In this work, we computationally design radical nucleobases which possess improved electronic properties, especially diradical properties through introducing a cyclopentadiene radical. We predict that the detailed electromagnetic features of base assemblies are based on the orientation of the extra five-membered cyclopentadiene ring. Broken symmetry DFT calculations take into account the relevant structures and properties. Our results reveal that both the radicalized DNA bases and the base pairs formed when they combine with their counterparts remain stable and display larger spin delocalization. The mode of embedding the cyclopentadiene free radical in the structures has some influence on the degree of π-conjugation, which results in various diradical characteristics. Single-layered radical base pairs all have an open-shell singlet ground state, but the energy difference between singlet and triplet is not significant. For two-layered radical base pairs, the situation is more complex. All of them have an open-shell state as their ground state, including an open-shell singlet state and an open-shell triplet state. That is, the majority of radical base pairs possess anti-ferromagnetic or ferromagnetic characteristics. We present here a more in-depth discussion and analyses to study the magnetic characteristics of radical bases and base pairs. As an important factor, two-layered radical base pairs also have been carefully analyzed. We hope that all the measurements and results presented here will stimulate further detailed insights into the related mechanisms in modified DNA bases and the design of better ring-expanded DNA magnetic materials.

In the current work, the nitroxide radical groups are utilized to functionalize the nucleobases, obtaining the nucleobase diradical building blocks for magnetic DNA with significant ferromagnetic or antiferromagnetic coupling characteristics. The nitroxide functionalization strategies include introduction of nitroxide radical group to the carbon site and oxidization of the amino group in nucleobases, and the diradical-functionalized nucleobases are denoted by 2NO X, where X = A, G, T, and C bases. The density functional theory calculations reveal that these nitroxide diradicalized nucleobases are stable and have large magnetic spin coupling magnitudes. Almost all of them possess antiferromagnetic-like spin coupling characteristics with considerably large spin coupling constants [J = −671.7 ( 2NO A1), −463.3 ( 2NO A3), −370.5 ( 2NO G), −494.9 ( 2NO C1), −3265.5 ( 2NO T), and −2445.5 cm −1 ( 2NO C3)] expect for 2NO C2 and 2NO A2 which have the ferromagnetic-like spin coupling characteristics (J = 149.1 and 440.7 cm −1 ), respectively. The spin alternation rule works well for these nitroxide-diradicalized nucleobases in interpreting the magnetic spin coupling characters although such heterocyclic nucleobases (purine and pyrimidine) are as the couplers, and the spin coupling constants present good linear relationships with the highest occupied molecular orbital−lowest unoccupied molecular orbital energy gaps and the energy gaps between the closed-shell singlet and triplet state of these nucleobase diradicals. Besides, their magnetic coupling properties are also analyzed by the shape of the singly occupied molecular orbitals (SOMOs) and SOMO−SOMO energy splitting of the triplet state, the H-bonding with their complementary nucleobases, and the nitroxide radical group orientations. Clearly, this work provides a novel strategy for the rational design of the magnetic DNA motifs with well-defined diradical characters and also provides insights into the spin coupling interactions in these nucleobasebased magnet building blocks of the magnetic DNA nanowires.

Possible electron-induced ruptures of C3'-O3', C5'-O5', and N1-C1' bonds in O4-hydrogenated 2'-deoxythymidine-3'-monophosphate (3'-dT(O4H)MPH) and 2'-deoxythymidine-5'-monophosphate (5'-dT(O4H)MPH) are investigated using density functional theory calculations, and efficient pathways are proposed. Electron attachment causes remarkable structural relaxation in the thymine C6 site. A concerted process of intramolecular proton transfer (IPT) from the C2' site of 2'-deoxyribose to the C6 site and the C3'-O3' bond rupture is observed in [3'-dT(O4H)MPH](-). A low activation barrier (9.32 kcal/mol) indicates that this pathway is the most efficient one as compared to other known pathways leading to backbone breaks of a single strand DNA at the non-3'-end thymine, which prevents the N1-C1' bond cleavage in [3'-dT(O4H)MPH](-). However, essentially spontaneous N1-C1' bond cleavage following similar IPT is predicted in [5'-dT(O4H)MPH](-). A moderate activation barrier (13.02 kcal/mol) for the rate-controlling IPT step suggests that base release from the N1-C1' cleavage arises readily at the 3'-end of single strand DNA with the strand ended by a thymine. The C5'-O5' bond has only an insignificant change in the IPT process. Solvent effects are found to increase slightly the energy requirements for either bond ruptures (11.23 kcal/mol (C3'-O3') vs 16.18 kcal/mol (N1-C1')), but not change their relative efficiencies.