blue-shifts the resulting absorbance wavelength by ca. 100 nm. Though photochemical and oxidative chain-shortening reactions had been noted previously, it is simple heating alone or with amine bases that effects this unexpected net C2H2 excision. Explicit acetylene loss would be too endothermic to merit consideration. Our mechanistic studies using 2H labeling, mass spectrometric and NMR spectroscopic analyses, and quantum chemical modeling point instead to electrocyclic closure and aromatization of the heptamethine chain in Cy7 forming Fischer's base FB (1,3,3-trimethyl-2-methyleneindoline), a reactive carbon nucleophile that initiates chain shortening of the cyanine dyes by attack on their polymethine backbones. The byproduct is the cationic indolium species TMP (IUPAC: 1,3,3 trimethyl-2-phenyl indolium).

Synthesis and Optoelectronic Properties of Threaded BODIPYs

We report on the synthesis of two new threaded BODIPYs 5 and 6 in good yields using boron as a gathering atom and a macrocycle with a 2,2'-biphenol unit. In addition to usual techniques, they were characterized by X-ray crystallography. Their electrochemical and optical properties were investigated. In particular, both compounds are highly emissive with photoluminescence quantum yields of 54 and 81 % respectively. In addition, they both show a high photostability.

BODIPY-based photocages: rational design and their biomedical application

Photocages, also known as photoactivated protective groups (PPGs), have been utilized to achieve controlled release of target molecules in a non-invasive and spatiotemporal manner. In the past decade, BODIPY fluorophores, a well-established class of fluorescent dyes, have emerged as a novel type of photoactivated protective group capable of efficiently releasing cargo species upon irradiation. This is due to their exceptional properties, including high molar absorption coefficients, resistance to photochemical and thermal degradation, multiple modification sites, favorable uncaging quantum yields, and highly adjustable spectral properties. Compared to traditional photocages that mainly absorb UV light, BODIPY-based photocages that absorb visible/near-infrared (Vis/NIR) light offer advantages such as deeper tissue penetration and reduced bio-autofluorescence, making them highly suitable for various biomedical applications. Consequently, different types of photoactivated protective groups based on the BODIPY skeleton have been established. This highlight provides a comprehensive overview of the strategies employed to construct BODIPY photocages by substituting leaving groups at different positions within the BODIPY fluorophore, including the meso-methyl position, boron position, 2,6-position, and 3,5-position. Furthermore, the application of these BODIPY photocages in biomedical fields, such as fluorescence imaging and controlled release of active species, is discussed.

Leveraging a Phage-Encoded Noncanonical Amino Acid: A Novel Pathway to Potent and Selective Epigenetic Reader Protein Inhibitors

Epigenetic reader proteins interpret histone epigenetic marks to regulate gene expression. Given their vital roles and the link between their dysfunction and various diseases, these proteins present compelling targets for therapeutic interventions. Nevertheless, designing selective inhibitors for these proteins poses significant challenges, primarily due to their unique properties such as shallow binding sites and similarities with homologous proteins. To overcome these challenges, we propose an innovative strategy that uses phage display with a genetically encoded noncanonical amino acid (ncAA) containing an epigenetic mark. This ncAA guides binding to the reader protein's active site, allowing the identification of peptide inhibitors with enhanced affinity and selectivity. In this study, we demonstrate this novel approach's effectiveness by identifying potent inhibitors for the ENL YEATS domain that plays a critical role in leukemogenesis. Our strategy involved genetically incorporating Nε-butyryl-l-lysine (BuK), known for its binding to ENL YEATS, into a phage display library for enriching the pool of potent inhibitors. One resultant hit was further optimized by substituting BuK with other pharmacophores to exploit a unique π-π-π stacking interaction with ENL YEATS. This led to the creation of selective ENL YEATS inhibitors with a KD value of 2.0 nM and a selectivity 28 times higher for ENL YEATS than its close homologue AF9 YEATS. One such inhibitor, tENL-S1f, demonstrated robust cellular target engagement and on-target effects to inhibit leukemia cell growth and suppress the expression of ENL target genes. As a pioneering study, this work opens up extensive avenues for the development of potent and selective peptidyl inhibitors for a broad spectrum of epigenetic reader proteins.

