Fragmentation of electrospray-produced oligodeoxynucleotide ions adducted to metal ions

In this article, we describe the unique fragmentations of oligodeoxynucleotides (ODNs) whose phosphate groups are completely depleted of protons and replaced with metal ions. The production of the ubiquitous [a(n) - base] ions still occurs, but no longer by transfer of an acidic phosphate proton to an adjoining 3' base. Nor is the extent of the reaction determined by the proton affinity of that base. Rather, the reaction now occurs via a cleavage 3' to both pyrimidines and purines; cleavage 3' to pyrimidine is more favorable than that 3' to purine. We also demonstrate that an ODN is more stable in the gas phase when its phosphate groups are bound to metal ions than when its phosphate groups are attached to hydrogens. This study also provides further evidence for the ODN fragmentation mechanism that involves H transfer to a nucleobase. To establish the structural utility of this new fragmentation, we applied it to distinguishing small ODNs containing a photomodified cis,syn-cyclobutane pyrimidine dimer from the parent ODNs, a system that cannot be distinguished by collisional activation of precursor species that do not contain metal ions.     

Molecular recognition in a uradinyl-functionalized stable radical

Stable radical 2-(6-uradinyl)-4,4,5,5-tetramethyl-4,5-dihydro-1H-imidazole-1-oxyl (1) binds to hydrogen-bonding complement 2,6-di(propylamido)pyridine (DAP) in chloroform with Ka=220 M(-1) at 33 degrees C; ESI-MS shows not only 1:DAP complementary dyad formation, but also 1:(DAP)2 formation at higher concentrations of DAP.     

Synthesis and structural characterization of acetatobis(triphenylphosphine)dicarbonylmanganese(I), (CH3CO2)Mn(CO)2[P(C6H5)3]2: An organometallic complex containing a chelating acetate ligand

The accidental but intriguing synthesis of acetatobis(triphenylphosphine)dicarbonylmanganese(I), (CH₃CO₂)Mn(CO)₂[P(C₆H₅)₃]₂, has been accomplished by the reaction of NaMn(CO)₅ with (CH₃)₃SiCl followed by the addition of triphenylphosphine and acetic acid. A three-dimensional single-crystal X-ray diffraction analysis has shown an octahedral-like molecule containing a symmetrically oxygen-chelating acetate group, the first such group to be reported in a metal carbonyl complex. The two triphenylphosphine ligands occupy mutually trans positions with the two carbonyl ligands possessing the remaining cis sites in the octahedral complex. The compound crystallizes with four molecules in a monoclinic unit cell of space group symmetry $\text{P}\text{2}{}_1\text{c}$ and of dimensions a = 17.744(2) Å, b = 9.692(1) Å, c = 20.004(2) Å, and β = 106.195(4)°. The relatively long MnO(acetate) bond lengths [2.066(6) and 2.069(7) Å] and the relatively short MnCO bond lengths [1.701(12) and 1.760(13) Å] and the relatively short MnP(C₆H₅)₃ bond lengths [2.260(3) and 2.275(3) Å], compared to the corresponding MnCO and MnP(C₆H₅)₃ bond lengths in other manganese carbonyl triphenylphosphine complexes, are rationalized on the basis that the acetate ligand in this molecule functions primarily as a σ-donor.     

Determination of alcohol polyether average molar oligomer value/distribution via supercritical fluid chromatography coupled with UV and MS detection

Supercritical fluid chromatography (SFC) was used for the analysis of ethoxylated and propoxylated surfactants. Samples were derivatized to phenylated silyl ethers with a disilazane-chlorosilane mixture. Addition of a phenyl group to the surfactant allowed UV-absorbance detection of each oligomer. Acetonitrile and methanol were evaluated as mobile phase modifiers. Better peak shape was realized with methanol-modified CO2 on an octadecyl silica bonded phase than with acetonitrile-modified CO2. Peak assignments were made via SFC coupled with electrospray ionization-mass spectrometry (ESI-MS) in the positive ion mode. A sulfonamide-embedded alkyl stationary phase was also evaluated for separation of the derivatized samples. SFC-UV and SFC-ESI-MS data were jointly used for calculation of average molar oligomer values which were then compared to values calculated from 1H NMR data of non-derivatized samples. The derivatization or separation method using the sulfonamide embedded phase required no preliminary cleanup and yielded reproducible oligomer values that were consistent with those of the manufacturer's nominal values.     

