Reaction of hydroxocobalamin and ascorbic acid
Description
This dataset contains the experimental and computational data underlying the article "Kinetic Separation of Competing Pathways in the Ascorbate Reduction of Hydroxocobalamin by Singular Value Decomposition and the Dimensionality of the Normalized Score Space" by M. Ishiguro, Y. Suzuki, K. Kobayashi, R. Koga, T. Tsuchida, T. Hanawa, I. Shitanda and S. Goto. Time-resolved UV–vis spectra (20260829Ishiguro1_raw_spectra.xlsx). All reactions were followed in 80 vol% ethanol–water at 298.15 K over 430–600 nm at a 0.5 nm pitch (341 wavelength points), with spectra recorded at 2-min intervals. The workbook contains a README sheet followed by eleven data sheets. Each data sheet holds wavelength in column A and elapsed time in minutes in row 1; t = 0 is the moment of complete mixing, and the tabulated values are absorbances. Eight sheets cover the reaction of hydroxocobalamin with ascorbic acid: five under air at [OHCbl]:[ASC] molar ratios of 1:75, 1:100, 1:125, 1:150 and 1:200, and three under N₂ at 1:100, 1:150 and 1:200. Assembled column-by-column in the order listed in the README, these eight sheets form the 341 × 492 matrix (312 aerobic and 180 anaerobic time points) whose singular value decomposition is reported in the article; the decomposition reproduces the published singular values of 45.307, 6.714, 1.422 and 0.541. The remaining three sheets contain the Fenton reference experiment, in which hydroxocobalamin was treated with FeSO₄ and H₂O₂ at Fe/H₂O₂ ratios of 250/125, 125/62.5, and 62.5/31.25 µM in air, yielding a 341 × 186 matrix. The README also records, for each sheet, the source file and column range from which the data were taken. Density functional theory calculations (.out files). Ground-state geometries of hydroxo-Cob(III)alamin (neutral, singlet), aqua-Cob(III)alamin (cationic, singlet) and Cob(II)alamin (neutral, doublet) were optimized with Gaussian 09W at the UB3LYP level, using the LanL2DZ basis set with its effective core potential for cobalt and 6-31G(d) for hydrogen, carbon, nitrogen, oxygen and phosphorus. Each optimization terminated normally at a stationary point. Frequency analyses were not performed, so the optimized geometries are not verified as minima. The full route sections, basis set and pseudopotential definitions, optimization histories and final Cartesian coordinates are contained in the output files. Molecular graphics (.gif files). Rotating three-dimensional renderings of the three optimized geometries, corresponding one-to-one with the output files above. Vertical excitation energies were subsequently computed on the optimized geometries at the same level of theory; the corresponding output files report the excited states and oscillator strengths from which the simulated absorption spectra in the article were constructed.
Files
Steps to reproduce
To provide qualitative computational support for the assignment of the transient 475-nm species to Cob(II)alamin, the electronic absorption spectra of hydroxo-Cob(III)alamin (OHCbl) and base-on Cob(II)alamin were calculated by time-dependent density functional theory (TD-DFT). Ground-state geometries were optimized at the (U)B3LYP level with the LanL2DZ basis set and effective core potential for cobalt and the 6-31G(d) basis set for all other atoms (H, C, N, O, P), using Gaussian 09W. OHCbl was treated as a closed-shell singlet (RB3LYP) and Cob(II)alamin as an open-shell doublet (UB3LYP). Vertical excitation energies of the 30 lowest singlet (OHCbl) or spin-unrestricted (Cob(II)alamin) excited states were computed at the same level of theory on the optimized geometries. The optimized structures are provided in the Supplementary Information (GIF animations and output files). Because the objective was a qualitative comparison of the spectral shift accompanying changes in cobalt oxidation state, rather than a quantitative reproduction of band positions, we discuss only excited states with oscillator strength f > 0.01.
Institutions
- Tokyo University of ScienceTokyo, Tokyo