Temporal and spatial resolution of distal protein motions that activate hydrogen tunneling in soybean lipoxygenase.

The enzyme soybean lipoxygenase (SLO) provides a prototype for deep tunneling mechanisms in hydrogen transfer catalysis. This work combines room temperature X-ray studies with extended hydrogen-deuterium exchange experiments to define a catalytically-linked, radiating cone of aliphatic side chains that connects an active site iron center of SLO to the protein-solvent interface. Employing eight variants of SLO that have been appended with a fluorescent probe at the identified surface loop, nanosecond fluorescence Stokes shifts have been measured. We report a remarkable identity of the energies of activation (Ea) for the Stokes shifts decay rates and the millisecond C-H bond cleavage step that is restricted to side chain mutants within an identified thermal network. These findings implicate a direct coupling of distal protein motions surrounding the exposed fluorescent probe to active site motions controlling catalysis. While the role of dynamics in enzyme function has been predominantly attributed to a distributed protein conformational landscape, the presented data implicate a thermally initiated, cooperative protein reorganization that occurs on a timescale faster than nanosecond and represents the enthalpic barrier to the reaction of SLO.

A near-infrared fluorescent probe with a substantial Stokes shift designed for the detection and imaging of ß-galactosidase within living cells and animals.

ß-Galactosidase serves as a pivotal biomarker for both cancer and cellular aging. The advancement of fluorescent sensors for tracking ß-galactosidase activity is imperative in the realm of cancer diagnosis. We have designed a near-infrared fluorescent probe (PTA-gal) for the detection of ß-galactosidase in living systems with large Stokes shifts. PTA-gal exhibits remarkable sensitivity and selectivity in detecting ß-galactosidase, producing near-infrared fluorescent signals with a remarkably low detection limit (2.2 × 10-5 U/mL) and a high quantum yield (0.30). Moreover, PTA-gal demonstrates biocompatibility and can effectively detect ß-galactosidase in cancer cells as well as within living animals.

Design and synthesis of large Stokes shift DNA dyes with reduced genotoxicity.

Despite intensive search over the past decades, only a few small-molecule DNA fluorescent dyes were found with large Stokes shifts. These molecules, however, are often too toxic for widespread usage. Here, we designed DNA-specific fluorescent dyes rooted in benzimidazole architectures with a hitherto unexplored molecular framework based on thiazole-benzimidazole scaffolding. We further incorporated a pyrazole ring with an extended sidechain to prevent cell penetration. These novel benzimidazole derivatives were predicted by quantum calculations and subsequently validated to have large Stokes shifts ranging from 135 to 143 nm, with their emission colors changed from capri blue for the Hoechst reference compound to iguana green. These readily-synthesized compounds, which displayed improved DNA staining intensity and detection limits along with a complete loss of capability for cellular membrane permeation and negligible mutagenic effects as designed, offer a safer alternative to the existing high-performance small-molecule DNA fluorescent dyes.

Central Ring Puckering Enhances the Stokes Shift of Xanthene Dyes.

Small-molecule dyes are generally designed based on well-understood electronic effects. However, steric hindrance can promote excited-state geometric relaxation, increasing the difference between the positions of absorption and emission bands (the Stokes shift). Accordingly, we hypothesized that sterically induced central ring puckering in xanthene dyes could be used to systematically increase their Stokes shift. Through a combined experimental/quantum-chemical approach, we screened a group of (9-acylimino)-pyronin dyes with a perturbed central ring geometry. Our results showed that an atom with sp3 hybridization in position 10 of (9-acylimino)-pyronins induces central ring puckering and facilitates excited-state geometric relaxation, thereby markedly enhancing their Stokes shifts (by up to ~2000 cm-1). Thus, we prepared fluorescent (9-acylimino)-pyronin pH sensors, which showed a Stokes shift disparity between acid and base forms of up to ~8700 cm-1. Moreover, the concept of ring puckering-enhanced Stokes shift can be applied to a wide range of xanthene analogues found in the literature. Therefore, central ring puckering may be reliably used as a strategy for enhancing Stokes shifts in the rational design of dyes.

