Support Information for: The Quest for Insight into Ultra Short CH π Proximities in Molecular Iron Maidens

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1 Support Information for: The Quest for Insight into Ultra Short CH π Proximities in Molecular Iron Maidens Ina Østrøm, Alexandre O. Ortolan, Felipe S. S. Schneider, Giovanni F. Caramori, and Renato L. T. Parreira. March 26, 2018 Contents 1 Computational Methodology S1 2 Geometrical Parameters S4 3 QTAIM analysis S8 4 NBO analysis S10 5 NCI analysis S13 6 GIAO 1 H NMR chemical shifts S13 7 XYZ files S13 References S42 1 Computational Methodology The geometries were optimized at DFT-D level of theory, employing the hybrid density functional PBE0 of Ernzerhof-Scuseria 1 and Adamo-Barone, 2 (25% of hartree-fock exchange), together with the Ahlrich s triple-zeta quality basis set, def2-tzvpp. 3,4 The RIJCOSX approximation was applied to speed up the calculation of the HF exchange integrals. 5 The description of long-range dispersion effects was taken into account by the D3 Grimme s dispersion correction 6,7 together with the Becke-Johnson damping functions. 8,9 All geometries were verified as true minima by the absence of negative eigenvalues of the Hessian matrix. For comparison, we also optimized a set of Corresponding author giovanni.caramori@ufsc.br. Departamento de Química, Universidade Federal de Santa Catarina, Campus Universitário Trindade, CP 476, Florianópolis, SC, , Brazil. Núcleo de Pesquisas em Ciências Exatas e Tecnológicas, Universidade de Franca, , Franca, SP, Brazil. S1

2 compounds with RI-SCS-MP2/def2-TZVPP level of theory. 3,4,10 12 The geometry optimization and numerical vibrational frequencies were performed in ORCA software (v.3.0.1). 13 Nuclear magnetic resonance (NMR) chemical shifts were computed by the use of the Gauge- Including Atomic Orbital approach (GIAO), 14,15 as implemented in ADF (PBE0- D3/TZ2P 15,19 ). Values are reported relative to tetramethylsilane (TMS) by the use of the experimental chemical shift of BZN(S) (-2.84 ppm 20 ). The electronic structure of all compounds were verified through the Non-Covalent Index (NCI), Natural Bond Orbitals (NBO) and the Quantum Theory of Atoms in Molecules (QTAIM). In the same way as the geometry optimization and vibrational frequencies, the NCI, NBO and QTAIM analyses were also performed at PBE0-D3(BJ)/def2-TZVPP level of theory. The NCI analysis 21 was performed with the NCI plot 22 code and visualized with the VMD software. 23 This analysis finds regions with small electron density and lower reduced density gradient, s, 1 ρ s = (1) 2(3π 2 ) 1/3 ρ 4/3 and it colors each region according to the sign of the second eigenvalue of the Hessian matrix times the electron density. The second Hessian eigenvalue reports the electron density curvature in the plane perpendicular to the internuclear direction, and allows one to differentiate the strongly attractive interactions from strongly repulsive ones, as well as from the non-covalent weak interactions. The attractive interactions (such as the dipole-dipole and hydrogen bonds) are represented in blue, whereas repulsive interactions (e.g. steric repulsion) are represented in red, and weak interactions (dispersive interactions) in green. The NBO (Natural Bond Orbital) method was performed at GAMESS-US v.2013 (R1) software. 27 The NBOs of a compound can be seen as two different set of orbitals: The (a) Lewis- Type (LT) NBOs, which have occupations of almost 2.0 electrons and are classified as a bonding orbital, and the (b) Non-Lewis-Type (NL) NBOs, which have a very small residual occupation of almost 0.0 electrons (but non-zero), and are anti-bonding orbitals. In this model, the LT NBOs are related to the classical Lewis structures, whereas the NL orbitals are the deviation from the those ideal structures; deviations that are necessary for a complete description of the final wave function. It is thus possible to interpret the final electronic structure through donoracceptor interactions between the LT (donors) and NL (acceptors) NBOs. The usefulness of the NBO technique is that it provides an estimate of the energy stabilization of these donor-acceptor interactions by the second order perturbation theory analysis of the Fock matrix ( ˆF ), according to E (2) i j = q i φ i ˆF 2 φ j ε j ε i where q i is the occupation of the donor NBO, φ i and φ j are the donor and acceptor NBOs, and ε i and ε j are their respective energy. In this sense, the NBO donor-acceptor orbital interactions are necessary to explain the final wave function. QTAIM analysis 28 was employed for selected structures, as implemented in MultiWFN QTAIM makes use exclusive use of the electron density (ρ( r)), which makes the method very robust and versatile, and uniquely defines one atomic basin for each atom within any molecule or crystal. It does so by the use of the well known condition of zero flux between atomic basins. The atomic charges from the QTAIM method are then calculated by integration of each atomic basin, giving rise to a unambiguous assignment of electrons, and consequently charge, to atoms in molecules. Furthermore, critical points (CP) of the electron density ( ρ( r) = 0) are assigned to special features of the molecule such as bonds, rings and cages. The density on (2) S2

