Clickable report tags for identification of modified peptides by mass spectrometry

The identification and quantification of modified peptides are critical for the functional characterization of post-translational protein modifications (PTMs) to elucidate their biological function. Nowadays, quantitative mass spectrometry coupled with various bioinformatic pipelines has been successfully used for the determination of a wide range of PTMs. However, direct characterization of low abundant protein PTMs in bottom-up proteomic workflow remains challenging. Here, we present the synthesis and evaluation of tandem mass spectrometry tags (TMT) which are introduced via click-chemistry into peptides bearing alkyne handles. The fragmentation properties of the two mass tags were validated and used for screening in a model system and analysis of AMPylated proteins. The presented tags provide a valuable tool for diagnostic peak generation to increase confidence in the identification of modified peptides and potentially for direct peptide-PTM quantification from various experimental conditions.     

Reaction Products of β-Aminopropioamidoximes Nitrobenzenesulfochlorination: Linear and Rearranged to Spiropyrazolinium Salts with Antidiabetic Activity

Nitrobenzenesulfochlorination of β-aminopropioamidoximes leads to a set of products depending on the structure of the initial interacting substances and reaction conditions. Amidoximes, functionalized at the terminal C atom with six-membered N-heterocycles (piperidine, morpholine, thiomorpholine and phenylpiperazine), as a result of the spontaneous intramolecular heterocyclization of the intermediate reaction product of an S_N2 substitution of a hydrogen atom in the oxime group of the amidoxime fragment by a nitrobenzenesulfonyl group, produce spiropyrazolinium ortho- or para-nitrobenzenesulfonates. An exception is ortho-nitrobenzenesulfochlorination of β-(thiomorpholin-1-yl)propioamidoxime, which is regioselective at room temperature, producing two spiropyrazolinium salts (ortho-nitrobezenesulfonate and chloride), and regiospecific at the boiling point of the solvent, when only chloride is formed. The para-Nitrobezenesulfochlorination of β-(benzimidazol-1-yl)propioamidoxime, due to the reduced nucleophilicity of the aromatic β-amine nitrogen atom, is regiospecific at both temperatures, and produces the O-para-nitrobenzenesulfochlorination product. The antidiabetic screening of the new nitrobezenesulfochlorination amidoximes found promising samples with in vitro α-glucosidase activity higher than the reference drug acarbose. ¹H-NMR spectroscopy and X-ray analysis revealed the slow inversion of six-membered heterocycles, and experimentally confirmed the presence of an unfavorable stereoisomer with an axial N–N bond in the pyrazolinium heterocycle.     

Optical constants of organic insulators in the UV range extracted from reflection electron energy loss spectra

Reflection electron energy loss spectroscopy (REELS) spectra were measured for seven insulating organic compounds (DNA, Irganox 1010, Kapton, polyethylene [PE], poly(methyl methacrylate) [PMMA], polystyrene [PS] and polytetrafluoroethylene [PTFE]). Optical constants and energy band gaps were extracted from the measured REELS spectra after elimination of multiple electron scattering via a deconvolution and fitting the normalised single scattering energy loss spectra to Drude and Drude–Lindhard model dielectric functions, constrained by the Kramers–Kronig sum and f-sum rules. Satisfactory agreement is found for those optical constants for which literature data exists. For PTFE, the observed features in the optical data correspond to its electronic structure.     

The unique structure of [(C4H9)4N]3[Pb(NO3)5]—one step forward in understanding transport properties in tetra-n-butylammonium-based solid electrolytes

Structural Chemistry - The crystal and molecular structure of tris(tetrabutylammonium) pentanitratoplumbate(II) was determined and characterized by single-crystal and powder X-ray diffraction and...     

