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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 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.
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fig4: 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.

Mentions: We use as CVs the oxygen–hydrogen distancesof the breakingand forming bonds, rO1H* and rO2H* where H* denotes the sharedproton. All four force fields in this study predict approximatelycircular, symmetric arcs for the reaction path projected onto thesecoordinates (Figure 3A). The ML runs relaxto the same circular arc as does the BLYP simulation (Figure 3B), passing through the saddle at rO1H* = rO2H* = 1.22 Å in agreement with earlier BLYP findings (1.223Å via DZP38 and 1.227 Å via cc-pVTZ37). The barrier heights for the converged pathsare fairly close to each other at ≈1.32 kcal/mol even thoughP-only predictions are different by up to an orderof magnitude (Figure 4). BLYP is known to underestimatethis barrier, particularly with smaller basis sets;37 our DZVP value falls in between the published values of1.0 kcal/mol via DZP38 and 2.0 kcal/molvia cc-pVTZ.37


Finding Chemical Reaction Paths with a Multilevel Preconditioning Protocol.

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

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.
© Copyright Policy
Related In: Results  -  Collection

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

fig4: 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.
Mentions: We use as CVs the oxygen–hydrogen distancesof the breakingand forming bonds, rO1H* and rO2H* where H* denotes the sharedproton. All four force fields in this study predict approximatelycircular, symmetric arcs for the reaction path projected onto thesecoordinates (Figure 3A). The ML runs relaxto the same circular arc as does the BLYP simulation (Figure 3B), passing through the saddle at rO1H* = rO2H* = 1.22 Å in agreement with earlier BLYP findings (1.223Å via DZP38 and 1.227 Å via cc-pVTZ37). The barrier heights for the converged pathsare fairly close to each other at ≈1.32 kcal/mol even thoughP-only predictions are different by up to an orderof magnitude (Figure 4). BLYP is known to underestimatethis barrier, particularly with smaller basis sets;37 our DZVP value falls in between the published values of1.0 kcal/mol via DZP38 and 2.0 kcal/molvia cc-pVTZ.37

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