Mixing water, sugar, and lipid: Conformations of isolated and micro-hydrated glycolipids in the gas phase.

Both sugars and lipids are important biomolecular building blocks with exceptional conformational flexibility and adaptability to their environment. Glycolipids bring together these two molecular components in the same assembly and combine the complexity of their conformational landscapes. In the present study, we have used selective double resonance vibrational spectroscopy, in combination with a computational approach, to explore the conformational preferences of two glycolipid models (3-0-acyl catechol and guaiacol α-D-glucopyranosides), either fully isolated in the gas phase or controlled interaction with a single water molecule. We could identify the preferred conformation and structures of the isolated and micro-hydrated species and evidence of the presence of a strong water pocket, which may influence the conformational flexibility of such systems, even in less controlled environments.

Conformationally Restricted ß-Sheet Breaker Peptides Incorporating Cyclic α-Methylisoserine Sulfamidates.

Peptides containing variations of the ß-amyloid hydrophobic core and five-membered sulfamidates derived from ß-amino acid α-methylisoserine have been synthesized and fully characterized in the gas phase, solid state and in aqueous solution by a combination of experimental and computational techniques. The cyclic sulfamidate group effectively locks the secondary structure at the N-terminus of such hybrid peptides imposing a conformational restriction and stabilizing non-extended structures. This conformational bias, which is maintained in the gas phase, solid state and aqueous solution, is shown to be resistant to structure templating through assays of in vitro ß-amyloid aggregation, acting as ß-sheet breaker peptides with moderate activity.

Isotopic dependence of intramolecular and intermolecular vibrational couplings in cooperative hydrogen bond networks: singly hydrated phenyl-α-D-mannopyranoside as a case study.

Hydrogen bonding (HB) is associated with frequency shifts, spectral broadening and intensity variation of the vibrational bands of the donor stretching modes. This is true in all systems, from the most basic molecular models, to more complex ones, and biological molecules. In the gas phase, the latter can be either fully isolated, with only intramolecular HB, or micro-solvated. The conformations of such systems are stabilized by networks of intramolecular and intermolecular HB where the donor groups can be coupled. This has been well-identified in the case of singly hydrated monosaccharides and in particular for phenyl-α-D-mannopyranoside, where the addition of a single water molecule reduces the number of observed conformations to a unique one, stabilized by such a cooperative network of intramolecular and intermolecular HB. In the present study we have re-examined this prototypical system to scrutinize subtle effects of isotopic substitution in the solvent molecule. Besides the obvious isotopic shift, coupling between intramolecular modes of sugar and water is observed, promoted by the intermolecular HB. The systematic substitution of water with heavy water, or methanol, also allowed the decomposition of the relation between HB strength and frequency shift.

Consistent characterization of the electronic ground state of iron(II) phthalocyanine from valence and core-shell electron spectroscopy.

We studied the iron(II) phthalocyanine molecule in the gas-phase. It is a complex transition organometallic compound, for which, the characterization of its electronic ground state is still debated more than 50 years after the first published study. Here, we show that to determine its electronic ground state, one needs a large corpus of data sets and a consistent theoretical methodology to simulate them. By simulating valence and core-shell electron spectra, we determined that the ground state is a 3Eg and that the ligand-to-metal charge transfer has a large influence on the spectra.

Investigating the Conformation of the Bridged Monosaccharide Levoglucosan.

Levoglucosan is one of the main products of the thermal degradation of glucose and cellulose and is commonly used as a tracer for biomass burning. Herein we report a conformational analysis of levoglucosan under isolation conditions, by means of microwave spectroscopy coupled with ultrafast laser vaporization in supersonic expansions. We observed three different conformations of levoglucosan in the gas phase. They all share a common heavy atom rigid bicyclic structure. The difference between the three of them lies in the network of intramolecular hydrogen bonds that arises from the OH groups at positions 2, 3 and 4. The different combinations of H-bonds give richness to the conformational landscape of levoglucosan. The gas phase conformers obtained in this work are compared to the crystal structure of levoglucosan previously reported. Although the heavy atom frame remains unchanged, there are significant differences in the positions of the H-atoms. In addition, the levoglucosan structure can be compared to the related glucose, for which gas phase conformational studies exist in the literature. In this case, in going from glucose to levoglucosan, there is an inversion in the chair conformation of the pyranose ring. This forces the OH groups to adopt axial positions (instead of the more favorable equatorial positions in glucose) and completely changes the pattern of intramolecular H-bonds.

Sensing the anomeric effect in a solvent-free environment.

