title: First-principles data set of 45,892 isolated and cation-coordinated conformers of 20 proteinogenic amino acids.
abstract: 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.
authors.affiliation: Fritz Haber Institute of the Max Planck Society, 14195 Berlin, Germany.|Department of Physics, Tampere University of Technology, 33720 Tampere, Finland.|COMP, Department of Applied Physics, Aalto University, 00076 Aalto, Finland.
authors.forename: Matti
authors.identifier: http://orcid.org/0000-0002-5098-7590
authors.initials: M
authors.lastname: Ropo
authors.affiliation: Fritz Haber Institute of the Max Planck Society, 14195 Berlin, Germany.
authors.forename: Markus
authors.initials: M
authors.lastname: Schneider
authors.affiliation: Fritz Haber Institute of the Max Planck Society, 14195 Berlin, Germany.
authors.forename: Carsten
authors.initials: C
authors.lastname: Baldauf
authors.affiliation: Fritz Haber Institute of the Max Planck Society, 14195 Berlin, Germany.|Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, USA.
authors.forename: Volker
authors.initials: V
authors.lastname: Blum
mesh_terms: D000596:Amino Acids; D002413:Cations, Divalent; D004151:Dipeptides; D008968:Molecular Conformation
chemical_list: D000596:Amino Acids; D002413:Cations, Divalent; D004151:Dipeptides