Supporting materials SI Theoretical Backgrounds SI.1 Breaking of orbital and spin symmetries In the supporting material a brief explanation of our generalized molecular orbital (GMO) approach to unstable molecule is presented in comparison with the valence-bond (VB) approach since the mathematical formulation is completely neglected in the text. The closed-shell molecular orbital (MO) picture often breaks down in the case of unstable molecules with diradical character, indicating the existence of more stable broken-symmetry (BS) solutions. Therefore we first construct BS Hartree-Fock (HF), BS Kohn-Sham density functional theory (DFT) and their hybrid solutions such as UB3LYP for diradical and polyradical species. In order to obtain the localized MO (LMO) picture used in Fig. 2 (see text), the first-order density matrix ( 1(r1,r2 )) of these BS solutions is diagonalized as [91] 1(r1,r2 ) i†i ds nii†i , i i (S1) where i denotes the BS MO i, and i and n i mean, respectively, the natural molecular orbitals (NMO) and the occupation number. The BS MOs are expressed with the bonding and antibonding NMOs pair as i cos i + sin i* (S2a) i– cos i sin i* (S2b) where denotes the orbital mixing parameter. Since i and i* are symmetry-adapted and usually belong to different spatial symmetries, BS MOs are often spatially symmetry-broken. The orbital overlap Ti between BS MOs under the NMO approximation is defined as (S3) Ti = i+ i– cos2 . Then Ti becomes 1.0 in the case of the closed-shell case; i+ i– i , whereas Ti is 0.0 for the complete mixing case (= /4). In order to express the decrease of chemical bonding via orbital the effective bond order b is defined by symmetry breaking, n i n *i 1 cos2 1 cos2 bi (S4a) 2 2 cos2 Ti, where n i and n *i denote the occupation numbers of the bonding and antibonding NMOs, respectively. The effective bond order (b) is nothing but the orbital overlap between BS MOs under the generalized MO approximation. The localized MO (LMO) are defined as the completely spin polarized BS MOs as i+ 4 (S4b) 1 i i* LMOa 2 (S5a) 1 i– 4 1 i i* LMOb, 2 (S5b) where LMOa and LMOb are more or less localized on the sites a and b of molecular systems, respectively. The LMOs are utilized for derivation of localized MO pictures of unstable molecules as illustrated in Fig. 2 in the text. However, it is noteworthy that LMOs are quite different from the atomic orbitals (AO) in the simple valence-bond (VB) theory since LMO are orthogonal and still molecular orbitals in nature. Then the expression of LMOs with AO-like orbitals in Fig. 2 is symbolic and qualitative for lucid understanding of diradicals and polydiradical species. We can depict their exact shapes with the computer graphics as shown in this series of papers. The delocalized MO picture via NMO can be transformed into LMO picture. To this end, the BS MOs in eq. S2 are re-expressed with LMOs as follows i cos LMOa + sin LMOb (S6a) i– cos LMOb + sin LMOa , (S6b) where the mixing parameter is given by 4 . Then the BS MO configuration can be expanded with using LMOs as BSI i i cos LMOa +sin LMOb cos LMOb +sin LMOa 1 2 cos2SD 2TD sin2ZWa ZWb , 2 (S7a) (S7b) where the pure singlet (SD) and triplet (TD) diradical wavefunctions are given by (S8a) (S8b) SD 1 LMOa LMOb LMOb LMOa 2 TD 1 LMOa LMOb LMOb LMOa . 