Photophysical and structural properties of the fluorescent nucleobase analogues of the tricyclic cytosine (tC) family

Literature Information

Publication Date 2010-06-08
DOI 10.1039/C000625D
Impact Factor 3.676
Authors

Søren Preus, Kristine Kilså, L. Marcus Wilhelmsson, Bo Albinsson


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Abstract

Fundamental insight into the unique fluorescence and nucleobase-mimicking properties of the fluorescent nucleobase analogues of the tC family is not only vital in explaining the behaviour of these probes in nucleic acid environments, but will also be profitable in the development of new and improved fluorescent base analogues. Here, temperature-dependent fluorescence quantum yield measurements are used to successfully separate and quantify the temperature-dependent and temperature-independent non-radiative excited-state decay processes of the three nucleobase analogues tC, tCO and tCnitro; all of which are derivatives of a phenothiazine or phenoxazine tricyclic framework. These results strongly suggest that the non-radiative decay process dominating the fast deactivation of tCnitro is an internal conversion of a different origin than the decay pathways of tC and tCO. tCnitro is reported to be fluorescent only in less dipolar solvents at room temperature, which is explained by an increase in excited-state dipole moment along the main non-radiative decay pathway, a suggestion that applies in the photophysical discussion of large polycyclic nitroaromatics in general. New insight into the ground and excited-state potential energy surfaces of the isolated tC bases is obtained by means of high level DFT and TDDFT calculations. The S0 potential energy surfaces of tC and tCnitro possess two global minima corresponding to geometries folded along the middle sulfur–nitrogen axis separated by an energy barrier of 0.05 eV as calculated at the B3LYP/6-311+G(2d,p) level. The ground-state potential energy surface of tCO is also predicted to be shallow along the bending coordinate but with an equilibrium geometry corresponding to the planar conformation of the tricyclic framework, which may explain some of the dissimilar properties of tC and tCO in various confined (biological) environments. The S1 equilibrium geometries of all three base analogues are predicted to be planar. These results are discussed in the context of the tC bases positioned in double-stranded DNA scenarios.

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Physical Chemistry Chemical Physics

Physical Chemistry Chemical Physics
CiteScore: 5.5
Self-citation Rate: 10.3%
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Physical Chemistry Chemical Physics (PCCP) is an international journal co-owned by 19 physical chemistry and physics societies from around the world. This journal publishes original, cutting-edge research in physical chemistry, chemical physics and biophysical chemistry. To be suitable for publication in PCCP, articles must include significant innovation and/or insight into physical chemistry; this is the most important criterion that reviewers and Editors will judge against when evaluating submissions. The journal has a broad scope and welcomes contributions spanning experiment, theory, computation and data science. Topical coverage includes spectroscopy, dynamics, kinetics, statistical mechanics, thermodynamics, electrochemistry, catalysis, surface science, quantum mechanics, quantum computing and machine learning. Interdisciplinary research areas such as polymers and soft matter, materials, nanoscience, energy, surfaces/interfaces, and biophysical chemistry are welcomed if they demonstrate significant innovation and/or insight into physical chemistry. Joined experimental/theoretical studies are particularly appreciated when complementary and based on up-to-date approaches.

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