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Concept: Organic compound


The fluorescence lifetimes of most red emitting organic probes are under 4 nanoseconds, which is a limiting factor in studying interactions and conformational dynamics of macromolecules. In addition, the nanosecond background autofluorescence is a significant interference during fluorescence measurements in cellular environment. Therefore, red fluorophores with longer lifetimes will be immensely helpful. Azaoxa-triangulenium fluorophores ADOTA and DAOTA are red emitting small organic molecules with high quantum yield, long fluorescence lifetime and high limiting anisotropy. In aqueous environment, ADOTA and DAOTA absorption and emission maxima are respectively 540 nm and 556 nm, and 556 nm and 589 nm. Their emission extends beyond 700 nm. Both probes have the limiting anisotropy between 0.36-0.38 at their absorption peak. In both protic and aprotic solvents, their lifetimes are around 20 ns, making them among the longest-lived red emitting organic fluorophores. Upon labeling of avidin, streptavidin and immunoglobulin their absorption and fluorescence are red-shifted. Unlike in free form, the protein-conjugated probes have heterogeneous fluorescence decays, with the presence of both significantly quenched and unquenched populations. Despite the presence of significant local motions due to a flexible trimethylene linker, we successfully measured both intermediate nanosecond intra-protein motions and slower rotational correlation times approaching 100 ns. Their long lifetimes are unaffected by the cell membrane (hexadecyl-ADOTA) and the intra-cellular (DAOTA-Arginine) localization. Their long lifetimes also enabled successful time-gating of the cellular autofluorescence resulting in background-free fluorescence lifetime based images. ADOTA and DAOTA retain a long fluorescence lifetime when free, as protein conjugate, in membranes and inside the cell. Our successful measurements of intermediate nanosecond internal motions and long correlations times of large proteins suggest that these probes will be highly useful to study slower intra-molecular motions and interactions among macromolecules. The fluorescence lifetime facilitated gating of cellular nanosecond autofluorescence should be of considerable help in in vitro and in vivo applications.

Concepts: Protein, Fluorescence, Cell membrane, In vivo, Organic compound, In vitro, Small molecule, 175


Small-molecule synthesis usually relies on procedures that are highly customized for each target. A broadly applicable automated process could greatly increase the accessibility of this class of compounds to enable investigations of their practical potential. Here we report the synthesis of 14 distinct classes of small molecules using the same fully automated process. This was achieved by strategically expanding the scope of a building block-based synthesis platform to include even Csp3-rich polycyclic natural product frameworks and discovering a catch-and-release chromatographic purification protocol applicable to all of the corresponding intermediates. With thousands of compatible building blocks already commercially available, many small molecules are now accessible with this platform. More broadly, these findings illuminate an actionable roadmap to a more general and automated approach for small-molecule synthesis.

Concepts: Protein, Organic compound, Biochemistry, Organic chemistry, Class, Social class, Small molecule, Accessibility


Structural characteristics of the active layers in organic photovoltaic (OPV) devices play a critical role in charge generation, separation and transport. Here we report on morphology and structural control of p-DTS(FBTTh2)2:PC71BM films by means of thermal annealing and 1,8-diiodooctane (DIO) solvent additive processing, and correlate it to the device performance. By combining surface imaging with nanoscale depth-sensitive neutron reflectometry (NR) and X-ray diffraction, three-dimensional morphologies of the films are reconstituted with information extending length scales from nanometers to microns. DIO promotes the formation of a well-mixed donor-acceptor vertical phase morphology with a large population of small p-DTS(FBTTh2)2 nanocrystals arranged in an elongated domain network of the film, thereby enhancing the device performance. In contrast, films without DIO exhibit three-sublayer vertical phase morphology with phase separation in agglomerated domains. Our findings are supported by thermodynamic description based on the Flory-Huggins theory with quantitative evaluation of pairwise interaction parameters that explain the morphological changes resulting from thermal and solvent treatments. Our study reveals that vertical phase morphology of small-molecule based OPVs is significantly different from polymer-based systems. The significant enhancement of morphology and information obtained from theoretical modeling may aid in developing an optimized morphology to enhance device performance for OPVs.

