Disentangling the subcycle electron momentum spectrum in strong-field ionization
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74 ATOMIC AND MOLECULAR PHYSICS↗
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Results for “molecular spectrum”
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Extragalactic CO emission lines in the CMB experiments: A forgotten signal and a foreground
High resolution cosmic microwave background (CMB) experiments have allowed us to precisely measure the CMB temperature power spectrum down to very small scales (multipole ℓ ~ 3000). Such measurements at multiple frequencies enable separating the power spectrum of the primary CMB anisotropies with the power spectrum of other signals like CMB lensing, thermal and kinematic Sunyaev-Zel’dovich effects (tSZ and kSZ), and cosmic infrared background (CIB). Here, in this paper, we explore another signal of interest at these frequencies that should be present in the CMB maps: extragalactic CO molecular rotational line emissions, which are the most widely used tracers of molecular gas in the line intensity mapping experiments. Using the SIDES simulations adopted for top hat bandpasses at 150 and 220 GHz, we show that the cross-correlation of the CIB with CO lines has a contribution similar to the CIB-tSZ correlation and the kSZ power, thereby contributing a non-negligible amount to the total power at these scales. This signal, therefore, may significantly impact the recently reported ≥3σ detection of the kSZ power spectrum from the South Pole Telescope collaboration, as the contribution of the CO lines is not considered in such analyses. Our results also provide a new way of measuring the CO power spectrum in cross-correlation with the CIB. Finally, these results show that the CO emissions present in the CMB maps will have to be accounted for in all the CMB auto-power spectrum and cross-correlation studies involving a large-scale structure tracer.
79 ASTRONOMY AND ASTROPHYSICS↗
Table-Top High Photon Energy Sources for Chemical Dynamics Investigations
Time-resolved spectroscopies using high-energy photons in the vacuum ultraviolet (VUV) to the X-ray region of the electromagnetic spectrum, have proven to be powerful probes of chemical dynamics. These high-energy photons can access valence and core orbitals of molecules and materials, providing key information on molecular and electronic structure and their time evolution. This report details the development of table-top sources of extreme ultraviolet (XUV) and VUV pulses at Sandia National Laboratories for use in studies of gas phase chemical dynamics. Femtosecond duration XUV pulses are produced using laser-driven high harmonic generation and their detected range span ~40-140 eV photon energies. These pulses are used in conjunction with ultraviolet pulses in a pump-probe scheme to study excited state dynamics of gas phase molecules. VUV pulses at 7.75 eV are generated using a four-wave-mixing scheme driven by 800 nm and 266 nm pulses in an argon-filled hollow-core fiber.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Computational optimal transport for molecular spectra: The fully continuous case
Computational optimal transport is used to analyze the difference between pairs of continuous molecular spectra. It is demonstrated that transport distances which are derived from this approach may be a more appropriate measure of the difference between two continuous spectra than more familiar measures of distance under many common circumstances. Associated with the transport distances is the transport map which provides a detailed analysis of the difference between two molecular spectra and is a key component of our study of quantitative differences between two continuous spectra. The use of optimal transport for comparing molecular spectra is developed in detail here with a set of model spectra, so that the discussion is self-contained. The difference between the transport distance and more common definitions of distance is elucidated for some well-chosen examples and it is shown where transport distances may be very useful alternatives to standard definitions of distance. The transport distance between a theoretical and experimental electronic absorption spectrum for SO 2 is studied and it is shown how the theoretical spectrum can be modified to fit the experimental spectrum better adjusting the theoretical band origin and the resolution of the theoretical spectrum. In conclusion, this analysis includes the calculation of transport maps between the theoretical and experimental spectra suggesting future applications of the methodology.
