Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Commentary
  • Published:

Computational prediction of small-molecule catalysts

Abstract

Most organic and organometallic catalysts have been discovered through serendipity or trial and error, rather than by rational design. Computational methods, however, are rapidly becoming a versatile tool for understanding and predicting the roles of such catalysts in asymmetric reactions. Such methods should now be regarded as a first line of attack in the design of catalysts.

This is a preview of subscription content, access via your institution

Relevant articles

Open Access articles citing this article.

Access options

Buy this article

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Time required to compute molecular structures.
Figure 2: Successful computational predictions of non-catalytic reactions.
Figure 3: Transition structures of the Hajos–Parrish reaction.
Figure 4: Successful computational predictions of catalysts.

References

  1. Gaussian 03, Revision C.02 (Gaussian, Wallingford, Connecticut, 2004).

  2. Zhao, Y. & Truhlar, D. G. Density functionals with broad applicability in chemistry. Acc. Chem. Res. 2, 157–167 (2008).

    Article  Google Scholar 

  3. Cramer, C. J. Essentials of Computational Chemistry: Theories and Models 2nd edn (Wiley, 2004).

    Google Scholar 

  4. Weik, M. H. in A Third Survey of Domestic Electronic Digital Computing Systems. Report No. 1115, 526–536 (Ballistic Research Laboratories, Aberdeen Proving Ground, Maryland, 1961).

    Book  Google Scholar 

  5. Rudolf, K., Spellmeyer, D. C. & Houk, K. N. Prediction and experimental verification of the stereoselective electrocyclization of 3-formylcyclobutene. J. Org. Chem. 52, 3708–3710 (1987).

    Article  CAS  Google Scholar 

  6. Murakami, M., Miyamoto, Y. & Ito, Y. A silyl substituent can dictate a concerted electrocyclic pathway: inward torquoselectivity in the ring opening of 3-silyl-1-cyclobutene. Angew. Chem. Int. Edn Engl. 40, 189–190 (2001).

    Article  CAS  Google Scholar 

  7. Murakami, M., Hasegawa, M. & Igawa, H. Theoretical and experimental studies on the thermal ring-opening reaction of cyclobutene having a stannyl substituent at the 3-position. J. Org. Chem., 69, 587–590 (2004).

    Article  CAS  Google Scholar 

  8. Mukherjee, D., Wu, Y.-D., Fronczek, F. R. & Houk, K. N. Experimental tests of models to predict nucleophilic addition stereochemistries. J. Am. Chem. Soc. 110, 3328–3330 (1998).

    Article  Google Scholar 

  9. Bahmanyar, S. & Houk, K. N. Transition states of amine-catalyzed aldol reactions involving enamine intermediates: theoretical studies of mechanism, reactivity, and stereoselectivity. J. Am. Chem. Soc. 123, 11273–11283 (2001).

    Article  CAS  Google Scholar 

  10. Rankin, K. R., Gauld, J. W. & Boyd, R. J. Density functional study of the proline-catalyzed direct aldol reaction. J. Phys. Chem. A 106, 5155–5159 (2002).

    Article  CAS  Google Scholar 

  11. Clemente, F. R. & Houk, K. N. Computational evidence for the enamine mechanism of intramolecular aldol reaction catalyzed by proline. Angew. Chem. Int. Edn Engl. 43, 5766–5768 (2004).

    Article  CAS  Google Scholar 

  12. Bahmanyar, S. & Houk, K. N. The origin of stereoselectivity in proline-catalyzed intramolecular aldol reactions. J. Am. Chem. Soc. 123, 12911–12912 (2001).

    Article  CAS  Google Scholar 

  13. Tang, Z. et al. Novel small organic molecules for a highly enantioselective direct aldol reaction. J. Am. Chem. Soc. 125, 5262–5263 (2003).

    Article  CAS  Google Scholar 

  14. Shinisha, C. B. & Sunoj, R. B. Bicyclic proline analogues as organocatalysts for stereoselective aldol reactions: an in silico DFT study. Org. Biomol. Chem. 5, 1287–1294 (2007).

    Article  CAS  Google Scholar 

  15. Cheong, P. H.-Y. & Houk, K. N. Origins of predictions of stereoselectivity in intramolecular aldol reactions catalyzed by proline derivatives. Synthesis 9, 1533–1537 (2005).

    Google Scholar 

  16. Mitsumori, S. et al. Direct asymmetric anti-Mannich-type reactions catalyzed by a designed amino acid. J. Am. Chem. Soc. 128, 1040–1041 (2006).

    Article  CAS  Google Scholar 

  17. Cheong, P. H.-Y. et al. Pipecolic acid-catalyzed direct asymmetric Mannich reactions. Org. Lett. 8, 811–814 (2006).

    Article  CAS  Google Scholar 

  18. Schreiner, P. R. & Wittkopp, A. H-bonding additives act like Lewis acid catalysts. Org. Lett. 4, 217–220 (2002).

    Article  CAS  Google Scholar 

  19. Fleming, E. M., Quigley, C., Rozas, I. &; Connon, S. J. Computational study-led organocatalyst design: a novel, highly active urea-based catalyst for addition reactions to epoxides. J. Org. Chem. 73, 948–956 (2008).

