Solving the OH + Glyoxal Problem: A Complete Theoretical Description of Post-Transition-State Energy Deposition in Activated Systems.

Activated chemistry in coupled reaction systems has broadened our understanding of the chemical kinetics. In the case of intermediates formed in gas phase abstraction reactions (e.g., OH + HC(O)C(O)H (glyoxal) →HC(O)CO + H2O), it is particularly crucial to understand how the reaction energy is partitioned between product species as this determines the propensity for a given product to undergo "prompt" dissociation (e.g., HC(O)CO → HCO + CO) before the excess reaction energy is removed. An example of such an activated system is the OH + glyoxal + O2 coupled reaction system. In this work, we develop a molecular dynamics pipeline, which, combined with a master equation analysis, accurately models previous experimental measurements. This new work resolves previous complexities and discrepancies from earlier master equation modeling for this reaction system. The detailed molecular dynamics approach employed here is a powerful new tool for modeling challenging activated reaction systems.

Temperature-Dependent, Site-Specific Rate Coefficients for the Reaction of OH (OD) with Methyl Formate Isotopologues via Experimental and Theoretical Studies.

Methyl esters are an important component of combustion and atmospheric systems. Reaction with the OH radical plays an important role in the removal of the simplest methyl ester, methyl formate (MF, CH3OCHO). In this paper, the overall rate coefficients for the reactions of OH and OD with MF isotopologues, studied under pseudo-first-order conditions, are reported using two different laser flash photolysis systems with the decay of OH monitored by laser-induced fluorescence. The room-temperature rate coefficient for OH + MF, (1.95 ± 0.34) × 10-13 cm3 molecule-1 s-1, is in good agreement with the literature. The rate coefficient exhibits curved Arrhenius behavior, and our results bridge the gap between previous low-temperature and shock tube studies. In combination with the literature, the rate coefficient for the reaction of OH with MF between 230 and 1400 K can be parametrized as kOH+MF = (3.2 × 10-13) × (T/300 K)2.3 × exp(-141.4 K/T) cm3 molecule-1 s-1 with an overall estimated uncertainty of ∼30%. The reactions of OD with MF isotopologues show a small enhancement (inverse secondary isotope effect) compared to the respective OH reactions. The reaction of OH/OD with MF shows a normal primary isotope effect, a decrease in the rate coefficient when MF is partially or fully deuterated. Experimental studies have been supported by ab initio calculations at the CCSD(T)-F12/aug-cc-pVTZ//M06-2X/6-31+G** level of theory. The calculated, zero-point-corrected, barrier heights for abstraction at the methyl and formate sites are 1.3 and 6.0 kJ mol-1, respectively, and the ab initio predictions of kinetic isotope effects are in agreement with experiment. Fitting the experimental isotopologue data refines these barriers to 0.9 ± 0.6 and 4.1 ± 0.9 kJ mol-1. The branching ratio is approximately 50:50 at 300 K. Between 300 and 500 K, abstraction via the higher-energy, higher-entropy formate transition state becomes more favored (60:40). However, experiment and calculations suggest that as the temperature increases further, with higher energy, less constrained conformers of the methyl transition state become more significant. The implications of the experimental and theoretical results for the mechanisms of MF atmospheric oxidation and low-temperature combustion are discussed.

Knowing What We Don't Know: A Survey of School Nurse Information Needs.

Providing complex care for students requires an informed school nurse workforce. However, school nurses, many of whom work independently, may not know where to find necessary information. This study seeks to understand the information needs of school nurses by conducting a needs assessment survey within the state of Illinois. A survey was disseminated through three statewide professional listservs to determine the types of care-related questions school nurses ask as part of their regular duties and which resources they use to answer those questions. School nurses' information needs vary widely, and they rely on numerous sources to answer clinical questions. They are responsible for the well-being of hundreds to thousands of children. While they are comfortable searching for information, they are motivated to further develop research skills.

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.

A Model for Developing Evidence-Based Clinical Practice Guidelines for School Nursing.

School nurses need evidence-based clinical practice guidelines (CPGs) to provide quality care for students with special health-care needs. However, a gap analysis revealed a paucity of rigorous school nursing CPGs. To fill this gap, a Model for Developing Evidence-based Clinical Practice Guidelines for School Nursing (School Nursing CPG Model) was designed under the auspices of the National Association of School Nurses to offer school nurse scholars, school health leaders, and pediatric clinical experts a standardized structure and systematic process to create rigorous evidence-based CPGs. The aim is to employ the School Nursing CPG Model to build a repository of CPGs that are projected to improve the quality of school nursing practice, thereby improving health and educational outcomes for students with special health-care needs. The School Nursing CPG Model is anticipated to apply to CPG development for other nursing specialties.

Validation of a Model for Developing Evidence-Based Clinical Practice Guidelines for School Nursing.

The paucity of scientifically rigorous school nursing clinical practice guidelines (CPGs) presents barriers to evidence-based care of students with special health-care needs. A Model for Developing Evidence-Based Clinical Practice Guidelines for School Nursing (School Nursing CPG Model) was developed under the auspices of the National Association of School Nurses (NASN) to address this need. To test and validate this School Nursing CPG Model, a trial CPG development project was conducted to (1) identify structure and process gaps and areas for improvement within the School Nursing CPG Model and (2) develop an evidence-based CPG for school nursing practice that addresses a priority student health condition: seizures and epilepsy. The School Nursing CPG Model was validated through a trial CPG project which followed the systematic, standardized process of the School Nursing CPG Model while responsively implementing quality improvement measures through the Plan-Do-Study-Act cycle. Both specific aims were accomplished.

