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1. Modelling the insertion of O(1D) into methane on the surface of interstellar ice mantles

   https://doi.org/10.1093/mnras/stab2619  

   Carder, Joshua T; Ochs, Wyatt; Herbst, Eric (October 2021, Monthly Notices of the Royal Astronomical Society)

   ABSTRACT The detection of many complex organic molecules (COMs) in interstellar space has sparked the study of their origins. While the formation of COMs detected in hot cores is attributed to photochemistry on warming grain surfaces followed by recombination of radicals and desorption, the formation routes in colder regions are still a debated issue with a number of theories such as cosmic ray bombardment on interstellar ice mantles or non-diffusive surface chemistry. Here, we present another method with reactions involving metastable atomic oxygen in the O(1D) state, which is initially produced by photodissociation of oxygen-containing species in interstellar ices. As a first example, we study the reactions of metastable oxygen atoms and methane in ices to form both formaldehyde and methanol. The reaction is studied incorporating two different surface processes: diffusive and non-diffusive chemistry. The formation of methanol and formaldehyde via metastable oxygen atoms is compared with well-known formation routes of both to understand the O(1D) contributions at different temperatures. 

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2. Water dissociation and association on mirror twin boundaries in two-dimensional MoSe ₂ : insights from density functional theory calculations

   https://doi.org/10.1039/d1na00429h  

   Joseph, T.; Ghorbani-Asl, M.; Batzill, M.; Krasheninnikov, Arkady V. (December 2021, Nanoscale Advances)

   The adsorption and dissociation of water molecules on two-dimensional transition metal dichalcogenides (TMDs) is expected to be dominated by point defects, such as vacancies, and edges. At the same time, the role of grain boundaries, and particularly, mirror twinboundaries (MTBs), whose concentration in TMDs can be quite high, is not fully understood. Using density functional theory calculations, we investigate the interaction of water, hydroxyl groups, as well as oxygen and hydrogen molecules with MoSe 2 monolayers when MTBs of various types are present. We show that the adsorption of all species on MTBs is energetically favorable as compared to that on the basal plane of pristine MoSe 2 , but the interaction with Se vacancies is stronger. We further assess the energetics of various surface chemical reactions involving oxygen and hydrogen atoms. Our results indicate that water dissociation on the basal plane should be dominated by vacancies even when MTBs are present, but they facilitate water clustering through hydroxyl groups at MTBs, which can anchor water molecules and give rise to the decoration of MTBs with water clusters. Also, the presence of MTBs affects oxygen reduction reaction (ORR) on the MoSe 2 monolayer. Unlike Se vacancies which inhibit ORR due to a high overpotential, it is found that the ORR process on MTBs is more efficient, indicating their important role in the catalytic activity of MoSe 2 monolayer and likely other TMDs. 

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3. Pushing the limits of concertedness. A waltz of wandering carbocations

   https://doi.org/10.1039/c8sc03567a  

   Castiñeira Reis, Marta; López, Carlos Silva; Nieto Faza, Olalla; Tantillo, Dean J. (February 2019, Chemical Science)

   Among the array of complex terpene-forming carbocation cyclization/rearrangement reactions, the so-called “triple shift” reactions are among the most unexpected. Such reactions involve the asynchronous combination of three 1, n -shifts into a concerted process, e.g. , a 1,2-alkyl shift followed by a 1,3-hydride shift followed by a second 1,2-alkyl shift. This type of reaction so far has been proposed to occur during the biosynthesis of diterpenes and the sidechains of sterols. Here we describe efforts to push the limits of concertedness in this type of carbocation reaction by designing, and characterizing with quantum chemical computations, systems that could couple additional 1, n -shift events to a triple shift leading, in principle to quadruple, pentuple, etc. shifts. While our designs did not lead to clear-cut examples of quadruple, etc. shifts, they did lead to reactions with surprisingly flat energy surfaces where more than five chemical events connect reactants and plausible products. Ab initio molecular dynamics simulations demonstrate that the formal minima on these surfaces interchange on short timescales, both with each other and with additional unexpected structures, allowing us a glimpse into a very complex manifold that allows ready access to great structural diversity. 

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4. Shear-activation of mechanochemical reactions through molecular deformation

   https://doi.org/10.1038/s41598-024-53254-2  

   Bhuiyan, Fakhrul H.; Li, Yu-Sheng; Kim, Seong H.; Martini, Ashlie (February 2024, Scientific Reports)

   Abstract Mechanical stress can directly activate chemical reactions by reducing the reaction energy barrier. A possible mechanism of such mechanochemical activation is structural deformation of the reactant species. However, the effect of deformation on the reaction energetics is unclear, especially, for shear stress-driven reactions. Here, we investigated shear stress-driven oligomerization reactions of cyclohexene on silica using a combination of reactive molecular dynamics simulations and ball-on-flat tribometer experiments. Both simulations and experiments captured an exponential increase in reaction yield with shear stress. Elemental analysis of ball-on-flat reaction products revealed the presence of oxygen in the polymers, a trend corroborated by the simulations, highlighting the critical role of surface oxygen atoms in oligomerization reactions. Structural analysis of the reacting molecules in simulations indicated the reactants were deformed just before a reaction occurred. Quantitative evidence of shear-induced deformation was established by comparing bond lengths in cyclohexene molecules in equilibrium and prior to reactions. Nudged elastic band calculations showed that the deformation had a small effect on the transition state energy but notably increased the reactant state energy, ultimately leading to a reduction in the energy barrier. Finally, a quantitative relationship was developed between molecular deformation and energy barrier reduction by mechanical stress. 

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5. Minimum reaction network necessary to describe Ar/CF4 plasma etch

   https://doi.org/10.1117/12.2297502  

   Chopra, Meghali J.; Bonnecaze, Roger T.; Helpert, Sofia (March 2018, Proc. SPIE 10589, Advanced Etch Technology for Nanopatterning VII)

   Predicting the etch and deposition profiles created using plasma processes is challenging due to the complexity of plasma discharges and plasma-surface interactions. Volume-averaged global models allow for efficient prediction of important processing parameters and provide a means to quickly determine the effect of a variety of process inputs on the plasma discharge. However, global models are limited based on simplifying assumptions to describe the chemical reaction network. Here a database of 128 reactions is compiled and their corresponding rate constants collected from 24 sources for an Ar/CF4 plasma using the platform RODEo (Recipe Optimization for Deposition and Etching). Six different reaction sets were tested which employed anywhere from 12 to all 128 reactions to evaluate the impact of the reaction database on particle species densities and electron temperature. Because many the reactions used in our database had conflicting rate constants as reported in literature, we also present a method to deal with those uncertainties when constructing the model which includes weighting each reaction rate and filtering outliers. By analyzing the link between a reaction’s rate constant and its impact on the predicted plasma densities and electron temperatures, we determine the conditions at which a reaction is deemed necessary to the plasma model. The results of this study provide a foundation for determining which minimal set of reactions must be included in the reaction set of the plasma model. 

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