Single oligomer spectra probe chromophore nanoenvironments of tetrameric fluorescent proteins

When analyzing the emission of a large number of individual chromophores embedded in a matrix, the spread of the observed parameters is a characteristic property for the particular chromophore-matrix system. To quantitatively assess the influence of the matrix on the single molecule emission parameters, it is imperative to have a system with a well-defined chromophore nanoenvironment and the possibility to alter these surroundings in a precisely controlled way. Such a system is available in the form of the visible fluorescent proteins, where the chromophore nanoenvironment is defined by the specific protein sequence. We analyze the influence of the chromophore embedding within this defined protein environment on the distribution of the emission maximum wavelength for a number of variants of the fluorescent protein DsRed, and show that this parameter is characteristic of the chromophore-protein matrix combination and largely independent of experimental conditions. We observe that the chemical changes in the vicinity of the chromophore of different variants do not account for the different distributions of emission maximum positions but that the flexibility of the chromophore surrounding has a dominant role in determining the distribution. We find, surprisingly, that the more rigid the chromophore surrounding, the broader the distribution of observed maximum positions. We hypothesize that, after a thermally induced reorientation in the chromophore surrounding, a more flexible system can easily return to its energetic minimum position by fast reorientation, while in more rigid systems the return to the energetic minimum occurs in a stepwise fashion, leading to the broader distribution observed.     

Absorption and emission spectra of fluorescent silica nanoparticles from TD-DFT/MM/PCM calculations

A multi-scale computational protocol, which combines Quantum Mechanics and Molecular Mechanics (QM/MM) calculations with the polarisable continuum model (PCM), has been used to study the tetramethylrhodamine isothiocyanate (TRITC) fluorophore, embedded in three different environments, namely in water, on an amorphous silica surface and covalently encapsulated in a silica nanoparticle (C dot). Absorption and emission spectra have been simulated by using TD-B3LYP/PCM calculations, performed on the TRITC ground and excited state geometries, optimized at the QM/MM level. The results are in good agreement with experimental data confirming the caging effect played by the silica shell on the mobility of the TRITC molecule when covalently encapsulated in silica nanoparticles. This could result in a decrease of the nonradiative decay rate and thus an increase of the quantum yield of the molecule.     

Simultaneous determination of chlorophyll a and chlorophyll b by derivative spectrophotometry

Chlorophyll a (Chl a) and chlorophyll b (Chl b) plant pigments, which are important in the food industry and are beneficial as environmental pollution indicators, have been extracted with a novel solvent mixture (1:1 v/v acetone–propanol) not containing chloroform and simultaneously determined by first-derivative spectrophotometry. The results were statistically compared to those obtained by the ordinary absorption spectrophotometric reference utilizing the principle of additivity of absorbances. The testing of the developed method in synthetic mixtures of Chl a and Chl b and in real plant material samples (grass, spinach, chard, purslane, black cabbage, crisp lettuce, rocket, dill and seaweed) proved successful in that the developed extractive derivative spectrophotometric method was both rapid and precise, and was not dependent on the Chl a/b ratio in contrast to the reference method which was adversely affected by the latter parameter.     

A priori resolution of the intermediate spectra in the bacteriorhodopsin photocycle: the time evolution of the L spectrum revealed

Resolution of the spectra of the intermediates in the photocycle of wild-type bacteriorhodopsin (BR) was achieved by singular value decomposition with exponential-fit-assisted self-modeling (SVD-EFASM) treatment of multichannel difference spectra measured at 5 degrees C during the course of the photocycle. New is the finding that two spectrally distinct L intermediates, L(1) and L(2), form sequentially. Our conclusion is that the photocycle is more complex than most published schemes. The dissection of the spectrally different L forms eliminates stoichiometric discrepancies usually appearing as systematically varying total intermediate concentrations before the onset of BR recovery. In addition, our analysis reveals that the red tails in the spectra of K and L(1) are more substantial than those of L(2) and BR. We suggest that these subtle differences in the shapes of the spectra reflect torsional and/or environmental differences in the retinyl chromophore.     