2 On the other hand, zwitterionic (ZW) configurations are resulted from the charge transfer from LMOa to LMOb (vice versa) as follows: ZWa LMOa LMOa , ZWb LMOb LMOb . (S9) The low-spin (LS) BSI MO configuration involves the pure triplet DR (TD) component, showing the spin-symmetry breaking property. This in turn indicates that BS solution more or less overestimates the diradical character, suggesting the necessity of careful examination of diradical mechanism concluded with the BS calculations in general. Similarly, the low-spin (LS) BSII MO configuration is expressed by BSII i– i (S10) 1 2 cos2 2 sin2 . ZWa ZWb SD TD 2 The LS BSII MO solution also involves the pure triplet component. Thus both orbital and spin 2 symmetry breakings are inevitable for diradical species in the case of the single-determinant (reference) BS solution on the basis of the independent particle model. However, both orbital and spin symmetries are conserved in finite systems, leading to the recovery of them. SI.2 Recovery of symmetry breaking The BSI and BSII solutions are degenerate in energy. Then the quantum-mechanical resonance of them is feasible as follows: RBS(+) RBS(–) 1 BSI BSII 2 (S11a) 1 2 cos2SD sin2ZWa ZWb , 2 (S11b) 1 BSI BSII 2 (S12a) TD. (S12b) Thus the in- and out-of-phase resonating BS (RBS) solutions are nothing but the pure singlet and triplet states wave functions, respectively. The chemical bonding between a and b sites is expressed with the mixing of the SD and ZW configurations under the LMO approximation. The valence-bond (VB)-type configuration interaction (CI) explanation of electronic structures becomes feasible under the LMO approximation. For example, the effective bond order becomes zero for the pure SD state, but it increases with the increase of mixing with the ZW configuration until the ZW/SD ratio becomes 1.0, namely closed-shell limit: it is noteworthy that BS solutions in eqs. (S7b) and (S10) involve the ZW configuration partly in the VB CI scheme. In order to obtain the effective bond order for the RBS(+) solution, it is transformed into the symmetry-adapted NMO expression as 1 cos2 1 cos2 , 2(1 T ) 1 RBS(+) i 2 * i i (S13) * i i where the first and second terms denote the ground and doubly excited configurations, respectively, in the MO-CI and 2x2 CASSCF approaches. The effective bond order (B) for RBS( ) is given by n i RBS () n *i RBS () B 2 1 T 1 T 21 T 2 2 i i 2 i (S14a) 2Ti 1 Ti2 (S14b) 2bi bi . 1 bi2 (S14c) The effective bond order (B) after elimination of triplet contamination part is larger than that (b) of the BS solution itself. The diradical character (y) is defined by the weight of the doubly excited configuration under the NMO approximation as 3 1 T 2 y 2W D i 1 Ti 2 1 2Ti 1 Ti2 (S15a) 1 B. (S15b) Thus the diradical character y is directly related to the decrease of the effective bond order B. The chemical indices, b, B, and y, are mutually related in the GMO approach. B and y values are also obtained by using the MO-CI and CASSCF methods. The simple pairing relation in eqs S2 and S6 is lost beyond BS approximation. Information entropy is introduced as an alternative to the effective bond orders as Ii ni ln ni . (S15c) Then the information entropy for closed-shell pair is given by Ic 2ln 2. (S15d) The normalized information entropy is defined as 2ln 2 ni ln ni (S15e) I˜i . 2ln 2 The I˜i values is zero for closed-shell orbital with ni 2 , whereas it becomes 1.0 for the singly occupied orbital with n 1. The I˜i value is also a measure of decrease of the bonding property i and it is applicable even for RBS and MR wave functions where the pairing property of the occupation numbers ni n*i 2 is lost. These chemical indices for transition-metal complexes in biology have been presented in this series of papers. structure of compound I SI. 3 Electronic Compound I (CpdI) is consisted of the Fe(IV)=O core and ligand radical (·L) parts. Here, CpdI is regarded as the three-center system (O-Fe-L) for simple explanation. Three -orbitals with the A1, S and A2 symmetries are available