title: Spectroscopic polarizable force field for amide groups in polypeptides.
abstract: The infrared spectra of polypeptides are dominated by the so-called amide bands. These bands originate from the electrostatically coupled vibrations of the strongly polar amide groups (AGs) making up the polypeptide backbone. Because the AGs are highly polarizable, external electric fields can shift the frequencies of the amide normal modes over wide spectral ranges. The sensitivity to external fields and the strong polarity are the reasons why the shapes of the amide bands can code the structure of the polypeptide backbone. Aiming at a decoding of these band shapes, Schultheis et al. (J. Phys. Chem. B 2008, 112, 12217) have recently suggested a polarizable molecular mechanics (PMM) force field for AGs, which employs field dependent force constants and enables the computation of the amide bands from molecular dynamics simulations. Here we extend and refine this first suggestion of such a PMM force field. The extension rests on the choice of suitable internal coordinates for the AGs and on the inclusion of the complete AG Hessian and of its field dependence. The force field parameters are calculated from density functional theory. The improved quality of the resulting PMM descriptions is demonstrated using very simple examples and an outlook is given.
authors.affiliation: Lehrstuhl für Biomolekulare Optik, Ludwig-Maximilians-Universität, Oettingenstrasse 67, 80538 München, Germany.
authors.forename: Bernhard
authors.initials: B
authors.lastname: Schropp
authors.forename: Christoph
authors.initials: C
authors.lastname: Wichmann
authors.forename: Paul
authors.initials: P
authors.lastname: Tavan
mesh_terms: D000081:Acetamides / Q000737:chemistry; D000577:Amides / Q000737:chemistry*; D056004:Molecular Dynamics Simulation; D010455:Peptides / Q000737:chemistry*; D013055:Spectrophotometry, Infrared; D055672:Static Electricity; D014732:Vibration
chemical_list: D000081:Acetamides; D000577:Amides; D010455:Peptides; C018595:N-methylacetamide