Resolving Sphingolipid Isomers Using Cryogenic Infrared Spectroscopy

1‐Deoxysphingolipids are a recently described class of sphingolipids that have been shown to be associated with several disease states including diabetic and hereditary neuropathy. The identification and characterization of 1‐deoxysphingolipids and their metabolites is therefore highly important. However, exact structure determination requires a combination of sophisticated analytical techniques due to the presence of various isomers, such as ketone/alkenol isomers, carbon–carbon double‐bond (C=C) isomers and hydroxylation regioisomers. Here we demonstrate that cryogenic gas‐phase infrared (IR) spectroscopy of ionized 1‐deoxysphingolipids enables the identification and differentiation of isomers by their unique spectroscopic fingerprints. In particular, C=C bond positions and stereochemical configurations can be distinguished by specific interactions between the charged amine and the double bond. The results demonstrate the power of gas‐phase IR spectroscopy to overcome the challenge of isomer resolution in conventional mass spectrometry and pave the way for deeper analysis of the lipidome.     

Tandem mass spectrometry for the analysis of self‐sorted pseudorotaxanes: the effects of Coulomb interactions

The increasing complexity of self‐assembled supramolecules generates the need for analytical techniques that can accurately elucidate their structures. Here, we explore the ability of tandem mass spectrometry to deliver structural information on a series of self‐sorted crown ether/ammonium pseudorotaxanes. Of these intertwined molecules, different charge states are accessible and the effects of Coulomb interactions on the fragmentation pattern can be examined. Three different cases can be distinguished: (1) one or more counterions are present in the complex and compete with the crown for binding to the ammonium ion. This destabilizes the supramolecular bond. (2) In multiply charged complexes, charge repulsion significantly alters the fragmentation behavior as compared with singly charged ions. (3) If guest and host are both charged, the supramolecular bond becomes very weak. The different charge states provide different pieces of information about the supramolecules under study. Although singly charged complexes provide data on the building block connectivity, the doubly charged analogs are more reliable with respect to complex stoichiometry. As there are several factors which may cause differences in the gas phase and solution behavior of supramolecules (the presence and absence of solvation, changes in the strength of non‐covalent interactions upon ionization), it is important to establish well understood correlations between the complexes' gas‐phase behavior and their solution structures. A more detailed understanding will help to characterize the structures of even more complex supramolecular architectures by mass spectrometry. Copyright © 2010 John Wiley & Sons, Ltd.     

Very Long‐Range Effects: Cooperativity between Anion–π and Hydrogen‐Bonding Interactions

The interplay between two important non‐covalent interactions involving aromatic rings (namely anion–π and hydrogen bonding) is investigated. Very interesting cooperativity effects are present in complexes where anion–π and hydrogen bonding interactions coexist. These effects are found in systems where the distance between the anion and the hydrogen‐bond donor/acceptor molecule is as long as ～11 Å. These effects are studied theoretically using the energetic and geometric features of the complexes, which were computed using ab initio calculations. We use and discuss several criteria to analyze the mutual influence of the non‐covalent interactions studied herein. In addition we use Bader’s theory of atoms‐in‐molecules to characterize the interactions and to analyze the strengthening or weakening of the interactions depending upon the variation of the charge density at the critical points.     

ESI‐MS/MS of expanded porphyrins: a look into their structure and aromaticity

Electrospray mass spectrometry/mass spectrometry was used to investigate the gas‐phase properties of protonated expanded porphyrins, in order to correlate those with their structure and conformation. We have selected five expanded meso‐pentafluorophenyl porphyrins, respectively, a pair of oxidized/reduced fused pentaphyrins (22 and 24 π electrons), a pair of oxidized/reduced regular hexaphyrins (26 and 28 π electrons) and a regular doubly N‐fused hexaphyrin (28 π electrons). The gas‐phase behavior of the protonated species of oxidized and reduced expanded porphyrins is different. The oxidized species (aromatic Hückel systems) fragment more extensively, mainly by the loss of two HF molecules. The reduced species (Möbius aromatic or Möbius‐like aromatic systems) fragment less than their oxidized counterparts because of their increased flexibility. The protonated regular doubly fused hexaphyrin (non‐aromatic Hückel system) shows the least fragmentation even at higher collision energies. In general, cyclization through losses of HF molecules decreases from the aromatic Hückel systems to Möbius aromatic or Möbius‐like aromatic systems to non‐aromatic Hückel systems and is related to an increase in conformational distortion. Copyright © 2016 John Wiley & Sons, Ltd.     