Photophysical Investigation of One Pot Synthesized Novel Indenofluorene Derivative (BDP) as a Fluorescent Chemosensor for the Detection of Fe3+ Ion.

An Indane-1-one derivative 11-(1-benzyl-1H-indol-3-yl)-10,12-dihydrodiindeno[1,2-b:2',1'-e]-pyridine (BDP) has been synthesized by the reaction of Indan-1-one with 1-benzyl-1H-indole-3-carbaldehyde. FT-IR, 1H-NMR, 13N-NMR and Mass spectroscopic techniques has been used to confirmed the structure of BDP. The observed photophysical changes in BDP across various solvents were associated. The impact of various interactions on photophysical parameters, including Stokes shift, dipole moment, oscillator strength, and fluorescence quantum yields, has been assessed in relation to solvent polarity. Moreover, BDP demonstrates potential as a selective fluorescent chemosensor for detecting Fe3+ ion within a range of cations in an aqueous DMSO environment. A thorough investigation into the recognition mechanism of BDP towards Fe3+ ion has been conducted using Benesi-Hildebrand and Stern-Volmer, measurements. BDP forms a 2:1 complex with the Fe3+ ion, exhibiting fluorescent quenching behaviour.

A Reaction-based Ratiometric Fluorescent Probe with Large STOKES Shift for Cu2+ in Neat Aqueous Solution.

A novel reaction-based ratiometric fluorescent probe 1 for Cu2+ using picolinate as the reaction site and hemicyanine as the fluorophore was developed. 1 displayed maximum absorption peak at 355 nm and fluorescence emission peak at 500 nm, with large Stokes shift of 145 nm. Upon reaction with Cu2+, the maximum absorption and fluorescence emission peaks red-shifted to 390 nm and 570 nm respectively, owing to Cu2+-induced hydrolysis of the picolinate moiety in 1. Meanwhile, the solution of 1 turned from green to orange under a 365 nm UV lamp. 1 not only could detect Cu2+ ratiometrically by the ratios of both absorbance (A390 nm/A355 nm) and fluorescence intensity (F570 nm/F500 nm), but also displayed large Stokes shift, fast response, high sensitivity and excellent selectivity over other metal ions in neat aqueous solution.

Synthesis, Physicochemical and Third Order Nonlinear Optical Properties of Bis-Chalcone (BBDP) as Donor-pi Acceptor Chromophore in Organize Medium.

Bis-Chalcone (BBDP) has been prepared by condensation of N, N-dimethyl benzaldehyde and 1,1'-([1,1'-biphenyl]-4,4'-diyl) di (ethan-1-one), and structure of BBDP was characterized by Mass Spectra, 13C-NMR, 1H-NMR, and IR. Physicochemical properties including Dipole-moments, Stoke-Shifts, Oscillator-strength, dielectric constant and quantum-yields of fluorescence of BBDP were investigated by the emission and absorbances in different solvents. Compound (BBDP) displayed bathochromic shift upon increasing the solvent polarity (from n-Hexane to DMSO). Furthermore, we have exploited third-order nonlinear optical characteristics of the bisChalone were invigilated by the Z-scan techniques in Chloroform. The measurements were taken with a continuous-wave (CW) diode laser having a wavelength of 520 nm in CHCl3 solvent. The third-order nonlinear optical properties, such as the nonlinear refractive index (NLRI) n2, nonlinear absorption coefficient (NLAC) ß, and nonlinear susceptibility χ(3), were measured at various solution concentrations and laser powers. The obtained values of n2, ß, and χ(3) were estimated to be high, of the order of 10-7(cm2/W), 10-3 (cm/W), and 10-6 (esu), respectively. As a result, bis-chalcone (BBDP) is considered as a promising candidate for applications in nonlinear optical (NLO) devices and optical limiting (OL).

A dual-function fluorescence 'turn-on' probe that allows Zn (II) bioimaging and quantification of water in the organic solvent.

