Theoretical H + O3 rate coefficients from ring polymer molecular dynamics on an accurate global potential energy surface: assessing experimental uncertainties

Thermal rate coefficients and kinetic isotope effects have been calculated for an important atmospheric reaction H/D + O3 → OH/OD + O2 based on an accurate permutation invariant polynomial-neural network potential energy surface, using ring polymer molecular dynamics (RPMD), quasi-classical trajectory (QCT) and variational transition-state theory (VTST) with multidimensional tunneling. The RPMD approach yielded results that are generally in better agreement with experimental rate coefficients than the VTST and QCT ones, especially at low temperatures, attributable to its capacity to capture quantum effects such as tunneling and zero-point energy. The theoretical results support one group of existing experiments over the other. In addition, rate coefficients for the D + O3 → OD + O2 reaction are also reported using the same methods, which will allow a stringent assessment of future experimental measurements, thus helping to reduce the uncertainty in the recommended rate coefficients of this reaction.

Reactive Oxygen Species Penetrate Persister Cell Membranes of Escherichia coli for Effective Cell Killing

Persister cells are difficult to eliminate because they are tolerant to antibiotic stress. In the present study, using artificially induced Escherichia coli persister cells, we found that reactive oxygen species (ROS) have greater effects on persister cells than on exponential cells. Thus, we examined which types of ROS could effectively eliminate persister cells and determined the mechanisms underlying the effects of these ROS. Ultraviolet (UV) light irradiation can kill persister cells, and bacterial viability is markedly increased under UV shielding. UV induces the production of ROS, which kill bacteria by moving toward the shielded area. Electron spin resonance-based analysis confirmed that hydroxyl radicals are produced by UV irradiation, although singlet oxygen is not produced. These results clearly revealed that ROS sterilizes persister cells more effectively compared to the sterilization of exponential cells (^**p < 0.01). These ROS do not injure the bacterial cell wall but rather invade the cell, followed by cell killing. Additionally, the sterilization effect on persister cells was increased by exposure to oxygen plasma during UV irradiation. However, vapor conditions decreased persister cell sterilization by reducing the levels of hydroxyl radicals. We also verified the effect of ROS against bacteria in biofilms that are more resistant than planktonic cells. Although UV alone could not completely sterilize the biofilm bacteria, UV with ROS achieved complete sterilization. Our results demonstrate that persister cells strongly resist the effects of antibiotics and starvation stress but are less able to withstand exposure to ROS. It was shown that ROS does not affect the cell membrane but penetrates it and acts internally to kill persister cells. In particular, it was clarified that the hydroxy radical is an effective sterilizer to kill persister cells.

Hydrogen-Atom Tunneling in Metaphosphorous Acid

Metaphosphorous acid (HOPO), a key intermediate in phosphorus chemistry, has been generated in syn- and anti-conformations in the gas phase by high-vacuum flash pyrolysis (HVFP) of a molecular precursor ethoxyphosphinidene oxide (EtOPO→C₂ H₄ +HOPO) at ca. 1000 K and subsequently trapped in an N₂ -matrix at 2.8 K. Unlike the two conformers of the nitrogen analogue HONO, the anti-conformer of HOPO undergoes spontaneous rotamerization at 2.8 K via hydrogen-atom tunneling (HAT) with noticeable kinetic isotope effects for H/D (>10⁴ for DOPO) and ¹⁶ O/¹⁸ O (1.19 for H¹⁸ OPO and 1.06 for HOP¹⁸ O) in N₂ -matrices.

