Identifying the protonation site and the scope of non-proline <i>cis</i>-peptide bond conformations: a first-principles study on protonated oligopeptides

Xiong, Rui; Li, Xu; Tang, Yong; Cao, Mengge; Li, Hong-Bao

doi:10.1039/d3cp00690e

Cited by 3 publications

(2 citation statements)

References 56 publications

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“…Our calculated structures and the DFT/ROCIS spectrum are in agreement with those obtained by Li and coworkers. 62 Fig. S14 and S16 (ESI †) show the respective calculated DFT spectra of conformers 1 and 2 with the different molecular orbitals responsible for the main transitions.…”

Section: Different Protonation Sites On Amino Groups In Peptidesmentioning

confidence: 99%

Mapping the electronic transitions of protonation sites in peptides using soft X-ray action spectroscopy

Leroux,

Kotobi,

Hirsch

et al. 2023

Phys. Chem. Chem. Phys.

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Section: Different Protonation Sites On Amino Groups In Peptidesmentioning

confidence: 99%

Mapping the electronic transitions of protonation sites in peptides using soft X-ray action spectroscopy

Leroux,

Kotobi,

Hirsch

et al. 2023

Phys. Chem. Chem. Phys.

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“…Consequently, X-ray spectroscopy is highly sensitive to processes such as proton transfer occurring in close proximity to the probed atom. It has been widely utilized to determine protonation states in various contexts, including gas-phase molecules, , solutions, and organic crystals. ,, X-ray photoelectron (XPS) − and absorption (XAS) ,, spectra are the two most common techniques for organic crystals, providing detailed information on proton dynamics associated with hydrogen bonding.…”

mentioning

confidence: 99%

Mapping Hydrogen Positions along the Proton Transfer Pathway in an Organic Crystal by Computational X-ray Spectra

Ge,

Zhang,

Wang

et al. 2024

J. Phys. Chem. Lett.

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Understanding proton transfer (PT) dynamics in condensed phases is crucial in chemistry. We computed a 2D map of N 1s X-ray photoelectron/absorption spectroscopy (XPS/XAS) for an organic donor–acceptor salt crystal against two varying N–H distances to track proton motions. Our results provide a continuous spectroscopic mapping of O–H···N↔O–··· H+–N processes via hydrogen bonds at both nitrogens, demonstrating the sensitivity of N 1s transient XPS/XAS to hydrogen positions and PT. By reducing the O–H length at N1 by only 0.2 Å, we achieved excellent theory-experiment agreement in both XPS and XAS. Our study highlights the challenge in refining proton positions in experimental crystal structures by periodic geometry optimizations and proposes an alternative scaled snapshot protocol as a more effective approach. This work provides valuable insights into X-ray spectra for correlated PT dynamics in complex crystals, benefiting future experimental studies.

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Pillar[5]arene/albumin biosupramolecular systems for simultaneous native protein preservation and encapsulation of a water-soluble substrate

Sultanaev,

Yakimova,

Nazarova

et al. 2024

J. Mater. Chem. B

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Identifying the protonation site and the scope of non-proline cis-peptide bond conformations: a first-principles study on protonated oligopeptides

Abstract: The existence of our proposed non-proline cis-peptide bond conformations of protonated triglycine has been verified through a recent IR-IR double resonance experiment. However, the scope of such unique structures in...

Cited by 3 publications

References 56 publications

Mapping the electronic transitions of protonation sites in peptides using soft X-ray action spectroscopy

Mapping the electronic transitions of protonation sites in peptides using soft X-ray action spectroscopy

Mapping Hydrogen Positions along the Proton Transfer Pathway in an Organic Crystal by Computational X-ray Spectra

Pillar[5]arene/albumin biosupramolecular systems for simultaneous native protein preservation and encapsulation of a water-soluble substrate

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