Herein, a Eugenol-derived fluorescence 'turn-on' probe FLHE was synthesized by condensing 2-((3-(trifluoromethyl)phenyl)amino)benzohydrazide with 5-allyl-2-hydroxy-3-methoxybenzaldehyde. FLHE demonstrated very low fluorescence in the studied organic solvents of varying polarities. However, upon titration with Zn2+ in HEPES buffer (pH = 7.4, 50% ACN, v/v), FLHE showed 40-fold higher fluorescence signals indicating the formation of the FLHE-Zn2+ complex. The fluorescence turn-on phenomenon upon FLHE-Zn2+ complex formation results from a chelation-enhanced fluorescence (CHEF) effect. The FLHE-Zn2+ complexation demonstrated a stokes shift of 156 nm (λex = 350 nm, λem = 506 nm) and an about 33-fold increase in the quantum yield (FLHE, Φ = 0.007; FLHE-Zn2+ complex, Φ = 0.23). The binding constant (Ka) determined by the Benesi-Hildebrand plot for interaction between FLHE and Zn2+ was 5.33 × 103 M-1. FLHE demonstrated a LOD of 31.8 nM for detecting Zn2+ in the environmental samples without interference from other cations and anions. FLHE-based paper strip (FLHE-PS) assay was developed to quantify the Zn2+ ions in water and the water content of organic solvent. FLHE-PS allows the detection of Zn2+ in aqueous solutions with a LOD of 63.2 nM and quantifying water in acetonitrile with a LOD of 0.14%. These results indicate that the FLHE has high applicability for detecting Zn2+ in living cells and environmental samples and detecting the presence of water in the organic solvents.

Golgi-targeted NIR fluorescent probe with large stokes shift for real-time monitoring of nitric oxide in depression model.

Depression is a debilitating mental illness that poses a serious threat to human health. Nitric Oxide (NO), as an important gasotransmitter, is closely associated with the pathogenesis of depressive disorders. Effective monitoring of NO fluctuation is beneficial for the diagnosis of depression and therapy assessment of antidepressants. Currently, there is a lack of effective methods for rapidly and sensitively identifying NO and elucidating its relationship with depression diseases. Herein, we developed a NIR dye TJ730-based fluorescent probe TJ730-Golgi-NO incorporating benzenesulfonamide as a Golgi-targeted moiety and the thiosemicarbazide group for NO detection. The probe exhibited turn-on fluorescence ability and a large Stokes shift of 158 nm, which shows high sensitivity, selectivity, and rapid response (<1 min) for NO detection. TJ730-Golgi-NO could detect exogenous and endogenous NO in cells stimulated by Glu and LPS, and target Golgi apparatus. Moreover, we disclose a significant increase of NO in the depression model and a weak fluorescence evidenced in the fluoxetine-treated depression mice. This study provides a competent tool for studying the function of NO and helping improve the effective treatment of depression diseases.

Pd(II)-Catalyzed Site-Selective Cross Coupling Reaction: Synthesis of Highly Fluorescent Aryl-Formyl-Chromenes and its Iminoantipyrine Analogues as Selective AChE Inhibitors.

A versatile and efficient chemo selective synthesis of 4-aryl-3-formyl-2H-chromenes (AFC) was undertaken using Pd-catalyzed cross-coupling conditions. The key oxidative transmetalation was successfully applied to a significant range of substitutions on the chromene moiety and aryl ring in Ar(BOH)3, accommodating both electron-rich and electron-deficient groups. These π-extended scaffolds exhibited green-yellow fluorescence with a large Stokes shift and high quantum yield. Measurement of photophysical properties revealed that the compound with methoxy substitution in the chromene ring, 3t, caused a significant bathochromic shift. The AFCs obtained from this method can be transformed into biologically active 4-aryl-3-iminoantipyrine-2H-chromenes (AAC) through functionalization of the formyl chromenes. The AFCs and AACs with methoxy substitutions (3t and 4e) were docked against AChE inhibition, and compound 4e had the lowest binding energy of -11.20 kcal/mol. DFT calculations performed on representative compounds revealed that compound 4e is more reactive than 3t, which is in accordance with the docking studies.

Lead Halide Perovskite Nanocrystals with Low Inhomogeneous Broadening and High Coherent Fraction through Dicationic Ligand Engineering.

