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Structural-topological preferences and protonation sequence of aliphatic polyamines: a theoretical case study of tetramine trien

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Abstract

A large set of lowest and medium energy conformers of aliphatic tetramine trien was used to uncover structural-topological preferences of poliamines. Numerous common structural features among HL and H 2 L tautomers were identified, e.g., H-atoms of protonated functional groups are always involved in intramolecular NH•••N interactions and they result in as large and as many as possible rings in lowest energy conformers. Largest, 11-membered, molecular rings stabilize a molecule most and they appeared to be strain free whereas 5-memebred intramolecular rings were most strained (all formed due to NH•••N interactions). The CH•••HC interactions with QTAIM-defined atomic interaction lines were also found but, surprisingly, mainly in the lowest energy conformers of HL tautomers. According to the non-covalent interaction-based (NCI) analysis, 5-memebered rings formed by CH•••HC interactions are not strained and, in general, 3D NCI isosurfaces mimic those obtained for weaker NH•••N interactions. Also, 3D NCI isosurfaces found for NH•••N and CH•••HC interactions, regardless whether linked or not by an atomic interaction line, appeared to be indistinguishable. Using lowest energy conformers, theoretically predicted mixture of primary (HL p ) and secondary (HL s ) forms of trien was found to be in accord with the literature reports; using linear conformers resulted in predicting HL s as the only tautomer formed. In contrast to HF, the overall performance of B3LYP was found satisfactory for the purpose of the study.

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Acknowledgments

This work is based on the research supported in part by the National Research Foundation of South Africa (Grant Numbers 87777) and the University of Pretoria.

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This work fully complies with Ethical Standards. An informed consent was reached to publish this work.

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The authors declare that they have no conflict of interest.

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  1. Department of Chemistry, Faculty of Natural and Agricultural Sciences, University of Pretoria, Lynnwood Road, Hatfield, 0002, Pretoria, South Africa

    Adedapo S. Adeyinka & Ignacy Cukrowski

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  1. Adedapo S. Adeyinka
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  2. Ignacy Cukrowski
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Correspondence to Ignacy Cukrowski.

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Adeyinka, A.S., Cukrowski, I. Structural-topological preferences and protonation sequence of aliphatic polyamines: a theoretical case study of tetramine trien . J Mol Model 21, 162 (2015). https://doi.org/10.1007/s00894-015-2709-y

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