Threading a Linear Molecule Through a Macrocycle Thanks to Boron: Optical Properties of the Threaded Species and Synthesis of a Rotaxane

Two BODIPYs and two boron β-diketonates were threaded through a macrocycle bearing a 2,2'-biphenol unit, showing thus the ability of boron to act as a gathering atom. The new threaded species were characterized by 1D and 2D NMR spectroscopy as well as by X-ray crystallography for one of them and their properties rationalized with quantum chemistry to unravel the vibronic contributions. The BODIPYs exhibited interesting fluorescence features with quantum yields up to 91 % and enhanced photostability compared to their non-threaded homologues. A rotaxane was synthesized using this threading strategy after stoppering and removing the boron with potassium hydroxide.

Design, Synthesis, and Characterization of Organometallic BODIPY-Ru(II) Dyads: Redox and Photophysical Properties with Singlet Oxygen Generation Capability†

A series of Ru(II)-acetylide complexes (Ru1, Ru2, and Ru1m) with alkynyl-functionalized borondipyrromethene (BODIPY) conjugates were designed by varying the position of the linker that connects the BODIPY unit to the Ru(II) metal center through acetylide linkage at either the 2-(Ru1) and 2,6-(Ru2) or the meso-phenyl (Ru1m) position of the BODIPY scaffold. The Ru(II) organometallic complexes were characterized by various spectroscopic methods, including nuclear magnetic resonance (NMR) spectroscopy, infrared (IR) spectroscopy, CHN, and high-resolution mass spectrometry (HRMS) analyses. The Ru(II)-BODIPY conjugates exhibit fascinating electrochemical and photophysical properties. All BODIPY-Ru(II) complexes exhibit strong absorption (εmax = 29,000-72,000 M-1 cm-1) in the visible region (λmax = 502-709 nm). Fluorescence is almost quenched for Ru1 and Ru2, whereas Ru1m shows the residual fluorescence of the corresponding BODIPY core at 517 nm. The application of the BODIPY-Ru(II) dyads as nonporphyrin-based triplet photosensitizers was explored by a method involving the singlet oxygen (1O2)-mediated photo-oxidation of diphenylisobenzofuran. Effective π-conjugation between the BODIPY chromophore and Ru(II) center in the case of Ru1 and Ru2 was found to be necessary to improve intersystem crossing (ISC) and hence the 1O2-sensitizing ability. In addition, electrochemical studies indicate electronic interplay between the metal center and the redox-active BODIPY in the BODIPY-Ru(II) dyads.

Easy access to strongly fluorescent higher homologues of BODIPY

We present the easy and high yield synthesis of several group 13 MesDPM compounds (Al-In) with alkyl substituents at the metal atom. All these compounds were fully characterized using techniques including X-ray diffraction analysis and photoluminescence measurements. It shows that for aluminium and gallium pronounced green fluorescence is observed, which is absent for indium. DFT calculations confirm that the first electronic transition corresponds to a ligand-based π-π* transition.

Access to isoindole-derived BODIPYs by an aminopalladation cascade

Here, we present a new route to dyes of the BODIPY family. We first built up a N-Boc-protected dipyrromethene scaffold via an aminopalladation cascade. Subsequentially, the pyrrole moiety was deprotected and the BF2 unit inserted. Depending on the terminating reaction, BODIPYs with either aryl or alkynyl moieties were accessible.

Red-Colored Circularly Polarized Luminescence from a Benzo-Fused BODIPY-BINOL Complex

Red emission with sharp bandwidth and high quantum yield is a desired characteristic for organic chromophores in optoelectronic, spintronic, and biomedical applications. Here, we observe circularly polarized luminescence (CPL) with these characteristics from a benzo-fused BODIPY-BINOL complex (1). Using time-resolved optical spectroscopy, electrochemistry, and density functional theory calculations, we showed that the emissive excited state of 1 does not have a charge-transfer (CT) character, unlike that of the regular BODIPY counterpart (2). The rigidity and the lack of CT character make this class of molecules an appealing platform for CPL-active molecules in the red spectral region, with ample room for improvement in the dissymmetry factor and brightness.

