pinecone/core-2020-05-10-deduplication huggingface dataset:
Dynamic covalent nanoparticle building blocks

The author thanks the Royal Society of Edinburgh and Scottish Government for a personal research fellowship and gratefully acknowledge the EPSRC (EP/K016342/1) and Leverhulme Trust (RPG-2015-042) for funding our work on dynamic nanomaterials.Rational and generalizable methods for engineering surface functionality will be crucial to realizing the technological potential of nanomaterials. Nanoparticle-bound dynamic covalent exchange combines the error-correcting and environment-responsive features of equilibrium processes with the stability, structural precision and vast diversity of covalent chemistry, defining a new and powerful approach for manipulating structure, function and properties at nanomaterial surfaces. Dynamic covalent nanoparticle (DCNP) building blocks thus present a whole host of possibilities for constructing adaptive systems, devices and materials that incorporate both nanoscale and molecular functional components. At the same time, DCNPs have the potential to reveal fundamental insights regarding dynamic and complex chemical systems confined to nanoscale interfaces.Publisher PDFPeer reviewe
Modular construction of fluoroarenes from a new difluorinated building block via cross-coupling/electrocyclisation/ dehydrofluorination reactions

Palladium-catalysed coupling reactions based on a novel and easy-to-synthesise difluorinated organotrifluoroborate were used to assemble precursors to 6π-electrocyclisations of three different types. Electrocyclisations took place at temperatures between 90 and 240 oC, depending on the central component of the π-system; non-aromatic trienes were most reactive, but even systems which required the temporary dearomatisation of two arenyl sub-units underwent electrocyclisation, albeit at elevated temperatures. Photochemical conditions were effective for these more demanding reactions. The package of methods delivered a structurally-diverse set of fluorinated arenes, spanning a 20 kcal mol-1 range of reactivity, by a flexible route
Toward fluorescence-based high-throughput screening for enantiomeric excess in amines and amino acid derivatives

A highly accurate and reliable screening method for enantiomeric excess of amine derivatives in the presence of water is reported. The fluorescence-based screening system has been realized by self-assembly of chiral diol-type dyes (BINOL, VANOL and VAPOL), 2-formylphenylboronic acid, and chiral amines forming iminoboronate esters. The structure and chirality of the amine analytes determine the stability of the diastereomeric iminoboronate esters, which in turn display differential fluorescence. The fluorescence signal reflects the enantiomeric purity of the chiral amines and was utilized in high-throughput arrays. The arrays were able to recognize enantiomeric excess of amines, amino esters, and amino alcohols. In addition to qualitative analysis, quantitative experiments were successfully performed. Studies of the role of additives such as water or citrate were carried out to gain insight into the stability of the iminoboronate esters. It is shown that the above additives destabilize less stable esters while the stable esters remain unchanged. Thus, the presence of water and citrate leads to increased difference between the diastereomeric iminoboronates and contributes to the enantiodiscrimination of the chiral amines
The catalytic mechanism of the marine-derived macrocyclase PatGmac

This work received financial support from the European Union (FEDER funds through COMPETE) and National Funds (Fundação para a Ciência e Tecnologia, FCT) through Projects EXCL/QEQ-COM/0394/2012, EXCL-II/QEQ-COM/0394/2012, and Pest-C/EQB/LA0006/2013. N.F.B. would like to thank the FCT for her IF starting grant (IF/01355/2014).Cyclic peptides are a class of compounds with high therapeutic potential, possessing bioactivities including antitumor and antiviral (including anti-HIV). Despite their desirability, efficient design and production of these compounds has not been achieved to date. The catalytic mechanism of patellamide macrocyclization by the PatG macrocyclase domain has been computationally investigated by using quantum mechanics/molecular mechanics methodology, specifically ONIOM(M06/6-311++G(2d,2p):ff94//B3LYP/6-31G(d):ff94). The mechanism proposed herein begins with a proton transfer from Ser783 to His 618 and from the latter to Asp548. Nucleophilic attack of Ser783 on the substrate leads to the formation of an acyl–enzyme covalent complex. The leaving group Ala-Tyr-Asp-Gly (AYDG) of the substrate is protonated by the substrate's N terminus, leading to the breakage of the P1−P1′ bond. Finally, the substrate's N terminus attacks the P1 residue, decomposing the acyl–enzyme complex forming the macrocycle. The formation and decomposition of the acyl–enzyme complex have the highest activation free energies (21.1 kcal mol−1 and 19.8 kcal mol−1 respectively), typical of serine proteases. Understanding the mechanism behind the macrocyclization of patellamides will be important to the application of the enzymes in the pharmaceutical and biotechnological industries.PostprintPostprintPeer reviewe
Reductive coupling of diynes at rhodium gives fluorescent\ud
rhodacyclopentadienes or phosphorescent rhodium 2,2’-biphenyl complexes.

