Mass spectrometry and combinatorial chemistry: new approaches for direct support-bound compound identification

Mass spectrometry is a powerful analytical tool allowing rapid and sensitive structural elucidation of a wide range of molecules issued from solution-, solid- and liquid-phase syntheses. Therefore, mass spectrometry has become the most widely used tool to probe combinatorial libraries. A significant portion of the reported combinatorial data are being produced using solid phase organic synthesis. In contrast to indirect strategies where the tethered structures were released from the support into solution to undergo standard mass spectrometric analyses, static - secondary ion mass spectrometry (S-SIMS) has enabled the identification of support-bound molecules without any chemical treatment of the resin bead. Such non-destructive characterization was applied at the bead level and facilitated the step-by-step monitoring of solid-phase peptide syntheses. Side-reactions were also detected. The relevance of S-SIMS in the rehearsal phase of combinatorial chemistry is demonstrated by comparison with infrared and nuclear magnetic resonance (NMR) spectroscopies, the two other techniques investigated in that field. An alternative to solid-phase synthesis consists of assembling molecules on a soluble polymer. This methodology is termed liquid-phase synthesis. Compound characterization is facilitated since the derivatized support is soluble in spectroscopic solvents used in NMR or in electrospray ionization mass spectrometry. The advantages and drawbacks of this approach will be discussed in terms of the direct monitoring of supported reactions during chemistry optimization and rehearsal library validation.     

Resolving the structure of ligands bound to the surface of superparamagnetic iron oxide nanoparticles by high-resolution magic-angle spinning NMR spectroscopy

A major challenge in magnetic nanoparticle synthesis and (bio)functionalization concerns the precise characterization of the nanoparticle surface ligands. We report the first analytical NMR investigation of organic ligands stably anchored on the surface of superparamagnetic nanoparticles (MNPs) through the development of a new experimental application of high-resolution magic-angle spinning (HRMAS). The conceptual advance here is that the HRMAS technique, already being used for MAS NMR analysis of gels and semisolid matrixes, enables the fine-structure-resolved characterization of even complex organic molecules bound to paramagnetic nanocrystals, such as nanosized iron oxides, by strongly decreasing the effects of paramagnetic disturbances. This method led to detail-rich, well-resolved (1)H NMR spectra, often with highly structured first-order couplings, essential in the interpretation of the data. This HRMAS application was first evaluated and optimized using simple ligands widely used as surfactants in MNP synthesis and conjugation. Next, the methodology was assessed through the structure determination of complex molecular architectures, such as those involved in MNP3 and MNP4. The comparison with conventional probes evidences that HRMAS makes it possible to work with considerably higher concentrations, thus avoiding the loss of structural information. Consistent 2D homonuclear (1)H- (1)H and (1)H- (13)C heteronuclear single-quantum coherence correlation spectra were also obtained, providing reliable elements on proton signal assignments and carbon characterization and opening the way to (13)C NMR determination. Notably, combining the experimental evidence from HRMAS (1)H NMR and diffusion-ordered spectroscopy performed on the hybrid nanoparticle dispersion confirmed that the ligands were tightly bound to the particle surface when they were dispersed in a ligand-free solvent, while they rapidly exchanged when an excess of free ligand was present in solution. In addition to HRMAS NMR, matrix-assisted laser desorption ionization time-of-flight MS analysis of modified MNPs proved very valuable in ligand mass identification, thus giving a sound support to NMR characterization achievements.     

A Cleavable Scaffold Strategy for the Synthesis of One-Bead One-Compound Cyclic Peptoid Libraries That Can Be Sequenced By Tandem Mass Spectrometry

Many macrocyclic depsipeptides or related compounds have interesting medicinal properties and often display more favorable pharmacokinetic properties than linear analogues. Therefore, there is considerable interest in the development of large combinatorial libraries of macrocyclic peptidomimetic compounds. However, such molecules cannot be easily sequenced by tandem mass spectrometry, making it difficult to identify hits isolated from library screens using one bead one compound libraries. Here we report a strategy to solve this problem by placing a methionine in both the linker connecting the cyclic molecule to the bead as well as within the cycle itself. Treatment with CNBr both linearizes the molecule at a specific position and releases the molecule from the bead, making its characterization by tandem MALDI mass spectrometry straightforward.     

