The Role of Torsion/Torsion Coupling in the Vibrational Spectrum of Cis−Cis HOONO

A three-dimensional model of the vibrational dynamics of HOONO is investigated. This model focuses on the couplings between the OH stretch vibration and the two torsions. The model is based on electronic energies, calculated at the CCSD(T)/cc-pVTZ level of theory and basis and dipole moment functions calculated at the CCSD/aug-cc-pVDZ level. The resulting points were fit to explicit functional forms, and the energies, wave functions, and intensities were evaluated using an approach in which the OH stretching motion was adiabatically separated from the torsional modes. It is found that the HOON torsion is strongly coupled to both the OONO torsion and OH stretch. Despite this, many of the conclusions that were drawn from earlier two-dimensional treatments, which did not include the OONO torsion, hold up on a semiquantitative level. In addition, we use this model to investigate the assignment of recently reported matrix isolated spectra of HOONO and DOONO. Finally, by comparing the results of this three-dimensional calculation to two-dimensional calculations and to the results of second-order perturbation theory, we investigate the question of how one determines the size of the reduced-dimensional system that is needed to describe the vibrational spectrum of molecules, like HOONO, that contain several large amplitude motions

Kinetics of n-Butoxy and 2-Pentoxy Isomerization and Detection of Primary Products by Infrared Cavity Ringdown Spectroscopy

The primary products of n-butoxy and 2-pentoxy isomerization in the presence and absence of O_2 have been detected using pulsed laser photolysis-cavity ringdown spectroscopy (PLP-CRDS). Alkoxy radicals n-butoxy and 2-pentoxy were generated by photolysis of alkyl nitrite precursors (n-butyl nitrite or 2-pentyl nitrite, respectively), and the isomerization products with and without O_2 were detected by infrared cavity ringdown spectroscopy 20 μs after the photolysis. We report the mid-IR OH stretch (ν_1) absorption spectra for δ-HO-1-C_4H_8•, δ-HO-1-C_4H_8OO•, δ-HO-1-C_5H_(10)•, and δ-HO-1-C_5H_(10)OO•. The observed ν_1 bands are similar in position and shape to the related alcohols (n-butanol and 2-pentanol), although the HOROO• absorption is slightly stronger than the HOR• absorption. We determined the rate of isomerization relative to reaction with O_2 for the n-butoxy and 2-pentoxy radicals by measuring the relative ν_1 absorbance of HOROO• as a function of [O_2]. At 295 K and 670 Torr of N_2 or N_2/O_2, we found rate constant ratios of k_(isom)/k_(O2) = 1.7 (±0.1) × 10^(19) cm^(–3) for n-butoxy and k_(isom)/k_(O2) = 3.4(±0.4) × 10^(19) cm^(–3) for 2-pentoxy (2σ uncertainty). Using currently known rate constants k_(O2), we estimate isomerization rates of k_(isom) = 2.4 (±1.2) × 10^5 s^(–1) and k_(isom) ≈ 3 × 10^5 s^(–1) for n-butoxy and 2-pentoxy radicals, respectively, where the uncertainties are primarily due to uncertainties in k_(O2). Because isomerization is predicted to be in the high pressure limit at 670 Torr, these relative rates are expected to be the same at atmospheric pressure. Our results include corrections for prompt isomerization of hot nascent alkoxy radicals as well as reaction with background NO and unimolecular alkoxy decomposition. We estimate prompt isomerization yields under our conditions of 4 ± 2% and 5 ± 2% for n-butoxy and 2-pentoxy formed from photolysis of the alkyl nitrites at 351 nm. Our measured relative rate values are in good agreement with and more precise than previous end-product analysis studies conducted on the n-butoxy and 2-pentoxy systems. We show that reactions typically neglected in the analysis of alkoxy relative kinetics (decomposition, recombination with NO, and prompt isomerization) may need to be included to obtain accurate values of k_(isom)/k_(O2)

