Input SMILES

Warning

This section is crucial for understanding how to get the input for any program that uses epic-mace, be it a python library, a CLI tool, or a GUI program.

SMILES specifications

The main problem that the epic-mace package solves is a stereomer search and generation of 3D atomic coordinates for mononuclear octahedral and square-planar metal complexes. Thus, any program that uses the mace package must receive the structure of the complex or the corresponding ligands as input. mace uses the SMILES notation to describe structure of input molecules, or rather two versions: RDKit SMILES extension and ChemAxon SMILES. The reason is that these are fairly popular SMILES formats that support dative bonds used in mace to describe metal-ligand bonds.

SMILES requirements

SMILES of complex or ligands must satisfy the following conditions:

  1. Donor atoms have non-zero atom map numbers describing their spatial arrangement around a central atom:

../_images/geoms_scheme.png

If one aims to generate all stereomers and is not interested in specifying the stereochemistry of the complex, when any non-zero map number can be used.

  1. Non-DA atoms must have zero map numbers.

  2. Bonds between central (CA) and donor (DA) atoms are dative, directed from DA to CA.

  3. The complex contains one central atom only.

  4. Substituents can be represented by dummy atoms with isotope number corresponding to the number of substituent (or R-groups for ChemAxon SMILES). Other atoms must have zero isotope numbers.

  5. Substituents must be monovalent (may change in the future) and cannot be bound to the central atom.

ChemAxon Marvin

For those who is familiar with the practical side of chemoinformatics, getting SMILES will not be a problem. For others the easiest way is to use the ChemAxon Marvin chemical editor:

  1. To set map numbers, right click on the atom and select the map option.

  2. To add dummy atoms describing substituents, use the R-group option.

  3. To save the structure in SMILES format, select the molecule, right click on it and select Save as. Use ChemAxon SMILES for metal complexes and Daylight SMILES for ligands.

../_images/marvin_get_smiles.png

  1. Now the SMILES string is copied to the clipboard and can be pasted via the Ctrl+V keyboard shortcut.