pinecone/core-2020-05-10-deduplication huggingface dataset:
Synthesis of Natural and Unnatural Cyclooligomeric Depsipeptides Enabled by Flow Chemistry

Flow chemistry has been successfully integrated into the synthesis of a series of cyclooligomeric depsipeptides of three different ring sizes including the natural products beauvericin (1a), bassianolide (2b) and enniatin C (1b). A reliable flow chemistry protocol was established for the coupling and macrocyclisation to form challenging N‐methylated amides. This flexible approach has allowed the rapid synthesis of both natural and unnatural depsipeptides in high yields, enabling further exploration of their promising biological activity.The authors gratefully acknowledge the EPSRC for financial support (grants EP/K009494/1 and EP/K039520/1).  This is the final version of the article. It first appeared from Wiley via http://dx.doi.org/10.1002/chem.20150445
Enantiopure Ferrocene-Based Planar-Chiral Iridacycles:Stereospecific Control of Iridium-Centred Chirality

Reaction of [IrCp*Cl-2](2) with ferrocenylimines (Fc=NAr, Ar=Ph, p-MeOC6H4) results in ferrocene C-H activation and the diastereoselective synthesis of half-sandwich iridacycles of relative configuration S-p*,R-Ir*. Extension to (S)-2-ferrocenyl-4-(1-methylethyl)oxazoline gave highly diastereoselective control over the new elements of planar chirality and metal-based pseudo-tetrahedral chirality, to give both neutral and cationic half-sandwich iridacycles of absolute configuration S-c,S-p,R-Ir. Substitution reactions proceed with retention of configuration, with the planar chirality controlling the metal-centred chirality through an iron-iridium interaction in the coordinatively unsaturated cationic intermediate
Methyl Complexes of the Transition Metals

Organometallic chemistry can be considered as a wide area of knowledge that combines concepts of classic organic chemistry, that is, based essentially on carbon, with molecular inorganic chemistry, especially with coordination compounds. Transition-metal methyl complexes probably represent the simplest and most fundamental way to view how these two major areas of chemistry combine and merge into novel species with intriguing features in terms of reactivity, structure, and bonding. Citing more than 500 bibliographic references, this review aims to offer a concise view of recent advances in the field of transition-metal complexes containing M-CH fragments. Taking into account the impressive amount of data that are continuously provided by organometallic chemists in this area, this review is mainly focused on results of the last five years. After a panoramic overview on M-CH compounds of Groups 3 to 11, which includes the most recent landmark findings in this area, two further sections are dedicated to methyl-bridged complexes and reactivity.Ministerio de Ciencia e Innovación Projects CTQ2010–15833, CTQ2013-45011 - P and Consolider - Ingenio 2010 CSD2007 - 00006Junta  de  Andalucía FQM - 119,  Projects  P09 - FQM - 5117  and  FQM - 2126EU 7th Framework Program, Marie Skłodowska - Curie actions C OFUND – Agreement nº 26722
Mechanistic Insights in the Mode of Action of Bifunctional Pyrrolidine-Squaramide-derived Organocatalysts

The modes of catalytic action of three squaramide-derived
bifunctional organocatalysts have been investigated using DFT
methods. The [5+2] cycloaddition between oxidopyrilium ylides and
enals has been used as model reaction. Two primary modes are
possible for the different catalysts studied. The preference for one
mode over the other is due to the possibility of additional favourable
π,π-interactions between the H-bond activated pyrilium ylide and an
electron-deficient aromatic ring bonded to a squaramide NH-group.
The model can be extended to other reactions catalyzed by the
same catalysts such as formal [2+2] cycloadditions between
nitroalkenes and α,β-unsaturated aldehydes. The computational
results are in excellent concurrence with the available experimental
reports on the observed total enantioselectivity and differences in
diastereoselectivity depending on the substrate and the reactionThis work was supported by Spanish MINECO Contracts CTQ2013-44367-C2-1-P (to P.M.) and CTQ2014-52107 (to J.L.V.). We also acknowledge the Government of Aragón (Spain) (Group E-10), the Basque Government (Spain) (IT328-10) and Aarhus University (Denmark) for financial support. We acknowledge the Institute of Biocomputation and Physics of Complex Systems (BIFI) at the University of Zaragoza (Spain) for computer time at clusters Terminus and Memento. D.R.-L. Thanks the Spanish Ministry of Education (MEC) for a predoctoral grant (FPU program)
One-pot approach to organo phosphorus-chalcogen macrocycles incorporating double OP(S)SCn or OP(Se)SeCn scaffolds : a synthetic and structural study

