Chiral Truxene-Based Self-Assembled Cages: Triple Interlocking and Supramolecular Chirogenesis.

Incorporating chiral elements in host-guest systems currently attracts much attention because of the major impact such structures may have in a wide range of applications, from pharmaceuticals to materials science and beyond. Moreover, the development of multi-responsive and -functional systems is highly desirable since they offer numerous benefits. In this context, we describe herein the construction of a metal-driven self-assembled cage that associates a chiral truxene-based ligand and a bis-ruthenium complex. The maximum separation between both facing chiral units in the assembly is fixed by the intermetallic distance within the lateral bis-ruthenium complex (8.4 Å). The resulting chiral cavity was shown to encapsulate polyaromatic guest molecules, but also to afford a chiral triply interlocked [2]catenane structure. The formation of the latter occurs at high concentration, while its disassembly could be achieved by the addition of a planar achiral molecule. Interestingly the planar achiral molecule exhibits induced circular dichroism signature when trapped within the chiral cavity, thus demonstrating the ability of the cage to induce supramolecular chirogenesis.

Nucleos'ID: A New Search Engine Enabling the Untargeted Identification of RNA Post-transcriptional Modifications from Tandem Mass Spectrometry Analyses of Nucleosides.

As RNA post-transcriptional modifications are of growing interest, several methods were developed for their characterization. One of them established for their identification, at the nucleosidic level, is the hyphenation of separation methods, such as liquid chromatography or capillary electrophoresis, to tandem mass spectrometry. However, to our knowledge, no software is yet available for the untargeted identification of RNA post-transcriptional modifications from MS/MS data-dependent acquisitions. Thus, very long and tedious manual data interpretations are required. To meet the need of easier and faster data interpretation, a new user-friendly search engine, called Nucleos'ID, was developed for CE-MS/MS and LC-MS/MS users. Performances of this new software were evaluated on CE-MS/MS data from nucleoside analyses of already well-described Saccharomyces cerevisiae transfer RNA and Bos taurus total tRNA extract. All samples showed great true positive, true negative, and false discovery rates considering the database size containing all modified and unmodified nucleosides referenced in the literature. The true positive and true negative rates obtained were above 0.94, while the false discovery rates were between 0.09 and 0.17. To increase the level of sample complexity, untargeted identification of several RNA modifications from Pseudomonas aeruginosa 70S ribosome was achieved by the Nucleos'ID search following CE-MS/MS analysis.

Next Challenges for the Comprehensive Molecular Characterization of Complex Organic Mixtures in the Field of Sustainable Energy.

The conversion of lignocellulosic biomass by pyrolysis or hydrothermal liquefaction gives access to a wide variety of molecules that can be used as fuel or as building blocks in the chemical industry. For such purposes, it is necessary to obtain their detailed chemical composition to adapt the conversion process, including the upgrading steps. Petroleomics has emerged as an integral approach to cover a missing link in the investigation bio-oils and linked products. It relies on ultra-high-resolution mass spectrometry to attempt to unravel the contribution of many compounds in complex samples by a non-targeted approach. The most recent developments in petroleomics partially alter the discriminating nature of the non-targeted analyses. However, a peak referring to one chemical formula possibly hides a forest of isomeric compounds, which may present a large chemical diversity concerning the nature of the chemical functions. This identification of chemical functions is essential in the context of the upgrading of bio-oils. The latest developments dedicated to this analytical challenge will be reviewed and discussed, particularly by integrating ion source features and incorporating new steps in the analytical workflow. The representativeness of the data obtained by the petroleomic approach is still an important issue.

Exciton Coupling in Redox-Active Salen based Self-Assembled Metallacycles.

The incorporation of a redox-active nickel salen complex into supramolecular structures was explored via coordination-driven self-assembly with homobimetallic ruthenium complexes (bridged by oxalato or 5,8-dihydroxy-1,4-naphthoquinato ligands). The self-assembly resulted in the formation of a discrete rectangle using the oxalato complex and either a rectangle or a catenane employing the larger naphthoquinonato complex. The formation of the interlocked self-assembly was determined to be solvent and concentration dependent. The electronic structure and stability of the oxidized metallacycles was probed using electrochemical experiments, UV-Vis-NIR absorption, EPR spectroscopy and DFT calculations, confirming ligand radical formation. Exciton coupling of the intense near-infrared (NIR) ligand radical intervalence charge transfer (IVCT) bands provided further confirmation of the geometric and electronic structures in solution.

Reversible pH-Controlled Catenation of a Benzobisimidazole-Based Tetranuclear Rectangle.

