A Novel MS-Cleavable Azo Cross-Linker for Peptide Structure Analysis by Free Radical Initiated Peptide Sequencing (FRIPS)

The chemical cross-linking/mass spectrometry (MS) approach is a growing research field in structural proteomics that allows gaining insights into protein conformations. It relies on creating distance constraints between cross-linked amino acid side chains that can further be used to derive protein structures. Currently, the most urgent task for designing novel cross-linking principles is an unambiguous and automated assignment of the created cross-linked products. Here, we introduce the homobifunctional, amine-reactive, and water soluble cross-linker azobisimidoester (ABI) as a prototype of a novel class of cross-linkers. The ABI-linker possesses an innovative modular scaffold combining the benefits of collisional activation lability with open shell chemistry. This MS-cleavable cross-linker can be efficiently operated via free radical initiated peptide sequencing (FRIPS) in positive ionization mode. Our proof-of-principle study challenges the gas phase behavior of the ABI-linker for the three amino acids, lysine, leucine, and isoleucine, as well as the model peptide thymopentin. The isomeric amino acids leucine and isoleucine could be discriminated by their characteristic side chain fragments. Collisional activation experiments were conducted via positive electrospray ionization (ESI) on two Orbitrap mass spectrometers. The ABI-mediated formation of odd electron product ions in MS/MS and MS³ experiments was evaluated and compared with a previously described azo-based cross-linker. All cross-linked products were amenable to automated analysis by the MeroX software, underlining the future potential of the ABI-linker for structural proteomics studies.

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TEMPO-Assisted Free Radical-Initiated Peptide Sequencing Mass Spectrometry (FRIPS MS) in Q-TOF and Orbitrap Mass Spectrometers: Single-Step Peptide Backbone Dissociations in Positive Ion Mode

The present study demonstrates that one-step peptide backbone fragmentations can be achieved using the TEMPO [2-(2,2,6,6-tetramethyl piperidine-1-oxyl)]-assisted free radical-initiated peptide sequencing (FRIPS) mass spectrometry in a hybrid quadrupole time-of-flight (Q-TOF) mass spectrometer and a Q-Exactive Orbitrap instrument in positive ion mode, in contrast to two-step peptide fragmentation in an ion-trap mass spectrometer (reference Anal. Chem. 85, 7044–7051 (30)). In the hybrid Q-TOF and Q-Exactive instruments, higher collisional energies can be applied to the target peptides, compared with the low collisional energies applied by the ion-trap instrument. The higher energy deposition and the additional multiple collisions in the collision cell in both instruments appear to result in one-step peptide backbone dissociations in positive ion mode. This new finding clearly demonstrates that the TEMPO-assisted FRIPS approach is a very useful tool in peptide mass spectrometry research.

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Characterizing Peptide Neutral Losses Induced by Negative Electron-Transfer Dissociation (NETD)

We implemented negative electron-transfer dissociation (NETD) on a hybrid ion trap/Orbitrap mass spectrometer to conduct ion/ion reactions using peptide anions and radical reagent cations. In addition to sequence-informative ladders of a•- and x-type fragment ions, NETD generated intense neutral loss peaks corresponding to the entire or partial side-chain cleavage from amino acids constituting a given peptide. Thus, a critical step towards the characterization of this recently introduced fragmentation technique is a systematic study of synthetic peptides to identify common neutral losses and preferential fragmentation pathways. Examining 46 synthetic peptides with high mass accuracy and high resolution analysis permitted facile determination of the chemical composition of each neutral loss. We identified 19 unique neutral losses from 14 amino acids and three modified amino acids, and assessed the specificity and sensitivity of each neutral loss using a database of 1542 confidently identified peptides generated from NETD shotgun experiments employing high-pH separations and negative electrospray ionization. As residue-specific neutral losses indicate the presence of certain amino acids, we determined that many neutral losses have potential diagnostic utility. We envision this catalogue of neutral losses being incorporated into database search algorithms to improve peptide identification specificity and to further advance characterization of the acidic proteome.     

