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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

Potential energy profiles for the Claissen rearrangement. (A) PBE,PM3, and BLYP alone. (B) PBE compared with the results from the MLscheme with PM3 (green) and BLYP (blue) preconditioning. Energiesfrom geometry optimization are indicated with orange dashed lines.
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fig8: Potential energy profiles for the Claissen rearrangement. (A) PBE,PM3, and BLYP alone. (B) PBE compared with the results from the MLscheme with PM3 (green) and BLYP (blue) preconditioning. Energiesfrom geometry optimization are indicated with orange dashed lines.

Mentions: The initial and finalpaths predicted by the two DFT methods indeedresemble each other more closely than that of PM3 (Figure 7A). Starting from an initial linear interpolation(black), both PBE (red) and BLYP (blue) converge to an extended transitionstate characterized by simultaneously long CO and CC distances aroundcentral images. PM3 (green), on the other hand, predicts a compacttransition state, and the bonds that are ruptured maintain their covalentcharacter longer as indicated by their near-equilibrium distances(∼1.5 Å) in the basins. In comparison, all final ML pathsagree fairly well with the PBE prediction (Figure 7B) as well as the basin and saddle points from geometry optimization(orange). As for the energies, PBE predicts the activation barrierand reaction enthalpy to be 22.0 and −19.7 kcal/mol (Figure 8A, red), which is close to earlier estimates of17.5 and −20.8 kcal/mol, respectively, using the same basisset but a lower plane wave cutoff and different software.20 The BLYP and PBE barriers are similar (19.0and −17.2 kcal/mol, respectively), while the PM3 barrier isfar higher (53.1 kcal/mol; the reaction enthalpy is −23.9 kcal/mol).ML energies (Figure 8B) are comparable withPBE.


Finding Chemical Reaction Paths with a Multilevel Preconditioning Protocol.

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

Potential energy profiles for the Claissen rearrangement. (A) PBE,PM3, and BLYP alone. (B) PBE compared with the results from the MLscheme with PM3 (green) and BLYP (blue) preconditioning. Energiesfrom geometry optimization are indicated with orange dashed lines.
© Copyright Policy
Related In: Results  -  Collection

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

fig8: Potential energy profiles for the Claissen rearrangement. (A) PBE,PM3, and BLYP alone. (B) PBE compared with the results from the MLscheme with PM3 (green) and BLYP (blue) preconditioning. Energiesfrom geometry optimization are indicated with orange dashed lines.
Mentions: The initial and finalpaths predicted by the two DFT methods indeedresemble each other more closely than that of PM3 (Figure 7A). Starting from an initial linear interpolation(black), both PBE (red) and BLYP (blue) converge to an extended transitionstate characterized by simultaneously long CO and CC distances aroundcentral images. PM3 (green), on the other hand, predicts a compacttransition state, and the bonds that are ruptured maintain their covalentcharacter longer as indicated by their near-equilibrium distances(∼1.5 Å) in the basins. In comparison, all final ML pathsagree fairly well with the PBE prediction (Figure 7B) as well as the basin and saddle points from geometry optimization(orange). As for the energies, PBE predicts the activation barrierand reaction enthalpy to be 22.0 and −19.7 kcal/mol (Figure 8A, red), which is close to earlier estimates of17.5 and −20.8 kcal/mol, respectively, using the same basisset but a lower plane wave cutoff and different software.20 The BLYP and PBE barriers are similar (19.0and −17.2 kcal/mol, respectively), while the PM3 barrier isfar higher (53.1 kcal/mol; the reaction enthalpy is −23.9 kcal/mol).ML energies (Figure 8B) are comparable withPBE.

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