The anomeric effect is a chemical phenomenon that refers to an observed stabilization of six-membered carbohydrate rings when they contain an electronegative substituent at the C1 position of the ring. This stereoelectronic effect influences the three-dimensional shapes of many biological molecules. It can be manifested not only in this classical manner involving interaction of the endocyclic oxygen atom (O5) found in such sugars with the C1 substituent (endo-anomeric effect) but also through a corresponding interaction of the electronegative exocyclic substituent with O5 (exo-anomeric effect). However, the underlying physical origin(s) of this phenomenon is still not clear. Here we show, using a combination of laser spectroscopy and computational analysis, that a truncated peptide motif can engage the two anomers of an isolated sugar in the gas phase, an environment lacking extraneous factors which could confound the analysis. (Anomers are isomers that differ in the orientation of the substituent at C1.) Complexes formed between the peptide and the α- or ß-anomers of d-galactose are nearly identical structurally; however, the strength of the polarization of their interactions with the peptide differs greatly. Natural bond order calculations support this observation, and together they reveal the dominance of the exo- over the endo-anomeric effect. As interactions between oxygen atoms at positions C1 and C2 (O1 and O2, respectively) on the pyranose ring can alter the exo/endo ratio of a carbohydrate, our results suggest that it will be important to re-evaluate the influence, and biological effects, of substituents at position C2 in sugars.

Using high harmonic radiation to reveal the ultrafast dynamics of radiosensitiser molecules.

5-Fluorouracil (5FU) is a radiosensitiser molecule routinely used in combined chemo- and radio-therapies to enhance and localize cancer treatments. We have employed ultra-short XUV pulses produced by high harmonic generation (HHG) as a pump pulse to study the dynamics underlying the photo-stability and the radiation damage of this molecule. This work shows that it is possible to resolve individual dynamics even when using unselected HH. By comparing the results with those obtained in the multiphoton absorption at 400 nm, we were able to identify the frequencies of the HH comb relevant to the recorded dynamics: HH5 and HH3. The latter excites a high-lying Rydberg state interacting with a valence state and its dynamics is revealed by a 30 fs decay signal in the parent ion transient. Our results suggest that the same photoprotection mechanisms as those conferring photostability to the neutral nucleobases and to the DNA appear to be activated: HH5 excites the molecule to a state around 10.5 eV that undergoes an ultrafast relaxation on a timescale of 30 fs due to nonadiabatic interactions. This is followed sequentially by a 2.3 ps internal conversion as revealed by the dynamics observed for another fragment ion. These dynamics are extracted from the fragment ion signals. Proton or hydrogen transfer processes are required for the formation of three fragments and we speculate that the time scale of one of the processes is revealed by a H+ transient signal.

Molecular gels in the gas phase? Gelator-gelator and gelator-solvent interactions probed by vibrational spectroscopy.

Benzylidene glucose (BzGlc) is a member of the benzylidene glycoside family. These molecules have the ability to form molecular physical gels. These materials are formed when gelator molecules create a non-covalently bound frame where solvent molecules are trapped. Since the gel formation process and its properties are determined by the subtle balance between non-covalent forces, it is difficult to anticipate them. Quantitative and qualitative understanding of the gelator-gelator and gelator-solvent interactions is needed to better control these materials for important potential applications. We have used gas phase vibrational spectroscopy and theoretical chemistry to study the conformational choices of BzGlc, its dimer and the complexes it forms with water or toluene. To interpret the vibrational spectra we have used the dispersion corrected functional B97D which we have calibrated for the calculation of OH stretching frequencies. Even at the most basic molecular level, it is possible to interrogate a large range of non-covalent interactions ranging from OH → OH hydrogen bonding, to OH → π, and CH → π, all being at the center of gel properties at the macroscopic level.

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).

Solvent contribution to the stability of a physical gel characterized by quasi-elastic neutron scattering.

The dynamics of a physical gel, namely, low-molecular-mass organic gelator methyl-4,6-O-benzylidene-α-D-mannopyranoside (α-manno) in water and toluene, are probed by neutron scattering. Using high gelator concentrations, we were able to determine, on a time scale from a few picoseconds to 1 nanosecond, the number of solvent molecules that are immobilized by the rigid network formed by the gelators. We found that only a few toluene molecules per gelator participate in the network which is formed by hydrogen bonding between the gelators' sugar moieties. In water, however, the interactions leading to the gel formations are weaker, involving dipolar, hydrophobic, or π-π interactions, and hydrogen bonds are formed between the gelators and the surrounding water. Therefore, around 10 to 14 water molecules per gelator are immobilized by the presence of the network. This study shows that neutron scattering can give valuable information about the behavior of solvent confined in a molecular gel.

'Naked' and hydrated conformers of the conserved core pentasaccharide of N-linked glycoproteins and its building blocks.

