Cyanines during the 1990s: A Review

Biomedical-Optical-Window Tailored Cyanines for Steerable Inflammatory Bowel Disease Theranostic

Tailored photophysical properties and chemical activity is the ultimate pursuit of functional dyes for in vivo biomedical theranostics. In this work, the independent regulation of the absorption and fluorescence emission wavelengths of heptamethine cyanines is reported. These dyes retain near-infrared fluorescence emission (except a nitro-modified dye) while feature variable absorption wavelengths ranging from 590 to 860 nm. This enables to obtain customized functional dyes that meet the excitation and fluorescence wavelength requirements defined by the optical properties of tissues for in vivo biomedical applications. Typically, a nitro-modified photothermal active derivative Cy-Mu-7-9 is used, which features strong absorption at 810 nm in PBS, a wavelength that balanced the tissue penetration depth and non-specific photothermal effect, to realize non-destructive inflammatory bowel disease (IBD) therapy via photothermal induced up-regulation of heat shock protein 70 in the intestinal epithelial cells. The corresponding amino-modified dye Cy-Mu-7-9-NH2, which can be formed in health enteric cavity by Cy-Mu-7-9 after oral administration, is a fluorescence compound with the emission of 800 nm in PBS. Based on the IBD sensitive transformation of Cy-Mu-7-9 and Cy-Mu-7-9-NH2, in vivo IBD theranostic and therapeutic effect evaluation is realized via the synergy of fluorescence imaging and photothermal therapy for the first time.

Zwitterionic nanoparticles from indocyanine green dimerization for imaging-guided cancer phototherapy

Indocyanine green (ICG), the only near-infrared (NIR) dye approved for clinical use, has received increasing attention as a theranostic agent wherein diagnosis (fluorescence) is combined with therapy (phototherapy), but suffers rapid hepatic clearance, poor photostability, and limited accumulation at tumor sites. Here we report that dimerized ICG can self-assemble to form zwitterionic nanoparticles (ZN-dICG), which generate fluorescence self-quenching but exhibit superior photothermal and photodynamic properties over ICG. The zwitterionic moieties confer ZN-dICG an ultralow critical micelle concentration and high colloidal stability with low non-specific binding in vivo. In addition, ZN-dICG can respond to the over-generated reactive oxygen species (ROSs) and dissociate to restore NIR fluorescence of ICG, amplifying the sensitivity via albumin binding for low-background imaging of tumors. Following systemic administration, ZN-dICG accumulated in tumors of xenograft-bearing mice for imaging primary and metastatic tumors, and induced tumor ablation under laser irradiation. The discovery of ZN-dICG would contribute to the design of translational phototheranostic platform with high biocompatibility. STATEMENT OF SIGNIFICANCE: Indocyanine green (ICG) has been extensively studied as a phototheranostic agent that combines imaging with phototherapies, but it suffers from rapid hepatic clearance, poor photostability, and limited accumulation at tumor sites. Here, we report a strategy to construct ICG dimers (ICG-tk-ICG) by conjugating two ICG molecules via a thioketal bond, which can self-assemble into zwitterionic nanoparticles (ZN-dICG) at ultralow critical micelle concentrations, exhibiting superior photothermal and photodynamic properties over ICG. ZN-dICG responds to the over-generated ROS in tumors and dissociates to restore the NIR fluorescence of ICG, enhancing the sensitivity via albumin binding for low-background imaging of tumors. This study offers a supramolecular strategy that may potentiate the clinical translation of ICG in imaging-guided cancer phototherapy.

Oxidation of Weakly Interacting Diradicals: An Approach for Strong and Tunable Near-Infrared-Absorbing Dyes Based on Small Chromophores

Near-infrared (NIR)-absorbing dyes are valuable for various applications, such as bioimaging and electronic devices. This work introduces a novel approach for designing NIR dyes, oxidation of weakly coupled diradicals. Our approach features a weak exchange interaction in diradicals, which potentially leads to bonding/antibonding molecular orbitals with a small energy gap. We found that removing one of two singly occupied molecular orbital electrons of the diradicals results in an exceptionally narrow frontier orbital energy gap. We examined a series of Blatter radical dimers, and the most weakly coupled diradical prepared in this work (ΔEST ∼ 0.12 eV) with a molecular weight of 590 Da exhibited a strong NIR absorption band reaching 2200 nm upon one-electron oxidation. The optical band gaps of the radical cations strongly correlate to the exchange interaction in the precursor neutral species, offering prediction and fine-tuning of the optical band gap in the NIR region.

Exploring solvatochromism: a comprehensive analysis of research data of the solvent -solute interactions of 4-nitro-2-cyano-azo benzene-meta toluidine

This study investigates the solvatochromic behavior of a new D1 disperse dye, focusing on the 4-nitro-2-cyano-azo-Benzene-metaToluidine type. Using UV-visible spectroscopy, we analyze the dye's performance in single solvents and binary mixtures. Our analysis includes the evaluation of solvent polarity parameters and dye structure parameters, with emphasis on the longest wavelength intramolecular charge transfer absorption band. We identify nonlinear and linear patterns in the electronic transition energies plots with respect to solvent composition. Statistical analysis considers correlation coefficients, root mean squared error, mean absolute percentage error, and other parameters, providing insights into data accuracy and precision. This experimental and statistical study explores the absorption spectrum, wavelength characteristics, absorption energy, and polarity of a novel azo dye across various solvent and solute environments. These findings contribute to a comprehensive understanding of the dye's photophysical and photochemical properties, potentially enabling applications in optical sensors and advanced materials.

A Cyanine Dye for Highly Specific Recognition of Parallel G-Quadruplex Topology and Its Application in Clinical RNA Detection for Cancer Diagnosis

G-quadruplex (G4), an unconventional nucleic acid structure, shows polymorphism in its topological morphology. The parallel G4 topology is the most prevalent form in organisms and plays a regulatory role in many biological processes. Designing fluorescent probes with high specificity for parallel G4s is important but challenging. Herein, a supramolecular assembly of the anionic cyanine dye SCY-5 is reported, which selectively identifies parallel G4 topology. SCY-5 can clearly distinguish parallel G4s from other G4s and non-G4s, even including hybrid-type G4s with parallel characteristics. The high specificity mechanism of SCY-5 involves a delicate balance between electrostatic repulsion and π-π interaction between SCY-5 and G4s. Using SCY-5, cellular RNA extracted from peripheral venous blood was quantitatively detected, and a remarkable increase in RNA G4 content in cancer patients compared to healthy volunteers was confirmed for the first time. This study provides new insights for designing specific probes for parallel G4 topology and opens a new path for clinical cancer diagnosis using RNA G4 as a biomarker.

Cyanine dyes in the mitochondria-targeting photodynamic and photothermal therapy

Mitochondrial dysregulation plays a significant role in the carcinogenesis. On the other hand, its destabilization strongly represses the viability and metastatic potential of cancer cells. Photodynamic and photothermal therapies (PDT and PTT) target mitochondria effectively, providing innovative and non-invasive anticancer therapeutic modalities. Cyanine dyes, with strong mitochondrial selectivity, show significant potential in enhancing PDT and PTT. The potential and limitations of cyanine dyes for mitochondrial PDT and PTT are discussed, along with their applications in combination therapies, theranostic techniques, and optimal delivery systems. Additionally, novel approaches for sonodynamic therapy using photoactive cyanine dyes are presented, highlighting advances in cancer treatment.

