Help & Documentation

Getting Started
  1. Insert your molecule: Paste SMILES/InChI strings or molecular data into the input field
  2. Select analysis options: Choose which analyses to perform
  3. Analyze: Click "Analyze Molecule" to evaluate COF and MOP formation potential
  4. Review results: Examine the comprehensive analysis results
  5. Export data: Download results in various formats
COF Chemistry Background
What are COFs?

Covalent Organic Frameworks (COFs) are crystalline porous materials constructed from organic building blocks linked by covalent bonds. They offer:

  • High surface areas (up to 2000+ m²/g)
  • Tunable pore sizes and shapes
  • Chemical stability
  • Design flexibility
Tripodal Molecules

Tripodal molecules have three-fold symmetry with a central core and three extending arms. They are ideal for COF formation because:

  • Provide structural rigidity
  • Enable predictable topology
  • Allow for systematic design
Analysis Types

Analyzes the 3D structure of your molecule:

  • Tripodal Detection: Identifies three-fold symmetry
  • Arm Angles: Measures angles between molecular arms
  • Planarity: Assesses molecular flatness
  • Flexibility: Evaluates conformational freedom

Identifies COF-forming functional groups:

  • Aldehydes: React with amines to form imines
  • Amines: React with aldehydes and acids
  • Boronic Acids: Form boronate esters
  • Carboxylic Acids: Form amides and esters
  • Phenols: Participate in condensation reactions

Predicts possible COF topologies:

  • STP (SrSi₂): 3D tetrahedral topology
  • DIA (Diamond): 3D diamond-like structure
  • HEX (Hexagonal): 2D hexagonal topology
  • SQL (Square): 2D square lattice

Analyzes synthetic feasibility:

  • Disconnection Sites: Identifies strategic bond breaks
  • Synthetic Routes: Suggests synthesis pathways
  • Building Blocks: Identifies required starting materials
  • Reaction Partners: Suggests suitable comonomers
Topology Types
STP (SrSi₂)

3D tetrahedral topology with mesoporous structure. Typical pore size: 2.5 nm. Suitable for gas storage and separation.

DIA (Diamond)

3D diamond-like topology with interconnected pores. Typical pore size: 3.0 nm. Excellent mechanical properties.

HEX (Hexagonal)

2D hexagonal topology with planar structure. Typical pore size: 2.0 nm. Good for membrane applications.

SQL (Square)

2D square lattice topology. Typical pore size: 1.8 nm. Suitable for selective adsorption.

Input Formats
SMILES (Simplified Molecular Input Line Entry System)

A text-based notation for molecules. Examples:

  • c1ccc(cc1)C(=O)O - Benzoic acid
  • c1nc(nc(n1)N)N - Melamine
  • c1ccc(cc1)N(c2ccccc2)c3ccccc3 - Triphenylamine
InChI (International Chemical Identifier)

A standard identifier for chemical substances. More verbose than SMILES but provides unique identification.

Export Formats
JSON

Complete analysis results in JSON format for further processing.

CSV

Tabular data format for spreadsheet analysis.

CIF (Crystallographic Information File)

Standard format for crystallographic data, including predicted COF structures.

PDB (Protein Data Bank)

3D structure format for visualization in molecular viewers.

Troubleshooting
Common Issues

If you get an "Invalid molecule structure" error:

  • Check your SMILES syntax
  • Ensure all atoms have valid valencies
  • Verify ring closures are properly numbered

Analysis might be slow for large molecules:

  • Complex molecules take longer to analyze
  • Multiple analyses increase processing time
  • Consider disabling unnecessary analyses
Need More Help?

For additional support or questions about COF chemistry:

  • Check the analysis results for specific recommendations
  • Consult the literature for COF synthesis protocols
  • Consider experimental validation of predictions