HO2 + NO2: Kinetics, Thermochemistry, and Evidence for a Bimolecular Product Channel.

A master equation (ME) analysis of available experimental data has been carried out on the reaction HO2 + NO2 + M ⇋ HO2NO2 + M (1a)/(-1a). The analysis, based on the ME code MESMER, uses both the association and dissociation kinetic data from the literature, and provides improved thermochemistry on reaction 1a. Our preferred model assigns two low-frequency vibrations of HO2NO2 as hindered rotors and couples these to the external rotations. This model gives ΔrH°0(1a) = -93.9 ± 1.0 kJ mol-1, which implies that ΔfH°0 HO2NO2 = -42.0 ± 1.0 kJ mol-1 (uncertainties are 2σ). A significant contributor to the uncertainty derives from modeling the interaction between the internal and external rotors. Using this improved kinetics for reaction 1a/-1a, data at elevated temperatures, 353-423 K, which show no evidence of the expected equilibration, have been reanalyzed, indicating that an additional reaction is occurring that masks the equilibration. Based on a published ab initio study, this additional channel is assigned to the bimolecular reaction HO2 + NO2 → H-NO2 + O2 (1b); H-NO2 is nitryl hydride and has not previously been directly observed in experiments. The output of the master equation analysis has been parametrized and Troe expressions are provided for an improved description of k1a(p,T) and k-1a(p,T).

AutoMeKin2021: An open-source program for automated reaction discovery.

AutoMeKin2021 is an updated version of tsscds2018, a program for the automated discovery of reaction mechanisms (J. Comput. Chem. 2018, 39, 1922). This release features a number of new capabilities: rare-event molecular dynamics simulations to enhance reaction discovery, extension of the original search algorithm to study van der Waals complexes, use of chemical knowledge, a new search algorithm based on bond-order time series analysis, statistics of the chemical reaction networks, a web application to submit jobs, and other features. The source code, manual, installation instructions and the website link are available at: https://rxnkin.usc.es/index.php/AutoMeKin.

Nonadiabatic Kinetics in the Intermediate Coupling Regime: Comparing Molecular Dynamics to an Energy-Grained Master Equation.

We propose and test an extension of the energy-grained master equation (EGME) for treating nonadiabatic (NA) hopping between different potential energy surfaces, which enables us to model the competition between stepwise collisional relaxation and kinetic processes which transfer population between different electronic states of the same spin symmetry. By incorporating Zhu-Nakamura theory into the EGME, we are able to treat NA passages beyond the simple Landau-Zener approximation, along with the corresponding treatments of zero-point energy and tunneling probability. To evaluate the performance of this NA-EGME approach, we carried out detailed studies of the UV photodynamics of the volatile organic compound C6-hydroperoxy aldehyde (C6-HPALD) using on-the-fly ab initio molecular dynamics and trajectory surface hopping. For this multichromophore molecule, we show that the EGME is able to capture important aspects of the dynamics, including kinetic timescales, and diabatic trapping. Such an approach provides a promising and efficient strategy for treating the long-time dynamics of photoexcited molecules in regimes which are difficult to capture using atomistic on-the-fly molecular dynamics.

Exploring human-guided strategies for reaction network exploration: Interactive molecular dynamics in virtual reality as a tool for citizen scientists.

The emerging fields of citizen science and gamification reformulate scientific problems as games or puzzles to be solved. Through engaging the wider non-scientific community, significant breakthroughs may be made by analyzing citizen-gathered data. In parallel, recent advances in virtual reality (VR) technology are increasingly being used within a scientific context and the burgeoning field of interactive molecular dynamics in VR (iMD-VR) allows users to interact with dynamical chemistry simulations in real time. Here, we demonstrate the utility of iMD-VR as a medium for gamification of chemistry research tasks. An iMD-VR "game" was designed to encourage users to explore the reactivity of a particular chemical system, and a cohort of 18 participants was recruited to playtest this game as part of a user study. The reaction game encouraged users to experiment with making chemical reactions between a propyne molecule and an OH radical, and "molecular snapshots" from each game session were then compiled and used to map out reaction pathways. The reaction network generated by users was compared to existing literature networks demonstrating that users in VR capture almost all the important reaction pathways. Further comparisons between humans and an algorithmic method for guiding molecular dynamics show that through using citizen science to explore these kinds of chemical problems, new approaches and strategies start to emerge.

