In chemical kinetics research, kinetic models containing hundreds of species and tens of thousands of elementary reactions are commonly used to understand and predict the behavior of reactive chemical systems. Reaction Mechanism Generator (RMG) is a software suite developed to automatically generate such models by incorporating and extrapolating from a database of known thermochemical and kinetic parameters.Here, we present the recent version 3 release of RMG and highlight improvements since the previously published description of RMG v1.0. One important change is that RMG v3.0 is now Python 3 compatible, which supports the most up-to-date versions of cheminformatics and machine learning packages that RMG depends on. Additionally, RMG can now generate heterogeneous catalysis models, in addition to the previously available gas-and liquid-phase capabilities. For model analysis, new methods for local and global uncertainty analysis have been implemented to supplement first-order sensitivity analysis. The RMG database of thermochemical and kinetic parameters has been significantly expanded to cover more types of chemistry. The present release also includes parallelization for reaction generation and on-the-fly quantum calculations, and a new molecule isomorphism approach to improve computational performance. Overall, RMG v3.0 includes many changes which improve the accuracy of the generated chemical mechanisms and allow for exploration of a wider range of chemical systems.

Advances in deep neural network (DNN) based molecular property prediction have recently led to the development of models of remarkable accuracy and generalization ability, with graph convolution neural networks (GCNNs) reporting state-of-the-art performance for this task. However, some challenges remain and one of the most important that needs to be fully addressed concerns uncertainty quantification. DNN performance is affected by the volume and the quality of the training samples. Therefore, establishing when and to what extent a prediction can be considered reliable is just as important as outputting accurate predictions, especially when out-of-domain molecules are targeted. Recently, several methods to 1 arXiv:1910.03127v1 [cs.LG] 7 Oct 2019 account for uncertainty in DNNs have been proposed, most of which are based on approximate Bayesian inference. Among these, only a few scale to the large datasets required in applications. Evaluating and comparing these methods has recently attracted great interest, but results are generally fragmented and absent for molecular property prediction. In this paper, we aim to quantitatively compare scalable techniques for uncertainty estimation in GCNNs. We introduce a set of quantitative criteria to capture different uncertainty aspects, and then use these criteria to compare MC-Dropout, deep ensembles, and bootstrapping, both theoretically in a unified framework that separates aleatoric/epistemic uncertainty and experimentally on the QM9 dataset. Our experiments quantify the performance of the different uncertainty estimation methods and their impact on uncertainty-related error reduction. Our findings indicate that ensembling and bootstrapping consistently outperform MC-Dropout, with different context-specific pros and cons. Our analysis also leads to a better understanding of the role of aleatoric/epistemic uncertainty and highlights the challenge posed by out-of-domain uncertainty.

Quantitative predictions of reaction properties, such as activation energy, have been limited due to a lack of available training data. Such predictions would be useful for computer-assisted reaction mechanism generation and organic synthesis planning. We develop a template-free deep learning model to predict the activation energy given reactant and product graphs and train the model on a new, diverse data set of gas-phase quantum chemistry reactions. We demonstrate that our model achieves accurate predictions and agrees with an intuitive understanding of chemical reactivity. With the continued generation of quantitative chemical reaction data and the development of methods that leverage such data, we expect many more methods for reactivity prediction to become available in the near future.

Abstract:Femtosecond laser micromachining has emerged in recent years as a new technique for micro/nano structure fabrication because of its applicability to virtually all kinds of materials in an easy one-step process that is scalable. In the past, much research on femtosecond laser micromachining was carried out to understand the complex ablation mechanism, whereas recent works are mostly concerned with the fabrication of surface structures because of their numerous possible applications. The state-of-the-art knowledge on the fabrication of these structures on metals with direct femtosecond laser micromachining is reviewed in this article. The effect of various parameters, such as fluence, number of pulses, laser beam polarization, wavelength, incident angle, scan velocity, number of scans, and environment, on the formation of different structures is discussed in detail wherever possible. Furthermore, a guideline for surface structures optimization is provided. The authors' experimental work on laser-inscribed regular pattern fabrication is presented to give a complete picture of micromachining processes. Finally, possible applications of laser-machined surface structures in different fields are briefly reviewed.

Ketohydroperoxides are important in liquid-phase autoxidation and in gas-phase partial oxidation and pre-ignition chemistry, but because of their low concentration, instability, and various analytical chemistry limitations, it has been challenging to experimentally determine their reactivity, and only a few pathways are known. In the present work, 75 elementary-step unimolecular reactions of the simplest γ-ketohydroperoxide, 3-hydroperoxypropanal, were discovered by a combination of density functional theory with several automated transition-state search algorithms: the Berny algorithm coupled with the freezing string method, single- and double-ended growing string methods, the heuristic KinBot algorithm, and the single-component artificial force induced reaction method (SC-AFIR). The present joint approach significantly outperforms previous manual and automated transition-state searches - 68 of the reactions of γ-ketohydroperoxide discovered here were previously unknown and completely unexpected. All of the methods found the lowest-energy transition state, which corresponds to the first step of the Korcek mechanism, but each algorithm except for SC-AFIR detected several reactions not found by any of the other methods. We show that the low-barrier chemical reactions involve promising new chemistry that may be relevant in atmospheric and combustion systems. Our study highlights the complexity of chemical space exploration and the advantage of combined application of several approaches. Overall, the present work demonstrates both the power and the weaknesses of existing fully automated approaches for reaction discovery which suggest possible directions for further method development and assessment in order to enable reliable discovery of all important reactions of any specified reactant(s).