Dissecting and reducing the heterogeneity of excited-state energy transport in DNA-based photonic wires

Molecular photonic wires are one-dimensional representatives of a family of nanoscale molecular devices that transport excited-state energy over considerable distances in analogy to optical waveguides in the far-field. In particular, the design and synthesis of such complex supramolecular devices is challenging concerning the desired homogeneity of energy transport. On the other hand, novel optical techniques are available that permit direct investigation of heterogeneity by studying one device at a time. In this article, we describe our efforts to synthesize and study DNA-based molecular photonic wires that carry several chromophores arranged in an energetic downhill cascade and exploit fluorescence resonance energy transfer to convey excited-state energy. The focus of this work is to understand and control the heterogeneity of such complex systems, applying single-molecule fluorescence spectroscopy (SMFS) to dissect the different sources of heterogeneity, i.e., chemical heterogeneity and inhomogeneous broadening induced by the nanoenvironment. We demonstrate that the homogeneity of excited-state energy transport in DNA-based photonic wires is dramatically improved by immobilizing photonic wires in aqueous solution without perturbation by the surface. In addition, our study shows that the in situ construction of wire molecules, i.e., the stepwise hybridization of differently labeled oligonucleotides on glass cover slides, further decreases the observed heterogeneity in overall energy-transfer efficiency. The developed strategy enables efficient energy transfer between up to five chromophores in the majority of molecules investigated along a distance of approximately 14 nm. Finally, we used multiparameter SMFS to analyze the energy flow in photonic wires in more detail and to assign residual heterogeneity under optimized conditions in solution to different leakages and competing energy-transfer processes.     

Current-induced rotation of helical molecular wires

We show that electric current running through a nanojunction with a biased helical molecule can induce unidirectional rotation of the molecular component. In an electric field, conduction electrons injected into the molecule are accelerated along the helical path going through its body, thereby gaining directed angular momentum. Conservation laws require that an angular momentum of the same size but opposite sense is imparted to the rigid-body rotation of the helix. We describe the angular momentum exchange processes that underlie the operation of the nanorotor, discuss factors limiting its efficiency, and propose potential applications.     

Conduction properties of bipyridinium-functionalized molecular wires

We present a detailed analysis of the coherent electron transport through a redox-active, 4,4'-bipyridinium (viologen)-functionalized molecular wire, which was studied in several recent experiments. Our calculations for the bare viologen predict conductances differing by 2 orders of magnitude depending on the contact geometry. For the alkyl-wired viologen unit, we obtain an exponential decay of the conductance with the wire length. Because this exponent also governs the conductance in the incoherent transport regime, comparison with experiments is legitimate and we find a good agreement. Furthermore, our calculations indicate that the experimentally observed conductance switching behavior is not amenable to an explanation inside a coherent transport picture. A possible incoherent mechanism is being discussed.     

Efficient synthesis of thioamide terminated molecular wires

Bis-thioamide terminated ‘molecular wires’ are formed in a high yield under mild conditions from readily synthesised bis-nitrile terminated molecules and aqueous ammonium sulfide in DMF.     

Effect of bond-length alternation in molecular wires

Current-voltage (I-V) characteristics for metal-molecule-metal junctions formed from three classes of molecules measured with a simple crossed-wire molecular electronics test-bed are reported. Junction conductance as a function of molecular structure is consistent with I-V characteristics calculated from extended Hückel theory coupled with a Green's function approach, and can be understood on the basis of bond-length alternation.     

Optical properties of current carrying molecular wires

We consider several fundamental optical phenomena involving single molecules in biased metal-molecule-metal junctions. The molecule is represented by its highest occupied and lowest unoccupied molecular orbitals, and the analysis involves the simultaneous consideration of three coupled fluxes: the electronic current through the molecule, energy flow between the molecule and electron-hole excitations in the leads, and the incident and/or emitted photon flux. Using a unified theoretical approach based on the nonequilibrium Green's function method we derive expressions for the absorption line shape (not an observable but a useful reference for considering yields of other optical processes) and for the current induced molecular emission in such junctions. We also consider conditions under which resonance radiation can induce electronic current in an unbiased junction. We find that current driven molecular emission and resonant light induced electronic currents in single molecule junctions can be of observable magnitude under appropriate realizable conditions. In particular, light induced current should be observed in junctions involving molecular bridges that are characterized by strong charge-transfer optical transitions. For observing current induced molecular emission we find that in addition to the familiar need to control the damping of molecular excitations into the metal substrate the phenomenon is also sensitive to the way in which the potential bias is distributed on the junction.     

