M-DNA: a self-assembling molecular wire for nanoelectronics and biosensing.

M-DNA is a complex between divalent metal ions such as Zn2+ and duplex DNA which forms at pH 8.5. Unlike B-DNA, M-DNA does not bind ethidium so that M-DNA formation can be monitored conveniently by an ethidium fluorescence assay. M-DNA was shown to be a better conductor than B-DNA by fluorometric measurements of electron transport in donor-acceptor labelled duplexes; by direct conductivity measurements of M-DNA bound between gold electrodes and by cyclic voltammetric studies on ferrocene labelled duplexes attached to gold microelectrodes. As is the case with B-DNA, M-DNA can self-assemble into a variety of structures and is anticipated to find widespread use in nanoelectronics and biosensing.     

Gamma and ultraviolet radiation cause DNA crosslinking in the presence of metal ions at high pH.

M-DNA is a novel duplex conformation in which metal ions such as Co2+, Ni2+ or Zn2+ replace the imino protons of every base pair. An ethidium fluorescence assay was used to estimate lesions in M-DNA induced by gamma- and UV radiation. General damage to DNA was assessed from the loss of ethidium fluorescence after irradiation of calf thymus DNA. Crosslinks were measured from the return of ethidium fluorescence after a heating and cooling step. Strand breaks were estimated from the loss of fluorescence in covalently closed circular plasmid DNA after a heating and cooling step. For the Co2+ form of M-DNA, gamma-radiation caused the very efficient formation of crosslinks which was not observed with B-DNA nor with the Ni2+ or Zn2+ forms of M-DNA. The crosslinks occurred in both A-T and G-C base pairs but did not form in the presence of a free radical scavenger. Crosslinks induced by UV radiation also formed at a faster rate in the Co2+, Ni2+ and Zn2+ forms of M-DNA compared to B-DNA; crosslinking occurred in all DNA but was more prominent in AT-rich sequences and was not inhibited by a free radical scavenger. Therefore, the presence of certain metal ions may lead to large increases in the formation of radiation-induced crosslinks in DNA.     

Fluorescence measurements of duplex DNA oligomers under conditions conducive for forming M-DNA (a metal-DNA complex)

M-DNA (a metal complex of DNA with millimolar concentrations of Zn2+, Co2+, or Ni2+ and basic pH) has been proposed to undergo electron transfer over long distances along the helix and has generated interest as a potential building block for nanoelectronics. We show that DNA aggregates form under solvent conditions favorable for M-DNA (millimolar zinc and pH = 8.6) by fluorescence correlation spectroscopy. We have performed steady-state F?rster resonance energy transfer (FRET) experiments with DNA oligomers conjugated with 6-carboxyfluorescein and tetramethylrhodamine to the opposite ends of double-stranded DNA (dsDNA) molecules. Enhanced acceptor emission is observed for distances larger than expected for identical DNA molecules with no zinc. To avoid intermolecular FRET, the fluorescently labeled dsDNA is diluted with a 100-fold excess of unlabeled dsDNA. The intramolecular FRET efficiency increases 25-fold for a 30-mer doubly labeled duplex DNA molecule upon addition of millimolar concentrations of zinc ions. Without zinc, this oligomer has less than 1% FRET efficiency. This dramatic increase in the FRET efficiency points to either significant changes in the F?rster radius or fraying of the ends of the DNA helices. The latter hypothesis is supported by our experiments with a 9-mer that show dissociation of the duplex by zinc ions.     

Scanning electrochemical microscopy. 51. Studies of self-assembled monolayers of DNA in the absence and presence of metal ions

