Combination of solid-state NMR, molecular mechanics and DFT calculations for the molecular structure determination of me
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ORIGINAL RESEARCH
Combination of solid-state NMR, molecular mechanics and DFT calculations for the molecular structure determination of methyl glycoside benzoates Łukasz Szeleszczuk 1 Dariusz M. Pisklak 1
&
Tomasz Gubica 1
&
Sebastian Szmeja 1 & Arkadiusz Ciesielski 2 & Michał K. Cyrański 2 &
Received: 4 August 2020 / Accepted: 23 September 2020 # The Author(s) 2020
Abstract A reliable method for molecular structure determination, excluding single-crystal X-ray diffraction (SCXRD), has been applied to six methyl glycoside tetrabenzoates. The proposed method is based on a global conformational search using molecular mechanics and subsequent DFT calculations guided by a solid-state NMR experiment. The accuracy of the applied method has been verified on three methyl glycoside benzoates for which the SCXRD analysis has been completed. It appeared that the calculated conformations of unprivileged energy could be found in the solid state. Bulky substituents (benzoates) exerted less energetically favored interactions in crystals in contrast to isolated molecules. Therefore, solid-state NMR was revealed to be an indispensable approach for choosing credible conformations from the calculated conformations. Keywords Carbohydrates . Molecular structure . Molecular mechanics . DFT . Solid-state NMR . X-ray diffraction
Abbreviations Bz-Me-α-Glc Bz-Me-β-Glc Bz-Me-α-Gal Bz-Me-β-Gal Bz-Me-α-Man Bz-Me-β-Man
Methyl α-D-glucoside tetrabenzoate Methyl β-D-glucoside tetrabenzoate Methyl α-D-galactoside tetrabenzoate Methyl β-D-galactoside tetrabenzoate Methyl α-D-mannoside tetrabenzoate Methyl β-D-mannoside tetrabenzoate
Introduction It is always worthwhile to compare the molecular structures of similar chemical species. Structural studies are the most basic studies and should precede further physicochemical analysis. The most credible molecular structures are obtained from single-crystal X-ray diffraction (SCXRD). However, this technique requires the formation of appropriate monocrystals, which can be a challenging task even for crystalline substances. Therefore, the accessibility of molecular structures derived from SCXRD is limited.
Supplementary Information The online version of this article (https:// doi.org/10.1007/s11224-020-01654-1) contains supplementary material, which is available to authorized users. * Tomasz Gubica [email protected]
Michał K. Cyrański [email protected] Dariusz M. Pisklak [email protected]
Łukasz Szeleszczuk [email protected] Sebastian Szmeja [email protected]
1
Department of Physical Chemistry, Faculty of Pharmacy, Medical University of Warsaw, Banacha 1, 02-097 Warsaw, Poland
Arkadiusz Ciesielski [email protected]
2
Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
Struct Chem
R
OBz
5
R
6
R BzO
3
O
H H
Bz-MeBz-MeBz-MeBz-MeBz-MeBz-Me-
Table 2 Calculated root-mean-square deviation (RMSD, Å) between experimental (unoptimized) and CASTEP- and Gaussian-optimized conformations
R R
4
R
1
2
-Glc: R1=R3=R5=H, R2=OMe, R4=R6=OBz
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