pinecone/core-2020-05-10-deduplication huggingface dataset:
Surviving mass extinctions through biomineralized DNA

Even in the worst of conditions, such as those which occurred during mass extinction events, life on Earth never totally stopped. Aggressive chemical and physical attacks able to sterilize or poison living organisms occurred repeatedly. Surprisingly, DNA was not degraded, denatured or modified to the point of losing the capability of transferring the genetic information to the next generations. After the events of mass extinction life was able to survive and thrive. DNA was passed on despite being an extremely fragile biomolecule. The potential implications of hydroxyapatite protection of DNA are discussed in this Concept article including how DNA acts as a template for hydroxyapatite (HAp) formation, how cell death can trigger biomineralization, and how DNA can be successfully released from HAp when the conditions are favorable for life.Peer ReviewedPostprint (published version
On the mechanism of the digold(I) hydroxide-catalyzed hydrophenoxylation of alkynes

Herein we present a detailed investigation of the mechanistic aspects of the dual gold-catalysed hydrophenoxylation of alkynes, using both experimental and computational methods. The dissociation of [{Au(NHC)}2(µ-OH)][BF4] is essential to enter the catalytic cycle; this step is favored in the presence of bulky, non-coordinating counterions. Moreover, in silico studies confirmed that phenol does not only act as a reactant, but as a co-catalyst, lowering the energy barriers for several transition states. A gem-diaurated species might form during the reaction, but this lies deep within a potential energy well, and is likely to be an ‘off-cycle’ rather than an ‘in-cycle’ intermediate
Chemoproteomic Approach to Explore the Target Profile of GPCR ligands: Application to 5-HT1A and 5-HT6 Receptors

Determination of the targets of a compound remains  an essential aspect in drug discovery. A complete understanding of all binding interactions is critical to recognize in advance both therapeutic effects and undesired consequences. However, the complete polypharmacology of many drugs currently in clinical development is still unknown, especially in the case of G-protein-coupled receptor (GPCR) ligands. In this work we have developed a chemoproteomic platform based on the use of chemical probes to explore the target profile of a compound in biological systems. As proof of concept, this methodology has been applied to selected ligands of the therapeutically relevant serotonin 5-HT1A and 5-HT6 receptors, and we have identified and validated some of their off-targets. This approach could be extended to other drugs of interest to study the targeted proteome in disease-relevant systems
Stabilization of the low-spin state in a mononuclear Iron(II) complex and high-temperature cooperative spin crossover mediated by hydrogen bonding

The tetrapyridyl ligand bbpya (bbpya=N,N-bis(2,2'-bipyrid-6-yl)amine) and its mononuclear coordination compound [Fe(bbpya)(NCS)(2)] (1) were prepared. According to magnetic susceptibility, differential scanning calorimetry fitted to Sorai's domain model, and powder X-ray diffraction measurements, 1 is low-spin at room temperature, and it exhibits spin crossover (SCO) at an exceptionally high transition temperature of T-1/2=418 K. Although the SCO of compound 1 spans a temperature range of more than 150 K, it is characterized by a wide (21 K) and dissymmetric hysteresis cycle, which suggests cooperativity. The crystal structure of the LS phase of compound 1 shows strong N-H center dot center dot center dot S intermolecular H-bonding interactions that explain, at least in part, the cooperative SCO behavior observed for complex 1. DFT and CASPT2 calculations under vacuum demonstrate that the bbpya ligand generates a stronger ligand field around the iron(II) core than its analogue bapbpy (N,N'-di(pyrid-2yl)-2,2'-bipyridine-6,6'-diamine); this stabilizes the LS state and destabilizes the HS state in 1 compared with [Fe(bapbpy)( NCS)(2)] (2). Periodic DFT calculations suggest that crystal-packing effects are significant for compound 2, in which they destabilize the HS state by about 1500 cm(-1). The much lower transition temperature found for the SCO of 2 compared to 1 appears to be due to the combined effects of the different ligand field strengths and crystal packing
Stereo- and chemodivergent NHC-promoted functionalisation of arylalkylketenes with chloral

Funding: UK Engineering and Physical Sciences Research Council EP/G501742/1Stereo- and chemodivergent enantioselective reaction pathways are observed upon treatment of alkylarylketenes and trichloroacetaldehyde (chloral) with N-heterocyclic carbenes, giving selectively either β-lactones (up to 88:12 dr, up to 94 % ee) or α-chloroesters (up to 94 % ee). Either 2-arylsubstitution or an α-branched iPr alkyl substituent within the ketene favours the chlorination pathway, allowing chloral to be used as an electrophilic chlorinating reagent in asymmetric catalysis.Publisher PDFPeer reviewe
Facile, catalytic dehydrocoupling of phosphines using β-diketiminate iron(II) complexes

