Preface. Part One: Optical Methods. 1. Developments in Classical Optical Spectroscopy J. Amesz. 2. Linear and Circular Dichroism G. Garab. 3. Fluorescence K. Sauer, M. Debreczeny. 4. Ultrafast Spectroscopy of Photosynthetic Systems R. Jimenez, G.R. Fleming. 5. Data Analysis of Time-Resolved Measurements A.R. Holzwarth. 6. Photosynthetic Thermoluminescence as a Simple Probe of Photosystem II Electron Transport Y. Inoue. 7. Accumulated Photon Echo Measurements of Excited State Dynamics in Pigment-Protein Complexes T.J. Aartsma, R.J.W. Louwe, P. Schellenberg. 8. Spectral Hole Burning: Methods and Applications to Photosynthesis N. Raja, S. Reddy, G.J. Small. 9. Infrared and Fourier-Transform Infrared Spectroscopy W. Mantele. 10. Resonance Raman Studies in Photosynthesis - Chlorophyll and Carotenoid Molecules B. Robert. 11. Stark Spectroscopy of Photosynthetic Systems S.G. Boxer. 12. The Photoacoustic Method in Photosynthesis - Monitoring and Analysis of Phenomena which Lead to Pressure Changes Following Light Excitation S. Malkin. Part Two: Magnetic Resonance. 13. Magnetic Resonance: an Introduction A.J. Hoff. 14. Time-Resolved Electron Paramagnetic Resonance Spectroscopy - Principles and Applications H. Levanon. 15. Electron Spin Echo Methods in Photosynthesis Research R.D. Britt. 16. ENDOR Spectroscopy W. Lubitz, F. Lendzian. 17. Optically Detected Magnetic Resonance (ODMR) of Triplet States in Photosynthesis A.J. Hoff. 18. MagicAngle Spinning Nuclear Magnetic Resonance of Photosynthetic Components H.J.M. de Groot. Part Three: Structure and Oxygen. 19. Structure Determination of Proteins by X-Ray Diffraction M. Schiffer. 20. Electron Microscopy E.J. Boekema, M. Roegner. 21. X-Ray Absorption Spectroscopy:Determination of Transition Metal Site Structures in Photosynthesis V.K. Yachandra, M.P. Klein. 22. Moessbauer Spectroscopy P.G. Debrunner. 23. Characterization of Photosynthetic Supramolecular Assemblies Using Small Angle Neutron Scattering D.M. Tiede, P. Thiyagarajan. 24. Measurements of Photosynthetic Oxygen Evolution H.J. van Gorkom, P. Gast.

Biophysical techniques in photosynthesis

A theory of optical echo spectroscopies of large polyatomic molecules in condensed phases is developed. Using phase space correlation functions, we examine the interrelationships among the following optical measurements: ordinary photon echo, stimulated photon echo, accumulated photon echo, incoherent accumulated photon echo, and pump–probe absorption. Conditions for the elimination of inhomogeneous broadening in these experiments are specified. A multimode Brownian oscillator model is used to account for high frequency molecular vibrations, as well as solvent modes, and electronic dephasing processes. The effects of quantum beats, spectral diffusion, and homogeneous dephasing on the echo signals are studied and compared in detail with pump–probe and hole burning spectroscopy.

/pdf/photon-echoes-of-polyatomic-molecules-in-condensed-phases-yrj78raz2h.pdf

Photon echoes of polyatomic molecules in condensed phases

Femtosecond visible and infrared analogues of multiple-pulse nuclear magnetic resonance techniques provide novel snapshot probes into the structure and electronic and vibrational dynamics of complex molecular assemblies such as photosynthetic antennae, proteins, and hydrogen-bonded liquids A classical-oscillator description of these spectroscopies in terms of interacting quasiparticles (rather than transitions among global eigenstates) is developed and sets the stage for designing new pulse sequences and inverting the multidimensional signals to yield molecular structures Considerable computational advantages and a clear physical insight into the origin of the response and the relevant coherence sizes are provided by a real-space analysis of the underlying coherence-transfer pathways in Liouville space

/pdf/multidimensional-femtosecond-correlation-spectroscopies-of-2a19t8t3z0.pdf

Multidimensional femtosecond correlation spectroscopies of electronic and vibrational excitons

X-ray luminescent nanoparticles (NPs), including lanthanide fluorides, have been evaluated for application to deep tissue in vivo molecular imaging using optical tomography. A combination of high material density, higher atomic number and efficient NIR luminescence from compatible lanthanide dopant ions indicates that particles that consist of ALnF4 (A = alkaline, Ln = lanthanide element) may offer a very attractive class of materials for high resolution, deep tissue imaging with X-ray excitation. NaGdF4:Eu3+ NPs produced an X-ray excited luminescence that was among the most efficient of nanomaterials that have been studied thus far. We have systematically studied factors such as (a) the crystal structure that changes the lattice environment of the doped Eu3+ ions within the unit cell; and extrinsic factors such as (b) a gold coating (with attendant biocompatibility) that couples to a plasmonic excitation, and (c) changes in the NPs surface properties via changes in the pH of the suspending medium-all with a significant impact on the X-ray excited luminescence of NaGdF4:Eu3+NPs. The luminescence from an optimally doped hexagonal phase NaGdF4:Eu3+ nanoparticle was 25% more intense compared to that of a cubic structure. We observed evidence of plasmonic reabsorption of midwavelength emission by a gold coating on hexagonal NaGdF4:Eu3+ NPs; fortunately, the NaGdF4:Eu3+ @Au core-shell NPs retained the efficient 5D0→7F4 NIR (692 nm) luminescence. The NaGdF4:Eu3+ NPs exhibited sensitivity to the ambient pH when excited by X-rays, an effect not seen with UV excitation. The sensitivity to the local environment can be understood in terms of the sensitivity of the excitons that are generated by the high energy X-rays (and not by UV photons) to crystal structure and to the surface state of the particles.

