Unexpected influence of substituents on the binding affinities of polycyclic aromatic hydrocarbons with a tetra-Au(I) metallorectangle

A tetra-gold supramolecular organometallic cage constructed with two pyrene-bis-imidazolylidene ligands and two carbazolyl-bis-alkynyl linkers (1) was studied as host for a series of substituted polycyclic aromatic hydrocarbons (PAHs). For the two smaller PAHs used (2-naphthalenol and 1-pyrenemethanol), the presence of the - OH groups at the periphery of the molecules did not enhance the binding affinity of the guest, compared with the unsubstituted PAHs. This observation indicated no hydrogen bonding of these two guests with the NH of the carbazole linker, as well as negligible dispersive interactions of the substituents with the π-system of 1. In the case of 3- perylenemethanol, the CH2OH group produced a significant increase in the binding affinity, vs perylene. Similarly, 3- methylperylene shows an increased binding affinity compared to perylene. MN15-L/def2-QZVP calculations gave Gibbs reaction energies for the displacement of perylene from the host by the substituted perylenes becoming more exergonic in the order: -1.6 (3-methylperylene) > -4.3 (3-ethylperylene) > -4.5 kcal/mol (3-perylenemethanol). The experimental and DFT results indicate that the peripheral dispersive interactions can make a significant contribution to the host-guest bonding energy, in addition to the conventional π–π stacking interactions. Our work highlights the importance of dispersive interactions in the contribution to the binding affinity of host-guest chemistry complexe

First homoleptic MIC and heteroleptic NHC-MIC coordination cages from 1,3,5-triphenylbenzene-bridged tris-MIC and tris-NHC ligands

The preparation of a triphenylbenzene-bridged tris-(1,2,3-triazolium) salt allowed us to obtain the first homoleptic tris-MIC cylinder-like cages of Ag and Au. The silver MIC-based cage reacts with the trisNHC-Ag analogue to form the corresponding heteroleptic NHC–MIC silver cage in an unusual reaction involving the simultaneous exchange of the tris-NHC and tris-MIC ligands.MINECO (CTQ2014-51999-P) and UJI (P11B2014-02).Published versio

Ion Mobility Mass Spectrometry Uncovers Guest-Induced Distortions in a Supramolecular Organometallic Metallosquare

The encapsulation of the tetracationic palladiummetallosquare with four pyrene-bis-imidazolylidene ligands[1]4+with aseries of organic molecules was studied byElectrosprayionization Travelling Wave Ion-Mobility MassSpectrometry (ESI TWIM-MS). The method allowed todetermine the Collision Cross Sections (CCSs), whichwereused to assess the sizechanges experienced by the host uponencapsulation of the guest molecules.When fullerenes wereused as guests,the host is expanded DCCS 13 2and 23 2,forC60or C70,respectively.The metallorectangle [1]4+was alsoused for the encapsulation of aseries of polycyclic aromatichydrocarbons (PAHs) and naphthalenetetracarboxylic diimide(NTCDI), to form complexes of formula [(NTCDI)2-(PAH)@1]4+.For these host:guest adducts,the ESI IM-MSstudies revealed that [1]4+is expanded by 47–49 2.. Theenergy-minimized structures of [1]4+,[C60@1]4+,[C70@1]4+,[(NTCDI)2(corannulene)@1]4+in the gas phase were obtainedby DFT calculations.IntroductionFunding for open access charge: CRUE-Universitat Jaume

Domestication as Enskilment : Harnessing Reindeer in Arctic Siberia

Acknowledgements Funding for this project was provided by the Wenner-Gren Foundation (SFR1725) to R. Losey, the JPI HUMANOR project (ESRC ES/M011054/1) to D. Anderson, ERC GRETPOL to D. Arzyutov, and the Russian Foundation for Basic Research to N.Fedorova (18-09-40011). The authors wish to express their gratitude to the Nenets families, the Okotettos and Yaungads, who hosted us during our stay in Iamal, which is greatly appreciated. Special thanks are also offered to the staff of Iamal-Nenets Autonomous District, and the staff of the Iamal-Nenets Regional Museum and Exhibition Complex of I.S. Shemanovskii, Peter the Great Museum of Anthropology and Ethnography, and British Museum for providing access to their collections.Peer reviewedPostprin

The Milstein Bipyridyl PNN Pincer Complex of Ruthenium Becomes a Noyori-Type Catalyst under Reducing Conditions

