Using semiempirical methods for fast and automated predictions

Using semiempirical methods for fast and automated predictions
Feel free to tweet, record, …
#WATOC
@janhjensen
Jan H. Jensen, University of Copenhagen

Fast and Accurate Prediction of the Regioselectivity
of Electrophilic Aromatic Substitution Reactions of
Heteroaromatic Systems
Jimmy C. Kromann and Jan H. Jensen
University of Copenhagen
Morten Jørgensen, Monika Kruszyk, Mikkel Jessing
Lundbeck A/S
Contact me for a preprint
N
H
N + Br+
-H+
N
H
N N
H
N N
H
N
Br
Br
Br
or ?

Streitwieser: Proton affinity correlated with reaction rate
i.e. reaction occurs at site with highest PA
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
90% success rate for 520 compounds
Kcal/mol

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

Lessons learned – Asking the right questions
N
H
N
N
H
N H
H
H
N
H
N
H
N
H
N
169.4182.2 181.1
H HH
H
“Which atom has the highest PA?” instead of “What is the PA?”
“What is the relative pKa?” instead of “What is the pKa?”
Jensen, Swain, Olsen JPCA 2017 (10.1021/acs.jpca.6b10990 )

Lessons learned – Newer SQM methods not more accurate
pKa prediction
PM3 AM1PM6 PM7PM6-DH+
Accuracy of solvation energy may play a role
COSMO Errors for MNSOL database
Kcal/mol AM1 PM3 PM6
MAE 3.6 3.4 3.9
ME 0.0 0.5 1.8

Lessons learned – Learn cheminformatics
All aspects of calculation must be automated – including “chemical transformation” and analysis
Cheminformatics toolkits, e.g. RDKit, are incredibly useful for “chemical transformation” problems
Datasets must include SMILES. XYZ -> SMILES unsolved problem.
Protonate
here
But not
here

Lessons learned - Cheminformatics
Creating intermediate/products as easy as creating protonation states
Setup for TS search?
Must solve atom mapping problem

Lessons learned – Use by non-experts
Automation ✔
Interface ✔
(SMILES input/HTML)
Installation ?
(MOPAC, Python, RDKit, oBabel)
Parallel computing/queueing ?
N
N
N
Cl
Cl
O
O
O
Si
N
H
O
~100 geometry optimizations -> 100-200 minutes on 1 core
-> 4-8 minutes on 24 cores
Options
Webserver/dedicated node
Pay-per-use cloud computing

Using semiempirical methods for fast and automated predictions

Using semiempirical methods for fast and automated predictions

More Related Content

More from molmodbasics (20)

Recently uploaded (20)

Using semiempirical methods for fast and automated predictions