Scanning electrochemical microscopy was used to examine electron transfer across a self-assembled monolayer of thiol-modified DNA duplexes on a gold electrode. The apparent rate constant for heterogeneous ET from a solution redox probe, Fe(CN)6(3-/4-), to the gold surface through ds-DNA was 4.6 (+/-0.2) x 10(-7) cm/s. With the addition of Zn2+, which resulted in the formation of a metalated DNA (M-DNA) monolayer, the rate constant increased to 5.0 (+/-0.3) x 10(-6) cm/s. Upon treating M-DNA with EDTA, the zinc ions were released from the monolayer and the original rate constant for the DNA duplexes was restored. The enhanced ET rate was also observed at a DNA monolayer treated with Ca2+ or Mg2+, which does not complex by the DNA bases to form M-DNA. The binding of these cations facilitated the monolayer penetration by the probe mediator Fe(CN)6(3-/4-) and accordingly caused an increased redox signal of the mediator at the ds-DNA-modified electrode. Cationic or neutral mediators were not blocked by the ds-DNA monolayer. These results suggest that although the increased electron transport through M-DNA could partially be ascribed to the intrinsic enhancement of electric conductivity of M-DNA, which has been confirmed by photochemical studies, the change in the surface charge of DNA monolayers on the electrode caused by the binding of metal ions to DNA molecules may play a more important role in the enhancement of current with M-DNA.     

Targeted proton delivery in the catalyzed reduction of oxygen to water by bimetallic pacman porphyrins

A combined experimental and theoretical investigation of the role of proton delivery in determining O2 reduction pathways catalyzed by cofacial bisporphyrins is presented. A homologous family of dicobalt(II) Pacman porphyrins anchored by xanthene [Co2(DPX) (1) and Co2(DPXM) (3)] and dibenzofuran [Co2(DPD) (2) and Co2(DPDM) (4)] have been synthesized, characterized, and evaluated as catalysts for the direct four-proton, four-electron reduction of O2 to H2O. Structural analysis of the intramolecular diiron(III) mu-oxo complex Fe2O(DPXM) (5) and electrochemical measurements of 1-4 establish that Pacman derivatives bearing an aryl group trans to the spacer possess structural flexibilities and redox properties similar to those of their parent counterparts; however, these trans-aryl catalysts exhibit markedly reduced selectivities for the direct reduction of O2 to H2O over the two-proton, two-electron pathway to H2O2. Density functional theory calculations reveal that trans-aryl substitution results in inefficient proton delivery to O2-bound catalysts compared to unsubstituted congeners. In particular, the HOMO of [Co2(DPXM)(O2)]+ disfavors proton transfer to the bound oxygen species, funneling the O-O activation pathway to single-electron chemistry and the production of H2O2, whereas the HOMO of [Co2(DPX)(O2)]+ directs protonation to the [Co2O2] core to facilitate subsequent multielectron O-O bond activation to generate two molecules of H2O. Our findings highlight the importance of controlling both proton and electron inventories for specific O-O bond activation and offer a unified model for O-O bond activation within the clefts of bimetallic porphyrins.     

Rational Design for Building Blocks of DNA‐Based Conductive Nanowires through Multi‐Copper Incorporation into Mismatched Base Pairs

Metal‐modified DNA base pairs, which possess potential electrical conductivity and can serve as conductive nanomaterials, have recently attracted much attention. Inspired by our recent finding that multicopper incorporation into natural DNA base pairs could improve the electronic properties of base pairs, herein, we designed two novel multi‐copper‐mediated mismatched base pairs (G_3CuT and A_2CuC), and examined their structural and electronic properties by means of density functional theory calculations. The results reveal that these multi‐Cu‐mediated mismatched base pairs still have planar geometries that are thermodynamically favorable to stability, and their binding energies are close to those of multi‐Cu‐mediated normal base pairs (G_3CuC and A_2CuT). Their HOMO–LUMO gaps and ionization potentials decrease significantly compared to the corresponding natural base pairs. As evidenced by the charge transfer excitation transitions, transverse electronic communication of G_3CuT and A_2CuC is remarkably enhanced, suggesting that they facilitate electron migration along the DNA wires upon incorporation. Further examinations also clarify the possibility to build promising DNA helices using the G_3CuT and/or A_2CuC base pairs. The calculated electronic properties of the three‐layer‐stacked multi‐Cu‐mediated mismatched base pairs illustrate that the Cu_m‐DNA have better conductivity. This work provides perspectives for the development and application of DNA nanowires.     

