Isotope Labeling Research Articles

Molecular Engineering of Metal–Organic Frameworks for Boosting Photocatalytic Hydrogen Peroxide Production

AbstractThe development of novel metal–organic frameworks (MOFs) as efficient photocatalysts for hydrogen peroxide production from water and oxygen is particularly interesting, yet remains a challenge. Herein, we have prepared four cyclic trinuclear units (CTUs) based MOFs, exhibiting good light absorption ability and suitable band gaps for photosynthesis of H2O2. However, Cu‐CTU‐based MOFs are not able to photocatalyzed the formation of H2O2, while the alteration of metal nodes from Cu‐CTU to Ag‐CTU dramatically enhances the photocatalytic performance for H2O2 production and the production rates can reach as high as 17476 μmol g−1 h−1 with an apparent quantum yield of 4.72 %, at 420 nm, which is much higher than most reported MOFs. The photocatalytic mechanism is comprehensively studied by combining the isotope labeling experiments and DFT calculation. This study provides new insights into the preparation of MOF photocatalysts with high activity for H2O2 production through molecular engineering.

Incorporating Zinc Metal Sites in Aluminum-Coordinated Porphyrin Metal-Organic Frameworks for Enhanced Photocatalytic Nitrogen Reduction to Ammonia.

Rationally designing photocatalysts is crucial for the solar-driven nitrogen reduction reaction (NRR) due to the stable N≡N triple bond. Metal-organic frameworks (MOFs) are considered promising candidates but suffer from insufficient active sites and inferior charge transport. Herein, it is demonstrated that incorporating 3d metal ions, such as zinc (Zn) or iron (Fe) ions, into Al-coordinated porphyrin MOFs (Al-PMOFs) enables the enhanced ammonia yield of 88.7 and 65.0µggcat -1h-1, 2.5- and 1.8-fold increase compared to the pristine Al-PMOF (35.4µggcat -1h-1), respectively. The origin of ammonia (NH3) is verified via isotopic labeling experiments. Incorporating Zn or Fe into Al-PMOF generates active sites in Al-PMOF, that is, Zn-N4 or Fe-N4 sites, which not only facilitates the adsorption and activation of N2 molecules but suppresses the charge recombination. Photophysical and theoretical studies further reveal the upshift of the lowest unoccupied molecular orbital (LUMO) level to a more energetic position upon inserting 3d metal ions (with a more significant shift in Zn than Fe). The promoted nitrogen activation, suppressed charge recombination, and more negative LUMO levels in Al-PMOF(3d metal) contribute to a higher photocatalytic activity than pristine Al-PMOF. This work provides a promising strategy for designing photocatalysts for efficient solar-to-chemical conversion.

Microplastic exposure inhibits nitrate uptake and assimilation in wheat plants

Microplastic (MP) contamination in soil severely impairs plant growth. However, mechanisms underlying the effects of MPs on plant nutrient uptake remain largely unknown. In this study, we revealed that NO3− content was significantly decreased in shoots and roots of wheat plants exposed to high concentrations (50–100 mg L−1) of MPs (1 μm and 0.1 μm; type: polystyrene) in the hydroponic solution. Isotope labeling experiments demonstrated that MP exposure led to a significant inhibition of NO3− uptake in wheat roots. Further analysis indicated that the presence of MPs markedly inhibited root growth and caused oxidative damage to the roots. Additionally, superoxide dismutase and peroxidase activities in wheat roots decreased under all MP treatments, whereas catalase and ascorbate peroxidase activities significantly increased under the 100 mg L−1 MP treatment. The transcription levels of most nitrate transporters (NRTs) in roots were significantly downregulated by MP exposure. Furthermore, exposure to MPs distinctly suppressed the activity of nitrate reductase (NR) and nitrite reductase (NiR), as well as the expression levels of their coding genes in wheat shoots. These findings indicate that a decline in root uptake area and root vitality, as well as in the expression of NRTs, NR, and NiR genes caused by MP exposure may have adverse effects on NO3− uptake and assimilation, consequently impairing normal growth of plants.

