title: Instantaneous normal mode analysis of the vibrational relaxation of the amide I mode of alanine dipeptide in water.
abstract: Nonequilibrium Molecular Dynamics (MD) simulations coupled to instantaneous normal modes (INMs) analysis are used to study the vibrational relaxation of the acetyl and amino-end amide I modes of the alanine dipeptide (AlaD) molecule dissolved in water (D2O). The INMs are assigned in terms of the equilibrium normal modes using the Effective Atomic Min-Cost algorithm as adapted to make use of the outputs of standard MD packages, a method which is well suited for the description of flexible molecules. The relaxation energy curves of both amide I modes show multiexponential decays, in good agreement with the experimental findings. It is found that ~85%-90% of the energy relaxes through intramolecular vibrational redistribution. The main relaxation pathways are also identified. The rate at which energy is transferred into the solvent is similar for the acetyl-end and amino-end amide I modes. The conformational changes occurring during relaxation are investigated, showing that the populations of the alpha and beta region conformers are altered by energy transfer in such a way that it takes 15 ps for the equilibrium conformational populations to be recovered after the initial excitation of the AlaD molecule.
authors.affiliation: Departamento de Química Física, Regional Campus of International Excellence Campus Mare Nostrum, Universidad de Murcia, 30100 Murcia, Spain.
authors.forename: Marwa H
authors.initials: MH
authors.lastname: Farag
authors.forename: José
authors.initials: J
authors.lastname: Zúñiga
authors.forename: Alberto
authors.initials: A
authors.lastname: Requena
authors.forename: Adolfo
authors.initials: A
authors.lastname: Bastida
mesh_terms: D000409:Alanine / Q000737:chemistry*; D000577:Amides / Q000737:chemistry*; D004151:Dipeptides / Q000737:chemistry*; D056004:Molecular Dynamics Simulation; D014732:Vibration; D014867:Water / Q000737:chemistry*
chemical_list: D000577:Amides; D004151:Dipeptides; D014867:Water; D000409:Alanine