ROS generating BODIPY loaded nanoparticles for photodynamic eradication of biofilms

Bacterial biofilms can pose a serious health risk to humans and are less susceptible to antibiotics and disinfection than planktonic bacteria. Here, a novel method for biofilm eradication based on antimicrobial photodynamic therapy utilizing a nanoparticle in conjunction with a BODIPY derivative as photosensitizer was developed. Reactive oxygen species are generated upon illumination with visible light and lead to a strong, controllable and persistent eradication of both planktonic bacteria and biofilms. One of the biggest challenges in biofilm eradication is the penetration of the antimicrobial agent into the biofilm and its matrix. A biocompatible hydrophilic nanoparticle was utilized as a delivery system for the hydrophobic BODIPY dye and enabled its accumulation within the biofilm. This key feature of delivering the antimicrobial agent to the site of action where it is activated resulted in effective eradication of all tested biofilms. Here, 3 bacterial species that commonly form clinically relevant pathogenic biofilms were selected: Escherichia coli, Staphylococcus aureus and Streptococcus mutans. The development of this antimicrobial photodynamic therapy tool for biofilm eradication takes a promising step towards new methods for the much needed treatment of pathogenic biofilms.

Halogen Bonding in Brominated BODIPY Crystals: a Crystallographic and Computational Study

The study of halogen bonds (XBs) has been a subject of great interest in recent years due to its clear application in catalysis, liquid crystals, and crystal engineering. In this study, we analyzed the intermolecular interactions, in particular halogen bonds in BODIPYs with an increasing number of bromine atoms. The computational study included analyses through three different methods: the first approach of close contacts provided by mercury, then the expanded approach of the electron density partition of the molecules in the crystals provided by the analysis of Hirshfeld surfaces, and finally, the approach of the Quantum Theory of Atoms in Molecules (QT-AIM) to characterize the non-covalent interactions through finding electron density critical points between atoms and between neighboring molecules. The use of different computational methods allowed to gain insight into the interactions directing the crystal packing as the number of bromine atoms increased in the BODIPY moiety. Monocoordinated and bifurcated halogen bonds involving halide/halide were found. The penta-brominated BODIPY showed four-center cyclic nodes where each node is linked via XBs. This kind of motif can be useful in supramolecular chemistry and self-assembly.

π-Extended Pyrazinepyrene-Fused Zinc Phthalocyanines: Synthesis and Excited-State Charge Separation Involving Coordinated C60

A series of pyrazinepyrene-fused zinc phthalocyanines (ZnPc-Pyr_n) have been newly synthesized by reacting quinoxaline and the corresponding diamino-functionalized phthalocyanines as a new class of π-extended phthalocyanine systems. Bathochromically shifted absorption as a function of the number of pyrazinepyrene entities due to extended π-conjugation and quenched fluorescence due to the presence of fused pyrazinepyrene were witnessed. The electronic structures of these phthalocyanines were probed by systematic computational and electrochemical studies, while the excited-state properties were examined by pump-probe spectroscopies operating at the femto- and nanosecond time scales. Similar to the excited singlet lifetimes, the excited triplet states also revealed diminished lifetimes with an increased number of pyrazinepyrene entities. Further, the coordinatively unsaturated zinc in these molecules was coordinated with phenyl imidazole-functionalized fullerene, ImC₆₀, to form a new series of donor-acceptor conjugates. Upon full characterization of these conjugates, the occurrence of excited-state charge separation was established by transient pump-probe spectroscopy, covering wide temporal and spatial regions. The lifetime of the final charge-separated states was ∼2 ns and decreased with an increase in the number of fused pyrazinepyrene units.

In house synthesized novel distyryl-BODIPY dye and polymer assembly as deep-red emitting probe for protamine detection

In this contribution, we designed and synthesized a deep-red emitting distyryl-BODIPY dye (dye 3) which is non-fluorescent in aqueous solution due to the formation of non-emissive aggregates. However, in presence of an amphiphilic polymer (polystyrene sulfonate, PSS), the aggregated dye molecules de-aggregate and form dye 3-PSS complex, which significantly modulates the optical features of the bound dye. Interestingly, the dye 3-PSS complex shows turn-on fluorescence response in deep-red region in presence of protamine (Pr) due to the formation of dye 3-PSS-Pr ternary complex. Such enhancement follows a linear trend in the dynamic range of 0-8.75 μM of Pr which has been utilized to determine Pr with limit of detection (LOD) of 15.04(±0.5) nM in phosphate buffer. Furthermore, excellent selectivity of the dye 3-PSS system towards Pr allows us to determine Pr even in complex biological matrix like 1% human serum. Thus, dye 3-PSS system can be applied as a very effective tool for the detection and quantification of Pr in deep-red region, overcoming several limitations encountered with the probes in the shorter wavelength region. This is the first report on BODIPY dye based supramolecular assembly for sensing and quantification of protamine.