Lead halide perovskite nanocrystals (LHP NCs) are an emerging materials system with broad potential applications, including as emitters of quantum light. We apply design principles aimed at the structural optimization of surface ligand species for CsPbBr3 NCs, leading us to the study of LHP NCs with dicationic quaternary ammonium bromide ligands. Through the selection of linking groups and aliphatic backbones guided by experiments and computational support, we demonstrate consistently narrow photoluminescence line shapes with a full-width-at-half-maximum below 70 meV. We observe bulk-like Stokes shifts throughout our range of particle sizes, from 7 to 16 nm. At cryogenic temperatures, we find sub-200 ps lifetimes, significant photon coherence, and the fraction of photons emitted into the coherent channel increasing markedly to 86%. A 4-fold reduction in inhomogeneous broadening from previous work paves the way for the integration of LHP NC emitters into nanophotonic architectures to enable advanced quantum optical investigation.

A Red-Emission Fluorescent Probe with Large Stokes Shift for Detection of Viscosity in Living Cells and Tumor-Bearing Mice.

Abnormal viscosity is closely related to the occurrence of many diseases, such as cancer. Therefore, real-time detection of changes in viscosity in living cells is of great importance. Fluorescent molecular rotors play a critical role in detecting changes in cellular viscosity. Developing red emission viscosity probes with large Stokes shifts and high sensitivity and specificity remains an urgent and important topic. Herein, a novel viscosity-sensitive fluorescent probe (TCF-VIS1) with a large stokes shift and red emission was prepared based on the 2-dicyanomethylene-3-cyano-4,5,5-trimethyl-2,5-dihydrofuran (TCF) skeleton. Due to intramolecular rotation, the probe itself does not fluorescence at low viscosity. With the increase in viscosity, the rotation of TCF-VIS1 is limited, and its fluorescence is obviously enhanced. The probe has the advantages of simple preparation, large Stokes shift, good sensitivity and selectivity, and low cytotoxicity, which make it successfully used for viscosity detection in living cells. Moreover, TCF-VIS1 showed its potential for cancer diagnosis at the cell level and in tumor-bearing mice by detecting viscosity. Therefore, the probe is expected to enrich strategies for the detection of viscosity in biological systems and offer a potential tool for cancer diagnosis.

A Coumarin-Hemicyanine Deep Red Dye with a Large Stokes Shift for the Fluorescence Detection and Naked-Eye Recognition of Cyanide.

In this study, we synthesized a coumarin-hemicyanine-based deep red fluorescent dye that exhibits an intramolecular charge transfer (ICT). The probe had a large Stokes shift of 287 nm and a large molar absorption coefficient (ε = 7.5 × 105 L·mol-1·cm-1) and is best described as a deep red luminescent fluorescent probe with λem = 667 nm. The color of probe W changed significantly when it encountered cyanide ions (CN-). The absorption peak (585 nm) decreased gradually, and the absorption peak (428 nm) increased gradually, so that cyanide (CN-) could be identified by the naked eye. Moreover, an obvious fluorescence change was evident before and after the reaction under irradiation using 365 nm UV light. The maximum emission peak (667 nm) decreased gradually, whilst the emission peak (495 nm) increased gradually, which allowed for the proportional fluorescence detection of cyanide (CN-). Using fluorescence spectrometry, the fluorescent probe W could linearly detect CN- over the concentration range of 1-9 µM (R2 = 9913, RSD = 0.534) with a detection limit of 0.24 µM. Using UV-Vis spectrophotometry, the linear detection range for CN- was found to be 1-27 µM (R2 = 0.99583, RSD = 0.675) with a detection limit of 0.13 µM. The sensing mechanism was confirmed by 1H NMR spectroscopic titrations, 13C NMR spectroscopy, X-ray crystallographic analysis and HRMS. The recognition and detection of CN- by probe W was characterized by a rapid response, high selectivity, and high sensitivity. Therefore, this probe provides a convenient, effective and economical method for synthesizing and detecting cyanide efficiently and sensitively.

Dithieno[2,3-b;3,2-f]phosphepinium-Based Near-Infrared Fluorophores: px-π* Conjugation Inherent to Seven-Membered Phosphacycles.

