Photolabile coumarins with improved efficiency through azetidinyl substitution

The fate of the contact ion pair determines the photochemistry of coumarin-based photocleavable protecting groups

Photocleavable protecting groups (PPGs) enable the precise spatiotemporal control over the release of a payload of interest, in particular a bioactive substance, through light irradiation. A crucial parameter that determines the practical applicability of PPGs is the efficiency of payload release, largely governed by the quantum yield of photolysis (QY). Understanding which parameters determine the QY will prove crucial for engineering improved PPGs and their effective future applications, especially in the emerging field of photopharmacology. The Contact Ion Pair (CIP) has been recognized as an important intermediate in the uncaging process, but the key influence of its fate on the quantum yield has not been explored yet, limiting our ability to design improved PPGs. Here, we demonstrate that the CIP escape mechanism of PPGs is crucial for determining their payload- and solvent-dependent photolysis QY, and illustrate that an intramolecular type of CIP escape is superior over diffusion-dependent CIP escape. Furthermore, we report a strong correlation of the photolysis QY of a range of coumarin PPGs with the DFT-calculated height of all three energy barriers involved in the photolysis reaction, despite the vastly different mechanisms of CIP escape that these PPGs exhibit. Using the insights obtained through our analysis, we were able to predict the photolysis QY of a newly designed PPG with particularly high accuracy. The level of understanding of the factors determining the QY of PPGs presented here will move the ever-expanding field of PPG applications forward and provides a blueprint for the development of PPGs with QYs that are independent of payload-topology and solvent polarity.

Inactivation of Competitive Decay Channels Leads to Enhanced Coumarin Photochemistry

In the development of photolabile protecting groups, it is of high interest to selectively modify photochemical properties with structural changes as simple as possible. In this work, knowledge of fluorophore optimization was adopted and used to design new coumarin‐ based photocages. Photolysis efficiency was selectively modulated by inactivating competitive decay channels, such as twisted intramolecular charge transfer (TICT) or hydrogen‐bonding, and the photolytic release of the neurotransmitter serotonin was demonstrated. Structural modifications inspired by the fluorophore ATTO 390 led to a significant increase in the uncaging cross section that can be further improved by the simple addition of a double bond. Ultrafast transient absorption spectroscopy gave insights into the underlying solvent‐dependent photophysical dynamics. The chromophores presented here are excellently suited as new photocages in the visible wavelength range due to their simple synthesis and their superior photochemical properties.

Synthesis, Optical Characterization in Solution and Solid-State, and DFT Calculations of 3-Acetyl and 3-(1'-(2'-Phenylhydrazono)ethyl)-coumarin-(7)-substituted Derivatives

Intramolecular charge transfer (ICT) effects are responsible for the photoluminescent properties of coumarins. Hence, optical properties with different applications can be obtained by ICT modulation. Herein, four 3-acetyl-2H-chromen-2-ones (1a–d) and their corresponding fluorescent hybrids 3- (phenylhydrazone)-chromen-2-ones (2a–d) were synthesized in 74–65% yields. The UV-Vis data were in the 295–428 nm range. The emission depends on the substituent in position C-7 bearing electron-donating groups. Compounds 1b–d showed good optical properties due to the D-π-A structural arrangement. In compounds 2a–d, there is a quenching effect of fluorescence in solution. However, in the solid, an increase is shown due to an aggregation-induced emission (AIE) effect given by the rotational restraints and stacking in the crystal. Computational calculations of the HOMO-LUMO orbitals indicate high absorbance and emission values of the molecules, and gap values represent the bathochromic effect and the electronic efficiency of the compounds. Compounds 1a–d and 2a–d are good candidates for optical applications, such as OLEDs, organic solar cells, or fluorescence markers.

Rethinking Uncaging: A New Antiaromatic Photocage Driven by a Gain of Resonance Energy

Photoactivatable compounds for example photoswitches or photolabile protecting groups (PPGs, photocages) for spatiotemporal light control, play a crucial role in different areas of research. For each application, parameters such as the absorption spectrum, solubility in the respective media and/or photochemical quantum yields for several competing processes need to be optimized. The design of new photochemical tools therefore remains an important task. In this study, we exploited the concept of excited-state-aromaticity, first described by N. Colin Baird in 1971, to investigate a new class of photocages, based on cyclic, ground-state-antiaromatic systems. Several thio- and nitrogen-functionalized compounds were synthesized, photochemically characterized and further optimized, supported by quantum chemical calculations. After choosing the optimal scaffold, which shows an excellent uncaging quantum yield of 28 %, we achieved a bathochromic shift of over 100 nm, resulting in a robust, well accessible, visible light absorbing, compact new photocage with a clean photoreaction and a high quantum product (ϵ⋅Φ) of 893 M-1  cm-1 at 405 nm.

