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Linking in silico MS/MS spectra with chemistry data to improve identification of unknowns

Confident identification of unknown chemicals in high resolution mass spectrometry (HRMS) screening studies requires cohesive workflows and complementary data, tools, and software. Chemistry databases, screening libraries, and chemical metadata have become fixtures in identification workflows. To increase confidence in compound identifications, the use of structural fragmentation data collected via tandem mass spectrometry (MS/MS or MS2) is vital. However, the availability of empirically collected MS/MS data for identification of unknowns is limited. Researchers have therefore turned to in silico generation of MS/MS data for use in HRMS-based screening studies. This paper describes the generation en masse of predicted MS/MS spectra for the entirety of the US EPA’s DSSTox database using competitive fragmentation modelling and a freely available open source tool, CFM-ID. The generated dataset comprises predicted MS/MS spectra for ~700,000 structures, and mappings between predicted spectra, structures, associated substances, and chemical metadata. Together, these resources facilitate improved compound identifications in HRMS screening studies. These data are accessible via an SQL database, a comma-separated export file (.csv), and EPA’s CompTox Chemicals Dashboard.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Photoionization of C 4 H 5 Isomers

In this work, single-photon, photoelectron–photoion coincidence spectroscopy is used to record the mass-selected ion spectra and slow photoelectron spectra of C 4 H 5 radicals produced by the abstraction of hydrogen atoms from three C 4 H 6 precursors by fluorine atoms generated by a microwave discharge. Three different C 4 H 5 isomers are identified, with the relative abundances depending on the nature of the precursor (1-butyne, 1,2-butadiene, and 1,3-butadiene). The results are compared with our previous work using 2-butyne as a precursor [ Hrodmarsson, H. R. J. Phys. Chem. A 2019 , 123 , 1521-1528]. The slow photoelectron spectra provide new information on the three radical isomers that is in good agreement with previous experimental and theoretical results [ Lang, M. J. Phys. Chem. A 2015 , 119 , 3995-4000; Hansen, N. J. Phys. Chem. A 2006 , 110 , 3670–3678]. The energy scans of the C 4 H 5 photoionization signal are recorded with substantially better resolution and signal-to-noise ratio than those in earlier work, allowing the observation of autoionizing resonances based on excited states of the C 4 H 5 cation. Photoelectron images recorded at several energies are also reported, providing insight into the decay processes of these excited states. Finally, in contrast to the earlier work using 2-butyne as a precursor, where H-atom abstraction was the only observed process, F- and H-atom additions to the present precursors are also observed through the detection of C 4 H 6 F, C 4 H 5 F, and C 4 H 7

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Scaling Properties of φ -Meson and Light Charged Hadron Production in Small and Large Systems at PHENIX

Recent results on the identified charged-hadron (π ± , K ± , p, p¯) production vat midrapidity region (|η| < 0.35) have been measured by the PHENIX experiment in p + Al, 3 He + Au, Cu + Au collisions at $\sqrt{s_{NN}}$ = 200 GeV and U + U collisions at $\sqrt{s_{NN}}$ = 193 GeV. These measurements are presented through the invariant transverse-momentum (p T ) and transverse-mass (m T ) spectra for different collision centralities. The averaged freeze-out temperature value for different systems was found to be 166.1 ± 2.2 MeV, and do not exhibit any dependence on the collision centrality and $\langle$N parti $\rangle$ values. The particle ratios of K/π and p/π have been measured in different centrality ranges of large and small collision systems. The values of K/π ratios measured in all considered collision systems were found to be consistent with those measured in p+p collisions. Furthermore, the identified charged-hadron nuclear-modification factors (R AB ) are also presented. Enhancement of proton R AB values over meson R AB values was observed in central 3 He+Au, Cu+Au, and U+U collisions. The proton R AB values measured in p+Al collision system were found to be consistent with R AB values of Φ, π ± , K ± , and π 0 mesons, suggesting that the size of the system produced in p+Al collisions is too small for recombination to cause a noticeable increase in proton production.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

