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References

References

Graph-driven sampling methodology

These papers describe the core principles and ideas of the main reaction-discovery methods implemented in CDE.

  • Sampling reactive pathways with random walks in chemical space: Applications to molecular dissociation and catalysis, S Habershon, Journal of Chemical Physics, 143, 094106 (2015)

  • Automated prediction of catalytic mechanism and rate law using graph-based reaction path sampling, S Habershon, Journal of chemical theory and computation, 12, 1786 (2016)

  • Automatic Proposal of Multistep Reaction Mechanisms using a Graph-Driven Search, I. Ismail, H. B. V. A. Stuttaford-Fowler, C. Ochan Ashok, C. Robertson and S. Habershon, J. Phys. Chem. A, 123, 3407 (2019)

  • Fast screening of homogeneous catalysis mechanisms using graph-driven searches and approximate quantum chemistry, C. Robertson and S. Habershon, Cat. Sci. Tech., dx.doi.org/10.1039/C9CY01997A (in press, 2019)

Minimum energy path refinement.

These papers describe the MEP finding algorithms which are implemented in CDE.

  • Improved tangent estimate in the nudged elastic band method for finding minimum energy paths and saddle points, G. Henkelman and H. Jonsson, Journal of Chemical Physics, 113, 9978 (2000)

  • A climbing image nudged elastic band method for finding saddle points and minimum energy paths, G. Henkelman, B. P. Uberuaga and H. Jonsson, Journal of Chemical Physics, 113, 9901 (2000)

  • An automated nudged elastic band method, E. L. Kolsbjerg, M. N. Groves, and B. Hammer Journal of Chemical Physics, 145, 094107 (2016)

ReaxFF and LAMMPS

  • ReaxFF:  A Reactive Force Field for Hydrocarbons, A. C. T. van Duin and S. Dasgupta and F. Lorant and W. A. Goddard, J. Phys. Chem. A, 105, 9396-9409 (2001) (https://doi.org/10.1021/jp004368u)

  • Information and full documentation on the LAMMPS molecular dynamics code can be found at: https://lammps.sandia.gov