NMRium: Teaching nuclear magnetic resonance spectra interpretation in an online platform.

NMRium is the first web-based software that allows displaying, processing, interpretation, and teaching of 1D and 2D NMR data in a user-friendly interface. It can import the most common data formats (e.g., JCAMP-DX, Bruker, Varian, and Jeol). While the scope for the use of NMRium encompasses a variety of applications such as being a component in data repositories or electronic lab notebooks (ELN), performing structure elucidation or preparing raw spectral data for publication, it also excels in enhancing teaching of NMR interpretation. In this paper, we present some current possibilities of this new tool. Several series of exercises are already provided on https://www.nmrium.org/teaching.

Formation of Breslow Intermediates from N-Heterocyclic Carbenes and Aldehydes Involves Autocatalysis by the Breslow Intermediate, and a Hemiacetal.

Under aprotic conditions, the stoichiometric reaction of N-heterocyclic carbenes (NHCs) such as imidazolidin-2-ylidenes with aldehydes affords Breslow Intermediates (BIs), involving a formal 1,2-C-to-O proton shift. We herein report kinetic studies (NMR), complemented by DFT calculations, on the mechanism of this kinetically disfavored H-translocation. Variable time normalization analysis (VTNA) revealed that the kinetic orders of the reactants vary for different NHC-to-aldehyde ratios, indicating different and ratio-dependent mechanistic regimes. We propose that for high NHC-to-aldehyde ratios, the H-shift takes place in the primary, zwitterionic NHC-aldehyde adduct. With excess aldehyde, the zwitterion is in equilibrium with a hemiacetal, in which the H-shift occurs. In both regimes, the critical H-shift is auto-catalyzed by the BI. Kinetic isotope effects observed for R-CDO are in line with our proposal. Furthermore, we detected an H-bonded complex of the BI with excess NHC (NMR).

NMReDATA: Tools and applications.

The nuclear magnetic resonance extracted data (NMReDATA) format has been proposed as a way to store, exchange, and disseminate nuclear magnetic resonance (NMR) data and physical and chemical metadata of chemical compounds. In this paper, we report on analytical workflows that take advantage of the uniform and standardized NMReDATA format. We also give access to a repository of sample data, which can serve for validating software packages that encode or decode files in NMReDATA format.

Acyl Donor Intermediates in N-Heterocyclic Carbene Catalysis: Acyl Azolium or Azolium Enolate?

Azolium enolates and acyl azolium cations have been proposed as intermediates in numerous N-heterocyclic carbene (NHC) catalyzed transformations. Acetyl azolium enolates were generated from the reaction of 2-propenyl acetate with both saturated (SIPr) and aromatic (IPr) NHCs, isolated, and characterized (NMR, XRD). Protonation with triflic acid gave the corresponding acetyl azolium triflates which were isolated and characterized (NMR, XRD). Acyl azolium cations have been proposed as immediate precursors of the ester product, for example, in the redox esterification of α,ß-enals. Studies with d3 -acetyl azolium triflate suggest that ester formation originates instead from an azolium enolate intermediate. Furthermore, the acetyl azolium enolate selectively reacted with alcohol nucleophiles in the presence of amines. While the acetyl azolium cation did not react with alcohols, an ester-selective reaction was induced by addition of base, by intermediate formation of the acetyl azolium enolate.

Pursuing Experimental Reproducibility: An Efficient Protocol for the Preparation of Cerebrospinal Fluid Samples for NMR-based Metabolomics and Analysis of Sample Degradation.

NMR-based metabolomics investigations of human biofluids offer great potential to uncover new biomarkers. In contrast to protocols for sample collection and biobanking, procedures for sample preparation prior to NMR measurements are still heterogeneous, thus compromising the comparability of the resulting data. Herein, we present results of an investigation of the handling of cerebrospinal fluid (CSF) samples for NMR metabolomics research. Origins of commonly observed problems when conducting NMR experiments on this type of sample are addressed, and suitable experimental conditions in terms of sample preparation and pH control are discussed. Sample stability was assessed by monitoring the degradation of CSF samples by NMR, hereby identifying metabolite candidates, which are potentially affected by sample storage. A protocol was devised yielding consistent spectroscopic data as well as achieving overall sample stability for robust analysis. We present easy to adopt standard operating procedures with the aim to establish a shared sample handling strategy that facilitates and promotes inter-laboratory comparison, and the analysis of sample degradation provides new insights into sample stability.

Technical Synthesis of 1,5,9-Cyclododecatriene Revisited: Surprising Byproducts from a Venerable Industrial Process.

