High accuracy calculations of the rotation-vibration spectrum of H3+_3^+

Calculation of the rotation-vibration spectrum of H3+, as well as of its deuterated isotopologues, with near-spectroscopic accuracy requires the development of sophisticated theoretical models, methods, and codes. The present paper reviews the state-of-the-art in these fields. Computation of rovibrational states on a given potential energy surface (PES) has now become standard for triatomic molecules, at least up to intermediate energies, due to developments achieved by the present authors and others. However, highly accurate Born--Oppenheimer energies leading to highly accurate PESs are not accessible even for this two-electron system using conventional electronic structure procedures e.g., configuration-interaction or coupled-cluster techniques with extrapolation to the complete basis set limit). For this purpose highly specialized techniques must be used, e.g., those employing explicitly correlated Gaussians and nonlinear parameter optimizations. It has also become evident that a very dense grid of \ai\ points is required to obtain reliable representations of the computed points extending from the minimum to the asymptotic limits. Furthermore, adiabatic, relativistic, and QED correction terms need to be considered to achieve near-spectroscopic accuracy during calculation of the rotation-vibration spectrum of H3+. The remaining and most intractable problem is then the treatment of the effects of non-adiabatic coupling on the rovibrational energies, which, in the worst cases, may lead to corrections on the order of several \cm. A promising way of handling this difficulty is the further development of effective, motion- or even coordinate-dependent, masses and mass surfaces. Finally, the unresolved challenge of how to describe and elucidate the experimental pre-dissociation spectra of H$_3^+$ and its isotopologues is discussed.Comment: Topical review to be published in J Phys B: At Mol Opt Phy

Experimental energy levels and partition function of the 12^{12}C2_2 molecule

The carbon dimer, the $^{12}$C$_2$ molecule, is ubiquitous in astronomical environments. Experimental-quality rovibronic energy levels are reported for $^{12}$C$_2$, based on rovibronic transitions measured for and among its singlet, triplet, and quintet electronic states, reported in 42 publications. The determination utilizes the Measured Active Rotational-Vibrational Energy Levels (MARVEL) technique. The 23,343 transitions measured experimentally and validated within this study determine 5,699 rovibronic energy levels, 1,325, 4,309, and 65 levels for the singlet, triplet, and quintet states investigated, respectively. The MARVEL analysis provides rovibronic energies for six singlet, six triplet, and two quintet electronic states. For example, the lowest measurable energy level of the \astate\ state, corresponding to the $J=2$ total angular momentum quantum number and the $F_1$ spin-multiplet component, is 603.817(5) \cm. This well-determined energy difference should facilitate observations of singlet--triplet intercombination lines which are thought to occur in the interstellar medium and comets. The large number of highly accurate and clearly labeled transitions that can be derived by combining MARVEL energy levels with computed temperature-dependent intensities should help a number of astrophysical observations as well as corresponding laboratory measurements. The experimental rovibronic energy levels, augmented, where needed, with {\it ab initio} variational ones based on empirically adjusted and spin-orbit coupled potential energy curves obtained using the \Duo\ code, are used to obtain a highly accurate partition function, and related thermodynamic data, for $^{12}$C$_2$ up to 4,000 K.Comment: ApJ Supplements (in press), 48 page

Uncertainty Estimates for Theoretical Atomic and Molecular Data

Sources of uncertainty are reviewed for calculated atomic and molecular data that are important for plasma modeling: atomic and molecular structure and cross sections for electron-atom, electron-molecule, and heavy particle collisions. We concentrate on model uncertainties due to approximations to the fundamental many-body quantum mechanical equations and we aim to provide guidelines to estimate uncertainties as a routine part of computations of data for structure and scattering.Comment: 65 pages, 18 Figures, 3 Tables. J. Phys. D: Appl. Phys. Final accepted versio

MARVEL Analysis of the Measured High-Resolution Rovibronic Spectra of 90Zr16O

Zirconium oxide(ZrO) is an important astrophysical molecule that defines the S-star classification class for cool giant stars. Accurate, empirical rovibronic energy levels, with associated labels and uncertainties, are reported for 9 low-lying electronic states of the diatomic 90Zr16O molecule. These 8088 empirical energy levels are determined using the Marvel (Measured Active Rotational-Vibrational Energy Levels) algorithm with 23 317 input assigned transition frequencies, 22 549 of which were validated. A temperature-dependent partition function is presented alongside updated spectroscopic constants for the 9 low-lying electronic states