Experimental and computational studies of Criegee intermediate reactions with NH3 and CH3NH2.

Ammonia and amines are emitted into the troposphere by various natural and anthropogenic sources, where they have a significant role in aerosol formation. Here, we explore the significance of their removal by reaction with Criegee intermediates, which are produced in the troposphere by ozonolysis of alkenes. Rate coefficients for the reactions of two representative Criegee intermediates, formaldehyde oxide (CH2OO) and acetone oxide ((CH3)2COO) with NH3 and CH3NH2 were measured using cavity ring-down spectroscopy. Temperature-dependent rate coefficients, k(CH2OO + NH3) = (3.1 ± 0.5) × 10-20T2 exp(1011 ± 48/T) cm3 s-1 and k(CH2OO + CH3NH2) = (5 ± 2) × 10-19T2 exp(1384 ± 96/T) cm3 s-1 were obtained in the 240 to 320 K range. Both the reactions of CH2OO were found to be independent of pressure in the 10 to 100 Torr (N2) range, and average rate coefficients k(CH2OO + NH3) = (8.4 ± 1.2) × 10-14 cm3 s-1 and k(CH2OO + CH3NH2) = (5.6 ± 0.4) × 10-12 cm3 s-1 were deduced at 293 K. An upper limit of ≤2.7 × 10-15 cm3 s-1 was estimated for the rate coefficient of the (CH3)2COO + NH3 reaction. Complementary measurements were performed with mass spectrometry using synchrotron radiation photoionization giving k(CH2OO + CH3NH2) = (4.3 ± 0.5) × 10-12 cm3 s-1 at 298 K and 4 Torr (He). Photoionization mass spectra indicated production of NH2CH2OOH and CH3N(H)CH2OOH functionalized organic hydroperoxide adducts from CH2OO + NH3 and CH2OO + CH3NH2 reactions, respectively. Ab initio calculations performed at the CCSD(T)(F12*)/cc-pVQZ-F12//CCSD(T)(F12*)/cc-pVDZ-F12 level of theory predicted pre-reactive complex formation, consistent with previous studies. Master equation simulations of the experimental data using the ab initio computed structures identified submerged barrier heights of -2.1 ± 0.1 kJ mol-1 and -22.4 ± 0.2 kJ mol-1 for the CH2OO + NH3 and CH2OO + CH3NH2 reactions, respectively. The reactions of NH3 and CH3NH2 with CH2OO are not expected to compete with its removal by reaction with (H2O)2 in the troposphere. Similarly, losses of NH3 and CH3NH2 by reaction with Criegee intermediates will be insignificant compared with reactions with OH radicals.

Interactive molecular dynamics in virtual reality from quantum chemistry to drug binding: An open-source multi-person framework.

As molecular scientists have made progress in their ability to engineer nanoscale molecular structure, we face new challenges in our ability to engineer molecular dynamics (MD) and flexibility. Dynamics at the molecular scale differs from the familiar mechanics of everyday objects because it involves a complicated, highly correlated, and three-dimensional many-body dynamical choreography which is often nonintuitive even for highly trained researchers. We recently described how interactive molecular dynamics in virtual reality (iMD-VR) can help to meet this challenge, enabling researchers to manipulate real-time MD simulations of flexible structures in 3D. In this article, we outline various efforts to extend immersive technologies to the molecular sciences, and we introduce "Narupa," a flexible, open-source, multiperson iMD-VR software framework which enables groups of researchers to simultaneously cohabit real-time simulation environments to interactively visualize and manipulate the dynamics of molecular structures with atomic-level precision. We outline several application domains where iMD-VR is facilitating research, communication, and creative approaches within the molecular sciences, including training machines to learn potential energy functions, biomolecular conformational sampling, protein-ligand binding, reaction discovery using "on-the-fly" quantum chemistry, and transport dynamics in materials. We touch on iMD-VR's various cognitive and perceptual affordances and outline how these provide research insight for molecular systems. By synergistically combining human spatial reasoning and design insight with computational automation, technologies such as iMD-VR have the potential to improve our ability to understand, engineer, and communicate microscopic dynamical behavior, offering the potential to usher in a new paradigm for engineering molecules and nano-architectures.