The synthesis of 1,5,9-cyclododecatriene by selective trimerization of butadiene catalyzed by TiCl4 and ethylaluminum sesquichloride has been commercially used since 1965. Although thoroughly investigated, not all details of the mechanism are completely understood. The recent development of a new process to produce cyclododecanone involving oxidation of 1,5,9-cyclododecatriene with N2O has led to the serendipitous discovery of an array of hitherto unknown byproducts, formed in the trimerization of butadiene: eleven tricyclic C12H20 and one tetracyclic C12H18 hydrocarbons, three of which had never been described before. The identification of these byproducts became possible by using a combination of chemical enrichment, high-resolution distillation, 13C-2D-INADEQUATE NMR, and comparison with ab initio calculated spectra, thus demonstrating the power of these combined techniques. The identification of these byproducts contributes to a better understanding of the mechanism of this centrally important reaction.

Breslow Intermediates from Aromatic N-Heterocyclic Carbenes (Benzimidazolin-2-ylidenes, Thiazolin-2-ylidenes).

We report the first generation and characterization of elusive Breslow intermediates derived from aromatic N-heterocyclic carbenes (NHCs), namely benzimidazolin-2-ylidenes (NMR, X-ray analysis) and thiazolin-2-ylidenes (NMR). In the former case, the diamino enols were generated by reaction of the free N,N-bis(2,6-diisopropylphenyl)- and N,N-bis(mesityl)-substituted benzimidazolin-2-ylidenes with aldehydes while the dimer of 3,4,5-trimethylthiazolin-2-ylidene served as the starting material in the latter case. The unambiguous NMR identification of the first thiazolin-2-ylidene-based Breslow intermediate rests on double 13 C labeling of both the NHC and the aldehyde component. The acyl anion reactivity was confirmed by benzoin formation with excess aldehyde.

NMReDATA, a standard to report the NMR assignment and parameters of organic compounds.

Even though NMR has found countless applications in the field of small molecule characterization, there is no standard file format available for the NMR data relevant to structure characterization of small molecules. A new format is therefore introduced to associate the NMR parameters extracted from 1D and 2D spectra of organic compounds to the proposed chemical structure. These NMR parameters, which we shall call NMReDATA (for nuclear magnetic resonance extracted data), include chemical shift values, signal integrals, intensities, multiplicities, scalar coupling constants, lists of 2D correlations, relaxation times, and diffusion rates. The file format is an extension of the existing Structure Data Format, which is compatible with the commonly used MOL format. The association of an NMReDATA file with the raw and spectral data from which it originates constitutes an NMR record. This format is easily readable by humans and computers and provides a simple and efficient way for disseminating results of structural chemistry investigations, allowing automatic verification of published results, and for assisting the constitution of highly needed open-source structural databases.

Exploring the Role of Solvent on Carbohydrate-Aryl Interactions by Diffusion NMR-Based Studies.

Carbohydrate-protein interactions play an important role in many molecular recognition processes. An exquisite combination of multiple factors favors the interaction of the receptor with one specific type of sugar, whereas others are excluded. Stacking CH-aromatic interactions within the binding site provide a relevant contribution to the stabilization of the resulting sugar-protein complex. Being experimentally difficult to detect and analyze, the key CH-π interaction features have been very often dissected using a variety of techniques and simple model systems. In the present work, diffusion NMR spectroscopy has been employed to separate the components of sugar mixtures in different solvents on the basis of their differential ability to interact through CH-π interactions with one particular aromatic cosolute in solution. The experimental data show that the properties of the solvent did also influence the diffusion behavior of the sugars present in the mixture, inhibiting or improving their separation. Overall, the results showed that, for the considered monosaccharide derivatives, their diffusion coefficient values and, consequently, their apparent molecular sizes and/or shapes depend on the balance between solute/cosolute as well as solute/solvent interactions. Thus, in certain media and in the presence of the aromatic cosolute, the studied saccharides that are more suited to display CH-π interactions exhibited a lower diffusion coefficient than the noncomplexing sugars in the mixture. However, when dissolved in another medium, the interaction with the solvent strongly competes with that of the aromatic cosolute.

Kirmse-Doyle- and Stevens-Type Rearrangements of Glutarate-Derived Oxonium Ylides.

A novel chemoenzymatic synthetic cascade enables the preparation of densely decorated tetrahydrofuran building blocks. Here, the lipase-catalyzed desymmetrization of 3-alkoxyglutarates renders highly enantioenriched carboxylic acid intermediates, whose subsequent activation and oxonium ylide rearrangement by means of rhodium or copper complexes furnishes functionalized O-heterocycles with excellent diastereoselectivity. The two-step protocol offers a streamlined and flexible synthesis of tetrahydrofuranones bearing different benzylic, allylic or allenylic side chains with full control over multiple stereogenic centers.