Combined effects of metal complexation and size expansion in the electronic structure of DNA base pairs

Novel DNA derivatives have been recently investigated in the pursuit of modified DNA duplexes to tune the electronic structure of DNA-based assemblies for nanotechnology applications. Size-expanded DNAs (e.g., xDNA) and metalated DNAs (M-DNA) may enhance stacking interactions and induce metallic conductivity, respectively. Here we explore possible ways of tailoring the DNA electronic structure by combining the aromatic size expansion with the metal-doping. We select the salient structures from our recent study on natural DNA pairs complexed with transition metal ions and consider the equivalent model configurations for xDNA pairs. We present the results of density functional theory electronic structure calculations of the metalated expanded base-pairs with various localized basis sets and exchange-correlation functionals. Implicit solvent and coordination water molecules are also included. Our results indicate that the effect of base expansion is largest in Ag-xGC complexes, while Cu-xGC complexes are the most promising candidates for nanowires with enhanced electron transfer and also for on-purpose modification of the DNA double-helix for signal detection.     

Effective manipulation of the electronic effects and its influence on the emission of 5-substituted tris(8-quinolinolate) aluminum(III) complexes

The unique electron-transport and emissive properties of tris(8-quinolinolate) aluminum(III) (Alq(3)) have resulted in extensive use of this material for small molecular organic light-emitting diode (OLED) fabrication. So far, efforts to prepare stable and easy-to-process red/green/blue (RGB)-emitting Alq(3) derivatives have met with only a limited success. In this paper, we describe how the electronic nature of various substituents, projected via an arylethynyl or aryl spacer to the position of the highest HOMO density (C5), may be used for effective emission tuning to obtain blue-, green-, and red-emitting materials. The synthetic strategy consists of four different pathways for the attachment of electron-donating and electron-withdrawing aryl or arylethynyl substituents to the 5-position of the quinolinolate ring. Successful tuning of the emission color covering the whole visible spectrum (lambda=450-800 nm) was achieved. In addition, the photophysical properties of the luminophores were found to correlate with the Hammett constant of the respective substituents, providing a powerful strategy with which to predict the optical properties of new materials. We also demonstrate that the electronic nature of the substituent affects the emission properties of the resulting complex through effective modification of the HOMO levels of the quinolinolate ligand.     

Singular crystalline beta'-layered topologies directed by ribbons of self-complementary amide...amide ring motifs in [EDT-TTF-(CONH(2))(2)](2)X (X = HSO(4)(-), ClO(4)(-), ReO(4)(-), AsF(6)(-)): coupled activation of ribbon curvature, electron interactions, and magnetic susceptibility

The deliberate design of a series of single crystals of conducting two-dimensional radical cation salts of o-bis(amide)-appended ethylenedithiotetrathiafulvalene, beta'-[EDT-TTF-(CONH(2))(2)](2)X (X = HSO(4)(-), ClO(4)(-), ReO(4)(-), or AsF(6)(-)) and of their parent monocomponent solid EDT-TTF-(CONH(2))(2) is demonstrated and allows us to reach a level of prediction of the structure of molecular conductors. Their conductivity is activated with a gap of 1650 K and a sizable room-temperature conductivity of 0.15 S.cm(-)(1) (for X = ClO(4)(-)) and a singular spin susceptibility for a beta'-type salt that, in addition, changes very remarkably with the anion. The key design element is that of a recurrent, puckered ribbon constructed out of self-complementary, hydrogen-bonded amide...amide ring motifs whose minute modulations of curvature and shape throughout the series have been shown to correlate to very remarkable differences in the intrastack beta(HOMO)(-)(HOMO) interaction energies and changes in the density of states at the Fermi level and on to important differences of spin susceptibility behavior in a system where electron correlations are significant. The coupled activation of structure, electron interactions, and magnetic susceptibility discovered and discussed throughout the paper is unprecedented and is seen as a genuine expression of interfacial hydrogen-bond interactions onto the collective electronic properties.     