in the x-z plane as illustrated in Fig. S1, and the A1 and S orbitals are doubly occupied under the closed-shell approximation. The S and A2 orbitals are HOMO and LUMO, respectively. Similarly three -orbitals with the A1, S and A2 symmetries are also formed in the y-z plane and the A2 orbital becomes the singly occupied MO (SOMO). This A2 orbital is mainly consisted of the dyz orbital of iron (Fe) ion, and therefore it is regarded as a localized MO; LMO(Fe). CpdI is formally regarded as a doublet species with the restricted open-shell MO configuration; (S)LMO (Fe) (S) . However, the energy gap between the S (HOMO) and A2 (LUMO) orbital is small in the case of CpdI, leading to the HOMO-LUMO mixing under the BS approximation cosS sin A2 . (S16) Then the localized natural molecular orbitals (LMO) are defined by ( 4) 1 S A2 LMO (O), 2 (S17a) 4 – ( 4) 1 S A2 LMO (L). 2 (S17b) These LMO are mainly localized on the oxygen (O) and ligand (L) parts, respectively. The electronic structure of the -electron system in the x-y plane is more or less spin-polarized like 1,3-diradical species. The electronic structure of CpdI is regarded as an exchange coupled state between diradical and doublet radicals. Having obtained the MOs, we now consider the electronic structures of eight configurations in Fig. 1. The three localized MO (LMO) are used to define the LMO configurations in Fig. 1 (see text) as follows: (4 1) LMO (O)LMO (Fe)LMO (L), (S18a) ( 1) LMO (O)LMO (Fe)LMO (L), (S18b) ( 1) LMO (O)LMO (Fe)LMO (L), (S18c) ( 1) LMO (O)LMO (Fe)LMO (L). (S18d) 2 2 2 These configurations correspond to the LMO descriptions of the active radical states depicted in On the other hand, the charge transfer from LMO(O) to LMO(L) (vice versa) provides the Fig.2. doublet zwitterionic (ZW) configuration: (2 1) LMO (L)LMO (Fe)LMO (L), ( 1) LMO (O)LMO (Fe)LMO (O). (S19a) 2 (S19b) The four doublet configurations (21, 21', 21'', and 21''') are used to describe the diradicaloid state in the x-z -electron system with extra one spin in eq. 4 (see text) RBSCI C1 ( 2 1) C 2 ( 2 1) C 3( 2 1) C 4 ( 2 1), (S20) where Ci means the CI coefficient in the resonating BS (RBS) configuration interaction (CI). The RBS CI description is also possible for transition structures and intermediates of hydroxylation reactions as discussed in the text. The key points of the RBS CI is that increase of the weight of the ZW configuration with CI gives rise to the increase of the effective bond order of local singlet diradical bond as shown in eqs. S13-S15. This means that rebound step becomes stereoselective because of decrease of diradical character (y) (see text). As an extension of configuration correlation diagrams at the BS level, RBS CI provides potential curves and states correlation diagrams for hydroxylation reactions, which are under progress in our group. SI. 4 Spin polarization of the d-p bond of Fe(IV)=O The d-p bond of Fe(IV)=O core embedded in the strong ligand field is usually strong, exhibiting no biradical character as illustrated in Fig. S2. However, the energy gap between the bonding () aand antibonding (*) orbitals often becomes small in the case of weak ligand field, giving rise to the HOMO-LUMO mixing. This entails the BS MOs as shown in Fig. S2. cos ( ) sin ( * ), (S21a) * sin ( ) cos ( * ). (S21b) 5 The oxygen radical character is not negligible in this situation. The up-spin (HOMO) orbital is more or less localized on the iron site because of the exchange stabilization (see below). On the other hand, the up-spin * (LUMO) orbital ( * ) is more or less localized on the oxygen site and acts as an electron acceptor as shown in Fig. 5 (see text). The spin polarization