Electronic and vibrational excitations in some biologically relevant molecules

Chlorophyll a (Chla) aggregates in 3-methylpentane solution were studied by pico- and femtosecond absorption and picosecond fluorescence spectroscopy and molecular modeling. Time dependent anisotropies were used to follow rotational diffusion of some of the aggregates. The rotational diffusion of a chlorophyll a monomer and (Chla·2H2O)2 dimer was hydrodynamic over the viscosity range studied (0.29-1.8 cP). Molecular mechanics calculations were used to predict the minimum energy structures of several chlorophyll dimers suggested earlier in the literature. These structures were used to estimate excitonic splitting of the Qy-band of chlorophyll a and compared to experimentally observed spectral shifts. Femtosecond measurements of a strongly redshifted large chlorophyll a-water aggregate indicated fast 1.5 ps energy transfer and trapping within the aggregate. No indication of exciton annihilation was observed in an excitation intensity range from 7x1010 to lxI017 photons/(pulse cm2). In the second part of this work a non-linear theoretical model describing energy transfer in ex-helical proteins was tested experimentally. The temperature dependence of the infrared spectra of polypeptides tryptophan-alanine15 and tyrosine-alanine15 was studied. Anomalous red-shifted side-bands in the NH-stretch region were observed. Temperature dependence of the anomalous side-bands was studied by using multivariate principal component analysis. The functional form of the temperature dependence suggests that the anomalous band in crystalline acetanilide at amide-I region and in the polypeptides at NH-stretch region originates from a common mechanism. A non-linear mechanism based on coupling between phonons and a NH-vibration, suggested first by Davydov, seems to explain the temperature dependence. To our knowledge this is the first experimental observation of a soliton in an α-helical polypeptide.