Molecular dynamics simulation study of N-methylacetamide in water. I. Amide I mode frequency fluctuation

Abstract

Carrying out molecular dynamics simulations of an N-methylacetamide (NMA) in H2O and D2O solutions, we investigated the amide I mode frequency fluctuation and dynamics. The ensemble averaged amide I mode frequency shift was found to be −78 cm−1 in comparison to that of the gas-phase NMA molecule, which is in excellent agreement with the experimental value of −81 cm−1. Similar to the solvation correlation function of a polar solute in liquid water, the correlation function of the fluctuating amide I mode frequency exhibits a bimodal decaying pattern and both the hindered translational and the librational motions of the water molecules directly hydrogen-bonded to the NMA are found to play critical roles in the pure dephasing of the amide I mode. The pure dephasing constant is estimated to be 11 cm−1. The vibrational broadening mechanism is mainly determined by the motional narrowing process. The vibrational Stokes shift of the amide I mode was estimated to be as small as 1.2 cm−1. The amide I IR absorption spectrum thus calculated without any adjustable parameters except for the lifetime of the first excited state has a full width at half maximum of 26.9 cm−1 and is found to be in good agreement with the experiment.

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.…”

Collective Solvent Coordinates for the Infrared Spectrum of HOD in D2O Based on an ab Initio Electrostatic Map

“…The solvent-solute interaction and the solute are described by a map that accounts for the interaction only through the electrostatic field generated by the solvent force field. 13,44,[76][77][78][79] The vibrational Stark effect, in which a uniform external field is applied and the effect on the vibrational spectrum is observed, has been applied to probe the local environment in proteins. 42,80,81 The map provides the frequencies as a function of the electrostatic potential [77][78][79] or its first derivative.…”

“…13,44,[76][77][78][79] The vibrational Stark effect, in which a uniform external field is applied and the effect on the vibrational spectrum is observed, has been applied to probe the local environment in proteins. 42,80,81 The map provides the frequencies as a function of the electrostatic potential [77][78][79] or its first derivative. 13,44,76 The simplest map utilized a quadratic Stark effect model based on a Morse potential for a single vibrational mode.…”

“…13 Other maps were based on fits to ab initio calculations on small clusters, establishing an empirical relation between the fundamental frequency and the electrostatic potential generated by a specific solvent force field. 44,[77][78][79] These empirical maps provide a fast method for obtaining the fluctuating frequencies without constructing the full vibrational Hamiltonian at every time step. The solute polarization built into the ab initio maps is likely to be more important for the vibrational frequency than for the polarization of the solvent.…”

Simulation of vibrational energy transfer in two-dimensional infrared spectroscopy of amide I and amide II modes in solution

“…N-methyl acetamide ͑NMA͒ has been frequently used as a model for the peptide bond, [3][4][5][6][7][8][9][10][11][12][13][14][15][16][17] which is omnipresent in the backbone of proteins. The amide I mode has been the subject of most studies due to its strong intensity and the strong coupling between different amide I modes, which allow the use of this mode for structural determination.…”