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

Abstract

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, [sUrd+H], and 4-thiouridine, [sUrd+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. Graphical Abstract ᅟ.

IRMPD Spectroscopy of [PC (4:0/4:0) + M]+ (M = H, Na, K) and Corresponding CID Fragment Ions

“…For the experiments described here, settings for the MS were chosen to give an approximate 0.5 Da mass resolution for the precursor ion masses under investigation. Wavenumbers were calibrated using a grating spectrometer (±0.02 μm), and observed vibrational band widths in the IRMPD spectra are typically on the order of 30 cm –1 . Precursor isolation was performed with a mass isolation window of Δ m / z = ±1 centered around the precursor mass.…”

“…Wavenumbers were calibrated using a grating spectrometer (±0.02 μm), and observed vibrational band widths in the IRMPD spectra are typically on the order of 30 cm −1 . 32 Precursor isolation was performed with a mass isolation window of Δm/z = ±1 centered around the precursor mass. Ions were generated using electrospray ionization (ESI), employing a flow rate of 2−3 μL•min −1 with a voltage difference of approximately 4 kV in positive ion mode.…”

Benzoxazine Formation Mechanism Evaluation by Direct Observation of Reaction Intermediates

“…The formation of benzoxazine was conducted by stirring aniline (5.3 mmol) and formaldehyde (10.6 mmol) in ethyl acetate (10.0 mL) for 4.0 h at 293 K using a magnetic stirrer. After 4.0 h, the temperature of the reaction media was gradually raised to 343 K, 5.3 mmol of phenol was added, and the mixture was stirred for an additional 4.0 h. An aliquot of 10 μL was withdrawn at every hour and diluted in acetonitrile to a concentration of approximately 10 –5 mol L –1 for analysis by direct infusion ESI­(+)-MS at our in-house modified AmaZon SL ion trap mass spectrometer. − The samples were also analyzed after addition of 1 μL of formic acid to allow detection of the final reaction products and other intermediates. All MS experiments were carried out at the higher mass resolution mode (enhanced mode – fwhm = 0.2) after calibration against tune mix ESI-L calibrant mixture (Agilent) in a standard source and typical ion optics conditions (4.5 kV).…”

Development of a photoinduced fragmentation ion trap for infrared multiple photon dissociation spectroscopy

“…To support the IRMPD spectral assignments, IR harmonic frequencies of the compounds under study were calculated using the Gaussian09 This Amazon SL setup is similar to other developments reported in the literature. [77][78][79][80] This model has a slightly larger trap than the one used in AmaZon ETD and Speed models, enhancing ion storage and detection limit.…”