The development of methodologies to control on demand and reversibly supramolecular transformations from self-assembled metalla-structures requires the rational design of architectures able to answer to an applied stimulus. While solvent or concentration changes, light exposure or addition of a chemical have been largely explored to provide these transformations, the case of pH sensitive materials is less described. Herein, we report the first example of a pH-triggered dissociation of a coordination-driven self-assembled interlocked molecular link. It incorporates a pH sensitive benzobisimidazole-based ligand that can be selectively protonated on its bisimidazole moieties. This generates intermolecular electrostatic repulsions that reduces drastically the stability of the interlocked structure, leading to its dissociation without any sign of protonation of the pyridine moieties involved in the coordination bonds. Importantly, the dissociation process is reversible through addition of a base.

Investigation of polymer-based composites by laser desorption/ionization study of their photo-oxidative aging.

RATIONALE: Polybutadiene (PB) is one of the most widely used polymers. Its aging occurs by reaction with oxygen under illumination and may modify its mechanical and/or aesthetic properties. To modify its properties, organic and/or inorganic compounds are generally added to PB. The aging of such composite materials is poorly known. METHODS: PB and its mixtures with TiO2 and/or the Orange 13 pigment are subjected to an accelerated photo-oxidative aging step for one week. The analysis of PB and its composites with regard to their composition and the aging time is carried out by 266 nm and/or 355 nm laser desorption/ionization Fourier transform ion cyclotron resonance mass spectrometry (LDI-FTICR-MS). RESULTS: Both PB and its degradation products are detected by (+) LDI-FTICR-MS. The oxidation mechanism of PB is not significantly affected by the used organic or inorganic fillers, which results from the cleavage of the polymer chain and the formation of carbonyl compounds. The crosslinking of PB is significantly reduced by the two investigated fillers. Analysis in negative mode [(-) LDI-FTICR-MS] ensures the specific detection of the Orange 13 pigment. CONCLUSIONS: LDI-FTICR-MS has demonstrated its ability to provide relevant information on the degradation of polymer-based composites. The main advantages of this approach are its ability to probe the surface, which is specifically affected by photo-oxidation aging processes, and to access the insoluble degradation compounds.

Metalla-Assembled Electron-Rich Tweezers: Redox-Controlled Guest Release Through Supramolecular Dimerization.

Developing methodologies for on-demand control of the release of a molecular guest requires the rational design of stimuli-responsive hosts with functional cavities. While a substantial number of responsive metallacages have already been described, the case of coordination-tweezers has been less explored. Herein, we report the first example of a redox-triggered guest release from a metalla-assembled tweezer. This tweezer incorporates two redox-active panels constructed from the electron-rich 9-(1,3-dithiol-2-ylidene)fluorene unit that are facing each other. It dimerizes spontaneously in solution and the resulting interpenetrated supramolecular structure can dissociate in the presence of an electron-poor planar unit, forming a 1:1 host-guest complex. This complex dissociates upon tweezer oxidation/dimerization, offering an original redox-triggered molecular delivery pathway.

Study of the mainstream cigarette smoke aerosols by Fourier transform ion cyclotron resonance mass spectrometry coupled to laser/desorption and electrospray ionization - Additional insights on the heteroaromatic components.

RATIONALE: The chemical composition of the particulate phase of cigarette smoke inhaled by the active smoker is still poorly known in spite of its importance from a health point of view. A non-targeted approach is applied to cigarette smoke particles collected on a quartz filter to obtain an as complete as possible description of this complex mixture. METHODS: A home-made smoking machine including devices for volatile organic compounds (VOCs) and particle sampling was used. The validation of the cigarette smoking and cigarette smoke collection procedures was conducted by the quantification of some compounds by gas chromatography/mass spectrometry (GC/MS). The particles were investigated by Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) directly after their collection on quartz filters by laser/desorption ionization (LDI) or after extraction with CH2 Cl2 by electrospray ionization (ESI). RESULTS: The determination of the benzene, toluene, ethylbenzene and xylenes (from 2 to 35 µg/cigarette) and nicotine (0.68 ± 0.05 mg/cigarette) validated the used sampling method. The complementarity of the LDI and ESI sources for the cigarette smoke analysis was established. The ESI analyses evidenced polar compounds and components with a pyridine group and LDI ensured the detection of poly-condensed heteroaromatic species. Finally, this methodology was employed to characterize particles from cigarettes with or without flavoring additives. CONCLUSIONS: Some insights into the composition of cigarette smoke inhaled by active smokers have been obtained. The ~1750 observed features revealed the huge complexity of cigarette smoke particles and the diversity of the possible associated health issues. Both heteroaromatic and highly oxygenated compounds produced by combustion and pyrolysis have been highlighted.

