MARVEL analysis of high-resolution rovibrational spectra of ¹³C¹⁶O₂

A set of empirical rovibrational energy levels, obtained through the MARVEL (measured active rotational-vibrational energy levels) procedure, is presented for the 13C16O2 isotopologue of carbon dioxide. This procedure begins with the collection and analysis of experimental rovibrational transitions from the literature, allowing for a comprehensive review of the literature on the high-resolution spectroscopy of 13C16O2, which is also presented. A total of 60 sources out of more than 750 checked provided 14,101 uniquely measured and assigned rovibrational transitions in the wavenumber range of 579–13,735 cm-1. This is followed by a weighted leastsquares refinement yielding the energy levels of the states involved in the measured transitions. Altogether 6318 empirical rovibrational energies have been determined for 13C16O2. Finally, estimates have been given for the uncertainties of the empirical energies, based on the experimental uncertainties of the transitions. The detailed analysis of the lines and the spectroscopic network built from them, as well as the uncertainty estimates, all serve to pinpoint possible errors in the experimental data, such as typos, misassignment of quantum numbers, and misidentifications. Errors found in the literature data were corrected before including them in the final MARVEL dataset and analysi

An update to the MARVEL data set and ExoMol line list for ¹²C₂

The spectrum of dicarbon (C_{2}) is important in astrophysics and for spectroscopic studies of plasmas and flames. The C_{2} spectrum is characterized by many band systems with new ones still being actively identified; astronomical observations involve eight of these bands. Recently, Furtenbacher et al. presented a set of 5699 empirical energy levels for {12}^C_{2}, distributed among 11 electronic states and 98 vibronic bands, derived from 42 experimental studies and obtained using the MARVEL (Measured Active Rotational-Vibrational Energy Levels) procedure. Here, we add data from 13 new sources and update data from 5 sources. Many of these data sources characterize high-lying electronic states, including the newly detected 3 {3}^Π_{g} state. Older studies have been included following improvements in the MARVEL procedure that allow their uncertainties to be estimated. These older works in particular determine levels in the C {1}^Π_{g} state, the upper state of the insufficiently characterized Deslandres–d’Azambuja (C {1}^Π_{g}–A {1}^Π_{u}) band. The new compilation considers a total of 31 323 transitions and derives 7047 empirical (MARVEL) energy levels spanning 20 electronic and 142 vibronic states. These new empirical energy levels are used here to update the 8states C_{2} ExoMol line list This updated line list is highly suitable for high-resolution cross-correlation studies in astronomical spectroscopy of, for example, exoplanets, as 99.4 per cent of the transitions with intensities over 10^{−18} cm molecule^{−1} at 1000 K have frequencies determined by empirical energy levels

MARVEL analysis of the measured high-resolution spectra of 14NH3

Accurate, experimental rotational–vibrational energy levels and line positions, with associated labels and uncertainties, are reported for the ground electronic state of the symmetric-top 14NH3 molecule. All levels and lines are based on critically reviewed and validated high-resolution experimental spectra taken from 56 literature sources. The transition data are in the 0.7–17 000 cm−1 region, with a large gap between 7000 and 15 000 cm−1. The MARVEL (Measured Active Rotational–Vibrational Energy Levels) algorithm is used to determine the energy levels. Out of the 29 450 measured transitions 10 041 and 18 947 belong to ortho- and para-14NH3, respectively. A careful analysis of the related experimental spectroscopic network (SN) allows 28 530 of the measured transitions to be validated, 18 178 of these are unique, while 462 transitions belong to floating components. Despite the large number of spectroscopic measurements published over the last 80 years, the transitions determine only 30 vibrational band origins of 14NH3, 8 for ortho- and 22 for para-14NH3. The highest J value, where J stands for the rotational quantum number, for which an energy level is validated is 31. The number of experimental-quality ortho- and para-14NH3 rovibrational energy levels is 1724 and 3237, respectively. The MARVEL energy levels are checked against ones in the BYTe first-principles database, determined previously. The lists of validated lines and levels for 14NH3 are deposited in the Supporting Information to this paper. Combination of the MARVEL energy levels with first-principles absorption intensities yields a huge number of experimental-quality rovibrational lines, which should prove to be useful for the understanding of future complex high-resolution spectroscopy on 14NH3; these lines are also deposited in the Supporting Information to this paper

An improved rovibrational linelist of formaldehyde, H₂¹²C¹⁶O

Published high-resolution rotation-vibration transitions of H₂¹²C¹⁶O the principal isotopologue of methanal, are analyzed using the MARVEL (Measured Active Rotation-Vibration Energy Levels) procedure. The literature results are augmented by new, high-accuracy measurements of pure rotational transitions within the ground, ν_{3}, ν_{4}, and ν_{6} vibrational states. Of the 16 596 non-redundant transitions processed, which come from 43 sources including the present work, 16 403 could be validated, providing 5029 empirical energy levels of H₂¹²C¹⁶O with statistically well-defined uncertainties. All the empirical rotational-vibrational energy levels determined are used to improve the accuracy of ExoMol’s AYTY line list for hot formaldehyde. The complete list of collated experimental transitions, the empirical energy levels determined, as well as the extended and improved line list are provided as Supplementary Material

Distribution and Phylogeny of EFL and EF-1α in Euglenozoa Suggest Ancestral Co-Occurrence Followed by Differential Loss

