Exploring the conformational and reactive dynamics of biomolecules in solution using an extended version of the glycine reactive force field

Susanna Monti, Alessandro Corozzi, Peter Fristrup, Kaushik L. Joshi, Yun Kyung Shin, Peter Oelschlaeger, Adri C.T. Van Duin, Vincenzo Barone

Research output: Contribution to journalArticle

49 Citations (Scopus)

Abstract

In order to describe possible reaction mechanisms involving amino acids, and the evolution of the protonation state of amino acid side chains in solution, a reactive force field (ReaxFF-based description) for peptide and protein simulations has been developed as an expansion of the previously reported glycine parameters. This expansion consists of adding to the training set more than five hundred molecular systems, including all the amino acids and some short peptide structures, which have been investigated by means of quantum mechanical calculations. The performance of this ReaxFF protein force field on a relatively short time scale (500 ps) is validated by comparison with classical non-reactive simulations and experimental data of well characterized test cases, comprising capped amino acids, peptides, and small proteins, and reaction mechanisms connected to the pharmaceutical sector. A good agreement of ReaxFF predicted conformations and kinetics with reference data is obtained.

Original languageEnglish (US)
Pages (from-to)15062-15077
Number of pages16
JournalPhysical Chemistry Chemical Physics
Volume15
Issue number36
DOIs
StatePublished - Sep 28 2013

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Biomolecules
glycine
Glycine
field theory (physics)
amino acids
peptides
Amino Acids
proteins
Peptides
Proteins
expansion
Protonation
Conformations
education
sectors
simulation
Kinetics
kinetics
Pharmaceutical Preparations

All Science Journal Classification (ASJC) codes

  • Physics and Astronomy(all)
  • Physical and Theoretical Chemistry

Cite this

Monti, Susanna ; Corozzi, Alessandro ; Fristrup, Peter ; Joshi, Kaushik L. ; Shin, Yun Kyung ; Oelschlaeger, Peter ; Van Duin, Adri C.T. ; Barone, Vincenzo. / Exploring the conformational and reactive dynamics of biomolecules in solution using an extended version of the glycine reactive force field. In: Physical Chemistry Chemical Physics. 2013 ; Vol. 15, No. 36. pp. 15062-15077.
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Exploring the conformational and reactive dynamics of biomolecules in solution using an extended version of the glycine reactive force field. / Monti, Susanna; Corozzi, Alessandro; Fristrup, Peter; Joshi, Kaushik L.; Shin, Yun Kyung; Oelschlaeger, Peter; Van Duin, Adri C.T.; Barone, Vincenzo.

In: Physical Chemistry Chemical Physics, Vol. 15, No. 36, 28.09.2013, p. 15062-15077.

Research output: Contribution to journalArticle

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