Probing the Rotary Cycle of Amine-Substituted Molecular Motors.

An understanding of the rotary cycle of molecular motors (MMs), a key component of an approach to opening cells using mechanical motion, is important in furthering the research. Nuclear magnetic resonance (NMR) spectroscopy was used for in situ analysis of illuminated light-active MMs. We found that the presence of a N,N-dimethylethylenediamine in a position conjugated to the central olefin results in changes to the rotation of a second-generation Feringa-type MM. Importantly, the addition decreases the photostability of the compound. The parent compound 1 can withstand >2 h of illumination with no signs of decomposition, while the amino 7 decomposes after 10 min. We found that the degradation can be mitigated by implementing the simple techniques of modulating the light dose, dilution, and stirring the sample while illuminating. Additionally, the presence of moisture affects the rate of the motor's rotation. The addition of the amino group to 1, without moisture present, makes the rotation of motor 7 three times slower than the unfunctionalized parent compound. We also report the use of a method that can be used to determine the molar extinction coefficient of a light-generated metastable species. This method can be used when in situ NMR illumination is not available.

Interrogating Amyloid Aggregates using Fluorescent Probes.

Amyloids are a broad class of proteins and peptides that can misfold and assemble into long unbranched fibrils with a cross-ß conformation. These misfolding and aggregation events are associated with the onset of a variety of human diseases, among them, Alzheimer's disease, Parkinson's disease, and Huntington disease. Our understanding of amyloids has been greatly supported by fluorescent molecular probes, such as thioflavin-T, which shows an increase in fluorescence emission upon binding to fibrillar aggregates. Since the first application of thioflavin-T in amyloid studies nearly 30 years ago, many probes have emerged exhibiting a variety of responses to amyloids, such as intensity changes, shifts in fluorescence maxima, and variations in lifetimes, among many others. These probes have shed light on a variety of topics including the kinetics of amyloid aggregation, the effectiveness of amyloid aggregation inhibitors, the elucidation of binding sites in amyloid structures, and the staining of amyloids aggregates in vitro, ex vivo, and in vivo. In this Review, we discuss the design, properties, and application of photoactive probes used to study amyloid aggregation, as well as the challenges faced by current probes and techniques, and the novel approaches that are emerging to address these challenges.

Monitoring the Formation of Amyloid Oligomers Using Photoluminescence Anisotropy.

The formation of oligomeric soluble aggregates is related to the toxicity of amyloid peptides and proteins. In this manuscript, we report the use of a ruthenium polypyridyl complex ([Ru(bpy)2(dpqp)]2+) to track the formation of amyloid oligomers at different times using photoluminescence anisotropy. This technique is sensitive to the rotational correlation time of the molecule under study, which is consequently related to the size of the molecule. [Ru(bpy)2(dpqp)]2+ presents anisotropy values of zero when free in solution (due to its rapid rotation and long lifetime) but larger values as the size and concentration of amyloid-ß (Aß) oligomers increase. Our assays show that Aß forms oligomers immediately after the assay is started, reaching a steady state at ∼48 h. SDS-PAGE, DLS, and TEM were used to confirm and characterize the formation of oligomers. Our experiments show that the rate of formation for Aß oligomers is temperature dependent, with faster rates as the temperature of the assay is increased. The probe was also effective in monitoring the formation of α-synuclein oligomers at different times.

Lead-Free Double Perovskite Cs2 SnX6 : Facile Solution Synthesis and Excellent Stability.

Long-term instability and possible lead contamination are the two main issues limiting the widespread application of organic-inorganic lead halide perovskites. Here a facile and efficient solution-phase method is demonstrated to synthesize lead-free Cs2 SnX6 (X = Br, I) with a well-defined crystal structure, long-term stability, and high yield. Based on the systematic experimental data and first-principle simulation results, Cs2 SnX6 displays excellent stability against moisture, light, and high temperature, which can be ascribed to the unique vacancy-ordered defect-variant structure, stable chemical compositions with Sn4+ , as well as the lower formation enthalpy for Cs2 SnX6 . Additionally, photodetectors based on Cs2 SnI6 are also fabricated, which show excellent performance and stability. This study provides very useful insights into the development of lead-free double perovskites with high stability.

