From Canonical to Unique: Extension of A Lipophilicity Scale of Amino Acids to Non-Standard Residues

31 January 2024, Version 1
This content is a preprint and has not undergone peer review at the time of posting.


The lipophilicity of amino acids plays a pivotal role in determining their physicochemical properties as it gives an estimate of solubility, binding propensity, and bioavailability. Herein, we applied the IEFPCM/MST implicit solvation model to compute the n-octanol/water partition coefficient as lipophilic descriptor for non-standard amino acids. Thus, extending our previous work on the hydrophobicity scale of amino acids. To this end, we employed two structural models, named Model 1 and 2, differentiated solely by their C-terminal capping groups using an N- or O- methyl substituent, respectively. Our findings revealed substantial similarities between the models, validating the lipophilicity values for the non-standard side chains. Differences were observed in fewer cases, indicating an effect of the capping group on the side chain hydrophobicity. This effect is expected as one model contains an hydrogen bond donor (Model 1) while the other one uses an hydrogen bond acceptor (Model 2). Overall, both models exhibit strong correlations with the experimental values, with Model 1 showing lower statistical errors. In addition, our predictions were able to correctly predict the experimental hydrophobicity change due to the number of acetylated lysines in peptide pairs determined by HPLC, suggesting that our scale can be employed for proteomics studies that include post-translational modifications beyond acetylation.


Partition coefficient
Non-natural amino acids
Post-translational modifications
Acetyl lysine

Supplementary materials

Additional material


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