We are grateful to the University of St. Andrews for financial support and the EPSRC National Mass Spectrometry Service Centre (Swansea) for mass spectral measurements.The development of new methodology for the preparation of functional macrocycles with practical applications is a fundamental important research area in macromolecular science. In this study, we report a new one-pot route for the synthesis of a series of macro-heterocycles by incorporating two phosphorus atoms and two chalcogen atoms and two oxygen atoms (double OP(S)SCn or OP(Se)SeCn scaffolds). The three-component condensation reactions of 2,4-diferrocenyl-1,3,2,4-diathiadiphosphetane 2,4-disulfide ( FcLR , a ferrocene analogue of Lawesson’s reagent) or 2,4-bis(4-methoxyphenyl)-1,3,2,4-dithiadiphosphetane 2,4-disulfide ( LR , Lawesson’s reagent), or 2,4-diphenyl-1,3,2,4-diselenadiphosphetane 2,4-diselenide ( WR , Woollins’ reagent), disodium alkenyl-diols, and dihalogenated alkanes are performed giving rise to soluble and air or moisture-stable macrocycloes in good to excellent yields (up to 92%). This is the first systemically preparative and readily scalable example of one-pot ring opening/ring extending reaction of three-components to prepare phosphorus-chalcogen containing macrocycles. We also provide a systematic crystallographic study.PostprintPostprintPeer reviewe
Structural and magnetic diversity in alkali-metal Manganate chemistry : evaluating donor and alkali-metal effects in co-complexation processes

By exploring co-complexation reactions between the manganese alkyl Mn(CH2SiMe3)2 and the heavier alkali-metal alkyls M(CH2SiMe3) (M=Na, K) in a benzene/hexane solvent mixture and in some cases adding Lewis donors (bidentate TMEDA, 1,4-dioxane, and 1,4-diazabicyclo[2,2,2] octane (DABCO)) has produced a new family of alkali-metal tris(alkyl) manganates. The influences that the alkali metal and the donor solvent impose on the structures and magnetic properties of these ates have been assessed by a combination of X-ray, SQUID magnetization measurements, and EPR spectroscopy. These studies uncover a diverse structural chemistry ranging from discrete monomers [(TMEDA)2MMn(CH2SiMe3)3] (M=Na, 3; M=K, 4) to dimers [(KMn(CH2SiMe3)3C6H6)2] (2) and [(NaMn(CH2SiMe3)3)2(dioxane)7] (5); and to more complex supramolecular networks [(NaMn(CH2SiMe3)3)∞] (1) and [(Na2Mn2(CH2SiMe3)6(DABCO)2)∞] (7)). Interestingly, the identity of the alkali metal exerts a significant effect in the reactions of 1 and 2 with 1,4-dioxane, as 1 produces coordination adduct 5, while 2 forms heteroleptic [((dioxane)6K2Mn2(CH2SiMe3)4(O(CH2)2OCH=CH2)2)∞] (6) containing two alkoxide-vinyl anions resulting from α-metalation and ring opening of dioxane. Compounds 6 and 7, containing two spin carriers, exhibit antiferromagnetic coupling of their S=5/2 moments with varying intensity depending on the nature of the exchange pathways
Triple Helix Formation in a Topologically Controlled DNA Nanosystem

In the present study, we demonstrate single-molecule imaging of triple helix formation in DNA nanostructures. The binding of the single-molecule third strand to double-stranded DNA in a DNA origami frame was examined using two different types of triplet base pairs. The target DNA strand and the third strand were incorporated into the DNA frame, and the binding of the third strand was controlled by the formation of Watson-Crick base pairing. Triple helix formation was monitored by observing the structural changes in the incorporated DNA strands. It was also examined using a photocaged third strand wherein the binding of the third strand was directly observed using high-speed atomic force microscopy during photoirradiation. We found that the binding of the third strand could be controlled by regulating duplex formation and the uncaging of the photocaged strands in the designed nanospace
CO2 Conversion to Esters by Fluoride-mediated Carboxylation of Organosilanes and Halide Derivatives