Photoacoustic imaging of a cyanine dye targeting bacterial infection

The development of a non-invasive infection-specific diagnostic probe holds the potential to vastly improve early-stage detection of infection, enabling precise therapeutic intervention and potentially reducing the incidence of antibiotic resistance. Towards this goal, a commercially available bacteria-targeting Zinc(II)-dipicolylamine (ZnDPA)-derived fluorophore, PSVue794, was assessed as a photoacoustic (PA) imaging probe (PIP). A radiolabeled version of the dye, [99mTc]Tc-PSVue794, was developed to facilitate quantitative biodistribution studies beyond optical imaging methods, which showed a target-to-non-target ratio of 10.1 ± 1.1, 12 h post-injection. The ability of the PIP to differentiate between bacterial infection, sterile inflammation, and healthy tissue in a mouse model, was then evaluated via PA imaging. The PA signal in sites of sterile inflammation (0.062 ± 0.012 a.u.) was not statistically different from that of the background (0.058 ± 0.006 a.u.). In contrast, high PA signal was detected at sites of bacterial infection (0.176 ± 0.011 a.u.) as compared to background (0.081 ± 0.04 a.u., where P ≤ 0.03). This work demonstrates the potential of utilizing established fluorophores towards PAI and utilizing PAI as a modality in the distinction of bacterial infection from sites of sterile inflammation.

Mechanisms of delayed indocyanine green fluorescence and applications to clinical disease processes

BACKGROUND

Delayed indocyanine green fluorescence imaging is under investigation in various clinical disease processes. Understanding the mechanisms of indocyanine green accumulation and retention is essential to correctly interpreting and analyzing imaging data. The purpose of this scoping review was to synthesize what is known about the mechanism of indocyanine green retention at the cellular level to better understand the clinical nuances of delayed indocyanine green imaging and identify critical gaps in our knowledge to guide future studies.

METHODS

We performed a scoping review of 7,087 citations after performing database searches of PubMed, Scopus, the Cochrane Library, and the Web of Science Core Collection electronic databases. Studies were eligible for inclusion if they were peer-reviewed original research discussing the mechanism of indocyanine green retention in the results section in disease processes involving inflammation and/or necrosis, including cancer, and were available in English. Data were extracted using Covidence software.

RESULTS

Eighty-nine studies were included in the final analysis. Several features of indocyanine green retention were identified.

CONCLUSION

We identified several mechanistic features involved in indocyanine green accumulation in diseased tissue that overall had distinct mechanisms of indocyanine green retention in tumors, nontumor inflammation, and necrosis. Our study also reveals new insights on how inflammatory infiltrate influences indocyanine green fluorescence imaging. These findings are noteworthy because they add to our understanding of how fluorescence-guided surgery may be optimized based on the pathology of interest via specific indocyanine green dosing and timing of image acquisition.

Shortwave infrared polymethine dyes for bioimaging: ultrafast relaxation dynamics and excited-state decay pathways

Excited-state relaxation in two prototypical shortwave infrared (SWIR) polymethine dyes developed for bioimaging, heptamethine chromenylium Chrom7 and flavylium Flav7, is studied by means of femtosecond transient absorption with broadband ultraviolet-to-SWIR probing complemented by steady-state and time-resolved fluorescence and phosphorescence measurements. The relaxation processes of the dyes in dichloromethane are resolved with sub-100 fs temporal resolution using SWIR, near-IR, and visible photoexcitation. Different population members of the ground-state inhomogeneous ensemble are found to equilibrate via skeletal deformation changes with time constants of 90 fs and either 230 fs (Chrom7) and 350 fs (Flav7) followed by slower evolution matching the 1-ps timescale of diffusive solvation dynamics. Molecules excited into high-lying singlet electronic states (Sn) by visible excitation repopulate with time constants of 400 fs (Chrom7) and 450 fs (Flav7) the corresponding first excited singlet S1 states, which decay within several hundreds of picoseconds in dichloromethane and chloroform solvents. Vibrational relaxation in S1 for both Chrom7 and Flav7 in dichloromethane occurs with time constants of 350 and 800 fs for excess of vibrational energy of ∼1000 and 10 000 cm-1 deposited by near-IR and visible excitation, respectively. Two competing non-radiative processes are present in S1: temperature-independent internal conversion, and thermally-activated twisting about a carbon-carbon bond of the conjugated chain, which is substantial at room temperature but essentially nonreactive, producing traces of isomer product. Intersystem crossing in S1, and thus the triplet quantum yield, is minor. The importance of absorption bands from the excited S1 state in applications requiring high-intensity excitation conditions is discussed.

Development of Polymethine Dyes for NIR-II Fluorescence Imaging and Therapy

Fluorescence imaging in the second near-infrared window (NIR-II) is burgeoning because of its higher imaging fidelity in monitoring physiological and pathological processes than clinical visible/the second near-infrared window fluorescence imaging. Notably, the imaging fidelity is heavily dependent on fluorescence agents. So far, indocyanine green, one of the polymethine dyes, with good biocompatibility and renal clearance is the only dye approved by the Food and Drug Administration, but it shows relatively low NIR-II brightness. Importantly, tremendous efforts are devoted to synthesizing polymethine dyes for imaging preclinically and clinically. They have shown feasibility in the customization of structure and properties to fulfill various needs in imaging and therapy. Herein, a timely update on NIR-II polymethine dyes, with a special focus on molecular design strategies for fluorescent, photoacoustic, and multimodal imaging, is offered. Furthermore, the progress of polymethine dyes in sensing pathological biomarkers and even reporting drug release is illustrated. Moreover, the NIR-II fluorescence imaging-guided therapies with polymethine dyes are summarized regarding chemo-, photothermal, photodynamic, and multimodal approaches. In addition, artificial intelligence is pointed out for its potential to expedite dye development. This comprehensive review will inspire interest among a wide audience and offer a handbook for people with an interest in NIR-II polymethine dyes.

The Influence of the Alkylamino Group on the Solvatochromic Behavior of 5-(4-substituted-arylidene)-1,3-dimethylpyrimidine-2,4,6-triones: Synthesis, Spectroscopic and Computational Studies

Advances in electronics and medical diagnostics have made organic dyes extremely popular as key functional materials. From a practical viewpoint, it is necessary to assess the spectroscopic and physicochemical properties of newly designed dyes. In this context, the condensation of 1,3-dimethylbarbituric acid with electron-rich alkylaminobenzaldehyde derivatives has been described, resulting in a series of merocyanine-type dyes. These dyes exhibit intense blue-light absorption but weak fluorescence. An electron-donating alkylamino group at position C4 is responsible for the solvatochromic behavior of the dyes since the lone electron pair of the nitrogen atom is variably delocalized toward the barbituric ring, which exhibits electron-withdrawing properties. This was elucidated, taking into account the different geometry of the amino group. The intramolecular charge transfer in the molecules is responsible for the relatively high redshift in absorption and fluorescence spectra. Additionally, an increase in solvent polarity moves the absorption and fluorescence to lower energy regions. The observed solvatochromism is discussed in terms of the four-parameter Catalán solvent polarity scale. The differences in the behavior of the dyes were quantified with the aid of time-dependent density functional theory calculations. The obtained results made it possible to find regularities linking the basic spectroscopic properties of the compounds with their chemical structure. This is important in the targeted search for new, practically important dyes.

