Publications

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69
Farrera-Soler, L.; Daguer, J.-P.; Raunft, P.; Barluenga, S.; Imberty, A.; Winssinger, N. “PNA-Based Dynamic Combinatorial Libraries (PDCL) and screening of lectins”, Bioorg. Med. Chem. 2020, in press.

Selections from dynamic combinatorial libraries (DCL) benefit from the dynamic nature of the library that can change constitution upon addition of a selection pressure, such as ligands binding to a protein. This technology has been predominantly used with small molecules interacting with each other through reversible covalent interaction. However, application of this technology in biomedical research and drug discovery has been limited by the reversibility of covalent exchange and the analytical deconvolution of small molecule fragments. Here we report a supramolecular approach based on the use of a constant short PNA tag to direct the combinatorial pairing of fragment. This PNA tag yields fast exchange kinetics, while still delivering the benefits of cooperativity, and provides favourable properties for analytical deconvolution by MALDI. A selection from >6,000 assemblies of glycans (mono-, di-, tri-saccharides) targeting AFL, a lectin from pathogenic fungus, yielded a 95 nM assembly, nearly three orders of magnitude better in affinity than the corresponding glycan alone (41 µM).

68
Liu, Y.; Mazet, C. “A Catalytic Dual Isomerization/Allylboration Sequence for the Stereoselective Construction of Congested Secondary Homoallylic Alcohols”, J. Org. Chem. 2020, in press.

A catalytic sequence for the diastereo- and enantioselective preparation of homoallylic alcohols with an adjacent quaternary (stereo)center is reported. The one-pot process relies on the use of a single (achiral or chiral) iridium complex to catalyze the concomitant isomerization of primary allylic alcohols and homoallylboronates into (chiral) aldehydes and allylboronates respectively. In the same flask, a chiral Brønsted acid is added next to engage the isomerization products into a stereocontrolled allylboration reaction. Structural variations have been performed on both the allylic alcohols and the homoallylboronates. This mild process affords an array of stereochemically congested and complex chiral secondary homoallylic alcohols in high yield, excellent diastereoselectivity and usually high enantioselectivity.

67
Huang, J.; Zajforoushan Moghaddam, S.; Maroni, P.; Thormann, E. “Swelling behavior, interaction, and electrostatic properties of chitosan/alginate dialdehyde multilayer films with different outermost layer”, Langmuir 2020, in press.

In this study, self-cross-linked chitosan/alginate dialdehyde multilayer films, capped with either alginate dialdehyde (6 layers) or chitosan (7 layers), are fabricated using the layer-by-layer method. The disruption of the electrostatic equilibrium when exposing the fabricated layers to acidic and alkaline conditions causes swelling within the film and independently in the outermost layer, showing dependence on the ionic strength. Spectroscopic ellipsometry and quartz crystal microbalance with dissipation monitoring are employed to examine the swelling behavior. Atomic force microscopy colloidal probe measurements are conducted to assess the surface forces between the multilayer films at different pH and ionic strengths. Finally, the electrostatic properties of the multilayer films are examined at different pH and ionic strengths using zeta potential measurements. The results suggest that stimuli-responsiveness and overall swelling behavior of the polysaccharide multilayer films significantly depend on the outermost layer, an effect that should expectedly become more pronounced the thinner the film becomes.

66
Kim, K. T.; Winssinger, N. “Enhanced SNP-sensing using DNA-templated reactions through confined hybridization of minimal substrates (CHOMS)”, Chem. Sci. 2020, in press.

DNA or RNA templated reactions are attractive for nucleic acid sensing and imaging. As for any hybridization-based sensing, there is a tradeoff between sensitivity (detection threshold) and resolution (single nucleotide discrimination). Longer probes afford better sensitivity but compromise single nucleotide resolution due to the small thermodynamic penalty of a single mismatch. Herein we report a design that overcomes this tradeoff. The reaction is leveraged on the hybridization of a minimal substrate (covering 4 nucleotides) which is confined by two guide DNAs functionalized respectively with a ruthenium photocatalyst. The use of a catalytic reaction is essential to bypass the exchange of guide DNAs while achieving signal amplification through substrate turnover. The guide DNAs restrain the reaction to a unique site and enhance the hybridization of short substrates by providing two π-stacking interactions. The reaction was shown to enable the detection of SNPs and SNVs down to 50 pM with a discrimination factor ranging from 24 to 309 (median 82, 27 examples from 3 oncogenes). The clinical diagnostic potential of the technology was demonstrated with the analysis of RAS amplicons obtained directly from cell culture.

65
Mottet, M.; Soldati, T. “AI842, AI843, AI844 and AI177 antibodies do not recognize a FLAG-tagged protein by immunofluorescence in D. discoideum cells”, Antib. Rep. 2020, 3, e126.archive ouverte unige:134087 pdf texte intégral [accès libre]

The recombinant antibodies AI842, AI843, AI844 and AI177 failed to detect by immunofluorescence a C-terminally FLAG-tagged LmpA fusion protein expressed in Dictyostelium discoideum.

64
Bisio, A.; Schito, A. M.; Pedrelli, F.; Danton, O.; Reinhardt, J. K.; Poli, G.; Tuccinardi, T.; Bürgi, T.; De Riccardis, F.; Giacomini, M.; Calzia, D.; Panfoli, I.; Schito, G. C.; Hamburger, M.; De Tommasi, N. “Antibacterial and ATP Synthesis Modulating Compounds from Salvia tingitana”, J. Nat. Prod. 2020, in press.

A surface extract of the aerial parts of Salvia tingitana afforded a nor-sesterterpenoid (1) and eight new sesterterpenoids (29), along with five known sesterterpenoids, five labdane and one abietane diterpenoid, one sesquiterpenoid, and four flavonoids. The structures of the new compounds were established by 1D and 2D NMR spectroscopy, HRESIMS, and VCD data and Mosher’s esters analysis. The antimicrobial activity of compounds was evaluated against 30 human pathogens including 27 clinical strains and three isolates of marine origin for their possible implications on human health. The methyl ester of salvileucolide (10), salvileucolide-6,23-lactone (11), sclareol (15), and manool (17) were the most active against Gram-positive bacteria. The compounds were also tested for the inhibition of ATP production in purified mammalian rod outer segments. Terpenoids 101115, and 17 inhibited ATP production, while only 17 inhibited also ATP hydrolysis. Molecular modeling studies confirmed the capacity of 17 to interact with mammalian ATP synthase. A significant reduction of ATP production in the presence of 17 was observed in Enterococcus faecalis and E. faecium isolates.

63
Paraja, M.; Hao, X.; Matile, S. “Polyether Natural Product Inspired Cascade Cyclizations: Autocatalysis on π-Acidic Aromatic Surfaces”, Angew. Chem. Int. Ed. 2020, in press.

Anion-π catalysis functions by stabilizing anionic transition states on aromatic π surfaces, thus providing a new approach to molecular transformation. The delocalized nature of anion–π interactions suggests that they serve best in stabilizing long-distance charge displacements. Aiming therefore for an anionic cascade reaction that is as charismatic as the steroid cyclization is for conventional cation-π biocatalysis, reported here is the anion-π-catalyzed epoxide-opening ether cyclizations of oligomers. Only on π-acidic aromatic surfaces having a positive quadrupole moment, such as hexafluorobenzene to naphthalenediimides, do these polyether cascade cyclizations proceed with exceptionally high autocatalysis (rate enhancements kauto/kcat >104 m−1). This distinctive characteristic adds complexity to reaction mechanisms (Goldilocks-type substrate concentration dependence, entropy-centered substrate destabilization) and opens intriguing perspectives for future developments.

62
Sosnowski, P.; Hopfgartner, G. “Application of 3D printed tools for customized open port probe-electrospray mass spectrometry”, Talanta 2020, 215, 120894.

Three dimensional printed open port probe (3DP-OPP) and air displacement based liquid handler, were designed and optimized using fused deposition modeling (FDM) and stereolitography (SLA) 3D printing. The performance of the devices were investigated for the analysis of solid and liquid samples with electrospray ionization mass spectrometry (ESI-MS). Direct analysis in less than 1 min and without any sample preparation, enabled detection of pesticides (azoxtystrobin/imazalil) on fruits peel surface and illegal substances (MDMA/MDEA) in home-made pills. Conjunction of OPP in the overspill mode with a customized autosampler, equipped with disposable pipette tips, enables direct quantitative analysis of drugs of abuse in urine and plasma, with minimized carry-over and reduced matrix effect compared to flow injection analysis.

61
Cadoux, C. M.; Milton, R. D. “Recent enzymatic electrochemistry for reductive reactions”, ChemElectroChem 2020, in press.

Enzymatic electrochemistry is the coupling of oxidoreductase enzymes to electrodes, where electrons are transferred between the electrode and an enzyme's cofactor(s). In addition to enzymatic electrochemistry enabling mechanistic study [such as the determination of cofactor reduction potential(s)], enzymatic electrocatalysis also enables substrate reduction or oxidation by exploiting the catalytic properties of enzymes. This Minireview illustrates some recent examples, in which electrodes are coupled with enzymes that catalyze the reduction of substrates such as dinitrogen (N2), carbon dioxide (CO2) and protons (H+), performed by metalloenzymes such as nitrogenases, formate dehydrogenases and hydrogenases. We review some strategies to achieve electron transfer (such as mediated and direct electron transfer), as well as some key results of recent studies.

60
Homberg, A.; Lacour, J. “From reactive carbenes to chiral polyether macrocycles in two steps – synthesis and applications made easy?”, Chem. Sci. 2020, in press.

Chiral polyether macrocycles are versatile molecules. For their preparation, original two-step procedures were recently developed and present the advantage of high concentration conditions and simple starting reagents (stable diazo reagents, small cyclic ethers, aliphatic or aromatic amines). Enantiopure materials are readily afforded by CSP-HPLC on semi preparative scale. Flexibility and adaptability in the macrocyclic design is provided by a large selection of amines to choose from while ring size and chemical nature is controlled by the choice of 5 to 7-membered cyclic ether precursors. Such macrocycles have been used already as asymmetric catalysts, mono and ditopic receptors, fluorescent sensors and probes, and chiroptical reversible switches.

