Total Synthesis of Anti-MRSA Active Diorcinols and Analogues

Diorcinols and related prenylated diaryl ethers were reported to exhibit activity against methicillin-resistant clinical isolates of Staphylococcus aureus (MRSA). Within these lines, we report the first total synthesis of diorcinol D, I, J, the proposed structure of verticilatin and recently isolated antibacterial diaryl ether by using an efficient and highly divergent synthetic strategy. These total syntheses furnish the diaryl ethers in only five to seven steps employing a Pd-catalyzed diaryl ether coupling as the key step. The total synthesis led to the structural revision of the natural product verticilatin, which has been isolated from a plant pathogenic fungus. Furthermore, these structures were tested in order to determine their antibacterial activities against different MRSA strains as well as further Gram-positive and -negative bacteria.

Predicting Absolute Rate Constants for Huisgen Reactions of Unsaturated Iminium Ions with Diazoalkanes

The kinetics and stereochemistry of the reactions of iminium ions derived from cinnamaldehydes and MacMillan's imidazolidinones with diphenyldiazomethane and aryldiazomethanes were investigated experimentally and with DFT calculations. The reactions of diphenyldiazomethane with iminium ions derived from MacMillan's second-generation catalysts gave 3-aryl-2,2-diphenylcyclopropanecarbaldehydes with yields >90 % and enantiomeric ratios of ≥90:10. Predominantly 2:1 products were obtained from the corresponding reactions with monoaryldiazomethanes. The measured rate constants are in good agreement with the rate constants derived from the one-center nucleophilicity parameters N and sN of diazomethanes and the one-center electrophilicity parameters E of iminium ions as well as with quantum chemically calculated activation energies.

Molecular Features and Metal Ions That Influence 10-23 DNAzyme Activity

Deoxyribozymes (DNAzymes) with RNA hydrolysis activity have a tremendous potential as gene suppression agents for therapeutic applications. The most extensively studied representative is the 10-23 DNAzyme consisting of a catalytic loop and two substrate binding arms that can be designed to bind and cleave the RNA sequence of interest. The RNA substrate is cleaved between central purine and pyrimidine nucleotides. The activity of this DNAzyme in vitro is considerably higher than in vivo, which was suggested to be related to its divalent cation dependency. Understanding the mechanism of DNAzyme catalysis is hindered by the absence of structural information. Numerous biological studies, however, provide comprehensive insights into the role of particular deoxynucleotides and functional groups in DNAzymes. Here we provide an overview of the thermodynamic properties, the impact of nucleobase modifications within the catalytic loop, and the role of different metal ions in catalysis. We point out features that will be helpful in developing novel strategies for structure determination and to understand the mechanism of the 10-23 DNAzyme. Consideration of these features will enable to develop improved strategies for structure determination and to understand the mechanism of the 10-23 DNAzyme. These insights provide the basis for improving activity in cells and pave the way for developing DNAzyme applications.

Poly-γ-S-perillyl-l-glutamate and Poly-γ-S-perillyl-d-glutamate: Diastereomeric Alignment Media Used for the Investigation of the Alignment Process

Residual dipolar couplings (RDCs) offer additional information for structure elucidation by NMR spectroscopy. They are measured in anisotropic media, such as lyotropic liquid crystalline phases of polypeptides. Today, some suitable polypeptides are known. Nevertheless, structural influences of these polypeptides on the alignment properties are not really understood. Thus, which influence a chiral side chain has on enantiodiscrimination and whether we can improve the enantiodifferentiation significantly by adding an additional chiral center in the side chain are questions of interest. Therefore, new diastereomeric polypeptide-based alignment media with an additional chiral center in the side chain derived from perillyl alcohol were synthesized and their properties were investigated (secondary structure, liquid crystallinity, etc.). The enantiomers of isopinocampheol and β-pinene were used as model analytes for the study of enantiodiscrimination. Additionally, the usage of 1 H-1 H-RDCs to improve the alignment tensor quality is demonstrated.

Electro-organic synthesis - a 21st century technique

The severe limitations of fossil fuels and finite resources influence the scientific community to reconsider chemical synthesis and establish sustainable techniques. Several promising methods have emerged, and electro-organic conversion has attracted particular attention from international academia and industry as an environmentally benign and cost-effective technique. The easy application, precise control, and safe conversion of substrates with intermediates only accessible by this method reveal novel pathways in synthetic organic chemistry. The popularity of electricity as a reagent is accompanied by the feasible conversion of bio-based feedstocks to limit the carbon footprint. Several milestones have been achieved in electro-organic conversion at rapid frequency, which have opened up various perspectives for forthcoming processes.