H-bond engineering as a general strategy for inhibiting twisted intramolecular charge transfer in donor-acceptor fluorescent probes: Reshaping the pre-twisting method

Twisted intramolecular charge transfer (TICT) is a fluorescence quenching mechanism that occurs in donor-acceptor (D‒A) molecules. Chemical engineering research into TICT regulation over the past 50 years has primarily focused on manipulating steric factors by introducing alkyl groups at the D-A junction (pre-twisting). Herein, we report a significant advance in TICT-based probes through the introducing of H-bond as an efficient strategy for suppressing TICT. Accordingly, ortho-Cl installation in the N-phenylpyrazine-2-carboxamide (PPC) platform can achieve complete reversal from the quenching mode to the light-up mode. This specific H-bonding (N-H⋯Cl) effectively blocks N-C(Ar) bond rotation, leading to fluorescence-ON. This suggested that TICT inhibition may be involved. Therefore, in a sharp contrast to the general nature of the pre-twisting method in rotor molecules, which involves incorporating steric hindrance at either the donor or acceptor moiety to enhance intramolecular rotation (promotion TICT), the ortho-H bonding strategy completely freezes D‒A bond twisting (suppression TICT), resulting in improved fluorescent intensity. Furthermore, the fluorophores were evaluated for Hg2+ detection and in vivo bio-imaging. Notably, Hg-complexation induced another fluorescence inversion (OFF-ON) by imposing spatial constraints on twisting freedom in 3,4-Cl-PPC. Taken together, this work provides a valid and generalizable tactic for the development of high-performance sensing fluorophores through inhibition of TICT.

How to Build Plasmon-Driven Molecular Jackhammers that Disassemble Cell Membranes and Cytoskeletons in Cancer

Plasmon-driven molecular machines with ultrafast motion at the femtosecond scale are effective for the treatment of cancer and other diseases. It is recently shown that cyanine dyes act as molecular jackhammers (MJH) through vibronic (vibrational and electronic mode coupling) driven activation that causes the molecule to stretch longitudinally and axially through concerted whole molecule vibrations. However, the theoretical and experimental underpinnings of these plasmon-driven motions in molecules are difficult to assess. Here the use of near-infrared (NIR) light-activated plasmons in a broad array of MJH that mechanically disassemble membranes and cytoskeletons in human melanoma A375 cells is described. The characteristics of plasmon-driven molecular mechanical disassembly of supramolecular biological structures are observed and recorded using real-time fluorescence confocal microscopy. Molecular plasmon resonances in MJH are quantified through a new experimental plasmonicity index method. This is done through the measurement of the UV-vis-NIR spectra in various solvents, and quantification of the optical response as a function of the solvent polarity. Structure-activity relationships are used to optimize the synthesis of plasmon-driven MJH, applying them to eradicate human melanoma A375 cells at low lethal concentrations of 75 nm and 80 mW cm-2 of 730 nm NIR-light for 10 min.

Chemical Approaches to Optimize the Properties of Organic Fluorophores for Imaging and Sensing

Organic fluorophores are indispensable tools in cells, tissue and in vivo imaging, and have enabled much progress in the wide range of biological and biomedical fields. However, many available dyes suffer from insufficient performances, such as short absorption and emission wavelength, low brightness, poor stability, small Stokes shift, and unsuitable permeability, restricting their application in advanced imaging technology and complex imaging. Over the past two decades, many efforts have been made to improve these performances of fluorophores. Starting with the luminescence principle of fluorophores, this review clarifies the mechanisms of the insufficient performance for traditional fluorophores to a certain extent, systematically summarizes the modified approaches of optimizing properties, highlights the typical applications of the improved fluorophores in imaging and sensing, and indicates existing problems and challenges in this area. This progress not only proves the significance of improving fluorophores properties, but also provide a theoretical guidance for the development of high-performance fluorophores.

Molecular jackhammers eradicate cancer cells by vibronic-driven action

Through the actuation of vibronic modes in cell-membrane-associated aminocyanines, using near-infrared light, a distinct type of molecular mechanical action can be exploited to rapidly kill cells by necrosis. Vibronic-driven action (VDA) is distinct from both photodynamic therapy and photothermal therapy as its mechanical effect on the cell membrane is not abrogated by inhibitors of reactive oxygen species and it does not induce thermal killing. Subpicosecond concerted whole-molecule vibrations of VDA-induced mechanical disruption can be achieved using very low concentrations (500 nM) of aminocyanines or low doses of light (12 J cm-2, 80 mW cm-2 for 2.5 min), resulting in complete eradication of human melanoma cells in vitro. Also, 50% tumour-free efficacy in mouse models for melanoma was achieved. The molecules that destroy cell membranes through VDA have been termed molecular jackhammers because they undergo concerted whole-molecule vibrations. Given that a cell is unlikely to develop resistance to such molecular mechanical forces, molecular jackhammers present an alternative modality for inducing cancer cell death.

Cyclopentene ring effects in cyanine dyes: a handle to fine-tune photophysical properties

The aim of this study is to investigate the photophysical properties of a cyanine dye analogue by performing first-principles calculations based on density functional theory (DFT) and time dependent-DFT. Cationic cyanine dyes are the subject of great importance due to their versatile applications and the tunability of their photophysical properties, such as by modifying their end groups and chain length. An example of this is the vinylene shift, which is experimentally known for these molecules, and it consists of a bathochromic (red) shift of approximately 100 nm of the 0-0 vibronic transition when a vinyl group is added to the polymethine chain. Our study shows that when the saturated moiety C2H4 of the cyclopentene ring is added to the chain, it interacts with the conjugated π-system, resulting in a smaller HOMO-LUMO gap. Here, we demonstrate the origin of this interaction and how it can be used to fine tune the absorption energies of this class of dyes.

Insights into extended coupled polymethines through the investigation of dual UV-to-NIR acidochromic switches based on heptamethine-oxonol dyes

A series of heptamethine-oxonol dyes featuring different heterocyclic end groups were designed with the aim to explore structure-property relationships in π-extended coupled polymethines. These dyes can be stabilised under three different protonation states, affording dicationic derivatives with an aromatic core, cationic heptamethines, and zwitterionic bis-cyanine forms. The variation of the end groups directly impacts the absorption and emission properties and mostly controls reaching either a colourless neutral dispirocyclic species or near-infrared zwitterions. The acidochromic switching between the three states involves profound electronic rearrangements leading to notable shifts of their optical properties that were investigated using a parallel experiment-theory approach, providing a comprehensive description of these unique systems.

Growth of Merocyanine Dye J-Aggregate Nanosheets by Living Supramolecular Polymerization

J-aggregates are highly desired dye aggregates but so far there has been no general concept how to accomplish the required slip-stacked packing arrangement for dipolar merocyanine (MC) dyes whose aggregation commonly affords one-dimensional aggregates composed of antiparallel, co-facially stacked MCs with H-type coupling. Herein we describe a strategy for MC J-aggregates based on our results for an amphiphilic MC dye bearing alkyl and oligo(ethylene glycol) side chains. In an aqueous solvent mixture, we observe the formation of two supramolecular polymorphs for this MC dye, a metastable off-pathway nanoparticle showing H-type coupling and a thermodynamically favored nanosheet showing J-type coupling. Detailed studies concerning the self-assembly mechanism by UV-Vis spectroscopy and the packing structure by atomic force microscopy and wide-angle X-ray scattering show how the packing arrangement of such amphiphilic MC dyes can afford slip-stacked two-dimensional nanosheets whose macrodipole is compensated by the formation of a bilayer structure. As an additional feature we demonstrate how the size of the nanosheets can be controlled by seeded living supramolecular polymerization.

