Fluorogenic probes for detecting deacylase and demethylase activity towards post-translationally-modified lysine residues

Reversible enzymatic post-translational modification of the ε-amino groups of lysine residues (e.g. N-acylation reactions) plays an important role in regulating the cellular activities of numerous proteins. This study describes how enzyme catalyzed N-deprotection of lysine residues of non-fluorescent peptide-coumarin probes can be used to generate N-deprotected peptides that undergo spontaneous O- to N-ester transfer reactions (uncatalyzed) to generate a highly fluorescent N-carbamoyl peptide. This enables detection of enzyme catalyzed N-deacetylation, N-demalonylation, N-desuccinylation and N-demethylation reactions activities towards the N-modified lysine residues of these probes using simple ‘turn on’ fluorescent assays.

We developed “turn-on” fluorescent probes that detect enzymatic lysine deacylation and demethylation critical for epigenetic and other cellular phenomena, using intramolecular O- to N-ester transfer reactions.     

Solid-state NMR spectroscopy: an advancing tool to analyse the structure and properties of metal–organic frameworks

Metal–organic frameworks (MOFs) gain increasing interest due to their outstanding properties like extremely high porosity, structural variability, and various possibilities for functionalization. Their overall structure is usually determined by diffraction techniques. However, diffraction is often not sensitive for subtle local structural changes and ordering effects as well as dynamics and flexibility effects. Solid-state nuclear magnetic resonance (ssNMR) spectroscopy is sensitive for short range interactions and thus complementary to diffraction techniques. Novel methodical advances make ssNMR experiments increasingly suitable to tackle the above mentioned problems and challenges. NMR spectroscopy also allows study of host–guest interactions between the MOF lattice and adsorbed guest species. Understanding the underlying mechanisms and interactions is particularly important with respect to applications such as gas and liquid separation processes, gas storage, and others. Special in situ NMR experiments allow investigation of properties and functions of MOFs under controlled and application-relevant conditions. The present minireview explains the potential of various solid-state and in situ NMR techniques and illustrates their application to MOFs by highlighting selected examples from recent literature.

Metal–organic frameworks (MOFs) gain increasing interest due to their outstanding properties like extremely high porosity, structural variability, and various possibilities for functionalization.     

Enhanced catalytic reaction at an air–liquid–solid triphase interface

Gaseous reactant involved heterogeneous catalysis is critical to the development of clean energy, environmental management, health monitoring, and chemical synthesis. However, in traditional heterogeneous catalysis with liquid–solid diphase reaction interfaces, the low solubility and slow transport of gaseous reactants strongly restrict the reaction efficiency. In this minireview, we summarize recent advances in tackling these drawbacks by designing catalytic systems with an air–liquid–solid triphase joint interface. At the triphase interface, abundant gaseous reactants can directly transport from the air phase to the reaction centre to overcome the limitations of low solubility and slow transport of the dissolved gas in liquid–solid diphase reaction systems. By constructing a triphase interface, the efficiency and/or selectivity of photocatalytic reactions, enzymatic reactions, and (photo)electrochemical reactions with consumption of gaseous reactants oxygen, carbon dioxide, and nitrogen are significantly improved.

Gaseous reactant involved liquid–solid diphase interface reactions can be significantly enhanced using rationally designed and constructed air–liquid–solid triphase systems.     

A germaaluminocene

The reactions of dipotassium germacyclopentadienediide with two Group 13 dichlorides, Cp*BCl₂ and Cp*AlCl₂, yield two structurally different products. In the case of boron a borole complex of germanium(ii) is obtained. The aluminium halide gives an unprecedented neutral germaaluminocene. Both compounds were fully characterised by multinuclear NMR spectroscopy supported by DFT computations. The molecular structure of the germaaluminocene was determined by XRD.

Boron vs. aluminum: the synthesis of a borole complex of Ge(ii) is reported. Changing just the element from boron to aluminum unexpectedly yields an unprecedented neutral germaaluminocene.     

Ultrasensitive small molecule fluorogenic probe for human heparanase

Heparanase (HPA) is a critical enzyme involved in the remodeling of the extracellular matrix (ECM), and its elevated expression has been linked with diseases such as various types of cancer and inflammation. The detection of heparanase enzymatic activity holds tremendous value in the study of the cellular microenvironment, and search of molecular therapeutics targeting heparanase, however, no structurally defined probes are available for the detection of heparanase activity. Here we present the development of the first ultrasensitive fluorogenic small-molecule probe for heparanase enzymatic activity via tuning the electronic effect of the substrate. The probe exhibits a 756-fold fluorescence turn-on response in the presence of human heparanase, allowing one-step detection of heparanase activity in real-time with a picomolar detection limit. The high sensitivity and robustness of the probe are exemplified in a high-throughput screening assay for heparanase inhibitors.