Sequential ortho effects: characterization of novel [M - 35]+ fragment ions in the mass spectra of 2-alkyl-4, 6-dinitrophenols

High-resolution mass spectrometry (HRMS), hybrid tandem mass spectrometry (MS/MS) (EBqQ), and photoelectron-photoion coincidence (PEPICO) experiments were conducted to examine a possible ortho-ortho effect resulting in a novel [M - 35]⁺ fragment ion in 2-alkyl-4, 6-dinitrophenols. For compounds having ethyl or larger alkyl substituents, [M35]⁺ was observed only when [M - 18]⁺ ions were present, with the ortho nitro group being involved in the reaction to [M- 35]⁺. For [M - 18]⁺ and [M - 35]⁺, HRMS results were consistent with losses of H₂O and H₂O + OH, respectively, whereas MS/MS results indicated a sequential reaction due to metastable dissociations. The appearance energy determined by PEPICO for [M - 35]⁺ was found to be greater than the appearance energy for [M - 18]⁺, thus supporting a sequential reaction. 69–75).     

Automated site-directed drug design: An assessment of the transferability of atomic residual charges (CNDO) for molecular fragments

Summary In this paper a database of atomic residual charges has been constructed for all the molecular fragments defined previously in a combinatorial search of the Cambridge Structural Database. The charges generated for the atoms in each fragment are compared with charges calculated for whole molecules containing those fragments. The fragment atomic charges lie within 1 S.D. of the mean for 68%, and within 2 S.D. for 91%, of the atoms whose charges were computed for whole molecules. The actual charges on any atom are strongly influenced by the adjacent connected atoms. There is a large spread of atomic residual charge within the fragments database.     

Reactive intermediates in asymmetric cross-coupling catalysed by palladium P-N chelates

The palladium dibromide complexes of (S,R)-(1,1′-bis-diphenylphosphino)-2-ferrocencylthyldimethylamine and (S,R)-(1-diphenylphosphino)-2-ferrocenylethyldimethylamine have been reduced with dilithiocyclooctatetraene to form the corresponding Pd⁰ cyclooctatetraene complexes. Their reactions with E-4-methoxy-2′-bromophenylethene, and then benzylmagnesium chloride at −60 to −30°C, provide information on the structure of intermediates in asymmetric cross-coupling.     

Sulfur hexafluoride as a mobile phase for supercritical fluid chromatography

Summary The capabilities of sulfur hexafluoride as a mobile phase for supercritical-fluid chromatography are investigated. An evaluation of its overall utility on the basis of separations of standard aromatic hydrocarbon odel mixtures performed on a variety of bonded-phase, packed columns with UV detection is presented. The dependence of separation performance upon operational parameters is also examined. A comparative evaluation of the chroamtographic properties of supercitrical sulfur hexafluoride and those of supercritical carbon dioxide is developed from these separations under corresponding supercritical state conditions.     

International Measurement Evaluation Programme: IMEP-9, trace elements in water

The International Measurement Evaluation Programme (IMEP) is an interlaboratory comparison scheme, founded, owned and coordinated by the Institute for Reference Materials and Measurements (IRMM) since 1988. IMEP-9 is the third round of trace elements in water evaluation following IMEP-3 and IMEP-6. Reference values for 15 elements stating total concentrations and combined uncertainties (according to GUM) were established. The reference values were established mainly by isotope dilution mass spectrometry (IDMS) as a primary method of measurement, and values traceable to the SI were obtained. The four elements that could not be certified by IDMS were assigned values by means of other measurement techniques. Results from 201 laboratories from 35 countries and four continents were evaluated against the reference values and the comparability between the laboratories is presented graphically.