Recommended isolated-line profile for representing high-resolution spectroscopic transitions (IUPAC Technical Report)

The report of an IUPAC Task Group, formed in 2011 on "Intensities and line shapes in high-resolution spectra of water isotopologues from experiment and theory" (Project No. 2011-022-2-100), on line profiles of isolated high-resolution rotational-vibrational transitions perturbed by neutral gas-phase molecules is presented. The well-documented inadequacies of the Voigt profile (VP), used almost universally by databases and radiative-transfer codes, to represent pressure effects and Doppler broadening in isolated vibrational-rotational and pure rotational transitions of the water molecule have resulted in the development of a variety of alternative line-profile models. These models capture more of the physics of the influence of pressure on line shapes but, in general, at the price of greater complexity. The Task Group recommends that the partially Correlated quadratic-Speed-Dependent Hard-Collision profile should be adopted as the appropriate model for high-resolution spectroscopy. For simplicity this should be called the Hartmann--Tran profile (HTP). The HTP is sophisticated enough to capture the various collisional contributions to the isolated line shape, can be computed in a straightforward and rapid manner, and reduces to simpler profiles, including the Voigt profile, under certain simplifying assumptions.Comment: Accepted for publication in Pure and Applied Chemistr

IUPAC Critical Evaluation of the Rotational-Vibrational Spectra of Water Vapor, Part III: Energy Levels and Transition Wavenumbers for H216O

This is the third of a series of articles reporting critically evaluated rotational-vibrational line positions, transition intensities, and energy levels, with associated critically reviewed labels and uncertainties, for all the main isotopologues of water. This paper presents experimental line positions, experimental-quality energy levels, and validated labels for rotational-vibrational transitions of the most abundant isotopologue of water, H216O. The latest version of the MARVEL (Measured Active Rotational-Vibrational Energy Levels) line-inversion procedure is used to determine the rovibrational energy levels of the electronic ground state of H216O from experimentally measured lines, together with their self-consistent uncertainties, for the spectral region up to the first dissociation limit. The spectroscopic network of H216O contains two components, an ortho (o) and a para (p) one. For o-H216O and p-H216O, experimentally measured, assigned, and labeled transitions were analyzed from more than 100 sources. The measured lines come from one-photon spectra recorded at room temperature in absorption, from hot samples with temperatures up to 3000K recorded in emission, and from multiresonance excitation spectra which sample levels up to dissociation. The total number of transitions considered is 184667 of which 182156 are validated: 68027 between para states and 114129 ortho ones. These transitions give rise to 18486 validated energy levels, of which 10446 and 8040 belong to o-H216O and p-H216O, respectively. The energy levels, including their labeling with approximate normal-mode and rigid-rotor quantum numbers, have been checked against ones determined from accurate variational nuclear motion computations employing exact kinetic energy operators as well as against previous compilations of energy levels. The extensive list of MARVEL lines and levels obtained are deposited in the supplementary data of this paper, as well as in a distributed information system applied to water, W@DIS, where they can easily be retrieved

PERT: A Method for Expression Deconvolution of Human Blood Samples from Varied Microenvironmental and Developmental Conditions

The cellular composition of heterogeneous samples can be predicted using an expression deconvolution algorithm to decompose their gene expression profiles based on pre-defined, reference gene expression profiles of the constituent populations in these samples. However, the expression profiles of the actual constituent populations are often perturbed from those of the reference profiles due to gene expression changes in cells associated with microenvironmental or developmental effects. Existing deconvolution algorithms do not account for these changes and give incorrect results when benchmarked against those measured by well-established flow cytometry, even after batch correction was applied. We introduce PERT, a new probabilistic expression deconvolution method that detects and accounts for a shared, multiplicative perturbation in the reference profiles when performing expression deconvolution. We applied PERT and three other state-of-the-art expression deconvolution methods to predict cell frequencies within heterogeneous human blood samples that were collected under several conditions (uncultured mono-nucleated and lineage-depleted cells, and culture-derived lineage-depleted cells). Only PERT's predicted proportions of the constituent populations matched those assigned by flow cytometry. Genes associated with cell cycle processes were highly enriched among those with the largest predicted expression changes between the cultured and uncultured conditions. We anticipate that PERT will be widely applicable to expression deconvolution strategies that use profiles from reference populations that vary from the corresponding constituent populations in cellular state but not cellular phenotypic identity

