Synthesis of three-dimensionally arranged porphyrin arrays via intramolecular meso-meso coupling

The synthesis and photophysical properties of three-dimensionally arranged porphyrin arrays with through-space electronic communication are reported. 1,3,5-Trioxamethylphenylene bridged Zn(II) porphyrin trimer 3 was coupled by Ag(I)-promoted oxidative coupling reaction to give porphyrin cage 5 comprising three meso-meso linked diporphyrins, which was then transformed by oxidation with DDQ and Sc(OTf)₃ into porphyrin cage 7 comprising three fused diporphyrins. Intramolecular meso-meso coupling reaction was applied to porphyrin pentamer 11 to provide porphyrin array 12 consisting of a porphyrin core flanked by two meso-meso linked diporphyrins. Further oxidation of 12 with DDQ and Sc(OTf)₃ afforded triply stacked porphyrin array 13 that is comprised of a porphyrin core flanked by two porphyrin tapes. UV-vis-NIR absorption and fluorescence spectra of 5, 7, 12, and 13 showed their distorted conformations and electronic interaction within the stacked porphyrin arrays.     

Structural Feature Ions for Distinguishing N- and O-Linked Glycan Isomers by LC-ESI-IT MS/MS

Glycomics is the comprehensive study of glycan expression in an organism, cell, or tissue that relies on effective analytical technologies to understand glycan structure–function relationships. Owing to the macro- and micro-heterogeneity of oligosaccharides, detailed structure characterization has required an orthogonal approach, such as a combination of specific exoglycosidase digestions, LC-MS/MS, and the development of bioinformatic resources to comprehensively profile a complex biological sample. Liquid chromatography-electrospray ionization-mass spectrometry (LC-ESI-MS/MS) has emerged as a key tool in the structural analysis of oligosaccharides because of its high sensitivity, resolution, and robustness. Here, we present a strategy that uses LC-ESI-MS/MS to characterize over 200 N- and O-glycans from human saliva glycoproteins, complemented by sequential exoglycosidase treatment, to further verify the annotated glycan structures. Fragment-specific substructure diagnostic ions were collated from an extensive screen of the literature available on the detailed structural characterization of oligosaccharides and, together with other specific glycan structure feature ions derived from cross-ring and glycosidic-linkage fragmentation, were used to characterize the glycans and differentiate isomers. The availability of such annotated mass spectrometric fragmentation spectral libraries of glycan structures, together with such substructure diagnostic ions, will be key inputs for the future development of the automated elucidation of oligosaccharide structures from MS/MS data.

SEC ICP MS and CZE ICP MS investigation of medium and high molecular weight complexes formed by cadmium ions with phytochelatins

Size-exclusion chromatography (SEC) and capillary zone electrophoresis (CZE) coupled with inductively coupled plasma mass spectrometry were applied to characterize low, medium, and high molecular weight cadmium complexes with glutathione and phytochelatins (PCs). The dominant stoichiometry of the complexes formed in vitro was established as 1:1 using electrospray ionization mass spectrometry. Calculated molecular masses of Cd₁L₁ complexes were used for calibration of the SEC and CZE methods. The results showed a lower (2 kDa) SEC column exclusion limit for cadmium complexes compared with free peptides (10 kDa), and most of the high molecular weight cadmium species were eluted in the void volume of the column. Moreover, the CZE method based on the semiempirical model of Offord to elucidate peptide migration allowed us to show a high propensity of Cd–PC complexes for polymorphism on complexation, which was also observed for extracts of Arabidopsis thaliana treated with cadmium. All the information presented is vital for understanding the mechanism of metal deactivation in plants.

