On the Magnetic Alignment of Metal Ions in a DNA-Mimic Double Helix

New Dimension in Magnetism and Superconductivity: 3D and Curvilinear Nanoarchitectures

Traditionally, the primary field, where curvature has been at the heart of research, is the theory of general relativity. In recent studies, however, the impact of curvilinear geometry enters various disciplines, ranging from solid-state physics over soft-matter physics, chemistry, and biology to mathematics, giving rise to a plethora of emerging domains such as curvilinear nematics, curvilinear studies of cell biology, curvilinear semiconductors, superfluidity, optics, 2D van der Waals materials, plasmonics, magnetism, and superconductivity. Here, the state of the art is summarized and prospects for future research in curvilinear solid-state systems exhibiting such fundamental cooperative phenomena as ferromagnetism, antiferromagnetism, and superconductivity are outlined. Highlighting the recent developments and current challenges in theory, fabrication, and characterization of curvilinear micro- and nanostructures, special attention is paid to perspective research directions entailing new physics and to their strong application potential. Overall, the perspective is aimed at crossing the boundaries between the magnetism and superconductivity communities and drawing attention to the conceptual aspects of how extension of structures into the third dimension and curvilinear geometry can modify existing and aid launching novel functionalities. In addition, the perspective should stimulate the development and dissemination of research and development oriented techniques to facilitate rapid transitions from laboratory demonstrations to industry-ready prototypes and eventual products.

Curvilinear One-Dimensional Antiferromagnets

Antiferromagnets host exotic quasiparticles, support high frequency excitations and are key enablers of the prospective spintronic and spin-orbitronic technologies. Here, we propose a concept of a curvilinear antiferromagnetism where material responses can be tailored by a geometrical curvature without the need to adjust material parameters. We show that an intrinsically achiral one-dimensional (1D) curvilinear antiferromagnet behaves as a chiral helimagnet with geometrically tunable Dzyaloshinskii-Moriya interaction (DMI) and orientation of the Néel vector. The curvature-induced DMI results in the hybridization of spin wave modes and enables a geometrically driven local minimum of the low-frequency branch. This positions curvilinear 1D antiferromagnets as a novel platform for the realization of geometrically tunable chiral antiferromagnets for antiferromagnetic spin-orbitronics and fundamental discoveries in the formation of coherent magnon condensates in the momentum space.

Structures, physicochemical properties, and applications of T–HgII–T, C–AgI–C, and other metallo-base-pairs

In this feature article, recent progress and future perspectives of metal-mediated base-pairs such as T–Hg(ii)–T and C–Ag(i)–C are presented.

Structural and magnetic properties of a variety of transition metal incorporated DNA double helices

By using density functional theory calculations, the structural, energetic, magnetic, and optical properties for a variety of transition metal (M = Mn, Fe, Co, Ni and Cu) ions incorporated modified-DNA (M-DNA) double helices has been investigated. The DNA is modified with either hydroxypyridone (H) or bis(salicylaldehyde)ethylenediamine (S-en) metalated bases. We find the formation of extended M-O network leading to the ferromagnetic interactions for the case of H-DNA for all the metal ions. More ordered stacking arrangement was found for S-en-DNA. We calculate the exchange coupling constant (J) considering Heisenberg Hamiltonian for quantitative description of magnetic interactions. The ferromagnetic and antiferromagnetic interactions are obtained by varying different transition metal ions. The extent of the magnetic interaction depends on the number of transition metal ions. Optical profiles show peaks below 2 eV, a clear signature of spin-spin coupling.

Thieno analogues of RNA nucleosides: a detailed theoretical study

We use first-principles density functional theory calculations to investigate the structural, energetic, bonding aspects, and optical properties of recently synthesized thieno-analogues of RNA nucleosides. The results are compared against the findings obtained for both the natural nucleosides as well as available experimental data. We find that the modified nucleosides form the hydrogen bonded Watson-Crick (WC) base pairing with similar H-bonding energy as obtained for the natural nucleosides. We have calculated and compared the charge transfer integrals for the H-bonded natural and thieno-modified nucleosides. We find that the thieno modification of these nucleosides strongly affects the charge transfer integrals due to the difference in extent of orbital delocalization in these two types of nucleosides. We also find that the degree of reduction of charge transfer integrals is larger for the H-bonded A-U pair than in the G-C pair. We also focus on the optical absorption properties of these thieno-modified nucleosides and their WC H-bonded base pairs in gas phase as well as with implicit water. Our calculated results show that the low energy peaks in the absorption spectra mainly arise because of the π-π* electronic transition for both the nucleosides, and the observed red shift for thieno-nucleosides compared to natural nucleosides are consistent with the calculated decrease in electronic gaps. Our results demonstrate that the thieno modification of natural nucleosides significantly modifies their electronic and optical properties, although the basic structural and bonding aspects remained the same. It also gives a microscopic understanding of the experimentally observed optical behaviors.