Cost-Effective Simulations of Vibrationally-Resolved Absorption Spectra of Fluorophores with Machine-Learning-Based Inhomogeneous Broadening

The results of electronic and vibrational structure simulations are an invaluable support for interpreting experimental absorption/emission spectra, which stimulates the development of reliable and cost-effective computational protocols. In this work, we contribute to these efforts and propose an efficient first-principle protocol for simulating vibrationally-resolved absorption spectra, including nonempirical estimations of the inhomogeneous broadening. To this end, we analyze three key aspects: (i) a metric-based selection of density functional approximation (DFA) so to benefit from the computational efficiency of time-dependent density function theory (TD-DFT) while safeguarding the accuracy of the vibrationally-resolved spectra, (ii) an assessment of two vibrational structure schemes (vertical gradient and adiabatic Hessian) to compute the Franck-Condon factors, and (iii) the use of machine learning to speed up nonempirical estimations of the inhomogeneous broadening. In more detail, we predict the absorption band shapes for a set of 20 medium-sized fluorescent dyes, focusing on the bright ππ^★ S₀ → S₁ transition and using experimental results as references. We demonstrate that, for the studied 20-dye set which includes structures with large structural variability, the preselection of DFAs based on an easily accessible metric ensures accurate band shapes with respect to the reference approach and that range-separated functionals show the best performance when combined with the vertical gradient model. As far as band widths are concerned, we propose a new machine-learning-based approach for determining the inhomogeneous broadening induced by the solvent microenvironment. This approach is shown to be very robust offering inhomogeneous broadenings with errors as small as 2 cm^-1 with respect to genuine electronic-structure calculations, with a total CPU time reduced by 98%.

Photoactivatable BODIPYs for Live-Cell PALM

Photoactivated localization microscopy (PALM) relies on fluorescence photoactivation and single-molecule localization to overcome optical diffraction and reconstruct images of biological samples with spatial resolution at the nanoscale. The implementation of this subdiffraction imaging method, however, requires fluorescent probes with photochemical and photophysical properties specifically engineered to enable the localization of single photoactivated molecules with nanometer precision. The synthetic versatility and outstanding photophysical properties of the borondipyrromethene (BODIPY) chromophore are ideally suited to satisfy these stringent requirements. Specifically, synthetic manipulations of the BODIPY scaffold can be invoked to install photolabile functional groups and photoactivate fluorescence under photochemical control. Additionally, targeting ligands can be incorporated in the resulting photoactivatable fluorophores (PAFs) to label selected subcellular components in live cells. Indeed, photoactivatable BODIPYs have already allowed the sub-diffraction imaging of diverse cellular substructures in live cells using PALM and can evolve into invaluable analytical probes for bioimaging applications.

Stability of Dibromo-Dipyrromethene Complexes Coordinated with B, Zn, and Cd in Solutions of Various Acidities

The spectral luminescent properties of dipyrromethenates halogenated with bromine on both ends of the long axis and coordinated using boron fluoride, zinc, or cadmium in neutral ethanol and acidified with hydrochloric acid solutions were studied. The constants of the acid-base equilibrium of the complexes in the proton-donor solvents in the ground and excited states was determined. The mechanisms of complex protonation were discussed, depending on the structure of the compounds. The electronic structures of the neutral and protonated compounds were modeled and analyzed based on the quantum-chemical method. The structures and spectral-luminescence properties were calculated using the SMD model of ethanol solvent using the TD-DFT theory with the B3LYP functional and the composite def2-SVP/def2-TZVP/def2-TZVPP_ECP basis sets, depending on the atomic number of the elements.

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.

Structure and Conformation of Novel BODIPY Ugi Adducts

Two novel BODIPY-Ugi (boron dipyrromethene) adducts exhibit peculiar room temperature (T=20 °C) H-1 NMR spectra in that several protons located at the aromatic aniline-type ring are lost in the baseline. This observation revealed the existence of a dynamic conformational process where rotation around the C-N bond is hindered. Variable-temperature H-1 and C-13 NMR spectroscopic analysis confirmed this conclusion; that is, low-temperature spectra show distinct signals for all four aromatic protons below coalescence, whereas average signals are recorded above coalescence (T=+120 °C). Particularly interesting was the rather large difference in chemical shifts for the ortho protons below coalescence, Δδ=1.45 ppm, which was explained based on DFT computational analysis. Indeed, the calculated lowest-energy gas-phase conformation of the BODIPY Ugi adducts locates one half of the aniline-type ring in the shielding anisotropic cone of the bridge phenyl ring in the BODIPY segment. This is in contrast to the solid-state conformation established by X-ray diffraction analysis that shows a nearly parallel arrangement of the aromatic rings, probably induced by crystal packing forces.

