Amide Spectral Fingerprints are Hydrogen Bonding-Mediated

Abstract

The origin of the peculiar amide spectral features of proteins in aqueous solution is investigated, by exploiting a combined theoretical and experimental approach to study UV Resonance Raman (RR) spectra of peptide molecular models, namely N -acetylglycine- N -methylamide (NAGMA) and N -acetylalanine- N -methylamide (NALMA). UVRR spectra are recorded by tuning Synchrotron Radiation at several excitation wavelengths and modeled by using a recently developed multiscale protocol based on a polarizable QM/MM approach. Thanks to the unparalleled agreement between theory and experiment, we demonstrate that specific hydrogen bond interactions, which dominate hydration dynamics around these solutes, play a crucial role in the selective enhancement of amide signals. These results further argue the capability of vibrational spectroscopy methods as valuable tools for refined structural analysis of peptides and proteins in aqueous solution.

Multiple Facets of Modeling Electronic Absorption Spectra of Systems in Solution

“…11 Many works have greatly benefited from one or another parametrization as can be read in Table 1. Overall, changing parameters improves the description of the position of the absorption bands 68 or relative intensities. 56 It is worth recalling here that what is changing when varying parameters is the degree of polarization that the solute can induce on the surrounding solvent molecules, thus directly affecting the solute's spectral response.…”

“…This is due to the fact that there are no specific solute–solvent interactions according to the radial distribution functions from the MD sampling. Also, for NAGMA and NALMA dipeptides, a shift toward the experimental results is recovered by using the QM/FQ model rather than QM/TIP3P. Concerning a very popular solute, caffeine, some repercussions are noted too.…”

“…To retain a more accurate description of the directionality of the key O···H–O and N···H–O molecule–water interactions, in some works, ,,, additional interaction sites (also known as virtual sites, VS) have been added to the molecular topology of the solutes. An improvement of the agreement between QM/FQ and experimental spectra was reported by Skoko et al in the UV–vis study of flavonoids in aqueous solution.…”

“…That strategy can be extended to the QM/FQ methodology, where explicit water molecules are included in the QM portion in what is called QM/QM w /FQ . Sometimes results achieved in that way have been in better agreement with experiments ,, or have been taken as reference, but it also happens that the QM/FQ approach is more than enough in the description of the solvent since it outperforms other solvation models at a lower computational cost …”

Nonadiabatic Vibrational Resonance Raman Spectra from Quantum Dynamics Propagations with LVC Models. Application to Thymine

“…In the future, we will investigate the possibility to run the computation of vRR spectra in explicit solvent models, generalizing to resonance Raman the mixed quantum classical approach for absorption spectra in the condensed phase, which we proposed recently both for single-state and for nonadiabatic systems . It should be mentioned that, for vRR in explicit water models of systems with negligible nonadiabatic couplings, remarkable progress has been done recently by Gómez et al, − also accounting for the mutual solute/solvent polarization.…”