title: Conformational structures of a decapeptide validated by first principles calculations and cold ion spectroscopy.
abstract: Calculated structures of the two most stable conformers of a protonated decapeptide gramicidin S in the gas phase have been validated by comparing the vibrational spectra, calculated from first- principles and measured in a wide spectral range using infrared (IR)-UV double resonance cold ion spectroscopy. All the 522 vibrational modes of each conformer were calculated quantum mechanically and compared with the experiment without any recourse to an empirical scaling. The study demonstrates that first-principles calculations, when accounting for vibrational anharmonicity, can reproduce high-resolution experimental spectra well enough for validating structures of molecules as large as of 200 atoms. The validated accurate structures of the peptide may serve as templates for in silico drug design and absolute calibration of ion mobility measurements.
authors.affiliation: Institute of Chemistry, The Hebrew University Jerusalem 91904 (Israel).
authors.forename: Tapta Kanchan
authors.initials: TK
authors.lastname: Roy
authors.affiliation: Laboratoire de Chimie Physique Molèculaire, École Polytechnique Fèdèrale de Lausanne, 1015 Lausanne (Switzerland).
authors.forename: Vladimir
authors.initials: V
authors.lastname: Kopysov
authors.affiliation: Laboratoire de Chimie Physique Molèculaire, École Polytechnique Fèdèrale de Lausanne, 1015 Lausanne (Switzerland).
authors.forename: Natalia S
authors.initials: NS
authors.lastname: Nagornova
authors.affiliation: Laboratoire de Chimie Physique Molèculaire, École Polytechnique Fèdèrale de Lausanne, 1015 Lausanne (Switzerland).
authors.forename: Thomas R
authors.initials: TR
authors.lastname: Rizzo
authors.affiliation: Laboratoire de Chimie Physique Molèculaire, École Polytechnique Fèdèrale de Lausanne, 1015 Lausanne (Switzerland).
authors.forename: Oleg V
authors.initials: OV
authors.lastname: Boyarkin
authors.affiliation: Institute of Chemistry, The Hebrew University Jerusalem 91904 (Israel). benny@fh.huji.ac.il.|Department of Chemistry, University of California, Irvine, CA 92697 (USA). benny@fh.huji.ac.il.|Department of Chemistry, University of Helsinki, P.O. BOX, 55, 00014 Helsinki(Finland). benny@fh.huji.ac.il.
authors.forename: R Benny
authors.initials: RB
authors.lastname: Gerber
mesh_terms: D006096:Gramicidin / Q000737:chemistry*; D015394:Molecular Structure; D011789:Quantum Theory; D015203:Reproducibility of Results; D013055:Spectrophotometry, Infrared
chemical_list: D006096:Gramicidin
keywords: ab initio calculations; cold-ion spectroscopy; gramicidin S; peptides; vibrational self-consistent field theory