Synthesis and Reactivity of Tricoordinate Organoberyllium Azides.

A series of terminal mono- and disubstituted beryllium azides of the form [(CAAC)Be(N3)R] (R=CAACH, Dur; CAACH/CAAC=1-(2,6-diisopropylphenyl)-3,3,5,5-tetramethylpyrrolidin-2-yl/idene, Dur=2,3,5,6-tetramethylphenyl) and [L2Be(N3)2] (L=CAACNH=1-(2,6-diisopropylphenyl)-3,3,5,5-tetramethylpyrrolidin-2-imine, IiPrMe=1,3-diisopropyl-4,5-dimethylimidazol-2-ylidene), respectively, were synthesized and characterized by NMR spectroscopy and X-ray crystallography. Thermolysis and photolysis products of these first examples of tricoordinate azidoberyllium complexes evidence extensive ligand scrambling and the formal insertion of nitrenes into the CAAC-Be bond, generating cyclic alkyl(amino)imine (CAAI) ligands. Furthermore, the reaction with a small N-heterocyclic carbene (NHC) leads to unexpected CAAC-NHC ligand exchange, while the reaction with pentaphenylborole yields the first γ-azide adduct of a borole, long postulated to be the first step in the synthesis of 1,2-azaborinines from boroles and azides.

Synthesis, reduction and C-H activation chemistry of azaborinines with redox-active organoboryl substituents.

The 2,3,4,5,6-pentaphenyl-1,2-azaborinin-1-yl (PPAB) potassium complex 1 undergoes facile salt metathesis with 9,10-dibromo-9,10-dihydroboraanthracene (DBABr2), 5-bromodibenzo[b,d]borole (DBBBr), 1-chlorotetraphenylborole (TPBCl) and dibromo(phenyl)borane (BBr2Ph) to yield the corresponding N-borylated azaborinines N-DBABr-PPAB (2, which hydrolyses and dimerises to the oxo-bridged N,N'-O(DBA)2-(PPAB)2, 3), N,N'-DBA-(PPAB)2 (4), N-DBB-PPAB (5), N-PPB-PPAB (7) and N-BBrPh-PPBA (9). Stepwise reduction of 4 yields the corresponding stable radical anion 4˙- and dianion 42-. One-electron reduction of 5 with KC8 yields the purple radical anion 5˙-, which forms a highly insoluble coordination polymer. 5˙- undergoes very slow radical intramolecular ortho-C-H activation at the C4-phenyl substituent of the PPAB moiety, yielding a BN-analogue of the 5,5'-spiro-bi[dibenzoborole] anion, [6]K. Compound 7 cannot be isolated and undergoes spontaneous and diastereoselective 2,5-anti-addition of the ortho-C-H bond of the PPAB C4-phenyl substituent to yield a novel BNB-analogue of the triply fused dihydrocyclopenta[l]phenanthrene cation, compound 8. Finally the one-electron reduction of 9 results in the ortho-C-H activation of the PPAB C4-phenyl substituent at an in situ-generated dicoordinate boryl anion (10), resulting in the formation of a BNB-analogue of 9H-fluorene, the borate 11-. DFT calculations provide a rationale for the diverse C-H activations observed in these reactions.

Coinage metal complexes of BN analogues of m-terphenyl ligands.

We report the synthesis of a series of group 11 metal complexes with sterically demanding anionic nitrogen ligands based on the 1,2-azaborinine motif. The ligands, which share structural similarities with m-terphenyls, have been used to stabilize two-coordinate phosphine complexes and dimeric complexes with close contacts between the metal centers. Spectroscopic, crystallographic, and theoretical investigations reveal close parallels to the related m-terphenyl complexes, including metallophilic interactions in the dimers.

Aromatic 1,2-Azaborinin-1-yls as Electron-Withdrawing Anionic Nitrogen Ligands for Main Group Elements.