Positively charged phosphorus-containing heterocycles are characteristic core skeletons for functional molecules. While various phosphonium-containing five- or six-membered ring compounds have been reported, seven-membered ring phosphepinium has not yet been fully studied. In this study, dithieno[2,3-b;3,2-f]phosphepinium ions containing electron-donating aminophenyl groups were synthesized. An X-ray crystallographic analysis of the resulting donor-acceptor-donor dyes revealed a bent conformation of the central seven-membered ring. This compound exhibited fluorescence in the near-infrared region with a bathochromic shift of 70 nm compared to phosphepine oxide congener and a large Stokes shift. High fluorescence quantum yields were obtained even in polar solvents due to the suppression of the nonradiative decay process. The theoretical study revealed that the phosphepinium skeleton is highly electron-accepting owing to the orbital interaction between a px orbital of the phosphonium moiety and a π* orbital of the 1,3,5-hexatriene moiety. Owing to the lower-lying px orbital in the phosphonium moiety compared with that of the phosphine oxide and the bent conformation of the seven-membered ring, the phosphepinium ring effectively furnishes a px-π* conjugation. A large structural relaxation with the contribution of a quinoidal resonance structure is suggested in the excited state, which is responsible for the intense emission with a large Stokes shift.

PyrAtes: Modular Organic Salts with Large Stokes Shifts for Fluo-rescence Microscopy.

The deployment of small-molecule fluorescent agents plays an ever-growing role in medicine and drug development. Herein, we complement the portfolio of powerful fluorophores, reporting the serendipitous discovery and development of a novel class with an imidazo[1,2-a]pyridinium triflate core, which we term PyrAtes. These fluorophores are synthesized in a single step from readily available materials (>60 examples) and display Stokes shifts as large as 240 nm, while also reaching NIR-I emissions at λmax as long as 720 nm. Computational studies allow the development of a platform for the prediction of λmax and λEm. Furthermore, we demonstrate the compatibility of these novel fluorophores with live cell imaging in HEK293 cells, suggesting PyrAtes as potent intracellular markers.

Organic Fluorophores with Large Stokes Shift for the Visualization of Rapid Protein and Nucleic Acid Assays.

Organic small-molecule fluorophores, characterized by flexible chemical structure and adjustable optical performance, have shown tremendous potential in biosensing. However, classical organic fluorophore motifs feature large overlap between excitation and emission spectra, leading to the requirement of advanced optical set up to filter desired signal, which limits their application in scenarios with simple settings. Here, a series of wavelength-tunable small-molecule fluorescent dyes (PTs) bearing simple organic moieties have been developed, which exhibit Stokes shift up to 262 nm, molar extinction coefficients ranged 30,000-100,000 M-1 cm-1, with quantum yields up to 54.8 %. Furthermore, these dyes were formulated into fluorescent nanoparticles (PT-NPs), and applied in lateral flow assay (LFA). Consequently, limit of detection for SARS-CoV-2 nucleocapsid protein reached 20 fM with naked eye, a 100-fold improvement in sensitivity compared to the pM detection level for colloidal gold-based LFA. Besides, combined with loop-mediated isothermal amplification (LAMP), the LFA system achieved the visualization of single copy level nucleic acid detection for monkeypox (Mpox).

Evolution of Amino Acid Propensities under Stability-Mediated Epistasis.

Site-specific amino acid preferences are influenced by the genetic background of the protein. The preferences for resident amino acids are expected to, on average, increase over time because of replacements at other sites-a nonadaptive phenomenon referred to as the "evolutionary Stokes shift." Alternatively, decreases in resident amino acid propensity have recently been viewed as evidence of adaptations to external environmental changes. Using population genetics theory and thermodynamic stability constraints, we show that nonadaptive evolution can lead to both positive and negative shifts in propensities following the fixation of an amino acid, emphasizing that the detection of negative shifts is not conclusive evidence of adaptation. By examining propensity shifts from when an amino acid is first accepted at a site until it is subsequently replaced, we find that ≈50% of sites show a decrease in the propensity for the newly resident amino acid while the remaining sites show an increase. Furthermore, the distributions of the magnitudes of positive and negative shifts were comparable. Preferences were often conserved via a significant negative autocorrelation in propensity changes-increases in propensities often followed by decreases, and vice versa. Lastly, we explore the underlying mechanisms that lead propensities to fluctuate. We observe that stabilizing replacements increase the mutational tolerance at a site and in doing so decrease the propensity for the resident amino acid. In contrast, destabilizing substitutions result in more rugged fitness landscapes that tend to favor the resident amino acid. In summary, our results characterize propensity trajectories under nonadaptive stability-constrained evolution against which evidence of adaptations should be calibrated.