International audienceThe one-step conversion of CO2 to hetero-aromatic esters is presented under metal-free conditions. Using fluoride anions as promoters for C-Si bond activation, pyridyl, furanyl and thiophenyl organosilanes are successfully carboxylated with CO2, in the presence of an electrophile. The mechanism of this unprecedented reaction has been elucidated based on experimental and computational results, which show a unique catalytic influence of CO2 in the C-Si bond activation of pyridylsilanes. The methodology is applied to 18 different esters and it has enabled the incorporation of CO2 to a polyester material, for the first time
Synthesis and Evaluation of a 2,11-Cembranoid-Inspired Library

The 2,11-cembranoid family of natural products has been used as inspiration for the synthesis of a structurally simplified, functionally diverse library of octahydroisobenzofuran-based compounds designed to augment a typical medicinal chemistry library screen. Ring-closing metathesis, lactonisation and SmI2-mediated methods were exemplified and applied to the installation of a third ring to mimic the nine-membered ring of the 2,11-cembranoids. The library was assessed for aqueous solubility and permeability, with a chemical-space analysis performed for comparison to the family of cembranoid natural products and a sample set of a screening library. Preliminary investigations in cancer cells showed that the simpler scaffolds could recapitulate the reported anti-migratory activity of the natural products
The Influence of Substituent Orientation on the Photovoltaic Performance of Phthalocyanine-Sensitized Solar Cells

This is the peer reviewed version of the following article:Chemistry - A European Journal 22.13 (2016): 4369-4373, which has been published in final form at http://dx.doi.org/10.1002/chem.201600166. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Self-ArchivingPhthalocyanines (Pcs) are used as sensitizers in dye-sensitized solar cells (DSSCs) because of their stability and intense absorption in the red and near-IR regions. Impressive progress has been made in photovoltaic efficiencies by introduction of bulky peripheral substituents to help suppress macrocycle aggregation. To reach benchmark efficiencies reported for other related dyes, new designs need to be explored. Single carboxy-ZnPc regioisomers substituted at the non-peripheral positions by rigid aryl groups have now been studied, which has shed light on the influence of steric hindrance and/or orientation of the substituent around the anchoring group on the photovoltaic response. The regioisomer bearing the aryl group far away from the anchoring group produces a more effective sensitization of the TiO2 films and higher short-circuit photocurrent density (Jsc). Taking advantage of the good photovoltaic performance in the near-IR region of this ZnPc, it was combined with another appropriate dye for panchromatic sensitization of the mesoporous photoelectrode and an increase of the overall device efficiencyFinancial support from the European Union (FP7-ENERGY-2012- 1 framework, GLOBASOL project, Proposal No 309194-2), from the Spanish MINECO (CTQ2014-52869-P), Comunidad de Madrid (FOTOCARBON S2013/MIT-2841), and MECD (F.P.U. fellowship to L.T.) is gratefully acknowledge
Two-Dimensional Ketone-Driven Metal-Organic Coordination on Cu(111)

Two-dimensional metal-organic nanostructures based on the binding of ketone groups and metal atoms were fabricated by depositing pyrene-4,5,9,10-tetraone (PTO) molecules on a Cu(111) surface. The strongly electronegative ketone moieties bind to either copper adatoms from the substrate or codeposited iron atoms. In the former case, scanning tunnelling microscopy images reveal the development of an extended metal-organic supramolecular structure. Each copper adatom coordinates to two ketone ligands of two neighbouring PTO molecules, forming chains that are linked together into large islands through secondary van der Waals interactions. Deposition of iron atoms leads to a transformation of this assembly resulting from the substitution of the metal centres. Density functional theory calculations reveal that the driving force for the metal substitution is primarily determined by the strength of the ketone-metal bond, which is higher for Fe than for Cu. This second class of nanostructures displays a structural dependence on the rate of iron deposition
Fluorinated musk fragrances : the CF2 group as a conformational bias influencing the odour of civetone and (R)-muscone

This work was supported by the Engineering and Physical Sciences Research Council (EPSRC) and the European Research Council (ERC). The authors acknowledge the EPSRC National Mass Spectrometry Facility (Swansea). M.Y. thanks the China Scholarship Council for financial support. D.O'H. thanks the Royal Society for a Wolfson Research Merit Award.The difluoromethylene (CF2) group has a strong tendency to adopt corner over edge locations in aliphatic macrocycles. In this study, the CF2 group has been introduced into musk relevant macrocyclic ketones. Nine civetone and five muscone analogues have been prepared by synthesis for structure and odour comparisons. X-ray studies indeed show that the CF2 groups influence ring structure and they give some insight into the preferred ring conformations, triggering a musk odour as determined in a professional perfumery environment. The historical conformational model of Bersuker and co-workers for musk fragrance generally holds, and structures that become distorted from this consensus, by the particular placement of the CF2 groups, lose their musk fragrance and become less pleasant.PostprintPeer reviewe
The mechanism of phosphonium ylide alcoholysis and hydrolysis: concerted addition of the O-H bond across the P=C bond

