Characterization of a new qQq-FTICR mass spectrometer for post-translational modification analysis and top-down tandem mass spectrometry of whole proteins

The use of a new electrospray qQq Fourier transform ion cyclotron mass spectrometer (qQq-FTICR MS) instrument for biologic applications is described. This qQq-FTICR mass spectrometer was designed for the study of post-translationally modified proteins and for top-down analysis of biologically relevant protein samples. The utility of the instrument for the analysis of phosphorylation, a common and important post-translational modification, was investigated. Phosphorylation was chosen as an example because it is ubiquitous and challenging to analyze. In addition, the use of the instrument for top-down sequencing of proteins was explored since this instrument offers particular advantages to this approach. Top-down sequencing was performed on different proteins, including commercially available proteins and biologically derived samples such as the human E2 ubiquitin conjugating enzyme, UbCH10. A good sequence tag was obtained for the human UbCH10, allowing the unambiguous identification of the protein. The instrument was built with a commercially produced front end: a focusing rf-only quadrupole (Q0), followed by a resolving quadrupole (Q1), and a LINAC quadrupole collision cell (Q2), in combination with an FTICR mass analyzer. It has utility in the analysis of samples found in substoichiometric concentrations, as ions can be isolated in the mass resolving Q1 and accumulated in Q2 before analysis in the ICR cell. The speed and efficacy of the Q2 cooling and fragmentation was demonstrated on an LCMS-compatible time scale, and detection limits for phosphopeptides in the 10 amol/muL range (pM) were demonstrated. The instrument was designed to make several fragmentation methods available, including nozzle-skimmer fragmentation, Q2 collisionally activated dissociation (Q2 CAD), multipole storage assisted dissociation (MSAD), electron capture dissociation (ECD), infrared multiphoton induced dissociation (IRMPD), and sustained off resonance irradiation (SORI) CAD, thus allowing a variety of MS(n) experiments. A particularly useful aspect of the system was the use of Q1 to isolate ions from complex mixtures with narrow windows of isolation less than 1 m/z. These features enable top-down protein analysis experiments as well structural characterization of minor components of complex mixtures.     

Synthesis and structures of a 3-sila-beta-diketiminatomagnesium bromide, ketenimide and triflate

The crystalline compounds [Mg(Br)(L)(thf)].0.5Et2O [L = {N(R)C(C6H3Me2-2,6)}2SiR, R = SiMe3] (1), [Mg(L){N=C=C(C(Me)=CH)2CH2}(D)2] [D = NCC6H3Me2-2,6 (2), thf (3)] and [{Mg(L)}2{mu-OSO(CF3)O-[mu}2] (4) were prepared from (a) Si(Br)(R){C(C6H3Me2-2,6)=NR}2 and Mg for (1), (b) [Mg(SiR3)2(thf)2] and 2,6-Me2C6H3CN (5 mol for (2), 3 mol for (3)), and (c) (2) + Me3SiOS(O)2CF3 for (4); a coproduct from (c) is believed to have been the trimethylsilyl ketenimide Me3SiN=C=C{C(Me)=CH}2CH2 (5).     

Stereoselective hydroxylation of an achiral cyclopentanecarboxylic acid derivative using engineered P450s BM-3

Substrate engineered, achiral carboxylic acid derivative was biohydroxylated with various mutants of cytochrome P450 BM-3 to give two out of the four possible diastereoisomers in high de and ee. The BM-3 mutants exhibit up to 9200 total turnovers for hydroxylation of the engineered substrate, which without the protecting group is not transformed by this enzyme.     