Second hyperpolarizability of ethynyl-linked azobenzene molecular wires

A series of oligomers consisting of ethynyl-linked azobenzene units was prepared using Pd-catalyzed cross coupling. The linear and nonlinear optical properties of the oligomers were investigated. The molecular second hyperpolarizability, gamma, followed the power law gamma proportional, variant n(2.12+/-0.05) (n is the number of repeat units) for unusually large molecular lengths exceeding 360 conjugated bonds (>49 nm). The exceptional exciton delocalization length is attributed to the rigidity of the conjugated backbone.     

p-Phenyleneethynylene molecular wires: influence of structure on photoinduced electron-transfer properties

A series of donor-acceptor arrays (exTTF-oPPE-C60) containing pi-conjugated oligo(phenyleneethynylene) wires (oPPE) of different length between pi-extended tetrathiafulvalene (exTTF) as electron donor and fullerene (C60) as electron acceptor has been prepared by following a convergent synthesis. The key reaction in these approaches is the bromo-iodo selectivity of the Hagihara-Sonogashira reaction and the deprotecting of acetylenes with different silyl groups to afford the corresponding donor-acceptor conjugates in moderate yields. The electronic interactions between the three electroactive species were determined by using UV-visible spectroscopy and cyclic voltammetry. Our studies clearly confirm that, although the C60 units are connected to the exTTF donor through pi-conjugated oPPE frameworks, no significant electronic interactions are observed in the ground state. Theoretical calculations predict how a simple exchange from C=C double bonds (i.e., oligo(p-phenylenevinylene) to C triple chemical bond C triple bonds (i.e., oPPE) in the electron donor-acceptor conjugates considerably alters long-range electron transfer. Photoexcitation of exTTF-oPPE-C60 leads to the following features: a transient photoproduct with maxima at 660 and 1000 nm, which are unambiguously attributed to the photolytically generated radical-ion-pair state, [exTTF*+-oPPE-C60*]. Both charge-separation and charge-recombination processes give rise to a molecular-wire behaviour of the oPPE moiety with an attenuation factor (beta) of (0.2+/-0.05) A(-1).     

A comparison of potential molecular wires as components for molecular electronics

The field of electronics using single-molecule components has recently received much attention as a possible new design concept for the continued miniturisation of electronics. Molecular wires are the conceptually simplest components of such electronic systems and several different compound types have been used to produce molecular wires. Examples of some of the most promising families of molecular wires are presented, namely conjugated hydrocarbons, carbon nanotubes, porphyrin oligomers and DNA. Discussion centres around their potential use in functioning electronic architectures in terms of their electronic properties, ease and controllability of synthesis and potential for self-assembly.     

Communication: Time-resolved fluorescence of highly single crystalline molecular wires of azobenzene

We report the enhanced fluorescence with the remarkably long lifetime (1.17 ns) in the first excited state (S(1)) of highly crystalline molecular wires of azobenzene at the excitation wavelength of 467 nm for the first time. This observation suggests that trans-cis photoisomerization through the rotation or inversion mechanism may not be a favorable pathway after excitation to the S(1) state in highly single crystalline molecular wires of azobenzene due to the hindered motion within densely packed crystal structure. We also measured the fluorescence lifetime image of a single crystalline molecular wire of azobenzene, indicating that the lifetime was remarkably uniform and that there was only a very minor variation within the crystal.     

