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The thymidine analogue 1 is a blue-to-red energy transfer cassette designed to absorb UV light in the 300 nm region and emit it as fluorescence at around 520 nm. When incorporated into DNA, the fluorescence intensity of this modified nucleobase is not significantly reduced by the surrounding structure in the oligonucleotides. more...

Rotational coherence spectroscopy has been used to measure the inertial properties of 1:1 complexes of perylene with water and several different aliphatic alcohols, under supersonic expansion conditions. Hole-burning experiments confirm that several complexes, including ethanol, 1-propanol, and 2-propanol, are present in at least two distinct structural forms. On the other hand, for the methanol and tert-butyl alcohol complexes, only a single structure was detected. The water complex also exists in two ground-state forms, but so far only one of these has been structurally identified. Structures calculated via molecular mechanics procedures, using the CVFF and CFF91 force fields and parameters from the Biosym protein database, are remarkably consistent with experimental inertial measurements. Some comparisons with other molecular mechanics procedures are also presented. We have determined that all these complexes involve a hydrogen bond to π-electrons in the outer rings of the aromatic molecule. The structural variants usually involve rotation about this bond site to different registry positions with the perylene aromatic rings, effectively conserving the alcohol geometry. However, one form of the 1-propanol complex may involve a gauche isomer of the alcohol molecule. more...

Coumarin 151, when complexed 1:1 by a water molecule in a supersonic jet, develops two sets of resonances, based on features displaced by −45 cm^-1 (species A) and −690 cm^-1 (species B) from the uncomplexed molecule. The vertical ionization thresholds of these species differ by a much greater amount (0.5 eV) than the bound states, confirming that the attachment sites are functionally different. When two water molecules are present, there appears to be a single cluster type, having an origin shifted from the bare chromophore by −1214 cm^-1. In this case, fluorescence excitation spectra recorded simultaneously at two emission wavelengths show that the 2:1 species exhibit a Stokes shift for excitation energies ≥60 cm^-1. Also, above this energy barrier, the ionization energy shifts downward by >1000 cm^-1. The bare molecule also undergoes vibronically induced nonradiative relaxation, but this occurs at higher energies (i.e., >450 cm^-1) and results in a large increase in the effective ionization threshold. The fluorescence decay time of the 2:1 water aggregate, excited into the zero-point level of S1, was found to be twice that of the bare molecule (6.7 ns vs 3.5 ns). Above the relaxation barrier, the decay time of the initial state rapidly decreased below the instrument resolution of 35 ps. On the other hand, the fluorescence decay time of the product state increased to ≈9.5 ns and remained constant up to >400 cm^-1 excess vibrational energy. more...