pinecone/core-2020-05-10-deduplication huggingface dataset:
A structural, spectroscopic and computational examination of the dative interaction in constrained phosphine–stibines and phosphine–stiboranes

This work was financially supported by the EPSRC and COST actions CM0802 PhoSciNet and CM1302 SIPs.A series of phosphine–stibine and phosphine–stiborane peri–substituted acenaphthenes containing all permutations of pentavalent groups –SbClnPh4-n (5–9), as well as trivalent groups –SbCl2, –Sb(R)Cl, and –SbPh2 (2–4, R = Ph, Mes), were synthesised and fully characterised including single crystal diffraction and multinuclear NMR. In addition, the bonding in these species was studied by DFT computational methods. The P–Sb dative interactions in both series range from strongly bonding to non-bonding as the Lewis acidity of the Sb acceptor is decreased. In the pentavalent antimony series, a significant change in the P–Sb distance is observed between –SbClPh3 and –SbCl2Ph2 derivatives 6 and 7, consistent with a change from a bonding to a non-bonding interaction in a response to relatively small change in Lewis acidity of the acceptor. In the SbIII series, two geometric forms are observed. The P–Sb bond length in the SbCl2 derivative 2 is as expected for a normal (rather than a dative) bond. Rather unexpectedly, the phosphine–stiborane complexes 5–9 represent the first examples of σ4P→σ6Sb structural motif.PostprintPeer reviewe
Synthetic Active Site Model of the [NiFeSe] Hydrogenase

A dinuclear synthetic model of the [NiFeSe] hydrogenase active site and a structural, spectroscopic and electrochemical analysis of this complex is reported. [NiFe(‘S2Se2’)(CO)3] (H2‘S2Se2’=1,2-bis(2-thiabutyl-3,3-dimethyl-4-selenol)benzene) has been synthesized by reacting the nickel selenolate complex [Ni(‘S2Se2’)] with [Fe(CO)3bda] (bda=benzylideneacetone). X-ray crystal structure analysis confirms that [NiFe(‘S2Se2’)(CO)3] mimics the key structural features of the enzyme active site, including a doubly bridged heterobimetallic nickel and iron center with a selenolate terminally coordinated to the nickel center. Comparison of [NiFe(‘S2Se2’)(CO)3] with the previously reported thiolate analogue [NiFe(‘S4’)(CO)3] (H2‘S4’=H2xbsms=1,2-bis(4-mercapto-3,3-dimethyl-2-thiabutyl)benzene) showed that the selenolate groups in [NiFe(‘S2Se2’)(CO)3] give lower carbonyl stretching frequencies in the IR spectrum. Electrochemical studies of [NiFe(‘S2Se2’)(CO)3] and [NiFe(‘S4’)(CO)3] demonstrated that both complexes do not operate as homogenous H2 evolution catalysts, but are precursors to a solid deposit on an electrode surface for H2 evolution catalysis in organic and aqueous solution.This work was supported by the Engineering and Physical Sciences
Research Council (EP/H00338X/2), the Christian Doppler
Research Association, and the OMV group. We thank Mr Dirk
Mersch for recording SEM and EDX, Dr John Davies for collecting
and refining the crystallographic data, and the National
EPSRC XPS User’s Service (NEXUS) at Newcastle University for
recording XPS data. Benjamin C. M. Martindale is acknowledged
for his help with XPS analysis. Dr Christine Caputo and
Janina Willkomm are acknowledged for helpful comments.This is the final published version. It first appeared at http://onlinelibrary.wiley.com/doi/10.1002/chem.201500311/abstract
Stabilization of a Bimolecular Triplex by 3′-S-Phosphorothiolate Modifications: An NMR and UV Thermal Melting Investigation

YesTriplexes formed from oligonucleic acids are key to a number of biological processes. They have attracted attention as molecular biology tools and as a result of their relevance in novel therapeutic strategies. The recognition properties of single-stranded nucleic acids are also relevant in third-strand binding. Thus, there has been considerable activity in generating such moieties, referred to as triplex forming oligonucleotides (TFOs). Triplexes, composed of Watson–Crick (W–C) base-paired DNA duplexes and a Hoogsteen base-paired RNA strand, are reported to be more thermodynamically stable than those in which the third strand is DNA. Consequently, synthetic efforts have been focused on developing TFOs with RNA-like structural properties. Here, the structural and stability studies of such a TFO, composed of deoxynucleic acids, but with 3′-S-phosphorothiolate (3′-SP) linkages at two sites is described. The modification results in an increase in triplex melting temperature as determined by UV absorption measurements. 1H NMR analysis and structure generation for the (hairpin) duplex component and the native and modified triplexes revealed that the double helix is not significantly altered by the major groove binding of either TFO. However, the triplex involving the 3′-SP modifications is more compact. The 3′-SP modification was previously shown to stabilise G-quadruplex and i-motif structures and therefore is now proposed as a generic solution to stabilising multi-stranded DNA structures
Supramolecular Interaction of Fullerenes with a Curved π-Surface of a Monomeric Quadruply Ring-Fused Porphyrin

