Development of High-Performance Pyrimidine Nucleoside and Oligonucleotide Diarylethene Photoswitches

Second Generation Zwitterionic Aza-Diarylethene: Photoreversible CN Bond Formation, Three-State Photoswitching, Thermal Energy Release, and Facile Photoinitiation of Polymerization

Diarylethenes are a well-studied and optimized class of photoswitches with a wide range of applications, including data storage, smart materials, or photocontrolled catalysis and biological processes. Most recently, aza-diarylethenes have been developed in which carbon-carbon bond connections are replaced by carbon-nitrogen connections. This structural elaboration opens up an entire new structure and property space expanding the versatility and applicability of diarylethenes. In this work, we present the second generation of zwitterionic aza-diarylethenes, which finally allows for fully reversible photoswitching and precise control over all three switching states. High-yielding photoswitching between the neutral open form and a zwitterionic Z isomer is achieved with two different wavelengths of light. The third zwitterionic E isomeric state can be reached in up to 87 % upon irradiation with a third wavelength. Its high energy content of >10 kcal/mol can be released thermally by deliberate solvent change as trigger mechanism, rendering aza-diarylethenes into interesting candidates for molecular solar thermal energy storage (MOST) applications. The third state also serves as locking state, allowing to toggle light-responsiveness reversibly between thermally labile and thermally stable switching. Further, irradiation of the zwitterionic states leads to highly efficient photopolymerization of methyl acrylate (MA), directly harnessing the unleashed chemical reactivity of our aza-diarylethene in a materials application.

Pd(ii)-catalyzed enantioselective C-H olefination and photoregulation of sterically hindered diarylethenes

Sterically hindered diarylethenes with intrinsic chirality have shown great potential in chiral signal regulation, light-controlled liquid crystals (LCs), etc. Their unique enantiospecific phototransformation between axial chirality of ring-open isomers and central chirality of ring-closed isomers can break through the bottleneck of interference between multiple chiral centers in traditional chiral diarylethenes. However, these intrinsic chiral diarylethenes require necessary chiral resolution through preparative chiral HPLC, typically resulting in limited separation efficiency and production scale. Here, we present an enantioselective olefination strategy to directly construct intrinsic chiral diarylethenes from a prochiral sterically hindered diarylethene, achieving high yields and enantioselectivity. The resulting isomers can be further decorated by incorporating mesogenic units, and the derivatives enable the successful reversible photoregulation of blue, green, and red reflection colors of LCs with excellent thermal stability, fatigue resistance, and little texture disorderliness, demonstrating the practical application potential of direct enantioselective olefination in photoregulation with intrinsic chiral diarylethenes.

Synthesis and Development of Inverse-Type Nucleoside Diarylethene Photoswitches

Nucleosidic diarylethenes (DAEs) have evolved from an emerging class of photochromes into a well-established option for integrating photochromic functionalities into biological systems. However, a comprehensive understanding of how chemical structure influences their photochromic properties remains essential. While structural features, such as an inverse connection between the aryl residues and the ethene bridge, are well-documented for classical DAEs, their application to nucleosidic DAEs has been underexplored. In this study, we address this gap by developing three distinct types of inverse nucleosidic DAEs-semi-inverse thiophenes, semi-inverse uridines and inverse uridines. We successfully synthesized these compounds and conducted comprehensive analyses of their photostationary states, thermal stability, reversibility, and reaction quantum yields. Additionally, we conducted an in-depth comparison of their photochromic properties with those of their normal-type counterparts. Among the synthesized compounds, seven semi-inverse thiophenes exhibited the most promising characteristics. Notably, these compounds demonstrated excellent fatigue resistance, with up to 96 % retention of photochromic activity over 40 switching cycles, surpassing the performance of all comparable nucleosidic DAEs reported to date. These findings hold significant promise for future applications in various fields.

Reversible C═N Bond Formation Controls Charge-Separation in an Aza-Diarylethene Photoswitch

Diarylethenes belong to the most eminent photoswitches and have been studied for many decades. They are found in virtually every field of application and have become highly valuable molecular tools for instilling light-responsiveness into materials, catalysts, biological systems, or pharmacology. In this work, we present a novel and distinct type of pyrimidine-based aza-diarylethene, which undergoes a highly unusual zwitterion-forming photoreaction. During this fully reversible process, a CN double bond is established under concomitant aromatization and thiophene-ring opening. The metastable zwitterion thus possesses a positively charged extended aromatic structure and an independent conjugated thiolate function. It can further photoisomerize between a more stable Z and a less stable E isomer, resulting in effective four-state photoswitching. Unusual for diarylethenes, the metastable isomers show negative solvatochromism and red-shifted absorption in apolar solvents. With this behavior, aza-diarylethenes effectively bridge the properties of merocyanines and diarylethenes. Thermal stability of the zwitterions can be modulated from very labile to highly stable behavior in response to pH, again in a fully reversible manner. Pyrimidine-based aza-diarylethene thus establishes a unique photoreaction mechanism for diarylethenes, allowing control of charge separation, thermal stability, and color generation in a different way than hitherto possible.