Polysulfonylamine. CLXIII [1] Kristallstrukturen von Metall‐di(methansulfonyl)amiden. 12 [1] Das orthorhombische Doppelsalz Na2Cs2[(CH3SO2)2N]4·3H2O: Ein dreidimensionales Koordinationspolymer aus (Caesium‐Anion‐Wasser)‐Schichten und intercalierten Natriumionen

Polysulfonylamines. CLXIII. Crystal Structures of Metal Di(methanesulfonyl)amides. 12. The Orthorhombic Double Salt Na₂Cs₂[(CH₃SO₂)₂N]₄·3H₂O: A Three‐Dimensional Coordination Polymer Built up from Cesium‐Anion‐Water Layers and Intercalated Sodium Ions The packing arrangement of the three‐dimensional coordination polymer Na₂Cs₂[(MeSO₂)₂N]₄·3H₂O (orthorhombic, space group Pna2₁, Z′ = 1) is in some respects similar to that of the previously reported sodium‐potassium double salt Na₂K₂[(MeSO₂)₂N]₄·4H₂O (tetragonal, P4₃2₁2, Z′ = 1/2). In the present structure, four multidentately coordinating independent anions, three independent aquo ligands and two types of cesium cation form monolayer substructures that are associated in pairs to form double layers via a Cs(1)—H₂O—Cs(2) motif, thus conferring upon each Cs⁺ an irregular O₈N₂ environment drawn from two N, O‐chelating anions, two O, O‐chelating anions and two water molecules. Half of the sodium ions occupy pseudo‐inversion centres situated between the double layers and have an octahedral O₆ coordination built up from four anions and two water molecules, whereas the remaining Na⁺ are intercalated within the double layers in a square‐pyramidal and pseudo‐C₂ symmetric O₅ environment provided by four anions and the water molecule of the Cs—H₂O—Cs motif. The net effect is that each of the four independent anions forms bonds to two Cs⁺ and two Na⁺, two independent water molecules are involved in Cs—H₂O—Na motifs, and the third water molecule acts as a μ₃‐bridging ligand for two Cs⁺ and one Na⁺. The crystal cohesion is reinforced by a three‐dimensional network of conventional O—H···O=S and weak C—H···O=S/N hydrogen bonds.     

C[triple‐bond]C—H systems as hydrogen‐bond donors and acceptors: trans‐1,2‐diethynylcyclo­hexane‐1,2‐diol and trans‐1,4‐diprop‐2‐ynylcyclo­hexane‐1,4‐diol monohydrate

The title 1,2‐diol derivative, C₁₀H₁₂O₂, crystallizes with two independent but closely similar mol­ecules in the asymmetric unit. Only two of the four OH groups are involved in classical hydrogen bonding; the mol­ecules thereby associate to form chains parallel to the short c axis. The other two OH groups are involved in O—H⋯(C[triple‐bond]C) systems. Additionally, three of the four C[triple‐bond]C—H groups act as donors in C—H⋯O inter­actions. The 1,4‐diol derivative crystallizes with two independent half‐mol­ecules of the diol (each associated with an inversion centre) and one water mol­ecule in the asymmetric unit, C₁₂H₁₆O₂·H₂O. Both OH groups and one water H atom act as classical hydrogen‐bond donors, leading to layers parallel to the ac plane. The second water H atom is involved in a three‐centre contact to two C[triple‐bond]C bonds. One acetyl­enic H atom makes a very short `weak' hydrogen bond to a hydr­oxy O atom, and the other is part of a three‐centre system in which the acceptors are a hydroxy O atom and a C[triple‐bond]C bond.     

Axially Dissymmetric Diphosphines in the Biphenyl Series: Synthesis of (6,6′-Dimethoxybiphenyl-2,2′-diyl)bis(diphenylphosphine)(‘MeO-BIPHEP’) and Analogues via an ortho-Lithiation/Iodination Ullmann-Reaction Approach

The new axially dissymmetric diphosphines (R)- and (S)-(6,6′-dimethoxybiphenyl-2,2′-diyl)bis(diphenyl phosphine) ((R)- and (S)- 5a ; ‘MeO-BIPHEP’) and the analogues (R)- and (S)- 5b and 5c have been synthesized in enantiomerically pure form. These ligands have become readily available by a synthetic scheme which employs, as key steps, an ortho-lithiation/iodination reaction of the (m-methoxyphenyl)diprienylphosphine oxides 8 and a subsequent Ullmann reaction of the resulting iodides 9 to provide the racemic bis(phosphine oxides) 10 . The bis(phosphine oxides) 10 subsequently are resolved with (?)-(2R,3R)- and (+)-(2S,3S)-O-2,3-dibenzoyltartaric acid and reduced to diphosphines 5 . The Ullmann reaction constitutes a new and efficient route to 2,2′-bis(phosphinoyl)-substituted biphenyl systems. Absolute configurations were established for (R)- 5a by X-ray analysis of the derived Pd complex (R,R)- 17a , and for 5b and 5c by means of ¹H-NMR comparisons of the derived Pd complexes 16 or 17 , respectively, and by means of CD comparisons. The MeO-BIPHEP diphosphine 5a proved to be as efficient as the previously described BIPHEMP diphosphine ((6,6′-dimethylbiphenyl-2,2′-diyl)bis(diphenylphosphine)) in enantioselective isomerizations and hydrogenations.     