Catalytic dehydrocoupling of primary and secondary phosphines has been achieved for the first time using an iron pre-catalyst. The reaction proceeds under mild reaction conditions and is successful with a range of diarylphosphines. A proton acceptor is not needed for the transformation to take place, but addition of 1-hexene does allow for turnover at 50 °C. The catalytic system developed also facilitates the dehydrocoupling of phenylphosphane and dicyclohexylphosphane. A change in solvent switches off dehydrocoupling to allow hydrophosphination of alkenes
Studies of a large odd-numbered odd-electron metal ring : inelastic neutron scattering and muon spin relaxation spectroscopy of Cr8Mn.

The spin dynamics of Cr8Mn, a nine-membered antiferromagnetic (AF) molecular nanomagnet, are investigated. Cr8Mn is a rare example of a large odd-membered AF ring, and has an odd-number of 3d-electrons present. Odd-membered AF rings are unusual and of interest due to the presence of competing exchange interactions that result in frustrated-spin ground states. The chemical synthesis and structures of two Cr8Mn variants that differ only in their crystal packing are reported. Evidence of spin frustration is investigated by inelastic neutron scattering (INS) and muon spin relaxation spectroscopy (μSR). From INS studies we accurately determine an appropriate microscopic spin Hamiltonian and we show that μSR is sensitive to the ground-spin-state crossing from S=1/2 to S=3/2 in Cr8Mn. The estimated width of the muon asymmetry resonance is consistent with the presence of an avoided crossing. The investigation of the internal spin structure of the ground state, through the analysis of spin-pair correlations and scalar-spin chirality, shows a non-collinear spin structure that fluctuates between non-planar states of opposite chiralities
Reversed crystal growth of RHO zeolite imidazolate framework (ZIF)

KS and MT would like to thank the University of St Andrews for the studentship, Dr Jürgen Kahr and Professor Paul Wright for their help with this work, Mr Ross Blackley for his help on using the SEM and TEM microscopes and Mrs Sylvia Williamson for her assistance with the N2 adsorption tests. HFG would like to thank EPSRC for the funding (EP/K015540/1). WZZ thanks EPSRC for the financial support to purchase the FEG SEM (EP/F019580/1).RHO zeolitic imidazolate framework (ZIF), Zn1.33(O.OH)0.33(nim)1.167(pur), crystals with a rhombic dodecahedral morphology were synthesized by a solvothermal process. The growth of the crystals was studied over time using scanning electron microscopy (SEM), transmission electron microscopy (TEM), powder X-ray diffraction (PXRD) and Brunauer–Emmett–Teller (BET) analyses, and a reversed crystal growth mechanism was revealed. Initially, precursor materials joined together to form disordered aggregates, which then underwent surface recrystallization forming a core–shell structure, in which a disordered core is encased in a layer of denser, less porous crystal. When the growth continued, the shell became less and less porous, until it was a layer of true single crystal. The crystallization then extended from the surface to the core over a six-week period until, eventually, true single crystals were formed.Publisher PDFPeer reviewe
Trinuclear Cage-Like ZnII Macrocyclic Complexes: Enantiomeric Recognition and Gas Adsorption Properties

Three zinc(II) ions in combination with two units of enantiopure 3+3 triphenolic Schiff base macrocycles 1, 2, 3 or 4 form cage-like chiral complexes. The formation of these complexes is accompanied by the enantioselective self-recognition of chiral macrocyclic units. The X-ray crystal structures of these trinuclear complexes show hollow metal-organic molecules. In some crystal forms, these barrel-shaped complexes are arranged in a window-to-window fashion which results in formation of 1-D channels and combination of intrinsic porosity with extrinsic porosity. The microporous nature of the [Zn312] complex is reflected in its N2, Ar, H2 and CO2 adsorption properties. The N2 and Ar adsorption isotherms showed pressure gating behaviour which is without precedent for any noncovalent porous material. The comparison of the structures of the [Zn312] and [Zn332] complexes with that of the free macrocycle H31 reveals a striking structural similarity. In the latter compound two macrocyclic units stitched together by hydrogen bonds form a cage very similar to that formed by two macrocyclic units stitched together by Zn(II) ions. This structural similarity is manifested also by the gas adsorption properties of the free H31 macrocycle. Recrystallization of [Zn312] in the presence of racemic 2-butanol results in enantioselective binding of the (S)-2-butanol inside the cage via coordination to one of Zn(II) ions.This work was supported by the NCN (NarodoweCentrumNauki, Poland) (grant 2011/03/B/ST5/01060).D.P.and J.L.thank the FNP Program“Mistrz” for financial support, and D.F.-J. thanks the Royal Society for funding through a University Research Fellowship.This is the author accepted manuscript. The final version is available from Wiley via http://dx.doi.org/10.1002/chem.20150347
Unprecedented strongly panchromic absorption from proton switchable iridium(III) azoimidazolate complexes