74 ATOMIC AND MOLECULAR PHYSICS↗
CFM-ID 4.0: More Accurate ESI MS/MS Spectral Prediction and Compound Identification
In the field of metabolomics, mass spectrometry (MS) is the method most commonly used for identifying and annotating metabolites. As this typically involves matching a given MS spectrum against an experimentally acquired reference spectral library, this approach is limited by the coverage and size of such libraries (which typically number in the thousands). These experimental libraries can be greatly extended by predicting the MS spectra of known chemical structures (which number in the millions) to create computational reference spectral libraries. To facilitate the generation of predicted spectral reference libraries we developed CFM-ID, a computer program that can accurately predict ESI-MS/MS spectrum for a given compound structure. CFM-ID is one of the best-performing methods for compound-to-mass-spectrum prediction, and also one of the top tools for in silico mass-spectrum-to-compound identification. This work improves CFM-ID’s ability to predict ESI-MS/MS spectra from compounds by: (1) learning parameters from features based on the molecular topology, (2) adding a new approach to ring cleavage that models such cleavage as a sequence of simple chemical bond dissociations and (3) expanding its hand-written rule-based predictor to cover more chemical classes, including acylcarnitines, acylcholines, flavonols, flavones, flavanones, and flavonoid glycosides. We demonstrate that this new version of CFM-ID (version 4.0) is significantly more accurate than previous CFM-ID versions, in terms of both EI-MS/MS spectral prediction and compound identification. CFM-ID 4.0 is available at http://cfmid4.wishartlab.com/ as a webservice and docker images can be downloaded at https://hub.docker.com/r/wishartlab/cfmid
Wang, Fei↗
Mutations in penicillin-binding protein 2 from cephalosporin-resistant Neisseria gonorrhoeae hinder ceftriaxone acylation by restricting protein dynamics
The global incidence of the sexually transmitted disease gonorrhea is expected to rise due to the spread of Neisseria gonorrhoeae strains with decreased susceptibility to extended-spectrum cephalosporins (ESCs). ESC resistance is conferred by mosaic variants of penicillin-binding protein 2 (PBP2) that have diminished capacity to form acylated adducts with cephalosporins. To elucidate the molecular mechanisms of ESC resistance, we conducted a biochemical and high-resolution structural analysis of PBP2 variants derived from the decreased-susceptibility N. gonorrhoeae strain 35/02 and ESC-resistant strain H041. Our data reveal that mutations both lower affinity of PBP2 for ceftriaxone and restrict conformational changes that normally accompany acylation. Specifically, we observe that a G545S substitution hinders rotation of the β3 strand necessary to form the oxyanion hole for acylation and also traps ceftriaxone in a noncanonical configuration. In addition, F504L and N512Y substitutions appear to prevent bending of the β3–β4 loop that is required to contact the R1 group of ceftriaxone in the active site. Other mutations also appear to act by reducing flexibility in the protein. Overall, our findings reveal that restriction of protein dynamics in PBP2 underpins the ESC resistance of N. gonorrhoeae.
60 APPLIED LIFE SCIENCES↗
SF6 Negative Ion Formation in Charge Transfer Experiments
In the present work, we report an update and extension of the previous ion-pair formation study of Hubers, M.M.; Los, J. Chem. Phys. 1975, 10, 235–259, noting new fragment anions from time-of-flight mass spectrometry. The branching ratios obtained from the negative ions formed in K + SF6 collisions, in a wide energy range from 10.7 up to 213.1 eV in the centre-of-mass frame, show that the main anion is assigned to SF5− and contributing to more than 70% of the total ion yield, followed by the non-dissociated parent anion SF6− and F−. Other less intense anions amounting to <20% are assigned to SF3− and F2−, while a trace contribution at 32u is tentatively assigned to S− formation, although the rather complex intramolecular energy redistribution within the temporary negative ion is formed during the collision. An energy loss spectrum of potassium cation post-collision is recorded showing features that have been assigned with the help of theoretical calculations. Quantum chemical calculations for the lowest-lying unoccupied molecular orbitals in the presence of a potassium atom are performed to support the experimental findings. Apart from the role of the different resonances participating in the formation of different anions, the role of higher-lying electronic-excited states of Rydberg character are noted.