Photochromic Nucleosides and Oligonucleotides

Photochromism is a reversible phenomenon wherein a material undergoes a change in color upon exposure to light. In organic photochromes, this effect often results from light-induced isomerization reactions, leading to alterations in either the spatial orientation or electronic properties of the photochrome. The incorporation of photochromic moieties into biomolecules, such as proteins or nucleic acids, has become a prevalent approach to render these biomolecules responsive to light stimuli. Utilizing light as a trigger for the manipulation of biomolecular structure and function offers numerous advantages compared to other stimuli, such as chemical or electrical treatments, due to its non-invasive nature. Consequently, light proves particularly advantageous in cellular and tissue applications. In this review, we emphasize recent advancements in the field of photochromic nucleosides and oligonucleotides. We provide an overview of the design principles of different classes of photochromes, synthetic strategies, critical analytical challenges, as well as structure-property relationships. The applications of photochromic nucleic acid derivatives encompass diverse domains, ranging from the precise photoregulation of gene expression to the controlled modulation of the three-dimensional structures of oligonucleotides and the development of DNA-based fluorescence modulators. Moreover, we present a future perspective on potential modifications and applications.

Photoswitchable Quadruple Hydrogen-Bonding Motif

Multiple hydrogen-bonding motifs serve as important building blocks for molecular recognition and self-assembly. Herein, a photoswitchable quadruple hydrogen-bonding motif featuring near-complete, reversible, and thermostable conversion between DADA and AADD arrays associated with an alteration of their dimerization constants by over 3 orders of magnitude is reported. The system is based on a diarylethene featuring a ureidopyrimidin-4-ol moiety, which upon photoinduced ring closure and associated loss of aromaticity undergoes enol-keto tautomerization to a ureidopyrimidinone moiety. The latter causes a transformation of the hydrogen-bonding arrays and significantly weakens the free energy of dimerization in the case of the closed isomer. This photoswitchable quadruple hydrogen-bonding motif should allow us to spatially and temporarily direct self-assembly and supramolecular polymerization processes by light.

Ion valence-gated photochromism of an aza-crowned diarylethene

A non-photochromic diarylethene 2o with an N-phenylaza-15-crown-5 was synthesized. When the nitrogen atom in the aza-crown ring was protonated, it became photochromic due to the prevention of a twisted intramolecular charge transfer (TICT). Although addition of a monovalent metal cation (Li+, Na+, K+, Rb+, Cs+, Cu+, Ag+) in acetonitrile could not stop the TICT so that it was not photochromic, the addition of a multivalent metal cation (Mg2+, Ca2+, Sr2+, Ba2+, Fe2+, Ni2+, Al3+, Sb5+) changed 2o to be photochromic due to the strong attraction of the lone pair on the nitrogen atom. In the presence of excess Cu2+, 2o was oxidized to be EPR-detectable 2o·+, which was thermally unstable as well as inert towards visible-light irradiation. However, 2o·+ was further oxidized to be fairly stable 2o2+ by the irradiation of 365-nm light in the presence of Cu2+. ESI-MS measurements strongly suggested the generation of 2o·+ by mixing 2o with Cu(ClO4)2 in acetonitrile, and the transformation of 2o·+ to 2o2+ by successive 365-nm light irradiation. Fe3+ similarly worked as the oxidant, but the two-step oxidation of 2o to 2o2+ occurred more easily.

Gonçalves DP, Zhu C, Tilki T, Prévôt ME, Hegmann T. Controlling the Structure and Morphology of Organic Nanofilaments Using External Stimuli

In our continuing pursuit to generate, understand, and control the morphology of organic nanofilaments formed by molecules with a bent molecular shape, we here report on two bent-core molecules specifically designed to permit a phase or morphology change upon exposure to an applied electric field or irradiation with UV light. To trigger a response to an applied electric field, conformationally rigid chiral (S,S)-2,3-difluorooctyloxy side chains were introduced, and to cause a response to UV light, an azobenzene core was incorporated into one of the arms of the rigid bent core. The phase behavior as well as structure and morphology of the formed phases and nanofilaments were analyzed using differential scanning calorimetry, cross-polarized optical microscopy, circular dichroism spectropolarimetry, scanning and transmission electron microscopy, UV-vis spectrophotometry, as well as X-ray diffraction experiments. Both bent-core molecules were characterized by the coexistence of two nanoscale morphologies, specifically helical nanofilaments (HNFs) and layered nanocylinders, prior to exposure to an external stimulus and independent of the cooling rate from the isotropic liquid. The application of an electric field triggers the disappearance of crystalline nanofilaments and instead leads to the formation of a tilted smectic liquid crystal phase for the material featuring chiral difluorinated side chains, whereas irradiation with UV light results in the disappearance of the nanocylinders and the sole formation of HNFs for the azobenzene-containing material. Combined results of this experimental study reveal that in addition to controlling the rate of cooling, applied electric fields and UV irradiation can be used to expand the toolkit for structural and morphological control of suitably designed bent-core molecule-based structures at the nanoscale.