Chemical effects in the X-ray emission spectra of sulphur

X-ray emission spectroscopy can be utilised to characterise and distinguish specific central to ligand atom bonding. The K_β emission spectra of sulphur have been extensively studied with the central sulphur atom in a variety of chemical environments, each showing a distinctive peak profile that reflects the sulphur 3p orbital participation in the bonding.     

High resolution emission Fourier transform infrared spectra of the 4p-5s and 5p-6s bands of ArH

In the 2500-8500 cm(-1) region several strong emission bands of (40)ArH were observed by Fourier transform spectroscopy through a dc glow discharge in a mixture of argon and hydrogen. Rotational-electronic transitions of the two previously unstudied 4p-5s and 5p-6s,v = 0-0, bands of (40)ArH were measured and assigned in the 6060 and 3770 cm(-1) regions, respectively. A simultaneous fit of the emission transitions of the 4p-5s and 5p-6s bands and an extended set of transitions of the 6s-4p band observed by Dabrowski, Tokaryk, and Watson [J. Mol. Spectrosc. 189, 95 (1998)] and remeasured in the present work yielded consistent values of the spectroscopic parameters of the electronic states under investigation. In the branch of the 4p-5s band with transitions of type (Q)Q(f(3)e) we observed a narrowing in the linewidths with increasing rotational quantum number N. The rotational dependence of the linewidth is caused by predissociation of the 5s state by the repulsive ground 4s state through homogeneous coupling and changes in overlap integrals of the vibrational wave functions with the rotational level. Analysis was based on the Fermi's golden rule approximation model. In the 4p-5s band region a vibrational sequence ofv(')-v(")=1-1, 2-2, and 3-3 were recorded and a number of transitions belonging to the strongest (Q)Q(f(3)e) form branch of the 1-1 band were analyzed.     

Absorption and emission spectra of isomeric tolunitriles

Absorption and emission characteristics ofo-, m- andp-tolunitriles in polar and non-polar solvents under different conditions have been investigated in detail. Solvatochromic shifts of band origin of these molecules in non-polar solvents show that their dipolemoments in the first excited singlet state are almost the same while its value in the second excited singlet is larger in the metathan in the para-isomer. Vibronic analyses of the low temperatures absorption, fluorescence and phosphorescence spectra of all the three molecules have provided evidence that these molecules are slightly distorted in the first excited singlet state while such distortion in the phosphorescence emitting triplet state is larger. The data on fluorescence and phosphorescence quantum yield and phosphorescence lifetime of the tolunitriles are reasonably interpreted as showing that in these molecules, particularly m-andp- tolunitriles, the internal conversion rate from the first excited singlet to the ground state is probably small and that the charge transfer character of the triplet state in thep-isomer is larger than that in the meta.     

Absorption and emission spectra of the lowest triplet state in hexachloroacetone

T₁ ← S₀ absorption and T₁ → S₀ phosphorescence spectra of neat cystalline hexachloroacetone have been analyzed at 4.2°K. From the lifetime and energy the upper state is assigned as ³nπ^*. The spectra are sharp compared to other aliphatic ketones, with the 0-0 band at 26 248 ± 2 cm ^?1. The phosphorescence shows two strong progressions; one involving the CO stretching mode at 1784 cm^?1 (x), the other a long progression of at least 8 bands involving a mode at 143 cm^t-1 (a). The 143 cm^?1 progression forming mode can best be asigned to the CO out-of-plane wagging vibration. The absorption shows the same two strong progressions, reduced in frequency to 1270 cm^t-1 and 123 cm^?1, respectively, but with the progression in mode a broadened with increasing n. The broadening is interpreted as arising from inversion doublets; the close harmonicity up to n = 5 allowing the potential barrier to inversion to be estimated as > 700 cm^?1. A feature of the spectra is the absence of low frequency torsional modes suggesting lack of pseudo Jahn-Teller distortion of the triplet state potential surface. For comparison, the phosphorescence of crystalline hexafluoroacetone was also studied at 4.2°K. The spectrum exhibits broad bandedness with a 00 band tentatively assigned at 26 870 ± 20 cm^?1.     

