The need for enzymatic steering in abietic acid biosynthesis: Gas-phase chemical dynamics simulations of carbocation rearrangements on a bifurcating potential energy surface

Journal of the American Chemical Society

Volumn 133, Issue 21, 2011, Pages 8335-8343

  Siebert, Matthew R ^a   Zhang, Jiaxu ^a   Addepalli, Srirangam V ^a,c   Tantillo, Dean J ^b   Hase, William L ^a  

^a TEXAS TECH UNIVERSITY   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c UNIVERSITY OF ARKANSAS   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ABIETADIENE; CARBOCATIONS; CHEMICAL DYNAMICS; COMPLEX PROCESSES; DIPHOSPHATES; DIRECT DYNAMICS; ELECTRONIC STRUCTURE CALCULATIONS; GASPHASE; GERANYLGERANYL DIPHOSPHATE; METHYL GROUP; MOLECULAR ARCHITECTURE; PINE RESIN; REACTION PATHWAYS; SYNTHASES; TRANSITION STATE STRUCTURE; TWO-PRODUCT;

BIFURCATION (MATHEMATICS); BIOCHEMISTRY; BYPRODUCTS; CARBOXYLIC ACIDS; ELECTRONIC STRUCTURE; ENZYMES; FUNCTIONAL GROUPS; POTENTIAL ENERGY; POTENTIAL ENERGY SURFACES; QUANTUM CHEMISTRY; RESINS;

SURFACE REACTIONS;

ABIETIC ACID;

ARTICLE; BIOSYNTHESIS; CHEMICAL REACTION; CHEMICAL STRUCTURE; ENERGY CONVERSION; ENZYME ACTIVATION;

DITERPENES, ABIETANE; ISOMERASES; MODELS, CHEMICAL; MOLECULAR DYNAMICS SIMULATION; PHOSPHORIC ACID ESTERS; RESINS, PLANT;

EID: 79957762465     PISSN: 00027863     EISSN: 15205126     Source Type: Journal    
DOI: 10.1021/ja201730y     Document Type: Article

References (102)

