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  • Title: Nonadiabatic effects in the two-dimensional infrared spectra of peptides: application to alanine dipeptide.
    Author: Jansen Tl, Knoester J.
    Journal: J Phys Chem B; 2006 Nov 16; 110(45):22910-6. PubMed ID: 17092043.
    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.
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