Unprecedented Dual Light-Switching Response of a Metal Dipyridophenazine Complex toward Amyloid-ß Aggregation.

Probes for monitoring protein aggregation with a variety of photophysical properties are of importance for the fundamental understanding of the aggregation process as well as for drug discovery. In this manuscript we report the photoluminescence response of the metal dipyridophenazine complex [Re(CO)3(dppz)(Py)](+) in the presence of aggregated Aß. [Re(CO)3(dppz)(Py)](+) shows an instantaneous increase in photoluminescence with fibrillar Aß (primary light-switching), and an unprecedented further increase in photoluminescence upon light irradiation at 362 nm (secondary light switching). The total increase in photoluminescence amounts to 105-fold, which we show can be used to monitor Aß aggregation in real time.

Unimolecular Submersible Nanomachines. Synthesis, Actuation, and Monitoring.

Unimolecular submersible nanomachines (USNs) bearing light-driven motors and fluorophores are synthesized. NMR experiments demonstrate that the rotation of the motor is not quenched by the fluorophore and that the motor behaves in the same manner as the corresponding motor without attached fluorophores. No photo or thermal decomposition is observed. Through careful design of control molecules with no motor and with a slow motor, we found using single molecule fluorescence correlation spectroscopy that only the molecules with fast rotating speed (MHz range) show an enhancement in diffusion by 26% when the motor is fully activated by UV light. This suggests that the USN molecules give ∼9 nm steps upon each motor actuation. A non-unidirectional rotating motor also results in a smaller, 10%, increase in diffusion. This study gives new insight into the light actuation of motorized molecules in solution.

Arresting amyloid with coulomb's law: acetylation of ALS-linked SOD1 by aspirin impedes aggregation.

Although the magnitude of a protein's net charge (Z) can control its rate of self-assembly into amyloid, and its interactions with cellular membranes, the net charge of a protein is not viewed as a druggable parameter. This article demonstrates that aspirin (the quintessential acylating pharmacon) can inhibit the amyloidogenesis of superoxide dismutase (SOD1) by increasing the intrinsic net negative charge of the polypeptide, i.e., by acetylation (neutralization) of multiple lysines. The protective effects of acetylation were diminished (but not abolished) in 100 mM NaCl and were statistically significant: a total of 432 thioflavin-T amyloid assays were performed for all studied proteins. The acetylation of as few as three lysines by aspirin in A4V apo-SOD1-a variant that causes familial amyotrophic lateral sclerosis (ALS)-delayed amyloid nucleation by 38% and slowed amyloid propagation by twofold. Lysines in wild-type- and ALS-variant apo-SOD1 could also be peracetylated with aspirin after fibrillization, resulting in supercharged fibrils, with increases in formal net charge of ∼2 million units. Peracetylated SOD1 amyloid defibrillized at temperatures below unacetylated fibrils, and below the melting temperature of native Cu2,Zn2-SOD1 (e.g., fibril Tm = 84.49°C for acetylated D90A apo-SOD1 fibrils). Targeting the net charge of native or misfolded proteins with small molecules-analogous to how an enzyme's Km or Vmax are medicinally targeted-holds promise as a strategy in the design of therapies for diseases linked to protein self-assembly.

Ascertaining free histidine from mixtures with histidine-containing proteins using time-resolved photoluminescence spectroscopy.