IR mass-resolved spectroscopy of complexes without chromophore: Cyclohexanol·(H{sub 2}O){sub n}, n = 1–3 and cyclohexanol dimer

Mass-resolved IR spectra of cyclohexanol-water clusters and cyclohexanol dimer in supersonic expansions are presented for the first time. A combination of ns and fs IR lasers made possible recording such spectra without inclusion of a chromophore or a messenger atom. Furthermore, employment of the recently developed IR{sup 3} technique [I. León, R. Montero, F. Castaño, A. Longarte, and J. A. Fernández, J. Phys. Chem. A 116, 6798 (2012)] allowed us to discriminate between the contribution of different species to the IR spectrum. Comparison of the experimental spectra with the predictions at the M06-2X/6-311++G(d,p) calculation level confirmed the assignment of the spectrum of cyclohexanol·(H{sub 2}O){sub 1} to a structure in which water is accepting a proton from cyclohexanol's OH group, and those of cyclohexanol·(H{sub 2}O){sub 2,3} to structures with cyclic hydrogen bond networks. A comparative analysis of the results obtained with those reported on other aromatic alcohols is also offered.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

The viability of aluminum Zintl anion moieties within magnesium-aluminum clusters

Through a synergetic combination of anion photoelectron spectroscopy and density functional theory based calculations, we have investigated the extent to which the aluminum moieties within selected magnesium-aluminum clusters are Zintl anions. Magnesium-aluminum cluster anions were generated in a pulsed arc discharge source. After mass selection, photoelectron spectra of Mg{sub m}Al{sub n}{sup −} (m, n = 1,6; 2,5; 2,12; and 3,11) were measured by a magnetic bottle, electron energy analyzer. Calculations on these four stoichiometries provided geometric structures and full charge analyses for the cluster anions and their neutral cluster counterparts, as well as photodetachment transition energies (stick spectra). Calculations revealed that, unlike the cases of recently reported sodium-aluminum clusters, the formation of aluminum Zintl anion moieties within magnesium-aluminum clusters was limited in most cases by weak charge transfer between the magnesium atoms and their aluminum cluster moieties. Only in cases of high magnesium content, e.g., in Mg{sub 3}Al{sub 11} and Mg{sub 2}Al{sub 12}{sup −}, did the aluminum moieties exhibit Zintl anion-like characteristics.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

An integrated time-of-flight versus residual energy subsystem for a compact dual ion composition experiment for space plasmas

We have developed a novel concept for a Compact Dual Ion Composition Experiment (CoDICE) that simultaneously provides high quality plasma and energetic ion composition measurements over 6 decades in ion energy in a wide variety of space plasma environments. CoDICE measures the two critical ion populations in space plasmas: (1) mass and ionic charge state composition and 3D velocity and angular distributions of ∼10 eV/q–40 keV/q plasma ions—CoDICE-Lo and (2) mass composition, energy spectra, and angular distributions of ∼30 keV–10 MeV energetic ions—CoDICE-Hi. CoDICE uses a common, integrated Time-of-Flight (TOF) versus residual energy (E) subsystem for measuring the two distinct ion populations. This paper describes the CoDICE design concept, and presents results of the laboratory tests of the TOF portion of the TOF vs. E subsystem, focusing specifically on (1) investigation of spill-over and contamination rates on the start and stop microchannel plate (MCP) anodes vs. secondary electron steering and focusing voltages, scanned around their corresponding model-optimized values, (2) TOF measurements and resolution and angular resolution, and (3) cross-contamination of the start and stop MCPs’ singles rates from CoDICE-Lo and -Hi, and (4) energy resolution of avalanche photodiodes near the lower end of the CoDICE-Lo energy range. We also discuss physical effects that could impact the performance of the TOF vs. E subsystem in a flight instrument. Finally, we discuss advantages of the CoDICE design concept by comparing with capabilities and resources of existing flight instruments.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Breaking through the false coincidence barrier in electron–ion coincidence experiments

