Literature DB >> 26119005

Anharmonic simulations of the vibrational spectrum of sulfated compounds: application to the glycosaminoglycan fragment glucosamine 6-sulfate.

Loïc Barnes1, Baptiste Schindler, Abdul-Rahman Allouche, Daniel Simon, Stéphane Chambert, Jos Oomens, Isabelle Compagnon.   

Abstract

Mid-infrared spectroscopy coupled with mass spectrometry is an appealing tool for the sequencing and structural elucidation of functional modifications in biopolymers, as it offers direct spectroscopic identification of the functionality where the traditional mass spectrometric approach is insufficient. Whereas the gas phase vibrational spectroscopy of peptides (and to a lesser extent saccharides) has been widely investigated, sulfation has attracted much less attention, despite its prevalence in natural polymers. The simulation of the vibrational spectra of such functionalized compounds is however notoriously challenging, which impairs the interpretation of spectroscopic data in terms of structure. Driven by a striking case of such a failure for a sulfated glycosaminoglycan fragment, we elaborate on an original hybrid GVPT2 anharmonic approach. This strategy offers a significantly improved accuracy in the description of the sulfate modes, without the recourse to empirical scaling factors, and with a greatly reduced computational cost which is otherwise prohibitive for molecules of this size. Alternatively, we propose a selection of reasonably accurate harmonic methods with adequate scaling factors optimized on a set of benchmark compounds.

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Year:  2015        PMID: 26119005     DOI: 10.1039/c5cp02079d

Source DB:  PubMed          Journal:  Phys Chem Chem Phys        ISSN: 1463-9076            Impact factor:   3.676


  7 in total

1.  Analysis of Sulfate Patterns in Glycosaminoglycan Oligosaccharides by MSn Coupled to Infrared Ion Spectroscopy: the Case of GalNAc4S and GalNAc6S.

Authors:  G Renois-Predelus; B Schindler; I Compagnon
Journal:  J Am Soc Mass Spectrom       Date:  2018-04-26       Impact factor: 3.109

Review 2.  Glycosaminoglycanomics: where we are.

Authors:  Sylvie Ricard-Blum; Frédérique Lisacek
Journal:  Glycoconj J       Date:  2016-11-30       Impact factor: 2.916

3.  Fast and accurate hybrid QM//MM approach for computing anharmonic corrections to vibrational frequencies.

Authors:  Loïc Barnes; Baptiste Schindler; Isabelle Compagnon; Abdul-Rahman Allouche
Journal:  J Mol Model       Date:  2016-11-02       Impact factor: 1.810

Review 4.  Mass Spectrometry-Based Techniques to Elucidate the Sugar Code.

Authors:  Márkó Grabarics; Maike Lettow; Carla Kirschbaum; Kim Greis; Christian Manz; Kevin Pagel
Journal:  Chem Rev       Date:  2021-09-07       Impact factor: 72.087

5.  Anomeric memory of the glycosidic bond upon fragmentation and its consequences for carbohydrate sequencing.

Authors:  Baptiste Schindler; Loïc Barnes; Gina Renois; Christopher Gray; Stéphane Chambert; Sébastien Fort; Sabine Flitsch; Claire Loison; Abdul-Rahman Allouche; Isabelle Compagnon
Journal:  Nat Commun       Date:  2017-10-17       Impact factor: 14.919

Review 6.  Gas-Phase Infrared Spectroscopy of Neutral Peptides: Insights from the Far-IR and THz Domain.

Authors:  Sjors Bakels; Marie-Pierre Gaigeot; Anouk M Rijs
Journal:  Chem Rev       Date:  2020-02-19       Impact factor: 60.622

7.  Characterization of Cyclic N-Acyliminium Ions by Infrared Ion Spectroscopy.

Authors:  Jona Merx; Kas J Houthuijs; Hidde Elferink; Eva Witlox; Jasmin Mecinović; Jos Oomens; Jonathan Martens; Thomas J Boltje; Floris P J T Rutjes
Journal:  Chemistry       Date:  2021-12-29       Impact factor: 5.020

  7 in total

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