The use of photoluminescent probes for differentiating free amino acids from biomolecules containing the same amino acids is challenging. Photoluminescent probes generally present similar emission spectra when in the presence of either free-amino acids or protein containing those same amino acids. Probes based on cyclometalated iridium(III) complexes Ir(L)2(sol)2 (where L is 2-phenylpyridine, 2-(2,4-difluorophenyl)pyridine, or benzo[h]quinolone, and sol is a solvent molecule) present long-lived emission when bound to histidine. This emission is tuned by the microenvironment around the complex and therefore its lifetime is different for free histidine (487 ns) than from histidine-containing proteins such as bovine serum albumin (average lifetime > 700 ns). As a proof-of-concept we demonstrate that free histidine can be discerned from a mixture with histidine-containing proteins by using time-resolved photoluminescence decays. In the presence of multiple sources of histidine, iridium(III) probes display a multiexponential decay, which can be fitted by nonlinear least-squares methods to separate the different components. Because the pre-exponential factor of the 487 ns lifetime is proportional to the concentration of free histidine, we can use it to assess the amount of free histidine in solution even in the presence of proteins such as bovine serum albumin. We also show that iridium(III) probes displaying different photoluminescence maxima can be produced by modifying the ancillary ligands of the metal complex.

Brownian Diffusion of Hexagonal Boron Nitride Nanosheets and Graphene in Two Dimensions.

Two-dimensional (2D) nanomaterials have numerous interesting chemical and physical properties that make them desirable building blocks for the manufacture of macroscopic materials. Liquid-phase processing is a common method for forming macroscopic materials from these building blocks including wet-spinning and vacuum filtration. As such, assembling 2D nanomaterials into ordered functional materials requires an understanding of their solution dynamics. Yet, there are few experimental studies investigating the hydrodynamics of disk-like materials. Herein, we report the lateral diffusion of hexagonal boron nitride nanosheets (h-BN and graphene) in aqueous solution when confined in 2-dimensions. This was done by imaging fluorescent surfactant-tagged nanosheets and visualizing them by using fluorescence microscopy. Spectroscopic studies were conducted to characterize the interactions between h-BN and the fluorescent surfactant, and atomic force microscopy (AFM) was conducted to characterize the quality of the dispersion. The diffusion data under different gap sizes and viscosities displayed a good correlation with Kramers' theory. We propose that the yielded activation energies by Kramers' equation express the magnitude of the interaction between fluorescent surfactant tagged h-BN and glass because the energies remain constant with changing viscosity and decrease with increasing confinement size. The diffusion of graphene presented a similar trend with similar activation energy as the h-BN. This relationship suggests that Kramers' theory can also be applied to simulate the diffusion of other 2D nanomaterials.

Unraveling the photoluminescence response of light-switching ruthenium(II) complexes bound to amyloid-ß.

Photoluminescent molecules are widely used for real-time monitoring of peptide aggregation. In this Article, we detail both experimental and computational modeling to elucidate the interaction between [Ru(bpy)2dppz](2+) and amyloid-ß (Aß(1-40)) aggregates. The transition from monomeric to fibrillar Aß is of interest in the study of Alzheimer's disease. Concentration-dependent experiments allowed the determination of a dissociation constant of 2.1 µM, while Job plots provided a binding stoichiometry of 2.6 Aß monomers per [Ru(bpy)2dppz](2+). Our computational approach that combines molecular docking (both rigid and flexible) and all-atom molecular dynamics (MD) simulations predicts that the hydrophobic cleft between Val18 and Phe20 is a plausible binding site, which could also explain the increase in photoluminescence of [Ru(bpy)2dppz](2+) upon binding. This binding site is parallel to the fibril axis, in marked contrast to the binding site of these complexes in DNA (perpendicular to the DNA axis). Other binding sites may exist at the edges of the Aß fibril, but they are actually of low abundance in an Aß fibril several micrometers long. The assignment of the binding site was confirmed by binding studies in an Aß fragment (Aß(25-35)) that lacked the amino acids necessary to form the binding site. The agreement between the experimental and computational work is remarkable and provides a general model that can be used for studying the interaction of amyloid-binding molecules to Aß.

Deamidation of asparagine to aspartate destabilizes Cu, Zn superoxide dismutase, accelerates fibrillization, and mirrors ALS-linked mutations.