Peptide‐binding specificity of the prosurfactant protein C Brichos domain analyzed by electrospray ionization mass spectrometry

The C‐terminal domain of lung surfactant protein C (CTC) precursor (proSP‐C) is involved in folding of the transmembrane segment of proSP‐C. CTC includes a Brichos domain with homologs in cancer‐ and dementia‐associated proteins. Mutations in the Brichos domain cause misfolding of proSP‐C and hence amyloid fibril formation in interstitial lung disease. Electrospray ionization mass spectrometry (ESI‐MS) with collision‐induced dissociation (CID) experiments was applied to study non‐covalent interactions between human recombinant CTC or its Brichos domain, and SP‐C analogs, homotripeptides and peptides designed to model amyloid fibril formation. The results show that the Brichos domain contains the peptide‐binding function of CTC. In titration experiments, apparent dissociation constants (K_D) were in the micromolar range where triple‐valine showed the lowest K_D and triple‐tyrosine the highest. Non‐hydrophobic peptides failed to form complexes with Brichos. CID revealed that complexes with aromatic peptide ligands are more stable in the gas phase than complexes with non‐aromatic ligands. The Brichos domain was also shown to bind fibril‐forming peptides containing aromatic/hydrophobic residues. Copyright © 2009 John Wiley & Sons, Ltd.     

Mass Spectrometry Quantifies Protein Interactions—From Molecular Chaperones to Membrane Porins

Proteins possess an intimate relationship between their structure and function, with folded protein structures generating recognition motifs for the binding of ligands and other proteins. Mass spectrometry (MS) can provide information on a number of levels of protein structure, from the primary amino acid sequence to its three‐dimensional fold and quaternary interactions. Given that MS is a gas‐phase technique, with its foundations in analytical chemistry, it is perhaps counter‐intuitive to use it to study the structure and non‐covalent interactions of proteins that form in solution. Herein we show, however, that MS can go beyond simply preserving protein interactions in the gas phase by providing new insight into dynamic interaction networks, dissociation mechanisms, and the cooperativity of ligand binding. We consider potential pitfalls in data interpretation and place particular emphasis on recent studies that revealed quantitative information about dynamic protein interactions, in both soluble and membrane‐embedded assemblies.     

Molecular Complexes of Simple Anions with Electron‐Deficient Arenes: Spectroscopic Evidence for Two Types of Structural Motifs for Anion–Arene Interactions

Anion–π interactions between a π‐acidic aromatic system and an anion are gaining increasing recognition in chemistry and biology. Herein, the binding features of an electron‐deficient aromatic system (1,3,5‐trinitrobenzene (TNB)) and selected anions (OH^?, Br^?, and I^?) are examined in the gas phase by using the combined information derived from collision‐induced dissociation experiments at variable energy, infrared multiple‐photon dissociation spectroscopy, and quantum chemical calculations. We provide spectroscopic evidence for two different structural motifs of anion–arene complexes depending on the nature of the anion. The TNB–OR^? complexes (R=H, or alkyl groups which were studied earlier) adopt an anionic σ‐complex structure whereby RO^? attacks the aromatic ring with covalent bond formation, and develops a tetrahedral ring carbon bound to H and OR. The halide complexes rather conform to a structure in which the TNB moiety is hardly altered, and the halogen is placed on an unsubstituted carbon atom over the periphery of the ring at a C–X distance that is appreciably longer than a typical covalent bond length. The ensuing structural motif, previously characterized in the solid state and named weak σ interaction, is now confirmed by an IR spectroscopic assay in the gas phase, in which the sampled species are unperturbed by crystal packing or solvation effects.     

