Work Description

Date: 2 February, 2024

Dataset Title: Data from "Ultrafast X-ray Absorption Spectroscopy Reveals Excited State Dynamics of B12 Coenzymes Controlled by the Axial Base"

Dataset Creators: Taewon Chung, Taylor P. McClain, Roberto Alonso-Mori, Matthieu Chollet, Aniruddha Deb, Angel T. Garcia-Esparza, Joel Huang Ze En, Ryan M. Lamb, Lindsay B. Michocki, Marco
Reinhard, Tim B. van Driel, James E. Penner-Hahn1, and Roseanne J. Sension

Dataset Contact: James Penner-Hahn, jeph@umich.edu

Funding: NSF-CHE 1836435, NSF-CHE 2154157), NIH grant P41GM139687DOE Contract No. DE-AC02-76SF00515.

Methodology:
The referenced manuscript describes the excited state dynamics of methyl cobalamin at low pH. 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, and the Stanford Synchrotron Radiation Light Source. Detailed methods for the collection and analysis of these data are described in the associated manuscript.

UV-visible, X-ray absorption, and X-ray emission data used to characterize the dynamics of methyl 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.

Related publication(s):
Chung, T., et al. (2024). "Ultrafast X-ray Absorption Spectroscopy Reveals Excited State Dynamics of B12 Coenzymes Controlled by the Axial Base". J. Phys. Chem. B. 2024, in press https://pubs.acs.org/doi/10.1021/acs.jpcb.3c07779

Use and Access:
This data set is made available under a Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0).The referenced manuscript describes the excited state dynamics of base-off methyl cobalamin. This dataset includes all of the data that are referenced in the manuscript. These data were measured at the University of Michigan and at the LCLS. Detailed methods for the collection and analysis of these data are described in the associated manuscript as are details of data collection and reduction. UV-visible and X-ray absorption data and theoretical calculations used to characterize the dynamics of base-off methyl cobalamin are included in the data files. Data files are all text files which contain tab-delimited columns of data corresponding to each figure in the manuscript. In addition to the data files, also included are representative input files for calculations using FDMNES and ORCA.

Figures are:

Figure 1. UV-visible absorption spectrum of base-on MeCbl (pH 7), base-off MeCbl (pH 2), base-on cob(II)alamin (pH 7) and base-off cob(II)alamin (pH 2). The -band region in the visible and the -band region in the UV are indicated on the plot. Spectra of the base-on and base-off forms of AdoCbl are plotted in Figure S1.

Figure 2. (a) Summary of UV-visible transient absorption measurements for base-off MeCbl following excitation at 407 nm. The data for wavelengths >350 nm was reported previously.8 The evolution associated difference spectra are plotted in the upper panel of (a) and compared with the ground state spectrum of base-off MeCbl. The spectrum of the short-lived species A is complicated by stimulated Raman scattering around 470 nm and by stimulated Raman scattering and cross phase modulation for wavelengths below 380 nm. The region below 380 nm is omitted from the plot for this species. The 250 ps spectrum (red line) is compared with the difference spectrum that is obtained by subtracting the base-off MeCbl spectrum from that for authentic cob(II)alamin at pH ~2 (black dashed line, see text for details). For reference, the ground-state spectrum of base-off MeCbl is shown in grey (b) False-color image showing the full time-dependent evolution of the difference signal as a function of wavelength (c) Time dependent populations of A, B, and C as determined from a global analysis of the transient absorption spectra. The vertical lines represent the time-delays used to measure excited-state XANES for A and C, and the time-delay range used to measure excited-state XANES for B

Figure 3. Estimated decay-associated excited state UV-visible spectra for base-off MeCbl at different times, calculated using Eq. 1. The excited states are designated by their lifetimes. The spectrum of the short-lived species A is complicated by stimulated Raman scattering around 470 nm and by stimulated Raman scattering and cross phase modulation for wavelengths below 380 nm. These regions are omitted from the plot. For reference, the ground-state spectra of the starting base-off MeCbl (black line) and authentic Cob(II)alamin (dashed grey line) are also included. The latter shows that the 250 ps spectrum is identical to Cob(II)alamin.

Figure 4. (a) Experimental isotropic difference spectra (DS, see text) for base-off MeCbl at different times (top) and the estimated excited state spectra at the same times, calculated using Eq. 2. All XANES spectra are normalized to an edge jump of 1 at 7.78 keV and plotted with the scale on the left axis. The difference spectra are plotted with the amplitude on the right axis. For comparison, the ground state XANES spectrum of base-off MeCbl (black line) and for Cob(II)alamin (light blue line) are included on the lower plot. . The vertical dashed line indicates the energy below which the pre-edge transitions dominate. The inset emphasizes the changes in the pre-edge region and shows both the XANES and the difference spectra, scaled vertically in order to highlight the energy shift. For comparison, the base-off MeCbl spectrum is also shown (gray dashed line) in order to illustrate the fact that only the higher energy portion of the pre-edge feature is bleached in the base-off MeCbl excited states. (b) Equivalent plot to (a), comparing the ground state XANES spectrum of base-off MeCbl and base-off AdoCbl and their estimated excited state spectra at 10 ps.