Concepts: Protein, Diffraction, X-ray, Orders of magnitude, Organic compound, Solar cell, Photovoltaics, Theory


Fluorescent imaging of biological systems in the second near-infrared window (NIR-II) can probe tissue at centimetre depths and achieve micrometre-scale resolution at depths of millimetres. Unfortunately, all current NIR-II fluorophores are excreted slowly and are largely retained within the reticuloendothelial system, making clinical translation nearly impossible. Here, we report a rapidly excreted NIR-II fluorophore (∼90% excreted through the kidneys within 24 h) based on a synthetic 970-Da organic molecule (CH1055). The fluorophore outperformed indocyanine green (ICG)-a clinically approved NIR-I dye-in resolving mouse lymphatic vasculature and sentinel lymphatic mapping near a tumour. High levels of uptake of PEGylated-CH1055 dye were observed in brain tumours in mice, suggesting that the dye was detected at a depth of ∼4 mm. The CH1055 dye also allowed targeted molecular imaging of tumours in vivo when conjugated with anti-EGFR Affibody. Moreover, a superior tumour-to-background signal ratio allowed precise image-guided tumour-removal surgery.

Concepts: Oncology, Brain tumor, Organic compound, Organ, Tumor, Spleen, Dyes, Fluorophore


Carbon nanotubes (CNTs), tubular molecular entities that consist of sp(2)-hybridized carbon atoms, are currently produced as mixtures that contain tubes of various diameters and different sidewall structures. The electronic and optical properties of CNTs are determined by their diameters and sidewall structures and so a controlled synthesis of uniform-diameter, single-chirality CNTs-a significant chemical challenge-would provide access to pure samples with predictable properties. Here we report a rational bottom-up approach to synthesize structurally uniform CNTs using carbon nanorings (cycloparaphenylenes) as templates and ethanol as the carbon source. The average diameter of the CNTs formed is close to that of the carbon nanorings used, which supports the operation of a ‘growth-from-template’ mechanism in CNT formation. This bottom-up organic chemistry approach is intrinsically different from other conventional approaches to making CNTs and, if it can be optimized sufficiently, offers a route to the programmable synthesis of structurally uniform CNTs.

Concepts: Chemistry, Atom, Organic compound, Chemical element, Carbon, Carbon nanotube, Allotropes of carbon, Graphite


Fossil biomolecules from an endogenous source were previously identified in Cretaceous to Pleistocene fossilized bones, the evidence coming from molecular analyses. These findings, however, were called into question and an alternative hypothesis of the invasion of the bone by bacterial biofilm was proposed. Herewith we report a new finding of morphologically preserved blood-vessel-like structures enclosing organic molecules preserved in iron-oxide-mineralized vessel walls from the cortical region of nothosaurid and tanystropheid (aquatic and terrestrial diapsid reptiles) bones. These findings are from the Early/Middle Triassic boundary (Upper Roetian/Lowermost Muschelkalk) strata of Upper Silesia, Poland. Multiple spectroscopic analyses (FTIR, ToF-SIMS, and XPS) of the extracted “blood vessels” showed the presence of organic compounds, including fragments of various amino acids such as hydroxyproline and hydroxylysine as well as amides, that may suggest the presence of collagen protein residues. Because these amino acids are absent from most proteins other than collagen, we infer that the proteinaceous molecules may originate from endogenous collagen. The preservation of molecular signals of proteins within the “blood vessels” was most likely made possible through the process of early diagenetic iron oxide mineralization. This discovery provides the oldest evidence of in situ preservation of complex organic molecules in vertebrate remains in a marine environment.

Concepts: Protein, Oxygen, Amino acid, Collagen, Organic compound, Organic chemistry, Fossil, Dinosaur


The beginning of the twenty-first century has witnessed significant advances in the field of C-H bond activation, and this transformation is now an established piece in the synthetic chemists' toolbox. This methodology has the potential to be used in many different areas of chemistry, for example it provides a perfect opportunity for the late-stage diversification of various kinds of organic scaffolds, ranging from relatively small molecules like drug candidates, to complex polydisperse organic compounds such as polymers. In this way, C-H activation approaches enable relatively straightforward access to a plethora of analogues or can help to streamline the lead-optimization phase. Furthermore, synthetic pathways for the construction of complex organic materials can now be designed that are more atom- and step-economical than previous methods and, in some cases, can be based on synthetic disconnections that are just not possible without C-H activation. This Perspective highlights the potential of metal-catalysed C-H bond activation reactions, which now extend beyond the field of traditional synthetic organic chemistry.