3 each bond CP, for instance, is a measure of electron density accumulation and thus a measure for bond strength. S3

4 2 Geometrical Parameters π-system Label A B Benzene BZN C C(H) Cyanuric Acid CA N C(O) Triaminobenzene TAB C C(NH 2 ) Trithiocyanuric Acid TCA N C(S) Trifluorobenzene TFB C C(F) Trihydroxybenzene THB C C(OH) Trinitrobenzene TNB C C(NO 2 ) s-triazine TRZ C N Scheme S1: Atom labeling. Table S1: Comparison between the calculated (at PBE0-D3/def2-TZVPP and RI-MP2- SCS/def2-TZVPP level of theories) and experimental [a] bond lengths (Å) for the BZN compound with sulfur bridges (5). Since no symmetry restrictions were imposed in the geometry optimization, the final molecule does not possess the perfect C 3v symmetry (root-mean-square displacement of atomic coordinates necessary to apply the C 3v point group = (PBE0-D3) and (RI-MP2-SCS)). Mean signed deviation (MSD)= Å (PBE0-D3) and Å (RI-MP2-SCS). Mean absolute error (MAE)=0.008 Å (PBE0-D3) and Å (RI-MP2-SCS). Parameter (Å) C 3 A C 3 B H B C 1 S C 2 S A C 1 C 2 C 3 A B X-ray [a] PBE0-D3(BJ) [avg] RI-MP2-SCS [avg] [a] From Cambridge Structural Database (CSD) cod. VAMMEB. S4

5 BZN(CH 2 ) TRZ(CH 2 ) CA(CH 2 ) TCA(CH 2 ) BZN(O) TRZ(O) CA(O) TCA(O) BZN(S) TRZ(S) CA(S) TCA(S) BZN(NH) TRZ(NH) CA(NH) TCA(NH) BZN(NH + 2 ) TRZ(NH + 2 ) CA(NH + 2 ) TCA(NH + 2 ) Figure S1: Optimized structures of compounds 1 20 (BZN, TRZ, CA and TCA rings with the CH 2, O, S, NH and NH + 2 bridges). S5

6 TFB(CH 2 ) TNB(CH 2 ) THB(CH 2 ) TAB(CH 2 ) TFB(O) TNB(O) THB(O) TAB(O) TFB(S) TNB(S) THB(S) TAB(S) TFB(NH) TNB(NH) THB(NH) TAB(NH) TFB(NH + 2 ) TNB(NH + 2 ) THB(NH + 2 ) TAB(NH + 2 ) Figure S2: Optimized structures of compounds (TFB, TNB, THB and TAB rings with the CH 2, O, S, NH and NH + 2 bridges). S6

