Online coupling of liquid chromatography and two-dimensional diffusion ordered spectroscopy for the analysis of oligostyrenes.

The aim of this study was to introduce a powerful coupling of Liquid Adsorption Chromatography (LAC) and Diffusion-Ordered Spectroscopy (DOSY) for comprehensive structure analysis. This new hyphenation approach facilitated the simultaneous separation of a polymer mixture and the determination of molar masses within a single 3D experiment. The online coupling of High-Performance Liquid Chromatography (HPLC) and two-dimensional DOSY-NMR will be called 3D-LAC-NMR-DOSY experiment. Our methodology enabled the chromatographic separation of analytes based on their chemical heterogeneity, and provided accurate molar masses of the analytes through 2D-DOSY. This new method was demonstrated on a polystyrene oligomer mixture. In this case, the oligostyrenes could be separated with LAC according to their tacticity and chain length in protonated acetonitrile as eluent and DOSY measurements provided the molar masses of each oligomer. In order to show the power of the 3D-LAC-NMR-DOSY method, the comparison to 2D-DOSY, 3D-DOSY and LAC-NMR was separately evaluated. Furthermore, the recently published solvent-independent molar mass calibration of diffusion coefficients was also successfully applied in our LAC-DOSY studies for molar mass predictions of the oligomers in acetonitrile. The predicted molar masses were in good agreement with the LAC-DOSY measurements and were verified by calibrations of diffusion coefficients and mass spectrometry. Finally, this pioneering 3D technique offers a powerful new tool for advancing structure analysis and enhancing our understanding of complex systems such as oligostyrenes.

The accuracy limit of chemical shift predictions for species in aqueous solution.

Interpreting NMR experiments benefits from first-principles predictions of chemical shifts. Reaching the accuracy limit of theory is relevant for unambiguous structural analysis and dissecting theoretical approximations. Since accurate chemical shift measurements are based on using internal reference compounds such as trimethylsilylpropanesulfonate (DSS), a detailed comparison of experimental with theoretical data requires simultaneous consideration of both target and reference species ensembles in the same solvent environment. Here we show that ab initio molecular dynamics simulations to generate liquid-state ensembles of target and reference compounds, including explicitly their short-range solvation environments and combined with quantum-mechanical solvation models, allows for predicting highly accurate 1H (∼0.1-0.5 ppm) and aliphatic 13C (∼1.5 ppm) chemical shifts for aqueous solutions of the model compounds trimethylamine N-oxide (TMAO) and N-methylacetamide (NMA), referenced to DSS without any system-specific adjustments. This encompasses the two peptide bond conformations of NMA identified by NMR. The results are used to derive a general-purpose guideline set for predictive NMR chemical shift calculations of NMA in the liquid state and to identify artifacts of force field models. Accurate predictions are only obtained if a sufficient number of explicit water molecules is included in the quantum-mechanical calculations, disproving a purely electrostatic model of the solvent effect on chemical shifts.

The Universal Calibration for Structure- and Solvent-Independent Molar Mass Determinations of Polymers Using Diffusion-Ordered Spectroscopy.

It will be shown how diffusion-ordered spectroscopy (DOSY) can produce a universal calibration of molar mass dependences of polymers compared to size exclusion chromatography (SEC) or recently published DOSY methods. Whereas SEC can deliver only structure-independent universal calibrations for a particular solvent, DOSY was used for creating solvent-independent calibrations for a certain polymer. Now, we can demonstrate a universal calibration method that generates both a structure- and solvent-independent molar mass calibration. Only one mathematical function describes the structure- and solvent-independent calibrations for DOSY by implementing the Mark-Houwink approach. The derived equation is tested on polystyrene (PS), poly(ethylene oxide), and poly(methyl methacrylate) of different molar masses and in different solvents. Altogether, 94 diffusion coefficients representing 16 molar mass calibrations of the diffusion coefficients in 10 different solvents could be perfectly matched to one universal calibration function with an average deviation of just 2.5%. It was also found that the Mark-Houwink parameters calculated by DOSY are very close to the SEC data. In any case, this new approach is a very useful tool for the determination of molar masses and new Mark-Houwink parameters via DOSY.

Gauging the Strength of the Molecular Halogen Bond via Experimental Electron Density and Spectroscopy.

