Benchmarking quantum mechanical methods for calculating reaction energies of reactions catalyzed by enzymes

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Edited by our new EiC @janhjensen, “Benchmarking quantum mechanical methods for calculating reaction energies of reactions catalyzed by enzymes” has accrued 7 citations and 3.7k views since being published in PeerJ Physical Chemistry https://t.co/eE3O3XcgUx
Edited by our new EiC @janhjensen, “Benchmarking quantum mechanical methods for calculating reaction energies of reactions catalyzed by enzymes” has accrued 7 citations and 3.7k views since being published in PeerJ Physical Chemistry https://t.co/kZqWGx7NY0
RT @janhjensen: An article I handled as editor has been published today @PeerJPhysChem: Benchmarking quantum mechanical methods for calcu…
RT @janhjensen: An article I handled as editor has been published today @PeerJPhysChem: Benchmarking quantum mechanical methods for calcu…
RT @janhjensen: An article I handled as editor has been published today @PeerJPhysChem: Benchmarking quantum mechanical methods for calcu…
RT @AdrianMulholla1: Benchmarking quantum mechanical methods for calculating reaction energies for enzymes: Jitnapa Sirirak, @narinlawan @m…
1779 days ago
RT @AdrianMulholla1: Benchmarking quantum mechanical methods for calculating reaction energies for enzymes: Jitnapa Sirirak, @narinlawan @m…
RT @AdrianMulholla1: Benchmarking quantum mechanical methods for calculating reaction energies for enzymes: Jitnapa Sirirak, @narinlawan @m…
RT @AdrianMulholla1: Benchmarking quantum mechanical methods for calculating reaction energies for enzymes: Jitnapa Sirirak, @narinlawan @m…
RT @AdrianMulholla1: Benchmarking quantum mechanical methods for calculating reaction energies for enzymes: Jitnapa Sirirak, @narinlawan @m…
RT @AdrianMulholla1: Benchmarking quantum mechanical methods for calculating reaction energies for enzymes: Jitnapa Sirirak, @narinlawan @m…
1779 days ago
RT @AdrianMulholla1: Benchmarking quantum mechanical methods for calculating reaction energies for enzymes: Jitnapa Sirirak, @narinlawan @m…
RT @AdrianMulholla1: Benchmarking quantum mechanical methods for calculating reaction energies for enzymes: Jitnapa Sirirak, @narinlawan @m…
1779 days ago
RT @AdrianMulholla1: Benchmarking quantum mechanical methods for calculating reaction energies for enzymes: Jitnapa Sirirak, @narinlawan @m…
RT @AdrianMulholla1: Benchmarking quantum mechanical methods for calculating reaction energies for enzymes: Jitnapa Sirirak, @narinlawan @m…
RT @AdrianMulholla1: Benchmarking quantum mechanical methods for calculating reaction energies for enzymes: Jitnapa Sirirak, @narinlawan @m…
1779 days ago
RT @AdrianMulholla1: Benchmarking quantum mechanical methods for calculating reaction energies for enzymes: Jitnapa Sirirak, @narinlawan @m…
Benchmarking quantum mechanical methods for calculating reaction energies for enzymes: Jitnapa Sirirak, @narinlawan @marcvanderkamp and Jeremy Harvey @PeerJPhysChem https://t.co/II9vtE6D9J #Catalysis #QM #enzyme #TheoreticalandComputationalChemistry
RT @janhjensen: An article I handled as editor has been published today @PeerJPhysChem: Benchmarking quantum mechanical methods for calcu…
1779 days ago
My article has been published today in @PeerJPhysChem https://t.co/i4qYD84n6s #Catalysis #TheoreticalandComputationalChemistry
1779 days ago
An article I handled as editor has been published today @PeerJPhysChem: Benchmarking quantum mechanical methods for calculating reaction energies of reactions catalyzed by enzymes https://t.co/KmHdfFpfhm #compchem
PeerJ Physical Chemistry

Main article text

 

Introduction

Materials & Methods

Results

Discussion

Conclusions

Supplemental Information

Molecular xyz coordinates

DOI: 10.7717/peerj-pchem.8/supp-1

Coordinates of 29 molecules optimized at the B3LYP/6-311+G(d) level

DOI: 10.7717/peerj-pchem.8/supp-2

Molecular energies of molecular No.1 (M1) to molecular No.29 (M29) (in kcal mol−1) calculated by 24 QM methods using the structure optimized at the B3LYP/6-311+G(d) level as starting structures

DOI: 10.7717/peerj-pchem.8/supp-3

Reaction energies (in kcal mol−1) of reaction 1–20 calculated by 24 quantum mechanics methods

DOI: 10.7717/peerj-pchem.8/supp-4

Errors of reaction energies (in kcal mol−1) of reaction 1–20, relative to the CCSD(T)/aug-cc-pVTZ results

DOI: 10.7717/peerj-pchem.8/supp-5

Mean signed errors, standard deviations, maximum errors and minimum errors along with their reaction number (Rxn No.) of reaction energies (in kcal mol−1) of reaction 1–20

The absolute errors are given relative to the CCSD(T)/aug-cc-pVTZ results

DOI: 10.7717/peerj-pchem.8/supp-6

Absolute errors, mean absolute errors and standard deviations of reaction energies (in kcal mol−1) of reaction 1–20. The absolute errors are given relative to the CCSD(T)/aug-cc-pVTZ results

DOI: 10.7717/peerj-pchem.8/supp-7

Comparison of mean absolute errors (MAEs), standard deviations (SDs), large absolute errors (LAEs) with reaction number (Rxn No.), and coefficient of determinations (R2) of reaction energies groups

Three groups of reaction energies include reaction 1–20, proton transfer reactions (reaction 1–13), and non-proton transfer reactions. The mean absolute errors and coefficient of determinations (R2) were given in relative to the CCSD(T)/aug-cc-pVTZ in kcal mol−1.

DOI: 10.7717/peerj-pchem.8/supp-8

Additional Information and Declarations

Competing Interests

The authors declare there are no competing interests.

Author Contributions

Jitnapa Sirirak and Marc W. Van der Kamp performed the experiments, analyzed the data, performed the computation work, prepared figures and/or tables, authored or reviewed drafts of the paper, and approved the final draft.

Narin Lawan, Jeremy N. Harvey and Adrian J. Mulholland performed the computation work, authored or reviewed drafts of the paper, and approved the final draft.

Data Availability

The following information was supplied regarding data availability:

The raw data are available in the Supplementary Files.

Funding

This work was supported by EPSRC (grant numbers EP/M022609/1 and EP/M013219/1), BBSRC (BB/M026280/1, BB/R001332/1), Chiang Mai University, and the Royal Thai Government Scholarship. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

13 Citations 4,672 Views 1,444 Downloads

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