Article
Chemistry, Multidisciplinary
Tom A. Young, Joseph J. Silcock, Alistair J. Sterling, Fernanda Duarte
Summary: autodE is an open-source Python package that can calculate reaction energy profiles for organic and organometallic reactions, locating transition states and minima and compatible with multiple electronic structure packages.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Chemistry, Multidisciplinary
Emilio Martinez-Nunez, George L. Barnes, David R. Glowacki, Sabine Kopec, Daniel Pelaez, Aurelio Rodriguez, Roberto Rodriguez-Fernandez, Robin J. Shannon, James J. P. Stewart, Pablo G. Tahoces, Saulo A. Vazquez
Summary: AutoMeKin2021 is an updated program for the automated discovery of reaction mechanisms, featuring new capabilities such as rare-event molecular dynamics simulations and the use of chemical knowledge.
JOURNAL OF COMPUTATIONAL CHEMISTRY
(2021)
Article
Chemistry, Multidisciplinary
Cyrille Lavigne, Gabe Gomes, Robert Pollice, Alan Aspuru-Guzik
Summary: This study demonstrates that complex reaction pathways can be efficiently predicted using chemical activation imposed by geometrical constraints. The method is successfully applied to various realistic chemical reactions and requires minimal human involvement and prior knowledge compared to traditional methods.
Review
Chemistry, Multidisciplinary
Alberto Baiardi, Stephanie A. Grimmel, Miguel Steiner, Paul L. Turtscher, Jan P. Unsleber, Thomas Weymuth, Markus Reiher
Summary: Quantum mechanical methods are crucial for elucidating reaction paths and molecular dynamics. Recent developments cover strategies ranging from heuristic rules based on quantum mechanics, external biases to enforce reactive events, manual steering facilitated by interactive quantum mechanics, to new approaches for transition-state optimization. These explorative approaches are likely to lead to surprising discoveries in computational chemistry by reducing human effort and covering more extensive regions of configuration space.
ACCOUNTS OF CHEMICAL RESEARCH
(2022)
Article
Chemistry, Physical
Eric C. Geistfeld, Erik Torres, Thomas Schwartzentruber
Summary: In this study, a simulation method is proposed to investigate three-body collisions and recombination in mixtures of oxygen and nitrogen. The results show that long-lived atom-diatom collisions are rare and do not play a dominant role in the recombination process. The recombination rate constants are in agreement with the predictions of detailed balance.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Multidisciplinary
Jacqueline R. Santhouse, Jeremy M. G. Leung, Lillian T. Chong, W. Seth Horne
Summary: By studying the folding kinetics and mechanism of the BdpA sequence, researchers found that altering the backbone connectivity can affect protein folding. This suggests that protein mimetic chains have a significant degree of plasticity in transitioning between unfolded and folded states.
Article
Engineering, Chemical
Qilei Liu, Kun Tang, Lei Zhang, Jian Du, Qingwei Meng
Summary: Organic synthesis is important for converting raw materials into valuable chemicals, and computer-assisted synthetic planning plays a vital role in designing synthetic pathways. However, the evaluation of these pathways based on reaction probabilities using deep learning models often fails to consider real reaction behaviors such as reaction kinetics. This article proposes a reaction kinetics-based retrosynthesis planning framework that aims to design synthetic pathways with well-performed reaction kinetics, and introduces a method for generating initial guesses of transition states for reaction kinetic models.
Article
Chemistry, Physical
Robin J. Shannon, Emilio Martinez-Nunez, Dmitrii Shalashilin, David R. Glowacki
Summary: This work introduces a new approach that combines molecular dynamics and statistical rate theory to automatically discover kinetically important reactions and solve the time evolution of species in the evolving network. Mapping chemical networks through combined dynamics and ME simulation, the concept of kinetic convergence constrains the search for new reactions to kinetically favorable species.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2021)
Article
Chemistry, Physical
Victoria P. Barber, William H. Green, Jesse H. Kroll
Summary: Automatic reaction network generation is used as a screening tool for new pathways in atmospheric oxidation chemistry, revealing unconventional reaction pathways that differ from traditional oxidation mechanisms. These findings highlight the potential for further experimental and theoretical study on promising targets in atmospheric chemistry. This approach represents a new and efficient way to explore atmospheric chemical space and discover overlooked reaction steps in atmospheric oxidation.
JOURNAL OF PHYSICAL CHEMISTRY A
(2021)
Article
Multidisciplinary Sciences
Jiangxu Li, Jiaxi Liu, Stanley A. Baronett, Mingfeng Liu, Lei Wang, Ronghan Li, Yun Chen, Dianzhong Li, Qiang Zhu, Xing-Qiu Chen
Summary: Researchers have discovered over 5000 topological phononic (TP) materials through a high-throughput screening and data-driven approach, revealing the mechanisms of their occurrence in various materials, including Weyl and nodal-line types. The discovery of these materials opens up new possibilities for exploring their structure-property relationships and designing devices related to TPs in the future.
