Interaction Of Chromophores Research Articles

Detection of Free Thiols and Fluorescence Response of Phycoerythrin Chromophore after Ultraviolet-B Radiation Stress

The chemistry of thiol-chromophore linkage plays a central role in the nature of fluorescence of phycoerythrin (PE). Interaction of thiol and chromophore is crucial for the energy transfer, redox signal and inhibition of oxidative damage. In the present investigation the effects of ultraviolet-B radiation on an emission fluorescence intensity and wavelength shift in PE due to interaction between thiol and chromophore by remarkable strategy of detection technique was studied. Purification of PE was done by using a gel permeation and ion exchange chromatography that yielded a quite high purity index (6.40) in a monomeric (αβ) form. UV-B radiation accelerated the quenching efficiency (24.9±1.52%) by reducing fluorescence emission intensity of thiol linked chromophore after 240min of UV-B exposure. However, after blocking of transiently released free thiol by N-ethylmaleimide, quenching efficiency was increased (36.8±2.80%) with marked emission wavelength shift towards shorter wavelengths up to 562nm as compared to 575nm in control. Emission fluorescence of free thiol was at maximum after 240min that was detected specifically by monobromobimane (mBrB) molecular probe. The association/dissociation of bilin chromophore was analyzed by SDS- and Native-PAGE that also indicated a complete reduction in emission fluorescence. Our work clearly shows an early detection of free thiols and relative interaction with chromophore after UV-B radiation which might play a significant role in structural and functional integrity of terminal PE.

<b>Opsin genes: research perspectives with Neotropical cichlids (Perciformes: Cichlidae) and their relevance in floodplain studies

Vision not only plays an important role in the behavior and exploration capacity of new ecology niches but also influences the evolution of species exposed to the heterogeneity of light. Floodplain environments have high habitat heterogeneity and, thus, different light gradients. Cichlids are a group of vertebrates that has stirred interest in evolutionary studies due to their morphological and behavioral diversity and their widely used vision. The molecular basis of vertebrates’ vision occurs through the interaction of opsin proteins and retinal chromophores. Proteins are expressed by opsin genes where each is responsible for absorbing certain light wavelengths. Current review analyzes the main characteristics of opsin genes family and the possibility of using them in floodplain and Neotropical cichlids studies. Opsins may have different levels of expression and molecular polymorphisms according to the dispersion of the species. They are also related to such behavior as sexual selection, nourishment and exploration of new habitats. Floodplains are natural experiments and dynamic environments that provide a wide range of habitats. In fact, the integration of studies in floodplains and the opsin genes in Neotropical cichlids seems to be a promising and still unexplored area in Neotropical regions.

Structurally Controlled Dynamics in Azobenzene-Based Supramolecular Self-Assemblies in Solid State

Light-responsive supramolecular self-assemblies exhibit interplay between order and dynamics of the self-assembling motifs, through which the thermal isomerization rate of azobenzene chromophores can be tuned by orders of magnitude. By using supramolecular complexes of 4-(4-alkylphenylazo)phenols hydrogen-bonded to poly(4-vinylpyridine) as model systems, we demonstrate that the thermal isomerization rate of the hydroxyazobenzene derivatives increases 5700-fold when the material undergoes a transformation from a disordered, low-azobenzene-concentration state to a high-concentration state exhibiting lamellar, smectic-like self-assembly. Drastically smaller thermal isomerization rates are observed in disordered structures. This allows us to attribute the change to a combination of increased number density of the hydroxyazobenzenes inducing plasticization, and cooperativity created by the chromophore–chromophore interactions through self-assembled molecular order and alignment. Our results pinpoint the import...

Molecular Recognition of Parallel DNA Quadruplex d(TTAGGGT)4 by Mitoxantrone: Binding with 1:2 Stoichiometry Leading to Thermal Stabilization and Telomerase Inhibition

The interaction of the anthraquinone derivative mitoxantrone, a semisynthetic anti-cancer drug with two non-planar side chains, with heptamer G-quadruplex d(TTAGGGT)4 , which contains the human telomere DNA sequence, was evaluated by differential scanning calorimetry, fluorescence Job plotting, absorption, and NMR and CD spectroscopy. Binding led to thermal stabilization of DNA (ΔTm =13-20 °C). The spectra revealed that two mitoxantrone molecules bind externally at two sites of the DNA quadruplex as monomers, by partial insertion of the chromophore and side-chain interaction at the grooves. The inhibition of telomerase (IC50 =2 μM), as determined by a TRAP assay, can be attributed to thermal stabilization of the DNA quadruplex because of the interactions with mitoxantrone. The studies revealed highly specific molecular recognition between a ligand and a parallel-stranded G-quadruplex; this might serve as a platform for the rational design of new drugs.

