Paper Citing NAMD - Abstract
Falvo, Cyril; Hayashi, Tomoyuki; Zhuang, Wei; Mukamel, Shaul
Coherent two dimensional infrared spectroscopy of a cyclic decapeptide Antamanide. A simulation study of the amide-I and A bands
JOURNAL OF PHYSICAL CHEMISTRY B, 112:12479-12490, OCT 2 2008
The two-dimensional infrared photon echo spectrum of Antamanide (-(1)Val-(2)Pro-(3)Pro-(4)Ala-(5)Phe-(6)Phe-(7)Pro-(8)Pro-(9)Phe-(10)Pro -) in chloroform is calculated using an explicit solvent molecular dynamics (MD) simulation combined with a density functional theory (DFT) map for the effective vibrational Hamiltonian. Evidence for a strong intramolecular hydrogen bonding network is found. Comparison with experimental absorption allows the identification of the dominant conformation. Multidimensional spectroscopy reveals intramolecular couplings and gives information on its dynamics. A two-color amide-I and amide-A crosspeak is predicted and analyzed in terms of local structure.
