Amide I Vibrational Dynamics of N-Methylacetamide in Polar Solvents:  The Role of Electrostatic Interactions

Abstract

The vibrational frequency of the amide I transition of peptides is known to be sensitive to the strength of its hydrogen bonding interactions. In an effort to account for interactions with hydrogen bonding solvents in terms of electrostatics, we study the vibrational dynamics of the amide I coordinate of N-methylacetamide in prototypical polar solvents: D2O, CDCl3, and DMSO-d6. These three solvents have varying hydrogen bonding strengths, and provide three distinct solvent environments for the amide group. The frequency-frequency correlation function, the orientational correlation function, and the vibrational relaxation rate of the amide I vibration in each solvent are retrieved by using three-pulse vibrational photon echoes, two-dimensional infrared spectroscopy, and pump-probe spectroscopy. Direct comparisons are made to molecular dynamics simulations. We find good quantitative agreement between the experimentally retrieved and simulated correlation functions over all time scales when the solute-solvent interactions are determined from the electrostatic potential between the solvent and the atomic sites of the amide group.

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.…”

Ultrafast 2D IR Vibrational Echo Spectroscopy

“…Ultrafast 2D IR vibrational echo spectroscopy [1][2][3][4][5][6][7][8][9][10][11] is an ultrafast IR analog of 2D NMR 12 that directly probes the structural degrees of freedom of molecules. 13 The 2D IR vibrational echo technique involves a three-pulse sequence that induces and then probes the coherent evolution of excitations (vibrations) of a molecular system.…”

“…2D IR experiments can also be useful as a tool for chemical structural analysis by revealing the relationship among different mechanical degrees of freedom of a molecular 14,15 or biomolecular system. 3,10,16 2D IR vibrational echo experiments have been successfully applied to study fast chemical exchange reactions and solution dynamics, 9,17,18 water dynamics, 19,20 hydrogen network evolution, 6 intramolecular vibrational energy relaxations, 5 protein structures and dynamics, 3,10,16,21 and mixed chemicals analysis. 15 In 1995 an Accounts of Chemical Research article was published 22 summarizing recent fast condensed phase vibrational echo experiments.…”

“…In this Account we will first introduce the experimental technique and then describe its applications in the study of chemical exchange reactions, 9,18 water dynamics, 19 and chemical analysis. 15 Interesting topics that are not covered here are experiments by Tokmakoff and co-workers on the coupling between vibrational modes, 14 population relaxation, 5 and structure and dynamics of proteins, 10 experiments by Hochstrasser and co-workers on solution dynamics of small molecules, 25 hydrogenbond chemical exchange, 17 and small peptide models of biological systems, 26 experiments by Zanni and co-workers on fifth-order vibrational echo spectroscopy 8 and membrane peptides, 7 and experiments by Fayer and co-workers on hydrogen-bonded oligomers, 6 nanoscopic water, 27 and protein structure and dynamics. 16,28 …”

Calculation of two-dimensional infrared spectra of ultrafast chemical exchange with numerical Langevin simulations

“…2DIR has already been used to reveal several chemical exchange processes experimentally. 7,[9][10][11][12][13] The observed processes typically involve solvent rearrangement or conformational changes.…”