Vibrational echo correlation spectroscopy probes of hydrogen bond dynamics in water and methanol

Asbury, John B.; Steinel, Tobias; Fayer, M. D.

doi:10.1016/j.jlumin.2003.12.035

Cited by 83 publications

(114 citation statements)

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“…The frequency changes are reflected in the change in shapes of the 2D-IR vibrational echo spectra. Full descriptions of the method have been presented (16,(38)(39)(40). (41) and are shifted along the m -axis by the CO stretching mode's anharmonicity.…”

Section: Resultsmentioning

confidence: 99%

Neuroglobin dynamics observed with ultrafast 2D-IR vibrational echo spectroscopy

Ishikawa

Finkelstein

Kim

et al. 2007

Proc. Natl. Acad. Sci. U.S.A.

104

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Neuroglobin (Ngb), a protein in the globin family, is found in vertebrate brains. It binds oxygen reversibly. Compared with myoglobin (Mb), the amino acid sequence has limited similarity, but key residues around the heme and the classical globin fold are conserved in Ngb. The CO adduct of Ngb displays two CO absorption bands in the IR spectrum, referred to as N 3 (distal histidine in the pocket) and N 0 (distal histidine swung out of the pocket), which have absorption spectra that are almost identical with the Mb mutants L29F and H64V, respectively. The Mb mutants mimic the heme pocket structures of the corresponding Ngb conformers. The equilibrium protein dynamics for the CO adduct of Ngb are investigated by using ultrafast 2D-IR vibrational echo spectroscopy by observing the CO vibration's spectral diffusion (2D-IR spectra time dependence) and comparing the results with those for the Mb mutants. Although the heme pocket structure and the CO FTIR peak positions of Ngb are similar to those of the mutant Mb proteins, the 2D-IR results demonstrate that the fast structural fluctuations of Ngb are significantly slower than those of the mutant Mbs. The results may also provide some insights into the nature of the energy landscape in the vicinity of the folded protein free energy minimum.myoglobin mutants ͉ protein dynamics ͉ energy landscape N euroglobin (Ngb) is a recently discovered family of vertebrate globin proteins. Ngb is expressed predominantly in nerve tissue. It has been hypothesized that Ngb facilitates O 2 diffusion to protect neuronal cells from hypoxia and ischemia (1). Ngb concentration in the brain is fairly low, too low to play the role that myoglobin (Mb) plays in the red muscles. However, because the expression level of Ngb is enhanced under hypoxic conditions in vitro as well as ischemia in vivo (2, 3), Ngb may be involved in neuronal responses to ischemia. A much higher concentration of Ngb is found in the retina. The concentration is high enough to deliver O 2 to mitochondria (4) and may facilitate O 2 diffusion in a manner similar to Mb. Another possibility is that Ngb is involved in redox-coupled sensor regulation for signal transduction in the brain. Ngb binds to the GDP-bound form of the ␣-subunit of heterotrimeric G protein under oxidative stress (5).The 3D structures of Ngb from human and mouse, both having 151 amino acids, have been published (6, 7). Comparisons of Ngb with vertebrate Mb and Hb sequences show only minor similarities at the amino acid level (1), but Ngb features the conserved classical globin fold and contains heme (6). The heme iron in both the ferrous and ferric forms of Ngb is hexacoordinated (8), in contrast to mammalian Mb and Hb, which contain pentacoordinated heme iron. Although hexacoordinated heme has been reported in plant, bacteria, and invertebrate globins, its physiological significance is not yet understood (9). In Ngb, an external gaseous ligand must compete with the sixth ligand, the distal histidine (E7 in helix notation), for binding. Several key residues...

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Section: Resultsmentioning

confidence: 99%

Neuroglobin dynamics observed with ultrafast 2D-IR vibrational echo spectroscopy

Ishikawa

Finkelstein

Kim

et al. 2007

Proc. Natl. Acad. Sci. U.S.A.