N-glycosylation of eukaryotic proteins is widespread and vital to survival. The pentasaccharide unit -Man3GlcNAc2- lies at the protein-junction core of all oligosaccharides attached to asparagine side chains during this process. Although its absolute conservation implies an indispensable role, associated perhaps with its structure, its unbiased conformation and the potential modulating role of solvation are unknown; both have now been explored through a combination of synthesis, laser spectroscopy, and computation. The proximal -GlcNAc-GlcNAc- unit acts as a rigid rod, while the central, and unusual, -Man-ß-1,4-GlcNAc- linkage is more flexible and is modulated by the distal Man-α-1,3- and Man-α-1,6- branching units. Solvation stiffens the 'rod' but leaves the distal residues flexible, through a ß-Man pivot, ensuring anchored projection from the protein shell while allowing flexible interaction of the distal portion of N-glycosylation with bulk water and biomolecular assemblies.

Exploring carbohydrate-peptide interactions in the gas phase: structure and selectivity in complexes of pyranosides with N-acetylphenylalanine methylamide.

The physical basis of carbohydrate-peptide interactions has been explored by probing the structures of a series of complexes generated 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 of the model, N-acetyl-L-phenylalanine methylamide, bound to the α and ß anomers of methyl D-gluco- and D-galactopyranoside as guests. In all cases, the carbohydrates are bound through hydrogen bonding to the dipeptide chain, although with some differing patterns. The amino acid host "engages" with the most suitable pair of neighboring conjugate sites on each carbohydrate; the specific choice depends on the conformation of the peptide backbone and the configuration and conformation of the carbohydrate ligand. None of the structures is supported by "stacking" interactions with the aromatic ring, despite their common occurrence in bound carbohydrate-protein structures.

Dehalogenation of 5-halo-uracil molecules induced by 100 keV proton collisions.

Neutral and cationic halogen loss of singly and doubly ionised 5-X-uracil (X = F, Cl, Br, I) after collisions with 100 keV protons have been studied in the gas phase. The rates of these dissociation channels are strongly dependant on the nature of the halogen substituent. It is very weak in the case of fluorine but is a dominant channel for iodine. Dissociation mechanisms are proposed for a number of significant channels associated to dehalogenation. It is suggested that some final ion products originate from specific processes. For instance, ion products of mass 38, 39 and 40 amu are very sensitive to the nature of the primarily ejected halogen and result from pathways associated to dehydrogenation and transient formation of the dehalogenated uracil cation.

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 ß anomers of methyl d-gluco- and d-galacto- and l-fucopyranosides (α/ßMeGlc, 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/ßMeGal. These adopt stacked intermolecular structures in marked contrast to those with α/ßMeGlc; 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.

Building up key segments of N-glycans in the gas phase: intrinsic structural preferences of the alpha(1,3) and alpha(1,6) dimannosides.

The intrinsic conformer specific vibrational spectra of two important subunits of the core pentasaccharide of N-linked glycans, the alpha(1,3) and alpha(1,6) dimannosides, have been recorded in the gas phase. Coupling these measurements with a computational exploration of their conformational landscapes has enabled their conformational assignment and has identified characteristic vibrational signatures associated with particular conformational families-including those that do or do not display inter-ring hydrogen bonding across the glycosidic linkage. In addition, the IR spectra of the monosaccharide moieties provide benchmarks, through which the conformational assignments can be refined. This introduces a general concept of modularity and secondary structure in oligosaccharides--essential for the success of similar studies on larger oligosaccharides in the future.

Spectral signatures and structural motifs in isolated and hydrated monosaccharides: phenyl alpha- and beta-l-fucopyranoside.

The conformation and structure of phenyl-alpha-l-fucopyranoside (alpha-PhFuc), phenyl-beta-L-fucopyranoside (beta-PhFuc) and their singly hydrated complexes (alpha,beta-PhFuc.H(2)O) isolated in a molecular beam, have been investigated by means of resonant two photon ionization (R2PI) spectroscopy and ultraviolet and infrared ion-dip spectroscopy. Conformational and structural assignments have been based on comparisons between their experimental and computed near IR spectra, calculated using density functional theory (DFT) and their relative energies, determined from ab initio (MP2) calculations. The near IR spectra of "free" and hydrated alpha- and beta-PhFuc, and many other mono- and di-saccharides, provide extremely sensitive probes of hydrogen-bonded interactions which can be finely tuned by small (or large) changes in the molecular conformation. They provide characteristic "signatures" which reflect anomeric, or axial vs. equatorial differences, both revealed through comparisons between alpha/beta-PhFuc and alpha/beta-PhXyl; or similarities, revealed through comparisons between fucose (6-deoxy galactose) and galactose; or binding motifs, for example, "insertion" vs. "addition" structures in hydrated complexes. At the monosaccharide level (the first step in the carbohydrate hierarchy), these trends appear to be general. In contrast to the monohydrates of galactose (beta-PhGal) and glucose (beta-PhGlc), the conformations of alpha- and beta-PhFuc are unaffected by the binding of a single water molecule though changes in the R2PI spectra of multiply hydrated alpha-PhFucW(n) however, may reflect a conformational transformation when n> or = 3.