NATURE COMMUNICATIONS
(2021)
Article
Chemistry, Physical
Xu Zhang, Hoang Nguyen, Jeffrey T. Paci, Subramanian K. R. S. Sankaranarayanan, Jose L. Mendoza-Cortes, Horacio D. Espinosa
Summary: This investigation introduces a generally applicable framework for parameterizing interatomic potentials to accurately capture large deformation pathways. By utilizing a multi-objective genetic algorithm, training and screening property sets, and correlation and principal component analyses, this framework enables iterative definition of properties in the training and screening sets, aiming to achieve optimal parametrizations for the properties of interest. The study demonstrates good reproducibility of training/screening properties and superior transferability, with the best performance achieved using the Tersoff potential for exploring mechanical and phononic properties of a large library of two-dimensional and bulk materials, specifically focusing on the case study of MoSe2.
NPJ COMPUTATIONAL MATERIALS
(2021)
Article
Chemistry, Physical
Jason Ford, Stefan Seritan, Xiaolei Zhu, Michael N. Sakano, Md Mahbub Islam, Alejandro Strachan, Todd J. Martinez
Summary: In this study, kinetic models were constructed for the decomposition of nitromethane by using accelerated molecular dynamics simulations and the ReaxFF reactive force field. Thermochemical data from density functional theory was combined with ReaxFF minimal energy paths to correct reaction barriers. The models were validated by predicting gas phase CO and NO concentrations as well as high-pressure induction times similar to experimental data, and fundamental decomposition reactions were identified in different thermodynamic regimes.
JOURNAL OF PHYSICAL CHEMISTRY A
(2021)
Article
Chemistry, Physical
Dhiman Ray, Sharon Emily Stone, Ioan Andricioaei
Summary: The Markovian Weighted Ensemble Milestoning (M-WEM) introduces a scheme for efficiently calculating thermodynamic and kinetic properties of biomolecular processes. It has been tested on various models and systems, demonstrating high accuracy and low computational cost, making it a potential tool for computational drug design.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Chemistry, Physical
Patrick E. Schneider, Zhen Tao, Fabijan Pavosevic, Evgeny Epifanovsky, Xintian Feng, Sharon Hammes-Schiffer
Summary: The NEO method is a multicomponent quantum chemistry theory that describes electronic and nuclear quantum effects simultaneously while avoiding the Born-Oppenheimer approximation. By optimizing stationary points, generating minimum energy paths, and calculating thermochemical properties, the NEO method provides a theoretical foundation for a wide range of chemical reactions.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Chemistry, Physical
Eli Pollak, Jianshu Cao
Summary: This paper answers Wigner's challenge from ninety years ago by deriving the h(2) expansion term for the tunneling rate through an asymmetric barrier. It is shown that the expansion derived in this paper should be used for heavy atom tunneling instead of the parabolic barrier approximation. The results of this study provide critical insights into the validity of approximate theories such as classical Wigner theory.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Thermodynamics
Alina Wildenberg, Malte Doentgen, Indu Sekhar Roy, Can Huang, Benoite Lefort, Luis Le Moyne, Alan Keromnes, Kai Leonhard, Karl Alexander Heufer
Summary: This paper describes improvements made to the high-temperature chemistry model of 1,3-dioxolane through new experiments and quantum chemical calculations. The existing model was unable to reproduce the results of the new experiments, necessitating the inclusion of new reaction pathways and ab-initio rate parameters. Additionally, the low-temperature chemistry of linear intermediates was found to be critical even at high temperatures. The presented new mechanism successfully reproduces all experimental results.
PROCEEDINGS OF THE COMBUSTION INSTITUTE
(2023)
Article
Engineering, Chemical
Lorenz Fleitmann, Christoph Gertig, Jan Scheffczyk, Johannes Schilling, Kai Leonhard, Andre Bardow
Summary: This paper integrates computer-aided molecular design of solvents with heat-integrated process design to select and design optimal solvents for maximum process performance. The results of two case studies show that designed solvents improve process performance compared to previous heuristics, highlighting the importance of integrating molecular and process design.
CHEMIE INGENIEUR TECHNIK
(2023)
Article
Chemistry, Physical
Lukas Krep, Felix Schmalz, Florian Solbach, Leonid Komissarov, Thomas Nevolianis, Wassja A. Kopp, Toon Verstraelen, Kai Leonhard
Summary: In our two-paper series, we developed ReaxFF CHOCl parameters using ParAMS parametrization tool and updated the ChemTraYzer scheme to study chlorinated dibenzofurans. Our self-learning method improved the success rate of transition-state searches in ChemTraYzer by 10 percentage points. Using ChemTraYzer, we discovered and quantified over 500 reactions, including new reactions not found in the literature. Three case studies focused on relevant reactions in the dibenzofuran literature.
