Geometry and vibrational frequencies of the helical polypeptide complexes with ligand molecules

Abstract

The complexes of alpha helical polypeptides and individual molecules of water, acetonitrile, and 1,4-dioxane have been investigated. We used 16-mer of polyalanine (PA), polyglutamic acid (PGA) and poly-c-benzyl-L-glutamate (PBG). Full geometry optimization was performed for polypeptides and their complexes with ligands, each structure has been characterized by the vibrational analysis and the interaction energy including the correction for zero point vibrational energy. Polyalanine creates by single complex with water molecule, acetonitrile, and dioxane. Polyglutamic acid forms five different complexes with water molecule, and three complexes with acetonitrile and two complexes with dioxane. Two complexes of poly-c-benzyl-L-glutamate with each ligand were found. Carbonyl oxygen of PGA and PBG confirms its strong acceptor character by participation in formation of all obtained complexes with water and acetonitrile. The long side chains of PGA and PBG aid the formation of complexes with two hydrogen bonds where ligand molecule bridges two polar sites of polypeptide. Most of complexes of dioxane with polypeptides are produced due to weak hydrogen bonds of type CAHÁÁÁO. Strong shifts for the stretching vibrations of the interacting group of polypeptides and ligands under the complex formation are detected. Obtained frequencies are in a good agreement with known experimental data.

Hyperconjugation

“…As early as 1937, it was found that a linear relationship exists between H‐bond strength and the shift in the IR H–X stretching frequency, termed the Badger–Bauer rule (Figure ) . The qualitative correlation between H‐bond strengths and stretching frequencies has been observed in many chemical systems . Although a single linear relationship does not hold throughout the many diverse types of H‐bonding, satisfactory linear correlations between enthalpy of H‐bond formation, the IR stretching frequency shift, and the X–H bond elongation were found for structurally related compounds …”

The Badger–Bauer Rule Revisited: Correlation of Proper Blue Frequency Shifts in the OC Hydrogen Acceptor with Morphed Hydrogen Bond Dissociation Energies in OC–HX (X = F, Cl, Br, I, CN, CCH)

“…In the initially published paper, it was proposed that the enthalpy of formation of hydrogen bonds, Δ H , was linearly related to the infrared frequency shifts, Δν for hydroxylic electron acceptors involved in such hydrogen bonding. Since this time, it has been extensively used to correlate experimentally determined red frequency shifts of B–HO– and related stretching vibrations with intermolecular binding strengths for a large range of hydrogen bonded acceptors, B. − A number of models have also been developed theoretically to account for the basis of the Badger–Bauer relationship. − Further applications have, in addition, involved a wide range of studies including H–X red frequency shifts with force constants or bond length changes. − There have been varying degrees of success with such correlations, − in part due to a number of factors such as solvent and steric effects in experimental studies and the influence of anharmonicity. ,,, Despite these issues, Badger–Bauer relationships still continue to be invoked in a wide range of applications. − These have also included proton acceptor carbonyl frequency shifts , because of the facility of experimental measurements. In particular, spectroscopically determined frequency shifts on complexation are used as a means of qualitatively or quantitatively probing of the strength of noncovalent interactions as well as the environment of hydrogen bonded interactions.…”

Aqueous Solvation of Polyalanine α-Helices with Specific Water Molecules and with the CPCM and SM5.2 Aqueous Continuum Models Using Density Functional Theory

“…6–8 Our group 9–13 and others 14–17 have reported density functional theory (DFT) calculations on the stabilities of these helices without solvation, and solvated using the SM5.2 aqueous solvation model. 18 Kubelka has reported the effects of explicit waters on vibrational spectra of helices, 19 Ermakova has reported other studies of α-helices 20,21 and Ireta has reported studies of β-sheets 22 interacting with individual water molecules…”