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.

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.
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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.
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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.

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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