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Finding Chemical Reaction Paths with a Multilevel Preconditioning Protocol.

Kale S, Sode O, Weare J, Dinner AR - J Chem Theory Comput (2014)

Bottom Line: Chem.Phys. 2014, 140, 184114) can be used to accelerate quantum-chemical string calculations.The approach also shows promise for free energy calculations when thermal noise can be controlled.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry, James Franck Institute, Institute for Biophysical Dynamics, Computation Institute, Department of Statistics, University of Chicago , Chicago, Illinois 60637, United States ; Department of Chemistry, James Franck Institute, Institute for Biophysical Dynamics, Computation Institute, Department of Statistics, University of Chicago , Chicago, Illinois 60637, United States.

ABSTRACT

Finding transition paths for chemical reactions can be computationally costly owing to the level of quantum-chemical theory needed for accuracy. Here, we show that a multilevel preconditioning scheme that was recently introduced (Tempkin et al. J. Chem. Phys. 2014, 140, 184114) can be used to accelerate quantum-chemical string calculations. We demonstrate the method by finding minimum-energy paths for two well-characterized reactions: tautomerization of malonaldehyde and Claissen rearrangement of chorismate to prephanate. For these reactions, we show that preconditioning density functional theory (DFT) with a semiempirical method reduces the computational cost for reaching a converged path that is an optimum under DFT by several fold. The approach also shows promise for free energy calculations when thermal noise can be controlled.

No MeSH data available.


Related in: MedlinePlus

Convergence of the malonaldehydetautomerization for the stringmethod with only DFT (black) and in the ML preconditioning schemewith various inexpensive P models (red, PM3; green, PM6; and blue,SCC-DFTB). Progress is measured by the norm of the net string displacementas projected on the CV subspace and averaged over all images. Insetshows reaction diagram.
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fig5: Convergence of the malonaldehydetautomerization for the stringmethod with only DFT (black) and in the ML preconditioning schemewith various inexpensive P models (red, PM3; green, PM6; and blue,SCC-DFTB). Progress is measured by the norm of the net string displacementas projected on the CV subspace and averaged over all images. Insetshows reaction diagram.

Mentions: Potential energy profilesalong the string for the malonaldehydetautomerization after 100 R- or P-only (A) or 20 ML (B) iterationsof refinement. Color convention is as in Figure 5. The predicted barrier height is ≈1.32 kcal/mol. Energiesfrom geometry optimization are indicated with orange dashed lines.


Finding Chemical Reaction Paths with a Multilevel Preconditioning Protocol.

Kale S, Sode O, Weare J, Dinner AR - J Chem Theory Comput (2014)

Convergence of the malonaldehydetautomerization for the stringmethod with only DFT (black) and in the ML preconditioning schemewith various inexpensive P models (red, PM3; green, PM6; and blue,SCC-DFTB). Progress is measured by the norm of the net string displacementas projected on the CV subspace and averaged over all images. Insetshows reaction diagram.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4263463&req=5

fig5: Convergence of the malonaldehydetautomerization for the stringmethod with only DFT (black) and in the ML preconditioning schemewith various inexpensive P models (red, PM3; green, PM6; and blue,SCC-DFTB). Progress is measured by the norm of the net string displacementas projected on the CV subspace and averaged over all images. Insetshows reaction diagram.
Mentions: Potential energy profilesalong the string for the malonaldehydetautomerization after 100 R- or P-only (A) or 20 ML (B) iterationsof refinement. Color convention is as in Figure 5. The predicted barrier height is ≈1.32 kcal/mol. Energiesfrom geometry optimization are indicated with orange dashed lines.

Bottom Line: Chem.Phys. 2014, 140, 184114) can be used to accelerate quantum-chemical string calculations.The approach also shows promise for free energy calculations when thermal noise can be controlled.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry, James Franck Institute, Institute for Biophysical Dynamics, Computation Institute, Department of Statistics, University of Chicago , Chicago, Illinois 60637, United States ; Department of Chemistry, James Franck Institute, Institute for Biophysical Dynamics, Computation Institute, Department of Statistics, University of Chicago , Chicago, Illinois 60637, United States.

ABSTRACT

Finding transition paths for chemical reactions can be computationally costly owing to the level of quantum-chemical theory needed for accuracy. Here, we show that a multilevel preconditioning scheme that was recently introduced (Tempkin et al. J. Chem. Phys. 2014, 140, 184114) can be used to accelerate quantum-chemical string calculations. We demonstrate the method by finding minimum-energy paths for two well-characterized reactions: tautomerization of malonaldehyde and Claissen rearrangement of chorismate to prephanate. For these reactions, we show that preconditioning density functional theory (DFT) with a semiempirical method reduces the computational cost for reaching a converged path that is an optimum under DFT by several fold. The approach also shows promise for free energy calculations when thermal noise can be controlled.

No MeSH data available.


Related in: MedlinePlus