Using Computational Chemistry to Understand & Discover Chemical Reactions

Daedalus

Volumn 143, Issue 4, 2014, Pages 49-66

  Houk, K N ^a   Liu, Peng ^b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF PITTSBURGH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84907450711     PISSN: 00115266     EISSN: 15486192     Source Type: Journal    
DOI: 10.1162/DAED_a_00305     Document Type: Article

References (33)

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3. Christopher J. Cramer, Essentials of Computational Chemistry: Theories and Models, 2nd ed. (Malden, Mass.: John Wiley & Sons, 2004).
4. M. J. Frisch et al., Gaussian 09, Revision D. 01 [electronic structure modeling program] (Wallingford, Conn.: Gaussian, Inc., 2009).
5. A. B. Richon, “An Early History of the Molecular Modeling Industry,” Drug Discovery Today 13 (2008): 659-664.
6. See R. Hoffmann and R. B. Woodward, “Stereochemistry of Electrocyclic Reactions,” Journal of the American Chemical Society 87 (1965): 395-397.
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11. Henry Eyring, “The Activated Complex in Chemical Reactions,” The Journal of Chemical Physics 3 (1935): 107-115.
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13. See also N. G. Rondan and K. N. Houk, “Theory of Stereoselection in Conrotatory Electrocyclic Reactions of Substituted Cyclobutenes,” Journal of the American Chemical Society 107 (1985): 2099-2111.
14. K. Rudolf, D. C. Spellmeyer, and K. N. Houk, “Prediction and Experimental Veriffication of the Stereoselective Electrocyclization of 3-Formylcyclobutene,” The Journal of Organic Chemistry 52 (1987): 3708-3710.
15. These Nobel Prizes in Chemistry were awarded for asymmetric hydrogenations and oxidations (William S. Knowles, Ryoji Noyori, and K. Barry Sharpless; 2001), oleffin metathesis (Yves Chauvin, Robert H. Grubbs, and Richard R. Schrock; 2005), and palladium-catalyzed cross couplings (Richard F. Heck, Ei-ichi Negishi, and Akira Suzuki; 2010).
16. A. J. Jiang, Y. Zhao, R. R. Schrock, and A. H. Hoveyda, “Highly Z-Selective Metathesis Homocoupling of Terminal Oleffins,” Journal of the American Chemical Society 131 (2009): 16630-16631.
17. S. J. Meek, R. V. O'Brien, J. Llaveria, R. R. Schrock, and A. H. Hoveyda, “Catalytic Z-Selective Oleffin Cross-Metathesis for Natural Product Synthesis,” Nature 471 (2011): 461-466.
18. K. Endo and R. H. Grubbs, “Chelated Ruthenium Catalysts for Z-Selective Oleffin Metathesis,” Journal of the American Chemical Society 133 (2011): 8525-8527.
19. B. K. Keitz, K. Endo, M. B. Herbert, and R. H. Grubbs, “Z-Selective Homodimerization of Terminal Oleffins with a Ruthenium Metathesis Catalyst,” Journal of the American Chemical Society 133 (2011): 9686-9688.
20. Even though we evaluate only the reasonable possibilities, we use a lot of computer time. Last year we used about ten million hours of fast computer time, equivalent to one thousand years on one fast computer.
21. P. Liu, X. Xu, X. Dong, B. K. Keitz, M. B. Herbert, R. H. Grubbs, and K. N. Houk, “Z-Selectivity in Oleffin Metathesis with Chelated Ru Catalysts: Computational Studies of Mechanism and Selectivity,” Journal of the American Chemical Society 134 (2012): 1464-1467.
22. L. E. Rosebrugh, M. B. Herbert, V. M. Marx, B. K. Keitz, and R. H. Grubbs, “Highly Active Ruthenium Metathesis Catalysts Exhibiting Unprecedented Activity and Z-Selectivity,” Journal of the American Chemical Society 135 (2013): 1276-1279.
23. J. K. Nørskov, T. Bligaard, J. Rossmeisl, and C. H. Christensen, “Towards the Computational Design of Solid Catalysts,” Nature Chemistry 1 (2009): 37-46.
24. For a review of this procedure, see G. Kiss, N. Çelebi-Ölçüm, R. Moretti, D. Baker, and K. N. Houk, “Computational Enzyme Design,” Angewandte Chemie International Edition 52 (2013): 5700-5725.
25. See http://www. pdb. org/.
26. H. M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T. N. Bhat, H. Weissig, I. N. Shindyalov, and P. E. Bourne, “The Protein Data Bank,” Nucleic Acids Research 28 (2000): 235-242.
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28. L. Jiang, E. A. Althoff, F. R. Clemente, L. Doyle, D. Rothlisberger, A. Zanghellini, J. L. Gallaher, J. L. Betker, F. Tanaka, C. F. Barbas III, D. Hilvert, K. N. Houk, B. L. Stoddard, and D. Baker, “De Novo Computational Design of Retro-Aldol Enzymes,” Science 319 (2008): 1387-1391.
29. J. B. Siegel, A. Zanghellini, H. M. Lovick, G. Kiss, A. R. Lambert, J. L. St. Clair, J. L. Gallaher, D. Hilvert, M. H. Gelb, B. L. Stoddard, K. N. Houk, F. E. Michael, and D. Baker, “Computational Design of an Enzyme Catalyst for a Stereoselective Bimolecular Diels-Alder Reaction,” Science 329 (2010): 309-313.
30. William L. Jorgensen, “The Many Roles of Computation in Drug Discovery,” Science 303 (2004): 1813-1818.
31. National Science and Technology Council, “Materials Genome Initiative for Global Competitiveness” (Washington, D. C.: Executive Offfice of the President of the United States, 2011).
32. Andreas W. Götz, Mark J. Williamson, Dong Xu, Duncan Poole, Scott Le Grand, and Ross C. Walker, “Routine Microsecond Molecular Dynamics Simulations with amber on gpus. 1. Generalized Born,” The Journal of Chemical Theory and Computation 8 (2012): 1542-1555.
33. Satoshi Maeda and Keiji Morokuma, “Communications: A Systematic Method for Locating Transition Structures of A+B → X Type Reactions,” The Journal of Chemical Physics 132 (24) (2010): 241102.