Structure and hydrogen bonding in neat N-methylacetamide: classical molecular dynamics and Raman spectroscopy studies of a liquid of peptidic fragments.
The results of classical molecular dynamics (MD) simulations and Raman spectroscopy studies of neat liquid N-methylacetamide (NMA), the simplest model system relevant to the peptides, are reported as a function of temperature and pressure. The MD simulations predict that near ambient conditions, the molecules form a hydrogen bond network consisting primarily of linear chains. Both the links between molecules within the hydrogen-bonded chains and the associations between chains are stabilized by weak methyl-donated "improper" hydrogen bonds. The three-dimensional structural motifs observed in the liquid show some similarity to protein beta-sheets. The temperature and pressure dependence of the hydrogen bond network, as probed by the mode frequency of the experimentally determined amide-I Raman band, blue shifts on heating and red shifts under compression, respectively, suggesting weakened and enhanced hydrogen bonding in response to temperature and pressure increases. Disruption of the hydrogen-bonding network is clearly observed in the simulation data as temperature is increased, whereas the improper hydrogen bonding is enhanced under compression to reduce the energetic cost of increasing the packing fraction. Because of the neglect of polarizability in the molecular model, the computed dielectric constant is underestimated compared to the experimental value, indicating that the simulation may underestimate dipolar coupling in the liquid.
IBM T. J. Watson Research Center, Yorktown Heights, New York 10598, USA.
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Whitfield
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Martyna
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Allison
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Bates
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Vass
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Crain
D000081:Acetamides / Q000737:chemistry*; D000465:Algorithms; D003198:Computer Simulation; D006860:Hydrogen Bonding; D010455:Peptides / Q000737:chemistry*; D011312:Pressure; D017433:Protein Structure, Secondary; D013059:Spectrum Analysis, Raman; D013696:Temperature; D025801:Ubiquitin / Q000737:chemistry
D000081:Acetamides; D010455:Peptides; D025801:Ubiquitin; C018595:N-methylacetamide