Molecular Dynamical and Quantum Mechanical Exploration of the Site-Specific Dynamics of Cy3 Dimers Internally Linked to dsDNA

Performing spectroscopic measurements on biomolecules labeled with fluorescent probes is a powerful approach to locating the molecular behavior and dynamics of large systems at specific sites within their local environments. The indocarbocyanine dye Cy3 has emerged as one of the most commonly used chromophores. The incorporation of Cy3 dimers into DNA enhances experimental resolution owing to the spectral characteristics influenced by the geometric orientation of excitonically coupled monomeric units. Various theoretical models and simulations have been utilized to aid in the interpretation of the experimental spectra. In this study, we employ all-atom molecular dynamics simulations to study the structural dynamics of Cy3 dimers internally linked to the dsDNA backbone. We used quantum mechanical calculations to derive insights from both the linear absorption spectra and the circular dichroism data. Furthermore, we explore potential limitations within a commonly used force field for cyanine dyes. The molecular dynamics simulations suggest the presence of four possible Cy3 dimeric populations. The spectral simulations on the four populations show one of them to agree better with the experimental signatures, suggesting it to be the dominant population. The relative orientation of Cy3 in this population compares very well with previous predictions from the Holstein-Frenkel Hamiltonian model.

Neutral Cyanine: Ultra-Stable NIR-II Merocyanines for Highly Efficient Bioimaging and Tumor-Targeted Phototheranostics

Fluorescence imaging (FLI)-guided phototheranostics using emission from the second near-infrared (NIR-II) window show significant potential for cancer diagnosis and treatment. Clinical imaging-used polymethine ionic indocyanine green (ICG) dye is widely adopted for NIR fluorescence imaging-guided photothermal therapy (PTT) research due to its exceptional photophysical properties. However, ICG has limitations such as poor photostability, low photothermal conversion efficiency (PCE), short-wavelength emission peak, and liver-targeting issues, which restrict its wider use. In this study, two ionic ICG derivatives are transformed into neutral merocyanines (mCy) to achieve much-enhanced performance for NIR-II cancer phototheranostics. Initial designs of two ionic dyes show similar drawbacks as ICG in terms of poor photostability and low photothermal performance. One of the modified neutral molecules, mCy890, shows significantly improved stability, an emission peak over 1000 nm, and a high photothermal PCE of 51%, all considerably outperform ICG. In vivo studies demonstrate that nanoparticles of the mCy890 can effectively accumulate at the tumor sites for cancer photothermal therapy guided by NIR-II fluorescence imaging. This research provides valuable insights into the development of neutral merocyanines for enhanced cancer phototheranostics.

Tetraanionic Oligo-Dioxaborines: Strongly Absorbing Near-Infrared Dyes

Polymethine dyes of tetraanionic nature comprising 1,3,2-dioxaborine rings in the polymethine chain and end-groups of different electron-accepting abilities have been synthesized. They can be considered as oligomeric polymethines, where a linear conjugated π-system passes through three 1,3,2-dioxaborine units and a number of tri- and dimethine π-bridges between two end-groups. The obtained dyes exhibit near-infrared absorption and fluorescence, with molar absorption coefficients reaching as high as 564000 M-1 cm-1 in DMF, rendering them among the strongest absorbers known. The novel compounds are bright NIR fluorophores, with fluorescence quantum yields up to 0.13 in DMF. A comparative analysis of the electronic structure of the obtained dyes with respective dianionic and trianionic oligomers was conducted through quantum chemical calculations.

Push-Pull Heptamethines Near the Cyanine Limit Exhibiting Large Quadratic Electro-Optic Effect

Harnessing the quadratic electro-optic (QEO) of near-infrared polymethine chromophores over broad telecom wavelength bands is a subject of immense potential but remains largely under-investigated. Herein a series of push-pull heptamethines containing the tricyanofuran (TCF) acceptors and indoline or benzo[e]indoline donors are reported. These dipolar chromophores can attain a highly delocalized "cyanine-like" electronic ground state in solvents spanning a wide range of polarities, in some cases even closer to the ideal polymethine state than symmetrical cyanines. A transmission-mode electromodulation spectroscopy is used to study the electric-field-induced changes in optical absorption and refraction of polymer films doped with heptamethine chromophores, and large and thermally stable QEO effect with high efficiency-loss figure-of-merits that compare favorably to those from dipolar polyenes in poled or unpoled polymers and III-V semiconductors is obtained. The study opens a path for developing organic materials based on cyanine-like merocyanines for complementary metal oxide semiconductor -compatible, fast, efficient, and low-loss electro-optic modulation.

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.