Synthesis and photophysical properties of a new BODIPY-based siloxane dye

A fluorescent dye comprising four BODIPY derivatives conjugated to a cyclotetrasiloxane core was synthesized by consecutive hydrosilylation and esterification reactions. Photophysical properties of the dye in various organic solvents were investigated. It was shown that due to a fourfold extinction coefficient increase and a moderate quantum yield decrease the brightness of the tetra-BODIPY dye in low-polarity solvents, calculated per molecule, increased 3 times when compared to mono-BODIPY. By contrast, in polar solvents there was a dramatic drop in brightness apparently associated with intramolecular interactions of the low-polar BODIPY chromophores.

Allosteric effects of chromophore interaction with dimeric near-infrared fluorescent proteins engineered from bacterial phytochromes.

Fluorescent proteins (FPs) engineered from bacterial phytochromes attract attention as probes for in vivo imaging due to their near-infrared (NIR) spectra and use of available in mammalian cells biliverdin (BV) as chromophore. We studied spectral properties of the iRFP670, iRFP682 and iRFP713 proteins and their mutants having Cys residues able to bind BV either in both PAS (Cys15) and GAF (Cys256) domains, in one of these domains, or without these Cys residues. We show that the absorption and fluorescence spectra and the chromophore binding depend on the location of the Cys residues. Compared with NIR FPs in which BV covalently binds to Cys15 or those that incorporate BV noncovalently, the proteins with BV covalently bound to Cys256 have blue-shifted spectra and higher quantum yield. In dimeric NIR FPs without Cys15, the covalent binding of BV to Сys256 in one monomer allosterically inhibits the covalent binding of BV to the other monomer, whereas the presence of Cys15 allosterically promotes BV binding to Cys256 in both monomers. The NIR FPs with both Cys residues have the narrowest blue-shifted spectra and the highest quantum yield. Our analysis resulted in the iRFP713/Val256Cys protein with the highest brightness in mammalian cells among available NIR FPs.

Synthesis and Properties of (3‐Phenyl‐1‐azulenyl)tetracyanobetadienes and Tris(aryltetracyanobetadiene)s Connected with 1,3,5‐Tri(1‐azulenyl)benzene Core

AbstractTris[(3‐phenyl‐1‐azulenyl)tetracyanobutadiene]s and tris(aryltetracyanobutadiene)s connected to a 1,3,5‐tri(1‐azulenyl)benzene core (tris‐AzTCBDs) have been prepared by the Pd‐catalyzed alkynylation of tris(3‐iodo‐1‐azulenyl)benzene derivative with the corresponding 1‐ethynylazulene or ethynylbenzene derivatives under Sonogashira–Hagihara cross‐coupling conditions, followed by the reaction with tetracyanoethylene (TCNE) in a formal [2 + 2] cycloaddition‐retroelectrocyclization (CA–RE) reaction. The intramolecular charge‐transfer (ICT) interactions of the new chromophores were investigated by the comparison with those of the model tetracyanobutadiene derivatives with azulene substituents (AzTCBDs), which were prepared by the reaction of the corresponding 1‐ethynylazulene derivative with iodoarenes, followed by the CA–RE reaction with TCNE, utilizing UV/Vis spectroscopy and theoretical calculations. The redox behavior of the alkyne precursors and the tetracyanobutadiene derivatives was examined by cyclic voltammetry (CV) and differential pulse voltammetry (DPV), which revealed their multistep electrochemical reduction properties. Moreover, significant color changes of these compounds were observed by visible spectroscopy under the electrochemical reduction conditions.

Chromophore interactions leading to different absorption spectra in mNeptune1 and mCardinal red fluorescent proteins.

