Gas-phase infrared spectroscopy of glycans and glycoconjugates

Greis, Kim; Kirschbaum, Carla; Helden, Gert von; Pagel, Kevin

doi:10.1016/j.sbi.2021.11.006

Cited by 15 publications

(16 citation statements)

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“…Their selectivities were compared to acetylated and benzylated building blocks 4Ac and 4Bn . In parallel, the glycosyl cation intermediates of the 4/6/4,6Piv building blocks were structurally characterized using cryogenic gas-phase infrared (IR) spectroscopy in helium nanodroplets and density functional theory (DFT). , This approach allows investigating the intermediate of S N 1-like glycosylation reactions. Finally, the most promising building block, 4Piv , was used in automated glycan assembly to synthesize an α(1,3)- d -trigalactopyranoside.…”

Section: Introductionmentioning

confidence: 99%

The Influence of the Electron Density in Acyl Protecting Groups on the Selectivity of Galactose Formation

et al. 2022

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The stereoselective formation of 1,2-cis-glycosidic bonds is a major bottleneck in the synthesis of carbohydrates. We here investigate how the electron density in acyl protecting groups influences the stereoselectivity by fine-tuning the efficiency of remote participation. Electron-rich C4-pivaloylated galactose building blocks show an unprecedented α-selectivity. The trifluoroacetylated counterpart with electron-withdrawing groups, on the other hand, exhibits a lower selectivity. Cryogenic infrared spectroscopy in helium nanodroplets and density functional theory calculations revealed the existence of dioxolenium-type intermediates for this reaction, which suggests that remote participation of the pivaloyl protecting group is the origin of the high α-selectivity of the pivaloylated building blocks. According to these findings, an α-selective galactose building block for glycosynthesis is developed based on rational considerations and is subsequently employed in automated glycan assembly exhibiting complete stereoselectivity. Based on the obtained selectivities in the glycosylation reactions and the results from infrared spectroscopy and density functional theory, we suggest a mechanism by which these reactions could proceed.

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Section: Introductionmentioning

confidence: 99%

The Influence of the Electron Density in Acyl Protecting Groups on the Selectivity of Galactose Formation

et al. 2022

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Section: Glycosaminoglycansmentioning

confidence: 99%

“…Most conventional approaches are action spectroscopy techniques 65 in which a photon-mediated “action” such as dissociation or fragmentation is monitored as a function of the wavelength. InfraRed multiple photon dissociation (IRMPD) spectroscopy is based on the sequential absorption of multiple photons.…”

Section: Glycosaminoglycansmentioning

confidence: 99%

“… 68 This problem can be overcome by cryogenic gas-phase IR spectroscopy in which the ions are cooled prior to irradiation, either in a cold trap with subsequent messenger tagging 69 or by encapsulation in superfluid helium nanodroplets 70 ( Figure 5 ). Even though the underlying principles and the temperature are different in both techniques, 65 the spectra are generally comparable: they exhibit narrow and well-resolved vibrational bands that are diagnostic to minute structural details. In combination with sophisticated molecular calculations at the density functional theory (DFT) level, the resulting spectra can be used to obtain detailed structural models of the investigated ions.…”

Section: Glycosaminoglycansmentioning

confidence: 99%

“…The better availability of tunable benchtop lasers, which can cover a broad range of wavelengths, leads to increasing interest in applying gas-phase IR spectroscopy for various classes of biomolecules, 64 including sugars. 65 Most conventional approaches are action spectroscopy techniques 65 in which a photon-mediated "action" such as dissociation or fragmentation is monitored as a function of the wavelength. InfraRed multiple photon dissociation (IRMPD) spectroscopy is based on the sequential absorption of multiple photons.…”

Section: Ion Mobility Spectrometry (Ims)mentioning

confidence: 99%

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Glycosaminoglycans: What Remains To Be Deciphered?

Pérez

Makshakova

Angulo

et al. 2023

JACS Au

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Glycosaminoglycans (GAGs) are complex polysaccharides exhibiting a vast structural diversity and fulfilling various functions mediated by thousands of interactions in the extracellular matrix, at the cell surface, and within the cells where they have been detected in the nucleus. It is known that the chemical groups attached to GAGs and GAG conformations comprise “glycocodes” that are not yet fully deciphered. The molecular context also matters for GAG structures and functions, and the influence of the structure and functions of the proteoglycan core proteins on sulfated GAGs and vice versa warrants further investigation. The lack of dedicated bioinformatic tools for mining GAG data sets contributes to a partial characterization of the structural and functional landscape and interactions of GAGs. These pending issues will benefit from the development of new approaches reviewed here, namely (i) the synthesis of GAG oligosaccharides to build large and diverse GAG libraries, (ii) GAG analysis and sequencing by mass spectrometry (e.g., ion mobility-mass spectrometry), gas-phase infrared spectroscopy, recognition tunnelling nanopores, and molecular modeling to identify bioactive GAG sequences, biophysical methods to investigate binding interfaces, and to expand our knowledge and understanding of glycocodes governing GAG molecular recognition, and (iii) artificial intelligence for in-depth investigation of GAGomic data sets and their integration with proteomics.

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