title: Neural-network analysis of the vibrational spectra of N-acetyl L-alanyl N'-methyl amide conformational states.
abstract: Density-functional theory (DFT) calculations utilizing the Becke 3LYP hybrid functional have been carried out for N-acetyl L-alanine N'-methylamide and examined with respect to the effect of water on the structure, the vibrational frequencies, vibrational absorption (VA), vibrational circular dichroism (VCD), Raman spectra, and Raman optical activity (ROA) intensities. The large changes due to hydration in the structures, and the relative stability of the conformer, reflected in the VA, VCD, Raman spectra, and ROA spectra observed experimentally, are reproduced by the DFT calculations. A neural network has been constructed for reproducing the inverse scattering data (we infer the structural coordinates from spectroscopic data) that the DFT method could produce. The purpose of the network has also been to generate the large set of conformational states associated with each set of spectroscopic data for a given conformer of the molecule by interpolation. Finally the neural network performances are used to monitor a sensitivity analysis of the importance of secondary structures and the influence of the solvent. The neural network is shown to be good in distinguishing the different conformers of the small alanine peptide, especially in the gas phase.
authors.affiliation: Department of Physics, The Technical University of Denmark, DK-2800 Lyngby, Denmark.
authors.forename: H G
authors.initials: HG
authors.lastname: Bohr
authors.forename: K
authors.initials: K
authors.lastname: Frimand
authors.forename: K J
authors.initials: KJ
authors.lastname: Jalkanen
authors.forename: R M
authors.initials: RM
authors.lastname: Nieminen
authors.forename: S
authors.initials: S
authors.lastname: Suhai
mesh_terms: D000409:Alanine / Q000031:analogs & derivatives* / Q000737:chemistry*; D000465:Algorithms; D001665:Binding Sites; D002942:Circular Dichroism / Q000379:methods; D003198:Computer Simulation; D004151:Dipeptides / Q000737:chemistry*; D008958:Models, Molecular; D008968:Molecular Conformation; D009415:Nerve Net; D011485:Protein Binding; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D012996:Solutions; D012997:Solvents / Q000737:chemistry; D013057:Spectrum Analysis / Q000379:methods*; D013059:Spectrum Analysis, Raman / Q000379:methods; D014732:Vibration; D014867:Water / Q000737:chemistry*
chemical_list: D004151:Dipeptides; D011506:Proteins; D012996:Solutions; D012997:Solvents; D014867:Water; C024314:N-acetylalanyl-N-methylamide; D000409:Alanine