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.     

Design of molecular photonic wires based on multistep electronic excitation transfer.

Light-harvesting complexes, one of nature's supreme examples of nanoscale engineering, have inspired researchers to construct molecular optical devices, such as photonic wires, which are optimised for efficient transfer of excited-state energy over large distances. The control parameters for the design and the advantages of single-molecule fluorescence spectroscopy for the study of such complex systems are discussed with respect to energy-transfer mechanisms, chromophore selection and arrangement as well as static and dynamic heterogeneity.     

Multistep energy transfer in single molecular photonic wires

We demonstrate the synthesis and spectroscopic characterization of an unidirectional photonic wire based on four highly efficient fluorescence energy-transfer steps (FRET) between five spectrally different chromophores covalently attached to double-stranded DNA. The DNA-based modular conception enables the introduction of various chromophores at well-defined positions and arbitrary interchromophore distances. While ensemble fluorescence measurements show overall FRET efficiencies between 15 and 30%, single-molecule spectroscopy performed on four spectrally separated detectors easily uncovers subpopulations that exhibit overall FRET efficiencies of up to approximately 90% across a distance of 13.6 nm and a spectral range of approximately 200 nm. Fluorescence trajectories of individual photonic wires show five different fluorescence intensity patterns which can be ascribed to successive photobleaching events.     

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.     

A Study of Excitation Delocalization/Localization in Multibranched Chromophores by Using Fluorescence Excitation Anisotropy Spectroscopy

We describe a simple approach to study the excitation localization/delocalization in multibranched chromophores by using fluorescence excitation anisotropy spectroscopy at room temperature. As examples, the electronic excitations in three different multibranched chromophores (dimers) are investigated. For a weakly coupled dimer, fluorescence anisotropy is independent of excitation wavelength, due to localized excitation as well as the degenerate electronic excited states. In contrast, in the case of a strongly coupled dimer, owing to excitonic splitting, a redistribution of the excitation energy is demonstrated by the dependence of anisotropy spectra on the excitation wavelength, which leads to significant deviation from the anisotropy signal of localized excitation. In particular, based on the law of additivity for anisotropy, the degree of delocalized excitation can be simply estimated for a given dimer.     

Linear absorbance of the pheophorbide-a butanediamine dendrimer P(4) in solution: computational studies using a mixed quantum classical methodology

The linear absorbance of a particular chromophore complex P(4) dissolved in ethanol is computed. P(4) is formed by a butanediamine dendrimer to which four pheophorbide-a molecules are covalently linked. The computations utilize a mixed quantum classical methodology and different approximations are compared. The electronic states of the P(4) chromophores which form Frenkel excitons in the excited states are treated quantum mechanically, whereas the intramolecular, intermolecular, as well as solvent coordinates are described classically. The computations use an improved exciton model, where the charge and transition densities of the chromophores are described by atomic partial charges, derived from a fit of the respective ab initio electrostatic potentials. Room temperature molecular dynamics simulations of all nuclear coordinates result in a time-dependent exciton model. It includes modulations of chromophore excitation energies due to charge density coupling between all chromophores as well as between the chromophores and solvent molecules, and, finally, modulations of the interchromophore excitonic couplings. The different approximations to the absorbance agree rather well. In particular, they confirm the reliability of adiabatic excitonic states which energies and oscillator strengths are altered by the overall temporal evolution of P(4) conformations. The fluctuations of solute-solvent interactions have a significantly larger effect on the absorbance broadening than the excitonic couplings but cannot completely explain the measured spectrum. The additional account for intrachromophore vibrations overcomes this discrepancy.     

A 3.0 micros room temperature excited state lifetime of a bistridentate RuII-polypyridine complex for rod-like molecular arrays

A bistridentate RuII-polypyridine complex [Ru(bqp)2]2+ (bqp = 2,6-bis(8'-quinolinyl)pyridine) has been prepared, which has a coordination geometry much closer to a perfect octahedron than the typical Ru(terpyridine)2-type complex. Thus, the complex displays a 3.0 mus lifetime of the lowest excited metal-to-ligand charge transfer (3MLCT) state at room temperature. This is, to the best of our knowledge, the longest MLCT state lifetime reported for a RuII-polypyridyl complex at room temperature. The structure allows for the future construction of rod-like, isomer-free molecular arrays by substitution of donor and acceptor moieties on the central pyridine units. This makes it a promising photosensitizer for applications in molecular devices for artificial photosynthesis and molecular electronics.     

