Detection and Characterization of Hydride Ligands in Copper Complexes by Hard X-ray Spectroscopy.

Transition metal complexes, particularly copper hydrides, play an important role in various catalytic processes and molecular inorganic chemistry. This study employs synchrotron hard X-ray spectroscopy to gain insights into the geometric and electronic properties of copper hydrides as potential catalysts for CO2 hydrogenation. The potential of high energy resolution X-ray absorption near-edge structure (HERFD-XANES) and valence-to-core X-ray emission (VtC-XES) is demonstrated with measurement on Stryker's reagent (Cu6H6) and [Cu3(µ3-H)(dpmppe)2](PF6)2 (Cu3H), alongside a non-hydride copper compound (Cu-I). The XANES analysis reveals that coordination geometries strongly influence the spectra, providing only indirect details about hydride coordination. The VtC-XES analysis exhibits a distinct signal around 8975 eV, offering a diagnostic tool to identify hydride ligands. Theoretical calculations support and extend these findings by comparing hydride-containing complexes with their hydride-free counterparts.

mRNA Display Identifies Potent, Paralog-Selective Peptidic Ligands for ARID1B.

The ARID1A and ARID1B subunits are mutually exclusive components of the BAF variant of SWI/SNF chromatin remodeling complexes. Loss of function mutations in ARID1A are frequently observed in various cancers, resulting in a dependency on the paralog ARID1B for cancer cell proliferation. However, ARID1B has never been targeted directly, and the high degree of sequence similarity to ARID1A poses a challenge for the development of selective binders. In this study, we used mRNA display to identify peptidic ligands that bind with nanomolar affinities to ARID1B and showed high selectivity over ARID1A. Using orthogonal biochemical, biophysical, and chemical biology tools, we demonstrate that the peptides engage two different binding pockets, one of which directly involves an ARID1B-exclusive cysteine that could allow covalent targeting by small molecules. Our findings impart the first evidence of the ligandability of ARID1B, provide valuable tools for drug discovery, and suggest opportunities for the development of selective molecules to exploit the synthetic lethal relationship between ARID1A and ARID1B in cancer.

Optimization of Potent Ligands for the E3 Ligase DCAF15 and Evaluation of Their Use in Heterobifunctional Degraders.

Unlocking novel E3 ligases for use in heterobifunctional PROTAC degraders is of high importance to the pharmaceutical industry. Over-reliance on the current suite of ligands used to recruit E3 ligases could limit the potential of their application. To address this, potent ligands for DCAF15 were optimized using cryo-EM supported, structure-based design to improve on micromolar starting points. A potent binder, compound 24, was identified and subsequently conjugated into PROTACs against multiple targets. Following attempts on degrading a number of proteins using DCAF15 recruiting PROTACs, only degradation of BRD4 was observed. Deconvolution of the mechanism of action showed that this degradation was not mediated by DCAF15, thereby highlighting both the challenges faced when trying to expand the toolbox of validated E3 ligase ligands for use in PROTAC degraders and the pitfalls of using BRD4 as a model substrate.

Electronic Structure and Excited-State Dynamics of the NIR-II Emissive Molybdenum(III) Analogue to the Molecular Ruby.

Photoactive chromium(III) complexes saw a conceptual breakthrough with the discovery of the prototypical molecular ruby mer-[Cr(ddpd)2]3+ (ddpd = N,N'-dimethyl-N,N'-dipyridin-2-ylpyridine-2,6-diamine), which shows intense long-lived near-infrared (NIR) phosphorescence from metal-centered spin-flip states. In contrast to the numerous studies on chromium(III) photophysics, only 10 luminescent molybdenum(III) complexes have been reported so far. Here, we present the synthesis and characterization of mer-MoX3(ddpd) (1, X = Cl; 2, X = Br) and cisfac-[Mo(ddpd)2]3+ (cisfac-[3]3+), an isomeric heavy homologue of the prototypical molecular ruby. For cisfac-[3]3+, we found strong zero-field splitting using magnetic susceptibility measurements and electron paramagnetic resonance spectroscopy. Electronic spectra covering the spin-forbidden transitions show that the spin-flip states in mer-1, mer-2, and cisfac-[3]3+ are much lower in energy than those in comparable chromium(III) compounds. While all three complexes show weak spin-flip phosphorescence in NIR-II, the emission of cisfac-[3]3+ peaking at 1550 nm is particularly low in energy. Femtosecond transient absorption spectroscopy reveals a short excited-state lifetime of 1.4 ns, 6 orders of magnitude shorter than that of mer-[Cr(ddpd)2]3+. Using density functional theory and ab initio multireference calculations, we break down the reasons for this disparity and derive principles for the design of future stable photoactive molybdenum(III) complexes.