Reliable Determination of Site-Specific In Vivo Protein N-Glycosylation Based on Collision-Induced MS/MS and Chromatographic Retention Time

Site-specific glycopeptide mapping for simultaneous glycan and peptide characterization by MS is difficult because of the heterogeneity and diversity of glycosylation in proteins and the lack of complete fragmentation information for either peptides or glycans with current fragmentation technologies. Indeed, multiple peptide and glycan combinations can readily match the same mass of glycopeptides even with mass errors less than 5 ppm providing considerably ambiguity and analysis of complex mixtures of glycopeptides becomes quite challenging in the case of large proteins. Here we report a novel strategy to reliably determine site-specific N-glycosylation mapping by combining collision-induced dissociation (CID)-only fragmentation with chromatographic retention times of glycopeptides. This approach leverages an experimental pipeline with parallel analysis of glyco- and deglycopeptides. As the test case we chose ABCA4, a large integral membrane protein with 16 predicted sites for N-glycosylation. Taking advantage of CID features such as high scan speed and high intensity of fragment ions together combined with the retention times of glycopeptides to conclusively identify the non-glycolytic peptide from which the glycopeptide was derived, we obtained virtually complete information about glycan compositions and peptide sequences, as well as the N-glycosylation site occupancy and relative abundances of each glycoform at specific sites for ABCA4. The challenges provided by this example provide guidance in analyzing complex relatively pure glycoproteins and potentially even more complex glycoprotein mixtures.

Synthesis and application of head-to-head-type styrene dimers bearing two fluoroalkyl end-groups

Head-to-head-type styrene and substituted styrene dimers bearing two fluoroalkyl end-groups have been efficiently synthesized by a simple reaction of perfluoroalkyl iodide with styrene under radical conditions as a mixture of meso and racemic forms. The meso form obtained from the mixture by recrystallization gave a crystal suitable for X-ray diffraction study and the crystal structure was found to be based on π-stacking of benzene rings and aggregation of fluoroalkyl chains. Dynamic light scattering measurements showed that meso-styrene dimers bearing two fluoroalkyl end-groups can form the nanometer size-controlled self-assemblies through the intermolecular π-stacking of benzene rings and aggregation of end-capped fluoroalkyl groups in methanol.

Implementation of Dipolar Resonant Excitation for Collision Induced Dissociation with Ion Mobility/Time-of-Flight MS

An ion mobility/time-of-flight mass spectrometer (IMS/TOF MS) platform that allows for resonant excitation collision induced dissociation (CID) is presented. Highly efficient, mass-resolved fragmentation without additional excitation of product ions was accomplished and over-fragmentation common in beam-type CID experiments was alleviated. A quadrupole ion guide was modified to apply a dipolar AC signal across a pair of rods for resonant excitation. The method was characterized with singly protonated methionine enkephalin and triply protonated peptide angiotensin I, yielding maximum CID efficiencies of 44 % and 84 %, respectively. The Mathieu q_x,y parameter was set at 0.707 for these experiments to maximize pseudopotential well depths and CID efficiencies. Resonant excitation CID was compared with beam-type CID for the peptide mixture. The ability to apply resonant waveforms in mobility-resolved windows is demonstrated with a peptide mixture yielding fragmentation over a range of mass-to-charge (m/z) ratios within a single IMS-MS analysis.

Facile dearomatisation of porphyrins using palladium-catalysed hydrazination: the 5,15-diiminoporphodimethenes and their redox products

The synthesis, electronic absorption and ¹H NMR spectra of a suite of novel porphyrinoids derived from meso-bromoporphyrins by palladium-catalysed aminations using ethyl and tert-butylcarbazates are reported. Instead of the expected carbazate-substituted porphyrins, a facile oxidative dearomatisation of the porphyrin ring occurs in high yield, especially for the nickel(II) complexes, resulting in high yields of 5,15-diiminoporphodimethenes (DIPDs). The analogous zinc(II) and free base DIPDs were also characterised, the former by X-ray crystallography. The oxidation and reduction reactions of DIPDs and their precursor carbazate porphyrins were studied. Density Functional Theory (DFT) was used to calculate the optimised geometries and frontier molecular orbitals of DIPD Ni8c and bis(azocarboxylate) 19c, and Time Dependent DFT calculations allowed the prediction of electronic absorption spectra, whose characteristics corresponded well with those of the observed solution spectra. In the latter case, the calculated low-energy absorptions were unlike those of a typical porphyrin, due to the near-degeneracy of the highest filled frontier orbitals, and the wide energy separation between the unfilled orbitals. This feature was present in the observed spectrum.     

