The Atmospherically Important Reaction of Hydroxyl Radicals with Methyl Nitrate: A Theoretical Study Involving the Calculation of Reaction Mechanisms, Enthalpies, Activation Energies, and Rate Coefficients

A theoretical study, involving the calculation of reaction enthalpies, activation energies, mechanisms, and rate coefficients, was made of the reaction of hydroxyl radicals with methyl nitrate, an important process for methyl nitrate removal in the earth’s atmosphere. Four reaction channels were considered: formation of H₂O + CH₂ONO₂, CH₃OOH + NO₂, CH₃OH + NO₃, and CH₃O + HNO₃. For all channels, geometry optimization and frequency calculations were performed at the M06-2<i>X</i>/6-31+G** level, while relative energies were improved at the UCCSD­(T*)-F12/CBS level. The major channel is found to be the H abstraction channel, to give the products H₂O + CH₂ONO₂. The reaction enthalpy (Δ<i>H</i>_298 K^RX) of this channel is computed as −17.90 kcal mol^–1. Although the other reaction channels are also exothermic, their reaction barriers are high (>24 kcal mol^–1), and therefore these reactions do not contribute to the overall rate coefficient in the temperature range considered (200–400 K). Pathways via three transition states were identified for the H abstraction channel. Rate coefficients were calculated for these pathways at various levels of variational transition state theory including tunneling. The results obtained are used to distinguish between two sets of experimental rate coefficients, measured in the temperature range of 200–400 K, one of which is approximately an order of magnitude greater than the other. This comparison, as well as the temperature dependence of the computed rate coefficients, shows that the lower experimental values are favored. The implications of the results to atmospheric chemistry are discussed

Prediction of Peptide Fragment Ion Mass Spectra by Data Mining Techniques

Accurate prediction of peptide fragment ion mass spectra is one of the critical factors to guarantee confident peptide identification by protein sequence database search in bottom-up proteomics. In an attempt to accurately and comprehensively predict this type of mass spectra, a framework named MS²PBPI is proposed. MS²PBPI first extracts fragment ions from large-scale MS/MS spectra data sets according to the peptide fragmentation pathways and uses binary trees to divide the obtained bulky data into tens to more than 1000 regions. For each adequate region, stochastic gradient boosting tree regression model is constructed. By constructing hundreds of these models, MS²PBPI is able to predict MS/MS spectra for unmodified and modified peptides with reasonable accuracy. Moreover, high consistency between predicted and experimental MS/MS spectra derived from different ion trap instruments with low and high resolving power is achieved. MS²PBPI outperforms existing algorithms MassAnalyzer and PeptideART

Reaction between CH₃O₂ and BrO Radicals: A New Source of Upper Troposphere Lower Stratosphere Hydroxyl Radicals

Over the last two decades it has emerged that measured hydroxyl radical levels in the upper troposphere are often underestimated by models, leading to the assertion that there are missing sources. Here we report laboratory studies of the kinetics and products of the reaction between CH₃O₂ and BrO radicals that shows that this could be an important new source of hydroxyl radicals:BrO + CH₃O₂ → products (1). The temperature dependent value in Arrhenius form of <i>k</i>(<i>T</i>) is <i>k</i>₁ = (2.42_–0.72^+1.02) × 10^–14 exp­[(1617 ± 94)/<i>T</i>] cm³ molecule^–1 s^–1. In addition, CH₂OO and HOBr are believed to be the major products. Global model results suggest that the decomposition of H₂COO to form OH could lead to an enhancement in OH of up to 20% in mid-latitudes in the upper troposphere and in the lower stratosphere enhancements in OH of 2–9% are inferred from model integrations. In addition, reaction 1 aids conversion of BrO to HOBr and slows polar ozone loss in the lower stratosphere

Direct Measurements of Unimolecular and Bimolecular Reaction Kinetics of the Criegee Intermediate (CH₃)₂COO

The Criegee intermediate acetone oxide, (CH₃)₂COO, is formed by laser photolysis of 2,2-diiodopropane in the presence of O₂ and characterized by synchrotron photoionization mass spectrometry and by cavity ring-down ultraviolet absorption spectroscopy. The rate coefficient of the reaction of the Criegee intermediate with SO₂ was measured using photoionization mass spectrometry and pseudo-first-order methods to be (7.3 ± 0.5) × 10^–11 cm³ s^–1 at 298 K and 4 Torr and (1.5 ± 0.5) × 10^–10 cm³ s^–1 at 298 K and 10 Torr (He buffer). These values are similar to directly measured rate coefficients of <i>anti</i>-CH₃CHOO with SO₂, and in good agreement with recent UV absorption measurements. The measurement of this reaction at 293 K and slightly higher pressures (between 10 and 100 Torr) in N₂ from cavity ring-down decay of the ultraviolet absorption of (CH₃)₂COO yielded even larger rate coefficients, in the range (1.84 ± 0.12) × 10^–10 to (2.29 ± 0.08) × 10^–10 cm³ s^–1. Photoionization mass spectrometry measurements with deuterated acetone oxide at 4 Torr show an inverse deuterium kinetic isotope effect, <i>k</i>_H/<i>k</i>_D = (0.53 ± 0.06), for reactions with SO₂, which may be consistent with recent suggestions that the formation of an association complex affects the rate coefficient. The reaction of (CD₃)₂COO with NO₂ has a rate coefficient at 298 K and 4 Torr of (2.1 ± 0.5) × 10^–12 cm³ s^–1 (measured with photoionization mass spectrometry), again similar to rate for the reaction of <i>anti</i>-CH₃CHOO with NO₂. Cavity ring-down measurements of the acetone oxide removal without added reagents display a combination of first- and second-order decay kinetics, which can be deconvolved to derive values for both the self-reaction of (CH₃)₂COO and its unimolecular thermal decay. The inferred unimolecular decay rate coefficient at 293 K, (305 ± 70) s^–1, is similar to determinations from ozonolysis. The present measurements confirm the large rate coefficient for reaction of (CH₃)₂COO with SO₂ and the small rate coefficient for its reaction with water. Product measurements of the reactions of (CH₃)₂COO with NO₂ and with SO₂ suggest that these reactions may facilitate isomerization to 2-hydroperoxypropene, possibly by subsequent reactions of association products