Hello,
Nowadays, I am trying to filter MOF crystals according to their linkers. To do this, I take the SMILES strings belonging to the linker from Pubchem and paste it to the Organic Linker subsection in Building Blocks section, However, there is no corresponding MOF arise based on my choice even if I am confident there are.
What kind of steps I may skip? If there are differences between SMILES strings, what is the true type of them for Materials Project?
Emre
Hey @Emre_Genc are you using the MOF explorer from MP? The linkers are entered as SMILES, however they were probably made with MOF ID
Can you provide an example of a MOF where you know the linker is available in MP but you get no results for a specific SMILES?
Dear @Aaron_Kaplan ,
Thank you for your interest.
For instance, for benzene 1,4 dicarboxylic acid, the SMILES string is given in Pubchem as C1=CC(=CC=C1C(=O)O)C(=O)O. As opposed to that, QMOF database (the excel file) gives the same smiles code as [O-]C(=O)c1ccc(cc1)C(=O)[O-] . I am totally stuck about these two. The same situation is in effect for all linkers.
(By the way, I found the same linker in QMOF database excel through its InChI Key)
(Using this web site https://www.cheminfo.org/Chemistry/Cheminformatics/Smiles/index.html, I observed structural difference for these two SMILES string)
Best regards
Emre
The two SMILES represent the same molecule, the second (with lowercase “c”) SMILES is the canonical variant