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

▪ 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

Conventional vibrational spectroscopies such as infrared absorption and spontaneous or coherent Raman scattering provide a one-dimensional projection of intermolecular and intramolecular vibrational structure and motions onto a single frequency (or time) axis. For simple molecules with well-separated eigenstates, this gives direct information on energy levels and their oscillator strengths. The situation is very different in complex systems with highly congested levels such as biological molecules, liquids, polymers, and glasses.1-5 Here the microscopic information is highly averaged, and is often totally buried under broad, featureless lineshapes, whose precise interpretation remains a mystery. Typical examples are the amide band in proteins,6,7 and hydrogen-bonded liquids.8,9 For decades, optical spectroscopists have dreamt about using multidimensional coherent nonlinear spectroscopic techniques to overcome these difficulties and unravel the microscopic picture underlining complex spectra. Coherent spectroscopy uses several laser beams to generate signals that propagate along new directions, different from those of the incoming pulses. “Coherent” implies that phase information plays an important role. In this context, coherence has a dual meaning corresponding to both the radiation field and the molecules. First, the signal field is generated by many molecules whose externally driven charge distributions oscillate in phase, creating a signal field with a well-defined phase. This is in contrast to incoherent techniques such as fluorescence where individual molecules contribute additively to the signal’s intensity rather than to the amplitude, and there is no phase relation between the light emitted by different molecules. In addition to the phase of the field, the laser beams create wavepackets of molecular states; coherence thus further implies a definite phase relationship between different states. Multiple pulses can create, manipulate, and probe this coherence which carries important signatures of molecular structure, coupling patterns, and dynamics. Many modern techniques in spectroscopy make use of coherence. For example, one of the major accomplishments of nuclear magnetic resonance has been its capacity to disentangle hopelessly complicated spectra by spreading them in more dimensions onto several frequency or time axes.10 Carefully designed pulse sequences make it possible to eliminate dipolar interactions which dominate the line widths. Since their inception in the 1970s, multidimensional NMR techniques have turned into a powerful tool which provides structures with resolution comparable to X-rays, and dynamics of very complex molecules, crystals, and proteins with up to a few thousand atoms. Multidimensional spectroscopy probes correlations between signals and offers an unusual sensitivity and selectivity. Magnetic resonance is the elder brother of coherent optical spectroscopy: the two share many basic concepts. Since the ability to shape and control radiowave pulses predated similar advances in laser technology, many of the optical techniques had been invented in NMR 20-30 years earlier. By extending these ideas to the optical regime, it should be possible to come up with novel classes of spectroscopies which could probe complex vibrational motions. Picosecond coherent spectroscopy of atoms and small molecules in the gas phase is very similar to that of nuclear spins.11,12 The extension to complex molecules in the condensed phase has been a much more difficult task which requires some significant advances. The large transition dipoles and strong interactions induce line broadenings resulting from ultrashort dephasing processes, which the excitation pulses need to overcome. The necessary impulsive excitation requires laser pulses shorter than the corresponding vibrational periods and dephasing timescales. In recent years, femtosecond laser techniques have made giant strides, and Shaul Mukamel, Professor of Chemistry at the University of Rochester, NY, and at the Rochester Theory Center for Optical Science and Engineering, received the Ph.D. degree in chemical physics in 1976 from Tel-Aviv University, Israel, and held postdoctoral positions at MIT, Cambridge, and the University of California, Berkeley. His research interests include theoretical studies of ultrafast nonlinear optical spectroscopy in condensed phases, electronic excitations in conjugated and aggregated molecules and semiconductor nanostructures, and biological electron and energy transfer. He is a coauthor of 350 publications and a graduate-level textbook, Principles of Nonlinear Optical Spectroscopy; Oxford University Press, 1995. Dr. Mukamel is a fellow of the American Physical Society and of the Optical Society of America, and a recipient of the Fulbright, Alfred P. Sloan, Camille and Henry Dreyfus, Guggenheim, and Alexander von Humboldt Senior Awards.

