Brant Billinghurst

pH-dependent UV resonance Raman spectra of cytosine and uracil.

Cytosine is a nucleobase found in both DNA and RNA, while uracil is found only in RNA. Uracil has abstractable protons at N3 and N1. Cytosine has only one abstractable proton at N1 but can also accept a proton at N3. The pKa values of these protons are well-known, but the effect of the change in protonation on the rest of the molecule is not well understood and is very important in base stacking, base pairing, and protein-nucleic acid interactions. In this paper, UV resonance Raman (UVRR) spectroscopy is used to probe the structures of both cytosine and uracil at varying pH to determine the structural changes that take place. The results show that cytosine has increased electronic delocalization when moving to either basic or acidic environments, whereas uracil shows no significant change in acidic environment but increases its electronic delocalization in basic environment.

High-resolution spectroscopy of the C–N stretching band of methylamine

The C-N stretching infrared fundamental of CH(3)NH(2) has been investigated by high-resolution laser sideband and Fourier transform synchrotron spectroscopy to explore the energy level structure and to look for possible interactions with high-lying torsional levels of the ground state and other vibrational modes. The spectrum is complicated by two coupled large-amplitude motions in the molecule, the CH(3) torsion and the NH(2) inversion, which lead to rich spectral structure with a wide range of energy level splittings and relative line intensities. Numerous sub-bands have been assigned for K values ranging up to 12 for the stronger a inversion species for the v(t) = 0 torsional state, along with many of the weaker sub-bands of the s species. The C-N stretching sub-state origins have been determined by fitting the upper-state term values to J(J + 1) power-series expansions. For comparison with the ground-state behaviour, both ground and C-N stretch origins have been fitted to a phenomenological Fourier series model that produces an interesting pattern with the differing periodicities of the torsional and inversion energies. The amplitude of the torsional energy oscillation increases substantially for the C-N stretch, while the amplitude of the inversion energy oscillation is relatively unchanged. Independent inertial scale factors ρ were fitted for the torsion and the inversion and differ significantly in the upper state. The C-N stretching vibrational energy is determined to be 1044.817 cm(-1), while the effective upper state B-value is 0.7318 cm(-1). Several anharmonic resonances with v(t) = 4 ground-state levels have been observed and partially characterized. A variety of J-localized level-crossing resonances have also been seen, five of which display forbidden transitions arising from intensity borrowing that allow determination of the interaction coupling constants.

High-resolution synchrotron-based Fourier transform spectroscopy of in the 120–350 cm−1 far-infrared region

The Fourier transform spectrum of the isotopologue of methanol has been recorded in the 120–350 cm−1 far-infrared region at a resolution of 0.00096 cm−1 using synchrotron source radiation at the Canadian Light Source. The study, motivated by astrophysical applications, is aimed at generating a sufficiently accurate set of energy level term values for the ground vibrational state to allow prediction of the centres of the quadrupole hyperfine multiplets for astronomically observable sub-millimetre transitions to within an uncertainty of a few MHz. To expedite transition identification, a new function was added to the Ritz program in which predicted spectral line positions were generated by an adjustable interpolation between the known assignments for the and isotopologues. By displaying the predictions along with the experimental spectrum on the computer monitor and adjusting the predictions to match observed features, rapid assignment of numerous sub-bands was possible. The least squares function of the Ritz program was then used to generate term values for the identified levels. For each torsion-K-rotation substate, the term values were fitted to a Taylor-series expansion in powers of J(J + 1) to determine the substate origin energy and effective B-value. In this first phase of the study we did not attempt a full global fit to the assigned transitions, but instead fitted the sub-band J-independent origins to a restricted Hamiltonian containing the principal torsional and K-dependent terms. These included structural and torsional potential parameters plus quartic distortional and torsion–rotation interaction terms.

Far-infrared spectrum of S(CN)2 measured with synchrotron radiation: global analysis of the available high-resolution spectroscopic data.

The high resolution Fourier transform spectrum of the chemically challenging sulfur dicyanide, S(CN)2, molecule was recorded at the far-infrared beamline of the synchrotron at the Canadian Light Source. The spectrum covered 50-350 cm(-1), and transitions in three fundamentals, ν4, ν7, and ν8, as well as in the hot-band sequence (n + 1)ν4 - nν4, n = 1-4, have been assigned and measured. Global analysis of over 21,300 pure rotation and rotation vibration transitions allowed determination of precise energies for 12 of the lowest vibrationally excited states of S(CN)2, including the five lowest fundamentals. These results constitute an extensive set of benchmarks for ab initio anharmonic force field calculations and the observed and calculated vibration-rotation constants and anharmonic frequencies are compared. The semiexperimental equilibrium, r(e)(SE), geometry of S(CN)2 has also been evaluated. In the course of the measurements, new information concerning the physical chemistry of S(CN)2 has been obtained.

Photoacoustic spectroscopy using coherent synchrotron radiation: application to α-lactose monohydrate

We produced coherent synchrotron radiation at the Canadian Light Source between about 5 and 30 cm(-1) in bursting and continuous emission modes and used it to acquire photoacoustic spectra of solids. A band was observed in the spectrum of α-lactose monohydrate at 18 cm(-1) and attributed to a rotational mode, in agreement with published data obtained using other numerical and experimental techniques.