Heparanase, a critical enzyme involved in the remodeling of the extracellular matrix, activates a disaccharide probe HADP to give a strong fluorescence signal.     

Fluorescent small organic probes for biosensing

Small-molecule based fluorescent probes are increasingly important for the detection and imaging of biological signaling molecules due to their simplicity, high selectivity and sensitivity, whilst being non-invasive, and suitable for real-time analysis of living systems. With this perspective we highlight sensing mechanisms including Förster resonance energy transfer (FRET), intramolecular charge transfer (ICT), photoinduced electron transfer (PeT), excited state intramolecular proton transfer (ESIPT), aggregation induced emission (AIE) and multiple modality fluorescence approaches including dual/triple sensing mechanisms (DSM or TSM). Throughout the perspective we highlight the remaining challenges and suggest potential directions for development towards improved small-molecule fluorescent probes suitable for biosensing.

Small-molecule based fluorescent probes are increasingly important for the detection and imaging of biological signaling molecules due to their simplicity, high selectivity and sensitivity, whilst being non-invasive, and suitable for real-time analysis of living systems.     

Tandem aza-Heck Suzuki and carbonylation reactions of O-phenyl hydroxamic ethers: complex lactams via carboamination

The palladium-catalysed tandem aza-Heck–Suzuki and aza-Heck–carbonylation reactions of O-phenyl hydroxamic ethers are reported. These formal alkene carboamination reactions provide highly versatile access to wide range complex, stereogenic secondary lactams and exhibit outstanding functional group tolerance and high diastereoselectivity.

The palladium-catalysed tandem aza-Heck–Suzuki and aza-Heck–carbonylation reactions of O-phenyl hydroxamic ethers are reported.     

Chemoenzymatic elaboration of the Raper–Mason pathway unravels the structural diversity within eumelanin pigments

Melanin is a central polymer in living organisms, yet our understanding of its molecular structure remains unresolved. Here, we apply a biosynthetic approach to explore the composite structures accessible in one type of melanin, eumelanin. Using a combination of solid-state NMR, dynamic nuclear polarization, and electron microscopy, we reveal how a variety of monomers are enzymatically polymerized into their corresponding eumelanin pigments. We demonstrate how this approach can be used to unite structure with an understanding of enzymatic activity, substrate scope, and the regulation of nanostructural features. Overall, this data reveals how intermediate metabolites of the Raper–Mason metabolic pathway contribute to polymerization, allowing us to revisit the original proposal of how eumelanin is biosynthesized.

Melanin is a central polymer in living organisms, yet our understanding of its molecular structure remains unresolved.     

Identifying key mononuclear Fe species for low-temperature methane oxidation

The direct functionalization of methane into platform chemicals is arguably one of the holy grails in chemistry. The actual active sites for methane activation are intensively debated. By correlating a wide variety of characterization results with catalytic performance data we have been able to identify mononuclear Fe species as the active site in the Fe/ZSM-5 zeolites for the mild oxidation of methane with H₂O₂ at 50 °C. The 0.1% Fe/ZSM-5 catalyst with dominant mononuclear Fe species possess an excellent turnover rate (TOR) of 66 mol_MeOH mol_Fe⁻¹ h⁻¹, approximately 4 times higher compared to the state-of-the-art dimer-containing Fe/ZSM-5 catalysts. Based on a series of advanced in situ spectroscopic studies and ¹H- and ¹³C- nuclear magnetic resonance (NMR), we found that methane activation initially proceeds on the Fe site of mononuclear Fe species. With the aid of adjacent Brønsted acid sites (BAS), methane can be first oxidized to CH₃OOH and CH₃OH, and then subsequently converted into HOCH₂OOH and consecutively into HCOOH. These findings will facilitate the search towards new metal-zeolite combinations for the activation of C–H bonds in various hydrocarbons, for light alkanes and beyond.

The monomeric Fe species in Fe/ZSM-5 have been identified as the intrinsic active sites for the low-temperature methane oxidation.     

Supramolecular strategies in artificial photosynthesis

Artificial photosynthesis is a major scientific endeavor aimed at converting solar power into a chemical fuel as a viable approach to sustainable energy production and storage. Photosynthesis requires three fundamental actions performed in order; light harvesting, charge-separation and redox catalysis. These actions span different timescales and require the integration of functional architectures developed in different fields of study. The development of artificial photosynthetic devices is therefore inherently complex and requires an interdisciplinary approach. Supramolecular chemistry has evolved to a mature scientific field in which programmed molecular components form larger functional structures by self-assembly processes. Supramolecular chemistry could provide important tools in preparing, integrating and optimizing artificial photosynthetic devices as it allows precise control over molecular components within such a device. This is illustrated in this perspective by discussing state-of-the-art devices and the current limiting factors – such as recombination and low stability of reactive intermediates – and providing exemplary supramolecular approaches to alleviate some of those problems. Inspiring supramolecular solutions such as those discussed herein will incite expansion of the supramolecular toolbox, which eventually may be needed for the development of applied artificial photosynthesis.