Stable isotope labeling and functional gene prediction elucidate the carbon metabolism in fermentative bacteria and microalgae coupling system

The application of the fermentative bacteria and microalgae coupling system in the wastewater treatment has been studied, but there remains few knowledge regarding the organic and inorganic carbon metabolism within this system. In this study, the carbon metabolism of microalgae and fermentative bacteria was elucidated by 13C stable isotope labeling and functional gene prediction, respectively. The 13C glucose and 13C NaHCO3 were used as stable isotope tracers to clarify the organic and inorganic carbon metabolism of microalgae, indicating that approximately 71.5 % of the Acetyl-CoA in microalgae was synthesized from organic carbon sources, while 26.8 % was synthesized through the utilization of inorganic carbon sources. Inorganic carbon sources can enhance the activity of photosynthetic system and facilitate the Calvin cycle. Considering the adequate organic carbon sources and insufficient inorganic carbon sources in the fermentative bacteria and microalgae coupling system, NaHCO3 was added to improve carbon utilization of microalgae. The maximum microalgal lipid yield reached 1130.37 mg/L with 1000 mg/L NaHCO3 supplementation. Functional gene prediction was used to analysis the effect of various carbon composition on the bacterial carbon metabolism. Notably, the additional inorganic carbon sources increased the abundance of bacterial functional genes associated with the fermentation and acetic acids synthesis, which was advantageous for VFAs production and further promoted microalgae growth. This study can gain a deeper understanding of microbial metabolic mechanisms during the operation of fermentative bacteria and microalgae system, and improve its sustained operational stability.

Mechanism of bioactive 3,3′-diindolylmethane formation in flaxseed meal-xylose-tryptophan maillard reaction

3,3′-Diindolylmethane (DIM) has attracted extensive attention due to its bioactivity, and is applied to the fields of food, medicine and so on. In the study, DIM was isolated from the flaxseed meal-xylose-tryptophan Maillard reaction products. Its formation mechanism was investigated using the isotope labeling method. The reactive sites in DIM were analyzed by quantum chemistry calculation. The results showed that the Maillard reaction of tryptophan and xylose produced indole-3-formaldehyde, which further reacted to generate indole-3-methanol. Indole-3-methanol was unstable and eventually formed DIM. The molecular structure of DIM was determined and then the best configuration was obtained by frequency calculation. The molecular potential energy and frontier molecular orbital analysis showed that the main action site in DIM was near the indole ring. This study may provide a theoretical basis for in-depth studies on the relationship between the molecular structure and properties of DIM, broaden its applications in food, and offer a reference for the rational development of functional foods.

Copper Deposited on Reduced Titania as Catalyst for the Production of CH4 from Sunlight and Air

AbstractAtmospheric CO2 and H2O adsorbed on the photocatalyst surface undergo sunlight‐assisted conversion to solar products that bridge the gaps between artificial and natural photosynthesis. Herein, we report a Lewis acid‐base interaction derived photocatalyst, Cu deposited on reduced titania, that harvests CO2 and H2O from the air and transforms them to CH4. Photocatalyst surface studies confirm that coordinately unsaturated Cu atoms and oxygen vacancies are formed that facilitate CO2 and H2O adsorption. The mechanistic studies, combined with tandem secondary ion mass spectroscopy and isotopic labelling, confirm the CH4 origin from atmosphere‐adsorbed CO2 and H2O. The contributing factors to photocatalyst instability are explored. We expect that this study will have an impact on the widespread application and economic viability of photocatalytic CO2 reduction.

Spectroscopic Investigation of the Role of Water in Copper Zeolite Methane Oxidation.

Methane is one of the most potent greenhouse gases; developing technology for its abatement is essential for combating climate change. Copper zeolites can activate methane at low temperatures and pressures, demonstrating promise for this technology. However, a barrier to industrial implementation is the inability to recycle the Cu(II) active site. Anaerobic active site regeneration has been reported for copper-loaded mordenite, where it is proposed that water oxidizes Cu(I) formed from the methane reaction, producing H2 gas as a byproduct. However, this result has been met with skepticism given the overall reaction is thermodynamically unfavorable. In this study, we use X-ray absorption and electron paramagnetic resonance spectroscopies to study the role of water in copper zeolite methane oxidation. We find that water does not oxidize Cu(I) to Cu(II) in CH4-reacted Cu-MOR. Further, using isotope label mass spectrometry, we detail an alternate source of the hydrogen byproduct. We uncover that, although water does not oxidize Cu(I), it has the potential to facilitate low temperature methane abatement through promotion of product decomposition to carbon dioxide and H2.

