Evaluation of the rate constant for the reaction OH+H2CO: Application of modeling and sensitivity analysis techniques for determination of the product branching ratio

Gas-Phase vs. Grain-Surface Formation of Interstellar Complex Organic Molecules: A Comprehensive Quantum-Chemical Study

Several organic chemical compounds (the so-called interstellar complex organic molecules, iCOMs) have been identified in the interstellar medium (ISM). Examples of iCOMs are formamide (HCONH2), acetaldehyde (CH3CHO), methyl formate (CH3OCHO), or formic acid (HCOOH). iCOMs can serve as precursors of other organic molecules of enhanced complexity, and hence they are key species in chemical evolution in the ISM. The formation of iCOMs is still a subject of a vivid debate, in which gas-phase or grain-surface syntheses have been postulated. In this study, we investigate the grain-surface-formation pathways for the four above-mentioned iCOMs by transferring their primary gas-phase synthetic routes onto water ice surfaces. Our objective is twofold: (i) to identify potential grain-surface-reaction mechanisms leading to the formation of these iCOMs, and (ii) to decipher either parallelisms or disparities between the gas-phase and the grain-surface reactions. Results obtained indicate that the presence of the icy surface modifies the energetic features of the reactions compared to the gas-phase scenario, by increasing some of the energy barriers. Therefore, the investigated gas-phase mechanisms seem unlikely to occur on the icy grains, highlighting the distinctiveness between the gas-phase and the grain-surface chemistry.

Photochemical Synthesis of Ammonia and Amino Acids from Nitrous Oxide

Abiotic synthesis of ammonia (NH₃) and amino acids is important for the origin of life and early evolution. Ammonia and organic nitrogen species may be produced from nitrous oxide (N₂O), which is a second abundant nitrogen species in the atmosphere. Here, we report a new photochemical experiment and evaluate whether N₂O can be used as a nitrogen source for prebiotic synthesis in the atmosphere. We conducted a series of experiments by using a gas mixture of N₂O+CO, N₂O+CO₂, or N₂O + H₂ in the presence of liquid water. The results demonstrate that NH₃, methylamine (CH₃NH₂), and some amino acids such as glycine, alanine, and serine can be synthesized through photochemistry from N₂O even without metal catalysts. NH₃ can be produced not only from CO + N₂O, but also from H₂+N₂O. Glycine can be synthesized from CH₃NH₂ and CO₂, which can be produced from N₂O and CO under ultraviolet irradiation. Our work demonstrates, for the first time, that N₂O could be an important nitrogen source and provide a new process for synthesizing ammonia and organic nitrogen species, which has not been previously considered. The contribution of organic synthesis from N₂O should, therefore, be considered when discussing the prebiotic chemistry on primitive Earth.

Neural network potential energy surface for the low temperature ring polymer molecular dynamics of the H2CO + OH reaction

A new potential energy surface (PES) and dynamical study of the reactive process of H₂CO + OH toward the formation of HCO + H₂O and HCOOH + H are presented. In this work, a source of spurious long range interactions in symmetry adapted neural network (NN) schemes is identified, which prevents their direct application for low temperature dynamical studies. For this reason, a partition of the PES into a diabatic matrix plus a NN many-body term has been used, fitted with a novel artificial neural network scheme that prevents spurious asymptotic interactions. Quasi-classical trajectory (QCT) and ring polymer molecular dynamics (RPMD) studies have been carried on this PES to evaluate the rate constant temperature dependence for the different reactive processes, showing good agreement with the available experimental data. Of special interest is the analysis of the previously identified trapping mechanism in the RPMD study, which can be attributed to spurious resonances associated with excitations of the normal modes of the ring polymer.

Photo-oxidation of Acetone to Formic Acid in Synthetic Air and Its Atmospheric Implication

Acetone photo-oxidation in synthetic air under exposure of 311 nm ultraviolet light has been studied, and the photo-oxidation products are identified by means of infrared spectroscopy. Analysis reveals that formic acid is one of the major products, although there have been debates in the past concerning the authenticity of formation of this acid in synthetic air via the photo-oxidation pathway. The quantum yield of formation of this acid is similar to that of other major photoproducts like methanol, formaldehyde, and carbon monoxide. The reaction yield, however, decreases with an increase in total air pressure in the reaction cell, but it is still significant at pressures relevant to tropospheric conditions. A kinetic model has been used to simulate the measured reaction kinetics, and the quantum yields predicted by the model are found to be consistent with the measured yields for different durations of light exposure. The same model has also been used to investigate the effect of atmospheric nitric oxide on the fate of formation of this acid in the troposphere. Although nitric oxide is known to be a quencher of peroxy radicals, the precursors of formaldehyde and formic acid in acetone photo-oxidation, but our model predicts that this oxide plays a positive role in the overall reaction kinetics for production of this acid in the troposphere.