This review describes supramolecular strategies for optimization and integration of components needed for the fundamentals of artificial photosynthesis: light harvesting, charge-separation and catalysis, which are relevant for solar-to-fuel devices.     

Broad-band spectroscopy of a vanadyl porphyrin: a model electronuclear spin qudit

We explore how to encode more than a qubit in vanadyl porphyrin molecules hosting a S = 1/2 electronic spin coupled to a I = 7/2 nuclear spin. The spin Hamiltonian and its parameters, as well as the spin dynamics, have been determined via a combination of electron paramagnetic resonance, heat capacity, magnetization and on-chip magnetic spectroscopy experiments performed on single crystals. We find low temperature spin coherence times of micro-seconds and spin relaxation times longer than a second. For sufficiently strong magnetic fields (B > 0.1 T, corresponding to resonance frequencies of 9–10 GHz) these properties make vanadyl porphyrin molecules suitable qubit realizations. The presence of multiple equispaced nuclear spin levels then merely provides 8 alternatives to define the ‘1’ and ‘0’ basis states. For lower magnetic fields (B < 0.1 T), and lower frequencies (<2 GHz), we find spectroscopic signatures of a sizeable electronuclear entanglement. This effect generates a larger set of allowed transitions between different electronuclear spin states and removes their degeneracies. Under these conditions, we show that each molecule fulfills the conditions to act as a universal 4-qubit processor or, equivalently, as a d = 16 qudit. These findings widen the catalogue of chemically designed systems able to implement non-trivial quantum functionalities, such as quantum simulations and, especially, quantum error correction at the molecular level.

We show that a sizeable electronuclear entanglement of the S = 1/2 and I = 7/2 spins of a vanadyl porphyrin provides the conditions to act as a universal 4-qubit processor, and thus implement quantum error correction at the molecular level.     

Shaping non-noble metal nanocrystals via colloidal chemistry

Non-noble metal nanocrystals with well-defined shapes have been attracting increasingly more attention in the last decade as potential alternatives to noble metals, by virtue of their earth abundance combined with intriguing physical and chemical properties relevant for both fundamental studies and technological applications. Nevertheless, their synthesis is still primitive when compared to noble metals. In this contribution, we focus on third row transition metals Mn, Fe, Co, Ni and Cu that are recently gaining interest because of their catalytic properties. Along with providing an overview on the state-of-the-art, we discuss current synthetic strategies and challenges. Finally, we propose future directions to advance the synthetic development of shape-controlled non-noble metal nanocrystals in the upcoming years.

This minireview describes the state-of-the-art of shape-controlled nanocrystals of third raw transition metals and discusses future directions to advance their synthetic development, which is important for many applications.     

Recent progress in the improvement of hydrothermal stability of zeolites

Zeolites have been successfully employed in many catalytic reactions of industrial relevance. The severe conditions required in some processes, where high temperatures are frequently combined with the presence of steam, highlight the need of considering the evolution of the catalyst structure during the reaction. This review attempts to summarize the recently developed strategies to improve the hydrothermal framework stability of zeolites.

This review attempts to summarize the recently developed strategies to improve the hydrothermal framework stability of zeolites.     

A ground-state-dominated magnetic field effect on the luminescence of stable organic radicals

Organic radicals are an emerging class of luminophores possessing multiplet spin states and potentially showing spin-luminescence correlated properties. We investigated the mechanism of recently reported magnetic field sensitivity in the emission of a photostable luminescent radical, (3,5-dichloro-4-pyridyl)bis(2,4,6-trichlorophenyl)methyl radical (PyBTM) doped into host αH-PyBTM molecular crystals. The magnetic field (0–14 T), temperature (4.2–20 K), and the doping concentration (0.1, 4, 10, and 22 wt%) dependence on the time-resolved emission were examined by measuring emission decays of the monomer and excimer. Quantum mechanical simulations on the decay curves disclosed the role of the magnetic field; it dominantly affects the spin sublevel population of radical dimers in the ground states. This situation is distinctly different from that in conventional closed-shell luminophores, where the magnetic field modulates their excited-state spin multiplicity. Namely, the spin degree of freedom of ground-state open-shell molecules is a new key for achieving magnetic-field-controlled molecular photofunctions.

