Work Description

Title: Dataset from "Structural Evolution of Photoexcited Methylcobalamin Towards a CarH-like Metastable State: Evidence from Time-Resolved X-ray Absorption and X-ray Emission" Open Access Deposited

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Methodology
  • The referenced manuscript describes a comparative analysis of the excited state dynamics of methyl cobalamin and adenosylcobalamin in water or in the protein CarH. This dataset includes all of the data that are referenced in the manuscript. These data were measured at the University of Michigan, at the LCLS, at SSRL, and at the European XFEL. Details are described below.

  • Methylcobalamin was purchased from MilliporeSigma and used as received. Solutions were prepared by dissolving methylcobalamin in deionized water to produce ~0.6 mM solutions for UV-visible measurements and ~5 mM solutions for X-ray absorption and X-ray emission measurements. Sample preparation took place under red light to avoid photolysis. Solutions for UV-visible measurements were deoxygenated by bubbling nitrogen for at least an hour and maintained under a positive pressure of nitrogen during measurements. The sample was circulated through a fused silica flow cell with an optical path length of 1 mm to refresh the sample between laser pulses. For XANES measurements, the samples were filtered, centrifuged, and pumped through a glass nozzle to achieve a stable 50 ?m diameter jet of solution. For XES measurements, the sample was delivered as a 100 um thick cylindrical jet running with a linear speed of about 60 m/s. Samples were monitored using UV-visible absorption to ensure that any buildup of photoproducts remained insignificant. UV-visible TA spectra of MeCbl were obtained using a 1 KHz kHz Ti:sapphire laser system produced producing ca. 70 fs compressed pulses centered around 814 nm. Pump pulses were generated by frequency doubling the fundamental in a-barium borate crystal to ca. 407 nm, summing 407 nm and 814 nm to produce 270 nm pulses, or pumping a noncollinear optical parametric amplifier to generate 540 nm pulses. A portion of the 407 nm beam was used to produce a broadband continuum probe in a translating CaF2 window, spanning the range from 290 nm to 600 nm. Alternatively, the 814 nm fundamental was used to produce a broadband continuum probe spanning the range from 320 nm to 750 nm. All measurements were performed with the polarization of the pump and probe pulses at magic angle with respect to each other. These measurements characterize the spectral evolution out to hundreds of picoseconds complementing our earlier measurements which were only performed at specific wavelengths or select time delays. Time-resolved polarized XANES measurements of MeCbl were performed using the XPP instrument of the x-ray free electron laser LCLS at SLAC. The X-ray beam and laser beam travel in a nearly collinear geometry (~1? crossing angle) and were overlapped with the sample about 500 ?m from the nozzle producing the sample jet. The optical pump pulse was 520 nm, ~50 fs FWHM and the X-ray probe pulse (~50 fs) was scanned from 7.7 to 7.76 keV. Cobalt X-ray fluorescence was collected and used as a measure of X-ray absorption where the signal was normalized to the small-angle scattering from the solvent. Both the optical and X-ray pulses were linearly polarized. A waveplate in the optical beam was used to rotate the polarization to acquire transient spectra with the polarization of the optical pulse parallel and perpendicular to the X-ray pulses. The excitation fraction of ~0.25 was estimated as described previously.30 The XANES spectrum of ground state MeCbl was also obtained at SSRL beamline 9-3 for intensity scaling of the simulated and experimental spectra. The synchrotron data were measured on frozen solutions at ~10K as fluorescence excitation spectra, detected with a 100-element solid-state Ge detector array with an Fe filter and Soller slits. XES difference spectra of MeCbl in the Co Kà1,2, Co Kb1,3 and valence-to-core (VtC) regions were obtained at the FXE instrument of the European X-ray free electron laser (EuXFEL). The experiments were performed using the dedicated chamber for experiments on liquid samples.34 The incident X-ray energy of the SASE pulses was set to 9.3 keV and the intra-train repetition rate was either 0.564 or 0.282 MHz. Emission spectra were measured with a dispersive X-ray spectrometer operating in the von Hamos geometry and equipped with 7-10 Ge(111) analyzers at ~83 degrees for measuring the Co Kb and 5-8 Si(531) analyzers at ~77 degrees for the Co Kà over two experimental campaigns. All cylindrical analyzers have 500 mm radius of curvature. The Co Kà and K? signals were recorded simultaneously using two distinct detectors, namely a Jungfrau 1M and a 500K, respectively. The von Hamos spectrometer has a limited dispersion window in the Co K? region and did not allow detecting the complete K?1,3 and VtC at once. Measurements of the VtC region were performed by slightly changing the Bragg angle on the Ge(111) analyzers and moving the Jungfrau detector accordingly. Both Jungfrau detectors integrated all pulses (total 140 or 200 ) in each train from the European XFEL burst mode operation. The pump-probe signal was generated by pumping every second train (5 Hz) and the differences are constructed by first integrating all of pump-on and all of the pump-off trains for a given delay time, normalizing each of these to the total integrated Kà or Kb intensity and then subtracting one train ON minus one train OFF after normalization to the total integrated Kà or Kb intensity the normalized pump-off from the normalized pump-on signal. The optical excitation wavelength was 550 nm or 400 nm, ~70 fs duration (FWHM), with a laser/X-ray crossing angle of ca. 2?. The sample integrity throughout each run was checked at all times confirmed by measuring UV-Vis spectra spectroscopy using a parallel flowing circuit connected to the main sample reservoir . The Finite Difference Method Near Edge Structure (FDMNES) program was used to simulate the ground and excited state XANES spectra as a function of molecular structure. For most FDMNES simulations the cobalamin structure was truncated by removing the tail and replacing the peripheral groups on the corrin ring with methyl groups. The quantum chemical package Orca 4.2.1 was used to perform time-dependent density functional theory (TD-DFT) calculations with the B3LYP functional, ZORA-def2-TZVP basis, and CPCM solvent to model the pre-edge region of the ground state spectra of MeCbl as well as the ground state valence-to-core emission spectrum. These calculations were performed on a truncated structure replacing the peripheral groups on the corrin ring with hydrogen. Some calculations were performed without the CPCM solvent model and the resulting spectra are nearly identical to those presented here. Optical transient absorption measurements, XANES pre-edge, and time-resolved XES measurements were fit to a model consisting of a sum of exponential decay components using the global analysis program Glotaran.
Description
  • The dataset contains the numerical data used to produce figures 2-14 and S1-S8 (Figure 1 is purely schematic and is uploaded as a tif file for completeness - it does not contain any new data). These files contain the transient UV-visible, X-ray absorption, and X-ray emission data that were used to characterize the dynamics of methyl cobalamin at neutral pH and to compare this to adenosyl cobalamin. Details of data collection and reduction are provided in the associated manuscript. Data files are all text files which contain tab-delimited columns of data corresponding to each figure in the manuscript.
Creator
Creator ORCID
Depositor
  • jeph@umich.edu
Contact information
Discipline
Funding agency
  • National Science Foundation (NSF)
ORSP grant number
  • AWD021319
Keyword
Citations to related material
Related items in Deep Blue Documents
  • Sension et al. Structural Evolution of Photoexcited Methylcobalamin Towards a CarH-like Metastable State: Evidence from Time-Resolved X-ray Absorption and X-ray Emission. Journal of Physical Chemistry B (accepted version). 2024. dx.doi.org/10.7302/23559
Resource type
Last modified
  • 08/26/2024
Published
  • 08/26/2024
Language
DOI
  • https://doi.org/10.7302/9ycc-t185
License
To Cite this Work:
Penner-Hahn, J. E., Alonso Mori, R., Ardana-Lamas, F., Biednov, M., Chung, T., Deb, A., Jiang, Y., Kaneshiro, A. K., Khakhulin, D., Kubarych, K. J., Lamb, R., Lima, F. A., McClain, T. P., Meadows, J. H., Michocki, L., Miller, N. A., Otte, F., Sension, R. J., Sofferman, D. L., Song, S., Uemura, Y., van Driel, T. B. (2024). Dataset from "Structural Evolution of Photoexcited Methylcobalamin Towards a CarH-like Metastable State: Evidence from Time-Resolved X-ray Absorption and X-ray Emission" [Data set], University of Michigan - Deep Blue Data. https://doi.org/10.7302/9ycc-t185