Carbon Nanomembranes from Aromatic Carboxylate Precursors

Self-assembled monolayers (SAMs) serve as convenient platform for fabricating carbon nanomembranes (CNMs) of extended lateral dimensions. Highly porous CNMs are emerging as interesting materials for membrane technologies as they exhibit selectivity for water permeation and, owing to their reduced dimensionality, promise increased energy efficiency compared to established systems. In the present study terphenylcarboxylate SAMs, prepared on silver underpotential deposited on Au and irradiated by 100 eV electrons, were successfully converted into free-standing CNMs. Infrared and X-ray photoelectron spectroscopy reveal pronounced chemical changes both of the anchoring carboxylate moiety and the aromatic backbone upon electron irradiation. Permeation studies showed high specificity for water as demonstrated by the separation from tetrahydrofuran. Compared to thiols on gold, the standard CNM precursor system, the carboxylic acid based SAM exhibits equivalent characteristics. This suggests that electron-induced carbonization is insensitive to the particular choice of the anchor moiety and, therefore, the choice of precursor molecules can be extended to the versatile class of aromatic carboxylic acids.

Probing the Validity of the Zintl-Klemm Concept for Alkaline-Metal Copper Tellurides by Means of Quantum-Chemical Techniques

Understanding the nature of bonding in solid-state materials is of great interest for their designs, because the bonding nature influences the structural preferences and chemical as well as physical properties of solids. In the cases of tellurides, the distributions of valence-electrons are typically described by applying the Zintl-Klemm concept. Yet, do these Zintl-Klemm treatments provide adequate pictures that help us understanding the bonding nature in tellurides? To answer this question, we followed up with quantum-chemical examinations on the electronic structures and the bonding nature of three alkaline-metal copper tellurides, i.e., NaCu3Te2, K2Cu2Te5, and K2Cu5Te5. In doing so, we accordingly probed the validity of the Zintl-Klemm concept for these ternary tellurides, based on analyses of the respective projected crystal orbital Hamilton populations (-pCOHP) and Mulliken as well as Löwdin charges. Since all of the inspected tellurides are expected to comprise Cu-Cu interactions, we also paid particular attention to the possible presence of closed-shell interactions.

Unusual Racemization of Tertiary P-Chiral Ferrocenyl Phosphines

Tertiary phosphines are generally known to withstand inversion under moderate conditions. In this work, a remarkable racemization process of three P-chiral ferrocenyl phosphines is reported. Subjected to conventional column chromatography as highly enantioenriched compounds, they greatly experienced racemization when collected at the column outlet within minutes. Initially, attention was drawn to this unusual inversion behavior after observing that the superb enantiomeric excess of these ligands (>95 % ee in all cases) was almost lost in their corresponding ruthenium(II) complexes. Successively excluding possible racemization causes, these P-chiral ferrocenyl phosphines were found to undergo a significant, acid-catalyzed racemization process at room temperature within a few minutes. This process is mainly observed during standard column chromatography by using conventional silica or alumina, but can also be triggered deliberately by addition of certain acids. Therefore, the stereochemical preservation of P-chiral phosphines during their purification may per se not always be guaranteed, since column chromatography is the most frequently used technique for purifying such types of compounds.

Redox-inactive ions control the redox-activity of molecular vanadium oxides

Polyoxometalates are key materials for energy conversion and storage due to their unique chemical tunability and electrochemical reactivity. Herein, we report that functionalization of molecular vanadium oxides, polyoxovanadates, with redox-inert Ca2+ cations leads to a significant increase in their electron storage capabilities. The electrochemical performance of the Ca2+-functionalized dodecavanadate [Ca2V12O32Cl(DMF)3]2- (={Ca 2 V 12 }) was thus compared with that of the precursor compound (H2NMe2)2[V12O32Cl]3- (={V 12 }). {Ca 2 V 12 } can store up to five electrons per cluster, while {V 12 } only shows one reversible redox transition. In initial studies, we demonstrated that {Ca 2 V 12 } can be used as an active material in lithium-ion cathodes. Our results show how redox-inert cations can be used as structural and electrostatic stabilizers, leading to major changes in the redox-chemistry of polyoxovanadates.

