Literature DB >> 26609572

Evaluation of Density Functionals and Basis Sets for Carbohydrates.

Gábor I Csonka1, Alfred D French1, Glenn P Johnson1, Carlos A Stortz1.   

Abstract

Correlated ab initio wave function calculations using MP2/aug-cc-pVTZ model chemistry have been performed for three test sets of gas phase saccharide conformations to provide reference values for their relative energies. The test sets consist of 15 conformers of α- and β-d-allopyranose, 15 of 3,6-anhydro-4-O-methyl-d-galactitol, and four of β-d-glucopyranose. For each set, conformational energies varied by about 7 kcal/mol. Results obtained with the Hartree-Fock method, with pure density functional approximations (DFAs) like LSDA, PBEsol, PBE, and TPSS and with hybrid DFAs like B3PW91, B3LYP, PBEh, and M05-2X, were then compared to the reference and local MP2 relative energies. Basis sets included 6-31G*, 6-31G**, 6-31+G*, 6-31+G**, 6-311+G**, 6-311++G**, cc-pVTZ(-f), cc-pVTZ, and aug-cc-pVTZ(-f). The smallest basis set that gives good DFA relative energies is 6-31+G**, and more converged results can be obtained with 6-311+G**. The optimized geometries obtained from a smaller basis set, 6-31+G*, were useful for subsequent single point energy calculations with larger basis sets. The best agreement with MP2 was shown by M05-2X, but only when using a dense DFT grid. The popular B3LYP functional is not the best for saccharide conformational studies. The B3PW91 functional gives systematically better results, but other hybrid functionals like PBEh or TPSSh are even better. Overall, the nonempirical PBE GGA and TPSS meta-GGA functionals also performed better than B3LYP.

Entities:  

Year:  2009        PMID: 26609572     DOI: 10.1021/ct8004479

Source DB:  PubMed          Journal:  J Chem Theory Comput        ISSN: 1549-9618            Impact factor:   6.006


  17 in total

1.  Theoretical studies on the reaction of mono- and ditriflate derivatives of 1,4:3,6-dianhydro-D-mannitol with trimethylamine--Can a quaternary ammonium salt be a source of the methyl group?

Authors:  Justyna Bednarko; Justyna Wielińska; Karol Sikora; Beata Liberek; Andrzej Nowacki
Journal:  J Comput Aided Mol Des       Date:  2015-12-14       Impact factor: 3.686

2.  Probing deoxysugar conformational preference: A comprehensive computational study investigating the effects of deoxygenation.

Authors:  Alison E Vickman; Nicola L B Pohl
Journal:  Carbohydr Res       Date:  2018-12-12       Impact factor: 2.104

3.  Characterization and Modeling of the Collision Induced Dissociation Patterns of Deprotonated Glycosphingolipids: Cleavage of the Glycosidic Bond.

Authors:  Marko Rožman
Journal:  J Am Soc Mass Spectrom       Date:  2015-08-22       Impact factor: 3.109

4.  Testing the CP-correction procedure with different DFT methods on H-bonding complexes of κ-carrabiose with water molecules.

Authors:  Rachida Fodil; Majda Sekkal-Rahal; Adlane Sayede
Journal:  J Mol Model       Date:  2017-01-14       Impact factor: 1.810

5.  Effects of varying the 6-position oxidation state of hexopyranoses: a systematic comparative computational analysis of 48 monosaccharide stereoisomers.

Authors:  Alison E Vickman; Daniel C Ashley; Mu-Hyun Baik; Nicola L B Pohl
Journal:  J Mol Model       Date:  2017-06-27       Impact factor: 1.810

6.  Integration Grid Errors for Meta-GGA-Predicted Reaction Energies: Origin of Grid Errors for the M06 Suite of Functionals.

Authors:  Steven E Wheeler; K N Houk
Journal:  J Chem Theory Comput       Date:  2010-02-09       Impact factor: 6.006

7.  Conformational analysis of thioether musks using density functional theory.

Authors:  William N Setzer
Journal:  Int J Mol Sci       Date:  2009-08-04       Impact factor: 5.923

8.  Thermal reaction of the ionic liquid 1,2-dimethyl-(3-aminoethyl) imidazolium tetrafluoroborate: a kinetic and theoretical study.

Authors:  Xinming Zhou; Bobo Cao; Shuangyue Liu; Xuejun Sun; Xiao Zhu; Hu Fu
Journal:  J Mol Model       Date:  2016-05-18       Impact factor: 1.810

9.  Density functional conformational study of 2-O-sulfated 3,6 anhydro-α-D-galactose and of neo-κ- and ι-carrabiose molecules in gas phase and water.

Authors:  Noreya Bestaoui-Berrekhchi-Berrahma; Philippe Derreumaux; Majda Sekkal-Rahal; Michael Springborg; Adlane Sayede; Noureddine Yousfi; Abd-Ed-Daim Kadoun
Journal:  J Mol Model       Date:  2012-10-20       Impact factor: 1.810

10.  Deprotonation and acidity characterization of biomass sugars: a first-principles study.

Authors:  Gang Yang; Chang Zhu; Lijun Zhou
Journal:  J Mol Model       Date:  2016-04-13       Impact factor: 1.810

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