Cobalt and manganese nets via their wires: facile transformation in metal-diorganophosphates

The manganese and cobalt complexes [M(dtbp)2]n (M=Mn, Co; dtbp=di-tert-butyl phosphate), which exist as one-dimensional molecular wires, transform to [M(dtbp)2(bpy)2.2H2O]n by the addition of 4,4-bipyridine (bpy) at room temperature; the latter compounds form noninterpenetrating rectangular grid structures.     

Activating charge-transfer state formation in strongly-coupled dimers using DNA scaffolds

Strongly-coupled multichromophoric assemblies orchestrate the absorption, transport, and conversion of photonic energy in natural and synthetic systems. Programming these functionalities involves the production of materials in which chromophore placement is precisely controlled. DNA nanomaterials have emerged as a programmable scaffold that introduces the control necessary to select desired excitonic properties. While the ability to control photophysical processes, such as energy transport, has been established, similar control over photochemical processes, such as interchromophore charge transfer, has not been demonstrated in DNA. In particular, charge transfer requires the presence of close-range interchromophoric interactions, which have a particularly steep distance dependence, but are required for eventual energy conversion. Here, we report a DNA-chromophore platform in which long-range excitonic couplings and short-range charge-transfer couplings can be tailored. Using combinatorial screening, we discovered chromophore geometries that enhance or suppress photochemistry. We combined spectroscopic and computational results to establish the presence of symmetry-breaking charge transfer in DNA-scaffolded squaraines, which had not been previously achieved in these chromophores. Our results demonstrate that the geometric control introduced through the DNA can access otherwise inaccessible processes and program the evolution of excitonic states of molecular chromophores, opening up opportunities for designer photoactive materials for light harvesting and computation.

DNA scaffolds enable the activation and suppression of photochemistry between strongly-coupled synthetic chromophores.     

DNA-based molecular wires: multiple emission pathways of individual constructs

The extent of photon energy transfer through individual DNA-based molecular wires composed of five dyes is investigated at the single molecular level. Combining single-molecule spectroscopy and pulse interleaved excitation imaging, we have directly resolved the time evolution spectral response of individual constructs, while simultaneously probing DNA integrity. Our data clearly show that intact wires exhibit photon-transfer efficiencies close to 100% across five dyes. Dynamical and multiple pathways for the photon emission resulting from conformational freedom of the wire are readily uncovered. These results provide the basis for guiding the synthesis of DNA-based supramolecular arrays with improved photon transport at the nanometer scale.     

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.     

Spontaneous S–Si bonding of alkanethiols to Si(111)–H: towards Si–molecule–Si circuits

We report the synthesis of covalently linked self-assembled monolayers (SAMs) on silicon surfaces, using mild conditions, in a way that is compatible with silicon-electronics fabrication technologies. In molecular electronics, SAMs of functional molecules tethered to gold via sulfur linkages dominate, but these devices are not robust in design and not amenable to scalable manufacture. Whereas covalent bonding to silicon has long been recognized as an attractive alternative, only formation processes involving high temperature and/or pressure, strong chemicals, or irradiation are known. To make molecular devices on silicon under mild conditions with properties reminiscent of Au–S ones, we exploit the susceptibility of thiols to oxidation by dissolved O₂, initiating free-radical polymerization mechanisms without causing oxidative damage to the surface. Without thiols present, dissolved O₂ would normally oxidize the silicon and hence reaction conditions such as these have been strenuously avoided in the past. The surface coverage on Si(111)–H is measured to be very high, 75% of a full monolayer, with density-functional theory calculations used to profile spontaneous reaction mechanisms. The impact of the Si–S chemistry in single-molecule electronics is demonstrated using STM-junction approaches by forming Si–hexanedithiol–Si junctions. Si–S contacts result in single-molecule wires that are mechanically stable, with an average lifetime at room temperature of 2.7 s, which is five folds higher than that reported for conventional molecular junctions formed between gold electrodes. The enhanced “ON” lifetime of this single-molecule circuit enables previously inaccessible electrical measurements on single molecules.

