Ab initio molecular dynamics simulations of amino acids and their ammonia-based analogues in ammonia

Niemöller, Henrik and Ingenmey, Johannes and Hollóczki, Oldamur and Kirchner, Barbara (2025) Ab initio molecular dynamics simulations of amino acids and their ammonia-based analogues in ammonia. THE JOURNAL OF PHYSICAL CHEMISTRY B : A JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 129 (11). pp. 3007-3017. ISSN 1520-6106 (print); 1520-5207 (online)

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Abstract

α-Amino acids are the fundamental building blocks for complex molecular structures within the water-based biochemistry of Earth. In a hypothetical ammonia-based biochemistry, α-amino amidines may serve an equivalent role. In this study, we explore the basic properties of α-amino amidines in comparison to α-amino acids solvated in ammonia, utilizing ab initio molecular dynamics simulations. The investigation of the time-resolved molecular dipole moment reveals, in intricate detail, the relationship among the conformation, state, and magnitude of the dipole moment. Moreover, it allows for the tracking of proton-transfer reactions. In ammonia, α-amino acids tend to adopt an anionic state, with the zwitterionic state still being accessible. In contrast, the α-amino amidines remain neutral. Grotthuss diffusion is induced by the deprotonation of zwitterionic alanine. The charge transferred upon solvation serves as an indicator for the interaction strength between the solute and solvent. It is much stronger for α-amino acids, while, on average, the α-amino amidines exchange no charge with ammonia. The analyses reveal that in terms of structure, anionic α-amino acids behave very similarly to neutral α-amino amidines.

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