59
Soda, Y.; Robinson, K. J.; Cherubini, T. J.; Bakker, E. “Colorimetric absorbance mapping and quantitation on paper-based analytical devices”, Lab Chip 2020, in press.

A wide range of microfluidic paper-based analytical devices (μPADs) have been developed in the last decade. Despite this, the quality of colorimetric analysis has not substantially improved as the data is vulnerable to heterogeneous color distribution (e.g., coffee ring effects), non-uniform shapes of colored detection area, and noise from the underlying paper structure. These limitations are here addressed by a colorimetric method to quantify freely discharged dye on paper substrate, without the need for a defined channel or hydrophobic barrier. For accurate quantification, colorimetric absorbance values are calculated for each pixel based on the recorded RGB values and noise from the paper structure eliminated, to extract accurate absorbance information at the pixel level. Total analyte quantity is then calculated through the conversion of absorbance values into quantity values for each pixel followed by integration across the entire image. The resulting quantity is shown to be independent of the shape of the applied colored dye spot, with a cross, circle or rod shape all giving the same quantity information. The approach is applied to a capillary-based potassium-selective sensor, where the sample solution is loaded with the dye thioflavin T (ThT) obtained by quantitative exchange with K+ in a sensing capillary, which is discharged onto a bare paper substrate without any channels. The resulting dye quantity is successfully obtained by flatbed scanner and smartphone. The successful automated computation of colorimetric data on μPADs will help realize simpler paper-based assay and reaction systems that should be more applicable to addressing real world analytical problems.

58
Levernier, N.; Bénichou, O.; Voituriez, R.; Guérin, T. “Kinetics of rare events for non-Markovian stationary processes and application to polymer dynamics”, Phys. Rev. Res. 2020, 2, 012057(R).

How much time does it take for a fluctuating system, such as a polymer chain, to reach a target configuration that is rarely visited—typically because of a high energy cost? This question generally amounts to the determination of the first-passage time statistics to a target zone in phase space with lower occupation probability. Here, we present an analytical method to determine the mean first-passage time of a generic non-Markovian random walker to a rarely visited threshold, which goes beyond existing weak-noise theories. We apply our method to polymer systems, to determine (i) the first time for a flexible polymer to reach a large extension, and (ii) the first closure time of a stiff inextensible wormlike chain. Our results are in excellent agreement with numerical simulations and provide explicit asymptotic laws for the mean first-passage times to rarely visited configurations.

57
Lamrabet, O.; Melotti, A.; Burdet, F.; Hanna, N.; Perrin, J.; Nitschke, J.; Pagni, M.; Hilbi, H.; Soldati, T.; Cosson, P. “Transcriptional Responses of Dictyostelium discoideum Exposed to Different Classes of Bacteria”, Front. Microbiol. 2020, 11, art. 410.

Dictyostelium discoideum amoebae feed by ingesting bacteria, then killing them in phagosomes. Ingestion and killing of different bacteria have been shown to rely on largely different molecular mechanisms. One would thus expect that D. discoideum adapts its ingestion and killing machinery when encountering different bacteria. In this study, we investigated by RNA sequencing if and how D. discoideum amoebae respond to the presence of different bacteria by modifying their gene expression patterns. Each bacterial species analyzed induced a specific modification of the transcriptome. Bacteria such as Bacillus subtilis, Klebsiella pneumoniae, or Mycobacterium marinum induced a specific and different transcriptional response, while Micrococcus luteus did not trigger a significant gene regulation. Although folate has been proposed to be one of the key molecules secreted by bacteria and recognized by hunting amoebae, it elicited a very specific and restricted transcriptional signature, distinct from that triggered by any bacteria analyzed here. Our results indicate that D. discoideum amoebae respond in a highly specific, almost non-overlapping manner to different species of bacteria. We additionally identify specific sets of genes that can be used as reporters of the response of D. discoideum to different bacteria.

56
Chang, D.; Kim, K. T.; Lindberg, E.; Winssinger, N. “Smartphone DNA or RNA-Sensing Using Semisynthetic Luciferase-Based Logic Device”, ACS Sens. 2020, 5, 807-813.archive ouverte unige:132816 pdf texte intégral [accès restreint]

Detection of specific oligonucleotide sequences is central to numerous applications and technologies amenable to point-of-care diagnostics or end users are needed. Here we report a technology making use of a bioluminescent readout and smartphone quantification. The sensor is a semisynthetic luciferase (H-Luc-PNA conju-gate) that is turned on by a strand-displacement reaction. We demonstrated sensing of three different microRNAs (miRs), as representative cancer biomarker, and demonstrate the possibility to integrate an AND gate to sense two sequences simultaneously.

55
Kraikaew, P.; Jeanneret, S.; Soda, Y.; Cherubini, T.; Bakker, E. “Ultra-Sensitive Seawater pH Measurement by Capacitive Readout of Potentiometric Sensors”, ACS Sens. 2020, 5, 650-654.

Potentiometric pH probes remain the gold standard for the detection of pH but are not sufficiently sensitive to reliably detect ocean acidification at adequate frequency. Here, potentiometric probes are made dramatically more sensitive by placing a capacitive electronic component in series to the pH probe while imposing a constant potential over the measurement circuit. Each sample change now triggers a capacitive current transient that is easily identified between the two equilibrium states, and is integrated to reveal the accumulated charge. This affords dramatically higher precision than with traditional potentiometric probes. pH changes down to 0.001 pH units are easily distinguished in buffer and seawater samples, at a precision (standard deviation) of 28 μpH and 67 µpH, respectively, orders of magnitude better than what is possible with potentiometric pH probes.

54
López-Andarias, J.; Saarbach, J.; Moreau, D.; Cheng, Y.; Derivery, E.; Laurent, Q.; González-Gaitán, M.; Winssinger, N.; Sakai, N.; Matile, S. “Cell-Penetrating Streptavidin:  A General Tool for Bifunctional Delivery with Spatiotemporal Control, Mediated by Transport Systems such as Adaptive Benzopolysulfane Networks”, J. Am. Chem. Soc. 2020, 142, 4784-4792.archive ouverte unige:132259 pdf texte intégral [accès restreint]

In this report, cell-penetrating streptavidin (CPS) is introduced to exploit the full power of streptavidin–biotin biotechnology in cellular uptake. For this purpose, transporters, here cyclic oligochalcogenides (COCs), are covalently attached to lysines of wild-type streptavidin. This leaves all four biotin binding sites free for at least bifunctional delivery. To maximize the standards of the quantitative evaluation of cytosolic delivery, the recent chloroalkane penetration assay (CAPA) is coupled with automated high content (HC) imaging, a technique that combines the advantages of fluorescence microscopy and flow cytometry. According to the resulting HC-CAPA, cytosolic delivery of CPS equipped with four benzopolysulfanes was the best among all tested CPSs, also better than the much smaller TAT peptide, the original cell-penetrating peptide from HIV. HaloTag-GFP fusion proteins expressed on mitochondria were successfully targeted using CPS carrying two different biotinylated ligands, HaloTag substrates or anti-GFP nanobodies, interfaced with peptide nucleic acids, flipper force probes, or fluorescent substrates. The delivered substrates could be released from CPS into the cytosol through desthiobiotin–biotin exchange. These results validate CPS as a general tool which enables unrestricted use of streptavidin–biotin biotechnology in cellular uptake.

53
Maroni, P.; Gvaramia, M.; Kosior, D.; Kubiak, K.; Scarratt, L.; Smith, A. M.; Merkel, D. G.; Bottyán, L.; Borkovec, M. “Structuring of colloidal silica nanoparticle suspensions near water–silica interfaces probed by specular neutron reflectivity”, Phys. Chem. Chem. Phys. 2020, 22, 6449-6456.archive ouverte unige:132164 pdf texte intégral [accès libre]

Structuring of aqueous suspensions of colloidal silica nanoparticles near an isolated planar silica–water interface is studied by specular neutron reflectivity. The reflectivity data clearly show that the suspensions develop a damped, oscillatory concentration profile in the normal direction to the interface. The wavelengths of these oscillations agree well with those independently determined by direct force measurements in the slit-geometry. The reflectivity data further demonstrate that the oscillatory structure persists over several layers and that the first particle layer is separated from the interface by a particle-free region.

52
Hanna, N.; Kicka, S.; Chiriano, G.; Harrison, C.; Sakouhi, H. O.; Trofimov, V.; Kranjc, A.; Nitschke, J.; Pagni, M.; Cosson, P.; Hilbi, H.; Scapozza, L.; Soldati, T. “Identification of Anti-Mycobacterium and Anti-Legionella Compounds With Potential Distinctive Structural Scaffolds From an HD-PBL Using Phenotypic Screens in Amoebae Host Models”, Front. Microbiol. 2020, 11, art. 266.

Tubercular Mycobacteria and Legionella pneumophila are the causative agents of potentially fatal respiratory diseases due to their intrinsic pathogenesis but also due to the emergence of antibiotic resistance that limits treatment options. The aim of our study was to explore the antimicrobial activity of a small ligand-based chemical library of 1255 structurally diverse compounds. These compounds were screened in a combination of three assays, two monitoring the intracellular growth of the pathogenic bacteria, Mycobacterium marinum and L. pneumophila, and one assessing virulence of M. marinum. We set up these assays using two amoeba strains, the genetically tractable social amoeba Dictyostelium discoideum and the free-living amoeba Acanthamoeba castellanii. In summary, 64 (5.1%) compounds showed anti-infective/anti-virulence activity in at least one of the three assays. The intracellular assays hit rate varied between 1.7% (n = 22) for M. marinum and 2.8% (n = 35) for L. pneumophila with seven compounds in common for both pathogens. In parallel, 1.2% (n = 15) of the tested compounds were able to restore D. discoideum growth in the presence of M. marinum spiked in a lawn of food bacteria. We also validated the generality of the hits identified in the A. castellaniiM. marinum anti-infective screen using the D. discoideumM. marinum host–pathogen model. The characterization of anti-infective and antibacterial hits in the latter infection model revealed compounds able to reduce intracellular growth more than 50% at 30 μM. Moreover, the chemical space and physico-chemical properties of the anti-M. marinum hits were compared to standard and candidate Mycobacterium tuberculosis (Mtb) drugs using ChemGPS-NP. A principle component analysis identified separate clusters for anti-M. marinum and anti-L. pneumophila hits unveiling the potentially new physico-chemical properties of these hits compared to standard and candidate M. tuberculosis drugs. Our studies underscore the relevance of using a combination of low-cost and low-complexity assays with full 3R compliance in concert with a rationalized focused library of compounds to identify new chemical scaffolds and to dissect some of their properties prior to taking further steps toward compound development.

