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1 Supplementary information doi: /nchem.287 A Potential Energy Surface Bifurcation in Terpene Biosynthesis Young J. Hong and Dean J. Tantillo* Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, CA tantillo@chem.ucdavis.edu Table of Contents I. Gaussian03 Reference Page 2 II. Conformation change of conformer 1. Page 2 5 III. Energetics of a small model system. Page 5 6 IV. Coordinates and Energies Page 6 53 V. IRC Plots.... Page S1 nature chemistry 1
2 I. Gaussian03 Full Reference GAUSSIAN03, Revision D.01 M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria, M. A. Robb, J. R. Cheeseman, J. A. Montgomery, Jr., T. Vreven, K. N. Kudin, J. C. Burant, J. M. Millam, S. S. Iyengar, J. Tomasi, V. Barone, B. Mennucci, M. Cossi, G. Scalmani, N. Rega, G. A. Petersson, H. Nakatsuji, M. Hada, M. Ehara, K. Toyota, R. Fukuda, J. Hasegawa, M. Ishida, T. Nakajima, Y. Honda, O. Kitao, H. Nakai, M. Klene, X. Li, J. E. Knox, H. P. Hratchian, J. B. Cross, V. Bakken, C. Adamo, J. Jaramillo, R. Gomperts, R. E. Stratmann, O. Yazyev, A. J. Austin, R. Cammi, C. Pomelli, J. W. Ochterski, P. Y. Ayala, K. Morokuma, G. A. Voth, P. Salvador, J. J. Dannenberg, V. G. Zakrzewski, S. Dapprich, A. D. Daniels, M. C. Strain, O. Farkas, D. K. Malick, A. D. Rabuck, K. Raghavachari, J. B. Foresman, J. V. Ortiz, Q. Cui, A. G. Baboul, S. Clifford, J. Cioslowski, B. B. Stefanov, G. Liu, A. Liashenko, P. Piskorz, I. Komaromi, R. L. Martin, D. J. Fox, T. Keith, M. A. Al-Laham, C. Y. Peng, A. Nanayakkara, M. Challacombe, P. M. W. Gill, B. Johnson, W. Chen, M. W. Wong, C. Gonzalez, and J. A. Pople, Gaussian, Inc., Wallingford CT, II. Conformation change of conformer 1 Scheme S1 TS (1b'-1c') H 3.50 [3.51] 2.94 [3.12] 0.00 [0.00] H H 1c' 1b' S2 nature chemistry 2
3 [3.51] 1.34 TS (1b'-1c') [3.12] 0.00 [0.00] c' b' Figure S1. Conformation change of 1b to 1c involved in the rearrangement of the small model system. Computed geometries (selected distances in Å) and relative energies (in kcal/mol) of intermediates and transition structures are shown by B3LYP/6-31+G(d,p) and mpw1pw91/631+g(d,p)//b3lyp/631+g(d,p) in brackets. S3 nature chemistry 3
4 Scheme S2 H TS (1b-1c) 4.66 [4.46] 3.89 [3.57] 0.00 [0.00] H H 1c 1b 0.00 [0.00] TS (1b-1c) [4.46] 3.89 [3.57] c b S4 nature chemistry 4
5 Figure S2. Conformation change of 1b to 1c. Computed geometries (selected distances in Å) and relative energies (in kcal/mol) of intermediates and transition structures are shown by B3LYP/6-31+G(d,p) and mpw1pw91/631+g(d,p)//b3lyp/631+g(d,p) in brackets. III. Energetics of a small model system Our study began with an examination of the model system shown in Figure S3, in the absence of the enzyme active site. This model system includes only one of the 6- membered rings of 1a/b. The two conformers of this ring that are productive for proton transfer were examined, and rearrangements from both (1a and 1b ) are shown in Figure S3. Two pathways for each conformer are shown; these differ in which -face of the alkene attacks the proton (H c ). H c H c relative energy (kcal/mol) 1.73 [1.94] H c H c TS re (1a'-2a') 1a' pathway 1 H a Ha H b H b [25.37] pathway [0.00] H a H c 1b' TS si (1a'-2a') H b [27.66] H a H b H b Ha 3.64 [3.46] CH 3 2a' pathway 3 TS re (1b'-3b'/4b') [24.54] 7.13 [7.89] CH 3 CH 3 TS (2a'-3a') 4.07 [3.55] CH 3 TS (2a'-4a') pathway [10.56] [25.41] CH 3 TS (2a'-4b') H c H a H b TS si (1b-4b') BIFURCATION 7.33 [7.95] CH 3 CH 3 TS (3b'-4b') 2 CATION 4a' CH [-17.08] [-27.26] [-18.49] 4b' CH 3 CH 3 enantiomers [-27.26] CH 3 TS (3b'-3c') [-26.49] [-26.61] 3a' 3c' CH 3 3b' CH 3 S5 nature chemistry 5
6 Figure S3. Computed energies (top: B3LYP/6-31+G(d,p); in brackets: mpw1pw91/6-31+g(d,p)//b3lyp/6-31+g(d,p)) for structures involved in the rearrangement of the small model system. The italicized methyl group is the one that results from the proton transfer. Note that the energy surface corresponding to the rotation of the iso-propyl group (i.e., 3b -to-ts (3b -3c )-to-3c ) is very flat. IV. Coordinates and Energies Figure S3. 1a HF = hartrees ( kcal/mol) Imaginary Frequencies: none found Zero-point correction = (Hartree/Particle) HF = hartrees ( kcal/mol) S6 nature chemistry 6
7 TS re (1a -2a ) HF = hartrees ( kcal/mol) Imaginary Frequencies: 1 ( /cm) Zero-point correction = (Hartree/Particle) HF = hartrees ( kcal/mol) S7 nature chemistry 7
8 TS si (1a -2a ) o HF = hartrees ( kcal/mol) Imaginary Frequencies: 1 ( /cm) Zero-point correction = (Hartree/Particle) HF = hartrees ( kcal/mol) S8 nature chemistry 8
9 a HF = hartrees ( kcal/mol) Imaginary Frequencies: none found Zero-point correction = (Hartree/Particle) HF = hartrees ( kcal/mol) S9 nature chemistry 9
10 TS (2a -3a ) o HF = hartrees ( kcal/mol) Imaginary Frequencies: 1 ( /cm) Zero-point correction = (Hartree/Particle) HF = hartrees ( kcal/mol) S10 nature chemistry 10
11 a HF = hartrees ( kcal/mol) Imaginary Frequencies: none found Zero-point correction = (Hartree/Particle) HF = hartrees ( kcal/mol) S11 nature chemistry 11
12 TS (2a -4b ) HF = hartrees ( kcal/mol) Imaginary Frequencies: 1 ( /cm) Zero-point correction = (Hartree/Particle) HF = hartrees ( kcal/mol) S12 nature chemistry 12
13 b HF = hartrees ( kcal/mol) Imaginary Frequencies: none found Zero-point correction = (Hartree/Particle) HF = hartrees ( kcal/mol) S13 nature chemistry 13
14 TS (2a -4a ) o HF = hartrees ( kcal/mol) Imaginary Frequencies: 1 ( /cm) Zero-point correction = (Hartree/Particle) HF = hartrees ( kcal/mol) S14 nature chemistry 14
15 a HF = hartrees ( kcal/mol) Imaginary Frequencies: none found Zero-point correction = (Hartree/Particle) HF = hartrees ( kcal/mol) S15 nature chemistry 15
16 b HF = hartrees ( kcal/mol) Imaginary Frequencies: none found Zero-point correction = (Hartree/Particle) HF = hartrees ( kcal/mol) S16 nature chemistry 16
17 TS re (1b -3b /4b ) HF = hartrees ( kcal/mol) Imaginary Frequencies: 1 ( /cm) Zero-point correction = (Hartree/Particle) HF = hartrees ( kcal/mol) S17 nature chemistry 17
18 TS si (1b -4b ) o HF = hartrees ( kcal/mol) Imaginary Frequencies: 1 ( /cm) Zero-point correction = (Hartree/Particle) HF = hartrees ( kcal/mol) S18 nature chemistry 18