The previous work on the hydrolysis and alcoholysis reactions of phosphonium ylides is summarized and reviewed in the context of their currently accepted mechanisms. Several experimental facts relating to ylide hydrolysis and to salt and ylide alcoholysis are shown to conflict with those mechanisms. In particular, we demonstrate that the pK(a) values of water and alcohols are too high in organic media to bring about protonation of ylide. Therefore, we propose concerted addition of the water or alcohol O-H bond across the ylide P=C bond. In support of this, we provide NMR spectroscopic evidence for equilibrium between ylide and aclohol that does not require the involvement of phosphonium hydroxide. We report the first P-alkoxyphosphorane to be characterised by NMR spectroscopy that does not undergo exchange on an NMR timescale. Two-dimensional NMR spectroscopic techniques have been applied to the characterisation to P-alkoxyphosphoranes for the first time
Mechanism of oxidative amidation of nitroalkanes with oxygen and amine nucleophiles using electrophilic iodine

Recently, we developed a direct way to oxidatively convert primary nitroalkanes into amides. This entailed mixing an iodonium source with an amine, a base, and oxygen. Herein, we systematically investigated the mechanism and likely intermediates. We conclude that an amine-iodonium complex first forms through N-halogen bonding. This complex reacts with aci-nitronates to give both alpha-iodo and alpha-,alpha-diiodo nitroalkanes. These iodinated species can act as alternative sources of electrophilic iodine and also generate an extra equimolar amount of “I+” under O2. In particular, evidence supports alpha-,alpha-diiodo nitroalkanes reacting with molecular oxygen to form a peroxy adduct; alternatively, these tetrahedral intermediates rearrange anaerobically into a cleavable nitrite ester. In either case, activated esters are proposed form, which eventually react with nucleophilic amines in a traditional fashion
Dissolving hydroxyolite: a DNA molecule into its hydroxyapatite mold

In spite of the clinical importance of hydroxyapatite (HAp), the mechanism that controls its dissolution in acidic environments remains unclear. Knowledge of such a process is highly desirable to provide better understanding of different pathologies, as for example osteoporosis, and of the HAp potential as vehicle for gene delivery to replace damaged DNA. In this work, the mechanism of dissolution in acid conditions of HAp nanoparticles encapsulating double-stranded DNA has been investigated at the atomistic level using computer simulations. For this purpose, four consecutive (multi-step) molecular dynamics simulations, involving different temperatures and proton transfer processes, have been carried out. Results are consistent with a polynuclear decalcification mechanism in which proton transfer processes, from the surface to the internal regions of the particle, play a crucial role. In addition, the DNA remains protected by the mineral mold and transferred proton from both temperature and chemicals. These results, which indicate that biomineralization imparts very effective protection to DNA, also have important implications in other biomedical fields, as for example in the design of artificial bones or in the fight against osteoporosis by promoting the fixation of Ca2+ ions.Peer ReviewedPostprint (published version
Nucleosome Assembly Alters the Accessibility of the Antitumor Agent Duocarmycin B2 to Duplex DNA

To evaluate the reactivity of antitumor agents in a nucleosome architecture, we conducted in vitro studies to assess the alkylation level of duocarmycin B2 on nucleosomes with core and linker DNA using sequencing gel electrophoresis. Our results suggested that the alkylating efficiencies of duocarmycin B2 were significantly decreased in core DNA and increased at the histone-free linker DNA sites when compared with naked DNA conditions. Our finding that nucleosome assembly alters the accessibility of duocarmycin B2 to duplex DNA could advance its design as an antitumor agent
Star-shaped conjugated molecules with oxa- or thiadiazole bithiophene side arms.