Synthesis, structure, and physical properties for a series of trigonal bipyramidal M(II)-Cl complexes with intramolecular hydrogen bonds

A series of transition metal chloro complexes with the tetradentate tripodal tris(2-amino-oxazoline)amine ligand (TAO) have been synthesized and characterized. X-Ray structural analyses of these compounds demonstrate the formation of the mononuclear complexes [M(II)(TAO)(Cl)](+), where M(II) = Cr, Mn, Fe, Co, Ni, Cu and Zn. These complexes exhibit distorted trigonal-bipyramidal geometry, coordinating the metal through an apical tertiary amine, three equatorial imino nitrogen atoms, and an axial chloride anion. All the complexes possess an intramolecular hydrogen-bonding (H-bonding) network within the cavity occupied by the metal-bound chloride ion. The metal-chloride bond distances are atypically long, which is attributed to the effects of the H-bonding network. Nuclear magnetic resonance (NMR) spectroscopy of the Zn complex suggests that the solid-state structures are representative of that observed in solution, and that the H-bonding interactions persist as well. Additionally, density functional theory (DFT) calculations were carried out to probe the electronic structures of the complexes.     

Synthesis and characterization of mixed ligand complexes of copper(II), nickel(II), cobalt(II) and zinc(II) with glycine and uracil or 2-thiouracil

Mixed ligand complexes of Cu(II), Ni(II), Co(II) and Zn(II) formed with glycine and uracil or 2-thiouracil have been synthesized and characterized by elemental analysis, conductance, spectral (IR and electronic spectra) and magnetochemical measurements. Results show that glycine is bidentate in all cases; uracil behaves as a bidentate ligand in Cu(II) complex, coordinating through its one carbonyl oxygen and nitrogen, whereas in other cases it is only monodentate, coordinating only through nitrogen. With thiouracil, coordination occurs from carbonyl oxygen and one nitrogen in Cu(II) and Ni(II) complexes, but in the Co(II) complex coordination occurs from thionyl sulphur and nitrogen. In the Zn(II) complex it shows tridentate behaviour, coordinating through oxygen, sulphur and one nitrogen. Mixed Cu(II), Co(II) and Zn(II) complexes of uracil and of Ni(II) and Zn(II) with thiouracil are octahedral, whereas the mixed Ni(II) complex with uracil shows distorted tetrahedral geometry, and the mixed Co(II)-thiouracil complex is square planar. The mixed Cu(II)-thiouracil complex has a binuclear structure, with square planar arrangement around each copper atom.     

Metal chelates of ampicillin versus amoxicillin: synthesis,structural investigation,and biological studies

Solid chelates derived from some alkaline earth and transition metal complexes with ampicillin (Hamp, a) and amoxicillin (Hamox, b) were synthesized and characterized using elemental analysis, molar conductivity, IR, magnetic susceptibility, and thermogravimetric studies. Both drugs behave as tetradentate ligands coordinating to metal through amino, imino, and carboxylate as well as through β-lactamic carbonyl. All chelates have octahedral geometry except Cu(II) complexes which have square planar structure and uranium has pentagonal bipyramidal coordination. ¹H- and ¹³C-NMR of the Zn(II) and UO₂(VI) chelates are compared with the free ligands. The antimicrobial activity of the prepared chelates was determined.     

Structural character and energetics of tyrosyl radical formation by electron/proton transfers of a covalently linked histidine-tyrosine: a model for cytochrome C oxidase

The structural, energetic, and electronic and IR spectroscopic properties for a model of the cross-linked histidine-tyrosine (His-Tyr) residues as found in cytochrome c oxidase (CcO) are investigated by ab initio methods. The formation of a His-Tyr radical is studied by two paths: proton release followed by electron release and vice versa. The energetics for the proton/electron releases of the Tyr depend modestly on the cross-linked His substituent and, more sensitively, on the charge of the cation attached to the imino N site of the His residue. Protonation of the imino N site significantly increases the electron ionization potential and decreases the proton dissociation energy, making them competitive processes. A positive charge placed at the imino N site, whose value is scanned from zero to one, shows a continuous increase in ionization potential and a decrease in proton dissociation energy, with the +1 limit agreeing well with the protonated imino N site result, indicating a dominant electrostatic effect. The charge populations and the spin density distributions of the His-Tyr model, the radical cation formed by electron ionization, the anion formed by proton dissociation, and the final His-Tyr radical depend sensitively on the substituents, implying a modulation role on the charge transfer between the phenol and imidazole rings, especially for the charged species. His-Tyr and protonated His-Tyr exhibit differences among their respective structural isomers with consequences on their IR absorptions. Small barriers between their pseudo-cis and pseudo-trans rotamers demonstrate the relative flexibility between the two rings, and these may facilitate proton release and charge transfer. The cation effect demonstrates that the cationized cross-linked His-Tyr should be the best candidate to mimic the covalently ring-linked histidine-tyrosine structure in CcO.     

