Graphical aids and scanning modes for tandem mass spectrometry

In tandem mass spectrometry, where typically one analyser is used to study the reactions of ions selected by another analyser from a mixture leaving the ion source, the output contains an additional dimension of information compared to that from conventional mass spectrometry. The increase in dimensionality tends to make the results less easy to assimilate and interpret, but the difficulties may be overcome in large measure by presenting the results in an appropriate graphical form. This review deals with the use of graphical representations of three-dimensional data to display the results of experiments in tandem mass spectrometry. Perspective diagrams or contour maps can be used to show the identity of the parent and daughter ions for all of the reactions occurring in a tandem mass spectrometer, including reactions of positive ions, reactions of negative ions and charge inversion reactions. A graphical approach is particularly valuable when double focusing mass spectrometers are used for tandem mass spectrometry, because it can make it much easier to establish the origin of the ions contributing to an observed peak and thus to determine whether interference is occurring. Factors bearing on the choice of a coordinate system are discussed. Relationships characterizing the more important simple and linked scanning modes are listed and the features to which they correspond in two selected coordinate systems are shown. Factors that influence the resolution of neighbouring peaks by sector field tandem mass spectrometers are discussed.     

Rates of base-catalysed cleavage of pyridyl-, quinolyl-, picolyl- and (quinolylmethyl)-trimethylsilanes

Rates of cleavage of some picoyl- and (quinolylmethyl)-trimethylsilanes (RSiMe₃, where R = PyCH₂ or QnCH₂SiMe₃) have been measured in “90%” aqueous methanolic sodium methoxide at 50°C. Relative reactivities are: 2-PyCH₂, 1.0; 3-PyCH₂, 0.030; 4-PyCH₂, 8.9; 2-QnCH₂, 41; 3-QnCH₂, 0.161; 4-QnCH₂, 37. The rates correlate well with those for base-catalysed hydrogen-exchange in the parent carbon acids RH. Approximate pK_a's (based on the scale of ion-pair acidities in CsNHC₆H₁₁H₂NC₆H₁₁, with pK_a of 9-phenylfluorene = 18.6) for the carbon acids, RH, can be derived as follows: 2-PyCH₃, 29.5; 3-PyCH₃, 34; 4-PyCH₃, 27; 2-QnCH₃, 25; 3-QnCH₃, 32; 4-QnCH₃, 25.Rates of cleavage of pyridyl- and quinolyl-trimethylsilanes (PySiMe₃ and QnSiMe₃) by sodium hydroxide in 4 : 1 v/v Me₂SO/H₂O at 50°C have also been measured; and the relative reactivities are: 2-Py, 1.0; 3-Py, 2.9; 4-Py, 8.4; 2-Qn, 15.9; 3-Qn, 12.7; 4-Qn, 184. The sequence of reactivity differes from that for base-catalysed hydrogen-exchange at the relevant positions of pyridine and quinoline, indicating that the reactivities are not determined in both cases (if in either) solely by the stabilities of the corresponding carbanions.     

Fluorinations with potassium tetrafluorocobaltate(III) Part VII. Further investigations on the fluorination of pyridine

The product from the fluorination of pyridine by KCoF₄ at ca. 220° contains eleven fluoropyridines, two fluoro-2-azahex-enes, three azahexa- dienes, and two fluoro-N-methylpyrrolidines, besides an azacyclohexa-1,3- diene. Four products were isolated from a fluorination of pyridine by CoF₃ at ca. 150°, a 2-azahexene, two N-methylpyrrolidines, and 4H-nona- fluoropiperidine.     

[2,6‐Bis(3,5‐dimethylpyrazol‐1‐ylmethyl)pyridine]iodocopper(I) dichloromethane solvate

The title compound, [CuI(C₁₇H₂₁N₅)]·CH₂Cl₂, contains a tetracoordinate Cu^I centre with an unusual distorted tetrahedral stereochemistry, which has also been observed in other Cu^I complexes containing this tridentate ligand. This distortion is probably a result of intermolecular steric contacts between the I^? ligand and a neighbouring CH₂Cl₂ mol­ecule.     

Solid State Structures and Solution Dynamics of Unsolvated and Diethyl Ether Solvated Dilithium N,N'-Bis(trimethylsilyl)ethylenediamide Complexes

The lithiation of N,N'-bis(trimethylsilyl)ethylenediamine, 1, by 2 equiv of methyllithium in diethyl ether yields the dimeric diethyl ether adduct [{Li[N(SiMe(3))CH(2)CH(2)NSiMe(3)]Li.OEt(2)}(2)], 2. Recrystallization of 2 from benzene gives quantitatively the unsolvated trimer [{Li[N(SiMe(3))CH(2)CH(2)NSiMe(3)]Li}(3)], 3. The solution dynamics of 2 and 3 in toluene have been investigated using variable temperature multinuclear NMR spectroscopy. In solution, 2 is undergoing a rapid exchange process involving an equilibrium between unsolvated and diethyl ether solvated dimers, whereas compound 3 exists in a temperature dependent equilibrium of dimeric and trimeric species, of which the trimer is fluxional and exchanges inequivalent ligands by an intramolecular distortion of the Li(6)N(6) cage structure. Crystals of 2 are monoclinic, of space group P2(1)/n (No. 14), with a = 10.692(9) ?, b = 16.192(2) ?, c = 24.04(4) ?, beta = 101.16(5) degrees, V = 4083(8) ?(3), and Z = 4. Crystals of 3 are trigonal, of space group R&thremacr;m(No. 166), a = 17.765(1) ?, c = 13.394(1) ?, V = 3660.5(5) ?(3), Z = 3.     

