pinecone/core-2020-05-10-deduplication huggingface dataset:
Modeling Fungal Melanin Buildup: Biomimetic Polymerization of 1,8-Dihydroxynaphthalene Mapped by Mass Spectrometry

Due to the emerging biomedical relevance and technological potential of fungal melanins, and prompted by the virtual lack of information about their structural arrangement, an optimized synthetic protocol has been devised for a potential structural model of Ascomyces allomelanin through enzyme-catalyzed oxidative polymerization of 1,8-dihydroxynaphthalene (1,8-DHN). Electrospray ionization mass spectrometry (ESI-MS) measurements of freshly synthesized DHN-polymer recorded in the negative ion mode allowed detection of oligomers up to m/z 4000, separated by 158 Da, corresponding to the in-chain DHN-unit. The dominant peaks were assigned to singly-charged distribution, up to 23 repeating units, whereas a doubly charged polymer distribution was also detectable. Chemical derivatization, ultra-performance liquid chromatography (UPLC)-ESI MS, and MS/MS data confirmed that oxidative polymerization of 1,8-DHN proceeds through C−C coupling of the naphthalene rings. The new insights reported here into synthetic 1,8-DHN oligomers/polymers as a mimic of fungal melanins may guide novel interesting advances and applications in the field of biomimetic functional material
Molecules Designed to Contain Two Weakly Coupled Spins with a Photoswitchable Spacer

Controlling the charges and spins of molecules lies at the heart of spintronics. A photoswitchable molecule consisting of two independent spins separated by a photo- switchable moiety was designed in the form of new ligand H4L, which features a dithienylethene photochromic unit and two lateral coordinating moieties, and yields molecules with [MM···MM] topology. Compounds [M4L2(py)6] (M = Cu, 1; Co, 2; Ni, 3; Zn, 4) were prepared and studied by single-crys- tal X-ray diffraction (SCXRD). Different metal centers can be selectively distributed among the two chemically distinct sites of the ligand, and this enables the preparation of many double-spin systems. Heterometallic [MM'···M'M] analogues with formulas [Cu2Ni2L2(py)6] (5), [Co2Ni2L2(py)6] (6), [Co2Cu2L2(py)6] (7), [Cu2Zn2L2(py)6] (8), and [Ni2Zn2L2(py)6] (9) were prepared and analyzed by SCXRD. Their composition was established unambiguously. All complexes exhibit two weakly interacting [MM'] moieties, some of which embody two-level quantum systems. Compounds 5 and 8 each ex- hibit a pair of weakly coupled S = 1=2 spins that show quan- tum coherence in pulsed Q-band EPR spectroscopy, as re- quired for quantum computing, with good phase memory times (TM = 3.59 and 6.03 ms at 7 K). Reversible photoswitch- ing of all the molecules was confirmed in solution. DFT cal- culations on 5 indicate that the interaction between the two spins of the molecule can be switched on and off on photo- cyclization
Halide abstraction competes with oxidative addition in the reactions of aryl halides with [Ni(PMenPh(3-n))4]

Density functional theory (DFT) calculations have been used to study the oxidative addition of aryl halides to complexes of the type [Ni(PMenPh(3-n))4], revealing the crucial role of an open shell singlet transition state for halide abstraction. The formation of NiI versus NiII has been rationalised through the study of three different pathways: (i) halide abstraction by [Ni(PMenPh(3-n))3], via an open shell singlet transition state; (ii) SN2-type oxidative addition to [Ni(PMenPh(3-n))3], followed by phosphine dissociation; and (iii) oxidative addition to [Ni(PMenPh(3-n))2]. For the case of [Ni(PMe3)4], a microkinetic model was used to show that these data are consistent with the experimentally-observed ratios of NiI and NiII. Importantly, [Ni(PMenPh(3-n))2] complexes often have little if any role in the oxidative addition reaction because they are relatively high in energy. The behaviour of [Ni(PR3)4] complexes in catalysis is therefore likely to differ considerably from those based on diphosphine ligands in which two coordinate Ni0 complexes are the key species undergoing oxidative addition
Tandem in situ monitoring for quantitative assessment of mechanochemical reactions involving structurally unknown phases