Strong and weak halogen bonds (XBs) in discrete aggregates involving the same acceptor are addressed by experiments in solution and in the solid state. Unsubstituted and perfluorinated iodobenzenes act as halogen donors of tunable strength; in all cases, quinuclidine represents the acceptor. NMR titrations reliably identify the strong intermolecular interactions in solution, with experimental binding energies of approx. 7 kJ/mol. Interaction of the σ hole at the halogen donor iodine leads to a redshift in the symmetric C-I stretching vibration; this shift reflects the interaction energy in the halogen-bonded adducts and may be assessed by Raman spectroscopy in condensed phase even for weak XBs. An experimental picture of the electronic density for the XBs is achieved by high-resolution X-ray diffraction on suitable crystals. Quantum theory of atoms in molecules (QTAIM) analysis affords the electron densities and energy densities in the bond critical points of the halogen bonds and confirms stronger interaction for the shorter contacts. For the first time, the experimental electron density shows a significant effect on the atomic volumes and Bader charges of the quinuclidine N atoms, the halogen-bond acceptor: strong and weak XBs are reflected in the nature of their acceptor atom. Our experimental findings at the acceptor atom match the discussed effects of halogen bonding and thus the proposed concepts in XB activated organocatalysis.

Extending Chirality in Group XIV Metallatranes.

The syntheses of the racemic amino alcohol rac-N(CH2CMe2OH)(CMe2CH2OH)(CH2CHMeOH) (L22'1*H3, 2) and its representative N(CH2CMe2OH)(CMe2CH2OH)(CH2C(R)HMeOH) (L22'1RH3, 3) with the stereogenic carbon center being R-configured are reported. Also reported are the stannatranes L22'1*SnOt-Bu (4) L22'1RSnOt-Bu (6) and germatranes L22'1*GeOEt (5) and L22'1RGeOEt (7) as well as the trinuclear tin oxocluster [(µ3-O)(µ3-O-t-Bu){SnL22'1R}3] (8). NMR and IR spectroscopy, electrospray ionization mass spectrometry (ESI MS), and single crystal X-ray diffraction analysis characterize these compounds. Computational studies accompany the experimental work and help understand the diastereoselectivity observed in the course of the metallatrane syntheses.

Fragtory: Pharmacophore-Focused Design, Synthesis, and Evaluation of an sp3-Enriched Fragment Library.

Fragment-based drug discovery has played an important role in medicinal chemistry and pharmaceutical research. Despite numerous demonstrated successes, the limited diversity and overrepresentation of planar, sp2-rich structures in commercial libraries often hamper the full potential of this approach. Hence, the thorough design of screening libraries inevitably determines the probability for meaningful hits and subsequent structural elaboration. Against this background, we present the generation of an exclusive fragment library based on iterative entry nomination by a specifically designed computational workflow: "Fragtory". Following a pharmacophore diversity-driven approach, we used Fragtory in an interdisciplinary academic setting to guide both tailored synthesis efforts and the implementation of in-house compounds to build a curated 288-member library of sp3-enriched fragments. Subsequent NMR screens against a model protein and hit validation by protein crystallography led to the identification of structurally novel ligands that were further characterized by isothermal titration calorimetry, demonstrating the applicability of our experimental approach.

Comprehensive Study of the Enhanced Reactivity of Turbo-Grignard Reagents.

Since its introduction in 2004, Knochel's so called Turbo-Grignard reagents revolutionized the usage of Grignard reagents. Through the simple addition of LiCl to a magnesium alkyl an outstanding increase in reactivity can be achieved. Though the exact composition of the reactive species remained mysterious, the reactive mixture itself is readily used not only in synthesis but also found its way into more distant fields like material science. To unravel this mystery, we combined single-crystal X-ray diffraction with in-solution NMR-spectroscopy and closed our investigations with quantum chemical calculations. Using such a variety of methods, we have gained insight into and an explanation for the extraordinary reactivity of this extremely convenient reagent by determining the structure of the first bimetallic reactive species [t-Bu2 Mg ⋅ LiCl ⋅ 4 thf] with two tert-butyl anions at the magnesium center and incorporated lithium chloride.

Generation of Aurachin Derivatives by Whole-Cell Biotransformation and Evaluation of Their Antiprotozoal Properties.

