Published October 25, 2024
| Version v1
Dataset
Open
Direct imaging of carbohydrate stereochemistry structural dataset
Contributors
Researchers:
Supervisors:
-
1.
Aalto University
Description
Dataset includes.
- Training data for the NequIP model (all_4NPxG_mod_E.extxyz) including structures, energies and force components.
- Zip file (4NPxG_training_run.zip) containing training parameters (config.yaml) and metrics (.csv files) and the deployed NequIP model (deployed_model.pth) used for minima hopping in the corresponding study.
- Bayesian Optimization Structure Search results for conformers (alpha/beta-4-Nitrophenyl-D-Galacturonide_opt.extxyz) and isolated adsorbates (alpha/beta_isolated_adsorbates_opt.extxyz) on Au(111). DFT relaxed structures.
- CREST NADG conformers (crest_conformers_alpha.extxyz).
- Initial monolayer structure relaxations (4NPaG/4NPbG_monolayer_relaxation_every_fifth.extxyz). Every fifth geometry from the relaxation.
- Results from NequIP minima hopping for monolayer structures as trajectory files (alpha/beta_minima_hopping_nequip.traj). Contains also protonated NADG structures (alpha_protonated_minima_hopping_nequip.traj).
- Final NADG and NBDG monolayer structures with Hartree potentials and STM images simulated with FHI-aims (Final_NADG/NBDG_hartree_potential.cube, Final_NADG/NBDG_stm_01.cube) with the z-maps (Final_NADG/NBDG_stm_z_map.cube) for creating STM image contrast.
Files
4NPxG_training_run.zip
Files
(381.0 MB)
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Additional details
Related works
- Is supplement to
- Journal article: arXiv:2410.20897 (arXiv)
Funding
- CSC - IT Center for Science (Finland)
- Bayesian optimization for the identification and characterization of lignocellulosic building blocks project 2008059
- Research Council of Finland
- Microscopy and machine learning in molecular characterization of lignocellulosic materials” (MIMIC) grant 347319