7 Table S2: Selected C H vibrational frequencies (cm 1 ) and bond lengths (Å). Labeling atoms are shown in Fig. S1. Comparison between the calculated (PBE0-D3/def2-TZVPP level of theory) and the crystallographic structure 30 lead to a mean signed error of Å. Values for calculations at RI-MP2-SCS/def2-TZVPP are shown in parentheses. Ring ν C H bond lengths (Å) X (cm 1 ) H centroid C 3 H H X (avg.) BZN 1 CH (1.623) (1.059) (2.645) 2 O (1.576) (1.056) (2.510) 5 S (1.688) (1.064) (2.905) 6 NH NH TRZ 3 CH (1.608) (1.053) (2.605) 4 O (1.564) (1.050) (2.476) 8 S NH NH CA 11 CH O S NH NH TCA 16 CH O S NH NH TFB 21 CH O S NH NH TNB 26 CH O S NH NH THB 31 CH O S NH NH TAB 36 CH O S NH NH S7

8 3 QTAIM analysis All QTAIM charges are shown in Table S3. Methine hydrogen (H) charges, which is directed Table S3: QTAIM charges for compounds 1 4. Labeling atoms are shown in Scheme S1. L H C 3 A avg B avg X avg C avg 1 C avg 2 BZN CH a O TRZ CH O a Units of e. towards the center of the aromatic ring, are found to be close to zero in all cases (between e and 0.044e). For benzene, both X = CH 2 and O deliver very similar H (0.021e and 0.034e, respectively). Triazine shows charges that are similar for the same ligands, although slightly negative (-0.028e for CH 2 and e for O). But the choice of ligand (X) influences H charge for triazine: (i) changing S for O makes H more positive (-0.006e for S versus e for O); and (ii) protonating the bridge makes H even more positive, e.g. for NH versus NH 2 + (-0.024e and 0.029e, respectively) and for O versus OH + (-0.015e and 0.044e, respectively). Comparing rings with the same ligand O, the following trend is observed for the charge on H: TRZ(O) and CA(O) (both e), TNB(O) (-0.009e), TCA(O) (-0.004e), TFB(O) (0.016e), BZN(O) (0.034e), TAB(O) (0.041e), THB(O) (0.042e). C 3 is always close to zero but positive, staying between 0.013e (THB(O)) and 0.086e (TRZ(S)). Changing X = S for O in TRZ makes C 3 less positive (0.086e for S versus 0.039e for O), while changing the THB ring for benzene makes C 3 more positive (0.013e for THB(O) versus 0.048e for The substitution of ligand CH 2 for oxygen when the ring is benzene makes the C 3 carbon less positive (0.048e for BZN(CH 2 ) versus 0.019e for BZN(O)). For triazine, C 3 charges stay between 0.039e (TRZ(O)) and 0.086e (TRZ(S)). When it comes to charges, bridges vary depending on their nature. For instance, oxygen bridges vary between e (TRZ(O)) and e (TCA(O)). For the two structures with CH 2 bridge, charges for the carbon of CH 2 were found between 0.044e (TRZ(CH 2 )) and 0.047e (BZN(CH 2 )). Lastly, TRZ(S) has almost zero charge on S (0.001e), while protonating TRZ(O) on the bridge, producing TRZ(OH + ), makes the oxygen slightly more negative (-1.042e for TRZ(O) versus e for TRZ(OH + )). Protonating the nitrogen of TRZ(NH) has the opposite effect: nitrogen has charge of e in TRZ(NH), but its charge becomes e in TRZ(NH 2 + ). Rings seem not to be particularly affected by ligands, which can be observed by essentially the same charges for A and B atoms for benzene and ligands CH 2 and O (between e and e for A and between e and e for B). Triazine also shows the same trend: the charge of A stays between 1.048e (TRZ(O)) and 1.112e (both TRZ(NH 2 + ) and TRZ(OH+ )) and B stays between e (TRZ(OH + )) and e (TRZ(CH 2 )) in this case. The QTAIM charge of bridge carbons bound to the ring (C 1 ) vary according to ring and ligand. For instance, for benzene, C 1 is more positive when the ligand is O (0.532e), but close to zero (0.056e) for CH 2. For triazine, S makes C 1 slightly negative (-0.046e) when compared to O (0.544e), while C 1 of TRZ(CH 2 ) is comparable to BZN(CH 2 ) (0.051e versus 0.056e, respectively). Protonating the ligand makes C 1 less positive; e.g. TRZ(OH + ) versus TRZ(O) (0.318e versus 0.544e) and TRZ(NH 2 + ) versus TRZ(NH) (0.261e versus 0.377e, respectively). For different rings with the same ligand O, we find C 1 charges in the order: CA(O) (0.856e), THB(O) (0.509e), S8