AIEE activated Pyrene-Dansyl coupled FRET probe for discriminating detection of lethal Cu2+ and CN-: Bio-Imaging, DNA binding studies and prompt prognosis of Menke's disease

In present work a pyrene-dansyl dyad functionalized chemoreceptor, DPNS is unveiled towards ultrasensitive chromo-fluorogenic detection of heavy and transition metal ions (HTMs) like Cu2+ and pernicious CN-. It demonstrated distinct chromogenic responses; colorless to faint yellow (Cu2+), intense yellow (CN-) from contaminant aqueous sources. Cu2+ instigated alteration in DPNS fluorescence from feeble emission to sparkling green with LOD: 37.75 × 10-9 M, cyan emission for CN- having LOD 61.51 × 10-8M. In particular, chemical scaffold of DPNS consists of -C = N, O = S = O donor entitities that escalates overall polarity thereby providing an excellent binding pocket for simultaneous Cu2+ and CN- recognition with distinct photophysical signaling. Impressively, presence of two fluorophoric moieties triggers FRET, CHEF phenomenon. The conceivable host:guest interactive pathway is manifested by LMCT- FRET-PET-CHEF, C = N isomerization for Cu2+ and ICT-H-bonding for CN-. An exquisite experimental and theoretical corroboration further strengthened the recognition phenomenon. In addition owing to pyrene excimer formation, DPNS exhibits AIEE with increasing water fraction. Notably, DPNS could successfully undergo intracellular tracking of Cu2+ in Tecoma Stans, Peperomia Pellucida. DPNS•••Cu2+ adduct displayed significant intercalative DNA binding activity rationalized by spectral investigation, competitive EB binding, viscosity study. The overall findings, excellent properties endows DPNS a potential contender towards discriminative detection of Cu2+ and CN- like toxic industrial contaminants.

Phospha-cyanines in Their Ideal Polymethine State: Synthesis and Structure-Property Relationships

We report the synthesis and full characterization of a family of phosphorus-containing polymethine cyanines (phospha-cyanines). The compounds are easily prepared in two steps, starting from readily available phosphanes. The impact of the P-substituents and the counterions on the structural and optical properties is investigated through a joint experimental/theoretical approach. Based on the study of the single-crystal X-ray diffraction structures, all phospha-cyanines present a bond length alternation close to zero, independently of the substituents and counterions, which indicates an ideal polymethine state. All these compounds display the typical cyanine-like UV-vis absorption with an intense and sharp transition with a vibronic shoulder despite possessing a reverse electronic configuration compared to "classical" cyanines. Time-dependent density-functional theory calculations allowed us to fully rationalize the optical properties (absorption/emission wavelengths, luminescence quantum yields). Interestingly, due to the tetrahedral shape of the P atom, the optical properties are independent of the counterion, which is in marked contrast with N-analogues, which enables predictive engineering of the phospha-cyanines regardless of the medium in which they are used.

Combination of quinoxaline with pentamethinium system: Mitochondrial staining and targeting

Pentamethinium indolium salts are promising fluorescence probes and anticancer agents with high mitochondrial selectivity. We synthesized two indolium pentamethinium salts: a cyclic form with quinoxaline directly incorporated in the pentamethinium chain (cPMS) and an open form with quinoxaline substitution in the γ-position (oPMS). To better understand their properties, we studied their interaction with mitochondrial phospholipids (cardiolipin and phosphatidylcholine) by spectroscopic methods (UV-Vis, fluorescence, and NMR spectroscopy). Both compounds displayed significant affinity for cardiolipin and phosphatidylcholine, which was associated with a strong change in their UV-Vis spectra. Nevertheless, we surprisingly observed that fluorescence properties of cPMS changed in complex with both cardiolipin and phosphatidylcholine, whereas those of oPMS only changed in complex with cardiolipin. Both salts, especially cPMS, display high usability in mitochondrial imaging and are cytotoxic for cancer cells. The above clearly indicates that conjugates of pentamethinium and quinoxaline group, especially cPMS, represent promising structural motifs for designing mitochondrial-specific agents.

Supra-Cyanines: Ultrabright Cyanine-Based Fluorescent Supramolecular Materials in Solution and in the Solid State

Fluorescent materials with high brightness play a crucial role in the advancement of various technologies such as bioimaging, photonics, and OLEDs. While significant efforts are dedicated to designing new organic dyes with improved performance, enhancing the brightness of existing dyes holds equal importance. In this study, we present a simple supramolecular strategy to develop ultrabright cyanine-based fluorescent materials by addressing long-standing challenges associated with cyanine dyes, including undesired cis-trans photoisomerization and aggregation-caused quenching. Supra-cyanines are obtained by incorporating cyanine moieties in a cyclic peptide-based supramolecular scaffold, and exhibit high fluorescence quantum yields (up to 50 %) in both solution and in the solid state. These findings offer a versatile approach for constructing highly emissive cyanine-based supramolecular materials.

Theoretical Study on the Optoelectronic Properties of Merocyanine-Dyes

Merocyanines, as prototypes of highly polar π-conjugated molecules, have been intensively investigated for their self-assembly and optoelectronic properties, both experimentally and theoretically. However, an accurate description of their structural and electronic properties remains challenging for quantum-chemical methods. We assessed several theoretical approaches, TD-DFT, GW-BSE, STEOM-DLPNO-CCSD, and CASSCF/NEVPT2-FIC for their reliability in reproducing optoelectronic properties of a series of donor/acceptor (D/A) merocyanines, focusing on the first excitation energy. Additionally, we tested an all-electron perturbative method based on time-dependent coupled-perturbed density functional theory, denoted as TDCP-DFT. Particular focus was set on direct and indirect solvent effects, which affect excited-state energies by electrostatic interaction and molecular geometry. The molecular configuration space was sampled at the semiempirical tight-binding level. Our results corroborate previous investigations, showing that the S0 - S1 excitation energy strongly depends on the merocyanine molecular structure and the dielectric constant of the solvent. We found significant effects of the polar solution environment on the geometry of the merocyanines, which strongly affect the calculated excitation energies. Taking these effects into account, the best agreement between calculated and measured excitation energies was obtained with TDCP-DFT and GW-BSE. We also calculated excitation energies of molecular crystals at the TDCP-DFT level and compared the results to the corresponding monomers.

Unravelling the Origin of the Vibronic Spectral Signatures in an Excitonically Coupled Indocarbocyanine Cy3 Dimer

The indocarbocyanine Cy3 dye is widely used to probe the dynamics of proteins and DNA. Excitonically coupled Cy3 dimers exhibit very unique spectral signatures that depend on the interchromophoric geometrical orientation induced by the environment, making them powerful tools to infer the dynamics of their surroundings. Understanding the origin of the dimeric spectral signatures is a necessity for an accurate interpretation of the experimental results. In this work, we simulate the vibronic spectrum of an experimentally well-studied Cy3 dimer, and we explain the origin of the experimental signatures present in its linear absorption spectrum. The Franck-Condon harmonic approximations, among other tests, are used to probe the factors contributing to the spectrum. It is found that the first peak in the absorption spectrum originates from the lower energy excitonic state, while the next two peaks are vibrational progressions of the higher energy excitonic state. The polar solvent plays a crucial role in the appearance of the spectrum, being responsible for the localized S1 minimum, which results in an increased intensity of the first peak.