Redox-Driven Transformation of a Discrete Molecular Cage into an Infinite 3D Coordination Polymer.

Two M12 L6 redox-active self-assembled cages constructed from an electron-rich ligand based on the extended tetrathiafulvalene framework (exTTF) and metal complexes with a linear geometry (PdII and AgI ) are depicted. Remarkably, based on a combination of specific structural and electronic features, the polycationic self-assembled AgI coordination cage undergoes a supramolecular transformation upon oxidation into a three-dimensional coordination polymer, that is characterized by X-ray crystallography. This redox-controlled change of the molecular organization results from the drastic conformational modifications accompanying oxidation of the exTTF moiety.

Controlling the Host-Guest Interaction Mode through a Redox Stimulus.

A proof-of-concept related to the redox-control of the binding/releasing process in a host-guest system is achieved by designing a neutral and robust Pt-based redox-active metallacage involving two extended-tetrathiafulvalene (exTTF) ligands. When neutral, the cage is able to bind a planar polyaromatic guest (coronene). Remarkably, the chemical or electrochemical oxidation of the host-guest complex leads to the reversible expulsion of the guest outside the cavity, which is assigned to a drastic change of the host-guest interaction mode, illustrating the key role of counteranions along the exchange process. The reversible process is supported by various experimental data (1 H NMR spectroscopy, ESI-FTICR, and spectroelectrochemistry) as well as by in-depth theoretical calculations performed at the density functional theory (DFT) level.

Chemical Analysis of a "Miller-Type" Complex Prebiotic Broth: Part I: Chemical Diversity, Oxygen and Nitrogen Based Polymers.

In a famous experiment Stanley Miller showed that a large number of organic substances can emerge from sparking a mixture of methane, ammonia and hydrogen in the presence of water (Miller, Science 117:528-529, 1953). Among these substances Miller identified different amino acids, and he concluded that prebiotic events may well have produced many of Life's molecular building blocks. There have been many variants of the original experiment since, including different gas mixtures (Miller, J Am Chem Soc 77:2351-2361, 1955; Oró Nature 197:862-867, 1963; Schlesinger and Miller, J Mol Evol 19:376-382, 1983; Miyakawa et al., Proc Natl Acad Sci 99:14,628-14,631, 2002). Recently some of Miller's remaining original samples were analyzed with modern equipment (Johnson et al. Science 322:404-404, 2008; Parker et al. Proc Natl Acad Sci 108:5526-5531, 2011) and a total of 23 racemic amino acids were identified. To give an overview of the chemical variety of a possible prebiotic broth, here we analyze a "Miller type" experiment using state of the art mass spectrometry and NMR spectroscopy. We identify substances of a wide range of saturation, which can be hydrophilic, hydrophobic or amphiphilic in nature. Often the molecules contain heteroatoms, with amines and amides being prominent classes of molecule. In some samples we detect ethylene glycol based polymers. Their formation in water requires the presence of a catalyst. Contrary to expectations, we cannot identify any preferred reaction product. The capacity to spontaneously produce this extremely high degree of molecular variety in a very simple experiment is a remarkable feature of organic chemistry and possibly prerequisite for Life to emerge. It remains a future task to uncover how dedicated, organized chemical reaction pathways may have arisen from this degree of complexity.

Differentiation of Four Polyvinylidene Fluoride Polymers Based on Their End Groups by DART-FT-ICR MS and Kendrick Plots.

Nowadays, synthetic polymers are produced and used in many materials for different applications. Matrix-assisted laser desorption/ionization or electrospray mass spectrometry are classically used to investigate them, but these techniques require sample preparation steps, which are not always suitable for the study of insoluble or formulated polymers. Alternatively, direct real-time (DART) ionization analysis may be conducted without sample preparation. Four polyvinylidene fluoride (PVDF) polymers involving the C2H2F2 repeating unit coming from different suppliers have been analyzed by DART Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) in negative-ion mode. The obtained mass spectra systematically displayed an oligomeric distribution between m/z 400 and 1300 of [M - H]-, [M + O2]•-, and [M + NO2]- ions. Kendrick plots were used to ease the identification of PVDF end-groups and establish a difference between the samples. Both commercial PVDF polymers shared the same α+ω end groups formula, which confirmed a similar polymerization process for their synthesis. The two other PVDFs were clearly different from the commercial ones by the occurrence of specific end-groups. MS/MS and MS3 experiments were conducted to obtain structural information on these end-groups.

Hyphenation of Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) with separation methods: The art of compromises and the possible - A review.

