Exploring the interaction sites in glucose and galactose using phenol as a probe

Sugars, together with amino acids and nucleobases, are the fundamental building blocks of a cell. They are involved in many fundamental processes and they especially play relevant roles as part of the immune system. The latter is connected to their ability to establish a collection of intermolecular interactions, depending on the position of their hydroxyl groups. Here we explore how the position of the OH in C4, the anomeric conformation and the nature substituent affect the interaction with phenol, which serves as a probe of the preferred site for the interaction. Using mass-resolved excitation spectroscopy and density functional calculations, we unravel the structure of the dimers and compare their conformation with those found for similar systems. The main conclusion is that the hydroxymethyl group has a very strong influence, guiding the whole aggregation process and that the position of the substituent in C4 has a stronger influence on the final structure of the dimer than the anomeric conformation.

Laboratory Observation of, Astrochemical Search for, and Structure of Elusive Erythrulose in the Interstellar Medium

Rotational spectroscopy provides the most powerful means of identifying molecules of biological interest in the interstellar medium (ISM), but despite their importance, the detection of carbohydrates has remained rather elusive. Here, we present a comprehensive Fourier transform rotational spectroscopic study of elusive erythrulose, a sugar building block likely to be present in the ISM, employing a novel method of transferring the hygroscopic oily carbohydrate into the gas phase. The high sensitivity of the experiment allowed the rotational spectra of all monosubstituted isotopologue species of ¹³C-¹²C₃H₈O₄ to be recorded, which, together with quantum chemical calculations, enabled us to determine their equilibrium geometries (r_e^SE) with great precision. Searches employing the new experimental data for erythrulose have been undertaken in different ISM regions, so far including the cold areas Barnard 1, the pre-stellar core TMC-1, Sagittarius B2. Although no lines of erythrulose were found, this data will serve to enable future searches and possible detections in other ISM regions.

Conformational Landscape of the 1/1 Diacetyl/Water Complex Investigated by Infrared Spectroscopy and ab Initio Calculations

The complexes of diacetyl with water have been studied experimentally by Fourier transform infrared (FTIR) spectroscopy coupled to solid neon matrix and supersonic jet, and anharmonic ab initio calculations. The vibrational analysis of neon matrix spectra over the 100-7500 cm^-1 infrared range confirms the existence of two nearly isoenergetic one-to-one (1/1) diacetyl-water S₁ and S₂ isomers already evidenced in a previous argon matrix study. A third form (S₃) predicted slightly less stable ( J. Mol. Mod. 2015 , 21 , 214 ) is not observed. The correct agreement obtained between neon matrix and anharmonic calculated vibrational frequencies is exploited in several cases to derive band assignments for the vibrational modes of a specific isomer. Thereafter, theoretical x_ij anharmonic coupling constants are used for the attribution of combination bands and overtones relative to the 1/1 dimer. Finally, the most stable isomer of the one-to-two (1/2) diacetyl-water complex is identified in the OH stretching region of water on the grounds of comparison of experimental and calculated vibrational shifts between water dimer and the three most stable 1/2 isomers.

Physical characterization and in silico modeling of inulin polymer conformation during vaccine adjuvant particle formation

This study combined physical data from synchrotron SAXS, FTIR and microscopy with in-silico molecular structure predictions and mathematical modeling to examine inulin adjuvant particle formation and structure. The results show that inulin polymer chains adopt swollen random coil in solution. As precipitation occurs from solution, interactions between the glucose end group of one chain and a fructose group of an adjacent chain help drive organized assembly, initially forming inulin ribbons with helical organization of the chains orthogonal to the long-axis of the ribbon. Subsequent aggregation of the ribbons results in the layered semicrystalline particles previously shown to act as potent vaccine adjuvants. γ-Inulin adjuvant particles consist of crystalline layers 8.5 nm thick comprising helically organized inulin chains orthogonal to the plane of the layer. These crystalline layers alternate with amorphous layers 2.4 nm thick, to give overall particle crystallinity of 78%.

Local NH–π interactions involving aromatic residues of proteins: influence of backbone conformation and ππ* excitation on the π H-bond strength, as revealed from studies of isolated model peptides

Gas phase conformer-selective IR spectroscopy combined and relevant quantum chemistry methods document the NH–π interactions in Phe residues.

O-H⋅⋅⋅N and C-H⋅⋅⋅O hydrogen bonds control hydration of pivotal tropane alkaloids: tropinone⋅⋅⋅H(2)O complex

The effect of monohydration in equatorial/axial isomerism of the common motif of tropane alkaloids is investigated in a supersonic expansion by using Fourier-transform microwave spectroscopy. The rotational spectrum reveals the equatorial isomer as the dominant species in the tropinone⋅⋅⋅H2 O complex. The monohydrated complex is stabilized primarily by a moderate OH⋅⋅⋅N hydrogen bond. In addition, two CH⋅⋅⋅O weak hydrogen bonds also support this structure, blocking the water molecule and avoiding any molecular dynamics in the complex. The water molecule acts as proton donor and chooses the ternary amine group over the carbonyl group as a proton acceptor. The experimental work is supported by theoretical calculations; the accuracy of the B3LYP, M06-2X, and MP2 methods is also discussed.

Carbohydrates

Although carbohydrates represent one of the most important families of biomolecules, they remain under-studied in comparison to the other biomolecular families (peptides, nucleobases). Beyond their best-known function of energy source in living systems, they act as mediator of molecular recognition processes, carrying molecular information in the so-called "sugar code," just to name one of their countless functions. Owing to their high conformational flexibility, they encode extremely rich information conveyed via the non-covalent hydrogen bonds within the carbohydrate and with other biomolecular assemblies, such as peptide subunits of proteins. Over the last decade there has been tremendous progress in the study of the conformational preferences of neutral oligosaccharides, and of the interactions between carbohydrates and various molecular partners (water, aromatic models, and peptide models), using vibrational spectroscopy as a sensitive probe. In parallel, other spectroscopic techniques have recently become available to the study of carbohydrates in the gas phase (microwave spectroscopy, IRMPD on charged species).

Carbohydrate-aromatic interactions: vibrational spectroscopy and structural assignment of isolated monosaccharide complexes with p-hydroxy toluene and N-acetyl l-tyrosine methylamide

The nature of carbohydrate binding first to p-hydroxy toluene and then the capped amino acid, N-acetyl l-tyrosine methyl amide (AcTyrNHMe), has been investigated in a solvent-free environment under molecular beam conditions. A combination of double resonance IR-UV spectroscopy and quantum chemical calculations has established the structures of complexes with the α and β anomers of methyl d-gluco- and d-galacto- and l-fucopyranosides (α/βMeGlc, MeGal, MeFuc). The new results, when combined with dispersion-corrected DFT calculations, reveal gas phase structures which are dominated by hydrogen bonding but also with evidence of CH-π bonded interactions in complexes with α/βMeGal. These adopt stacked intermolecular structures in marked contrast to those with α/βMeGlc; p-OH → O bonds linking AcTyrNHMe, or p-hydroxy toluene, to the carbohydrate provide an anchor that facilitates further binding, both through OH → O and NH → O hydrogen bonds to the peptide backbone and through CH-π dispersion interactions with the aromatic side group. "Stacked" structures associated with dispersion interactions with the aromatic ring are not detected in the corresponding complexes of capped phenylalanine, despite their common occurrence in bound carbohydrate-protein structures.