Concepts: Oxygen, Chemistry, Atom, Organic compound, Biochemistry, Organic chemistry, C-H bond activation, Organometallic chemistry


The complexity of molecular recognition and assembly of biotic-abiotic interfaces at a scale of 1 to 1000 nm can be understood more effectively using simulation tools along with laboratory instrumentation. We discuss current capabilities and limitations of atomistic force fields and explain a strategy to obtain dependable parameters for inorganic compounds that has been developed and tested over the last decade. Parameter developments include several silicates, aluminates, metals, oxides, sulfates, and apatites that are summarized in what we call the INTERFACE force field. The INTERFACE force field operates as an extension of common harmonic force fields (PCFF, COMPASS, CHARMM, AMBER, GROMACS, and OPLS-AA) by employing the same functional form and combination rules to enable simulations of inorganic-organic and inorganic-biomolecular interfaces. The parameterization builds on in-depth understanding of physical-chemical properties at the atomic scale to assign each parameter, especially atomic charges and van-der-Waals constants, as well as on the validation of macroscale physical-chemical properties for each compound in comparison to measurements. The approach eliminates large discrepancies between computed and measured bulk and surface properties up to two orders of magnitude using other parameterization protocols and increases the transferability of the parameters by introducing thermodynamic consistency. As a result, a wide range of properties can be computed in quantitative agreement with experiment, including densities, surface energies, solid-water interface tensions, anisotropies of interfacial energies of different crystal facets, adsorption energies of biomolecules, thermal, and mechanical properties. Applications include insight into the assembly of inorganic-organic multiphase materials, recognition of inorganic facets by biomolecules, growth and shape preferences of nanocrystals and nanoparticles, as well as thermal transitions and nanomechanics. Limitations and opportunities for further development are described.

Concepts: Oxygen, Energy, Molecular dynamics, Organic compound, Parameter, CHARMM, Force field implementation, Parametrization


Nanocomposites, composed of organic and inorganic building blocks, can combine the properties from the parent constituents and generate new properties to meet current and future demands in functional materials. Recent developments in nanoparticle synthesis provide a plethora of inorganic building blocks, building the foundation for constructing hybrid nanocomposites with unlimited possibilities. The properties of nanocomposite materials depend not only on those of individual building blocks but also on their spatial organization at different length scales. Block copolymers, which microphase separate into various nanostructures, have shown their potential for organizing inorganic nanoparticles in bulk/thin films. Block copolymer-based supramolecules further provide more versatile routes to control spatial arrangement of the nanoparticles over multiple length scales. This review provides an overview of recent efforts to control the hierarchical assemblies in block copolymer-based hybrid nanocomposites.

Concepts: Nanoparticle, Polymer, Copolymer, Polymer chemistry, Organic compound, Nanomaterials, Nanocomposite


Taking into account the promising pharmacological actions of (Z)-2,3-bis(4-chlorophenylselanyl) prop-2-en-1-ol) (bis selenide), an organic compound containing the trace element selenium, and the constant search for drugs that improve the cognitive performance, the objective of the present study was to investigate whether bis selenide treatment ameliorates memory deficits induced by reserpine in rats. For this aim, male adult rats received a single subcutaneous injection of reserpine (1 mg/kg), a biogenic amine-depleting agent used to induce memory deficit. After 24 h, bis selenide at doses of 25 and 50 mg/kg was administered to rats by intragastric route, and 1 h later, the animals were submitted to behavior tasks. The effects of acute administration of bis selenide on memory were evaluated by social recognition, step-down passive avoidance, and object recognition paradigms. Exploratory and locomotor activities of rats were determined using the open-field test. Analysis of data revealed that the social memory disruption caused by reserpine was reversed by bis selenide at both doses. In addition, bis selenide, at the highest dose, prevented the memory deficit resulting from reserpine administration to rats in step-down passive avoidance and object recognition tasks. No significant alterations in locomotor and exploratory behaviors were found in animals treated with reserpine and/or bis selenide. Results obtained from distinct memory behavioral paradigms revealed that an acute treatment with bis selenide attenuated memory deficits induced by reserpine in rats.

Concepts: Psychology, Pharmacology, Organic compound, Dose, Behavior, Human behavior, Selenium, Deficit