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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

Reorientational dynamics of trimethoxyboroxine: A molecular glass former studied by dielectric spectroscopy and 11B nuclear magnetic resonance.

In this work, trimethoxyboroxine (TMB) is identified as a small-molecule glass former. In its viscous liquid as well as glassy states, static and dynamic properties of TMB are explored using various techniques. It is found that, on average, the structure of the condensed TMB molecules deviates from threefold symmetry so that TMB's electric dipole moment is nonzero, thus rendering broadband dielectric spectroscopy applicable. This method reveals the super-Arrhenius dynamics that characterizes TMB above its glass transition, which occurs at about 204 K. To extend the temperature range in which the molecular dynamics can be studied, 11B nuclear magnetic resonance experiments are additionally carried out on rotating and stationary samples: Exploiting dynamic second-order shifts, spin-relaxation times, line shape effects, as well as stimulated-echo and two-dimensional exchange spectroscopy, a coherent picture regarding the dynamics of this glass former is gained.

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).

Pd(II) Coordination Sphere Engineering: Pyridine Cages, Quinoline Bowls, and Heteroleptic Pills Binding One or Two Fullerenes.

Fullerenes and their derivatives are of tremendous technological relevance. Synthetic access and application are still hampered by tedious purification protocols, peculiar solubility, and limited control over regioselective derivatization. We present a modular self-assembly system based on a new low-molecular-weight binding motif, appended by two palladium(II)-coordinating units of different steric demands, to either form a [Pd2L14]4+ cage or an unprecedented [Pd2L23(MeCN)2]4+ bowl (with L1 = pyridyl, L2 = quinolinyl donors). The former was used as a selective induced-fit receptor for C60. The latter, owing to its more open structure, also allows binding of C70 and fullerene derivatives. By exposing only a fraction of the bound guests' surface, the bowl acts as fullerene protecting group to control functionalization, as demonstrated by exclusive monoaddition of anthracene. In a hierarchical manner, sterically low-demanding dicarboxylates were found to bridge pairs of bowls into pill-shaped dimers, able to host two fullerenes. The hosts allow transferring bound fullerenes into a variety of organic solvents, extending the scope of possible derivatization and processing methodologies.

Mechanistic Interplay between Light Switching and Guest Binding in Photochromic [Pd2Dithienylethene4] Coordination Cages.

Photochromic [Pd2L4] coordination cages based on dithienylethene (DTE) ligands L allow triggering guest uptake and release by irradiation with light of different wavelengths. The process involves four consecutive electrocyclic reactions to convert all chromophores between their open and closed photoisomeric forms. So far, guest affinity of the fully switched species was elucidated, but mechanistic details concerning the intermediate steps remained elusive. Now, a new member of the DTE cage family allows unprecedented insight into the interplay between photoisomerization steps and guest location inside/outside the cavity. Therefore, the intrinsic chirality of the DTE backbones was used as reporter for monitoring the fate of a chiral guest. In its "open" photoisomeric form ( o-L, [Pd2( o-L)4] = o-C), the C2-symmetric DTE chromophore quickly converts between energetically degenerate P and M helical conformations. After binding homochiral 1 R-( -) or 1 S-( +) camphor sulfonate ( R-CSA or S-CSA), guest-to-host chirality transfer was observed via a circular dichroism (CD) signal for the cage-centered absorption. Irradiating the R/S-CSA@ o-C host-guest complexes at 313 nm produced configurationally stable "closed" photoisomers, thus locking the induced chirality with an enantiomeric excess close to 25%. This value (corresponding to chiral induction for one out of four ligands), together with DOSY NMR, ion mobility mass spectrometry, and X-ray structure results, shows that closure of the first photoswitch is sufficient to expel the guest from the cavity.

Control of Λ- and Δ-Isomerization of the Atrane Cages in Group XIV Metallatranes by Chiral Axial Substituents.

The syntheses of the novel stannatranes N(CH2CMe2O)3Sn-(1 S)-(-)-OC(O)C(OMe)(CF3)(C6H5), 1( S, Δ), and N(CH2CMe2O)3Sn-(1 R)-(+)-OC(O)C(OMe)(CF3)(C6H5), 2( R, Λ), and germatranes N(CH2CMe2O)3Ge-(1 S)-(-)-OC(O)C(OMe)(CF3)(C6H5), 3( S, Δ), and N(CH2CMe2O)3Ge-(1 R)-(+)-OC(O)C(OMe)(CF3)(C6H5), 4( R, Λ) (with 1, S, Δ-configured/2, R, Λ-configured and 3, S, Δ-configured/4, R, Λ-configured being pairs of enantiomers) are reported. The compounds were characterized by NMR and IR spectroscopy, electrospray ionization mass spectrometry, and single crystal X-ray diffraction analysis. The epimerization via Λ â‡Œ Δ ring flip of the enantiomeric stannatrane pair 1( S, Δ)/2( R, Λ) was investigated by NMR experiments at variable temperatures and density functional theory (DFT) calculations.

