415 research outputs found

    The promise (or not) of quantum chemistry in QSAR

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    The effect of protein backbone hydration on the amide vibrations in Raman and Raman optical activity spectra

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    Raman and specifically Raman optical activity (ROA) spectroscopy are very sensitive to the solution structure and conformation of biomolecules. Because of this strong conformational sensitivity, density functional theory (DFT) calculations are often used to get a better understanding of the experimentally observed spectral patterns. While e.g. for carbohydrate structure the water molecules that surround the solute have been demonstrated to be of vital importance to get accurate modelled ROA spectra, the effect of explicit water molecules on the calculated ROA patterns of peptides and proteins is less well studied. Here, the effect of protein backbone hydration was studied using DFT calculations of HCO-(l-Ala)(5)-NH2 in specific secondary structure conformations with different treatments of the solvation. The effect of the explicit water molecules on the calculated spectra mainly arises from the formation of hydrogen bonds with the amide C?O and N-H groups. Hydrogen bonding of water with the C?O group determines the shape and position of the amide I band. The C?O bond length increases upon formation of C?OH2O hydrogen bonds. The effect of the explicit water molecules on the amide III vibrations arises from hydrogen bonding of the solvent with both the C?O and N-H group, but their contributions to this spectral region differ: geometrically, the formation of a C?OH2O bond decreases the C-N bond length, while upon forming a N-HH2O hydrogen bond, the N-H bond length increases
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