Berberine alleviates ulcerative colitis by inhibiting inflammation through targeting IRGM1

BackgroundBerberine (BBR), the main active component of Coptis chinensis Franch., has a variety of pharmacological effects, notably anti-inflammatory, which make it a potential treatment for ulcerative colitis (UC). Nevertheless, the specific target and the mode of action of BBR against UC are still unclear. PurposeHere, we aim to identify BBR's anti-inflammatory target and its mode of action in UC treatment. MethodsThe therapeutic effects of BBR and Coptis chinensis Franch. extract were first assessed in UC mice. Then, stable isotope labeling using amino acids in cell culture-activity-based protein profiling (SILAC-ABPP) was applied to identify the anti-inflammatory target proteins of BBR in an inflammation model of RAW264.7 cells stimulated by LPS. Molecular docking, drug affinity responsive target stability (DARTS), molecular dynamics simulation, cellular thermal shift assay (CETSA), and biological layer interference (BLI) measurement were employed to study the interaction between BBR and its targets. Lentiviral transfection was used to knock down the target protein and investigate BBR's anti-inflammatory mechanism. ResultsBBR and Coptis chinensis Franch. extracts both significantly alleviated UC in mice. SILAC-ABPP identified IRGM1 as BBR's anti-inflammatory target, with its overexpression reduced by BBR treatment in both RAW264.7 cell inflammation models stimulated by LPS and UC mice. BBR significantly reduced inflammatory cytokines in LPS-induced RAW264.7 cells by blocking the PI3K/AKT/mTOR pathway. Knockdown of IRGM1 weakened BBR's effects on cytokine expression and pathway regulation. ConclusionFor the first time, IRGM1 was identified as the direct anti-inflammatory target of BBR. BBR has the potential to inhibit IRGM1 expression in vitro as well as in vivo. The molecular mechanism of BBR's anti-inflammatory activity was inhibiting the PI3K/AKT/mTOR pathway by targeting IRGM1.

Metagenomic insights into nitrogen cycling functional gene responses to nitrogen fixation and transfer in maize-peanut intercropping.

The fixation and transfer of biological nitrogen from peanuts to maize in maize-peanut intercropping systems play a pivotal role in maintaining the soil nutrient balance. However, the mechanisms through which root interactions regulate biological nitrogen fixation and transfer remain unclear. This study employed a 15N isotope labelling method to quantify nitrogen fixation and transfer from peanuts to maize, concurrently elucidating key microorganisms and genera in the nitrogen cycle through metagenomic sequencing. The results revealed that biological nitrogen fixation in peanut was 50 mg and transfer to maize was 230 mg when the roots interacted. Moreover, root interactions significantly increased nitrogen content and the activities of protease, dehydrogenase (DHO) and nitrate reductase in the rhizosphere soil. Metagenomic analyses and structural equation modelling indicated that nrfC and nirA genes played important roles in regulating nitrogen fixation and transfer. Bradyrhizobium was affected by soil nitrogen content and DHO, indirectly influencing the efficiency of nitrogen fixation and transfer. Overall, our study identified key bacterial genera and genes associated with nitrogen fixation and transfer, thus advancing our understanding of interspecific interactions and highlighting the pivotal role of soil microorganisms and functional genes in maintaining soil ecosystem stability from a molecular ecological perspective.

