Ab initio-based kinetic study of zigzag edge reconstruction: formation and diffusion of residual defects

We have performed Density Functional Theory (DFT) and kinetic calculations to investigate the reconstruction of zigzag graphene edges. Specifically, we focused on the coalescence of reconstructed edge domains (comprising 57 pairs), which leads to the formation of residual topological defects. These defects serve as domain boundaries and we investigate their diffusion behavior to determine the conditions under which complete, defect-free edge reconstruction can be achieved. Using the Nudged Elastic Band (NEB) method [1,2] as implemented in the VASP code [3], we computed the energy barriers for the three final steps of domain coalescence and the diffusion of residual defects. Structure preoptimization was performed using MOPAC2016 [4]. A kinetic model [5], parameterized with the DFT results, was used to describe the time evolution of reconstructed edge domains and residual defects until their annihilation. The provided dataset contains the input and output files for the DFT calculations ("Edge*.tar.gz" and "TS_calc.tar.gz" for transition state energies), alongside output files from the kinetic model simulations conducted at various temperatures ("kinetic_model.tar.gz"). The input parameters for the kinetic model [5] are summarized in the file input_parameters within "kinetic_model.tar.gz". File "PM3_precalculated_structures.zip" contains PM3 preoptimized coordinates of hand-made structures. ZMT files with internal coordinates can be viewed by Hyperchem, GJF files with XYZ coordinates can be viewed by GaussView. References: G. Mills, H. Jónsson, G. K. Schenter, Surface Sci. 324 (1995) 305. H. Jónsson, G. Mills, K. W. Jacobsen, Nudged elastic band method for finding minimum energy paths of transitions, World Scientific, Singapore, 1998, pp. 385–404. G. Kresse, J. Furthmüller, Phys. Rev. B 54 (1996) 11169. J.J.P. Stewart. J. Computer-Aided Mol. Des. 4 (1990) 1–103. I. V. Lebedeva, Zenodo (2026), https://doi.org/10.5281/zenodo.18755409 Acknowledgements: Y.G.P. and A.M.P. acknowledge the support by the Russian Science Foundation grant No. 23-42-10010, https://rscf.ru/en/project/23-42-10010/. A.M.P. acknowledges the support by project FFUU-2024-0003 of the Institute of Spectroscopy of the Russian Academy of Sciences, Russia for the results described in Section 3. S.A.V. and N.A.P. acknowledge support by the Belarusian National Research Program ``Convergence-2030''. IL acknowledges support from the EuroHPC JU under the MAX (Materials design at the Exascale) project (grant no. 101093374), and from the Spanish MCIN/AEI/10.13039/501100011033 and the European Union NextGenerationEU/PRTR through grant no. PCI2022-134972-2. ICN2 is supported by the CERCA programme (Generalitat de Catalunya) and the Severo Ochoa Centres of Excellence programme (grant no. CEX2021-001214-S), funded by MCIN/AEI/10.13039/501100011033.