Gelation Mechanism Revealed in Organometallic Gels: Prevalence of van der Waals Interactions on Oligomerization by Coordination Chemistry.

Shaping of nanomaterials is a necessary step for their inclusion in electronic devices and batteries. For this purpose, the formulation of a moldable material including these nanomaterials is desirable. Organomineral gels are a very interesting option, since the components of the nanomaterial itself form a gel without the help of a binder. As a consequence, the properties of the nanomaterial are not diluted by the binder. In this article we studied organometallic gels based on a [ZnCy2 ] organometallic precursor and a primary alkyl amine which together forms spontaneously gels after few hours. We identified the main parameters controlling the gel properties monitored by rheology and NMR measurements The experiments demonstrate that the gelation time depends on the length of the alkyl chain of the amine and that the gelation mechanism derived firstly from the rigidification of the aliphatic chains of the amine, which takes precedence over the oligomerization of the inorganic backbone. This result highlights that the control of the rheological properties of organometallic gels remains mainly governed by the choice of the amine.

Evidence for genuine hydrogen bonding in gold(I) complexes.

The ability of gold to act as proton acceptor and participate in hydrogen bonding remains an open question. Here, we report the synthesis and characterization of cationic gold(I) complexes featuring ditopic phosphine-ammonium (P,NH+) ligands. In addition to the presence of short Au∙∙∙H contacts in the solid state, the presence of Au∙∙∙H-N hydrogen bonds was inferred by NMR and IR spectroscopies. The bonding situation was extensively analyzed computationally. All features were consistent with the presence of three-center four-electron attractive interactions combining electrostatic and orbital components. The role of relativistic effects was examined, and the analysis is extended to other recently described gold(I) complexes.

Synthesis of a Stable N-Hetero-RhI -Metallacyclic Silanone.

A novel N-hetero-RhI -metallacyclic silanone 2 has been synthesized. The silanone 2, showing an extremely large dimerization energy (ΔG=+86.2 kcal mol-1 ), displays considerable stability and persists in solution up to 60 °C. Above 120 °C, an intramolecular Csp3 -H insertion occurs slowly over a period of two weeks leading to the bicyclic silanol 5. The exceptional stability of 2, related to the unusual electronic and steric effects of RhI -substituent, should allow for a more profound study and understanding of these new species. Furthermore, the metallacyclic silanone 2 presents two reactive centers (Si=O and Rh), which can be involved depending upon the nature of reagents. Of particular interest, the reaction with H2 starts with the hydrogenation of RhI center leading to the corresponding RhIII -dihydride complex 7 and it undergoes a cis/trans-isomerization via a particular mechanism, demonstrating that addition-elimination processes can also happen for silanones just like for their carbon analogues!

A Stable N-Hetero-Rh-Metallacyclic Silylene.

A cyclic (amino)metal-substituted dicoordinated silylene derivative has been synthesized and fully characterized. Of particular interest is that the N-hetero-RhI -metallacyclic silylene exhibits a distorted tetrahedral geometry around the rhodium atom and a considerably shortened Si-Rh bond (2.138 Å) compared to classical Si-Rh single bonds (ca. 2.30-2.35 Å). A theoretical investigation reveals that the geometrical deviation around the rhodium center from the classical square-planar to a tetrahedral geometry increases the π-donating and σ-accepting character of the rhodium atom, thereby efficiently stabilizing the silylene moiety.

Room-Temperature Functionalization of N2 to Borylamine at a Molybdenum Complex.

Intermolecular, stepwise functionalization by BH bonds of a (triphosphine)MoIV -nitrido complex generated by N2 splitting is reported. The imido-hydride and di-hydride-amido MoIV complexes have been isolated and characterized. Addition of PinBH to the [Mo(H)2 (N(BPin)2 )]+ complex at room temperature results in the liberation of borylamines from the metal center.

Mechanochemical Synthesis and Biological Evaluation of Novel Isoniazid Derivatives with Potent Antitubercular Activity.