Biochemistry & Molecular Biology↗
Molecules in Cool Stars: The A 2 Π − X 2 Σ + and the B 2 Σ + − X 2 Σ + Band Systems of CaCl
Cool red giant stars exhibit absorption bands of calcium monochloride (CaCl) in the optical region. In this work, the bands of CaCl corresponding to the A 2 Π − X 2 Σ + transition with v' ≤ 4 and v'' ≤ 4, and B 2 Σ + − X 2 Σ + transition with v' ≤ 2 and v'' ≤ 2 are rotationally analyzed with PGOPHER, a multipurpose program for simulating and fitting molecular spectra. All bands were analyzed using high-resolution absorption spectra collected at the National Solar Observatory in 1985, calibrated with atomic lines from a high-resolution emission spectrum obtained in a separate hollow cathode experiment. The results are compared with previous laser-induced fluorescence measurements. Overall, the accuracy of spectroscopic constants for the A2Π and B2Σ+ states is improved. Scaled transition dipole moment calculations were used to obtain line strengths. Line lists are provided with Einstein A coefficients and oscillator strengths, which can be used to determine CaCl stellar abundances. Additionally, isotope splittings allowed us to estimate band origins for the 40 Ca 37 Cl isotopologue based on band-head positions.
Léo Lavy↗
The Evolution of Disks and Winds in Dwarf Nova Outbursts - FUSE
This project was a project to study the FUV spectra of two proto-typical dwarf novae, U Gem and SS Cygni, through an outburst cycle. The luminosity of the boundary layer in the two systems, as evidenced by earlier EUVE observations, is different in the two systems. Our intensive study of the two systems was intended to (1) probe the ionization and kinematic structure of the wind as a function of system brightness, (2) isolate the contributions of the disk to the FUV spectra, and (3) examine physical conditions and abundances of material just being accreted onto the disk from the secondary. The U Gem and SS Cyg observations took place in March and October 2000, respectively. The data obtained with FUSE was of excellent quality. Analysis of the both observations is now essentially complete, although some modeling of the SS Cyg spectra is ongoing, as we complete an ApJ manuscript on this object. Our main results for U Gem are as follows: The plateau spectra have continuum shapes and fluxes that are approximated by steady state accretion disk model spectra with an accretion rate 7x10(exp 9) Msolar/yr. The spectra also show numerous absorption lines of H I, He II, and 2-5 times ionized transitions of C, N, O, P, S, and Si. There are no emission features in the spectra, with the possible exception of a weak feature on the red wing of the 0 VI doublet. The absorption lines are narrow (FWHM approx. 50 km/s), too narrow to arise from the disk photosphere, and at low velocities (less than or equal to 700 km/s). The S VI and O VI doublets are optically thick. The absorption lines in the plateau spectra show orbital variability: in spectra obtained at orbital phases between 0.53 and 0.79, low-ionization absorption lines appear and the central depths of the preexisting lines increase. The increase in line absorption occurs at the same orbital phases as previously observed EUV and X-ray light-curve dips. If the absorbing material is in (near-) Keplerian rotation around the disk, it must be located at large disk radii. The final observation occurred when U Gem was about 2 mag from optical quiescence. The spectra are dominated by emission from an approx. 43,000 K, metal-enriched white dwarf (WD). The inferred radius of the WD is 4.95x10(exp 8) cm, close to that observed in quiescence. Allowing for a hot heated region on the surface of the WD improves the fit to the spectrum at short (less than 960 A) wavelengths. Our main results for SS Cyg are as follows: The first two of four observations of SS Cyg show disk dominated spectra with accretion rates of order 10(exp -8) Msolar/yr. Except for narrow interstellar features (atomic and molecular H), the lines are all broad consistent with a disk or wind origin. The O VI line in the spectra is mostly of wind origin as detailed modeling with our Monte Carlo code (developed in part using funds from this project) show. The continua from spectra in observations 3 and 4, observed during the decline phase, are not well fit with steady-state disks, and show considerable resemblance to quiescent spectra obtained with HUT. The most probable interpretation for the emission features seen in the spectrum in the last two observations is that they arise from a photo-illuminated choronosphere above the disk, rather than a wind.
