coherenttwodimensionalinfraredspectroscopyofproteinsconceptsandsimulations

The nonlinear optical response of peptide molecules to femtosecond infrared pulse sequences contains rich information on their structure,fluctuations and motions.We reviewed in this article the basic concepts as well as the simulation protocol for 2DIR signals associated with the amide backbone vibrational transitions of proteins.Starting with a general introduction of the perturbative picture of nonlinear optical response of excitonic systems,an introduction is given for constructing an effective fluctuating vibrational Hamiltonian based on classical MD simulation and a DFT electrostatic map.Several techniques for simulating the nonlinear response using the fluctuating Hamiltonian are then surveyed,these include the stochastic Liouville equations(SLE),numerical propagation(NP) and cumulant expansion of Gaussian fluctuation(CGF).Applications are presented to two dimensional infrared signal of peptides and peptide complexes