Divergent Reactivity of Triaryldivinyl Ketones: Competing 4π and Putative 6π Electrocyclization Pathways

This work describes an acid-promoted cyclization of triaryldivinyl ketones containing a thiophene moiety in the α-position. Two cyclization pathways are accessible: one a 4π-Nazarov cyclization and the other we propose to proceed through a 6π electrocyclic mechanism. The relative proportion of products from these divergent pathways is affected by reaction conditions and steric bulk in the substrate. We present experimental and computational evidence that when using HCl in dioxane, the 4π-conrotatory electrocyclization is more favorable, whereas GaCl₃ in methylene chloride shifts the chemoselectivity toward a putative 6π-disrotatory electrocyclization. DFT calculations suggest that a complex interplay between kinetic and thermodynamic factors is implicated in the chemodivergent behavior.

Unsymmetrical benzothiazole-based dithienylethene photoswitches

Herein, we investigate the structure-property relationships in a new series of benzothiazole based unsymmetrical hexafluorocyclopentene dithienylethenes (DTEs) and compare the results with the known facts for symmetric diarylethenes (DAEs). We reveal high photocyclization efficiency resulting from a significant shift of ground state equilibrium to the antiparallel conformation and a barrierless excited state pathway to conical intersection, which remains unperturbed even in polar solvents for most of the prepared DTEs. Furthermore, we uncover that the rate of back thermal cycloreversion correlates clearly more with the central C-C bond-length in the transition state than with the central C-C bond-length in the ground state of the cyclic form. Finally, our detailed vibrational spectral analysis of studied DTEs points out significant changes in Raman and infrared spectra during photoswitching cycles which pave the way for a non-destructive readout of stored information.

Future-Oriented Advanced Diarylethene Photoswitches: From Molecular Design to Spontaneous Assembly Systems

Diarylethene (DAE) photoswitch is a new and promising family of photochromic molecules and has shown superior performance as a smart trigger in stimulus-responsive materials. During the past few decades, the DAE family has achieved a leap from simple molecules to functional molecules and developed toward validity as a universal switching building block. In recent years, the introduction of DAE into an assembly system has been an attractive strategy that enables the photochromic behavior of the building blocks to be manifested at the level of the entire system, beyond the DAE unit itself. This assembly-based strategy will bring many unexpected results that promote the design and manufacture of a new generation of advanced materials. Here, recent advances in the design and fabrication of diarylethene as a trigger in materials science, chemistry, and biomedicine are reviewed.

A DNA-Based Two-Component Excitonic Switch Utilizing High-Performance Diarylethenes

Nucleosidic diarylethenes (DAEs) are an emerging class of photochromes but have rarely been used in materials science. Here, we have developed doubly methylated DAEs derived from 2'-deoxyuridine with high thermal stability and fatigue resistance. These new photoswitches not only outperform their predecessors but also rival classical non-nucleosidic DAEs. To demonstrate the utility of these new DAEs, we have designed an all-optical excitonic switch consisting of two oligonucleotides: one strand containing a fluorogenic double-methylated 2'-deoxyuridine as a fluorescence donor and the other a tricyclic cytidine (tC) as acceptor, which together form a highly efficient conditional Förster-Resonance-Energy-Transfer (FRET) pair. The system was operated in liquid and solid phases and showed both strong distance- and orientation-dependent photochromic FRET. The superior ON/OFF contrast was maintained over up to 100 switching cycles, with no detectable fatigue.

Photochemical modifications for DNA/RNA oligonucleotides

Light-triggered chemical reactions can provide excellent tools to investigate the fundamental mechanisms important in biology. Light is easily applicable and orthogonal to most cellular events, and its dose and locality can be controlled in tissues and cells. Light-induced conversion of photochemical groups installed on small molecules, proteins, and oligonucleotides can alter their functional states and thus the ensuing biological events. Recently, photochemical control of DNA/RNA structure and function has garnered attention thanks to the rapidly expanding photochemistry used in diverse biological applications. Photoconvertible groups can be incorporated in the backbone, ribose, and nucleobase of an oligonucleotide to undergo various irreversible and reversible light-induced reactions such as cleavage, crosslinking, isomerization, and intramolecular cyclization reactions. In this review, we gather a list of photoconvertible groups used in oligonucleotides and summarize their reaction characteristics, impacts on DNA/RNA thermal stability and structure, as well as their biological applications.