Merocyanines form bacteriorhodopsins with strongly bathochromic absorption maxima

There is a need to shift the absorbance of biomolecules to the optical transparency window of tissue for applications in optogenetics and photo-pharmacology. There are a few strategies to achieve the so-called red shift of the absorption maxima. Herein, a series of 11 merocyanine dyes were synthesized and employed as chromophores in place of retinal in bacteriorhodopsin (bR) to achieve a bathochromic shift of the absorption maxima relative to bR's [Formula: see text] of 568 nm. Assembly with the apoprotein bacterioopsin (bO) led to stable, covalently bound chromoproteins with strongly bathochromic absorbance bands, except for three compounds. Maximal red shifts were observed for molecules 9, 2, and 8 in bR where the [Formula: see text] was 766, 755, and 736 nm, respectively. While these three merocyanines have different end groups, they share a similar structural feature, namely, a methyl group which is located at the retinal equivalent position 13 of the polyene chain. The absorption and fluorescence data are also presented for the retinal derivatives in their aldehyde, Schiff base (SB), and protonated SB (PSB) forms in solution. According to their hemicyanine character, the PSBs and their analogue bRs exhibited fluorescence quantum yields (Φf) several orders of magnitude greater than native bR (Φf 0.02 to 0.18 versus 1.5 × 10-5 in bR) while also exhibiting much smaller Stokes shifts than bR (400 to 1000 cm-1 versus 4030 cm-1 in bR). The experimental results are complemented by quantum chemical calculations where excellent agreement between the experimental [Formula: see text] and the calculated [Formula: see text] was achieved with the second-order algebraic-diagrammatic construction [ADC(2)] method. In addition, quantum mechanics/molecular mechanics (QM/MM) calculations were employed to shed light on the origin of the bathochromic shift of merocyanine 2 in bR compared with native bR.

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.

Tunable Electronic Structure via DNA-Templated Heteroaggregates of Two Distinct Cyanine Dyes

Molecular excitons are useful for applications in light harvesting, organic optoelectronics, and nanoscale computing. Electronic energy transfer (EET) is a process central to the function of devices based on molecular excitons. Achieving EET with a high quantum efficiency is a common obstacle to excitonic devices, often owing to the lack of donor and acceptor molecules that exhibit favorable spectral overlap. EET quantum efficiencies may be substantially improved through the use of heteroaggregates-aggregates of chemically distinct dyes-rather than individual dyes as energy relay units. However, controlling the assembly of heteroaggregates remains a significant challenge. Here, we use DNA Holliday junctions to assemble homo- and heterotetramer aggregates of the prototypical cyanine dyes Cy5 and Cy5.5. In addition to permitting control over the number of dyes within an aggregate, DNA-templated assembly confers control over aggregate composition, i.e., the ratio of constituent Cy5 and Cy5.5 dyes. By varying the ratio of Cy5 and Cy5.5, we show that the most intense absorption feature of the resulting tetramer can be shifted in energy over a range of almost 200 meV (1600 cm^-1). All tetramers pack in the form of H-aggregates and exhibit quenched emission and drastically reduced excited-state lifetimes compared to the monomeric dyes. We apply a purely electronic exciton theory model to describe the observed progression of the absorption spectra. This model agrees with both the measured data and a more sophisticated vibronic model of the absorption and circular dichroism spectra, indicating that Cy5 and Cy5.5 heteroaggregates are largely described by molecular exciton theory. Finally, we extend the purely electronic exciton model to describe an idealized J-aggregate based on Förster resonance energy transfer (FRET) and discuss the potential advantages of such a device over traditional FRET relays.

Rational Design of a Near-Infrared Ratiometric Probe with a Large Stokes Shift: Visualization of Polarity Abnormalities in Non-Alcoholic Fatty Liver Model Mice

Tracking liver polarity with noninvasive and dynamic imaging techniques is helpful to better understand the non-alcoholic fatty liver (NAFL). Herein, a novel near-infrared (NIR) fluorescent probe Cy-Mp is constructed using a "symmetry collapse" strategy. The structure modification leads to the conversion of locally excited state fluorescence to charge transfer state fluorescence. Cy-Mp emits at near-infrared (NIR) wavelengths with high photostability as well as a large Stokes shift. Cy-Mp exhibits a ratiometric response to polarity, providing more accurate analysis of intracellular polarity via the built-in internal reference correction. Most importantly, the in vivo studies indicate that Cy-Mp can accumulate in the liver and the decreased polarity in the liver of mice with NAFL is verified by the ratiometric imaging, implying the great potential of Cy-Mp in the diagnosis of NAFL.

