Computed partial charges for protonated amines show discrepancies between Gasteiger and other methods
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SUPPORTED
the evidence backs this
refutedsupported
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A computational chemistry discussion specifically demonstrates that computed partial charges for a protonated amine show significant discrepancies when comparing the Gasteiger method to alternative methods like AM1-BCC or AtomicChargCalculator.
# Computed partial charges for protonated amine: discrepencies between Gasteiger and other methods
Tags: computational-chemistry, formal-charge
- Score: 8
- Views: 617
- Answers: 1
- Answered: yes
- Asked by: Eliane B. (183 rep)
- Asked: 2020-01-15
- Site: chemistry
## Question
Consider the following molecule:
SMILES: COC(=O)[C@@H](c1ccccc1)[C@@H]1CCCC[NH2+]1
I would expect the computed partial chage on the amine to be positive, due to its protonation state.
When using Gasteiger charges calculator, it is affected a positive charge of 0.2422.
However, when using more sophisticated methods (AtomicChargCalculator or Antechamber's AM1-BCC implementation) it is affected a negative charge (-0.649), in these results for example.
It seems the charges computed for the other atoms are roughly similar, as shown in this graph (x-axis: AtomicChargCalculator charge, y-axis: Gasteiger)
Does this amine really have a negative partial charge ? Why the discrepency ? Is there something I am missing ?
## Answers
### Answer by Geoff Hutchison (score: 4 [ACCEPTED])
tldr - atomic partial charges can be non-intuitive
Formal charges in a Lewis structure don't always match up with partial char