Manganese (III) Acetate Initiated Oxidative Free Radical Reaction of 3-Heteroaryl Substituted Malonates

The manganese (III) initiated oxidative free radical reaction of electron rich 3-heteroaryl substituted malonates is described.     

Bond Dissociation Free Energies (BDFEs) of the Acidic H-A Bonds in HA(*)(-) Radical Anions by Three Different Pathways

Cleavage of radical anions, HA(*)(-), have been considered to give either H(*) + A(-) (path a) or H(-) + A(*) (path b), and factors determining the preferred mode of cleavage have been discussed. It is conceivable that cleavage to give a proton and a radical dianion, HA(*)(-) right harpoon over left harpoon H(+) + A(*)(2)(-) (path c), might also be feasible. A method, based on a thermodynamic cycle, to estimate the bond dissociation free energy (BDFE) by path c has been devised. Comparison of the BDFEs for cleavage of the radical anions derived from 24 nitroaromatic OH, SH, NH, and CH acids by paths a, b, c has shown that path c is favored thermodynamically.     

Dissociation behavior of a bifunctional tempo‐active ester reagent for peptide structure analysis by free radical initiated peptide sequencing (FRIPS) mass spectrometry

We have synthesized a homobifunctional active ester cross‐linking reagent containing a TEMPO (2,2,6,6‐tetramethylpiperidine‐1‐oxy) moiety connected to a benzyl group (Bz), termed TEMPO‐Bz‐linker. The aim for designing this novel cross‐linker was to facilitate MS analysis of cross‐linked products by free radical initiated peptide sequencing (FRIPS). The TEMPO‐Bz‐linker was reacted with all 20 proteinogenic amino acids as well as with model peptides to gain detailed insights into its fragmentation mechanism upon collision activation. The final goal of this proof‐of‐principle study was to evaluate the potential of the TEMPO‐Bz‐linker for chemical cross‐linking studies to derive 3D‐structure information of proteins. Our studies were motivated by the well documented instability of the central NO―C bond of TEMPO‐Bz reagents upon collision activation. The fragmentation of this specific bond was investigated in respect to charge states and amino acid composition of a large set of precursor ions resulting in the identification of two distinct fragmentation pathways. Molecular ions with highly basic residues are able to keep the charge carriers located, i.e. protons or sodium cations, and consequently decompose via a homolytic cleavage of the NO―C bond of the TEMPO‐Bz‐linker. This leads to the formation of complementary open‐shell peptide radical cations, while precursor ions that are protonated at the TEMPO‐Bz‐linker itself exhibit a charge‐driven formation of even‐electron product ions upon collision activation. MS³ product ion experiments provided amino acid sequence information and allowed determining the cross‐linking site. Our study fully characterizes the CID behavior of the TEMPO‐Bz‐linker and demonstrates its potential, but also its limitations for chemical cross‐linking applications utilizing the special features of open‐shell peptide ions on the basis of selective tandem MS analysis. Copyright © 2015 John Wiley & Sons, Ltd.     

聚偏氟乙烯的氯化改性

研究了聚偏氟乙烯 (PVDF)自由基引发的氯化反应。考察了各种因素 ,如氯化剂、引发剂的种类及浓度 ,反应介质、反应温度和反应时间的影响 ,确定了合成氯化PVDF的最佳反应条件。采用碱熔法测定氯含量 ,用HNMR进行了结构表征 ,并用溶度参数法、接触角法、DTA TG等方法对PVDF氯化前后的溶解性、附着力、熔点等性能进行了测试。结果表明 ,氯原子成功地引入到了PVDF上 ,当氯含量增加到 8 3 %时 ,氯化PVDF的熔点由 1 63℃降至 1 3 0℃左右 ,附着力也有了明显的改善 ,与水的接触角由 90°降至 5 4°,由不溶于丙酮变为溶于丙酮 ,对甲醇和四氯化碳的溶度参数的变化也说明了氯化PVDF的溶解性能变好 ,由TG曲线可知 ,氯化PVDF的热稳定性比改性前虽有一定的降低 ,但其分解温度仍在 3 0 0℃以上     

通过RAFT自由基聚合合成含叠氮端基的聚N-异丙基丙烯酰胺

S-十二烷基-S′-(2-羧基-异丙基)三硫羧酸酯与叠氮乙醇反应合成了一种新型叠氮链转移剂(2);在2存在下通过可逆加成-断裂链转移(RAFT)自由基聚合合成了含叠氮端基的聚N-异丙基丙烯酰胺(3).其结构经1H NMR, IR和GPC表征.研究结果表明,3呈现较好的温敏性,低临界溶液温度为28.5 ℃.     