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Files (Count: 30; Size: 3.98 MB)

The dataset contains the numerical data used to produce figures 2-14 and S1-S8 (Figure 1 is purely schematic and is uploaded as a tif file for completeness - it does not contain any new data. These files contain the transient UV-visible, X-ray absorption, and X-ray emission data that were used to characterize the dynamics of methyl cobalamin at neutral pH and to compare this to adenosyl cobalamin. Details of data collection and reduction are provided in the associated manuscript. Data files are all text files which contain tab-delimited columns of data corresponding to each figure in the manuscript

Figure 1. UV-visible absorption spectrum of MeCbl at pH 7. The vertical lines indicate the center wavelength for pulses used to excited the MeCbl samples for UV-visible transient absorption (blue, 270 nm, 407 nm, and 540 nm), X-ray emission (red, 400 nm and 550 nm) and X-ray absorption (green, 520 nm).

Figure 2. Optical transient absorption results following excitation of MeCbl in water (pH ~7) at 540 nm.

Figure 3. Time resolved difference spectra and estimated excited state UV-visible spectra for the initial excited state, A, following excitation of MeCbl.

Figure 4. Estimated excited state UV-visible spectra for MeCbl.

Figure 5. Species associated difference spectra obtained from a global analysis of transient absorption data following excitation at 400 nm and 270 nm.

Figure 6. Isotropic XANES difference spectrum of MeCbl as a function of time delay following excitation at 520 nm.

Figure 7. Ground state XANES spectrum of MeCbl (GS black) and estimated excited state spectra.

Figure 8. Decomposition of the transient XANES signal at key energies following excitation of MeCbl.

Figure 9. Time-resolved X-ray emission spectra and X-ray absorption spectra for MeCbl.

Figure 10. Left: Evolution associated difference spectra obtained from a fit to the transient XES spectra.

Figure 11. (a) Difference spectra obtained at the indicated time delays following excitation of MeCbl at 400 nm.

Figure 12. Comparison of experimental difference spectra and estimated excited state spectra for MeCbl with simulated spectra.

Figure 13. (a) Comparison of the valence-to-core spectrum of MeCbl with a TD-DFT simulation of the transitions involved.

Figure 14. Fit of the XANES difference spectra of MeCbl averaged over select energy regions to a displaced step function convoluted with a Gaussian.

Figure S1. Contour surface plot of the broadband transient absorption difference spectrum of base-on MeCbl following excitation at 560 nm.

Figure S2. Comparison of experimental and fit difference spectra for select time delays

Figure S3. Fits at select energies in the Ka1 and Kb2 emission bands.

Figure S4. Fits at select energies in the Kb and valence-to-core (lower right) emission bands.

Figure S5. Comparison of exponential and displaced rise fits to the XAS pre-edge transient averaged around 7.714 keV.

Figure S6. Comparison of the exponential fit to the data in the pre-edge region.

Figure S7. Comparison of calculated ground state valence-to-core emission spectra for the parameters used in the XANES simulations.

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