Structural analysis of methyl 6-O-benzyl-2-deoxy-2-dimethylmaleimido- α-D-allopyranoside by X-ray crystallography, NMR, and QM calculations: Hydrogen bonding and comparison of density functionals
The crystal structure of methyl 6-O-benzyl-2-deoxy-2-dimethylmaleimido- α-d-allopyranoside was solved in order to gain insight into the hydrogen bond features which can be determining features in the glycosylation regioselectivity observed for this compound. An intramolecular hydrogen bond between t...
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2012
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| Acceso en línea: | https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_00086215_v353_n_p79_Colombo http://hdl.handle.net/20.500.12110/paper_00086215_v353_n_p79_Colombo |
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paper:paper_00086215_v353_n_p79_Colombo2023-06-08T14:33:01Z Structural analysis of methyl 6-O-benzyl-2-deoxy-2-dimethylmaleimido- α-D-allopyranoside by X-ray crystallography, NMR, and QM calculations: Hydrogen bonding and comparison of density functionals Stortz, Carlos Arturo Allosamine Conformation Crystal structure Density functional theory N-Dimethylmaleloyl group Allosamine Bond distance Carbonyl oxygen Complex carbohydrates Crystal geometry Density functionals Functionals Gain insight Hybrid method Intermolecular hydrogen bonds Intramolecular hydrogen bond N-Dimethylmaleloyl group Optimized geometries Quantum methods Sugar moiety Temperature shift Torsion angle Carbohydrates Complexation Conformations Crystal structure Density functional theory Geometry Optimization Oxygen X ray crystallography Hydrogen bonds 6 o benzyl 2 deoxy 2 dimethylmaleimido alpha dextro allopyranoside carbohydrate derivative carbonyl derivative dimethylmaleoyl hydroxyl group oxygen sugar unclassified drug article chemical structure density functional theory geometry hydrogen bond molecular model priority journal quantum mechanics X ray crystallography Crystallography, X-Ray Glycosides Hydrogen Bonding Magnetic Resonance Spectroscopy Molecular Structure The crystal structure of methyl 6-O-benzyl-2-deoxy-2-dimethylmaleimido- α-d-allopyranoside was solved in order to gain insight into the hydrogen bond features which can be determining features in the glycosylation regioselectivity observed for this compound. An intramolecular hydrogen bond between the hydroxyl H(O)3 and a carbonyl oxygen from the dimethylmaleoyl (DMM) group was observed. This was in agreement with previous NMR temperature shift determinations and molecular modeling. The determination has also found an intermolecular hydrogen bond between the second hydroxyl H(O)4 and the other carbonyl oxygen (generated by symmetry) from DMM. The crystal structure was optimized by five different functionals, namely the hybrid methods B3LYP, M06-2X, B3PW91, and PBE0, and the pure functional PBE, and the optimized geometries were compared with the crystal geometry and with MM3. An excellent coincidence of the geometries was found with the five quantum methods, with minor details deviating from this coincidence. PBE tends to yield larger bond distances, whereas M06-2X fails slightly to match the exocyclic torsion angles for the sugar moiety. In any case, the differences are small, implying that any of these functionals can accurately emulate the geometries of a complex carbohydrate derivative like this one. © 2012 Elsevier Ltd. All rights reserved. Fil:Stortz, C.A. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. 2012 https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_00086215_v353_n_p79_Colombo http://hdl.handle.net/20.500.12110/paper_00086215_v353_n_p79_Colombo |
| institution |
Universidad de Buenos Aires |
| institution_str |
I-28 |
| repository_str |
R-134 |
| collection |
Biblioteca Digital - Facultad de Ciencias Exactas y Naturales (UBA) |
| topic |
Allosamine Conformation Crystal structure Density functional theory N-Dimethylmaleloyl group Allosamine Bond distance Carbonyl oxygen Complex carbohydrates Crystal geometry Density functionals Functionals Gain insight Hybrid method Intermolecular hydrogen bonds Intramolecular hydrogen bond N-Dimethylmaleloyl group Optimized geometries Quantum methods Sugar moiety Temperature shift Torsion angle Carbohydrates Complexation Conformations Crystal structure Density functional theory Geometry Optimization Oxygen X ray crystallography Hydrogen bonds 6 o benzyl 2 deoxy 2 dimethylmaleimido alpha dextro allopyranoside carbohydrate derivative carbonyl derivative dimethylmaleoyl hydroxyl group oxygen sugar unclassified drug article chemical structure density functional theory geometry hydrogen bond molecular model priority journal quantum mechanics X ray crystallography Crystallography, X-Ray Glycosides Hydrogen Bonding Magnetic Resonance Spectroscopy Molecular Structure |
| spellingShingle |