Spectroscopic characterization of the first excited state and photochemistry of the HO3 radical

We report the one-dimensional cuts of the six-dimensional potential energy surfaces (PESs) of the ground and lowest doublet and quartet electronic states of trans-HO₃ at the MRCI-F12/aug-cc-pVTZ level of theory. Theoretical calculations predict that the first excited state (A²A) presents a real minimum on its PES and possesses a nonplanar structure. The adiabatic excitation energy at the MRCI+Q and MRCI-F12 levels shows that the A²A state lies in the near-infrared region. Both the transition dipole moment and the oscillator strength were predicted to be weak, which suggests that photodissociation of HO₃ to produce OH and O₂ after UV-Vis absorption is not a plausible mechanism. The harmonic vibrational frequencies and rotational constants of the weakly bound complex OH-O₂ in the two electronic states were predicted to help in its detection. Our PES shows that the reactions of H + O₃ or HO₂ + O in their ground states do not lead to trans-HO₃ in its ground electronic state if one of the component fragments, i.e., HO₂(A²A') + O(³P) or H(²S) + O₃(³B₂), is excited.

Riddles of the structure and vibrational dynamics of HO3 resolved near the ab initio limit

The hydridotrioxygen (HO₃) radical has been investigated in many previous theoretical and experimental studies over several decades, originally because of its possible relevance to the tropospheric HO_x cycle but more recently because of its fascinating chemical bonding, geometric structure, and vibrational dynamics. We have executed new, comprehensive research on this vexing molecule via focal point analyses (FPA) to approach the ab initio limit of optimized geometric structures, relative energies, complete quartic force fields, and the entire reaction path for cis-trans isomerization. High-order coupled cluster theory was applied through the CCSDT(Q) and even CCSDTQ(P) levels, and CBS extrapolations were performed using cc-pVXZ (X = 2-6) basis sets. The cis isomer proves to be higher than trans by 0.52 kcal mol^-1, but this energetic ordering is achieved only after the CCSDT(Q) milestone is reached; the barrier for cis → trans isomerization is a minute 0.27 kcal mol^-1. The FPA central r_e(O-O) bond length of trans-HO₃ is astonishingly long (1.670 Å), consistent with the semiexperimental r_e distance we extracted from microwave rotational constants of 10 isotopologues using FPA vibration-rotation interaction constants (α_i). The D₀(HO-O₂) dissociation energy converges to a mere 2.80 ± 0.25 kcal mol^-1. Contrary to expectation for such a weakly bound system, vibrational perturbation theory performs remarkably well with the FPA anharmonic force fields, even for the torsional fundamental near 130 cm^-1. Exact numerical procedures are applied to the potential energy function for the torsional reaction path to obtain energy levels, tunneling rates, and radiative lifetimes. The cis → trans isomerization occurs via tunneling with an inherent half-life of 1.4 × 10^-11 s and 8.6 × 10^-10 s for HO₃ and DO₃, respectively, thus resolving the mystery of why the cis species has not been observed in previous experiments executed in dissipative environments that allow collisional cooling of the trans-HO₃ product. In contrast, the pure ground eigenstate of the cis species in a vacuum is predicted to have a spontaneous radiative lifetime of about 1 h and 5 days for HO₃ and DO₃, respectively.

Anab initiobased full-dimensional potential energy surface for OH + O2⇄ HO3and low-lying vibrational levels of HO3

A full-dimensional potential energy surface for HO₃, including the HO + O₂dissociation asymptote, is developed and rigorous quantum dynamics calculations based on this PES have been carried out to compute the vibrational energy levels of HO₃.

