Correlating 3D atomic defects and electronic properties

of 2D transition metal dichalcogenides

[The experimental data, image reconstruction and data analysis source codes for: X. Tian, D. S Kim, S. Yang, C. J Ciccarino, Y. Gong, Yo. Yang, Ya. Yang, B. Duschatko, Y. Yuan, P. M Ajayan, J. C Idrobo, P. Narang, J. Miao, “Correlating 3D atomic defects and electronic properties of 2D transition metal dichalcogenides”, Nature Materials doi:10.1038/s41563-020-0636-5 (2020)]

Posted on March, 9,2020

The exceptional electronic, optical and chemical properties of two-dimensional materials strongly depend on the 3D atomic structure and crystal defects. Using Re-doped MoS2 as a model, here we develop scanning atomic electron tomography (sAET) to determine the 3D atomic positions and crystal defects such as dopants, vacancies and ripples with a precision down to 4 picometers. We measure the 3D bond distortion and local strain tensor induced by single dopants for the first time. By directly providing experimental 3D atomic coordinates to density functional theory (DFT), we obtain more truthful electronic band structures than those derived from conventional DFT calculations relying on relaxed 3D atomic models, which is confirmed by photoluminescence measurements. We anticipate that sAET is not only generally applicable to the determination of the 3D atomic coordinates of 2D materials, heterostructures and thin films, but also could transform ab initio calculations by using experimental 3D atomic coordinates as direct input to better predict and discover new physical, chemical and electronic properties.

To facilitate those who are interested in our work, we make the data, image reconstruction and data analysis source codes in Matlab freely available below.

1) Download the raw experimental projections for the datasets: 1 and 2 .

2) Download the denoised and deblurred experimental projections: 1 and 2 , as well as the refined tilt angles: 1 and 2 . We applied the Block-Matching and 3D filtering (BM3D) algorithm to denoised the two datasets, and the Lucy-Richardson deconvolution to remove the vibration blurry in the images. See our paper for details.

3) Download the 3D reconstructions from the two datasets: 1 and 2 . We used the GENeralized Fourier Iterative Reconstruction (GENFIRE) algorithm for our reconstruction, with scanning AET ( sAET) approach.

4) Download the source code to trace atomic positions from the 3D reconstruction.

5) Download the source code to identify the S atoms and S vacancies with atom flipping method. The Re and Mo atoms are directly identified from the images.

6) Download the source code to refine the atomic models.

7) The final 3D atomic models after refinement procedures are deposited in the Materials Data Bank(MDB). Here are the MDB IDs linked to the atomic models of each dataset: SMoX00001 and SMoX00002 .

If you use any of the above data and source codes in your publications and/or presentations, we request you cite our paper: X. Tian, D. S Kim, S. Yang, C. J Ciccarino, Y. Gong, Yo. Yang, Ya. Yang, B. Duschatko, Y. Yuan, P. M Ajayan, J. C Idrobo, P. Narang, J. Miao, “Correlating 3D atomic defects and electronic properties of 2D transition metal dichalcogenides”, Nature Materials doi:10.1038/s41563-020-0636-5 (2020).

This document was prepared by X. Tian, D. S Kim & J. Miao in the Department of Physics & Astronomy and California NanoSystems Institute, University of California, Los Angeles, California, 90095, USA. Email: miao@physics.ucla.edu.