Article | Published:

Discovering chemistry with an ab initio nanoreactor

Nature Chemistry volume 6, pages 10441048 (2014) | Download Citation

  • A Corrigendum to this article was published on 17 December 2014

This article has been updated

Abstract

Chemical understanding is driven by the experimental discovery of new compounds and reactivity, and is supported by theory and computation that provide detailed physical insight. Although theoretical and computational studies have generally focused on specific processes or mechanistic hypotheses, recent methodological and computational advances harken the advent of their principal role in discovery. Here we report the development and application of the ab initio nanoreactor—a highly accelerated first-principles molecular dynamics simulation of chemical reactions that discovers new molecules and mechanisms without preordained reaction coordinates or elementary steps. Using the nanoreactor, we show new pathways for glycine synthesis from primitive compounds proposed to exist on the early Earth, which provide new insight into the classic Urey–Miller experiment. These results highlight the emergence of theoretical and computational chemistry as a tool for discovery, in addition to its traditional role of interpreting experimental findings.

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Change history

  • 20 November 2014

    In the version of this Article originally published, the list of author affiliations was incomplete, and should have appeared as shown below. The list has been corrected in the online versions of the Article.  Lee-Ping Wang1,2, Alexey Titov1,2✝, Robert McGibbon2, Fang Liu1,2, Vijay S. Pande2 and Todd J. Martínez1,2,3*  1The PULSE Institute, Stanford University, Stanford, California 94305, USA. 2Department of Chemistry, Stanford University, Stanford, California 94305, USA. 3SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA. Present address: Advanced Micro Devices, Sunnyvale, California 94088, USA. *e-mail: toddjmartinez@gmail.com

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Acknowledgements

This work was supported by the National Science Foundation (OCI-1047577), the National Institutes of Health (U54 GM072970) and the Department of Defense through a National Security Science and Engineering Faculty Fellowship from the Office of the Assistant Secretary of Defense for Research and Engineering. This work included calculations performed on the Blue Waters supercomputer at the National Centre for Supercomputing Applications and funded by the National Science Foundation's Office of Cyber Infrastructure. Further computational support was provided by the AMOS program within the Chemical Sciences, Geosciences and Biosciences Division of the Office of Basic Energy Sciences, Office of Science, Department of Energy. We are grateful to E. G. Hohenstein, N. Luehr, S. D. Fried, S. Izmailov, Y. Zhao and C-Y. Wang for helpful suggestions.

Author information

Author notes

    • Alexey Titov

    Present address: Advanced Micro Devices, Sunnyvale, California 94088, USA

Affiliations

  1. The PULSE Institute, Stanford University, Stanford, California 94305, USA

    • Lee-Ping Wang
    • , Alexey Titov
    • , Fang Liu
    •  & Todd J. Martínez
  2. Department of Chemistry, Stanford University, Stanford, California 94305, USA

    • Lee-Ping Wang
    • , Alexey Titov
    • , Robert McGibbon
    • , Fang Liu
    • , Vijay S. Pande
    •  & Todd J. Martínez
  3. SLAC National Accelerator Laboratory, Menlo Park, California 94025, USA

    • Todd J. Martínez

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Contributions

L-P.W., A.T., F.L. and T.J.M. designed the nanoreactor simulation studies. L-P.W., R.M., V.S.P. and T.J.M. designed the energy refinement and network analysis. L.P.W. carried out the simulations and analysis. L-P.W., V.S.P. and T.J.M. co-wrote the manuscript. All authors discussed the results and commented on the manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Todd J. Martínez.

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https://doi.org/10.1038/nchem.2099

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