| name | mof-structure-creation |
| description | Workflow for building Metal-Organic Framework (MOF) structures (MOF-5, Cu-BTC, IRMOF series, custom). |
| when_to_use | Use when the user asks to construct a MOF or any metal-node + organic-linker porous framework. |
MOF Structure Creation Instructions
Common Workflow
-
Select MOF type
- MOF-5 (IRMOF-1): Zn4O(BDC)3, highly porous (~2900 m²/g)
- Cu-BTC (HKUST-1): Cu3(BTC)2, Cu paddlewheel nodes
- IRMOF series: Isoreticular MOFs with varying linkers
- Custom MOFs: Define metal nodes and organic linkers
-
Build MOF structure
- Use MOF builder tools with predefined templates
- Specify lattice parameter (MOF-5: a=25.9 Å)
- For custom MOFs: define metal, linker, and connectivity
-
Validate MOF structure
- Check metal coordination (Zn4O clusters, Cu paddlewheels)
- Verify pore sizes match expected values
- Check linker geometry and connectivity
- Ensure no overlapping atoms
-
Save and document
- Export in .extxyz and .vasp formats
- Document MOF type, lattice parameter, atom count
- Record surface area and pore size if available
Key Considerations
Common MOF Parameters
| MOF Type | Formula | Space Group | Lattice (Å) | Pore Size | Surface Area |
|---|
| MOF-5 | Zn4O(BDC)3 | Fm-3m (225) | 25.9 | ~12 Å | ~2900 m²/g |
| Cu-BTC | Cu3(BTC)2 | Fm-3m | 26.34 | ~9 Å | ~1500 m²/g |
| IRMOF-1 | Zn4O(BDC)3 | Fm-3m | 25.9 | ~12 Å | ~2900 m²/g |
MOF Building Blocks
- Metal nodes: Zn4O clusters, Cu paddlewheels, Zr6 clusters
- Linkers: BDC (benzenedicarboxylate), BTC (benzenetricarboxylate)
- Connectivity: 3-connected, 4-connected, 6-connected nodes
Structure Validation
- Metal-metal distances: Check cluster geometry
- Metal-linker bonds: Typically 1.9-2.2 Å for Zn-O, 1.9-2.0 Å for Cu-O
- Linker bond lengths: C-C aromatic ~1.40 Å, C-O ~1.27 Å
- Pore accessibility: Ensure channels are not blocked
Common Pitfalls and Fixes
| Pitfall | Symptom | Fix |
|---|
| Missing metal nodes | Wrong stoichiometry | Use proper builder function with correct cluster type |
| Incorrect lattice | Wrong pore size | Verify lattice parameter against literature |
| Linker disorder | Multiple orientations | Check symmetry and use ordered positions |
| Under-coordinated metals | Dangling bonds | Verify metal coordination environment |
Additional Tips
Available MOF Builder Functions
- build_mof5(a=25.9) - Build MOF-5 (IRMOF-1) structure
- build_cu_btc() - Build Cu-BTC (HKUST-1) MOF
- build_simple_mof(a=20.0, metal="Zn") - Customizable simple MOF
- build_irmof_1() - IRMOF-1 with accurate coordinates
- list_mof_types() - List all available MOF types
Usage Example
python3 toolbox/structure_modelling/mof_builder.py build_mof5
python3 toolbox/structure_modelling/mof_builder.py build_cu_btc
File Formats
- Output: .extxyz (preserves all structural info) and .vasp (for VASP)
- MOF-5 example: 99 atoms, a=25.9 Å
- Cu-BTC example: 22 atoms (unit cell), a=26.34 Å
Post-Processing Notes
- MOF structures from builder are ideal/uncollapsed
- For simulations, consider geometry optimization (DFT/force field)
- Check for framework flexibility in molecular simulations
- Porosity calculations may require specialized tools (ZeO++, PoreBlazer)