From the one-bead-one-compound concept to one-bead-one-reactor

The one-bead-one-compound method gives access to millions of compounds that can be screened directly on the bead. Although characterization techniques are increasingly potent and reliable, problems can still be encountered in deciphering the sequence of the active compound because of sensitiveness or manipulation of the bead. ChemMatrix, a totally PEG-based resin, has resolved the synthesis of peptides of outstanding difficulty. Like other PEG-based resins, it permits on-bead screening because of its compatibility in aqueous media and has the further advantage of having a high loading, comparable to polystyrene resins. ChemMatrix beads previously swelled in water can be nicely divided into four parts that can be characterized using different analytical techniques or just stored for safety or for further testing. The four bead parts show high homogeneity and can thus be considered to be replicas.     

DEUSS: a perdeuterated poly(oxyethylene)-based resin for improving HRMAS NMR studies of solid-supported molecules

A novel resin called DEUSS (perdeuterated poly(oxyethylene)-based solid support) has been prepared by anionic polymerization of deuterated [D4]ethylene oxide, followed by cross-linking with deuterated epichlorohydrin. DEUSS can be suspended in a wide range of solvents including organic and aqueous solutions, in which it displays a high swelling capacity. As measured by proton HRMAS of the swollen polymer, the signal intensity of the oxyethylene protons is reduced by a factor of 110 relative to the corresponding nondeuterated poly(oxyethylene)poly(oxypropylene) (POEPOP) resin, thus facilitating detailed HRMAS NMR studies of covalently linked molecules. This 1H NMR invisible matrix was used for the solid-phase synthesis of peptides, oligoureas, and a series of amides as well as their characterization by HRMAS NMR spectroscopy. On-bead NMR spectra of high quality and with resolution comparable to that of liquid samples were obtained and readily interpreted. The complete absence of the parasite resin signals will be of great advantage, for example, for the optimization of multistep solid-phase stereoselective reactions, and for the conformational study of resin-bound molecules in a large variety of solvents.     

Heats of adsorption from the Dubinin-Astakhov model applied to the characterization of pillared interlayered clays (PILCs)

Heats of adsorption of organic molecules are a useful tool for the characterization of porosity and surface chemistry of microporous materials. This work describes the possibility of using heats of adsorption of organic molecules, estimated from a methodology derived from the Dubinin-Astakhov equation, for the characterization of Pillared Interlayered Clays. The estimated heats were compared with data determined directly by adsorption microcalorimetry. It is shown that the chemical nature of the organic probe molecule strongly conditions the obtained results. The best agreement between calculated and experimental values, amongst the probe molecules studied, was found for toluene.     

Pulsed field gradient NMR on polybutylcyanoacrylate nanocapsules

The applicability of pulsed field gradient nuclear magnetic resonance spectroscopy to nanocapsule systems is demonstrated on dispersed poly-n-butylcyanoacrylate nanocapsules as a model system. Spectroscopic data are presented that allow for the structural characterization of the inner cavities, the observation of Brownian motion of the capsules and the detection of rapid molecular exchange through the capsule walls. An analytical formula is proposed that yields equilibrium populations and average residence times of a given tracer molecule, thus leading to crucial information regarding the permeability of the capsule walls. Based on these analytical methods, two varieties of nanocapsules are compared that derive from two different preparation procedures. It is found that thinner capsule walls obtained under acidic conditions of the organic phase during interfacial polymerization lead to correspondingly higher exchange rates of benzene as a tracer molecule.     

Progression of Organic Reactions on Resin Supports Monitored by Single Bead FTIR Microspectroscopy

We report the time courses of five solid-phase reactions obtained using single bead FTIR microspectroscopy. This time-resolved information aided in the determination of the required reaction time, the nature of the solid-phase reaction, and resin property, effectively assisting in the initial phase of our combinatorial chemistry efforts. Our results showed that solid-phase organic reactions proceed faster than generally speculated. In addition, we have shown that reactions on the surface and in the interior of the bead occur at the same rate for reactions studied. The reaction on the TentaGel resin was shown to be not faster than reactions on Wang resin, suggesting that the diffusion of the substrate into polystyrene bead copolymerized with 1% divinylbenzene is not rate-limiting. Finally, the capability of obtaining IR spectra from the partial surface of a single bead demonstrated the femtomolar detection limit of single bead FTIR microspectroscopy.     

