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Density functional theory and the harmonic approximation are used for calculating the temperature dependence of the stability of infinite poly-L-alanine [alpha], [pi], and [3.sub.10] helices with respect to the fully extended structure (FES). The temperature dependence is largest for the [pi] helix and smallest for the [3.sub.10] helix and these trends are a generic behavior related to the geometric peculiarities of the respective helical conformations and independent of the specific amino acid sequence.

The folding thermodynamics and kinetics of a polyalanine peptide is demonstrated by using newly developed computational method. The nonequilibrium relaxation of the populations of peptide is derived by using a mix of very efficient sampling techniques (REMD) to properly populate ensembles and conventional MD simulations.

The first-principles molecular dynamics simulations of the alanine hydration was carried out to test the validity of the cluster ansatz approach and the continuum model approach. Sufficient convergence of the cluster ansatz approach is observed for either of the two solvent shells around the polar groups and one solvent shell around the apolar groups or two solvent shells around the polar groups surrounded by a dielectric continuum.

Pure density functional theory calculations and ONIOM are used on infrared spectra of [alpha]-helical-capped polyalanines. The C[double bond] stretch of acetamide is used as a reference for calculating the red shifts for the most intense absorptions, which are greater than predicted by the transition dipole method.

[super 1]H NMR and molecular dynamics simulations are used for studying the interaction of alanyl-phenylalanyl-alanine (Ala-Phe-Ala) with the micelles formed by cesium perfluorooctanoate (CsPFO) in water. This combined approach has described the behavior of Ala-Phe-Ala in the micellar environment and has helped in understanding the interaction of small peptides with fluorinated micelles.

Density functional theory is used for calculating [super 17]O, [super 15]N, [super 13]C, and [super 1]H NMR chemical shieldings in order to differentiate among the three primarily helical forms, [[3.sub.10], [alpha] and [pi] in polyalanine peptides under periodic boundary conditions. The studies have shown [super 17]O as the best observable, as it is sensitive to hydrogen bonding and is affected by small changes in the polypeptide in helix conformations.