Theoretical studies on sulfur and metal cation (Cu(II), Ni(II), Pd(II), and Pt(II))-containing artificial DNA

We evaluated the stability, UV-vis spectra, and possibility of stacking of [S-M(II)-S] (M=Ni, Pd, Pt, S: hydroxypyridinethione) using density functional theory (DFT). We calculated the formation energies of modified bases with possible combinations of chalcogen atoms and metal cations. The results confirmed that [H-Ni(II)-H] (H: hydroxypyridone), [H-Cu(II)-H], and [S-Cu(II)-S] would form stable metal-base pairing; on the other hand, [H-Zn(II)-H], [S-Zn(II)-S], and [H-Pt(II)-H] would not. We predicted UV-vis excitations at 400-410 nm, mainly dominated by a d-pi* transition accompanied by a pi-pi* transition in [S-M(II)-S], where a metal-to-ligand charge transfer shifts the peak of S (without metal cations) by performing time-dependent density functional theory (TDDFT) calculations. By adding the Andersson-Langreth-Lundqvist van der Waals correction to the hybrid DFT results, we estimated the interaction energy between base pairs of [S-M(II)-S]. According to the results, the interaction between [S-M(II)-S] monomers for all cases is attractive, so that the selectivity of formation of the metal-containing DNA is governed mainly by the formation of the base pair in the aqueous phase and only slightly by the pi-pi stacking interaction between the modified bases.

Conformational tuning of magnetic interactions in metal-DNA complexes

The alignment of Cu(2+) ions along a modified DNA helix is studied with either hydroxypyridone (H) or bis(salicylaldehyde)ethylenediamine (S-en) metalated base pairs (MBPs). The conformational motion of H-MBP leads to the interlinking of the H-MBPs by an extended Cu-O network that is ferromagnetic, whereas the conformational freezing of the S-en-MBP leads to an ordered pairwise-stacked arrangement that is weakly antoferrimagnetic.

Combined density functional theory and Landauer approach for hole transfer in DNA along classical molecular dynamics trajectories

We investigate in detail the charge transport characteristics of DNA wires with various sequences and lengths in the presence of solvent. Our approach combines large-scale quantum/classical molecular dynamics (MD) simulations with transport calculations based on Landauer theory. The quantum mechanical transmission function of the wire is calculated along MD trajectories and thus encodes the influence of dynamical disorder arising from the environment (water, backbone, counterions) and from the internal base dynamics. We show that the correlated fluctuations of the base pair dynamics are crucial in determining the transport properties of the wire and that the effect of fluctuations can be quite different for sequences with low and high static disorders (differences in base ionization potentials). As a result, in structures with high static disorder as is the case of the studied Dickerson dodecamer, the weight of high-transmissive structures increases due to dynamical fluctuations and so does the calculated average transmission. Our analysis further supports the basic intuition of charge-transfer active conformations as proposed by Barton et al. [J. Am. Chem. Soc. 126, 11471 (2004)]. However, not DNA conformations with good stacking contacts leading to large interbase hopping values are necessarily the most important, but rather those where the average fluctuation of ionization potentials along the base stack is small. The reason behind this is that the ensemble of conformations leads to average electronic couplings, which are large enough for sufficient transmission. On the other hand, the alignment of onsite energies is the critical parameter which gates the charge transport.

Nature and magnitude of aromatic stacking of nucleic acid bases

This review summarises recent advances in quantum chemical calculations of base-stacking forces in nucleic acids. We explain in detail the very complex relationship between the gas-phase base-stacking energies, as revealed by quantum chemical (QM) calculations, and the highly variable roles of these interactions in nucleic acids. This issue is rarely discussed in quantum chemical and physical chemistry literature. We further extensively discuss methods that are available for base-stacking studies, complexity of comparison of stacking calculations with gas phase experiments, balance of forces in stacked complexes of nucleic acid bases, and the relation between QM and force field descriptions. We also review all recent calculations on base-stacking systems, including details analysis of the B-DNA stacking. Specific attention is paid to the highest accuracy QM calculations, to the decomposition of the interactions, and development of dispersion-balanced DFT methods. Future prospects of computational studies of base stacking are discussed.

