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On the fragmentation of biomolecules: Fragmentation of alanine dipeptide along the polypeptide chain

  • Statistical, Nonlinear, and Soft Matter Physics
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Abstract

The interaction potential between amino acids in alanine dipeptide has been studied for the first time taking into account exact molecular geometry. Ab initio calculation has been performed in the framework of density functional theory taking into account all electrons in the system. The fragmentation of dipeptide along the polypeptide chain, as well as the interaction between alanines, has been considered. The energy of the system has been analyzed as a function of the distance between fragments for all possible dipeptide fragmentation channels. Analysis of the energy barriers makes it possible to estimate the characteristic fragmentation times and to determine the degree of applicability of classical electrodynamics for describing the system energy.

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Authors and Affiliations

  1. Ioffe Physicotechnical Institute, Russian Academy of Sciences, Politekhnicheskaya ul. 26, St. Petersburg, 194021, Russia

    I. A. Solov’yov, A. V. Yakubovich & A. V. Solov’yov

  2. Frankfurt Institute for Advanced Studied, Johann Wolfgang Goethe University, Frankfurt am Main, 60438, Germany

    I. A. Solov’yov, A. V. Yakubovich, A. V. Solov’yov & W. Greiner

Authors
  1. I. A. Solov’yov
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  2. A. V. Yakubovich
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  3. A. V. Solov’yov
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  4. W. Greiner
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Original Russian Text © I.A. Solov’yov, A.V. Yakubovich, A. V. Solov’yov, W. Greiner, 2006, published in Zhurnal Éksperimental’noĭ i Teoreticheskoĭ Fiziki, 2006, Vol. 130, No. 3, pp. 534–543.

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Solov’yov, I.A., Yakubovich, A.V., Solov’yov, A.V. et al. On the fragmentation of biomolecules: Fragmentation of alanine dipeptide along the polypeptide chain. J. Exp. Theor. Phys. 103, 463–471 (2006). https://doi.org/10.1134/S1063776106090160

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  • DOI: https://doi.org/10.1134/S1063776106090160

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