Influence of immobilized biomolecules on magnetic bead plug formation and retention in capillary electrophoresis

Significant changes in the formation and retention of magnetic bead plugs in a capillary during electrophoresis were studied, and it was demonstrated that these effects were due to the type of biological molecule immobilized on the surface of these beads. Three biological molecules, an antibody, an oligonucleotide, and alkaline phosphatase (AP), were attached to otherwise identical streptavidin-coated magnetic beads through biotin-avidin binding in order to isolate differences in bead immobilization in a magnetic field resulting from the type of biological molecule immobilized on the bead surface. AP was also attached to the magnetic beads using epoxy groups on the bead surfaces (instead of avidin-biotin binding) to study the impact of immobilization chemistry. The formation and retention of magnetic bead plugs were studied quantitatively using light scattering detection of magnetic particles eluting from the bead plugs and qualitatively using microscopy. Both the types of biomolecule immobilized on the magnetic bead surface and the chemistry used to link the biomolecule to the magnetic bead impacted the formation and retention of the bead plugs.     

Single‐Molecule Sensors: Challenges and Opportunities for Quantitative Analysis

Measurement science has been converging to smaller and smaller samples, such that it is now possible to detect single molecules. This Review focuses on the next generation of analytical tools that combine single‐molecule detection with the ability to measure many single molecules simultaneously and/or process larger and more complex samples. Such single‐molecule sensors constitute a new type of quantitative analytical tool, as they perform analysis by molecular counting and thus potentially capture the heterogeneity of the sample. This Review outlines the advantages and potential of these new, quantitative single‐molecule sensors, the measurement challenges in making single‐molecule devices suitable for analysis, the inspiration biology provides for overcoming these challenges, and some of the solutions currently being explored.     

Selective and rapid immunomagnetic bead-based sample treatment for the liquid chromatography-electrospray ion-trap mass spectrometry detection of Ara h3/4 peanut protein in foods

Complex matrices commonly affect the sensitivity and selectivity of liquid chromatography-mass spectrometry (LC-MS) analysis. Thus, selective sample enrichment strategies are useful particularly to analyze organic biomarkers present in low abundance in samples. A selective immunomagnetic extraction procedure to isolate trace peanut allergen protein Ara h3/4 from breakfast cereals combined with microwave-assisted tryptic digestion and liquid chromatography-electrospray ion-trap tandem mass spectrometry (LC-ESI-IT-MS/MS) measurement was developed. Using protein A-coated magnetic bead (MB) support, anti-Ara h3/4 monoclonal antibodies (Abs) were used as selective capture molecules. The results obtained by LC-ESI-IT-MS/MS in terms of limit of detection (3mg peanuts/kg matrix) and a significantly reduced matrix effect demonstrated that the Ab-coated magnetic bead was very effective to selectively trap Ara h3/4 protein in breakfast cereals. The magnetic bead-based sample treatment followed by LC-IT-MS/MS method here developed can be proposed as very rapid and powerful confirmatory analytical method to verify the reliability of enzyme-linked immunosorbent assay (ELISA) screening methods, since the magnetic bead-LC-IT-MS/MS method combines good sensitivity to the identification capabilities of mass spectrometry.     

Aromatic resin characterisation by gas chromatography-mass spectrometry. Raw and archaeological materials

An analytical procedure based on alkaline hydrolysis, solvent extraction and trimethyl-silylation followed by gas chromatography-mass spectrometry (GC-MS) analysis was used to study the chemical composition of benzoe and storax resins, water-insoluble exudates of trees of the Styrax and Liquidambar genus. They are chemically characterised by having aromatic acids, alcohols and esters as their main components and are thus known as aromatic and/or balsamic resins. This analytical procedure allowed us to characterise the main components of the two resins and, even though cinnamic acid is the main component of both the resins, the presence of other characteristic aromatic compounds and triterpenes permitted us to distinguish between the two materials. All the compounds identified in benzoe resin were detected in an archaeological organic residue from an Egyptian ceramic censer (fifth to seventh centuries a.d.), thus proving that this resin was used as one of the components of the mixture of organic materials burned as incense. These results provide the first chemical evidence of the presence of benzoe resin in an archaeological material from Mediterranean area.     