Reactions of [Rh(κ2-O,O-acac)(PMe3)2] (acac=acetylacetonato) and α,ω-bis(arylbutadiynyl)alkanes afford two isomeric types of MC4 metallacycles with very different photophysical properties. As a result of a [2+2] reductive coupling at Rh, 2,5-bis(arylethynyl)rhodacyclopentadienes (A) are formed, which display intense fluorescence (Φ=0.07–0.54, τ=0.2–2.5 ns) despite the presence of the heavy metal atom. Rhodium biphenyl complexes (B), which show exceptionally long-lived (hundreds of μs) phosphorescence (Φ=0.01–0.33) at room temperature in solution, have been isolated as a second isomer originating from an unusual [4+2] cycloaddition reaction and a subsequent β-H-shift. We attribute the different photophysical properties of isomers A and B to a higher excited state density and a less stabilized T1 state in the biphenyl complexes B, allowing for more efficient intersystem crossing S1[RIGHTWARDS ARROW]Tn and T1[RIGHTWARDS ARROW]S0. Control of the isomer distribution is achieved by modification of the bis- (diyne) linker length, providing a fundamentally new route to access photoactive metal biphenyl compound
A Molecular Rotor that Measures Dynamic Changes of Lipid Bilayer Viscosity Caused by Oxidative Stress

Oxidation of cellular structures is typically an undesirable process that can be a hallmark of certain diseases. On the other hand, photooxidation is a necessary step of photodynamic therapy (PDT), a cancer treatment causing cell death upon light irradiation. Here, the effect of photooxidation on the microscopic viscosity of model lipid bilayers constructed of 1,2-dioleoyl-sn-glycero-3-phosphocholine has been studied. A molecular rotor has been employed that displays a viscosity-dependent fluorescence lifetime as a quantitative probe of the bilayer's viscosity. Thus, spatially-resolved viscosity maps of lipid photooxidation in giant unilamellar vesicles (GUVs) were obtained, testing the effect of the positioning of the oxidant relative to the rotor in the bilayer. It was found that PDT has a strong impact on viscoelastic properties of lipid bilayers, which ‘travels’ through the bilayer to areas that have not been irradiated directly. A dramatic difference in viscoelastic properties of oxidized GUVs by Type I (electron transfer) and Type II (singlet oxygen-based) photosensitisers was also detected
Heterogenized water oxidation catalysts prepared by immobilizing Klaui-type organometallic precursors

An efficient heterogenized water oxidation catalyst (2_TiO2) has been synthesized by immobilizing the Kläui-type organometallic precursor [Cp*Ir{P(O)(OH)2}3]Na (2, Cp*=1,2,3,4,5-pentamethylcyclopentadienyl ligand) onto rutile TiO2. Iridium is homogeneously distributed at the molecular and atomic/small cluster level in 2_TiO2 and 2'_TiO2 (solid catalyst recovered after the first catalytic run), respectively, as indicated by STEM-HAADF (scanning transmission electron microscopy - high angle annular dark field) studies. 2'_TiO2 exhibits TOF values up to 23.7 min-1 in the oxidation of water to O2 driven by NaIO4 at nearly neutral pH, and a TON only limited by the amount of NaIO4 used, as indicated by multiple run experiments. Furthermore, while roughly 40¿% leaching is observed during the first catalytic run, 2'_TiO2 does not undergo any further leaching even when in contact with strongly basic solutions and completely maintains its activity for thousands of cycles. NMR studies, in combination with ICP-OES (inductively coupled plasma optical emission spectrometry), indicate that the activation of 2_TiO2 occurs through the initial oxidative dissociation of PO43-, ultimately leading to active centers in which a 1:1 P/Ir ratio is present (derived from the removal of two PO43- units) likely missing the Cp* ligand.Peer ReviewedPostprint (author's final draft
Selective Hydrogenation of Acrolein Over Pd Model Catalysts: Temperature and Particle-Size Effects