Silicon amino acids

The existence and gas phase stability of silicon analogues of three natural amino acids (i.e., silicon glycine, silicon alanine, and silicon valine) belonging to the novel class of compounds termed silicon amino acids (SiAA) are investigated theoretically on the basis of ab initio QCISD/aug‐cc‐pVTZ and MP2/aug‐cc‐pVTZ calculations. All molecules studied (in their gas phase canonical forms) are structurally comparable to their proteinogenic counterparts (i.e., glycine, l ‐alanine, and l ‐valine) and capable of forming several structural isomers as such. These higher energy isomers are characterized by small relative energies (not exceeding 4 kcal mol⁻¹). The simulated IR spectra of the Si‐Gly, Si‐Ala, and Si‐Val global minima are also presented and discussed.     

Comprehensive Analysis of Fragment Orbital Interactions to Build Highly π‐Conjugated Thienylene‐Substituted Phenylene Oligomers

π‐Conjugated thienylene? phenylene oligomers with fluorinated and dialkoxylated phenylene fragments have been designed and prepared to understand the interactions in fragment orbitals, the influence of the substituents (F, OMe) on the HOMO–LUMO gap, and the role of intramolecular non‐covalent cumulative interactions in the construction of π‐conjugated nanostructures. Their strong conjugation was also evidenced in the gas phase by UV photoelectron spectroscopy and theoretical calculations. These results can be explained by the crucial role of the relative energetic positions of the π orbitals of the dimethoxyphenylene, which was used to model the dialkoxyphenylene entity, in determining the π/π^* orbital levels of the fluorinated phenylene entity. Dialkoxyphenylenes raise the HOMO orbitals, whereas fluorinated phenylenes lower the LUMO orbitals in the oligomers. In addition, the presence of S???F and H???F interactions in the fluorinated phenylene? thienylene compounds add to the S???O interactions in the mixed targets and contribute to the full conjugation in the oligomer, inducing weak inter‐ring angles between the involved aromatic cycles. These results, which showed extended conjugation of the π system, were corroborated by a narrow HOMO–LUMO gap (according to DFT calculations) and by a relatively strong maximum wavelength (as obtained by TD‐DFT calculations and experimental UV/Vis measurements). The crystallographic data of two mixed thienylene? (fluorinated and dialkoxylated phenylene) five‐ring oligomers agree with the above results and show the formation of quasi‐planar conformations with non‐covalent S???O, H???F, and S???F interactions. These studies in the solid and gas phases show the relevance of associating dialkoxyphenylene and fluorinated phenylene fragments with thiophene to lead to oligomers with improved electronic delocalization for electronic or optoelectronic devices.     

Ion‐Pair Recognition of Tetramethylammonium Salts by Halogenated Resorcinarenes

The non‐covalent interactions of different upper‐rim‐substituted C₂‐resorcinarenes with tetramethylammonium salts were analyzed in the gas phase in an Electrospray Ionization Fourier‐transform ion‐cyclotron‐resonance (ESI‐FTICR) mass spectrometer and by ¹H NMR titrations. The order of binding strengths of the hosts towards the tetramethylammonium cation in the gas phase reflects the electronic nature of the substituents on the upper rim of the resorcinarene. In solution, however, a different trend with particularly high binding constants for halogenated resorcinarenes has been observed. This trend can be explained by a synergetic effect originating from the interaction of the halogenated resorcinarenes with the counter anions through hydrogen bonding. This study highlights the importance of weak interactions in recognition processes and points out the benefits of comparing the gas‐phase data with results obtained from solution experiments.     

Non‐Covalent Polyvalent Ligands by Self‐Assembly of Small Glycodendrimers: A Novel Concept for the Inhibition of Polyvalent Carbohydrate–Protein Interactions In Vitro and In Vivo

Polyvalent carbohydrate–protein interactions occur frequently in biology, particularly in recognition events on cellular membranes. Collectively, they can be much stronger than corresponding monovalent interactions, rendering it difficult to control them with individual small molecules. Artificial macromolecules have been used as polyvalent ligands to inhibit polyvalent processes; however, both reproducible synthesis and appropriate characterization of such complex entities is demanding. Herein, we present an alternative concept avoiding conventional macromolecules. Small glycodendrimers which fulfill single molecule entity criteria self‐assemble to form non‐covalent nanoparticles. These particles—not the individual molecules—function as polyvalent ligands, efficiently inhibiting polyvalent processes both in vitro and in vivo. The synthesis and characterization of these glycodendrimers is described in detail. Furthermore, we report on the characterization of the non‐covalent nanoparticles formed and on their biological evaluation.     