Allosamine Conformation Crystal structure Density functional theory N-Dimethylmaleloyl group Allosamine Bond distance Carbonyl oxygen Complex carbohydrates Crystal geometry Density functionals Functionals Gain insight Hybrid method Intermolecular hydrogen bonds Intramolecular hydrogen bond N-Dimethylmaleloyl group Optimized geometries Quantum methods Sugar moiety Temperature shift Torsion angle Carbohydrates Complexation Conformations Crystal structure Density functional theory Geometry Optimization Oxygen X ray crystallography Hydrogen bonds 6 o benzyl 2 deoxy 2 dimethylmaleimido alpha dextro allopyranoside carbohydrate derivative carbonyl derivative dimethylmaleoyl hydroxyl group oxygen sugar unclassified drug article chemical structure density functional theory geometry hydrogen bond molecular model priority journal quantum mechanics X ray crystallography Crystallography, X-Ray Glycosides Hydrogen Bonding Magnetic Resonance Spectroscopy Molecular Structure Stortz, Carlos Arturo Structural analysis of methyl 6-O-benzyl-2-deoxy-2-dimethylmaleimido- α-D-allopyranoside by X-ray crystallography, NMR, and QM calculations: Hydrogen bonding and comparison of density functionals |
| topic_facet |
Allosamine Conformation Crystal structure Density functional theory N-Dimethylmaleloyl group Allosamine Bond distance Carbonyl oxygen Complex carbohydrates Crystal geometry Density functionals Functionals Gain insight Hybrid method Intermolecular hydrogen bonds Intramolecular hydrogen bond N-Dimethylmaleloyl group Optimized geometries Quantum methods Sugar moiety Temperature shift Torsion angle Carbohydrates Complexation Conformations Crystal structure Density functional theory Geometry Optimization Oxygen X ray crystallography Hydrogen bonds 6 o benzyl 2 deoxy 2 dimethylmaleimido alpha dextro allopyranoside carbohydrate derivative carbonyl derivative dimethylmaleoyl hydroxyl group oxygen sugar unclassified drug article chemical structure density functional theory geometry hydrogen bond molecular model priority journal quantum mechanics X ray crystallography Crystallography, X-Ray Glycosides Hydrogen Bonding Magnetic Resonance Spectroscopy Molecular Structure |
| description |
The crystal structure of methyl 6-O-benzyl-2-deoxy-2-dimethylmaleimido- α-d-allopyranoside was solved in order to gain insight into the hydrogen bond features which can be determining features in the glycosylation regioselectivity observed for this compound. An intramolecular hydrogen bond between the hydroxyl H(O)3 and a carbonyl oxygen from the dimethylmaleoyl (DMM) group was observed. This was in agreement with previous NMR temperature shift determinations and molecular modeling. The determination has also found an intermolecular hydrogen bond between the second hydroxyl H(O)4 and the other carbonyl oxygen (generated by symmetry) from DMM. The crystal structure was optimized by five different functionals, namely the hybrid methods B3LYP, M06-2X, B3PW91, and PBE0, and the pure functional PBE, and the optimized geometries were compared with the crystal geometry and with MM3. An excellent coincidence of the geometries was found with the five quantum methods, with minor details deviating from this coincidence. PBE tends to yield larger bond distances, whereas M06-2X fails slightly to match the exocyclic torsion angles for the sugar moiety. In any case, the differences are small, implying that any of these functionals can accurately emulate the geometries of a complex carbohydrate derivative like this one. © 2012 Elsevier Ltd. All rights reserved. |
| author |
Stortz, Carlos Arturo |
| author_facet |
Stortz, Carlos Arturo |
| author_sort |
Stortz, Carlos Arturo |
| title |
Structural analysis of methyl 6-O-benzyl-2-deoxy-2-dimethylmaleimido- α-D-allopyranoside by X-ray crystallography, NMR, and QM calculations: Hydrogen bonding and comparison of density functionals |
| title_short |
Structural analysis of methyl 6-O-benzyl-2-deoxy-2-dimethylmaleimido- α-D-allopyranoside by X-ray crystallography, NMR, and QM calculations: Hydrogen bonding and comparison of density functionals |
| title_full |
Structural analysis of methyl 6-O-benzyl-2-deoxy-2-dimethylmaleimido- α-D-allopyranoside by X-ray crystallography, NMR, and QM calculations: Hydrogen bonding and comparison of density functionals |
| title_fullStr |
Structural analysis of methyl 6-O-benzyl-2-deoxy-2-dimethylmaleimido- α-D-allopyranoside by X-ray crystallography, NMR, and QM calculations: Hydrogen bonding and comparison of density functionals |
| title_full_unstemmed |
Structural analysis of methyl 6-O-benzyl-2-deoxy-2-dimethylmaleimido- α-D-allopyranoside by X-ray crystallography, NMR, and QM calculations: Hydrogen bonding and comparison of density functionals |
| title_sort |
structural analysis of methyl 6-o-benzyl-2-deoxy-2-dimethylmaleimido- α-d-allopyranoside by x-ray crystallography, nmr, and qm calculations: hydrogen bonding and comparison of density functionals |
| publishDate |
2012 |
| url |
https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_00086215_v353_n_p79_Colombo http://hdl.handle.net/20.500.12110/paper_00086215_v353_n_p79_Colombo |
| work_keys_str_mv |
AT stortzcarlosarturo structuralanalysisofmethyl6obenzyl2deoxy2dimethylmaleimidoadallopyranosidebyxraycrystallographynmrandqmcalculationshydrogenbondingandcomparisonofdensityfunctionals |
| _version_ |
1768546472864776192 |