Non-linear vibrational modes in biomolecules: A periodic orbits description

The vibrational harmonic normal modes of a molecule, which are valid at energies close to an equilibrium point (a minimum, maximum or saddle of the potential energy surface), are extended by periodic orbits to high energies where anharmonicity and coupling of the degrees of freedom are significant. In this way the assignment of the spectra, and thus the extraction of dynamics in highly excited molecules, can be obtained. New vibrational modes emanating from bifurcations of periodic orbits and long living localized trajectories signal the birth and localization of new quantum states. In this article we review and further study non-linear vibrational modes for model biomolecules such as alanine dipeptide and the active site in the oxoferryl oxidation state of the enzyme cytochrome c oxidase. We locate periodic orbits which exhibit high anhamonicity and lead to center-saddle bifurcations. These modes are associated to an isomerization process in alanine dipeptide and to frequency shifts in the oxoferryl observed by modifying the Coulomb field around the Imidazole-FeIV = O species.

Vibrational frequency shifts in FeIV = O species of the active site of cytochrome c oxidase are attributed to changes in the surrounding Coulomb field. Periodic orbits analysis assists to find the most anharmonic modes in model biomolecules.Highlights► Periodic orbits are extended to multidimensional potentials of biomolecules. ► Highly anharmonic vibrational modes and center-saddle bifurcations are detected. ► Vibrational frequencies shifts in Oxoferryl species of CcO are observed.