High-Resolution X-ray Absorption and Emission Spectroscopy for Detailed Analysis of New CO2 Methanation Catalysts.

A new approach for the characterization of CO2 methanation catalysts prepared by thermal decomposition of a nickel MOF by hard X-ray photon-in/photon-out spectroscopy in form of high energy resolution fluorescence detected X-ray absorption near edge structure spectroscopy (HERFD-XANES) and valence-to-core X-ray emission (VtC-XES) is presented. In contrast to conventional X-ray absorption spectroscopy, the increased resolution of both methods allows a more precise phase determination of the final catalyst, which is influenced by the conditions during MOF decomposition.

Design and Evaluation of a Low Hydrogen Bond Donor Count Fragment Screening Set to Aid Hit Generation of PROTACs Intended for Oral Delivery.

The development of orally bioavailable PROTACs presents a significant challenge due to the inflated physicochemical properties of such heterobifunctional molecules. Molecules occupying this "beyond rule of five" space often demonstrate limited oral bioavailability due to the compounding effects of elevated molecular weight and hydrogen bond donor count (among other properties), but it is possible to achieve sufficient oral bioavailability through physicochemical optimization. Herein, we disclose the design and evaluation of a low hydrogen bond donor count (≤1 HBD) fragment screening set to aid hit generation of PROTACs intended for an oral route of delivery. We demonstrate that application of this library can enhance fragment screens against PROTAC proteins of interest and ubiquitin ligases, yielding fragment hits containing ≤1 HBD suitable for optimizing toward orally bioavailable PROTACs.

Janus-type emission from a cyclometalated iron(III) complex.

Although iron is a dream candidate to substitute noble metals in photoactive complexes, realization of emissive and photoactive iron compounds is demanding due to the fast deactivation of their charge-transfer states. Emissive iron compounds are scarce and dual emission has not been observed before. Here we report the FeIII complex [Fe(ImP)2][PF6] (HImP = 1,1'-(1,3-phenylene)bis(3-methyl-1-imidazol-2-ylidene)), showing a Janus-type dual emission from ligand-to-metal charge transfer (LMCT)- and metal-to-ligand charge transfer (MLCT)-dominated states. This behaviour is achieved by a ligand design that combines four N-heterocyclic carbenes with two cyclometalating aryl units. The low-lying π* levels of the cyclometalating units lead to energetically accessible MLCT states that cannot evolve into LMCT states. With a lifetime of 4.6 ns, the strongly reducing and oxidizing MLCT-dominated state can initiate electron transfer reactions, which could constitute a basis for future applications of iron in photoredox catalysis.

Correction: Distinct photodynamics of κ-N and κ-C pseudoisomeric iron(II) complexes.

Correction for 'Distinct photodynamics of κ-N and κ-C pseudoisomeric iron(II) complexes' by Philipp Dierks et al., Chem. Commun., 2021, 57, 6640-6643, https://doi.org/10.1039/D1CC01716K.

Synthesis and Characterization of Catalytically Active Au Core─Pd Shell Nanoparticles Supported on Alumina.

A two-step seeded-growth method was refined to synthesize Au@Pd core@shell nanoparticles with thin Pd shells, which were then deposited onto alumina to obtain a supported Au@Pd/Al2O3 catalyst active for prototypical CO oxidation. By the strict control of temperature and Pd/Au molar ratio and the use of l-ascorbic acid for making both Au cores and Pd shells, a 1.5 nm Pd layer is formed around the Au core, as evidenced by transmission electron microscopy and energy-dispersive spectroscopy. The core@shell structure and the Pd shell remain intact upon deposition onto alumina and after being used for CO oxidation, as revealed by additional X-ray diffraction and X-ray photoemission spectroscopy before and after the reaction. The Pd shell surface was characterized with in situ infrared (IR) spectroscopy using CO as a chemical probe during CO adsorption-desorption. The IR bands for CO ad-species on the Pd shell suggest that the shell exposes mostly low-index surfaces, likely Pd(111) as the majority facet. Generally, the IR bands are blue-shifted as compared to conventional Pd/alumina catalysts, which may be due to the different support materials for Pd, Au versus Al2O3, and/or less strain of the Pd shell. Frequencies obtained from density functional calculations suggest the latter to be significant. Further, the catalytic CO oxidation ignition-extinction processes were followed by in situ IR, which shows the common CO poisoning and kinetic behavior associated with competitive adsorption of CO and O2 that is typically observed for noble metal catalysts.

