Spectroscopy of Ru(II) polypyridyl complexes used as intercalators in DNA: Towards a theoretical study of the light switch effect

The absorption spectroscopy of [Ru(phen)₂dppz]²⁺ and [Ru(tap)₂dppz]²⁺ (phen = 1,10-phenanthroline, tap = 1,4,5,8-tetraazaphenanthrene; dppz = dipyridophenazine) complexes used as molecular light switches by intercalation in DNA has been analysed by means of Time-Dependent Density Functional Theory (TD-DFT). The electronic ground state structures have been optimized at the DFT (B3LYP) level of theory. The absorption spectra are characterized by a high density of excited states between 500 nm and 250 nm. The absorption spectroscopy of [Ru (phen)₂dppz]²⁺ in vacuum is characterized by metal-to-ligand-charge-transfer (MLCT) transitions corresponding to charge transfer from Ru(II) either to the phen ligands or to the dppz ligand with a strong MLCT () absorption at 411 nm. In contrast, the main feature of the lowest part of the vacuum theoretical spectrum of [Ru(tap)₂dppz]²⁺ between 522 nm and 400 nm is the presence of various excited states such as MLCT (), ligand-to-ligand-charge-transfer LLCT () or intra-ligand IL () states. When taking into account solvent corrections within the polarizable continuum model (PCM) approach (H₂O, CH₃CN) the absorption spectrum of [Ru(tap)₂dppz]²⁺ is dominated by a strong absorption at 388 nm (CH₃CN) or 390 nm (H₂O) assigned to a ¹IL () corresponding to a charge transfer from the outside end of the dppz ligand to the site of coordination to Ru(II). These differences in the absorption spectra of the two Ru(II) complexes have dramatic effects on the mechanism of deactivation of these molecules after irradiation at about 400 nm. In particular, the electronic deficiency at the outside end of the dppz ligand created by absorption to the ¹IL state will favour electron transfer from the guanine to the Ru(II) complex when it is intercalated in DNA.     

Ab initio study of single-molecule rotation switch based on nonequilibrium Green's function theory

The bistable molecular switches have been studied theoretically based on the first-principles calculation. The geometry structures of the switches studied in this paper can be triggered between two symmetrical structures by using an external applied electric field. I-V characteristic curves of the different molecule configurations have been calculated, and distinguishability of these characteristic curves indicates a switching behavior, the performance of which can be improved significantly by some suitable donors and acceptors.     

Structural and electronic properties of Al12X+ (X=C, Si, Ge, Sn, and Pb) clusters

Using the first-principles method with the generalized gradient approximation, the authors have studied the structural and electronic properties of Al(12)X(+) (X=C, Si, Ge, Sn, and Pb) clusters in detail. The ground state of Al(12)C(+) is a low symmetry C(s) structure instead of an icosahedron. However, the Si, Ge, Sn, and Pb atom doped cationic clusters favor icosahedral structures. The ground states for Al(12)Si(+) and Al(12)Ge(+) are icosahedra, while the C(5nu) structures optimized from an icosahedron with a vertex capped by a tetravalent atom have the highest binding energy for Al(12)Sn(+) and Al(12)Pb(+) clusters. The I(h) structure and the C(5nu) structure are almost degenerate for Al(12)Ge(+), whose binding energy difference is only 0.03 eV. The electronic properties are altered much by removing an electron from the neutral cluster. The binding strength of a valence electron is enhanced, while the binding energy of the cluster is reduced much. Due to the open electronic shell, the band gaps between the highest occupied molecular orbital and the lowest unoccupied molecular orbital are approximately 0.3 eV for the studied cationic clusters.     

Hexagonal supramolecular architectures from ferrocenium cations incorporating [Ni(mnt)2]- columns: structures and properties of [alkylferrocene][Ni(mnt)2]- charge-transfer complexes (mnt=maleonitriledithiolate)

The crystal architecture, magnetic properties, and thermodynamic properties of [n-butylferrocene][Ni(mnt)2] (1), [tert-butylferrocene][Ni(mnt)2] (2), [1,1'-diethylferrocene][Ni(mnt)2] (3), and [1,1'-diisopropylferrocene][Ni(mnt)2] (4) were investigated (mnt=maleonitriledithiolate). These complexes exhibit a unique supramolecular structure in which the ferrocenium cations constitute honeycomb-like assembled structures surrounding columns of the anions. For 1, the cations form a dimer through a very short intermolecular ferrocene-ferrocene distance of 3.28 A, which mediates an antiferromagnetic interaction with a singlet-triplet energy gap of 5 K. First-order phase transitions occur in 1-3 at 364, 361, and 350 K, respectively, accompanied by thermal hysteresis.     

Electrocatalytic formal [2+2] cycloaddition reactions between anodically activated enyloxy benzene and alkenes

Electrocatalytic formal [2+2] cycloadditions between anodically activated enyloxy benzene and alkenes have been accomplished in a lithium perchlorate/nitromethane electrolyte solution. The enyloxy benzene moiety of these electrolytic substrates played an important role in the formation of a radical cation that could accept nucleophilic alkenes, followed by intramolecular electron transfer between the cyclobutane and phenyl ether moieties of the intermediates.     

