Abstract
From quantum chemical computations, two sets of molecular mechanics force fields based on peptides and aldehydes were developed for the simplest sugar-glycolaldehyde. Molecular dynamics simulations demonstrated that the structure of glycolaldehyde and the solvent water distribution can be better described by aldehyde-like parameters. Probabilities of normal mode frequencies and dipole derivatives were obtained by instantaneous normal mode analysis. This is thus a new way to predict the parameters of femtosecond broadband two-dimensional infrared spectroscopy for biomolecules by combining quantum mechanics calculation and molecular dynamics simulation.
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