A series of isoniazid derivatives bearing a phenolic or heteroaromatic coupled frame were obtained by mechanochemical means. Their pH stability and their structural (conformer/isomer) analysis were checked. The activity of prepared derivatives against Mycobacterium tuberculosis cell growth was evaluated. Some compounds such as phenolic hydrazine 1a and almost all heteroaromatic ones, especially 2, 5 and 7, are more active than isoniazid, and their activity against some M. tuberculosis MDR clinical isolates was determined. Compounds 1a and 7 present a selectivity index >1400 evaluated on MRC5 human fibroblast cells. The mechanism of action of selected hydrazones was demonstrated to block mycolic acid synthesis due to InhA inhibition inside the mycobacterial cell.

Exceptionally Strong Electron-Donating Ability of Bora-Ylide Substituent vis-à-vis Silylene and Silylium Ion.

Electropositive boron-based substituent (phosphonium bora-ylide) with an exceptionally strong π- and σ-electron donating character dramatically increases the stability of a new type of N-heterocyclic silylene 2 featuring amino- and bora-ylide-substituents. Moreover, the related silylium ion 4 and transition-metal-silylene complexes, with trigonal-planar geometries around the silicon center, are also well stabilized. Therefore, the N,B-heterocyclic silylene 2 can be used as a strongly electron-donating innocent ligand in coordination chemistry similarly to N-heterocyclic carbenes.

Cyclic (Amino)(Phosphonium Bora-Ylide)Silanone: A Remarkable Room-Temperature-Persistent Silanone.

A silanone substituted by bulky amino and phosphonium bora-ylide substituents has been isolated in crystalline form. Thanks to the exceptionally strong electron-donating phosphonium bora-ylide substituent, the lifetime at room temperature of the silanone is dramatically extended (t1/2 =4 days) compared to the related (amino)(phosphonium ylide)silanone VI (t1/2 =5 h), allowing easier manipulation and its use as precursor of new valuable silicon compounds. The interaction of silanone with a weak Lewis acid such as MgBr2 increases further its stability (no degradation after 3 weeks at room temperature).

A ¹H NMR study of the specificity of α-l-arabinofuranosidases on natural and unnatural substrates.

BACKGROUND: The detailed characterization of arabinoxylan-active enzymes, such as double-substituted xylan arabinofuranosidase activity, is still a challenging topic. Ad hoc chromogenic substrates are useful tools and can reveal subtle differences in enzymatic behavior. In this study, enzyme selectivity on natural substrates has been compared with enzyme selectivity towards aryl-glycosides. This has proven to be a suitable approach to understand how artificial substrates can be used to characterize arabinoxylan-active α-l-arabinofuranosidases (Abfs). METHODS: Real-time NMR using a range of artificial chromogenic, synthetic pseudo-natural and natural substrates was employed to determine the hydrolytic abilities and specificity of different Abfs. RESULTS: The way in which synthetic di-arabinofuranosylated substrates are hydrolyzed by Abfs mirrors the behavior of enzymes on natural arabinoxylo-oligosaccharide (AXOS). Family GH43 Abfs that are strictly specific for mono-substituted d-xylosyl moieties (AXH-m) do not hydrolyze synthetic di-arabinofuranosylated substrates, while those specific for di-substituted moieties (AXH-d) remove a single l-arabinofuranosyl (l-Araf) group. GH51 Abfs, which are supposedly AXH-m enzymes, can release l-Araf from disubstituted d-xylosyl moieties, when these are non-reducing terminal groups. CONCLUSIONS AND GENERAL SIGNIFICANCE: The present study reveals that although the activity of Abfs on artificial substrates can be quite different from that displayed on natural substrates, enzyme specificity is well conserved. This implies that carefully chosen artificial substrates bearing di-arabinofuranosyl d-xylosyl moieties are convenient tools to probe selectivity in new Abfs. Moreover, this study has further clarified the relative promiscuity of GH51 Abfs, which can apparently hydrolyze terminal disubstitutions in AXOS, albeit less efficiently than mono-substituted motifs.

Isotopic studies of metabolic systems by mass spectrometry: using Pascal's triangle to produce biological standards with fully controlled labeling patterns.