Carbon-13 NMR spectra of chlorophyll a,chlorophyll a′, pyrochlorophyll a and the corresponding pheophytins

The ¹³C NMR spectra of C-10 epimeric chlorophylls a and a′, pheophytins a and a′, pyrochlorophyll a and pyropheophytin a have been recorded and assigned by chemical shift comparison, by long-range selective ¹H decoupling experiments and by the examination of the fully coupled spectra. Various factors influencing the ¹³C chemical shifts of the chlorophyll derivatives, e.g. the coordination of magnesium to the chlorin nucleus, the effect of solvent and the steric strain at the periphery of the macrocycle, have been examined. The ¹³C NMR spectra of chlorophyll a measured in acetone-d₆ and tetrahydrofuran-d₈ (THF) were compared, and remarkable solvent effects on the ¹³C chemical shifts were observed. These effects were interpreted mostly in terms of specific chlorophyll-solvent interactions. Different electron donor and steric properties of acetone and THF were considered to cause conformational alterations in the macrocycle, induced by the ligation of the solvent molecule(s) to the axial position(s) of the central magnesium atom of chlorophyll a. These results show that ¹³C NMR spectroscopy is a method of high information value for investigations of the unique electron donor acceptor (EDA) properties of the chlorophylls. The structural differences between the C-10 epimeric chlorophylls and pheophytins were examined in terms of the substituent chemical shift (SCS) parameters for the C-10 methoxycarbonyl group. The analysis showed that the change from the (10R) to the 10(S) configuration induces conformational alterations in the whole macrocycle which are, however, most prominent in rings IV and V. Owing to the increased steric interaction (repulsion) between the bulky substituents at C-7 and C-10, the peripheral strain is larger in the (10S) form, and is relieved by more pronounced deviations of rings IV and V from the macrocyclic plane compared with the (10R) form. The examination of the SCS parameters also showed that the peripheral steric strain is dissipated to a larger extent over the entire macrocycle in the Mg-free derivatives. These results confirm the previous conclusions based on ¹H NMR and CD data. The possible function of chlorophyll a′ in photosynthesis is briefly discussed.     

Photolysis and emission spectra of substituted polyacrylophenones

Poly-[3′,4′-dimethoxyacrylophenone], poly-4′-phenylacrylophenone, poly-2′-acrylonaphthone and copolymers of acrylophenone monomers with styrene and methyl methacrylate were prepared. Quantum yields of main chain scission in chlorobenzene by 313 nm radiation were 10³ times lower for all homopolymers and copolymers studied than for polyacrylophenone. The emission spectra of the polymers, copolymers and model compounds were taken for films at 77 K. The 3′,4′-dimethoxyacrylophenone, 4′-phenylacrylophenone and 2′-acrylonaphthone structural units exhibited poorly resolved emission spectra in homopolymer, copolymer and model compound. No difference in the emission spectra of films and dispersed homopolymer or copolymer in a poly(methyl methacrylate) matrix was observed. The decay of the emission of all homopolymers and copolymers under study was exponential, the life-time exceeding 0.20 sec.     

Detecting Hg2+ ions with an ICT fluorescent sensor molecule: remarkable emission spectra shift and unique selectivity

A fluorescent ratiometric Hg2+ ion sensor RMS, based on a coumarin platform coupled with a tetraamide receptor, is presented. This sensor, employing the ICT mechanism, could be used to specifically detect Hg2+ ions in a neutral buffered water solution with an approximately 100-nm blue shift in emission spectra.     

Enhanced emission and its switching in fluorescent organic nanoparticles

A new class of organic nanoparticles (CN-MBE nanoparticles) with a mean diameter of ca. 30-40 nm, which exhibit a strongly enhanced fluorescence emission, were prepared by a simple reprecipitation method. CN-MBE (1-cyano-trans-1,2-bis-(4'-methylbiphenyl)ethylene) is very weakly fluorescent in solution, but the intensity is increased by almost 700 times in the nanoparticles. Enhanced emission in CN-MBE nanoparticles is attributed to the synergetic effect of intramolecular planarization and J-type aggregate formation (restricted excimer formation) in nanopaticles. On/off fluorescence switching for organic vapor was demonstrated with CN-MBE nanoparticles.     