Improved synthesis of DA364, an NIR fluorescence RGD probe targeting αvβ3 integrin

Optical imaging (OI) is gaining increasing attention in medicine as a non-invasive diagnostic imaging technology and as a useful tool for image-guided surgery. OI exploits the light emitted in the near-infrared region by fluorescent molecules able to penetrate living tissues. Cyanines are an important class of fluorescent molecules and by their conjugation to peptides it is possible to achieve optical imaging of tumours by selective targeting. We report here the improvements obtained in the synthesis of DA364, a small fluorescent probe (1.5 kDa) prepared by conjugation of pentamethine cyanine Cy5.5 to an RGD peptidomimetic, which can target tumour cells overexpressing integrin αvβ3 receptors.

The full spectrum tuning of fluorescent molecules via a one-pot multicomponent reaction

Fluorogenic probes for imaging enable visualization and analysis of difficult-to-reach cells and organelles. However, there are limited efficient examples of tuning these fluorescent molecules to higher wavelengths. This is vital since different tissues are sensitive to varying wavelength emissions. To address this need, we report the discovery, tuning, structure-photophysical property relationships (SPPR), and time-dependent DFT (TD-DFT) computations of 400-700+ nm fluorescent pyrido[2',1':2,3]imidazo[4,5-c]isoquinolines and substituted imidazo[1,2-a]pyridin-3-amines. The syntheses involve the trimethylsilylcyanide (TMSCN) modified Groebke-Blackburn-Bienaymé (GBB) multicomponent reaction as well as the TMSCN modified GBB combined with subsequent condensation of an aldehyde, and Aza-Friedel-Crafts-Intramolecular Cyclization-Oxidation all in one pot. The SPPR reveals that electron-withdrawing strength in the para-position of the aminopyridine starting material has direct control over the absorption and fluorescence emission wavelengths of these molecules. The TD-DFT computations show the changes in the natural transition orbitals (NTOs) with differing substitutions to the parent molecule that dictate the observed excitations, emissions, and fluorescence intensities. These findings give insights and directions for tuning the fluorescent properties of these motifs for various uses as probes and imaging agents.

Near-Infrared Molecular Logic Gate for In Situ Construction and Quantification of Cell-Macromolecule Conjugates

Engineering cell surfaces with macromolecules offers the potential to manipulate and control their phenotype and function for cell-based therapies. In situ construction and real-time evaluation of cell-macromolecule conjugates are vital for characterizing their dynamics, mobility, and function but remain a great challenge. Herein, we design a near-infrared (NIR) heptamethine cyanine (LS)-bearing dibenzocyclooctyne (DBCO) and norbornene (NB) in its structure for rapid and selective bioorthogonal "click" coupling to azide-labeled cells and tetrazine-functionalized macromolecular precursors. Specifically, only orthogonal dual "click" cell-macromolecule conjugates turn on NIR fluorescence, in which LS behaves as an AND logic gate, with azide- and tetrazine-derivatives being "input" and the emission intensity as the output. LS enables in situ construction and real-time evaluation of the process and functional effects that macromolecules "graft to" cells with high cytocompatibility. This probe is tailor-made for live-cell microscopy technologies, which may open new opportunities for promoting further developments in cell-tracking and cell-based therapies.

π-Electronic ion pairs: building blocks for supramolecular nanoarchitectonics viaiπ-iπ interactions

The pairing of charged π-electronic systems and their ordered arrangement have been achieved by iπ-iπ interactions that are derived from synergetically worked electrostatic and dispersion forces. Charged π-electronic systems that provide ion pairs as building blocks for assemblies have been prepared by diverse strategies for introducing charge in the core π-electronic systems. One method to prepare charged π-electronic systems is the use of covalent bonding that makes π-electronic ions and valence-mismatched metal complexes as well as protonated and deprotonated states. Noncovalent ion complexation is another method used to create π-electronic ions, particularly for anion binding, producing negatively charged π-electronic systems. Charged π-electronic systems afford various ion pairs, consisting of both cationic and anionic π-systems, depending on their combinations. Geometries and electronic states of the constituents in π-electronic ion pairs affect the photophysical properties and assembling modes. Recent progress in π-electronic ion pairs has revealed intriguing characteristics, including the transformation into radical pairs through electron transfer and the magnetic properties influenced by the countercations. Furthermore, the assembly states exhibit diversity as observed in crystals and soft materials including liquid-crystal mesophases. While the chemistry of ion pairs (salts) is well-established, the field of π-electronic ion pairs is relatively new; however, it holds great promise for future applications in novel materials and devices.

Xanthene, cyanine, oxazine and BODIPY: the four pillars of the fluorophore empire for super-resolution bioimaging

In the realm of biological research, the invention of super-resolution microscopy (SRM) has enabled the visualization of ultrafine sub-cellular structures and their functions in live cells at the nano-scale level, beyond the diffraction limit, which has opened up a new window for advanced biomedical studies to unravel the complex unknown details of physiological disorders at the sub-cellular level with unprecedented resolution and clarity. However, most of the SRM techniques are highly reliant on the personalized special photophysical features of the fluorophores. In recent times, there has been an unprecedented surge in the development of robust new fluorophore systems with personalized features for various super-resolution imaging techniques. To date, xanthene, cyanine, oxazine and BODIPY cores have been authoritatively utilized as the basic fluorophore units in most of the small-molecule-based organic fluorescent probe designing strategies for SRM owing to their excellent photophysical characteristics and easy synthetic acquiescence. Since the future of next-generation SRM studies will be decided by the availability of advanced fluorescent probes and these four fluorescent building blocks will play an important role in progressive new fluorophore design, there is an urgent need to review the recent advancements in designing fluorophores for different SRM methods based on these fluorescent dye cores. This review article not only includes a comprehensive discussion about the recent developments in designing fluorescent probes for various SRM techniques based on these four important fluorophore building blocks with special emphasis on their effective integration into live cell super-resolution bio-imaging applications but also critically evaluates the background of each of the fluorescent dye cores to highlight their merits and demerits towards developing newer fluorescent probes for SRM.

A new twist on PIFE: photoisomerisation-related fluorescence enhancement

PIFE was first used as an acronym for protein-induced fluorescence enhancement, which refers to the increase in fluorescence observed upon the interaction of a fluorophore, such as a cyanine, with a protein. This fluorescence enhancement is due to changes in the rate ofcis/transphotoisomerisation. It is clear now that this mechanism is generally applicable to interactions with any biomolecule. In this review, we propose that PIFE is thereby renamed according to its fundamental working principle as photoisomerisation-related fluorescence enhancement, keeping the PIFE acronym intact. We discuss the photochemistry of cyanine fluorophores, the mechanism of PIFE, its advantages and limitations, and recent approaches to turning PIFE into a quantitative assay. We provide an overview of its current applications to different biomolecules and discuss potential future uses, including the study of protein-protein interactions, protein-ligand interactions and conformational changes in biomolecules.

Aggregation induced nucleic acids recognition by homodimeric asymmetric monomethyne cyanine fluorochromes in mesenchymal stem cells

In the light of recent retrovirus pandemics, the issue of discovering new and diverse RNA-specific fluorochromes for research and diagnostics became of acute importance. The great majority of nucleic acid-specific probes either do not stain RNA or cannot distinguish between DNA and RNA. The versatility of polymethine dyes makes them suitable as stains for visualization, analysis, and detection of nucleic acids, proteins, and other biomolecules. We synthesized the asymmetric dicationic homodimeric monomethine cyanine dyes 1,1'-(1,3-phenylenebis(methylene))bis(4-((3-methylbenzo[d]thiazol-2(3H)-ylidene)methyl)pyridin-1-ium) bromide (Т1) and 1,1'-(1,3-phenylenebis(methylene))bis(4-((3-methylbenzo[d]thiazol-2(3H)-ylidene)methyl)quinolin-1-ium) bromide (M1) and tested their binding specificity, spectral characteristics, membrane penetration in living and fixed cells, cellular toxicity, and stability of fluorescent emission. Mesenchymal cells have diverse phenotypes and extensive proliferation and differentiation properties. We found dyes T1 and M1 to show high photochemical stability in living mesenchymal stem cells from apical papilla (SCAP) with a strong fluorescent signal when bound to nucleic acids. We found M1 to perform better than control fluorochrome (Hoechst 33342) for in vivo DNA visualization. T1, on the other hand, stains granular cellular structures resembling ribosomes in living cells and after permeabilization of the nuclear membrane stains the nucleoli and not the chromatin in the nucleus. This makes T1 suitable for the visualization of structures rich in RNA in living and fixed cells.