BODIPYs in PDT: A Journey through the Most Interesting Molecules Produced in the Last 10 Years

Over the past 30 years, photodynamic therapy (PDT) has shown great development. In the clinical setting the few approved molecules belong almost exclusively to the porphyrin family; but in the scientific field, in recent years many researchers have been interested in other families of photosensitizers, among which BODIPY has shown particular interest. BODIPY is the acronym for 4,4-difluoro-4-bora-3a, 4a-diaza-s-indacene, and is a family of molecules well-known for their properties in the field of imaging. In order for these molecules to be used in PDT, a structural modification is necessary which involves the introduction of heavy atoms, such as bromine and iodine, in the beta positions of the pyrrole ring; this change favors the intersystem crossing, and increases the ¹O₂ yield. This mini review focused on a series of structural changes made to BODIPYs to further increase ¹O₂ production and bioavailability by improving cell targeting or photoactivity efficiency.

Spanning BODIPY fluorescence with self-assembled micellar clusters

BODIPY dyes possess favorable optical properties for a variety of applications including in vivo and in vitro diagnostics. However, their utilization might be limited by their water insolubility and incompatibility with chemical modifications, resulting in low aggregation stability. Here, we outline the route for addressing this issue. We have demonstrated two approaches, based on dye entrapment in micellar coordination clusters (MCCs); this provides a general solution for water solubility as well as aggregation stability of the seven BODIPY derivatives. These derivatives have various bulky aromatic substituents in the 2,3,5,6- and meso-positions and can rotate relative to a dipyrrin core, which also provides molecular rotor properties. The molecular structural features and the presence of aromatic groups allows BODIPY dyes to be used as "supporting molecules", thus promoting micelle-micelle interaction and micellar network stabilization. In the second approach, self-micellization, following BODIPY use, leads to MCC formation without the use of any mediators, including chelators and/or metal ions. In both approaches, BODIPY exhibits an excellent optical response, at a concentration beyond its solubilization limit in aqueous media and without undesired crystallization. The suggested approaches represent systems used to encapsulate BODIPY in a capsule-based surfactant environment, enabling one to track the aggregation of BODIPY; these approaches represent an alternative system to study and apply BODIPY's molecular rotor properties. The stabilized compounds, i.e., the BODIPY-loaded MCCs, provide a unique feature of permeability to hydrophilic ligand-switching proteins such as BSA; they exhibit a bright "turn-on" fluorescence signal within the clusters via macromolecular complexation, thus expanding the possibilities of water-soluble BODIPY-loaded MCCs utilization for functional indicators.

A porphyrin(2.1.2.1) bis-boron complex as a deep-red AIE luminophore induced by intermolecular F-π interaction

Mono-/diboron complexes with saddle-shaped molecular conformations were synthesized from porphyrins(2.1.2.1). The boron complexes have unique structure-dependent photophysical properties: (a) monoboron complexes 2a and 2b are not emissive in solution and the solid state, (b) diboron complex 3a shows red emission in toluene, and (c) diboron complex 3b shows aggregation-induced emission (AIE) in the deep-red region due to intermolecular secondary interactions (F-π). This is the first case of a boron porphyrinoid complex that shows AIE emission in the deep-red region in decades.

Near-Infrared Fluorescent Probes as Imaging and Theranostic Modalities for Amyloid-Beta and Tau Aggregates in Alzheimer's Disease

A person suspected of having Alzheimer's disease (AD) is clinically diagnosed for the presence of principal biomarkers, especially misfolded amyloid-beta (Aβ) and tau proteins in the brain regions. Existing radiotracer diagnostic tools, such as PET imaging, are expensive and have limited availability for primary patient screening and pre-clinical animal studies. To change the status quo, small-molecular near-infrared (NIR) probes have been rapidly developed, which may serve as an inexpensive, handy imaging tool to comprehend the dynamics of pathogenic progression in AD and assess therapeutic efficacy in vivo. This Perspective summarizes the biochemistry of Aβ and tau proteins and then focuses on structurally diverse NIR probes with coverages of their spectroscopic properties, binding affinity toward Aβ and tau species, and theranostic effectiveness. With the summarized information and perspective discussions, we hope that this paper may serve as a guiding tool for designing novel in vivo imaging fluoroprobes with theranostic capabilities in the future.

