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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

Reaction diagram for malonaldehyde tautomerization.Arrows indicatethe flow of electron pairs.
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fig1: Reaction diagram for malonaldehyde tautomerization.Arrows indicatethe flow of electron pairs.

Mentions: In this article,we explore an analogous procedure for quantumchemical calculations. Here, a less computationally expensive, presumablyless accurate method plays the role of the CG model and a more computationallyexpensive, presumably more accurate model plays the role of the FGmodel. An advantage in this context is that both models have the samenumber of degrees of freedom, simplifying their coupling. Hence, throughoutthe paper we refer to them as the reference (R) and preconditioning(P) levels of theory. We first demonstrate that our multilevel schemeaccelerates refinement of the minimum energy paths of two chemicalreactions: tautomerization of malonaldehyde (Figure 1) and Claissen rearrangement of chorismate to prephanate (Figure 2). We choose these reactions because they have servedas prototypes for intrinsic reaction coordinate search and the reactionprogress can be readily traced via the chemical bonds formed and broken.19,20 We then illustrate how the approach can be extended to room-temperaturefree energy simulations with a phosphate hydrolysis reaction. Whileour approach is general, we specifically employ the string methodfor finding reaction paths; our preconditioning couples density functionaltheory (DFT) with semiempirical (SE) force fields. We provide evidencethat better correspondence between the models leads to greater reductionin the number of iterations.


Finding Chemical Reaction Paths with a Multilevel Preconditioning Protocol.

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

Reaction diagram for malonaldehyde tautomerization.Arrows indicatethe flow of electron pairs.
© Copyright Policy
Related In: Results  -  Collection

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

fig1: Reaction diagram for malonaldehyde tautomerization.Arrows indicatethe flow of electron pairs.
Mentions: In this article,we explore an analogous procedure for quantumchemical calculations. Here, a less computationally expensive, presumablyless accurate method plays the role of the CG model and a more computationallyexpensive, presumably more accurate model plays the role of the FGmodel. An advantage in this context is that both models have the samenumber of degrees of freedom, simplifying their coupling. Hence, throughoutthe paper we refer to them as the reference (R) and preconditioning(P) levels of theory. We first demonstrate that our multilevel schemeaccelerates refinement of the minimum energy paths of two chemicalreactions: tautomerization of malonaldehyde (Figure 1) and Claissen rearrangement of chorismate to prephanate (Figure 2). We choose these reactions because they have servedas prototypes for intrinsic reaction coordinate search and the reactionprogress can be readily traced via the chemical bonds formed and broken.19,20 We then illustrate how the approach can be extended to room-temperaturefree energy simulations with a phosphate hydrolysis reaction. Whileour approach is general, we specifically employ the string methodfor finding reaction paths; our preconditioning couples density functionaltheory (DFT) with semiempirical (SE) force fields. We provide evidencethat better correspondence between the models leads to greater reductionin the number of iterations.

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