Photoelectron Photoion Coincidence (PEPICO) spectroscopy holds the promise of a universal, isomer-selective, and sensitive analytical technique for time-resolved quantitative analysis of bimolecular chemical reactions. Unfortunately, its low dynamic range of ~10 3 has largely precluded its use for this purpose, where a dynamic range of at least 10 5 is generally required. This limitation is due to the false coincidence background common to all coincidence experiments, especially at high count rates. Electron/ion pairs emanating from separate ionization events but arriving within the ion time of flight (TOF) range of interest constitute the false coincidence background. Although this background has uniform intensity at every m/z value, the Poisson scatter in the false coincidence background obscures small signals. In this paper, temporal ion deflection coupled with a position-sensitive ion detector enables suppression of the false coincidence background, increasing the dynamic range in the PEPICO TOF mass spectrum by 2–3 orders of magnitude. The ions experience a time-dependent electric deflection field at a well-defined fraction of their time of flight. This deflection defines an m/z- and ionization-time dependent ion impact position for true coincidences, whereas false coincidences appear randomly outside this region and can be efficiently suppressed. When cold argon clusters are ionized, false coincidence suppression allows us to observe species up to Ar 9 + , whereas Ar 4 + is the largest observable cluster under traditional operation. As a result, this advance provides mass-selected photoelectron spectra for fast, high sensitivity quantitative analysis of reacting systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Predissociation-based measurements of bond dissociation energies: US 2 , OUS, and USe

The uranium-containing molecules US 2 , OUS, and USe have been investigated using a pulsed laser ablation supersonic beam molecular source with time-of-flight mass spectrometric detection. Spectra have been recorded using the resonant two-photon ionization method over the spectroscopic range from 277 to 238 nm. These species have a myriad of excited electronic states in this spectroscopic region, leading to spectra that are highly congested and appear quasicontinuous. Sharp predissociation thresholds are observed, allowing precise bond dissociation energies to be measured. In the case of the triatomic molecules, it was necessary to use one laser for excitation and a delayed laser for ionization in order to observe a sharp predissociation threshold that allowed a precise bond dissociation energy to be measured. The resulting thermochemical values are D 0 (SU-S) = 4.910 ± 0.003 eV, D 0 (OU-S) = 5.035 ± 0.004 eV, and D 0 (USe) = 4.609 ± 0.009 eV. These results provide the first measurement of D 0 (USe) and reduce the error limits in the previous values of D 0 (SU-S) and D 0 (OU-S) by a factor of more than 70.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DECOMPOSING STAR FORMATION AND ACTIVE GALACTIC NUCLEUS WITH SPITZER MID-INFRARED SPECTRA: LUMINOSITY FUNCTIONS AND CO-EVOLUTION

We present Spitzer 7-38 {mu}m spectra for a 24 {mu}m flux-limited sample of galaxies at z {approx} 0.7 in the COSMOS field. The detailed high-quality spectra allow us to cleanly separate star formation (SF) and active galactic nucleus (AGN) in individual galaxies. We first decompose mid-infrared luminosity functions (LFs). We find that the SF 8 {mu}m and 15 {mu}m LFs are well described by Schechter functions. AGNs dominate the space density at high luminosities, which leads to the shallow bright-end slope of the overall mid-infrared LFs. The total infrared (8-1000 {mu}m) LF from 70 {mu}m selected galaxies shows a shallower bright-end slope than the bolometrically corrected SF 15 {mu}m LF, owing to the intrinsic dispersion in the mid-to-far-infrared spectral energy distributions. We then study the contemporary growth of galaxies and their supermassive black holes (BHs). Seven of the thirty-one luminous infrared galaxies with Spitzer spectra host luminous AGNs, implying an AGN duty cycle of 23% {+-} 9%. The time-averaged ratio of BH accretion rate and SF rate matches the local M{sub BH} - M{sub bulge} relation and the M{sub BH} - M{sub host} relation at z {approx} 1. These results favor co-evolution scenarios in which BH growth and intense SF happen in the same event but the former spans a shorter lifetime than the latter. Finally, we compare our mid-infrared spectroscopic selection with other AGN identification methods and discuss candidate Compton-thick AGNs in the sample. While only half of the mid-infrared spectroscopically selected AGNs are detected in X-ray, {approx}90% of them can be identified with their near-infrared spectral indices.