104

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“…49 Here, we present a detailed account of the vibrational echo experiments on AOT reverse micelles that have been reported previously, 49 including new frequency-dependent data, as well as vibrational pump-probe experiments that examine the population dynamics of the hydroxyl stretch. Vibrational echo spectroscopy [16][17][18]20,[50][51][52][53][54][55][56] is uniquely capable of determining system dynamics by removing the inhomogeneous broadening contribution from the line shape 16,[56][57][58][59][60][61][62] and tracking the underlying dynamics. 63, 64 The properties of hydrogen-bond networks can be studied using IR spectroscopy of the hydroxyl stretching mode, because of the strong influence of the number and strength of hydrogen bonds on the hydroxyl stretch frequency.…”

Section: Introductionmentioning

confidence: 99%

Dynamics of Nanoscopic Water: Vibrational Echo and Infrared Pump−Probe Studies of Reverse Micelles

2005

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The dynamics of water in nanoscopic pools 1.7-4.0 nm in diameter in AOT reverse micelles were studied with ultrafast infrared spectrally resolved stimulated vibrational echo and pump-probe spectroscopies. The experiments were conducted on the OD hydroxyl stretch of low-concentration HOD in the H 2 O, providing a direct examination of the hydrogen-bond network dynamics. Pump-probe experiments show that the vibrational lifetime of the OD stretch mode increases as the size of the reverse micelle decreases. These experiments are also sensitive to hydrogen-bond dissociation and reformation dynamics, which are observed to change with reverse micelle size. Spectrally resolved vibrational echo data were obtained at several frequencies. The vibrational echo data are compared to data taken on bulk water and on a 6 M NaCl solution, which is used to examine the role of ionic strength on the water dynamics in reverse micelles. Two types of vibrational echo measurements are presented: the vibrational echo decays and the vibrational echo peak shifts. As the water nanopool size decreases, the vibrational echo decays become slower. Even the largest nanopool (4 nm, ∼1000 water molecules) has dynamics that are substantially slower than bulk water. It is demonstrated that the slow dynamics in the reverse micelle water nanopools are a result of confinement rather than ionic strength. The data are fit using time-dependent diagrammatic perturbation theory to obtain the frequency-frequency correlation function (FFCF) for each reverse micelle. The results are compared to the FFCF of water and show that the largest differences are in the slowest time scale dynamics. In bulk water, the slowest time scale dynamics are caused by hydrogen-bond network equilibration, i.e., the making and breaking of hydrogen bonds. For the smallest nanopools, the longest time scale component of the water dynamics is ∼10 times longer than the dynamics in bulk water. The vibrational echo data for the smallest reverse micelle displays a dependence on the detection wavelength, which may indicate that multiple ensembles of water molecules are being observed.

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“…Recent experiments had demonstrated that two-dimensional infrared (2D IR) lineshapes can probe the picosecond dynamics of chemical exchange by observing coherence transfer in molecular vibrations through time-dependent spectral jumps 1,2,3 . This spectroscopic technique 4,5,6 is an optical analogue of 2D NMR commonly used to study slower (ms) chemical exchange processes 7,8,9,10 .…”

Section: Introductionmentioning

confidence: 99%

Stochastic simulation of chemical exchange in two dimensional infrared spectroscopy

Šanda

Mukamel

2006

The Journal of Chemical Physics

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Vibrational echo correlation spectroscopy probes of hydrogen bond dynamics in water and methanol

Cited by 83 publications

References 56 publications

Neuroglobin dynamics observed with ultrafast 2D-IR vibrational echo spectroscopy

Neuroglobin dynamics observed with ultrafast 2D-IR vibrational echo spectroscopy

Dynamics of Nanoscopic Water: Vibrational Echo and Infrared Pump−Probe Studies of Reverse Micelles

Stochastic simulation of chemical exchange in two dimensional infrared spectroscopy

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