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NSD data for more than 1500 hemes of protein structures contained in the Protein Data Bank are available in reference 29
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0346522523
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note
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Most of the in-plane deformation found in the NSD analysis (Tables S8 and S9) trivially results from the out-of-plane deformations, as illustrated in Figure 6. For a nonplanar porphyrin, the projections of the atomic positions into the ring mean plane, when expressed by NSD in terms of the equivalent in-plane vibrational mode displacements, can appear to be significant even though the porphyrin bonds and angles do not change much. In fact, the NSD in-plane deformations would occur even if there were no changes in bond length and only the bond angle changes necessary to accommodate the out-of-plane distortion. In contrast, IPNR represents structural changes due to a direct substituent effect. In the NSD analysis, IPNR appears as additional small normal mode displacements caused by substituent-induced internal strain; the IPNR displacements will appear along only in-plane modes for planar porphyrins but along both the inplane and out-of-plane modes for nonplanar porphyrins.
-
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51
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0346522522
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-
note
-
1u modes (see Figure S2).
-
-
-
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53
-
-
0345891722
-
-
note
-
g orbitals probably results from orbital mixing.
-
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-
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54
-
-
0345891721
-
-
note
-
π orbital overlaps or if they involve the σ-electron system as well.
-
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-
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55
-
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0345891720
-
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note
-
7)P that may not exist in other environments such as in solution.
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57
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62
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0345891719
-
-
note
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56
-
-
-
-
63
-
-
0347152853
-
-
note
-
An important additional feature of the series of bridled porphyrins is that IPNR, if it is not negligible, should be largest for the short straps because they force the bulky substituents nearer to the mean plane and, consequently, to interact more strongly with the macrocycle atoms than for long straps, which relax these repulsive interactions by out-of-plane deformation. This stronger interaction with the macrocycle for the short straps must take place within a more planar macrocycle, leading to greater IPNR. Thus, if IPNR were important and caused a significant red shift, then we would expect the largest red shift for the short straps and the more planar porphyrin, contrary to the observed trend in the UV - visible data (Figure 8A and Table S13).
-
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64
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0016691711
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Spiro, T.G.1
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66
-
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0346522517
-
-
note
-
m bond length through the α carbon. Nevertheless, even this correlation is somewhat indirect.
-
-
-
-
67
-
-
0030479176
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