The reactivity of asparagine residues in Cu, Zn superoxide dismutase (SOD1) to deamidate to aspartate remains uncharacterized; its occurrence in SOD1 has not been investigated, and the biophysical effects of deamidation on SOD1 are unknown. Deamidation is, nonetheless, chemically equivalent to Asn-to-Asp missense mutations in SOD1 that cause amyotrophic lateral sclerosis (ALS). This study utilized computational methods to identify three asparagine residues in wild-type (WT) SOD1 (i.e., N26, N131, and N139) that are predicted to undergo significant deamidation (i.e., to >20%) on time scales comparable to the long lifetime (>1 year) of SOD1 in large motor neurons. Site-directed mutagenesis was used to successively substitute these asparagines with aspartate (to mimic deamidation) according to their predicted deamidation rate, yielding: N26D, N26D/N131D, and N26D/N131D/N139D SOD1. Differential scanning calorimetry demonstrated that the thermostability of N26D/N131D/N139D SOD1 is lower than WT SOD1 by ~2-8 °C (depending upon the state of metalation) and <3 °C lower than the ALS mutant N139D SOD1. The triply deamidated analog also aggregated into amyloid fibrils faster than WT SOD1 by ~2-fold (p < 0.008**) and at a rate identical to ALS mutant N139D SOD1 (p > 0.2). A total of 534 separate amyloid assays were performed to generate statistically significant comparisons of aggregation rates among WT and N/D SOD1 proteins. Capillary electrophoresis and mass spectrometry demonstrated that ~23% of N26 is deamidated to aspartate (iso-aspartate was undetectable) in a preparation of WT human SOD1 (isolated from erythrocytes) that has been used for decades by researchers as an analytical standard. The deamidation of asparagine--an analytically elusive, sub-Dalton modification--represents a plausible and overlooked mechanism by which WT SOD1 is converted to a neurotoxic isoform that has a similar structure, instability, and aggregation propensity as ALS mutant N139D SOD1.

Graphene quantum dots derived from carbon fibers.

Graphene quantum dots (GQDs), which are edge-bound nanometer-size graphene pieces, have fascinating optical and electronic properties. These have been synthesized either by nanolithography or from starting materials such as graphene oxide (GO) by the chemical breakdown of their extended planar structure, both of which are multistep tedious processes. Here, we report that during the acid treatment and chemical exfoliation of traditional pitch-based carbon fibers, that are both cheap and commercially available, the stacked graphitic submicrometer domains of the fibers are easily broken down, leading to the creation of GQDs with different size distribution in scalable amounts. The as-produced GQDs, in the size range of 1-4 nm, show two-dimensional morphology, most of which present zigzag edge structure, and are 1-3 atomic layers thick. The photoluminescence of the GQDs can be tailored through varying the size of the GQDs by changing process parameters. Due to the luminescence stability, nanosecond lifetime, biocompatibility, low toxicity, and high water solubility, these GQDs are demonstrated to be excellent probes for high contrast bioimaging and biosensing applications.

Hexagonal boron nitride exfoliation and dispersion.

Research on hexagonal boron nitride (hBN) 2-dimensional nanostructures has gained traction due to their unique chemical, thermal, and electronic properties. However, to make use of these exceptional properties and fabricate macroscopic materials, hBN often needs to be exfoliated and dispersed in a solvent. In this review, we provide an overview of the many different methods that have been used for dispersing hBN. The approaches that will be covered in this review include solvents, covalent functionalization, acids and bases, surfactants and polymers, biomolecules, intercalating agents, and thermal expansion. The properties of the exfoliated sheets obtained and the dispersions are discussed, and an overview of the work in the field throughout the years is provided.

Evaluating the inhibitory activity of ferrocenyl Schiff bases derivatives on 5-lipoxygenase: Computational and biological studies.