51
Delarue Bizzini, L.; Bürgi, T.; Mayor, M. “The Enantiomers of Trinorbornane and Derivatives Thereof”, Helv. Chim. Acta 2020, 103, e2000019.

Herein, we report the synthesis of the enantiomers of trinorbornane, a tetracyclic saturated hydrocarbon with the chemical formula C 11 H 16 . The preparation of these rigid carbon scaffolds was enabled by the successful chiral separation of its tricyclic precursor, thus allowing the enantiomers to be synthesized via a reductive radical cyclization rection. Assignment of the absolute conformation of the enantiomers was achieved via VCD experiments. Further we report an alternative cyclization procedure providing access to hydroxyl and phenyl sulfone functionalized trinorbornanes.

50
Paraja, M.; Matile, S. “Primary Anion-π Catalysis of Epoxide-Opening Ether Cyclizations into Rings of Different Sizes:  Access to New Reactivity”, Angew. Chem. Int. Ed. 2020, 59, 6273-6277.archive ouverte unige:134081 pdf texte intégral [accès restreint]

The concept of anion–π catalysis focuses on the stabilization of anionic transition states on aromatic π surfaces. Recently, we demonstrated the occurrence of epoxide-opening ether cyclizations on aromatic π surfaces. Although the reaction proceeded through unconventional mechanisms, the obtained products are the same as those from conventional Brønsted acid catalysis, and in agreement with the Baldwin selectivity rules. Different mechanisms, however, should ultimately lead to new products, a promise anion–π catalysis has been reluctant to live up to. Herein, we report non-trivial reactions that work with anion–π catalysis, but not with Brønsted acids, under comparable conditions. Namely, we show that the anion–π templated autocatalysis and epoxide opening with alcoholate–π interactions can provide access to unconventional ring chemistry. For smaller rings, anion–π catalysis affords anti-Baldwin oxolanes, 2-oxabicyclo[3.3.0]octanes, and the expansion of Baldwin oxetanes by methyl migration. For larger rings, anion–π templated autocatalysis is thought to alleviate the entropic penalty of folding to enable disfavored anti-Baldwin cyclizations into oxepanes and oxocanes.

49
Chen, W.; Egly, J.; Poblador-Bahamonde, A. I.; Maisse-Francois, A.; Bellemin-Laponnaz, S.; Achard, T. “Synthesis, characterization, catalytic and biological application of half-sandwich ruthenium complexes bearing hemilabile (κ2-C,S )-thioether-functionalised NHC ligands”, Dalton Trans. 2020, 49, 3243-3252.archive ouverte unige:132257 pdf texte intégral [accès restreint]

A series of cationic Ru(II)(η6-p-cymene) complexes with thioether-functionalised N-heterocyclic carbene ligands have been prepared and fully characterized. Steric and electronic influence of the R thioether substituent on the coordination of the sulfur atom was investigated. The molecular structure of three of them has been determined by means of X-ray diffractrometry and confirmed the bidentate (κ2-C,S) coordination mode of the ligand. Interestingly, only a single diastereomer, as an enantiomeric couple, was observed in the solid state for complexes 1c, 1i and 1j. DFT calculations established a low energy inversion barrier between the two diastereomers through a sulfur pyramidal inversion pathway with R donating group while a dissociative/associative mechanism is more likely with R substituents that contain electron withdrawing group, thus suggesting that the only species observed by the 1H-NMR correspond to an average resonance position of a fluxional mixtures of isomers. All these complexes were found to catalyse the oxydant-free double dehydrogenation of primary amine into nitrile. Ru complex bearing NHC-functionalised S-tBu group was further investigated in a wide range of amines and was found more selective for alkyl amine substrates than for benzylamine derivatives. Finally, preliminary results of the biological effects on various human cancer cells of four selected Ru complexes are reported.

48
Ziarati, A.; Badiei, A.; Luque, R.; Dadras, M.; Burgi, T. “Visible Light CO2 Reduction to CH4 Using Hierarchical Yolk@shell TiO2-xHx Modified with Plasmonic Au-Pd Nanoparticles”, ACS Sustainable Chem. Eng. 2020, 8, 3689-3696.

Engineering of advanced semiconductor photocatalysts for CO2 conversion to solar fuels is a promising strategy to solve the greenhouse effect and energy crisis. Herein, hierarchical urchin like yolk@shell TiO2-xHx decorated with core/shell Au-Pd plasmonic nanoparticles (HUY@S-TOH/AuPd) have been prepared using a multi-step process and employed as advanced visible light active photocatalyst in CO2 conversion to CH4 with rate of 47 µmol/gcat.h (up to 126 µmol/gcat after 7h). Different engineered sites in this structure for high gas adsorption, powerful visible light activation and intense electron transformation are responsible for the observed high photocatalytic CO2 conversion efficiency. The present smart designing process can produce a considerable cooperation, not only to disclose the architectural engineering to improvement of photo-conversion efficiency, but also as a viable and appropriate photocatalytic process to sustainable energy production.

47
Bierwagen, J.; Delgado, T.; Jiranek, G.; Yoon, S.; Gartmann, N.; Walfort, B.; Pollnau, M.; Hagemann, H. “Probing traps in the persistent phosphor SrAl2O4:Eu2+,Dy3+,B3+ - A wavelength, temperature and sample dependent thermoluminescence investigation”, J. Lumin. 2020, 222, 117113.

Wavelength-dependent thermoluminescence (TL) experiments were performed on SrAl2O4:Eu, SrAl2O4:Eu,B, SrAl2O4:Eu,Dy and SrAl2O4:Eu,Dy,B polycrystalline samples. Excitation at 445 nm allows to selectively excite one of the two different Eu2+ ions substituting for Sr in the crystal, whereas excitation at 375 nm excites both Eu2+ ions. Incorporation of boron generates the deepest traps which contribute to the very long afterglow in this material, while dysprosium increases significantly (by a factor of about 4–8) the total number of traps involved in the afterglow of this persistent phosphor. Increasing the temperature at which the samples are irradiated (loaded) from 173 K to 248 K reveals that many new traps can only be occupied or activated at higher temperatures, leading to a strong increase of the integrated TL intensity, in particular for the Dy-containing samples. Boron does not appear to contribute to these thermally-activated traps significantly responsible for the long afterglow of SrAl2O4:Eu,Dy,B. The results of this study reveal that the diversity of traps leading to the long afterglow is much larger than previously reported in the literature. We propose that boron stabilizes F centers (which absorb in the far UV), while the presence of dysprosium induces an excitation-induced charge-transfer reaction Eu2+ + Dy3+ → Eu3+ + Dy2+. However, the principal traps responsible for the efficient afterglow are temperature-activated and appear to be associated with the green emitting Eu2+ ion on the Sr2 site coupled to a nearby dysprosium ion.

46
Gao, W.; Xie, X.; Bakker, E. “Direct Potentiometric Sensing of Anion Concentration (Not Activity)”, ACS Sens. 2020, 5, 313-318.

Potentiometric probes used in direct potentiometry are attractive sensing tools. They give information on ion activities, which is often uniquely useful. If, instead, concen-trations are desired as sensor output, the ionic strength of the sample must be precisely known, which is often not possible. Here, for the first time, direct potentiometry can be made to report concentrations, rather than activities. It is demonstrat-ed for the detection of monovalent anionic species by using a self-referencing Ag/AgI pulstrode as reference element in-stead of a traditional reference electrode. This reference pul-strode releases a discrete quantity of iodide ions from the electrode and the resulting reference potential varies with the activity coefficient of iodide. The effects of activity coefficient on the indicator and reference electrode are therefore com-pensated and the observed cell potential may now be de-scribed in a nernstian manner against anion concentration, rather than activity. Theoretical simulations and experimental results support the validity of this approach. For most mono-valent anions of practical relevance, the potential difference between this approach and from a traditional activity coeffi-cient calculation is less than 0.5 mV. The concept is validated with an all-solid-state nitrate sensor as well as a commercial fluoride-selective electrode, giving nernstian responses in different ionic strength backgrounds against concentration without the need for correcting activity coefficients or liquid junction potentials.

45
Baghdasaryan, A.; Besnard, C.; Lawson Daku, L. M.; Delgado, T.; Burgi, T. “Thiolato Protected Copper Sulfide Cluster with the Tentative Composition Cu74S15(2-PET)45”, Inorg. Chem. 2020, 59, 2200-2208.

Ligand protected copper nanoclusters with precise compositions have attracted considerable attention due to their unique photoluminescent properties. However, the acquisition of structural information, knowledge of the factors affecting the stability, and high quantum yields are prerequisites for assessing their applications in biomedicine as fluorescent contrast agents, biosensors, and probes for cells. Despite all the effort, only finite examples of single crystal structures of CuNCs are reported. Herein, we report the phosphine-free synthesis and structure determination of 2-PET protected CuNCs. The structure analysis established by single crystal X-ray diffraction reveals the formation of binary Cu74S15(2-PET)45 sulfide cluster. A similar phenomenon has been observed for several other chalcogenide-bridged copper clusters. The synthesized cluster possesses a rod-like structure, protected with 45 thiol ligands on the surface. Fifteen independent bridged-sulfur atoms couple to the copper atoms inside the core. Calculations for both a neutral and negatively charged cluster showed no major differences in their geometrical structures. Further analysis of frontier MO levels of the closed-shell anion predicts the HOMO–LUMO transition to be intramolecular L7 → L1 charge transfer, where “L7” and “L1” abbreviations refer to the corresponding sulfur layer in the structure. For the neutral cluster, the calculated spin density is delocalized over the two moieties. On the basis of TDDFT+TB calculations, the onset of the measured absorption spectrum could be satisfactorily reproduced.

44
Sethio, D.; Martins, J. B. L.; Lawson Daku, L. M.; Hagemann, H.; Kraka, E. “Modified Density Functional Dispersion Correction for Inorganic Layered MFX Compounds (M = Ca, Sr, Ba, Pb and X = Cl, Br, I)”, J. Phys. Chem. A 2020, 124, 1619-1633.