The 2-aryl-3,4,5,6-tetraphenyl-1,2-azaborinines 1-EMe3 and 2-EMe3 (E=Si, Sn; aryl=Ph (1), Mes (=2,4,6-trimethylphenyl, 2)) were synthesized by ring-expansion of borole precursors with N3 EMe3 -derived nitrenes. Desilylative hydrolysis of 1- and 2-SiMe3 yielded the corresponding N-protonated azaborinines, which were deprotonated with nBuLi or MN(SiMe3 )2 (M=Na, K) to the corresponding group 1 salts, 1-M and 2-M. While the lithium salts crystallized as monomeric Lewis base adducts, the potassium salts formed coordination polymers or oligomers via intramolecular K⋅⋅⋅aryl π interactions. The reaction of 1-M or 2-M with CO2 yielded N-carboxylate salts, which were derivatized by salt metathesis to methyl and silyl esters. Salt metathesis of 1-M or 2-M with methyl triflate, [Cp*BeCl] (Cp*=C5 Me5 ), BBr2 Ar (Ar=Ph, Mes, 2-thienyl), ECl3 (E=B, Al, Ga) and PX3 (X=Cl, Br) afforded the respective group 2, 13 and 15 1,2-azaborinin-2-yl complexes. Salt metathesis of 1-K with BBr3 resulted not only in N-borylation but also Ph-Br exchange between the endocyclic and exocyclic boron atoms. Solution 11 B NMR data suggest that the 1,2-azaborinin-2-yl ligand is similarly electron-withdrawing to a bromide. In the solid state the endocyclic bond length alternation and the twisting of the C4 BN ring increase with the sterics of the substituents at the boron and nitrogen atoms, respectively. Regression analyses revealed that the downfield shift of the endocyclic 11 B NMR resonances is linearly correlated to both the degree of twisting of the C4 BN ring and the tilt angle of the N-substituent. Calculations indicate that the 1,2-azaborinin-1-yl ligand has no sizeable π-donor ability and that the aromaticity of the ring can be subtly tuned by the electronics of the N-substituent.

C-C and C-N Bond Activation, Lewis-Base Coordination and One- and Two-Electron Oxidation at a Linear Aminoborylene.

A cyclic alkyl(amino)carbene (CAAC)-stabilized dicoordinate aminoborylene is synthesized by the twofold reduction of a [(CAAC)BCl2 (TMP)] (TMP=2,6-tetramethylpiperidyl) precursor. NMR-spectroscopic, X-ray crystallographic and computational analyses confirm the cumulenic nature of the central C=B=N moiety. Irradiation of [(CAAC)B(TMP)] (2) resulted in an intramolecular C-C bond activation, leading to a doubly-fused C10 BN heterocycle, while the reaction with acetonitrile resulted in an aryl migration from the CAAC to the acetonitrile nitrogen atom, concomitant with tautomerization of the latter to a boron-bound allylamino ligand. One-electron oxidation of 2 with CuX (X=Cl, Br) afforded the corresponding amino(halo)boryl radicals, which were characterized by EPR spectroscopy and DFT calculations. Placing 2 under an atmosphere of CO afforded the tricoordinate (CAAC,CO)-stabilized aminoborylene. Finally, the twofold oxidation of 2 with chalcogens led, in the case of N2 O and sulfur, to the splitting of the B-CCAAC bond and formation of the 2,4-diamino-1,3,2,4-dichalcogenadiboretanes and CAAC-chalcogen adducts, whereas with selenium a monomeric boraselenone was isolated, which showed some degree of B-Se multiple bonding.

Introducing the FAIR Principles for research software.

Research software is a fundamental and vital part of research, yet significant challenges to discoverability, productivity, quality, reproducibility, and sustainability exist. Improving the practice of scholarship is a common goal of the open science, open source, and FAIR (Findable, Accessible, Interoperable and Reusable) communities and research software is now being understood as a type of digital object to which FAIR should be applied. This emergence reflects a maturation of the research community to better understand the crucial role of FAIR research software in maximising research value. The FAIR for Research Software (FAIR4RS) Working Group has adapted the FAIR Guiding Principles to create the FAIR Principles for Research Software (FAIR4RS Principles). The contents and context of the FAIR4RS Principles are summarised here to provide the basis for discussion of their adoption. Examples of implementation by organisations are provided to share information on how to maximise the value of research outputs, and to encourage others to amplify the importance and impact of this work.

