Super-resolution Imaging of Plasmonic Near-Fields: Overcoming Emitter Mislocalizations.

Plasmonic nano-objects have shown great potential in enhancing applications like biological/chemical sensing, light harvesting and energy transfer, and optical/quantum computing. Therefore, an extensive effort has been vested in optimizing plasmonic systems and exploiting their field enhancement properties. Super-resolution imaging with quantum dots (QDs) is a promising method to probe plasmonic near-fields but is hindered by the distortion of the QD radiation pattern. Here, we investigate the interaction between QDs and "L-shaped" gold nanoantennas and demonstrate both theoretically and experimentally that this strong interaction can induce polarization-dependent modifications to the apparent QD emission intensity, polarization, and localization. Based on FDTD simulations and polarization-modulated single-molecule microscopy, we show that the displacement of the emitter's localization is due to the position-dependent interference between the emitter and the induced dipole, and can be up to 100 nm. Our results help pave a pathway for higher precision plasmonic near-field mapping and its underlying applications.

Far-Field Super-resolution Detection of Plasmonic Near-Fields.

We demonstrate a far-field single molecule super-resolution method that maps plasmonic near-fields. The method is largely invariant to fluorescence quenching (arising from probe proximity to a metal), has reduced point-spread-function distortion compared to fluorescent dyes (arising from strong coupling to nanoscopic metallic features), and has a large dynamic range (of 2 orders of magnitude) allowing mapping of plasmonic field-enhancements regions. The method takes advantage of the sensitivity of quantum dot (QD) stochastic blinking to plasmonic near-fields. The modulation of the blinking characteristics thus provides an indirect measure of the local field strength. Since QD blinking can be monitored in the far-field, the method can measure localized plasmonic near-fields at high throughput using a simple far-field optical setup. Using this method, propagation lengths and penetration depths were mapped-out for silver nanowires of different diameters and for different dielectric environments, with a spatial accuracy of ∼15 nm. We initially use sparse sampling to ensure single molecule localization for accurate characterization of the plasmonic near-field with plans to increase density of emitters in further studies. The measured propagation lengths and penetration depths values agree well with Maxwell finite-difference time-domain calculations and with published literature values. This method offers advantages such as low cost, high throughput, and superresolved mapping of localized plasmonic fields at high sensitivity and fidelity.

Photon-HDF5: An Open File Format for Timestamp-Based Single-Molecule Fluorescence Experiments.

We introduce Photon-HDF5, an open and efficient file format to simplify exchange and long-term accessibility of data from single-molecule fluorescence experiments based on photon-counting detectors such as single-photon avalanche diode, photomultiplier tube, or arrays of such detectors. The format is based on HDF5, a widely used platform- and language-independent hierarchical file format for which user-friendly viewers are available. Photon-HDF5 can store raw photon data (timestamp, channel number, etc.) from any acquisition hardware, but also setup and sample description, information on provenance, authorship and other metadata, and is flexible enough to include any kind of custom data. The format specifications are hosted on a public website, which is open to contributions by the biophysics community. As an initial resource, the website provides code examples to read Photon-HDF5 files in several programming languages and a reference Python library (phconvert), to create new Photon-HDF5 files and convert several existing file formats into Photon-HDF5. To encourage adoption by the academic and commercial communities, all software is released under the MIT open source license.

Photon-HDF5: Open Data Format and Computational Tools for Timestamp-based Single-Molecule Experiments.

Archival of experimental data in public databases has increasingly become a requirement for most funding agencies and journals. These data-sharing policies have the potential to maximize data reuse, and to enable confirmatory as well as novel studies. However, the lack of standard data formats can severely hinder data reuse. In photon-counting-based single-molecule fluorescence experiments, data is stored in a variety of vendor-specific or even setup-specific (custom) file formats, making data interchange prohibitively laborious, unless the same hardware-software combination is used. Moreover, the number of available techniques and setup configurations make it difficult to find a common standard. To address this problem, we developed Photon-HDF5 (www.photon-hdf5.org), an open data format for timestamp-based single-molecule fluorescence experiments. Building on the solid foundation of HDF5, Photon-HDF5 provides a platform- and language-independent, easy-to-use file format that is self-describing and supports rich metadata. Photon-HDF5 supports different types of measurements by separating raw data (e.g. photon-timestamps, detectors, etc) from measurement metadata. This approach allows representing several measurement types and setup configurations within the same core structure and makes possible extending the format in backward-compatible way. Complementing the format specifications, we provide open source software to create and convert Photon-HDF5 files, together with code examples in multiple languages showing how to read Photon-HDF5 files. Photon-HDF5 allows sharing data in a format suitable for long term archival, avoiding the effort to document custom binary formats and increasing interoperability with different analysis software. We encourage participation of the single-molecule community to extend interoperability and to help defining future versions of Photon-HDF5.

Substituent effects on the reversibility of furan-maleimide cycloadditions.

The effects of furan and maleimide substitution on the dynamic reversibility of their Diels-Alder reactivity have been investigated computationally and by (1)H NMR spectroscopy. Furan and furan derivatives bearing methoxy, methyl, or formyl groups at their 2- or 3-positions were investigated with maleimide and maleimide derivatives bearing N-methyl, N-allyl, and N-phenyl substituents. Computational predictions indicate that electronic and regiochemical effects of furan substitution significantly influence their Diels-Alder reactivity with maleimide, with reaction free energies of exo adduct formation ranging from ΔG = -9.4 to 0.9 kcal/mol and transition state barriers to exo adduct formation ranging from ΔG(‡) = 18.9 to 25.6 kcal/mol. Much less variation was observed for the reactivity of N-substituted maleimide derivatives and furan, with reaction and transition state free energies each falling within a range of 1.1 kcal/mol. Dynamic exchange experiments monitored by (1)H NMR spectroscopy support computational predictions. The results indicate the reactivity and reversibility of furan-maleimide cycloadditions can be tuned significantly through the addition of appropriate substituents and have implications in the use of furan and maleimide derivatives in the construction of thermally responsive organic materials.