MFX (M = Ca, Ba, Sr, Pb and X = Cl, Br, I) compounds have received considerable attention due to their technological application as X-ray detectors, pressure sensors and optical data storage materials, when doped with rare-earth ions. MFX compounds belong to the class of layered materials with a tetragonal Matlockite crystal structure, characterized by weakly stacked double-halide layers along the crystallographic $c$-axis. These layers predominantly determine phase transitions, elastic and mechanical properties. However, the correct description of the lattice parameter $c$ is a challenge for most standard DFT functionals, which tend to overestimate the lattice parameter $c$. Because of the weak interactions between the halide layers dispersion corrected functionals seem to be a better choice. We investigated 11 different inorganic layered MFX compounds for which experimental data is available, with standard and dispersion-corrected functionals to assess their performance in reproducing the lattice parameter $c$, structural and vibrational properties of the MFX compounds. Our results revealed that these functionals do not describe the weak interactions between the halide layers in a balanced way. Therefore, we modified Grimme's popular DFT-D2 dispersion correction scheme in two different ways by (i) replacing the dispersion coefficients and van der Waals radii with those of noble gas atoms, or (ii) increasing the van der Waals radii of the MFX atoms up to 40 percent. Comparison with the available experimental data revealed that the latter approach applied to the PBE (Perdew-Burke-Ernzerhof)-D2 functional with 30 percent increased van der Waals radii, which we coined PBE-D2* (Stextsubscript{rvdw}1.30) is best suited to fine-tune the description of the weak interlayer interactions in MFX compounds, thus significantly improving the description of their structural and vibrational properties. Work is in progress applying this new, computationally inexpensive scheme to other inorganic layered compounds and periodic systems with weakly stacked layers.

43
Zdrachek, E.; Bakker, E. “Potentiometric Sensor Array with Multi-Nernstian Slope”, Anal. Chem. 2020, 92, 2926-2930.

The sensitivity of potentiometric sensors functioning in equilibrium mode is limited by the value predicted according to the Nernst equation and inversely proportional to the charge of the analyte ion. Therefore, an increased ion charge results in a dramatic decrease of sensor sensitivity. We propose an approach to allow one to increase the sensitivity of potentiometric measurements by using a combined electrochemical cell composed of several identical ion-selective electrodes immersed into separate sample solutions of equal composition. The combination of n electrodes demonstrating individually a Nernstian slope in one elec-trochemical cell allows to amplify the signal and associated response slope by n times. The proposed approach is shown to provide a double and triple Nernstian slope for potassium-, calcium-, nitrate and carbonate-selective electrodes by combining two or three identical electrodes, correspondingly. Each ion-selective electrode functions in an equilibrium mode, hence ensuring response sta-bility and reproducibility.

42
Kosior, D.; Morga, M.; Maroni, P.; Cieśla, M.; Adamczyk, Z. “Formation of Poly-L-lysine Monolayers on Silica: Modeling and Experimental Studies”, J. Phys. Chem. C 2020, 124, 4571-4581.

Modification of solid substrates by poly-L-lysine (PLL) layers has been widely employed in order to improve their biocompatibility, for promoting protein and cell immobilization for fabrication of biosensor arrays and antibacterial coatings. However, despite many studies conducted in the literature there is deficiency in a quantitative description of PLL adsorption processes. It is postulated that this becomes feasible applying direct experimental techniques combined with through theoretical modeling. In this work the kinetic of PLL adsorption on silica for various ionic strengths was determined in situ under controlled flow conditions using the optical reflectometry and the streaming potential methods. Both, the initial adsorption rates and longer time kinetic runs, were acquired and quantitatively interpreted in terms of the convective-diffusion and the random sequential adsorption theoretical modeling based on the coarse grained Monte-Carlo approach. This unique combination of experimental and theoretical approaches enabled to gain a new insight into the mechanism of macroion adsorption controlled by the electrostatic interactions, which affect both the molecule conformations and the blocking effects. Beside significance for basic science, the results obtained in this work can be exploited for developing reliable procedures for preparing stable PLL monolayers of well controlled coverage and electrokinetic properties.

41
Gooding, J. J.; Mazur, A.; Bakker, E.; Kelley, S.; Tao, N.; Sailor, M.; Merkx, M.; Mao, L.; Clark, H. “Editorial - Happy 5th Anniversary for ACS Sensors”, ACS Sens. 2020, 5, 1-2.

40
Christmann, J.; Mansouri, A.; Grinderslev, J. B.; Jensen, T. R.; Hagemann, H. “Probing the local symmetry of Tb3+ in borohydrides using luminescence spectroscopy”, J. Lumin. 2020, 221, 117065.

Rare-earth borohydrides have recently attracted a strong interest as potential hydrogen storage materials. While the local structure of the BH4 ion can be probed using vibrational spectroscopy, the local structure of the rare-earth ion can be studied using luminescence spectroscopy. This is reported here for Tb(BH4)3 and its solvate with S(CH3)2. The spectra clearly show smaller CF splittings for the unsolvated compound. These experimental data are compared with recent DFT+U calculations of the energy levels and CF splittings for Tb(BH4)3 and show that these calculations significantly overestimate the experimental results.

39
Cao, T.; Trefalt, G.; Borkovec, M. “Measuring slow heteroaggregation rates in the presence of fast homoaggregation”, J. Colloid Interface Sci. 2020, 566, 143-152.archive ouverte unige:134082 pdf texte intégral [accès restreint]

Homoaggregation and heteroaggregation involving amidine and sulfate latex particles in the presence of the anionic surfactant octyl sulfate (OS) is studied by light scattering. This surfactant causes a charge reversal of the amidine particles. This reversal induces a rapid homoaggregation near the charge reversal point. In the presence of the same surfactant, the sulfate particles remain negatively charged and stable. The heteroaggregation process is probed in mixed suspensions of amidine and sulfate latex particles with multi-angle time-resolved dynamic light scattering. This technique allows differentiating between the contributions of homoaggregation and heteroaggregation, and permits to measure the heteroaggregation rate. By optimally choosing the sizes of the particles, one can optimize the contrast and extract heteroaggregation stability ratio over a wide range. The heteroaggregation rate is fast at low OS concentrations, where the two particles are oppositely charged. This rate slows down at higher OS concentrations due to double layer repulsion between the negatively charged particles. However, the onset of this slow heteroaggregation occurs at lower OS concentrations than for homoaggregation. The reason for this shift is that the double layer repulsion between two OS-decorated amidine particles is weaker than between one sulfate particle and one OS-decorated amidine particle. These measurements compare favorably with calculations with the theory by Derjaguin, Landau, Verwey, and Overbeek (DLVO). These calculations suggest that constant potential boundary conditions are more appropriate than the ones of constant charge. In the system studied, the present light scattering technique permits to extract heteroaggregation stability ratios over almost three orders of magnitude. This study is the first of its kind, where such a large range is being probed.

38
Golesorkhi, B.; Nozary, H.; Fürstenberg, A.; Piguet, C. “Erbium complexes as pioneers for implementing linear light-upconversion in molecules”, Mater. Horiz. 2020, in press.archive ouverte unige:132163 pdf texte intégral [accès libre]

Since the non-linear optical (NLO) response of matter to incident excitation light does not require long-lived intermediate excited states working as relays, the conversion of low-energy photons into high energy light beams using second-harmonic generation (second-order NLO process) or two-photon absorption (third-order NLO process) can be implemented either in low-phonon macroscopic solids or in molecules containing high-energy vibrations. However, harnessing the very weak non-linear absorption coefficients requires (very) intense excitation sources, typically lasers, for getting reasonable emitted intensities. In contrast, the piling of successive near-infrared photons to get visible emission using linear optics, i.e. upconversion, is much more efficient, but it depends on the existence of intermediate excited states possessing long residence lifetimes. Therefore, upconversion usually occurs in low-phonon ionic solids or nanoparticles doped with pertinent activators. The recent recognition that trivalent erbium coordination complexes possessing high-frequency oscillators may act as dual visible/near-infrared activators, which implies the existence of at least one long-lived intermediate excited state in these complexes, paved the way for the implementation of the first upconversion processes within isolated molecules. Beyond a justification for using trivalent lanthanides, and especially erbium, for the manipulation of the energy of photons in molecules using linear optics, this tutorial review summarizes the current level of developments in the field of molecular-based upconversion and discusses some forthcoming challenges.

37
Knobloch, P.; Koliwer-Brandl, H.; Arnold, F. M.; Hanna, N.; Gonda, I.; Adenau, S.; Personnic, N.; Barisch, C.; Seeger, M. A.; Soldati, T.; Hilbi, H. “Mycobacterium marinum produces distinct mycobactin and carboxymycobactin siderophores to promote growth in broth and phagocytes”, Cell. Microbiol. 2020, 22, e13163.

Mycobacterium marinum is a model organism for pathogenic Mycobacterium species, including Mycobacterium tuberculosis, the causative agent of tuberculosis. These pathogens enter phagocytes and replicate within the Mycobacterium-containing vacuole (MCV), possibly followed by vacuole exit and growth in the host cell cytosol. Mycobacteria release siderophores called mycobactins to scavenge iron, an essential, yet poorly soluble and available micro-nutrient. To investigate the role of M. marinum mycobactins, we purified by organic solvent extraction and identified by mass spectrometry the lipid-bound mycobactin (MBT) and the water-soluble variant carboxymycobactin (cMBT). Moreover, we generated by specialized phage transduction a defined M. marinum ΔmbtB deletion mutant predicted to be defective for mycobactin production. The M. marinum ΔmbtB mutant strain showed a severe growth defect in broth and phagocytes, which was partially complemented by supplying the mbtB gene on a plasmid. Furthermore, purified Fe-MBT or Fe-cMBT improved the growth of wild-type as well as ΔmbtB mutant bacteria on minimal plates, but only Fe-cMBT promoted the growth of wild-type M. marinum during phagocyte infection. Finally, the intracellular growth of M. marinum ΔmbtB in Acanthamoeba castellanii amoebae was restored by co-infection with wild-type bacteria. Our study identifies and characterizes the M. marinum MBT and cMBT siderophores and reveals the requirement of mycobactins for extra- and intracellular growth of the pathogen.

