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Title: Finding Chemical Reaction Paths with a Multilevel Preconditioning Protocol

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. In conclusion, the approach also shows promise for free energy calculations when thermal noise can be controlled.

Authors:
 [1];  [2];  [3];  [4]
+ Show Author Affiliations
  1. Univ. of Chicago, IL (United States). Dept. of Chemistry; Univ. of Chicago, IL (United States). James Franck Inst.
  2. Univ. of Chicago, IL (United States). Dept. of Chemistry; Univ. of Chicago, IL (United States). James Franck Inst.; Univ. of Chicago, IL (United States). Inst. for Biophysical Dynamics; Univ. of Chicago, IL (United States). Computation Inst.; Argonne National Lab. (ANL), Argonne, IL (United States)
  3. Univ. of Chicago, IL (United States). James Franck Inst.; Univ. of Chicago, IL (United States). Computation Inst.; Univ. of Chicago, IL (United States). Dept. of Statistics
  4. Univ. of Chicago, IL (United States). Dept. of Chemistry; Univ. of Chicago, IL (United States). James Franck Inst.; Univ. of Chicago, IL (United States). Inst. for Biophysical Dynamics; Univ. of Chicago, IL (United States). Computation Inst.
Publication Date:
Research Org.:
Argonne National Laboratory (ANL), Argonne, IL (United States)
Sponsoring Org.:
USDOE; National Institutes of Health (NIH); National Science Foundation (NSF)
OSTI Identifier:
1261135
Grant/Contract Number:  
CHE-1136709; R01 GM109455-02; S10 RR029030-01; GM109455-02
Resource Type:
Accepted Manuscript
Journal Name:
Journal of Chemical Theory and Computation
Additional Journal Information:
Journal Volume: 10; Journal Issue: 12; Journal ID: ISSN 1549-9618
Publisher:
American Chemical Society
Country of Publication:
United States
Language:
English
Subject:
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY

Citation Formats

Kale, Seyit, Sode, Olaseni, Weare, Jonathan, and Dinner, Aaron R. Finding Chemical Reaction Paths with a Multilevel Preconditioning Protocol. United States: N. p., 2014. Web. doi:10.1021/ct500852y.
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Kale, Seyit, Sode, Olaseni, Weare, Jonathan, & Dinner, Aaron R. Finding Chemical Reaction Paths with a Multilevel Preconditioning Protocol. United States. https://doi.org/10.1021/ct500852y
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Kale, Seyit, Sode, Olaseni, Weare, Jonathan, and Dinner, Aaron R. Fri . "Finding Chemical Reaction Paths with a Multilevel Preconditioning Protocol". United States. https://doi.org/10.1021/ct500852y. https://www.osti.gov/servlets/purl/1261135.
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@article{osti_1261135,
title = {Finding Chemical Reaction Paths with a Multilevel Preconditioning Protocol},
author = {Kale, Seyit and Sode, Olaseni and Weare, Jonathan and Dinner, Aaron R.},
abstractNote = {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. In conclusion, the approach also shows promise for free energy calculations when thermal noise can be controlled.},
doi = {10.1021/ct500852y},
journal = {Journal of Chemical Theory and Computation},
number = 12,
volume = 10,
place = {United States},
year = {Fri Nov 07 00:00:00 EST 2014},
month = {Fri Nov 07 00:00:00 EST 2014}
}
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https://doi.org/10.1021/ct500852y
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Works referenced in this record:

Extending molecular simulation time scales: Parallel in time integrations for high-level quantum chemistry and complex force representations
journal, August 2013

  • Bylaska, Eric J.; Weare, Jonathan Q.; Weare, John H.
  • The Journal of Chemical Physics, Vol. 139, Issue 7
  • DOI: 10.1063/1.4818328

Addressing Open Questions about Phosphate Hydrolysis Pathways by Careful Free Energy Mapping
journal, December 2012

  • Prasad, B. Ram; Plotnikov, Nikolay V.; Warshel, Arieh
  • The Journal of Physical Chemistry B, Vol. 117, Issue 1
  • DOI: 10.1021/jp309778n

Revisiting the finite temperature string method for the calculation of reaction tubes and free energies
journal, May 2009

  • Vanden-Eijnden, Eric; Venturoli, Maddalena
  • The Journal of Chemical Physics, Vol. 130, Issue 19
  • DOI: 10.1063/1.3130083

