Intramolecular interactions of L-phenylalanine revealed by inner shell chemical shift

Abstract

Intramolecular interactions of the functional groups, carboxylic acid, amino, and phenyl in L-phenylalanine have been revealed through inner shell chemical shift. The chemical shift and electronic structures are studied using its derivatives, 2-phenethylamine (PEA) and 3-phenylpropionic acid (PPA), through substitutions of the functional groups on the chiral carbon C(alpha), i.e., carboxylic acid (-COOH) and amino (-NH(2)) groups. Inner shell ionization spectra of L-phenylalanine are simulated using density functional theory based B3LYP/TZVP and LB94/et-pVQZ models, which achieve excellent agreement with the most recently available synchrotron sourced x-ray photoemission spectroscopy of L-phenylalanine (Elettra, Italy). The present study reveals insight into behavior of the peptide bond (CO-NH) through chemical shift of the C(1)-C(alpha)-C(beta)(-C(gamma)) chain and intramolecular interactions with phenyl. It is found that the chemical shift of the carbonyl C(1)(=O) site exhibits an apparently redshift (smaller energy) when interacting with the phenyl aromatic group. Removal of the amino group (-NH(2)) from L-phenylalanine (which forms PPA) brings this energy on C(1) close to that in L-alanine (delta<0.01 eV). Chemical environment of C(alpha) and C(beta) exhibits more significant differences in L-alanine than in the aromatic species, indicating that the phenyl group indeed affects the peptide bond in the amino acid fragment. No direct evidences are found that the carbonyl acid and amino group interact with the phenyl ring through conventional hydrogen bonds.

Intramolecular interactions of L‐phenylalanine: Valence ionization spectra and orbital momentum distributions of its fragment molecules

“…2 It has been recognised 3 that the most populated conformer of L-phenylalanine (L-phe) in gas phase is stabilized by hydrogen bonds (Hbonds) which are enhanced by the aromatic ring. A most recent study 4 reveals that H-bonds and intramolecular interaction network of an aliphatic amino acid, i.e., L-alanine and the alanyl moiety of L-phe, an aromatic amino acid, are significantly different: hydrogen bonds in L-alanine are not necessary hydrogen bonds in the alanyl moiety of L-phe in their global minimum structures. Larger molecules such as phenylalanine can be simplified when they are reduced into smaller fragments or groups of structurally related molecules and their intramolecular interactions.…”

“…Larger molecules such as phenylalanine can be simplified when they are reduced into smaller fragments or groups of structurally related molecules and their intramolecular interactions. 4,5 Several excellent reviews discussed a range of aromatic interactions in chemical and biological systems. [5][6][7] These interactions include aiding the stability of DNA base pair stacking and determining molecular recognition in drug docking.…”

“…We addressed this problem by separating L-phe into fragments whose chemical environment and bonding mechanisms are already known. For example, in our previous study, 4 intramolecular interactions of fragments within L-phe were revealed using model molecules of 2-phenethylamine and 3-phenylpropionic acid. It is found 4 that all hydrogen bonds of the phenyl derivatives including L-phe are different from those within the L-alanine moiety (canonical structures).…”

“…For example, in our previous study, 4 intramolecular interactions of fragments within L-phe were revealed using model molecules of 2-phenethylamine and 3-phenylpropionic acid. It is found 4 that all hydrogen bonds of the phenyl derivatives including L-phe are different from those within the L-alanine moiety (canonical structures). That is, none of the hydrogen bonds in L-alanine remains hydrogen bond in the phenyl derivatives.…”

Structures of Cycloserine and 2-Oxazolidinone Probed by X-ray Photoelectron Spectroscopy: Theory and Experiment

“…The B3LYP model has proven to provide reliable geometries for several bio-molecules. [31][32][33] The outer valence Green's function (OVGF) 34,35 theory, which is coupled with the 6-311++G** basis set, was used to calculate valence spectra.…”