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 ICu(dtbppOH) (Cuy-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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

Fundamental Characterization, Photophysics and Photocatalysis of a Base Metal Iron(II)-Cobalt(III) Dyad.

A new base metal iron-cobalt dyad has been obtained by connection between a heteroleptic tetra-NHC iron(II) photosensitizer combining a 2,6-bis[3-(2,6-diisopropylphenyl)imidazol-2-ylidene]pyridine with 2,6-bis(3-methyl-imidazol-2-ylidene)-4,4'-bipyridine ligand, and a cobaloxime catalyst. This novel iron(II)-cobalt(III) assembly has been extensively characterized by ground- and excited-state methods like X-ray crystallography, X-ray absorption spectroscopy, (spectro-)electrochemistry, and steady-state and time-resolved optical absorption spectroscopy, with a particular focus on the stability of the molecular assembly in solution and determination of the excited-state landscape. NMR and UV/Vis spectroscopy reveal dissociation of the dyad in acetonitrile at concentrations below 1 mM and high photostability. Transient absorption spectroscopy after excitation into the metal-to-ligand charge transfer absorption band suggests a relaxation cascade originating from hot singlet and triplet MLCT states, leading to the population of the 3 MLCT state that exhibits the longest lifetime. Finally, decay into the ground state involves a 3 MC state. Attachment of cobaloxime to the iron photosensitizer increases the 3 MLCT lifetime at the iron centre. Together with the directing effect of the linker, this potentially makes the dyad more active in photocatalytic proton reduction experiments than the analogous two-component system, consisting of the iron photosensitizer and Co(dmgH)2 (py)Cl. This work thus sheds new light on the functionality of base metal dyads, which are important for more efficient and sustainable future proton reduction systems.

Electronic Structure of a Diiron Complex: A Multitechnique Experimental Study of [(dppf)Fe(CO) 3]+/0.

Here we explore the electronic structure of the diiron complex [(dppf)Fe(CO)3]0/+ [10/+; dppf = 1,1'-bis(diphenylphosphino)ferrocene] in two oxidation states by an advanced multitechnique experimental approach. A combination of magnetic circular dichroism, X-ray absorption and emission, high-frequency electron paramagnetic resonance (EPR), and Mössbauer spectroscopies is used to establish that oxidation of 10 occurs on the carbonyl iron ion, resulting in a low-spin iron(I) ion. It is shown that an unequivocal result is obtained by combining several methods. Compound 1+ displays slow spin dynamics, which is used here to study its geometric structure by means of pulsed EPR methods. Surprisingly, these data show an association of the tetrakis[3,5-bis(trifluoromethylphenyl)]borate counterion with 1+.

η3 -Coordination and Functionalization of the 2-Phosphaethynthiolate Anion at Lanthanum(III)*.

We present the η3 -coordination of the 2-phosphaethynthiolate anion in the complex (PN)2 La(SCP) (2) [PN=N-(2-(diisopropylphosphanyl)-4-methylphenyl)-2,4,6-trimethylanilide)]. Structural comparison with dinuclear thiocyanate-bridged (PN)2 La(µ-1,3-SCN)2 La(PN)2 (3) and azide-bridged (PN)2 La(µ-1,3-N3 )2 La(PN)2 (4) complexes indicates that the [SCP]- coordination mode is mainly governed by electronic, rather than steric factors. Quantum mechanical investigations reveal large contributions of the antibonding π*-orbital of the [SCP]- ligand to the LUMO of complex 2, rendering it the ideal precursor for the first functionalization of the [SCP]- anion. Complex 2 was therefore reacted with CAACs which induced a selective rearrangement of the [SCP]- ligand to form the first CAAC stabilized group 15-group 16 fulminate-type complexes (PN)2 La{SPC(R CAAC)} (5 a,b, R=Ad, Me). A detailed reaction mechanism for the SCP-to-SPC isomerization is proposed based on DFT calculations.

A von Hamos-type hard X-ray spectrometer at the PETRA III beamline P64.