Hydrogenation of the dearomatized PNN ligand of the Milstein bipyridyl complex RuH(CO)[PNN] (2) gives a square-pyramidal Ru(II) product RuH(CO)[pPNN] (5). The central ring of the pPNN ligand is a piperidine. A minor byproduct of the hydrogenation reaction is complex 6 which has a dimeric structure made of two Ru(II) fragments each possessing a partly hydrogenated PNN ligand. The structures of 5 and 6 have been elucidated by NMR spectroscopy and X-ray crystallography. The PNN ligand of 2 is also hydrogenated under the conditions of the catalytic dehydrogenative coupling of ethanol to ethyl acetate. No direct evidence of the aromatized dihydride RuH2(CO)[PNN] (4) was found in this study. However, treating RuHCl(CO)[PNN] with Li[HBEt3] or reacting 2 with H2 at low temperature resulted in a structurally characterized hydride-bridged dimer (7) bearing intact aromatized bipyridyl ligands. M06-L/def2-QZVP DFT calculations provided insights into the thermodynamics of the stoichiometric reactions of this work and into the nature of the intermediates of the catalytic ester hydrogenation facilitated by RuH2(CO)[pPN(H)N] (8) formed from 5 under H2

Ion Mobility Mass Spectrometry Uncovers Guest‐Induced Distortions in a Supramolecular Organometallic Metallosquare

The encapsulation of the tetracationic palladium metallosquare with four pyrene-bis-imidazolylidene ligands [1]4+ with a series of organic molecules was studied by Electrospray ionization Travelling Wave Ion-Mobility Mass Spectrometry (ESI TWIM-MS). The method allowed to determine the Collision Cross Sections (CCSs), which were used to assess the size changes experienced by the host upon encapsulation of the guest molecules. When fullerenes were used as guests, the host is expanded ΔCCS 13 Å2 and 23 Å2 , for C60 or C70 , respectively. The metallorectangle [1]4+ was also used for the encapsulation of a series of polycyclic aromatic hydrocarbons (PAHs) and naphthalenetetracarboxylic diimide (NTCDI), to form complexes of formula [(NTCDI)2 (PAH)@1]4+ . For these host:guest adducts, the ESI IM-MS studies revealed that [1]4+ is expanded by 47-49 Å2 .. The energy-minimized structures of [1]4+ , [C60 @1]4+ , [C70 @1]4+ , [(NTCDI)2 (corannulene)@1]4+ in the gas phase were obtained by DFT calculations

North Atlantic simulations in Coordinated Ocean-ice Reference Experiments phase II (CORE-II). Part I: Mean states

Simulation characteristics from eighteen global ocean–sea-ice coupled models are presented with a focus on the mean Atlantic meridional overturning circulation (AMOC) and other related fields in the North Atlantic. These experiments use inter-annually varying atmospheric forcing data sets for the 60-year period from 1948 to 2007 and are performed as contributions to the second phase of the Coordinated Ocean-ice Reference Experiments (CORE-II). The protocol for conducting such CORE-II experiments is summarized. Despite using the same atmospheric forcing, the solutions show significant differences. As most models also differ from available observations, biases in the Labrador Sea region in upper-ocean potential temperature and salinity distributions, mixed layer depths, and sea-ice cover are identified as contributors to differences in AMOC. These differences in the solutions do not suggest an obvious grouping of the models based on their ocean model lineage, their vertical coordinate representations, or surface salinity restoring strengths. Thus, the solution differences among the models are attributed primarily to use of different subgrid scale parameterizations and parameter choices as well as to differences in vertical and horizontal grid resolutions in the ocean models. Use of a wide variety of sea-ice models with diverse snow and sea-ice albedo treatments also contributes to these differences. Based on the diagnostics considered, the majority of the models appear suitable for use in studies involving the North Atlantic, but some models require dedicated development effort

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

A community effort in SARS-CoV-2 drug discovery.

peer reviewedThe COVID-19 pandemic continues to pose a substantial threat to human lives and is likely to do so for years to come. Despite the availability of vaccines, searching for efficient small-molecule drugs that are widely available, including in low- and middle-income countries, is an ongoing challenge. In this work, we report the results of an open science community effort, the "Billion molecules against Covid-19 challenge", to identify small-molecule inhibitors against SARS-CoV-2 or relevant human receptors. Participating teams used a wide variety of computational methods to screen a minimum of 1 billion virtual molecules against 6 protein targets. Overall, 31 teams participated, and they suggested a total of 639,024 molecules, which were subsequently ranked to find 'consensus compounds'. The organizing team coordinated with various contract research organizations (CROs) and collaborating institutions to synthesize and test 878 compounds for biological activity against proteases (Nsp5, Nsp3, TMPRSS2), nucleocapsid N, RdRP (only the Nsp12 domain), and (alpha) spike protein S. Overall, 27 compounds with weak inhibition/binding were experimentally identified by binding-, cleavage-, and/or viral suppression assays and are presented here. Open science approaches such as the one presented here contribute to the knowledge base of future drug discovery efforts in finding better SARS-CoV-2 treatments.R-AGR-3826 - COVID19-14715687-CovScreen (01/06/2020 - 31/01/2021) - GLAAB Enric