Spontaneously formed Si–S bonds enable monolayer and single-molecule Si–molecule–Si circuits.     

Tessellation of porphyrazines with porphyrins by design

The efficient self-assembly and functional characterization of arrays containing multiple types of chromophores will provide a basis for the design and applications of functional photonic materials that are unobtainable using only one type of molecule. The design, synthesis, and characterization of supramolecular systems bearing two different types of porphyrinic chromophores, porphyrins and porphyrazines, are reported. Because the porphyrins and porphyrazines bear different exocyclic ligands for self-assembly by metal ion coordination, these systems require new supramolecular synthetic strategies wherein reactants are added in a specific order. These arrays display unique photophysical properties derived from the component chromophores, the metal geometry, and the supramolecular nanoarchitecture.     

单分子电导测量技术及其影响因素

Molecular electronics is an important field for the application of nanotechnologies with an ultimate goal of building functional devices using single molecules or molecular arrays to realize the same functionality as macroscopic devices. To attain this goal, reliable techniques for measuring and manipulating electron transfer processes through single molecules are essential. There are various techniques and many environmental factors influencing single-molecule electronic conductance measurements. In this review, we first provide a detailed introduction and classification of the current well-accepted techniques in this field for measuring single-molecule conductance. All available techniques are summarized into two categories: the fixed junction technique and break junction technique. The break junction technique involves repeatedly forming and breaking molecular junctions by mechanically controlling a pair of electrodes moving into and out of contact in the presence of target molecules. Single-molecule conductance can be determined from the conductance plateaus that appear in typical conductance decay traces when molecules bind two electrodes during their separation process. In contrast, the fixed junction technique is to fix the distance between a pair of electrodes and measure the conductance fluctuations when a single molecule binds the two electrodes stochastically. Both techniques comprise different application methods and have been employed preferentially by different groups. Specific features of both techniques and their intrinsic advantages are compared and summarized in Section 4.     

Long-Lived Photocharges in Supramolecular Polymers of Low-Band-Gap Chromophores

Photoinduced charge separation in supramolecular aggregates of π-conjugated molecules is a fundamental photophysical process and a key criterion for the development of advanced organic electronics materials. Herein, the self-assembly of low-band-gap chromophores into helical one-dimensional aggregates, due to intermolecular hydrogen bonding, is reported. Chromophores confined in these supramolecular polymers show strong excitonic coupling interactions and give rise to charge-separated states with unusually long lifetimes of several hours and charge densities of up to 5 mol % after illumination with white light. Two-contact devices exhibit increased photoconductivity and can even show Ohmic behavior. These findings demonstrate that the confinement of organic semiconductors into one-dimensional aggregates results in a considerable stabilization of charge carriers for a variety of π-conjugated systems, which may have implications for the design of future organic electronic materials.     

Integrating DNA Photonic Wires into Light‐Harvesting Supramolecular Polymers

An approach combining DNA nanoscaffolds with supramolecular polymers for the efficient and directional propagation of light‐harvesting cascades has been developed. A series of photonic wires with different arrangements of fluorophores in DNA‐organized nanostructures were linked to light‐harvesting supramolecular phenanthrene polymers (SPs) in a self‐assembled fashion. Among them, a light‐harvesting complex (LHC) composed of SPs and a photonic wire of phenanthrene, Cy3, Cy5, and Cy5.5 chromophores reveals a remarkable energy transfer efficiency of 59 %. Stepwise transfer of the excitation energy collected by the light‐harvesting SPs via the intermediate Cy3 and Cy5 chromophores to the final Cy5.5 acceptor proceeds through a Förster resonance energy transfer mechanism. In addition, the light‐harvesting properties are documented by antenna effects ranging from 1.4 up to 23 for different LHCs.     