Mass spectrometry (MS) is widely used for isotopic studies of metabolism in which detailed information about biochemical processes is obtained from the analysis of isotope incorporation into metabolites. The biological value of such experiments is dependent on the accuracy of the isotopic measurements. Using MS, isotopologue distributions are measured from the quantitative analysis of isotopic clusters. These measurements are prone to various biases, which can occur during the experimental workflow and/or MS analysis. The lack of relevant standards limits investigations of the quality of the measured isotopologue distributions. To meet that need, we developed a complete theoretical and experimental framework for the biological production of metabolites with fully controlled and predictable labeling patterns. This strategy is valid for different isotopes and different types of metabolisms and organisms, and was applied to two model microorganisms, Pichia augusta and Escherichia coli, cultivated on (13)C-labeled methanol and acetate as sole carbon source, respectively. The isotopic composition of the substrates was designed to obtain samples in which the isotopologue distribution of all the metabolites should give the binomial coefficients found in Pascal's triangle. The strategy was validated on a liquid chromatography-tandem mass spectrometry (LC-MS/MS) platform by quantifying the complete isotopologue distributions of different intracellular metabolites, which were in close agreement with predictions. This strategy can be used to evaluate entire experimental workflows (from sampling to data processing) or different analytical platforms in the context of isotope labeling experiments.

A novel platform for automated high-throughput fluxome profiling of metabolic variants.

Advances in metabolic engineering are enabling the creation of a large number of cell factories. However, high-throughput platforms do not yet exist for rapidly analyzing the metabolic network of the engineered cells. To fill the gap, we developed an integrated solution for fluxome profiling of large sets of biological systems and conditions. This platform combines a robotic system for (13)C-labelling experiments and sampling of labelled material with NMR-based isotopic fingerprinting and automated data interpretation. As a proof-of-concept, this workflow was applied to discriminate between Escherichia coli mutants with gradual expression of the glucose-6-phosphate dehydrogenase. Metabolic variants were clearly discriminated while pathways that support metabolic flexibility towards modulation of a single enzyme were elucidating. By directly connecting the data flow between cell cultivation and flux quantification, considerable advances in throughput, robustness, release of resources and screening capacity were achieved. This will undoubtedly facilitate the development of efficient cell factories.

Sampling of intracellular metabolites for stationary and non-stationary (13)C metabolic flux analysis in Escherichia coli.

The analysis of metabolic intermediates is a rich source of isotopic information for (13)C metabolic flux analysis ((13)C-MFA) and extends the range of its applications. The sampling of labeled metabolic intermediates is particularly important to obtain reliable isotopic information. The assessment of the different sampling procedures commonly used to generate such data, therefore, is crucial. In this work, we thoroughly evaluated several sampling procedures for stationary and non-stationary (13)C-MFA using Escherichia coli. We first analyzed the efficiency of these procedures for quenching metabolism and found that procedures based on cold or boiling solvents are reliable, in contrast to fast filtration, which is not. We also showed that separating the cells from the broth is not necessary in isotopic stationary state conditions. On the other hand, we demonstrated that the presence of metabolic intermediates outside the cells strongly affects the transient isotopic data monitored during non-stationary (13)C-labeling experiments. Meaningful isotopic data can be obtained by recovering intracellular labeled metabolites from pellets of cells centrifuged in cold solvent. We showed that if the intracellular pools are not separated from the extracellular ones, accurate flux maps can be established provided that the contribution of exogenous compounds is taken into account in the metabolic flux model.

The ethylmalonyl-CoA pathway is used in place of the glyoxylate cycle by Methylobacterium extorquens AM1 during growth on acetate.