36
Leuba, F.; Soldati, T. “AI842, AI843, AI844 and AI177 antibodies do not recognize a FLAG-tagged protein expressed in D. discoideum by western blot”, Antib. Rep. 2020, 3, e111.archive ouverte unige:131083 pdf texte intégral [accès libre]

The recombinant antibodies AI842, AI843, AI844 and AI177 do not detect by western blot an N-terminal FLAG-tagged RavZ protein expressed in Dictyostelium discoideum.

35
Klont, F.; Jahn, S.; Grivet, C.; König, S.; Bonner, R.; Hopfgartner, G. “SWATH data independent acquisition mass spectrometry for screening of xenobiotics in biological fluids: Opportunities and challenges for data processing”, Talanta 2020, 211, 120747.

SWATH data independent acquisition (DIA) mass spectrometry (MS) has become an established technique in MS-based ‘omics’ research and is increasingly used for the screening of xenobiotics (e.g. drugs, drug metabolites, pesticides, toxicants). Such xenobiotic screening methods are mostly applied for tentative compound identification purposes based on spectral library searching, while additional data processing techniques are scarcely used thereby leaving the full potential of these methods often unused. Here we present an analytical workflow for screening xenobiotics in human samples using SWATH/MS based on which we highlight opportunities for unlocking unused potential of these methods. The workflow was applied to urine samples from subjects who tested positive for THC and/or cocaine during roadside drug testing with the goal of confirming the positive roadside drug tests and identifying compounds that relate to illicit drug use (e.g. cutting agents, tobacco components) or associate with corresponding lifestyle choices (e.g. nasal decongestants, painkillers). These goals could only be reached by complementing spectral library search procedures with additional multivariate data analyses due to inherent incompleteness of the spectral library that was employed. Such incompleteness represents a common challenge for applications where limited or no metadata is available for study samples, for example in toxicology, doping control in sports, and workplace or roadside drug testing. It furthermore sets the stage for employing additional data processing techniques as is outlined in the presented work.

34
Levernier, N.; Kruse, K. “Spontaneous formation of chaotic protrusions in a polymerizing active gel layer”, New J. Phys. 2020, 22, 013003.

The actin cortex is a thin layer of actin filaments and myosin motors beneath the outer membrane of animal cells. It determines the cells' mechanical properties and forms important morphological structures. Physical descriptions of the cortex as a contractile active gel suggest that these structures can result from dynamic instabilities. However, in these analyses the cortex is described as a two-dimensional layer. Here, we show that the dynamics of the cortex is qualitatively different when gel fluxes in the direction perpendicular to the membrane are taken into account. In particular, an isotropic cortex is then stable for arbitrarily large active stresses. If lateral contractility exceeds vertical contractility, the system can either from protrusions with an apparently chaotic dynamics or a periodic static pattern of protrusions.

33
Szabo, T.; Maroni, P.; Szilagyi, I. “Size-dependent aggregation of graphene oxide”, Carbon 2020, 160, 145-155.

Graphene oxides (GO) of highly polydisperse size distribution were prepared by the Brodie method and their dispersion stability was characterized. Exfoliation and fractionation led to well-defined particle populations in the Nano, classical Colloidal (submicron) and Micrometer size ranges, as revealed by atomic force microscopy and light scattering measurements. Time-resolved dynamic light scattering experiments revealed that aggregation processes are fully impeded in the intermediate pH regime of 3–13 in the absence of electrolytes. While the resistance against salt-induced aggregation increases with the pH due to the progressive ionization of the surface functional groups of GO sheets, their dispersions are inherently unstable at supramillimolar concentrations of strong acids and submolar concentrations of bases, in line with the DLVO theory. However, the aggregation behavior quantified by the critical coagulation concentrations (CCCs) shows surprisingly substantial platelet size dependence. The CCC of Nano Brodie-GO reaches 360 mm at pH = 12, which is one of the highest values ever reported for GO aqueous dispersions. These results provide useful quantitative information to design processable GO dispersions of pH- and size-tunable stability for future applications.

32
Nazarov, A. E.; Ivanov, A. I.; Vauthey, E. “Modeling Infrared Spectral Dynamics upon Symmetry Breaking of a Photo-Excited Quadrupolar Dye”, J. Phys. Chem. C 2020, 124, 2357-2369.

A significant number of quadrupolar dyes with a D-π-A-π-D or A-π-D-π-A structure,where D and A are electron donor and acceptor groups, were shown to undergosymmetry breaking (SB) upon optical excitation. During this process, the electronicexcitation, originally distributed evenly over the molecule, concentrates on one D-π-Abranch, and the molecule becomes dipolar. This process can be monitored by timeresolved infra-red (TRIR) spectroscopy and causes significant spectral dynamics. Atheoretical model of excited-state SB developed earlier ( Ivanov, A. I.J. Phys. Chem.C,2018,122, 29165-29172) is extended to account for the temporal changes takingplace in the IR spectrum upon SB. This model can reproduce the IR spectral dynamicsobserved in the−C≡C−stretching region with a D-π-A-π-D dye in two polar solventsusing a single set of molecular parameters. This approach allows estimating the degreeof asymmetry of the excited state in different solvents as well as its change during SB.Additionally, the relative contribution of the different mechanisms responsible for thesplitting of the symmetric and antisymmetric−C≡C−stretching bands, which areboth IR active upon SB, can be determined.

31
Doistau, B.; Jiménez, J.-R.; Guerra, S.; Besnard, C.; Piguet, C. “Key Strategy for the Rational Incorporation of Long-Lived NIR Emissive Cr(III) Chromophores into Polymetallic Architectures”, Inorg. Chem. 2020, 59, 1424-1435.archive ouverte unige:129610 pdf texte intégral [accès restreint]

The CrIIIN6 chromophores are particularly appealing for low-energy sensitization via energy transfer processes since they show extremely long excited state lifetimes reaching the millisecond range in the technologically crucial near-infrared domain. However, their properties were barely harnessed in multimetallic structures because of the lack of both monitoring methods and accessible synthetic pathways. We herein report a remedy to monitor and control the formation of CrIII-containing assemblies in solution via the design of a CrIIIN6 inert “complex-as-ligand” that can be included into polymetallic architectures. As a proof of concept, these CrN6 building blocks were reacted in solution with ZnII or FeII to give extended trinuclear linear Cr–M–Cr assemblies, the structure of which could be addressed by NMR spectroscopy despite the presence of two slowly relaxing CrIII paramagnetic centers. In addition to long CrIII excited state lifetimes and weak sensitivity to oxygen quenching, these polymetallic assemblies display controlled CrIII to MII energy transfers, which pave the way for use of the “complex-as-ligand” strategy for introducing photophysically active CrIII probes into light-converting polymetallic devices.

Supporting Information (pdf, 4.63 MB)

30
Hopfgartner, G. “Books Review Wenkui Li, Wenying Jian, and Yunlin Fu (Eds.): Sample preparation in LC-MS bioanalysis”, Anal. Bioanal. Chem. 2020, 412, 803-804.

29
Butler, R. E.; Smith, A. A.; Mendum, T. A.; Chandran, A.; Wu, H.; Lefrançois, L.; Chambers, M.; Soldati, T.; Stewart, G. R. “Mycobacterium bovis uses the ESX-1 Type VII secretion system to escape predation by the soil-dwelling amoeba Dictyostelium discoideum”, ISME J. 2020, 14, 919-930.

Mycobacterium bovis is the causative agent of bovine tuberculosis and the predominant cause of zoonotic tuberculosis in people. Bovine tuberculosis occurs in farmed cattle but also in a variety of wild animals, which form a reservoir of infection. Although direct transmission of tuberculosis occurs between mammals, the low frequency of contact between different host species and abundant shedding of bacilli by infected animals suggests an infectious route via environmental contamination. Other intracellular pathogens that transmit via the environment deploy strategies to survive or exploit predation by environmental amoebae. To explore if M. bovis has this capability, we investigated its interactions with the soil and dung-dwelling amoeba, Dictyostelium discoideum. We demonstrated that M. bovis evades phagocytosis and destruction by D. discoideum and actively transits through the amoeba using the ESX-1 Type VII Secretion System as part of a programme of mechanisms, many of which have been co-opted as virulence factors in the mammalian host. This capacity of M. bovis to utilise an environmental stage between mammalian hosts may enhance its transmissibility. In addition, our data provide molecular evidence to support an evolutionary role for amoebae as training grounds for the pathogenic M. tuberculosis complex.

28
Lathion, T.; Fürstenberg, A.; Besnard, C.; Hauser, A.; Bousseksou, A.; Piguet, C. “Monitoring Fe(II) Spin-State Equilibria via Eu(III) Luminescence in Molecular Complexes: Dream or Reality?”, Inorg. Chem. 2020, 59, 1091-1103.archive ouverte unige:129611 pdf texte intégral [accès restreint]

The modulation of light emission by Fe(II) spin-crossover processes in multifunctional materials has recently attracted major interest for the indirect and noninvasive monitoring of magnetic information storage. In order to approach this goal at the molecular level, three segmental ligand strands, L4L6, were reacted with stoichiometric mixtures of divalent d-block cations (M(II) = Fe(II) or Zn(II)) and trivalent lanthanides (Ln(III) = La(III) or Eu(III)) in acetonitrile to give C3-symmetrical dinuclear triple-stranded helical [LnM(Lk)3]5+ cations, which can be crystallized with noncoordinating counter-anions. The divalent metal M(II) is six-coordinate in the pseudo-octahedral sites produced by the facial wrapping of the three didentate binding units, the ligand field of which induces variable Fe(II) spin-state properties in [LnFe(L4)3]5+ (strictly high-spin), [LnFe(L5)3]5+ (spin-crossover (SCO) around room temperature), and [LnFe(L6)3]5+ (SCO at very low temperature). The introduction of the photophysically active Eu(III) probe in [EuFe(Lk)3]5+ results in europium-centered luminescence modulated by variable intramolecular Eu(III) → Fe(II) energy-transfer processes. The kinetic analysis implies Eu(III) → Fe(II) quenching efficiencies close to 100% for the low-spin configuration and greater than 95% for the high-spin state. Consequently, the sensitivity of indirect luminescence detection of Fe(II) spin crossover is limited by the resulting weak Eu(III)-centered emission intensities, but the dependence of the luminescence on the temperature unambiguously demonstrates the potential of indirect lanthanide-based spin-state monitoring at the molecular scale.