Near-infrared photodynamic and photothermal co-therapy based on organic small molecular dyes

Near-infrared (NIR) organic small molecule dyes (OSMDs) are effective photothermal agents for photothermal therapy (PTT) due to their advantages of low cost and toxicity, good biodegradation, and strong NIR absorption over a wide wavelength range. Nevertheless, OSMDs have limited applicability in PTT due to their low photothermal conversion efficiency and inadequate destruction of tumor regions that are nonirradiated by NIR light. However, they can also act as photosensitizers (PSs) to produce reactive oxygen species (ROS), which can be further eradicated by using ROS-related therapies to address the above limitations of PTT. In this review, the synergistic mechanism, composition, and properties of photodynamic therapy (PDT)-PTT nanoplatforms were comprehensively discussed. In addition, some specific strategies for further improving the combined PTT and PDT based on OSMDs for cancer to completely eradicate cancer cells were outlined. These strategies include performing image-guided co-therapy, enhancing tumor infiltration, increasing H2O2 or O2 in the tumor microenvironment, and loading anticancer drugs onto nanoplatforms to enable combined therapy with phototherapy and chemotherapy. Meanwhile, the intriguing prospects and challenges of this treatment modality were also summarized with a focus on the future trends of its clinical application.

Enhanced Lifetime of Cyanine Salts in Dilute Matrix Luminescent Solar Concentrators via Counterion Tuning

Organic luminophores offer great potential for energy harvesting and light emission due to tunable spectral properties, strong luminescence, high solubility, and excellent wavelength-selectivity. To realize their full potential, the lifetimes of luminophores must extend to many years under illumination. Many organic luminophores, however, have a tendency to degrade and undergo rapid photobleaching, leading to the perception of intrinsic instability of organic molecules. In this work we demonstrate that by exchanging the counterion of a heptamethine cyanine salt the photostability and corresponding lifetime of dilute cyanine salts can be enhanced by orders of magnitude from 10 hours to an extrapolated lifetime of greater than 65,000 hours under illumination. To help correlate and comprehend the underlying mechanism behind this phenomenon, the water contact angle and binding energy of each pairing were measured and calculated. We find that increased water contact angle, and therefore increasing hydrophobicity, generally correlate to improved lifetimes. Similarly, a lower absolute binding energy between cation and anion correlates to increased lifetimes. Utilizing the binding energy formalism, we predict the stability of a new anion and experimentally verify with good consistency. Moving forward, these factors could be used to rapidly screen and identify highly photostable organic luminophore salt systems for a range of energy harvesting and light emitting applications.

Cyclohexene-Embedded Dicyanomethylene Merocyanines - Consecutive Three-Component Coupling-Addition Synthesis and Chromophore Characteristics

A concise and efficient consecutive three-component alkynylation-addition synthesis of cyclohexene-embedded dicyanomethylene merocyanines furnishes a small library of dyes in moderate to excellent yield. The dyes possess strong absorption coefficients of the longest wavelength absorption bands. According to the crystal structure, the small bond length alternations account for a highly delocalized electronic ground state. The electronic structure of the absorption bands is qualitatively rationalized by TDDFT calculations, which explain that intense HOMO-LUMO transitions along the merocyanine axis lead to cyanine similar Stokes shifts.

Two-photon nanoprobes based on bioorganic nanoarchitectonics with a photo-oxidation enhanced emission mechanism

Two-photon absorption (TPA) fluorescence imaging holds great promise in diagnostics and biomedicine owing to its unparalleled spatiotemporal resolution. However, the adaptability and applicability of currently available TPA probes, which act as a critical element for determining the imaging contrast effect, is severely challenged by limited photo-luminescence in vivo. This is particularly a result of uncontrollable aggregation that causes fluorescence quenching, and inevitable photo-oxidation in harsh physiological milieu, which normally leads to bleaching of the dye. Herein, we describe the remarkably enhanced TPA fluorescence imaging capacity of self-assembling near-infrared (NIR) cyanine dye-based nanoprobes (NPs), which can be explained by a photo-oxidation enhanced emission mechanism. Singlet oxygen generated during photo-oxidation enables chromophore dimerization to form TPA intermediates responsible for enhanced TPA fluorescence emission. The resulting NPs possess uniform size distribution, excellent stability, more favorable TPA cross-section and anti-bleaching ability than a popular TPA probe rhodamine B (RhB). These properties of cyanine dye-based TPA NPs promote their applications in visualizing blood circulation and tumoral accumulation in real-time, even to cellular imaging in vivo. The photo-oxidation enhanced emission mechanism observed in these near-infrared cyanine dye-based nanoaggregates opens an avenue for design and development of more advanced TPA fluorescence probes.

A multifunctional 'golden cicada' nanoplatform breaks the thermoresistance barrier to launch cascade augmented synergistic effects of photothermal/gene therapy

BACKGROUND

Photothermal therapy (PTT) is taken as a promising strategy for cancer therapy, however, its applicability is hampered by cellular thermoresistance of heat shock response and insufficient accumulation of photothermal transduction agents in the tumor region. In consideration of those limitations, a multifunctional "Golden Cicada" nanoplatform (MGCN) with efficient gene delivery ability and excellent photothermal effects is constructed, overcoming the thermoresistance of tumor cells and improving the accumulation of indocyanine green (ICG).

RESULTS

Down-regulation of heat shock protein 70 (HSP70) makes tumor cells more susceptible to PTT, and a better therapeutic effect is achieved through such cascade augmented synergistic effects. MGCN has attractive features with prolonged circulation in blood, dual-targeting capability of CD44 and sialic acid (SA) receptors, and agile responsiveness of enzyme achieving size and charge double-variable transformation. It proves that, on the one hand, MGCN performs excellent capability for HSP70-shRNA delivery, resulting in breaking the cellular thermoresistance mechanism, on the other hand, ICG enriches in tumor site specifically and possesses a great thermal property to promoted PTT.

CONCLUSIONS

In short, MGCN breaks the protective mechanism of cellular heat stress response by downregulating the expression of HSP70 proteins and significantly augments synergistic effects of photothermal/gene therapy via cascade augmented synergistic effects.

Research on dye sensitized solar cells: recent advancement toward the various constituents of dye sensitized solar cells for efficiency enhancement and future prospects

It is universally accepted that the financial advancement of a state is essentially dependent upon the energy sector as it is essential in the growth, development, and improvement of the farming, mechanical, and defense sectors. A dependable source of energy is expected to enhance society's expectation of everyday comforts. Modern industrial advancement, which is indispensable for any nation, relies upon electricity. The principal explanation behind the energy emergency is rapidly increasing the use of hydrocarbon resources. Thus, the use of renewable resources is essential to overcome this dilemma. The consumption of hydrocarbon fuels and their discharge has destructive consequences on our surroundings. Third-generation photovoltaic (solar) cells are latest encouraging option in solar cells. Currently, dye-sensitized solar cells (DSSC) utilize organic (natural and synthetic) dye and inorganic (ruthenium) as a sensitizer. The nature of this dye combined with different variables has brought about a change in its use. Natural dyes are a feasible alternative in comparison to expensive and rare ruthenium dye owing to their low cast, easy utility, abundant supply of resources, and no environmental threat. In this review, the dyes generally utilized in DSSC are discussed. The DSSC criteria and components are explained, and the progress in inorganic and natural dyes is monitored. Scientists involved in this emerging technology will benefit from this examination.

