Raman spectroscopy reveals direct chromophore interactions in the Leu/Gln105 spectral tuning switch of proteorhodopsins

Proteorhodopsins are an extensive family of photoactive membrane proteins found in proteobacteria distributed throughout the world's oceans which are often classified as green- or blue-absorbing (GPR and BPR, respectively) on the basis of their visible absorption maxima. GPR and BPR have significantly different properties including photocycle lifetimes and wavelength dependence on pH. Previous studies revealed that these different properties are correlated with a single residue, Leu105 in GPR and Gln105 in BPR, although the molecular basis for the different properties of GPR and BPR has not yet been elucidated. We have studied the unexcited states of GPR and BPR using resonance Raman spectroscopy which enhances almost exclusively chromophore vibrations. We find that both spectra are remarkably similar, indicating that the retinylidene structure of GPR and BPR are almost identical. However, the frequency of a band assigned to the retinal C13-methyl-rock vibration is shifted from 1006 cm (-1) in GPR to 1012 cm (-1) in BPR. A similar shift is observed in the GPR mutant L105Q indicating Leu and Gln residues interact differently with the retinal C13-methyl group. The environment of the Schiff base of GPR and BPR differ as indicated by differences in the H/D induced down-shift of the Schiff base vibration. Residues located in transmembrane helices (D-G) do not contribute to the observed differences in the protein-chromophore interaction between BPR and GPR based on the Raman spectra of chimeras. These results support a model whereby the substitution of the hydrophilic Gln105 in BPR with the smaller hydrophobic Leu105 in GPR directly alters the environment of both the retinal C13 group and the Schiff base.     

Ultrafast vibrational spectroscopy of the flavin chromophore

Ultrafast time-resolved infrared (TRIR) spectra of flavin adenine dinucleotide (FAD) and the anion of lumiflavin (Lf-) are described. Ground-state recovery and excited-state decay of FAD reveal a common dominant ultrafast relaxation and a minor slower component. The Lf- transient lacks a fast component. No intermediate species are observed, suggesting that the quenching mechanism is internal conversion promoted by interaction of the adenine and isoalloxazine rings in FAD. Modes are assigned, and the potential for extension of the TRIR method to photoactive proteins is discussed.     

Kinetics of acid-induced spectral changes in the GFPmut2 chromophore

We have used a nanosecond pH-jump technique, coupled with simultaneous transient absorption and fluorescence emission detection, to characterize the dynamics of the acid-induced spectral changes in the GFPmut2 chromophore. Disappearance of the absorbance at 488 nm and the green fluorescence emission occurs with a thermally activated, double exponential relaxation. To understand the source of the two transients we have introduced mutations in amino acid residues that interact with the chromophore (H148G, T203V, and E222Q). Results indicate that the faster transient is associated with proton binding from the solution, while the second process, smaller in amplitude, is attributed to structural rearrangement of the amino acids surrounding the chromophore. The protonation rate shows a 3-fold increase for the H148G mutant, demonstrating that His148 plays a key role in protecting the chromophore from the solvent. The deprotonation rate for T203V is an order of magnitude smaller, showing that the hydrogen bond with the hydroxyl of Thr203 is important in stabilizing the deprotonated form of the chromophore. A kinetic model suggests that, in addition to protecting the chromophore from the solvent, His148 may act as the primary acceptor for the protons on the way to the chromophore.     

Structure, spectroscopy, and spectral tuning of the gas-phase retinal chromophore: the beta-ionone "handle" and alkyl group effect

The low-lying singlet states (i.e. S0, S1, and S2) of the chromophore of rhodopsin, the protonated Schiff base of 11-cis-retinal (PSB11), and of its all-trans photoproduct have been studied in isolated conditions by using ab initio multiconfigurational second-order perturbation theory. The computed spectroscopic features include the vertical excitation, the band origin, and the fluorescence maximum of both isomers. On the basis of the S0-->S1 vertical excitation, the gas-phase absorption maximum of PSB11 is predicted to be 545 nm (2.28 eV). Thus, the predicted absorption maximum appears to be closer to that of the rhodopsin pigment (2.48 eV) and considerably red-shifted with respect to that measured in solution (2.82 eV in methanol). In addition, the absorption maxima associated with the blue, green, and red cone visual pigments are tentatively rationalized in terms of the spectral changes computed for PSB11 structures featuring differently twisted beta-ionone rings. More specifically, a blue-shifted absorption maximum is explained in terms of a large twisting of the beta-ionone ring (with respect to the main conjugated chain) in the visual S-cone (blue) pigment chromophore. In contrast, the chromophore of the visual L-cone (red) pigment is expected to have a nearly coplanar beta-ionone ring yielding a six double bond fully conjugated framework. Finally, the M-cone (green) chromophore is expected to feature a twisting angle between 10 and 60 degrees. The spectroscopic effects of the alkyl substituents on the PSB11 spectroscopic properties have also been investigated. It is found that they have a not negligible stabilizing effect on the S1-S0 energy gap (and, thus, cause a red shift of the absorption maximum) only when the double bond of the beta-ionone ring conjugates significantly with the rest of the conjugated chain.     

