Twenty years of nmrshiftdb2: A case study of an open database for analytical chemistry.

In October 2003, 20 years ago, the open-source and open-content database NMRshiftDB was announced. Since then, the database, renamed as nmrshiftdb2 later, has been continuously available and is one of the longer-running projects in the field of open data in chemistry. After 20 years, we evaluate the success of the project and present lessons learnt for similar projects.

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.

Prediction of chemical shift in NMR: A review.

Calculation of solution-state NMR parameters, including chemical shift values and scalar coupling constants, is often a crucial step for unambiguous structure assignment. Data-driven (sometimes called empirical) methods leverage databases of known parameter values to estimate parameters for unknown or novel molecules. This is in contrast to popular ab initio techniques that use detailed quantum computational chemistry calculations to arrive at parameter estimates. Data-driven methods have the potential to be considerably faster than ab inito techniques and have been the subject of renewed interest over the past decade with the rise of high-quality databases of NMR parameters and novel machine learning methods. Here, we review these methods, their strengths and pitfalls, and the databases they are built on.

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.

New Insights into the Metabolism of Methyltestosterone and Metandienone: Detection of Novel A-Ring Reduced Metabolites.

Metandienone and methyltestosterone are orally active anabolic-androgenic steroids with a 17α-methyl structure that are prohibited in sports but are frequently detected in anti-doping analysis. Following the previously reported detection of long-term metabolites with a 17ξ-hydroxymethyl-17ξ-methyl-18-nor-5ξ-androst-13-en-3ξ-ol structure in the chlorinated metandienone analog dehydrochloromethyltestosterone ("oral turinabol"), in this study we investigated the formation of similar metabolites of metandienone and 17α-methyltestosterone with a rearranged D-ring and a fully reduced A-ring. Using a semi-targeted approach including the synthesis of reference compounds, two diastereomeric substances, viz. 17α-hydroxymethyl-17ß-methyl-18-nor-5ß-androst-13-en-3α-ol and its 5α-analog, were identified following an administration of methyltestosterone. In post-administration urines of metandienone, only the 5ß-metabolite was detected. Additionally, 3α,5ß-tetrahydro-epi-methyltestosterone was identified in the urines of both administrations besides the classical metabolites included in the screening procedures. Besides their applicability for anti-doping analysis, the results provide new insights into the metabolism of 17α-methyl steroids with respect to the order of reductions in the A-ring, the participation of different enzymes, and alterations to the D-ring.

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.

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.

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.

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.

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.

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.

Aryl-phenyl scrambling in intermediate organopalladium complexes: a gas-phase study of the Mizoroki-Heck reaction.

The intramolecular aryl-phenyl scrambling reaction within palladium-DPPP-aryl complex (DPPP=1,3-bis(diphenylphosphino)propane) ions was analyzed by state-of-the-art tandem MS, including gas-phase ion/molecule reactions. The Mizoroki-Heck cross-coupling reaction was performed in the gas phase, and the intrinsic reactivity of important intermediates could be examined. Moreover, linear free-energy correlations were applied, and a mechanism for the scrambling reaction proceeding via phosphonium cations was assumed.

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.

Biotransformation of anabolic androgenic steroids in human skin cells.

In comparison to well-known drug-metabolizing organs such as the liver, the metabolic capacity of human skin is still not well elucidated despite the widespread use of topical drug application. To gain a comprehensive insight into anabolic steroid metabolism in the skin, six structurally related anabolic androgenic steroids, testosterone, metandienone, methyltestosterone, clostebol, dehydrochloromethyltestosterone, and methylclostebol, were applied to human keratinocytes and fibroblasts derived from the juvenile foreskin. Phase I metabolites obtained from incubation media were analyzed by gas chromatography-mass spectrometry. The 5α-reductase activity was predominant in the metabolic pathways as supported by the detection of 5α-reduced metabolites after incubation of testosterone, methyltestosterone, clostebol, and methylclostebol. Additionally, the stereochemistry structures of fully reduced metabolites (4α,5α-isomers) of clostebol and methylclostebol were newly confirmed in this study by the help of inhouse synthesized reference materials. The results provide insights into the steroid metabolism in human skin cells with respect to the characteristics of the chemical structures.

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.

Total synthesis of cyclo-mumbaistatin analogues through anionic homo-Fries rearrangement.

The structurally unique polyketide mumbaistatin is the strongest naturally occurring inhibitor of glucose-6-phosphate translocase-1 (G6P-T1), which is a promising target for drugs against type-2 diabetes mellitus and angiogenic processes associated with brain tumor development. Despite its high relevance, mumbaistatin has so far withstood all attempts towards its total synthesis. In the present study an efficient total synthesis of a deoxy-mumbaistatin analogue containing the complete carbon skeleton and a spirolactone motif closely resembling the natural product in its cyclized form was elaborated. Key steps of the synthesis are a Diels-Alder cycloaddition for the construction of the fully functionalized anthraquinone moiety and an anionic homo-Fries rearrangement to build up the tetra-ortho-substituted benzophenone core motif, from which a spiroketal lactone forms in a spontaneous process. The elaborated strategy opens an entry to a variety of new analogs of mumbaistatin and cyclo-mumbaistatin and may be exploited for the total synthesis of the natural product itself in the future.

Structure characterisation of urinary metabolites of the cannabimimetic JWH-018 using chemically synthesised reference material for the support of LC-MS/MS-based drug testing.

As recently reported, the synthetic cannabinoid JWH-018 is the subject of extensive phase I and II metabolic reactions in vivo. Since these studies were based on LC-MS/MS and/or GC-MS identification and characterisation of analytes, the explicit structural assignment of the metabolites was only of preliminary nature, if possible at all. Here, we report the chemical synthesis of five potential in vivo metabolites of JWH-018 derivatives featuring an alkylcarboxy (M1), a terminal alkylhydroxy (M2), a 5-indolehydroxy (M3), an N-dealkylated 5-indolehydroxy (M4) and a 2'-naphthylhydroxy (5) analogue, respectively, and their characterisation by nuclear magnetic resonance spectroscopy. The collision-induced dissociation (CID) patterns of the protonated compounds were studied by high-resolution/high-accuracy tandem mass spectrometry (MS( n )) applying an LTQ Orbitrap with direct infusion and electrospray ionisation of target analytes. An unusual dissociation behaviour including a reversible ion-molecule reaction between a naphthalene cation (m/z 127) and water in the gas phase of the MS was shown to be responsible for nominal neutral losses of 10 u in the course of the CID pathway. LC-MS/MS-supported comparison of synthesised reference standards with an authentic urine sample using an API 4000 QTrap mass spectrometer identified the synthetic JWH-018 analogues M1-M4 as true in vivo metabolites, presuming a chromatographic separation of potentially present regioisomeric analogues. Existing doping control methods were expanded and validated according to international guidelines in order to allow for the detection of the carboxy and the alkylhydroxy metabolites, respectively, as urinary markers for the illegal intake of the synthetic cannabinoid JWH-018. Both metabolites were quantified in authentic doping control urine samples that had been suspicious of JWH-018 abuse after routine screening procedures, and a stable isotope-labelled (13)C(8)-(15)N-carboxy metabolite was synthesised for future analytical applications.