Pyridine-based strategies towards nitrogen isotope exchange and multiple isotope incorporation

Isotopic labeling is at the core of health and life science applications such as nuclear imaging, metabolomics and plays a central role in drug development. The rapid access to isotopically labeled organic molecules is a sine qua non condition to support these societally vital areas of research. Based on a rationally driven approach, this study presents an innovative solution to access labeled pyridines by a nitrogen isotope exchange reaction based on a Zincke activation strategy. The technology conceptualizes an opportunity in the field of isotope labeling. 15N-labeling of pyridines and other relevant heterocycles such as pyrimidines and isoquinolines showcases on a large set of derivatives, including pharmaceuticals. Finally, we explore a nitrogen-to-carbon exchange strategy in order to access 13C-labeled phenyl derivatives and deuterium labeling of mono-substituted benzene from pyridine-2H5. These results open alternative avenues for multiple isotope labeling on aromatic cores.

Incorporation of the 15N-labeled simulated arthropod rain in the soil food web.

Direct trophic links between aboveground and belowground animal communities are rarely considered in food web models. Most invertebrate animals inhabiting aboveground space eventually become prey of soil predators and scavengers forming a gravity-driven spatial subsidy to detrital food webs, but its importance remains unquantified. We used laboratory-grown 15N-labeled Collembola to trace the incorporation of arthropod rain into soil food webs. Live or euthanized Collembola were supplemented once to field mesocosms in the amount equivalent to the mean daily input of the arthropod rain (19mg d.w. m-2). After the addition of live Collembola, the isotopic label was found most often in predatory Trombidiformes (83% of samples) and Mesostigmata mites (85%), followed by Araneae (58%), Chilopoda (45%), and Coleoptera (29%). Among non-predatory groups, the isotopic label was recorded in Thysanoptera (27%), Collembola (24%), and Oribatida (18%). The 15N-label was also detected in Symphyla, Formicidae, Diplura, Diplopoda, Opiliones, Diptera, Hemiptera, Oligochaeta, and Nematoda. There was a positive correlation between natural 15N abundance and the frequency of the isotopic label among predators, but not among decomposers. In the non-replicated treatment, in which dead collembolans were added, the label was found in predators and decomposers in approximately equal proportions (21-25%). Unlike other forms of the aboveground subsidy (such as leaflitter, frass, or honeydew) that are primarily processed by microorganisms, arthropod rain is assimilated directly by the animals. The high frequency of consumption of the aboveground subsidy suggests that it plays a significant role in maintaining the abundance of soil predators.

Biosynthesis of the Non-canonical C17 Sesquiterpenoids Chlororaphen A and B from Pseudomonas chlororaphis.

Chlororaphens A and B are structurally unique non-canonical C17 sesquiterpenoids from Pseudomonas chlororaphis that are made by two SAM-dependent methyltransferases and a type I terpene synthase. This study addresses the mechanism of their formation in isotopic labelling experiments and DFT calculations. The results demonstrate an astonishing complexity with distribution of labellings within a cyclopentane core that is reversely connected to two acyclic fragments in chlororaphen A and B. In addition, the uptake of up to 14 deuterium atoms from D2O was observed. These findings are explainable by a repeated late stage multistep rearrangement sequence. The absolute configurations of the chlororaphens and their biosynthetic intermediates were elucidated in stereoselective labelling experiments.

Coupling photocatalytic CO2 reduction and CH3OH oxidation for selective dimethoxymethane production

Currently, conventional dimethoxymethane synthesis methods are environmentally unfriendly. Here, we report a photo-redox catalysis system to generate dimethoxymethane using a silver and tungsten co-modified blue titanium dioxide catalyst (Ag.W-BTO) by coupling CO2 reduction and CH3OH oxidation under mild conditions. The Ag.W-BTO structure and its electron and hole transfer are comprehensively investigated by combining advanced characterizations and theoretical studies. Strikingly, Ag.W-BTO achieve a record photocatalytic activity of 5702.49 µmol g−1 with 92.08% dimethoxymethane selectivity in 9 h of ultraviolet-visible irradiation without sacrificial agents. Systematic isotope labeling experiments, in-situ diffuse reflectance infrared Fourier-transform analysis, and theoretical calculations reveal that the Ag and W species respectively catalyze CO2 conversion to *CH2O and CH3OH oxidation to *CH3O. Subsequently, an asymmetric carbon-oxygen coupling process between these two crucial intermediates produces dimethoxymethane. This work presents a CO2 photocatalytic reduction system for multi-carbon production to meet the objectives of sustainable economic development and carbon neutrality.

