(C)C)NC(=O)C
RDKitRDKit
N
N
N
Cl
Cl
O
O
O
Si
N
H
O
1
RegioSQM
23
4
5
6
6 isomers x 20 confs
SMILES
github.com/jensengroup/RegioSQM](https://image.slidesharecdn.com/2019rdkitugmhamborg-190922091406/85/A-Quantum-Chemist-Meets-Cheminformatics-4-320.jpg)
A Quantum Chemist Meets Cheminformatics
- 1. A Quantum Chemist Meets Cheminformatics @janhjensen Jan H. Jensen, University of Copenhagen Feel free to tweet, record, … #WATOC
- 2. 2018 2017 2016 How I met RDKit RDKit
- 3. N H N + Br+ -H+ N H N N H N N H N Br Br Br or ? N H N N H N H H H N H N H N H N 169.4182.2 181.1 H HH H PM3/COSMOheat of formation Kcal/mol 90% success rate for 520 compounds
- 4. Workflow / Automation Molecule Protonated isomers Conformational search Find lowest energy isomer Display result Check for proton transfer ChemDraw RDKit SMILES c1cnc(cc1c1n(c(c(n1)c1ccc(cc1Cl)Cl)C(=O)OC)COCC[Si](C)(C)C)NC(=O)C RDKitRDKit N N N Cl Cl O O O Si N H O 1 RegioSQM 23 4 5 6 6 isomers x 20 confs SMILES github.com/jensengroup/RegioSQM
- 6. xyz2mol Molecule Protonated isomers Conformational search Find lowest energy isomer Display result Check for proton transfer ChemDraw RDKit SMILES RDKitRDKit xyz2mol 6 isomers x 20 confs N N N Cl Cl O O O Si N H O N N N Cl Cl O O O Si N H O xyx2mol converts an xyz file to an RDKit mol object (needs the molecular charge) github.com/jensengroup/xyz2mol
- 7. 2019 2004 2013 github.com/jensengroup/GB-GA An RDKit implementation of and Last example
- 8. crossover
- 11. Unpublished: finding molecules that absorb at 600 nm Mating pool size: 20, mutation rate: 0.05, sTDA-xTB, 10 runs Starting from random molecule in the ZINC data base O N NH O O F O NH2 N O NH N H O O N N N NH2 Does it work? H N O N N N O O O N O
- 12. Summary/Outlook RDKit changed my research life Quantum chemical studies need to be automated Manual work replacing CPU power as rate limiting step Mistakes become increasingly common QM students need to learn Python/RDKit “QM-needs” for RDKit Conf search for finding global minimum Generalized Born solvation model