Polystyrene‐Supported Core–Shell Beads with Aluminium MOF Coating for Extraction of Organic Pollutants

Aluminium‐based metal–organic framework (MOF) coatings on polystyrene bead surfaces were easily synthesized by reacting an intermediate metal hydroxide coating with an organic linker. Several different sizes of polystyrene beads were coated with aluminium metal hydroxide to construct Al@PS core–shell bead materials. The activated Al@PS core–shell beads were involved to make a homogenous MOF‐based layer in the presence of the organic linker. By using different sizes of the PS support the size of MOFs on the PS composites could be fine‐tuned under specific reaction conditions. MOF‐coated core–shell bead materials (Al‐1,4‐NDC@PS and MIL‐53(Al)@PS) were characterized using various analytical techniques. Al‐1,4‐NDC@PS and MIL‐53(Al)@PS were evaluated for solid‐phase microextraction (SPME) of hydrophobic polycyclic aromatic hydrocarbons (PAHs) and hydrophilic non‐steroidal anti‐inflammatory drugs (NSAIDs), respectively. Al‐1,4‐NDC@PS‐1000 displayed high extraction recoveries ranging from 79.2 % to 99.8 % in the SPME of PAHs. Meanwhile, MIL‐53(Al)@PS‐1000 showed 85.9–99.0 % extraction recoveries in the SPME of NSAIDs. These results show that the proposed approach holds potential to extract organic analytes on an industrial scale.     

Amino-carboxylic recognition on surfaces: from 2D to 2D + 1 nano-architectures

The control of the electronic properties of the interfaces between small organic molecules and the substrate is key for the development of efficient and reliable organic-based devices. A promising and widely covered route is to interpose a Self-Assembled Monolayer (SAM) to bridge the molecular film and the electrode. The morphology and the electronic level alignment of the triple substrate-SAM-organic layered system can be tuned by properly selecting the SAM composition. We have recently proposed a novel approach to the problem where, under ultra-high vacuum conditions, a molecular film is anchored to the SAM by exploiting the recognition between molecules functionalized, respectively, with -NH(2) and -COOH end-groups. Here we briefly review the role of the amino-carboxylic interaction in the formation of ordered organic 2-dimensional architectures on solid surfaces. We then describe the anchoring process of carboxylic molecules on amine based SAMs we have recently reported on. New results are presented showing how multiple anchoring sites per molecule may be exploited for tailoring the molecular orientation as well as the density of the anchored molecules.     

Combined elemental analysis of ancient glass beads by means of ion beam,portable XRF,and EPMA techniques

Ion beam analysis (IBA)- and X-ray fluorescence (XRF)-based techniques have been well adopted in cultural-heritage-related analytical studies covering a wide range of diagnostic role, i.e., from screening purposes up to full quantitative characterization. In this work, a systematic research was carried out towards the identification and evaluation of the advantages and the limitations of laboratory-based (IBA, electron probe microanalyzer) and portable (milli-XRF and micro-XRF) techniques. The study focused on the analysis of an Archaic glass bead collection recently excavated from the city of Thebes (mainland, Greece), in order to suggest an optimized and synergistic analytical methodology for similar studies and to assess the reliability of the quantification procedure of analyses conducted in particular by portable XRF spectrometers. All the employed analytical techniques and methodologies proved efficient to provide in a consistent way characterization of the glass bead composition, with analytical range and sensitivity depending on the particular technique. The obtained compositional data suggest a solid basis for the understanding of the main technological features related to the raw major and minor materials utilized for the manufacture of the Thebian ancient glass bead collection.     

