Limits...
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

Diagram of hydrolysis of MPP catalyzed by twowater molecules.Arrows indicate directions of electron pair movements. Nucleophilicand catalytic water molecules are indicated.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4263463&req=5

fig10: Diagram of hydrolysis of MPP catalyzed by twowater molecules.Arrows indicate directions of electron pair movements. Nucleophilicand catalytic water molecules are indicated.

Mentions: We consider hydrolysis in thepresence of two water molecules,one nucleophilic and the other catalytic (Figure 10). For visualization purposes only, the reaction path is projectedonto the breaking and forming oxygen–phosphate distances, thoseof the β-phosphorus with the anhydride bridging or the nucleophilicwater oxygens (Figure 11). This representationis known as a More O’Ferrall–Jencks (MOFJ) plot. A perfectlyassociative reaction corresponds to a path that goes through the lowerleft corner, while a perfectly dissociative path would go throughthe upper right corner.


Finding Chemical Reaction Paths with a Multilevel Preconditioning Protocol.

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

Diagram of hydrolysis of MPP catalyzed by twowater molecules.Arrows indicate directions of electron pair movements. Nucleophilicand catalytic water molecules are indicated.
© Copyright Policy
Related In: Results  -  Collection

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

fig10: Diagram of hydrolysis of MPP catalyzed by twowater molecules.Arrows indicate directions of electron pair movements. Nucleophilicand catalytic water molecules are indicated.
Mentions: We consider hydrolysis in thepresence of two water molecules,one nucleophilic and the other catalytic (Figure 10). For visualization purposes only, the reaction path is projectedonto the breaking and forming oxygen–phosphate distances, thoseof the β-phosphorus with the anhydride bridging or the nucleophilicwater oxygens (Figure 11). This representationis known as a More O’Ferrall–Jencks (MOFJ) plot. A perfectlyassociative reaction corresponds to a path that goes through the lowerleft corner, while a perfectly dissociative path would go throughthe upper right corner.

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