Nonadiabatic effects in the two-dimensional infrared spectra of peptides: application to alanine dipeptide.
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.
Jansen
Thomas la Cour
Tl
Institute for Theoretical Physics and Materials Science Centre, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands. t.l.c.jansen@rug.nl
Knoester
Jasper
J
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
D000577:Amides; D004151:Dipeptides; D000409:Alanine