Acetyl-CoA assimilation was extensively studied in organisms harboring the glyoxylate cycle. In this study, we analyzed the metabolism of the facultative methylotroph Methylobacterium extorquens AM1, which lacks isocitrate lyase, the key enzyme in the glyoxylate cycle, during growth on acetate. MS/MS-based proteomic analysis revealed that the protein repertoire of M. extorquens AM1 grown on acetate is similar to that of cells grown on methanol and includes enzymes of the ethylmalonyl-CoA (EMC) pathway that were recently shown to operate during growth on methanol. Dynamic 13C labeling experiments indicate the presence of distinct entry points for acetate: the EMC pathway and the TCA cycle. 13C steady-state metabolic flux analysis showed that oxidation of acetyl-CoA occurs predominantly via the TCA cycle and that assimilation occurs via the EMC pathway. Furthermore, acetyl-CoA condenses with the EMC pathway product glyoxylate, resulting in malate formation. The latter, also formed by the TCA cycle, is converted to phosphoglycerate by a reaction sequence that is reversed with respect to the serine cycle. Thus, the results obtained in this study reveal the utilization of common pathways during the growth of M. extorquens AM1 on C1 and C2 compounds, but with a major redirection of flux within the central metabolism. Furthermore, our results indicate that the metabolic flux distribution is highly complex in this model methylotroph during growth on acetate and is fundamentally different from organisms using the glyoxylate cycle.

Fast spatially encoded 3D NMR strategies for (13)C-based metabolic flux analysis.

The measurement of site-specific (13)C enrichments in complex mixtures of (13)C-labeled metabolites is a powerful tool for metabolic flux analysis. One of the main methods to measure such enrichments is homonuclear (1)H 2D NMR. However, the major limitation of this technique is the acquisition time, which can amount to a few hours. This drawback was recently overcome by the design of fast COSY experiments for measuring specific (13)C-enrichments, based on single-scan 2D NMR. However, these experiments are still limited by overlaps because of(1)H-(13)C splittings, thus limiting the metabolic information accessible for complex biological mixtures. To circumvent this limitation, we propose to tilt the (1)H-(13)C coupling into a third dimension via fast-hybrid 3D NMR methods combining the speed of ultrafast 2D NMR with the high resolution of conventional methods. Two strategies are described that allow the acquisition of a complete 3D J-resolved-COSY spectrum in 12 min (for concentrations as low as 10 mM). The analytical potentialities of both methods are evaluated on a series of (13)C-enriched glucose samples and on a biomass hydrolyzate obtained from Escherichia coli cells. Once optimized, the two complementary experiments lead to a trueness and a precision of a few percent and an excellent linearity. The advantages and drawbacks of these approaches are discussed and their potentialities are highlighted.

A versatile and colorful screening tool for the identification of arabinofuranose-acting enzymes.

Selecting wall-nibblers: Three 4-nitrocatechol derivatives were designed to facilitate high-throughput screening of arabinofuranose hydrolases, enzymes that typically digest plant cell walls. The designed compounds can be used in solid and liquid media, and, importantly, one allows the specific detection of AXH-d, a specialized enzyme that only releases L-arabinose from disubstituted D-xylosyl moieties.

Isotopic profiling of ¹³C-labeled biological samples by two-dimensional heteronuclear J-resolved nuclear magnetic resonance spectroscopy.

The use of two-dimensional heteronuclear J-resolved (2D H-JRES) nuclear magnetic resonance (NMR) spectroscopy for fast and reliable measurement of isotopic patterns from ¹³C-enriched compounds resulting from carbon labeling experiments was evaluated. Its use with biological samples of increasing complexity showed that 2D H-JRES spectroscopy is suitable for high-throughput isotopic profiling of any kind of labeled samples. Moreover, the method enabled accurate quantification of ¹³C enrichments and, thus, can be used for metabolic flux analysis. The excellent trade-off between reduced experimental time and the number of measurable isotopic data makes 2D H-JRES NMR a promising approach for high-throughput flux analysis of samples of intermediate complexity.

Limitation of diffusion effects in ultrafast 2D nuclear magnetic resonance by encapsulation of analytes in phospholipidic vesicles.

Increased sensitivity: A new sample-preparation procedure is described to limit molecular diffusion effects in NMR experiments. It is based on analyte encapsulation in liposomes and is particularly useful for ultrafast multidimensional NMR experiments.