19 b HF = hartrees ( kcal/mol) Imaginary Frequencies: none found Zero-point correction = (Hartree/Particle) HF = hartrees ( kcal/mol) S19 nature chemistry 19
20 TS (3b -3c ) HF = hartrees ( kcal/mol) Imaginary Frequencies: 1 ( /cm) Zero-point correction = (Hartree/Particle) HF = hartrees ( kcal/mol) S20 nature chemistry 20
21 c HF = hartrees ( kcal/mol) Imaginary Frequencies: none found Zero-point correction = (Hartree/Particle) HF = hartrees ( kcal/mol) S21 nature chemistry 21
22 TS (3b -4b ) HF = hartrees ( kcal/mol) Imaginary Frequencies: 1 ( /cm) Zero-point correction = (Hartree/Particle) HF = hartrees ( kcal/mol) S22 nature chemistry 22
23 Figure 2. 1a HF = hartrees ( kcal/mol) Imaginary Frequencies: none found Zero-point correction = (Hartree/Particle) HF = hartrees ( kcal/mol) MPWB1K/6-31+G(d,p)//B3LYP/6-31+G(d,p) HF = hartrees ( kcal/mol) S23 nature chemistry 23
24 S24 nature chemistry 24
25 TS re (1a-2a) HF = hartrees ( kcal/mol) Imaginary Frequencies: 1 ( /cm) Zero-point correction = (Hartree/Particle) HF = hartrees ( kcal/mol) MPWB1K/6-31+G(d,p)//B3LYP/6-31+G(d,p) HF = hartrees ( kcal/mol) S25 nature chemistry 25
26 TS si (1a-2a) HF = hartrees ( kcal/mol) Imaginary Frequencies: 1 ( /cm) Zero-point correction = (Hartree/Particle) HF = hartrees ( kcal/mol) MPWB1K/6-31+G(d,p)//B3LYP/6-31+G(d,p) HF = hartrees ( kcal/mol) 2 S26 nature chemistry 26
27 S27 nature chemistry 27
28 a o HF = hartrees ( kcal/mol) Imaginary Frequencies: none found Zero-point correction = (Hartree/Particle) HF = hartrees ( kcal/mol) MPWB1K/6-31+G(d,p)//B3LYP/6-31+G(d,p) HF = hartrees ( kcal/mol) S28 nature chemistry 28
29 TS (2a-3a) o HF = hartrees ( kcal/mol) Imaginary Frequencies: 1 ( /cm) Zero-point correction = (Hartree/Particle) S29 nature chemistry 29
30 HF = hartrees ( kcal/mol) MPWB1K/6-31+G(d,p)//B3LYP/6-31+G(d,p) HF = hartrees ( kcal/mol) S30 nature chemistry 30
31 a HF = hartrees ( kcal/mol) Imaginary Frequencies: none found Zero-point correction = (Hartree/Particle) HF = hartrees ( kcal/mol) MPWB1K/6-31+G(d,p)//B3LYP/6-31+G(d,p) HF = hartrees ( kcal/mol) S31 nature chemistry 31
32 TS (2a-4a) o HF = hartrees ( kcal/mol) S32 nature chemistry 32
33 Imaginary Frequencies: 1 ( /cm) Zero-point correction = (Hartree/Particle) HF = hartrees ( kcal/mol) MPWB1K/6-31+G(d,p)//B3LYP/6-31+G(d,p) HF = hartrees ( kcal/mol) S33 nature chemistry 33
34 a HF = hartrees ( kcal/mol) Imaginary Frequencies: none found Zero-point correction = (Hartree/Particle) HF = hartrees ( kcal/mol) MPWB1K/6-31+G(d,p)//B3LYP/6-31+G(d,p) HF = hartrees ( kcal/mol) S34 nature chemistry 34
35 b S35 nature chemistry 35
36 HF = hartrees ( kcal/mol) Imaginary Frequencies: none found Zero-point correction = (Hartree/Particle) HF = hartrees ( kcal/mol) MPWB1K/6-31+G(d,p)//B3LYP/6-31+G(d,p) HF = hartrees ( kcal/mol) S36 nature chemistry 36
37 TS re (1b-3b/4b) HF = hartrees ( kcal/mol) Imaginary Frequencies: 1 ( /cm) Zero-point correction = (Hartree/Particle) HF = hartrees ( kcal/mol) MPWB1K/6-31+G(d,p)//B3LYP/6-31+G(d,p) HF = hartrees ( kcal/mol) S37 nature chemistry 37
