An affordable accurate evaluation of the binding conformations predicted by molecular docking studies in bio-system

Franck-Condon factors bridge the gap between theoretical modeling and experimental observations for molecular electronic spectroscopy and electron transfer.Under the displaced harmonic oscillator approximation,multidimensional Franck-Condon factors are decomposed into a product of many one-dimensional(1D)Franck-Condon(FC)factors,and each 1D-FC factor is associated with one Huang-Rhys factor that determines the leading contribution of

Anharmonic and Damped Oscillators on Franck-Condon Factors with Application to Molecular Electronic Spectroscopy

Franck-Condon factors bridge the gap between theoretical modeling and experimental observations for molecular electronic spectroscopy and electron transfer. Under the displaced harmonic oscillator approximation, multidimensional Franck-Condon factors are decomposed into a product of many one-dimensional (1D) Franck-Condon (FC) factors, and each 1D-FC factor is associated with one HuangRhys factor that determines the leading contribution of band shape and intensity of corresponding normal-mode vibronic spectrum. Duschinsky rotation effect and anharmonic effect may be introduced into FC factors to further improve simulation in gaseous phase. We recently developed analytical formulas of anharmonic correction in FC factors in terms of HuangRhys factors for modeling absorption and fluorescence spectra in gaseous phase. The analytical formulas were successfully applied to simulate absorption and fluorescence spectra for pyridine, fluorobenzene, and pyrimidine molecules and its results agree well with experimental observations. On the other hand, we developed the scaling method leading to direct modification of HuangRhys factors by damped oscillators for modeling absorption and fluorescence spectra in solution phase and this method was applied to perylene molecule in benzene solution. The present method can be also extended to interfacial molecular spectroscopy with linear and nonlinear optical consideration. Absorption spectra and photovoltaic performance of benzoic acid on titanium dioxide surface is briefly addressed.