FRET Enhancement in Aluminum Zero‐Mode Waveguides

Zero‐mode waveguides (ZMWs) can confine light into attoliter volumes, which enables single molecule fluorescence experiments at physiological micromolar concentrations. Of the fluorescence spectroscopy techniques that can be enhanced by ZMWs, Förster resonance energy transfer (FRET) is one of the most widely used in life sciences. Combining zero‐mode waveguides with FRET provides new opportunities to investigate biochemical structures or follow interaction dynamics at micromolar concentrations with single‐molecule resolution. However, prior to any quantitative FRET analysis on biological samples, it is crucial to establish first the influence of the ZMW on the FRET process. Here, we quantify the FRET rates and efficiencies between individual donor–acceptor fluorophore pairs that diffuse into aluminum zero‐mode waveguides. Aluminum ZMWs are important structures thanks to their commercial availability and the large amount of literature that describe their use for single‐molecule fluorescence spectroscopy. We also compared the results between ZMWs milled in gold and aluminum, and found that although gold has a stronger influence on the decay rates, the lower losses of aluminum in the green spectral region provide larger fluorescence brightness enhancement factors. For both aluminum and gold ZMWs, we observed that the FRET rate scales linearly with the isolated donor decay rate and the local density of optical states. Detailed information about FRET in ZMWs unlocks their application as new devices for enhanced single‐molecule FRET at physiological concentrations.     

The Nephelauxetic Effect Becomes an Important Design Factor for Photoactive First-Row Transition Metal Complexes

The expansion of d-orbitals as a result of metal-ligand bond covalence, the so-called nephelauxetic effect, is a well-established concept of coordination chemistry, yet its importance for the design of new photoactive complexes based on first-row transition metals is only beginning to be recognized. Until recently, much focus has been on optimizing the ligand field strength, coordination geometries, and molecular rigidity, but now it becomes evident that the nephelauxetic effect can be a game changer regarding the photophysical properties of 3d metal complexes in solution at room temperature. In Cr^III and Mn^IV complexes with the d³ valence electron configuration, the nephelauxetic effect was exploited to shift the well-known ruby-like red luminescence to the near-infrared spectral region. In Fe^II and Co^III complexes with the low-spin d⁶ electron configuration, charge-transfer excited states were stabilized with respect to detrimental metal-centered excited states, to improve their properties and to enhance their application potential. In isoelectronic (3d⁶) isocyanide complexes of Cr⁰ and Mn^I, the nephelauxetic effect is likely at play as well, enabling luminescence and other favorable photoreactivity. This minireview illustrates the broad applicability of the nephelauxetic effect in tailoring the photophysical and photochemical properties of new coordination compounds made from abundant first-row transition metals.     

Is Iron the New Ruthenium?

Ruthenium complexes with polypyridine ligands are very popular choices for applications in photophysics and photochemistry, for example, in lighting, sensing, solar cells, and photoredox catalysis. There is a long-standing interest in replacing ruthenium with iron because ruthenium is rare and expensive, whereas iron is comparatively abundant and cheap. However, it is very difficult to obtain iron complexes with an electronic structure similar to that of ruthenium(II) polypyridines. The latter typically have a long-lived excited state with pronounced charge-transfer character between the ruthenium metal and ligands. These metal-to-ligand charge-transfer (MLCT) excited states can be luminescent, with typical lifetimes in the range of 100 to 1000 ns, and the electrochemical properties are drastically altered during this time. These properties make ruthenium(II) polypyridine complexes so well suited for the abovementioned applications. In iron(II) complexes, the MLCT states can be deactivated extremely rapidly (ca. 50 fs) by energetically lower lying metal-centered excited states. Luminescence is then no longer emitted, and the MLCT lifetimes become much too short for most applications. Recently, there has been substantial progress on extending the lifetimes of MLCT states in iron(II) complexes, and the first examples of luminescent iron complexes have been reported. Interestingly, these are iron(III) complexes with a completely different electronic structure than that of commonly targeted iron(II) compounds, and this could mark the beginning of a paradigm change in research into photoactive earth-abundant metal complexes. After outlining some of the fundamental challenges, key strategies used so far to enhance the photophysical and photochemical properties of iron complexes are discussed and recent conceptual breakthroughs are highlighted in this invited Concept article.     

Post-acquisition ETD spectral processing for increased peptide identifications

Tandem mass spectra (MS/MS) produced using electron transfer dissociation (ETD) differ from those derived from collision-activated dissociation (CAD) in several important ways. Foremost, the predominant fragment ion series are different: c- and z ^·-type ions are favored in ETD spectra while b- and y-type ions comprise the bulk of the fragments in CAD spectra. Additionally, ETD spectra possess charge-reduced precursors and unique neutral losses. Most database search algorithms were designed to analyze CAD spectra, and have only recently been adapted to accommodate c- and z ^·-type ions; therefore, inclusion of these additional spectral features can hinder identification, leading to lower confidence scores and decreased sensitivity. Because of this, it is important to pre-process spectral data before submission to a database search to remove those features that cause complications. Here, we demonstrate the effects of removing these features on the number of unique peptide identifications at a 1% false discovery rate (FDR) using the open mass spectrometry search algorithm (OMSSA). When analyzing two biologic replicates of a yeast protein extract in three total analyses, the number of unique identifications with a ∼1% FDR increased from 4611 to 5931 upon spectral pre-processing—an increase of ∼28. 6%. We outline the most effective pre-processing methods, and provide free software containing these algorithms.     