(19)F-encoded combinatorial libraries: discovery of selective metal binding and catalytic peptoids

A (19)F NMR method for encoding of combinatorial libraries has been developed. Aryl fluorides whose chemical shifts are modified by aromatic substituents were prepared and attached to resin support beads that were used in the split-pool synthesis of peptoids. The detection of the (19)F NMR signal of tags derived from a single "big bead" was demonstrated. The library diversity arises from peptoid amines and the cyclic anhydrides used in their acylation. The resulting 90-compound library was examined for metal ion binding, and novel ligands for iron and copper were discovered. Their binding constants were determined to be in the low micromolar range using conventional methods. The library was also examined for autocatalysis of acylation, and a molecule possessing the catalytic triad of serine proteases was deduced.     

Intercalation of cyclic ethers into vanadyl phosphate

Two cyclic ethers, tetrahydrofuran (THF) and tetrahydropyran (THP), were intercalated into vanadyl phosphate and characterized by X-ray powder diffraction, thermogravimetry, and IR and Raman spectroscopy. Both compounds contain one molecule of ether per formula unit of VOPO(4) and show high thermal stability in comparison with VOPO(4) intercalates with other organic guest molecules. Both ethers are anchored to the VOPO(4) host layers by their oxygen atoms, which are coordinated to the vanadium atoms of the host. The probable arrangement of the tetrahydropyran molecules in the host interlayer space is derived from molecular simulations by the Cerius(2) 4.5 program.     

Detection of volatile organic compounds by temperature-programmed desorption combined with mass spectrometry and Fourier transform infrared spectroscopy

A temperature-programmed desorption (TPD) device connected to a mass spectrometer was used to detect volatile organic compounds from air samples. The main aim was to develop an analytical method, by which both non-polar and polar organic components can be detected in the same run. In TPD, the adsorbed compounds are desorbed from the resin more slowly than in the conventional trapping techniques, such as purge-and-trap technique, in which the resin is flash-heated and the compounds are desorbed at the same time to a cryogenic trap or an analytical column. In TPD, the adsorbent resin acts also as an analytical column. In this way it is possible to obtain more rapid analysis, and also a more simple instrumentation, which can be used on-line and on-site. In this work, a new version of TPD device, which uses a resistor for heating and a Peltier element for rapid cooling, was designed and constructed. Various adsorbent resins were tested for their adsorption and desorption properties of both polar and non-polar compounds. When using a mixture of adsorbent resins, Tenax TA and HayeSep D, it was possible to analyze both polar, low-molecular weight compounds, such as methanol and ethanol, and non-polar volatile organic compounds, such as benzene and toluene, in the same run within 15 min including sampling. The same TPD principle was also tested using a Fourier transform infrared spectrometer as an analytical instrument, and the results showed that it was possible to obtain a separation of similar compounds, such as hexane and heptane, and still retaining the same sensitivity as the original on-line FTIR instrument.     

Profiling eicosanoids and phospholipids using LC-MS/MS: principles and recent applications

Eicosanoids are potent lipid mediators involved in numerous physiological and pathophysiological processes. Precursors are polyunsaturated fatty acids liberated from membrane phospholipids. Thus, profiling and quantification of these molecules has gained a lot of attention during last years. Eicosanoids and phospholipids are commonly profiled by LC-MS/MSbecause this technique allows accurate quantification within acceptable run-times. This article therefore focuses on liquid chromatography and the ESI-MS/MS analysis of proinflammatory lipid mediators, particularly arachidonic acid (C20:4) derived eicosanoids and their precursors phospholipids. Recent analytical developments for quantification of these compounds are highlighted and analytical challenges are discussed. Furthermore, applications such as the use of these molecules as biomarkers are presented.     

Characterizing the surface chemistry of nanoparticles: an analogy to solid-phase synthesis samples

Chemical modifications of nanoparticle's (NP's) surfaces can be used to regulate their activities, remove their toxic effects, and enable them to perform desired functions. Similar to SPS samples, modified NPs also have small-molecules on the surface of a solid support. The need to monitor synthesis, optimize reaction conditions, and characterize the products is quite similar in both situations. FTIR, NMR, MS and other analytical methods have been used as effective methods to analyze surface bound molecules and monitor organic reactions directly, or indirectly, on a solid phase of a resin or a NPs.