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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

Monotonic relaxation of the potential energy profiles in R-onlyand ML (P: PM3) refinements for malonaldehyde tautomerization. Initialprofiles and first iterations are indicated as m =0 and m = 1, respectively. Last energies (100th R-onlyiteration and 20th ML iteration) are indicated with circles for eachimage. All iterations are shown.
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fig6: Monotonic relaxation of the potential energy profiles in R-onlyand ML (P: PM3) refinements for malonaldehyde tautomerization. Initialprofiles and first iterations are indicated as m =0 and m = 1, respectively. Last energies (100th R-onlyiteration and 20th ML iteration) are indicated with circles for eachimage. All iterations are shown.

Mentions: To visualize the speed of convergence,we plot the norm of thedisplacement vector at each step of the iteration in Figure 5. This quantity shouldapproach zero near convergence. We find that the ML scheme reachesthe BLYP path 3–5 times faster than the R simulation. A similarspeedup can be observed by following the barrier in the energy profilestep-by-step (Figure 6).


Finding Chemical Reaction Paths with a Multilevel Preconditioning Protocol.

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

Monotonic relaxation of the potential energy profiles in R-onlyand ML (P: PM3) refinements for malonaldehyde tautomerization. Initialprofiles and first iterations are indicated as m =0 and m = 1, respectively. Last energies (100th R-onlyiteration and 20th ML iteration) are indicated with circles for eachimage. All iterations are shown.
© Copyright Policy
Related In: Results  -  Collection

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

fig6: Monotonic relaxation of the potential energy profiles in R-onlyand ML (P: PM3) refinements for malonaldehyde tautomerization. Initialprofiles and first iterations are indicated as m =0 and m = 1, respectively. Last energies (100th R-onlyiteration and 20th ML iteration) are indicated with circles for eachimage. All iterations are shown.
Mentions: To visualize the speed of convergence,we plot the norm of thedisplacement vector at each step of the iteration in Figure 5. This quantity shouldapproach zero near convergence. We find that the ML scheme reachesthe BLYP path 3–5 times faster than the R simulation. A similarspeedup can be observed by following the barrier in the energy profilestep-by-step (Figure 6).

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