In the search for new 5-LOX inhibitors, two ferrocenyl Schiff base complexes functionalized with catechol ((ƞ5-(E)-C5H4-NCH-3,4-benzodiol)Fe(ƞ5-C5H5) (3a)) and vanillin ((ƞ5-(E)-C5H4-NCH-3-methoxy-4-phenol)Fe(ƞ5-C5H5) (3b)) were obtained. Complexes 3a and 3b were biologically evaluated as 5-LOX inhibitors showed potent inhibition compared to their organic analogs (2a and 2b) and known commercial inhibitors, with IC50 = 0.17 ± 0.05 µM for (3a) and 0.73 ± 0.06 µM for (3b) demonstrated a highly inhibitory and potent effect against 5-LOX due to the incorporation of the ferrocenyl fragment. Molecular dynamic studies showed a preferential orientation of the ferrocenyl fragment toward the non-heme iron of 5-LOX, which, together with electrochemical and in-vitro studies, allowed us to propose a competitive redox deactivation mechanism mediated by water, where Fe(III)-enzyme can be reduced by the ferrocenyl fragment. An Epa/IC50 relationship was observed, and the stability of the Schiff bases was evaluated by SWV in the biological medium, observing that the hydrolysis does not affect the high potency of the complexes, making them interesting alternatives for pharmacological applications.

Photochemical iron-catalyzed decarboxylative azidation via the merger of ligand-to-metal charge transfer and radical ligand transfer catalysis.

Ligand-to-metal charge transfer (LMCT) using stoichiometric copper salts has recently been shown to permit decarboxylative C-N bond formation via an LMCT/radical polar crossover (RPC) mechanism; however, this method is unable to function catalytically and cannot successfully engage unactivated alkyl carboxylic acids, presenting challenges to the general applicability of this approach. Leveraging the concepts of ligand-to-metal charge transfer (LMCT) and radical-ligand-transfer (RLT), we herein report the first photochemical, iron-catalyzed direct decarboxylative azidation. Simply irradiating an inexpensive iron nitrate catalyst in the presence of azidotrimethylsilane allows for a diverse array of carboxylic acids to be converted to corresponding organic azides directly with broad functional group tolerance and mild conditions. Intriguingly, no additional external oxidant is required for this reaction to proceed, simplifying the reaction protocol. Finally, mechanistic studies are consistent with a radical mechanism and suggest that the nitrate counteranion serves as an internal oxidant for turnover of the iron catalyst.

Deconvoluting binding sites in amyloid nanofibrils using time-resolved spectroscopy.

Steady-state fluorescence spectroscopy has a central role not only for sensing applications, but also in biophysics and imaging. Light switching probes, such as ruthenium dipyridophenazine complexes, have been used to study complex systems such as DNA, RNA, and amyloid fibrils. Nonetheless, steady-state spectroscopy is limited in the kind of information it can provide. In this paper, we use time-resolved spectroscopy for studying binding interactions between amyloid-ß fibrillar structures and photoluminescent ligands. Using time-resolved spectroscopy, we demonstrate that ruthenium complexes with a pyrazino phenanthroline derivative can bind to two distinct binding sites on the surface of fibrillar amyloid-ß, in contrast with previous studies using steady-state photoluminescence spectroscopy, which only identified one binding site for similar compounds. The second elusive binding site is revealed when deconvoluting the signals from the time-resolved decay traces, allowing the determination of dissociation constants of 3 and 2.2 µM. Molecular dynamic simulations agree with two binding sites on the surface of amyloid-ß fibrils. Time-resolved spectroscopy was also used to monitor the aggregation of amyloid-ß in real-time. In addition, we show that common polypyridine complexes can bind to amyloid-ß also at two different binding sites. Information on how molecules bind to amyloid proteins is important to understand their toxicity and to design potential drugs that bind and quench their deleterious effects. The additional information contained in time-resolved spectroscopy provides a powerful tool not only for studying excited state dynamics but also for sensing and revealing important information about the system including hidden binding sites.

Detection of α-synuclein amyloidogenic aggregates in vitro and in cells using light-switching dipyridophenazine ruthenium(II) complexes.