Investigations on the Synthesis, Reactivity, and Properties of Perfluoro-α-Benzo-Fused BOPHY Fluorophores

The synthesis and reactivity of 3,8-dibromo-dodecafluoro-benzo-fused BOPHY 2 are reported, via S_N Ar with O-, N- S- and C-nucleophiles, and in Pd(0)-catalyzed cross-coupling reactions (Suzuki and Stille). The resulting perfluoro-BOPHY derivatives were investigated for their reactivity in the presence of various nucleophiles. BOPHY 3 displays reversible color change and fluorescence quenching in the presence of bases (Et₃ N, DBU), whereas BOPHY 7 reacts preferentially at the α-pyrrolic positions, and BOPHY 8 undergoes regioselective fluorine substitution in the presence of thiols. The structural and electronic features of the fluorinated BOPHYs were studied by TD-DFT computations. In addition, their spectroscopic and cellular properties were investigated; BOPHY 10 shows the most red-shifted absorption/emission (λ_max 659/699 nm) and 7 the highest fluorescence (Φ_f =0.95), while all compounds studied showed low cytotoxicity toward human HEp2 cells and were efficiently internalized.

Substitution at boron in BODIPYs

Recent synthetic achievements have led to 4,4-disubstituted-4-bora-3a,4a-diaza-s-indacenes (BODIPYs) with varying substituents at the meso, pyrrolic and/or boron sites, with each influencing photophysical properties and utility. This Feature article gives an overview of chemistry at the boron atom in BODIPYs, highlighting our contributions that evolved from synthetic curiosities and now offer this dipyrrolic skeleton potential across a wider range of applications. We first summarise preparative routes to BODIPYs through complexation of boron with the dipyrrinato ligand. The role of boron in protecting dipyrrins is then discussed, followed by strategies by which to achieve facile substitution at the boron atom.

Small-molecule ambipolar transistors

Ambipolar transistor properties have been observed in various small-molecule materials. Since a small energy gap is necessary, many types of molecular designs including extended π-skeletons as well as the incorporation of donor and acceptor units have been attempted. In addition to the energy levels, an inert passivation layer is important to observe ambipolar transistor properties. Ambipolar transport has been observed in extraordinary π-electron systems such as antiaromatic compounds, biradicals, radicals, metal complexes, and hydrogen-bonded materials. Several donor/acceptor cocrystals show ambipolar transport as well.

Circularly polarized luminescence from helical N,O-boron-chelated dipyrromethene (BODIPY) derivatives

We report N,O-boron-chelated dipyrromethene derivatives exhibiting circularly polarized luminescence (CPL) in the red/near-infrared region, both in solution and the aggregated state. The CPL is originated from the helical chirality through intramolecular substitution of fluorine by an alkenolic substituent. The self-assembly of the fluorophores significantly enhances the |g_lum| values from 10^-4 to 10^-2.

Light-Harvesting Crystals Formed from BODIPY-Proline Biohybrid Conjugates: Antenna Effects and Excitonic Coupling

A boron dipyrromethene (BODIPY) derivative bearing a cis-proline residue at the meso-position crystallizes in the form of platelets with strong (i.e., Φ_F = 0.34) red fluorescence, but the absorption and emission spectra differ markedly from those for dilute solutions. A key building block for the crystal is a pseudo-dimer where hydrogen bonding aligns the proline groups and separates the terminal chromophores by ca. 25 Å. Comparison with a covalently linked bichromophore suggests that one-dimensional (1D) excitonic coupling between the terminals is too small to perturb the optical properties. However, accretion of the pseudo-dimer forms narrow channels possessing a high density of chromophores. The resultant absorption spectrum exhibits strong excitonic splitting, which can be explained quantitatively using the extended dipole approach and allowing for coupling between ca. 30 BODIPY units. Fluorescence, which decays with a lifetime of 2.2 ns, is assigned to a delocalized and (slightly) super-radiant BODIPY dimer situated at the interface and populated via electronic energy transfer from the interior.

