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.

DNA--metal base pairs.

We introduce the development of conductive organic molecular assemblies including organic metals, superconductors, single component conductors, conductive films, and conductive liquids, particularl...

Development of Conductive Organic Molecular Assemblies: Organic Metals, Superconductors, and Exotic Functional Materials

The charge ordering phenomena in quasi two-dimensional 1/4-filled organic compounds (ET)_2X (ET=BEDT-TTF) are investigated theoretically for the $\theta$ and $\alpha$-type structures, based on the Hartree approximation for the extended Hubbard models with both on-site and intersite Coulomb interactions. It is found that charge ordered states of stripe-type are stabilized for the relevant values of Coulomb energies, while the spatial pattern of the stripes sensitively depends on the anisotropy of the models. By comparing the results of calculations with the experimental facts, where the effects of quantum fluctuation is incorporated by mapping the stripe-type charge ordered states to the S=1/2 Heisenberg Hamiltonians, the actual charge patterns in the insulating phases of $\theta$-(ET)_2MM'(SCN)_4 and $\alpha$-(ET)_2I_3 are deduced. Furthermore, to obtain a unified view among the $\theta$, $\alpha$ and $\kappa$-(ET)_2X families, the stability of the charge ordered state in competition with the dimeric antiferromagnetic state viewed as the Mott insulating state, which is typically realized in $\kappa$-type compounds, and with the paramagnetic metallic state, is also pursued by extracting essential parameters.

https://arxiv.org/pdf/cond-mat/9911329.pdf

Charge Ordering in Organic ET Compounds

Historically most materials in magnetic applications are based on inorganic materials. Recently, however, organic and molecular materials have begun to show increasing promise. Purely organic ferromagnets, based upon nitronyl nitroxide radicals, show long range magnetic order at very low temperatures in the region of 1 K, while sulfur based radicals show weak ferromagnetism at temperatures up to 36 K. It is also possible to prepare molecule based magnets in which transition metal ions are used to provide the magnetic moment, but organic groups mediate the interactions. This strategy has produced magnetic materials with a large variety of structures, including chains, layered systems and three-dimensional networks, some of which show ordering at room temperature and some of which have very high coercivity. Even if long range magnetic order is not achieved, the spin crossover effect may be observed, which has important applications. Further magnetic materials may be obtained by constructing charge transfer salts, which can produce metallic molecular magnets. Another development is single-molecule magnets, formed by preparing small magnetic clusters. These materials can show macroscopic quantum tunnelling of the magnetization and may have uses as memory devices or in quantum computation applications.

https://iopscience.iop.org/article/10.1088/0953-8984/16/24/R03/pdf

Organic and molecular magnets

The structure, dynamical, and electronic properties of liquid water utilizing different hybrid density functionals were tested within the plane wave framework of first-principles molecular dynamics simulations. The computational approach, which employs modified functionals with short-ranged Hartree-Fock exchange, was first tested in calculations of the structural and bonding properties of the water dimer and cyclic water trimer. Liquid water simulations were performed at the state point of 350 K at the experimental density. Simulations included three different hybrid functionals, a meta-functional, four gradient-corrected functionals, and the local density and Hartree-Fock approximations. It is found that hybrid functionals are superior in reproducing the experimental structure and dynamical properties as measured by the radial distribution function and self-diffusion constant when compared to the pure density functionals. The local density and Hartree-Fock approximations show strongly over- and understructured liquids, respectively. Hydrogen bond analysis shows that the hybrid functionals give slightly smaller average numbers of hydrogen bonds than pure density functionals but similar hydrogen bond populations. The average molecular dipole moments in the liquid from the three hybrid functionals are lower than those of the corresponding pure density functionals.