Despite recent advances in real-time and in situ monitoring techniques, a thorough mechanistic understanding of mechanochemical milling reactions is often hindered by the inability of their quantitative evaluation. Here, a tandem approach combining in situ powder X-ray diffraction and Raman spectroscopy enabled quantitative assessment and kinetic analysis of mechanochemical reaction, even when involving new phases of unknown crystal structures, and short-lived intermediates. We also introduce in situ Raman monitoring as a standalone laboratory technique for quantitative assessment of mechanochemical reactions. Our approach is demonstrated on a complex and multi-step mechanochemical cocrystallization of benzoic acid and the model active pharmaceutical ingredient nicotinamide under neat and liquid-assisted grinding, which resulted in complex transformations between four polymorphs. Reaction pathways and polymorph selectivity can be tuned by both the choice of a liquid additive and its amount. Our results provide an important step toward a complete and high-throughput quantitative approach to mechanochemical reaction kinetics and mechanisms, necessary for the development of the mechanistic framework of milling reactions
An Efficient Route to Highly Substituted Indoles via Tetrahydroindol-4(5H)-one Intermediates Produced by Ring-Opening Cyclization of Spirocyclopropanes with Amines

An efficient route to highly substituted indoles was developed. It includes regioselective functionalization of tetrahydroindol-4(5H)-ones, prepared by ring-opening cyclization of cyclohexane-1,3-dione-2-spirocyclopropanes with primary amines, and subsequent oxidation. 6-Substituted indoles were synthesized from a readily available 5-substituted cyclohexane-1,3-dione-2-spirocyclopropane. Synthesis of 5- and 7-substituted indoles was achieved by regioselective electrophilic alkylation of tetrahydroindol-4(5H)-one, followed by oxidation. 4-Substituted indoles were synthesized by nucleophilic alkylation of the corresponding pyrrole derivative, prepared by partial oxidation of tetrahydroindol-4(5H)-one, and a sequential oxidation. Synthesis of 4-substituted indoles was also accomplished by Pd-catalyzed coupling of 4-hydroxyindole-derived triflates. Furthermore, synthesis of 4,5,6,7-tetrasubstituted indoles was achieved by using these regioselective alkylations
In-Situ and Real-time Monitoring of Mechanochemical Preparation of Li2 Mg(NH2 BH3 )4 and Na2 Mg(NH2 BH3 )4 and Their Thermal Dehydrogenation

For the first time, in-situ monitoring of uninterrupted mechanochemical synthesis of two bimetallic amidoboranes, M2Mg(NH2BH3)4 (M = Li, Na), by means of Raman spectroscopy has been applied. This approach allowed real-time observation of key intermediate phases and a straightforward follow-up of the reaction course. Detailed analysis of time-dependent spectra revealed a two-step mechanism through MNH2BH3.NH3BH3 adducts as key intermediate phases which further reacted with MgH2, giving M2Mg(NH2BH3)4 as final products. The intermediates partially take a competitive pathway toward the oligomeric M(BH3NH2BH2NH2BH3) phases. The crystal structure of the novel bimetallic amidoborane Li2Mg(NH2BH3)4 was solved from high-resolution powder diffraction data and showed an analogous metal coordination as in Na2Mg(NH2BH3)4, but a significantly different crystal packing. Li2Mg(NH2BH3)4 thermally dehydrogenates releasing highly pure H2 in the amount of 7 wt% and at a lower temperature then its sodium analogue making it significantly more viable for practical applications
Azulene-Based Donor-Acceptor Systems: Synthesis, Optical, and Electrochemical Properties

First published: 07 Aug 2017We describe the synthesis and properties of azulene-substituted 1,1,4,4-tetracyanobutadienes (AzTCBDs) and heteroazulenyl TCBDs. TCBD derivatives were prepared in good to excellent yields through reaction of the corresponding 1-ethynylazulenes with tetracyanoethylene (TCNE). In contrast, the reaction between propargyl alcohols and the 1-azulenyl group in TCNE generated 2-aminofuran derivatives, which were transformed into 6-aminofulvenes with a 1-azulenyl substituent upon treatment with several amines. The optical and electrochemical properties of the AzTCBDs were clarified by UV/Vis and voltammetry. The AzTCBD derivatives exhibited electrochromism, showing a multi-step color change under electrochemical redox conditions. The multistage redox properties of AzTCBDs could be useful for the development of novel organic electronic materials
Total Synthesis of Two Possible Diastereomers of Natural 6-Chlorotetrahydrofuran Acetogenin and Its Stereostructural Elucidation

The first total synthesis of two possible diastereomers of natural 6-chlorotetrahydrofuran acetogenin 1 has been achieved. The synthetic route features 5-exo-tet cyclization, Z selective Wittig reaction and Julia olefination for the construction of conjugated diene and enyne moieties, and stereoselective chlorination. Comparison of their 1 H and 13 C NMR data and specific rotation with those of the natural product elucidated the absolute configuration of natural (-)-6-chlorotetrahydrofuran acetogenin 1
Homochiral emissive Λ8- andΔ8-[Ir8Pd4]16+ supramolecular cages