Effect of the Aza-N-Bridge and Push-Pull Moieties: A Comparative Study between BODIPYs and Aza-BODIPYs

In the field of fluorescent dyes, difluoroboron-dipyrromethenes (BODIPY) have a highly respected position. To predict their photophysical properties prior to synthesis and therefore to successfully design molecules specifically for one's needs, a solid structure-function understanding based on experimental observations is vital. This work delivers a photophysical evaluation of BODIPY and aza-BODIPY derivatives equipped with different electron-withdrawing/-donating substituents. Using combinatorial chemistry, pyrroles substituted with electron-donating/-withdrawing substituents were condensed together in two different manners, thus providing two sets of molecules. The only difference between the two sets is the bridging unit providing a so far lacking comparison between BODIPYs and aza-BODIPYs structural homologues. Replacing the meso-methine bridge with an aza-N bridge results in a red-shifted transition and considerably different, temperature-activated, excited-state relaxation pathways. The effect of electron-donating units on the absorption but not emission for BODIPYs was suppressed compared to aza-BODIPYs. This result could be evident in a substitution pattern-dependent Stokes shift. The outlook of this study is a deeper understanding of the structure-optics relationship of the (aza)-BODIPY-dye class, leading to an improvement in the de novo design of tailor-made molecules for future applications.

Synthesis and photophysical properties of 1,7-aroyl BODIPYs: an experimental and theoretical study

The introduction of electron donating groups or electron withdrawing groups into the phenyl ring at the meso position of 1,7-aroyl BODIPY significantly influences the fluorescence quantum yield.

An acid-triggered BODIPY-based photosensitizer for enhanced photodynamic antibacterial efficacy

An acid-triggered photodynamic antibacterial nanoplatform (IBPAAs) was constructed by co-assembly of an acid-triggered photosensitizer BODIPY (I-NBDP) and the POEGMA-b-PDEAEMA block copolymer for enhancing the antibacterial efficacy.

Data-driven modeling of S0 → S1 excitation energy in the BODIPY chemical space: High-throughput computation, quantum machine learning, and inverse design

Derivatives of BODIPY are popular fluorophores due to their synthetic feasibility, structural rigidity, high quantum yield, and tunable spectroscopic properties. While the characteristic absorption maximum of BODIPY is at 2.5 eV, combinations of functional groups and substitution sites can shift the peak position by ±1 eV. Time-dependent long-range corrected hybrid density functional methods can model the lowest excitation energies offering a semi-quantitative precision of ±0.3 eV. Alas, the chemical space of BODIPYs stemming from combinatorial introduction of-even a few dozen-substituents is too large for brute-force high-throughput modeling. To navigate this vast space, we select 77 412 molecules and train a kernel-based quantum machine learning model providing <2% hold-out error. Further reuse of the results presented here to navigate the entire BODIPY universe comprising over 253 giga (253 × 10⁹) molecules is demonstrated by inverse-designing candidates with desired target excitation energies.

Intracellular Localization Studies of the Luminescent Analogue of an Anticancer Ruthenium Iminophosphorane with High Efficacy in a Triple-Negative Breast Cancer Mouse Model

The potential of ruthenium(II) compounds as an alternative to platinum-based clinical anticancer agents has been unveiled after extensive research for over 2 decades. As opposed to cisplatin, ruthenium(II) compounds have distinct mechanisms of action that do not rely solely on interactions with DNA. In a previous report from our group, we described the synthesis, characterization, and biological evaluation of a cationic, water-soluble, organometallic ruthenium(II) iminophosphorane (IM) complex of p-cymene, ([(η6-p-cymene)Ru{(Ph3P═N-CO-2N-C5H4)-κ-N,O}Cl]Cl (1 or Ru-IM), that was found to be highly cytotoxic against a panel of cell lines resistant to cisplatin, including triple-negative breast cancer (TNBC) MDA-MB-231, through canonical or caspase-dependent apoptosis. Studies on a MDA-MB-231 xenograft mice model (after 28 days of treatment) afforded an excellent tumor reduction of 56%, with almost negligible systemic toxicity, and a favored ruthenium tumor accumulation compared to other organs. 1 is known to only interact weakly with DNA, but its intracellular distribution and ultimate targets remain unknown. To gain insight on potential mechanisms for this highly efficacious ruthenium compound, we have developed two luminescent analogues containing the BOPIPY fluorophore (or a modification) in the IM scaffold with the general structure of [(η6-p-cymene)Ru{(BODIPY-Ph2P═N-CO-2-NC5H4)-κ-N,O}Cl]Cl {BODIPY-Ph2P = 8-[(4-diphenylphosphino)phenyl]-4,4-dimethyl-1,3,5,7-tetramethyl-2,6-diethyl-4-bora-3a,4a-diaza-s-indacene (3a) and 4,4-difluoro-8-[4-[[2-[4-(diphenylphosphino)benzamido]ethyl]carbamoyl]phenyl]-1,3,5,7-tetramethyl,2,6-diethyl-4-bora-3a,4a-diaza-s-indacene (3b)}. We report on the synthesis, characterization, lipophilicity, stability, luminescence properties, and cell viability studies in the TNBC cell line MDA-MB-231, nonmalignant breast cells (MCF10a), and lung fibroblasts (IMR-90) of the new compounds. The ruthenium derivative 3b was studied by fluorescence confocal microscopy. These studies point to a preferential accumulation of the compound in the endoplasmic reticulum, mitochondria, and lysosomes. Inductively coupled plasma optical emission spectrometry (ICP-OES) analysis also confirms a greater ruthenium accumulation in the cytoplasmic fraction, including endoplasmic reticulum and lysosomes, and a smaller percentage of accumulation in mitochondria and the nucleus. ICP-OES analysis of the parent compound 1 indicates that it accumulates preferentially in the mitochondria and cytoplasm. Subsequent experiments in 1-treated MDA-MB-231 cells demonstrate significant reactive oxygen species generation.