Ultra-Thin 2D Ionic Salt Supported with Strong Hydrogen-Bonding Assisted Ionic Interaction.

2D materials have attracted great interest since the report of graphene. However, because of the fragile stability of ultra-thin nanosheets, most studies are restricted to sheets maintained by strong covalent or coordination bonds. The research on which kind of bonds can maintain the free-standing existence of 2D nanosheets is still of great significance. Recently, 2D ionic salts are successfully synthesized on substrates, but whether 2D ionic salts can free-stand is still a problem. Herein this problem is addressed by a free-standing 2D ionic salt (thickness: ≈2 nm) exfoliated from a 4,4'-bipyridinium hydrochloride salt crystal. The stability of this 2D salt is supported by a strong NH···Cl hydrogen (H)-bonding assisted ionic interaction (17.99 kcal mol-1 ), which is verified by density functional theory calculation and natural bond orbital analysis. The salt crystal has strong air-stable radicals inside and the 2D ionic salt exhibits red fluorescence in solution and in solid-state, especially in solution the stokes shifts are very large (≈ 386 nm). This breakthrough work is not only beneficial for the construction of novel 2D materials but also for the understanding of H-bonding interactions.

Cryogenic Ion Fluorescence Spectroscopy: FRET in Rhodamine Homodimers and Heterodimers.

The internal electronic communication between two or more light-absorbers is fundamental for energy-transport processes, a field of large current interest. Here the intrinsic photophysics of homo- and heterodimers of rhodamine cations were studied where just two methylene units bridge the dyes. Gas-phase experiments were done on frozen molecular ions at cryogenic temperatures using the newly built LUNA2 mass spectroscopy setup in Aarhus. Both absorption (from fluorescence excitation) and dispersed-fluorescence spectra were measured. In the gas phase, there is no dielectric screening from solvent molecules, and the effect of charges on transition energies is maximum. Indeed, bands are redshifted compared to those of monomer dyes due to the electric field that each dye senses from the other in a dimer. Importantly, also, as two chemically identical dyes in a homodimer do not experience the same field along the long axis, each dye has separate absorption. At low temperatures, it is therefore possible to selectively excite one dye. Fluorescence is dominantly from the dye with the lowest transition energy no matter which dye is photoexcited. Hence this work unequivocally demonstrates Förster Resonance Energy Transfer even in homodimers where one dye acts as donor and the other as acceptor.

Selective and Sensitive Detection of Hg2+ and Ag+ by a Fluorescent and Colorimetric Probe with Large Stokes Shift.

Development of fluorescent sensors with large Stokes shift for selective detection of heavy metals is of great importance. A novel fluorescent probe with extremely large Stokes shift (212 nm) was synthesized for selective and simultaneous detection of Hg2+ and Ag+ ions. The deep yellow probe turned colorless or pale yellow after addition of Hg2+ or Ag+. The new probe could be utilized for absorption spectral detection of Hg2+ and Ag+ both in ethanol and aqueous solution. Addition of Hg2+ and Ag+ ions caused significant decrease in the fluorescence intensity of the new probe and the selective recognition of Hg2+ and Ag+ was not interfered by common competitive metal ions including Li+, Na+, K+, Cu2+, Fe2+, Zn2+, Co2+, Ni2+, Mn2+, Sr2+, Ca2+, Mg2+, Al3+, Cr3+ and Fe3+. The detection limit for Hg2+ and Ag+ was calculated to be 4.68 µM and 4.29 µM, respectively. Application of the new probe for quantitative determination of Hg2+ and Ag+ concentrations in real water samples was accomplished.