The design and performance of the high-resolution wavelength-dispersive multi-crystal von Hamos-type spectrometer at PETRA III beamline P64 are described. Extended analyzer crystal collection available at the beamline allows coverage of a broad energy range from 5 keV to 20 keV with an energy resolution of 0.35-1 eV. Particular attention was paid to enabling two-color measurements by a combination of two types of analyzer crystals and two two-dimensional detectors. The performance of the spectrometer is demonstrated by elastic-line and emission-line measurements on various compounds.

Intersystem Crossing and Triplet Dynamics in an Iron(II) N-Heterocyclic Carbene Photosensitizer.

The electronic excited states of the iron(II) complex [FeII(tpy)(pyz-NHC)]2+ [tpy = 2,2':6',2″-terpyridine; pyz-NHC = 1,1'-bis(2,6-diisopropylphenyl)pyrazinyldiimidazolium-2,2'-diylidene] and their relaxation pathways have been theoretically investigated. To this purpose, trajectory surface-hopping simulations within a linear vibronic coupling model including a 244-dimensional potential energy surface (PES) with 20 singlet and 20 triplet coupled states have been used. The simulations show that, after excitation to the lowest-energy absorption band of predominant metal-to-ligand charge-transfer character involving the tpy ligand, almost 80% of the population undergoes intersystem crossing to the triplet manifold in about 50 fs, while the remaining 20% decays through internal conversion to the electronic ground state in about 300 fs. The population transferred to the triplet states is found to deactivate into two different regions of the PESs, one where the static dipole moment is small and shows increased metal-centered character and another with a large static dipole moment, where the electron density is transferred from the tpy to pyz-NHC ligand. Coherent oscillations of 400 fs are observed between these two sets of triplet populations, until the mixture equilibrates to a ratio of 60:40. Finally, the importance of selecting suitable normal modes is highlighted-a choice that can be far from straightforward in transition-metal complexes with hundreds of degrees of freedom.

Ground- and Excited-State Properties of Iron(II) Complexes Linked to Organic Chromophores.

Two new bichromophoric complexes, [Fe(bim-ant)2]2+ and [Fe(bim-pyr)2]2+ ([H2-bim]2+ = 1,1'-(pyridine-2,6-diyl)bis(3-methyl-1H-imidazol-3-ium); ant = 9-anthracenyl; pyr = 1-pyrenyl), are investigated to explore the possibility of tuning the excited-state behavior in photoactive iron(II) complexes to design substitutes for noble-metal compounds. The ground-state properties of both complexes are characterized thoroughly by electrochemical methods and optical absorption spectroscopy, complemented by time-dependent density functional theory calculations. The excited states are investigated by static and time-resolved luminescence and femtosecond transient absorption spectroscopy. Both complexes exhibit room temperature luminescence, which originates from singlet states dominated by the chromophore (1Chrom). In the cationic pro-ligands and in the iron(II) complexes, the emission is shifted to red by up to 110 nm (5780 cm-1). This offers the possibility of tuning the organic chromophore emission by metal-ion coordination. The fluorescence lifetimes of the complexes are in the nanosecond range, while triplet metal-to-ligand charge-transfer (3MLCT) lifetimes are around 14 ps. An antenna effect as in ruthenium(II) polypyridine complexes connected to an organic chromophore is found in the form of an internal conversion within 3.4 ns from the 1Chrom to the 1MLCT states. Because no singlet oxygen forms from triplet oxygen in the presence of the iron(II) complexes and light, efficient intersystem crossing to the triplet state of the organic chromophore (3Chrom) is not promoted in the iron(II) complexes.

Electronic Structure of the Hieber Anion [Fe(CO)3(NO)]- Revisited by X-ray Emission and Absorption Spectroscopy.