Cavity Ringdown Spectroscopy of the Hydroxy-Methyl-Peroxy Radical

We report vibrational and electronic spectra of the hydroxy-methyl-peroxy radical (HOCH_2OO^• or HMP), which was formed as the primary product of the reaction of the hydroperoxy radical, HO_2^•, and formaldehyde, HCHO. The ν_1 vibrational (OH stretch) spectrum and the à ← X electronic spectrum of HMP were detected by infrared cavity ringdown spectroscopy (IR-CRDS), and assignments were verified with density functional calculations. The HMP radical was generated in reactions of HCHO with HO_2^•. Free radical reactions were initiated by pulsed laser photolysis (PLP) of Cl_2 in the presence of HCHO and O_2 in a flow reactor at 300–330 Torr and 295 K. IR-CRDS spectra were measured in mid-IR and near-IR regions over the ranges 3525–3700 cm^(–1) (ν_1) and 7250–7800 cm^(–1) (à ← X) respectively, at a delay time 100 μs after photolysis. The ν_1 spectrum had an origin at 3622 cm^(–1) and exhibited partially resolved P- and R-branch contours and a small Q-branch. At these short delay times, spectral interference from HOOH and HCOOH was minimal and could be subtracted. From B3LYP/6-31+G(d,p) calculations, we found that the anharmonic vibrational frequency and band contour predicted for the lowest energy conformer, HMP-A, were in good agreement with the observed spectrum. In the near-IR, we observed four well spaced vibronic bands, each with partially resolved rotational contours. We assigned the apparent origin of the à ← X electronic spectrum of HMP at 7389 cm^(–1) and two bands to the blue to a progression in ν15′, the lowest torsional mode of the à state (ν_(15′) = 171 cm^(–1)). The band furthest to the red was assigned as a hot band in ν^(15″), leading to a ground state torsional frequency of (ν^(15″) = 122 cm^(–1)). We simulated the spectrum using second order vibrational perturbation theory (VPT2) with B3LYP/6-31+G(d,p) calculations at the minimum energy geometries of the HMP-A conformer on the X and à states. The predictions of the electronic origin frequency, torsional frequencies, anharmonicities, and rotational band contours matched the observed spectrum. We investigated the torsional modes more explicitly by computing potential energy surfaces of HMP as a function of the two dihedral angles τ_(HOCO) and τ_(OOCO). Wave functions and energy levels were calculated on the basis of this potential surface; these results were used to calculate the Franck–Condon factors, which reproduced the vibronic band intensities in the observed electronic spectrum. The transitions that we observed all involved states with wave functions localized on the minimum energy conformer, HMP-A. Our calculations indicated that the observed near-IR spectrum was that of the lowest energy X state conformer HMP-A, but that this conformer is not the lowest energy conformer in the à state, which remains unobserved. We estimated that the energy of this lowest conformer (HMP-B) of the à state is E_0 (Ã, HMP-B) ≈ 7200 cm^(–1), on the basis of the energy difference E_0(HMP-B) – E_0(HMP-A) on the à state computed at the B3LYP/6-31+G(d,p) level

The Structural Biology Knowledgebase: a portal to protein structures, sequences, functions, and methods

The Protein Structure Initiative’s Structural Biology Knowledgebase (SBKB, URL: http://sbkb.org) is an open web resource designed to turn the products of the structural genomics and structural biology efforts into knowledge that can be used by the biological community to understand living systems and disease. Here we will present examples on how to use the SBKB to enable biological research. For example, a protein sequence or Protein Data Bank (PDB) structure ID search will provide a list of related protein structures in the PDB, associated biological descriptions (annotations), homology models, structural genomics protein target status, experimental protocols, and the ability to order available DNA clones from the PSI:Biology-Materials Repository. A text search will find publication and technology reports resulting from the PSI’s high-throughput research efforts. Web tools that aid in research, including a system that accepts protein structure requests from the community, will also be described. Created in collaboration with the Nature Publishing Group, the Structural Biology Knowledgebase monthly update also provides a research library, editorials about new research advances, news, and an events calendar to present a broader view of structural genomics and structural biology

SNAPSHOT USA 2019 : a coordinated national camera trap survey of the United States

This article is protected by copyright. All rights reserved.With the accelerating pace of global change, it is imperative that we obtain rapid inventories of the status and distribution of wildlife for ecological inferences and conservation planning. To address this challenge, we launched the SNAPSHOT USA project, a collaborative survey of terrestrial wildlife populations using camera traps across the United States. For our first annual survey, we compiled data across all 50 states during a 14-week period (17 August - 24 November of 2019). We sampled wildlife at 1509 camera trap sites from 110 camera trap arrays covering 12 different ecoregions across four development zones. This effort resulted in 166,036 unique detections of 83 species of mammals and 17 species of birds. All images were processed through the Smithsonian's eMammal camera trap data repository and included an expert review phase to ensure taxonomic accuracy of data, resulting in each picture being reviewed at least twice. The results represent a timely and standardized camera trap survey of the USA. All of the 2019 survey data are made available herein. We are currently repeating surveys in fall 2020, opening up the opportunity to other institutions and cooperators to expand coverage of all the urban-wild gradients and ecophysiographic regions of the country. Future data will be available as the database is updated at eMammal.si.edu/snapshot-usa, as well as future data paper submissions. These data will be useful for local and macroecological research including the examination of community assembly, effects of environmental and anthropogenic landscape variables, effects of fragmentation and extinction debt dynamics, as well as species-specific population dynamics and conservation action plans. There are no copyright restrictions; please cite this paper when using the data for publication.Publisher PDFPeer reviewe