Excitation and emission spectra of rubidium in rare-gas thin-films

To understand the optical properties of atoms in solid state matrices, the absorption, excitation, and emission spectra of rubidium doped thin-films of argon, krypton, and xenon were investigated in detail. A two-dimensional spectral analysis extends earlier reports on the excitation and emission properties of rubidium in rare-gas hosts. We found that the doped crystals of krypton and xenon exhibit a simple absorption-emission relation, whereas rubidium in argon showed more complicated spectral structures. Our sample preparation employed in the present work yielded different results for the Ar crystal, but our peak positions were consistent with the prediction based on the linear extrapolation of Xe and Kr data. We also observed a bleaching behavior in rubidium excitation spectra, which suggests a population transfer from one to another spectral feature due to hole-burning. The observed optical response implies that rubidium in rare-gas thin-films is detectable with extremely high sensitivity, possibly down to a single atom level, in low concentration samples.     

Simultaneous imaging of multiple fluorescent probes in bio-cells.

In order to obtain the full spectrum from 400 to 800 nm of each pixel of a microscopic image, a unique spectro-imaging system was developed using an image slicer. The image slicer is composed of 100 photo fibers which are arranged in a matrix of 10 x 10 at the entrance and 100 x 1 at the exit. A line of this 100 signals is passed through a glism and projected onto a CCD. This system was applied to the fluorescent imaging of bio-cells. One of the demonstrative examples was simultaneous measurements of the Ca2+ concentration and the pH using of respective fluorescent probes. An electric signal was applied to BY-2 protoplasts and the fluorescent spectrum from 500 nm to 800 nm was measured every 5 s. The spectrum of the BY-2 protoplasts changed in response to the electric signal and the Ca2+ concentration, and the pH changes could be monitored. The wavelength resolution was satisfactory, but the space resolution was still rough in comparison with the usual microscopic systems. Notwithstanding these conditions, we could obtain discrete data from more than several tens of sites in a single-cell or a chain of several cells.     

On the relation between absorption and emission spectra of molecules in solution

The universal relation between absorption and fluorescence spectra derived by Stepanov in 1957 is reexamined to assess the relative merits of two of the inferences usually drawn from its use in the analysis of data: elevated excited state temperatures (“warm fluorescence”) and inhomogeneous broadening of the molecular spectra. Of these, only the latter appears to give a satisfactory explanation of the anomalous temperatures derived using the Stepanov method in condensed media, and in particular, a purely “warm fluorescence” interpretation implies that a distinct curvature should appear in plots which experimentally appear to be straight lines.     

Preparation and emission spectra of polymeric 1,2-diketones

Monomers of the methacrylate type, viz. 1-[4-(2-methacroyloxyethoxy)phenyl] propandione-1,2 (7a) and 1-phenyl-2-[4-(2-methacroyloxyethoxy)phenyl] ethandione-1,2 (7b) having the 1,2-dicarbonyl chromophore in the side-chain, were synthesized. The soluble homopolymer of monomer 76 and copolymers of both monomers 7a and 7b with styrene and methyl methacrylate were prepared by radical polymerization in solution. The absorption and emission spectra of a model compound and the homopolymer showed that the 1,2-dicarbonyl chromophore behaved as an isolated unit. No fluorescence was observed for the model compound or the homopolymer in emission spectra of poly(methyl methacrylate)-doped films. Phosphorescence of low- and high-molecular carbonyls was quenched by ferrocene in solution. Comparison of Stern-Volmer constants indicates partial steric hindrance of energy transfer for high-molecular donor.     

Excitation and emission spectra of jet-cooled naphthylmethyl radicals

Gas phase excitation and emission spectra of three naphthylmethyl radical chromophores are presented. These resonance-stabilized species, 1-naphthylmethyl, 2-naphthylmethyl, and α-acenaphthenyl, each possessing an sp(2) carbon adjacent to a naphthalene moiety, are studied by resonant two-color two-photon ionization, laser induced fluorescence, and dispersed fluorescence spectroscopy. Identification of the radicals is made through a combination of dispersed fluorescence and density functional theory calculations. All three species possess spectra in the 580 nm region. The possible relevance to unidentified spectroscopic features such as the diffuse interstellar bands and emission from the Red Rectangle nebula is discussed.