Molecular binding of fullerenes, C60 and C70, with the ZnII complex of a monomeric ring-fused porphyrin derivative (2-py) as a host molecule, which has a concave π-conjugated surface, has been confirmed spectroscopically. The structures of associated complexes composed of fullerenes and 2-py were explicitly established by X-ray diffraction analysis. The fullerenes in the 2:1 complexes, which consist of two 2-py molecules and one fullerene molecule, are fully covered by the concave surfaces of the two 2-py molecules in the crystal structure. In contrast, in the crystal structure of the 1:1 complex consisting of one 2-py molecule and one C60 molecule, the C60 molecule formed a π–π stacked pair with a C60 molecule in the neighboring complex using a partial surface, which was uncovered by the 2-py molecule. Additionally, the molecular size of fullerene adopted significantly affects the 1H NMR spectral changes and the redox properties of 2-py upon the molecular binding
Coordination polymer flexibility leads to polymorphism and enables a crystalline solid-vapour reaction : a multi-technique mechanistic study

Despite an absence of conventional porosity, the 1D coordination polymer [Ag4(O2C(CF2)2CF3)4(TMP)3] ( 1 ; TMP=tetramethylpyrazine) can absorb small alcohols from the vapour phase, which insert into AgO bonds to yield coordination polymers [Ag4(O2C(CF2)2CF3)4(TMP)3(ROH)2] ( 1-ROH ; R=Me, Et, iPr). The reactions are reversible single-crystal-to-single-crystal transformations. Vapour-solid equilibria have been examined by gas-phase IR spectroscopy (K=5.68(9)×10−5 (MeOH), 9.5(3)×10−6 (EtOH), 6.14(5)×10−5 (iPrOH) at 295 K, 1 bar). Thermal analyses (TGA, DSC) have enabled quantitative comparison of two-step reactions 1-ROH 1 2 , in which 2 is the 2D coordination polymer [Ag4(O2C(CF2)2CF3)4(TMP)2] formed by loss of TMP ligands exclusively from singly-bridging sites. Four polymorphic forms of 1 ( 1-ALT , 1-AHT , 1-BLT and 1-BHT ; HT=high temperature, LT=low temperature) have been identified crystallographically. In situ powder X-ray diffraction (PXRD) studies of the 1-ROH 1 2 transformations indicate the role of the HT polymorphs in these reactions. The structural relationship between polymorphs, involving changes in conformation of perfluoroalkyl chains and a change in orientation of entire polymers (A versus B forms), suggests a mechanism for the observed reactions and a pathway for guest transport within the fluorous layers. Consistent with this pathway, optical microscopy and AFM studies on single crystals of 1-MeOH / 1-AHT show that cracks parallel to the layers of interdigitated perfluoroalkyl chains develop during the MeOH release/uptake process
Cross-aldol reactions of ketones catalyzed by leucinol: a mechanistic investigation

This is the peer reviewed version of the following article: MALKOV, A.V. ...et al., 2015. Cross-aldol reactions of ketones catalyzed by leucinol: a mechanistic investigation. Chemistry - A European Journal, 21 (34), pp. 12026-12033, which has been published in final form at http://dx.doi.org/10.1002/chem.201500536. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Self-Archiving."Comprehensive mechanistic studies on the enantioselective aldol reaction between isatin (1 a) and acetone, catalyzed by L-leucinol (3 a), unraveled that isatin, apart from being a substrate, also plays an active catalytic role. Conversion of the intermediate oxazolidine 4 into the reactive syn-enamine 6, catalyzed by isatin, was identified as the rate-determining step by both the calculations (ΔG≠=26.1 kcal mol−1 for the analogous L-alaninol, 3 b) and the kinetic isotope effect (kH/kD=2.7 observed for the reaction using [D6]acetone). The subsequent reaction of the syn-enamine 6 with isatin produces (S)-2 a (calculated ΔG≠=11.6 kcal mol−1). The calculations suggest that the overall stereochemistry is controlled by two key events: 1) the isatin-catalyzed formation of the syn-enamine 6, which is thermodynamically favored over its anti-rotamer 7 by 2.3 kcal mol−1; and 2) the high preference of the syn-enamine 6 to produce (S)-2 a on reaction with isatin (1 a) rather than its enantiomer (ΔΔG≠=2.6 kcal mol−1)
Are nanoparticles spherical or quasi-spherical?