We investigated the mechanism of the magnetic field effect (MFE) on the emission of a luminescent radical doped into host crystals. It was revealed that the spin sublevel population of radical dimers in the ground states is the key that governs the MFE.     

Identifying reactive intermediates by mass spectrometry

Development of new reactions requires finding and understanding of novel reaction pathways. In challenging reactions such as C–H activations, these pathways often involve highly reactive intermediates which are the key to our understanding, but difficult to study. Mass spectrometry has a unique sensitivity for detecting low abundant charged species; therefore it is increasingly used for detection of such intermediates in metal catalysed- and organometallic reactions. This perspective shows recent developments in the field of mass spectrometric research of reaction mechanisms with a special focus on going beyond mass-detection. Chapters discuss the advantages of collision-induced dissociation, ion mobility and ion spectroscopy for characterization of structures of the detected intermediates. In addition, we discuss the relationship between the condensed phase chemistry and mass spectrometric detection of species from solution.

Modern approaches of mass spectrometry can identify reaction intermediates and provide a unique insight into their structure, properties and kinetics.     

Salient features of the aza-Wacker cyclization reaction

The intramolecular aza-Wacker reaction has unparalleled potential for the site-selective amination of olefins, but it is perhaps underappreciated relative to other alkene oxidations. The first part of this review makes the distinction between classical and tethered aza-Wacker cyclization reactions and summarizes examples of the latter. The second portion focuses on developments in asymmetric aza-Wacker cyclization technology. The final part of the review summarizes applications of all classes of aza-Wacker cyclization reactions to natural product assembly.

The aza-Wacker cyclization reaction is a powerful strategy for alkene amination.     

Synthesis of oxalamides by acceptorless dehydrogenative coupling of ethylene glycol and amines and the reverse hydrogenation catalyzed by ruthenium

A sustainable, new synthesis of oxalamides, by acceptorless dehydrogenative coupling of ethylene glycol with amines, generating H₂, homogeneously catalyzed by a ruthenium pincer complex, is presented. The reverse hydrogenation reaction is also accomplished using the same catalyst. A plausible reaction mechanism is proposed based on stoichiometric reactions, NMR studies, X-ray crystallography as well as observation of plausible intermediates.

Ruthenium catalyzed acceptorless dehydrogenative coupling of ethylene glycol and amines to oxalamides is reported. The reverse hydrogenation reaction is also accomplished.     

In situ visualization of peroxisomal viscosity in the liver of mice with non-alcoholic fatty liver disease by near-infrared fluorescence and photoacoustic imaging

Non-alcoholic fatty liver disease (NAFLD) can gradually develop into hepatic failure, and early diagnosis is crucial to improve treatment efficiency. The occurrence of NAFLD is closely related to lipid metabolism. Peroxisomes act as the first and main site for lipid metabolism in the hepatocytes, so abnormal lipid metabolism might directly affect peroxisomal viscosity. Herein, we developed a new near-infrared fluorescence (NIRF) and photoacoustic (PA) imaging probe (PV-1) for the real-time visualization of peroxisomal viscosity in vivo. This PV-1 encompasses the malononitrile group as the rotor, which emits strong NIRF (at 705 nm) and PA (at 680 nm) signals when rotation is hindered as viscosity increases. Through dual-mode imaging, we discovered distinctly higher viscosity in the liver of NAFLD mice for the first time. We further found the remarkable amelioration of NAFLD upon treatment with N-acetylcysteine (NAC). Therefore, we anticipate that the PV-1 imaging method is promising for the early diagnosis and prognostic evaluation of NAFLD.

We report a novel near-infrared fluorescence/photoacoustic imaging method for peroxisomal viscosity, enabling an accurate diagnosis and drug evaluation of non-alcoholic fatty liver disease.     

Et3SiH + KOtBu provide multiple reactive intermediates that compete in the reactions and rearrangements of benzylnitriles and indolenines

The combination of potassium tert-butoxide and triethylsilane is unusual because it generates multiple different types of reactive intermediates simultaneously that provide access to (i) silyl radical reactions, (ii) hydrogen atom transfer reactions to closed shell molecules and to radicals, (iii) electron transfer reductions and (iv) hydride ion chemistry, giving scope for unprecedented outcomes. Until now, reactions with this reagent pair have generally been explained by reference to one of the intermediates, but we now highlight the interplay and competition between them.

The combination of potassium tert-butoxide and triethylsilane provides simultaneous access to multiple reactive intermediates, radicals, H-atom donors, hydride donors and electron donors, giving scope for unprecedented reaction outcomes.