Modeling the Electronic Absorption Spectra of the Indocarbocyanine Cy3

Accurate modeling of optical spectra requires careful treatment of the molecular structures and vibronic, environmental, and thermal contributions. The accuracy of the computational methods used to simulate absorption spectra is limited by their ability to account for all the factors that affect the spectral shapes and energetics. The ensemble-based approaches are widely used to model the absorption spectra of molecules in the condensed-phase, and their performance is system dependent. The Franck-Condon approach is suitable for simulating high resolution spectra of rigid systems, and its accuracy is limited mainly by the harmonic approximation. In this work, the absorption spectrum of the widely used cyanine Cy3 is simulated using the ensemble approach via classical and quantum sampling, as well as, the Franck-Condon approach. The factors limiting the ensemble approaches, including the sampling and force field effects, are tested, while the vertical and adiabatic harmonic approximations of the Franck-Condon approach are also systematically examined. Our results show that all the vertical methods, including the ensemble approach, are not suitable to model the absorption spectrum of Cy3, and recommend the adiabatic methods as suitable approaches for the modeling of spectra with strong vibronic contributions. We find that the thermal effects, the low frequency modes, and the simultaneous vibrational excitations have prominent contributions to the Cy3 spectrum. The inclusion of the solvent stabilizes the energetics significantly, while its negligible effect on the spectral shapes aligns well with the experimental observations.

Sensitization of Nd3+ Luminescence by Simultaneous Two-Photon Excitation through a Coordinating Polymethinic Antenna

We have designed and synthesized two new cyaninic Nd³⁺ complexes where the lanthanide emission can be induced from simultaneous two-photon absorption followed by energy migration. These complexes correspond to a molecular design that uses an antenna ligand formed by the functionalization of a heptamethine dye with 5-ol-phenanthroline or 4-phenyl-terpyridine derivatives. These complexes employ the important nonlinear optical properties of symmetric polymethines to sensitize the lanthanide ion. We verified that simultaneous biphotonic excitation indirectly induces the ⁴F_3/2 → ⁴I_11/2 Nd³⁺ emission using femtosecond laser pulses tuned below the first electronic transition of the antenna. The simultaneous two-photon excitation events initially form the nonlinear-active second excited singlet of the polymethine antenna, which rapidly evolves into its first excited singlet. This state in turn induces the formation of the emissive Nd³⁺ states through energy transfer. The role of the first excited singlet of the antenna as the donor state in this process was verified through time resolution of the antenna's fluorescence. These measurements also provided the rates for antenna-lanthanide energy transfer, which indicate that the phenanthroline-type ligand is approximately five times more efficient for energy transfer than the phenyl-terpyridine derivative due to their relative donor-acceptor distances. The simultaneous two-photon excitation of this polymethine antenna allows for high spatial localization of the Nd³⁺excitation events.

Far-Red Absorbing Rhodopsins, Insights From Heterodimeric Rhodopsin-Cyclases

The recently discovered Rhodopsin-cyclases from Chytridiomycota fungi show completely unexpected properties for microbial rhodopsins. These photoreceptors function exclusively as heterodimers, with the two subunits that have very different retinal chromophores. Among them is the bimodal photoswitchable Neorhodopsin (NeoR), which exhibits a near-infrared absorbing, highly fluorescent state. These are features that have never been described for any retinal photoreceptor. Here these properties are discussed in the context of color-tuning approaches of retinal chromophores, which have been extensively studied since the discovery of the first microbial rhodopsin, bacteriorhodopsin, in 1971 (Oesterhelt et al., Nature New Biology, 1971, 233 (39), 149-152). Further a brief review about the concept of heterodimerization is given, which is widely present in class III cyclases but is unknown for rhodopsins. NIR-sensitive retinal chromophores have greatly expanded our understanding of the spectral range of natural retinal photoreceptors and provide a novel perspective for the development of optogenetic tools.

General and practical synthesis of naphtho[2,1-d]oxazoles from naphthols and amines

A general and practical synthesis of naphtho[2,1-d]oxazoles from readily available naphthols and amines is developed using TEMPO as the oxygen source with outstanding functional group tolerance, especially for the construction...