Compehensive two-dimensional gas chromatography (GC×GC) and its applicability to the characterization of complex (petrochemical) mixtures

In general, petrochemical products contain only a limited number of chemical classes of compounds (sample dimensionality). The enormous number of individual components within these classes, however, soon puts limitations upon a single chromatographic technique when it comes to adequate characterization of these products. Comprehensive two-dimensional gas chromatography (GC×GC) clearly opens the possibility of estimating the composition of hydrocarbon mixtures in a far more detailed fashion than hitherto possible. Although the emphasis of papers of GCxGC thus far almost exclusively applies to the unsurpassed peak-capacity, in the oil industry there is a need for characterization, rather than for analyzing all the individual compounds. In principle a GCxGC system can provide an almost perfect match between its intrinsic properties and the dimensionality of oil samples. To establish the applicability of GCxGC towards petrochemical analytical challenges, a commercially aavailable prototype instrument was subjected to an exhaustive characterization of a typical hydrocarbon precess stream and a fast characterization of a light gas oil. Although there are no fundamental limitations towards the quantitative aspects of a GCxGC system, this paper confines itself to qualitative results only. Quantitative aspects of GCxGC will be published in a forthcoming paper.     

Energetics of the loss of H2 from [C3H7]+

The internal energies of [C₃H₇]⁺ ions contributing to the metastable peak [C₃H₇]⁺ → [C₃H₅]⁺ + H₂ are higher (by perhaps > 100 kJ mol^?1) than those of the ion contributing to the threshold current in appearance energy measurements on [C₃H₅]⁺. The measured appearance energy may lead to an underestimation of the activation energy, i.e. negative ‘kinetic shift’, due to quantum, mechanical tunnelling. The distribution of energy released in the decomposition can be explained on the basis that much of the reverse activation energy and a statistical proportion of the excess energy is released as translation.     

Preparation of Protected β2‐ and β3‐Homocysteine, β2‐ and β3‐Homohistidine,and β2‐Homoserine for Solid‐Phase Syntheses

The Ser, Cys, and His side chains play decisive roles in the syntheses, structures, and functions of proteins and enzymes. For our structural and biomedical investigations of β‐peptides consisting of amino acids with proteinogenic side chains, we needed to have reliable preparative access to the title compounds. The two β³‐homoamino acid derivatives were obtained by Arndt–Eistert methodology from Boc‐His(Ts)‐OH and Fmoc‐Cys(PMB)‐OH (Schemes 2–4), with the side‐chain functional groups' reactivities requiring special precautions. The β²‐homoamino acids were prepared with the help of the chiral oxazolidinone auxiliary DIOZ by diastereoselective aldol additions of suitable Ti‐enolates to formaldehyde (generated in situ from trioxane) and subsequent functional‐group manipulations. These include OH→O^tBu etherification (for β²hSer; Schemes 5 and 6), OH→STrt replacement (for β²hCys; Scheme 7), and CH₂OH→CH₂N₃→CH₂NH₂ transformations (for β²hHis; Schemes 9–11). Including protection/deprotection/re‐protection reactions, it takes up to ten steps to obtain the enantiomerically pure target compounds from commercial precursors. Unsuccessful approaches, pitfalls, and optimization procedures are also discussed. The final products and the intermediate compounds are fully characterized by retention times (t_R), melting points, optical rotations, HPLC on chiral columns, IR, ¹H‐ and ¹³C‐NMR spectroscopy, mass spectrometry, elemental analyses, and (in some cases) by X‐ray crystal‐structure analysis.