Changes in charge distribution, molecular volume, accessible surface area and electronic structure along the reaction coordinate for a carbocationic triple shift rearrangement of relevance to diterpene biosynthesis

Journal of Physical Chemistry A

Volumn 116, Issue 35, 2012, Pages 8902-8909

  Hong, Young J ^a   Ponec, Robert ^b   Tantillo, Dean J ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b INSTITUTE OF CHEMICAL PROCESS FUNDAMENTALS   (Czech Republic)

Author keywords

[No Author keywords available]

Indexed keywords

ACCESSIBLE SURFACE AREAS; ACTIVE SITE; BONDING INDEX; CARBOCATIONS; DITERPENES; MOLECULAR VOLUME; REACTION COORDINATES; SYNTHASES;

BIOCHEMISTRY; CHARGE DISTRIBUTION; ELECTRONIC STRUCTURE;

OLEFINS;

CARBON; DITERPENE;

ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; CONFORMATION; ELECTRON; METABOLISM; SURFACE PROPERTY; THERMODYNAMICS;

CARBON; DITERPENES; ELECTRONS; MODELS, MOLECULAR; MOLECULAR CONFORMATION; SURFACE PROPERTIES; THERMODYNAMICS;

EID: 84865966694     PISSN: 10895639     EISSN: 15205215     Source Type: Journal    
DOI: 10.1021/jp3047328     Document Type: Article

References (58)