Rational Selection of Cyanines to Generate Conjugate Acid and Free Radicals for Photopolymerization upon Exposure at 860 nm

Different cyanines absorbing in the NIR between 750 and 930 nm were applied to study the efficiency of both radical and cationic polymerization in combination with diaryliodonium salt. Variation of the connecting methine chain and structure of the terminal indolium moiety provided a deeper insight in the structure of the cyanine NIR‐sensitizer and the efficiency to generate initiating radicals and conjugate acid. Photophysical studies were pursued by fluorescence spectroscopy providing a deeper understanding regarding the lifetime of the excited state and contribution of nonradiative deactivation resulting in generation of additional heat in the polymerization process. Furthermore, electrochemical experiments demonstrated connection to oxidation and reduction capability as influenced by the structural pattern of the sensitizer. LC–MS measurements provided a deeper pattern about the photoproducts formed. A nonamethine‐based cyanine showed the best performance regarding bleaching in combination with an iodonium salt at 860 nm.

Aggregation of Amphiphilic Carbocyanines: Fluorination Favors Cylindrical Micelles over Bilayered Tubes

The synthesis of a new amphiphilic 5,5',6,6'-tetrachlorobenzimidacarbocyanine dye derivative with -(CH₂)₂-(CF₂)₅-CF₃ chains attached to the nitrogen atoms in the 1,1'-position, CF8O3, is reported. Depending on the dye concentration and the addition of MeOH, CF8O3 forms J- and H-aggregates in aqueous solutions. The aggregation behavior was investigated using steady-state absorption, linear dichroism, and fluorescence spectroscopy, as well as by cryogenic transmission electron microscopy (cryo-TEM). The J-band of the MeOH-free solution is monomer-like, rather broad, and less red-shifted with respect to the monomer absorption, indicating weak excitonic coupling and disorder effects. Cryo-TEM reveals a diversity of supramolecular structures, wherein linear and branched cylindrical micelles dominate. It is concluded that the high stiffness of fluoroalkyl chains does not allow the chains to splay and completely fill up the hydrophobic gap between opposing chromophores. This destabilizes the bilayers and favors the micellar structure motifs instead. The aggregates appearing at 30% MeOH show a split absorption spectrum consisting of a broad blue-shifted H-band and an accompanying sharp red-shifted J-band with perpendicular polarizations. These HJ-type aggregates are also composed of micellar fibers, but these bundle into rope-like strands. For 10% MeOH, a narrow bilayered tube is the dominating morphology. The observed MeOH dependence of aggregation reveals a clear cosolvent effect.

Merocyanine dyes

Merocyanine dyes belong to the class of neutral polymethine dyes, where one terminal component is typically found in cyanine dyes and the second obtained from an active methylene compound. The different electron acceptor/donator abilities of the two terminal components have a marked impact on the electronic structure of a merocyanine dye and its equilibrium structure and electronic spectra. Their first technical application was spectral sensitization in silver halide photography. Today they have numerous of applications in textile dyeing and as membrane potential sensitive fluorescent dyes.

Delocalized Two-Exciton States in DNA Scaffolded Cyanine Dimers

The engineering and manipulation of delocalized molecular exciton states is a key component for artificial biomimetic light harvesting complexes as well as alternative circuitry platforms based on exciton propagation. Here we examine the consequences of strong electronic coupling in cyanine homodimers on DNA duplex scaffolds. The most closely spaced dyes, attached to positions directly across the double-helix from one another, exhibit pronounced Davydov splitting due to strong electronic coupling. We demonstrate that the DNA scaffold is sufficiently robust to support observation of the transition from the lowest energy (J-like) one-exciton state to the nonlocal two-exciton state, where each cyanine dye is in the excited state. This transition proceeds via sequential photon absorption and persists for the lifetime of the exciton, establishing this as a controlled method for creating two-exciton states. Our observations suggest that DNA-organized dye networks have potential as platforms for molecular logic gates and entangled photon emission based on delocalized two-exciton states.

DNA scaffold supports long-lived vibronic coherence in an indodicarbocyanine (Cy5) dimer

Vibronic coupling between pigment molecules is believed to prolong coherences in photosynthetic pigment–protein complexes. Reproducing long-lived coherences using vibronically coupled chromophores in synthetic DNA constructs presents a biomimetic route to efficient artificial light harvesting. Here, we present two-dimensional (2D) electronic spectra of one monomeric Cy5 construct and two dimeric Cy5 constructs (0 bp and 1 bp between dyes) on a DNA scaffold and perform beating frequency analysis to interpret observed coherences. Power spectra of quantum beating signals of the dimers reveal high frequency oscillations that correspond to coherences between vibronic exciton states. Beating frequency maps confirm that these oscillations, 1270 cm⁻¹ and 1545 cm⁻¹ for the 0-bp dimer and 1100 cm⁻¹ for the 1-bp dimer, are coherences between vibronic exciton states and that these coherences persist for ∼300 fs. Our observations are well described by a vibronic exciton model, which predicts the excitonic coupling strength in the dimers and the resulting molecular exciton states. The energy spacing between those states closely corresponds to the observed beat frequencies. MD simulations indicate that the dyes in our constructs lie largely internal to the DNA base stacking region, similar to the native design of biological light harvesting complexes. Observed coherences persist on the timescale of photosynthetic energy transfer yielding further parallels to observed biological coherences, establishing DNA as an attractive scaffold for synthetic light harvesting applications.

