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Abstract 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. 

Electron attachment to pyridine results in electronic resonances, metastable states that can decay through electronic or nuclear degrees of freedom. This study uses orbital stabilization techniques combined with bound electronic structure methods, based on equation of motion coupled cluster or multi-reference methods, to calculate positions and widths of electronic resonances in pyridine that exist below 10 eV. We report four 2B1 and four 2A2 resonances, including one 2B1 not previously reported experimentally and two 2A2 resonances not reported at all in the literature. The two lower energy resonances are one-particle shape resonances, while the remaining are mixed or primarily core-excited resonances. Multi-reference perturbation theory provides the best description of these resonances, especially when their character is mixed. We describe the character of these resonances qualitatively and calculate Dyson orbitals, which provide information about their decay channels. 

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.