1. Phillips, M. A.; Croteau, R. B. Trends Plant Sci. 1999, 4, 184-190
2. McCoy, M. Chem. Eng. News 2000, 78, 13-15
3. LaFever, R. E.; Stofer Vogel, B.; Croteau, R. Arch. Biochem. Biophys. 1994, 313, 139-149
4. Peters, R. J.; Flory, J. E.; Jetter, R.; Ravn, M. M.; Lee, H.-J.; Coates, R. M.; Croteau, R. B. Biochemistry 2000, 39, 15592-15602
5. Peters, R. J.; Croteau, R. B. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 580-584
6. Peters, R. J.; Ravn, M. M.; Coates, R. M.; Croteau, R. B. J. Am. Chem. Soc. 2001, 123, 8974-8978
7. Funk, C.; Croteau, R. Arch. Biochem. Biophys. 1994, 308, 258-266
8. Ravn, M. M.; Coates, R. M.; Jetter, R.; Croteau, R. B. Chem. Commun. 1998, 21-22
9. Ravn, M. M.; Coates, R. M.; Flory, J. E.; Peters, R. J.; Croteau, R. Org. Lett. 2000, 2, 573-576
10. Ravn, M. M.; Peters, R. J.; Coates, R. M.; Croteau, R. J. Am. Chem. Soc. 2002, 124, 6998-7006
11. Wilderman, P. R.; Peters, R. J. J. Am. Chem. Soc. 2007, 129, 15736-15737
12. Numbering of abietic acid adopted from ref 3a.
13. Hong, Y. J.; Tantillo, D. J. J. Am. Chem. Soc. 2009, 131, 7999-8015
14. Ho, G. A.; Nouri, D. H.; Tantillo, D. J. Tetrahedron Lett. 2009, 50, 1578-1584
15. Wang, S. C.; Tantillo, D. J. Org. Lett. 2008, 10, 4827-4830
16. Lodewyk, M. W.; Gutta, P.; Tantillo, D. J. J. Org. Chem. 2008, 73, 6570-6579
17. Gutta, P.; Tantillo, D. J. Org. Lett. 2007, 9, 1069-1071
18. Hong, Y. J.; Tantillo, D. J. Org. Lett. 2006, 8, 4601-4604
19. Gutta, P.; Tantillo, D. J. J. Am. Chem. Soc. 2006, 128, 6172-6179
20. Ho, G. A.; Nouri, D. H.; Tantillo, D. J. J. Org. Chem. 2005, 70, 5139-5143
21. Hong, Y. J.; Tantillo, D. J. Nature Chem. 2009, 1, 384-389
22. Tantillo, D. J. Chem. Soc. Rev. 2010, 39, 2847-2854
23. Christianson, D. W. Curr. Opin. Chem. Biol. 2008, 12, 141-150
24. Christianson, D. W. Chem. Rev. 2006, 106, 3412-3442
25. Davis, E. M.; Croteau, R. Top. Curr. Chem. 2000, 209, 53-95
26. Cane, D. E. Chem. Rev. 1990, 90, 1089-1103
27. Tantillo, D. J. J. Phys. Org. Chem. 2008, 21, 561-570 The term two-stage has also been proposed to describe a reaction that takes place in a single kinetic step but with asynchronous events: Dewar, M. J. S. J. Am. Chem. Soc. 1984, 106, 209-219
28. Ess, D. H.; Wheeler, S. E.; Iafe, R. G.; Xu, L.; Çelebi- Ölçüm, N.; Houk, K. N. Angew. Chem., Int. Ed. 2008, 47, 7592-7601
29. Ramquet, M.-N.; Dive, G.; Dehareng, D. J. Chem. Phys. 2000, 112, 4923-4934
30. Valtazanos, P.; Ruedenberg, K. Theor. Chim. Acta 1986, 69, 281-307
31. Lourderaj, U.; Park, K.; Hase, W. L. Int. J. Phys. Chem. 2008, 27, 361-403
32. Thomas, J. B.; Waas, J. R.; Harmata, M.; Singleton, D. A. J. Am. Chem. Soc. 2008, 130, 14544-14555
33. Hamaguchi, M.; Nakishi, M.; Nagai, T.; Nakamura, T.; Abe, M. J. Am. Chem. Soc. 2007, 129, 12981-12988
34. Singleton, D. A.; Hang, C.; Szymanski, M. J.; Meyer, M. P.; Leach, A. G.; Kuwata, K. T.; Chen, J. S.; Greer, A.; Foote, C. S.; Houk, K. N. J. Am. Chem. Soc. 2003, 125, 1319-1328
35. Wales, D. J. J. Chem. Phys. 2000, 113, 3926-3927
36. Williams, T.; Kelley, C. GNUPlot 4.0.0; broeker, 2004.
37. Sun, L.; Hase, W. L. Rev. Comput. Chem. 2003, 19, 79-146
38. Bolton, K.; Hase, W. L.; Peslherbe, G. H. Direct Dynamics Simulations of Reactive Systems. In Multidimensional Molecular Dynamics Methods; Thompson, D. L., Ed.; World Scientific Publishing, Inc.: London, 1998; pp 143-189.
39. Bylaska, E. J.; de Jong, W. A.; Govind, N.; Kowalski, K.; Straatsma, T. P.; Valiev, M.; Wang, D.; Apra, E.; Windus, T. L.; Hammond, J.; Nichols, P.; NWChem, A Computational Chemistry Package for Parallel Computers, Version 5.1; Pacific Northwest National Laboratory: Richland, WA, 2007.