The natural product aurachin D is a farnesylated quinolone alkaloid, which is known to possess activity against the causative agent of malaria, Plasmodium spp. In this study, we show that aurachin D inhibits other parasitic protozoa as well. While aurachin D had only a modest effect on Trypanosoma brucei rhodesiense, two other trypanosomatids, T. cruzi and Leishmania donovani, were killed at low micromolar and nanomolar concentrations, respectively, in an in vitro assay. The determined IC50 values of aurachin D were even lower than those of the reference drugs benznidazole and miltefosine. Due to these promising results, we set out to explore the impact of structural modifications on the bioactivity of this natural product. In order to generate aurachin D derivatives with varying substituents at the C-2, C-6 and C-7 position of the quinolone ring system, we resorted to whole-cell biotransformation using a recombinant Escherichia coli strain capable of aurachin-type prenylations. Quinolone precursor molecules featuring methyl, methoxy and halogen groups were fed to this E. coli strain, which converted the substrates into the desired analogs. None of the generated derivatives exhibited improved antiprotozoal properties in comparison to aurachin D. Obviously, the naturally occurring aurachin D features already a privileged structure, especially for the inhibition of the causative agent of visceral leishmaniasis.

Maximized axial helicity in a Pd2L4 cage: inverse guest size-dependent compression and mesocate isomerism.

Helicity is an archetypal structural motif of many biological systems and provides a basis for molecular recognition in DNA. Whilst artificial supramolecular hosts are often helical, the relationship between helicity and guest encapsulation is not well understood. We report a detailed study on a significantly coiled-up Pd2L4 metallohelicate with an unusually wide azimuthal angle (∼176°). Through a combination of NMR spectroscopy, single-crystal X-ray diffraction, trapped ion mobility mass spectrometry and isothermal titration calorimetry we show that the coiled-up cage exhibits extremely tight anion binding (K of up to 106 M-1) by virtue of a pronounced oblate/prolate cavity expansion, whereby the Pd-Pd separation decreases for mono-anionic guests of increasing size. Electronic structure calculations point toward strong dispersion forces contributing to these host-guest interactions. In the absence of a suitable guest, the helical cage exists in equilibrium with a well-defined mesocate isomer that possesses a distinct cavity environment afforded by a doubled Pd-Pd separation distance.

Myxococcus xanthus as Host for the Production of Benzoxazoles.

Benzoxazoles are important structural motifs in pharmaceutical drugs. Here, we present the heterologous production of 3-hydroxyanthranilate-derived benzoxazoles in the host bacterium Myxococcus xanthus following the expression of two genes from the nataxazole biosynthetic gene cluster of Streptomyces sp. Tü 6176. The M. xanthus expression strain achieved a benzoxazole titer of 114.6±7.4 mg L-1 upon precursor supplementation, which is superior to other bacterial production systems. Crosstalk between the heterologously expressed benzoxazole pathway and the endogenous myxochelin pathway led to the combinatorial biosynthesis of benzoxazoles featuring a 2,3-dihydroxybenzoic acid (2,3-DHBA) building block. Subsequent in vitro studies confirmed that this crosstalk is not only due to the availability of 2,3-DHBA in M. xanthus, rather, it is promoted by the adenylating enzyme MxcE from the myxochelin pathway, which contributes to the activation of aryl carboxylic acids and delivers them to benzoxazole biosynthesis.

Amamistatins isolated from Nocardia altamirensis.

Four new phenolic siderophores were isolated from the actinomycete Nocardia altamirensis along with the known natural product amamistatin B and a putative biosynthetic shunt product. The structures of all compounds were elucidated through 1D and 2D NMR analyses as well as mass spectrometry. The iron-chelating properties of the retrieved metabolites were evaluated in a chrome azurol S assay.

Discovery, Biosynthetic Origin, and Heterologous Production of Massinidine, an Antiplasmodial Alkaloid.

Bacteria of the genus Massilia represent an underexplored source of bioactive natural products. Here, we report the discovery of massinidine (1), a guanidine alkaloid with antiplasmodial activity, from these microbes. The unusual scaffold of massinidine is shown to originate from l-phenylalanine, acetate, and l-arginine. Massinidine biosynthesis genes were identified in the native producer and validated through heterologous expression in Myxococcus xanthus. Bioinformatic analyses indicate that the potential for massinidine biosynthesis is distributed in various proteobacteria.

Polyurea Thickened Lubricating Grease-The Effect of Degree of Polymerization on Rheological and Tribological Properties.