Myxochelin- and Pseudochelin-Derived Lipoxygenase Inhibitors from a Genetically Engineered Myxococcus xanthus Strain.

Precursor-directed biosynthesis was used to introduce selected aryl carboxylic acids into the pseudochelin pathway, which had recently been assembled in Myxococcus xanthus. Overall, 14 previously undescribed analogues of the natural products myxochelin B and pseudochelin A were generated and structurally characterized. A subset of 10 derivatives together with their parental molecules were evaluated for their activity toward human 5-lipoxygenase. This testing revealed pseudochelin A as the most potent 5-lipoxygenase inhibitor among the naturally occurring compounds, whereas myxochelin A is the least active. Replacement of the catechol moieties in myxochelin B and pseudochelin A affected the bioactivity to different degrees.

Entropically driven Polymeric Enzyme Inhibitors by End-Group directed Conjugation.

A new generic concept for polymeric enzyme inhibitors is presented using the example of poly(2-methyl-2-oxazoline) (PMOx) terminated with an iminodiacetate (IDA) function. These polymers are shown to be non-competitive inhibitors for horseradish peroxidase (HRP). Mechanistic investigations revealed that the polymer is directed to the protein by its end group and collapses at the surface in an entropy-driven process as shown by isothermal titration calorimetry. The dissociation constant of the complex was determined as the inhibition constant Ki using HRP kinetic activity measurements. Additional experiments suggest that the polymer does not form a diffusion layer around the protein, but might inhibit by inducing minor conformational changes in the protein. This kind of inhibitor offers new avenues towards designing bioactive compounds.

N-Functionalized Ferrocenes: Subvalent Group†XIV Element Chlorides and tert-Butyllithium-Induced C-C Bond Cleavage under Mild Conditions.

The ferrocene derivative (η5 -Cp)Fe{η5 -C5 H3 -1-(ArNCH)-2-(CH2 NMe2 )} (1; Ar=2,6-iPr2 C6 H3 )) reacts diastereoselectively with LiR by carbolithiation and subsequent hydrolysis to give (η5 -Cp)Fe{η5 -C5 H3 -1-(ArHNCHR)-2-(CH2 NMe2 )} (3: R=tBu; 4: R=Ph; 5: R=Me) in high yields. For R=tBu, the organolithium derivative (η5 -Cp)Fe{η5 -C5 H3 -1-(ArLiNCHR)-2-(CH2 NMe2 )} (2) was isolated. Compound 2 reacts with GeCl2 ⋅dioxane and SnCl2 to give the metallylene amide chlorides (η5 -Cp)Fe{η5 -C5 H3 -1-(ArMNCHtBu)-2-(CH2 NMe2 )} 6 (M=GeCl) and 7 (M=SnCl), respectively, which each contain three stereogenic centers. The potential of 7 as a ligand in transition-metal chemistry is demonstrated by formation of its complex (η5 -Cp)Fe{η5 -C5 H3 -1-(ArMNCHtBu)-2-(CH2 NMe2 )} [9, M= Sn(Cl)W(CO)5 ]. Treatment of 3 with tert-butyllithium at room temperature causes an unprecedented carbon-carbon bond cleavage whereas under kinetic control, lithiation at the Cp-3 position takes place, which leads to the isolation of (η5 -Cp)Fe{η5 -C5 H3 -1-(ArHNCHtBu)-2-(CH2 NMe2 )-3-SiMe3 } (10).

Hierarchical Assembly of an Interlocked M8 L16 Container.

The self-assembly of eight PdII cations and sixteen phenanthrene-derived bridging ligands with 60° bite angles yielded a novel M8 L16 metallosupramolecular architecture composed of two interlocked D4h -symmetric barrel-shaped containers. Mass spectrometry, NMR spectroscopy, and X-ray analysis revealed this self-assembled structure to be a very large "Hopf link" catenane featuring channel-like cavities, which are occupied by NO3- anions. The importance of the anions as catenation templates became imminent when we observed the nitrate-triggered structural rearrangement of a mixture of M3 L6 and M4 L8 assemblies formed in the presence of BF4- anions into the same interlocked molecule. Furthermore, the densely packed structure of the M8 L16 catenane was exploited in the preparation of a hexyloxy-functionalized analogue, which further self-assembled into vesicle-like aggregates in a reversible manner.