This is the peer reviewed version of the following article: SOKOLOV, S.V. ... et al, 2015. Are nanoparticles spherical or quasi-spherical? Chemistry - A European Journal, 21 (30), pp. 10741 - 10746., which has been published in final form at http://dx.doi.org/10.1002/chem.201500807. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Self-Archiving."The geometry of quasi-spherical nanoparticles is\ud
investigated. The combination of SEM imaging and electrochemical\ud
nano-impact experiments is demonstrated to allow sizing and characterization of the geometry of single silver\ud
nanoparticles
Selective Single-Step Separation of a Mixture of Three Metal Ions by a Triphasic Ionic-Liquid-Water-Ionic-Liquid Solvent Extraction System

In a conventional solvent extraction system, metal
ions are distributed between two immiscible phases, typically an aqueous and an organic phase. In this paper, the proof-of-principle is given for the distribution of metal ions between three immiscible phases, two ionic liquid phases with an aqueous phase in between them. Three-liquid-phase solvent extraction allows separation of a mixture of three metal ions in a single step, whereas at least two steps are required to separate three metals in the case of two-liquid phase solvent extraction. In the triphasic system, the lower organic phase is comprised of the ionic liquid betainium- or choline bis(trifluoromethylsulfonyl)imide, whereas the upper
organic phase is comprised of the ionic liquid trihexyl(tetradecyl)phosphonium bis(trifluoromethylsulfonyl)imide. The triphasic system was used for the separation of a mixture of tin(II), yttrium(III), and scandium(III) ions.status: publishe
On the functional group tolerance of ester hydrogenation and polyester depolymerisation catalysed by ruthenium complexes of tridentate aminophosphine ligands

The synthesis of a range of phosphine-diamine, phosphine-amino-alcohol, and phosphine-amino-amide ligands and their ruthenium(II) complexes are reported. Five of these were characterised by X-ray crystallography. The activity of this collection of catalysts was initially compared for the hydrogenation of two model ester hydrogenations. Turnover frequencies up to 2400 h-1 were observed at 85 oC. The catalysts turnover, albeit slowly at near ambient temperatures. Using a phosphine diamine RuII complex that was identified as the most active catalyst, a range of aromatic esters were reduced in high yield. The hydrogenation of alkene-, diene-, and alkyne functionalised esters was also studied. Substrates with a remote, but reactive terminal alkene substitutent could be reduced chemoselectively in the presence of 4-dimethylaminopyridine (DMAP) co-catalyst. The chemoselective reduction of the ester function in conjugated dienoate ethyl sorbate could deliver (2E,4E)-hexa-2,4-dien-1-ol, a precursor to leaf alcohol. The mono-unsaturated alcohol (E)-hex-4-en-1-ol was produced with reasonable selectivity, but complete chemoselectivity of C=O over the diene is elusive. High chemoselectivity for the reduction of an ester over an alkyne group was observed in the hydrogenation of an alkynoate for the first time. The catalysts were also active in the depolymerisation reduction of samples of waste PET to produce benzene dimethanol. These depolymerisations were found to be poisoned by the ethylene glycol side product, although good yields could still be achieved.PostprintPeer reviewe
Radical CH Alkylation of BODIPY Dyes Using Potassium Trifluoroborates or Boronic Acids

A one-step synthetic procedure for the radical C-H alkylation of BODIPY dyes has been developed. This new reaction generates alkyl radicals through the oxidation of boronic acids or potassium trifluoroborates and allows the synthesis of mono-, di-, tri-, and tetraalkylated fluorophores in a good to excellent yield for a broad range of organoboron compounds. Using this protocol, multiple bulky alkyl groups can be introduced onto the BODIPY core thus creating solid-state emissive BODIPY dyes.status: publishe
Speciation control during Suzuki-Miyaura cross-coupling of haloaryl and haloalkenyl MIDA boronic esters

Boronic acid solution speciation can be controlled during the Suzuki-Miyaura cross-coupling of haloaryl MIDA boronic esters to enable the formal homologation of boronic acid derivatives. The reaction is contingent upon control of the basic biphase and is thermodynamically driven: temperature control provides highly chemoselective access to either BMIDA adducts at room temperature or BPin products at elevated temperature. Control experiments and solubility analyses have provided some insight into the mechanistic operation of the formal homologation process
A Tetraferrocenyl-Resorcinarene Cavitand as a Redox-Switchable Host of Ammonium Salts