Regioselective hydroamination of unactivated olefins with diazirines as a diversifiable nitrogen source

Nitrogen-containing compounds, such as amines, hydrazines, and heterocycles, play an indispensable role in medicine, agriculture, and materials. Alkylated derivatives of these compounds, especially in sterically congested environments, remain a challenge to prepare. Here we report a versatile method for the regioselective hydroamination of readily available unactivated olefins with diazirines. Over fifty examples are reported, including the protecting group-free amination of fourteen different natural products. A broad functional group tolerance includes alcohols, ketones, aldehydes, and epoxides. The proximate products of these reactions are diaziridines, which, under mild conditions, are converted to primary amines, hydrazines, and heterocycles. Five target- and diversity-oriented syntheses of pharmaceutical compounds are shown, along with the preparation of a bis-15N diazirine validated in the late-stage isotopic labeling of an RNA splicing modulator candidate. In this work, we report using diazirine (1) as an electrophilic nitrogen source in a regioselective hydroamination reaction, and the diversification of the resulting diaziridines.

Synthesis of isotope‐substituted conjugated ladder polymers

AbstractConjugated ladder polymers (cLPs) represent an intriguing class of macromolecules, characterized by their multi‐stranded structure, with continuous fused π‐conjugated rings forming the backbone. Isotope substitution, such as deuteration and carbon‐13 labeling, offers unique approaches to address the significant challenges associated with elucidating the structure and solution phase dynamics of these polymers. For instance, selective deuteration can highlight parts of the polymer by controlling the scattering length density of specific molecular sections, thereby enhancing the contrast for neutron scattering experiments. In this context, deuteration of side‐chains in cLPs represents a promising approach to uncover the elusive polymer physics properties of their backbone. The synthesis of two distinct types of cLPs with perdeuterated side‐chains are reported here. During the synthesis, 13C isotope labeling was also employed to verify the low levels of defects in the synthesized polymers. Demonstrating these synthetic successes lays the foundation for rigorous characterization of the defects, conformation, and dynamics of cLPs.

Isotopomer labeling and oxygen dependence of hybrid nitrous oxide production

Abstract. Nitrous oxide (N2O) is a potent greenhouse gas and ozone depletion agent, with a significant natural source from marine oxygen-deficient zones (ODZs). Open questions remain, however, about the microbial processes responsible for this N2O production, especially hybrid N2O production when ammonia-oxidizing archaea are present. Using 15N-labeled tracer incubations, we measured the rates of N2O production from ammonium (NH4+), nitrite (NO2-), and nitrate (NO3-) in the eastern tropical North Pacific ODZ and the isotopic labeling of the central (α) and terminal (β) nitrogen (N) atoms of the N2O molecule. We observed production of both doubly and singly labeled N2O from each tracer, with the highest rates of labeled N2O production at the same depths as the near-surface N2O concentration maximum. At most stations and depths, the production of 45N2Oα and 45N2Oβ were statistically indistinguishable, but at a few depths there were significant differences in the labeling of the two nitrogen atoms in the N2O molecule. Implementing the rates of labeled N2O production in a time-dependent numerical model, we found that N2O production from NO3- dominated at most stations and depths, with rates as high as 1600 ± 200 pM N2O d−1. Hybrid N2O production, one of the mechanisms by which ammonia-oxidizing archaea produce N2O, had rates as high as 230 ± 80 pM N2O d−1 that peaked in both the near-surface and deep N2O concentration maxima. Based on the equal production of 45N2Oα and 45N2Oβ in the majority of our experiments, we infer that hybrid N2O production likely has a consistent site preference, despite drawing from two distinct substrate pools. We also found that the rates and yields of hybrid N2O production were enhanced at low dissolved oxygen concentrations ([O2]), with hybrid N2O yields as high as 20 % at depths where [O2] was below detection (880 nM) but nitrification was still active. Finally, we identified a few incubations with [O2] up to 20 µM where N2O production from NO3- was still active. A relatively high O2 tolerance for N2O production via denitrification has implications for the feedbacks between marine deoxygenation and greenhouse gas cycling.

