The potential for the indirect crystal structure verification of methyl glycosides based on acetates’ parent structures: GIPAW and solid-state NMR approaches

Szeleszczuk, Łukasz; Gubica, Tomasz; Zimniak, Andrzej; Pisklak, Dariusz Maciej; Dąbrowska, Kinga; Cyrański, Michał K.; Kańska, Marianna

doi:10.1016/j.cplett.2017.08.028

Cited by 5 publications

(5 citation statements)

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“…It is often difficult to obtain diffraction quality structures from sugars, while their acetate derivatives often crystallise more readily. The crystal structures of acetates of three methyl glycosides were determined and the conformation of the molecules used as the basis for structure solutions [320]; the acetate was replaced by H in a random orientation and a unit cell constructed in the relevant space group before geometry optimisation using dispersion-corrected DFT. In two cases, the resulting structures were in good agreement with the known crystal structures, and showed good matches with predicted 13 C shifts.…”

Section: Validation Of Structures From Powder Xrd Datamentioning

confidence: 99%

NMR crystallography of molecular organics

Hodgkinson

2020

Progress in Nuclear Magnetic Resonance Spectroscopy

125

112

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Section: Validation Of Structures From Powder Xrd Datamentioning

confidence: 99%

NMR crystallography of molecular organics

Hodgkinson

2020

Progress in Nuclear Magnetic Resonance Spectroscopy

125

112

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“…The hydrogen bond networks are shown by dashed lines with calculated bond length (blue) and O–H∙∙∙O bond angles (green). Reproduced from Kibalchenko et al [ 118 ] with the permission of Elsevier.…”

Section: Monosaccharidesmentioning

confidence: 99%

“…Implementation of GIPAW into a parallelized planewave pseudopotential code allows the calculation of NMR chemical shifts in large, low-symmetry extended systems. As an example, Szeleszczuk and coauthors [118] demonstrated a convenient method for the indirect crystal structure verification of methyl glycosides using the GIPAW method. In that paper, instead of using various time consuming methods of conformational search, the crystal structures of methyl glycoside acetates were used for the desired crystal structure preparation and optimization.…”

Section: Monosaccharidesmentioning

confidence: 99%

“…It was thus concluded that temperature effects were not essential in the case of methyl glycosides, which may not be so in the case of other classes of saccharides. Coming back to the paper by Kibalchenko and coauthors [118], a partial geometry optimization in that study was carried out prior to calculating the NMR parameters. The isotropic chemical shifts (represented here with 13 C-NMR chemical shifts in Table 2) were obtained from the isotropic average of the shielding tensors evaluated with the PBE and KT3 functionals.…”

Section: Monosaccharidesmentioning

confidence: 99%

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Computational NMR of Carbohydrates: Theoretical Background, Applications, and Perspectives

Krivdin

2021

Molecules

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This review is written amid a marked progress in the calculation of NMR parameters of carbohydrates substantiated by a vast amount of experimental data coming from several laboratories worldwide. By no means are we trying to cover in the present compilation a huge amount of all available data. The main idea of the present review was only to outline general trends and perspectives in this dynamically developing area on the background of a marked progress in theoretical and computational NMR. Presented material is arranged in three basic sections: (1)—a brief theoretical introduction; (2)—applications and perspectives in computational NMR of monosaccharides; and (3)—calculation of NMR chemical shifts and spin-spin coupling constants of di- and polysaccharides.

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“…For complex structures calculations offer the opportunity to evaluate the effect of structural changes upon the NMR parameters. Besides, if there is no experimentally confirmed structure for a studied material, calculated NMR parameters for candidate structures can be compared to those determined experimentally as a complementary method of structure validation …”

Section: Introductionmentioning

confidence: 99%

Does the choice of the crystal structure influence the results of the periodic DFT calculations? A case of glycine alpha polymorph GIPAW NMR parameters computations

2018

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Glycine is a common amino acid with relatively complex chemistry in solid state. Although several polymorphs (α, β, δ, γ, ε) of crystalline glycine are known, for NMR spectroscopy the most important is a polymorph, which is used as a standard for calibration of spectrometer performance and therefore it is intensively studied by both experimental methods and theoretical computation. The great scientific interest in a glycine results in a large number of crystallographic information files (CIFs) deposited in Cambridge Structural Database (CSD). The aim of this study was to evaluate the influence of the chosen crystal structure of α glycine obtained in different crystallographic experimental conditions (temperature, pressure and source of radiation of α glycine) on the results of periodic DFT calculation. For this purpose the total of 136 GIPAW calculations of α glycine NMR parameters were performed, preceded by the four approaches ("SP", "only H", "full", "full+cell") of structure preparation. The analysis of the results of those computations performed on the representative group of 34 structures obtained at various experimental conditions revealed that though the structures were generally characterized by good accuracy (R < 0.05 for most of them) the results of the periodic DFT calculations performed using the unoptimized structures differed significantly. The values of the standard deviations of the studied NMR parameters were in most cases decreasing with the number of optimized parameters. The most accurate results (of the calculations) were in most cases obtained using the structures with solely hydrogen atoms positions optimized. © 2018 Wiley Periodicals, Inc.

show abstract

The potential for the indirect crystal structure verification of methyl glycosides based on acetates’ parent structures: GIPAW and solid-state NMR approaches

Cited by 5 publications

References 30 publications

NMR crystallography of molecular organics

NMR crystallography of molecular organics

Computational NMR of Carbohydrates: Theoretical Background, Applications, and Perspectives

Does the choice of the crystal structure influence the results of the periodic DFT calculations? A case of glycine alpha polymorph GIPAW NMR parameters computations

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