Tetraannulation of a resorcinarene-octaamino cavitand with ferrocenecarboxaldehyde allows the preparation of a tetrabenzimidazole-resorcinarene cavitand with four ferrocenyl moieties directly linked to the C2 atom of the imidazole units. Oxidation of the four ferrocenyl moieties produces important structural modifications of the molecule, as indicated by DFT calculations performed for the neutral and tetraoxidized forms of the cavitand. By means of 1H NMR spectroscopic analysis, the encapsulating properties of the new tetraferrocenyl-resorcinarene cavitand toward a series of ammonium salts were evaluated, and a clear cutoff point in binding affinity with respect to size was observed. Cyclic voltammetric studies allowed us to estimate the relative association constants for the neutral and oxidized forms of the cavitand, thus indicating that the guest was bound to the neutral (reduced) state of the cavitand and was released from the oxidized form. These redox-addressable conformational and binding properties of the resorcinarene-tetraferrocenyl cavitand constitute all the necessary features of a redox-switchable molecular gripper. By means of mass-spectrometric analysis, we could unambiguously confirm the molar stoichiometry of the host–guest complex (1:1) and assess the strong guest encapsulation, as indicated by triggering the covalent coupling between host and guest in the gas phase.MEC of Spain (CTQ2011-24055/BQU and CTQ2014-54071-P) and the Universitat Jaume I (P11B2014-02
Circularly Polarized Luminescence from Simple Organic Molecules

This article aims to show the identity of “circularly polarized luminescent active simple organic molecules” as a new concept in organic chemistry due to the potential interest of these molecules, as availed by the exponentially growing number of research articles related to them. In particular, it describes and highlights the interest and difficulty in developing chiral simple (small and non-aggregated) organic molecules able to emit left- or right-circularly polarized light efficiently, the efforts realized up to now to reach this challenging objective, and the most significant milestones achieved to date. General guidelines for the preparation of these interesting molecules are also presented
Asymmetric isothiourea-catalysed formal [3+2] cycloadditions of ammonium enolates with oxaziridines

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 (C.F. and J.E.T.), GSK (CASE award to S.R.S.) and EPSRC grant No. EP/J018139/1 (D.S.B.D.) for funding.A highly enantioselective Lewis base-catalysed formal [3+2] cycloaddition of ammonium enolates and oxaziridines to give stereodefined oxazolidin-4-ones in high yield is described. Employing an enantioenriched oxaziridine in this process leads to a matched/mis-matched effect with the isothiourea catalyst and allowed the synthesis of either syn- or anti-stereodefined oxazolidin-4-ones in high dr, yield and ee. Additionally, the oxazolidin-4-one products have been derivatised to afford functionalised enantioenriched building blocks.Publisher PDFPeer reviewe
Group 2 Catalysis for the atom-efficient synthesis of imidazolidine and thiazolidine derivatives

A wide variety of functionalised imidazolidine-2-ones and -thiones, 2-imino-imidazolidines and thiazolidine-2-thiones have been synthesised under very mild reaction conditions by using simple and cost-effective alkaline earth bis(amide) precatalysts, [Ae{N(SiMe<inf>3</inf>)<inf>2</inf>}<inf>2</inf>(THF)<inf>2</inf>] (Ae=Mg, Ca, Sr). The reactions ensue with 100 % atom efficiency as one-pot cascades from simple, commercially available terminal alkyne and heterocumulene reagents. The reactions take place through the initial assembly of propargylamidines, which are utilised in subsequent cyclisation reactions through addition of the isocyanate, isothiocyanate and, in one case, carbon disulfide reagents. This reactivity is deduced to take place through a well-defined sequence of heterocumulene hydroacetylenation and alkyne hydroamidation steps, which are all mediated at the alkaline earth centre. The rate and regioselectivity of the cyclisation reactions are, thus, found to be heavily dependent upon the identity of the catalytic alkaline earth centre employed. Similarly, the selectivity of the reactions was observed to be profoundly affected by stereoelectronic variations in the individual substrates, albeit by a similar Group 2-centred reaction mechanism in all cases studied
A visible light induced α-H chlorination of alkylarenes with inorganic chloride under nanoAg@AgCl.