Unveiling the In Situ Evolution of Li2O-Rich Solid Electrolyte Interface on CoOx Embedded Carbon Fibers as Li Anode Host.

Modification of three-dimensional (3D) carbon hosts with metal oxides has been considered as advantageous for the formation of Li2O-rich solid electrolyte interface (SEI), which can show fast Li+ diffusion, and meanwhile alleviate dendrite problems caused by fragility and nonuniformity of native SEIs. However, the lack of convincing experimental evidence has made it difficult to unveil the true origin of oxygen in Li2O-rich SEIs until now. Herein, CoOx embedded carbon nanofibers (CNF-CoOx) are successfully prepared as high-performance Li anode hosts. By employing 18O isotope labeling, the role of CoOx during SEI evolution is elucidated, revealing that CoOx contributes significantly to Li2O formation by delivering oxygen. Benefiting from the rich Li2O content, the as-formed SEIs greatly improve the Li+ migration kinetics, and therefore, the CNF-CoOx@Li anode can exhibit excellent cycling stability in half, symmetrical, and full cells.

Deuteration of Arenes via Pd-Catalyzed C-H Activation: A Lesson in Nondirected C-H Activation, Isotopic Labeling, and NMR Characterization.

Isotopic labeling is an important tool in medicinal research, metabolomics, and for understanding reaction mechanisms. In this context, transition metal-catalyzed C-H activation has emerged as a key technology for deuterium incorporation via hydrogen isotope exchange. A detailed and easy-to-implement experimental procedure for a nondirected arene deuteration has been developed that exclusively uses commercial equipment and chemicals. The protocol is ideally suited for students and other prospective applicants who are not experts in catalysis. The degree of deuterium incorporation was analyzed via different means like mass spectrometry and 1H and 2H nuclear magnetic resonance (NMR). A hands-on understanding of quantitative NMR, as well as the influence of H/D exchange on experimental spectra, was conveyed by comparative NMR spin simulations. Students were measurably familiarized with the concepts of C-H activation, isotope effects, and basics in experimental catalysis.

Exploring formation of turanose in honey via stable isotope labelling and high-resolution mass spectrometry analysis

Turanose, an isomer of sucrose, naturally exists in honey. Previous study indicated that turanose content increased gradually in acacia honey as honeybees brewed honey in the hive. However, it is unclear how turanose is generated in honey. We hypothesised that turanose was produced by enzymes from honeybees and performed a series of simulation experiments to prove this hypothesis. We found turanose in honey was produced by honeybees processing sucrose. Furthermore, we determined that sugar composition of simulated nectar influenced the turanose concentration in honey: when sucrose concentration was below 5%, turanose was difficult to form, whereas high concentration of fructose and limited glucose were beneficial in producing turanose. Using 13C-labelled sucrose tests combined with proteomics analysis, we identified that α-glucosidase converted sucrose to turanose through an intermolecular isomerisation process. This study reveals the formation mechanism of turanose in honey and assists in the scientific control and improvement of honey quality.

Global protein turnover quantification in Escherichia coli reveals cytoplasmic recycling under nitrogen limitation

Protein turnover is critical for proteostasis, but turnover quantification is challenging, and even in well-studied E. coli, proteome-wide measurements remain scarce. Here, we quantify the turnover rates of ~3200 E. coli proteins under 13 conditions by combining heavy isotope labeling with complement reporter ion quantification and find that cytoplasmic proteins are recycled when nitrogen is limited. We use knockout experiments to assign substrates to the known cytoplasmic ATP-dependent proteases. Surprisingly, none of these proteases are responsible for the observed cytoplasmic protein degradation in nitrogen limitation, suggesting that a major proteolysis pathway in E. coli remains to be discovered. Lastly, we show that protein degradation rates are generally independent of cell division rates. Thus, we present broadly applicable technology for protein turnover measurements and provide a rich resource for protein half-lives and protease substrates in E. coli, complementary to genomics data, that will allow researchers to study the control of proteostasis.