Contrasting Patterns of Coral Bleaching Susceptibility in 2010 Suggest an Adaptive Response to Thermal Stress

Background: \ud Coral bleaching events vary in severity, however, to date, the hierarchy of susceptibility to bleaching among coral taxa has been consistent over a broad geographic range and among bleaching episodes. Here we examine the extent of spatial and temporal variation in thermal tolerance among scleractinian coral taxa and between locations during the 2010 thermally induced, large-scale bleaching event in South East Asia.\ud \ud Methodology/Principal Findings: \ud Surveys to estimate the bleaching and mortality indices of coral genera were carried out at three locations with contrasting thermal and bleaching histories. Despite the magnitude of thermal stress being similar among locations in 2010, there was a remarkable contrast in the patterns of bleaching susceptibility. Comparisons of bleaching susceptibility within coral taxa and among locations revealed no significant differences between locations with similar thermal histories, but significant differences between locations with contrasting thermal histories (Friedman = 34.97; p,0.001). Bleaching was much less severe at locations that bleached during 1998, that had greater historical temperature variability and lower rates of warming. Remarkably, Acropora and Pocillopora, taxa that are typically highly susceptible, although among the most susceptible in Pulau Weh (Sumatra, Indonesia) where respectively, 94% and 87% of colonies died, were among the least susceptible in Singapore, where only 5% and 12% of colonies died.\ud \ud Conclusions/Significance: \ud The pattern of susceptibility among coral genera documented here is unprecedented. A parsimonious explanation for these results is that coral populations that bleached during the last major warming event in 1998 have adapted and/or acclimatised to thermal stress. These data also lend support to the hypothesis that corals in regions subject to more variable temperature regimes are more resistant to thermal stress than those in less variable environments

Effects of Restrained Sampling Space and Nonplanar Amino Groups on Free-Energy Predictions for RNA with Imino and Sheared Tandem GA Base Pairs Flanked by GC, CG, iGiC or iCiG Base Pairs

Guanine-adenine (GA) base pairs play important roles in determining the structure, dynamics, and stability of RNA. In RNA internal loops, GA base pairs often occur in tandem arrangements and their structure is context and sequence dependent. Calculations reported here test the thermodynamic integration (TI) approach with the amber99 force field by comparing computational predictions of free energy differences with the free energy differences expected on the basis of NMR determined structures of the RNA motifs (5′-GCGGACGC-3′)2, (5′-GCiGGAiCGC-3′)2, (5′-GGCGAGCC-3′)2, and (5′-GGiCGAiGCC-3′)2. Here, iG and iC denote isoguanosine and isocytidine, which have amino and carbonyl groups transposed relative to guanosine and cytidine. The NMR structures show that the GA base pairs adopt either imino (cis Watson−Crick/Watson−Crick A-G) or sheared (trans Hoogsteen/Sugar edge A-G) conformations depending on the identity and orientation of the adjacent base pair. A new mixing function for the TI method is developed that allows alchemical transitions in which atoms can disappear in both the initial and final states. Unrestrained calculations gave ΔG° values 2−4 kcal/mol different from expectations based on NMR data. Restraining the structures with hydrogen bond restraints did not improve the predictions. Agreement with NMR data was improved by 0.7 to 1.5 kcal/mol, however, when structures were restrained with weak positional restraints to sample around the experimentally determined NMR structures. The amber99 force field was modified to partially include pyramidalization effects of the unpaired amino group of guanosine in imino GA base pairs. This provided little or no improvement in comparisons with experiment. The marginal improvement is observed when the structure has potential cross-strand out-of-plane hydrogen bonding with the G amino group. The calculations using positional restraints and a nonplanar amino group reproduce the signs of ΔG° from the experimental results and are, thus, capable of providing useful qualitative insights complementing the NMR experiments. Decomposition of the terms in the calculations reveals that the dominant terms are from electrostatic and interstrand interactions other than hydrogen bonds in the base pairs. The results suggest that a better description of the backbone is key to reproducing the experimental free energy results with computational free energy predictions