On R(4) symmetries in atomic structure

By defining a new rotation group in four dimensions we show that previous phase discrepancies can be accounted for. Furthermore we demonstrate that the new R(4) group is the one to be used in the study of atomic correlation.     

Effect of molecular oxygen on the variable-temperature 29Si MAS NMR spectra of zeolite-sorbate complexes

Structure determinations of siliceous zeolite-sorbate host-guest complexes by solid-state NMR require highly resolved 29Si MAS NMR spectra. As the temperature is lowered, the 29Si MAS NMR spectra of many zeolite-sorbate complexes become broadened such that the resolution of the individual 29Si peaks is lost, limiting the application of solid-state NMR for structure determination. It is shown that the 29Si peak widths are related to the 29Si T2 relaxation times and that the source of the 29Si relaxation and the line broadening is paramagnetic molecular oxygen in the channels of the zeolite. Removal of the oxygen by purging the sample with nitrogen gas leads to a dramatic increase in the resolution of the 29Si MAS NMR spectrum of the p-dibromobenzene/ZSM-5 complex. An analysis of the individual 29Si T1 relaxation times reveals that the oxygen molecules are localized mainly in the zigzag channels of ZSM-5, suggesting that the p-dibromobenzene molecules are located in the channel intersections.     

Effects of As(III) binding on alpha-helical structure

As(III) displays a wide range of effects in cellular chemistry. Surprisingly, the structural consequences of arsenic binding to peptides and proteins are poorly understood. This study utilizes model alpha-helical peptides containing two cysteine (Cys) residues in various sequential arrangements and spatial locations to study the structural effects of arsenic binding. With i, and i + 1, i + 2, or i + 3 arrangements, CD spectroscopy shows that As(III) coordination causes helical destabilization when Cys residues are located at central or C-terminal regions of the helix. Interestingly, arsenic binding to i, i + 3 positions results in the elimination of helical structure and the formation of a relatively stable alternate fold. In contrast, helical stabilization is observed for peptides containing i, i + 4 Cys residues, with corresponding pseudo pairwise interaction energies (Delta G(pw) degrees) of -1.0 and -0.7 kcal/mol for C-terminal and central placements, respectively. Binding affinities and association rate constants show that As(III) binding is comparatively insensitive to the location of the Cys residues within these moderately stable helices. These data demonstrate that As(III) binding can be a significant modulator of helical secondary structure.     

Aggregate, Polymer and Cluster Formation from Metal-Imino Carboxylate Complexes

Reaction of tris-(2-aminoethyl)amine (tren) andthe sodium salt of an -ketocarboxylic acid, typically sodium pyruvate, affordsin the presence of a lanthanide ion aseries of complexes and aggregates includingmononuclear, cyclic tetranuclear and polymerspecies of [L¹]^3- ([L¹]^3-=N[CH₂CH₂N=C(CH₃)COO^-]³).The aggregation of these and related d-block elementcomplexes with Na⁺ ions leadsto the formation of polymeric materials, and thefactors influencing the formation and controlof these various aggregation states are discussed.Metal cations also template the aggregationof the fragment [Ni(L²)] ([L²]^2- =CH₂[CH₂N = C(CH₃)COO^-]₂)to give, in high yield, the polynuclearaggregates {[Ni(L²)]₆M}^x+(M = Nd, Pr, Ce, La, x = 3; M = Sr, Ba, x = 2). The structures of{[Ni(L²)]₆M}^x+ show aninterstitial twelve co-ordinate, icosahedralcation M^x+ encapsulated by six [Ni(L²)]fragments. In the presence ofNa⁺, aggregation of [Ni(L²)] fragments affords {[Ni(L²)]₉Na₄(H₂O)(MeOH)(ClO₄)}³⁺ thestructure of whichshows four Na⁺ ions templating the formation ofa distorted tricapped trigonal prismatic[Ni(L²)]₉ cage. Thus, control overconstruction of various polynuclear cages viaself-assembly at octahedral junctions can beachieved using main group, transition metaland lanthanide ion templates.     

The Dyeing of Nylon and Cotton Cloth with Azo Dyes: Kinetics and Mechanism

The mechanism of the dyeing of cotton and nylon cloth by the azo dyes Orange G and Sunset Yellow FCF was investigated using a channel flow cell. The variation in dyeing with flow rate was found to proceed via a mechanism in which the flux of dye entering the cloth relative to the flux of dye to the cloth surfacedecreasedwith increasing flow rate. A mechanism is deduced in which the dye passes from bulk solution, through a porous surface layer within the cloth, before passing into the bulk cloth. Adsorption onto surface sites in this porous layer blocks the passage of further dye into the cloth. Kinetic parameters for such a mechanism are given.