Article
Chemistry, Physical
Leonid Komissarov, Lukas Krep, Felix Schmalz, Wassja A. Kopp, Kai Leonhard, Toon Verstraelen
Summary: This work presents a new parametrization method for investigating reaction processes of chlorinated organic compounds using ReaxFF formalism. The force field parameters for C, H, O, Cl elements were obtained through an optimization approach involving relaxed potential energy surface scans as training targets. The resulting ReaxFF parametrization exhibits good transferability, as demonstrated on two independent ab initio validation sets. In Part II of this two-paper series, we apply these parameters to simulate the formation and decomposition processes of chlorinated dibenzofuran.
Article
Energy & Fuels
Lorenz Fleitmann, Philipp Ackermann, Johannes Schilling, Johanna Kleinekorte, Jan G. Rittig, Florian vom Lehn, Artur M. Schweidtmann, Heinz Pitsch, Kai Leonhard, Alexander Mitsos, Andre Bardow, Manuel Dahmen
Summary: Co-design of alternative fuels and future SI engines achieves high engine efficiencies. Computer-aided molecular design (CAMD) of renewable fuels has gained attention for tailoring molecular structure to the needs of SI engines. An optimization-based fuel design method targeting SI engine efficiency is proposed, integrating automated prediction of various fuel properties and considering their combined impact.
Article
Computer Science, Interdisciplinary Applications
Artur M. Schweidtmann, Jan G. Rittig, Jana M. Weber, Martin Grohe, Manuel Dahmen, Kai Leonhard, Alexander Mitsos
Summary: Graph neural networks (GNNs) are used in chemical engineering to learn physico-chemical properties based on molecular graphs. The pooling function in GNNs is important for combining atom feature vectors into molecular fingerprints. Unsuitable pooling functions can lead to unphysical GNNs that have poor generalization. This study compares and selects meaningful GNN pooling methods based on physical knowledge about the learned properties, and demonstrates the impact of physical pooling functions on molecular properties.
COMPUTERS & CHEMICAL ENGINEERING
(2023)
Article
Chemistry, Physical
Indu Sekhar Roy, Malte Doentgen, Can Huang, Wassja Kopp, Kai Leonhard
Summary: Biohybrid fuels, such as 1,3-dioxolane produced from inedible biomass, show promise in making transportation more environmentally friendly. However, there is limited data on the kinetics of low-temperature oxidation of 1,3-dioxolane. This study presents the reaction kinetics of O-2 addition to 1,3-dioxolanyl radicals and compares it to similar fuel molecules. The results show that the ring-opening beta-scission reactions dominate the oxidation of 1,3-dioxolanyl radicals.
JOURNAL OF PHYSICAL CHEMISTRY A
(2023)
Article
Chemistry, Physical
Dzmitry H. Zaitsau, Maxim Papusha, Wassja A. Kopp, Kai Leonhard
Summary: This study investigates the decomposition pathways of 1-Ethyl-3-methylimidazolium acetate ([C2Mim][OAc]) through a combination of experiments and computations. The activation energy for the decomposition of [C2Mim][OAc] is found to be around 135 kJ & sdot;mol- 1 in experiments and approximately 142-144 kJ & sdot;mol- 1 in computations. The study reveals that the thermal decomposition of [C2Mim][OAc] is primarily dominated by the SN2 pathway.
JOURNAL OF MOLECULAR LIQUIDS
(2023)
Article
Chemistry, Physical
Wassja A. A. Kopp, Matthias L. L. Moedden, Narasimhan Viswanathan, Gabriel Rath, Kai Leonhard
Summary: This study presents the TAMkinTools extension for improved modeling of one-dimensional hindered rotation, which enables a more standardized workflow. The structures from the Goebench challenge were chosen as test cases, and the probability density analysis of TAMkinTools provides zero-point energies for all conformations, showing a significant effect on the conformational order.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Indu Sekhar Roy, Malte Doentgen, Can Huang, Wassja Kopp, Kai Leonhard
Summary: Biohybrid fuels, including 1,3-dioxolane, offer a promising solution for greener transportation. However, there is limited data on the oxidation kinetics of 1,3-dioxolane. This study presents the reaction kinetics of O2 addition to 1,3-dioxolanyl radicals and compares it to similar fuel molecules. The dominant pathway following the oxidation of 1,3-dioxolanyl radicals is the ring-opening beta-scission reactions of the dioxolane hydroperoxy species.
JOURNAL OF PHYSICAL CHEMISTRY A
(2023)
Article
Chemistry, Physical
Thomas Nevolianis, Raja A. Ahmed, Arnim Hellweg, Michael Diedenhofen, Kai Leonhard
Summary: Accurately predicting partition coefficients is crucial for drug design, but the performance of existing methods is unclear. In this study, the COSMO-RS approach is used to predict the toluene/water partition coefficients for 16 molecules in the SAMPL9 challenge. Both submissions achieve high R2 values, but there are deviations compared to previous challenges.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)