/pdf/molecular-dynamics-simulation-of-liquid-water-hybrid-density-3lpqrnp1p5.pdf

Molecular Dynamics Simulation of Liquid Water: Hybrid Density Functionals†

Magnetic properties in polypyrrole doped by series of dopants

T SP 以上における(DMe-DCNQI) 2 Liの絶縁性状態における電荷輸送 ±1/2eの分数電荷ソリトン伝導の可能性

The magnetic properties of the pristine and metal ion doped deoxyribonucleic acid (DNA) of salmon are investigated with electron paramagnetic resonance (EPR), superconducting quantum interference device and energy dispersive x-ray flourescence spectroscopy. Purified salmon DNA gives intrinsically no EPR signal, which is consistent with DNA being a semiconductor, but not with DNA having metallic or superconducting properties as reported previously. Several kinds of divalent ions (Zn, Mn, Ca, \dots{}) are used as dopants, resulting in no substantial EPR signal except in the case of Mn. This leads to the conclusion that a metal ion counterbalances two phosphate anions instead of Na counterions in $B$-DNA, which contradicts the metallic behavior reported previously [A. Rakitin et al., Phys. Rev. Lett. 86, 3670 (2001)].

Magnetic study of the electronic states of B -DNA and M -DNA doped with metal ions

Infrared spectra at room temperature under relative humidity (RH) of 0% and 90% have been measured on dry salmon-sperm DNA incorporating various metallic ions ($M\text{-DNA}$, $M=\text{Li}$, Na, Mg, Ca, Mn, Fe, and Zn); the effects of which are examined from the molecular-vibrational points of view. Among many absorption bands, the antisymmetric and symmetric stretching modes of the phosphate group $({\text{PO}}_{2}^{\ensuremath{-}})$ are found to show distinct spectral change depending on $M$. At $\text{RH}=90%$, the band shifts appear for both modes, reflecting that the magnitude of the electric dipole of ${\text{PO}}_{2}^{\ensuremath{-}}$ is affected by $M$. At $\text{RH}=0%$, a band splitting induced by the spatial anisotropy around ${\text{PO}}_{2}^{\ensuremath{-}}$ is detected in the antisymmetric stretching mode for Mg-DNA, Ca-DNA, Mn-DNA, Zn-DNA with divalent counterions, and Fe-DNA with trivalent counterions. The configurational change in $M$ leads to these shifts and splittings; the divalent or trivalent ions do not connect to ${\text{PO}}_{2}^{\ensuremath{-}}$ but are incorporated into the base-pair sequence as already pointed out by the previous measurements of NMR, ESR, and fluorescence. In $M\text{-DNA}$ with $M=\text{Mg}$, Ca, Mn, Fe, and Zn, a kink appears around $3100\text{ }{\text{cm}}^{\ensuremath{-}1}$ corresponding to the NH stretching, and additionally a slight minimum disappears around $310\text{ }{\text{cm}}^{\ensuremath{-}1}$. These phenomena are caused by a generation of $\text{N-}M$ stretching vibrations due to the replacement of proton in the imino group to $M$.

Infrared spectroscopic studies on incorporating the effect of metallic ions into a M -DNA double helix

Effects of hydrostatic pressure on TDAE-${\mathrm{C}}_{60}$ are investigated by electron spin resonance to reveal a mechanism of the ferromagnetism, where TDAE is tetrakis-dimethylamino-ethylene ${T}_{\mathrm{C}}$ decreases with increasing pressure, reaching zero around 9 kbar, following a relation of $\ensuremath{\approx}{T}_{\mathrm{C}}(0)(1\ensuremath{-}{\mathrm{aP}}^{2})$ The orbital-ordering model of Jahn-Teller distorted ${\mathrm{C}}_{60}$ molecules reproduces such a dependence successfully Furthermore, above $\ensuremath{\approx}10$ kbar at 300 K, $\ensuremath{\alpha}\ensuremath{-}\mathrm{TDAE}\ensuremath{-}{\mathrm{C}}_{60}$ transforms to the \ensuremath{\beta} phase with a [2+2] cycloadditive one-dimensional polymer, stable even after pressure release Remarkably, a missing spin in ${\mathrm{TDAE}}^{+}$ revives in the polymer with $g=20028$

/pdf/pressure-effect-in-tdae-c-60-ferromagnet-mechanism-and-48j6ru4r20.pdf

Hirokazu Sakamoto

Papers

Magnetic properties in polypyrrole doped by series of dopants

T SP 以上における(DMe-DCNQI) 2 Liの絶縁性状態における電荷輸送 ±1/2eの分数電荷ソリトン伝導の可能性

Magnetic study of the electronic states of B -DNA and M -DNA doped with metal ions

Infrared spectroscopic studies on incorporating the effect of metallic ions into a M -DNA double helix

Pressure effect in TDAE-C 60 ferromagnet: Mechanism and polymerization