EZ-C acknowledges the University of St Andrews and EPSRC (EP/M02105X/1) for financial support. DE thanks funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No 700961. DJ acknowledges the European Research Council (Marches grant n°278845) and the RFI Lumomat for financial support.Synthetic self-assembly is a powerful technique for the bottom-up construction of discrete and well-defined polyhedral nanostructures resembling the spherical shape of large biological systems. In recent years, numerous Archimedean-shaped coordination cages have been reported based on the assembly of bent monodentate organic ligands containing two or more distal pyridyl rings and square planar PdII ions. The formation of photoactive PdII metallamacrocycles and cages, however, remain rare. Here we report the first examples of emissive and homochiral supramolecular cages of the form of [Ir8Pd4]16+. These cages provide a suitably sized cavity to host large guest molecules. Importantly, encapsulation and energy transfer have been observed between the blue-emitting NBu4[Ir(dFppy)2(CN)2] guest and the red-emitting Δ8-[Ir8Pd4]16+ cage.Publisher PDFPeer reviewe
Role of the diphosphine chelate in emissive, charge-neutral iridium(III) complexes.

A class of neutral tris-bidentate Ir(III) metal complexes incorporating a diphosphine as a chelate is prepared and characterized here for the first time. Treatment of [Ir(dppb)(tht)Cl3] (1) with fppzH afforded the dichloride complexes, trans-(Cl,Cl)[Ir(dppb)(fppz)Cl2] (2) and cis-(Cl,Cl)[Ir(dppb)(fppz)Cl2] (3). The reaction of 3 with the dianionic chelate precursor bipzH2 or mepzH2, in DMF gave the complex [Ir(dppb)(fppz)(bipz)] (4) or [Ir(dppb)(fppz)(mepz)] (5), respectively. In contrast, a hydride complex [Ir(dppb)(fppz)(bipzH)H] (6) was isolated instead of 4 in protic solvent, namely: DGME. All complexes 2 - 6 are luminescent in powder forms and thin films where the dichlorides (2, 3) emit with maxima at 590-627 nm (orange) and quantum yields (Q.Y.s) up to 90% whereas the tris-bidentate (4, 5) and hydride (6) complexes emit at 455-458 nm (blue) with Q.Y.s up to 70%. Hybrid TD-DFT calculations showed considerable MLCT contribution to the orange-emitting 2 and 3 but substantial ligand-centered 3ππ* transition character in the blue-emitting 4 - 6. The dppb does not participate to these radiative transitions in 4 - 6, but it provides the rigidity and steric bulk needed to promote the luminescence by suppressing the self-quenching in the solid state. Fabrication of an OLED with dopant 5 gave a deep blue CIE chromaticity of (0.16, 0.15). Superior blue emitters, which are vital in OLED applications, may be found in other neutral Ir(III) complexes containing phosphine chelates
Peptide-Based Probes with an Artificial Anion Binding Motif for Direct Fluorescence 'Switch-On' Detection of Nucleic Acid in Cells

We report two new peptide based fluorescence probes 1 and 2 for the detection of ds-DNA at physiological pH. 1 and 2 contain amino-naphthalimide and diethyl-aminocoumarin fluorophores, respectively, with two identical peptide arms each equipped with a guanidiniocarbonylpyrrole (GCP) artificial anion-binding motif. 1 and 2 show ‘switch-on’ fluorescence response upon binding to ds-DNA, whereby they can differentiate between various types of polynucleotides. For instance they exhibit more pronounced fluorescence response for AT-rich polynucleotides than GC-rich polynucleotides, and both give only negligible response to ds-RNA. The fluorimetric response of 1 is proportional to the AT-basepair content in DNA, while the fluorescence of 2 is sensitive to secondary structure of polynucleotide. Fluorescence experiments, thermal melting experiments and circular dichroism studies reveal that 1 interacts with ds-DNA in a combined intercalation and minor groove binding, while 2 interacts mainly with the outer surface of DNA/RNA. As 1 and 2 have a very low cytotoxicity, 1 can be applied for the imaging of nuclear DNA in cells
Synthesis and Demonstration of the Biological Relevance of sp3 -rich Scaffolds Distantly Related to Natural Product Frameworks.

