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Efficient exploration of reaction paths via a freezing string method
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10.1063/1.3664901
/content/aip/journal/jcp/135/22/10.1063/1.3664901
http://aip.metastore.ingenta.com/content/aip/journal/jcp/135/22/10.1063/1.3664901

Figures

Image of FIG. 1.
FIG. 1.

Algorithm flowchart for the freezing string method with parameter definitions.

Image of FIG. 2.
FIG. 2.

Cartoon depiction of the FSM algorithm on the MB potential energy surface.

Image of FIG. 3.
FIG. 3.

An illustration of the practical operation of FSM: strings on the MB 2D potential energy surface with increasing number of perpendicular steps taken (inward step size held constant, 1 to 15 perpendicular gradients). As the number of gradients increases, the string approaches the minimum energy path.

Image of FIG. 4.
FIG. 4.

An illustration of the operation of FSM in practice: FSM strings on the MB 2D potential energy surface with decreasing inward step size on the string (number of perpendicular gradients is held constant at 3). As the number of nodes increases, the string appears to approach the minimum energy pathway.

Image of FIG. 5.
FIG. 5.

Structures of the minima and transition states for the reaction cis,cis-2,4-hexadiene to trans-3,4-dimethylcyclobutene. All energies shown are relative to the reactant structure.

Image of FIG. 6.
FIG. 6.

Exact IRC, FSM with large and small spacing, and GSM strings plotted in reduced coordinates for the conversion of cis,cis-2,4-hexadiene to trans-3,4-dimethylcyclobutene. The first frame corresponds to cartesian interpolation FSM and GSM, while the second frame corresponds to LST interpolation. The circled nodes of the FSM and GSM strings correspond to those taken as the transition state guess structures for further refinement.

Image of FIG. 7.
FIG. 7.

Reactant, transition state, and product structures for the alanine dipeptide rearrangement. The angles ϕ and ψ denote the important dihedral angle rotations of this reaction pathway.

Image of FIG. 8.
FIG. 8.

Reduced coordinates plots of the exact IRC, FSM strings with large and small spacing, and the first fully grown GSM string of the alanine dipeptide rearrangement. The first frame corresponds to cartesian interpolation FSM and GSM, while the second frame corresponds to LST interpolation. The dihedral angles plotted are illustrated in Figure 7. The circled nodes of the FSM and GSM strings correspond to those taken as the transition state guess structures for further refinement.

Image of FIG. 9.
FIG. 9.

Energy profiles of the final FSM strings, the first fully grown GSM string, and the exact IRC for the alanine dipeptide conformational transition. The top frame corresponds to FSM and GSM performed with cartesian interpolation, while the second frame corresponds to LST interpolation.

Image of FIG. 10.
FIG. 10.

Reactant, TS, and product for ethylene dimerization in the Ni zeolite.

Tables

Generic image for table
Table I.

Qualitative comparison of FSM and GSM methods.

Generic image for table
Table II.

Comparison of the number of QM gradient calculations necessary to complete the FSM for large and small step sizes, as well as to converge the corresponding GSM calculations for all three example applications. The FSM was performed with interpolation spacings of 1/10th and 1/20th the initial distance from reactant to product for the large and small step FSM runs, respectively, a scaling factor of γ = 1.75 hartree/Å2, and 3 optimization steps. GSM was performed with 11 nodes and a scaling factor of γ = 5.0 hartree/Å2.

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/content/aip/journal/jcp/135/22/10.1063/1.3664901
2011-12-13
2014-04-25
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752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: Efficient exploration of reaction paths via a freezing string method
http://aip.metastore.ingenta.com/content/aip/journal/jcp/135/22/10.1063/1.3664901
10.1063/1.3664901
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