Direct electron transfer and biocatalytic activity of iron storage protein molecules immobilized on electrodeposited cobalt oxide nanoparticles

Ferritin was immobilized on a glassy carbon electrode with electrodeposited cobalt oxide nanoparticles, and its direct electron transfer behavior was studied. It exhibits a pair of redox peaks due to direct electron transfer between ferritin and the nanoparticles. Electrochemical parameters including the formal potential (E^0??), the charge transfer coefficient (??), and the apparent heterogeneous electron transfer rate constant (k_s) were determined. The sensor displays excellent biocatalytic activity in terms of reduction of hydrogen peroxide, and this was applied to electrochemical sensing of hydrogen peroxide.

Discovery of safety biomarkers for realgar in rat urine using UFLC-IT-TOF/MS and 1H NMR based metabolomics

As an arsenical, realgar (As₄S₄) is known as a poison and paradoxically as a therapeutic agent. However, a complete understanding of the precise biochemical alterations accompanying the toxicity and therapy effects of realgar is lacking. Using a combined ultrafast liquid chromatography (UFLC) coupled with ion trap time-of-flight mass spectrometry (IT-TOF/MS) and ¹H NMR spectroscopy based metabolomics approach, we were able to delineate significantly altered metabolites in the urine samples of realgar-treated rats. The platform stability of the liquid chromatography LC/MS and NMR techniques was systematically investigated, and the data processing method was carefully optimized. Our results indicate significant perturbations in amino acid metabolism, citric acid cycle, choline metabolism, and porphyrin metabolism. Thirty-six metabolites were proposed as potential safety biomarkers related to disturbances caused by realgar, and glycine and serine are expected to serve as the central contacts in the metabolic pathways related to realgar-induced disturbance. The LC/MS and NMR based metabolomics approach established provided a systematic and holistic view of the biochemical effects of realgar on rats, and might be employed to investigate other drugs or xenobiotics in the future.

Solid-phase extraction of mercury(II) with magnetic core-shell nanoparticles, followed by its determination with a rhodamine-based fluorescent probe

Magnetic Fe₃O₄@SiO₂ core shell nanoparticles containing diphenylcarbazide in the shell were utilized for solid phase extraction of Hg(II) from aqueous solutions. The Hg(II) loaded nanoparticles were then separated by applying an external magnetic field. Adsorbed Hg(II) was desorbed and its concentration determined with a rhodamine-based fluorescent probe. The calibration graph for Hg(II) is linear in the 60 nM to 7.0 μM concentration range, and the detection limit is at 23 nM. The method was applied, with satisfying results, to the determination of Hg(II) in industrial waste water.

Synthesis, spectroscopic studies of new water-soluble Co(II) and Cu(II) macrocyclic complexes of 4,15-bis(2-hydroxyethyl)-2,4,6,13,15,17-hexaazatricyclodocosane: their interaction studies with calf thymus DNA and guanosine 5′ monophosphate

New water soluble Co(II) 1, Ni(II) 2 and Cu(II) 3 complexes of 4,15-bis(2-hydroxyethyl)-2,4,6,13,15,17-hexaazatricyclodocosane Co(II) were synthesized and characterized by various techniques, viz. elemental analysis, conductivity measurements, infrared, electronic, ESI-MS, ¹H and ¹³C NMR spectroscopy. Molar conductance measurements in aqueous solution showed that complexes 1, 2 and 3 are ionic in nature. On the basis of spectroscopic data, a square planar geometry was assigned to the complexes involving four N-atoms of the two cyclohexane moieties. Interaction studies of 1 and 3 with CT-DNA were carried using UV/Visible absorption spectroscopy, fluorescence spectrophotometry, cyclic voltammetry and viscosity measurements. Absorption spectral traces reveal 27.7 and 23.3% hyperchromism for complexes 1 and 3, respectively indicative of strong binding to CT-DNA. These results were authenticated by fluorescence quenching experiments and viscosity measurements. The intrinsic binding constants K _b of 1 and 3 are 2.94 × 10⁴ and 2.71 × 10⁴ M^?1, respectively. Early transition metals show preference for O6 position while later ones copper and cobalt prefer N7 position of DNA base guanine. To validate this hypothesis, interaction studies of copper (II) and cobalt (II) complexes were carried out with 5′GMP, which revealed electrostatic interactions are more favored along with hydrogen bonding than coordinate covalent interaction to N7 position of guanine.     