Hydrophobic Self‐Assembly Affords Robust Noncovalent Polymer Isomers

In covalent polymerization, a single monomer can result in different polymer structures due to positional, geometric, or stereoisomerism. We demonstrate that strong hydrophobic interactions result in stable noncovalent polymer isomers that are based on the same covalent unit (amphiphilic perylene diimide). These isomers have different structures and electronic/photonic properties, and are stable in water, even upon prolonged heating at 100 °C. Such combination of covalent‐like stability together with structural/functional variation is unique for noncovalent polymers, substantially advancing their potential as functional materials.     

Parallel Water/Aromatic Interactions of Non‐Coordinated and Coordinated Water

The parallel interactions of non‐coordinated and coordinated water molecules with an aromatic ring were studied by analyzing data in the Cambridge structural database (CSD) and by using quantum chemical calculations. The CSD data show that water/aromatic contacts prefer parallel to OH/π interactions, which indicates the importance of parallel interactions. The results reveal the influence of water coordination to a metal ion; the interactions of aqua complexes are stronger. Coordinated water molecules prefer a parallel‐down orientation in which one O?H bond is parallel to the aromatic ring, whereas the other O?H bond points to the plane of the ring. The interactions of aqua complexes with parallel‐down water/benzene orientation are as strong as the much better known OH/π orientations. The strongest calculated interaction energy is ?14.89 kcal mol^?1. The large number of parallel contacts in crystal structures and the quite strong interactions indicate the importance of parallel orientation in water/benzene interactions.     

Non‐covalent dimers of the lysine containing protonated peptide ions in gaseous state: electrospray ionization mass spectrometric study

Study of the non‐covalent molecular complexes in gas phase by electrospray ionization mass spectrometry (ESI‐MS) represents a promising strategy to probe the intrinsic nature of these complexes. ESI‐MS investigation of a series of synthetic octapeptides containing six alanine and two lysine residues differing only by their positions showed the formation of non‐covalent dimers, which were preserved in the gas phase. Unlike the monomers, the dimers were found to show only singly protonated state. The decrease in the solvent polarity from water to alcohol showed enhanced propensity of formation of the dimer indicating that the electrostatic interaction plays a crucial role to stabilize the dimer. Selective functionalization studies showed that ε‐NH₂ of lysine and C‐terminal amide (? CONH₂) facilitate the dimerization through intermolecular hydrogen bonding network. Copyright © 2010 John Wiley & Sons, Ltd.     

Spectroscopic Observation of the Hydroxy Position in Butanol Hydrates and Its Effect on Hydrate Stability

In this study, we investigate the crystal structures and phase equilibria of butanols+CH₄+H₂O systems to reveal the hydroxy group positioning and its effects on hydrate stability. Four clathrate hydrates formed by structural butanol isomers are identified with powder X‐ray diffraction (PXRD). In addition, Raman spectroscopy is used to analyze the guest distributions and inclusion behaviors of large alcohol molecules in these hydrate systems. The existence of a free OH indicates that guest molecules can be captured in the large cages of structure II hydrates without any hydrogen‐bonding interactions between the hydroxy group of the guests and the water‐host framework. However, Raman spectra of the binary (1‐butanol+CH₄) hydrate do not show the free OH signal, indicating that there could be possible hydrogen‐bonding interactions between the guests and hosts. We also measure the four‐phase equilibrium conditions of the butanols+CH₄+H₂O systems.     