Two novel heteroleptic iridium(III) complexes bearing an aryldiazoimidazole ligand are reported. These complexes differ structurally with respect to the protonation state of the imidazole ring, but can be independently accessed by varying the synthetic conditions. Their structures have been unequivocally confirmed by X-ray crystal structure analysis, with surprising differences in the structural parameters of the two complexes. The strongly absorbing nature of the free diazoimidazole ligand is enhanced in these iridium complexes, with the protonated cationic complex demonstrating extraordinarily strong panchromic absorption up to 700 nm. The absorption profile of the deprotonated neutral complex is blue-shifted by about 100 nm and thus the interconversion between the two complexes as a function of the acidity/basicity of the environment can be readily monitored by absorption spectroscopy. Theoretical calculations reveal the origins of these markedly different absorption properties. Finally, the protonated analogue has been targeted as an acceptor material for organic photovoltaic (OPV) applications and preliminary results are reported.Publisher PDFPeer reviewe
Developing the Saegusa-Ito cyclisation for the synthesis of difluorinated cyclohexenones

Palladium(II)-catalysed cycloalkenylation (Saegusa-Ito cyclisation) has been used for the first time to transform difluorinated silylenol ethers to difluorinated cycloalkenones under mild conditions. The silylenol ether precursors were prepared in two high-yielding steps from trifluoroethanol, and cyclised in moderate to good yields. A combination of air and copper(I) chloride in acetonitrile achieved the turnover of the initial palladium(II) salt, while the provision of an oxygen atmosphere ensured more rapid reaction. Annulations required a minimum level of substitution on the chain, but failed when the alkene was substituted. Annelations allowed a range of n,6-bicyclic systems to be prepared and afforded three products in which heterocycles were fused to the new cyclohexenone. The least substituted system explored underwent cyclisation followed by terminal oxidation to a cyclic enal, which corresponded to a Wacker product of unusual regiochemistry
Probing the limits of selectivity in a recognition-mediated reaction network embedded within a dynamic covalent library

This work was supported by the award of a Postgraduate Studentship from EPSRC (EP/K503162/1) to TK.Two recognition-mediated reaction processes operating through a reactive binary complex drive resolution of a 24-component dynamic covalent library, assembled from individual aldehydes and nucleophiles. The effectiveness of the library resolution and selective amplification of one recognition-enabled species over another is limited by the difference in the rates of the recognition-mediated reactive processes and strength of the recognition processes employed in the dynamic system.PostprintPeer reviewe
Approaching the kinetic inertness of macrocyclic gadolinium(III)-based MRI contrast agents with highly rigid open-chain derivatives

[Abstract] A highly rigid open-chain octadentate ligand (H4cddadpa) containing a diaminocylohexane unit to replace the ethylenediamine bridge of 6,6′-[(ethane-1,2 diylbis{(carboxymethyl)azanediyl})bis(methylene)] dipicolinic acid (H4octapa) was synthesized. This structural modification improves the thermodynamic stability of the Gd3+ complex slightly (log KGdL=20.68 vs. 20.23 for [Gd(octapa)]−) while other MRI-relevant parameters remain unaffected (one coordinated water molecule; relaxivity r1=5.73 mm−1 s−1 at 20 MHz and 295 K). Kinetic inertness is improved by the rigidifying effect of the diaminocylohexane unit in the ligand skeleton (half-life of dissociation for physiological conditions is 6 orders of magnitude higher for [Gd(cddadpa)]− (t1/2=1.49×105 h) than for [Gd(octapa)]−. The kinetic inertness of this novel chelate is superior by 2–3 orders of magnitude compared to non-macrocyclic MRI contrast agents approved for clinical use.Hungarian Scientific Research Fund. OTKA; K-84291Hungarian Scientific Research Fund. OTKA; K-109029European Social Fund; TÁMOP-4.2.2A-11/1/KONV-2012-004
Stereoselective Synthesis of the Proposed C79-C104 Fragment of Symbiodinolide

