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Using metadynamics to build neural network potentials for reactive events: the case of urea decomposition in water

Manyi Yang1,2*, Luigi Bonati1,3, Daniela Polino1,2, Michele Parrinello1,2

1 Department of Chemistry and Applied Biosciences, ETH Zurich, 8092, Zurich, Switzerland

2 Institute of Computational Sciences, Faculty of Informatics, Università della Svizzera italiana, Via Buffi 13, 6900, Lugano, Switzerland

3 Department of Physics, ETH Zurich, 8092, Zurich, Switzerland

* Corresponding authors emails: ymy0664@163.com
DOI10.24435/materialscloud:4v-0w [version v1]

Publication date: Apr 08, 2021

How to cite this record

Manyi Yang, Luigi Bonati, Daniela Polino, Michele Parrinello, Using metadynamics to build neural network potentials for reactive events: the case of urea decomposition in water, Materials Cloud Archive 2021.55 (2021), doi: 10.24435/materialscloud:4v-0w.

Description

The study of chemical reactions in aqueous media is very important for its implications in several fields of science, from biology to industrial processes. However, modeling these reactions is difficult when water directly participates in the reaction, since it requires a fully quantum mechanical description of the system. Ab-initio molecular dynamics is the ideal candidate to shed light on these processes. However, its scope is limited by a high computational cost. A popular alternative is to perform molecular dynamics simulations powered by machine learning potentials, trained on an extensive set of quantum mechanical calculations. Doing so reliably for reactive processes is difficult because it requires including very many intermediate and transition state configurations. In this study we used an active learning procedure accelerated by enhanced sampling to harvest such structures and to build a neural-network potential to study the urea decomposition process in water. This allowed us to obtain the free energy profiles of this important reaction in a wide range of temperatures, to discover several novel metastable states, and improve the accuracy of the kinetic rates calculations. Furthermore, we found that the formation of the zwitterionic intermediate has the same probability of occurring via an acidic or a basic pathway, which could be the cause of the insensitivity of reaction rates to the solution pH.

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Files

File name Size Description
Urea_decomposition.tar.gz
MD5md5:5909ef1e44cddff45162593a65481d76
19.8 MiB Input files and the final NN model used in this work
README.txt
MD5md5:57909e5894209b992620b9610f47ed19
316 Bytes README

License

Files and data are licensed under the terms of the following license: Creative Commons Attribution 4.0 International.
Metadata, except for email addresses, are licensed under the Creative Commons Attribution Share-Alike 4.0 International license.

Keywords

Neural network potentials Metadynamics Urea decomposition Free energy surface Kinetic rates MARVEL/DD1 ERC

Version history:

2021.55 (version v1) [This version] Apr 08, 2021 DOI10.24435/materialscloud:4v-0w