Icolos: a workflow manager for structure-based post-processing of de novo generated small molecules.

SUMMARY: We present Icolos, a workflow manager written in Python as a tool for automating complex structure-based workflows for drug design. Icolos can be used as a standalone tool, for example in virtual screening campaigns, or can be used in conjunction with deep learning-based molecular generation facilitated for example by REINVENT, a previously published molecular de novo design package. In this publication, we focus on the internal structure and general capabilities of Icolos, using molecular docking experiments as an illustrative example. AVAILABILITY AND IMPLEMENTATION: The source code is freely available at https://github.com/MolecularAI/Icolos under the Apache 2.0 license. Tutorial notebooks containing minimal working examples can be found at https://github.com/MolecularAI/IcolosCommunity. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Electronic Signature of Subnanometer Interfacial Broadening in Heterostructures.

Interfaces are ubiquitous in semiconductor low-dimensional systems used in electronics, photonics, and quantum computing. Understanding their atomic-level properties has thus been crucial to controlling the basic behavior of heterostructures and optimizing the device performance. Herein, we demonstrate that subnanometer interfacial broadening in heterostructures induces localized energy states. This phenomenon is predicted within a theory incorporating atomic-level interfacial details obtained by atom probe tomography. The experimental validation is achieved using heteroepitaxial (Si1-xGex)m/(Si)m superlattices as a model system demonstrating the existence of additional paths for hole-electron recombination. These predicted interfacial electronic transitions and the associated absorptive effects are evaluated at variable superlattice thickness and periodicity. By mapping the energy of the critical points, the optical transitions are identified between 2 and 2.5 eV, thus extending the optical absorption to lower energies. This phenomenon is shown to provide an optical fingerprint for a straightforward and nondestructive probe of the subnanometer broadening in heterostructures.

Pseudo-Octahedral Iron(II) Complexes with Near-Degenerate Charge Transfer and Ligand Field States at the Franck-Condon Geometry.

Increasing the metal-to-ligand charge transfer (MLCT) excited state lifetime of polypyridine iron(II) complexes can be achieved by lowering the ligand's π* orbital energy and by increasing the ligand field splitting. In the homo- and heteroleptic complexes [Fe(cpmp)2 ]2+ (12+ ) and [Fe(cpmp)(ddpd)]2+ (22+ ) with the tridentate ligands 6,2''-carboxypyridyl-2,2'-methylamine-pyridyl-pyridine (cpmp) and N,N'-dimethyl-N,N'-di-pyridin-2-ylpyridine-2,6-diamine (ddpd) two or one dipyridyl ketone moieties provide low energy π* acceptor orbitals. A good metal-ligand orbital overlap to increase the ligand field splitting is achieved by optimizing the octahedricity through CO and NMe units between the coordinating pyridines which enable the formation of six-membered chelate rings. The push-pull ligand cpmp provides intra-ligand and ligand-to-ligand charge transfer (ILCT, LL'CT) excited states in addition to MLCT excited states. Ground and excited state properties of 12+ and 22+ were accessed by X-ray diffraction analyses, resonance Raman spectroscopy, (spectro)electrochemistry, EPR spectroscopy, X-ray emission spectroscopy, static and time-resolved IR and UV/Vis/NIR absorption spectroscopy as well as quantum chemical calculations.

Olefin Metathesis in Confinement: Towards Covalent Organic Framework Scaffolds for Increased Macrocyclization Selectivity.

Covalent organic frameworks (COFs) offer vast structural and chemical diversity enabling a wide and growing range of applications. While COFs are well-established as heterogeneous catalysts, so far, their high and ordered porosity has scarcely been utilized to its full potential when it comes to spatially confined reactions in COF pores to alter the outcome of reactions. Here, we present a highly porous and crystalline, large-pore COF as catalytic support in α,ω-diene ring-closing metathesis reactions, leading to increased macrocyclization selectivity. COF pore-wall modification by immobilization of a Grubbs-Hoveyda-type catalyst via a mild silylation reaction provides a molecularly precise heterogeneous olefin metathesis catalyst. An increased macro(mono)cyclization (MMC) selectivity over oligomerization (O) for the heterogeneous COF-catalyst (MMC:O=1.35) of up to 51 % compared to the homogeneous catalyst (MMC:O=0.90) was observed along with a substrate-size dependency in selectivity, pointing to diffusion limitations induced by the pore confinement.