is enhanced if the iron site becomes high-spin (HS) because of the stabilization of the Coulombic exchange interaction. The closed-shell ()2 pair is triplet-unstable at the HS state, providing the triplet (*)2 configuration. Then the sextet and quartet configurations in Fig. 1 are contributable to the hydroxylation as ( 6 1) LMO (O) LMO (Fe) LMO (L) ( ) ( * ), (S22a) ( 4 1) LMO (O) LMO (Fe) LMO (L) ( ) ( * ) , (S22b) ( 4 1) LMO (O) LMO (Fe) LMO (L) ( ) ( * ) , (S22c) ( 4 1) LMO (O) LMO (Fe) LMO (L) ( ) ( * ) . (S22d) Since these HS configurations have the reactive *-LUMO, the hydrogen abstraction reaction is expected as illustrated in Fig. 6 (see text). The LMO descriptions of orbital reorganization processes along the radical reaction pathways as illustrated in Fig. 2. The key conclusion elucidated with this analysis is that the spin exchange coupling modes in the configurations determine local singlet (SD) and triplet (TD) diradical mechanisms for rebound process in hydroxylation reactions with CpdI as summarized in Table 1. This is the reason why the spin exchange coupling modes in metalloenzymes have been investigated thoroughly in this series of papers. The local SD and TD mechanisms for CpdI are regarded as an extention of previous SD and TD mechanisms on the basis of the isolobal analogy among O, O2 and Fe(IV)=O (see text). SI. 5 Pair and spin correlation functions The spin densities appear under the BS approximation even in the low-spin (LS) singlet-type BS configuration, though they should disappear in the exact singlet state. So, there is a basic question what is spin density in the LS BS solution; only spin contamination errors? Important roles of spin densities emerge via the analysis of pair and spin correlation functions derived from second-order density matrices of the BS solutions as shown in previous papers [92,93]. The on-site pair function (P2) for electrons with different spins is given by P2 (r1 ,r1;r1 ,r1 ) P1 (r1 ,r1 ) 2 Q(r1 ,r1 ) 2 2, (S23) where P1 (r1 ,r1 ) 2 and Q1 (r1 ,r1 ) 2 denotes, respectively, the density and spin density. This means that the magnitude of spin density is parallel to the size of Coulombic hole for electrons with different spins, namely electron correlations. Then the unpaired electron density U responsible for deviation from the single determinant [94] is expressed by the sqaure of spin density under the BS 6 approximation as U (r1 ) Q(r1 ,r1 ) 2 Q(r1 ) 2 . (S24) The magnitude of spin densities reported in various recent BS calculations can be understood from the view point of nondynamical correlations between electrons with different spins [23-27]. Next, how about the sign of spin densities is a basic problem under the BS approximation. In order to elucidate this problem, the spin correlation function is introduced since it can be observed in the case of infinite systems with neutron diffraction technique [23-27]. In fact, the spin correlation function K 2 (r1 ,r2 ) is approximately given by K 2 (r1 ,r2 ) s(1) s(2)P (r ,r ;r ,r )ds 2 1 2 1 (S25a) 2 Q(r1 )Q(r2 ). where P2 denotes the second-order density matrix. (S25b) This means that the spin correlation is singlet-type if the sign of spin density product is negative; () or (). Thus the sign of spin density is closely related to the spin correlation function. Although the spin densities arising from the first-order density P1 (r1 ,r2 ) disappears at the pure singlet state, the unpaired electron density (U) and spin correlation function (K2) still exist as important indices of spin and electron correlations even in the resonating BS (RBS) and symmetry-adapted MR wave functions such as CASSCF and CASDFT. Therefore sign and