Abstract:Articles you may be interested inAnalysis of cross peaks in two-dimensional electronic photon-echo spectroscopy for simple models with vibrations and dissipation J. Chem. Phys. 126, 074314 (2007); 10.1063/1.2435353Photoelectron spectroscopy of S 1 toluene: II. Intramolecular dynamics of selected vibrational levels in S 1 toluene studied by nanosecond and picosecond time-resolved photoelectron spectroscopies Site-specific vibrational dynamics of the CD3ζ membrane peptide using heterodyned two-dimensional infrar… Show more
“…Eqs. (56,57)], and the corresponding experimental result I exp (ω) [42]. The peak of I B850 is located at 1.46 eV (≈ 849 nm), and coincides with the position of the other two spectra.…”
Section: E Absorption Spectrum For Distribution Of Phononsmentioning
confidence: 99%
“…We note that the autocorrelation function in Fig. 11a, resembles the transition frequency autocorrelation function for Nile Blue [57], obtained through a model that combines in both the intramolecular vibrations and solvent dependent contributions.…”
Section: E Absorption Spectrum For Distribution Of Phononsmentioning
The dynamics of pigment-pigment and pigment-protein interactions in light-harvesting complexes is studied with a novel approach that combines molecular dynamics simulations with quantum chemistry calculations and a polaron model analysis. The molecular dynamics simulation of lightharvesting complexes was performed on an 87,055 atom system comprised of an LH-II complex of Rhodospirillum molischianum embedded in a lipid bilayer and surrounded with appropriate water layers. The simulation provided information about the extent and timescales of geometrical deformations of pigment and protein residues at physiological temperatures, revealing also a pathway of a water molecule into the B800 binding site, as well as increased dimerization within the B850 BChl ring, as compared to the dimerization found for the crystal structure. For each of the 16 B850 BChls we performed 400 ab initio quantum chemistry calculations on geometries that emerged from the molecular dynamical simulations, determining the fluctuations of pigment excitation energies as a function of time. From the results of these calculations we construct a time-dependent Hamiltonian of the B850 exciton system from which we determine within linear response theory the absorption spectrum. Finally, a polaron model is introduced to describe both the excitonic and coupled phonon degrees of freedom by quantum mechanics. The exciton-phonon coupling that enters into the polaron model, and the corresponding phonon spectral function are derived from the molecular dynamics and quantum chemistry simulations. The model predicts that excitons in the B850 bacteriochlorophyll ring are delocalized over five pigments at room temperature. Also, the polaron model permits the calculation of the absorption spectrum of the B850 excitons from the sole knowledge of the autocorrelation function of the excitation energies of individual BChls, which is readily available from the combined molecular dynamics and quantum chemistry simulations. The obtained result is found to be in good agreement with the experimentally measured absorption spectrum. PACS number(s): 87.15. Aa, 87.15.Mi, 87.16.Ac
“…Eqs. (56,57)], and the corresponding experimental result I exp (ω) [42]. The peak of I B850 is located at 1.46 eV (≈ 849 nm), and coincides with the position of the other two spectra.…”
Section: E Absorption Spectrum For Distribution Of Phononsmentioning
confidence: 99%
“…We note that the autocorrelation function in Fig. 11a, resembles the transition frequency autocorrelation function for Nile Blue [57], obtained through a model that combines in both the intramolecular vibrations and solvent dependent contributions.…”
Section: E Absorption Spectrum For Distribution Of Phononsmentioning
The dynamics of pigment-pigment and pigment-protein interactions in light-harvesting complexes is studied with a novel approach that combines molecular dynamics simulations with quantum chemistry calculations and a polaron model analysis. The molecular dynamics simulation of lightharvesting complexes was performed on an 87,055 atom system comprised of an LH-II complex of Rhodospirillum molischianum embedded in a lipid bilayer and surrounded with appropriate water layers. The simulation provided information about the extent and timescales of geometrical deformations of pigment and protein residues at physiological temperatures, revealing also a pathway of a water molecule into the B800 binding site, as well as increased dimerization within the B850 BChl ring, as compared to the dimerization found for the crystal structure. For each of the 16 B850 BChls we performed 400 ab initio quantum chemistry calculations on geometries that emerged from the molecular dynamical simulations, determining the fluctuations of pigment excitation energies as a function of time. From the results of these calculations we construct a time-dependent Hamiltonian of the B850 exciton system from which we determine within linear response theory the absorption spectrum. Finally, a polaron model is introduced to describe both the excitonic and coupled phonon degrees of freedom by quantum mechanics. The exciton-phonon coupling that enters into the polaron model, and the corresponding phonon spectral function are derived from the molecular dynamics and quantum chemistry simulations. The model predicts that excitons in the B850 bacteriochlorophyll ring are delocalized over five pigments at room temperature. Also, the polaron model permits the calculation of the absorption spectrum of the B850 excitons from the sole knowledge of the autocorrelation function of the excitation energies of individual BChls, which is readily available from the combined molecular dynamics and quantum chemistry simulations. The obtained result is found to be in good agreement with the experimentally measured absorption spectrum. PACS number(s): 87.15. Aa, 87.15.Mi, 87.16.Ac
“…For τ 12 =0 fs in particular, this process known as transient grating (TG) is a special case of the PE process and the weak quantum beats are not pronounced as shown in Figures 4(b) and 4(e). When two vibrational states are excited and they are closely spaced in energy, the coherent superposition is created, and the quantum beats in signal are observed in the time domain [12,13]. In our system the PE and FID can obtain the dynamics of vibrational states both on the excited and ground states.…”
The poly-[2-methoxy, (5-2′-ethyl-hexyloxy)-p-phenylene vinylene] (MEH-PPV) film is investigated by means of the Multi-Color Photon Echo (MCPE) technique. Under the three-order nonlinear response theory, the reason for the occurrence of the quantum beats in the time domain and the relations among signal wavevector, pulse sequence and response function are discussed. The analysis of the Raman spectrum of MEH-PPV and the fast Fourier transformation (FFT) results of photon echo (PE) signal dynamics demonstrate the coherent coupling between the C==C bonds and the CC-H bonds and the coherent coupling between the C-C stretching of the phenyl group and the C==C stretching of the vinylene group. MCPE, quantum beats, coherent coupling PACS: 34.50.Ez, 42.50.Md, 42.70.Jk
“…The timescale of the initial decay of FFTCF is $60 fs [3]. It has been observed in vibrational peak shift measurements (PS) that the amplitude and the phase characteristics of the pulse strongly influence the initial value and early decay timescale [41]. In Fig.…”
Section: Simulation Details Results and Discussionmentioning
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