Quadrupolar Dyes Based on Highly Polarized Coumarins

The fluorescence and other photophysical parameters of highly polarized, quadrupolar bis-coumarins possessing an electron-rich pyrrolo[3,2-b]pyrrole bridging unit are highly dependent on the linking position between both chromophores. Delocalization of the LUMO on the entire π-system results in intense emission and strong two-photon absorption.

Polarized Helical Coumarins: [1,5] Sigmatropic Rearrangement and Excited-State Intramolecular Proton Transfer

The tandem process of phenol addition to a cyclic α,β-unsaturated ester followed by intramolecular transesterification and [1,5] sigmatropic rearrangement affords a series of helical coumarins based upon a previously unknown 3-amino-7-hydroxybenzo[3,4]cyclohepta[1,2-c]chromen-6-one core. These novel polarized coumarins, possessing a β-ketoester moiety, have been employed to synthesize more rigid and helical coumarin–pyrazolones, which display green fluorescence. The enhanced emission of coumarin–pyrazolones in polar solvents depends on the nature of the S₁ state. The coumarin–pyrazolones are predicted to have two vertical states close in energy: a weakly absorbing S₁ (¹LE) followed by a bright S₂ state (¹CT). In polar solvents, the ¹CT can be stabilized below the ¹LE and may become the fluorescent state. Solvatochromism of the fluorescence spectra confirms this theoretical prediction. The presence of an N—H···O=C intramolecular hydrogen bond in these coumarin–pyrazolone hybrids facilitates excited-state intramolecular proton transfer (ESIPT). This process leads to a barrierless conical intersection with the ground electronic state and opens a radiationless deactivation channel effectively competing with fluorescence. Solvent stabilization of the CT state increases the barrier for ESIPT and decreases the efficiency of the nonradiative channel. This results in the observed correlation between solvatochromism and an increase of fluorescence intensity in polar solvents.

Selective Modification for Red-Shifted Excitability: A Small Change in Structure, a Huge Change in Photochemistry

We developed three bathochromic, green-light activatable, photolabile protecting groups based on a nitrodibenzofuran (NDBF) core with D-π-A push-pull structures. Variation of donor substituents (D) at the favored ring position enabled us to observe their impact on the photolysis quantum yields. Comparing our new azetidinyl-NDBF (Az-NDBF) photolabile protecting group with our earlier published DMA-NDBF, we obtained insight into its excitation-specific photochemistry. While the "two-photon-only" cage DMA-NDBF was inert against one-photon excitation (1PE) in the visible spectral range, we were able to efficiently release glutamic acid from azetidinyl-NDBF with irradiation at 420 and 530 nm. Thus, a minimal change (a cyclization adding only one carbon atom) resulted in a drastically changed photochemical behavior, which enables photolysis in the green part of the spectrum.

Visible-to-NIR-Light Activated Release: From Small Molecules to Nanomaterials

Photoactivatable (alternatively, photoremovable, photoreleasable, or photocleavable) protecting groups (PPGs), also known as caged or photocaged compounds, are used to enable non-invasive spatiotemporal photochemical control over the release of species of interest. Recent years have seen the development of PPGs activatable by biologically and chemically benign visible and near-infrared (NIR) light. These long-wavelength-absorbing moieties expand the applicability of this powerful method and its accessibility to non-specialist users. This review comprehensively covers organic and transition metal-containing photoactivatable compounds (complexes) that absorb in the visible- and NIR-range to release various leaving groups and gasotransmitters (carbon monoxide, nitric oxide, and hydrogen sulfide). The text also covers visible- and NIR-light-induced photosensitized release using molecular sensitizers, quantum dots, and upconversion and second-harmonic nanoparticles, as well as release via photodynamic (photooxygenation by singlet oxygen) and photothermal effects. Release from photoactivatable polymers, micelles, vesicles, and photoswitches, along with the related emerging field of photopharmacology, is discussed at the end of the review.

