title: Molecular mechanics force field-based map for peptide amide-I mode in solution and its application to alanine di- and tripeptides.
abstract: A molecular mechanics (MM) force field-based empirical electrostatic potential map (MM map) for amide-I vibrations is developed with the aim of seeking a quick and reasonable approach to computing local mode parameters and their distributions in solution phase. Using N-methylacetamide (NMA) as a model compound, the instantaneous amide-I normal-mode parameters (transition frequency and dipole) obtained at the level of MM force fields are converted to solution phase values by a four-site potential scheme, but without the need for quantum mechanical frequency computations of solute-solvent clusters as are required in constructing ab initio-based electrostatic potential or field maps. The linear IR line shape of the amide-I mode in NMA obtained from the frequency-time correlation function on the basis of the MM map are found to be comparable to those from the ab initio-based maps. Our results show that the amide-I local mode parameters are largely determined by the solvated peptide structure rather than by explicit solvent molecules, suggesting an inherent local structure sensitivity of the amide-I mode in solvated peptides. Applications to alanine di- and tripeptides are satisfactorily demonstrated, showing its usefulness as an alternative approach in providing vibrational parameters for the simulation of linear IR and 2D IR spectra of the amide-I modes in polypeptides.
authors.affiliation: Beijing National Laboratory for Molecular Sciences, State Key Laboratory of Molecular Reaction Dynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, People's Republic of China.
authors.forename: Kaicong
authors.initials: K
authors.lastname: Cai
authors.forename: Chen
authors.initials: C
authors.lastname: Han
authors.forename: Jianping
authors.initials: J
authors.lastname: Wang
mesh_terms: D000081:Acetamides / Q000737:chemistry; D000577:Amides / Q000737:chemistry*; D004121:Dimethyl Sulfoxide / Q000737:chemistry; D004151:Dipeptides / Q000737:chemistry*; D056004:Molecular Dynamics Simulation; D009842:Oligopeptides / Q000737:chemistry*; D011487:Protein Conformation; D012996:Solutions; D012997:Solvents / Q000737:chemistry; D017550:Spectroscopy, Fourier Transform Infrared
chemical_list: D000081:Acetamides; D000577:Amides; D004151:Dipeptides; D009842:Oligopeptides; D012996:Solutions; D012997:Solvents; C002956:alanylalanine; C039944:alanyl-alanyl-alanine; C018595:N-methylacetamide; D004121:Dimethyl Sulfoxide