Dyes coupled to DNA display distance-dependent vibronic couplings that prolongs quantum coherences detected with 2D spectroscopy.

Identification of Nonradiative Decay Pathways in Cy3

Photoexcited fluorescent markers are extensively used in spectroscopy, imaging, and analysis of biological systems. The performance of fluorescent markers depends on high levels of emission, which are limited by competing nonradiative decay pathways. Small-molecule fluorescent dyes have been increasingly used as markers due to their high and stable emission. Despite their prevalence, the nonradiative decay pathways of these dyes have not been determined. Here, we investigate these pathways for a widely used indocarbocyanine dye, Cy3, using transient grating spectroscopy. We identify a nonradiative decay pathway via a previously unknown dark state formed within ∼1 ps of photoexcitation. Our experiments, in combination with electronic structure calculations, suggest that the generation of the dark state is mediated by picosecond vibrational mode coupling, likely via a conical intersection. We further identify the vibrational modes, and thus structural elements, responsible for the formation and dynamics of the dark state, providing insight into suppressing nonradiative decay pathways in fluorescent markers such as Cy3.

Stereochemistry-Controlled Supramolecular Architectures of New Tetrahydroxy-Functionalised Amphiphilic Carbocyanine Dyes

The syntheses of novel amphiphilic 5,5',6,6'-tetrachlorobenzimidacarbocyanine (TBC) dye derivatives with aminopropanediol head groups, which only differ in stereochemistry (chiral enantiomers, meso form and conformer), are reported. For the achiral meso form, a new synthetic route towards asymmetric cyanine dyes was established. All compounds form J aggregates in water, the optical properties of which were characterised by means of spectroscopic methods. The supramolecular structure of the aggregates is investigated by means of cryo-transmission electron microscopy, cryo-electron tomography and AFM, revealing extended sheet-like aggregates for chiral enantiomers and nanotubes for the mesomer, respectively, whereas the conformer forms predominately needle-like crystals. The experiments demonstrate that the aggregation behaviour of compounds can be controlled solely by head group stereochemistry, which in the case of enantiomers enables the formation of extended hydrogen-bond chains by the hydroxyl functionalities. In case of the achiral meso form, however, such chains turned out to be sterically excluded.

Dye-Loaded Quatsomes Exhibiting FRET as Nanoprobes for Bioimaging

Fluorescent organic nanoparticles (FONs) are emerging as an attractive alternative to the well-established fluorescent inorganic nanoparticles or small organic dyes. Their proper design allows one to obtain biocompatible probes with superior brightness and high photostability, although usually affected by low colloidal stability. Herein, we present a type of FONs with outstanding photophysical and physicochemical properties in-line with the stringent requirements for biomedical applications. These FONs are based on quatsome (QS) nanovesicles containing a pair of fluorescent carbocyanine molecules that give rise to Förster resonance energy transfer (FRET). Structural homogeneity, high brightness, photostability, and high FRET efficiency make these FONs a promising class of optical bioprobes. Loaded QSs have been used for in vitro bioimaging, demonstrating the nanovesicle membrane integrity after cell internalization, and the possibility to monitor the intracellular vesicle fate. Taken together, the proposed QSs loaded with a FRET pair constitute a promising platform for bioimaging and theranostics.

Cyanine dyes

Cyanine dyes are characterized by an odd number 2n + 3 of π-centers and 2n + 4 π-electrons (where n is the number of vinyl groups –CH = CH–). This special feature has a marked impact on their electronic structure and thus their equilibrium structure in the electronic ground state as well their color and electronic spectrum, respectively. Their first technical application was the use as spectral sensitizers in silver halide photography. Today they have numerous of applications in digital optical data storage, Computer-to-Plate lithographic printing plates, bio-analysis and medical diagnostics.