Observation of a new channel, the production of CH3, in the abstraction reaction of OH radicals with acetaldehyde.

Using laser flash photolysis coupled to photo-ionization time-of-flight mass spectrometry (PIMS), methyl radicals (CH3) have been detected as primary products from the reaction of OH radicals with acetaldehyde (ethanal, CH3CHO) with a yield of ∼15% at 1-2 Torr of helium bath gas. Supporting measurements based on laser induced fluorescence studies of OH recycling in the OH/CH3CHO/O2 system are consistent with the PIMS study. Master equation calculations suggest that the origin of the methyl radicals is from prompt dissociation of chemically activated acetyl products and hence is consistent with previous studies which have shown that abstraction, rather than addition/elimination, is the sole route for the OH + acetaldehyde reaction. However, the observation of a significant methyl product yield suggests that energy partitioning in the reaction is different from the typical early barrier mechanism where reaction exothermicity is channeled preferentially into the newly formed bond. The master equation calculations predict atmospheric yields of methyl radicals of ∼9%. The implications of the observations in atmospheric and combustion chemistry are briefly discussed.

Measurements of Rate Coefficients for Reactions of OH with Ethanol and Propan-2-ol at Very Low Temperatures.

The low temperature kinetics of the reactions of OH with ethanol and propan-2-ol have been studied using a pulsed Laval nozzle apparatus coupled with pulsed laser photolysis-laser-induced fluorescence (PLP-LIF) spectroscopy. The rate coefficients for both reactions have been found to increase significantly as the temperature is lowered, by approximately a factor of 18 between 293 and 54 K for ethanol, and by ∼10 between 298 and 88 K for OH + propan-2-ol. The pressure dependence of the rate coefficients provides evidence for two reaction channels: a zero pressure bimolecular abstraction channel leading to products and collisional stabilization of a weakly bound OH-alcohol complex. The presence of the abstraction channel at low temperatures is rationalized by a quantum mechanical tunneling mechanism, most likely through the barrier to hydrogen abstraction from the OH moiety on the alcohol.

Mechanism of the reaction of OH with alkynes in the presence of oxygen.

Previous work has shown that the branching ratio of the reaction of OH/C2H2/O2 to glyoxal and formic acid is dependent on oxygen fraction, and a significant component of the product yield under atmospheric conditions is formed from reaction of chemically activated OH-C2H2 adduct. In this article, isotopic substitution is used to determine the mechanism of the OH/C2H2/O2 reaction resolving previous contradictory observations in the literature. Using laser flash photolysis and probing OH concentrations via laser induced fluorescence, a rate coefficient of kHO-C2H2+O2 = (6.17 ± 0.68) × 10(-12) cm(3) molecule(-1) s(-1) is determined at 298 K from the analysis of biexponential OH decays in the presence of C2H2 and low concentrations of O2. The studies have been extended to propyne and but-2-yne. The reactions of OH with propyne and but-2-yne have been studied as a function of pressure in the absence of oxygen. The reaction of OH with propyne is in the fall off region from 2-25 Torr of nitrogen at room temperature. A pressure independent value of (4.21 ± 0.47) × 10(-12) cm(3) molecule(-1) s(-1) was obtained from averaging the eight independent measurements at 25 and 75 Torr. The reaction of OH with but-2-yne at 298 K is pressure independent (5-25 Torr N2) with a value of (1.87 ± 0.19) × 10(-11) cm(3) molecule(-1) s(-1). Analysis of biexpontial OH decays in alkyne/low O2 conditions gives the following rate coefficients at 298 K: kHO-C3H4+O2 = (8.00 ± 0.82) × 10(-12) cm(3) molecule(-1) s(-1) and kHO-C4H6+O2 = (6.45 ± 0.68) × 10(-12) cm(3) molecule(-1) s(-1). The branching ratio of bicarbonyl to organic acid in the presence of excess oxygen also shows an oxygen fraction dependence for propyne and but-2-yne, qualitatively similar to that for acetylene. For an oxygen fraction of 0.2 at 298 K, pressure independent yields of methylglyoxal (0.70 ± 0.03) and biacetyl (0.74 ± 0.03) were determined for the propyne and but-2-yne systems, respectively. The yield of acid increases with temperature from 212-500 K. Master equation calculations show that, under atmospheric conditions, the acetyl cofragment of organic acid production will dissociate, consistent with experimental observations.

