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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

Journal Article · · ACS Omega
ORCiD logo [1]; ORCiD logo [2]; ORCiD logo [3]; ORCiD logo [4]
  1. Nagoya University (Japan); Univ. of Tennessee, Knoxville, TN (United States)
  2. Bradley University, Peoria, IL (United States)
  3. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
  4. Nagoya University (Japan); Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
+ Show Author Affiliations

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 lowest-energy 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.

Research Organization:
Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)
Sponsoring Organization:
USDOE; USDOE Office of Science (SC), Basic Energy Sciences (BES)
Grant/Contract Number:
AC05-00OR22725; AC02-05CH11231
OSTI ID:
1484977
Alternate ID(s):
OSTI ID: 1488722; OSTI ID: 1508802
Journal Information:
ACS Omega, Vol. 3, Issue 12; ISSN 2470-1343
Publisher:
American Chemical Society (ACS)Copyright Statement
Country of Publication:
United States
Language:
English
Citation Metrics:
Cited by: 10 works
Citation information provided by
Web of Science

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Density functional tight binding
  • Elstner, Marcus; Seifert, Gotthard
  • Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, Vol. 372, Issue 2011 https://doi.org/10.1098/rsta.2012.0483
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Improvement of DNA and RNA sugar pucker profiles from semiempirical quantum methods image January 2017
Assessment of Performance of G3B3 and CBS-QB3 Methods in Calculation of Bond Dissociation Energies journal February 2005
Less is more when simulating unsulfated glycosaminoglycan 3D-structure: Comparison of GLYCAM06/TIP3P, PM3-CARB1/TIP3P, and SCC-DFTB-D/TIP3P predictions with experiment journal January 2010
Effect of the damping function in dispersion corrected density functional theory journal March 2011
General atomic and molecular electronic structure system journal November 1993
Possible improvements to the self-consistent-charges density-functional tight-binding method within the second order journal December 2011
The SCC-DFTB method and its application to biological systems journal December 2005
Comparison of the accuracy of semiempirical and some DFT methods for predicting heats of formation journal February 2004
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B3LYP/6-311++G** study of monohydrates of α- and β-d-glucopyranose: hydrogen bonding, stress energies, and effect of hydration on internal coordinates journal February 2004
DFT study of α- and β-d-mannopyranose at the B3LYP/6-311++G** level journal February 2005
DFT study of α- and β-d-galactopyranose at the B3LYP/6-311++G** level of theory journal March 2006
Conformation, dynamics, solvation and relative stabilities of selected β-hexopyranoses in water: a molecular dynamics study with the gromos 45A4 force field journal October 2007
On the path to glycan conformer identification: Gas-phase study of the anomers of methyl glycosides of N-acetyl-d-glucosamine and N-acetyl-d-galactosamine journal December 2012
Proper basis set for quantum mechanical studies of potential energy surfaces of carbohydrates journal April 2002
Dispersion-Corrected Mean-Field Electronic Structure Methods journal April 2016
Accurate Hydrogen Bond Energies within the Density Functional Tight Binding Method journal March 2015
Divide-and-Conquer-Type Density-Functional Tight-Binding Simulations of Hydroxide Ion Diffusion in Bulk Water journal February 2017
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Benchmarking the Conductor-like Polarizable Continuum Model (CPCM) for Aqueous Solvation Free Energies of Neutral and Ionic Organic Molecules journal October 2004
Advanced Corrections of Hydrogen Bonding and Dispersion for Semiempirical Quantum Mechanical Methods journal December 2011
Performance of the SCC-DFTB Model for Description of Five-Membered Ring Carbohydrate Conformations: Comparison to Force Fields, High-Level Electronic Structure Methods, and Experiment journal June 2012
Parametrization and Benchmark of DFTB3 for Organic Molecules journal November 2012
Improvement of DNA and RNA Sugar Pucker Profiles from Semiempirical Quantum Methods journal March 2014
Density-Functional Tight-Binding Combined with the Fragment Molecular Orbital Method journal October 2014
Parameterization of the DFTB3 Method for Br, Ca, Cl, F, I, K, and Na in Organic and Biological Systems journal December 2014
Description of Phosphate Hydrolysis Reactions with the Self-Consistent-Charge Density-Functional-Tight-Binding (SCC-DFTB) Theory. 1. Parameterization journal November 2008
Emil Fischer's discovery of the configuration of glucose. A semicentennial retrospect journal August 1941
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Theoretical Study of the Relative Stability of Rotational Conformers of α and β- d -Glucopyranose in Gas Phase and Aqueous Solution journal May 2004
Pyranose Ring Transition State Is Derived from Cellobiohydrolase I Induced Conformational Stability and Glycosidic Bond Polarization journal September 2010
Intramolecular Hydrogen Bonding and Cooperative Interactions in Carbohydrates via the Molecular Tailoring Approach journal January 2008
The Self-Consistent Charge Density Functional Tight Binding Method Applied to Liquid Water and the Hydrated Excess Proton: Benchmark Simulations journal May 2010
Ring Puckering: A Metric for Evaluating the Accuracy of AM1, PM3, PM3CARB-1, and SCC-DFTB Carbohydrate QM/MM Simulations journal December 2010
DFT Energy Optimization of a Large Carbohydrate: Cyclomaltohexaicosaose (CA-26) journal December 2011
Molecular Simulation of Water and Hydration Effects in Different Environments: Challenges and Developments for DFTB Based Models journal September 2014
Atomic-scale insights on hydrogen trapping and exclusion at incoherent interfaces of nanoprecipitates in martensitic steels journal July 2022
Stepwise gating of the Sec61 protein-conducting channel by Sec63 and Sec62 journal January 2021
Toward elimination of discrepancies between theory and experiment: The gas-phase reaction of N2O5 with H2O journal December 2002
Application of London-type dispersion corrections to the solid-state density functional theory simulation of the terahertz spectra of crystalline pharmaceuticals journal January 2011
Dispersion interactions of carbohydrates with condensate aromatic moieties: Theoretical study on the CH–π interaction additive properties journal January 2011
Stability of conformationally locked free fructose: theoretical and computational insights journal January 2015
Assessment of Gaussian-3 and density-functional theories on the G3/05 test set of experimental energies journal September 2005
A new mixing of Hartree–Fock and local density‐functional theories journal January 1993
Gaussian-3 (G3) theory for molecules containing first and second-row atoms journal November 1998
Assessment of Gaussian-3 and density functional theories for a larger experimental test set journal May 2000
An extension of the GROMOS force field for carbohydrates, resulting in improvement of the crystal structure determination of α- D -galactose journal April 1995
Taking a snapshot of the triplet excited state of an OLED organometallic luminophore using X-rays text January 2020

Cited By (1)

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

Figures / Tables (25)

Figure 1.(p. 2)figure Figure 1.
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Figure 19.(p. 13)figure Figure 19.
Table 5.(p. 13)table Table 5.
Table 6.(p. 13)table Table 6.

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Related Subjects

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