The productive exploration of chemical space is an enduring challenge in chemical biology and medicinal chemistry. Natural products are biologically relevant, and their frameworks have facilitated chemical tool and drug discovery. A "top-down" synthetic approach is described that enabled a range of complex bridged intermediates to be converted with high step efficiency into 26 diverse sp3 -rich scaffolds. The scaffolds have local natural product-like features, but are only distantly related to specific natural product frameworks. To assess biological relevance, a set of 52 fragments was prepared, and screened by high-throughput crystallography against three targets from two protein families (ATAD2, BRD1 and JMJD2D). In each case, 3D fragment hits were identified that would serve as distinctive starting points for ligand discovery. This demonstrates that frameworks that are distantly related to natural products can facilitate discovery of new biologically relevant regions within chemical space.Peer-reviewedPublisher Versio
First principles calculation of the reaction rates for ligand binding to myoglobin: the cases of NO and CO

Ligand binding by proteins is among the most fundamental processes in nature. Among these processes the binding of small gas molecules, such as O2, CO and NO to heme proteins has traditionally received vivid interest, which was further boosted by their recently recognized significant role in gas sensing in the body. At the heart of the binding of these ligands to the heme group is the spin-forbidden reaction between high-spin iron(II) and the ligand yielding a low spin adduct. We use computational means to address the complete mechanism of CO and NO binding by myoglobin. As it involves several steps occurring on different time-scales, molecular dynamics simulations were performed to address the diffusion of the ligand through the enzyme, and DFT calculations in combination with statistical rate calculation to investigate the spin-forbidden reaction. The calculations yielded rate constants in qualitative agreement with experiment and revealed that the bottle-neck of NO and CO binding is different: for NO diffusion was found to be rate-limiting, while for CO the spin-forbidden step is the slowest
Recent advances in the synthesis of peptoid macrocycles.

Over the past two decades, developing medical applications for peptides has, and continues to be a highly active area of research. At present there are over 60 peptide-based drugs on the market and more than 140 in various stages of clinical trials. The interest in peptide-based therapeutics arises from their biocompatibility and their ability to form defined secondary and tertiary structures, resulting in a high selectivity for complex targets. However, there are significant challenges associated with the development of peptide-based therapeutics, namely peptides are readily metabolised in vivo. Peptoids are an emerging class of peptidomimetic and they offer an alternative to peptides. Peptoids are comprised of N-substituted glycines where side-chains are located on the nitrogen atom of the amide backbone rather than the α-carbon as is the case in peptides. This change in structure confers a high degree of resistance to proteolytic degradation but the absence of any backbone hydrogen bonding means that peptoids exhibit a high degree of conformational flexibility. Cyclisation has been explored as one possible route to rigidify peptoid structures, making them more selective, and, therefore more desirable as potential therapeutics. This review outlines the various strategies that have been developed over the last decade to access new types of macrocyclic peptoids
Synthesis of α-l -Fucopyranoside-Presenting Glycoclusters and Investigation of Their Interaction with Photorhabdus asymbiotica Lectin (PHL)

Photorhabdus asymbiotica is a gram-negative bacterium that is not only as effective an insect pathogen as other members of the genus, but it also causes serious diseases in humans. The recently identified lectin PHL from P. asymbiotica verifiably modulates an immune response of humans and insects, which supports the idea that the lectin might play an important role in the host-pathogen interaction. Dimeric PHL contains up to seven Lfucose specific binding sites per monomer, and in order to target multiple binding sites of PHL, a-L-fucoside-containing di-, tri- and tetravalent glycoclusters were synthesized. Methyl gallate and pentaerythritol were chosen as multivalent scaffolds, and the fucoclusters were built from the above-mentioned cores by coupling with different oligoethylene bridges and propargyl a-L-fucosides using 1,3-dipolar azide-alkyne cycloaddition. The interaction between fucoside derivates and PHL was investigated by several biophysical and biological methods, ITC and SPR measurements, hemagglutination inhibition assay and an investigation of bacterial aggregation properties were carried out. Moreover, details of the interaction between PHL and propargyl a-L-fucoside as a monomer unit were revealed using X-ray crystallography. Besides this, the interaction with multivalent compounds was studied by NMR techniques. The newly synthesized multivalent fucoclusters proved to be up to several orders of magnitude better ligands than the \ud
natural ligand, L-fucose
Polymorphism, weak interactions and phase transitions in chalcogen-phosphorus heterocycles