magnitude of spin densities in several tables in this article should be understood from the above theoretical view points in eqs. S23, S24, and S25. The pair and spin correlation functions can be used to elucidate the nature of chemical bonds in the case of RBS and MR approaches as alternative indices for spin density at the BS level of theory. The above theoretical formulations in turn mean that discrimination between local singlet (SD) and triplet (TD) diradical mechanisms in Table 1 works well even at RBS and MR levels of theory, though the spin correlation function (K2) should be used as an alternative to spin density. More detailed derivations of eqs (S23-S25) are given in the refs [92-94]. It is noteworthy that recent many BS calculations of metalloenzymes are understood and analyzed from these theoretical viewpoints as described in the text. The present local SD and TD mechanisms are also applicable for binuclear transition metal oxides with antiferromagnetic and ferromagnetic exchange couplings as shown elsewhere [95]. Therefore it is concluded that magnetic coupling modes in several transition-metal oxides cores in metalloenzymes determine local exchange coupling modes for rebound diradical pairs, which are directly responsible for radical reaction pathways of oxygenations. Thus magnetism and chemical bond is a basic and fundamental notion even in the theory of chemical reaction mechanisms as shown in this series of papers. SII. Supporting Figures Figures S1-S6 are given here as the supporting materials for MO-theoretical illumination of local SD and TD mechanisms of hydroxylation with CpdI. 7 Figure S1. Isoelectronic analogy among O, O2, Fe(IV)=O, Cu(III)=O and Au(III)=O. Figure S2. Orbital interaction schemes of substrates with the compound I (CpdI) along the diradical-type reaction pathway for 2[3(↑Fe(IV)=O↓) 2(•L↑)] (21’’)(see text). Figure S3. Orbital interaction schemes of substrates with the compound I (CpdI) along the diradical-type reaction pathway for 4[3(↓Fe(IV)=O↑) 3(↑*↑) 2(•L↑)] (41’) (see text). Figure S4. Orbital interaction schemes of substrates with the compound I (CpdI) along the diradical-type reaction pathway for 4[3(↓Fe(IV)=O↑) 3(↑*↑) 2(•L↑)] (41’’) (see text). Figure S5. Orbital interaction schemes of substrates with the compound I (CpdI) along the diradical-type reaction pathway for 4[3(↓Fe(IV)=O↑) 3(↑*↑) 2(•L↑)] (41’’’) (see text). Figure S6. Molecular structures of substrates for hydroxylations. SIII. Supporting Tables Tables S1-S5 are given here as the supporting materials. Table S1 Opimized geometrical parameters and activation barriers for campjor (III) Computational results for camphor by the B3LYP method are taken from several groups. Table S2 The optimized geometrical parameters and x-values for the transition structures (4TS1 and 2TS1’ ) of IV-XII by UB3LYP. The geometrical parameters are taken from refs [36-50]. Table S3 The spin density population on key groups of CpdI at the transition structures (4TS1 and 2TS1 ) of I, II, III and IV-XII by UB3LYP. Table S4 The spin density population on key groups of CpdI at the transition structures (4TS1 ) of I, II, III and IV-XII by UB3LYP. Table S5 The spin density population on key groups of CpdI at the transition structures ( 2TS1’ ) of II and IV-XII by UB3LYP. 8 Fig. S1 K. Yamaguchi et al. 9 Fig. S2 K. Yamaguchi et al. 10 Fig. S3 K. Yamaguchi et al. 11 Fig. S4 K. Yamaguchi et al. 12 Fig. S5 K. Yamaguchi et al. 13 Fig. S6 K. Yamaguchi et al. 14 Table S1 Optimized geometrical parameters and x-values for transition structures of hydroxylation of camphor with CpdI by hybrid DFT (HDFT) calculations No. III (a) R1 R2 Rt q x (%) DE‡(DFT) Ref. 