Performance of Density-Functional Tight-Binding in Comparison to Ab Initio and First-Principles Methods for Isomer Geometries and Energies of Glucose Epimers in Vacuo and Solution

Lee, Ka Hung; Schnupf, Udo; Sumpter, Bobby G.; Irle, Stephan

doi:10.1021/acsomega.8b02213

Title: Performance of Density-Functional Tight-Binding in Comparison to Ab Initio and First-Principles Methods for Isomer Geometries and Energies of Glucose Epimers in Vacuo and Solution

Abstract

Density functional theory (DFT) is a widely used methodology for the computation of molecular and electronic structure, and we confirm that B3LYP and the high-level ab initio G3B3 method are in excellent agreement for the lowestenergy isomers of the 16 glucose epimers. Density-functional tight-binding (DFTB) is an approximate version of DFT with typically comparable accuracy that is 2 to 3 orders of magnitude faster, therefore generally very suitable for processing large numbers of complex structures. Conformational isomerism in sugars is well known to give rise to a large number of isomer structures. On the basis of a comprehensive study of glucose epimers in vacuo and aqueous solution, we found that the performance of DFTB is on par to B3LYP in terms of geometrical parameters excluding hydrogen bonds and isomer energies. However, DFTB underestimates both hydrogen bonding interactions as well as torsional barriers associated with rotations of the hydroxy groups, resulting in a counterintuitive overemphasis of hydrogen bonding in both gas phase as well as in water. Although the associated root mean squared deviation from B3LYP within epimer isomer groups is only on the order of 1 kcal/mol, this deviation affects the correct assignment of major isomer ordering, which span lessmore »« less

Authors:

^[1]; Schnupf, Udo ^[2];

;

^[3]

Department of Chemistry, Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan, Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, Tennessee 37996, United States
Department of Chemistry and Biochemistry, Bradley University, Peoria, Illinois 61625, United States
Department of Chemistry, Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan

Publication Date:: Fri Dec 07 00:00:00 EST 2018

Research Org.:: Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)

Sponsoring Org.:: USDOE Office of Science (SC), Basic Energy Sciences (BES)

OSTI Identifier:: 1484977

Alternate Identifier(s):: OSTI ID: 1488722; OSTI ID: 1508802

Grant/Contract Number:: AC05-00OR22725; AC02-05CH11231

Resource Type:: Published Article

Journal Name:: ACS Omega

Additional Journal Information:: Journal Name: ACS Omega Journal Volume: 3 Journal Issue: 12; Journal ID: ISSN 2470-1343

Publisher:: American Chemical Society

Country of Publication:: United States

Language:: English

Subject:: 37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY; 59 BASIC BIOLOGICAL SCIENCES; Carbohydrates; Electronic structure; Molecular structure; Potential energy; Quantum mechanical methods; Thermodynamic properties

Citation Formats


                    Lee, Ka Hung, Schnupf, Udo, Sumpter, Bobby G., and Irle, Stephan. Performance of Density-Functional Tight-Binding in Comparison to Ab Initio and First-Principles Methods for Isomer Geometries and Energies of Glucose Epimers in Vacuo and Solution.  United States: N. p., 2018. 
Web.  doi:10.1021/acsomega.8b02213.

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                    Lee, Ka Hung, Schnupf, Udo, Sumpter, Bobby G., & Irle, Stephan. Performance of Density-Functional Tight-Binding in Comparison to Ab Initio and First-Principles Methods for Isomer Geometries and Energies of Glucose Epimers in Vacuo and Solution.  United States.  https://doi.org/10.1021/acsomega.8b02213

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                    Lee, Ka Hung, Schnupf, Udo, Sumpter, Bobby G., and Irle, Stephan. Fri .  
"Performance of Density-Functional Tight-Binding in Comparison to Ab Initio and First-Principles Methods for Isomer Geometries and Energies of Glucose Epimers in Vacuo and Solution".  United States.  https://doi.org/10.1021/acsomega.8b02213.

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@article{osti_1484977,

  title        = {Performance of Density-Functional Tight-Binding in Comparison to Ab Initio and First-Principles Methods for Isomer Geometries and Energies of Glucose Epimers in Vacuo and Solution},

  author       = {Lee, Ka Hung and Schnupf, Udo and Sumpter, Bobby G. and Irle, Stephan},

  abstractNote = {Density functional theory (DFT) is a widely used methodology for the computation of molecular and electronic structure, and we confirm that B3LYP and the high-level ab initio G3B3 method are in excellent agreement for the lowestenergy isomers of the 16 glucose epimers. Density-functional tight-binding (DFTB) is an approximate version of DFT with typically comparable accuracy that is 2 to 3 orders of magnitude faster, therefore generally very suitable for processing large numbers of complex structures. Conformational isomerism in sugars is well known to give rise to a large number of isomer structures. On the basis of a comprehensive study of glucose epimers in vacuo and aqueous solution, we found that the performance of DFTB is on par to B3LYP in terms of geometrical parameters excluding hydrogen bonds and isomer energies. However, DFTB underestimates both hydrogen bonding interactions as well as torsional barriers associated with rotations of the hydroxy groups, resulting in a counterintuitive overemphasis of hydrogen bonding in both gas phase as well as in water. Although the associated root mean squared deviation from B3LYP within epimer isomer groups is only on the order of 1 kcal/mol, this deviation affects the correct assignment of major isomer ordering, which span less than 10 kcal/mol. Both second- as well as third-order DFTB methods are exhibiting similar deviations from B3LYP. Even after the inclusion of empirical dispersion corrections in vacuum, these deviations remain for a large majority of isomer energies and geometries when compared to dispersion-corrected B3LYP.},

  doi          = {10.1021/acsomega.8b02213},

  journal      = {ACS Omega},

  number       = 12,

  volume       = 3,

  place        = {United States},

  year         = {Fri Dec 07 00:00:00 EST 2018},

  month        = {Fri Dec 07 00:00:00 EST 2018}

}

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Figure 1.: Chair conformations of ⁴C₁ D-aldopyranoses.

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Works referencing / citing this record:

Artificial neural network correction for density-functional tight-binding molecular dynamics simulations
journal, June 2019

Zhu, Junmian; Vuong, Van Quan; Sumpter, Bobby G.
MRS Communications, Vol. 9, Issue 3
DOI: 10.1557/mrc.2019.80

Artificial neural network correction for density-functional tight-binding molecular dynamics simulations
journal, June 2019

Zhu, Junmian; Vuong, Van Quan; Sumpter, Bobby G.
MRS Communications, Vol. 9, Issue 3
DOI: 10.1557/mrc.2019.80

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Title: Performance of Density-Functional Tight-Binding in Comparison to Ab Initio and First-Principles Methods for Isomer Geometries and Energies of Glucose Epimers in Vacuo and Solution

Abstract

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