Long, Knox↗
Infrared absorption and emission characteristics of interstellar PAHs
The mid-infrared interstellar emission spectrum with features at 3.28, 6.2, 7.7, 8.7 and 11.3 microns is discussed in terms of the Polycyclic Aromatic Hydrocarbon (PAH) hypothesis, which is based on the suggestive, but inconclusive comparison between the interstellar emission spectrum with the infrared absorption and Raman spectra of a few PAHs. The fundamental vibrations of PAHs and PAH-like species which determine the IR and Raman properties are discussed. Interstellar IR band emission is due to relaxation from highly vibrationally excited PAHs excited by ultraviolet photons. The excitation/emission process is described and the IR fluorescence from one PAH, chrysene, is traced. Generally, there is sufficient energy to populate several vibrational levels in each mode. Molecular vibrational potentials are anharmonic and emission from these higher levels will fall at lower frequencies and produce weak features to the red of the stronger fundamentals. This process is also described and can account for some spectroscopic details of the interstellar emission spectra previously unexplained. Analysis of the interstellar spectrum shows that PAHs contain between 20 and 30 carbon atoms are responsible for the emission.
Barker, J. R.↗
Infrared absorption and emission characteristics of interstellar PAHs
The mid-infrared interstellar emission spectrum with features at 3.28, 6.2, 7.7, 8.7 and 11.3 microns is discussed in terms of the Polycyclic Aromatic Hydrocarbon (PAH) hypothesis, which is based on the suggestive, but inconclusive comparison between the interstellar emission spectrum with the infrared absorption and Raman spectra of a few PAHs. The fundamental vibrations of PAHs and PAH-like species which determine the IR and Raman properties are discussed. Interstellar IR band emission is due to relaxation from highly vibrationally excited PAHs excited by ultraviolet photons. The excitation/emission process is described and the IR fluorescence from one PAH, chrysene, is traced. Generally, there is sufficient energy to populate several vibrational levels in each mode. Molecular vibrational potentials are anharmonic and emission from these higher levels will fall at lower frequencies and produce weak features to the red of the stronger fundamentals. This process is also described and can account for some spectroscopic details of the interstellar emission spectra previously unexplained. Analysis of the interstellar spectrum shows that PAHs contain between 20 and 30 carbon atoms and are responsible for the emission.
Allamandola, L. J.↗
Electron-ion coincidence measurements of molecular dynamics with intense X-ray pulses
Molecules can sequentially absorb multiple photons when irradiated by an intense X-ray pulse from a free-electron laser. If the time delay between two photoabsorption events can be determined, this enables pump-probe experiments with a single X-ray pulse, where the absorption of the first photon induces electronic and nuclear dynamics that are probed by the absorption of the second photon. Here we show a realization of such a single-pulse X-ray pump-probe scheme on N 2 molecules, using the X-ray induced dissociation process as an internal clock that is read out via coincident detection of photoelectrons and fragment ions. By coincidence analysis of the kinetic energies of the ionic fragments and photoelectrons, the transition from a bound molecular dication to two isolated atomic ions is observed through the energy shift of the inner-shell electrons. Via ab-initio simulations, we are able to map characteristic features in the kinetic energy release and photoelectron spectrum to specific delay times between photoabsorptions. In contrast to previous studies where nuclear motions were typically revealed by measuring ion kinetics, our work shows that inner-shell photoelectron energies can also be sensitive probes of nuclear dynamics, which adds one more dimension to the study of light-matter interactions with X-ray pulses.
74 ATOMIC AND MOLECULAR PHYSICS↗
Digital quantum simulation of NMR experiments
Simulations of nuclear magnetic resonance (NMR) experiments can be an important tool for extracting information about molecular structure and optimizing experimental protocols but are often intractable on classical computers for large molecules such as proteins and for protocols such as zero-field NMR. We demonstrate the first quantum simulation of an NMR spectrum, computing the zero-field spectrum of the methyl group of acetonitrile using four qubits of a trapped-ion quantum computer. We reduce the sampling cost of the quantum simulation by an order of magnitude using compressed sensing techniques. We show how the intrinsic decoherence of NMR systems may enable the zero-field simulation of classically hard molecules on relatively near-term quantum hardware and discuss how the experimentally demonstrated quantum algorithm can be used to efficiently simulate scientifically and technologically relevant solid-state NMR experiments on more mature devices. Our work opens a practical application for quantum computation.