38 S38 nature chemistry 38
39 TS si (1b-4b) HF = hartrees ( kcal/mol) Imaginary Frequencies: 1 ( /cm) Zero-point correction = (Hartree/Particle) HF = hartrees ( kcal/mol) MPWB1K/6-31+G(d,p)//B3LYP/6-31+G(d,p) HF = hartrees ( kcal/mol) S39 nature chemistry 39
40 b HF = hartrees ( kcal/mol) Imaginary Frequencies: none found Zero-point correction = (Hartree/Particle) S40 nature chemistry 40
41 HF = hartrees ( kcal/mol) MPWB1K/6-31+G(d,p)//B3LYP/6-31+G(d,p) HF = hartrees ( kcal/mol) S41 nature chemistry 41
42 TS (3b-3c) HF = hartrees ( kcal/mol) Imaginary Frequencies: 1 ( /cm) Zero-point correction = (Hartree/Particle) HF = hartrees ( kcal/mol) MPWB1K/6-31+G(d,p)//B3LYP/6-31+G(d,p) HF = hartrees ( kcal/mol) S42 nature chemistry 42
43 c S43 nature chemistry 43
44 HF = hartrees ( kcal/mol) Imaginary Frequencies: none found Zero-point correction = (Hartree/Particle) HF = hartrees ( kcal/mol) MPWB1K/6-31+G(d,p)//B3LYP/6-31+G(d,p) HF = hartrees ( kcal/mol) S44 nature chemistry 44
45 TS (3b-4b) HF = hartrees ( kcal/mol) Imaginary Frequencies: 1 ( /cm) Zero-point correction = (Hartree/Particle) HF = hartrees ( kcal/mol) MPWB1K/6-31+G(d,p)//B3LYP/6-31+G(d,p) HF = hartrees ( kcal/mol) S45 nature chemistry 45
46 S46 nature chemistry 46
47 b HF = hartrees ( kcal/mol) Imaginary Frequencies: none found Zero-point correction = (Hartree/Particle) HF = hartrees ( kcal/mol) MPWB1K/6-31+G(d,p)//B3LYP/6-31+G(d,p) HF = hartrees ( kcal/mol) S47 nature chemistry 47
48 Figure S1. 1c HF = hartrees ( kcal/mol) Imaginary Frequencies: none found Zero-point correction = (Hartree/Particle) S48 nature chemistry 48
49 HF = hartrees ( kcal/mol) TS (1b -1c ) HF = hartrees ( kcal/mol) Imaginary Frequencies: 1 ( /cm) Zero-point correction = (Hartree/Particle) S49 nature chemistry 49
50 HF = hartrees ( kcal/mol) Figure S2. 1c HF = hartrees ( kcal/mol) Imaginary Frequencies: none found Zero-point correction = (Hartree/Particle) S50 nature chemistry 50
51 HF = hartrees ( kcal/mol) MPWB1K/6-31+G(d,p)//B3LYP/6-31+G(d,p) HF = hartrees ( kcal/mol) S51 nature chemistry 51
52 TS (1b-1c) HF = hartrees ( kcal/mol) Imaginary Frequencies: 1 ( /cm) Zero-point correction = (Hartree/Particle) HF = hartrees ( kcal/mol) MPWB1K/6-31+G(d,p)//B3LYP/6-31+G(d,p) HF = hartrees ( kcal/mol) S52 nature chemistry 52
53 V. IRC Plots Specification for IRC calculations relevant to the bifurcating path in the full system TS re (1b-3b/4b) : Figure 4a in the main paper. S53 nature chemistry 53
54 1. IRC calculation was incomplete; both forward and reverse proceeded to 25 points by calcfc. But 1b is verified. Insufficient to verify either 1b-3b or 1b-4b. 2. Additional calculation toward 3b/4b was attempted. Additional calculation by calcfc proceeded to specified 100 points and verified 1b-4b. The second additional calculation was unsuccessful and proceeded to only 2 points. 3. TS (3b-4b) was located by full optimization of the geometry selected in the flat region of TS re (1b-3b/4b) IRC. TS re (3b-4b) : Figure 4b in the main paper. Both forward and reverse proceeded to specified 100 points by calcfc (sufficient for verification). Figure S4. IRC results (B3LYP/6-31+G(d,p); energies do not include zero point energy corrections) for TS re (1b -3b /4b ) from Figure S3. Selected distances are shown in Å. Complete IRC calculations (both forward and reverse) were obtained by calcfc S54 nature chemistry 54
