The role of the mobile proton in fucose migration

Fucose migration reactions represent a substantial challenge in the analysis of fucosylated glycan structures by mass spectrometry. In addition to the well-established observation of transposed fucose residues in glycan-dissociation product ions, recent experiments show that the rearrangement can also occur in intact glycan ions. These results suggest a low-energy barrier for migration of the fucose residue and broaden the relevance of fucose migration to include other types of mass spectrometry experiments, including ion mobility-mass spectrometry and ion spectroscopy. In this work, we utilize cold-ion infrared spectroscopy to provide further insight into glycan scrambling in intact glycan ions. Our results show that the mobility of the proton is a prerequisite for the migration reaction. For the prototypical fucosylated glycans Lewis x and blood group antigen H-2, the formation of adduct ions or the addition of functional groups with variable proton affinity yields significant differences in the infrared spectra. These changes correlate well with the promotion or inhibition of fucose migration through the presence or absence of a mobile proton

an ion mobility-mass spectrometry study

Coordinative halogen bonds have recently gained interest for the assembly of supramolecular capsules. Ion mobility-mass spectrometry and theoretical calculations now reveal the well-defined gas-phase structures of dimeric and hexameric [N⋯I+⋯N] halogen-bonded capsules with counterions located inside their cavities as guests. The solution reactivity of the large hexameric capsule shows the intriguing solvent-dependent equilibrium between the hexamer and an unprecedented pentameric [N⋯I+⋯N] halogen-bonded capsule, when the solvent is changed from chloroform to dichloromethane. The intrinsic flexibility of the cavitands enables this novel structure to adopt a pseudo-trigonal bipyramidal geometry with nine [N⋯I+⋯N] bonds along the edges and two pyridine binding sites uncomplexed

Publisher Correction: Unravelling the structure of glycosyl cations via cold-ion infrared spectroscopy

Correction to: Nature Communications https://doi.org/10.1038/s41467-018-06764-3; published online 09 October 2018 The original version of this Article contained an error in Fig. 1, in which an oxygen atom was missing from the ‘Acetoxonium type’ structure. The correct version of Fig.

H-Bond Isomerization in Crystalline Cellulose IIII: Proton Hopping versus Hydroxyl Flip-Flop

Based on density-functional theory calculations, we discuss three forms of cellulose III_I that are characterized by different intersheet H-bonding patterns. Two alternative mechanisms can facilitate the interconversion between these H-bonding patterns: the rotation of hydroxy groups (“flip-flop”) or a concerted proton transfer from one hydroxy group to the other (“proton hopping”). Both mechanisms have energy barriers of very similar height. Electronic structure theory methods allow us to study effects that involve the breaking/forming bonds, like the hopping of protons. In many of the force field formulations, in particular, the ones that are typically used to study cellulose, such effects are not considered. However, such insight at the atomistic and electronic scale can be the key to finding energy-efficient means for cellulose deconstruction

Aqueous Solvation of Polyalanine α-Helices with Specific Water Molecules and with the CPCM and SM5.2 Aqueous Continuum Models Using Density Functional Theory

We present density functional theory (DFT) calculations at the X3LYP/D95(d,p) level on the solvation of polyalanine α-helices in water. The study includes the effects of discrete water molecules and the CPCM and AMSOL SM5.2 solvent continuum model both separately and in combination. We find that individual water molecules cooperatively hydrogen-bond to both the C- and N-termini of the helix, which results in increases in the dipole moment of the helix/water complex to more than the vector sum of their individual dipole moments. These waters are found to be more stable than in bulk solvent. On the other hand, individual water molecules that interact with the backbone lower the dipole moment of the helix/water complex to below that of the helix itself. Small clusters of waters at the termini increase the dipole moments of the helix/water aggregates, but the effect diminishes as more waters are added. We discuss the somewhat complex behavior of the helix with the discrete waters in the continuum models

Assessing the stability of alanine-based helices by conformer-selective IR spectroscopy

Polyalanine based peptides that carry a lysine at the C-terminus ([Ac-Ala(n)Lys + H](+)) are known to form alpha-helices in the gas phase. Three factors contribute to the stability of these helices: (i) the interaction between the helix macro dipole and the charge, (ii) the capping of dangling C=O groups by lysine and (iii) the cooperative hydrogen bond network. In previous studies, the influence of the interaction between the helix dipole and the charge as well as the impact of the capping was studied intensively. Here, we complement these findings by systematically assessing the third parameter, the H-bond network. In order to selectively remove one H-bond along the backbone, we use amide-to-ester substitutions. The resulting depsi peptides were analyzed by ion-mobility and m/z-selective infrared spectroscopy as well as theoretical calculations. Our results indicate that peptides which contain only one ester bond still maintain the helical conformation. We conclude that the interaction between the charge and the helix macro-dipole is most crucial for the formation of the alpha-helical conformation and a single backbone H-bond has only little influence on the overall stability.114Nsciescopu

Assessing the Accuracy of Across-the-Scale Methods for Predicting Carbohydrate Conformational Energies for the Examples of Glucose and α‑Maltose

A big hurdle when entering the field of carbohydrate research stems from the complications in the analytical and computational treatment. In effect, this extremely important class of biomolecules remains underinvestigated when compared, for example, with the maturity of genomics and proteomics research. On the theory side, the commonly used empirical methods suffer from an insufficient amount of high-quality experimental data against which they can be thoroughly validated. In order to provide a pivotal point for an ascent of accurate carbohydrate simulations, we present here a structure/energy benchmark set of diverse glucose (in three isomeric forms) and α-maltose conformations at the coupled-cluster level as well as an assessment of commonly used energy functions. We observe that empirical force fields and semiempirical approaches, on average, do not reproduce accurately the reference energy hierarchies. While the force fields maintain accuracy for the low-energy structures, the semiempirical methods perform unsatisfactory for the entire range. On the contrary, density-functional approximations reproduce the reference energy hierarchies with better than chemical accuracy already at the generalized gradient approximation level (GGA). Particularly, the novel meta-GGA functional SCAN provides the accuracy of more expensive hybrid functionals at fraction of their computational cost. In conclusion, we advocate for electronic-structure theory methods to become the routine tool for simulations of carbohydrates

Surprising solvent-induced structural rearrangements in large [N center dot center dot center dot I+center dot center dot center dot N] halogen-bonded supramolecular capsules : an ion mobility-mass spectrometry study

Coordinative halogen bonds have recently gained interest for the assembly of supramolecular capsules. Ion mobility-mass spectrometry and theoretical calculations now reveal the well-defined gas-phase structures of dimeric and hexameric [NI+N] halogen-bonded capsules with counterions located inside their cavities as guests. The solution reactivity of the large hexameric capsule shows the intriguing solvent-dependent equilibrium between the hexamer and an unprecedented pentameric [NI+N] halogen-bonded capsule, when the solvent is changed from chloroform to dichloromethane. The intrinsic flexibility of the cavitands enables this novel structure to adopt a pseudo-trigonal bipyramidal geometry with nine [NI+N] bonds along the edges and two pyridine binding sites uncomplexed