Selective Benzylic CH-Borylations by Tandem Cobalt Catalysis.

Metal-catalyzed C-H activations are environmentally and economically attractive synthetic strategies for the construction of functional molecules as they obviate the need for pre-functionalized substrates and minimize waste generation. Great challenges reside in the control of selectivities, the utilization of unbiased hydrocarbons, and the operation of atom-economical dehydrocoupling mechanisms. An especially mild borylation of benzylic CH bonds was developed with the ligand-free pre-catalyst Co[N(SiMe3 )2 ]2 and the bench-stable and inexpensive borylation reagent B2 pin2 that produces H2 as the only by-product. A full set of kinetic, spectroscopic, and preparative mechanistic studies are indicative of a tandem catalysis mechanism of CH-borylation and dehydrocoupling via molecular CoI catalysts.

DockStream: a docking wrapper to enhance de novo molecular design.

Recently, we have released the de novo design platform REINVENT in version 2.0. This improved and extended iteration supports far more features and scoring function components, which allows bespoke and tailor-made protocols to maximize impact in small molecule drug discovery projects. A major obstacle of generative models is producing active compounds, in which predictive (QSAR) models have been applied to enrich target activity. However, QSAR models are inherently limited by their applicability domains. To overcome these limitations, we introduce a structure-based scoring component for REINVENT. DockStream is a flexible, stand-alone molecular docking wrapper that provides access to a collection of ligand embedders and docking backends. Using the benchmarking and analysis workflow provided in DockStream, execution and subsequent analysis of a variety of docking configurations can be automated. Docking algorithms vary greatly in performance depending on the target and the benchmarking and analysis workflow provides a streamlined solution to identifying productive docking configurations. We show that an informative docking configuration can inform the REINVENT agent to optimize towards improving docking scores using public data. With docking activated, REINVENT is able to retain key interactions in the binding site, discard molecules which do not fit the binding cavity, harness unused (sub-)pockets, and improve overall performance in the scaffold-hopping scenario. The code is freely available at https://github.com/MolecularAI/DockStream .

Rh(I)/(III)-N-Heterocyclic Carbene Complexes: Effect of Steric Confinement Upon Immobilization on Regio- and Stereoselectivity in the Hydrosilylation of Alkynes.

Rh(I) NHC and Rh(III) Cp* NHC complexes (Cp*=pentamethylcyclopentadienyl, NHC=N-heterocyclic carbene=pyrid-2-ylimidazol-2-ylidene (Py-Im), thiophen-2-ylimidazol-2-ylidene) are presented. Selected catalysts were selectively immobilized inside the mesopores of SBA-15 with average pore diameters of 5.0 and 6.2 nm. Together with their homogenous progenitors, the immobilized catalysts were used in the hydrosilylation of terminal alkynes. For aromatic alkynes, both the neutral and cationic Rh(I) complexes showed excellent reactivity with exclusive formation of the ß(E)-isomer. For aliphatic alkynes, however, selectivity of the Rh(I) complexes was low. By contrast, the neutral and cationic Rh(III) Cp* NHC complexes proved to be highly regio- and stereoselective catalysts, allowing for the formation of the thermodynamically less stable ß-(Z)-vinylsilane isomers at room temperature. Notably, the SBA-15 immobilized Rh(I) catalysts, in which the pore walls provide an additional confinement, showed excellent ß-(Z)-selectivity in the hydrosilylation of aliphatic alkynes, too. Also, in the case of 4-aminophenylacetylene, selective formation of the ß(Z)-isomer was observed with a neutral SBA-15 supported Rh(III) Cp* NHC complex but not with its homogenous counterpart. These are the first examples of high ß(Z)-selectivity in the hydrosilylation of alkynes by confinement generated upon immobilization inside mesoporous silica.

Multicenter Evaluation of a Fully Automated High-Throughput SARS-CoV-2 Antigen Immunoassay.