DNA-Enabled Chiral Gold Nanoparticle-Chromophore Hybrid Structure with Resonant Plasmon-Exciton Coupling Gives Unusual and Strong Circular Dichroism

Circular dichroism (CD) from hybrid complexes of plasmonic nanostructures and chiral molecules has recently attracted significant interest. However, the hierarchical chiral self-assembly of molecules on surfaces of metal nanostructures has remained challenging. As a result, a deep understanding of plasmon-exciton coupling between surface plasmons and chiral collective molecular excitations has not been achieved. In particular, the critical impact of resonant plasmon-exciton coupling within the hybrid is unclear. Here, we employed DNA-templated strategies to control the chiral self-assembly of achiral chromophores with rationally tuned exciton transitions on gold nanosphere (AuNP) or gold nanorod (AuNR) surfaces. Unlike many previous chiral plasmonic hybrids utilizing chiral biomolecules with CD signals in the UV range, we designed structures with the chiral excitonic resonances at visible wavelengths. The constructed hybrid complexes displayed strong chiroptical activity that depends on the spectral overlap between the chiral collective molecular excitations and the plasmon resonances. We find that when spectral overlap is optimized, the molecular CD signal originating from the chiral self-assemblies of chromophores was strongly enhanced (maximum enhancement of nearly an order of magnitude) and a plasmonic CD signal was induced. Surprisingly, the sign of the molecular CD was reversed despite different self-assembly mechanisms of the Au nanoparticle-chromophore hybrids. Our results provide new insight into plasmonic CD enhancements and will inspire further studies on chiral light-matter interactions in strongly coupled plasmonic-excitonic systems.

Photochemistry with Cyanines in the Near Infrared: A Step to Chemistry 4.0 Technologies

Cyanines covering the absorption in the near infrared (NIR) are attractive for distinct applications. They can interact either with lasers exhibiting line-shaped focus emitting at both 808 and 980 nm or bright high intensity NIR-LEDs with 805 nm emission, respectively. This is drawing attention to Industry 4.0 applications. The major deactivation occurs through a non-radiative process resulting in the release of heat into the surrounding, although a small fraction of radiative deactivation also takes place. Most of these NIR-sensitive systems possess an internal activation barrier to react in a photonic process with initiators resulting in the generation of reactive radicals and acidic cations. Thus, the heat released by the NIR absorber helps to bring the system, consisting of an NIR sensitizer and initiator, above such internal barriers. Molecular design strategies making these systems more compatible with distinct applications in a certain oleophilic surrounding are considered as a big challenge. This includes variations of the molecular pattern and counter ions derived from super acids exhibiting low coordinating properties. Further discussion focusses on the use of such systems in Chemistry 4.0 related applications. Intelligent software tools help to improve and optimize these systems combining chemistry, engineering based on high-throughput formulation screening (HTFS) technologies, and machine learning algorithms to open up novel solutions in material sciences.

Unified Model for Photophysical and Electro-Optical Properties of Green Fluorescent Proteins

Green fluorescent proteins (GFPs) have become indispensable imaging and optogenetic tools. Their absorption and emission properties can be optimized for specific applications. Currently, no unified framework exists to comprehensively describe these photophysical properties, namely the absorption maxima, emission maxima, Stokes shifts, vibronic progressions, extinction coefficients, Stark tuning rates, and spontaneous emission rates, especially one that includes the effects of the protein environment. In this work, we study the correlations among these properties from systematically tuned GFP environmental mutants and chromophore variants. Correlation plots reveal monotonic trends, suggesting that all these properties are governed by one underlying factor dependent on the chromophore's environment. By treating the anionic GFP chromophore as a mixed-valence compound existing as a superposition of two resonance forms, we argue that this underlying factor is defined as the difference in energy between the two forms, or the driving force, which is tuned by the environment. We then introduce a Marcus-Hush model with the bond length alternation vibrational mode, treating the GFP absorption band as an intervalence charge transfer band. This model explains all of the observed strong correlations among photophysical properties; related subtopics are extensively discussed in the Supporting Information. Finally, we demonstrate the model's predictive power by utilizing the additivity of the driving force. The model described here elucidates the role of the protein environment in modulating the photophysical properties of the chromophore, providing insights and limitations for designing new GFPs with desired phenotypes. We argue that this model should also be generally applicable to both biological and nonbiological polymethine dyes.

Improvement of Photostability and NIR Activity of Cyanine Dye through Nanohybrid Formation: Key Information from Ultrafast Dynamical Studies