A novel synthesis of polymeric CO via useful hard x-ray photochemistry

Abstract We report on the synchrotron hard X-ray-induced decomposition of strontium oxalate (SrC2O4) pressurized to 7 GPa inside a diamond anvil cell (DAC). After some 4 h of irradiation in a white X-ray synchrotron beam, a dark reddish/brown region formed in the area of irradiation which was surrounded by a yellowish brown remainder in the rest of the sample. Upon depressurization of the sample to ambient conditions, the reacted/decomposed sample was recoverable as a dark brown/red and yellow waxy solid. Synchrotron infrared spectroscopy confirmed the strong presence of CO2 even under ambient conditions with the sample exposed to air and other strongly absorbing regions, suggesting that the sample may likely be polymerized CO (in part) with dispersed CO2 and SrO trapped within the polymer. These results will have significant implications in the ability to readily produce and trap CO2 in situ via irradiation of a simple powder for useful hard X-ray photochemistry and in the ability to easily manufacture polymeric CO (via loading of powders in a DAC or high volume press) without the need for the dangerous and complex loading of toxic CO. A novel means of X-ray-induced polymerization under extreme conditions has also been demonstrated.

FTIR synchrotron spectroscopy of the S–H stretching fundamental of the 12CH332SH species of methyl mercaptan

ABSTRACT The infrared Fourier transform spectrum of the S–H stretching fundamental band of 12CH3 32SH has been recorded using synchrotron radiation at the far-infrared beamline of the Canadian Light Source in Saskatoon. The S–H stretch is a hybrid band predominantly of perpendicular b-type with a small parallel a-component. With both ΔK = +1 and ΔK = −1 sub-bands present, the assignments are well determined from ground-state combination difference relations. The identified sub-bands access S–H stretching ground torsional substates from K′ = 0–14 for A and E torsional species. The substate origins have been obtained by expanding the term values in J(J + 1) power series, and have been fitted to a simple 6-parameter Fourier Hamiltonian to deduce the torsional energies. The oscillation amplitude of the S–H stretching torsional curves is 0.547 cm− 1 compared to 0.653 cm− 1 for the ground state, implying an increase on the order of 6.9% in the torsional barrier height. The vibrational wavenumber for the S–H stretch mode is found to be 2603.5 cm− 1. GRAPHICAL ABSTRACT

Observation of Wakefields and Resonances in Coherent Synchrotron Radiation.

We report on high resolution measurements of resonances in the spectrum of coherent synchrotron radiation (CSR) at the Canadian Light Source (CLS). The resonances permeate the spectrum at wave number intervals of 0.074  cm(-1), and are highly stable under changes in the machine setup (energy, bucket filling pattern, CSR in bursting or continuous mode). Analogous resonances were predicted long ago in an idealized theory as eigenmodes of a smooth toroidal vacuum chamber driven by a bunched beam moving on a circular orbit. A corollary of peaks in the spectrum is the presence of pulses in the wakefield of the bunch at well-defined spatial intervals. Through experiments and further calculations we elucidate the resonance and wakefield mechanisms in the CLS vacuum chamber, which has a fluted form much different from a smooth torus. The wakefield is observed directly in the 30-110 GHz range by rf diodes, and indirectly by an interferometer in the THz range. The wake pulse sequence found by diodes is less regular than in the toroidal model, and depends on the point of observation, but is accounted for in a simulation of fields in the fluted chamber. Attention is paid to polarization of the observed fields, and possible coherence of fields produced in adjacent bending magnets. Low frequency wakefield production appears to be mainly local in a single bend, but multibend effects cannot be excluded entirely, and could play a role in high frequency resonances. New simulation techniques have been developed, which should be invaluable in further work.

Carbon Dioxide Line Shapes for Atmospheric Remote Sensing

We present a detailed spectroscopic study of carbon dioxide in support of atmospheric remote sensing. We have studied two weak absorption bands near the strong ν2 band that is used to derive atmospheric temperature profiles. We have analyzed our laboratory spectra recorded with the synchrotron and globar sources with spectral line profiles that reproduce the absorption features with high accuracy. The Q‐branch transitions exhibited asymmetric line shape due to weak line‐mixing. For these weak transitions, we have retrieved accurate experimental line strengths, self‐ and air‐broadening, self‐ and air‐induced shift coefficients and weak line mixing parameters. The experimental precision is sufficient to reveal inherent variations of the width and shift coefficients according to transition quantum numbers.

Progress in the rotational analysis of the ground and low-lying vibrationally excited states of malonaldehyde

Despite being an important prototype molecule for intramolecular proton tunnelling, the far-IR spectrum of the internally hydrogen-bonded species malonaldehyde (C3O2H4) is not yet well understood. In the talk I gave at the ISMS meeting in 2015 I discussed the high-resolution spectra we obtained at the Canadian Light Source synchrotron in Saskatoon, Saskatchewan. These spectra include a number of fundamental vibrational bands in the 100-2000 cm−1 region. In our efforts to analyze these bands we have noticed that our ground state combination differences show a large drift (up to an order of magnitude larger than our experimental error) away from those calculated using constants established by Baba et al.,a particularly in regions of high J (above 30) and low Ka (below 5). An examination of the previous microwave and far-IR studiesbc reveals that this region of J-Ka space was not represented in the lines that Baba et al. used to generate the values for their fitting parameters. By including our own measurements in the fitting, we were able to improve the characterization of the ground state so that it is now consistent with all of the existing data. This characterization now covers a much larger range of J-Ka space and has enabled us to make significant progress in analyzing our far-IR synchrotron spectra. These include an excited vibrational state at 241 cm−1 as well as several states split by the tunnelling effect at higher wavenumber.