Laser saturation studies of spectral broadening of electrons in alcohols

Kinetic laser saturation experiments are reported in which evidence is presented for homogeneous photobleaching across 1.5 eV of the optical absorption band of solvated electrons in a range of alcohols. Competition between vibronic relaxation and photochemistry of the excited state is discussed.     

The scavenging of the precursors of the solvated electron from the positron lifetime spectroscopy and the doppler broadening of annihilation line shape technique

The electron scavenging properties of aqueous solutions of two series of solutes are investigated, using the positron as a probe. For a better interpretation of the data, both lifetime spectroscopy and the Doppler broadening of annihilation line shape technique are used. All solutes inhibit the positronium (Ps) formation, by the scavenging of electrons. The first series consists of the halate ions, that should follow the Hunt linear relation between the rate constant for reaction with the solvated electrons, k_(e^?aq+S), and that for its precursor(s), 1/C₃₇. The Ps inhibition constants, k, are 0.14, 1.44 and 3.45 M^?1 for ClO^?₃, BrO^?₃ and IO^?₃, respectively. This sequence is quantitatively consistent with that of the respective k_(e^?eq+S). The second series includes the SeO⁼₄, Te(OH)₆ and BrO^?₄ species, and the Ps inhibition constants are 5.62, 10.5 and 14.3 M^?1 respectively. These values are much higher than expected from the k_(e^?aq+S) constants, on basis of the Hunt relation, in agreement with previous results from pulse radiolysis experimets.     

Stark broadening and shift of OII spectral lines in higher multiplets

Stark widths and shifts of nineteen singly-ionized oxygen spectral lines, mostly of higher multiplets, have been measured in a pulsed linear arc plasma in an oxygen-nitrogen mixture at 8.1×10²² m^?3 electron density and 60000 K electron temperature. The measured widths and shifts values are compared, for eight multiplets, with existing theoretical results.     

Single chromophore spectroscopy of MEH-PPV: homing-in on the elementary emissive species in conjugated polymers.

Low-temperature, single-molecule spectroscopy can provide unparalleled access to the primary emissive species of conjugated polymers. We demonstrate this with the example of one of the most commonly studied polymers, poly(2-methoxy-5-(2'-ethylhexoxy)-1,4-phenylenevinylene), MEH-PPV, which is shown to exhibit sharp fluorescence signatures over one hundred times narrower than the ensemble. These unprecedented narrow emission features can be assigned to single chromophores on the polymer chain, which are selectively addressed by the narrow band excitation. As with organic dye systems, the emission from single chromophores is not static with time, but shows a substantial spectral fluctuation. We find that, for single chromophores, this spectral fluctuation always follows a universal Gaussian statistical distribution. High-resolution spectroscopy provides unique insight into low-energy vibrational modes in the polymer emission, which are generally inaccessible with conventional spectroscopic methods such as site-selective fluorescence or Raman spectroscopy. Interchromophoric coupling can also occur owing to the flexible nature of the polymer backbone. This leads to substantial spectral broadening and a loss of resolution in the vibronic progression. We observe reversible switching within one single molecule between narrow and broad emission, which directly correlates with a discrete switching in emission intensity. We conclude that one and the same single molecule can support aggregated and nonaggregated emission, that is, emission from isolated and aggregated chromophores in one single molecule, rather than the tendency for aggregate emission being intrinsic to the molecule.     

