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In the present work, a comprehensive theoretical investigation on the excited state properties of the isomorphic emissive RNA nucleobase analogues, namely tzA, tzG, tzC, and tzU, was performed. Vertical transition energies are determined with the time-dependent density functional theory method at both the B3LYP and CAM-B3LYP levels using the 6-311++G(d,p) basis set. The nature of the low-lying singlet excited states is discussed and the results are compared with the findings from experiment and those for thieno analogues and natural bases. In gas phase, it was found that the S1 state is ππ* in nature for all the tz-bases except for tzA, for which the S1 state is predicted to be nπ* in nature with the ππ* state being the S2. While in water solution, the S1 state for all tz-bases are predicted to be ππ* dominated by the configuration HOMO→LUMO. Compared with natural bases, the lowest ππ* states are about 0.85-1.22 eV red-shifted. When compared with thieno analogues, it is interesting to note that the S1 state (ππ*) transition energies of the two counterparts from the two alphabets are nearly equal due to the very little differences of their HOMO-LUMO gaps. In addition, it was found that the hydration + PCM model can perfectly reproduce the photophysical properties of the tz-bases since the calculated excitation maxima and fluorescence are in good agreement with the experimental data. The microenvironment effects of linking to ribose, base pairing, and further hydration of base pairs were also studied. [ABSTRACT FROM AUTHOR]

Unnatural nucleobases are under intense research due to their widespread applications in nucleic acids research. In this work, four new thieno‐expanded purine analogs comprising ttzA, tthA, ttzG, and tthG were computationally designed based on the isomorphic tz‐ and th‐bases. These base analogs can also be seen as modified derivatives of the previously reported tricyclic purine analogs (ttA and ttG). The structural, electronic, and photophysical properties are studied by means of DFT and TDDFT calculations. We find out that these new bases can form stable Watson‐Crick base pairs with natural counterparts, thus potentially mimicking natural nucleobases in DNA/RNA duplexes. Calculations reveal that these bases have smaller AIPs and HOMO‐LUMO gaps than natural ones, suggesting that they are candidates for applications in nanowire technology. Particularly, the photophysical properties were explored, and the results are compared with those for tz‐, th‐, and tt‐bases. The nature of the low‐lying excited states is discussed, and analyses reveal that the thiophene‐homologation would not change excitation maxima of thA and tzA, while it will result in large red‐shifts of those of thG and tzG. Meanwhile, thiophene insertion has relatively larger influences on the emissions thA and tzG, for which the fluorescence was 37 nm blue‐shifted and 19 nm red‐shifted, respectively. Taking these new bases as derivatives of ttA and ttG, it was found that the modifications would result in large red‐shifts of both the excitation maxima and the fluorescence. The effects of water solution and base paring on the phtotophysical properties were also considered. Four new thieno‐expanded purine analogs are computationally designed based on the isomorphic th‐ and tz‐bases. The structural, electronic, and photophysical properties are studied by means of DFT and TDDFT calculations. Micro‐environment effects of hydration, base pairing, and further hydration of base pairs on photophysical properties are examined and the results are compared with their parental bases. The predictions may be helpful for experimental design of novel nucleobase analogs. [ABSTRACT FROM AUTHOR]