Supporting Information (pdf, 1.5 MB)

27
Stankevicins, L.; Ecker, N.; Terriac, E.; Maiuri, P.; Schoppmeyer, R.; Vargas, P.; Lennon-Duménil, A.-M.; Piel, M.; Qu, B.; Hoth, M.; Kruse, K.; Lautenschläger, F. “Deterministic actin waves as generators of cell polarization cues”, Proc. Natl. Acad. Sci. USA 2020, 117, 826-835.

Dendritic cells “patrol” the human body to detect pathogens. In their search, dendritic cells perform a random walk by amoeboid migration. The efficiency of pathogen detection depends on the properties of the random walk. It is not known how the dendritic cells control these properties. Here, we quantify dendritic cell migration under well-defined 2-dimensional confinement and in a 3-dimensional collagen matrix through recording their long-term trajectories. We find 2 different migration states: persistent migration, during which the dendritic cells move along curved paths, and diffusive migration, which is characterized by successive sharp turns. These states exhibit differences in the actin distributions. Our theoretical and experimental analyses indicate that this kind of motion can be generated by spontaneous actin polymerization waves that contribute to dendritic cell polarization and migration. The relative distributions of persistent and diffusive migration can be changed by modification of the molecular actin filament nucleation and assembly rates. Thus, dendritic cells can control their migration patterns and adapt to specific environments. Our study offers an additional perspective on how dendritic cells tune their searches for pathogens.

26
Galli, V.; Sadhu, K. K.; Masi, D.; Saarbach, J.; Roux, A.; Winssinger, N. “Caprin-1 Promotes Cellular Uptake of Nucleic Acids with Backbone and Sequence Discrimination”, Helv. Chim. Acta 2020, 103, e1900255.archive ouverte unige:129366 pdf texte intégral [accès libre]

The cellular delivery of oligonucleotides has been a major obstacle in the development of therapeutic antisense agents. PNAs (Peptide Nucleic Acid) are unique in providing a modular peptidic backbone that is amenable to structural and charge modulation. While cationic PNAs have been shown to be taken up by cells more efficiently than neutral PNAs, the generality of uptake across different nucleobase sequences has never been tested. Herein, we quantified the relative uptake of PNAs across a library of 10 000 sequences for two different PNA backbones (cationic and neutral) and identified sequences with high uptake and low uptake. We used the high uptake sequence as a bait for target identification, leading to the discovery that a protein, caprin-1, binds to PNA with backbone and sequence discrimination. We further showed that purified caprin-1 added to cell cultures enhanced the cellular uptake of PNA as well as DNA and RNA.

Supporting Information: PDF (1 MB) / XSLX (1.7 MB)

25
Patel, J.; Cai, R.; Milton, R.; Chen, H.; Minteer, S. D. “Pyrene-Based Noncovalent Immobilization of Nitrogenase on Carbon Surfaces”, ChemBioChem 2020, in press.

Early work with viologen-mediated nitrogenase bio-electrochemistry focused on bio-electrocatalysis with the enzyme in solution, but biocatalyst immobilization at electrode surfaces is favorable as it provides a high effective concentration of biocatalyst at the electrode surface. We have used a pyrene–peptide linker as a method for immobilizing nitrogenase on carbon electrode surfaces for nitrogenase bio-electrocatalysis.

24
Forrest, T.; Zdrachek, E.; Bakker, E. “Thin Layer Membrane Systems as Rapid Development Tool for Potentiometric Solid Contact Ion-selective Electrodes”, Electroanalysis 2020, in press.

The use of thin membrane layer ion selective electrodes (of ∼200 nm thickness) as rapid diagnosis tool is proposed. While conventional solid contact systems (with a membrane of ∼250 μm thickness) may exhibit a satisfactory stability for regular laboratory use, a signal degradation can still be distinguished over a longer period of time but this requires tedious and time consuming tests. By diminishing the thickness of the membrane by a factor of 103 approximately, diffusion processes happen faster, and the lifetime is significantly reduced. This would ordinarily be a strong drawback but not if the aim is to detect a membrane deterioration in a shorter time frame. This characteristic makes thin membrane systems an ideal tool for rapid complications identification in the development process of conventional solid contact electrodes. The approach is demonstrated here in the development of an all new solid contact probe for anions. PEDOT−C14, a conducting polymer, was used for the first time in a solid contact electrode with an anion exchange membrane for the detection of nitrate. The thin layer configuration was used to optimise the polymerisation parameters as well as the membrane composition without having to run week long trials. A stable conventional solid contact electrode was in the end successfully developed and exhibited a lower detection limit of 10−5.5 M for nitrate with a stable Nernstian response for several days.

23
Yang, J.; Chatelet, B.; Hérault, D.; Dufaud, V.; Robert, V.; Grass, S.; Lacour, J.; Vanthuyne, N.; Jean, M.; Albalat, M.; Dutasta, J.-P.; Martinez, A. “Enantiopure encaged Verkade's superbases: Synthesis, chiroptical properties, and use as chiral derivatizing agent”, Chirality 2020, 32, 139-146.archive ouverte unige:129075 pdf texte intégral [accès restreint]

Verkade's superbases, entrapped in the cavity of enantiopure hemicryptophane cages, have been synthesized with enantiomeric excess (ee) superior to 98%. Their absolute configuration has been determined by using electronic circular dichroism (ECD) spectroscopy. These enantiopure encaged superbases turned out to be efficient chiral derivatizing agents for chiral azides, underlining that the chirality of the cycloveratrylene (CTV) macrocycle induces different magnetic and chemical environments around the phosphazide functions.

Supporting Information (PDF / 2 MB)

22
Hopfgartner, G. “Editorial Bioanalytical method validation: How much should we do and how should we document?”, Anal. Bioanal. Chem. 2020, 412, 531-532.

21
Humeniuk, H. V.; Licari, G.; Vauthey, E.; Sakai, N.; Matile, S. “Mechanosensitive Membrane Probes:  Push-Pull Papillons”, Supramol. Chem. 2020, 33, 106-111.archive ouverte unige:131618 pdf texte intégral [accès libre]

Design, synthesis and evaluation of push-pull N,N′-diphenyl-dihydrodibenzo[a,c]phenazines are reported. Consistent with theoretical predictions, donors and acceptors attached to the bent mechanophore are shown to shift absorption maxima to either red or blue, depending on their positioning in the chromophore. Redshifted excitation of push-pull fluorophores is reflected in redshifted emission of both bent and planar excited states. The intensity ratios of the dual emission in more and less polar solvents imply that excited-state (ES) planarization decelerates with increasing fluorophore macrodipole, presumably due to attraction between the wings of closed papillons. ES planarization of highly polarisable papillons is not observed in lipid bilayer membranes. All push-pull papillon amphiphiles excel with aggregation-induced emission (AIE) from bent ES as micelles in water and mechanosensitivity in viscous solvents. They are not solvatochromic and only weakly fluorescent (QY < 4%).

Supplemental material (pdf)

20
Stojimirovic, B.; Vis, M.; Tuinier, R.; Philipse, A. P.; Trefalt, G. “Experimental Evidence for Algebraic Double-Layer Forces”, Langmuir 2020, 36, 47-54.

According to textbook wisdom electric double-layer forces decay exponentially with separation distance. Here we present experimental evidence of algebraically decaying double-layer interactions. We show that algebraic interactions arise in both strongly overlapping as well as counterion-only regimes. In both of these cases the disjoining pressure profile assumes an inverse square distance dependence. At small separation distances another algebraic regime is recovered. In this regime the pressure decays as the inverse of separation distance.

Supporting Information (pdf / 191.56 kb)

19
Fiorito, D.; Liu, Y.; Besnard, C.; Mazet, C. “Direct Access to Chiral Secondary Amides by Copper-Catalyzed Borylative Carboxamidation of Vinylarenes with Isocyanates”, J. Am. Chem. Soc. 2020, 142, 623-632.archive ouverte unige:128621 pdf texte intégral [accès restreint]

A Cu-catalyzed borylative carboxamidation reaction has been developed using vinylarenes and isocyanates. Alkynes, branched 1,3-dienes and bicyclic alkenes were also found to be competent coupling partners. Using a chiral phosphan-amine ligand, an enantioselective variant of this transformation was developed, affording a set of α-chiral amides with unprecedented levels of enantioselectivity. The synthetic utility of the method was demonstrated through a series of representative stereoretentive post-catalytic derivatizations.

Supporting Information: Experimental procedures, characterization of all new compounds, spectroscopic, spectrometric, and X-ray data for compounds 3wa, (E)-5ab, and 3ja (CCDC 1914320–1914322) (PDF / 21.13 MB)
Crystallographic information files (CIF): #1 ( 276.58 kb) / #2 (730.19 kb) / #3 (405.19 kb)

18
Oberhauser, L.; Granziera, S.; Colom, A.; Goujon, A.; Lavallard, V.; Matile, S.; Roux, A.; Brun, T.; Maechler, P. “Palmitate and Oleate Modify Membrane Fluidity and Kinase Activities of INS-1E ß-Cells Alongside Altered Metabolism-Secretion Coupling”, Biochim. Biophys. Acta, Mol. Cell Biol. Lipids 2020, 1867, 118619.archive ouverte unige:127987 pdf texte intégral [accès restreint]

Chronic exposure to elevated levels of glucose and free fatty acids impairs beta-cell function, leading to insulin secretion defects and eventually beta-cell failure. Using a semi-high throughput approach applied to INS-1E beta-cells, we tested multiple conditions of chronic exposure to basal, intermediate and high glucose, combined with saturated versus mono- and polyunsaturated fatty acids in order to assess cell integrity, lipid metabolism, mitochondrial function, glucose-stimulated calcium rise and secretory kinetics. INS-1E beta-cells were cultured for 3 days at different glucose concentrations (5.5, 11.1, 25 mM) without or with BSA-complexed 0.4 mM saturated (C16:0 palmitate), monounsaturated (C18:1 oleate) or polyunsaturated (C18:2 linoleate, C18:3 linolenate) fatty acids, resulting in 0.1–0.5 μM unbound fatty acids. Accumulation of triglycerides in cells exposed to fatty acids was glucose-dependent, oleate inducing the strongest lipid storage and protecting against glucose-induced cytotoxicity. The combined chronic exposure to both high glucose and either palmitate or oleate altered mitochondrial function as well as glucose-induced calcium rise. This pattern did not directly translate at the secretory level since palmitate and oleate exhibited distinct effects on the first and the second phases of glucose-stimulated exocytosis. Both fatty acids changed the activity of kinases, such as the MODY-associated BLK. Additionally, chronic exposure to fatty acids modified membrane physicochemical properties by increasing membrane fluidity, oleate exhibiting larger effects compared to palmitate. Chronic fatty acids differentially and specifically exacerbated some of the glucotoxic effects, without promoting cytotoxicity on their own. Each of the tested fatty acids functionally modified INS-1E beta-cell, oleate inducing the strongest effects.