1. Although concertedness is usually defined in terms of a potential energy surface, the absence or presence of a given intermediate may vary when free energy is considered.(2) In addition, some intermediates have very small barriers for conversion into other species, leading some to prefer definitions based on lifetimes rather than the presence or absence of minima on a potential energy surface. For a recent study that deals with such issues, see Gonzalez-James, O. M.; Kwan, E. E.; Singleton, D. A. J. Am. Chem. Soc. 2012, 134, 1914
2. Tantillo, D. J. J. Phys. Org. Chem. 2008, 21, 561
3. Williams, A. Concerted Organic and Bio-Organic Mechanisms, CRC Press, Boca Raton, FL, 2000.
4. A classic paper on the issue that generated considerable debate: Dewar, M. J. S. J. Am. Chem. Soc. 1984, 106, 209. The definitions used in this paper: "In our terminology a synchronous reaction is one where all the bond-making and bond-breaking processes take place in unison, having all proceeded to comparable extents in the transition state. A concerted reaction is one that takes place in a single kinetic step without necessarily being synchronous. A two-stage reaction is concerted but not synchronous, some of the changes in bonding taking place in the first part of the reaction, followed by the rest. A two-step reaction takes place in two kinetically distinct steps, via a stable intermediate."
5. Cane, D. E. Compr. Nat. Prod. Chem. 1999, 2, 155
6. Cane, D. E. Chem. Rev. 1990, 90, 1089
7. Davis, E. M.; Croteau, R. Top. Curr. Chem. 2000, 209, 53
8. Christianson, D. W. Chem. Rev. 2006, 106, 3412
9. Ueberbacher, B. T.; Hall, M.; Faber, K. Nat. Prod. Rep. 2012, 29, 337
10. Christianson, D. W. Curr. Op. Chem. Biol. 2008, 12, 141
11. Dickschat, J. S. Nat. Prod. Rep. 2011, 28, 1917
12. Miller, D. J.; Allemann, R. K. Nat. Prod. Rep. 2012, 29, 60
13. Tantillo, D. J. Nat. Prod. Rep. 2011, 28, 1035
14. Tantillo, D. J. Chem. Soc. Rev. 2010, 39, 2847
15. Quantum calculations (and leading references): Hong, Y. J.; Tantillo, D. J. J. Am. Chem. Soc. 2010, 132, 5375
16. Note that the calculations described herein are for structures in the absence of the enzyme active site (and the departed diphosphate counterion); that is, here we are addressing the inherent reactivity of the carbocations in question.
17. A recent report on dedicated kaurene and atiserene syntheses in bacteria: Smanski, M. J.; Yu, Z.; Casper, J.; Lin, S.; Peterson, R. M.; Chen, Y.; Wendt-Pienkowski, E.; Rajski, S. R.; Shen, B. Proc. Natl. Acad. Sci. U.S.A. 2011, 108, 13498. Note that ent -kaurene and ent -atiserene are biosynthetic precursors to the platensimycin and platensin antibiotics
18. This report is part 7 in our diterpene series; for parts 4-6, see: Hong, Y. J.; Tantillo, D. J. J. Am. Chem. Soc. 2011, 133, 18249 and ref 7
19. Siebert, M. R.; Zhang, J.; Addepalli, S. V.; Tantillo, D. J.; Hase, W. L. J. Am. Chem. Soc. 2011, 133, 8335
20. Siebert, M. R.; Paranjothy, M.; Sun, R.; Tantillo, D. J.; Hase, W. L. J. Chem. Theor. Comput. 2012, 8, 1212
21. Gonzalez, C.; Schlegel, H. B. J. Phys. Chem. 1990, 94, 5523
22. Fukui, K. Acc. Chem. Res. 1981, 14, 363
23. Dewar, M. J. S.; Jie, C. Acc. Chem. Res. 1992, 25, 537
24. Houk, K. N.; Gonzales, J.; Li, Y. Acc. Chem. Res. 1995, 28, 81
25. Rynkiewicz, M. J.; Cane, D. E.; Christianson, D. W. Biochemistry 2002, 41, 1732
26. Shishova, E. Y.; Di Costanzo, L.; Cane, D. E.; Christianson, D. W. Biochemistry 2007, 46, 1941
27. Ma, J. C.; Dougherty, D. A. Chem. Rev. 1997, 97, 1303
28. Gokel, G. W. Chem. Commun. 2003, 2847
29. Jensen, C.; Jorgensen, W. L. J. Am. Chem. Soc. 1997, 119, 10946
30. Bojin, M. D.; Tantillo, D. J. J. Phys. Chem. A 2006, 110, 4810
31. Weitman, M.; Major, D. T. J. Am. Chem. Soc. 2010, 132, 6349
32. Hong, Y. J.; Tantillo, D. J. Org. Biomol. Chem. 2010, 8, 4589
33. Hong, Y. J.; Tantillo, D. J. Org. Lett. 2011, 13, 1294
34. Alabugin, I. V.; Gilmore, K. M.; Peterson, P. W. Wiley Interdiscip. Rev.: Comput. Mol. Sci. 2011, 1, 109
35. Wiberg, K. B. Tetrahedron 1968, 24, 1083
36. Mayer, I. Chem. Phys. Lett. 1986, 97, 270
37. Muszkat, K. A.; Shafari-Ozeri, S. Chem. Phys. Lett. 1973, 20, 397
38. Lendvay, G. J. Phys. Chem. 1989, 93, 4422
39. Ponec, R.; Cooper, D. L. J. Phys. Chem. A 2003, 107, 2100