Stable Mesoionic N-Heterocyclic Olefins (mNHOs)

We report a new class of stable mesoionic N-heterocyclic olefins, featuring a highly polarized (strongly ylidic) double bond. The ground-state structure cannot be described through an uncharged mesomeric Lewis-structure, thereby structurally distinguishing them from traditional N-heterocyclic olefins (NHOs). mNHOs can easily be obtained through deprotonation of the corresponding methylated N,N'-diaryl-1,2,3-triazolium and N,N'-diaryl-imidazolium salts, respectively. In their reactivity, they represent strong σ-donor ligands as shown by their coordination complexes of rhodium and boron. Their calculated proton affinities, their experimentally derived basicities (competition experiments), as well as donor abilities (Tolman electronic parameter; TEP) exceed the so far reported class of NHOs.

Radical C-N Borylation of Aromatic Amines Enabled by a Pyrylium Reagent

Herein, we report a radical borylation of aromatic amines through a homolytic C(sp2 )-N bond cleavage. This method capitalizes on a simple and mild activation via a pyrylium reagent (Sc Pyry-OTf) thus priming the amino group for reactivity. The combination of terpyridine and a diboron reagent triggers a radical reaction which cleaves the C(sp2 )-N bond and forges a new C(sp2 )-B bond. The unique non-planar structure of the pyridinium intermediate, provides the necessary driving force for the aryl radical formation. The method permits borylation of a wide variety of aromatic amines indistinctively of the electronic environment.

A Spherically Shielded Triphenylamine and Its Persistent Radical Cation

This work reports the design and synthesis of a sterically protected triphenylamine scaffold which undergoes one-electron oxidation to form an amine-centered radical cation of remarkable stability. Several structural adjustments were made to tame the inherent reactivity of the radical cation. First, the parent propeller-shaped triphenylamine was planarized with sterically demanding bridging units and, second, protecting groups were deployed to block the reactive positions. The efficiently shielded triphenylamine core can be reversibly oxidized at moderate potentials (+0.38 V, vs. Fc/Fc+ in CH2 Cl2 ). Spectroelectrochemistry and chemical oxidation studies were employed to monitor the evolution of characteristic photophysical features. To obtain a better understanding of the impact of one-electron oxidation on structural and electronic properties, joint experimental and computational studies were conducted, including X-ray structural analysis, electron paramagnetic resonance (EPR), and density functional theory (DFT) calculations. The sterically shielded radical cation combines various desirable attributes: A characteristic and unobstructed absorption in the visible region, high stability which enables storage for weeks without spectroscopically traceable degradation, and a reliable oxidation/re-reduction process due to effective screening of the planarized triphenylamine core from its environment.

N-Heterocyclic Carbene Catalyzed Photoenolization/Diels-Alder Reaction of Acid Fluorides

The combination of light activation and N-heterocyclic carbene (NHC) organocatalysis has enabled the use of acid fluorides as substrates in a UVA-light-mediated photochemical transformation previously observed only with aromatic aldehydes and ketones. Stoichiometric studies and TD-DFT calculations support a mechanism involving the photoactivation of an ortho-toluoyl azolium intermediate, which exhibits "ketone-like" photochemical reactivity under UVA irradiation. Using this photo-NHC catalysis approach, a novel photoenolization/Diels-Alder (PEDA) process was developed that leads to diverse isochroman-1-one derivatives.

A Simple Nickel Catalyst Enabling an E-Selective Alkyne Semihydrogenation

Stereoselective alkyne semihydrogenations are attractive approaches to alkenes, which are key building blocks for synthesis. With regards to the most atom-economic reducing agent dihydrogen (H2 ), only few catalysts for the challenging E-selective alkyne semihydrogenation have been disclosed, each with a unique substrate scope profile. Here, we show that a commercially available nickel catalyst facilitates the E-selective alkyne semihydrogenation of a wide variety of substituted internal alkynes. This results in a simple and broadly applicable overall protocol to stereoselectively access E-alkenes employing H2 , which could serve as a general method for synthesis.

Two π-Electrons Make the Difference: From BODIPY to BODIIM Switchable Fluorescent Dyes