Supplementary figures (PDF / 1 MB)

17
Brun, E.; Zhang, K.-F.; Guénée, L.; Lacour, J. “Photo-induced thiol–ene reactions for late-stage functionalization of unsaturated polyether macrocycles: regio and diastereoselective access to macrocyclic dithiol derivatives”, Org. Biomol. Chem. 2020, 18, 250-254.archive ouverte unige:128309 pdf texte intégral [accès libre]

Double hydrothiolation of bis enol ether macrocycles was achieved under photo-mediated conditions. The thiol–ene reactions afford a fully regioselective anti-Markovnikov post-functionalization. Thanks to the use of ethanedithiol as reagent, moderate to excellent diastereoselectivity was accomplished leading to macrocycles containing four defined stereocenters in only three steps from 1,4-dioxane, tetrahydrofuran (THF) or tetrahydropyran (THP).

Supplementary Information (PDF) / Crystal Structure data (CIF)

16
Duwald, R.; Bosson, J.; Pascal, S.; Grass, S.; Zinna, F.; Besnard, C.; Di Bari, L.; Jacquemin, D.; Lacour, J. “Merging polyacenes and cationic helicenes: from weak to intense chiroptical properties in the far red region”, Chem. Sci. 2020, 11, 1165-1169.archive ouverte unige:129838 pdf texte intégral [accès libre]

A series of helical tetracenes and pentacenes was synthesized from cationic [6] and [4]helicene precursors. These colorful acenes fluoresce in the far red region. While [4]helicene-based pentacenes exhibit chiroptical properties mainly in the UV region, [6]helicene-derived tetracenes show enhanced ECD in the visible range, in addition to clear CPL responses. This difference is rationalized using first principles.

Supplementary information (PDF) / Crystal structure data (CIF)

15
Zinna, F.; Brun, E.; Homberg, A.; Lacour, J. “Circularly polarized luminescence from intramolecular excimers”, In Circularly Polarized Luminescence of Isolated Small Organic Molecules”, Mori, T. (Ed.), Springer: Singapore 2020.

14
Figuerola-Conchas, A.; Saarbach, J.; Daguer, J.-P.; Cieren, A.; Barluenga, S.; Winssinger, N.; Gotta, M. “Small-molecule modulators of the ATPase VCP/p97 affect specific p97 cellular functions”, ACS Chem. Biol. 2020, 15, 243-253.archive ouverte unige:129089 pdf texte intégral [accès libre]

VCP/p97 belongs to the AAA+ ATPase family and has an essential role in several cellular processes ranging from cell division to protein homeostasis. Compounds targeting p97 inhibit the main ATPase domain and cause cell death. Here, using PNA-encoded chemical libraries, we have identified two small molecules that target the regulatory domain of p97, comprising the N-terminal and the D1 ATPase domains, and do not cause cell death. One molecule, NW1028, inhibits the degradation of a p97-dependent reporter, whereas the other, NW1030, increases it. ATPase assays show that NW1028 and NW1030 do not affect the main catalytic domain of p97. Mapping of the binding site using a photo-affinity conjugate points to a cleft at the interface of the N-terminal and the D1 ATPase domains. We have therefore discovered two new compounds that bind to the reg-ulatory domain of p97 and modulate specific p97 cellular functions. Using these compounds, we have revealed a role for p97 in the regulation of mitotic spindle orientation in HeLa cells.

Supporting Information:

Supplementary figures and synthetic procedures as well as analysis of the synthesized compounds (PDF / 4.27 MB)

Video 1: HeLa K cells expressing H2B-mCherry (red, to mark chromosomes) and α-tubulin-mEGFP (green, to mark microtubules) treated with 10 μM DBeQ (AVI / 1.91 MB)

Video 2: HeLa K cells expressing H2B-mCherry (red, to mark chromosomes) and α-tubulin-mEGFP (green, to mark microtubules) treated with 10 μM NW1028 (AVI / 90.02 kb)

Video 3: HeLa K cells expressing H2B-mCherry (red, to mark chromosomes) and α-tubulin-mEGFP (green, to mark microtubules) treated with 10 μM NW1030 (AVI / 112.48 kb)

Video 4: HeLa K cells expressing H2B-mCherry (red, to mark chromosomes) and α-tubulin-mEGFP (green, to mark microtubules) treated with 10 μM DMSO (AVI / 90.9 kb)

13
Rodrigues, T.; Brodier, L.; Matter, J.-M. “Investigating Neurogenesis in Birds”, In Retinal Development: Methods and Protocols”, Mao, C.-A. (Ed.), Collection “Methods in Molecular Biology” vol. 2092, Humana: New York 2020, p. 1-18.

The macula and fovea make human vision unique among mammals. An understanding of the genetic network underlying the development and maintenance of this highly specialized region is instrumental to address issues about human macula-related retinopathies. The pigeon retina, unlike currently available animal models, shares numerous key characteristics of the primate macula and represents a promising new model for the study of retinal development. We provide key elements to take advantage of this new model for the study of retina and brain development. This includes precise embryo staging, transfection of genetic material (reporter plasmid, expression vectors, siRNAs) using in ovo and ex vivo electroporation, live imaging, high-resolution confocal imaging, and data layout and instructions for data analysis.

12
Smith, A. M.; Borkovec, M.; Trefalt, G. “Forces between solid surfaces in aqueous electrolyte solutions”, Adv. Colloid Interface Sci. 2020, 275, 102078.

This review addresses experimental findings obtained with direct force measurements between two similar or dissimilar solid surfaces in aqueous electrolyte solutions. Interpretation of these measurements is mainly put forward in terms of the classical theory of Derjaguin, Landau, Verwey, and Overbeek (DLVO). This theory invokes a superposition of attractive van der Waals forces and repulsive double layer forces. DLVO theory is shown to be extremely reliable, even in the case of multivalent ions. However, such a description is only successful, when appropriate surface charge densities, charge regulation characteristics, and ion pairing or complexation equilibria in solution are considered. Deviations from DLVO theory only manifest themselves at distances of typically below few nm. More long-ranged non-DLVO forces can be observed in some situations, particularly, in concentrated electrolyte solutions, in the presence of strongly adsorbed layers, or for hydrophobic surfaces. The latter forces probably originate from patch-charge surface heterogeneities, which can be induced by ion-ion correlation effects, charge fluctuations, or other types of surface heterogeneities.

11
Gao, W.; Zdrachek, E.; Xie, X.; Bakker, E. “A Solid-State Reference Electrode Based on a Self-Referencing Pulstrode”, Angew. Chem. Int. Ed. 2020, 59, 2294-2298.

The design of solid-state reference electrodes without a liquid junction is important to allow miniature and cost-effective electrochemical sensors. To address this, a pulse control is proposed using an Ag/AgI element as reliable solid-state reference electrode. It involves the local release of iodide by a cathodic current that is immediately followed by an electromotive force (EMF) measurement that serves as the reference potential. The recapture of iodide ions is achieved by potentiostatic control. This results in intermittent potential values that are reproducible to less than one millivolt (SD=0.27 mV, n=50). The ionic strength is shown to influence the activity coefficient of released iodide in accordance with the extended Debye–Hückel equation, resulting in a predictable change of the potential reading. The principle is applied to potentiometric potassium detection with a valinomycin-based ion-selective electrode (ISE), demonstrating a completely solid-state sensor configuration.

Supporting Information (pdf / 1800.3 KB)

10
Zhang, X.; Sakai, N.; Matile, S. “Methyl Scanning for Mechanochemical Chalcogen-Bonding Cascade Switches”, ChemistryOpen 2020, 9, 18-22.archive ouverte unige:128620 pdf texte intégral [accès libre]

Chalcogen-bonding cascade switching was introduced recently to produce the chemistry tools needed to image physical forces in biological systems. In the original flipper probe, one methyl group appeared to possibly interfere with the cascade switch. In this report, this questionable methyl group is replaced by a hydrogen. The deletion of this methyl group in planarizable push-pull probes was not trivial because it required the synthesis of dithienothiophenes with four different substituents on the four available carbons. The mechanosensitivity of the resulting demethylated flipper probe was nearly identical to that of the original. Thus methyl groups in the switching region are irrelevant for function, whereas those in the twisting region are essential. This result supports the chalcogen-bonding cascade switching concept and, most importantly, removes significant synthetic demands from future probe development.

Supporting Information

9
Fedunov, R. G.; Yermolenko, I. P.; Nazarov, A. E.; Ivanov, A. I.; Rosspeintner, A.; Angulo, G. “Theory of fluorescence spectrum dynamics and its application to determining the relaxation characteristics of the solvent and intramolecular vibrations”, J. Mol. Liq. 2020, 298, 112016.

A general analytical expression for the transient fluorescence spectrum is derived. The formation of a wave packet in the excited state of a fluorophore is described, assuming that the pump pulse has a Gaussian time-profile. The expression explicitly connects the relaxation characteristics of the medium with the spectral dynamics of a fluorophore. Fitting the expression to experimental spectral dynamics allows obtaining the solvent relaxation function. So far this approach was applicable for the analysis of experimental data when the pump pulse does not populate excited sublevels of intramolecular high-frequency vibrational modes. Here, the approach is generalized to include vibrational relaxation in the excited electronic state. In this case, fitting to the experimental spectral dynamics provides reliable information not only on the solvent relaxation, but also on the relaxation time constants of intramolecular high-frequency vibrational modes. This approach is applied to the excited state dynamics of coumarin 153 in multiple solvents, obtained from broadband fluorescence upconversion spectroscopy.