Syntheses and Investigations of Conformationally Restricted, Linker-Free α-Amino Acid-BODIPYs via Boron Functionalization

A series of α-amino acid-BODIPY derivatives were synthesized using commercially available N-Boc-l-amino acids, via boron functionalization under mild conditions. The mono-linear, mono-spiro, and di-amino acid-BODIPY derivatives were obtained using an excess of basic (histidine, lysine, and arginine), acidic (aspartic acid), polar (tyrosine, serine), and nonpolar (methionine) amino acid residues, in yields that ranged from 37 to 66%. The conformationally restricted mono-spiro- and di-amino acid-BODIPYs display strong absorptions in the visible spectral region with high molar extinction coefficients and significantly enhanced fluorescence quantum yields compared with the parent BF₂-BODIPY. Cellular uptake and cytotoxicity studies using the human HEp2 cell line show that both the presence of an N,O-bidentate spiro-ring and basic amino acids (His and Arg) increase cytotoxicity and enhance cellular uptake. Among the series of BODIPYs tested, the spiro-Arg- and spiro-His-BODIPYs were found to be the most cytotoxic (IC₅₀ ∼ 22 μM), while the spiro-His-BODIPY was the most efficiently internalized, localizing preferentially in the cell lysosomes, ER, and mitochondria.

Benchmarking Density Functional Approximations for Excited-State Properties of Fluorescent Dyes

This study presents an extensive analysis of the predictive power of time-dependent density functional theory in determining the excited-state properties of two groups of important fluorescent dyes, difluoroboranes and hydroxyphenylimidazo[1,2-a]pyridine derivatives. To ensure statistically meaningful results, the data set is comprised of 85 molecules manifesting diverse photophysical properties. The vertical excitation energies and dipole moments (in the electronic ground and excited states) of the aforementioned dyes were determined using the RI-CC2 method (reference) and with 18 density functional approximations (DFA). The set encompasses DFAs with varying amounts of exact exchange energy (EEX): from 0% (e.g., SVWN, BLYP), through a medium (e.g., TPSSh, B3LYP), up to a major contribution of EEX (e.g., BMK, MN15). It also includes range-separated hybrids (CAM-B3LYP, LC-BLYP). Similar error profiles of vertical energy were obtained for both dye groups, although the errors related to hydroxyphenylimidazopiridines are significantly larger. Overall, functionals including 40-55% of EEX (SOGGA11-X, BMK, M06-2X) ensure satisfactory agreement with the reference vertical excitation energies obtained using the RI-CC2 method; however, MN15 significantly outperforms them, providing a mean absolute error of merely 0.04 eV together with a very high correlation coefficient (R2 = 0.98). Within the investigated set of functionals, there is no single functional that would equally accurately determine ground- and excited-state dipole moments of difluoroboranes and hydroxyphenylimidazopiridine derivatives. Depending on the chosen set of dyes, the most accurate μGS predictions were delivered by MN15 incorporating a major EEX contribution (difluoroboranes) and by PBE0 containing a minor EEX fraction (hydroxyphenylimidazopiridines). Reverse trends are observed for μES, i.e., for difluoroboranes the best results were obtained with functionals including a minor fraction of EEX, specifically PBE0, while in the case of hydroxyphenylimidazopiridines, much more accurate predictions were provided by functionals incorporating a major EEX contribution (BMK, MN15).