40. Kendall, R. A.; Apra, E.; Bernholdt, D. E.; Bylaska, E. J.; Dupuis, M.; Fann, G. I.; Harrison, R. J.; Ju, J.; Nichols, J. A.; Nieplocha, J.; Straatsma, T. P.; Windus, T. L.; Wong, A. T. Comput. Phys. Commun. 2000, 128, 260-283
41. Møller, C.; Plesset, M. S. Phys. Rev. 1934, 46, 618-622
42. Becke, A. D. J. Chem. Phys. 1993, 98, 5648-5652
43. Becke, A. D. J. Chem. Phys. 1993, 98, 1372-1377
44. Lee, C.; Yang, W.; Parr, R. G. Phys. Rev. B: Solid State 1988, 37, 785-789
45. Stevens, P. J.; Devlin, F. J.; Chabalowski, C. F.; Frisch, M. J. J. Phys. Chem. 1994, 98, 11623-11627
46. Zhao, Y.; Lynch, B. J.; Truhlar, D. G. J. Phys. Chem. A 2004, 108, 2715-2719
47. Zhao, Y.; Schultz, N. E.; Truhlar, D. G. J. Chem. Theory Comput. 2006, 2, 364-382
48. The 6-31+G(d,p) basis set is not standard in NWChem; it was generated as a composite of the 6-31G(d,p) and the diffuse function from 6-31+G(d) as acquired from the EMSL basis set exchange: Schuchardt, K. L.; Didler, B. T.; Elsethagen, T.; Sun, L.; Gurumoorthi, V.; Chase, J.; Li, J.; Windus, T. L. J. Chem. Inf. Model. 2007, 47, 1045-1052
49. Feller, D. J. Comput. Chem. 1996, 17, 1571-1586 Explicit basis set specifications used for the calculations herein can be found in the Supporting Information.
50. Dunning, T. H., Jr. J. Chem. Phys. 1989, 90, 1007-1023
51. Wheeler, S. E.; Houk, K. N. J. Chem. Theory Comput 2010, 6, 395-404
52. Tirado-Rives, J.; Jergensen, W. L. J. Chem. Theory Comput. 2008, 4, 297-306
53. Zhang, J.; Zhao, Y.; Truhlar, D. G. J. Chem. Theory Comput. 2007, 3, 569-582
54. Riley, K. E.; Opt Holt, B. T.; Merz, K. M., Jr. J. Chem. Theory Comput. 2007, 3, 407-433
55. Lynch, B. J.; Truhlar, D. G. J. Phys. Chem. A 2003, 107, 8996-8999
56. Curtiss, L. A.; Raghavachari, K.; Redfern, P. C.; Pople, J. A. J. Chem. Phys. 2000, 112, 7374-7383
57. Curtiss, L. A.; Raghavachari, K.; Redfern, P. C.; Pople, J. A. J. Chem. Phys. 1997, 106, 1063-1079 For comparisons in terpene related carbocations, see, for example: Hong, Y. J.; Tantillo, D. J. Org. Biomol. Chem. 2010, 8, 4589-4600
58. Weitman, M.; Major, D. T. J. Am. Chem. Soc. 2010, 132, 6349-6360
59. Raghavachari, K.; Trucks, G. W.; Pople, J. A.; Head-Gordon, M. Chem. Phys. Lett. 1989, 157, 479-483
60. Woodcock, H. L.; Schaefer, H. F.; Schreiner, P. R. J. Phys. Chem. A 2002, 106, 11923-11931
61. Tsuzuki, S.; Lüthi, H. P. J. Chem. Phys. 2001, 114, 3949-3957
62. Schreiner, P. R.; Fokin, A. A.; Pascal, R. A., Jr.; de Meijera, A. Org. Lett. 2006, 8, 3635-3638
63. Check, C. E.; Gilbert, T. M. J. Org. Chem. 2005, 70, 9828-9834
64. Redfern, P. C.; Zapol, P.; Curtiss, L. A.; Raghavachari, K. J. Phys. Chem. A 2000, 104, 5850-5854
65. Wodrich, M. D.; Wannere, C. S.; Mp, Y.; Jarowski, P. D.; Houk, K. N.; Schleyer, P. v. R. Chem. - Eur. J. 2007, 13, 7731-7744
66. Grimme, S. Angew. Chem., Int. Ed. 2006, 45, 4460-4464
67. Wodrich, M. D.; Corminboeuf, C.; Schleyer, P. v. R. Org. Lett. 2006, 8, 3631-3634
68. For a good overview of the problems associated with B3LYP, see: Kang, J. K.; Musgrave, C. B. J. Chem. Phys. 2001, 115, 11040-11051 For a report suggesting that B3LYP tends to underestimate reaction barriers and overestimate reaction thermochemistry, see: Lynch, B. J.; Fast, P. L.; Harris, M.; Truhlar, D. G. J. Phys. Chem. A 2000, 104, 4811-4815 For reports that indicate B3LYP underestimates the strength of hydrogen bonds, see ref 24 and Zhao, Y.; Tishchenko, O.; Truhlar, D. G. J. Phys. Chem. B 2005, 109, 19046-19051
69. Zheng, J.; Zhao, Y.; Truhlar, D. G. J. Chem. Theory Comput. 2007, 3, 569-582