1,4-Bis-Dipp/Mes-1,2,4-Triazolylidenes: Carbene Catalysts That Efficiently Overcome Steric Hindrance in the Redox Esterification of α- and ß-Substituted α,ß-Enals.

As reported by Scheidt and Bode in 2005, sterically nonencumbered α,ß-enals are readily converted to saturated esters in the presence of alcohols and N-heterocyclic carbene catalysts, e.g., benzimidazolylidenes or triazolylidenes. However, substituents at the α- or ß-position of the α,ß-enal substrate are typically not tolerated, thus severely limiting the substrate spectrum. On the basis of our earlier mechanistic studies, a set of N-Mes- or N-Dipp-substituted 1,2,4-triazolium salts were synthesized and evaluated as (pre)catalysts in the redox esterification of various α- or ß-substituted enals. In particular the 1,4-bis-Mes/Dipp-1,2,4-triazolylidenes overcome the above limitations and efficiently catalyze the redox esterification of a whole series of α/ß-substituted enals hitherto not amenable to NHC-catalyzed transformations. The synthetic value of 1,4-bis-Mes/Dipp-1,2,4-triazolylidenes is further demonstrated by the one-step bicyclization of 10-oxocitral to (racemic) nepetalactone in diastereomerically pure form.

Facilitating quality control for spectra assignments of small organic molecules: nmrshiftdb2--a free in-house NMR database with integrated LIMS for academic service laboratories.

nmrshiftdb2 supports with its laboratory information management system the integration of an electronic lab administration and management into academic NMR facilities. Also, it offers the setup of a local database, while full access to nmrshiftdb2's World Wide Web database is granted. This freely available system allows on the one hand the submission of orders for measurement, transfers recorded data automatically or manually, and enables download of spectra via web interface, as well as the integrated access to prediction, search, and assignment tools of the NMR database for lab users. On the other hand, for the staff and lab administration, flow of all orders can be supervised; administrative tools also include user and hardware management, a statistic functionality for accounting purposes, and a 'QuickCheck' function for assignment control, to facilitate quality control of assignments submitted to the (local) database. Laboratory information management system and database are based on a web interface as front end and are therefore independent of the operating system in use.

Carbene catalyzed umpolung of α,ß-enals: a reactivity study of diamino dienols vs. azolium enolates, and the characterization of advanced reaction intermediates.

Since their discovery by Bode and Glorius in 2004, N-heterocyclic carbene catalyzed conjugate umpolung reactions of α,ß-enals have been postulated to involve the formation of diamino dienols ("homoenolates") and/or azolium enolates ("enolates"), typically followed by addition to electrophiles, e.g. Michael-acceptors. In this article, we provide evidence, for the first time, for the postulated individual and specific reactivity patterns of diamino dienols (γ-C-C-bond formation) vs. azolium enolates (ß-C-C-bond formation). Our study is based on the pre-formation of well defined diamino dienols and azolium enolates, and the in situ NMR monitoring of their reactivities towards enone electrophiles. Additionally, reaction intermediates were isolated and characterized, inter alia by X-ray crystallography.

Anion recognition with hydrogen-bonding cyclodiphosphazanes.

Modular cyclodiphosph(V)azanes are synthesised and their affinity for chloride and actetate anions were compared to those of a bisaryl urea derivative (1). The diamidocyclodiphosph(V)azanes cis-[{ArNHP(O)(µ-tBu)}2 ] [Ar=Ph (2) and Ar=m-(CF3 )2 Ph (3)] were synthesised by reaction of [{ClP(µ-NtBu)}2 ] (4) with the respective anilines and subsequent oxidation with H2 O2 . Phosphazanes 2 and 3 were obtained as the cis isomers and were characterised by multinuclear NMR spectroscopy, FTIR spectroscopy, HRMS and single-crystal X-ray diffraction. The cyclodiphosphazanes 2 and 3 readily co-crystallise with donor solvents such as MeOH, EtOH and DMSO through bidentate hydrogen bonding, as shown in the X-ray analyses. Cyclodiphosphazane 3 showed a remarkably high affinity (log[K]=5.42) for chloride compared with the bisaryl urea derivative 1 (log[K]=4.25). The affinities for acetate (AcO(-) ) are in the same range (3: log[K]=6.72, 1: log[K]=6.91). Cyclodiphosphazane 2, which does not contain CF3 groups, exhibits weaker binding to chloride (log[K]=3.95) and acetate (log[K]=4.49). DFT computations and X-ray analyses indicate that a squaramide-like hydrogen-bond directionality and Cα H interactions account for the efficiency of 3 as an anion receptor. The Cα H groups stabilise the Z,Z-3 conformation, which is necessary for bidentate hydrogen bonding, as well as coordinating with the anion.