Stereoselective and streamlined synthesis of the proposed C79-C104 fragment 2 of symbiodinolide (1), a polyol marine natural product with a molecular weight of 2860, was achieved. In the synthetic route, the proposed C79-C104 fragment 2 was synthesized by utilizing a Julia-Kocienski olefination and subsequent Sharpless asymmetric dihydroxylation as key transformations in a convergent manner. Detailed comparison of the 13 C NMR chemical shifts between the natural product and the synthetic C79-C104 fragment 2 revealed that the stereostructure at the C91-C99 carbon chain moiety of symbiodinolide (1) should be reinvestigated
Stereodivergent Synthesis and Stereochemical Reassignment of the C79-C104 Fragment of Symbiodinolide

We have synthesized eight possible diastereoisomers 3 a-h of the C79-C97 fragment of symbiodinolide (1) in a stereodivergent manner by utilizing a dithiane addition to the aldehyde as a key step. Comparison of the 13 C NMR chemical shifts of the natural product 1 and the synthetic products 3 a-h indicated that the relative stereostructure of this fragment in symbiodinolide (1) is that represented in 3 a or f. We have stereodivergently synthesized eight possible diastereoisomers of the C94-C104 fragment 4 a-h, and we have compared their 13 C NMR chemical shifts with those of the natural product, which established the relative stereochemistry of this fragment to be that described in diastereoisomers 4 a or e. By combining the stereostructural outcomes of the C79-C97 and C94-C104 fragments, we have proposed four candidate compounds of the C79-C104 fragment 2 a-d. We also synthesized diastereoisomers 2 a and b (2 a in the preceding article; Chem. Eur. J. 2015, DOI: 10.1002/chem.201503880) by a Julia-Kocienski olefination and diastereoisomers 2 c and d by a Wittig reaction. By comparing the 13 C NMR chemical shifts of natural symbiodinolide (1) with those of the synthetic products 2 a-d, we have reassigned the stereostructure of the C79-C104 fragment of natural product 1 to be that depicted in diastereoisomer 2 b
A Modular Approach to Phosphoglycosyltransferase Inhibitors Inspired by Nucleoside Antibiotics

Phosphoglycosyltransferases (PGTs) represent “gatekeeper” enzymes in complex glycan assembly pathways by catalyzing transfer of a phosphosugar from an activated nucleotide diphosphosugar to a membrane-resident polyprenol phosphate. The unique structures of selected nucleoside antibiotics, such as tunicamycin and mureidomycin A, which are known to inhibit comparable biochemical transformations, are exploited as the foundation for the development of modular synthetic inhibitors of PGTs. Herein we present the design, synthesis, and biochemical evaluation of two readily manipulatable modular scaffolds as inhibitors of monotopic bacterial PGTs. Selected compounds show IC[subscript 50] values down to the 40 μm range, thereby serving as lead compounds for future development of selective and effective inhibitors of diverse PGTs of biological and medicinal interest.National Institutes of Health (U.S.) (NIH Grant Number: R21 AI101807
Large-Scale Synthesis of Helicene-Like Molecules for the Design of Enantiopure Thin Films with Strong Chiroptical Activity

International audienceHelicenes are fascinating molecules owing to their unusual properties and applications in many fields from catalysis to organic electronics. Herein, we report a straightforward pathway for the synthesis of helicene-like molecules on a gram scale in an enantiopure form. Thin-film materials with good propagating optical properties and very high chiroptical responses have been grown by using pulsed laser ablation without altering the structure or the enantiopurity of the molecules. Moreover, electronic and vibrational circular dichroism spectroscopies coupled with theoretical calculations enabled some dependences of the chiroptical properties with the structure to be highlighted, for example, effects of rigidification, aromatization, or the state of matter (liquid versus solid)
Nickel(II) meso-hydroxyporphyrin complexes revisited: Palladium-catalysed synthesis, electronic structures of derived oxy radicals, and oxidative coupling to a dioxoporphodimethene dyad