Lubricating greases based on urea thickeners are frequently used in high-performance applications since their invention in 1954. One property that has so far been neglected in the further development of these systems due to their low solubility and the resulting difficulty of analysis, is to better understand how the degree of polymerization affect such polyurea lubricating systems. In this work, we prepared three different oligo- or polyurea systemswith different degrees of polymerization (DP) and investigated the influence of DP on rheological and tribological properties. The results showed that the DP has an influence on the flow limit in rheology as well as on the extreme pressure (EP) and anti-wear (AW) properties as examined by tribology measurements. By optimizing the DP for a thickener system, comparable EP and AW properties can be achieved through the use of additives. The DP showed an increasing influence on the flow limit. This could reduce damage to rolling bearings due to lateral loading at rest. Therefore, modifying the DP of the polyurea systems shows similar effects as the addition of external additives. Overall, this would reduce the use of additives in industrial applications.

Hidden intermediates in Mango III RNA aptamer folding revealed by pressure perturbation.

Fluorescent RNA aptamers have the potential to enable routine quantitation and localization of RNA molecules and serve as models for understanding biologically active aptamers. In recent years, several fluorescent aptamers have been selected and modified to improve their properties, revealing that small changes to the RNA or the ligands can modify significantly their fluorescent properties. Although structural biology approaches have revealed the bound, ground state of several fluorescent aptamers, characterization of low-abundance, excited states in these systems is crucial to understanding their folding pathways. Here we use pressure as an alternative variable to probe the suboptimal states of the Mango III aptamer with both fluorescence and NMR spectroscopy approaches. At moderate KCl concentrations, increasing pressure disrupted the G-quadruplex structure of the Mango III RNA and led to an intermediate with lower fluorescence. These observations indicate the existence of suboptimal RNA structural states that still bind the TO1-biotin fluorophore and moderately enhance fluorescence. At higher KCl concentration as well, the intermediate fluorescence state was populated at high pressure, but the G-quadruplex remained stable at high pressure, supporting the notion of parallel folding and/or binding pathways. These results demonstrate the usefulness of pressure for characterizing RNA folding intermediates.

Mutasynthesis of Physostigmines in Myxococcus xanthus.

The alkaloid physostigmine is an approved anticholinergic drug and an important lead structure for the development of novel therapeutics. Using a complementary approach that merged chemical synthesis with pathway refactoring, we produced a series of physostigmine analogues with altered specificity and toxicity profiles in the heterologous host Myxococcus xanthus. The compounds that were generated by applying a simple feeding strategy include the promising drug candidate phenserine, which was previously accessible only by total synthesis.

Molecular Cage Assembly by Sn-O-Sn Bridging of Di-, Tri- and Tetranuclear Organotin Tectons: Extending the Spacing in Double Ladder Structures.

Hydrolysis reactions of di- and trinuclear organotin halides yielded large novel cage compounds containing Sn-O-Sn bridges. The molecular structures of two octanuclear tetraorganodistannoxanes showing double-ladder motifs, viz., [{Me3 SiCH2 (Cl)SnCH2 YCH2 Sn(OH)CH2 SiMe3 }2 (µ-O)2 ]2 [1, Y=p-(Me)2 SiC6 H4 -C6 H4 Si(Me)2 ] and [{Me3 SiCH2 (I)SnCH2 YCH2 Sn(OH)CH2 SiMe3 }2 (µ-O)2 ]2 ⋅0.48 I2 [2⋅0.48 I2 , Y=p-(Me)2 SiC6 H4 -C6 H4 Si(Me)2 ], and the hexanuclear cage-compound 1,3,6-C6 H3 (p-C6 H4 Si(Me)2 CH2 Sn(R)2 OSn(R)2 CH2 Si(Me)2 C6 H4 -p)3 C6 H3 -1,3,6 (3, R=CH2 SiMe3 ) are reported. Of these, the co-crystal 2⋅0.48 I2 exhibits the largest spacing of 16.7 Šreported to date for distannoxane-based double ladders. DFT calculations for the hexanuclear cage and a related octanuclear congener accompany the experimental work.

Weak yet Decisive: Molecular Halogen Bond and Competing Weak Interactions of Iodobenzene and Quinuclidine.

The halogen bonded adduct between the commonly used constituents quinuclidine and iodobenzene is based on a single weak nitrogen-iodine contact, and the isolation of this adduct was initially unexpected. Iodobenzene does not contain any electron-withdrawing group and therefore represents an unconventional halogen bond donor. Based on excellent diffraction data of high resolution, an electron density study was successfully accomplished and confirmed one of the longest N···I molecular halogen bonds with a distance of 2.9301(4) Å. The topological analysis identified the XB as a directional but weak σ hole interaction and revealed secondary contacts between peripheral regions of opposite charge. These additional contacts and their competition with a nitrogen-based interaction were confirmed by NOESY experiments in solution. Integration enabled us to determine the relative NOE ratios and provided insight regarding the existing interactions.