Star-shaped conjugated molecules, consisting of a benzene central unit symmetrically trisubstituted with either oxa- or thiadiazole bithiophene groups, were synthesized as promising molecules and building blocks for application in (opto)electronics and electrochromic devices. Their optical (Eg(opt)) as well as electrochemical (Eg(electro)) band gaps depended on the type of the side arm and the number of solubilizing alkyl substituents. Oxadiazole derivatives showed Eg(opt) slightly below 3 eV and by 0.2 eV larger than those determined for thiadiazole-based compounds. The presence of alkyl substituents in the arms additionally lowered the band gap. The obtained compounds were efficient electroluminophores in guest/host-type light-emitting diodes. They also showed a strong tendency to self-organize in monolayers deposited on graphite, as evidenced by scanning tunneling microscopy. The structural studies by X-ray scattering revealed the formation of supramolecular columnar stacks in which the molecules were organized. Differences in macroscopic alignment in the specimen indicated variations in the self-assembly mechanism between the molecules. The compounds as trifunctional monomers were electrochemically polymerized to yield the corresponding polymer network. As shown by UV/Vis-NIR spectroelectrochemical studies, these networks exhibited reversible electrochromic behavior both in the oxidation and in the reduction modes
Synthesis and Application of Tetrahydro-2H-fluorenes by a Pd(0)-Catalyzed Benzylic C(sp³)-H Functionalization

A new method has been developed for the synthesis of tetrahydro-2H-fluorenes based on a Pd(0)-catalyzed benzylic C(sp³)-H functionalization. Importantly, the success of the cyclization step was dependent on there being substituents at the two positions ortho to the benzylic group to avoid an undesired C(sp²)-H functionalization. This method was subsequently used to prepare the right-hand fragment of the hexacyclic triterpenoid benzohopanes, and therefore represents a powerful tool for the construction of the related compounds. A new method has been developed for the synthesis of tetrahydro-2H-fluorenes based on a Pd(0)-catalyzed benzylic C(sp³)-H alkenylation of an enol triflate bearing substituents at its two ortho positions (see scheme). This method was used to prepare the right-hand fragment of benzohopanes
Analysis of the Electronic Structure of Aqueous Urea and Its Derivatives  A Systematic Soft X Ray TD DFT Approach

Soft X ray emission  XE , absorption  XA , and resonant inelastic scattering  RIXS  experiments have been conducted at the nitrogen K edge of urea and its derivatives in aqueous solution and were compared with density functional theory and time dependent density functional theory calculations. This comprehensive study provides detailed information on the occupied and unoccupied molecular orbitals of urea, thiourea, acetamide, dimethylurea, and biuret at valence levels. By identifying the electronic transitions that contribute to the experimental spectral features, the energy gap between the highest occupied and the lowest unoccupied molecular orbital of each molecule is determined. Moreover, a theoretical approach is introduced to simulate resonant inelastic X ray scattering spectra by adding an extra electron to the lowest unoccupied molecular orbital, thereby mimicking the real initial state of the core electron absorption before the subsequent relaxation proces
Generalization of the copper to late-transition-metal transmetallation to carbenes beyond N-heterocyclic carbenes

The authors gratefully acknowledge the Royal Society (University Research Fellowship to C.S.J.C.), the EPSRC (EP/J500549/1) and the DOE (DE-FG02-13ER16370) for financial support.Carbene transition-metal complexes have become a prevalent family of catalysts enabling numerous organic transformations. Their facile synthetic access is a matter of great importance. To this end, the CuI-NHC transfer methodology has emerged as a powerful alternative presenting attractive advantages over other methods. Herein, we report the remarkable ability of copper to transfer not only NHCs but also other types of carbenes such as abnormal NHCs (aNHCs), cyclic (alkyl)(amino)carbenes (CAACs), and mesoionic carbenes (MICs) to various transition metal precursors.PostprintPeer reviewe
Last-step enzymatic [18F]-fluorination of cysteine-tethered RGD peptides using modified Barbas linkers

We thank the Engineering and Physical Sciences Research Council, UK, for a research grant.We report a last-step fluorinase-catalyzed [18F]-fluorination of a cysteine-containing RGD peptide. The peptide was attached through sulfur to a modified and more hydrophilic variant of the recently disclosed Barbas linker which was itself linked to a chloroadenosine moiety via a PEGylated chain. The fluorinase was able to use this construct as a substrate for a transhalogenation reaction to generate [18F]-radiolabeled RGD peptides, which retained high affinity to cancer-cell relevant αvβ3 integrins.PostprintPeer reviewe