Yong-Bin Zhuang^1*, Alfredo Pasquarello^1*

1 Chaire de Simulation à l’Echelle Atomique (CSEA), Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland

* Corresponding authors emails: yongbin.zhuang@epfl.ch, alfredo.pasquarello@epfl.ch

DOI10.24435/materialscloud:wq-w4 [version v2]

Publication date: Jun 01, 2025

How to cite this record

Yong-Bin Zhuang, Alfredo Pasquarello, Data and analyses for first proton-coupled electron transfer of water oxidation at the BiVO₄-water interface, Materials Cloud Archive 2025.90 (2025), https://doi.org/10.24435/materialscloud:wq-w4

Description

This entry provides original trajectories of on-the-fly probability enhanced sampling (OPES) and of molecular dynamics simulations and images of nudged-elastic band (NEB) calculation. Jupyter notebooks are provided for a NEB profile, NEB collective variables, free energy surface of the OPES simulations, hole transfer of the OPES simulations, proton transfer mechanisms of of the OPES simulations, water density profiles of MD simulations, radial distribution functions of MD simulations, reweight of Bi-O bonds of OPES simulations, coordination numbers of surface Bi atoms and hydrogen-bond analysis of proton transfer.

Materials Cloud sections using this data

Files

File name	Size	Description
00.raw_data.00.NEB_traj.tgz MD5md5:46e613715f643a1848833fda279c1825	220.6 MiB	NEB inputs and trajectory
00.raw_data.02.CLL.tgz MD5md5:ac90036d2dfe47077a0e595ac3d7c6b4	20.9 KiB	Active learning inputs for ai2-kit
00.raw_data.04.potentials.tgz MD5md5:5ef5a3ffc21cbe8b7f10cbc0cf8ff073	1.8 GiB	Machine learning potentials, training data sets, testing data sets, and testing results
00.raw_data.05.opes.tgz MD5md5:8834db6ce86dc3e62a2a483fd7d41a78	23.7 GiB	OPES inputs, trajectory, and spin cubes for important structures.
00.raw_data.06.1ns-MD.tgz MD5md5:518c1488e91590b13746164a845818b0	315.2 MiB	Trajectories of normal MD
01.NEB.tgz MD5md5:b3d8645c2489568a6f0646ba4e270f0d	354.9 KiB	NEB profiles and NEB collective variables (Jupyter Notebook Figure S4 and S5).
02.potential_test.tgz MD5md5:3a6c0a78b528d46e0d40dbe3f987676c	3.5 MiB	Fitting errors of machine learning potentials on training sets (Jupyter Notebook).
03.cutoff_test.tgz MD5md5:d8f41a1d35338b23a467b10d355e15a1	11.9 KiB	Results of cutoff test for CP2K.
04.opes.tgz MD5md5:ec8ea0d853a4fcbf26df113d48967902	21.2 MiB	Free-energy surfaces and convergence of OPES simulations (Jupyter Notebook Figure 2a,b, S6, and S7).
05.hole_transfer.tgz MD5md5:c3d5e001b49b2a8f96469b2c66388805	3.1 MiB	Selecting important structures according to weights, determining order of hole transfer, and free-energy profiles (Jupyter Notebook Figure 2c,d, and 3).
06.PT.tgz MD5md5:fcbb972087d3dd3aaed10f3e56f8afa6	108.7 MiB	Free-energy surfaces of direct and indirect proton transfer (Jupyter Notebook Figure 4).
07.NormalMD.tgz MD5md5:d304e64daa958b4e16274aee46f40724	256.8 KiB	Water density profiles and radial distribution functions of bulk water (Jupyter Notebook Figure S3).
08.BiObond.tgz MD5md5:2248d6581c56873e3fbda846d1e1d7e7	20.9 MiB	Reweight of Bi-O bond lengths (Jupyter Notebook Figure S8).
09.CNofBi.tgz MD5md5:234c56412fe30e56c286499f401c7153	1.6 MiB	Coordination numbers of surface Bi atoms (Jupyter Notebook Figure S1 and S2).
10.HB.tgz MD5md5:9972044d638fa5b8155b962d2bcff7e7	31.5 MiB	Hydrogen-bond analysis for proton transfer reactions (Jupyter Notebook Figure S10).
codes_for_reproduce.zip MD5md5:f584e6294c51b10ac87e9a1cdcd43b07	57.2 MiB	The key python packages for running jupyter notebooks.
README.txt MD5md5:fab26bdfaa5908e9daf1a8062cbfb86d	3.0 KiB	file description for all uploaded data

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.

External references

Keywords

BiVO4-water interface proton-couple electron transfer machine learning potentials on-the-fly probability sampling OPES reweighting