On the Heterogeneous Nature of Cisplatin-1-Methyluracil Complexes: Coexistence of Different Aggregation Modes and Partial Loss of NH3 Ligands as Likely Explanation.

The conversion of the 1 : 1-complex of Cisplatin with 1-methyluracil (1MeUH), cis-[Pt(NH3 )2 (1MeU-N3)Cl] (1 a) to the aqua species cis-[Pt(NH3 )2 (1MeU-N3)(OH2 )]+ (1 b), achieved by reaction of 1 a with AgNO3 in water, affords a mixture of compounds, the composition of which strongly depends on sample history. The complexity stems from variations in condensation patterns and partial loss of NH3 ligands. In dilute aqueous solution, 1 a, and dinuclear compounds cis-[(NH3 )2 (1MeU-N3)Pt(µ-OH)Pt(1MeU-N3)(NH3 )2 ]+ (3) as well as head-tail cis-[Pt2 (NH3 )4 (µ-1MeU-N3,O4)2 ]2+ (4) represent the major components. In addition, there are numerous other species present in minor quantities, which differ in metal nuclearity, stoichiometry, stereoisomerism, and Pt oxidation state, as revealed by a combination of 1 H NMR and ESI-MS spectroscopy. Their composition appears not to be the consequence of a unique and repeating coordination pattern of the 1MeU ligand in oligomers but rather the coexistence of distinctly different condensation patterns, which include µ-OH, µ-1MeU, and µ-NH2 bridging and combinations thereof. Consequently, the products obtained should, in total, be defined as a heterogeneous mixture rather than a mixture of oligomers of different sizes. In addition, a N2 complex, [Pt(NH3 )(1MeU)(N2 )]+ appears to be formed in gas phase during the ESI-MS experiment. In the presence of Na+ ions, multimers n of 1 a with n=2, 3, 4 are formed that represent analogues of non-metalated uracil quartets found in tetrastranded RNA.

MeSi(CH2 SnRO)3 (R=Ph, Me3 SiCH2 ): Building Blocks for Triangular-Shaped Diorganotin Oxide Macrocycles.

The syntheses of the novel silicon-bridged tris(tetraorganotin) compounds MeSi(CH2 SnPh2 R)3 (2, R=Ph; 5, R=Me3 SiCH2 ) and their halogen-substituted derivatives MeSi(CH2 SnPh(3-n) In )3 (3, n=1; 4, n=2) and MeSi(CH2 SnI2 R)3 (6, R=Me3 SiCH2 ) are reported. The reaction of compound 4 with di-t-butyltin oxide (t-Bu2 SnO)3 gives the oktokaideka-nuclear (18-nuclear) molecular diorganotin oxide [MeSi(CH2 SnPhO)3 ]6 (7) while the reaction of 6 with sodium hydroxide, NaOH, provides the trikonta-nuclear (30-nuclear) molecular diorganotin oxide [MeSi(CH2 SnRO)3 ]10 (8, R=Me3 SiCH2 ). Both 7 and 8 show belt-like ladder-type macrocyclic structures and are by far the biggest molecular diorganotin oxides reported to date. The compounds have been characterized by elemental analyses, electrospray mass spectrometry (ESI-MS), NMR spectroscopy, 1 H DOSY NMR spectroscopy (7), IR spectroscopy (7, 8), and single-crystal X-ray diffraction analysis (2, 7, 8).

Biosynthetic Plasticity Enables Production of Fluorinated Aurachins.

Enzyme promiscuity has important implications in the field of biocatalysis. In some cases, structural analogues of simple metabolic building blocks can be processed through entire pathways to give natural product derivatives that are not readily accessible by chemical means. In this study, we explored the plasticity of the aurachin biosynthesis pathway with regard to using fluoro- and chloroanthranilic acids, which are not abundant in the bacterial producers of these quinolone antibiotics. The incorporation rates of the tested precursor molecules disclosed a regiopreference for halogen substitution as well as steric limitations of enzymatic substrate tolerance. Three previously undescribed fluorinated aurachin derivatives were produced in preparative amounts by fermentation and structurally characterized. Furthermore, their antibacterial activities were evaluated in comparison to their natural congener aurachin D.