Extensive MD simulations combined with QM/MM calculations have been performed on mNeptune1 and mCardinal red fluorescent proteins to establish the reasons behind the red shift of the excitation wavelength of mCardinal with respect to mNeptune1. In both cases, it is seen that Arg197 stabilizes the chromophore but cannot be described as stabilizing preferentially the excited state because of the anchor point of the interaction. The interactions of the linking bonds to the α-helix of both proteins to the chromophore have been analyzed. It has been found that, besides the presence of a strategically placed residue Gln41 in mCardinal, solvation water molecules play an active role in the energetics of the stabilization of the excited state, which is preferentially stabilized in the case of mCardinal in contrast to mNeptune1.

Synthesis, structure and optical data storage properties of silver nanoparticles modified with azobenzene thiols

Silver nanoparticles modified with photoresponsive azobenzene thiol ligands are prepared and the interaction between them has been investigated through photoisomerization behaviour by UV–vis spectroscopy. Upon irradiation with UV light at 365 nm, an increase of the absorbance centered at 445 nm corresponding to the n–π* transition band of cis azobenzene isomers is observed for azobenzene solution without Ag and a decrease of the absorbance centered at 445 nm is observed for azobenzene solution with Ag, showing strong interaction of azo chromophores with surface plasmons of Ag nanoparticles, in particular when the absorption bands are overlapped with each other. The enhanced light-responsivity has been confirmed by two-photon induced optical data storage experiments. An image can be recorded on the photoactive film doped with 7 wt% silver nanoparticles modified with azobenzene thiol ligands under writing power of 25 mW, but is failed to be recorded in the azobenzene film without Ag even under the same recording condition.

Introduction of fluorine to change the dielectric environment of nonlinear optical chromophores for improved electro-optic activities

Fluorine was non-conjugatedly linked to the donor of nonlinear optical chromophore to investigate the effect of highly electronegative fluorine on intramolecular charge-transfer and electro-optic activities. 1HNMR spectra and UV–vis absorption were used to investigate that introduction of fluorine change the dielectric environment of intramolecular charge-transfer. Fluorinated chromophore showed more intensified absorption and its absorption properties was more stable to dielectric change in solution. In solid state of guest-host electro-optic polymer films, this dielectric environment stabilization was revealed to attenuate the dipole–dipole interactions of chromophores. Higher electro-optic coefficients (148pm/V) and higher chromophore loading density (30wt%) of fluorinated material chr-2/APC than benchmark material chr-1/APC (116pm/V at 25wt%) was achieved.

Excited‐State Deactivation of Branched Phthalocyanine Compounds

The excited-state relaxation dynamics and chromophore interactions in two phthalocyanine compounds (bis- and trisphthalocyanines) are studied by using steady-state and femtosecond transient absorption spectral measurements, where the excited-state energy-transfer mechanism is explored. By exciting phthalocyanine compounds to their second electronically excited states and probing the subsequent relaxation dynamics, a multitude of deactivation pathways are identified. The transient absorption spectra show the relaxation pathway from the exciton state to excimer state and then back to the ground state in bisphthalocyanine (bis-Pc). In trisphthalocyanine (tris-Pc), the monomeric and dimeric subunits are excited and the excitation energy transfers from the monomeric vibrationally hot S1 state to the exciton state of a pre-associated dimer, with subsequent relaxation to the ground state through the excimer state. The theoretical calculations and steady-state spectra also show a face-to-face conformation in bis-Pc, whereas in tris-Pc, two of the three phthalocyanine branches form a pre-associated face-to-face dimeric conformation with the third one acting as a monomeric unit; this is consistent with the results of the transient absorption experiments from the perspective of molecular structure. The detailed structure-property relationships in phthalocyanine compounds is useful for exploring the function of molecular aggregates in energy migration of natural photosynthesis systems.

