Hydrogen Isotope Labeling of Pharmaceuticals Via Dual Hydrogen Isotope Exchange Pathways Using CdS Quantum Dot Photocatalyst
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Maity, Rajendra↗
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Conclusions • Multimaterial and isotopically-labeled specimens were successfully fabricated via FFF-AM • Raman spectroscopy, atomic force microscopy, and neutron scattering show promise for direct measurements of interlayer diffusion in the multimaterial and isotopically-labeled specimens • Although isotopically-labeled specimens offer the greatest potential for experimentally verifying FFF-AM process models, substituting hydrogen with deuterium alters the thermal and rheological properties of the HDPE polymer
Multimaterial and Isotopically Labeled Specimen Fabrication via Material Extrusion Additive Manufacturing for Interlayer Diffusion Analysis
Jones, Haley W. [Savannah River National Laborator↗
Surface Functionalization of Black Phosphorus with Nitrenes: Identification of P=N Bonds Using Isotopic Labeling
Abstract: Surface functionalization of two-dimensional crystals is a key path to tuning their intrinsic physical and chemical properties. However, synthetic protocols and experimental strategies to directly probe chemical bonding in modified surfaces are scarce. Introduced here is a mild, surface-specific protocol for the surface functionalization of few-layer black phosphorus nanosheets using a family of photolytically generated nitrenes (RN) from the corresponding azides. By embedding spectroscopic tags in the organic backbone, a multitude of characterization techniques are employed to investigate in detail the chemical structure of the modified nanosheets, including vibrational (infrared, Raman), Xray (emission, photoelectron), CPMAS NMR, and UV-vis spectroscopy. To directly probe the functional groups introduced on the surface, R fragments were selected such that in conjunction with vibrational spectroscopy, 15N-labeling experiments, and DFT methods, diagnostic P=N vibrational modes indicative of iminophosphorane units on the nanosheet surface could be conclusively identified.
Walz, Kendall↗
Endogenous Production and Vibrational Analysis of Heavy-Isotope-Labeled Peptides from Cyanobacteria
Stable isotope labeling is an extremely useful tool for characterizing the structure, tracing the metabolism, and imaging the distribution of natural products in living organisms using mass-sensitive measurement techniques. In this study, a cyanobacterium was cultured in 15 N/ 13 C-enriched media to endogenously produce labeled, bioactive oligopeptides. The extent of heavy isotope incorporation in these peptides was determined with LC–MS, while the overall extent of heavy isotope incorporation in whole cells was studied with nanoSIMS and AFM-IR. Up to 98 % heavy isotope incorporation was observed in labeled cells. Three of the most abundant peptides, microcystin-LR (MCLR), cyanopeptolin-A (CYPA), and aerucyclamide-A (ACAA), were isolated and further studied with Raman and FTIR spectroscopies and DFT calculations. This revealed several IR and Raman active vibrations associated with functional groups not common in ribosomal peptides, like diene, ester, thiazole, thiazoline, and oxazoline groups, which could be suitable for future vibrational imaging studies. More broadly, this study outlines a simple and relatively inexpensive method for producing heavy-labeled natural products. Finally, manipulating the bacterial culture conditions by the addition of specific types and amounts of heavy-labeled nutrients provides an efficient means of producing heavy-labeled natural products for mass-sensitive imaging studies.
60 APPLIED LIFE SCIENCES↗
Tag you're it: Application of stable isotope labeling and LC-MS to identify the precursors of specialized metabolites in plants
Untargeted liquid chromatography/mass spectrometry (LC-MS) can contribute a comprehensive and unbiased picture of the metabolic space of plants. These data can be used to quantify natural metabolite variation for genome wide association studies, to compare global metabolic responses from environmental or genetic perturbations, and to identify previously undescribed metabolites in Nature. A major limitation with untargeted metabolomics is the classification and identification of the thousands of metabolite features that can be detected in a single analytical run. Isotopic labeling improves the informational value of these datasets by categorizing metabolites as being derived from specific upstream precursors and/or to known metabolic pathways. When a 13 C-labeled precursor is fed to either a plant or tissue, the downstream metabolites produced from it have a higher m/z value than the molecules in the pre-existing pool, generating an m/z peak pair that can be specifically identified within the MS data. In this paper, we outline methods and principles to consider when supplementing untargeted MS data with isotopic labeling, including how to choose the appropriate isotopic label, grow and feed plant tissues to maximize label uptake and incorporation into derivatives, optimize LC-MS methods, and interpret the resulting labeling data. Although the focus here is on annotation of amino acid-derived metabolites using LC-MS, we anticipate that the methods are generally adaptable to other precursors, plant species, and chromatographic approaches.