9 TNB(O) (0.569e), TAB(O) (0.535e), TCA(O) (0.845e), TFB(O) (0.554e). For C 2, charges depend more intensely on ligands. But when we look for triazine, the change of S for O makes C 2 negative (0.499e for TRZ(O) versus e for TRZ(S)), while TRZ(CH 2 ) has almost neutral charge on C 2 (0.041e). By proponating the bridges we get, for triazine ring, less positive charges on C 2 : 0.356e for TRZ(NH) versus 0.249e for TRZ(NH 2 + ) and 0.499e for TRZ(O) versus 0.342e for TRZ(OH + ). Values and Laplacians of the electron density evaluated at QTAIM critical points can be used as a measure of bond strength. 28 Generally, ρ > 0.2 au suggests covalent bonding, while ρ < 0.1 au indicates closed-shell interaction and ρ has a direct relationship with binding energy for a series of bonding interactions. 28 C H CP density between au and au and 2 ρ between au and au indicate, as expected, covalent bonding, which is the strongest for TRZ(NH 2 + ) (Table S4). Table S4: Values and Laplacians of the electron density evaluated at selected QTAIM critical points (CPs). Labeling atoms are shown in Scheme S1. L CP type ρ(r CP ) a 2 ρ(r CP ) b BZN 1 CH 2 B(C 3 H) d B avg(a H) R avg(a H A) e R(ring) C f O B(C 3 H) d B avg(a H) R avg(a H A) e R(ring) C f TRZ 4 O B(C 3 H) B avg(b H) R avg(b H B) R(ring) C NH + 2 B(C 3 H) B avg(b H) R avg(b H B) R(ring) C a, b Units of au. d Bond critical point, formally (3, 1). e Ring critical point, formally (3, +1). f Cage critical point, formally (3, +3). The charge held within a ring, which is itself a measure of ring basicity, can be correlated with the density at the ring critical point. For the studied systems, the density at this CP seems to depend mostly on the nature of the ring and is largest for TRZ(X) ( au). The ring-h interaction can be classified by QTAIM by the three types of critical points found: (i) up to three bond CPs found between H and atoms of the ring; (ii) up to three ring CPs between H and two atoms of the ring; and (iii) a single cage critical point between H and all the atoms of the ring. The electron density values at all these CPs suggest that the strongest interaction happens for TRZ(O) (Table S4), which correlates with ring basicity. Bond CPs (i), between H and atoms of the ring, are found either as A H or B H bonds, depending on the S9

10 nature of the ring (Table S4), and are very similar to ring CPs (ii) in terms of electron density values and Laplacian. Ring CPs (ii) are found accordingly in an alternated way between bond CPs (Scheme S2). Scheme S2: Schematic representation of selected QTAIM critical points (CPs) common to all structures: nuclei attractors are represented as blue spheres, bond critical points as small red dots, ring critical points as small yellow dots and the cage critical point as a small green dot. Data on selected critical points for selected structures can be seen in Table S4. 4 NBO analysis We have searched for all donor-acceptor interactions involving the NBOs of the methine hydrogen (H) in the compounds 1 (BZN(CH 2 )), 2 (BZN(O)), 3 (TRZ(CH 2 )) and 4 (TRZ(O)), in order to see the influence of the oxygen bridges as well the triazine ring in the CH π bond distances. In all cases, a σ(c H) bonding orbital acts as a NBO donor, and a σ (C H) anti-bonding orbital acts as a NBO acceptor. Although we did not found any relation between the interactions involving the σ (C H) NBOs and the CH π distances, we did see a relation with the σ(c-h) donor NBO. The NBO energy stabilization in which the σ(c H) acts as a donor are shown in Table 3, and spatially represented for compound 4 (TRZ(O)) in Fig. 4. Basically, four different types of interactions with σ(c H) are seen: (a) σ(c H) σ (C H) the sigma donation from the methine C H group to the sigma anti-bonding NBO of the neighbor carbon-hydrogen group; (b) σ(c H) σ (C C) the sigma donation from the methine C H group to the sigma antibonding NBO of the neighbor bridging carbon-carbon group; (c) σ(c H) σ (C O) the sigma donation from the methine C H group to the sigma anti-bonding NBO of the neighbor S10

