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The cyclization mechanism of cis DAA-DAA dipeptide: an ab initio study

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Abstract

The gas-phase cyclization mechanism of cis DAA-DAA dipeptide (where DAA stands for the earlier described double amino acid molecule of (NH2)2C(COOH)2 formula while DAA-DAA indicates the system formed by two DAAs linked via the peptide bond) is investigated in the absence of any catalysts. Two different paths, concerted and stepwise, each leading to the same cyclo(DAA-DAA) dipeptide product are examined on the basis of theoretical calculations carried out at the CCSD(T)/aug-cc-pVDZ//MP2/aug-cc-pVDZ level. The final product of the cyclization was found to adopt boat conformation of the six-membered 2,5-diketopiperazine ring and its formation was predicted to be thermodynamically favored by ca. 3.7 kcal/mol. The activation barrier estimated for the concerted mechanism (39 kcal/mol) was found to be higher than each of two barriers (30–33 kcal/mol) on the stepwise route which indicates that the cyclization process leading to the cyclo(DAA-DAA) dipeptide formation is more plausible when operating along the stepwise pathway.

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Funding

This research was supported by the Polish Ministry of Science and Higher Education Grants No. 538-8375-B370-16/17 and DS-530-8375-D499-17. The calculations have been carried out using resources provided by Wroclaw Centre for Networking and Supercomputing (http://wcss.pl) grants No. 436.

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  1. Laboratory of Quantum Chemistry, Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308, Gdańsk, Poland

    Sylwia Freza

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  1. Sylwia Freza
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Correspondence to Sylwia Freza.

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Freza, S. The cyclization mechanism of cis DAA-DAA dipeptide: an ab initio study. Struct Chem 29, 1025–1029 (2018). https://doi.org/10.1007/s11224-018-1085-5

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  • DOI: https://doi.org/10.1007/s11224-018-1085-5

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