79 ASTRONOMY AND ASTROPHYSICS↗

ICE CHEMISTRY ON OUTER SOLAR SYSTEM BODIES: ELECTRON RADIOLYSIS OF N{sub 2}-, CH{sub 4}-, AND CO-CONTAINING ICES

Radiation processing of the surface ices of outer Solar System bodies may be an important process for the production of complex chemical species. The refractory materials resulting from radiation processing of known ices are thought to impart to them a red or brown color, as perceived in the visible spectral region. In this work, we analyzed the refractory materials produced from the 1.2-keV electron bombardment of low-temperature N{sub 2}-, CH{sub 4}-, and CO-containing ices (100:1:1), which simulates the radiation from the secondary electrons produced by cosmic ray bombardment of the surface ices of Pluto. Despite starting with extremely simple ices dominated by N{sub 2}, electron irradiation processing results in the production of refractory material with complex oxygen- and nitrogen-bearing organic molecules. These refractory materials were studied at room temperature using multiple analytical techniques including Fourier-transform infrared spectroscopy, X-ray absorption near-edge structure (XANES) spectroscopy, and gas chromatography coupled with mass spectrometry (GC-MS). Infrared spectra of the refractory material suggest the presence of alcohols, carboxylic acids, ketones, aldehydes, amines, and nitriles. XANES spectra of the material indicate the presence of carboxyl groups, amides, urea, and nitriles, and are thus consistent with the IR data. Atomic abundance ratios for the bulk composition of these residues from XANES analysis show that the organic residues are extremely N-rich, having ratios of N/C ∼ 0.9 and O/C ∼ 0.2. Finally, GC-MS data reveal that the residues contain urea as well as numerous carboxylic acids, some of which are of interest for prebiotic and biological chemistries.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

The Spitzer survey of stellar structure in galaxies (S{sup 4}G): Precise STELLAR mass distributions from automated dust correction at 3.6 μm

The mid-infrared is an optimal window to trace stellar mass in nearby galaxies and the 3.6 μm IRAC band has been exploited to this effect, but such mass estimates can be biased by dust emission. We present our pipeline to reveal the old stellar flux at 3.6 μm and obtain stellar mass maps for more than 1600 galaxies available from the Spitzer Survey of Stellar Structure in Galaxies (S{sup 4}G). This survey consists of images in two infrared bands (3.6 and 4.5 μm), and we use the Independent Component Analysis (ICA) method presented in Meidt et al. to separate the dominant light from old stars and the dust emission that can significantly contribute to the observed 3.6 μm flux. We exclude from our ICA analysis galaxies with low signal-to-noise ratio (S/N<10) and those with original [3.6]–[4.5] colors compatible with an old stellar population, indicative of little dust emission (mostly early Hubble types, which can directly provide good mass maps). For the remaining 1251 galaxies to which ICA was successfully applied, we find that as much as 10%–30% of the total light at 3.6 μm typically originates from dust, and locally it can reach even higher values. This contamination fraction shows a correlation with specific star formation rates, confirming that the dust emission that we detect is related to star formation. Additionally, we have used our large sample of mass estimates to calibrate a relationship of effective mass-to-light ratio (M/L) as a function of observed [3.6]–[4.5] color: log(M/L) = −0.339(±0.057) × ([3.6]−[4.5])−0.336(±0.002). Our final pipeline products have been made public through IRSA, providing the astronomical community with an unprecedentedly large set of stellar mass maps ready to use for scientific applications.