Miniaturized Sequencing Gel System for Quick Analysis of DNA by Hydroxyl Radical Cleavage

We described a simple and quick miniaturized sequencing gel system for DNA analysis. Two major modifications were made to the previously reported miniaturized DNA sequencing gel system to achieve high-resolution hydroxyl radical cleavage analysis: including formamide in the miniaturized gel and providing uniform heating during electrophoresis. Our method enables one to reduce the cost for chemicals and to significantly reduce electrophoresis time. Furthermore, minimal gel handling simplifies the entire process. We show that the resolution of DNA fragments obtained by hydroxyl radical cleavage for the miniaturized gel is similar to that of a large conventional sequencing gel.     

Diastereoselective Radical Hydroacylation of Alkylidenemalonates with Aliphatic Aldehydes Initiated by Photolysis of Hypervalent Iodine(III) Reagents

Diastereoselective radical hydroacylation of chiral alkylidenemalonates with aliphatic aldehydes is realized by the combination of a hypervalent iodine(III) reagent and UV‐light irradiation. The reaction is initiated by the photolysis of hypervalent iodine(III) reagents under mild, metal‐free conditions, and is the first example of diastereoselective addition of acyl radicals to olefins to afford chiral ketones in a highly stereoselective fashion. The obtained optically active ketones are useful chiral synthons, as exemplified by the short formal synthesis of (?)‐methyleneolactocin.     

The Studies of Free Radical Cyclization Reactions Mediated by Sulfonyl Chloride (I)

A study of the free racinoal reaction of vinylcycloprelpane mediated by p-toluenesulfonyl chloride is described.     

The Studies of Free Radical Cyclization Reactions Mediated by Sulfonyl Chloride (II)

A study on the free radical cyclization reaction of substituted 1,6-dienes mediated by p-toluenesulfonyl chloride is described.     

Synthesis and Characterization of Poly(allyl methacrylate) Obtained by Free Radical Initiator

Allyl methacrylate was polymerized in CCl₄ solution by α,α′‐azoisobutyronitrile at 50, 60, and 70°C. The kinetic curves were auto‐accelarated types at 60 and 70°C, but almost linear at 50°C. Arrhenius activation energy was 77.5 kJ/mol. The polymer was insoluble in common organic solvents. It was characterized by FT‐IR, NMR, DSC, TGA and XPS methods. About 98–99% of allyl side groups were remained as pendant even after completion of the polymerization. The spectroscopic and thermal results showed that polymerization is not a cyclopolymerization type, but may have end group cyclization. The high molecular weight is the main cause of a polymer being insoluble even in the early stage of the polymerization. Molecular weight of 1.1×10⁶ for a soluble polymer fraction was measured by light scattering method. The Tg of polymer was 94°C, and after curing at 150–200°C, increased to 211°C. The thermal pyrolysis of polymer at about 350°C gave an anhydride by linkage type degradation, and side group cyclization. The XPS analysis showed the presence of radical fragments of AIBN (initiator) and CCl₄ (solvent) associated with oligomers.     

Effect of Temperature on Dynamic Physical Behavior of Poly(vinyl chloride) Gel Structure with Ester Plasticizers

Dynamic viscoelastic properties of poly(vinyl chloride) (PVC)/bis(2-ethylhexyl) phthalate (DOP) and PVC/di-n-butyl sebacate (DBS) gels with molecular weight distribution (M_w/M_n), of 2.16 and various polymer concentrations c, have been studied as a function of temperature. These PVC gels exhibited an elastic solid at room temperature T, and gradually became liquid (sol) with increasing temperature. The sol-gel transition took place at a critical gel temperature at which the scaling law of G′(ω) ∼ G″(ω) ∝ ωⁿ held, allowing an accurate determination of the critical gel temperature by means of the frequency ω independence of the loss tangent. In this study the scaling exponent n, was 0.75–0.77. This is in good agreement with the previous results observed at different temperatures and suggests the formation of a similar fractal structure of the PVC gels. The gel strength S_g, at the gel point increased with increasing PVC concentration. These results suggest a unique character and structure for the gel points of PVC-plasticizers.     