(aza-)BODIPY dyes (boron dipyrromethene dyes) are well-established fluorophores due to their large quantum yields, stability, and diversity, which led to promising applications including imaging techniques, sensors, organic (opto)electronic materials, or biomedical applications. Although the control of the optical properties in (aza-)BODIPY dyes by peripheral functional groups is well studied, we herein present a novel approach to modify the 12 π-electron core of the dipyrromethene scaffold. The replacement of two carbon atoms in the β-position of a BODIPY dye by two nitrogen atoms afforded a 14 π-electron system, which was termed BODIIM (boron diimidazolylmethene) in systematic analogy to the BODIPY dyes. Remarkably, the BODIIM dye was obtained with a BH2 -rigidifying entity, which is currently elusive and highly sought after for the BODIPY dye class. DFT-Calculations confirm the [12+2] π-electron relationship between BODIPY and BODIIM and reveal a strong shape correlation between LUMO in the BODIPY and the HOMO of the BODIIM. The modification of the π-system leads to a dramatic shift of the optical properties, of which the fluorescent emission is most noteworthy and occurs at much larger Stokes shift, that is, ≈500 cm-1 in BODIPY versus >4170 cm-1 in BODIIM system in all solvents investigated. Nucleophilic reactivity was found at the meso-carbon atom in the formation of stable borane adducts with a significant shift of the fluorescent emission, and this behavior contrasts the reactivity of conventional BODIPY systems. In addition, the reverse decomplexation of the borane adducts was demonstrated in reactions with a representative N-heterocyclic carbene to retain the strongly fluorescent BODIIM compound, which suggests applications as fully reversible fluorescent switch.

Labeling surface proteins with high specificity: Intrinsic limitations of phosphopantetheinyl transferase systems

Objective

Fluorescent labeling of specific cell-surface proteins enables a manifold of techniques to study their function in health and disease. A frequently cited family of methods employs phosphopantetheinyl transferases (PPTases) to attach probes, provided as conjugates of Coenzyme A. This method appears attractive, as only short peptide tags genetically fused to the protein of interest are needed as conjugation sites. Here, we describe observations we made when evaluating such protocols for delicate single-molecule applications where we require a particular combination of dyes, low background binding or low labeling of other proteins, and a high degree of labeling.

Results

When we tested a PPTase-acceptor peptide couple with several experimental protocols and various CoA conjugates for labeling of a protein on the cell surface, we noticed substantial non-specific labeling. For the first time, we provide here a quantification of the non-specific fraction of the signals obtained using appropriate controls. We further present evidence that this background is due to CoA-dye conjugates entering the cell, where they may be covalently attached to endogenous proteins. However, when studying cell-surface proteins, most fluorescent readouts require that labeling is strictly limited to the protein of interest located at the cell surface. While such data have so far been missing in the literature, they suggest that for applications where labeling of unwanted molecules would affect the conclusions, researchers need to be aware of this potential non-specificity of PPTase methods when selecting a labeling strategy. We show, again by quantitative comparison, that the HaloTag is a viable alternative.

Nucleophilicity of Glutathione: A Link to Michael Acceptor Reactivities

Deprotonated glutathione is among the most potent biological nucleophiles and plays an important physiological role in cellular detoxification by forming covalent conjugates with Michael acceptors. The electrophilicity E of various Michael acceptors was characterized recently according to the Patz-Mayr relation lg k2 =sN (N+E). We now determined the nucleophilic reactivity (N, sN ) of glutathione (GSH) in aqueous solution at 20 °C to connect published GSH reactivities (kGSH ) with Mayr's electrophilicity scale (E). In this way, electrophilicities E of more than 70 Michael acceptors could be estimated, which can now be used to systematically predict novel reactions with the multitude of nucleophiles whose nucleophilicity parameters N/sN are known.

An Experimental Acidity Scale for Intramolecularly Stabilized Silyl Lewis Acids

A new NMR-based Lewis acidity scale is suggested and its application is demonstrated for a family of silyl Lewis acids. The reaction of p-fluorobenzonitrile (FBN) with silyl cations that are internally stabilized by interaction with a remote chalcogenyl or halogen donor yields silylated nitrilium ions with the silicon atom in a trigonal bipyramidal coordination environment. The 19 F NMR chemical shifts and the 1 J(CF) coupling constants of these nitrilium ions vary in a predictable manner with the donor capability of the stabilizing group. The spectroscopic parameters are suitable probes for scaling the acidity of Lewis acids. These new probes allow for the discrimination between very similar Lewis acids, which is not possible with conventional NMR tests, such as the well-established Gutmann-Beckett method.

Light-Mediated Formal Radical Deoxyfluorination of Tertiary Alcohols through Selective Single-Electron Oxidation with TEDA2+

The synthesis of tertiary alkyl fluorides through a formal radical deoxyfluorination process is described herein. This light-mediated, catalyst-free methodology is fast and broadly applicable allowing for the preparation of C-F bonds from (hetero)benzylic, propargylic, and non-activated tertiary alcohol derivatives. Preliminary mechanistic studies support that the key step of the reaction is the single-electron oxidation of cesium oxalates-which are readily available from the corresponding tertiary alcohols-with in situ generated TEDA2+. (TEDA: N-(chloromethyl)triethylenediamine), a radical cation derived from Selectfluor®.