Stereoselective Ring Opening of Electronically Excited Cyclohexa-2, 4-dienones: Cause and effect

The two conformers of a cyclohexa-2, 4-dienone with different substituents at C(6) on irradiation are believed to undergo ring opening stereospecifically affording a mixture of two configurationally isomeric diene-ketenes (and descendents thereof)- Exceptions are generally found for those dienones with one C and one O substituent or even with two C substituents, if one of them carries a polar group at a site able to interact through space with the ring C?O group. In these cases, only one of the two anticipated diene-ketenes (and descendents thereof) is produced. A thorough investigation of the photochemistry of a series of structurally different cyclohexa-2, 4-dienones on analytical as well as on preparative scale extends our mechanistic knowledge of the various routes from diene-ketenes into a variety of compound classes. Novel compound classes accessible to diene-ketenes are seven-membered carbocycles (by intramolecular aldolization of the zwitterion of appropriately substituted, transiently formed diene-(N, O)-ketene acetals) and β-lactams (by Staudinger reaction).     

Assessment of the In Vivo Release and Biocompatibility of Novel Vesicles Containing Zinc in Rats

This paper is focused on the in vivo release and biocompatibility evaluation in rats of some novel systems entrapping zinc chloride in lipid vesicles. The particles were prepared by zinc chloride immobilization inside lipid vesicles made using phosphatidylcholine, stabilized with 0.5% chitosan solution, and dialyzed for 10 h to achieve a neutral pH. The submicrometric systems were physico-chemically characterized. White Wistar rats, assigned into four groups of six animals each, were treated orally with a single dose, as follows: Group I (control): deionized water 0.3 mL/100 g body weight; Group II (Zn): 2 mg/kg body weight (kbw) zinc chloride; Group III (LV-Zn): 2 mg/kbw zinc chloride in vesicles; Group IV (LVC-Zn): 2 mg/kbw zinc chloride in vesicles stabilized with chitosan. Haematological, biochemical, and immune parameters were assessed after 24 h and 7 days, and then liver fragments were collected for histopathological examination. The use of zinc submicrometric particles—especially those stabilized with chitosan—showed a delayed zinc release in rats. No substantial changes to blood parameters, plasma biochemical tests, serum complement activity, or peripheral neutrophils phagocytic capacity were noted; moreover, the tested substances did not induce liver architectural disturbances. The obtained systems provided a delayed release of zinc, and showed good biocompatibility in rats.     

A New Definition of the Stationary Phase Volume in Mixed-Mode Chromatographic Columns in Hydrophilic Liquid Chromatography

Polar columns used in the HILIC (Hydrophilic Interaction Liquid Chromatography) systems take up water from the mixed aqueous–organic mobile phases in excess of the water concentration in the bulk mobile phase. The adsorbed water forms a diffuse layer, which becomes a part of the HILIC stationary phase and plays dominant role in the retention of polar compounds. It is difficult to fix the exact boundary between the diffuse stationary and the bulk mobile phase, hence determining the column hold-up volume is subject to errors. Adopting a convention that presumes that the volume of the adsorbed water can be understood as the column stationary phase volume enables unambiguous determination of the volumes of the stationary and of the mobile phases in the column, which is necessary for obtaining thermodynamically correct chromatographic data in HILIC systems. The volume of the aqueous stationary phase, Vex, can be determined experimentally by frontal analysis combined with Karl Fischer titration method, yielding isotherms of water adsorbed on polar columns, which allow direct prediction of the effects of the composition of aqueous–organic mobile phase on the retention in HILIC systems, and more accurate determination of phase volumes in columns and consistent retention data for any mobile phase composition. The n phase volume ratios of 18 columns calculated according to the new phase convention strongly depend on the type of the polar column. Zwitterionic and TSK gel amide and amine columns show especially strong water adsorption.     

