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

TL;DR

This paper provides a comprehensive first-principles dataset of 45,892 conformers of amino acids and dipeptides, including various protonation states and metal cation complexes, useful for force field development and biophysical studies.

Contribution

It presents a large, curated density-functional theory dataset of amino acids and dipeptides with diverse protonation and metal-binding states, covering conformational hierarchies and energies.

Findings

Good agreement with experimental ion affinity data

Extensive conformational coverage of amino acids and dipeptides

Dataset suitable for force field parametrization and spectral calculations

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 an overall 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.