10 research outputs found
Comparison of DFT calculated and experimental ctv features.
<p>Lines, spectra from DFT; dots, experimental data (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0158681#pone.0158681.g003" target="_blank">Fig 3</a>); spectra were vertically shifted for comparison; note the doubled y-scale in (B). Calculated spectra represent the indicated model structures; solid lines and coloured annotations denote calculated spectra for the indicated structures, which show superior agreement with the experimental data (broken lines show calculation results less in agreement with the experimental data).</p
EXAFS simulation parameters<sup>a</sup>.
<p>EXAFS simulation parameters<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0158681#t002fn001" target="_blank"><sup>a</sup></a>.</p
EXAFS spectra of cobalamin systems.
<p>Panel (A) shows Fourier-transforms (FTs) of the EXAFS oscillations in panel (B) for indicated solution Cbl or CoFeSP-Cbl samples. Black lines, experimental data; coloured lines, simulations with parameters in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0158681#pone.0158681.t002" target="_blank">Table 2</a> (fits 2, 5, 7, 10, 12, 14, 16, 19, 21); spectra in (A) and (B) were vertically shifted for comparison.</p
HOMO and LUMO energies and natural population analysis charges from DFT<sup>a</sup>.
<p>HOMO and LUMO energies and natural population analysis charges from DFT<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0158681#t005fn001" target="_blank"><sup>a</sup></a>.</p
Cobalt-ligand bond lengths from crystallography, EXAFS, and DFT.
<p>Cobalt-ligand bond lengths from crystallography, EXAFS, and DFT.</p
Core-to-valence electronic transition characters.
<p>Core-to-valence electronic transition characters.</p
Molecular orbitals in Cbl model structures from DFT.
<p>LUMO, lowest unoccupied MO corresponding to the lowest energy core-to-valence electronic transition in the pre-edge absorption X-ray spectral region; ctv<sub>max</sub>, MO corresponding to the highest-intensity ctv transition of the pre-edge absorption. Cobalt oxidation state and axial ligation are indicated.</p
Metal content and cobalt oxidation state in the CoFeSP samples<sup>a</sup>.
<p>Metal content and cobalt oxidation state in the CoFeSP samples<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0158681#t001fn001" target="_blank"><sup>a</sup></a>.</p
Cobalt XANES spectra.
<p>(A) Indicated Cbl solution samples, (B) CoFeSP-Cbl samples. Dotted lines mark edge half-height. Spectra of Co<sup>III</sup><sub>2</sub>O<sub>3</sub> (solid black line) and Co<sup>II</sup>O (dashed black line) are shown for comparison in (A) and (B). Inset: Isolated pre-edge (core-to-valence, ctv) absorption features after subtraction of a smooth edge rise background (not shown) from the XANES spectra. For XANES spectra of further cobalt reference compounds see Fig C in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0158681#pone.0158681.s001" target="_blank">S1 File</a>.</p
Cobalamin crystal structures.
<p>(a) Structure of the Cbl cofactor in CoFeSP enzyme (PDB entry 2H9A, 1.9 Å resolution [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0158681#pone.0158681.ref012" target="_blank">12</a>]) showing a base-off configuration (dmb ligand not bound to cobalt in α-position). Ligand X at the ß-position (light green) at cobalt can be absent or can be a water species, a methyl group, or an oxygen from the side chain of RACo-Ser398 in the CoFeSP-RACo complex [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0158681#pone.0158681.ref014" target="_blank">14</a>]; red balls show resolved water molecules. (b) Structure of Cbl in base-on configuration [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0158681#pone.0158681.ref021" target="_blank">21</a>]; X can be a water, cyanide, or methyl species. Color code: magenta, Co; blue, N; red, O; grey, C; dark green, P; protons were omitted for clarity.</p