1. Neural-network analysis of the vibrational spectra of N-acetyl L-alanyl N'-methyl amide conformational states
H G Bohr, K Frimand, K J Jalkanen, R M Nieminen, S Suhai Phys Rev E Stat Nonlin Soft Matter Phys. 2001 Aug;64(2 Pt 1):021905. doi: 10.1103/PhysRevE.64.021905. Epub 2001 Jul 20.
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.
2. Energetics of the deformation of a peptide unit. Semi-empirical molecular orbital and ab initio study of N-methyl acetamide and N-acetyl-L-alanine N-methyl amide
V Renugopalakrishnan, R Rein Biochim Biophys Acta. 1976 May 20;434(1):164-8. doi: 10.1016/0005-2795(76)90046-5.
The problem of non-planarity of peptide unit has been investigated using N-methyl acetamide as a theoretical model. A semi-empirical molecular orbital method: Iterative Extended Hückel Theory viz. IEHT/2 (Adams S. (1974) Doctoral dissertation, State University of New York at Buffalo, U.S.A.) and non-empirical abinitio method with minimal basis set, STO-3G (Hehre, W.J., Stewart, R.F. and Pople, J.A. (1969) J. Chem. Phys. 51, 2657-2664) were used to probe the energetics of the distortion of a planar peptide unit. Distortion of one of the peptide units in a dipeptide, N-acetyl-L-alanine N-methyl amide has also been investigated using abinitio method. The studies amply demonstrate the possibility of the existence of a non-planar peptide unit. Distortion of about 10-15 degrees is predicted to bring about very small loss in energy. The results are substantiated by results from experimental studies.