Synthesis and hydrogenation of polycyclic aromatic hydrocarbon-substituted diborenes via uncatalysed hydrogenative B-C bond cleavage.

The classical route to the PMe3-stabilised polycyclic aromatic hydrocarbon (PAH)-substituted diborenes B2Ar2(PMe3)2 (Ar = 9-phenanthryl 7-Phen; Ar = 1-pyrenyl 7-Pyr) via the corresponding 1,2-diaryl-1,2-dimethoxydiborane(4) precursors, B2Ar2(OMe)2, is marred by the systematic decomposition of the latter to BAr(OMe)2 during reaction workup. Calculations suggest this results from the absence of a second ortho-substituent on the boron-bound aryl rings, which enables their free rotation and exposes the B-B bond to nucleophilic attack. 7-Phen and 7-Pyr are obtained by the reduction of the corresponding 1,2-diaryl-1,2-dichlorodiborane precursors, B2Ar2Cl2(PMe3)2, obtained from the SMe2 adducts, which are synthesised by direct NMe2-Cl exchange at B2Ar2(NMe2)2 with (Me2S)BCl3. The low-lying π* molecular orbitals (MOs) located on the PAH substituents of 7-Phen and 7-Pyr intercalate between the B-B-based π and π* MOs, leading to a relatively small HOMO-LUMO gap of 3.20 and 2.72 eV, respectively. Under vacuum or at high temperature 7-Phen and 7-Pyr undergo intramolecular hydroarylation of the B[double bond, length as m-dash]B bond to yield 1,2-dihydronaphtho[1,8-cd][1,2]diborole derivatives. Hydrogenation of 7-Phen, 7-Pyr and their 9-anthryl and mesityl analogues III and II, respectively, results in all cases in splitting of the B-B bond and isolation of the monoboranes (Me3P)BArH2. NMR-spectroscopic monitoring of the reactions, solid-state structures of isolated reaction intermediates and computational mechanistic analyses show that the hydrogenation of the three PAH-substituted diborenes proceeds via a different pathway to that of the dimesityldiborene. Rather than occurring exclusively at the B-B bond, hydrogenation of 7-Ar and III proceeds via a hydroarylated intermediate, which undergoes one B-B bond-centered H2 addition, followed by hydrogenation of the endocyclic B-C bond resulting from hydroarylation, making the latter effectively reversible.

Perspectives on automated composition of workflows in the life sciences.

Scientific data analyses often combine several computational tools in automated pipelines, or workflows. Thousands of such workflows have been used in the life sciences, though their composition has remained a cumbersome manual process due to a lack of standards for annotation, assembly, and implementation. Recent technological advances have returned the long-standing vision of automated workflow composition into focus. This article summarizes a recent Lorentz Center workshop dedicated to automated composition of workflows in the life sciences. We survey previous initiatives to automate the composition process, and discuss the current state of the art and future perspectives. We start by drawing the "big picture" of the scientific workflow development life cycle, before surveying and discussing current methods, technologies and practices for semantic domain modelling, automation in workflow development, and workflow assessment. Finally, we derive a roadmap of individual and community-based actions to work toward the vision of automated workflow development in the forthcoming years. A central outcome of the workshop is a general description of the workflow life cycle in six stages: 1) scientific question or hypothesis, 2) conceptual workflow, 3) abstract workflow, 4) concrete workflow, 5) production workflow, and 6) scientific results. The transitions between stages are facilitated by diverse tools and methods, usually incorporating domain knowledge in some form. Formal semantic domain modelling is hard and often a bottleneck for the application of semantic technologies. However, life science communities have made considerable progress here in recent years and are continuously improving, renewing interest in the application of semantic technologies for workflow exploration, composition and instantiation. Combined with systematic benchmarking with reference data and large-scale deployment of production-stage workflows, such technologies enable a more systematic process of workflow development than we know today. We believe that this can lead to more robust, reusable, and sustainable workflows in the future.

Rethinking Borole Cycloaddition Reactivity.

