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Using Atomic Charges to Describe the pKa of Carboxylic Acids

Abstract :
In this study, we present an accurate protocol for the fast prediction of pKa's of carboxylic acids based on the linear relationship between computed atomic charges of the anionic form of the carboxylate fragment and their experimental pKa values. Five charge descriptors, three charge models, three solvent models, gas phase calculations and several DFT methods (combination of eight DFT functionals and fifteen basis sets) were tested. Among those, the best combination to reproduce experimental pKa's is to compute NPA atomic charge using the SMD model at the M06L/6-311G(d,p) level of theory and selecting the maximum atomic charge on carboxylic oxygen atoms (R^2 = 0.955). The applicability of the suggested protocol and its stability along geometrical changes are verified by molecular dynamics simulations performed for a set of aspartate, glutamate and alanine peptides. By reporting the calculated atomic charge of the carboxylate form into the linear relationship derived in this work, it will be possible to estimate accurately the amino acid’s pKa's in protein environment.
Document type :
Preprints, Working Papers, ...
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Contributor : Gérald Monard Connect in order to contact the contributor
Submitted on : Sunday, June 13, 2021 - 1:22:03 PM
Last modification on : Sunday, June 26, 2022 - 3:09:42 AM

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Zeynep Pinar Haslak, Sabrina Zareb, Ilknur Dogan, Viktorya Aviyente, Gérald Monard. Using Atomic Charges to Describe the pKa of Carboxylic Acids. 2021. ⟨hal-03259113⟩



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