对二甲胺基二苯酮的吸收光谱行为及其敏化的甲基丙烯酸甲酯的光聚合

本文对对二甲胺基二苯酮的吸收光谱及其光敏引发甲基丙烯酸甲酯聚合反应动力学进行了研究，并简单考察了氧气对聚合反应的影响。     

A Study on End Group Characterization of Poly(phenacyl methacrylate) Polymer Produced by Free Radical Polymerization

Free‐radical homopolymerization and copolymerization of phenacyl methacrylate (PAMA) with methyl methacrylate (MMA) was done using 2,2′‐azobis(isobutyronitrile) (AIBN) as the initiator in 1,4‐dioxane at 60°C. ¹H‐NMR and FT‐IR spectroscopy confirmed the existence of OCH₂ and CH signals and unsaturated structure and CN stretch at the chain end of low molecular weight poly(phenacyl methacrylate) [poly(PAMA)], respectively. The six‐membered ring with both ester and ether at the end group was detected by ¹H‐NMR. In the poly(PAMA), the end groups formed due to chain transfer reactions were found in large concentrations. The mechanism of the formation of end groups has been presented. The behavior of free radical polymerization of PAMA was compared with that of phenoxycarbonylmethyl methacrylate (PCMMA). The molecular weight distribution of the homo and copolymers was determined using gel permeation chromatography. Thermal properties of the polymers were determined using differential thermal analysis (DTA) and thermogravimetric analysis (TGA).     

A Study on End Group Characterization of Poly(phenacyl methacrylate) Polymer Produced by Free Radical Polymerization

Free‐radical homopolymerization and copolymerization of phenacyl methacrylate (PAMA) with methyl methacrylate (MMA) was done using 2,2′‐azobis(isobutyronitrile) (AIBN) as the initiator in 1,4‐dioxane at 60°C. ¹H‐NMR and FT‐IR spectroscopy confirmed the existence of OCH₂ and CH signals and unsaturated structure and CN stretch at the chain end of low molecular weight poly(phenacyl methacrylate)[poly(PAMA)], respectively. The six‐membered ring with both ester and ether at the end group was detected by ¹H‐NMR. In the poly(PAMA), the end groups formed due to chain transfer reactions were found in large concentrations. The mechanism of the formation of end groups has been presented. The behavior of free radical polymerization of PAMA was compared with that of phenoxycarbonylmethyl methacrylate (PCMMA). The molecular weight distribution of the homo and copolymers was determined using gel permeation chromatography. Thermal properties of the polymers were determined using differential thermal analysis (DTA) and thermogravimetric analysis (TGA).     

Unexpected Behavior of Diastereomeric Ions in the GasPhase: A Stimulus for Pondering on ee Measurements by ESI-MS

The most common protocols for the quantitative determination of the enantiomeric excess (ee) of raw mixtures by ESI-MS reveal inadequate in cases where the distribution of diastereomeric derivatives diverges from the ee of original solutions. This phenomenon is attributable to a matrix effect, i.e., to the stereospecific formation of high order noncovalent adducts in the ESI droplets, which alters the actual availability of the diastereomeric species under MS analysis. In this frame, the assumption of classic protocols that the ionization correction factor q is independent on the composition of the mixture submitted to analysis is questionable. An alternative methodology is presented in this paper, which is aimed at circumventing the problem by excluding any chemical derivatization of the original raw mixture. It is based on the measurement of the actual distribution of ESI-formed proton-bound diastereomeric complexes from the enantiomeric mixture through a careful analysis of their reaction kinetics with a suitable reactant.