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The carboxylate side chains of Asp and Glu have significant coupling with the amide states of the backbone of the Villin headpiece. In two-dimensional spectroscopy, cross peaks are observed between these side chains and the main amide-I band. To model the absorption of the side chains, the electric field variations of vibrational frequencies of a carboxylic(More)
Revealing the structure and aggregation mechanism of amyloid fibrils is essential for the treatment of over 20 diseases related to protein misfolding. Coherent two-dimensional (2D) infrared spectroscopy is a novel tool that provides a wealth of new insight into the structure and dynamics of biomolecular systems. Recently developed ultrafast laser sources(More)
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(More)
We assess the performance of colored-noise thermostats to generate quantum mechanical initial conditions for molecular dynamics simulations, in the context of infrared spectra of large polyatomic molecules. Comparison with centroid molecular dynamics simulations taken as reference shows that the method is accurate in predicting line shifts and band widths(More)
Relaxation channels for two-vibron bound states in an anharmonic alpha-helix protein are studied. According to a recently established small polaron model [V. Pouthier, Phys. Rev. E 68, 021909 (2003)], it is shown that the relaxation originates in the interaction between the dressed anharmonic vibrons and the remaining phonons. This interaction is(More)
The two-vibron dynamics associated to amide-I vibrations in a three-dimensional (3D) alpha-helix is described according to a generalized Davydov model. The helix is modeled by three spines of hydrogen-bonded peptide units linked via covalent bonds. It is shown that the two-vibron energy spectrum supports both a two-vibron free states continuum and two kinds(More)
By using a Generalized Hubbard model for bosons, the energy transfer in a nonlinear quantum lattice is studied, with special emphasis on the interplay between local and nonlocal nonlinearity. For a strong local nonlinearity, it is shown that the creation of v quanta on one site excites a soliton band formed by bound states involving v quanta trapped on the(More)
Femtosecond infrared pump-probe spectroscopy of the N-H mode of a stable alpha-helix reveals two excited-state absorption bands, which disappear upon unfolding of the helix. A quantitative comparison with polaron theory shows that these two bands reflect two types of two-vibron bound states connected to the trapping of two vibrons at the same site and at(More)
We present mixed quantum-classical simulations on relaxation and dephasing of vibrationally excited carbon monoxide within a protein environment. The methodology is based on a vibrational surface hopping approach treating the vibrational states of CO quantum mechanically, while all remaining degrees of freedom are described by means of classical molecular(More)
This Letter presents a comparison between experimental and simulated 2D mid-infrared spectra of carboxy-hemoglobin in the spectral region of the carbon monoxide stretching mode. The simulations rely on a fluctuating potential energy surface that includes both the effect of heme and the protein surroundings computed from molecular dynamics simulations. A(More)