An efficient, photocatalytic chlorination of alkylarene α-H groups using NaCl/HCl as chlorine source has been developed involving a radical mechanism under visible light (including sunlight) conditions. A chlorine radical is proposed to be formed by an electron transfer from chloride ion to O2 in\ud
air via the band gap hole of the semiconductor AgCl. The chlorination protocol is characterized by its use of natural sunlight or other visible light, mild conditions, cheap source of chlorine, green solvent and high selectivity. The yield of benzylchloride is 95% with a toluene conversion as high as 40%,\ud
which rivals traditional chlorination methods
Peptide delta-turn: Literature survey and recent progress

Among the various types of a-peptide folding motifs, delta-turn, which requires a central cis-amide disposition, has been one of the least extensively investigated. In particular, this main-chain reversal topology has been studied in-depth neither in linear/cyclic peptides nor in proteins. This Minireview article assembles and critically analyzes relevant data from a literature survey on the d-turn conformation in those compounds. Unpublished results from recent conformational energy calculations and a preliminary solution-state analysis on a small model peptide, currently ongoing in our laboratories, are also briefly outlined.Postprint (published version
Self-assembly of tetraphenylalanine peptides

Three different tetraphenylalanine (FFFF) based peptides that differ at the N- and C-termini have been synthesized by using standard procedures to study their ability to form different nanoassemblies under a variety of conditions. The FFFF peptide assembles into nanotubes that show more structural imperfections at the surface than those formed by the diphenylalanine (FF) peptide under the same conditions. Periodic DFT calculations (M06L functional) were used to propose a model that consists of three FFFF molecules defining a ring through head-to-tail NH3\ud
+¿-OOC interactions, which in turn stack to produce deformed channels with internal diameters between 12 and 16 Å. Depending on the experimental conditions used for the peptide incubation, N-fluorenylmethoxycarbonyl (Fmoc) protected FFFF self-assembles into a variety of polymorphs: ultra-thin nanoplates, fibrils, and star-like submicrometric aggregates. DFT calculations indicate that Fmoc-FFFF prefers a parallel rather than an antiparallel ß-sheet assembly. Finally, coexisting multiple assemblies (up to three) were observed for Fmoc-FFFF-OBzl (OBzl = benzyl ester), which incorporates aromatic protecting groups at the two peptide terminals. This unusual and noticeable feature is attributed to the fact that the assemblies obtained by combining the Fmoc and OBzl groups contained in the peptide are isoenergetic. Variety show! Three different tetraphenylalanine-based peptides that differ at the N- and C-termini have been synthesized by using standard procedures to study their ability to form different nanoassemblies (e.g., nanotubes, see figure) under a variety of conditions.Peer ReviewedPostprint (author's final draft
Hybrid [5]Radialenes with Bispyrroloheteroles: New Electron-Donating Units.

Bispyrroloheteroles have been synthesized to address their intrinsic structural, optical, and electrochemical properties. The X-ray crystal structures and calculated natural bond orbital (NBO) bond orders unambiguously demonstrated the existence of a two pyrrole-fused five-membered ring with short exocyclic C-C double bonds and long endocyclic C-C single bonds, supporting that the bispyrroloheteroles are rare examples of structurally characterized hybrid [5]radialenes. The bispyrroloheteroles were found to act as an electron-donating unit, which would be fascinating for the rational design of new charge-transporting and donor-acceptor photovoltaic materials as well as versatile charge-transfer complexes
Selective Targeting of the KRAS Codon 12 Mutation Sequence by Pyrrole-Imidazole Polyamide seco-CBI Conjugates.

Mutation of KRAS is a key step in many cancers. Mutations occur most frequently at codon 12, but the targeting of KRAS is notoriously difficult. We recently demonstrated selective reduction in the volume of tumors harboring the KRAS codon 12 mutation in a mouse model by using an alkylating hairpin N-methylpyrrole-N-methylimidazole polyamide seco-1, 2, 9, 9a-tetrahydrocyclopropa[1, 2-c]benz[1, 2-e]indol-4-one conjugate (conjugate 4) designed to target the KRAS codon 12 mutation sequence. Herein, we have compared the alkylating activity of 4 against three other conjugates that were also designed to target the KRAS codon 12 mutation sequence. Conjugate 4 displayed greater affinity for the G12D mutation sequence than for the G12V sequence. A computer-minimized model suggested that conjugate 4 could bind more efficiently to the G12D match sequence than to a one-base-pair mismatch sequence. Conjugate 4 was modified for next-generation sequencing. Bind-n-Seq analysis supported the evidence showing that conjugate 4 could target the G12D mutation sequence with exceptionally high affinity and the G12V mutation sequence with much higher affinity than that for the wild-type sequence