We report the synthesis and characterisation of new examples of meso-hydroxynickel(II) porphyrins with 5,15-diphenyl and 10-phenyl-5,15-diphenyl/diaryl substitu- tion. The OH group was introduced by using carbonate or hydroxide as nucleophile by using palladium/phosphine cat- alysis. The NiPor OHs exist in solution in equilibrium with the corresponding oxy radicals NiPor OC. The 15-phenyl group stabilises the radicals, so that the 1H NMR spectra of {NiPor OH} are extremely broad due to chemical exchange with the paramagnetic species. The radical concentration for the diphenylporphyrin analogue is only 1%, and its NMR line-broadening was able to be studied by variable-tempera- ture NMR spectroscopy. The EPR signals of NiPor OC are con- sistent with somewhat delocalised porphyrinyloxy radicals, and the spin distributions calculated by using density func- tional theory match the EPR and NMR spectroscopic obser- vations. Nickel(II) meso-hydroxy-10,20-diphenylporphyrin was oxidatively coupled to a dioxo-terminated porphodimethene dyad, the strongly red-shifted electronic spectrum of which was successfully modelled by using time-dependent DFT calculations
Enantioselective NHC-catalyzed redox [2+2] cycloadditions with perfluoroketones; a route to fluorinated oxetanes

The authors thank the Royal Society for a University Research Fellowship (A.D.S.), and the European Research Council under the European Union's Seventh Framework Programme (FP7/2007-2013) ERC grant agreement no. 279850 (A.T.D.).The N-heterocyclic carbene (NHC) catalyzed redox formal [2+2] cycloaddition between α-aroyloxyaldehydes and perfluoroketones, followed by ring-opening in situ delivers a variety of perfluorinated β-hydroxycarbonyl compounds in good yield, and excellent diastereo- and enantioselectivity. Through a reductive work-up and subsequent cyclization, this protocol offers access to highly substituted fluorinated oxetanes in two steps and in high ee.PostprintPeer reviewe
Supramolecular Organization of Dye Molecules in Zeolite L Channels: Synthesis, Properties, and Composite Materials

Sequential insertion of different dyes into the 1D channels of zeolite L (ZL) leads to supramolecular sandwich structures and allows the formation of sophisticated antenna composites for light harvesting, transport, and trapping. The synthesis and properties of dye molecules, host materials, composites, and composites embedded in polymer matrices, including two- and three-color antenna systems, are described. Perylene diimide (PDI) dyes are an important class of chromophores and are of great interest for the synthesis of artificial antenna systems. They are especially well suited to advancing our understanding of the structure–transport relationship in ZL because their core fits tightly through the 12-ring channel opening. The substituents at both ends of the PDIs can be varied to a large extent without influencing their electronic absorption and fluorescence spectra. The intercalation/insertion of 17 PDIs, 2 terrylenes, and 1 quaterrylene into ZL are compared and their interactions with the inner surface of the ZL nanochannels discussed. ZL crystals of about 500 nm in size have been used because they meet the criteria that must be respected for the preparation of antenna composites for light harvesting, transport, and trapping. The photostability of dyes is considerably improved by inserting them into the ZL channels because the guests are protected by being confined. Plugging the channel entrances, so that the guests cannot escape into the environment is a prerequisite for achieving long-term stability of composites embedded in an organic matrix. Successful methods to achieve this goal are described. Finally, the embedding of dye–ZL composites in polymer matrices, while maintaining optical transparency, is reported. These results facilitate the rational design of advanced dye–zeolite composite materials and provide powerful tools for further developing and understanding artificial antenna systems, which are among the most fascinating subjects of current photochemistry and photophysics
In Situ Generation of ArCu from CuF2 Makes Coupling of Bulky Aryl Silanes Feasible and Highly Efficient

Producción CientíficaA bimetallic system Pd/CuF2, catalytic in Pd and stoichiometric in Cu, is very efficient and selective for the coupling of fairly hindered aryl silanes with aryl, anisyl, phenylaldehide, or pyridyl iodides of conventional size. The reaction involves the activation of the silane by CuII followed by disproportionation and
transmetalation from the CuI(aryl) to PdII, on which coupling takes place. The CuIII formed in the disproportionation is reduced to CuI(aryl) by the aryl silane in excess, so that the CuF2 used is fully converted into CuI(aryl) and used in the coupling. Moreover, no extra source of fluoride is needed. Interesting size selectivity towards coupling is found in competitive reactions of hindered aryl silanes. Easily accessible [PdCl2(IDM)(AsPh3)] is by far the best catalyst, and the isolated products are esentially free of As or Pd (< 1 ppm). The mechanistic aspects of the process are experimentally examined and discussed.Ministerio de Economía, Industria y Competitividad  (CTQ2013-48406-P)Junta de Castilla y León (programa de apoyo a proyectos de investigación – Ref. VA256U13