Weakly coupled molecular photonic wires: synthesis and excited-state energy-transfer dynamics

Molecular photonic wires, which absorb light and undergo excited-state energy transfer, are of interest as biomimetic models for photosynthetic light-harvesting systems and as molecular devices with potential applications in materials chemistry. We describe the stepwise synthesis of four molecular photonic wires. Each wire consists of an input unit, transmission element, and output unit. The input unit consists of a boron-dipyrrin dye or a perylene-monoimide dye (linked either at the N-imide or the C9 position); the transmission element consists of one or three zinc porphyrins affording short or long wires, respectively; and the output unit consists of a free base (Fb) porphyrin. The components in the arrays are joined in a linear architecture via diarylethyne linkers (an ethynylphenyl linker is attached to the C9-linked perylene). The wires have been examined by static absorption, static fluorescence, and time-resolved absorption spectroscopy. Each wire (with the exception of the C9-linked perylene wire) exhibits a visible absorption spectrum that is the sum of the spectra of the component parts, indicating the relatively weak electronic coupling between the components. Excitation of each wire at the wavelength where the input unit absorbs preferentially (typically 480-520 nm) results in emission almost exclusively from the Fb porphyrin. The static emission and time-resolved data indicate that the overall rate constants and quantum efficiencies for end-to-end (i.e., input to output) energy transfer are as follows: perylene-(N-imide)-linked short wire, (33 ps)(-1) and >99%; perylene-(C9)-linked short wire, (26 ps)(-1) and >99%; boron-dipyrrin-based long wire, (190 ps)(-1) and 81%; perylene-(N-imide)-linked long wire, (175 ps)(-1) and 86%. Collectively, the studies provide valuable insight into the singlet-singlet excited-state energy-transfer properties in weakly coupled molecular photonic wires.     

Mechanically untying a protein slipknot: multiple pathways revealed by force spectroscopy and steered molecular dynamics simulations

Protein structure is highly diverse when considering a wide range of protein types, helping to give rise to the multitude of functions that proteins perform. In particular, certain proteins are known to adopt a knotted or slipknotted fold. How such proteins undergo mechanical unfolding was investigated utilizing a combination of single molecule atomic force microscopy (AFM), protein engineering, and steered molecular dynamics (SMD) simulations to show the mechanical unfolding mechanism of the slipknotted protein AFV3-109. Our results reveal that the mechanical unfolding of AFV3-109 can proceed via multiple parallel unfolding pathways that all cause the protein slipknot to untie and the polypeptide chain to completely extend. These distinct unfolding pathways proceed via either a two- or three-state unfolding process involving the formation of a well-defined, stable intermediate state. SMD simulations predict the same contour length increments for different unfolding pathways as single molecule AFM results, thus providing a plausible molecular mechanism for the mechanical unfolding of AFV3-109. These SMD simulations also reveal that two-state unfolding is initiated from both the N- and C-termini, while three-state unfolding is initiated only from the C-terminus. In both pathways, the protein slipknot was untied during unfolding, and no tightened slipknot conformation was observed. Detailed analysis revealed that interactions between key structural elements lock the knotting loop in place, preventing it from shrinking and the formation of a tightened slipknot conformation. Our results demonstrate the bifurcation of the mechanical unfolding pathway of AFV3-109 and point to the generality of a kinetic partitioning mechanism for protein folding/unfolding.     

Unimolecular micelles: supramolecular use of dendritic constructs to create versatile molecular containers

A brief survey of host–guest interactions involving dendritic architectures is presented. Discussion begins with an examination of early examples of branched motifs described as ‘micelle-like’ and progresses through to current investigations of unimolecular micelles and their attendant supramolecular properties. To cite this article: C.N. Moorefield, G.R. Newkome, C. R. Chimie 6 (2003).     

Determination of the attenuation factor in fluorene-based molecular wires

Fluorene-based bridges exhibit a molecular wire-like behaviour in C(60)-wire-exTTF systems with a very low attenuation factor (beta = 0.09 A(-1)).     

Synthesis and electronic properties of alkyne-TTFAQ based molecular wires

We herein describe the first synthesis of a series of π-extend tetrathiafulvalene and alkyne based conjugated molecular wires. Electronic properties of these compounds were characterized by cyclic voltammetry, UV-vis absorption, and fluorescence spectroscopy.     

Ultraviolet emission of molecular chlorine

The UV emission of Cl₂ from a new valence-shell state having 0⁺_u symmetry (T_c ≈ 59774 cm^?1, r_c ≈ 3.0 Å) was observed by focusing ≈ 500 nm laser radiation to gaseous chlorine. Excitation was achieved by virtual two-photon absorption from the B ³Π_0⁺u state formed by single-photon absorption stepwisely. The emission spectra showed transitions to the ground state as well as to the repulsive grade estate dissociating to Cl²P) + Cl(²P) products.