Transformation of COUPY Fluorophores into a Novel Class of Visible-Light-Cleavable Photolabile Protecting Groups

Although photolabile protecting groups (PPGs) have found widespread applications in several fields of chemistry, biology and materials science, there is a growing interest in expanding the photochemical toolbox to overcome some of the limitations of classical caging groups. In this work, the synthesis of a new class of visible-light-sensitive PPGs based on low-molecular weight COUPY fluorophores with several attractive properties, including long-wavelength absorption, is reported. Besides being stable to spontaneous hydrolysis in the dark, COUPY-based PPGs can be efficiently photoactivated with yellow (560 nm) and red light (620 nm) under physiological-like conditions, thereby offering the possibility of unmasking functional groups from COUPY photocages under irradiation conditions in which other PPGs remain stable. Additionally, COUPY photocages exhibit excellent cellular uptake and accumulate selectively in mitochondria, opening the door to the delivery of caged analogues of biologically active compounds into these organelles.

Thiocoumarin Caged Nucleotides: Synthetic Access and Their Photophysical Properties

Photocages have been successfully applied in cellular signaling studies for the controlled release of metabolites with high spatio-temporal resolution. Commonly, coumarin photocages are activated by UV light and the quantum yields of uncaging are relatively low, which can limit their applications in vivo. Here, syntheses, the determination of the photophysical properties, and quantum chemical calculations of 7-diethylamino-4-hydroxymethyl-thiocoumarin (thio-DEACM) and caged adenine nucleotides are reported and compared to the widely used 7-diethylamino-4-hydroxymethyl-coumarin (DEACM) caging group. In this comparison, thio-DEACM stands out as a phosphate cage with improved photophysical properties, such as red-shifted absorption and significantly faster photolysis kinetics.

Regio- and Diastereoselective Synthesis of 2-Arylazetidines: Quantum Chemical Explanation of Baldwin's Rules for the Ring-Formation Reactions of Oxiranes†

A general, scalable two-step regio- and diastereoselective method has been described for the synthesis of versatile alkaloid-type azetidines from simple building blocks with excellent overall yields. In the kinetically controlled reaction, only the formation of the strained four-membered ring can be achieved instead of the thermodynamically favorable five-membered rings under appropriate conditions. Remarkable functional group tolerance has also been demonstrated. In this paper, we give a new scope of Baldwin’s rules by density functional theory (DFT) calculations with an explicit solvent model, confirming the proposed reaction mechanisms and the role of kinetic controls in the stereochemical outcome of the reported transition-metal-free carbon–carbon bond formation reactions.

A Systematic Study of Coumarin-Tetrazine Light-Up Probes for Bioorthogonal Fluorescence Imaging

Fluorescent probes that light-up upon reaction with complementary bioorthogonal reagents are superior tools for no-wash fluorogenic bioimaging applications. In this work, a thorough study is presented on a set of seventeen structurally diverse coumarin-tetrazine probes that produce fluorescent dyes with exceptional turn-on ratios when reacted with trans-cyclooctene (TCO) and bicyclononyne (BCN) dienophiles. In general, formation of the fully aromatic pyridazine-containing dyes resulting from the reaction with BCN was found superior in terms of fluorogenicity. However, evaluation of the probes in cellular imaging experiments revealed that other factors, such as reaction kinetics and good cell permeability, prevail over the fluorescence turn-on properties. The best compound identified in this study showed excellent performance in live cell-labeling experiments and enabled no-wash fluorogenic imaging on a timescale of seconds.

Rational design of small molecule fluorescent probes for biological applications

Fluorescent small molecules are powerful tools for visualizing biological events, embodying an essential facet of chemical biology. Since the discovery of the first organic fluorophore, quinine, in 1845, both synthetic and theoretical efforts have endeavored to "modulate" fluorescent compounds. An advantage of synthetic dyes is the ability to employ modern organic chemistry strategies to tailor chemical structures and thereby rationally tune photophysical properties and functionality of the fluorophore. This review explores general factors affecting fluorophore excitation and emission spectra, molar absorption, Stokes shift, and quantum efficiency; and provides guidelines for chemist to create novel probes. Structure-property relationships concerning the substituents are discussed in detail with examples for several dye families. We also present a survey of functional probes based on PeT, FRET, and environmental or photo-sensitivity, focusing on representative recent work in each category. We believe that a full understanding of dyes with diverse chemical moieties enables the rational design of probes for the precise interrogation of biochemical and biological phenomena.