Swallowtail porphyrins: synthesis, characterization and incorporation into porphyrin dyads

The incorporation of symmetrically branched tridecyl ("swallowtail") substituents at the meso positions of porphyrins results in highly soluble building blocks. Synthetic routes have been investigated to obtain porphyrin building blocks bearing 1-4 swallowtail groups. Porphyrin dyads have been synthesized in which the zinc or free base (Fb) porphyrins are joined by a 4,4'-diphenylethyne linker and bear swallowtail (or n-pentyl) groups at the nonlinking meso positions. The swallowtail-substituted Zn(2)- and ZnFb-dyads are readily soluble in common organic solvents. Static absorption and fluorescence spectra and electrochemical data show that the presence of the swallowtail groups slightly raises the energy level of the filled a(2u)(pi) HOMO. EPR studies of the pi-cation radicals of the swallowtail porphyrins indicate that the torsional angle between the proton on the alkyl carbon and p-orbital on the meso carbon of the porphyrin is different from that of a porphyrin bearing linear pentyl groups. Regardless, the swallowtail substituents do not significantly affect the photophysical properties of the porphyrins or the electronic interactions between the porphyrins in the dyads. In particular, time-resolved spectroscopic studies indicate that facile excited-state energy transfer occurs in the ZnFb dyad, and EPR studies of the monocation radical of the Zn(2)-dyad show that interporphyrin ground-state hole transfer is rapid.     

洛汾碱衍生物的电子结构及光谱性质的理论研究

采用密度泛函理论(DFT)的B3LYP/6-31G*方法,对4种洛汾碱类化合物的几何构型进行了优化,在此基础上计算分子的电子结构,并结合有限场FF方法研究了二阶非线性光学(NLO)性质.用含时密度泛函理论(TD-DFT)对上述化合物分子进行吸收光谱的研究.研究表明在4,5-二-苯基-2-对甲酰苯基咪唑生色团中4,5苯环上引入硝基和3位N原子引入苄基改变分子的共轭平面,使二阶非线性极化率总有效值(βtot)减小,吸收峰总体蓝移.同时还发现,在CH2Cl2溶剂中a和c分子的λmax主要来源于HOMO→LUMO的π一π*跃迁,b和d分子的λmax主要来源于HOMO→LUMO+2的π→π*跃迁.     

Electronic properties of mononuclear, dinuclear, and polynuclear cobaltacarboranes: electrochemical and spectroelectrochemical studies

Electronic interactions and metal-metal communication in a wide range of cobaltacarborane-hydrocarbon complexes containing one to six metal centers, and exhibiting a variety of modes of inter-cage connectivity and molecular architectures, have been investigated via cyclic voltammetry, controlled potential coulometry, and UV-visible spectroelectrochemistry. The properties of mixed-valent Co(III)/Co(IV) and Co(II)/Co(III) species that are generated on oxidation or reduction of dinuclear and polynuclear Co(III) complexes were examined and classified as Robin-Day Class I (localized), Class II (partially delocalized), or Class III (fully delocalized) systems. The extent of metal-metal communication between metallacarborane cage units is strongly influenced by the type of intercage connection (e.g., cage B-B or Cp-Cp); the vertexes involved (equatorial vs apical); the nature of the linking unit, if any; and the presence of substituents on the carborane cages. In multi-tripledecker complexes where three CpCo(C(2)B(3)H(4))CoCp units are linked through a central triethynyl benzene connector, the data suggest that Co-Co electronic communication is extensive (Class III) within individual sandwich units while intersandwich delocalization is weak or absent. An extended Hückel study of CpCoC(2)B(4)H(6) double-decker and CpCo(C(2)B(3)H(5))CoCp triple-decker sandwich model complexes shows significant differences in the orbital contributions involved in the HOMO and LUMO of the former vs the latter type. The calculations afford additional insight into the electronic structures and properties of these systems as elucidated by the experimental studies.     