Homogenous smooth sol gel films doped with organic compounds for nonlinear optics

The demand for protection of various types of optical sensors from laser-beam pulses has resulted in the search for optical limiting devices that have the property of being transparent at low intensity of light (normal light), but no transparent towards high intensity (laser) light. Organic material with nonlinear optical (NLO) properties as reverse saturable absorption and two-photon absorption can be used for optical limiting with the advantage of a very fast response and self-activation. A promising approach in the fabrication of thin films by low cost/easy use deposition methods for second-order nonlinear optics is sol–gel technique. The present paper reports on the sol–gel synthesis of some pyrazolone derivative doped SiO2–P2O5 smooth and homogenous films (Root mean square roughness (Rq)=1.1nm) using as precursors tetraethylorthosilicate (TEOS) and phosphoric acid (H3PO4). The structure of the deposited azo-derivatives doped thin films was examined by Fourier transform infrared spectroscopy and atomic force microscopy, while their optical properties of the films by UV–VIS spectroscopy. The nonlinear optical efficiencies due to the interaction of the NLO-active chromophores with the inorganic matrix have a significant influence on the second harmonic generation capabilities that was measured using a femtosecond Ti:Sapphire laser. The properties of the films were investigated and correlated with the concentration of the organic dopant and the thermal treatment temperature.

Spectral and fluorescent properties of cross-conjugated ω,ω′-bisaminopolyenes containing pyran or dihydropyridine cycle with acceptor groups of different structures

The spectral and fluorescent properties of cross-conjugated bichromophoric ω,ω′-aminopolyenes containing the pyran or dihydropyridine cycle with acceptor groups of different structures have been studied. According to the two-dimensional 1H NMR spectroscopy (NOESY and ROESY) data obtained earlier, chromophores are arranged at an acute or obtuse angle in compounds with the pyran or the dihydropyridine moiety, respectively, thereby leading to significant differences in the absorption spectra of these compounds. The absorption spectra have been considered on the basis of the theory of interaction of chromophores. Since the long-wavelength bands of the absorption spectra of the compounds with the dihydropyridine cycle are broad and poorly resolved, we used decomposition of the absorption spectra of these compounds into Gaussian components. The angles between the chromophores, estimated from the ratio of the intensities of the absorption bands, were found to comply with the NMR data. Fluorescence quantum yields of the compounds studied have been also determined. In the case of the dyes with carbonyl, dinitrile, or indandione acceptors, the fluorescence quantum yields were found to be significantly higher for the compounds with the pyran rather than the dihydropyridine cycle.

Characterization of Red/Green Cyanobacteriochrome NpR6012g4 by Solution Nuclear Magnetic Resonance Spectroscopy: A Hydrophobic Pocket for the C15-E,anti Chromophore in the Photoproduct.

Cyanobacteriochromes (CBCRs) are cyanobacterial photosensory proteins distantly related to phytochromes. Like phytochromes, CBCRs reversibly photoconvert between a dark-stable state and a photoproduct via photoisomerization of the 15,16-double bond of their linear tetrapyrrole (bilin) chromophores. CBCRs provide cyanobacteria with complete coverage of the visible spectrum and near-ultraviolet region. One CBCR subfamily, the canonical red/green CBCRs typified by AnPixJg2 and NpR6012g4, can function as sensors of light color or intensity because of their great variation in photoproduct stability. The mechanistic basis for detection of green light by the photoproduct state in this subfamily has proven to be a challenging research topic, with competing hydration and trapped-twist models proposed. Here, we use ¹³C-edited and ¹⁵N-edited ¹H-¹H NOESY solution nuclear magnetic resonance spectroscopy to probe changes in chromophore configuration and protein-chromophore interactions in the NpR6012g4 photocycle. Our results confirm a C15-Z,anti configuration for the red-absorbing dark state and reveal a C15-E,anti configuration for the green-absorbing photoproduct. The photoactive chromophore D-ring is located in a hydrophobic environment in the photoproduct, surrounded by both aliphatic and aromatic residues. Characterization of variant proteins demonstrates that no aliphatic residue is essential for photoproduct tuning. Taken together, our results support the trapped-twist model over the hydration model for the red/green photocycle of NpR6012g4.

Atomistic design of microbial opsin-based blue-shifted optogenetics tools.

Microbial opsins with a bound chromophore function as photosensitive ion transporters and have been employed in optogenetics for the optical control of neuronal activity. Molecular engineering has been utilized to create colour variants for the functional augmentation of optogenetics tools, but was limited by the complexity of the protein–chromophore interactions. Here we report the development of blue-shifted colour variants by rational design at atomic resolution, achieved through accurate hybrid molecular simulations, electrophysiology and X-ray crystallography. The molecular simulation models and the crystal structure reveal the precisely designed conformational changes of the chromophore induced by combinatory mutations that shrink its π-conjugated system which, together with electrostatic tuning, produce large blue shifts of the absorption spectra by maximally 100 nm, while maintaining photosensitive ion transport activities. The design principle we elaborate is applicable to other microbial opsins, and clarifies the underlying molecular mechanism of the blue-shifted action spectra of microbial opsins recently isolated from natural sources.