Selective and mild hydrogen production using water and formaldehyde.

With the increased efforts in finding new energy storage systems for mobile and stationary applications, an intensively studied fuel molecule is dihydrogen owing to its energy content, and the possibility to store it in the form of hydridic and protic hydrogen, for example, in liquid organic hydrogen carriers. Here we show that water in the presence of paraformaldehyde or formaldehyde is suitable for molecular hydrogen storage, as these molecules form stable methanediol, which can be easily and selectively dehydrogenated forming hydrogen and carbon dioxide. In this system, both molecules are hydrogen sources, yielding a theoretical weight efficiency of 8.4% assuming one equivalent of water and one equivalent of formaldehyde. Thus it is potentially higher than formic acid (4.4 wt%), as even when technical aqueous formaldehyde (37 wt%) is used, the diluted methanediol solution has an efficiency of 5.0 wt%. The hydrogen can be efficiently generated in the presence of air using a ruthenium catalyst at low temperature.

TEFDDOLs (α,α,α',α'-tetrakis(perfluoroaryl/alkyl)-2,2'-dimethyl-1,3-dioxolane-4,5-dimethanols): highly fluorinated chiral H-bond donors and Brønsted acids with distinct H-bonding patterns and supramolecular architectures.

The synthesis of six enantiopure α,α,α',α'-tetrakis(perfluoroalkyl/aryl)-2,2'-dimethyl-1,3-dioxolane-4,5-dimethanols (TEFDDOLs), by addition of perfluorinated organolithium reagents or Ruppert's reagent (TMS-CF(3)) to isopropylidene tartaric dichloride, is reported. X-ray crystal structures of the TEFDDOLs alone or in complexes with H-bond acceptors such as water and DABCO revealed that this new class of highly fluorinated chiral 1,4-diols forms distinct intra- and intermolecular H-bond patterns. Intramolecular OH-OH bonding accounts for the relatively high acidity of the perfluoroalkyl TEFDDOLs (pK(a) in DMSO: tetrakis-CF(3), 5.7; tetrakis-C(2)F(5), 2.4). For the tetrakis(perfluorophenyl) TEFDDOL, a quite unusual "pseudo-anti" conformation of the diol, with no intramolecular (and no intermolecular) OH-OH bonds, was found both in the crystal and in solution (DOSY and NOESY NMR). The latter conformation results from a total of four intramolecular OH-F(aryl) hydrogen bonds overriding OH-OH bonding. Due to their H-bonding properties, the TEFDDOLs are promising new building blocks for supramolecular and potentially catalytic applications.

Control of enantioselectivity with flexible biaryl axes: terpene-based alkylzinc catalysts in enantioselective dialkylzinc additions.

New enantiopure pyridyl alcohols are efficiently accessible through few synthetic steps from commercially available terpenes, that is, (+)-fenchone, (-)-menthone and (-)-verbenone as well as 2,6-diphenylpyridine. These chelating pyridyl alcohols exhibit flexible pyridyl-phenylene axes, which give rise to P and M conformers. Alkylzincation of the hydroxy groups eliminates equilibria of the conformers and generates alkylzinc complexes with adjusted biaryl axes, as it is demonstrated by NMR studies. These alkylzinc catalysts perform well in the addition of dimethylzinc or diethylzinc to benzaldehyde with yields up to 99% and ee's up to 95%. The adjusted pyridylphenylene conformations in the ligands now control enantioselectivities of the catalysts, which were also analysed by computations at the DFT level.

Jacobsen's catalyst for hydrolytic kinetic resolution: structure elucidation of paramagnetic Co(III) salen complexes in solution via combined NMR and quantum chemical studies.

NMR investigation of chiral Co(III) salen catalysts, important for enantioselective hydrolytic kinetic resolution (HKR), revealed the presence of a paramagnetic high-spin Co(III) species, which is in solvent- and temperature-dependent equilibrium with the known diamagnetic low-spin Co(III) complex. Combined with quantum chemical DFT calculations, the para- and diamagnetic chemical shifts were used to study the salen ligand conformation of the para- and diamagnetic complexes, resulting in a mechanistic proposal for the enantioselective step in catalysis.