A spectroscopic and magnetic study of complexes of bis(2-benzothiazolyl)methanate and bis(2-benzoxazolyl)methanate with Co(II), Ni(II), Cu(II) and Zn(II)

The co-ordination geometry of the complexes M(bbtm)2 and M(bbom)2 (M: Co, Ni, Cu, Zn; bbtm, bis(2-benzothiazolyl)methanate; bbom, bis(2-benzoxazolyl)methanate) are discussed on the basis of their IR, Raman, resonance Raman, electronic and ESR spectra. Compounds of Ni, Co, Zn with both ligands and Cu(bbom)2 resulted to have a distorted tetrahedral geometry. The distortion towards a square planar geometry is more marked for the M(bbtm)2 series than for the M(bbom)2 one. It has been impossible to suggest a co-ordination geometry for Cu(bbtm)2, that probably has a polymeric structure.     

Transition metal polymeric chelates: Spectral, magnetic, thermal behaviour of polymeric chelates of poly(resacetophenone diyl ethylene)s with Ni(II), Cu(II), Mn(II), Zn(II) and Co(II)

Polymeric chelates of the type [ML₂]_n where M = Ni(II), Cu(II), Zn(II) or Co(II), L = poly(resacetophenone diyl ethylene)s, andn= degree of polymerization, have been synthesized. Their structures have been elucidated on the basis of analytical, magnetic, electronic and IR spectral studies. Electronic spectra in conjunction with magnetic moments are in accord with an octahedral environment around the central metal ion in all polymeric chelates except Cu(II) and Zn(II) polymeric chelates which have been shown to possess square planar and tetrahedral geometries, respectively. IR spectral studies further suggest that the metal ions are coordinated through the oxygens of the carbonyl and the phenolic hydroxyl groups. All the chelates are paramagnetic except Zn(II), which is found to be diamagnetic.     

Quantum chemical analysis of electronic structure and n- and p-type charge transport in perfluoroarene-modified oligothiophene semiconductors

Density-functional theory (DFT) is employed to investigate the structural, electronic, and transport properties of several isomeric fluoroarene-oligothiophene-based semiconductors. Three oligothiophene systems varying in the perfluoroarene group positions within the molecule are studied to understand the electronic structure leading to the observed mobility values and to the n- or p-type behavior in these structures. Analyses of both intermolecular interactions in dimers and extended interactions in crystalline structures afford considerable insight into the electronic properties and carrier mobilities of these materials, as well as the polarity of the charge carriers. From the calculated carrier effective masses, we find that sterically governed molecular planarity plays a crucial role in the transport properties of these semiconductors. Our calculations correlate well with experimentally obtained geometries, highest-occupied molecular orbital (HOMO)/lowest-unoccupied molecular orbital (LUMO) energies, and the experimental carrier mobility trends among the systems investigated.     

Influence of the Absolute Configuration of NPE‐Caged Cytosine on DNA Single Base Pair Stability

Photolabile protecting groups are a versatile tool to trigger reactions by light irradiation. In this study, we have investigated the influence of the absolute configuration of the 1‐(2‐nitrophenyl)ethyl (NPE) cage group on a 15‐base‐pair duplex DNA. Using UV melting, we determined the global stability of the unmodified and the selectively (S)‐ and (R)‐NPE‐modified DNA sequences, respectively. We observe a differently destabilizing effect for the two NPE stereoisomers on the global stability. Analysis of the temperature dependence of imino proton exchange rates measured by NMR spectroscopy reveals that this effect can be attributed to decreased base pair stabilities of the caged and the 3′‐neighbouring base pair, respectively. Furthermore, our NMR based structural models of the modified duplexes provide a structural basis for the distinct effect of the (S)‐ and the (R)‐NPE group.