70. Zhao, Y.; Schultz, N. E.; Truhlar, D. G. J. Chem. Theory Comput. 2006, 2, 364-382
71. Zhao, Y.; Lynch, B. J.; Truhlar, D. G. J. Phys. Chem. A 2004, 108, 2715-2719
72. Lynch, B. J.; Truhlar, D. G. J. Phys. Chem. A 2003, 107, 8996-8999
73. Siebert, M. R.; Tantillo, D. J. J. Phys. Org. Chem. 2007, 20, 384-394
74. Siebert, M. R.; Tantillo, D. J. J. Org. Chem. 2006, 71, 645-654
75. Vrcek, I. V.; Vrcek, V.; Siehl, H.-U. J. Phys. Chem. A 2002, 106, 1604-1611
76. Farcasiu, D.; Lukinskas, P.; Pamidighantam, S. V. J. Phys. Chem. A 2002, 106, 11672-11675
77. Hase, W. L.; Bolton, K.; Sainte Claire, P. D.; Duchovic, R. J.; Hu, X.; Komornicki, A.; Li, G.; Lim, K. F.; Lu, D.-H.; Peslherbe, G. H.; Song, K.; Swamy, K. N.; Vande Linde, S. R.; Varandas, A.; Wang, H.; Wolf, R. J. Venus05, a general chemical dynamics computer program; 2004.
78. Hase, W. L.; Duchovic, R. J.; Hu, X.; Komornicki, A.; Lim, K. F.; Lu, D. H.; Peslherbe, G. H.; Swamy, S. R.; Vande Linde, S. R.; Varandas, A.; Wang, H.; Wolf, R. J. QCPE Bull. 1996, 16, 671
79. Hu, X.; Hase, W. L.; Pirraglia, T. J. Comput. Chem. 1991, 12, 1014-1024
80. Swope, W. C.; Anderson, H. C.; Berens, P. H.; Wilson, K. R. J. Chem. Phys. 1982, 76, 637-649
81. Schlier, C.; Seiter, A. Comput. Phys. Commun. 2000, 130, 176-189
82. Schlier, C.; Seiter, A. J. Phys. Chem. A 1998, 102, 9399-9404
83. Lourderaj, U.; Song, K.; Windus, T. L.; Zhuang, Y.; Hase, W. L. J. Chem. Phys. 2007, 126, 044105
84. Peslherbe, G. H.; Wang, H.; Hase, W. L. Adv. Chem. Phys. 1999, 105, 171-201
85. Sun, L.; Hase, W. L. J. Chem. Phys. 2010, 133, 034027
86. Truhlar, D. G.; Muckerman, J. T. In Atom-Molecule Collision Theory: A Guide fort he Experimentalist; Bernstein, R. B., Ed.; Plenum: New York, 1979; pp 505-566.
87. Each event was deemed complete at the first time that the interatomic distance in question fell below the distance for the equilibrium structure. For 4, key equilibrium interatomic distances are 1.10 and 1.56 Å for the C16-H18 and C11-C15 bonds, respectively; for 5, these distances are 1.09 and 1.54 Å for the C16-H18 and C1-C15 bonds, respectively; and for 8, these distances are 1.10 and 1.59 Å for the C16-H18 and C3-C15 bonds, respectively. Interatomic distances were printed every 10 fs, which represents the resolution in which the stated times reside.
88. Xu, L.; Doubleday, C. E.; Houk, K. N. J. Am. Chem. Soc. 2010, 132, 3029-3037
89. -1; these frequencies correspond to 11 and 42 fs, respectively.
90. López, J. G.; Vayner, G.; Lourderaj, U.; Addepalli, S. V.; Kato, S.; de Jong, W. A.; Windus, T. L.; Hase, W. L. J. Am. Chem. Soc. 2007, 129, 9976-9985
91. Sun, L.; Song, K.; Hase, W. L. Science 2002, 296, 875-878
92. Mann, D. J.; Hase, W. L. J. Am. Chem. Soc. 2002, 124, 3208-3209
93. Goodrow, A.; Bell, A. T.; Head-Gordon, M. J. Chem. Phys. 2009, 130, 244108
94. Kalra, B. L.; Cho, J. Y.; Lewis, D. K. J. Phys. Chem. A 1999, 103, 362-364
95. Setser, D. W.; Rabinovitch, B. S. J. Am. Chem. Soc. 1964, 86, 564-569
96. Chesick, J. P. J. Am. Chem. Soc. 1960, 82, 3277-3285
97. Nishio, M.; Hirota, M.; Umezawa, Y. The CH/π Interaction: Evidence, Nature, and Consequences; Wiley-VCH: New York, 1998.
98. Brandl, M.; Weiss, M. S.; Jabs, A.; Sühnel, J.; Hilgenfeld, R. J. Mol. Biol. 2001, 307, 357-377
99. Tsuzuki, S.; Honda, K.; Uchimaru, T.; Mikami, M.; Tanabe, K. J. Am. Chem. Soc. 2000, 122, 3746-3753
100. Ma., J. C.; Dougherty, D. A. Chem. Rev. 1997, 97, 1303-1324
101. Dougherty, D. A. Science 1996, 271, 163-168
102. Hong, Y. J.; Tantillo, D. J. J. Org. Chem. 2007, 72, 8877-8881