Comparative studies of IR spectra of deprotonated serine with classical and thermostated ring polymer molecular dynamics simulations

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Structural Dynamics


Here we report the vibrational spectra of deprotonated serine calculated from the classical molecular dynamics (MD) simulations and thermostated ring-polymer molecular dynamics (TRPMD) simulation with third-order density-functional tight-binding. In our earlier study [Inakollu and Yu, “A systematic benchmarking of computational vibrational spectroscopy with DFTB3: Normal mode analysis and fast Fourier transform dipole autocorrelation function,” J. Comput. Chem. 39, 2067 (2018)] of deprotonated serine, we observed a significant difference in the vibrational spectra with the classical MD simulations compared to the infrared multiple photon dissociation spectra. It was postulated that this is due to neglecting the nuclear quantum effects (NQEs). In this work, NQEs are considered in spectral calculation using the TRPMD simulations. With the help of potential of mean force calculations, the conformational space of deprotonated serine is analyzed and used to understand the difference in the spectra of classical MD and TRPMD simulations at 298.15 and 100K. The high-frequency vibrational bands in the spectra are characterized using Fourier transform localized vibrational mode (FT-νNAC) and interatomic distance histograms. At room temperature, the quantum effects are less significant, and the free energy profiles in the classical MD and the TRPMD simulations are very similar. However, the hydrogen bond between the hydroxyl-carboxyl bond is slightly stronger in TRPMD simulations. At 100K, the quantum effects are more prominent, especially in the 2600-3600cm−1, and the free energy profile slightly differs between the classical MD and TRPMD simulations. Using the FT-νNAC and the interatomic distance histograms, the high-frequency vibrational bands are discussed in detail.

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National Computational Infrastructure



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