40. Lendvay, G. J. Phys. Chem. 1994, 98, 6098
41. Sannigrahi, A. B.; Kar, T. Chem. Phys. Lett. 1990, 173, 569
42. Sannigrahi, A. B.; Kar, T. J. Mol. Struct. (THEOCHEM) 2000, 496, 1
43. Giambiagi, M.; Giambiagi, M. S.; Mundim, K. C. Struct. Chem. 1990, 1, 423
44. Mundim, K. C.; Giambiagi, M.; Giambiagi, M. S. J. Phys. Chem. 1994, 98, 6118
45. Ponec, R.; Uhlik, F. Croat. Chem. Acta 1996, 69, 941
46. Ponec, R.; Mayer, I. J. Phys. Chem. 1997, 101, 1738
47. Dewar, M. J. S. Angew. Chem., Int. Ed. Engl. 1971, 10, 761
48. Mandado, M.; Ponec, R. J. Phys. Org. Chem. 2009, 22, 1225
49. Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Montgomery, J. A., Jr.; Vreven, T.; Kudin, K. N.; Burant, J. C.; J. M., Millam; Lyengar, S. S.; Tomasi, J.; Barone, V.; Mennucci, B.; Cossi, M.; Scalmani, G.; Rega, N.; Petresson, G. A.; Nakatsuji, H.; Hada, M.; Ehara, M.; Toyota, K.; Fukuda, R.; Hasegawa, J.; Ishida, M.; Nakajima, T.; Honda, Y.; Kitao, O.; Nakai, H.; Klene, M.; Li, X.; Knox, J. E.; Hratchian, H. P.; Cross, J. B.; Adamo, C.; Jaramillo, J.; Gomperts, R.; Stratmann, R. E.; Yazyev, O.; Austin, A. J.; R. Cammi; Pomelli, C.; Ochterski, J. W.; Ayala, P. Y.; Morokuma, K.; G. A, Voth; Salvador, P.; Dannenberg, J. J.; Zakrzewski, V. G.; Dapprich, S.; Daniels, A. D.; Strain, M. C.; Farkas, O.; Malick, D. K.; Rabuck, A. D.; Raghavachari, K.; Foresman, J. B.; Ortiz, J. V.; Cui, Q.; Baboul, A. G.; Cliffordqq, S.; Cioslowski, J.; Stefanov, B. B.; Liu, G.; Liashenko, A.; Piskorz, P.; Komaromi, I.; Martin, R. L.; Martin, R. L.; Fox, D. J.; Keith, T.; M. A. Al-Laham; Peng, C. Y.; Nanayakkara, A.; Challacombe, M.; Gill, P. M. W.; Johnson, B.; Chen, W.; Wong, M. W.; Gonzalez, C.; Pople, J. A., Gaussian 03, revision B.04; Gaussian, Inc.: Pittsburgh, PA, 2003.
50. Becke, A. D. J. Chem. Phys. 1993, 98, 5648
51. Becke, A. D. J. Chem. Phys. 1993, 98, 1372
52. Lee, C.; Yang, W.; Parr, R. G. Phys. Rev. B 1988, 37, 785
53. Stephens, P. J.; Devlin, F. J.; Chabalowski, C. F.; Frisch, M. J. J. Phys. Chem. 1994, 98, 11623
54. Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Scalmani, G.; Barone, V.; Mennucci, B.; Petersson, G. A.; Nakatsuji, H.; Caricato, M.; Li, X.; Hratchian, H. P.; Izmaylov, A. F.; Bloino, J.; Zheng, G.; Sonnenberg, J. L.; Hada, M.; Ehara, M.; Toyota, K.; Fukuda, R.; Hasegawa, J.; Ishida, M.; Nakajima, T.; Honda, Y.; Kitao, O.; Nakai, H.; Vreven, T.; Montgomery, J. A.;, Jr.; Peralta, J. E.; Ogliaro, F.; Bearpark, M.; Heyd, J. J.; Brothers, E.; Kudin, K. N.; Staroverov, V. N.; Keith, T.; Kobayashi, R.; Normand, J.; Raghavachari, K.; Rendell, A.; Burant, J. C.; Iyengar, S. S.; Tomasi, J.; Cossi, M.; Rega, N.; Millam, J. M.; Klene, M.; Knox, J. E.; Cross, J. B.; Bakken, V.; Adamo, C.; Jaramillo, J.; Gomperts, R.; Stratmann, R. E.; Yazyev, O.; Austin, A. J.; Cammi, R.; Pomelli, C.; Ochterski, J. W.; Martin, R. L.; Morokuma, K.; Zakrzewski, V. G.; Voth, G. A.; Salvador, P.; Dannenberg, J. J.; Dapprich, S.; Daniels, A. D.; Farkas, O.; Foresman, J. B.; Ortiz, J. V.; Cioslowski, J.; Fox, D. J., Gaussian 09, revision B.01; Gaussian, Inc.: Wallingford CT, 2010.
55. Fraczkiewicz, R.; Braun, W. J. Comput. Chem. 1998, 19, 319
56. Müller, N.; Falk, A.; Gsaller, G. Ball & Stick Molecular Graphics Application for MacOS Computers, version 4.0a12; Johannes Kepler University: Linz, Austria, 2004.
57. Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb, M. A.; Cheeseman, J. R.; Zakrzewski, V. G.; Montgomery, J. A., Jr.; Stratmann, R. E.; Burant, J. C.; Dapprich, S.; Millam, J. M.; Daniels, A. D.; Kudin, K. N.; Strain, M. C.; Farkas, O.; Tomasi, J.; Barone, V.; Cossi, M.; Cammi, R.; Mennucci, B.; Pomelli, C.; Adamo, C.; Clifford, S.; Ochterski, J.; Petersson, G. A.; Ayala, P. Y.; Cui, Q.; Morokuma, K.; Malick, D. K.; Rabuck, A. D.; Raghavachari, K.; Foresman, J. B.; Cioslowski, J.; Ortiz, J. V.; Stefanov, B. B.; Liu, G.; Liashenko, A.; Piskorz, P.; Komaromi, I. R.; Gomperts, R.; Martin, L.; Fox, D. J.; Keith, T.; Al-Laham, M. A.; Peng, C. Y.; Nanayakkara, A.; Gonzalez, C.; Challacombe, M. P.; Gill, M. W.; Johnson, B.; Chen, W.; Wong, M. W.; Andres, J. L.; Gonzalez, C.; Head-Gordon, M.; Replogle, E. S.; Pople, J. A. Gaussian 98
58. revision A.9; Gaussian, Inc.: Pittsburgh, PA, 1998.