Boroles are attracting broad interest for their myriad and diverse applications, including in synthesis, small molecule activation and functional materials. Their properties and reactivity are closely linked to the cyclic conjugated diene system, which has been shown to participate in cycloaddition reactions, such as the Diels-Alder reaction with alkynes. The reaction steps leading to boranorbornadienes, borepins and tricyclic boracyclohexenes from the thermal reaction of boroles with alkynes are seemingly well understood as judged from the literature. Herein, we question the long-established mechanistic picture of pericyclic rearrangements by demonstrating that seven-membered borepins (i. e., heptaphenylborepin and two derivatives substituted with a thienyl and chloride substituent on boron) exist in a dynamic equilibrium with the corresponding bicyclic boranorbornadienes, the direct Diels-Alder products, but are not isolable products from the reactions. Heating gradually converts the isomeric mixtures into fluorescent tricyclic boracyclohexenes, the most stable isomers in the series. Results from mechanistic DFT calculations reveal that the tricyclic compounds derive from the boranorbornadienes and not the borepins, which were previously believed to be intermediates in purely pericyclic processes.

Adducts of the Parent Boraphosphaketene H2 BPCO and their Decarbonylative Insertion Chemistry.

The first examples of Lewis base adducts of the parent boraphosphaketene (H2 B-PCO) and their cyclodimers are prepared. One of these adducts is shown to undergo mild decarbonylation and phosphinidene insertion into a B-C bond of a borole, forming very rare examples of 1,2-phosphaborinines, B/P isosteres of benzene. The strong donor properties of these 1,2-phosphaborinines are confirmed by the synthesis of their π complexes with the Group 6 metals.

Loose programming of GIS workflows with geo-analytical concepts.

Loose programming enables analysts to program with concepts instead of procedural code. Data transformations are left underspecified, leaving out procedural details and exploiting knowledge about the applicability of functions to data types. To synthesize workflows of high quality for a geo-analytical task, the semantic type system needs to reflect knowledge of geographic information systems (GIS) at a level that is deep enough to capture geo-analytical concepts and intentions, yet shallow enough to generalize over GIS implementations. Recently, core concepts of spatial information and related geo-analytical concepts were proposed as a way to add the required abstraction level to current geodata models. The core concept data types (CCD) ontology is a semantic type system that can be used to constrain GIS functions for workflow synthesis. However, to date, it is unknown what gain in precision and workflow quality can be expected. In this article we synthesize workflows by annotating GIS tools with these types, specifying a range of common analytical tasks taken from an urban livability scenario. We measure the quality of automatically synthesized workflows against a benchmark generated from common data types. Results show that CCD concepts significantly improve the precision of workflow synthesis.

APE in the Wild: Automated Exploration of Proteomics Workflows in the bio.tools Registry.

The bio.tools registry is a main catalogue of computational tools in the life sciences. More than 17 000 tools have been registered by the international bioinformatics community. The bio.tools metadata schema includes semantic annotations of tool functions, that is, formal descriptions of tools' data types, formats, and operations with terms from the EDAM bioinformatics ontology. Such annotations enable the automated composition of tools into multistep pipelines or workflows. In this Technical Note, we revisit a previous case study on the automated composition of proteomics workflows. We use the same four workflow scenarios but instead of using a small set of tools with carefully handcrafted annotations, we explore workflows directly on bio.tools. We use the Automated Pipeline Explorer (APE), a reimplementation and extension of the workflow composition method previously used. Moving "into the wild" opens up an unprecedented wealth of tools and a huge number of alternative workflows. Automated composition tools can be used to explore this space of possibilities systematically. Inevitably, the mixed quality of semantic annotations in bio.tools leads to unintended or erroneous tool combinations. However, our results also show that additional control mechanisms (tool filters, configuration options, and workflow constraints) can effectively guide the exploration toward smaller sets of more meaningful workflows.

Ca2+ functions as a molecular switch that controls the mutually exclusive complex formation of pyridoxal phosphatase with CIB1 or calmodulin.