In this work, the selectivity in hydrogenation of acrolein over Fe 3 O 4 -supported Pd nanoparticles is investigated as a function of nanoparticle size in the 220-270 K temperature range. While Pd(111) shows nearly 100% selectivity towards the desired hydrogenation of the C=O bond to produce propenol, Pd nanoparticles were found to be much less selective towards this product. In-situ detection of surface species using infrared-reflection absorption spectroscopy shows that the selectivity towards propenol critically depends on the formation of an oxopropyl spectator 
species.  While an overlayer of oxopropyl species is effectively formed on Pd(111) turning the surface highly selective for propenol formation, this process is strongly hindered on Pd nanoparticles by acrolein decomposition resulting in CO formation. We show that the extent of 
acrolein decomposition can be tuned by varying the particle size and the reaction temperature. As a result, significant production of propenol is observed over 12 nm Pd nanoparticles at 250 K, while smaller (4 and 7 nm) nanoparticles did not produce propenol at any of the temperatures investigated. The possible origin of particle size dependence of propenol formation is discussed. 
This work demonstrates that the selectivity in hydrogenation of acrolein is controlled by the relative rates of acrolein partial hydrogenation to oxopropyl surface species and of acrolein decomposition, which has significant implications for rational catalyst design
Preferential 5-Methylcytosine Oxidation in the Linker Region of Reconstituted Positioned Nucleosomes by Tet1 Protein

Tet (ten-eleven translocation) family proteins oxidize 5-methylcytosine (mC) to 5-hydroxymethylcytosine (hmC), 5-formylcytosine (fC), and 5-carboxycytosine (caC), and are suggested to be involved in the active DNA demethylation pathway. In this study, we reconstituted positioned mononucleosomes using CpG-methylated 382bp DNA containing the Widom 601 sequence and recombinant histone octamer, and subjected the nucleosome to treatment with Tet1 protein. The sites of oxidized methylcytosine were identified by bisulfite sequencing. We found that, for the oxidation reaction, Tet1 protein prefers mCs located in the linker region of the nucleosome compared with those located in the core region
Asymmetric total synthesis of (-)-erogorgiaene and its C11 epimer and investigation of their antimycobacterial activity

This is the peer reviewed version of the following article: INCERTI-PRADILLOS, C.A. ... et al, 2016. Asymmetric total synthesis of (-)-erogorgiaene and its C11 epimer and investigation of their antimycobacterial activity. Chemistry - A European Journal, 22 (40), pp. 14390-14396., which has been published in final form at http://dx.doi.org/10.1002/chem.201602440. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Self-Archiving.A short, nine-step, highly enantioselective synthesis of (−)-erogorgiaene and its C-11 epimer is reported. The key stereochemistry controlling steps involve catalytic asymmetric crotylation, anionic oxy-Cope rearrangement and cationic cyclisation. (−)-Erogorgiaene exhibited promising antitubercular activity against multidrug-resistant strains of Mycobacterium tuberculosis
Aromatic cluster sensor of protein folding: near-UV ECD bands\ud
assigned to fold compactness\ud

Both far- and near-UV ECD spectra have bands sensitive to thermal unfolding of Trp and Tyr residues containing proteins. Beside spectral changes at 222 nm reporting secondary structural variations (far-UV range), Lb bands (near-UV range) are applicable as 3D-fold sensors of protein’s core structure. In this study we show that both Lb(Tyr) and Lb(Trp) ECD bands could be used as sensors of fold compactness. ECD is a relative method and thus requires NMR referencing and cross-validation, also provided here.\ud
The ensemble of 204 ECD spectra of Trp-cage miniproteins is analysed as training set for “calibrating” Trp↔Tyr folded systems of known NMR structure. While in the far-UV ECD spectra changes are linear as function of the temperature, near-UV ECD data indicate a non-linear and thus, cooperative unfolding mechanism of these proteins. Ensemble of ECD spectra deconvoluted gives both conformational weights\ud
and insight to protein folding↔unfolding mechanism. We found that the Lb293 band is reporting on the 3D-structure compactness. In addition, the pure near-UV ECD spectrum of the unfolded state is described here for the first time. Thus, ECD folding information now validated can be applied with confidence in a large thermal window (5≤T≤85 °C) compared to NMR for studying the unfolding of Trp↔Tyr residue pairs. In conclusion, folding propensities of important proteins (RNA polymerase II, ubiquitin protein\ud
ligase, tryptase-inhibitor etc.) can now be analysed with higher confidence.\u
Paramagnetic NMR of phenolic oxime copper complexes: a joint experimental and density functional study