Effect of lattice relaxation on spin density of nitrogen-vacancy centers in diamond and oscillator strength calculations

Using a generalized Hubbard Hamiltonian, many-electron wavefunctions of negatively charged (NV⁻) and neutral nitrogen-vacancy (NV⁰) centers in diamond were calculated. We report the effect of symmetric relaxation of surrounding atoms on the spin density, calculated from the many electron wavefunctions in the ground and excited states. We evaluated the error, that, arises in estimation of spin density when lattice relaxation effect is neglected in Electron Paramagnetic Resonance experiment and showed that the ground state spin density distribution is accessible in outward relaxations. The computed oscillator strengths give a higher efficiency for the 1.945 eV photoluminescence (PL) line of NV⁻ with respect to 2.156 eV PL line of NV⁰ which agrees well with experiment. This result is explained based on the largest the ground state spin among available values for the NV⁻ with respect to NV⁰. The transition probability between degenerate ground and excited states slightly depends on the S _z value. Finally, we report on the electronic configurations which contribute to the ground and excited states and discuss the population variation of electronic configurations with relaxation.     

Coinage metal (4, 4) nanotubes, simulated by first-principles calculations

The structural stability of coinage metal nanotubes with a square cross-section has been investigated by the first-principles numerical simulations. In addition to the reported (4, 4) silver tube, it is found that the hollow (4, 4) copper and gold nanotubes can also be formed by applying an appropriate stress to an 8(A)/8(B) fcc wire. The stability of these coinage metal (4, 4) nanotubes, formed by tip-stretching the wires, has been explained by a local minimum in the string tension variation with their tube lengths. Interestingly, we have explained why a low-stress stretching is needed to obtain the (4, 4) Cu tube in contrast to a higher one for both the (4, 4) Ag and Au tubes due to the larger stiffness coefficient of copper than those of silver and gold, which could be proved by future experiments.     

Triplet states of zigzag edged hexagonal graphene molecules C(6m∗∗2)H(6m) (m = 1, 2, 3, ..., 10) and carbon based magnetism

The geometry and magnetization (spin distribution) of the series of flat hexagonal zigzag edged molecules C(6m??2)H(6m) (m = 1,2, ..., 10) in their lowest triplet state (S(z) = 1) has been calculated using density functional theory and a connection established from the known benzene (m = 1) triplets to the triplets and singlet ground state of the largest molecules (m = 9, 10). The triplet state potential energy surface has two minima corresponding to distortions from the ground state geometry, such that CC bonds bisected by a C(2)" rotation axis are either longer or shorter. For both geometries, the spin on the carbon atoms forms a pattern that peaks at the middle of an edge and for large index (m) values is the same (apart from sign) as the edge pattern of the hexagonally sectored singlet radical ground state of the largest member C(600)H(60). This similarity suggests that the singlet ground state of the larger (m = 9, 10) zigzag edged hexangulenes is possibly a hex-radical, in some ways analogous to the di- and higher multiradical ground state of the linear acenes C(4m + 2)H(2m + 4) starting around m ≥ 8 and 9. The spin patterns provide guidance in interpreting the multiradical nature of ground and low lying excited states of large hexangulenes and how magnetism evolves with size in molecules with graphene cores.     

Electronic structures and spectra of symmetric meso‐substituted porphyrin: DFT and TDDFT—PCM investigations

DFT and TDDFT calculations at the level of PBE0/6‐31G(d)/6‐31+G(d) were performed systematically on seven porphyrins with symmetrical meso‐substitutents. Our results show that the planarity of the free base porphyrin (BP) are affected by the introduction of substitutents at the meso‐position of the ring. Geometrical studies show that the introduction of electron‐withdrawing groups brings about in‐plane deformation in the porphyrin ring, whereas the bulky substitutents make an out‐of‐plane deformation. However, FMO's diagram shows that electron‐withdrawing groups alter the degeneracy of the HOMO and HOMO ?1 orbtial. Up on introduction of substituents at the meso‐position, the Q band FMOs transitions were the same as in the case of free BP; however, the oscillator strength is changed. Electron releasing substituted at the meso‐position shows bathochromic shift in the Q band region. However, the intensity or the hyperchromic shift is higher for the electron withdrawing groups. Solvation studies show that Q bands are blue shifted and B bands are red shifted, whereas the intensity of the B bands was highly enhanced compared with the Q bands. These theoretical studies would be helpful in designing new porphyrins for the photodynamic therapy and dye‐sensitized solar cell applications. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Magnetism and bonding in graphene nanodots with H modified interior, edge, and apex

Ab initio density functional theory calculations of hexagonal shaped zigzag edged graphene nanodot molecules, modified by the addition of atomic H to interior and perimeter sites, predict significant changes to the hexagonally sectored spin distribution and chemical bonding of the originals. The redistribution of Kohn-Sham levels at the top of the valence manifold from parent to derivative hint at large changes in the electronic structure. A centrally added H atom creates an occupied level in the middle of the 0.3 eV band gap of the parent molecule and is surrounded by an island of spins. The latter is isolated enough from the perimeter to provide a calibration of the edge spins of the modified parent. Mid-edge addition of a H atom "quenches" the spin on the edge by drawing a p(z)-electron into the C-H bond without reducing the spin on the other edges. Addition of H to an apex carbon atom results in a localized spin freed from the double bond that coexists with the parent spin on the same edge. Saturating the apex double bond by adding two H atoms, returns π-levels shifted in energy and index and parent-like spin patterns on all edges, intact except for small changes on the edges joined at the apex. Taken in unison these results demonstrate how atomic hydrogen and other groups could be used to engineer the magnetism of graphene nanodots.