Spatially distributed stochastic systems: Equation-free and equation-assisted preconditioned computations
journal, November 2006

  • Qiao, Liang; Erban, Radek; Kelley, C. T.
  • The Journal of Chemical Physics, Vol. 125, Issue 20
  • DOI: 10.1063/1.2372492

Why nature really chose phosphate
journal, January 2013

  • Kamerlin, Shina C. L.; Sharma, Pankaz K.; Prasad, Ram B.
  • Quarterly Reviews of Biophysics, Vol. 46, Issue 1
  • DOI: 10.1017/s0033583512000157

Density-functional exchange-energy approximation with correct asymptotic behavior
journal, September 1988

Canonical sampling through velocity-rescaling
text, January 2008

Quantifying the Mechanism of Phosphate Monoester Hydrolysis in Aqueous Solution by Evaluating the Relevant Ab Initio QM/MM Free-Energy Surfaces
journal, May 2013

  • Plotnikov, Nikolay V.; Prasad, B. Ram; Chakrabarty, Suman
  • The Journal of Physical Chemistry B, Vol. 117, Issue 42
  • DOI: 10.1021/jp4020146

Mechanistic Insights into the Hydrolysis of a Nucleoside Triphosphate Model in Neutral and Acidic Solution
journal, April 2012

  • Glaves, Rachel; Mathias, Gerald; Marx, Dominik
  • Journal of the American Chemical Society, Vol. 134, Issue 16
  • DOI: 10.1021/ja2101533

Mapping the transition state for ATP hydrolysis: implications for enzymatic catalysis
journal, November 1995

Efficient Reconstruction of Complex Free Energy Landscapes by Multiple Walkers Metadynamics †
journal, March 2006

  • Raiteri, Paolo; Laio, Alessandro; Gervasio, Francesco Luigi
  • The Journal of Physical Chemistry B, Vol. 110, Issue 8
  • DOI: 10.1021/jp054359r

Optimization methods for finding minimum energy paths
journal, April 2008

  • Sheppard, Daniel; Terrell, Rye; Henkelman, Graeme
  • The Journal of Chemical Physics, Vol. 128, Issue 13
  • DOI: 10.1063/1.2841941

Nonequilibrium umbrella sampling in spaces of many order parameters
journal, February 2009

  • Dickson, Alex; Warmflash, Aryeh; Dinner, Aaron R.
  • The Journal of Chemical Physics, Vol. 130, Issue 7
  • DOI: 10.1063/1.3070677

The path of chemical reactions - the IRC approach
journal, December 1981

A climbing image nudged elastic band method for finding saddle points and minimum energy paths
journal, December 2000

  • Henkelman, Graeme; Uberuaga, Blas P.; Jónsson, Hannes
  • The Journal of Chemical Physics, Vol. 113, Issue 22, p. 9901-9904
  • DOI: 10.1063/1.1329672

Improved tangent estimate in the nudged elastic band method for finding minimum energy paths and saddle points
journal, December 2000

  • Henkelman, Graeme; Jónsson, Hannes
  • The Journal of Chemical Physics, Vol. 113, Issue 22
  • DOI: 10.1063/1.1323224

String method for the study of rare events
journal, August 2002

On-the-fly string method for minimum free energy paths calculation
journal, September 2007

Finding Transition Pathways Using the String Method with Swarms of Trajectories
journal, March 2008

  • Pan, Albert C.; Sezer, Deniz; Roux, Benoît
  • The Journal of Physical Chemistry B, Vol. 112, Issue 11
  • DOI: 10.1021/jp0777059

Phosphorylation Reaction in cAPK Protein Kinase-Free Energy Quantum Mechanical/Molecular Mechanics Simulations
journal, November 2007

  • Valiev, Marat; Yang, Jie; Adams, Joseph A.
  • The Journal of Physical Chemistry B, Vol. 111, Issue 47
  • DOI: 10.1021/jp074853q

Transition Path Sampling Study of the Reaction Catalyzed by Purine Nucleoside Phosphorylase
journal, August 2008

  • Saen-oon, Suwipa; Schramm, Vern L.; Schwartz, Steven D.
  • Zeitschrift für Physikalische Chemie, Vol. 222, Issue 8-9
  • DOI: 10.1524/zpch.2008.5395

