mof-structure-creation

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

1. 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

2. 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

3. 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

4. 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

1. build_mof5(a=25.9) - Build MOF-5 (IRMOF-1) structure
2. build_cu_btc() - Build Cu-BTC (HKUST-1) MOF
3. build_simple_mof(a=20.0, metal="Zn") - Customizable simple MOF
4. build_irmof_1() - IRMOF-1 with accurate coordinates
5. 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)