ArticleScientific data2016
First-principles data set of 45,892 isolated and cation-coordinated conformers of 20 proteinogenic amino acids.
Article in Scientific data, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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18 citing papers in PubMed.
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- Benchmark Ab Initio Determination of the Conformers, Proton Affinities, and Gas-Phase Basicities of Cysteine.The journal of physical chemistry. A · 2022Article
- Impact of anion polarizability on ion pairing in microhydrated salt clusters.Chemical science · 2022Article
- Better force fields start with better data: A data set of cation dipeptide interactions.Scientific data · 2022Article
- AB-DB: Force-Field parameters, MD trajectories, QM-based data, and Descriptors of Antimicrobials.Scientific data · 2022Article
- Local Kernel Regression and Neural Network Approaches to the Conformational Landscapes of Oligopeptides.Journal of chemical theory and computation · 2022Article
- TorsiFlex: an automatic generator of torsional conformers. Application to the twenty proteinogenic amino acids.Journal of cheminformatics · 2021Article
- Density Functional Theory Study of Reaction Equilibria in Signal Amplification by Reversible Exchange.Chemphyschem : a European journal of chemical physics and physical chemistry · 2021Article
- Machine learning-accelerated quantum mechanics-based atomistic simulations for industrial applications.Journal of computer-aided molecular design · 2021Article
- Toward accurate prediction of amino acid derivatives structure and energetics from DFT: glycine conformers and their interconversions.Journal of molecular modeling · 2020Article
- Atomic structures and orbital energies of 61,489 crystal-forming organic molecules.Scientific data · 2020Article
- Energy refinement and analysis of structures in the QM9 database via a highly accurate quantum chemical method.Scientific data · 2019Article
- In-depth structural analysis of glycans in the gas phase.Chemical science · 2019Review
- PEPCONF, a diverse data set of peptide conformational energies.Scientific data · 2019Article
- Machine learning unifies the modeling of materials and molecules.Science advances · 2017Article
- Mapping and classifying molecules from a high-throughput structural database.Journal of cheminformatics · 2017Article
- Trends for isolated amino acids and dipeptides: Conformation, divalent ion binding, and remarkable similarity of binding to calcium and lead.Scientific reports · 2016Article
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4 authors.
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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.
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