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Behn A, Zimmerman PM, Bell AT, et al. Incorporating Linear Synchronous Transit Interpolation into the Growing String Method: Algorithm and Applications. J Chem Theory Comput. 2011;7(12):4019-25doi: 10.1021/ct200654u.
Behn, A., Zimmerman, P. M., Bell, A. T., & Head-Gordon, M. (2011). Incorporating Linear Synchronous Transit Interpolation into the Growing String Method: Algorithm and Applications. Journal of chemical theory and computation, 7(12), 4019-25. https://doi.org/10.1021/ct200654u
Behn, Andrew, et al. "Incorporating Linear Synchronous Transit Interpolation into the Growing String Method: Algorithm and Applications." Journal of chemical theory and computation vol. 7,12 (2011): 4019-25. doi: https://doi.org/10.1021/ct200654u
Behn A, Zimmerman PM, Bell AT, Head-Gordon M. Incorporating Linear Synchronous Transit Interpolation into the Growing String Method: Algorithm and Applications. J Chem Theory Comput. 2011 Dec 13;7(12):4019-25. doi: 10.1021/ct200654u. Epub 2011 Nov 29. PMID: 26598348.
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J Chem Theory Comput. 2011 Dec 13;7(12):4019-25. doi: 10.1021/ct200654u. Epub 2011 Nov 29.

Incorporating Linear Synchronous Transit Interpolation into the Growing String Method: Algorithm and Applications.

Journal of chemical theory and computation

Andrew Behn, Paul M Zimmerman, Alexis T Bell, Martin Head-Gordon

Affiliations

  1. Department of Chemical and Biomolecular Engineering and ‡Department of Chemistry, University of California , Berkeley, California 94720-1462, United States.

PMID: 26598348 DOI: 10.1021/ct200654u

Abstract

The growing string method is a powerful tool in the systematic study of chemical reactions with theoretical methods which allows for the rapid identification of transition states connecting known reactant and product structures. However, the efficiency of this method is heavily influenced by the choice of interpolation scheme when adding new nodes to the string during optimization. In particular, the use of Cartesian coordinates with cubic spline interpolation often produces guess structures which are far from the final reaction path and require many optimization steps (and thus many energy and gradient calculations) to yield a reasonable final structure. In this paper, we present a new method for interpolating and reparameterizing nodes within the growing string method using the linear synchronous transit method of Halgren and Lipscomb. When applied to the alanine dipeptide rearrangement and a simplified cationic alkyl ring condensation reaction, a significant speedup in terms of computational cost is achieved (30-50%).

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