13C CP MAS NMR and crystal structure of methyl glycopyranosides

Paradowska, Katarzyna; Gubica, Tomasz; Temeriusz, Andrzej; Cyrański, Michał K.; Wawer, Iwona

doi:10.1016/j.carres.2008.05.015

Cited by 10 publications

(5 citation statements)

References 26 publications

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“…The calculations yielded 13 C shielding constants correlated with experimental chemical shifts with R 2 = 0.993 (isolated molecule) and R 2 = 0.992Á Á Á0.997 (hydrates). 269 The authors could not separate effects produced by different hydrogen bonds but confirmed an increase of stability with every next hydrogen bond observed for a-D-lyxofuranoside earlier. 292 NMR observables of methyl D-xylopyranosides were predicted with the use of DFT for geometries optimized with the fixed dihedral angle f of the C1-OMe bond.…”

Section: Monosaccharides and Derivativesmentioning

confidence: 73%

Recent advances in computational predictions of NMR parameters for the structure elucidation of carbohydrates: methods and limitations

2013

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All living systems are comprised of four fundamental classes of macromolecules--nucleic acids, proteins, lipids, and carbohydrates (glycans). Glycans play a unique role of joining three principal hierarchical levels of the living world: (1) the molecular level (pathogenic agents and vaccine recognition by the immune system, metabolic pathways involving saccharides that provide cells with energy, and energy accumulation via photosynthesis); (2) the nanoscale level (cell membrane mechanics, structural support of biomolecules, and the glycosylation of macromolecules); (3) the microscale and macroscale levels (polymeric materials, such as cellulose, starch, glycogen, and biomass). NMR spectroscopy is the most powerful research approach for getting insight into the solution structure and function of carbohydrates at all hierarchical levels, from monosaccharides to oligo- and polysaccharides. Recent progress in computational procedures has opened up novel opportunities to reveal the structural information available in the NMR spectra of saccharides and to advance our understanding of the corresponding biochemical processes. The ability to predict the molecular geometry and NMR parameters is crucial for the elucidation of carbohydrate structures. In the present paper, we review the major NMR spectrum simulation techniques with regard to chemical shifts, coupling constants, relaxation rates and nuclear Overhauser effect prediction applied to the three levels of glycomics. Outstanding development in the related fields of genomics and proteomics has clearly shown that it is the advancement of research tools (automated spectrum analysis, structure elucidation, synthesis, sequencing and amplification) that drives the large challenges in modern science. Combining NMR spectroscopy and the computational analysis of structural information encoded in the NMR spectra reveals a way to the automated elucidation of the structure of carbohydrates.

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Section: Monosaccharides and Derivativesmentioning

confidence: 73%

Recent advances in computational predictions of NMR parameters for the structure elucidation of carbohydrates: methods and limitations

2013

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“…hydrogen bond formed by the C3AO oxygen with methanol molecule present in the crystal. The effects of hydrogen bonds formed by OH groups of sugar moiety are smaller than 1.5 ppm, as usually observed [27]. The difference D in d(C30) may result from hindered rotation of the CH 3 group in the crystal; the steric hindrance is due to the presence of methanol molecule.…”

Section: Nmr Spectroscopymentioning

confidence: 89%

Molecular structure of actein: 13C CPMAS NMR, IR, X-ray diffraction studies and theoretical DFT–GIAO calculations

Jamróz

Bąk

Gliński³

et al. 2009

Journal of Molecular Structure

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“…[28] However, in this case the contributions to the chemical shifts from intermolecular and intramolecular sources should be considered to explain the differences between chemical shifts registered in solid state and in solution. 29 Chemical shifts for solid gentiobiose, its solution in D 2 O, and the differences between solution and solid state = δ solution − δ solid > 1 ppm are given in Table 3. The assignment was verified by theoretical calculations of the shielding constants.…”

Section: Cpmas Nmr Spectroscopymentioning

confidence: 99%

Conformational Analysis of Gentiobiose Using Genetic Algorithm Search and GIAO DFT Calculations with¹³C CPMAS NMR as a Verification Method

Bukowicki

Wawer

Paradowska

2015

Journal of Carbohydrate Chemistry

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The ALJAR03 software was implemented performing searches in the dihedral angle conformational space of disaccharides. The angles φ, ψ, and ω around glycosidic linkages, as well as the orientations of hydroxymethyl and hydroxyl groups, were considered. The energy maps were calculated using the MM+ force field. The searches were performed using a genetic algorithm (GA) combined with systematic grid search (GS). The application of a genetic algorithm-assisted grid search (GAAGS) approach yielded a significant reduction in the number of structures to be sampled in order to find the best low-energy conformation, as compared with the standard systematic grid search. Thus, time-consuming gauge-independent atomic orbital (GIAO) calculations of shielding constants can be rationalized and limited to some selected conformations. 13 C CP-MAS NMR chemical shifts for solid gentiobiose were measured and compared with the respective (GIAO DFT) shielding constants calculated for the crystallographic structure and for low-energy conformers. The differences in shielding are associated with the conformational effects (different arrangements of exocyclic groups) and hydrogen bonds. The best agreement (R 2 = 0.99) between the experimental and calculated chemical shifts was for the XRD structure and for the best conformer (R 2 = 0.98). Their geometries differ in the orientation of OH groups.

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13C CP MAS NMR and crystal structure of methyl glycopyranosides

Cited by 10 publications

References 26 publications

Recent advances in computational predictions of NMR parameters for the structure elucidation of carbohydrates: methods and limitations

Recent advances in computational predictions of NMR parameters for the structure elucidation of carbohydrates: methods and limitations

Molecular structure of actein: 13C CPMAS NMR, IR, X-ray diffraction studies and theoretical DFT–GIAO calculations

Conformational Analysis of Gentiobiose Using Genetic Algorithm Search and GIAO DFT Calculations with¹³C CPMAS NMR as a Verification Method

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13C CP MAS NMR and crystal structure of methyl glycopyranosides

Cited by 10 publications

References 26 publications

Recent advances in computational predictions of NMR parameters for the structure elucidation of carbohydrates: methods and limitations

Recent advances in computational predictions of NMR parameters for the structure elucidation of carbohydrates: methods and limitations

Molecular structure of actein: 13C CPMAS NMR, IR, X-ray diffraction studies and theoretical DFT–GIAO calculations

Conformational Analysis of Gentiobiose Using Genetic Algorithm Search and GIAO DFT Calculations with13C CPMAS NMR as a Verification Method

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Conformational Analysis of Gentiobiose Using Genetic Algorithm Search and GIAO DFT Calculations with¹³C CPMAS NMR as a Verification Method