Synthesis and conformations of cross-conjugated polyenes containing heterocyclic moieties with diverse structures

New non-linear cross-conjugated polyenes containing a central 4-ylidene-substituted pyran or N-methyldihydropyridine ring have been synthesized. Interaction of chromophores in these compounds occurs through the ylidene group linked to the heterocycles.

Novel pendant azobenzene/polymer systems for second harmonic generation and optical data storage

New poly(methyl methacrylate)s bearing push–pull azo-moieties, with the azo-dye content ranging from 31 wt% to 100 wt%, are synthesized by (co)polymerization of a methacrylamide-based azo-monomer. The high reactivity of the colored monomer allowed well-balanced structures to be achieved, characterized by a suitable thermal stability. The second harmonic generation efficiency of the poled samples is investigated by means of the SHG Maker fringes setup. Features that hinder the translation of the azo-moiety optical nonlinearity in the material at the macroscopic level are debated. The results underline the role of chromophore–chromophore and chromophore–polymer interactions on the alignment of the azo-moieties. The polarity of the polymer matrix is proven to influence the chromophore–chromophore interactions. Two-photon absorption is employed for gray scale encoding of second harmonic signals on poled thin films, thus pointing out the possibility to employ these new materials for optical data storage applications.

Silicophosphate films doped with organic compounds for nonlinear optical applications

Doped organic compounds are of great interest for optical communications and high-density optical data storage due to their large second-order nonlinearity and high-speed response. A promising approach in the fabrication of new materials for second-order nonlinear optics is sol–gel technique. The present paper reports on the sol–gel synthesis of some pyrazolone derivative doped SiO2–P2O5 films. The precursors used for sol gel synthesis were tetraethylorthosilicate and phosphoric acid (H3PO4). The organic compound was added under continuous stirring in the precursors’ mixture. The structure of the deposited azo-derivatives doped thin films was examined by Fourier transform infrared spectroscopy, and atomic force microscopy and their optical properties by UV–VIS spectroscopy. The nonlinear optical efficiencies due to the interaction of the NLO-active chromophores with the inorganic matrix has a significant influence on the second harmonic generation capabilities that was measured using a femtosecond Ti:sapphire laser. The properties of the films were investigated and correlated with the concentration of the organic dopant and the thermal treatment temperature.

The structure of a far-red fluorescent protein, AQ143, shows evidence in support of reported red-shifting chromophore interactions.

Engineering fluorescent proteins (FPs) to emit light at longer wavelengths is a significant focus in the development of the next generation of fluorescent biomarkers, as far-red light penetrates tissue with minimal absorption, allowing better imaging inside of biological hosts. Structure-guided design and directed evolution have led to the discovery of red FPs with significant bathochromic shifts to their emission. Here, we present the crystal structure of one of the most bathochromically shifted FPs reported to date, AQ143, a nine-point mutant of aeCP597, a chromoprotein from Actinia equina. The 2.19 Å resolution structure reveals several important chromophore interactions that contribute to the protein's far-red emission and shows dual occupancy of the green and red chromophores.

An “off–on” fluorescent and colorimetric probe bearing fluorescein moiety for Mg2 + and Ca2 + via a controlled supramolecular approach

In the present work, a new kind of fluorescein-based chemosensor L was designed and synthesized to selectively recognize Ca2+ or Mg2+ over other competing ions. The chemosensor showed “off–on” fluorescent and color changes upon the addition of Ca2+ and Mg2+. The dynamic binding events with the formation of 1:1(L/M) and 1:2(L/M) complexes were examined. The cation-driven conformation changes of L were understood and proposed rationally by the UV–vis, FL, and 1HNMR titrations. By this allosteric effect, Ca2+ and Mg2+ could be selectively recognized with the 1:2 stoichiometry by fluorescent changes, which were different from other known reports on chemosensors that the host-cation complexion was exploited for controlling chromophore interaction as the model of signaling.