Protein aggregation is the hallmark of a number of neurodegenerative diseases including Parkinson's and Huntington's diseases. There is a significant interest in understanding the molecular mechanisms involved in the self-association and fibrillization of monomeric soluble proteins into insoluble deposits in vivo and in vitro. Probes with novel properties, such as red-shifted emission, large Stokes shifts, and high photostability, are desirable for a variety of protein aggregation studies. To respond to the increasing need for aggregation-responsive compounds suitable to cellular studies, we present a ruthenium(II) dipyridophenazine derivative, [Ru(phen)(2)dppz](2+) (phen =1,10-phenanthroline, dppz = dipyrido[3,2-a:2'.3'-c]phenazine), to study aggregation of α-synuclein (αS), which is associated with the development of Parkinson's disease. We demonstrated the use of [Ru(phen)(2)dppz](2+) to monitor αS fibril formation in real-time and to detect and quantify αS aggregates in neuroglioma cells, thereby providing a novel molecular tool to study protein deposition diseases in vitro and in vivo.

Optimizing the sensitivity of photoluminescent probes using time-resolved spectroscopy: a molecular beacon case study.

Improving probes so that they can perform more sensitive and accurate detections is at the heart of much fundamental and applied research. Within the past few years a considerable amount of effort has been devoted to the study of photoluminescent probes in combination with time-resolved photoluminescence spectroscopy (TRPS). Although TRPS is a powerful and important technique for improving the sensitivity of long-lived probes, there is a lack of a general methodology that would allow one to unambiguously optimize the parameter affecting this technique. In this manuscript it will be shown how parameters that are probe- and technique-specific can affect the effectiveness of TRPS in improving sensitivity. Furthermore, it will be demonstrated that, when TRPS is used, the sensitivity of the probe is strongly dependent on the time window used to generate the time-resolved emission spectra (TRES). A method will be described that will allow one to remove the uncertainty in the selection of the time window that would yield the optimum improvement in probe performance, as well as the experimental parameters that need to be considered. Molecular beacon probes (MBs) were used to demonstrate these points. These probes show signal-to-background ratios (S/B) of less than 9 when SSPS is used, which can be easily enhanced to 17 using TRPS. The detection limits were also improved when TRPS is used allowing detecting target DNA with concentrations as low as 13.6 nM.

Highly luminescent-paramagnetic nanophosphor probes for in vitro high-contrast imaging of human breast cancer cells.

Highly luminescent-paramagnetic nanophosphors have a seminal role in biotechnology and biomedical research due to their potential applications in biolabeling, bioimaging, and drug delivery. Herein, the synthesis of high-quality, ultrafine, europium-doped yttrium oxide nanophosphors (Y(1.9)O(3):Eu(0.1)(3+)) using a modified sol-gel technique is reported and in vitro fluorescence imaging studies are demonstrated in human breast cancer cells. These highly luminescent nanophosphors with an average particle size of ≈6 nm provide high-contrast optical imaging and decreased light scattering. In vitro cellular uptake is shown by fluorescence microscopy, which visualizes the characteristic intense hypersensitive red emission of Eu(3+) peaking at 610 nm ((5)D(0)-(7)F(2)) upon 246 nm UV light excitation. No apparent cytotoxicity is observed. Subsequently, time-resolved emission spectroscopy and SQUID magnetometry measurements demonstrate a photoluminescence decay time in milliseconds and paramagnetic behavior, which assure applications of the nanophosphors in biomedical studies.

Recent trends in molecular beacon design and applications.

A molecular beacon (MB) is a hairpin-structured oligonucleotide probe containing a photoluminescent species (PLS) and a quencher at different ends of the strand. In a recognition and detection process, the hybridization of MBs with target DNA sequences restores the strong photoluminescence, which is quenched before hybridization. Making better MBs involves reducing the background photoluminescence and increasing the brightness of the PLS, which therefore involves the development of new PLS and quenchers, as well as innovative PLS-quencher systems. Heavy-metal complexes, nanocrystals, pyrene compounds, and other materials with excellent photophysical properties have been applied as PLS of MBs. Nanoparticles, nanowires, graphene, metal films, and many other media have also been introduced to quench photoluminescence. On the basis of their high specificity, selectivity, and sensitivity, MBs are developed as a general platform for sensing, producing, and carrying molecules other than oligonucleotides.