BACKGROUND: The eukaryotic elongation factor EF-1alpha (also known as EF1A) catalyzes aminoacyl-tRNA binding by the ribosome during translation. Homologs of this essential protein occur in all domains of life, and it was previously thought to be ubiquitous in eukaryotes. Recently, however, a number of eukaryotes were found to lack EF-1alpha and instead encode a related protein called EFL (for EF-Like). EFL-encoding organisms are scattered widely across the tree of eukaryotes, and all have close relatives that encode EF-1alpha. This intriguingly complex distribution has been attributed to multiple lateral transfers because EFL's near mutual exclusivity with EF-1alpha makes an extended period of co-occurrence seem unlikely. However, differential loss may play a role in EFL evolution, and this possibility has been less widely discussed. METHODOLOGY/PRINCIPAL FINDINGS: We have undertaken an EST- and PCR-based survey to determine the distribution of these two proteins in a previously under-sampled group, the Euglenozoa. EF-1alpha was found to be widespread and monophyletic, suggesting it is ancestral in this group. EFL was found in some species belonging to each of the three euglenozoan lineages, diplonemids, kinetoplastids, and euglenids. CONCLUSIONS/SIGNIFICANCE: Interestingly, the kinetoplastid EFL sequences are specifically related despite the fact that the lineages in which they are found are not sisters to one another, suggesting that EFL and EF-1alpha co-occurred in an early ancestor of kinetoplastids. This represents the strongest phylogenetic evidence to date that differential loss has contributed to the complex distribution of EFL and EF-1alpha

Marvel analysis of the measured high-resolution rovibrational spectra of H232S

44325 measured and assigned transitions of H232S, the parent isotopologue of the hydrogen sulfide molecule, are collated from 33 publications into a single database and reviewed critically. Based on this information, rotation-vibration energy levels are determined for the ground electronic state using the Measured Active Rotational-Vibrational Energy Levels (MARVEL) technique. The ortho and para principal components of the measured spectroscopic network of H232S are considered separately. The verified set of 25 293 ortho- and 18 778 para- H232S transitions determine 3969 ortho and 3467 para energy levels. The MARVEL results are compared with alternative data compilations, including a theoretical variational linelist

Total internal partition sums for 166 isotopologues of 51 molecules important in planetary atmospheres: Application to HITRAN2016 and beyond

Total internal partition sums (TIPS) are reported for 166 isotopologues of 51 molecules important in planetary atmospheres. Molecules 1 to 50 are taken from the HITRAN2016 list, and, in some cases, additional isotopologues are considered for some of the molecules. Molecules 51–53 are C3H4, CH3, and CS2, respectively. TIPS are not reported for the O atom and CF4; thus, while there are 53 species in the list, data are reported for 51 molecules. The TIPS are determined by various methods from 1 K to a Tmax that ensures the TIPS reported have converged. These data are provided with HITRAN2016 and a new version of the TIPS code is available in both FORTRAN and python languages

The HITRAN2020 molecular spectroscopic database

The HITRAN database is a compilation of molecular spectroscopic parameters. It was established in the early 1970s and is used by various computer codes to predict and simulate the transmission and emission of light in gaseous media (with an emphasis on terrestrial and planetary atmospheres). The HITRAN compilation is composed of five major components: the line-by-line spectroscopic parameters required for high-resolution radiative-transfer codes, experimental infrared absorption cross-sections (for molecules where it is not yet feasible for representation in a line-by-line form), collision-induced absorption data, aerosol indices of refraction, and general tables (including partition sums) that apply globally to the data. This paper describes the contents of the 2020 quadrennial edition of HITRAN. The HITRAN2020 edition takes advantage of recent experimental and theoretical data that were meticulously validated, in particular, against laboratory and atmospheric spectra. The new edition replaces the previous HITRAN edition of 2016 (including its updates during the intervening years). All five components of HITRAN have undergone major updates. In particular, the extent of the updates in the HITRAN2020 edition range from updating a few lines of specific molecules to complete replacements of the lists, and also the introduction of additional isotopologues and new (to HITRAN) molecules: SO, CH3F, GeH4, CS2, CH3I and NF3. Many new vibrational bands were added, extending the spectral coverage and completeness of the line lists. Also, the accuracy of the parameters for major atmospheric absorbers has been increased substantially, often featuring sub-percent uncertainties. Broadening parameters associated with the ambient pressure of water vapor were introduced to HITRAN for the first time and are now available for several molecules. The HITRAN2020 edition continues to take advantage of the relational structure and efficient interface available at www.hitran.org and the HITRAN Application Programming Interface (HAPI). The functionality of both tools has been extended for the new edition

Ancient and Recent Adaptive Evolution of Primate Non-Homologous End Joining Genes

In human cells, DNA double-strand breaks are repaired primarily by the non-homologous end joining (NHEJ) pathway. Given their critical nature, we expected NHEJ proteins to be evolutionarily conserved, with relatively little sequence change over time. Here, we report that while critical domains of these proteins are conserved as expected, the sequence of NHEJ proteins has also been shaped by recurrent positive selection, leading to rapid sequence evolution in other protein domains. In order to characterize the molecular evolution of the human NHEJ pathway, we generated large simian primate sequence datasets for NHEJ genes. Codon-based models of gene evolution yielded statistical support for the recurrent positive selection of five NHEJ genes during primate evolution: XRCC4, NBS1, Artemis, POLλ, and CtIP. Analysis of human polymorphism data using the composite of multiple signals (CMS) test revealed that XRCC4 has also been subjected to positive selection in modern humans. Crystal structures are available for XRCC4, Nbs1, and Polλ; and residues under positive selection fall exclusively on the surfaces of these proteins. Despite the positive selection of such residues, biochemical experiments with variants of one positively selected site in Nbs1 confirm that functions necessary for DNA repair and checkpoint signaling have been conserved. However, many viruses interact with the proteins of the NHEJ pathway as part of their infectious lifecycle. We propose that an ongoing evolutionary arms race between viruses and NHEJ genes may be driving the surprisingly rapid evolution of these critical genes