Visualizing and Manipulating Biological Processes by Using HaloTag and SNAP-Tag Technologies

Visualizing and manipulating the behavior of proteins is crucial to understanding the physiology of the cell. Methods of biorthogonal protein labeling are important tools to attain this goal. In this review, we discuss advances in probe technology specific for self-labeling protein tags, focusing mainly on the application of HaloTag and SNAP-tag systems. We describe the latest developments in small-molecule probes that enable fluorogenic (no wash) imaging and super-resolution fluorescence microscopy. In addition, we cover several methodologies that enable the perturbation or manipulation of protein behavior and function towards the control of biological pathways. Thus, current technical advances in the HaloTag and SNAP-tag systems means that they are becoming powerful tools to enable the visualization and manipulation of biological processes, providing invaluable scientific insights that are difficult to obtain by traditional methodologies. As the multiplex of self-labeling protein tag systems continues to be developed and expanded, the utility of these protein tags will allow researchers to address previously inaccessible questions at the forefront of biology.

Quantitative Design of Bright Fluorophores and AIEgens by the Accurate Prediction of Twisted Intramolecular Charge Transfer (TICT)

Inhibition of TICT can significantly increase the brightness of fluorescent materials. Accurate prediction of TICT is thus critical for the quantitative design of high-performance fluorophores and AIEgens. TICT of 14 types of popular organic fluorophores were modeled with time-dependent density functional theory (TD-DFT). A reliable and generalizable computational approach for modeling TICT formations was established. To demonstrate the prediction power of our approach, we quantitatively designed a boron dipyrromethene (BODIPY)-based AIEgen which exhibits (almost) barrierless TICT rotations in monomers. Subsequent experiments validated our molecular design and showed that the aggregation of this compound turns on bright emissions with ca. 27-fold fluorescence enhancement, as TICT formation is inhibited in molecular aggregates.

Single-Benzene-Based Solvatochromic Chromophores: Color-Tunable and Bright Fluorescence in the Solid and Solution States

The search for structurally simple chromophores with superior fluorescence brightness and a wide range of solvent compatibility is highly desirable. Herein, a new type of single-benzene-based solvatochromic chromophore with a symmetric bifunctional structure, in which azetidine and ethoxycarbonyl moieties serve as the electron-donating and -withdrawing groups, respectively, is reported. This chromophore exhibits an extraordinary wide range of solvent compatibility and preserves excellent fluorescence quantum yields from nonpolar n-hexane to polar methanol and even in water. Unusually, the symmetric structure of the chromophore shows a distinct color change from bright green to red with increasing solvent polarity and possesses large Stokes shifts (λ=132-207 nm) in the tested solvents. Moreover, this single-benzene-based chromophore displays good photochemical stability in both solution and solid states, and even exhibits reversible mechanochromic luminescence.

The Interplay between Solvation and Stacking of Aromatic Rings Governs Bright and Dark Sites of Benzo[g]coumarins

Coumarins are classic, strongly polarized fluorophores with multiple applications, and significant efforts have been put into modifying their emission characteristics and elucidating their photophysics. Expecting that π-expansion of these donor-acceptor chromophores could modify their ground- and excited-state characteristics, the authors performed combined, detailed photophysical and computational studies of linearly π-expanded coumarins, that is, 8-dialkylamino-3-carboxyalkyl-benzo[g]coumarins. The investigation led to the conclusion that emission is only possible thanks to the stabilizing effect of the solvent and that breaking of the lactone ring leads to the conical intersection with the ground state and induces the radiationless decay of the electronic excitation. Aiming at the fine-tuning the excited state properties through the construction of covalently linked dye assemblies, the authors designed and synthesized a new bis(benzo[g]coumarin), built from two similar moieties that exhibit different degrees of polarization due to the electron donor at position 8: one possesses a dialkylamino, and the other a weaker amide donor. Comprehensive studies have shown that the observed weak fluorescence of the system is the result of the interplay between the solvation-induced separation of the benzo[g]coumarin moieties, which stabilizes the emitting locally excited singlet state and the π-stacking interactions, favoring their sandwiched orientation and leading to the non-emissive charge-transfer state.