Near-infrared (NIR) light harvesting has enormous importance for different potential applications in the modern era of research. Some NIR cyanine dyes such as IR820 have achieved great success in energy harvesting and cancer therapy. However, their action is limited for low photostability, considerable thermal degradation, short circulation times, and nonspecific biodistribution. Our present study is an attempt to overcome such limitations by attaching a model cyanine dye IR820 with ZnO nanoparticles. We prepared an IR820-ZnO nanohybrid and characterized it using microscopic and optical spectroscopic tools. Thermogravimetric analysis depicted greater thermal stability of the IR820-ZnO nanohybrid compared to free dye. We explored the enhancement in the photostability of IR820 upon nanohybrid formation. We detected generation of photoinduced reactive oxygen species (ROS) such as superoxide, singlet oxygen, and so forth using appropriate molecular probes. The formation of IR820-ZnO nanohybrid reduced production of photoinduced singlet oxygen. However, it revealed an alternative trend in overall ROS formation (increases total ROS) under red light illumination. To correlate the enhanced photostability of IR820 on the ZnO surface, we explored excited-state dynamical processes at the interface in nanohybrids. We illustrated the photoinduced excited-state electron-transfer process from the lowest unoccupied molecular orbital of IR820 to the conduction band of ZnO. This photoelectron-transfer process enhances the production of ROS and decreases the formation of singlet oxygen that altogether leads to improvement in photostability and overall activity. A quencher of singlet oxygen sodium azide (NaN₃) was used to further confirm the direct association of singlet oxygen generation with the photostability issue of IR820. Also, ZnO is able to deliver the dye selectively in acidic environment, which suggests its diseased site-specific targeted activity. Our results provide promising improvement for potential use of IR820 through formation of a nanohybrid that could be translated for other NIR cyanine dyes.

Optical Properties of Vibronically Coupled Cy3 Dimers on DNA Scaffolds

We examine the effect of electronic coupling on the optical properties of Cy3 dimers attached to DNA duplexes as a function of base pair (bp) separation using steady-state and time-resolved spectroscopy. For close Cy3-Cy3 separations, 0 and 1 bp between dyes, intermediate to strong electronic coupling is revealed by modulation of the absorption and fluorescence properties including spectral band shape, peak wavelength, and excited-state lifetime. Using a vibronic exciton model, we estimate coupling strengths of 150 and 266 cm^-1 for the 1 and 0 bp separations, respectively, which are comparable to those found in natural light-harvesting complexes. For the strongest electronic coupling (0 bp separation), we observe that the absorption band shape is strongly affected by the base pairs that surround the dyes, where more strongly hydrogen-bonded G-C pairs produce a red-shifted absorption spectrum consistent with a J-type dimer. This effect is studied theoretically using molecular dynamics simulation, which predicts an in-line dye configuration that is consistent with the experimental J-type spectrum. When the Cy3 dimers are in a standard aqueous buffer, the presence of relatively strong electronic coupling is accompanied by decreased fluorescence lifetime, suggesting that it promotes nonradiative relaxation in cyanine dyes. However, we show that the use of a viscous solvent can suppress this nonradiative recombination and thereby restore the dimer fluorescent emission. Ultrafast transient absorption measurements of Cy3 dimers in both standard aqueous buffer and viscous glycerol buffer suggest that sufficiently strong electronic coupling increases the probability of excited-state relaxation through a dark state that is related to Cy3 torsional motion.

Fine Structure in Electronic Spectra of Cyanine Dyes: Are Sub-Bands Largely Determined by a Dominant Vibration or a Collection of Singly Excited Vibrations?

This work critically examines attempts to model the fine structure apparent in electronic spectra of cyanine dyes and their analogues. Numerous computational studies reported over the past decade attribute the origin of sub‐bands and their relative intensities to vibronic transitions in which the relevant electronic transition is coupled, irrespective of symmetry, with a collection of vibrations. It is contended that this type of approach is not supported by experimental evidence. An argument is reiterated for a more appropriate model that adheres closely to fundamental principles and fits the data. It stipulates that essentially just one symmetric vibration, carbon–carbon bond stretching of the cyanine polymethine chain, dominates the coupling and is responsible for the observed fine structure. Furthermore, it is pointed out that the intensities of the sub‐bands are readily explained by means of the Franck–Condon principle.

Tubular J-aggregates of a new thiacarbocyanine Cy5 dye for the far-red spectral region – a spectroscopic and cryo-transmission electron microscopy study

A new phenol-substituted Cy5 dye forms tubular J-aggregates that are active in the far-red spectral region.

Polarization, second-order nonlinear optical properties and electrochromism in 4H-pyranylidene chromophores with a quinoid/aromatic thiophene ring bridge

The second-order NLO responses and spectroelectrochemical properties of donor–π–acceptor systems featuring a quinoid/aromatic thiophene unit have been studied.

25th anniversary article: Design of polymethine dyes for all-optical switching applications: guidance from theoretical and computational studies

All-optical switching--controlling light with light--has the potential to meet the ever-increasing demand for data transmission bandwidth. The development of organic π-conjugated molecular materials with the requisite properties for all-optical switching applications has long proven to be a significant challenge. However, recent advances demonstrate that polymethine dyes have the potential to meet the necessary requirements. In this review, we explore the theoretical underpinnings that guide the design of π-conjugated materials for all-optical switching applications. We underline, from a computational chemistry standpoint, the relationships among chemical structure, electronic structure, and optical properties that make polymethines such promising materials.