Mammal responses to global changes in human activity vary by trophic group and landscape

Wildlife must adapt to human presence to survive in the Anthropocene, so it is critical to understand species responses to humans in different contexts. We used camera trapping as a lens to view mammal responses to changes in human activity during the COVID-19 pandemic. Across 163 species sampled in 102 projects around the world, changes in the amount and timing of animal activity varied widely. Under higher human activity, mammals were less active in undeveloped areas but unexpectedly more active in developed areas while exhibiting greater nocturnality. Carnivores were most sensitive, showing the strongest decreases in activity and greatest increases in nocturnality. Wildlife managers must consider how habituation and uneven sensitivity across species may cause fundamental differences in human–wildlife interactions along gradients of human influence.Peer reviewe

Circulating microRNAs in sera correlate with soluble biomarkers of immune activation but do not predict mortality in ART treated individuals with HIV-1 infection: A case control study

Introduction: The use of anti-retroviral therapy (ART) has dramatically reduced HIV-1 associated morbidity and mortality. However, HIV-1 infected individuals have increased rates of morbidity and mortality compared to the non-HIV-1 infected population and this appears to be related to end-organ diseases collectively referred to as Serious Non-AIDS Events (SNAEs). Circulating miRNAs are reported as promising biomarkers for a number of human disease conditions including those that constitute SNAEs. Our study sought to investigate the potential of selected miRNAs in predicting mortality in HIV-1 infected ART treated individuals. Materials and Methods: A set of miRNAs was chosen based on published associations with human disease conditions that constitute SNAEs. This case: control study compared 126 cases (individuals who died whilst on therapy), and 247 matched controls (individuals who remained alive). Cases and controls were ART treated participants of two pivotal HIV-1 trials. The relative abundance of each miRNA in serum was measured, by RTqPCR. Associations with mortality (all-cause, cardiovascular and malignancy) were assessed by logistic regression analysis. Correlations between miRNAs and CD4+ T cell count, hs-CRP, IL-6 and D-dimer were also assessed. Results: None of the selected miRNAs was associated with all-cause, cardiovascular or malignancy mortality. The levels of three miRNAs (miRs -21, -122 and -200a) correlated with IL-6 while miR-21 also correlated with D-dimer. Additionally, the abundance of miRs -31, -150 and -223, correlated with baseline CD4+ T cell count while the same three miRNAs plus miR- 145 correlated with nadir CD4+ T cell count. Discussion: No associations with mortality were found with any circulating miRNA studied. These results cast doubt onto the effectiveness of circulating miRNA as early predictors of mortality or the major underlying diseases that contribute to mortality in participants treated for HIV-1 infection

The Seventeenth Data Release of the Sloan Digital Sky Surveys: Complete Release of MaNGA, MaStar and APOGEE-2 Data

This paper documents the seventeenth data release (DR17) from the Sloan Digital Sky Surveys; the fifth and final release from the fourth phase (SDSS-IV). DR17 contains the complete release of the Mapping Nearby Galaxies at Apache Point Observatory (MaNGA) survey, which reached its goal of surveying over 10,000 nearby galaxies. The complete release of the MaNGA Stellar Library (MaStar) accompanies this data, providing observations of almost 30,000 stars through the MaNGA instrument during bright time. DR17 also contains the complete release of the Apache Point Observatory Galactic Evolution Experiment 2 (APOGEE-2) survey which publicly releases infra-red spectra of over 650,000 stars. The main sample from the Extended Baryon Oscillation Spectroscopic Survey (eBOSS), as well as the sub-survey Time Domain Spectroscopic Survey (TDSS) data were fully released in DR16. New single-fiber optical spectroscopy released in DR17 is from the SPectroscipic IDentification of ERosita Survey (SPIDERS) sub-survey and the eBOSS-RM program. Along with the primary data sets, DR17 includes 25 new or updated Value Added Catalogs (VACs). This paper concludes the release of SDSS-IV survey data. SDSS continues into its fifth phase with observations already underway for the Milky Way Mapper (MWM), Local Volume Mapper (LVM) and Black Hole Mapper (BHM) surveys