This review provides an overview of the online hyphenation of Fourier Transform Ion Cyclotron Resonance Mass Spectrometry (FT-ICR MS) with separation methods to date. The online coupling between separation techniques (gas and liquid chromatography, capillary electrophoresis) and FT-ICR MS essentially raises questions of compromise and is not look as straightforward as hyphenation with other analyzers (QTOF-MS for instance). FT-ICR MS requires time to reach its highest resolving power and accuracy in mass measurement capabilities whereas chromatographic and electrophoretic peaks are transient. In many applications, the strengths and the weaknesses of each technique are balanced by their hyphenation. Untargeted "Omics" (e.g. proteomics, metabolomics, petroleomics, …) is one of the main areas of application for FT-ICR MS hyphenated to online separation techniques because of the complexity of the sample. FT-ICR MS achieves the required high mass measurement accuracy to determine accurate molecular formulae and resolution for isobar distinction. Meanwhile separation techniques highlight isomers and reduce the ion suppression effects extending the dynamic range. Even if the implementation of FT-ICR MS hyphenated with online separation methods is a little trickier (the art of compromise), this review shows that it provides unparalleled results to the scientific community (the art of the possible), along with raising the issue of its future in the field with the relentless technological progress.

Optimization of nucleotides dephosphorylation for RNA structural characterization by tandem mass spectrometry hyphenated with separation methods.

As part of RNA characterization, the identification of post-transcriptional modifications can be performed using hyphenation of separation methods with mass spectrometry. To identify RNA modifications with those methods, a first total digestion followed by a dephosphorylation step are usually required to reduce RNA to nucleosides. Even though effective digestion and dephosphorylation are essential to avoid further complications in analysis and data interpretation, to our knowledge, no standard protocol is yet referenced in the literature. Therefore, the aim of this work is to optimize the dephosphorylation step using a total extract of transfer RNA (tRNA)1 from B. taurus as a model and to determine and fix two protocols, leading to complete dephosphorylation, based on time and bacterial alkaline phosphatase (BAP)2 consumptions. Capillary electrophoresis-tandem mass spectrometry (CE-MS/MS) was used to estimate the dephosphorylation efficiency of both protocols on many canonical and modified nucleotides. For a timesaving protocol, we established that full dephosphorylation was obtained after a 4-hour incubation at 37 °C with 7.5 U of BAP for 1 µg of tRNA. And for a BAP-saving protocol, we established that full dephosphorylation was obtained 3.0 U of BAP after an overnight incubation at 37 °C. Both protocols are suitable for quantitative analyses as no loss of analytes is expected. Moreover, they can be widely used for all other RNA classes, including messenger RNA or ribosomal RNA.

Protocol for Etching Bare-Fused Silica Capillaries for Sheathless Capillary Electrophoresis-Mass Spectrometry Coupling.

Homemade capillaries are a very common practice for the users of capillary electrophoresis (CE), notably in CE-UV. With the advent of the capillary electrophoresis-mass spectrometry coupling since the end of the 1980s, several interfaces have been developed. Among those interfaces, the porous tip sprayer allows great sensitivity at nano flow rates and has been used in numerous applications over the past few years. However, the homemade implementation of a suitable capillary for the porous tip sprayer is more challenging. The porous tip is created by etching the bare-fused silica capillary with hydrofluoric acid. Here we describe the complete process of etching bare-fused silica capillaries, from length cutting to quality control of the newly etched capillary.

Analysis of mainstream and sidestream cigarette smoke particulate matter by laser desorption mass spectrometry.

Laser desorption ionization Fourier transform ion cyclotron resonance mass spectrometry (LDI-FTICRMS) was used to investigate particulate matter (PM) associated with mainstream (MSS) and sidestream cigarette smokes (SSS). The high mass resolution and the high mass measurement accuracy allowed a molecular formula for each detected signal in the 150-500 m/z range to be assigned. The high number of peaks observed in mass spectra required additional data processing to extract information. In this context, Kendrick maps and Van Krevelen diagrams were drawn. These postacquisition treatments were used to more easily compare different cigarette smokes: (i) MSS from different cigarettes and (ii) MSS and SSS from the same cigarette. In both ion detection modes, most of the detected species were found to be attributed to C(6-31)H(2-35)N(0-7)O(0-9) compounds. The compounds observed in the study of SSS appeared to be more unsaturated and less oxygenated than those observed when MSS of the same cigarette was investigated.

Contributions to Lignomics: Stochastic Generation of Oligomeric Lignin Structures for Interpretation of MALDI-FT-ICR-MS Results.