55 (verification of 1b -3b ) IRC calculation toward 3b /4b specified by calcall proceded to only 7 points. Figure S5. IRC results (B3LYP/6-31+G(d,p); energies do not include zero point energy corrections) for TS (3b -4b ) from Figure 3S. Selected distances are shown in Å. Both forward (3b ) and reverse (4b ) proceeded to specified 100 points by calcfc (sufficient for verification). Additional points for both proceded to 100 points by calcfc (3b ) and rcfc (4b ). S55 nature chemistry 55
56 Figure S6. IRC results (B3LYP/6-31+G(d,p); energies do not include zero point energy corrections) for TS si (1b-4b) from Figure 2. Selected distances are shown in Å. The initial IRC calculation specified calcfc generated 17 points toward 4b. Until additional calculation, it appears too early to detect any sign of alkyl shifting. To verify the connection of TS si (1b-4b) to 4b, additional points were necessary. Geometries at the last point of each additional IRC calculations (Five consecutive IRC calculations were attempted; additional calculations each reached up to 26, 61, 8 and 38 points) are shown. Additional calculation specified by rcfc did not proceed at all (no convergence at all). This is a general trend in all additional IRC calculations when the initial calculation stopped at a point suffering from convergence problems. There is an energy drop between the last point from initial calculation and the first point from the first additional calculation, but note the energy surface becomes level. Geometrical changes along additional IRC calculations are consistent with 1,2-alkyl shifting (bridging). This suggests another concerted reaction consisting of proton transfer and alkyl shift (ring expansion). The geometries in the flat region resemble TS (3b-4b) and those in the flat region of the TSre (1b-3b/4b) IRC (e.g., the green point in Figure 4a). Thus, the pathway towards product from TS si (1b-4b) may also bifurcate. Figure 3S. TS re (1a -2a ) S56 nature chemistry 56
57 TS si (1a -2a ) TS (2a -3a ) S57 nature chemistry 57
58 TS (2a -4b ) TS (2a -4a ) TS si (1b -4b ) S58 nature chemistry 58
59 TS (3b -3c ) Figure 2. TS re (1a-2a) S59 nature chemistry 59
60 TS si (1a-2a) TS (2a-3a) S60 nature chemistry 60
61 TS (2a-4a) TS (3b-3c) S61 nature chemistry 61
62 Figure S1. TS (1b -1c ) Dihedral angle changes (highlighted atoms; decrease to 100º) along to IRC indicated the direction was toward 1c. IRC calculation in this direction was not successful, however dihedral angle changes (highlighted atoms; increase to 106º) indicated the direction was toward 1b. Figure S2. S62 nature chemistry 62
63 TS (1b-1c) S63 nature chemistry 63
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