Iminodiacetic acid functionalised monolithic silica chelating ion exchanger for rapid determination of alkaline earth metal ions in high ionic strength samples

Iminodiacetic acid has been covalently bonded to a bare silica monolith to produce the first reported high-performance monolithic chelating ion exchange column. Using the new column, separation and determination of traces of alkaline earth metal ions (low ppm) in high ionic strength samples (up to 2 M NaCl and KCl brines), could be achieved in under 40 s. At an eluent flow rate of 4 mL min(-1) retention time precision was < 1.2% (n = 9) for Mg(II) and Ca(II), with detector linearity (n = 5) over the range 2-10 mg L(-1) of between R2 = 0.985 and R2 = 0.995. In 1 M KCl and NaCl brine samples, detection limits of 0.2 mg L(-1) were possible.     

Structural and mechanistic look at the orthoplatination of aryl oximes by dichlorobis(sulfoxide or sulfide)platinum(II) complexes

Structural and mechanistic aspects of orthoplatination of acetophenone and benzaldehyde oximes by the platinum(II) sulfoxide and sulfide complexes [PtCl(2)L(2)] (2, L = SOMe(2) (a), rac-SOMePh (b), R-SOMe(C(6)H(4)Me-4) (c), and SMe(2) (d)) to afford the corresponding platinacycles cis-(C,S)-[Pt(II)(C(6)H(3)-2-CR'=NOH-5-R)Cl(L)] (3, R, R' = H, Me) have been investigated. The reaction of acetophenone oxime with sulfoxide complex 2a in methanol solvent occurs noticeably faster than with sulfide complex 2d due to the fact that the sulfoxide is a much better platinum(II) leaving ligand than the sulfide. Evidence is presented that the orthoplatination is a multistep process. The formation of unreactive dichlorobis(N-oxime)platinum(II) cations accounts for the rate retardation by excess acetophenone oxime and suggests the importance of pseudocoordinatively unsaturated species for the C-H bond activation by Pt(II). A comparative X-ray structural study of dimethyl sulfoxide platinacycle 3b (R = R' = Me) and its sulfide analogue 3e (R = H, R' = Me), as well as of SOMePh complex 3c (R = H, R' = Me), indicated that they are structurally similar and a sulfur ligand is coordinated in the cis position with respect to the sigma-bound phenyl carbon. The differences concern the Pt-S bond distance, which is notably longer in the sulfide complex 3e (2.2677(11) A) as compared to that in sulfoxide complexes 3b (2.201(2)-2.215(2) A) and 3c (2.2196(12) A). Whereas the metal plane is practically a plane of symmetry in 3b due to the H-bonding between the sulfoxide oxygen and the proton at carbon ortho to the Pt-C bond, an S-bonded methyl of SOMePh and SMe(2) is basically in the platinum(II) plane in complexes 3c and 3e, respectively. There are intra- and intermolecular hydrogen bond networks in complex 3b. An interesting structural feature of complex 3c is that the two independent molecules in the asymmetric unit of the crystal reveal an extremely short Pt-Pt contact of 3.337 A.     

Strain‐Induced Isomerization in One‐Dimensional Metal–Organic Chains

The ability to use mechanical strain to steer chemical reactions creates completely new opportunities for solution‐ and solid‐phase synthesis of functional molecules and materials. However, this strategy is not readily applied in the bottom‐up on‐surface synthesis of well‐defined nanostructures. We report an internal strain‐induced skeletal rearrangement of one‐dimensional (1D) metal–organic chains (MOCs) via a concurrent atom shift and bond cleavage on Cu(111) at room temperature. The process involves Cu‐catalyzed debromination of organic monomers to generate 1,5‐dimethylnaphthalene diradicals that coordinate to Cu adatoms, forming MOCs with both homochiral and heterochiral naphthalene backbone arrangements. Bond‐resolved non‐contact atomic force microscopy imaging combined with density functional theory calculations showed that the relief of substrate‐induced internal strain drives the skeletal rearrangement of MOCs via 1,3‐H shifts and shift of Cu adatoms that enable migration of the monomer backbone toward an energetically favorable registry with the Cu(111) substrate. Our findings on this strain‐induced structural rearrangement in 1D systems will enrich the toolbox for on‐surface synthesis of novel functional materials and quantum nanostructures.