74 ATOMIC AND MOLECULAR PHYSICS↗
High-resolution laser-induced fluorescence spectroscopy of 28 Si 16 O + and 29 Si 16 O + in a cryogenic buffer-gas cell
Here, the electronic, laser-induced fluorescence spectrum of the B 2 Σ + ← X 2 Σ + transition in 28 Si 16 O + and 29 Si 16 O + has been recorded in a cryogenic buffer gas cell at K. Molecular constants are extracted for both 28 Si 16 O + and 29 Si 16 O + , including the Fermi contact hyperfine constant for both the B and X states of 29 Si 16 O + , and used in a discussion of the suitability of SiO in future quantum information experiments.
47 OTHER INSTRUMENTATION↗
Defect-induced states, defect-induced phase transition, and excitonic states in bent tungsten disulfide (WS 2 ) nanoribbons: Density functional vs. many body theory
Two-dimensional (2D) transition metal dichalcogenide (TMD) materials have versatile electronic and optical properties. TMD nanoribbons exhibit interesting properties due to reduced dimensionality, quantum confinement, and edge states, which make them suitable for various electronic and optoelectronic applications. In a previous work conducted by our group, we demonstrated that the edge bands evolved with bending can tune the optical properties for various widths of TMD nanoribbons. Defects are commonly present in 2D TMD materials, and can dramatically change the material properties. Here, in this following work, we investigate the interaction between the edge and the defect states in tungsten disulfide (WS 2 ) nanoribbons with lines of W- or S-atom vacancies defects under different bending conditions, using density functional theory (DFT). To gain understanding about the limits of density functional approximations, we compare results on band gaps and energies of defect states with quasiparticle GW. We reveal interesting semiconductor-metal phase transitions, suggesting potential applications in nanoelectronics or molecular electronics. We also calculate the optical absorption of the bent and defective nanoribbons with the many-body GW-BSE (Bethe-Salpeter equation) approach, revealing a tunable optical spectrum and diverse exciton states in the defective WS 2 nanoribbons.
36 MATERIALS SCIENCE↗
Titan - Far-infrared and microwave remote sensing of methane clouds and organic haze
Titan's surface and plausible atmospheric thermal opacity sources, which include gaseous N2, CH4, and H2, together with CH4 clouds and organic haze, are sufficient to match available earth-based and Voyager observations of Titan's thermal emission spectrum. Dominant thermal emission sources are the surface, at greater than 1 cm wavelengths, atmospheric N2 for the 1-200 micron range, condensed and gaseous CH4 for 200-20 microns, and molecular bands and organic haze at less than 20 microns.
Thompson, W. R.↗
Atmospheric Pseudohalogen Chemistry
Hydrogen cyanide is not usually considered in atmospheric chemical models. The paper presents three reasons why hydrogen cyanide is likely to be significant for atmospheric chemistry. Firstly, HCN is a product and marker of biomass burning. Secondly, it is also likely that lightning is producing HCN, and as HCN is sparingly soluble it could be a useful long-lived "smoking gun" marker of lightning activity. Thirdly, the chemical decomposition of HCN leads to the production of small amounts of the cyanide (CN) and NCO radicals. The NCO radical can be photolyzed in the visible portion of the spectrum yielding nitrogen atoms (N). The production of nitrogen atoms is significant as it leads to the titration of total nitrogen from the atmosphere via N+N->N2, where N2 is molecular nitrogen.
Lary, David John↗
The Advanced Spectral Library (ASTRAL): Reference Spectra for Evolved M Stars
The HST Treasury Program Advanced Spectral Library Project: Cool Stars was designed to collect representative, high-quality UV spectra of eight evolved FM type cool stars. The Space Telescope Imaging Spectrograph (STIS)echelle spectra of these objects enable investigations of a broad range of topics, including stellar and interstellar astrophysics. This paper provides a guide to the spectra of the two evolved M stars, the M2 Iab supergiant Oriand the M3.4 giant Cru, with comparisons to the prototypical K1.5 giant Boo. It includes identifications of the significant atomic and molecular emission and absorption features and discusses the character of the photospheric and chromospheric continua and line spectra. The fluorescent processes responsible for a large portion of the emission-line spectrum, the characteristics of the stellar winds, and the available diagnostics for hot and cool plasmas are also summarized. This analysis will facilitate the future study of the spectra, outer atmospheres, and winds, not only of these objects but of numerous other cool, low-gravity stars, for years to come.
The HST Treasury Program Advanced Spectral Library↗