Activity of AC electrokinetically immobilized horseradish peroxidase

Dielectrophoresis (DEP) is an AC electrokinetic effect mainly used to manipulate cells. Smaller particles, like virions, antibodies, enzymes, and even dye molecules can be immobilized by DEP as well. In principle, it was shown that enzymes are active after immobilization by DEP, but no quantification of the retained activity was reported so far. In this study, the activity of the enzyme horseradish peroxidase (HRP) is quantified after immobilization by DEP. For this, HRP is immobilized on regular arrays of titanium nitride ring electrodes of 500 nm diameter and 20 nm widths. The activity of HRP on the electrode chip is measured with a limit of detection of 60 fg HRP by observing the enzymatic turnover of Amplex Red and H₂O₂ to fluorescent resorufin by fluorescence microscopy. The initial activity of the permanently immobilized HRP equals up to 45% of the activity that can be expected for an ideal monolayer of HRP molecules on all electrodes of the array. Localization of the immobilizate on the electrodes is accomplished by staining with the fluorescent product of the enzyme reaction. The high residual activity of enzymes after AC field induced immobilization shows the method's suitability for biosensing and research applications.     

Mixed Oligoureas Based on Constrained Bicyclic and Acyclic β‐Amino Acids Derivatives: On the Significance of the Subunit Configuration for Folding

The combination of a non‐functionalized constrained bicyclo[2.2.2]octane motif along with urea linkages allowed the formation of a highly rigid 2.5_12/14 helical system both in solution and the solid state. In this work, we aimed at developing stable and functionalized systems as promising materials for biological applications in investigating the impact of this constrained motif and its configuration on homo and heterochiral mixed‐oligourea helix formation. Di‐, tetra‐, hexa‐, and octa‐oligoureas alternating the highly constrained bicyclic motif of (R) or (S) configuration with acyclic (S)‐β³‐amino acid derivatives were constructed. Circular dichroism (CD), NMR experiments, and the X‐ray crystal structure of the octamer unequivocally proved that the alternating heterochiral R/S sequences form a stable left‐handed 2.5‐helix in contrast to the mixed (S/S)‐oligoureas, which did not adopt any defined secondary structure. We observed that the (?)‐synclinal conformation around the C_α? C_β bond of the acyclic residues, although sterically less favorable than the (+)‐synclinal conformation, was imposed by the (R)‐bicyclic amino carbamoyl (BAC) residue. This highlighted the strong ability of the BAC residue to drive helical folding in heterochiral compounds. The role of the stereochemistry of the BAC unit was assessed and a model was proposed to explain the misfolding of the S/S sequences.     

Electron Transfer between Hydrogen‐Bonded Pyridylphenols and a Photoexcited Rhenium(I) Complex

Two pyridylphenols with intramolecular hydrogen bonds between the phenol and pyridine units have been synthesized, characterized crystallographically, and investigated by cyclic voltammetry and UV/Vis spectroscopy. Reductive quenching of the triplet metal‐to‐ligand charge‐transfer excited state of the [Re(CO)₃(phen)(py)]⁺ complex (phen=1,10‐phenanthroline, py=pyridine) by the two pyridylphenols and two reference phenol molecules is investigated by steady‐state and time‐resolved luminescence spectroscopy, as well as by transient absorption spectroscopy. Stern–Volmer analysis of the luminescence quenching data provides rate constants for the bimolecular excited‐state quenching reactions. H/D kinetic isotope effects for the pyridylphenols are on the order of 2.0, and the bimolecular quenching reactions are up to 100 times faster with the pyridylphenols than with the reference phenols. This observation is attributed to the markedly less positive oxidation potentials of the pyridylphenols with respect to the reference phenols (≈0.5 V), which in turn is caused by proton coupling of the phenol oxidation process. Transient absorption spectroscopy provides unambiguous evidence for the photogeneration of phenoxyl radicals, that is, the overall photoreaction is clearly a proton‐coupled electron‐transfer process.     

4‐Benzoyl‐3,4‐dihydro‐2H‐1,4‐benzoxazine‐2‐carbonitrile: refinement using a multipolar atom model

The structural model for the title compound, C₁₆H₁₂N₂O₂, was refined using a multipolar atom model transferred from an experimental electron‐density database. The refinement showed some improvements of crystallographic statistical indices when compared with a conventional spherical neutral‐atom refinement. The title compound adopts a half‐chair conformation. The amide N atom lies almost in the plane defined by the three neighbouring C atoms. In the crystal structure, molecules are linked by weak intermolecular C—H...O and C—H...π hydrogen bonds.     

Computing finest mincut partitions of a graph and application to routing problems

Let G=(V,E,w) be an n-vertex graph with edge weights w>0. We propose an algorithm computing all partitions of V into mincuts of G such that the mincuts in the partitions cannot be partitioned further into mincuts. There are O(n) such finest mincut partitions. A mincut is a non-empty proper subset of V such that the total weight of edges with exactly one end in the subset is minimal. The proposed algorithm exploits the cactus representation of mincuts and has the same time complexity as cactus construction. An application to the exact solution of the general routing problem is described.