Photobioreactor design for isotopic non-stationary 13C-metabolic flux analysis (INST 13C-MFA) under photoautotrophic conditions.

Adaptive metabolic behavior of photoautotrophic microorganisms toward genetic and environmental perturbations can be interpreted in a quantitative depiction of carbon flow through a biochemical reaction network using isotopic non-stationary (13) C-metabolic flux analysis (INST (13) C-MFA). To evaluate (13) C-metabolic flux maps for Chlamydomonas reinhardtii, an original experimental framework was designed allowing rapid, reliable collection of high-quality isotopomer data against time. It involved (i) a short-time (13) C labeling injection device based on mixing control in a torus-shaped photobioreactor with plug-flow hydrodynamics allowing a sudden step-change in the (13) C proportion in the substrate feed and (ii) a rapid sampling procedure using an automatic fast filtration method coupled to a manual rapid liquid nitrogen quenching step. (13) C-substrate labeling enrichment was controlled through the total dissolved inorganic carbon concentration in the pulsed solution. First results were obtained from steady-state continuous culture measurements allowing the characterization of the kinetics of label incorporation into light-limited growing cells cultivated in a photobioreactor operating at the maximal biomass productivity for an incident photon flux density of 200 µmol m(-2) s(-1). (13)C label incorporation was measured for 21 intracellular metabolites using IC-MS/MS in 58 samples collected across a labeling experiment duration of 7 min. The fastest labeling rate was observed for 2/3-phosphoglycerate with an apparent isotopic stationary state reached after 300 s. The labeling rate was consistent with the optimized mixing time of about 4.9 s inside the reactor and the shortest reliable sampling period assessed at 5 s.

Demonstration of the ethylmalonyl-CoA pathway by using 13C metabolomics.

The assimilation of one-carbon (C1) compounds, such as methanol, by serine cycle methylotrophs requires the continuous regeneration of glyoxylate. Instead of the glyoxylate cycle, this process is achieved by a not yet established pathway where CoA thioesters are known to play a key role. We applied state-of-the-art metabolomics and (13)C metabolomics strategies to demonstrate how glyoxylate is generated during methylotrophic growth in the isocitrate lyase-negative methylotroph Methylobacterium extorquens AM1. High-resolution mass spectrometry showed the presence of CoA thioesters specific to the recently proposed ethylmalonyl-CoA pathway. The operation of this pathway was demonstrated by short-term (13)C-labeling experiments, which allowed determination of the sequence of reactions from the order of label incorporation into the different CoA derivatives. Analysis of (13)C positional enrichment in glycine by NMR was consistent with the predicted labeling pattern as a result of the operation of the ethylmalonyl-CoA pathway and the unique operation of the latter for glyoxylate generation during growth on methanol. The results also revealed that 2 molecules of glyoxylate were regenerated in this process. This work provides a complete pathway for methanol assimilation in the model methylotroph M. extorquens AM1 and represents an important step toward the determination of the overall topology of its metabolic network. The operation of the ethylmalonyl-CoA pathway in M. extorquens AM1 has major implications for the physiology of these methylotrophs and their role in nature, and it also provides a common ground for C1 and C2 compound assimilation in isocitrate lyase-negative bacteria.

Cordiasecosides G-J, 9,10-Seco-29-norcycloartane glycosides isolated from Cordia lutea and their antibacterial activities.

Four undescribed secocycloartane monoglycosides (1-4) were isolated from an ethanolic extract of the dry flowers of Cordia lutea Lam. Their structural assignment is based on NMR and MS analysis. Their stereochemistry is confirmed by molecular modelling studies using DFT-NMR calculations done for compound 3. In vitro antibacterial activity of the four compounds was moderate on Helicobacter pylori (MIC = 15.6 µg/mL), and much weaker on Staphylococcus aureus, Pseudomonas aeruginosa or Escherichia coli (MIC >125 µg/mL). Toxicity evaluated against RAW 264.7 cells was weak (IC50 values ranging from 24 to 41 µM i.e. 15 to 24 µg/mL), but in the same range as anti-Helicobacter activity.