Empirical modeling of the peptide amide I band IR intensity in water solution

Abstract

Articles you may be interested inSingle-conformation infrared spectra of model peptides in the amide I and amide II regions: Experiment-based determination of local mode frequencies and inter-mode coupling An empirical correction to amide group vacuum force fields is proposed in order to account for the influence of the aqueous environment on the CvO stretching vibration ͑amide I͒. The dependence of the vibrational absorption spectral intensities on the geometry is studied with density functional theory methods at the BPW91/6-31G** level for N-methyl acetamide interacting with a variety of of water molecule clusters hydrogen bonded to it. These cluster results are then generalized to form an empirical correction for the force field and dipole intensity of the amide I (CvO stretch͒ mode. As an example of its extension, the method is applied to a larger ͑␤-turn model͒ peptide molecule and its IR spectrum is simulated. The method provides realistic bandwidths for the amide I bands if the spectra are generated from the ab initio force field corrected by perturbation from an ensemble of solvent geometries obtained using molecular dynamic simulations.

Optimization of Model Parameters for Describing the Amide I Spectrum of a Large Set of Proteins

“…A computationally inexpensive way of including solvent effects on the amide I frequencies is to parametrize ab initio calculations of N-methylacetamide (NMA) and water clusters. [16][17][18][19][20][21][22][23][24][25][26][27][28][29][30] This method exploits the linear correlation found between the C=O bond length, stretching frequency and electrostatic potential at the atoms of NMA, 18,31,32 which provides a link between perturbation of molecular (and electronic) structure by the electric field of the solvent and the resulting shift of the vibrational frequency. Parametrized electrostatic calculations using the building block approach have been used in protein amide I sim-ulations of ubiquitin, 10,33 other proteins 34 as well as polypeptides in membrane environment.…”

Vibrational−Exciton Couplings for the Amide I, II, III, and A Modes of Peptides

“…The vibrational circular dichroism (VCD) of the amide I, II, and III has been extensively applied to protein structure determination, [8][9][10][11][12] and normal-mode analysis of ab initio calculations has been performed. 13,14 However, most simulation effort has focused on the amide I vibrations [15][16][17][18][19][20] which are highly localized (mostly CdO stretch) and the easiest to model. Coherent ultrafast vibrational spectroscopy is a powerful new technique for probing molecular structure and dynamics in the condensed phase.…”

Two-dimensional vibrational lineshapes of amide III, II, I and A bands in a helical peptide

“…Most simulation effort had so far focused on the highly-localized amide I vibrations [15][16][17][18][19][20] which are the easiest to model. Ab initio calculations of all amide band normal modes have been reported [21,22].…”