Oligosaccharide Shells as a Decisive Factor for Moderate and Strong Ionic Interactions of Dendritic Poly(ethylene imine) Scaffolds under Shear Forces

For better understanding and improving the non‐covalent interactions of dendritic core–shell, we evaluated the interactions of hyperbranched poly(ethylene imine) (PEI) decorated with various oligosaccharide shells with water‐soluble B vitamins, an estradiol derivative and pantoprazole. Depending on the different properties of the analyte molecules, dendritic core–shell glyco architectures showed (very) weak, moderate and strong interactions with the analyte molecules. Thus, ionic interactions are the strongest driving force for the formation of host–guest complexes. The core–shell glyco architecture is a necessary prerequisite for stable analyte/PEI complexes; the pure hyperbranched PEI did not show any sufficiently strong interactions with neutral, cationic or anionic analytes under the shear forces applied during ultrafiltration of pure aqueous solution without an adjusted pH. Thus, only robust non‐covalent interactions between analytes and the dendritic polyamine scaffold of the glycopolymer structure survive this separation step and allow isolation of stable host–guest complexes in aqueous solution.     

Development of carbohydrate-based scaffolds for restricted presentation of recognition groups. Extension to divalent ligands and implications for the structure of dimerized receptors

The solution structure of glycosyl amides has been studied by using NMR. A strong preference is displayed by tertiary aromatic glycosyl amides for E-anti structures in contrast with secondary aromatic glycosyl amides where Z-anti structures predominate. The structural diversity displayed by these classes of molecules would seem to be important as the directional properties of the aromatic ring, or groups attached to the aromatic ring, would be determined by choosing to have either a secondary or tertiary amide at the anomeric center and could be considered when designing bioactive molecules with carbohydrate scaffolds. The structural analysis was also carried out for related divalent secondary and tertiary glycosyl amides and these compounds display preferences similar to that of the monovalent compounds. The constrained divalent compounds have potential for promoting formation of clusters that will have restricted structure and thus have potential for novel studies of mechanisms of action of multivalent ligands. Possible applications of such compounds would be as scaffolds for the design and synthesis of ligands that will facilitate protein-protein or other receptor-receptor interactions. The affinity of restricted divalent (or higher order) ligands, designed to bind to proteins that recognize carbohydrates which would facilitate clustering and concomitantly promote protein-protein interactions, may be significantly higher than monovalent counterparts or multivalent ligands without these properties. This may be useful as a new approach in the development of therapeutics based on carbohydrates.     

Synthesis of Novel Phosphorylated Daidzein Derivatives and ESI Investigation on Their Non-Covalent Complexes with Lysozyme

Daidzein （7,4＇-dihydroxyisoflavone） was phosphorylated by a modified Atherton-Todd reaction. The structures of the five target product, were determined by X-ray, IR, NMR and ESI-MS. Electrospray ionization results show that in the gas phase all the phosphorylated daidzein derivatives could form non-covalent complexes with the protein lysozyme, while non-covalent complexes were not detected in the mixed solution of daidzein with lysozyme. Relative affinity of every non-covalent complex was obtained according to its different decomposition orifice voltage.     

Controlling the Regioselectivity of the Hydrosilylation Reaction in Carbon Nanoreactors

Hollow graphitized carbon nanofibres (GNF) are employed as nanoscale reaction vessels for the hydrosilylation of alkynes. The effects of confinement in GNF on the regioselectivity of addition to triple carbon–carbon bonds are explored. A systematic comparison of the catalytic activities of Rh and RhPt nanoparticles embedded in a nanoreactor with free‐standing and surface‐adsorbed nanoparticles reveals key mechanisms governing the regioselectivity. Directions of reactions inside GNF are largely controlled by the non‐covalent interactions between reactant molecules and the nanofibre channel. The specific π–π interactions increase the local concentration of the aromatic reactant and thus promote the formation of the E isomer of the β‐addition product. In contrast, the presence of aromatic groups on both reactants (silane and alkyne) reverses the effect of confinement and favours the formation of the Z isomer due to enhanced interactions between aromatic groups in the cis‐orientation with the internal graphitic step‐edges of GNF. The importance of π–π interactions is confirmed by studying transformations of aliphatic reactants that show no measurable changes in regioselectivity upon confinement in carbon nanoreactors.