Pyridoxal 5'-phosphate (PLP) is an essential cofactor for neurotransmitter metabolism. Pyridoxal phosphatase (PDXP) deficiency in mice increases PLP and γ-aminobutyric acid levels in the brain, yet how PDXP is regulated is unclear. Here, we identify the Ca2+ - and integrin-binding protein 1 (CIB1) as a PDXP interactor by yeast two-hybrid screening and find a calmodulin (CaM)-binding motif that overlaps with the PDXP-CIB1 interaction site. Pulldown and crosslinking assays with purified proteins demonstrate that PDXP directly binds to CIB1 or CaM. CIB1 or CaM does not alter PDXP phosphatase activity. However, elevated Ca2+ concentrations promote CaM binding and, thereby, diminish CIB1 binding to PDXP, as both interactors bind in a mutually exclusive way. Hence, the PDXP-CIB1 complex may functionally differ from the PDXP-Ca2+ -CaM complex.

Community curation of bioinformatics software and data resources.

The corpus of bioinformatics resources is huge and expanding rapidly, presenting life scientists with a growing challenge in selecting tools that fit the desired purpose. To address this, the European Infrastructure for Biological Information is supporting a systematic approach towards a comprehensive registry of tools and databases for all domains of bioinformatics, provided under a single portal (https://bio.tools). We describe here the practical means by which scientific communities, including individual developers and projects, through major service providers and research infrastructures, can describe their own bioinformatics resources and share these via bio.tools.

Automated workflow composition in mass spectrometry-based proteomics.

MOTIVATION: Numerous software utilities operating on mass spectrometry (MS) data are described in the literature and provide specific operations as building blocks for the assembly of on-purpose workflows. Working out which tools and combinations are applicable or optimal in practice is often hard. Thus researchers face difficulties in selecting practical and effective data analysis pipelines for a specific experimental design. RESULTS: We provide a toolkit to support researchers in identifying, comparing and benchmarking multiple workflows from individual bioinformatics tools. Automated workflow composition is enabled by the tools' semantic annotation in terms of the EDAM ontology. To demonstrate the practical use of our framework, we created and evaluated a number of logically and semantically equivalent workflows for four use cases representing frequent tasks in MS-based proteomics. Indeed we found that the results computed by the workflows could vary considerably, emphasizing the benefits of a framework that facilitates their systematic exploration. AVAILABILITY AND IMPLEMENTATION: The project files and workflows are available from https://github.com/bio-tools/biotoolsCompose/tree/master/Automatic-Workflow-Composition. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Lewis-Base-Induced Disproportionation of a Dialane.

The reaction of a pentamethylcyclopentadienyl-substituted dialane with a variety of Lewis bases results in unexpected disproportionation of the dialane into AlI and AlIII species. Use of a transition-metal Lewis base allows for the formation of metal-only Lewis pairs. Furthermore, the synthesis of a Lewis base bis-adduct was successful with the Lewis base 4-dimethylaminopyridine.

Dialumination of unsaturated species with a reactive bis(cyclopentadienyl) dialane.

A new bis(cyclopentadienyl) dialane is prepared, which shows controlled, selective dialumination reactions with a conventional alkyne, an electron-rich alkyne, and an azide. The reactions provide structurally diverse products, featuring a range of aluminium coordination numbers, cyclopentadienyl binding modes, and cyclic motifs. The variable nature of the bonding in the Cp*Al units allows a range of binding modes depending on the electronic requirements of the Al atom and provides new possibilities to the chemistry of dialanes, as demonstrated by the isolation of a double internal Lewis adduct with "ring-slipped" Cp* rings in this work.

TRPC4α and TRPC4ß Similarly Affect Neonatal Cardiomyocyte Survival during Chronic GPCR Stimulation.