Hydrogen bonding and cooperativity in isolated and hydrated sugars: mannose, galactose, glucose, and lactose.

The conformation of phenyl-substituted monosaccharides (mannose, galactose, and glucose) and their singly hydrated complexes has been investigated in the gas phase by means of a combination of mass selected, conformer specific ultraviolet and infrared double resonance hole burning spectroscopy experiments, and ab initio quantum chemistry calculations. In each case, the water molecule inserts into the carbohydrate at a position where it can replace a weak intramolecular interaction by two stronger intermolecular hydrogen bonds. The insertion can produce significant changes in the conformational preferences of the carbohydrates, and there is a clear preference for structures where cooperative effects enhance the stability of the monosaccharide conformers to which the water molecule chooses to bind. The conclusions drawn from the study of monosaccharide-water complexes are extended to the disaccharide lactose and discussed in the light of the underlying mechanisms that may be involved in the binding of carbohydrate assemblies to proteins and the involvement, or not, of key structural water molecules.

Adding water to sugar: a spectroscopic and computational study of alpha- and beta-phenylxyloside in the gas phase.

The gas phase structures of phenyl alpha- and beta-d-xylopyranoside (alpha- and beta-pXyl) and their mono-hydrates have been investigated using a combination of resonant two-photon ionization (R2PI), ultra-violet hole-burning and resonant infrared ion dip spectroscopy, coupled with density functional theory (DFT) and ab initio computation. The hole-burning experiments indicate the population of a single conformer only, in each of the two anomers. Their experimental and calculated infrared spectra are both consistent with a conformational assignment corresponding to the computed global minimum configuration. All three OH groups are oriented towards the oxygen atom (O1) on the anomeric carbon atom to form an all trans(ttt) counter-clockwise chain of hydrogen bonds. The mono-hydrates, alpha- and beta-pXyl(H(2)O) each populate two distinct structures in the molecular beam environment, with the water molecule inserted between OH4 and OH3 or between OH3 and OH2 in alpha-pXyl(H2O), and between OH2 and O1 in either of two alternative orientations, in beta-pXyl(H2O). In all of the mono-hydrated xyloside complexes, the water molecule inserts into the weakest link of the sugar molecules' hydrogen-bonded chain of hydroxy groups, creating a single extended chain, strengthened by co-operativity. The all-trans configuration of the xylose moiety is retained and the mono-hydrate structures correspond to those calculated to lie at the lowest relative energies.

UV spectra of benzene isotopomers and dimers in helium nanodroplets.

We report spectra of various benzene isotopomers and their dimers in helium nanodroplets in the region of the first Herzberg-Teller allowed vibronic transition 6(0)(1) (1)B(2u)<--(1)A(1g) (the A(0) (0) transition) at approximately 260 nm. Excitation spectra have been recorded using both beam depletion detection and laser-induced fluorescence. Unlike for many larger aromatic molecules, the monomer spectra consist of a single "zero-phonon" line, blueshifted by approximately 30 cm(-1) from the gas phase position. Rotational band simulations show that the moments of inertia of C(6)H(6) in the nanodroplets are at least six-times larger than in the gas phase. The dimer spectra present the same vibronic fine structure (though modestly compressed) as previously observed in the gas phase. The fluorescence lifetime and quantum yield of the dimer are found to be equal to those of the monomer, implying substantial inhibition of excimer formation in the dimer in helium.

Probing the glycosidic linkage: UV and IR ion-dip spectroscopy of a lactoside.

The beta(1-->4) glycosidic linkage found in lactose is a prevalent structural motif in many carbohydrates and glycoconjugates. Using UV and IR ion-dip spectroscopies to probe benzyl lactoside isolated in the gas phase, we find that the disaccharide unit adopts only a single, rigid structure. Its fully resolved infrared ion-dip spectrum is in excellent agreement with that of the global minimum structure computed ab initio. This has glycosidic torsion angles of phi(H) (H1-C1-O-C4') approximately 180 degrees and psi(H) (C1-O-C4'-H4') approximately 0 degrees which correspond to a rotation of approximately 150 degrees about the glycosidic bond compared to the accepted solution-phase conformation. We discuss the biological implications of this discovery and the generality of the strategies employed in making it.