Application of laser-induced plasma spectroscopy to the measurement of Stark broadening parameters

In this work, we have studied the main conditions that a laser-induced plasma must fulfill in order to be considered as adequate for the measurement of Stark broadening parameters. We investigated the effect of the temporal window, the self-absorption, the crater size, and the effect of the spatial inhomogeneity on the emission profiles coming from a laser-induced plasma. Starting from the spatially resolved values of the plasma parameters, obtained by emission spectroscopy, the error in the determination of the Stark electron width due to the spatial inhomogeneity has been estimated and, for the present experimental conditions, was found to be lower than 7%. As a test of the method, the Stark electron broadening constant of Fe I 381.58 nm has been measured using the Fe I 538.34 nm emission line as the reference to determine the electron density. The plasma was produced under a controlled atmosphere of argon at atmospheric pressure, on an iron–nickel alloy sample. The emission was collected by a system with high spectral resolution, for different temporal windows after the laser pulse. For time delays between 2.75 and 21 μs, the electron density showed an evolution in the range 2.0–0.13 × 10¹⁷ cm^− 3, while the temperature varied from 11 100 to 7100 K. The representation of the Stark electron width of Fe I 381.58 nm, measured for each temporal window, versus the Stark electron width of the reference line showed a linear behavior with a high correlation coefficient. From the slope of this linear fit and the Stark electron broadening constant of the reference line, the Stark width of Fe I 381.58 nm was obtained to be 1.10 ± 0.07 × 10^− 2 nm for an electron density of 10¹⁷ cm^− 3.     

Population branching in the conical intersection of the retinal chromophore revealed by multipulse ultrafast optical spectroscopy

The branching ratio of the excited-state population at the conical intersection between the S(1) and S(0) energy surfaces (Φ(CI)) of a protonated Schiff base of all-trans retinal in protic and aprotic solvents was studied by multipulse ultrafast transient absorption spectroscopy. In particular, pump-dump-probe experiments allowed to isolate the S(1) reactive state and to measure the photoisomerization time constant with unprecedented precision. Starting from these results, we demonstrate that the polarity of the solvent is the key factor influencing the Φ(CI) and the photoisomerization yield.     

Discrimination of structural order and chromophore aggregation as factors effecting the photo-reorientation of azobenzene in copolyglutamate LB films

Photo-reorientation experiments have been performed on LB films of polyglutamates with azobenzene side chains and copolyglutamates with azobenzene moieties and non-photochromic mesogens as side chains. Incorporation of the non-photochromic phenylbenzoate and methyl-substituted biphenyl side chains prevents aggregation of the chromophores, but does not change the LB film structure. Photo-reorientation upon irradiation with polarized light is suppressed by the side-chain structure in the LB film, independent of chromophore aggregation. This structure is disrupted if the amount of side chains which can be photo-isomerized exceeds a critical number. After the structure has been disrupted, photo-reorientation is possible. Not only the chromophores, but also the non-photochromic side chains are reoriented in a cooperative manner.     

Nanoparticle agglutination: acceleration of aggregation rates and broadening of the analyte concentration range using mixtures of various-sized nanoparticles

SiO(2) particles of various sizes were prepared and surface modified with biotin-chain-end-functionalized poly(ethylene glycol). Dispersions of these particles were prepared, and their aggregation was induced upon the addition of avidin. The aggregate size and growth rate were monitored by DLS analysis, and SEM and TEM images of freeze-dried samples of the aggregate solutions were used to confirm the DLS data and to image the aggregate size and dimension. A linear correspondence between apparent diameter and time was observed, and both the 20 and 300 nm particles aggregated at slower rates than for the 40 nm particles. These observations were attributed to differences in the average functionality of the systems and the different initial concentrations of particles and avidin. The observed aggregation rates of binary combinations of the three particle sizes (i.e., 20 + 40 nm or 40 + 300 nm) were faster than those of the single-sized mixtures. These results were attributed to the faster flux of smaller particles toward larger particles in the mixture solutions as well as to the potentially larger number of productive collisions possible between mixtures of small particles and large particles versus only similarly sized particles. Combinations of the three sizes of particles were studied to find an empirical optimum formulation for generating large aggregates on a short time scale and over a wide range of analyte concentrations.     

Femtosecond IR spectroscopy of peroxycarbonate photodecomposition: S1-lifetime determines decarboxylation rate

The ultrafast photofragmentation of arylperoxycarbonates R-O-C(O)O-O-tert-butyl (R = naphthyl, phenyl) is studied using femtosecond UV excitation at 266 nm and mid-infrared broadband probe pulses to elucidate the dissociation mechanism. Our experiments show that the rate of fragmentation is determined by the S1-lifetime of the peroxide, i.e., the time constants of S1 decay and of CO2 and R-O* formation are identical. The fragmentation times are solvent dependent and for tert-butyl-2-naphthylperoxycarbonate (TBNC) vary from 25 ps in CH2Cl2 to 52 ps in n-heptane. In the case of the tert-butylphenylperoxycarbonate (TBPC) the decomposition takes 5.5 ps in CD2Cl2 and 12 ps in n-heptane. The CO2 fragment is formed vibrationally hot with an excess energy of about 5000 cm(-1). The hot CO2 spectra at high energy can be modeled assuming Boltzmann distributions with initial vibrational temperatures of ca. 2500 K which relax to ambient temperature with time constants of 280 ps in CCl4 and 130 ps in n-heptane. In CCl4 the relaxed spectra at 1.5 ns show 3.5% residual excitation in the n = 1 level of the asymmetric stretch vibration.     