Development of Red-Shifted and Fluorogenic Nucleoside and Oligonucleotide Diarylethene Photoswitches

The reversible modulation of fluorescence signals by light is of high interest for applications in super‐resolution microscopy, especially on the DNA level. In this article we describe the systematic variation of the core structure in nucleoside‐based diarylethenes (DAEs), in order to generate intrinsically fluorescent photochromes. The introduction of aromatic bridging units resulted in a bathochromic shift of the visible absorption maximum of the closed‐ring form, but caused reduced thermal stability and switching efficiency. The replacement of the thiophene aryl unit by thiazol improved the thermal stability, whereas the introduction of a benzothiophene unit led to inherent and modulatable turn‐off fluorescence. This feature was further optimized by introducing a fluorescent indole nucleobase into the DAE core, resulting in an effective photoswitch with a fluorescence quantum yield of 0.0166 and a fluorescence turn‐off factor of 3.2. The site‐specific incorporation into an oligonucleotide resulted in fluorescence‐switchable DNA with high cyclization quantum yields and switching efficiency, which may facilitate future applications.

Molecular platforms based on biocompatible photoreactions for photomodulation of biological targets

Photoirradiation provides a convenient and biocompatible approach for spatiotemporal modulation of biological systems with photoresponsive components. The construction of molecular platforms with a photoresponse to be integrated into biomolecules for photomodulation has been of great research interest in optochemical biology. In this review, we summarize typical molecular platforms that are integratable with biomolecules for photomodulation purposes. We categorize these molecular platforms according to their excitation light source, namely ultraviolet (UV), visible (Vis) or near-infrared (NIR) light. The protype chemistry of these molecular platforms is introduced along with an overview of their most recent applications for spatiotemporal regulation of biomolecular function in living cells or mice models. Challenges and the outlook are also presented. We hope this review paper will contribute to further progress in the development of molecular platforms and their biomedical use.

"Click-switch" - one-step conversion of organic azides into photochromic diarylethenes for the generation of light-controlled systems

Diarylethenes (DAEs) are an established class of photochromic molecules, but their effective incorporation into pre-existing targets is synthetically difficult. Here we describe a new class of DAEs in which one of the aryl rings is a 1,2,3-triazole that is formed by “click” chemistry between an azide on the target and a matching alkyne–cyclopentene–thiophene component. This late-stage zero-length linking allows for tight integration of the DAE with the target, thereby increasing the chances for photomodulation of target functions. Nineteen different DAEs were synthesized and their properties investigated. All showed photochromism. Electron-withdrawing groups, and in particular −M-substituents at the triazole and/or thiophene moiety resulted in DAEs with high photo- and thermostability. Further, the chemical nature of the cyclopentene bridge had a strong influence on the behaviour upon UV light irradiation. Incorporation of perfluorinated cyclopentene led to compounds with high photo- and thermostability, but the reversible photochromic reaction was restricted to halogenated solvents. Compounds containing the perhydrogenated cyclopentene bridge, on the other hand, allowed the reversible photochromic reaction in a wide range of solvents, but had on average lower photo- and thermostabilities. The combination of the perhydrocyclopentene bridge and electron-withdrawing groups resulted in a DAE with improved photostability and no solvent restriction. Quantum chemical calculations helped to identify the photoproducts formed in halogenated as well as non-halogenated solvents. For two optimized DAE photoswitches, photostationary state composition and reaction quantum yields were determined. These data revealed efficient photochemical ring closure and opening. We envision applications of these new photochromic diarylethenes in photonics, nanotechnology, photobiology, photopharmacology and materials science.

New photochromic diarylethenes are reported in which one aryl ring is a 1,2,3-triazole that is formed by “click” chemistry between an azide on the target and a matching alkyne–cyclopentene–thiophene component.

Development of High-Performance Pyrimidine Nucleoside and Oligonucleotide Diarylethene Photoswitches

Nucleosidic and oligonucleotidic diarylethenes (DAEs) are an emerging class of photochromes with high application potential. However, their further development is hampered by the poor understanding of how the chemical structure modulates the photochromic properties. Here we synthesized 26 systematically varied deoxyuridine- and deoxycytidine-derived DAEs and analyzed reaction quantum yields, composition of the photostationary states, thermal and photochemical stability, and reversibility. This analysis identified two high-performance photoswitches with near-quantitative, fully reversible back-and-forth switching and no detectable thermal or photochemical deterioration. When incorporated into an oligonucleotide with the sequence of a promotor, the nucleotides maintained their photochromism and allowed the modulation of the transcription activity of T7 RNA polymerase with an up to 2.4-fold turn-off factor, demonstrating the potential for optochemical control of biological processes.