ChemDyME: Kinetically Steered, Automated Mechanism Generation through Combined Molecular Dynamics and Master Equation Calculations.

In many scientific fields, there is an interest in understanding the way in which chemical networks evolve. The chemical networks which researchers focus upon have become increasingly complex, and this has motivated the development of automated methods for exploring chemical reactivity or conformational change in a "black-box" manner, harnessing modern computing resources to automate mechanism discovery. In this work, we present a new approach to automated mechanism generation which couples molecular dynamics and statistical rate theory to automatically find kinetically important reactions and then solve the time evolution of the species in the evolving network. The key to this chemical network mapping through combined dynamics and ME simulation approach is the concept of "kinetic convergence", whereby the search for new reactions is constrained to those species which are kinetically favorable at the conditions of interest. We demonstrate the capability of the new approach for two systems, a well-studied combustion system and a multiple oxygen addition system relevant to atmospheric aerosol formation.

Observation of a large negative temperature dependence for rate coefficients of reactions of OH with oxygenated volatile organic compounds studied at 86-112 K.

The rate coefficients (k) for reactions of OH with acetone, methyl ethyl ketone (MEK) and dimethyl ether (DME) have been measured in the temperature range 86-112 K using a pulsed Laval nozzle apparatus. Large increases in k at lower temperatures were observed, with k(86K)/k(295K) = 334 for acetone, and k(93K)/k(295K) = 72 and 3, for MEK and DME respectively. A mechanism involving the formation of a hydrogen bonded complex prior to an overall barrier on the potential energy surface is proposed to explain this behaviour.

Adaptively Accelerating Reactive Molecular Dynamics Using Boxed Molecular Dynamics in Energy Space.

The problem of observing rare events is pervasive among the molecular dynamics community and an array of different types of methods are commonly used to accelerate these long time scale processes. Typically, rare event acceleration methods require an a priori specification of the event to be accelerated. In recent work, we have demonstrated the application of boxed molecular dynamics to energy space, as a way to accelerate rare events in the stochastic chemical master equation. Here we build upon this work and apply the boxed molecular dynamics algorithm to the energy space of a molecule in classical trajectory simulations. Through this new BXD in energy (BXDE) approach we demonstrate that generic rare events (in this case chemical reactions) may be accelerated by multiple orders of magnitude compared to unbiased simulations. Furthermore, we show that the ratios of products formed from the BXDE simulations are similar to those formed in unbiased simulations at the same temperature.

Accelerated chemistry in the reaction between the hydroxyl radical and methanol at interstellar temperatures facilitated by tunnelling.

Understanding the abundances of molecules in dense interstellar clouds requires knowledge of the rates of gas-phase reactions between uncharged species. However, because of the low temperatures within these clouds, reactions with an activation barrier were considered too slow to play an important role. Here we show that, despite the presence of a barrier, the rate coefficient for the reaction between the hydroxyl radical (OH) and methanol--one of the most abundant organic molecules in space--is almost two orders of magnitude larger at 63 K than previously measured at ∼200 K. We also observe the formation of the methoxy radical product, which was recently detected in space. These results are interpreted by the formation of a hydrogen-bonded complex that is sufficiently long-lived to undergo quantum-mechanical tunnelling to form products. We postulate that this tunnelling mechanism for the oxidation of organic molecules by OH is widespread in low-temperature interstellar environments.