/pdf/two-dimensional-raman-echoes-femtosecond-view-of-molecular-17795st4w8.pdf

Two-Dimensional Raman Echoes: Femtosecond View of Molecular Structure and Vibrational Coherence

https://web.stanford.edu/group/fayer/articles/135.pdf

High temperature optical dephasing mechanism for dye molecules in PMMA glass

http://web.stanford.edu/group/fayer/articles/144.pdf

Thermal history and temperature-dependent photon echo and hole burning linewidths in low temperature glycerol glasses

https://web.stanford.edu/group/fayer/articles/122.pdf

Low-temperature glass dynamics probed by optical dephasing measurements

Amorphous materials at low temperature have markedly different physical and thermal properties from crystals.' For example, the specific heats of crystals obey the Debye P law at low temperatures2 and the thermal conductivity also follows the same P temperature dependen~e .~ Many of these properties can be calculated because crystals have long-range spatial and orientational order.4 Twenty years ago, specific heat measurements on disordered materials revealed significant deviations from the Debye law at approximately 1 K.5-8 Measurements of thermal conductivity5y9 and dielectric responselOJ1 also deviated from crystalline behavior. These observations showed that the dynamics of ordered and disordered systems must be fundamentally different. Although ordered crystals are commonly found in nature, many other naturally occurring complex systems, such as proteins, are inherently disordered.12 Furthermore, many artificial materials, such as polymeric solids and amorphous semiconductors, are glasses. Therefore, understanding the microscopic behavior of the glassy state has been and continues to be13-15 an important problem in chemistry, physics, and materials science. Glasses are systems in which there is no translational or rotational order. More important, unlike a crystal, a glass is not in thermodynamic equilibrium. At low temperature, the equilibrium state of a substance like ethanol is crystalline. A glass is formed by rapid cooling, which traps the material in the glassy state. Thermodynamically the material should be a crystal, but kinetics prevent the system from finding the global potential minimum; Le., the kinetics at low temperature make the time scale for crystallization essentially infinitely long. Dynamics in simple crystals involve fast fluctuations about an equilibrium structure.16 In conlocal structures as well as time evolution of the nonequilibrium local structures them~e1ves.l~ Glass dynamics can occur through essentially all time scales from femtoseconds, to kiloseconds, and perhaps longer.lgZ0 Many concepts that are useful in describing dynamics in crystals cannot be extended to the amorphous state, e.g., translational symmetry, which gives rise to phonon bands and fast phonon fluctuations, providing a separation of time scales for a variety of processes.z1 In crystals at low temperatures, only the acoustic phonons are thermally excited. The phonon dispersion is well described by the Debye density of ~ t a t e s , ~ J ~ and this means that the distribution of fluctuation rates is known. A glass also has modes that are equivalent to a crystal's phonons. Even at low temperatures, however, there is a major contribution to the dynamical properties of glasses from the evolution of local structures, and it is these "extra" dynamics that make glasses fundamentally different from crystals. The anomalous heat capacities found in glasses show a term linear in temperature which is not present in crystals. This is true in such diverse substances as silicates and ceramics as well as poly(methy1 methacrylate) and Lexan polymer^.^-^>^^ In addition, heat capacities are time dependent; the heat capacity increases as time i n c r e a ~ e s . ~ ~ J ~ ~ ~ ~ ~ Thermal conductivity, which varies as P in crystals, varies as P? The phonon mean free path in a glass is substantially less than in the corresponding crystal, and a variation in the velocity of sound with temperature is seen in amorphous syst e m ~ . ~ ~ Many theoretical models have been developed to account for the various observations. The models invoke defect-induced scattering,26 localized electronic states,27 and defect and particle diffusionz8 to explain aspects of the observed behaviors. The two-level-system (TLS) model proposed independently by Anderson et al.29 and Phillips30 has been the most widely used, and it is frequently the point of departure in discussing the properties of low-temperature glasses. The TLS model postulates that, in an amorphous material, some atoms or molecules (or groups of atoms or molecules) can reside in not just one but two potential minima of the local structure potential surface (Figure 1). Each side of the double-well potential represents a distinct local structure of the glass. This is a simplified representation of what is almost certainly a complex multidimensional potential surface. At low temperatures, transitions from one side of the double well to the other represent changes in the local structure. Transitions occur by phonon-assisted tunneling. To model the complex distribution of local structures and transition rates, the TLS model states that there

/pdf/probing-organic-glasses-at-low-temperature-with-variable-4i9j027db8.pdf

Probing organic glasses at low temperature with variable time scale optical dephasing measurements

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High temperature optical dephasing mechanism for dye molecules in PMMA glass

Thermal history and temperature-dependent photon echo and hole burning linewidths in low temperature glycerol glasses

Low-temperature glass dynamics probed by optical dephasing measurements

Probing organic glasses at low temperature with variable time scale optical dephasing measurements