New insights in atmospheric acid-catalyzed gas phase hydrolysis of formaldehyde: a theoretical study

A two-step mechanism of the gas phase hydrolysis of formaldehyde catalyzed by nitric acid.

ReaxFF reactive force field for molecular dynamics simulations of hydrocarbon oxidation

To investigate the initial chemical events associated with high-temperature gas-phase oxidation of hydrocarbons, we have expanded the ReaxFF reactive force field training set to include additional transition states and chemical reactivity of systems relevant to these reactions and optimized the force field parameters against a quantum mechanics (QM)-based training set. To validate the ReaxFF potential obtained after parameter optimization, we performed a range of NVT-MD simulations on various hydrocarbon/O2 systems. From simulations on methane/O2, o-xylene/O2, propene/O2, and benzene/O2 mixtures, we found that ReaxFF obtains the correct reactivity trend (propene > o-xylene > methane > benzene), following the trend in the C-H bond strength in these hydrocarbons. We also tracked in detail the reactions during a complete oxidation of isolated methane, propene, and o-xylene to a CO/CO2/H2O mixture and found that the pathways predicted by ReaxFF are in agreement with chemical intuition and our QM results. We observed that the predominant initiation reaction for oxidation of methane, propene, and o-xylene under fuel lean conditions involved hydrogen abstraction of the methyl hydrogen by molecular oxygen forming hydroperoxyl and hydrocarbon radical species. While under fuel rich conditions with a mixture of these hydrocarbons, we observed different chemistry compared with the oxidation of isolated hydrocarbons including a change in the type of initiation reactions, which involved both decomposition of the hydrocarbon or attack by other radicals in the system. Since ReaxFF is capable of simulating complicated reaction pathways without any preconditioning, we believe that atomistic modeling with ReaxFF provides a useful method for determining the initial events of oxidation of hydrocarbons under extreme conditions and can enhance existing combustion models.

A closed-loop identification protocol for nonlinear dynamical systems

A previous work introduced an optimal identification (OI) technique for reliably extracting model parameters of biochemical reaction systems from tailored laboratory experiments. The notion of optimality enters through seeking an external control in the laboratory producing data that leads to minimum uncertainties in the identified parameter distributions. A number of algorithmic and operational improvements are introduced in this paper to OI, aiming to build a more practical and efficient closed-loop identification protocol/procedure (CLIP) for nonlinear dynamical systems. The improvements in CLIP include (a) inversion cost function modification to preferably search for the upper and lower boundaries of the parameter distributions consistent with the observed data, (b) dynamic search range updating of the unknown parameters to better exploit the information from the prior iterative experiments, (c) replacing the control genetic algorithm by the simplex method to enable better balance between operational cost and inversion quality, and (d) utilizing virtual sensitivity optimization techniques to further reduce the laboratory costs. The workings of CLIP utilizing these new algorithms are illustrated in indentifying a simulated tRNA proofreading model, and the results demonstrate enhanced performance of CLIP in terms of algorithmic reliability and efficiency.

Efficient chemical kinetic modeling through neural network maps

An approach to modeling nonlinear chemical kinetics using neural networks is introduced. It is found that neural networks based on a simple multivariate polynomial architecture are useful in approximating a wide variety of chemical kinetic systems. The accuracy and efficiency of these ridge polynomial networks (RPNs) are demonstrated by modeling the kinetics of H(2) bromination, formaldehyde oxidation, and H(2)+O(2) combustion. RPN kinetic modeling has a broad range of applications, including kinetic parameter inversion, simulation of reactor dynamics, and atmospheric modeling.

On the importance of prereactive complexes in molecule-radical reactions: hydrogen abstraction from aldehydes by OH

In this work, the OH + formaldehyde and OH + acetaldehyde reactions have been characterized using accurate ab initio methods with large basis sets. The results clearly indicate that the reaction occurs by hydrogen abstraction, and that the OH addition channel is unfavorable. Close to zero (for formaldehyde) and negative (for acetaldehyde) activation energy values are obtained, which are in excellent agreement with the experimentally observed values. The reaction rate constants, calculated using the classical transition-state theory as applied to a complex mechanism involving the formation of a prereactive complex, reproduce very well the reported experimental results. Consideration of the prereactive complex is shown to be essential for the determination of the height of the energy barrier and thus for the correct calculation of the tunneling factor.