While the Hieber anion [Fe(CO)3(NO)]- has been reincarnated in the last years as an active catalyst in organic synthesis, there is still a debate about the oxidation state of the central Fe atom and the resulting charge of the NO ligand. To shed new light on this question and to understand the Fe-NO interaction in the Hieber anion, it is investigated in comparison to the formal 3d8 reference Fe(CO)5 and the formal 3d10 reference [Fe(CO)4]2- by the combination of valence-to-core X-ray emission spectroscopy (VtC-XES), X-ray absorption near-edge structure spectroscopy (XANES), and high-energy-resolution fluorescence-detected XANES. In order to extract information about the electronic structure, time-dependent density functional theory and ground-state density functional theory calculations are applied. This combination of experimental and computational methods reveals that the electron density at the Fe center of the Hieber resembles that of the isoelectronic [Fe(CO)4]2-. These observations challenge recent descriptions of the Hieber anion and reopen the debate about the experimentally and computationally determined Fe oxidation state and charge on the NO ligand.

When Donors Turn into Acceptors: Ground and Excited State Properties of FeII Complexes with Amine-Substituted Tridentate Bis-imidazole-2-ylidene Pyridine Ligands.

In search of new ligand motifs for photoactive iron(II) complexes with long-lived MLCT states, a series of six complexes with tridentate amine-functionalized bis-n-heterocyclic carbene (NHC)-pyridine ligands is presented. In the homoleptic complexes imidazole-, methylimidazole-, or benzimidazole-2-ylidene, NHC donors are employed in combination with pyridine, functionalized in the 4-position by dimethylamine or dibenzylamine. The effects of these different functionalities on the electronic structure of the complexes are examined through detailed ground state characterization by NMR, single crystal X-ray diffraction, as well as electrochemical and spectroscopic methods. The net influence of these different functionalities on orbital-orbital and electrostatic ligand-iron interactions is investigated thoroughly by density functional theory, and changes in the excited state behavior and lifetimes are finally examined by ultrafast optical spectroscopy. Great deviations of the initially expected effects by substitution in 4-position on the photochemical properties are observed, together with a significantly increased π-acceptor interaction strength in the benzimidazole-2-ylidene functionalized complexes.

Exploring the light-induced dynamics in solvated metallogrid complexes with femtosecond pulses across the electromagnetic spectrum.

Oligonuclear complexes of d4-d7 transition metal ion centers that undergo spin-switching have long been developed for their practical role in molecular electronics. Recently, they also have appeared as promising photochemical reactants demonstrating improved stability. However, the lack of knowledge about their photophysical properties in the solution phase compared to mononuclear complexes is currently hampering their inclusion into advanced light-driven reactions. In the present study, the ultrafast photoinduced dynamics in a solvated [2 × 2] iron(II) metallogrid complex are characterized by combining measurements with transient optical-infrared absorption and x-ray emission spectroscopy on the femtosecond time scale. The analysis is supported by density functional theory calculations. The photocycle can be described in terms of intra-site transitions, where the FeII centers in the low-spin state are independently photoexcited. The Franck-Condon state decays via the formation of a vibrationally hot high-spin (HS) state that displays coherent behavior within a few picoseconds and thermalizes within tens of picoseconds to yield a metastable HS state living for several hundreds of nanoseconds. Systematic comparison with the closely related mononuclear complex [Fe(terpy)2]2+ reveals that nuclearity has a profound impact on the photoinduced dynamics. More generally, this work provides guidelines for expanding the integration of oligonuclear complexes into new photoconversion schemes that may be triggered by ultrafast spin-switching.

The curcumin analog HO-3867 selectively kills cancer cells by converting mutant p53 protein to transcriptionally active wildtype p53.

p53 is an important tumor-suppressor protein that is mutated in more than 50% of cancers. Strategies for restoring normal p53 function are complicated by the oncogenic properties of mutant p53 and have not met with clinical success. To counteract mutant p53 activity, a variety of drugs with the potential to reconvert mutant p53 to an active wildtype form have been developed. However, these drugs are associated with various negative effects such as cellular toxicity, nonspecific binding to other proteins, and inability to induce a wildtype p53 response in cancer tissue. Here, we report on the effects of a curcumin analog, HO-3867, on p53 activity in cancer cells from different origins. We found that HO-3867 covalently binds to mutant p53, initiates a wildtype p53-like anticancer genetic response, is exclusively cytotoxic toward cancer cells, and exhibits high anticancer efficacy in tumor models. In conclusion, HO-3867 is a p53 mutant-reactivating drug with high clinical anticancer potential.