The Structure of the Protonated Serine Octamer

Abstract

The amino acid serine has long been known to form a protonated "magic-number" cluster containing eight monomer units that shows an unusually high abundance in mass spectra and has a remarkable homochiral preference. Despite many experimental and theoretical studies, there is no consensus on a SerH structure that is in agreement with all experimental observations. Here, we present the structure of SerH determined by a combination of infrared spectroscopy and ab initio molecular dynamics simulations. The three-dimensional structure that we determine is ∼25 kcal mol more stable than the previous most stable published structure and explains both the homochiral preference and the experimentally observed facile replacement of two serine units.

Synthesis and Binding of Mannose‐Specific Synthetic Carbohydrate Receptors

“…While long‐time MD simulations of the SCR⋅glycan complexes using an empirical potential function (force field) could reproduce the experimental K a values, such modeling remains largely underexplored because of the lack of appropriate parameters for carbohydrate–receptor interactions in nonaqueous solutions, and, as such, is too preliminary to apply here. The alternative, ab initio MD, which utilizes density functional theory (DFT) for propelling the equation of motions, is prohibitively expensive for systematically deriving the structures of molecular complexes . Another computation hurdle is the complexity of the SCR⋅glycan conformational space.…”

Microhydration of protonated 5-hydroxyindole revealed by infrared spectroscopy

“…The PBE0 functional is frequently used to compute properties of molecular clusters and is less empirical than B3LYP. 28,30,[44][45][46] Furthermore, singlepoint energy calculations of selected optimized structures are performed at the CC2/aug-cc-pVDZ level. Comparison to neutral and cationic s/a5HI-W clusters previously studied at the same level (B3LYP-D3/aug-cc-pVTZ) yields the effects of protonation.…”

Identification of Active Sites and Structural Characterization of Reactive Ionic Intermediates by Cryogenic Ion Trap Vibrational Spectroscopy

“…For example, in combination with site‐specific isotopic labeling, the docking sites for small molecules in tripeptides have been identified by recording at 10 K conformationally frozen gas‐phase clusters, or the combination of ion‐mobility mass spectrometry with IR action spectroscopy permitted the structural characterization of the celebrated serine (Ser) octamer as a dichloride complex . Very recently, the long‐disputed structure of [Ser 8 H] +[64c] has been identified by using the He‐tagging technique …”