INTRODUCTION: Molecular testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to suffer from delays and shortages. Antigen tests have recently emerged as a viable alternative to detect patients with high viral loads, associated with elevated risk of transmission. While rapid lateral flow tests greatly improved accessibility of SARS-CoV-2 detection in critical areas, their manual nature limits scalability and suitability for large-scale testing schemes. The Elecsys® SARS-CoV-2 Antigen assay allows antigen immunoassays to be carried out on fully automated high-throughput serology platforms. METHODS: A total of 3139 nasopharyngeal and oropharyngeal swabs were collected at 3 different testing sites in Germany. Swab samples were pre-characterized by reverse transcription real-time polymerase chain reaction (RT-qPCR) and consecutively subjected to the antigen immunoassay on either the cobas e 411 or cobas e 801 analyzer. RESULTS: Of the tested respiratory samples, 392 were PCR positive for SARS-CoV-2 RNA. Median concentration was 2.95 × 104 (interquartile range [IQR] 5.1 × 102-3.5 × 106) copies/ml. Overall sensitivity and specificity of the antigen immunoassay were 60.2% (95% confidence interval [CI] 55.2-65.1) and 99.9% (95% CI 99.6-100.0), respectively. A 93.7% (95% CI 89.7-96.5) sensitivity was achieved at a viral RNA concentration ≥ 104 copies/ml (~ cycle threshold [Ct] value < 29.9). CONCLUSION: The Elecsys SARS-CoV-2 Antigen assay reliably detected patient samples with viral loads ≥ 10,000 copies/ml. It thus represents a viable high-throughput alternative for screening of patients or in situations where PCR testing is not readily available.

EASIX for Prediction of Outcome in Hospitalized SARS-CoV-2 Infected Patients.

BACKGROUND: The coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) and has evoked a pandemic that challenges public health-care systems worldwide. Endothelial cell dysfunction plays a key role in pathophysiology, and simple prognosticators may help to optimize allocation of limited resources. Endothelial activation and stress index (EASIX) is a validated predictor of endothelial complications and outcome after allogeneic stem cell transplantation. Aim of this study was to test if EASIX could predict life-threatening complications in patients with COVID-19. METHODS: SARS-CoV-2-positive, hospitalized patients were enrolled onto a prospective non-interventional register study (n=100). Biomarkers were assessed at hospital admission. Primary endpoint was severe course of disease (mechanical ventilation and/or death, V/D). Results were validated in 126 patients treated in two independent institutions. RESULTS: EASIX at admission was a strong predictor of severe course of the disease (odds ratio for a two-fold change 3.4, 95%CI 1.8-6.3, p<0.001), time to V/D (hazard ratio (HR) for a two-fold change 2.0, 95%CI 1.5-2.6, p<0.001) as well as survival (HR for a two-fold change 1.7, 95%CI 1.2-2.5, p=0.006). The effect was retained in multivariable analysis adjusting for age, gender, and comorbidities and could be validated in the independent cohort. At hospital admission EASIX correlated with increased suppressor of tumorigenicity-2, soluble thrombomodulin, angiopoietin-2, CXCL8, CXCL9 and interleukin-18, but not interferon-alpha. CONCLUSION: EASIX is a validated predictor of COVID19 outcome and an easy-to-access tool to segregate patients in need for intensive surveillance.

Higher MLCT lifetime of carbene iron(II) complexes by chelate ring expansion.

Combining strong σ-donating N-heterocyclic carbene ligands and π-accepting pyridine ligands with a high octahedricity in rigid iron(ii) complexes increases the 3MLCT lifetime from 0.15 ps in the prototypical [Fe(tpy)2]2+ complex to 9.2 ps in [Fe(dpmi)2]2+12+. The tripodal CNN ligand dpmi (di(pyridine-2-yl)(3-methylimidazol-2-yl)methane) forms six-membered chelate rings with the iron(ii) centre leading to close to 90° bite angles and enhanced iron-ligand orbital overlap.

Distinct photodynamics of κ-N and κ-C pseudoisomeric iron(II) complexes.

Two closely related FeII complexes with 2,6-bis(1-ethyl-1H-1,2,3-triazol-4yl)pyridine and 2,6-bis(1,2,3-triazol-5-ylidene)pyridine ligands are presented to gain new insights into the photophysics of bis(tridentate) iron(ii) complexes. The [Fe(N^N^N)2]2+ pseudoisomer sensitizes singlet oxygen through a MC state with nanosecond lifetime after MLCT excitation, while the bis(tridentate) [Fe(C^N^C)2]2+ pseudoisomer possesses a similar 3MLCT lifetime as the tris(bidentate) [Fe(C^C)2(N^N)]2+ complexes with four mesoionic carbenes.