The Transient Receptor Potential Channel Subunit 4 (TRPC4) has been considered as a crucial Ca2+ component in cardiomyocytes promoting structural and functional remodeling in the course of pathological cardiac hypertrophy. TRPC4 assembles as homo or hetero-tetramer in the plasma membrane, allowing a non-selective Na+ and Ca2+ influx. Gαq protein-coupled receptor (GPCR) stimulation is known to increase TRPC4 channel activity and a TRPC4-mediated Ca2+ influx which has been regarded as ideal Ca2+ source for calcineurin and subsequent nuclear factor of activated T-cells (NFAT) activation. Functional properties of TRPC4 are also based on the expression of the TRPC4 splice variants TRPC4α and TRPC4ß. Aim of the present study was to analyze cytosolic Ca2+ signals, signaling, hypertrophy and vitality of cardiomyocytes in dependence on the expression level of either TRPC4α or TRPC4ß. The analysis of Ca2+ transients in neonatal rat cardiomyocytes (NRCs) showed that TRPC4α and TRPC4ß affected Ca2+ cycling in beating cardiomyocytes with both splice variants inducing an elevation of the Ca2+ transient amplitude at baseline and TRPC4ß increasing the Ca2+ peak during angiotensin II (Ang II) stimulation. NRCs infected with TRPC4ß (Ad-C4ß) also responded with a sustained Ca2+ influx when treated with Ang II under non-pacing conditions. Consistent with the Ca2+ data, NRCs infected with TRPC4α (Ad-C4α) showed an elevated calcineurin/NFAT activity and a baseline hypertrophic phenotype but did not further develop hypertrophy during chronic Ang II/phenylephrine stimulation. Down-regulation of endogenous TRPC4α reversed these effects, resulting in less hypertrophy of NRCs at baseline but a markedly increased hypertrophic enlargement after chronic agonist stimulation. Ad-C4ß NRCs did not exhibit baseline calcineurin/NFAT activity or hypertrophy but responded with an increased calcineurin/NFAT activity after GPCR stimulation. However, this effect was not translated into an increased propensity towards hypertrophy but rather less hypertrophy during GPCR stimulation. Further analyses revealed that, although hypertrophy was preserved in Ad-C4α NRCs and even attenuated in Ad-C4ß NRCs, cardiomyocytes had an increased apoptosis rate and thus were less viable after chronic GPCR stimulation. These findings suggest that TRPC4α and TRPC4ß differentially affect Ca2+ signals, calcineurin/NFAT signaling and hypertrophy but similarly impair cardiomyocyte viability during GPCR stimulation.

The 3rd DBCLS BioHackathon: improving life science data integration with Semantic Web technologies.

BACKGROUND: BioHackathon 2010 was the third in a series of meetings hosted by the Database Center for Life Sciences (DBCLS) in Tokyo, Japan. The overall goal of the BioHackathon series is to improve the quality and accessibility of life science research data on the Web by bringing together representatives from public databases, analytical tool providers, and cyber-infrastructure researchers to jointly tackle important challenges in the area of in silico biological research. RESULTS: The theme of BioHackathon 2010 was the 'Semantic Web', and all attendees gathered with the shared goal of producing Semantic Web data from their respective resources, and/or consuming or interacting those data using their tools and interfaces. We discussed on topics including guidelines for designing semantic data and interoperability of resources. We consequently developed tools and clients for analysis and visualization. CONCLUSION: We provide a meeting report from BioHackathon 2010, in which we describe the discussions, decisions, and breakthroughs made as we moved towards compliance with Semantic Web technologies - from source provider, through middleware, to the end-consumer.

Flux-p: automating metabolic flux analysis.

Quantitative knowledge of intracellular fluxes in metabolic networks is invaluable for inferring metabolic system behavior and the design principles of biological systems. However, intracellular reaction rates can not often be calculated directly but have to be estimated; for instance, via 13C-based metabolic flux analysis, a model-based interpretation of stable carbon isotope patterns in intermediates of metabolism. Existing software such as FiatFlux, OpenFLUX or 13CFLUX supports experts in this complex analysis, but requires several steps that have to be carried out manually, hence restricting the use of this software for data interpretation to a rather small number of experiments. In this paper, we present Flux-P as an approach to automate and standardize 13C-based metabolic flux analysis, using the Bio-jETI workflow framework. Exemplarily based on the FiatFlux software, it demonstrates how services can be created that carry out the different analysis steps autonomously and how these can subsequently be assembled into software workflows that perform automated, high-throughput intracellular flux analysis of high quality and reproducibility. Besides significant acceleration and standardization of the data analysis, the agile workflow-based realization supports flexible changes of the analysis workflows on the user level, making it easy to perform custom analyses.