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First-principles data set of 45,892 isolated and cation-coordinated conformers of 20 proteinogenic amino acids.

Publication ,  Journal Article
Ropo, M; Schneider, M; Baldauf, C; Blum, V
Published in: Scientific data
February 2016

We present a structural data set of the 20 proteinogenic amino acids and their amino-methylated and acetylated (capped) dipeptides. Different protonation states of the backbone (uncharged and zwitterionic) were considered for the amino acids as well as varied side chain protonation states. Furthermore, we studied amino acids and dipeptides in complex with divalent cations (Ca(2+), Ba(2+), Sr(2+), Cd(2+), Pb(2+), and Hg(2+)). The database covers the conformational hierarchies of 280 systems in a wide relative energy range of up to 4 eV (390 kJ/mol), summing up to a total of 45,892 stationary points on the respective potential-energy surfaces. All systems were calculated on equal first-principles footing, applying density-functional theory in the generalized gradient approximation corrected for long-range van der Waals interactions. We show good agreement to available experimental data for gas-phase ion affinities. Our curated data can be utilized, for example, for a wide comparison across chemical space of the building blocks of life, for the parametrization of protein force fields, and for the calculation of reference spectra for biophysical applications.

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Published In

Scientific data

DOI

EISSN

2052-4463

ISSN

2052-4463

Publication Date

February 2016

Volume

3

Start / End Page

160009

Related Subject Headings

  • Molecular Conformation
  • Dipeptides
  • Cations, Divalent
  • Amino Acids
 

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Ropo, M., Schneider, M., Baldauf, C., & Blum, V. (2016). First-principles data set of 45,892 isolated and cation-coordinated conformers of 20 proteinogenic amino acids. Scientific Data, 3, 160009. https://doi.org/10.1038/sdata.2016.9
Ropo, Matti, Markus Schneider, Carsten Baldauf, and Volker Blum. “First-principles data set of 45,892 isolated and cation-coordinated conformers of 20 proteinogenic amino acids.Scientific Data 3 (February 2016): 160009. https://doi.org/10.1038/sdata.2016.9.
Ropo M, Schneider M, Baldauf C, Blum V. First-principles data set of 45,892 isolated and cation-coordinated conformers of 20 proteinogenic amino acids. Scientific data. 2016 Feb;3:160009.
Ropo, Matti, et al. “First-principles data set of 45,892 isolated and cation-coordinated conformers of 20 proteinogenic amino acids.Scientific Data, vol. 3, Feb. 2016, p. 160009. Epmc, doi:10.1038/sdata.2016.9.
Ropo M, Schneider M, Baldauf C, Blum V. First-principles data set of 45,892 isolated and cation-coordinated conformers of 20 proteinogenic amino acids. Scientific data. 2016 Feb;3:160009.

Published In

Scientific data

DOI

EISSN

2052-4463

ISSN

2052-4463

Publication Date

February 2016

Volume

3

Start / End Page

160009

Related Subject Headings

  • Molecular Conformation
  • Dipeptides
  • Cations, Divalent
  • Amino Acids