Dynamics in low temperature glasses: Theory and experiments on optical dephasing, spectral diffusion, and hydrogen tunneling

Berg, Mark A.; Walsh, Cecilia A.; Narasimhan, L. R.; Littau, Karl A.; Fayer, M. D.

doi:10.1063/1.454136

Cited by 228 publications

(119 citation statements)

References 81 publications

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“…2,3 In 1964, the basic concepts inherent in the spin echo were extended to visible spectroscopy using the earliest pulsed lasers to perform ''photon echo'' experiments on electronic excited states. 4,5 Photon echoes have been widely used to study electronic excited state dynamics in systems such as low temperature crystals [6][7][8][9][10] and glasses, [11][12][13][14] proteins, [15][16][17] and photosynthetic chromophore clusters. 18,19 The advent of short pulse infrared (IR) sources made it possible to perform ''vibrational echo'' experiments on the vibrations of condensed mater systems such as liquids, glasses and proteins beginning in the early 1990's.…”

Section: Introductionmentioning

confidence: 99%

Probing dynamics of complex molecular systems with ultrafast 2D IR vibrational echo spectroscopy

Finkelstein

Zheng

Ishikawa

et al. 2007

Phys. Chem. Chem. Phys.

148

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Ultrafast 2D IR vibrational echo spectroscopy is described and a number of experimental examples are given. Details of the experimental method including the pulse sequence, heterodyne detection, and determination of the absorptive component of the 2D spectrum are outlined. As an initial example, the 2D spectrum of the stretching mode of CO bound to the protein myoglobin (MbCO) is presented. The time dependence of the 2D spectrum of MbCO, which is caused by protein structural evolution, is presented and its relationship to the frequency-frequency correlation function is described and used to make protein structural assignments based on comparisons to molecular dynamics simulations. The 2D vibrational echo experiments on the protein horseradish peroxidase are presented. The time dependence of the 2D spectra of the enzyme in the free form and with a substrate bound at the active site are compared and used to examine the influence of substrate binding on the protein's structural dynamics. The application of 2D vibrational echo spectroscopy to the study of chemical exchange under thermal equilibrium conditions is described. 2D vibrational echo chemical exchange spectroscopy is applied to the study of formation and dissociation of organic solute-solvent complexes and to the isomerization around a carbon-carbon single bond of an ethane derivative.

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Section: Introductionmentioning

confidence: 99%

Probing dynamics of complex molecular systems with ultrafast 2D IR vibrational echo spectroscopy

Finkelstein

Zheng

Ishikawa

et al. 2007

Phys. Chem. Chem. Phys.

148

View full text Add to dashboard Cite

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“…As T w is increased, the echo decay increasingly reflects the effects of slower dynamics. 17,29 The signal at 1932 cm -1 decays more rapidly than the signal at 1946 cm -1 , and the signals at the two detection wavelengths change differently as the value of T w is increased. The time-dependent (T w -dependent) dynamic vibrational line shape is the Fourier transform of the vibrational echo decay.…”

mentioning

confidence: 99%

Structural Assignments and Dynamics of the A Substates of MbCO: Spectrally Resolved Vibrational Echo Experiments and Molecular Dynamics Simulations

et al. 2002

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Spectrally resolved three-pulse stimulated vibrational echo experiments are used as the basis for structural assignments of the A 1 and A 3 spectroscopic substates in the IR spectrum of the carbon monoxide (CO) stretch of carbonmonoxymyoglobin (MbCO). The measured dephasing dynamics of these substates is compared to the dephasing dynamics of MbCO predicted from molecular dynamics (MD) simulations. We assign the A 1 and A 3 substates to different protein conformations on the basis of the agreement between the measured and computed vibrational echoes. In the A 1 substate, the N -H proton and N δ of His64 are equidistant from the ligand, whereas in the A 3 substate, the N -H of His64 is oriented toward the CO.Structural information is essential for understanding the functions of proteins. Techniques such as X-ray diffraction, 1-3 neutron diffraction, 4 and 2D-NMR 5 have been used to investigate the structures of many proteins and a wide variety of other biomolecules. Despite the power of these methods, the identification of conformational substates that interconvert rapidly is difficult because of the limited time resolution of these techniques. A long-standing problem of this type is the assignment of the A conformational substates of the protein carbonmonoxymyoglobin (MbCO).The infrared (IR) spectrum of the CO stretching mode of MbCO has three absorption bands, denoted A 0 (∼1965 cm -1 ), A 1 (∼1944 cm -1 ), and A 3 (∼1930 cm -1 ), as shown in Figure 1. 6-8 It has been suggested that different electrostatic environments in the heme pocket arising from distinct structures are largely responsible for the observed bands. 9 The distal histidine His64 plays a prominent role in determining the CO stretching frequencies, but the tautomerization and orientation of this residue remain controversial. [1][2][3]10,11 His64 has two titratable nitrogens, N δ and N , either of which can be oriented toward the ligand through rotation of the imidazole ring. This residue is also fairly mobile and has been observed at a wide variety of distances from the CO ligand. 2,3,12 At low pH, His64 is thought to be doubly protonated and has been observed in the low pH crystal structure rotated out of the heme binding pocket away from the CO ligand. 12 This conformer, with little interaction between His64 and the ligand, is thought to correspond to the A 0 substate, because at low pH the A 0 line is the most intense IR absorption band. In addition, mutations of His64 to apolar residues produce an A substate band at approximately the same frequency as the A 0 line. 9,13 At pH greater than 6, the A 1 and A 3 substates are the most populated. 7,14 Crystal structures at neutral pH indicate that His64 is rotated into the heme pocket and is much closer to the ligand than in the A 0 substate, but the exact orientation of His64 is uncertain. 2,3 Also, the tautomerization state of the singly protonated His64 at neutral pH is unclear.Structural calculations have provided insight into the origins of the A 1 and A 3 substates. Rovira et al. 10 performed...