    Article  CAS  Google Scholar 

  20. Kozlowski, M. C., Dixon, S. L., Panda, M. & Lauri, G. Quantum mechanical models correlating structure with selectivity: predicting the enantioselectivity of β-amino alcohol catalysts in aldehyde alkylation J. Am. Chem. Soc. 125, 6614–6615 (2003).

    Article  CAS  Google Scholar 

  21. Ianni, J. C., Annamalai, V., Phuan, P.-W. & Kozlowski, M. C. A priori theoretical prediction of selectivity in asymmetric catalysis: design of new chiral catalysts using quantum molecular interaction fields. Angew. Chem. Int. Edn Engl. 45, 5502–5505 (2006).

    Article  CAS  Google Scholar 

  22. Yu, Z.-X. et al. Origins of differences in reactivities of alkenes, alkynes, and allenes in [Rh(CO)2Cl]2-catalyzed (5 + 2) cycloaddition reactions with vinylcyclopropanes. J. Am. Chem. Soc. 130, 2378–2379 (2008).

    Article  CAS  Google Scholar 

  23. Wang, Y. et al. A computationally designed Rh(i)-catalyzed two-component [5 + 2+ 1] cycloaddition of ene-vinylcyclopropanes and CO for the synthesis of cyclooctenones. J. Am. Chem. Soc. 129, 10060–10061 (2007).

    Article  CAS  Google Scholar 

  24. Corbeil, C. R., Thielges, S., Schwartzentruber, J. A. & Moitessier, N. Toward a computational tool predicting the stereochemical outcome of asymmetric reactions: development and application of a rapid and accurate program based on organic principles. Angew. Chem. Int. Edn Engl. 47, 2635–2638 (2008).

    Article  CAS  Google Scholar 

  25. Harriman, D. J., Lambropoulos, A. & Deslongchamps, G. In silico correlation of enantioselectivity for the TADDOL catalyzed asymmetric hetero-Diels–Alder reaction. Tetrahedr. Lett. 48, 689–692 (2007).

    Article  CAS  Google Scholar 

  26. Anderson, C. D., Dudding, T., Gordillo, R. & Houk, K. N. Origin of enantioselection in hetero-Diels–Alder reactions catalyzed by naphthyl-TADDOL. Org. Lett. 10, 2749–2752 (2008).

    Article  CAS  Google Scholar 

  27. Takano, Y. & Houk, K. N. Benchmarking the conductor-like polarizable continuum model (CPCM) for aqueous solvation free energies of neutral and ionic organic molecules. J. Chem. Theory Comput. 1, 70–77 (2005).

    Article  Google Scholar 

  28. van Erp, T. S. & Meijer, E. J. Ab initio molecular dynamics study of aqueous solvation of ethanol and ethylene. J. Chem. Phys. 118, 8831–8840 (2003).

    Article  ADS  CAS  Google Scholar 

  29. Pitcock, W. H. Jr, Lord, R. L. & Baik, M.-H. The mechanism of the rhodium(i)-catalyzed [2 + 2 + 1] carbocyclization reaction of dienes and CO: a computational study. J. Am. Chem. Soc. 130, 5821–5830 (2008).

    Article  CAS  Google Scholar 

  30. Tantillo, D. J., Chen, J. & Houk, K. N. Theozymes and compuzymes: theoretical models for biological catalysis. Curr. Opin. Chem. Biol. 2, 743–750 (1998).

    Article  CAS  Google Scholar 

  31. Zipse, H., Wang, L.-H. & Houk, K. N. Polyether catalysis of ester aminolysis — a computational and experimental study. Liebigs Ann. 1996, 1511–1522 (1996).

    Article  Google Scholar 

  32. Wang, L.-H. & Zipse, H. Bifunctional catalysis of ester aminolysis — a computational and experimental study. Liebigs Ann. 1996, 1501–1509 (1996).

    Article  Google Scholar 

  33. Rothlisberger, D. et al. Kemp elimination catalysts by computational enzyme design. Nature 453, 190–195 (2008).

    Article  ADS  Google Scholar 

  34. Jiang, L. et al. De novo computational design of retro-aldol enzymes. Science 319, 1387–1391 (2008).

    Article  ADS  CAS  Google Scholar 

  35. The PyMOL Molecular Graphics System v1.1 (DeLano Scientific, Palo Alto, 2007).

  36. Tarini, M., Cignoni, P. & Montani, C. Ambient occlusion and edge cueing to enhance real time molecular visualization. IEEE Trans. Vis. Comput. Graph. 12, 1237–1244 (2006).

    Article  Google Scholar 

  37. CYLview v.1.0b (C. Legault, 2007).

Download references

Acknowledgements

We are grateful to the University of California, Los Angeles, as well as to the National Institute of General Medical Sciences (grant GM 36700) and the National Science Foundation (grant CHE-0548209), for financial support. We also thank C. Legault for the use of CYLview, and M. Tarini, P. Cignoni and C. Montani for assistance in using QuteMol.

Author information

Authors and Affiliations

Authors

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Additional information

Reprints and permissions information is available at http://www.nature.com/reprints.

Correspondence should be addressed to K.N.H. (houk@chem.ucla.edu).

Rights and permissions

Reprints and permissions

About this article

Cite this article

Houk, K., Cheong, PY. Computational prediction of small-molecule catalysts. Nature 455, 309–313 (2008). https://doi.org/10.1038/nature07368

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nature07368

This article is cited by

Search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing