Exhaustive rotamer search of the 4C1 conformation of α- and β-D-galactopyranose
An exhaustive search approach was used to establish all possible rotamers of α- and β-D-galactopyranose using DFT at the B3LYP/6-311+G** and M06-2X/6-311+G** levels, both in vacuum calculations, and including two variants of continuum solvent models as PCM and SMD to simulate water solutions. Free e...
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| Acceso en línea: | https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_00086215_v448_n_p136_DelVigo http://hdl.handle.net/20.500.12110/paper_00086215_v448_n_p136_DelVigo |
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paper:paper_00086215_v448_n_p136_DelVigo2023-06-08T14:33:06Z Exhaustive rotamer search of the 4C1 conformation of α- and β-D-galactopyranose Stortz, Carlos Arturo Conformation Density functional theory Exhaustive search Galactose Rotamer Solvent model Chemical bonds Conformations Density functional theory Free energy Quantum chemistry Solvents Divergent behaviors Exhaustive search Experimental values Free-energy calculations Galactose Geometrical differences Rotamers Solvent model Hydrogen bonds galactopyranose galactose unclassified drug galactose solvent Article calculation chemical structure conformation density functional theory dielectric constant energy hydrogen bond priority journal rotamer solvation solvent effect vacuum X ray diffraction chemistry conformation molecular model quantum theory stereoisomerism Carbohydrate Conformation Galactose Models, Molecular Quantum Theory Solvents Stereoisomerism An exhaustive search approach was used to establish all possible rotamers of α- and β-D-galactopyranose using DFT at the B3LYP/6-311+G** and M06-2X/6-311+G** levels, both in vacuum calculations, and including two variants of continuum solvent models as PCM and SMD to simulate water solutions. Free energies were also calculated. MM3 was used as the starting point for calculations, using a dielectric constant of 1.5 for vacuum modeling, and 80 for water solution modeling. For the vacuum calculations, out of the theoretically possible 729 rotamers, only about a hundred rendered stable minima, highly stabilized by hydrogen bonding and scattered in a ca. 14 kcal/mol span. The rotamer with a clockwise arrangement of hydrogen bonds was the most stable for the α-anomer, whereas that with a counterclockwise arrangement was the most stable for the β-anomer. Free energy calculations, and especially solvent modeling, tend to flatten the potential energy surface. With PCM, the total range of energies was reduced to 9–10 kcal/mol (α-anomer) or 7–8 kcal/mol (β-anomer). These figures fall to 4.5–6 kcal/mol using SMD. At the same time, the total number of possible rotamers increases dramatically to about 300 with PCM, and to 400 with SMD. Both models show a divergent behavior: PCM tends to underestimate the effect of solvent, thus rendering as the most stable many common rotamers with vacuum calculations, and giving underestimations of populations of β-anomers and gt rotamers in the equilibrium. On the other hand, SMD gives a better estimation of the solvent effect, yielding correct populations of gt rotamers, but more β-anomers than expected by the experimental values. The best agreement is observed when the functional M06-2X is combined with SMD. Both DFT models show minimal geometrical differences between the optimized conformers. © 2017 Elsevier Ltd Fil:Stortz, C.A. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. 2017 https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_00086215_v448_n_p136_DelVigo http://hdl.handle.net/20.500.12110/paper_00086215_v448_n_p136_DelVigo |
| institution |
Universidad de Buenos Aires |
| institution_str |
I-28 |
| repository_str |
R-134 |
| collection |
Biblioteca Digital - Facultad de Ciencias Exactas y Naturales (UBA) |
| topic |
Conformation Density functional theory Exhaustive search Galactose Rotamer Solvent model Chemical bonds Conformations Density functional theory Free energy Quantum chemistry Solvents Divergent behaviors Exhaustive search Experimental values Free-energy calculations Galactose Geometrical differences Rotamers Solvent model Hydrogen bonds galactopyranose galactose unclassified drug galactose solvent Article calculation chemical structure conformation density functional theory dielectric constant energy hydrogen bond priority journal rotamer solvation solvent effect vacuum X ray diffraction chemistry conformation molecular model quantum theory stereoisomerism Carbohydrate Conformation Galactose Models, Molecular Quantum Theory Solvents Stereoisomerism |
| spellingShingle |
Conformation Density functional theory Exhaustive search Galactose Rotamer Solvent model Chemical bonds Conformations Density functional theory Free energy Quantum chemistry Solvents Divergent behaviors Exhaustive search Experimental values Free-energy calculations Galactose Geometrical differences Rotamers Solvent model Hydrogen bonds galactopyranose galactose unclassified drug galactose solvent Article calculation chemical structure conformation density functional theory dielectric constant energy hydrogen bond priority journal rotamer solvation solvent effect vacuum X ray diffraction chemistry conformation molecular model quantum theory stereoisomerism Carbohydrate Conformation Galactose Models, Molecular Quantum Theory Solvents Stereoisomerism Stortz, Carlos Arturo Exhaustive rotamer search of the 4C1 conformation of α- and β-D-galactopyranose |
| topic_facet |
Conformation Density functional theory Exhaustive search Galactose Rotamer Solvent model Chemical bonds Conformations Density functional theory Free energy Quantum chemistry Solvents Divergent behaviors Exhaustive search Experimental values Free-energy calculations Galactose Geometrical differences Rotamers Solvent model Hydrogen bonds galactopyranose galactose unclassified drug galactose solvent Article calculation chemical structure conformation density functional theory dielectric constant energy hydrogen bond priority journal rotamer solvation solvent effect vacuum X ray diffraction chemistry conformation molecular model quantum theory stereoisomerism Carbohydrate Conformation Galactose Models, Molecular Quantum Theory Solvents Stereoisomerism |
| description |
An exhaustive search approach was used to establish all possible rotamers of α- and β-D-galactopyranose using DFT at the B3LYP/6-311+G** and M06-2X/6-311+G** levels, both in vacuum calculations, and including two variants of continuum solvent models as PCM and SMD to simulate water solutions. Free energies were also calculated. MM3 was used as the starting point for calculations, using a dielectric constant of 1.5 for vacuum modeling, and 80 for water solution modeling. For the vacuum calculations, out of the theoretically possible 729 rotamers, only about a hundred rendered stable minima, highly stabilized by hydrogen bonding and scattered in a ca. 14 kcal/mol span. The rotamer with a clockwise arrangement of hydrogen bonds was the most stable for the α-anomer, whereas that with a counterclockwise arrangement was the most stable for the β-anomer. Free energy calculations, and especially solvent modeling, tend to flatten the potential energy surface. With PCM, the total range of energies was reduced to 9–10 kcal/mol (α-anomer) or 7–8 kcal/mol (β-anomer). These figures fall to 4.5–6 kcal/mol using SMD. At the same time, the total number of possible rotamers increases dramatically to about 300 with PCM, and to 400 with SMD. Both models show a divergent behavior: PCM tends to underestimate the effect of solvent, thus rendering as the most stable many common rotamers with vacuum calculations, and giving underestimations of populations of β-anomers and gt rotamers in the equilibrium. On the other hand, SMD gives a better estimation of the solvent effect, yielding correct populations of gt rotamers, but more β-anomers than expected by the experimental values. The best agreement is observed when the functional M06-2X is combined with SMD. Both DFT models show minimal geometrical differences between the optimized conformers. © 2017 Elsevier Ltd |
| author |
Stortz, Carlos Arturo |
| author_facet |
Stortz, Carlos Arturo |
| author_sort |
Stortz, Carlos Arturo |
| title |
Exhaustive rotamer search of the 4C1 conformation of α- and β-D-galactopyranose |
| title_short |
Exhaustive rotamer search of the 4C1 conformation of α- and β-D-galactopyranose |
| title_full |
Exhaustive rotamer search of the 4C1 conformation of α- and β-D-galactopyranose |
| title_fullStr |
Exhaustive rotamer search of the 4C1 conformation of α- and β-D-galactopyranose |
| title_full_unstemmed |
Exhaustive rotamer search of the 4C1 conformation of α- and β-D-galactopyranose |
| title_sort |
exhaustive rotamer search of the 4c1 conformation of α- and β-d-galactopyranose |
| publishDate |
2017 |
| url |
https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_00086215_v448_n_p136_DelVigo http://hdl.handle.net/20.500.12110/paper_00086215_v448_n_p136_DelVigo |
| work_keys_str_mv |
AT stortzcarlosarturo exhaustiverotamersearchofthe4c1conformationofaandbdgalactopyranose |
| _version_ |
1768544253501243392 |