Journal of Molecular Modeling

, Volume 18, Issue 3, pp 871–879 | Cite as

Influence of stereochemistry on proton transfer in protonated tripeptide models

  • Namat Ali Soliman
  • Petr Kulhánek
  • Jaroslav KočaEmail author
Original Paper


Vectorial proton transfer among carbonyl oxygen atoms was studied in two models of tripeptide via quantum chemical calculations using the hybrid B3LYP functional and the 6-31++G** basis set. Two principal proton transfer pathways were found: a first path involving isomerization of the proton around the double bond of the carbonyl group, and a second based on the large conformational flexibility of the tripeptide model where all carbonyl oxygen atoms cooperate. The latter pathway has a rate-determining step energy barrier that is only around half of that for the first pathway. As conformational flexibility plays a crucial role in second pathway, the effect of attaching methyl groups to the alpha carbon atoms was studied. The results obtained are presented for all four possible stereochemical configurations.


Conformational rearrangement Density functional theory Protonated peptides Proton transfer 



The access to the MetaCentrum supercomputing facilities provided under the research intent MSM6383917201 is appreciated. This work was supported by the Ministry of Education of the Czech Republic, under contracts MSM0021622413 and LC06030 (J.K.). The research leading to these results also received funding from the European Community's Seventh Framework Programme under grant agreement no. 205872 (P.K.).

Supplementary material

894_2011_1116_MOESM1_ESM.doc (34 kb)
ESM 1 (DOC 33 kb)


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Copyright information

© Springer-Verlag 2011

Authors and Affiliations

  • Namat Ali Soliman
    • 1
  • Petr Kulhánek
    • 1
    • 2
  • Jaroslav Koča
    • 1
    • 2
    Email author
  1. 1.Faculty of Science - National Centre for Biomolecular ResearchMasaryk UniversityBrnoCzech Republic
  2. 2.Central European Institute of Technology (CEITEC)Masaryk UniversityBrnoCzech Republic

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