This work was supported by EaStCHEM and the School of Chemistry. The authors would like to thank the EPSRC for computational support through the Collaborative Computational Project on NMR Crystallography (CCP-NC), via EP/M022501/1 and EP/J501542/1. SEA would like to thank the Royal Society and Wolfson Foundation for a merit award. Work at the TU Berlin has been carried out within the EU Marie-Curie Initial Training Network “pNMR”.1H and 13C pNMR properties of bis(salicylaldoximato)copper(II) were studied in the solid state using magic-angle-spinning NMR spectroscopy and, for the isolated complex and selected oligomers, using density-functional theory at the PBE0-1/3 // PBE0-D3 level. Large paramagnetic shifts are observed, up to δ(1H) = 272 ppm and δ(13C) = 1006 ppm (at 298 K), which are rationalised through spin delocalisation from the metal onto the organic ligand and the resulting contact shifts arising from hyperfine coupling. The observed shift ranges are best reproduced computationally using exchange-correlation functionals with a high fraction of exact exchange (such as PBE0-1/3). Through a combination of experimental techniques and first-principles computation, a near-complete assignment of the observed signals is possible. Intermolecular effects on the pNMR shifts, modelled computationally in the dimers and trimers through effective decoupling between the local spins via A-tensor and total spin rescaling in the pNMR expression, are indicated to be small. Addition of electron-donating substituents and benzannelation of the organic ligand is predicted computationally to induce notable changes in the NMR signal pattern, suggesting that pNMR spectroscopy can be a sensitive probe for the spin distribution in paramagnetic phenolic oxime copper complexes.PostprintPeer reviewe
Water-soluble triarylborane chromophores for one- and two-photon excited fluorescence imaging of mitochondria in cells.

Three water-soluble tetracationic quadrupolar chromophores comprising two three-coordinate boron π-acceptor groups bridged by thiophene-containing moieties were synthesised for biological imaging applications. Compound 3 containing the bulkier 5-(3,5-Me2C6H2)-2,2′-(C4H2S)2-5′-(3,5-Me2C6H2) bridge is stable over a long period of time, exhibits a high fluorescence quantum yield and strong one- and two-photon absorption (TPA), and has a TPA cross section of 268 GM at 800 nm in water. Confocal laser scanning fluorescence microscopy studies in live cells indicated localisation of the chromophore at the mitochondria; moreover, cytotoxicity measurements proved biocompatibility. Thus, chromophore 3 has excellent potential for one- and two-photon-excited fluorescence imaging of mitochondrial function in cells
Structural diversity in alkali metal and alkali metal magnesiate chemistry of the bulky 2,6-diisopropyl-N-(trimethylsilyl)anilino ligand

Bulky amido ligands are precious in s-block chemistry since they can implant complementary strong basic and weak nucleophilic properties within compounds. Recent work has shown the pivotal importance of the base structure with enhancement of basicity and extraordinary regioselectivities possible for cyclic alkali metal magnesiates containing mixed n-butyl/amido ligand sets. This work advances alkali metal and alkali metal magnesiate chemistry of the bulky aryl-silyl amido ligand [N(SiMe3)(Dipp)] (Dipp = 2,6-iPr2-C6H3). Infinite chain structures of the parent sodium and potassium amides are disclosed, adding to the few known crystallographically characterised unsolvated s-block metal amides. Solvation by PMDETA or TMEDA gives molecular variants of the lithium and sodium amides; whereas for potassium, PMDETA gives a molecular structure but TMEDA affords a novel, hemi-solvated infinite chain. Crystal structures of the first magnesiate examples of this amide in [MMg{N(SiMe3)(Dipp)}2(μ-nBu)]∞ (M = Na or K), are also revealed though these breakdown to their homometallic components in donor solvent as revealed through NMR and DOSY studies
Prenucleation self-assembly and chiral discrimination mechanisms during solution crystallisation of racemic diprophylline