Optimization methods for finding minimum energy paths
journal, April 2008

  • Sheppard, Daniel; Terrell, Rye; Henkelman, Graeme
  • The Journal of Chemical Physics, Vol. 128, Issue 13
  • DOI: 10.1063/1.2841941

Pericyclic Reaction Transition States: Passions and Punctilios, 1935-1995
journal, February 1995

  • Houk, Kendall N.; Gonzalez, Javier; Li, Yi
  • Accounts of Chemical Research, Vol. 28, Issue 2
  • DOI: 10.1021/ar00050a004

Using multiscale preconditioning to accelerate the convergence of iterative molecular calculations
journal, May 2014

  • Tempkin, Jeremy O. B.; Qi, Bo; Saunders, Marissa G.
  • The Journal of Chemical Physics, Vol. 140, Issue 18
  • DOI: 10.1063/1.4872021

Spatially distributed stochastic systems: Equation-free and equation-assisted preconditioned computations
journal, November 2006

  • Qiao, Liang; Erban, Radek; Kelley, C. T.
  • The Journal of Chemical Physics, Vol. 125, Issue 20
  • DOI: 10.1063/1.2372492

Estimating the hessian for gradient-type geometry optimizations
journal, January 1984

General methods for geometry and wave function optimization
journal, November 1992

  • Fischer, Thomas H.; Almlof, Jan
  • The Journal of Physical Chemistry, Vol. 96, Issue 24
  • DOI: 10.1021/j100203a036

Motif-based Hessian matrix for ab initio geometry optimization of nanostructures
journal, May 2006

The optimal tunneling path for the proton transfer in malonaldehyde
journal, August 2002

  • Tautermann, Christofer S.; Voegele, Andreas F.; Loerting, Thomas
  • The Journal of Chemical Physics, Vol. 117, Issue 5
  • DOI: 10.1063/1.1488924

A DFT-Based QM-MM Approach Designed for the Treatment of Large Molecular Systems:  Application to Chorismate Mutase
journal, December 2003

  • Crespo, Alejandro; Scherlis, Damián A.; Martí, Marcelo A.
  • The Journal of Physical Chemistry B, Vol. 107, Issue 49
  • DOI: 10.1021/jp036236h

Quickstep: Fast and accurate density functional calculations using a mixed Gaussian and plane waves approach
journal, April 2005

  • VandeVondele, Joost; Krack, Matthias; Mohamed, Fawzi
  • Computer Physics Communications, Vol. 167, Issue 2
  • DOI: 10.1016/j.cpc.2004.12.014

Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density
journal, January 1988

Generalized Gradient Approximation Made Simple
journal, October 1996

  • Perdew, John P.; Burke, Kieron; Ernzerhof, Matthias
  • Physical Review Letters, Vol. 77, Issue 18, p. 3865-3868
  • DOI: 10.1103/PhysRevLett.77.3865

Optimization of Gaussian-type basis sets for local spin density functional calculations. Part I. Boron through neon, optimization technique and validation
journal, February 1992

  • Godbout, Nathalie; Salahub, Dennis R.; Andzelm, Jan
  • Canadian Journal of Chemistry, Vol. 70, Issue 2
  • DOI: 10.1139/v92-079

Optimization of parameters for semiempirical methods I. Method
journal, March 1989

Development and use of quantum mechanical molecular models. 76. AM1: a new general purpose quantum mechanical molecular model
journal, June 1985

  • Dewar, Michael J. S.; Zoebisch, Eve G.; Healy, Eamonn F.
  • Journal of the American Chemical Society, Vol. 107, Issue 13
  • DOI: 10.1021/ja00299a024

Optimization of parameters for semiempirical methods V: Modification of NDDO approximations and application to 70 elements
journal, September 2007

Self-consistent-charge density-functional tight-binding method for simulations of complex materials properties
journal, September 1998

  • Elstner, M.; Porezag, D.; Jungnickel, G.
  • Physical Review B, Vol. 58, Issue 11, p. 7260-7268
  • DOI: 10.1103/PhysRevB.58.7260

Canonical sampling through velocity rescaling
journal, January 2007

  • Bussi, Giovanni; Donadio, Davide; Parrinello, Michele
  • The Journal of Chemical Physics, Vol. 126, Issue 1
  • DOI: 10.1063/1.2408420

A dimer method for finding saddle points on high dimensional potential surfaces using only first derivatives
journal, October 1999