11 bridging carbon-oxygen group; (d) σ(c H) π (C N) the sigma donation from the methine C H group to the π anti-bonding NBOs of the carbon-nitrogen atoms of the triazine ring. Although the interaction (a) σ(c H) σ (C H) provides almost the same stabilization (from kcal mol 1 ) in all compounds, the interaction (b) σ(c H) σ (C C) is a bit smaller (about 1 kcal mol 1 ) when the aromatic ring is the triazine unit. On the other hand, the triazine ring allows the interaction (d) σ(c H) π (C N), providing an stabilization of 3.1 and 2.9 kcal mol 1 to the 3(TRZ(CH 2 )) and 4 (TRZ(O)) compounds. In 1 (BZN(CH 2 )) and 2 (BZN(O)), no interactions with the anti-bonding π orbitals of the benzene ring was seen. In addition, in the oxygen bridged compounds, a extra interaction is found, (c) σ(c H) σ (C O), which gives an stabilization of 2.4 and 2.8 kcal mol 1 for 2 (BZN(O)) and 4 (TRZ(O)), which are not seen in the CH 2 -bridged compounds. These interactions provides extra stabilization to the compounds, and allows the electronic density to flow from the methine C H group to the remaining of the molecule, which probably is the reason of the CH π bond distance trend of 1 (BZN(CH 2 )) > 3 (TRZ(CH 2 )) > 2 (BZN(O)) > 4 (TRZ(O)). S11

σ(c-h) σ*(c-h) (a) σ(c-h)àσ*(c-h) E (2) i j* = -2.8 kcal.

mol -1 (b) σ(c-h) σ*(c-o) (c) σ(c-h)àσ*(c-o) E (2) i j* = -0.9 kcal.

mol -1 Figure S3: Representation of selected NBO interactions for compound TRZ(O) (4) and

12 σ(c-h) σ*(c-h) (a) σ(c-h)àσ*(c-h) E (2) i j* = -2.8 kcal.mol -1 σ(c-h) σ*(c-c) σ(c-h)àσ*(c-c) E (2) i j* = -0.7 kcal.mol -1 (b) σ(c-h) σ*(c-o) (c) σ(c-h)àσ*(c-o) E (2) i j* = -0.9 kcal.mol -1 σ(c-h) π*(c-n) (d) σ(c-h)àπ*(c-n) E (2) i j* = -0.9 kcal.mol -1 Figure S3: Representation of selected NBO interactions for compound TRZ(O) (4) and the donor-acceptor interactions with their respective second order energy stabilization ( E (2) i j ). (a) σ(c H) donor NBO and the σ of the bridging neighbor C H acceptor NBO; (b) σ(c H) donor NBO and the σ of the bridging neighbor C C acceptor NBO; (c) σ(c H) donor NBO and the σ of the bridging neighbor C O acceptor NBO; (d) σ(c H) donor NBO and the π acceptor NBO of the triazine ring. S12