Pinacyanol chloride forms mesoscopic H- and J-aggregates in aqueous solution – a spectroscopic and cryo-transmission electron microscopy study

Pinacyanol chloride self-assembles in aqueous solution into tubular H-aggregates and fibrillar J-aggregates.

Supramolecular structure of TTBC J-aggregates in solution and on surface

The aggregation behavior of cationic 5,5',6,6'-tetrachloro-1,1',3,3'-tetraethylbenzimidacarbocyanine with chloride (TTBC-Cl) or iodide counterions (TTBC-I) in aqueous solution is investigated by absorption, linear dichroism, and fluorescence spectroscopies, as well as cryogenic transmission electron microscopy (cryo-TEM) and atomic force microscopy (AFM). TTBC-Cl is found to form J-aggregates with a classical Davydov-split absorption band (type I spectrum) even under different preparation conditions. These aggregates remain stable for months. Unlike the chloride salt, the iodide salt TTBC-I forms two different types of J-aggregates depending on the pH of the aqueous solution. The TTBC-I aggregates prepared in pure water (pH = 6) are characterized by a single redshifted absorption band (type III spectrum), whereas those prepared in alkaline solution at pH = 13 show a typical Davydov-split (type I) absorption band. Despite differences in counterions, preparation method, stability, and spectroscopic behavior, cryo-TEM reveals an identical tubular architecture for all these J-aggregates. Among the new structure models discussed here is a cylindrical brickwork layer of dye molecules for single-banded J-aggregates (type III). For Davydov-split aggregates (type I), a molecular herringbone-like pattern is proposed instead. Moreover, absorption spectra have revealed an additional single redshifted absorption band (type II spectrum) that is assigned to a surface aggregate and is induced by a specific interaction of the dye cation with the negatively charged cuvette wall. AFM measurements of analogous preparations on negatively charged mica surfaces have supported this interpretation and revealed the formation of monolayered sheet structures.

Octupolar merocyanine dyes: a new class of nonlinear optical chromophores

A set of new octupolar merocyanine chromophores was designed and synthesized. These compounds were prepared from the reaction of 1,3,5-triformyl-2,4,6-trihydroxybenzene with heterocyclic nucleophiles. Octupolar dyes were formed exclusively in their open-dye form. The one- and two-photon-absorption spectra of the dyes consist of two bands: The long-wavelength band in the two-photon absorption spectrum (a few hundreds GM above 1000 nm) matches well with the intense, long-wavelength-absorption band that is located in the visible region in the linear spectrum. Interestingly, an additional, much-more-intense TPA band in the NIR region is observed at higher energy, which corresponds to a weakly allowed one-photon electronic transition. Changing the peripheral heterocyclic moieties allows tuning of the optical properties to approach the cyanine limit (i.e., polymethine state), thus resulting in a red-shift of the low-energy one-photon-absorption band as well as to the rise of an intense two-photon-absorption band in the NIR region. To the best of our knowledge, this is the first synthesis and TPA characterization of octupolar merocyanine chromophores with typical low-bond-length alternation.

Aromatic/proaromatic donors in 2-dicyanomethylenethiazole merocyanines: from neutral to strongly zwitterionic nonlinear optical chromophores

Push-pull compounds, in which a proaromatic electron donor is conjugated to a 2-dicyanomethylenethiazole acceptor, have been prepared, and their properties compared to those of model compounds featuring an aromatic donor. A combined experimental (X-ray diffraction, (1) H NMR, IR, Raman, UV/Vis, nonlinear optical (NLO) measurements) and theoretical study reveals that structural and solvent effects determine the ground-state polarisation of these merocyanines: whereas 4H-pyran-4-ylidene- and 4-pyridylidene-containing compounds are zwitterionic and 1,3-dithiol-2-ylidene derivatives are close to the cyanine limit, anilino-derived merocyanines are essentially neutral. This very large range of intramolecular charge transfer (ICT) gives rise to efficient second-order NLO chromophores with μβ values ranging from strongly negative to strongly positive. In particular, pyranylidene derivatives are unusual in that they show an increase in the degree of ICT on lengthening the π-spacer, a feature that lies behind the very large negative μβ values they display. The linking of the formally quinoidal 2-dicyanomethylenethiazole moiety to proaromatic donors seems a promising approach towards the optimisation of zwitterionic NLO chromophores.