My talk at the 2019 RDKit User Group Meeting in Hamburg

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

5. Web server
regiosqm.org

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 Unpublished: finding molecules that absorb at 600 nm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