Local Hydration Environments of Amino Acids and Dipeptides Studied by X-ray Spectroscopy of Liquid Microjets

Abstract

The nitrogen K-edge spectra of aqueous proline and diglycine solutions have been measured by total electron yield near-edge X-ray absorption fine structure (NEXAFS) spectroscopy at neutral and high pH. All observed spectral features have been assigned by comparison to the recently reported spectrum of aqueous glycine and calculated spectra of isolated amino acids and hydrated amino acid clusters. The sharp preedge resonances at 401.3 and 402.6 eV observed in the spectrum of anionic glycine indicate that the nitrogen terminus is in an "acceptor-only" configuration, wherein neither amine proton is involved in hydrogen bonding to the solvent, at high pH. The analogous 1s f σ* NH preedge transitions are absent in the NEXAFS spectrum of anionic proline, implying that the acceptor-only conformation observed in anionic glycine arises from steric shielding induced by free rotation of the amine terminus about the glycine CN bond. Anionic diglycine solutions exhibit a broadened 1s f π* CN resonance at 401.2 eV and a broad shoulder resonance at 403 eV, also suggesting the presence of an acceptor-only species. Although this assignment is not as unambiguous as for glycine, it implies that the nitrogen terminus of most proteins is capable of existing in an acceptor-only conformation at high pH. The NEXAFS spectrum of zwitterionic lysine solution was also measured, exhibiting features similar to those of both anionic and zwitterionic glycine, and leading us to conclude that the R amine group is present in an acceptor-only configuration, while the end of the butylammonium side chain is fully solvated.

Possible survival of simple amino acids to X-ray irradiation in ice: the case of glycine

“…The σ * (C-N) features are also at a lower energy in the neutral compounds, and the absorption cross section on the σ * (C-N) is also lower. This is consistent with ab initio quantum calculations performed on clusters of methylamine and its chlorine salt (Otero & Urquhart 2006), and with published results of amino acids in the solid phase (Gordon et al 2003;Messer et al 2005). Zubavichus et al (2004a,b) report a difference of -2 eV between the N 1s binding energies of neutral and protonated amine.…”

“…As we see in Sect. 2.2, our NEXAFS data in the O 1s → π * range are dominated by a single component at 532.5 eV assigned to the COO − moiety (Messer et al 2005). Messer et al report that the O 1s → π * in the neutral COOH group is downshifted by 0.25 eV with respect to the corresponding O 1s → π * (COO − ) in the negative ion.…”

Alanine: Then There Was Water

“…The experimental observations show free NH 3 + rotation of glycine in spectroscopy of water-amino acid microjets. 33 Discrete solvation with a small number of waters has also been explored. The N(H 2 O) complex has been explored with DFT/B3LYP, using the 6-311++G(d,p) basis set.…”

Beyond the electric-dipole approximation: A formulation and implementation of molecular response theory for the description of absorption of electromagnetic field radiation

“…[28][29][30][31] XAS can also be used to study the local atomic structure and displacement of the absorbing center in crystals 32,33 and in liquid phases to, for example, detect the local hydration environment of a solute. 34,35 In the present work, we conduct a critical assessment of the ED approximation in response theory calculations of linear absorption cross sections by developing the theory and implementing the code required to describe a molecular system subjected to a weak, linearly polarized electromagnetic plane wave. Since our work will not introduce any truncations whatsoever, the presented results are by construction gaugeorigin independent, and, in the language of multipolar expansions, the presented absorption spectra include contributions to infinite order.…”