DNA bases ring-expanded with a cyclopentadiene free radical: a theoretical investigation of building blocks with diradical character

Abstract

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.

Rational Design of Magnetic DNA Motifs with Diradical Character: Nitroxide Functionalization of Nucleobases

“…First, the development of new assembly structures include the incorporation of other nanoparticles, such as metal modification (M-DNA), hybridization, and so forth. Second, DNA bases are modified by ring expansion or metal modification, such as changing their magnetic, electrical, and optical properties. − In the latter case, our team has designed a series of basic monomer and base pair combinations and discussed in more detail and extensively. − We have successfully introduced radicals into DNA bases, giving them new magnetic properties, while also greatly improving their electronic properties, redox activity, and the like. , However, slightly less than that, while giving radical properties, the size of radical bases is also widened, which to some extent weakens the magnetic coupling between the radicals. Therefore, the magnetic coupling properties of such novel DNA diradicals are not very prominent.…”

Remarkable Differences in Spin Couplings for Various Self‐Paired Dimers of Ring‐Expansion‐Radicalized Uracil: A Basis for the Design of Magnetically Anisotropic Assemblies

“…[25][26][27] AlthoughUderivatives have been widely used as building blocks to create functional nanostructures on surfaces by exploiting molecular recognition, to the best of our knowledge, their radicalized derivatives are little investigated, and relevant information about their electronic properties, especially the magnetic properties, and even their assemblies are quite scarce. Indeed, as has been done for the nucleobases, which can be modified through expanding closed-shell rings, [28][29][30][31][32][33][34][35][36] U can be also expanded through fusing ac yclopentadienyl radical to its ÀC 5 =C 6 À unit to form ar adicalized Ud erivative( rU) with considerable spin delocalizationo ver its bicycle. More interestingly,r Uh as aG -like structure with four double H-bonding sites.…”

Azobenzene‐bridged diradical janus nucleobases with photo‐converted magnetic properties between antiferromagnetic and ferromagnetic couplings

“…Notably, DNA is a promising material for the development of nanotechnology applications, in part due to its ability to selectively hybridize complementary strands . In addition to the exploration of various nano‐structural assemblies of DNA, rational design of various function‐targeted base or base pair units has been the subject in much more recent works . In particular, we recently designed six radicalized nucleobases and examined the magnetic coupling properties of the corresponding Watson–Crick base pairs and their stacked structures and found some intriguing magnetic coupling characteristics .…”

“…In addition to the exploration of various nano‐structural assemblies of DNA, rational design of various function‐targeted base or base pair units has been the subject in much more recent works . In particular, we recently designed six radicalized nucleobases and examined the magnetic coupling properties of the corresponding Watson–Crick base pairs and their stacked structures and found some intriguing magnetic coupling characteristics . Besides, it should be noted that the AB‐based photoisomerizable compounds have been found to interact with or to be linked to DNA and the interaction of such photoisomerizable species with duplex DNA might allow the stability of the resulting double stranded DNA structures to be controlled by light .…”

“…Undoubtedly, the above properties are extremely important to the design of novel photo‐switchable organic magnetic materials. Inspired by these progresses, in this work, on the basis of the intriguing aspects of photo‐reversibility of AB and radicalized nucleobases (rG, rA, rC, rT), we theoretically design a series of the AB‐bridged radicalized nucleobases, a novel kind of diradical Janus nucleobases, and explore their spin coupling characteristics. Calculations prove that such AB‐linked Janus‐nucleobases exhibit well‐defined diradical characters of photo‐convertible intramolecular magnetic couplings (antiferromagnetic (AFM) vs. ferromagnetic (FM) coupling).…”