The crystallisation behaviour of (RS)-diprophylline (DPL) in two different solvents is investigated to assess the incidence of solvated pre-associations on nucleation, crystal growth and chiral discrimination. In the solvated state, Raman spectroscopy shows that dimeric associations similar to those depicted in the crystalline solid solution (ssRII) predominate in isopropanol (IPA), which may account for the systematic spontaneous nucleation of this crystal form from this solvent. By contrast, spontaneous nucleation in DMF yields the stable racemic compound RI, consistently with the distinct features of the Raman spectrum collected in this solvent. A crystal growth study of ssRII in IPA reveals that the crystal habitus is impacted by the solution enantiomeric excess; this is explained by increased competition between homo- and heterochiral pre-associations. This is supported by a molecular modelling study on the enantiomeric selectivity of the DPL crystal lattices. The combination of assessment methods on solution chemistry, nucleation and chiral discrimination provides methodological tools from which the occurrence of solid solutions can be rationalised
Cyclobuteno[60]fullerenes as efficient n-type organic\ud
semiconductors

Cyclobuteno[3,4:1,2][60]fullerenes have been prepared in a straightforward manner by a simple reaction between [60]fullerene and readily available allenoates or alkynoates as organic reagents under basic and mild conditions. The chemical structure of the new modified fullerenes has been determined by standard spectroscopic techniques and confirmed by X-Ray diffraction analysis. Some of these new fullerene derivatives exhibit a remarkable intrinsic electron mobility – determined by using flash-photolysis time-resolved microwave conductivity (FP-TRMC) measurements – which surpasses that of the well-known PCBM, thus behavi ng as promising n-type organic semiconductors
The relationship between NMR chemical shifts of thermally polarized and hyperpolarized 89Y complexes and their solution structures

[Abstract] Recently developed dynamic nuclear polarization (DNP) technology offers the potential of increasing the NMR sensitivity of even rare nuclei for biological imaging applications. Hyperpolarized 89Y is an ideal candidate because of its narrow NMR linewidth, favorable spin quantum number (I= ), and long longitudinal relaxation times (T1). Strong NMR signals were detected in hyperpolarized 89Y samples of a variety of yttrium complexes. A dataset of 89Y NMR data composed of 23 complexes with polyaminocarboxylate ligands was obtained using hyperpolarized 89Y measurements or 1H,89Y-HMQC spectroscopy. These data were used to derive an empirical equation that describes the correlation between the 89Y chemical shift and the chemical structure of the complexes. This empirical correlation serves as a guide for the design of 89Y sensors. Relativistic (DKH2) DFT calculations were found to predict the experimental 89Y chemical shifts to a rather good accuracy.España. Ministerio de Economía y Competitividad (CTQ2013-43243-P)España. Ministerio de Economía y Competitividad (CTQ2015-71211-REDT)Estados Unidos. National Institutes of Health (EB-015908)Estados Unidos. National Institutes of Health (CA-115531)Estados Unidos. Robert A. Welch Foundation (AT-584
Structural and mechanistic insights into s-block bimetallic catalysis : sodium magnesiate-catalyzed guanylation of amines

To advance the catalytic applications of s-block mixed-metal complexes, sodium magnesiate [NaMg(CH2SiMe3)3] (1) is reported as an efficient precatalyst for the guanylation of a variety of anilines and secondary amines with carbodiimides. First examples of hydrophosphination of carbodiimides by using a Mg catalyst are also described. The catalytic ability of the mixed-metal system is much greater than that of its homometallic components [NaCH2SiMe3 ] and [Mg(CH2SiMe3)2]. Stoichiometric studies suggest that magnesiate amido and guanidinate complexes are intermediates in these catalytic routes. Reactivity and kinetic studies imply that these guanylation reactions occur via (tris)amide intermediates that react with carbodiiimides in insertion steps. The rate law for the guanylation of N,N'-diisopropylcarbodiimide with 4-tert-butylaniline catalyzed by 1 is first order with respect to [amine], [carbodiimide], and [catalyst], and the reaction shows a large kinetic isotopic effect, which is consistent with an amine-assisted rate-determining carbodiimide insertion transition state. Studies to assess the effect of sodium in these transformations denote a secondary role with little involvement in the catalytic cycle
A new generation of smart amine donors for transaminase-mediated biotransformations

The application of ω-transaminase biocatalysts for the synthesis of optically pure chiral amines presents a number of challenges, including difficulties associated with displacing the challenging reaction equilibria. Herein, we report a highly effective approach using low equivalents of the novel diamine donor, cadaverine, which enables high conversions of challenging substrates to the corresponding chiral amines in excellent ee. This approach paves the way for the design of self-sufficient fermentation processes combining transaminase biotransformations with existing strategies for cadaverine production via decarboxylation of endogenous lysine