The lack of standards to identify oligomeric molecules is a challenge for the analysis of complex organic mixtures. High-resolution mass spectrometry-specifically, Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR MS)-offers new opportunities for analysis of oligomers with the assignment of formulae (Cx Hy Oz ) to detected peaks. However, matching a specific structure to a given formula remains a challenge due to the inability of FT-ICR MS to distinguish between isomers. Additional separation techniques and other analyses (e.g., NMR spectroscopy) coupled with comparison of results to those from pure compounds is one route for assignment of MS peaks. Unfortunately, this strategy may be impractical for complete analysis of complex, heterogeneous samples. In this study we use computational stochastic generation of lignin oligomers to generate a molecular library for supporting the assignment of potential candidate structures to compounds detected during FT-ICR MS analysis. This approach may also be feasible for other macromolecules beyond lignin.

Lignin Depolymerization: A Comparison of Methods to Analyze Monomers and Oligomers.

Catalytic liquefaction of lignin is an attractive process to produce fuels and chemicals, but it forms a wide range of liquid products from monomers to oligomers. Oligomers represent an important fraction of the products and their analysis is complex. Therefore, rapid characterization methods are needed to screen liquefaction conditions based on the distribution in monomers and oligomers. For this purpose, UV spectroscopy is proposed as a fast and simple method to assess the composition of lignin-derived liquids. UV absorption and fluorescence were studied on various model compounds and liquefaction products. Liquefaction of Soda lignin was conducted in an autoclave, in ethanol and with Pt/C catalyst (H2 , 250 °C, 110 bar). Liquids were sampled at isothermal conditions every 30 min for 4 h. UV fluorescence spectroscopy is related to GC-MS, gel-permeation chromatography (GPC), MALDI-TOF MS, and NMR characterizations. A depolymerization index is proposed from UV spectroscopy to rapidly assess the relative distribution of monomers and oligomers.

Cerium oxyhydroxide clusters: formation, structure, and reactivity.

Cerium oxyhydroxide cluster anions were produced by irradiating ceric oxide particles by using 355 nm laser pulses that were synchronized with pulses of nitrogen gas admitted to the irradiation chamber. The gas pulse stabilized the nascent clusters that are largely anhydrous [Ce(x)O(y)] ions and neutrals. These initially formed species react with water, principally forming oxohydroxy species that are described by the general formula [Ce(x)O(y)(OH)(z)](-) for which all the Ce atoms are in the IV oxidation state. In general, the extent of hydroxylation varies from a value of three OH per Ce atom when x = 1 to a value slightly greater than 1 for x >or= 8. The Ce(3) and Ce(6) species deviate significantly from this trend: the x = 3 cluster accommodates more hydroxyl moieties compared to neighboring congeners at x = 2 and 4. Conversely, the x = 6 cluster is significantly less hydroxylated than its x = 5 and 7 neighbors. Density functional theory (DFT) modeling of the cluster structures shows that the hydrated clusters are hydrolyzed, and contain one-to-multiple hydroxide moieties, but not datively bound water. DFT also predicts an energetic preference for formation of highly symmetric structures as the size of the clusters increases. The calculated structures indicate that the ability of the Ce(3) oxyhydroxide to accommodate more extensive hydroxylation is due to a more open, hexagonal structure in which the Ce atoms can participate in multiple hydrolysis reactions. Conversely the Ce(6) oxyhydroxide has an octahedral structure that is not conducive to hydrolysis. In addition to the fully oxidized (Ce(IV)) oxyhydroxides, reduced oxyhydroxides (containing a Ce(III) center) are also formed. These become more prominent as the size of the clusters increases, suggesting that the larger ceria clusters have an increased ability to accommodate a reduced Ce(III) moiety. In addition, the spectra offer evidence for the formation of superoxide derivatives that may arise from reaction of the reduced oxyhydroxides with dioxygen. The overall intensity of the clusters tends to monotonically decrease as the cluster size increases; however, this trend is interrupted at Ce(13), which is significantly more stable compared to neighboring congeners, suggesting formation of a dehydrated Keggin-type structure.

Laser ablation mass spectrometry of inorganic transition metal compounds. Additional knowledge for the understanding of ion formation.

Laser ablation of transition-metal oxides have been investigated to better understand the formation processes of inorganic cluster ions. The study of binary oxide mixtures and the relative distribution of the ions produced suggest three salient mechanisms that occur after laser/matter interaction, that function to produce the observed ensemble of ionic species. Molecular recombination reactions, unimolecular dissociation processes, emission of small neutrals, including molecular oxygen from transition-metal oxide samples, or from species expelled in gas phase appear to be a significant mechanism, especially under high laser irradiance conditions. These processes are used to propose a set of pathways to rationalize the envelope of ionic clusters formed under photon bombardment.