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

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.

The Influence of Methoxy and Ethoxy Groups on Supramolecular Arrangement of Two Methoxy-chalcones

“…T h e t h e o r e t i c a l c a l c u l a t i o n s u s i n g CAM-B3LYP/6-311+g(d) systematically over-estimated the IR vibrational spectra and to avoid this we used a scale factor 48 of 0.958 with the objective of better convergence with the experimental results. The spectroscopic data are consistent with the crystal structure.…”

“…Frontier molecular orbitals of chalcones 1 and 2, followed by calculated homo and lumo band-gaps. In order to make a better comparison between theoretical and experimental results, we apply in the theoretical values a scaling factor of 0.958 48 for the results obtained at CAM-B3LYP/6-311+g(d) level of theory. This procedure corrects the systematic overestimation of the vibrational frequencies that is characteristic of the DFT methods and, besides, makes easier the assignments of the vibrational modes.…”

Thermal and spectroscopic studies of 2,3,5-trisubstituted and 1,2,3,5-tetrasubstituted indoles as non-competitive antagonists of GluK1/GluK2 receptors

“…Gaussian09 was also used to calculate IR spectra. The computed IR spectra were corrected using the scaling factor of 0.962 as recommended for this level of theory [24]. Moreover, the computed vibrational frequencies have been unambiguously assigned by means of the potential energy distribution (PED) analysis of all the fundamental vibration modes by using VEDA 4 program [25,26] as described previously [27][28][29][30].…”

IRMPD Spectroscopy Sheds New (Infrared) Light on the Sulfate Pattern of Carbohydrates

“…38 Density Functional Theory at the CAMB3LYP 39 level of theory with the 6--311++G(2df,2pd) 40,41 basis set was chosen to take in account the difficulties to simulate vibrational spectra of sulfated species. 18 The mode analysis was performed using Gabedit 42 and an empirical scaling factor of 0.947 was used to correct the frequency of stretching modes in the 2700--3700 cm --1 spectral range.…”

“…The conformational analysis of glucosamine 6--sulfate was previousy reported. 18,19 It was found that it adopts the same 4 C 1 chair ring conformation. The differences between the two IRMPD spectra thus originate solely from the different positions of the sulfate group and the induced differences in intra--molecular hydrogen bonding.…”