Negative ion tandem mass spectrometry of prenylated fungal metabolites and their derivatives

Liquid chromatography negative ion electrospray ionisation tandem mass spectrometry has been used for characterisation of naturally occurring prenylated fungal metabolites and synthetic derivatives. The fragmentation studies allow an elucidation of the decomposition pathways for these compounds. It could be shown, that the prenyl side chain is degraded by successive radical losses of C₅ units. Both the benzoquinones and the phenolic derivatives display significant key ions comprising the aromatic ring. In some cases, the formation of significant oxygen-free key ions could be evidenced by high-resolution MS/MS measurements. Furthermore, the different types of basic skeletons, benzoquinones and phenol type as well as cyclic prenylated compounds, can be differentiated by their MS/MS behaviour.

Imidate-Based Cross-Linkers for Structural Proteomics: Increased Charge of Protein and Peptide Ions and CID and ECD Fragmentation Studies

Chemical cross-linking is an attractive low-resolution technique for structural studies of protein complexes. Distance constraints obtained from cross-linked peptides identified by mass spectrometry (MS) are used to construct and validate protein models. Amidinating cross-linkers such as diethyl suberthioimidate (DEST) have been used successfully in chemical cross-linking experiments. In this work, the application of a commercial diimidate cross-linking reagent, dimethyl suberimidate (DMS), was evaluated with model peptides and proteins. The peptides were designed with acetylated N-termini followed by random sequences containing two Lys residues separated by an Arg residue. After cross-linking reactions, intra- and intermolecular cross-linked species were submitted to CID and ECD dissociations to study their fragmentation features in the gas phase. Fragmentation of intramolecular peptides by collision induced dissociation (CID) demonstrates a unique two-step fragmentation pathway involving formation of a ketimine as intermediate. Electron capture and electron transfer dissociation (ECD and ETD) experiments demonstrated that the cyclic moiety is not dissociated. Intermolecular species demonstrated previously described fragmentation behavior in both CID and ECD experiments. The charge state distributions (CSD) obtained after reaction with DMS were compared with those obtained with disuccinimidyl suberate (DSS). CSDs for peptides and proteins were increased after their reaction with DMS, owing to the higher basicity of DMS modified species. These features were also observed in LC-MS experiments with bovine carbonic anhydrase II (BCA) after cross-linking with DMS and tryptic proteolysis. Cross-linked peptides derived from this protein were identified at high confidence and those species were in agreement with the crystal structure of BCA.

Soft Ionization of Saturated Hydrocarbons, Alcohols and Nonpolar Compounds by Negative-Ion Direct Analysis in Real-Time Mass Spectrometry

Large polarizable n-alkanes (approximately C18 and larger), alcohols, and other nonpolar compounds can be detected as negative ions when sample solutions are injected directly into the sampling orifice of the atmospheric pressure interface of the time-of-flight mass spectrometer with the direct analysis in real time (DART) ion source operating in negative-ion mode. The mass spectra are dominated by peaks corresponding to [M + O₂]￣^?. No fragmentation is observed, making this a very soft ionization technique for samples that are otherwise difficult to analyze by DART. Detection limits for cholesterol were determined to be in the low nanogram range.