  • Henkelman, Graeme; Jónsson, Hannes
  • The Journal of Chemical Physics, Vol. 111, Issue 15
  • DOI: 10.1063/1.480097

Swift: A language for distributed parallel scripting
journal, September 2011

Revisiting the finite temperature string method for the calculation of reaction tubes and free energies
journal, May 2009

  • Vanden-Eijnden, Eric; Venturoli, Maddalena
  • The Journal of Chemical Physics, Vol. 130, Issue 19
  • DOI: 10.1063/1.3130083

Nonequilibrium umbrella sampling in spaces of many order parameters
journal, February 2009

  • Dickson, Alex; Warmflash, Aryeh; Dinner, Aaron R.
  • The Journal of Chemical Physics, Vol. 130, Issue 7
  • DOI: 10.1063/1.3070677

Predicting proton transfer barriers with density functional methods
journal, June 1999

Proton transfer in the ground and lowest excited states of malonaldehyde: A comparative density functional and post‐Hartree–Fock study
journal, December 1996

  • Barone, Vincenzo; Adamo, Carlo
  • The Journal of Chemical Physics, Vol. 105, Issue 24
  • DOI: 10.1063/1.472900

Critical test of PM3-calculated proton transfer activation energies: a comparison with ab initio and AM1 calculations
journal, March 1998

Tunneling splittings in vibrational spectra of non-rigid molecules
journal, December 2000

Insights into Chorismate Mutase Catalysis from a Combined QM/MM Simulation of the Enzyme Reaction
journal, November 1995

  • Lyne, Paul D.; Mulholland, Adrian J.; Richards, W. Graham
  • Journal of the American Chemical Society, Vol. 117, Issue 45
  • DOI: 10.1021/ja00150a037

Quantifying the Mechanism of Phosphate Monoester Hydrolysis in Aqueous Solution by Evaluating the Relevant Ab Initio QM/MM Free-Energy Surfaces
journal, May 2013

  • Plotnikov, Nikolay V.; Prasad, B. Ram; Chakrabarty, Suman
  • The Journal of Physical Chemistry B, Vol. 117, Issue 42
  • DOI: 10.1021/jp4020146

Addressing Open Questions about Phosphate Hydrolysis Pathways by Careful Free Energy Mapping
journal, December 2012

  • Prasad, B. Ram; Plotnikov, Nikolay V.; Warshel, Arieh
  • The Journal of Physical Chemistry B, Vol. 117, Issue 1
  • DOI: 10.1021/jp309778n

Mechanistic Insights into the Hydrolysis of a Nucleoside Triphosphate Model in Neutral and Acidic Solution
journal, April 2012

  • Glaves, Rachel; Mathias, Gerald; Marx, Dominik
  • Journal of the American Chemical Society, Vol. 134, Issue 16
  • DOI: 10.1021/ja2101533

ATP Hydrolysis in Water − A Density Functional Study
journal, October 2003

  • Akola, J.; Jones, R. O.
  • The Journal of Physical Chemistry B, Vol. 107, Issue 42
  • DOI: 10.1021/jp035538g

Quantum and Classical Dynamics Simulations of ATP Hydrolysis in Solution
journal, June 2012

  • Harrison, Christopher B.; Schulten, Klaus
  • Journal of Chemical Theory and Computation, Vol. 8, Issue 7
  • DOI: 10.1021/ct200886j

Mechanisms of signaling and related enzymes
journal, December 1997

Mapping the transition state for ATP hydrolysis: implications for enzymatic catalysis
journal, November 1995

Well-Tempered Metadynamics: A Smoothly Converging and Tunable Free-Energy Method
journal, January 2008

Efficient Reconstruction of Complex Free Energy Landscapes by Multiple Walkers Metadynamics †
journal, March 2006

  • Raiteri, Paolo; Laio, Alessandro; Gervasio, Francesco Luigi
  • The Journal of Physical Chemistry B, Vol. 110, Issue 8
  • DOI: 10.1021/jp054359r

Extending molecular simulation time scales: Parallel in time integrations for high-level quantum chemistry and complex force representations
journal, August 2013

  • Bylaska, Eric J.; Weare, Jonathan Q.; Weare, John H.
  • The Journal of Chemical Physics, Vol. 139, Issue 7
  • DOI: 10.1063/1.4818328
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