A free and open-source tool to generate and analyse metallocage structures

Get Started

About

cgbind is available on github as a Python module. Note that the generated structures are stored in an anonymous and non-searchable database for fast retrieval. If you find cgbind useful in your research please consider citing the paper.

Start Building

To generate a metallocage enter a SMILES string of linker molecule, select the cage architecture and submit! Generate the linker SMILES string in the sketcher window and click Get Smiles, or copy and paste from ChemDraw™ with Edit/Copy As/SMILES. Architectures are depicted here.

Examples

Some example linkers suitable to form cages with different architectures. Click to insert the SMILES string and architecture.

Timeout

Due to limited computational resources the calculation has timed out. The server may be busy or the cage may need > 60 s to build. Consider trying a linker with fewer possible donor atoms and/or less conformational flexibility. Alternatively, use the Python module.

Couldn't build a cage

This could be for a variety of reasons including the linker containing invalid Xmotifs or >200 iterations being required to find a suitable conformer with the correct orientation to build a cage. Particularly flexible linkers may require using the Python module.

Results

If a metallocage geometry can be generated from the linker it will generated here, along with a minimal set of associated properties to describe the size, hydrophobicity and flexibility of the system.
Property
M-M Distance / Å None
Max. enclosed sphere / Å3 None
Max. escape sphere / Å3 None
H bond donors None
Rotatable bonds None

Electrostatic Potential

The electrostatic potential (ESP) is plotted on the van der Walls surface of the structure and is the work required to add a unit positive charge to that point. Blue areas are electron rich and red electron poor. Calculations are performed at the tight-binding DFT level and the ESP constructed from partial atomic charges.

None

Add Substrates

To add a substrate draw the molecule in the sketcher window and click Get Smiles, or copy and paste from ChemDraw™. The accuracy of the method ranges from using a purely repulsive FF to utilising tight-binding DFT partial atomic charges to estimate the electrostatic interaction.

Couldn't build a cage-substrate complex

Results

Cage-substrate complexes are generated here. The likelihood of binding is calculated using a simple force-field derived from ab initio calculations. Further work is ongoing to improve the accuracy.
Property
Size complementarity None
S. rotatable bonds None
S. H bond donors None
Substrate binds None
Confidence None
Written by Tom Young. Copyright © 2019
DOI