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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

Initial and final energy profiles forMPP hydrolysis. Final profilesare averaged over the regions indicated inside the boxes from Figure 13. Bars show standard deviation.
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fig14: Initial and final energy profiles forMPP hydrolysis. Final profilesare averaged over the regions indicated inside the boxes from Figure 13. Bars show standard deviation.

Mentions: Energies of the transitionstates found by reference and ML stringsare comparable (Figure 14); however, basinsexhibit differences because of hydrogen bonding rearrangements ofwater. This is more prominent in the product basin where the ML schemefinds more favorable interactions between the catalytic water andmagnesium ion. To verify that these are indeed PM6 solutions, we switchoff ML and continue PM6 string simulations for another 20 iterations.The path remains stable. We estimate activation barrier and the reactionenthalpy as 8.0 and −14.8 kcal/mol. While the level of theoryand limited solvent representation employed here preclude drawingconclusions about the reaction, the simulations show that the ML preconditioningscheme can accelerate convergence of complex systems at room temperature.A caveat is that, achieving this speedup requires averaging the displacementsand the correction term to control the noise, which the preconditioningamplifies.


Finding Chemical Reaction Paths with a Multilevel Preconditioning Protocol.

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

Initial and final energy profiles forMPP hydrolysis. Final profilesare averaged over the regions indicated inside the boxes from Figure 13. Bars show standard deviation.
© Copyright Policy
Related In: Results  -  Collection

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

fig14: Initial and final energy profiles forMPP hydrolysis. Final profilesare averaged over the regions indicated inside the boxes from Figure 13. Bars show standard deviation.
Mentions: Energies of the transitionstates found by reference and ML stringsare comparable (Figure 14); however, basinsexhibit differences because of hydrogen bonding rearrangements ofwater. This is more prominent in the product basin where the ML schemefinds more favorable interactions between the catalytic water andmagnesium ion. To verify that these are indeed PM6 solutions, we switchoff ML and continue PM6 string simulations for another 20 iterations.The path remains stable. We estimate activation barrier and the reactionenthalpy as 8.0 and −14.8 kcal/mol. While the level of theoryand limited solvent representation employed here preclude drawingconclusions about the reaction, the simulations show that the ML preconditioningscheme can accelerate convergence of complex systems at room temperature.A caveat is that, achieving this speedup requires averaging the displacementsand the correction term to control the noise, which the preconditioningamplifies.

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