We would like to thank the ERC (EU FP7 Consolidator Grant 614290 “EXONMR”) and EPSRC for computational support through the Collaborative Computational Project on NMR Crystallography (CCP-NC), via EP/M022501/1 and EP/J010510/1. SEA would like to thank the Royal Society and the Wolfson Foundation for a merit award. The research data (and/or materials) supporting this publication can be accessed at DOI: 10.17630/d0b365a1-b647-4556-b6f8-24d99d0c7a8a.A series of novel P-E containing heterocycles with aromatic backbones were synthesised and characterized by single crystal and powder X-ray diffraction, microanalysis and mass spectrometry. 31P and 77Se solution- and solid-state NMR spectroscopy revealed significant differences between the NMR parameters in solution and in the solid state, related to conformational changes in the molecules. Many compounds were shown to exhibit a number of different polymorphic structures (identified by single-crystal XRD), although the bulk material studied by solid-state NMR often contained just one major polymorph. For the unoxidised heterocycles, the presence of weak intermolecular J couplings were also investigated using DFT calcaulations.Publisher PDFPeer reviewe
Bifunctional Squaramide Organocatalysts for the Asymmetric Addition of Formaldehyde tert-Butylhydrazone to Simple Aldehydes

The nucleophilic addition of formaldehyde tert-butylhydrazone to simple aldehydes (a formal hetero-carbonyl–ene reaction) can be performed with good reactivity and excellent enantioselectivity by virtue of the dual hydrogen-bonding activation exerted by amide–squaramide organocatalysts. The resulting hydroxydiazenes (azo alcohols) were isolated in high yields as enantiomerically enriched azoxy compounds after a regioselective azo-to-azoxy transformation. Subsequent derivatization provides an entry to relevant amino alcohols, oxazolidinones, and derivatives thereof.Peer Reviewe
Progress in lanthionine and protected lanthionine synthesis

: Lanthionine (Lan), a non-proteinogenic natural amino acid, is an essential component of peptidoglycan found in the cell wall of Fusobacterium species. Lan and -methyllanthionine are also key constituents in lantibiotics, a prevalent class of peptide antibiotics. The development of those new antibacterial drugs with enhanced properties is the focus of recent research. Since multiple isomers of Lan are possible, a regio- and diastereoselective synthesis is challenging. This comprehensive review summarizes the known chemical syntheses of lanthionine from various precursors (e.g., -chloroalanine, cystine, dehydroalanine, -iodoalanine, aziridine, serine lactone, sulfamidate) since 1941. Methods for preparation of unprotected, protected, orthogonally protected, and mutually orthogonally protected lanthionine with relevant experimental details and perspectives on their usefulness are provided. The potential of these Lan derivatives is illustrated by one recent application. This review includes 102 references.Peer reviewe
Chemically Tunable Formation of Different Discrete, Oligomeric, and Polymeric Self‐Assembled Structures from Digold Metallotweezers

Digold metallotweezers whose complex supramolecular landscape is controlled by adding a series of metal cations are described. The metallotweezers have a strong tendency to form interesting supramolecular structures on addition of Tl+, Ag+, and Cu+. The choice of the cation can be used to direct the formation of a designated molecular architecture. The addition of thallium facilitates the formation of a self‐aggregated duplex structure in which the cation occupies the cavity of the dimer. The same type of structure is formed when Cu+ is added, and the resulting duplex inclusion complex shows interesting vapochromic properties. This copper‐encapsulating system evolves in solution to a 1D helical supramolecular polymer showing multiple aurophilic and Au⋅⋅⋅Cu interactions, in which the copper cation is bound to several alkynyl ligands of the tweezer. The addition of a small amount of silver cations to the digold tweezer yields a similar type of inclusion dimer complex, but adding an excess of the cation produces new discrete molecules presumably exhibiting multiple Au⋅⋅⋅Au, Au⋅⋅⋅Ag, and Ag⋅⋅⋅Ag metallophilic interactions. The differences in the supramolecular structures formed are ascribed to the different tendencies of the metal cations to exhibit interactions with the gold atoms and to coordinate to the alkynyl ligands of the tweezer
Redox-Driven Transformation of a Discrete Molecular Cage into an Infinite 3D Coordination Polymer

Two M12L6 redox‐active self‐assembled cages constructed from an electron‐rich ligand based on the extended tetrathiafulvalene framework (exTTF) and metal complexes with a linear geometry (PdII and AgI) are depicted. Remarkably, based on a combination of specific structural and electronic features, the polycationic self‐assembled AgI coordination cage undergoes a supramolecular transformation upon oxidation into a three‐dimensional coordination polymer, that is characterized by X‐ray crystallography. This redox‐controlled change of the molecular organization results from the drastic conformational modifications accompanying oxidation of the exTTF moiety