1H NMR spectroscopy quantifies visibility of lipoproteins, subclasses, and lipids at varied temperatures and pressures

NMR-based quantification of human lipoprotein (sub)classes is a powerful high-throughput method for medical diagnostics. We evaluated select proton NMR signals of serum lipoproteins for elucidating the physicochemical features and the absolute NMR visibility of their lipids. We separated human lipoproteins of different subclasses by ultracentrifugation and analyzed them by 1H NMR spectroscopy at different temperatures (283-323 K) and pressures (0.1-200 MPa). In parallel, we determined the total lipid content by extraction with chloroform/methanol. The visibility of different lipids in the 1H NMR spectra strongly depends on temperature and pressure: it increases with increasing temperatures but decreases with increasing pressures. Even at 313 K, only part of the lipoprotein is detected quantitatively. In LDL and in HDL subclasses HDL2 and HDL3, only 39%, 62%, and 90% of the total cholesterol and only 73%, 70%, and 87% of the FAs are detected, respectively. The choline head groups show visibilities of 43%, 75%, and 87% for LDL, HDL2, and HDL3, respectively. The description of the NMR visibility of lipid signals requires a minimum model of three different compartments, A, B, and C. The thermodynamic analysis of compartment B leads to melting temperatures between 282 K and 308 K and to enthalpy differences that vary for the different lipoproteins as well as for the reporter groups selected. In summary, we describe differences in NMR visibility of lipoproteins and variations in biophysical responses of functional groups that are crucial for the accuracy of absolute NMR quantification.

A benchmark driven guide to binding site comparison: An exhaustive evaluation using tailor-made data sets (ProSPECCTs)

The automated comparison of protein-ligand binding sites provides useful insights into yet unexplored site similarities. Various stages of computational and chemical biology research can benefit from this knowledge. The search for putative off-targets and the establishment of polypharmacological effects by comparing binding sites led to promising results for numerous projects. Although many cavity comparison methods are available, a comprehensive analysis to guide the choice of a tool for a specific application is wanting. Moreover, the broad variety of binding site modeling approaches, comparison algorithms, and scoring metrics impedes this choice. Herein, we aim to elucidate strengths and weaknesses of binding site comparison methodologies. A detailed benchmark study is the only possibility to rationalize the selection of appropriate tools for different scenarios. Specific evaluation data sets were developed to shed light on multiple aspects of binding site comparison. An assembly of all applied benchmark sets (ProSPECCTs–Protein Site Pairs for the Evaluation of Cavity Comparison Tools) is made available for the evaluation and optimization of further and still emerging methods. The results indicate the importance of such analyses to facilitate the choice of a methodology that complies with the requirements of a specific scientific challenge.

Binding site similarities are useful in the context of promiscuity prediction, drug repurposing, the analysis of protein-ligand and protein-protein complexes, function prediction, and further fields of general interest in chemical biology and biochemistry. Many years of research have led to the development of a multitude of methods for binding site analysis and comparison. On the one hand, their availability supports research. On the other hand, the huge number of methods hampers the efficient selection of a specific tool. Our research is dedicated to the analysis of different cavity comparison tools. We use several binding site data sets to establish guidelines which can be applied to ensure a successful application of comparison methods by circumventing potential pitfalls.

A set of conformationally well-defined L/D-peptide epitopes provides a serological bar code for autoantibody subtypes

Which conformational parameters lead to an antibody-affine peptide antigen? And in how many different conformations can we actually present the respective conformational epitope? To provide answers from a chemical point of view, we direct the bending and tethering of peptide backbones by the utilisation of a hydrophobic cluster, disulfides, and d-amino acids. Each mutation is employed pairwise on directly opposite sides of a β-hairpin. In combination, these synthetic modules guide the formation of complementary β-sheet-like structures, whereby the oppositely configured (l/d-)bi-disulfide pairs form with high regioselectivity. The conformational properties of the peptides are assessed by NMR spectroscopy and correlated with their antibody affinity in ELISA. From a pool of thus designed peptide antigens with distinctive complementary affinities against known rheumatoid arthritis (RA) autoantibodies, we select a set of epitopes for an immunoassay with sera of RA patients. We want to put emphasis on the idea, that the different conformational properties of the chosen antigens, containing the same epitope sequence, are mirrored in the distribution of autoantibody subtypes (or of the antibody polyclonality, respectively). Such directly comparable information can only be delivered by a set of peptides, rather than a single one. The hairpin-restriction technology of l/d-configured bi-disulfide amino acid pairs is not limited to RA but applicable to other shape-persistent hairpin motifs which are supposed to identify subgroups of protein receptors.