Tropospheric oxidation of methyl hydrotrioxide (CH3OOOH) by hydroxyl radical

We have employed high level theoretical methods to investigate the oxidation of methyl hydrotrioxide by hydroxyl radical, which is of interest in atmospheric chemistry research. The reaction can proceed by abstraction of either the terminal hydrogen atom of OOH group producing CH3O, O2 and H2O, or one hydrogen atom of the CH3 group forming H2CO, HO2 and H2O. The rate constants for both reactions at 298 K are computed to be 4.7 × 10-11 and 2.1 × 10-12 cm3 molecule-1 s-1, respectively, that is, the abstraction of terminal hydrogen atom of the OOH group is about 22 times faster than that of a hydrogen atom of the CH3 group. The rate constant for the overall CH3OOOH + OH reaction is computed to be 4.9 × 10-11 cm3 molecule-1 s-1. Our calculations predict branching ratios between 99.0 and 93.9% for the formation of methoxy radical plus molecular oxygen and water, and between 1.0 and 6.1% for the formation of formaldehyde plus hydroperoxyl radical and water, in the 225-325 K temperature range. The lifetime of CH3OOOH in the troposphere is predicted to range from of 1.8 hours at 225 K, up to 3.9 hours at 275 K and decreasing to 0.2 hours at 310 K. CH3OOO and CH2OOOH radicals have been also investigated.

Low temperature kinetics and theoretical studies of the reaction CN + CH3NH2: a potential source of cyanamide and methyl cyanamide in the interstellar medium

The reaction between cyano radicals (which are ubiquitous in interstellar clouds) and methylamine (a molecule detected in various interstellar sources) has been investigated in a synergistic experimental and theoretical study. The reaction has been found to be very fast in the entire range of temperatures investigated (23-297 K) by using a CRESU apparatus coupled to pulsed laser photolysis - laser induced fluorescence. The global experimental rate coefficient is given by In addition, dedicated electronic structure calculations of the underlying potential energy surface have been performed, together with capture theory and RRKM calculations. The experimental data have been interpreted in the light of the theoretical calculations and the product branching ratio has been established. According to the present study, in the range of temperatures investigated the title reaction is an efficient interstellar route of formation of cyanamide, NH₂CN, another interstellar species. The second most important channel is the one leading to methyl cyanamide, CH₃NHCN (an isomer of aminoacetonitrile), via a CN/H exchange mechanism with a yield of 12% of the global reaction in the entire range of temperatures explored. For a possible inclusion in future astrochemical models we suggest, by referring to the usual expression the following values: α = 3.68 × 10^-12 cm³ molec^-1 s^-1, β = -1.80, γ = 7.79 K for the channel leading to NH₂CN + CH₃; α = 5.05 × 10^-13 cm³ molec^-1 s^-1, β = -1.82, γ = 7.93 K for the channel leading to CH₃NHCN + H.

Quantitative probing of subtle interactions among H-bonds in alpha hydroxy carboxylic acid complexes

The alpha OH stretching frequency may be affected upon complexing with water and formic acid.

Dissection of H-bonding interactions in a glycolic acid–water dimer

The binding strength and collective effects of multiple H-bonds in the glycolic acid–water dimer were studied in comparison to the aromatic analog, 9-hydroxy-9-fluorene carboxylic acid (9HFCA).

An Evaluation of Gas Phase Enthalpies of Formation for Hydrogen-Oxygen (HxOy) Species

We have compiled gas phase enthalpies of formation for nine hydrogen-oxygen species (HxOy) and selected recommended values for H, O, OH, H2O, HO2, H2O2, O3, HO3, and H2O3. The compilation consists of values derived from experimental measurements, quantum chemical calculations, and prior evaluations. This work updates the recommended values in the NIST-JANAF (1985) and Gurvich et al. (1989) thermochemical tables for seven species. For two species, HO3 and H2O3 (important in atmospheric chemistry) and not found in prior thermochemical evaluations, we also provide supplementary data consisting of molecular geometries, vibrational frequencies, and torsional potentials which can be used to compute thermochemical functions. For all species, we also provide supplementary data consisting of zero point energies, vibrational frequencies, and ion reaction energetics.

Pressure dependent low temperature kinetics for CN + CH3CN: competition between chemical reaction and van der Waals complex formation

The gas phase reaction between the CN radical and acetonitrile CH₃CN was investigated experimentally with a CRESU apparatus and a slow flow reactor as well as theoretically to explore the temperature and pressure dependence of its rate coefficient from 354 K down to 23 K.