Many-body response of benzene at monolayer MoS2: Van der Waals interactions and spectral broadening

Models of surface enhancement of molecular electronic response properties are challenging for two reasons: (a) molecule-surface interactions require a simultaneous solution of the molecular and the surface dynamic response (a daunting task), and (b) when solving for the electronic structure of the combined molecule + surface system, it is not trivial to single out the particular physical effects responsible for enhancement. To tackle this problem, in this work, we apply a formally exact decomposition of the system's response function into subsystem contributions by using subsystem density functional theory (DFT), which grants access to dynamic polarizabilities and optical spectra. In order to access information about the interactions between the subsystems, we extend a previously developed subsystem-based adiabatic connection fluctuation-dissipation theorem of DFT to separate the additive from the nonadditive correlation energy and identify the nonadditive correlation as the van der Waals interactions. As an example, we choose benzene adsorbed on monolayer MoS₂. We isolate the contributions to benzene's dynamic response arising from the interaction with the surface, and for the first time, we evaluate the enhancements to the effectiveness of C₆ coefficients as a function of benzene-MoS₂ distance and adsorption site. We also quantify the spectral broadening of the benzene's electronic excited states due to their interaction with the surface. We find that the broadening has a similar decay law with the molecule-surface distance as the leading van der Waals interactions (ie, R⁻⁶ ) and that the surface enhancement of dispersion interactions between benzene molecules is less than 5% but is still large enough (0.5 kcal/mol) to likely play a role in the prediction of interface morphologies.     

Determination of critical micelle concentrations and aggregation numbers by fluorescence correlation spectroscopy: aggregation of a lipopolysaccharide

Fluorescence correlation spectroscopy (FCS) is often used to determine the mass or radius of a particle by using the dependence of the diffusion coefficient on the mass and shape. In this article we discuss how the particle size of aggregates can be measured by using the concentration dependence of the amplitude of the autocorrelation function (ACF) instead of the temporal decay. We titrate a solution of aggregates or micelles with a fluorescent label that possesses a high affinity for these structures and measure the changes in the amplitude of the ACF. We develop the theory describing the change of the ACF amplitude with increasing concentrations of labels and use it to fit experimental data. It is shown how this method can determine the aggregation number and critical micelle concentration of a standard detergent nonaethylene glycol monododecyl ether (C₁₂E₉) and a lipopolysaccharide (LPS: Escherichia coli 0111:B4).     

FT transmission spectroscopy in the visible and ultraviolet spectral ranges

Fourier transform spectroscopy can be applied as a useful measurement technique in the visible and ultraviolet spectral range. Examples of high resolution measurements in these spectral ranges are shown.     

Conformational study of the chromophore of C-phycocyanin by resonance raman and electronic absorption spectroscopy.

The conformation of the chromophore of C-phycocyanin (PC) was investigated by using electronic absorption and resonance Raman spectroscopy, and theoretical calculations. Using an A-dihydrobilindione as model compound, the syn, syn, syn conformation was established for the isolated chromophore in solution. For the native PC, the best results were obtained by considering the syn, syn, anti conformation, although the possibility of having a syn, anti, anti conformation could not be excluded.     

Ionization spectroscopy of conformational isomers of propanal: the origin of the conformational preference

Two different conformational isomers of propanal, cis and gauche, are investigated by the vacuum-UV mass-analyzed threshold ionization (VUV-MATI) spectroscopy to give accurate adiabatic ionization potentials of 9.9997 +/- 0.0006 eV and 9.9516 +/- 0.0006 eV, respectively. cis-Propanal, which is the more stable conformer in the neutral state, becomes less stable in the cation compared to gauche-propanal. Vibrational structures revealed in the MATI spectra indicate that cis and gauche isomers undergo their unique structural changes upon ionization. The ionization of gauche-propanal induces a geometrical change along the conformational coordinate, suggesting that the steric effect in the ground state is diminished upon ionization. Natural bonding orbital (NBO) calculations provide the extent of hyperconjugation in each conformational isomer of propanal.