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

Research output: Contribution to journalArticleScientificpeer-review

Researchers

  • Matti Ropo
  • Markus Schneider
  • Carsten Baldauf
  • Volker Blum

Research units

  • Aalto University
  • Duke University
  • Fritz-Haber-Institut der Max-Planck-Gesellschaft
  • Tampere University of Technology

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 (Ca2+, Ba2+, Sr2+, Cd2+, Pb2+, and Hg2+). 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.

Details

Original languageEnglish
Article number160009
Number of pages13
JournalScientific Data
Volume3
Publication statusPublished - 16 Feb 2016
MoE publication typeA1 Journal article-refereed

    Research areas

  • DENSITY-FUNCTIONAL THEORY, POTENTIAL-ENERGY SURFACE, CONFORMATION-DEPENDENT PROPERTIES, MOLECULAR-ORBITAL CALCULATIONS, AB-INITIO, GAS-PHASE, N-METHYLAMIDE, L-TRYPTOPHAN, METAL-IONS, L-PROLINE

ID: 13325302