Quaternary Piperazine-Substituted Rhodamines with Enhanced Brightness for Super-Resolution Imaging

Insufficient brightness of fluorophores poses a major bottleneck for the advancement of super-resolution microscopes. Despite being widely used, many rhodamine dyes exhibit sub-optimal brightness due to the formation of twisted intramolecular charge transfer (TICT) upon photoexcitation. Herein, we have developed a new class of quaternary piperazine-substituted rhodamines with outstanding quantum yields (Φ = 0.93) and superior brightness (ε × Φ = 8.1 × 10⁴ L·mol^-1·cm^-1), by utilizing the electronic inductive effect to prevent TICT. We have also successfully deployed these rhodamines in the super-resolution imaging of the microtubules of fixed cells and of the cell membrane and lysosomes of live cells. Finally, we demonstrated that this strategy was generalizable to other families of fluorophores, resulting in substantially increased quantum yields.

Building Molecular Complexity from Quinizarin: Conjoined Coumarins and Coronene Analogs

The double Knoevenagel condensation of 1,4-dibenzoyloxyanthraquinone with methyl esters of arylacetic acids affords a series of compounds based upon a previously unknown 1,8-dioxa-benzo[e]pyrene-2,7-dione heterocyclic core. The aryl groups incorporated in the 3- and 6-positions can be oxidatively coupled to the π-expanded backbone to produce a further new heterocyclic core: 1,10-dioxa-dibenzo[dj]coronene-2,9-dione. The intriguing optical properties of these π-expanded coumarin derivatives are discussed and rationalized through quantum chemical calculations. The broad absorption bands of 1,8-dioxa-benzo[e]pyrene-2,7-dione-based dyes are attributed to both HOMO-1→LUMO and HOMO→LUMO transitions, which have a similar energy. Weakly coupled electron-donating aryl substituents result in a moderate bathochromic shift of both the absorption and emission by 30-60 nm in toluene. The emissive properties of these compounds are in part determined by the oscillator strength of the main transition, lifetimes of the excited state, and by the energy match of the excited state with a triplet state of a similar energy. The 1,10-dioxa-dibenzo[dj]coronene-2,9-dione displays a much smaller Stokes shift, yet a markedly increased fluorescence quantum yield of 90 % owing to the increased rigidity compared with the 1,8-dioxa-benzo[e]pyrene-2,7-dione core.

A new efficient domino approach for the synthesis of coumarin-pyrazolines as antimicrobial agents targeting bacteriald-alanine-d-alanine ligase

The inhibition ofd-alanine-d-alanine ligase (Ddl) prevents bacterial growth, which makes this enzyme an attractive and viable target in the urgent search for novel effective antimicrobial drugs.

High Photostability in Nonconventional Coumarins with Far-Red/NIR Emission through Azetidinyl Substitution

Replacement of electron-donating N,N-dialkyl groups with three- or four-membered cyclic amines (e.g., aziridine and azetidine, respectively) has been described as a promising approach to improve some of the drawbacks of conventional fluorophores, including low fluorescent quantum yields (Φ_F) in polar solvents. In this work, we have explored the influence of azetidinyl substitution on nonconventional coumarin-based COUPY dyes. Two azetidine-containing scaffolds were first synthesized in four linear synthetic steps and easily transformed into far-red/NIR-emitting fluorophores through N-alkylation of the pyridine moiety. Azetidine introduction in COUPY dyes resulted in enlarged Stokes' shifts with respect to the N,N-dialkylamino-containing parent dyes, but the Φ_F were not significantly modified in aqueous media, which is in contrast with previously reported observations in other fluorophores. However, azetidinyl substitution led to an unprecedented improvement in the photostability of COUPY dyes, and high cell permeability was retained since the fluorophores accumulated selectively in mitochondria and nucleoli of HeLa cells. Overall, our results provide valuable insights for the design and optimization of novel fluorophores operating in the far-red/NIR region, since we have demonstrated that three important parameters (Stokes' shifts, Φ_F, and photostability) cannot be always simultaneously addressed by simply replacing a N,N-dialkylamino group with azetidine, at least in nonconventional coumarin-based fluorophores.

Cross-dehydrogenative coupling of coumarins with Csp3–H bonds using an iron–organic framework as a productive heterogeneous catalyst

The iron–organic framework VNU-20 was utilized as an active heterogeneous catalyst for the cross-dehydrogenative coupling of coumarins with Csp³–H bonds in alkylbenzenes, cyclohexanes, ethers, and formamides.