13 5 NCI analysis Through the NCI analysis, it is possible to see a strong attractive interaction (blue region in a bowl shape, Fig. 5) between the central methine hydrogen (H) and the center of the aromatic ring. These blue surfaces are characteristic of hydrogen-bonds, indicating that the CH π interaction in these compounds are not dispersive but electrostatic. In the opposite side of the surface, the blue regions also shows the attractive interactions between the ring and the H. Compounds with the benzene ring shows this feature between all carbon atoms of the ring, whereas compounds with triazine, this regions intensified above the nitrogen atoms. Fused in the center of the underside of this bowl structure, there is the characteristic inter-ring steric repulsion. Non-covalent interactions between the hydrogens of the methylene bridges, neighbor to methine group and the aromatic unit is also seen in all cases (green surfaces, Fig. 5). In addition, in methylene bridged compounds 1 (BZN(CH 2 ) and 3 (TRZ(CH 2 )), non-covalent interactions between their bridges is also present, whereas a much smaller interaction is seen in oxygen bridged compounds 3 (BZN(O)) and 4 (TRZ(O)). Interestingly, the NCI analysis did not show any sort non-covalent interactions between the H and either the methylene nor oxygen bridges. In summary, attractive interactions, similar to hydrogen bonds, of electrostatic character, was found between the hydrogen H and the aromatic units. Non-covalent interaction between the methylene of the bridges and the aromatic ring is present in all compounds. Weak interactions between the bridges is seen in methylene bridged compounds, but also in smaller extent in O compounds. No interactions between the methine hydrogen H and the bridges (both CH 2 and O) is seen. 6 GIAO 1 H NMR chemical shifts Table S5: Absolute total and relative isotropic NMR shieldings (in ppm) for H of selected structures. Relative chemical shifts are taken as δtms calc. = δ ref δ abs, where δ ref = δ TMS (BZN(S))+ δ abs (BZN(S)), in which δ TMS (BZN(S)) and δ abs (BZN(S)) are experimental and calculated values, respectively, for BZN(S). Experimental values are given in parentheses. Structure δ abs (ppm) δ TMS (ppm) 1 BZN(CH 2 ) (-4.03) 31 2 BZN(O) BZN(S) (-2.84) 20 3 TRZ(CH 2 ) TRZ(O) /out TRZ(O)/out XYZ files 5, BZN, X = S; Eh. S S S C S13

14 C C C C C C C C C C C C H H H H H H H H H H H H H H H H , BZN, X = NH 2 + ; Eh. N N N C C C C C C C C C C C C C H H H S14

15 H H H H H H H H H H H H H H H H H H H , BZN, X = CH 2 ; Eh. C C C C C C C C C C C C C C C C H H H H H H H H H H H H S15

16 H H H H H H H H H H , BZN, X = NH; Eh. N N N C C C C C C C C C C C C C H H H H H H H H H H H H H H H H H H H , BZN, X = O; Eh. S16

17 O O O C C C C C C C C C C C C C H H H H H H H H H H H H H H H H , CA, X = S; Eh. S S S N C N C N C C C C C C C S17

18 C O O O H H H H H H H H H H H H H , CA, X = NH 2 + ; Eh. N N N N C N C N C C C C C C C C O O O H H H H H H H H H H S18

19 H H H H H H H H H , CA, X = CH 2 ; Eh. C C C N C N C N C C C C C C C C O O O H H H H H H H H H H H H H H H H H H H S19

20 14, CA, X = NH; Eh. N N N N C N C N C C C C C C C C O O O H H H H H H H H H H H H H H H H , CA, X = O; Eh. O O O N C N C N C C S20

21 C C C C C C O O O H H H H H H H H H H H H H , TFB, X = S; Eh. S S S C C C C C C C C C C C C C F F F H H H H H H S21

22 H H H H H H H , TFB, X = NH 2 + ; Eh. N N N C C C C C C C C C C C C C F F F H H H H H H H H H H H H H H H H H H H , TFB, X = CH 2 ; Eh. S22

23 C C C C C C C C C C C C C C C C F F F H H H H H H H H H H H H H H H H H H H , TFB, X = NH; Eh. N N N C C C C C C S23

24 C C C C C C C F F F H H H H H H H H H H H H H H H H , TFB, X = O; Eh. O O O C C C C C C C C C C C C C F F F H H S24

25 H H H H H H H H H H H , TRZ, X = S; Eh. S S S C N C N C N C C C C C C C H H H H H H H H H H H H H , TRZ, X = NH 2 + ; Eh. N N N C N S25

Chapter 10. VSEPR Model: Geometries

Chapter 10. VSEPR Model: Geometries Chapter 10 Molecular Geometry VSEPR Model: Geometries Valence Shell Electron Pair Repulsion Theory Electron pairs repel and get as far apart as possible Example: Water Four electron pairs Farthest apart