79 ASTRONOMY AND ASTROPHYSICS↗

Rare-gas-cluster explosions under irradiation by intense short XUV pulses

High-intensity, extreme-ultraviolet (XUV) femtosecond interactions with large rare-gas clusters of xenon and argon have been studied at a wavelength of 38 nm. Pulses of XUV radiation with nJ energy are produced by high-order harmonic conversion from a 35-fs, near-infrared, terawatt laser. Mass resolved ion spectra show charge states up to Xe{sup 8+} and Ar{sup 4+}. Kinetic-energy measurements of ions and electrons indicate that a nanoplasma is formed and a hydrodynamic cluster explosion ensues after heating by the short wavelength pulse. It appears that the observed charge states and electron temperatures are consistent with sequential, single-photon ionization and collisional ionization of ions that have had their ionization potential depressed by plasma continuum lowering in the cluster nanoplasma.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Strange hadron production in Au + Au collisions at s N N = 7.7 , 11.5, 19.6, 27, and 39 GeV

In this paper, we present STAR measurements of strange hadron (K$0\atop{s}$, Λ, $\bar{Λ}$, $Ξ$ - , $\bar{Ξ}$ + , Ω - , $\bar{Ω}$ + , and Φ ) production at mid-rapidity (|y|<0.5) in Au+Au collisions at √s NN = 7.7 – 39 GeV from the Beam Energy Scan Program at the Relativistic Heavy Ion Collider (RHIC). Transverse momentum spectra, averaged transverse mass, and the overall integrated yields of these strange hadrons are presented versus the centrality and collision energy. Antibaryon-to-baryon ratios(Λ/$\bar{Λ}$, $Ξ$ - / $\bar{Ξ}$ + , Ω - / $\bar{Ω}$ + ) are presented as well, and used to test a thermal statistical model and to extract the temperature normalized strangeness and baryon chemical potentials at hadronic freeze-out (μ B / T ch μ S / T ch ) in central collisions. Strange baryon-to-pion ratios are compared to various model predictions in central collisions for all energies. The nuclear modification factors (R CP ) and antibaryon-to-meson ratios as a function of transverse momentum are presented for all collision energies. The K$0\atop{s}$ R CP shows no suppression for p T up to 3.5 GeV/c at energies of 7.7 and 11.5 GeV. The $\bar{Λ}$/ K$0\atop{s}$ ratio also shows baryon-to-meson enhancement at intermediate p T (~2.5 GeV/c) in central collisions at energies above 19.6 GeV. In conclusion, both observations suggest that there is likely a change of the underlying strange quark dynamics at collision energies below 19.6 GeV.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Identified charged-hadron production in 𝑝+Al, 3 He + Au, and Cu + Au collisions at $\sqrt{s_{NN}}$ = 200 GeV and in U + U collisions at $\sqrt{s_{NN}}$ = 193 GeV