/pdf/nagdf4-eu3-nanoparticles-for-enhanced-x-ray-excited-optical-4vx0xpp0ce.pdf

NaGdF4:Eu3+ Nanoparticles for Enhanced X-ray Excited Optical Imaging.

▪ Abstract IR vibrational echo experiments are used to study dynamics in myoglobin (Mb) by investigating the dephasing of the CO-stretching mode of CO bound at the active site of the protein (Mb-CO). The temperature dependence and the viscosity dependence of Mb-CO pure dephasing have been measured in several solvents. In low-temperature, glassy solvents, the pure dephasing has a power law temperature dependence, T1.3, that reflects glasslike protein dynamics. In liquids, the temperature dependence is much steeper and arises from a combination of pure temperature dependence and the influence of decreasing solvent viscosity with increasing temperature. As the solvent viscosity decreases, the ability of the protein's surface to undergo topological fluctuations increases, which in turn increases the internal protein-structural fluctuations. The protein-structural motions are coupled to the CO bound at the active site by electric field fluctuations that accompany movements of polar residues. The dynamic electr...

Fast protein dynamics probed with infrared vibrational echo experiments

Results of picosecond photon echo and optical hole burning experiments are reported for four ionic dyes in ethanol glass. At low temperatures, the dephasing times deduced from the hole widths are as much as nine times shorter than those measured by the two‐pulse echo because of the effect of spectral diffusion. The temperature dependences found are of the form aTα+b exp (−ΔE/kT) due to glass two level system dynamics (T<4 K) and a process that activates exponentially at higher temperatures, possibly from a pseudolocal mode or glass optical phonon. Comparing the ratios of echo to hole burning measured dephasing times for the four dyes suggests that the dephasing is influenced by the existence of distinct local ethanol solvation shells in addition to the dynamics of the bulk solvent. A theoretical description of solvent shell effects is achieved through the use of a two spatial domain model of the glass dynamics. Calculations of dynamic perturbations from distinct solvation shell and bulk solvent regions sh...

Solvation shell effects and spectral diffusion: Photon echo and optical hole burning experiments on ionic dyes in ethanol glass

Solute-solvent dynamics and interactions in glassy media: Photon echo and optical hole burning studies of cresyl violet in ethanol glass

Optical evidence of multiple Ce{sup 3+}:Na{sup +} charge-compensation sites in codoped Ce{sup 3+}:Na{sup +}:CaF{sub 2} and Ce{sup 3+}:Na{sup +}:SrF{sub 2} crystals is reported. High-resolution absorption and laser-excitation spectroscopy reveal the presence of numerous lines in the 32 200--32 400-cm{sup {minus}1} region indicating a quasirandom distribution of pair sites. The absorption spectra of annealed Ce{sup 3+}:CaF{sub 2} and Ce{sup 3+}:Na{sup +}:CaF{sub 2} crystals reveal isolated {ital O}{sub {ital h}} lines. This fact has aided the interpretation of the Ce{sup 3+}:Na{sup +} pair spectra. Evidence for photoionization of charge-compensated Ce{sup 3+} sites followed by trapping of the electron at remotely compensated ({ital O}{sub {ital h}}) Ce{sup 3+} sites is presented. Acceptor-type hole burning, the disappearance of the cubic Ce{sup 3+} site's absorption line while exciting the Ce{sup 3+}:Na{sup +} pair centers, is observed in both CaF{sub 2} and SrF{sub 2} hosts. The holes persist for weeks after their creation and survive thermal cycling to room temperature.

Ce3+:Na+ pairs in CaF2 and SrF2: Absorption and laser-excitation spectroscopy, and the observation of hole burning.

https://web.stanford.edu/group/fayer/articles/124.pdf

Hole burning line shapes in a two-dimensional glass a model for hole burning line shapes of molecules on surfaces

We report the first optical dephasing study of an inorganic impurity system possessing sharp, low frequency mode structure in its ground and excited state spectra. The total dephasing times T2 and population relaxation times T1 for the 1T2g and 1Eg d9s excited states of NaF:Cu+ are determined at a series of temperatures between 1.8 and 296 K. The T2 values are determined by extracting the Lorentzian components from one‐ and two‐photon excitation line shapes. The T1 values caused by nonradiative decay rates are obtained by detecting very low quantum yield emission from the fast‐relaxing excited states and applying the formula tnr=Qtr, where t’s are radiative and nonradiative lifetimes and Q is the quantum yield. T1(1T2g)=4.6 ps and T1(1Eg )=2.0 ps at 8 K. Significantly, these are very similar to the T1 values calculated from lowest temperature Lorentzian linewidths by the relationship 1/T2=1/T′2 +1/(2T1). The T1 values stay approximately constant over the temperature range 1.8–45 K, while the linewidths ra...

Pure dephasing and nonradiative decay processes in the excited electronic states of NaF:Cu+

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