Modified Quadrupole Ion Trap Mass Spectrometer for Infrared Ion Spectroscopy: Application to Protonated Thiated Uridines

Modifications to a Paul-type quadrupole ion trap mass spectrometer providing optical access to the trapped ion cloud as well as hardware and software for coupling to a table-top IR optical parametric oscillator laser (OPO) are detailed. Critical experimental parameters for infrared multiple photon dissociation (IRMPD) on this instrument are characterized. IRMPD action spectra, collected in the hydrogen-stretching region with this instrument, complemented by spectra in the IR fingerprint region acquired at the FELIX facility, are employed to characterize the structures of the protonated forms of 2-thiouridine, [s²Urd+H]⁺, and 4-thiouridine, [s⁴Urd+H]⁺. The measured spectra are compared with predicted linear IR spectra calculated at the B3LYP/6-311+G(d,p) level of theory to determine the conformers populated in the experiments. This comparison indicates that thiation at the 2- or 4-positions shifts the protonation preference between the 2,4-H tautomer and 4-protonation in opposite directions versus canonical uridine, which displays a roughly equal preference for the 2,4-H tautomer and O4 protonation. As found for canonical uridine, protonation leads to a mixture of conformers exhibiting C2′-endo and C3′-endo sugar puckering with an anti nucleobase orientation being populated for both 2- and 4-thiated uridine.

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Synthesis,X-ray crystal structure and cation binding properties of a tetrahomodioxacalix[4]arene tetraester

Treatment ofp-t-butyltetrahomodioxacalix[4]arene with ethyl bromoacetate yields a tetraester derivative (4) whose crystal and molecular structure have been determined and whose ion binding properties have been assessed by phase transfer and stability constant measurements. Colorless transparent triclinic crystals (obtained from methoxyethanol) C₆₂H₈₄O₁₄,a = 10.347(2),b = 11.583(2),c = 13.448(3) Å, = 72.04(2), = 86.50(2)°, = 81.23(2)°, space group ,Z = 1, MoK radiation = 0.70930 Å. Refinement was carried out using 2221 reflections withI > 1.5(I). The complexation properties resemble those of calix[6]arene hexaester (6), although weaker, with a preference for the larger alkali cations. Ca²⁺ and Ba²⁺; though not extracted, are more strongly complexed than alkali cations. Eu³⁺ is better complexed than Na⁺.Supplementary Data relating to this article are deposited with the British Library as Supplementary Publication No. SUP 82106 (22 pages) and at the Cambridge Crystallographic Data Centre, University Chemical Laboratory, Lensfield Road, Cambridge CB2 9EW, U.K.     

Identification and characterization of active and inactive species for surface-enhanced resonance Raman scattering

The surface-enhanced resonance Raman scattering (SERRS) activity of a statistically significant number of silver nanoparticles has been studied using a correlated SERRS mapping and transmission electron microscopy (TEM) method. TEM allowed the nature of each entity to be directly identified, and the SERRS activity was obtained from the corresponding SERRS map. Particles in various states of aggregation were analyzed to establish relative activities. It was established that SERRS activity is dependent on the specific batch of colloid tested. By averaging different colloid batches, it was shown that increasing SERRS activity is observed with increasing numbers of particles in the aggregates. By reducing the surface coverage of the particles to the extent that single moieties could be examined optically, the ratio of the relative activities of single particles, dimers, trimers, and larger aggregates was estimated. High-resolution TEM images of a number of active and inactive particles are reported. However, no clear correlation between microstructure and SERRS activity was observed.     

Friedel-crafts polymerisations with α,α′-dimethoxy-p-xylene—I The initiation step with stannic chloride as catalyst

A white insoluble 1:1 complex is formed between stannic chloride and α,α′-dimethoxy-p-xylene (DMPX) when the Friedel-Crafts copolymerisation of DMPX and benzene is carried out in a series of solvents using stannic chloride as catalyst. As the reaction proceeds, the precipitate dissolves, being converted to a 1:1 and later a 1:2 complex of stannic chloride and methanol, the latter being a product of the reaction. The 1:1 stannic chloride:methanol complex is an active catalyst for the polymerisation while the 1:2 complex is relatively inactive. The rate of the reaction is also strongly dependent upon the dielectric constant of the medium.For these reasons, a precise quantitative investigation of the kinetics of the polymerisation will be almost impossible but experimental conditions are specified whereby a partial investigation may be made for comparison with the SnCl₄/benzene/di(chloromethyl) benzene system previously studied.