1.173 1.365 2.538 – 53.8 18.0 [53] TS1 (SD) 1.124 1.424 2.548 – 55.9 20.2 TS1 (TD) 1.154 1.408 2.562 166.9 55.0 20.6 TS1 (SD) 1.158 1.390 2.548 166.4 54.6 19.5 TS1 (TD) 1.188 1.369 2.557 167.8 53.5 21.6 TS1 (SD) 1.195 1.359 2.554 167.6 53.2 20.8 TS1 (TD) 1.181 1.362 2.543 171.6 53.6 19.5 TS1 (SD) 1.152 1.371 2.523 170.6 54.3 19.5 TS1 (TD) 1.157 1.389 2.546 169.8 54.6 17.96 TS1 (SD) 1.129 1.404 2.533 170.4 55.4 18.39 TS1 (TD) 1.20 1.38 2.58 – 53.5 20.6 Spin State 4 TS1 (TD) 2 III (b) 4 2 III (c) 4 2 III (d) 4 2 III (e) 4 2 III (f) 4 15 [41] [41] [41] [50] [54] Table S2 Optimized geometrical parameters, x-values, bond dissociation energies and activation barriers for hydroxylation with CpdI obtained by HD No. Substrates Spin State R1 R2 Rt x (%) E(BDE) E‡(DFT) IV ethane HS(TD) 1.136 1.427 2.563 170.2 55.7 107.51 21.32 LS(SD) 1.215 1.327 2.542 174.0 52.2 HS(TD) 1.123 1.427 2.550 166.3 56.0 LS(SD) 1.198 1.321 2.519 168.2 52.4 HS(TD) 1.141 1.427 2.568 170.2 55.6 LS(SD) 1.220 1.327 2.547 173.6 52.1 HS(TD) 1.257 1.337 2.594 170.6 51.5 LS(SD) 1.318 1.244 2.562 171.3 48.6 HS(TD) 1.126 1.426 2.552 171.8 55.9 LS(SD) 1.215 1.300 2.515 172.3 51.7 HS(TD) 1.203 1.449 2.652 169.8 54.6 LS(SD) 1.426 1.209 2.635 172.6 45.9 HS(TD) 1.259 1.310 2.569 170.7 51.0 LS(SD) 1.377 1.222 2.599 172.3 47.0 HS(TD) 1.252 1.404 2.656 172.8 52.9 LS(SD) 1.227 1.402 2.629 172.2 53.3 HS(TD) 1.240 1.324 2.564 163.5 51.6 LS(SD) 1.289 1.269 2.558 166.6 49.6 V VI VII VIII i-propane n-propane propene methylphenyl- 20.23 103.39 19.05 17.68 107.98 21.47 20.36 91.48 14.68 15.15 103.66 18.28 cyclopropane IX isopropylphenyl- 17.31 95.92 16.03 cyclopropane X XI XII dimethylaniline toluene phenylethane 16 15.05 95.72 7.66 6.65 94.45 14.81 14.78 91.30 14.57 14.21 Table S3 Spin density populations for 4TS1, 2TS1 and 2TS1’’ of I, II and III. No. Type Fe O Por SR H Alk I (2TS1) SD 1.01 0.42 -0.58 -0.48 -0.08 0.70 III (2TS1) SD 1.00 0.45 -0.48 -0.51 -0.04 0.58 II (2TS1) SD 0.97 0.52 -0.33 -0.72 -0.07 0.63 II (2TS1’’) TD -1.00 0.37 0.34 0.74 -0.07 0.61 III (2TS1a) SD 1.038 0.504 -0.827 -0.210 -0.057 0.560 III (2TS1b) SD 1.157 0.546 -0.892 -0.257 -0.072 0.500 III (2TS1c) SD 0.963 0.502 -0.437 -0.518 -0.047 0.522 III ( TS1a) TD 0.887 0.594 0.761 0.191 -0.060 0.647 III (4TS1b) TD 0.947 0.612 0.717 0.211 -0.066 0.553 III (4TS1c) TD 1.269 0.681 0.123 0.397 -0.035 0.576 4 17 Table S4 Spin Density Populations for HS (4TS ) state of I-XII No. Type Fe O Por SR H Alk Q a) Ib) TD 0.89 0.52 0.46 0.48 -0.06 0.72 0.35 II b) TD 1.35 0.61 0.07 0.38 -0.06 0.72 0.27 III c) TD 1.34 0.60 0.08 0.39 -0.03 0.62 0.35 IV c) TD 1.35 0.61 0.07 0.38 -0.04 0.63 0.35 V c) TD 1.40 0.64 0.05 0.36 -0.02 0.58 0.35 VI c) TD 1.35 0.60 0.06 0.38 -0.04 0.64 0.35 VII c) TD 1.28 0.69 0.14 0.40 -0.03 0.53 0.29 VIII c) TD 1.38 0.63 0.05 0.36 -0.03 0.61 0.35 IX c) TD 1.39 0.68 0.05 0.36 -0.01 0.52 0.36 X c) TD 1.50 0.65 -0.05 0.25 0.00 0.66 0.49 XI c) TD 1.32 0.66 0.11 0.38 -0.03 0.55 0.31 XII c) TD 1.35 0.66 0.12 0.38 -0.02 0.52 0.31 a)Q: charge transfer from substrates b) Ref. [61] c) Refs [36-50]. 18 Table S5 Spin density populations for 2TS1’ of IV-XII No. Type Fe O Por SR H Alk Q a) IIb) SD 1.93 -0.20 -0.18 -0.09 0.05 -0.51 0.28 IVc) SD 1.86 -0.07 -0.19 -0.09 0.03 -0.54 0.37 Vc) SD 1.87 -0.05 -0.22 -0.17 0.02 -0.45 0.34 VIc) SD 1.85 -0.07 -0.19 -0.08 0.03 -0.54 0.37 VIIc) SD 1.82 0.12 -0.31 -0.24 0.01 -0.40 0.30 VIIIc) SD 1.82 -0.03 -0.22 -0.12 0.02 -0.47 0.36 IXc) SD 1.83 0.11 -0.29 -0.28 0.00 -0.37 0.34 Xc) SD 1.71 0.21 -0.23 -0.15 -0.01 -0.52 0.47 XIc) SD 1.81 0.11 -0.30 -0.22 0.01 -0.41 0.31 XIIc) SD 1.83 0.16 -0.32 -0.29 0.00 -0.39 0.31 a) Q: charge transfer from substrates b) Ref. [61] c) Refs [36-50]. 19