The effect of the number of parallel DNA molecules on electric charge transport through 'standing DNA'

We present morphological and electrical characterization of double-stranded DNA (dsDNA) molecules covalently bound to two metal electrodes: an underlying gold surface and a gold nanoparticle (GNP). Conductive atomic force microscope (cAFM) with a metallized tip is used to perform current-voltage (I-V) measurements through dsDNA molecules, connected to GNPs of different diameters 5, 10 and 20 nm. The number of DNA molecules coating the GNP is expected to vary with the surface area of the GNP. This number and the portion of the GNP surface area enabling hybridization of the DNA determine the number of DNA molecules connecting the GNP to the gold surface. The larger the diameter of the GNP the higher the expected number of dsDNA molecules connecting it to the gold surface and thus the expected current. Our results show similar currents for all three GNP sizes, indicating that current flows through the same number of molecules regardless of the diameter of the measured GNP. The measured currents, 220 nA at 2 V, are in accordance with our previous reports (Cohen et al 2005 Proc. Natl Acad. Sci. USA 102 11589-93; Cohen et al 2006 Faraday Discuss. 131 367-76) in which we demonstrated the validity of the experimental system. In particular, for the 5 nm GNP, we conclude that the current possibly flows through two to three molecules, likely only one, and that a single short dsDNA molecule can support at least ∼70 nA, and probably 220 nA.

DNA-Metal Base Pairs

Recent developments show encouraging results for the use of DNA as a construction material for nanometer-sized objects. Today, however, DNA-based molecular nanoarchitectures are constructed with mainly unmodified or at best end-modified oligonucleotides, thus shifting the development of functionalized DNA structures into the limelight. One of most recent developments in this direction is the substitution of the canonical Watson-Crick base pairs by metal complexes. In this way "metal-base pairs" are created, which could potentially impart magnetic or conductive properties to DNA-based nanostructures. This review summarizes research which started almost 45 years ago with the investigation of how metal ions interact with unmodified DNA and which recently culminated in the development of artificial ligand-like nucleobases so far able to coordinate up to ten metal ions inside a single DNA duplex in a programmable fashion.

Symmetry Selection in Artificial DNA Base Pairs

We report the results of density functional theory (DFT) studies on the formation of the complex H1--Cu2+-H1- consisting of two deprotonated hydroxypyridone ligands (H1-) and a Cu2+ ion. We compare the total energies of three possible structures with different symmetries and show that the structure with plane reflection symmetry has the lowest energy. The electronic structure of the periodic extended DNA-like double helix consisting of stacked H1--Cu2+-H1- units is then calculated within the density functional method, and the double helix is found to be an insulating ferromagnet.

Structure and transport characteristics of modified DNA with magnetic ions

Motivated by recent experiments we study the alignment of magnetic ions Cu2+ and Mn2+ along the modified DNA helix. We find that doping with magnetic ions induces conducting states in the gap region of natural DNA. These magnetic ions are found to interact ferromagnetically along the DNA helix. Calculations of optical conductivity about the helical axis suggest that the origin of magnetic characteristics depend on the metal ions; while Cu-DNA favors in-plane sigma-like delocalization over the base pairs, the Mn-DNA favors out-of-plane (pi) delocalizations. Such an alignment of magnetic ions offers promising perspectives for creating low-dimensional polarized spin channel within the DNA helix.

Stability and migration of metal ions in G4-wires by molecular dynamics simulations

We present a molecular dynamics investigation of guanine quadruple helices based on classical force fields. We analyze the dependence of the helical conformation on various compositional factors, such as the length of the G4-wire, as well as the incorporation into the helix channel of alkali ions of different species and in different amounts. In compliance with previous indications, our results suggest that monovalent alkali cations assist the stability of the quadruplex arrangement against disruption on the few nanoseconds time scale in the order of increasing van der Waals radius. Whereas very short G4-wire fragments immediately unfold in the absence of coordinating metal ions or in the presence of tiny ions (e.g., Li+) in agreement with the experimental evidence that empty short guanine quadruplexes are not formed in any synthetic conditions, our simulations show that longer empty helices do not discompose. This finding supports the possibility of producing long G4-wires with different guanine-cation stoichiometries than those routinely known. The classical trajectories allow us to identify different stationary axial sites for the different metal species, which are confirmed by complementary quantum calculations.