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.

Spin-Forbidden Channels in Reactions of Unsaturated Hydrocarbons with O(3P).

The electronic structure of four prototypical Cvetanovic diradicals, species derived by addition of O(3P) to unsaturated compounds, is investigated by high-level electronic structure calculations and kinetics modeling. The main focus of this study is on the electronic factors controlling the rate of intersystem crossing (ISC): minimal energy crossing points (MECPs) and spin-orbit couplings (SOCs). The calculations illuminate significant differences in the electronic structure of ethene- and ethyne-derived compounds and explain the effect of methylation. The computed MECP heights and SOCs reveal different mechanisms of ISC in ethene- and ethyne-derived species, thus explaining variations in the observed branching ratios between singlet and triplet products and a puzzling effect of methyl substitution. In the ethene- and propene-derived species, the MECP is very low and the rate is controlled by variations of SOC, whereas in the ethyne- and propyne-derived species the MECP is high and the changes in the ISC rate due to methyl substitutions are driven by the variations of MECP heights.

Temperature and Pressure Dependent Kinetics of QOOH Decomposition and Reaction with O2: Experimental and Theoretical Investigations of QOOH Radicals Derived from Cl + (CH3)3COOH.

QOOH radicals are key species in autoignition, produced by internal isomerizations of RO2 radicals, and are central to chain branching reactions in low-temperature combustion. The kinetics of QOOH radical decomposition and reaction with O2 have been determined as a function of temperature and pressure, using observations of OH radical production and decay following H-atom abstraction from t-butyl hydroperoxide ((CH3)3COOH) by Cl atoms to produce QOOH (CH2(CH3)2COOH) radicals. The kinetics of QOOH decomposition have been investigated as a function of temperature (251-298 K) and pressure (10-350 Torr) in helium and nitrogen bath gases, and those of the reaction between QOOH and O2 have been investigated as a function of temperature (251-304 K) and pressure (10-100 Torr) in He and N2. Decomposition of the QOOH radical was observed to display temperature and pressure dependence, with a barrier height for the decomposition of (44.7 ± 4.0) kJ mol-1 determined by master equation fitting to the experimental data. The rate coefficient for the reaction between QOOH and O2 was determined to be (5.6 ± 1.7) × 10-13 cm3 s-1 at 298 K, with no significant dependence on pressure, and can be described by the Arrhenius parameters A = (7.3 ± 6.8) × 10-14 cm3 s-1 and Ea = -(5.4 ± 2.1) kJ mol-1 in the temperature range of 251-304 K. This work represents the first measurements of any QOOH radical kinetics as a function of temperature and pressure.

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.

Reaction kinetics of OH + HNO3 under conditions relevant to the upper troposphere/lower stratosphere.

The OH initiated oxidation of HNO3 in the UT/LS plays an important role in controlling the O3 budget, removing HOx radicals whilst driving NOx/y partitioning chemistry by yielding NO3 radicals: OH + HNO3 → H2O + NO3. In this paper, k1(T, P) was measured using OH (A ← X) Laser Induced Fluorescence (LIF) and the data was modelled over the 223-298 K temperature and 25-750 Torr pressure ranges, using the modified Lindemann-Hinshelwood expression , where k0 = 5.2 × 10-14 exp(200/T) cm3 s-1, k2 = 8.4 × 10-17 exp(1900/T) cm3 s-1 and k3 = 1.6 × 10-34 exp(1745/T) cm3 s-1. A significant source of experimental uncertainty derives from accurate determination of HNO3 concentration, which is impacted by heterogeneous uptake of the low volatility HNO3 onto cold surfaces of the reactors. Our results represent the determination of k1(T, P) using two different in situ [HNO3] measurements: VUV absorption and a new two photon Photolysis Induced Fluoresence (PIF). Experimental results are discussed along with a computational master equation calculation (MESMER), which highlight the need for further theoretical study into the OH + HNO3 mechanism and potential energy surface. The atmospheric impact of these new rate constants were modelled using the STOCHEM-CRI chemistry transport global model, which have shown a small reduction in global budgets of key atmospheric species, with more significant changes in the NOx/HNO3 ratio, peaking in the tropical upper troposphere regions.

A Simple "Boxed Molecular Kinetics" Approach To Accelerate Rare Events in the Stochastic Kinetic Master Equation.

The chemical master equation is a powerful theoretical tool for analyzing the kinetics of complex multiwell potential energy surfaces in a wide range of different domains of chemical kinetics spanning combustion, atmospheric chemistry, gas-surface chemistry, solution phase chemistry, and biochemistry. There are two well-established methodologies for solving the chemical master equation: a stochastic "kinetic Monte Carlo" approach and a matrix-based approach. In principle, the results yielded by both approaches are identical; the decision of which approach is better suited to a particular study depends on the details of the specific system under investigation. In this Article, we present a rigorous method for accelerating stochastic approaches by several orders of magnitude, along with a method for unbiasing the accelerated results to recover the "true" value. The approach we take in this paper is inspired by the so-called "boxed molecular dynamics" (BXD) method, which has previously only been applied to accelerate rare events in molecular dynamics simulations. Here we extend BXD to design a simple algorithmic strategy for accelerating rare events in stochastic kinetic simulations. Tests on a number of systems show that the results obtained using the BXD rare event strategy are in good agreement with unbiased results. To carry out these tests, we have implemented a kinetic Monte Carlo approach in MESMER, which is a cross-platform, open-source, and freely available master equation solver.

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.