Aggregates of Cyanine Dyes: When Molecular Vibrations and Electrostatic Screening Make the Difference

Aggregates of cyanine dyes are currently investigated as promising materials for advanced electronic and photonic applications. The spectral properties of aggregates of cyanine dyes can be tuned by altering the supramolecular packing, which is affected by the length of the dye, the presence of alkyl chains, or the nature of the counterions. In this work, we present a joint experimental and theoretical study of a family of cyanine dyes forming aggregates of different types according to the length of the polymethinic chain. Linear and nonlinear optical spectra of aggregates are rationalized here in terms of an essential-state model accounting for intermolecular interactions together with the molecular polarizability and vibronic coupling. A strategy is implemented to properly account for screening effects, distinguishing between electrostatic intermolecular interactions relevant to the ground state (mean-field effect) and the interactions relevant to the excited states (excitonic effects). To the best of our knowledge, this is the first attempt to simulate nonlinear spectral properties of aggregates of symmetric dyes accounting for molecular vibrations.

Domino protocol for the synthesis of diversely functionalized derivatives of a novel fused pentacyclic antioxidant/anticancer fluorescent scaffold: Pyrazolo[5'',1'':2',3']pyrimido[4',5':5,6][1,4]thiazino[2,3-b]quinoxaline

Rising to the challenge of formidable multi-step reaction needed for the synthesis of polycyclic compounds, an efficient one-pot two-step procedure for the synthesis of densely functionalized novel pyrazolo[5″,1'':2',3']pyrimido[4',5':5,6] [1,4]thiazino[2,3-b]quinoxalines from synthetically accessible starting materials 6-bromo-7-chloro-3-cyano-2-(ethylthio)-5-methylpyrazolo[1,5-a]pyrimidine, 3-aminoquinoxaline-2-thiol and some readily accessible alkyl halides was established. The domino reaction pathway involves cyclocondensation/N-alkylation sequence in K₂CO₃/N,N-dimethyl formamide under heating condition. DPPH free radical scavenging activity of all synthesized pyrazolo[5″,1'':2',3']pyrimido[4',5':5,6][1,4]thiazino[2,3-b]quinoxalines was evaluated to determine their antioxidant potentials. IC₅₀ values were recorded in the range of 29-71 μM. N-benzyl substituted derivative represented the most effective antioxidant activity as well as antiproliferative activity against MCF-7 cells. Moreover, fluorescence in solution for these compounds exhibited strong red emission in the visible region (λ_flu. = 536-558 nm) with good to excellent quantum yields (61-95%). Due to their interesting fluorescence properties, these novel pentacyclic fluorophores can be used as fluorescent markers and probes for studies in biochemistry and pharmacology.

Recent progress in the development of fluorescent probes for imaging pathological oxidative stress

Oxidative stress is closely related to the physiopathology of numerous diseases. Reactive oxygen species (ROS), reactive nitrogen species (RNS), and reactive sulfur species (RSS) are direct participants and important biomarkers of oxidative stress. A comprehensive understanding of their changes can help us evaluate disease pathogenesis and progression and facilitate early diagnosis and drug development. In recent years, fluorescent probes have been developed for real-time monitoring of ROS, RNS and RSS levels in vitro and in vivo. In this review, conventional design strategies of fluorescent probes for ROS, RNS, and RSS detection are discussed from three aspects: fluorophores, linkers, and recognition groups. We introduce representative fluorescent probes for ROS, RNS, and RSS detection in cells, physiological/pathological processes (e.g., Inflammation, Drug Induced Organ Injury and Ischemia/Reperfusion Injury etc.), and specific diseases (e.g., neurodegenerative diseases, epilepsy, depression, diabetes and cancer, etc.). We then highlight the achievements, current challenges, and prospects for fluorescent probes in the pathophysiology of oxidative stress-related diseases.

Colorimetric and near-infrared spectrophotometric monitoring of bisulfite using glyoxal modified chromenylium-cyanine chemosensor: Smartphone and paper strip applications for on-site food and beverages control

Detection of bisulfite (HSO₃^-) in food and beverages has vital importance because the excessive amount leads to ill effects on the human body. Colorimetric and fluorometric chromenylium-cyanine-based chemosensor CyR was synthesized and applied for high selective and sensitive analysis of HSO₃^- in red wine, rose wine and, granulated sugar with high recovery ranges and very fast response time without any interference from other competitive species. The limits of detection (LOD) for the UV-Vis and fluorescence titrations were found as 11.5 μM and 3.77 μM, respectively. The on-site and very rapid methods based on paper strips and smartphone which depend on the color changes from yellow to green have been successfully developed to analyze HSO₃^- concentration (10^-5-10^-1 M for paper strip and 163-1205 μM for smartphone). CyR and the bisulfite-adduct formed in the nucleophilic addition reaction with HSO₃^- were verified by FT-IR, ¹H NMR, and MALDI-TOF results as well as Single-Crystal X-Ray Crystallography for CyR.

Synthesis of stable class 5 mesoionic benzo[c]tetrazolo[2,3-a]cinnolinium thiolate, dicyanomethylide, and amides

Although class 5 mesoionic compounds show interesting electrical behaviour, they are generally unstable, readily undergoing ring-opening reactions. We designed and synthesized a bridged mesoionic derivative, benzo[c]tetrazolo[2,3-a]cinolinium (BTC), as a stable class 5 mesoionic compound, which was further transformed to the corresponding thiolate, cicyanomethylide, and amide. The intramolecular bridging imparted stability to the BTC thiolates and amides: the BTC thiolates were unsusceptible to ring-opening at high temperatures, and the BTC amides were stable in the absence of electron-withdrawing groups on the amide nitrogen. The properties of the BTC thiolate were compared with those of 2,3-diphenyltetrazolium derivatives based on UV-Vis absorption spectroscopy, single-crystal X-ray diffraction and quantum calculations.

Photoisomerization of Heptamethine Cyanine Dyes Results in Red-Emissive Species: Implications for Near-IR, Single-Molecule, and Super-Resolution Fluorescence Spectroscopy and Imaging

Photoisomerization kinetics of the near-infrared (NIR) fluorophore Sulfo-Cyanine7 (SCy7) was studied by a combination of fluorescence correlation spectroscopy (FCS) and transient state (TRAST) excitation modulation spectroscopy. A photoisomerized state with redshifted emission was identified, with kinetics consistent with a three-state photoisomerization model. Combining TRAST excitation modulation with spectrofluorimetry (spectral-TRAST) further confirmed an excitation-induced redshift in the emission spectrum of SCy7. We show how this red-emissive photoisomerized state contributes to the blinking kinetics in different emission bands of NIR cyanine dyes, and how it can influence single-molecule, super-resolution, as well as Förster resonance energy transfer (FRET) and multicolor readouts. Since this state can also be populated at moderate excitation intensities, it can also more broadly influence fluorescence readouts, also readouts not relying on high excitation conditions. However, this additional red-emissive state and its photodynamics, as identified and characterized in this work, can also be used as a strategy to push the emission of NIR cyanine dyes further into the NIR and to enhance photosensitization of nanoparticles with absorption spectra further into the NIR. Finally, we show that the photoisomerization kinetics of SCy7 and the formation of its redshifted photoisomer depend strongly on local environmental conditions, such as viscosity, polarity, and steric constraints, which suggests the use of SCy7 and other NIR cyanine dyes as environmental sensors. Such environmental information can be monitored by TRAST, in the NIR, with low autofluorescence and scattering conditions and on a broad range of samples and experimental conditions.