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“…One goal of high-resolution spectroscopy was to measure the true homogeneous width of the zero phonon, purely electronic transition of molecules in solids without the interference from inhomogeneous broadening. It is for this reason that much research in the 1970's and 1980's was devoted to methods like fluorescence line narrowing (FLN) (13,14) and transient spectroscopies such as free induction decay, optical nutation, and photon echoes (15)(16)(17). While these were all powerful methods with advantages and disadvantages, there was another method to assess the homogeneous width under certain circumstances, persistent spectral hole-burning, illustrated in Figure 4.…”

Section: Figure 2 Herementioning

confidence: 99%

Nobel Lecture: Single-molecule spectroscopy, imaging, and photocontrol: Foundations for super-resolution microscopy

Moerner

2015

Rev. Mod. Phys.

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The initial steps toward optical detection and spectroscopy of single molecules in condensed matter arose out of the study of inhomogeneously broadened optical absorption profiles of molecular impurities in solids at low temperatures. Spectral signatures relating to the fluctuations of the number of molecules in resonance led to the attainment of the single-molecule limit in 1989 using frequency-modulation laser spectroscopy. In the early 90's, many fascinating physical effects were observed for individual molecules, and the imaging of single molecules as well as observations of spectral diffusion, optical switching and the ability to select different single molecules in the same focal volume simply by tuning the pumping laser frequency provided important forerunners of the later superresolution microscopy with single molecules. In the room temperature regime, imaging of single copies of the green fluorescent protein also uncovered surprises, especially the blinking and photoinduced recovery of emitters, which stimulated further development of photoswitchable fluorescent protein labels. Because each single fluorophore acts a light source roughly 1 nm in size, microscopic observation and localization of individual fluorophores is a key ingredient to imaging beyond the optical diffraction limit. Combining this with active control of the number of emitting molecules in the pumped volume led to the super-resolution imaging of Eric Betzig and others, a new frontier for optical microscopy beyond the diffraction limit. The background leading up to these observations is described and current developments are summarized. The early days Introduction and early inspirationsI want to thank the Nobel Committee for Chemistry, the Royal Swedish Academy of Sciences, and the Nobel Foundation for selecting me for this prize recognizing the development of super-resolved fluorescence microscopy. I am truly honored to share the prize with my two esteemed colleagues, Stefan Hell and Eric Betzig. My primary contributions center on the first optical detection and spectroscopy of single molecules in the condensed phase(1), and on the observations of imaging, blinking and photocontrol not only for single molecules at low temperatures in solids, but also for useful variants of the green fluorescent protein at room temperature (2). This lecture describes the context of the events leading up to these advances as well as a portion of the subsequent developments both around the world and in my laboratory.In the mid-1980's, I derived much early inspiration from amazing advances that were occurring around the world where single nanoscale quantum systems were detected and explored for both scientific and technological reasons. Some of these were (i) the spectroscopy of single electrons or ions confined in vacuum electromagnetic traps (3-5), (ii) scanning tunneling microscopy (STM) (6) and atomic force microscopy (AFM) (7), and (iii) the study of ion currents in single membrane-embedded ion channels (8). But why not optical detection and ...

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Dynamics in low temperature glasses: Theory and experiments on optical dephasing, spectral diffusion, and hydrogen tunneling

Cited by 228 publications

References 81 publications

Probing dynamics of complex molecular systems with ultrafast 2D IR vibrational echo spectroscopy

Probing dynamics of complex molecular systems with ultrafast 2D IR vibrational echo spectroscopy

Structural Assignments and Dynamics of the A Substates of MbCO: Spectrally Resolved Vibrational Echo Experiments and Molecular Dynamics Simulations

Nobel Lecture: Single-molecule spectroscopy, imaging, and photocontrol: Foundations for super-resolution microscopy

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