Figure 5. Decomposition of the XANES difference spectra for time delays around 0.8 ps, between 5 and 15 ps, labeled ~10 ps, and at 250 ps, labeled Cob(II), into contributions along (x) and perpendicular (y+z) to the transition dipole initially excited. The vertical dashed line indicates the approximate energy below which pre-edge transitions dominate the spectrum.

Figure 6. Comparison of the ground state spectrum of MeCbl at pH ~7 and pH 2 with FDMNES simulations. The ring is held constant and the axial bond lengths in Å are given in the legend. TD-DFT simulations of the pre-edge transitions are plotted in the inset. The inclusion of water in the base-off calculation is required for good agreement with experiment (see Figure S7).

Figure 7. Comparison of the ground state spectrum of MeCbl (gray) and cob(II)alamin (blue) at pH ~7 (left) and pH ~2 (right). FDMNES was used to simulate the XANES spectra and are plotted as a pink dashed line (MeCbl) and a light-blue dashed line(Cob(II)alamine). Experimental (dark blue) and calculated (light blue) differences for MeCbl minus Cob(II)alamine are plotted at the top of the figure. Both sets of absorption spectra use the vertical scale shown on the left; both sets of difference spectra use the scale shown on the right. Inset shows the and expansion of the pre-edge region for the experiment (dark blue and gray solid lines) and the TD-DFT calculations (pink and light-blue dashed lines). The pre-edge transitions that give rise to the predicted spectra are shown as vertical sticks.

Figure 8. Left: Comparison of the excited state XANES spectrum of the B (B=2.1 ps) state of base-off MeCbl with an FDMNES simulation assuming an 0.02 Å symmetric expansion of the corrin ring, an 0.02 Å expansion of the Co-C bond and an 0.04 Å expansion of the Co-O bond. Upper traces shown the experimental and calculated polarized difference spectra (see text) and the experimental and simulated isotropic difference spectra. In the lower plot the black and grey lines represent the experimental and calculated ground state spectra while the colored lines represent the excited state or the difference between the excited state and the ground state. The vertical dashed line indicates the approximate energy below which the pre-edge transitions dominate the spectrum. Center: Similar comparison of the excited state XANES spectrum of the C (C=47 ps) state of base-off MeCbl with an FDMNES simulation assuming an 0.04 Å symmetric expansion around the cobalt. The legend is the same as the plot to the left. Right: An enlargement of the pre-edge region illustrating the difference between the excited and ground states, B light blue, C dark blue. The TD-DFT simulations of the ground state predict that transitions from the Co 1s orbital to the orbitals plotted above the spectra make the dominant contribution to the indicated transitions. The pre-edge transitions that give rise to the predicted spectra are shown as vertical sticks.

Figure 9. (a) Comparison of the base-on (pH 7) and base-off (pH 2) XANES difference spectra for excitation of MeCbl. The 1 ps spectrum was obtained in the same run as the 100 ps spectrum.29 The dashed line indicates the approximate break between the pre-edge and XANES regions. (b) Comparison of the ground and estimated excited state XANES spectra for base-on AdoCbl in ethylene glycol (EG)13,48 and base-off AdoCbl in water at pH 2.

Figure S1. UV-visible absorption spectra of base-on AdoCbl (pH~7) and base-off AdoCbl (pH~2) compared with the base-off spectrum of cob(II)alamin

Figure S2. Fits to select kinetic traces following excitation of base-off MeCbl. Differences at each wavelength are plotted in color, as are the residuals (lines centered around 0). The fits are shown as black dashed lines. The 0.26 ps component is prominant at 600 nm and 580 nm (see also Figure S3), while the 2.1 ps and 47 ps components are clearly necessary at 325 nm and 478 nm.

Figure S3. Contour surface plot of the broadband transient absorption difference spectrum of base-off base-off MeCbl for early times. The predominant signature of the 0.26 ps component is the excited state absorption between 530 nm and 650 nm.

Figure S4. Comparison of the estimated excited state spectra for base-off MeCbl as a function of the anticipated quantum yield for bond dissociation and formation of cob(II)alamin. Predicted spectra for =0.65 are shown as solid lines of the indicated color; predicted spectra for =0.5 and =0.8 are shown in lighter color as dashed or dotted lines, respectively.

Figure S5. Left: comparison of base-on XANES spectra of MeCbl, PrCbl, and AdoCbl. Right: Comparison of base-on (pH ~7) XANES spectra for MeCbl and AdoCbl with the base-off spectra obtained at pH 2.

Figure S6. Schematic of structures used for FDMNES simulations

Figure S7. FDMNES Simulations of base-on and base-off methylcobalamin for the three truncations illustrated in Figure S8. The numbers in parentheses are the lower and upper axial bond lengths used in the simulation.

Figure S8. Comparison of the XAS measurement with FDMNES simulations of the XANES region and orca calculations of the pre-edge region for MeCbl and 5-coordinate base-off methylcobalamin

Figure S9. Left: Absorption spectra of base-on and base-off cob(II)alamin at the pH values indicated. Right: Estimated XANES spectra of base-on and base-off cob(II)alamin.