DNA and microfluidics: building molecular electronics systems

The development of molecular electronics using DNA molecules as the building blocks and using microfluidics to build nanowire arrays is reviewed. Applications of DNA conductivity to build sensors and nanowire arrays, and DNA conjugation with other nanostructures, offers an exciting opportunity to build extremely small analytical devices that are suitable for single-molecule detection and also target screening.     

On the influence of nonlocal molecular vibrations and charge transfer on the spectra of aggregated push-pull chromophores

Through their fluorescence spectrum, aggregates of push-pull chromophores are good reporters of their microenvironment temperature and polarity. The understanding of the fluorescence and charge-separation dynamics in arrays composed of this type of species is consequently of considerable interest. In this article, we study the effect of charge fluctuations induced by molecular nonlocal vibrations on the electronic coupling between a pair of linear push-pull chromophores, for side-to-side or head-to-tail orientations, using a valence-bond charge-transfer (VB-CT) model and the Redfield equation. The results show that the exciton-vibrational dynamics along the bond length alternation coordinate can significantly modify the inter-molecular electronic coupling, which determines the fluorescence spectral band redshift due to aggregation. Numerical results for the electronic and exciton-vibrational contributions to the Coulombic coupling between two of these chromophores are obtained using experimentally based parameters for polyene linker species. The exciton-vibrational contribution is significant relative to the electronic contribution at room temperature in some ranges of the energy gap between the VB and CT states, and it is more important for the side-to-side than for the head-to-tail configuration. Our calculations also show that, even without including solvation effects, the spectral band associated with an S(0) → S(1) transition is redshifted with increasing temperature.     

Structure-Based Calculations of the Optical Spectra of the LH2 Bacteriochlorophyll-Protein Complex from Rhodopseudomonas acidophila

Abstract— The molecular structure of the light-harvesting complex 2 (LH2) bacteriochlorophyll-protein antenna complex from the purple non-sulfur photosynthetic bacterium Rhodopseudomonas acidophila , strain 10050 provides the positions and orientations of the 27 bacteriochlorophyll (BChl) molecules in the complex. Our structure-based model calculations of the distinctive optical properties (absorption, CD, polarization) of LH2 in the near-infrared region use a point-monopole approximation to represent the BChl Q_y transition moment. The results of the calculations support the assignment of the ring of 18 closely coupled BChl to B850 (BChl absorbing at 850 nm) and the larger diameter, parallel ring of 9 weakly coupled BChl to B800. All of the significantly allowed transitions in the near infrared are calculated to be perpendicular to the C9 symmetry axis, in agreement with polarization studies of this membrane-associated complex. To match the absorption maxima of the B800 and B850 components using a relative permittivity (dielectric constant) of 2.1, we assign different site energies (12 500 and 12260 cm⁻¹, respectively) for the Q_y transitions of the respective BChl in their protein binding sites. Excitonic coupling is particularly strong among the set of B850 chromophores, with pairwise interaction energies nearly 300 cm between nearest neighbors, comparable with the experimental absorption bandwidths at room temperature. These strong interactions, for the full set of 18 B850 chromophores, result in an excitonic manifold that is 1200 cm⁻¹ wide. Some of the upper excitonic states should result in weak absorption and perhaps stronger CD features. These predictions from the calculations await experimental verification.     

Two-dimensional electronic conjugation: statics and dynamics at structural domains beyond molecular wires

Chemical architectures supporting a high degree of electronic conjugation serve as important functional components in devices and materials for advanced electronic and photonic applications. Increasing the spatial dimensionality of such constructs can fundamentally modify their optoelectronic properties and significantly alter intra- and intermolecular interactions that are crucial for understanding and controlling charge/energy-transfer processes. In this article, emerging design principles in the construction of well-defined conjugated platforms beyond molecular wires are highlighted. Both covalent and noncovalent approaches can be strategically employed to position one-dimensional (1D) substructures in a spatially well-defined manner in order to enhance both structural and functional complexity in a two-dimensional (2D) setting. A predictable and controllable switching mechanism can be designed and implemented with mobile 2D electronic conjugation that operates by correlated motions of inherently rigid 1D subunits. This emerging "dynamic" approach complements and challenges the prevailing "static" paradigm of conjugated chemical architectures.