Multicomponent synthesis of chromophores – The one-pot approach to functional π-systems

Multicomponent reactions, conducted in a domino, sequential or consecutive fashion, have not only considerably enhanced synthetic efficiency as one-pot methodology, but they have also become an enabling tool for interdisciplinary research. The highly diversity-oriented nature of the synthetic concept allows accessing huge structural and functional space. Already some decades ago this has been recognized for life sciences, in particular, lead finding and exploration in pharma and agricultural chemistry. The quest for novel functional materials has also opened the field for diversity-oriented syntheses of functional π-systems, i.e. dyes for photonic and electronic applications based on their electronic properties. This review summarizes recent developments in MCR syntheses of functional chromophores highlighting syntheses following either the framework forming scaffold approach by establishing connectivity between chromophores or the chromogenic chromophore approach by de novo formation of chromophore of interest. Both approaches warrant rapid access to molecular functional π-systems, i.e. chromophores, fluorophores, and electrophores for various applications.

RNA G-quadruplex in live cells lighted-up by a thiazole orange analogue for SCA36 identification

SCA36 is a neurodegenerative disease mainly caused by the abnormal expansion of the GGGCCT repeat sequence in intron 1 of NOP56. The RNA sequences of this gene are expected to form large amounts of G-quadruplexes in the cytoplasm, which may be a potential intervention and detection target for SCA36. Here, we have developed a small-molecular compound named TCB-1, which shows good selectivity to the G-quadruplex structure, and its fluorescence can be enhanced by hundreds of folds. Interestingly, TCB-1 can avoid lysosome capture, evenly disperse in the cytoplasm, and selectively light up the cytoplasmic RNA G-quadruplexes. This property allows TCB-1 to sensitively detect the increased formation of cytoplasmic RNA G-quadruplexes in SCA36 model cells. This work not only provides new ideas for the design of small-molecule compounds targeting RNA G-quadruplexes in living cells, but also intuitively demonstrates the increased formation of RNA G-quadruplexes caused by NOP56 gene mutation, providing a possible tool for the detection of SCA36.

Synthesis of Heptamethine Cyanines from Furfural Derivatives

Despite the widespread theranostic utilization of cyanine dyes (Cy7), their synthetic method is still limited with pyridine or cyclohexanone derivatives as starting materials. Herein, we report the synthesis of Cy7 from furfural derivatives. First, a one-pot reaction strategy is developed to solve the unstable problem of the Stenhouse salts. Second, a stepwise condensation strategy is exploited to regioselectively synthesize asymmetrical Cy7. The methodology possesses advantages, such as easy handling, high yield, wide substrate scopes, and good functional group tolerance.

Charge-Segregated Stacking Structure with Anisotropic Electric Conductivity in NIR-Absorbing and Emitting Positively Charged π-Electronic Systems

Squarylium-based π-electronic cation with an augmented dipole was synthesized by methylation of zwitterionic squarylium. The cation formed various ion pairs in combination with anions, and the ion pairs exhibited distinct photophysical properties in the dispersed state, ascribed to the formation of J- and H-aggregates. The ion pairs provided solid-state assemblies based on cation stacking. It is noteworthy that complete segregation of cations and anions was observed in a pseudo-polymorph of the ion pair with pentacyanocyclopentadienide as a π-electronic anion. In the crystalline state, the ion pairs exhibited photophysical properties and electric conductivity derived from cation stacking. In particular, the charge-segregated ion-pairing assembly induces an electric conductive pathway along the stacking axis. The charge-segregated mode and fascinating properties were derived from the reduced electrostatic repulsion between adjacent π-electronic cations via dipole-dipole interactions.

Combined Fluorescence Fluctuation and Spectrofluorometric Measurements Reveal a Red-Shifted, Near-IR Emissive Photo-Isomerized Form of Cyanine 5

Cyanine fluorophores are extensively used in fluorescence spectroscopy and imaging. Upon continuous excitation, especially at excitation conditions used in single-molecule and super-resolution experiments, photo-isomerized states of cyanines easily reach population probabilities of around 50%. Still, effects of photo-isomerization are largely ignored in such experiments. Here, we studied the photo-isomerization of the pentamethine cyanine 5 (Cy5) by two similar, yet complementary means to follow fluorophore blinking dynamics: fluorescence correlation spectroscopy (FCS) and transient-state (TRAST) excitation-modulation spectroscopy. Additionally, we combined TRAST and spectrofluorimetry (spectral-TRAST), whereby the emission spectra of Cy5 were recorded upon different rectangular pulse-train excitations. We also developed a framework for analyzing transitions between multiple emissive states in FCS and TRAST experiments, how the brightness of the different states is weighted, and what initial conditions that apply. Our FCS, TRAST, and spectral-TRAST experiments showed significant differences in dark-state relaxation amplitudes for different spectral detection ranges, which we attribute to an additional red-shifted, emissive photo-isomerized state of Cy5, not previously considered in FCS and single-molecule experiments. The photo-isomerization kinetics of this state indicate that it is formed under moderate excitation conditions, and its population and emission may thus deserve also more general consideration in fluorescence imaging and spectroscopy experiments.

Double Hybrid Density Functionals for the Electronic Excitation Energies of Linear Cyanines

The lowest bright electronic excitations of seven model linear cyanines (CN3-CN15) using 28 double-hybrid (DH) density functionals are benchmarked against accurate and recent CC3 results. Some of these DH functionals are recently designed specifically for excited electronic state calculations. In addition, CIS, CIS(D), SCS-CIS(D), and SOS-CIS(D) were also tested. Four different basis sets were used for the vertical electronic excitation calculations: cc-pVDZ, aug-cc-pVDZ, cc-pVTZ, and aug-cc-pVTZ basis. Augmented basis sets (e.g. aug-cc-pVDZ and aug-cc-pVTZ) are found to be required for accurate and consistent results using DH functionals. The DH functionals tested in this work are classified into four main groups: global double-hybrids (GDH), range-separated double-hybrids (RSDH), spin-component and spin-opposite scaling global double-hybrids (SCS/SOS-GDH), and spin-component and spin-opposite scaling range-separated double-hybrids (SCS/SOS-RSDH). Within these groups, the SCS/SOS-RSDH group of functionals is found to provide the lowest mean absolute error (MAE) values (in the range 0.020-0.148 eV) in comparison with the GDH group (0.195-0.441 eV), the RSDH group (0.186-0.511 eV), and the SCS/SOS-GDH group (0.079-0.461 eV). Of all the DH functionals and ab initio methods investigated in the present contribution, the following functionals are found to be the most accurate and consistent: SCS-ωB2GPPLYP (MAE = 0.036 eV), SOS-ωB2GPPLYP (MAE = 0.020 eV), SOS-ωB88PP86 (MAE = 0.035 eV), and SOS-ωPBEPP86 (MAE = 0.037 eV). In general, the ab initio methods tested here show mediocre performance as compared to many DH functionals.