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Spin densities from subsystem density-functional theory: Assessment and application to a photosynthetic reaction center complex model
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10.1063/1.4709771
/content/aip/journal/jcp/136/19/10.1063/1.4709771
http://aip.metastore.ingenta.com/content/aip/journal/jcp/136/19/10.1063/1.4709771

Figures

Image of FIG. 1.
FIG. 1.

Structure of the chromophores in the PRC of purple bacteria (from PDB ID 1AIJ). BCL: bacteriochlorophyll, BPH: bacteriophenophytin, and U: ubiquinone. Each chromophore is labelled with the PDB residue id. The two apparently equivalent electron transfer pathways are labelled with branch A and B respectively.

Image of FIG. 2.
FIG. 2.

(a) Geometry of the H2NO⋯20 H2O system. (b) Contour plots of the spin densities for the H2NO⋯20 H2O system from the KS-DFT (BP86/TZP) calculation, (c) the FDE calculation with H2NO as an active fragment, and (d) the FDE (BP86/TZP) calculation with H2NO⋯3H2O as an active fragment; the three water molecules included in the active system are highlighted. Also are shown contour plots from KS-DFT for (e) H2NO and (f) H2NO⋯3H2O. The contour plane is defined through nitrogen and hydrogen atoms of H2NO. Contour lines are drawn at ±1, 3, 5 · 10n , n = 1, 2, 3, 4, 5. Contours corresponding to positive values are plotted with solid lines, negative ones with dashed lines. Cyan dots represent the position of the hydrogen nuclei in H2NO, a blue dot indicates the nitrogen nucleus, and the red dots correspond to the oxygen nuclei of H2NO and H2O molecule bound to it. Coordinates are given in units of bohr.

Image of FIG. 3.
FIG. 3.

(a) to (e) Spin density isosurface plots for GT• +: KS-DFT calculations with different exchange–correlation potentials and a TZP basis set; FDE calculation (B3LYP/TZP) with (f) monomer and (g) supermolecular basis; (g) CASSCF(11,12) calculation with TZVP basis set. The isosurface value is set to 0.001. The blue surface corresponds to positive SD, red to negative.

Image of FIG. 4.
FIG. 4.

Model structures of the SP• + in the protein binding pocket.

Image of FIG. 5.
FIG. 5.

SD contour plots of the SP• + from KS-DFT (B3LYP/TZP) calculations: (a) SP• +, (b) SP• +-2HIS, (c) SP• +-3HIS, (d) SP• +-COSMO. The contour planes contain the nitrogen atoms of the P A (left column) and P B halves (right column) of the SP, respectively. Solid lines correspond to positive SD, dashed lines to negative. Atomic positions are specified with colored dots: Mg - green, N - blue, C - violet, O - red, H - cyan.

Image of FIG. 6.
FIG. 6.

SD contour plots of the SP• + from FDE (B3LYP/TZP) calculations: (a) SP• +-2HIS, (b) SP• +-3HIS, (c) SP• +-3HIS-2LEU-1PHE, (d) SP• +-protein. The contour planes contain the nitrogen atoms of the P A (left column) and P B halves (right column) of the SP, respectively. Solid lines correspond to positive SD, dashed lines to negative. Atomic positions are specified with colored dots: Mg - green, N - blue, C - violet, O - red, H - cyan.

Tables

Generic image for table
Table I.

Comparison of the calculated and experimental spin densities for the SP• +. Calculated values are obtained by summing Mulliken spin populations (supermolecular B3LYP/TZP calculations) over all atoms of P A and P B , respectively. Experimental values12 correspond to the total spin density in s-orbitals detected from all carbon atoms.

Generic image for table
Table II.

Effects of the protein environment on the Mulliken spin populations (B3LYP/TZP) of SP• + summed over P A and P B , respectively.

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/content/aip/journal/jcp/136/19/10.1063/1.4709771
2012-05-16
2014-04-18
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752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: Spin densities from subsystem density-functional theory: Assessment and application to a photosynthetic reaction center complex model
http://aip.metastore.ingenta.com/content/aip/journal/jcp/136/19/10.1063/1.4709771
10.1063/1.4709771
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