Synthesis,crystal structure,and photoluminescence of a zinc metalloporphyrin

A zinc metalloporphyrin, ZnTCPP(acetone) (1) (TCPP = meso-tetra(4-carboxyphenyl)porphyrin), has been prepared via a solvothermal reaction and structurally characterized by single-crystal X-ray diffraction. Compound 1 features an isolated structure with a planar macrocycle and an embedded zinc ion binded to four pyrrole nitrogen atoms and one acetone oxygen atom. Photoluminescent investigation reveals that compound 1 displays an intensive emission in the red region.     

Electrochemical chiral recognition of tryptophan using a glassy carbon electrode modified with β-cyclodextrin and graphene

We report on a method for electrochemical enantioselective recognition of tryptophan (Trp) enantiomers. It is based on competitive host-guest interaction between a deoxy-(2-aminoethylamino)-β-cyclodextrin (CD) bound to graphene nanosheets and the Cu(II) complexes of the Trp enantiomers via a ligand exchange mechanism. Chiral recognition was investigated via cyclic voltammetry and electrochemical impedance spectroscopy. The results reveal that the CD bound to graphene displays a stronger interaction with the Cu(II) complex of L-Trp than to that of D-Trp. The method was applied to the determination of the ratio of Trp enantiomers in mixtures.

Synthesis and spectral properties of sandwich <Emphasis Type="Italic">meso</Emphasis>-tetramethyltetrabenzoporphyrin-phthalocyanine complexes with lutetium,erbium, yttrium,and lanthanum

The reaction of phthalimide with zinc(II) propanoate gave meso-tetramethyltetrabenzoporphyrinatozinc(II) whose demetalation afforded the corresponding free base. The latter was used to synthesize complexes with lutetium, erbium, yttrium, and lanthanum. Heating of these complexes with excess phthalonitrile led to the formation of sandwich meso-tetramethyltetrabenzoporphyrin-phthalocyanine complexes. Spectral properties of the resulting compounds were studied.     

Microfluidic robotic device coupled with electrochemical sensor field for handling of paramagnetic micro-particles as a tool for determination of plant mRNA

The expression of genes responsible for the biosynthesis of stress proteins corresponds to the exposition of an organism to abiotic and/or biotic stress. We utilize two types of paramagnetic particles for isolation of total mRNA from early somatic embryos of Norway Spruce (Picea abies /L./ Karst.) and maize plants (Zea mays L.) treated with cadmium(II) ions. The paramagnetic particles were evaluated for analysis of real samples, and poly-adenine was used as a model mRNA. Various approaches (from non-automatic to fully automatic) were tested in terms of handling the particles.

Interpretation and Deconvolution of Nanodisc Native Mass Spectra

Nanodiscs are a promising system for studying gas-phase and solution complexes of membrane proteins and lipids. We previously demonstrated that native electrospray ionization allows mass spectral analysis of intact Nanodisc complexes at single lipid resolution. This report details an improved theoretical framework for interpreting and deconvoluting native mass spectra of Nanodisc lipoprotein complexes. In addition to the intrinsic lipid count and charge distributions, Nanodisc mass spectra are significantly shaped by constructive overlap of adjacent charge states at integer multiples of the lipid mass. We describe the mathematical basis for this effect and develop a probability-based algorithm to deconvolute the underlying mass and charge distributions. The probability-based deconvolution algorithm is applied to a series of dimyristoylphosphatidylcholine Nanodisc native mass spectra and used to provide a quantitative picture of the lipid loss in gas-phase fragmentation.

Differentiation of Diastereoisomers of Protected 1,2-Diaminoalkylphosphonic Acids by EI Mass Spectrometry and Density Functional Theory

Electron ionization mass spectrometry and density functional theory (DFT) calculations have been used to study the fragmentation of diastereoisomers of protected 1,2-diaminoalkylphosphonic acids. The loss of a diethoxyphosphoryl group and the elimination of diethyl phosphonate were found to be competitive fragmentation processes, which can be used to differentiate both stereoisomers. Selective deuterated analogs and product- and precursor-ion mass spectra allowed the elucidation of the fragmentation mechanisms. The structures of the transition states and product ions were optimized using the density functional theory (DFT), and free energy calculations confirmed the observed differences in the formation and relative intensities of specific fragment ions.