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n-Cyanoindole fluorescent probes hydrogen bonded with one or two water molecules can form cyclic or non-cyclic structures. These structures can lead to excited state proton or hydrogen transfer to the solvent molecules.

 

Exciton-coupled chromophore dimers are an emerging class of optical probes for studies of site-specific biomolecular interactions. Applying accurate theoretical models for the electrostatic coupling of a molecular dimer probe is a key step for simulating its optical properties and analyzing spectroscopic data. In this work, we compare experimental absorbance and circular dichroism (CD) spectra of ‘internally-labeled’ (iCy3)2 dimer probes inserted site-specifically into DNA fork constructs to theoretical calculations of the structure and geometry of these exciton-coupled dimers. We compare transition density models of varying levels of approximation to determine conformational parameters of the (iCy3)2 dimer-labeled DNA fork constructs. By applying an atomistically detailed transition charge (TQ) model, we can distinguish between dimer conformations in which the stacking and tilt angles between planar iCy3 monomers are varied. A major strength of this approach is that the local conformations of the (iCy3)2 dimer probes that we determined can be used to infer information about the structures of the DNA framework immediately surrounding the probes at various positions within the constructs, both deep in the duplex DNA sequences and at sites at or near the DNA fork junctions where protein complexes bind to discharge their biological functions.

 

Time-resolved photoionization measurements were performed on o-nitrophenol pumped with UV laser pulses at a central wavelength of 255 nm (4.9 eV) and probed with vacuum ultraviolet (VUV) pulses at 153 nm (8.1 eV). The photoelectron spectrum and time of flight mass spectrum for ions were recorded at each pump–probe delay. The measurements are interpreted with the aid of electronic structure calculations for both the neutral and ionic states. Evidence is found for the formation of a bicyclic intermediate followed by NO dissociation through a process of internal conversion and intersystem crossing. The combination of photoelectron and photoion spectroscopy, together with computational results, provides strong evidence of intersystem crossing that is difficult to establish with only a single technique.