Gold Nanocluster Transformation Dataset

Dataset Overview

This archive contains structural datasets and transformation pathways for magic-size gold nanoclusters investigated in:

Khajehpasha, Ehsan Rahmatizad, et al.
"The transformation mechanisms among cuboctahedra, Ino's decahedra and icosahedra structures of magic-size gold nanoclusters."
Nanoscale Advances (2026).

Paper link:
https://pubs.rsc.org/en/content/articlelanding/2026/na/d6na00012f

The archive contains atomistic structures and transformation pathways between high-symmetry and low-symmetry motifs of gold nanoclusters with sizes:

  • 55 atoms
  • 147 atoms
  • 309 atoms
  • 561 atoms

All structural files are provided in .extxyz format unless otherwise noted.

Folder Structure

1. barriers/

Contains saddle-point structures corresponding to high-symmetry transformations between gold cluster motifs.

Filename Format

<number_of_atoms>_<initial_structure>_<final_structure>_barrier.extxyz

Example

055_OH_IH_barrier.extxyz

This file corresponds to:

  • 55-atom gold cluster
  • Cuboctahedron (OH) → Icosahedron (IH)

Structure Labels

| Label | Structure | |---|---| | OH | Cuboctahedron | | DH | Ino's Decahedron | | IH | Icosahedron |

Available Sizes

  • 55
  • 147
  • 309
  • 561

2. Ionized_NEB/

Contains NEB transformation pathways for 55-atom gold clusters under different ionization states.

Filename Format

<number_of_atoms>_<initial_structure>_<final_structure>_<ionization>.extxyz

Example

055_DH_IH_M01.extxyz

This file corresponds to:

  • 55-atom gold cluster
  • Ino's Decahedron → Icosahedron
  • One extra electron added

Ionization Labels

| Label | Description | |---|---| | M02 | Two electrons added | | M01 | One electron added | | N00 | Neutral | | P01 | One electron removed | | P02 | Two electrons removed |

3. LowMinima/

Contains the 10 lowest-energy structures for each cluster size:

  • 55
  • 147
  • 309
  • 561

Structures are sorted in increasing energy order.

Contents

For each minimum:

  • CONTCAR : optimized geometry
  • INCAR : VASP input parameters used for DFT geometry optimization

4. NEB/

Contains nudged elastic band (NEB) transformation pathways between high-symmetry structures of magic-size gold clusters.

Transformations include pathways from:

  • Cuboctahedron → Icosahedron
  • Ino's Decahedron → Icosahedron

Filename Format

<number_of_atoms>_<initial_structure>_<final_structure>_NEB.extxyz

Example

055_DH_IH_NEB.extxyz

This file corresponds to:

  • 55-atom gold cluster
  • Ino's Decahedron → Icosahedron
  • Transformation pathway computed using NEB

5. pathway/

Contains low-barrier asymmetric transformation pathways of magic-size gold clusters explored using:

  • NequIP machine-learning potentials
  • COMPASS pathway exploration code

Filename Format

<number_of_atoms>_<initial_structure>_<final_structure>_pathway.extxyz

Example

055_DH_IH_pathway.extxyz

This file corresponds to:

  • 55-atom gold cluster
  • Ino's Decahedron → Icosahedron
  • Low-barrier asymmetric transformation pathway calculated using COMPASS

Notes

  • All clusters are composed of gold atoms (Au).
  • Structures and pathways are intended for atomistic simulation, transformation analysis, and machine-learning studies.
  • The .extxyz files can be visualized using software such as:
    • ASE
    • OVITO
    • VMD

Citation

If you use this dataset, please cite:

Khajehpasha, Ehsan Rahmatizad, et al.
"The transformation mechanisms among cuboctahedra, Ino's decahedra and icosahedra structures of magic-size gold nanoclusters."
Nanoscale Advances (2026).