title: Nonadiabatic effects in the two-dimensional infrared spectra of peptides: application to alanine dipeptide.
abstract: A method of simulating two-dimensional infrared spectra accounting for nonadiabatic effects is presented. The method is applied to the amide I modes of a dipeptide. The information necessary to construct the time-dependent Hamiltonian for the system is extracted from molecular dynamics simulations using a recently published ab initio-based model. It is shown that the linear absorption spectrum agrees with experiment only if the nonadiabatic effects are accounted for. The two-dimensional infrared spectrum is predicted for a range of mixing times. It is shown that population transfer between the amide I site vibrations affects the anisotropy at longer mixing times. It is also demonstrated that the population transfer can, to a good approximation, be extracted from the simulated spectra using a procedure that should also be applicable to experimental spectra.
authors.affiliation: Institute for Theoretical Physics and Materials Science Centre, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands. t.l.c.jansen@rug.nl
authors.forename: Thomas la Cour
authors.initials: Tl
authors.lastname: Jansen
authors.forename: Jasper
authors.initials: J
authors.lastname: Knoester
mesh_terms: D000409:Alanine / Q000737:chemistry*; D000465:Algorithms; D000577:Amides / Q000737:chemistry; D016880:Anisotropy; D003198:Computer Simulation; D004151:Dipeptides / Q000737:chemistry*; D006860:Hydrogen Bonding; D011487:Protein Conformation; D013055:Spectrophotometry, Infrared / Q000379:methods*; D013997:Time Factors
chemical_list: D000577:Amides; D004151:Dipeptides; D000409:Alanine