The PHENIX experiment has performed a systematic study of identified charged-hadron (𝜋 ± , 𝐾 ± , 𝑝, $\bar{𝑝}$) production at midrapidity in 𝑝 + Al, 3 He + Au, and Cu + Au collisions at $\sqrt{s_{NN}}$ = 200 GeV and U + U collisions at $\sqrt{s_{NN}}$ = 193 GeV. Identified charged-hadron invariant transverse-momentum (𝑝 𝑇 ) and transverse-mass (𝑚 𝑇 ) spectra are presented and interpreted in terms of radially expanding thermalized systems. The particle ratios of 𝐾/𝜋 and 𝑝/𝜋 have been measured in different centrality ranges of large (Cu + Au and U + U) and small (𝑝 + Al and 3 He + Au) collision systems. The values of 𝐾/𝜋 ratios measured in all considered collision systems were found to be consistent with those measured in 𝑝+𝑝 collisions. However, the values of 𝑝/𝜋 ratios measured in large collision systems reach the values of ≈0.6, which is a factor of ≈2 larger than in 𝑝 + 𝑝 collisions. These results can be qualitatively understood in terms of the baryon enhancement expected from hadronization by recombination. Identified charged-hadron nuclear-modification factors (𝑅 𝐴⁢𝐵 ) are also presented. Enhancement of proton 𝑅 𝐴⁢𝐵 values over meson 𝑅 𝐴⁢𝐵 values was observed in central 3 He + Au, Cu + Au, and U + U collisions. Finally, the proton 𝑅 𝐴⁢𝐵 values measured in the 𝑝 + Al collision system were found to be consistent with 𝑅 𝐴⁢𝐵 values of 𝜙, 𝜋 ± , 𝐾 ± , and 𝜋 0 mesons, which may indicate that the size of the system produced in 𝑝 + Al collisions is too small for recombination to cause a noticeable increase in proton production.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Electron capture decay of 58-min U-229(92) and levels in Pa-229(91)

Electron capture decay of U-229 is investigated by measuring the gamma-ray and conversion electron spectra of mass-separated and unseparated U-229 sources with high-resolution germanium and silicon detectors, respectively. Gamma-gamma coincidence measurements are also performed using germanium detectors. These studies provide level energies and level ordering in Pa-229. Single-particle assignments are given to these levels which are in agreement with the systematics in this region and also with theory. In a previous study, we report the observation of a 5/2(+/-) parity doublet in the Pa-229 ground state, which is a signature of octupole deformation. The present analysis of the data still shows a splitting of 60 +/- 50 eV, but with this large uncertainty the existence of the doublet is not certain.

Ahmad, I.↗

Evidence of Υ ( 1 S ) → J / ψ + χ c 1 and search for double-charmonium production in Υ ( 1 S ) and Υ ( 2 S ) decays

Using data samples of 102 × 10 6 Υ ( 1 S ) and 158 × 10 6 Υ ( 2 S ) events collected with the Belle detector, a first experimental search has been made for double-charmonium production in the exclusive decays Υ ( 1 S , 2 S ) → J / ψ ( ψ ' ) + X , where X = η c , χ c J ( J = 0 , 1 , 2 ) , η c ( 2 S ) , X ( 3940 ) , and X ( 4160 ) . No significant signal is observed in the spectra of the mass recoiling against the reconstructed J / ψ or ψ ' except for the evidence of χ c 1 production with a significance of 4.6 σ for Υ ( 1 S ) → J / ψ + χ c 1 . The measured branching fraction B ( Υ ( 1 S ) → J / ψ + χ c 1 ) is [ 3.90 ± 1.21 ( stat ) ± 0.23 ( syst ) ] × 10 - 6 . The 90% C.L. upper limits on the branching fractions of the other modes having a significance of less than 3 σ are determined. In conclusion, these results are consistent with theoretical calculations using the nonrelativistic QCD factorization approach.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Development of methods for calculating basic features of the nuclear contribution to single event upsets under the effect of protons of moderately high energy

As a continuation and a development of previous studies of our group that were devoted to the investigation of nuclear reactions induced by protons of moderately high energy (between 10 and 400 MeV) in silicon, aluminum, and tungsten atoms, the results obtained by exploring nuclear reactions on atoms of copper, which is among the most important components in materials for contact pads and pathways in modern and future ultralarge-scale integration circuits, especially in three-dimensional topology, are reported in the present article. The nuclear reactions in question lead to the formation of the mass and charge spectra of recoil nuclei ranging fromheavy target nuclei down to helium and hydrogen. The kineticenergy spectra of reaction products are calculated. The results of the calculations based on the procedure developed by our group are compared with the results of calculations and experiments performed by other authors.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