Weakly Bound Clusters in Astrochemistry? Millimeter and Submillimeter Spectroscopy of trans-HO3 and Comparison to Astronomical Observations

The emergence of chemical complexity during star and planet formation is largely guided by the chemistry of unstable molecules that are reaction intermediates in terrestrial chemistry. Our knowledge of these intermediates is limited by both the lack of laboratory studies and the difficulty in their astronomical detection. In this work, we focus on the weakly bound cluster HO3 as an example of the connection between laboratory spectroscopic study and astronomical observations. Here, we present a fast-sweep spectroscopic technique in the millimeter and submillimeter range to facilitate the laboratory search for trans-HO3 and DO3 transitions in a discharge supersonic jet and report their rotational spectra from 70 to 450 GHz. These new measurements enable full determination of the molecular constants of HO3 and DO3. We also present a preliminary search for trans-HO3 in 32 star-forming regions using this new spectroscopic information. HO3 is not detected, and column density upper limits are reported. This work provides additional benchmark information for computational studies of this intriguing radical, as well as a reliable set of molecular constants for extrapolation of the transition frequencies of HO3 for future astronomical observations.

Formation of hydrogen polyoxides as constituents of peroxy radical condensate upon low-temperature interaction of hydrogen atoms with liquid ozone

The composition of low-temperature condensates obtained by the reaction of hydrogen atoms with liquid ozone has been determined from the Raman spectra and data on the molar ratio of O2 to H2O2 in the decomposition products. The main constituents are hydrogen tetroxide H2O4, trioxide H2O3, and peroxide H2O2 in comparable amounts and also water H2O. The mechanism and quantitative kinetic model of their formation have been proposed. H2O4, H2O3, and H2O2 are formed in the diffusion-controlled reactions between OH and HO2 in the liquid ozone layer and stabilized by transfer to the solid phase. OH and HO2 radicals are generated via a sequence of the reactions initiated by the interaction H + O3(liq). The model adequately reproduces the properties of the real condensates.

Is HO3− multiple-minimum and floppy? Covalent to van der Waals isomerization and bond rupture of a peculiar anion

The HO₃⁻ anion is multiple-minimum and floppy: the two main isomers and isomerization barrier all lie quite below dissociation.

An experimental and theoretical investigation of the N(4S) + C2(1Σg+) reaction at low temperature

The N + C₂ reaction is shown to be an important source of CN radicals in dense interstellar clouds.

Detection and structure of HOON: microwave spectroscopy reveals an O-O bond exceeding 1.9 Å

Nitric oxide (NO) reacts with hydroxyl radicals (OH) in the gas phase to produce nitrous acid, HONO, but essentially nothing is known about the isomeric nitrosyl-O-hydroxide (HOON), owing to its perceived instability. We report the detection of gas-phase HOON in a supersonic molecular beam by Fourier transform microwave spectroscopy and a precise determination of its molecular structure by further spectroscopic analysis of its (2)H, (15)N, and (18)O isotopologs. HOON contains the longest O-O bond in any known molecule (1.9149 ± 0.0005 Å) and appears surprisingly stable, with an abundance roughly 3% that of HONO in our experiments.

Low temperature kinetics of unstable radical reactions

Recent advances in Earth and satellite based observations of molecules in interstellar environments and in planetary atmospheres have highlighted the lack of information regarding many important gas-phase formation mechanisms involving neutral species at low temperatures. Whilst significant progress has been made towards a better understanding of radical-molecule reactions in these regions, the inherent difficulties involved in the investigation of reactions between two unstable radical species have hindered progress in this area. This perspective article provides a brief review of the most common techniques applied to study radical-radical reactions below room temperature, before outlining the developments in our laboratory that have allowed us to extend such measurements to temperatures relevant to astrochemical environments. These developments will be discussed with particular emphasis on our recent investigations of the reactions of atomic nitrogen with diatomic radicals.