8
Caprice, K.; Aster, A.; Cougnon, F. B. L.; Kumpulainen, T. “Untying the Photophysics of Quinolinium-Based Molecular Knots and Links”, Chem. Eur. J. 2020, 26, 1576-1587.archive ouverte unige:129606 pdf texte intégral [accès restreint]

Today, complex molecular knots and links are still difficult to synthesize and the properties arising from their topology are mostly unknown. Here, we report on a comparative photophysical study carried out on a family of closely related quinolinium-based knots and links to determine the impact exerted by topology on the molecular backbone. Our results indicate that topology has a negligible influence on the behavior of loosely braided molecules, which mostly behave like their unbraided equivalents. On the other hand, tightly braided molecules display distinct features. Their higher packing density results in a pronounced ability to resist deformation, a significant reduction in the solvent-accessible surface area and favors close-range π-π interactions between the quinolinium-units and neighboring aromatics. Finally, the sharp alteration in behavior between loosely and tightly braided molecules sheds light upon the factors contributing to braiding tightness.

Supporting Information (pdf / 8 MB)

7
Laurent, Q.; Berthet, M.; Cheng, Y.; Sakai, N.; Barluenga, S.; Winssinger, N.; Matile, S. “Probing for Thiol-Mediated Uptake into Bacteria”, ChemBioChem 2020, 21, 69-73.archive ouverte unige:129267 pdf texte intégral [accès restreint]

Cellular uptake mediated by cyclic oligochalcogenides (COCs) is emerging as a conceptually innovative method to penetrate mammalian cells. Their mode of action is based on dynamic covalent oligochalcogenide exchange with cellular thiols. To test thiol-mediated uptake in bacteria, five antibiotics have been equipped with up to three different COCs: One diselenolane and two dithiolanes. We found that the COCs do not activate antibiotics in Gram-negative bacteria. In Gram-positive bacteria, the COCs inactivate antibiotics that act in the cytoplasm and reduce the activity of antibiotics that act on the cell surface. These results indicate that thiol-mediated uptake operates in neither of the membranes of bacteria. COCs are likely to exchange with thiols on the inner, maybe also on the outer membrane, but do not move on. Concerning mammalian cells, the absence of a COC-mediated uptake into bacteria observed in this study disfavors trivial mechanisms, such as passive diffusion, and supports the existence of more sophisticated, so far poorly understood uptake pathways.

Supporting Information (PDF / 1.9 MB)

6
Apichai, S.; Wang, L.; Grudpan, K.; Bakker, E. “Renewable magnetic ion-selective colorimetric microsensors based on surface modified polystyrene beads”, Anal. Chim. Acta 2020, 1094, 136-141.

Magnetic ion-selective colorimetric microspheres based on surface modification of polystyrene beads (0.8 μm diameter) are reported for the first time. The common components of ion-selective optode sensing (chromoionophore, ion-exchanger and ionophore) and magnetic nanoparticles are adsorbed onto the surface of the polystyrene particles using a simple mixed solvent method. The average diameter of the magnetic microspheres is evaluated by dynamic light scattering as 0.79 ± 0.06 μm. The reversible microsensors are circulated by flow and accumulated at a single spot by an applied magnet to become observable by digital camera. Hue signals are extracted from the recorded images to quantify the ratio of protonated and deprotonated form of the chromoionophore, which is the basis for optode response. The resulting magnetic microsensors respond to K+ with excellent selectivity over the range of 10−6 M to 10−2 M and a response time of t99 < 2.6±0.5 min above 10−5 M. The use of solvatochromic dyes as pH independent transducers was not successful in this application.

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Sheberstov, K. F.; Guardiola Sistare, E.; Jeannerat, D. “Everything you wanted to know about phase and reference frequency in one- and two-dimensional NMR Spectroscopy”, Magn. Reson. Chem. 2020, 58, 376-389.archive ouverte unige:132660 pdf texte intégral [accès restreint]

The fundamental concept of phase is discussed in this tutorial aimed at providing students with an explanation of the delays and processing parameters they may find in NMR pulse programs. We consider the phase of radio-frequency pulses, receiver, magnetization and how all these parameters are related to phases and offsets of signals in spectra. The impact of the off-resonance effect on the phase of the magnetization is discussed before presenting an overview of how adjustment of the time reference of the free induction decay (FID) avoids first-order correction of the phase of spectra. The main objective of this tutorial is to show how the relative phase of a pulse and the receiver can be used to change the reference frequency along direct and indirect dimensions of NMR experiments. Unusual applications of phase incrementation with non-90 degree angles will be illustrated on 1D and 2D NMR spectra.

Supporting Information (ZIP / 1.6 MB)

4
Akbal, L.; Hopfgartner, G. “Supercritical fluid chromatography–mass spectrometry using data independent acquisition for the analysis of polar metabolites in human urine”, J. Chromatogr. A 2020, 1609, 460449.

The application of supercritical fluid chromatography with mass spectrometric (MS) detection (SFC–MS) was compared towards generic reversed phase liquid chromatography (RPLC) and hydrophilic interaction liquid chromatography (HILIC) for the analysis of urine with regards of ionization performance and analyte identification. The different chromatographic conditions were characterized with a selected set of 51 metabolites from different classes reported in the Human Metabolome DataBase (HMDB) and previously detected in human urine and/or plasma. SFC using a diol column with a gradient of carbon dioxide (CO2) and methanol with 10?mM ammonium hydroxide as modifier was able to retain and separate 20 polar analytes co-eluting in the RPLC eluent front. In the conditions investigated and compared to HILIC where many metabolites were also co-eluting, SFC showed a different ratio between elution domain and analysis time. Similar peak width and symmetry were observed, while retention time variability was slightly lower compared to that of HILIC (0.15% versus 0.24% and 1.26% for RPLC and HILIC, respectively). In SFC–MS, a significant signal enhancement (2–150 times, average of about 10 times) was measured after post-column make-up addition (MeOH/H2O, 95/5, v/v + 25?mM ammonium acetate) for 28 analytes. Nine analytes measured by LC–MS could not be detected in SFC–MS. Applicability of SFC–MS for metabolomics was investigated with the analysis of urine samples using data independent acquisition (DIA) and more specifically Sequential Window Acquisition of all Theoretical Mass Spectra (SWATH/MS). Using a metabolomics library, 74 metabolites from human urine could be identified in positive mode in a single SFC–MS analysis of 15 min.

3
Baudet, K.; Kale, V.; Mirzakhani, M.; Babel, L.; Naseri, S.; Besnard, C.; Nozary, H.; Piguet, C. “Neutral Heteroleptic Lanthanide Complexes for Unravelling Host–Guest Assemblies in Organic Solvents: The Law of Mass Action Revisited”, Inorg. Chem. 2020, 59, 62-75.archive ouverte unige:128831 pdf texte intégral [accès restreint]

The binding of lanthanide containers [Ln(β-diketonate)3dig] [dig = 1-methoxy-2-(2-methoxyethoxy)ethane] to aromatic tridentate N-donor ligands (L) in dichloromethane produces neutral nine-coordinate heteroleptic [LLn(β-diketonate)3] complexes, the equilibrium reaction quotients of which vary with the total concentrations of the reacting partners. This problematic drift prevents the determination of both reliable thermodynamic stability constants and intrinsic host–guest affinities. The classical solution theory assigns this behavior to changes in the activity coefficients of the various partners in nonideal solutions, and a phenomenological approach attempts to quantitatively attribute this effect to some partition of the solvent molecules between bulk-innocent and contact-noninnocent contributors to the chemical potential. This assumption eventually predicts an empirical linear dependence of the equilibrium reaction quotient on the concentration of the formed [LLn(β-diketonate)3] complexes, a trend experimentally supported in this contribution for various ligands L differing in lipophilicity and nuclearity and for lanthanide containers grafted with diverse β-diketonate coligands. Even if the origin of the latter linear dependence is still the subject of debate, this work demonstrates that this approach can be exploited by experimentalists for extracting reliable thermodynamic constants suitable for analyzing and comparing host–guest affinities in organic solvents.

Supporting Information (pdf, 28.1 MB)

2
Sheberstov, K.; Sistaré Guardiola, E.; Pupier, M.; Jeannerat, D. “SAN plot: a Graphical representation of the signal, noise and artifacts content of spectra”, Magn. Reson. Chem. 2020, 58, 466-472.archive ouverte unige:132183 pdf texte intégral [accès libre]

The signal-to-noise ratio is an important property of NMR spectra. It allows to compare the sensitivity of experiments, the performance of hardware, etc. Its measurement is usually done in a rudimentary manner involving manual operation of selecting separately a region of the spectrum with signal and noise respectively, applying some operation and returning the SNR. We introduce here a simple method based on the analysis of the distribution of point intensities in one- and two-dimensional spectra. The Signal/Artifact/Noise plots, (SAN plots) allows one to present in a graphical manner qualitative and quantitative information about spectra. It will be shown that besides measuring signal and noise levels, SAN plots are also quite useful to visualize and compare artifacts within a series of spectra. Some basic properties of the SAN plots are illustrated with simple application.

Supporting Information (PDF / 506.5 KB)

1
Funato, K.; Riezman, H.; Muñiz, M. “Vesicular and non-vesicular lipid export from the ER to the secretory pathway”, Biochim. Biophys. Acta, Mol. Cell Biol. Lipids 2020, 1865, 158453.

The endoplasmic reticulum is the site of synthesis of most glycerophospholipids, neutral lipids and the initial steps of sphingolipid biosynthesis of the secretory pathway. After synthesis, these lipids are distributed within the cells to create and maintain the specific compositions of the other secretory organelles. This represents a formidable challenge, particularly while there is a simultaneous and quantitatively important flux of membrane components stemming from the vesicular traffic of proteins through the pathway, which can also vary depending on the cell type and status. To meet this challenge cells have developed an intricate system of interorganellar contacts and lipid transport proteins, functioning in non-vesicular lipid transport, which are able to ensure membrane lipid homeostasis even in the absence of membrane trafficking. Nevertheless, under normal conditions, lipids are transported in cells by both vesicular and non-vesicular mechanisms. In this review we will discuss the mechanism and roles of vesicular and non-vesicular transport of lipids from the ER to other organelles of the secretory pathway.