59 BASIC BIOLOGICAL SCIENCES↗
Studies on the Incorporation of Isotopically Labeled Nucleotides and Amino Acids in Planaria
Incorporation of isotopically labeled nucleotides and amino acids studies in planaria
PROTEIN METABOLISM↗
Improved chemical and isotopic labeling of biomembranes in Bacillus subtilis by leveraging CRISPRi inhibition of beta-ketoacyl-ACP synthase (fabF)
Assessing the structure of living microbial cell membranes is a challenging analytical goal. The cell membrane is defined by its transverse structure, an approximately 5 nm-thick selectively permeable bilayer that serves many important cellular functions. Compositionally complex, dynamic, and organized in both the transverse and lateral dimensions, understanding the cell membrane structure—and the role that structure plays in cellular function, communication, and environmental sensing is an active scientific effort. Previously, we have devised a novel isotopic labeling approach for membrane lipids to enable direct in vivo structural studies of the cell membrane in the Gram-positive bacterium, Bacillus subtilis , using small-angle neutron scattering. This was accomplished through a genetic inhibition of fatty acid (FA) degradation (Δ fadN ) and a chemical inhibition of FA biosynthesis using cerulenin, an irreversible inhibitor of type II fatty acid synthases. Here, we improve upon the previous system by introducing a dCas9/sgRNA- fabF complex that blocks transcription of the essential fabF gene when under xylose induction. This leads to greater sensitivity to cerulenin in the mutant strain (JEBS102) and more robust cell growth when supplementary FAs are introduced to the culture medium. A subtle change in FA uptake is noted when compared to the prior labeling strategy. This is seen in the gas chromatography/mass spectrometry (GC/MS) data as a higher ratio of n 16:0 to a 15:0, and manifests in an apparent increase in the membrane thickness determined via neutron scattering. This represents an improved method of isotopic labeling for the cell membrane of Bacillus subtilis; enabling improved investigations of cellular uptake and utilization of FAs, cell membrane structure and organization as a phenotypic response to metabolic and environmental changes.
59 BASIC BIOLOGICAL SCIENCES↗
Substrate-Directed Underlayer Growth of Bilayer MoS 2 Revealed by Mo Isotope Labeling
Direct control over the vertical formation sequence and stacking registry in van der Waals (vdW) bilayers is essential for device performance and moiré engineering yet difficult to resolve unambiguously with conventional probes. Here, we use Mo isotope labeling in a two-step chemical vapor deposition process to synthesize bilayer MoS 2 and trace its vertical formation on common substrates. By combining site-selective laser thinning, Raman spectroscopy, time-of-flight secondary ion mass spectrometry, and atomic-resolution scanning transimission electron microscopy (STEM), we find a clear substrate dependence: on SiO 2 /Si, the second layer nucleates and grows beneath the first (underlayer), whereas on sapphire, it forms on top (overlayer). Density functional theory indicates that a larger equilibrium interfacial separation and weaker MoS 2 –substrate interactions on amorphous SiO 2 permit confined interfacial diffusion and underlayer nucleation, whereas stronger interactions and smaller separations on sapphire favor overlayer growth. On SiO 2 , confined epitaxy templates commensurate 2H, 3R, and mixed bilayers, as confirmed by second harmonic generation spectroscopy and STEM. During underlayer coalescence, embedded mirror-twin grain boundaries stitch atomically sharp 2H|3R junctions via alternating 4|8 ring motifs. Molecular-dynamics simulations reveal that these alternating 4|8 motifs accommodate interlayer vdW coupling and locally modulate the stacking registry. These results provide mechanistic insight into confined epitaxial growth and establish isotope labeling as a powerful probe of two-dimensional materials synthesis.
MoS2↗
Using Multiple Isotope-Labeled Infrared Spectra for the Structural Characterization of an Intrinsically Disordered Peptide
Intrinsically disordered proteins (IDPs) rapidly interconvert between conformers, requiring an ensemble description. This complicates their experimental characterization, and force field limitations pose challenges for their simulation. Here, in this work, we use isotope-labeled and unlabeled infrared (IR) spectra to reweight simulated ensembles of the elastin-like peptide GVGVPGVG, a paradigmatic disordered peptide. By comparing the results obtained with different spectra, we explicitly show that the weights are underdetermined by the ensemble averaged data. We identify which labels and frequency regions maximize structural information while minimizing sensitivity to simulation error and show that these regions report on whether the peptide makes specific interactions. Our work shows the importance of incorporating simulations and simulated spectra at the planning stages of isotope-labeled IR experiments and more generally provides a framework for interpreting IR data for IDPs.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
An isotopic labeling investigation into the influence of the nitro group on LLM-105 thermal decomposition
Here, this work presents the first application of isotopically labeled LLM-105 (2,6-diamino-3,5-dinitropyrazine-1-oxide) to investigate thermal decomposition pathways. Specially synthesized LLM-105 isotopologues were utilized to isolate the influence of labeled 15 NO 2 nitro groups on the formation of lightgas products. Simultaneous differential scanning calorimetry, thermo-gravimetric, and mass spectrometry measurements were employed to track the evolution of product gases, enabling the direct comparison of isotopically shifted species with unlabeled LLM-105. Key findings show that C 2 N 2 production is mainly dependent on nitrogen sources from either the amine groups or the pyrazine ring (i.e., not the nitro groups). The formation of NO, N 2 , and N 2 O all involves the nitro groups to some extent. NO (nitric oxide) was found to be the predominant gas species directly formed from the nitro group of LLM-105. In contrast, mixed nitrogen isotopologues of N 2 and N 2 O (i.e., 14 N 15 N and 15 NNO) formed more readily in comparison to their pure counterparts (i.e., 15 N 2 and 15 N 2 O). This indicates the amine and/or pyrazine groups of LLM-105, in addition to the nitro group, are involved in the decomposition pathways forming N 2 and N 2 O. In addition, our investigation led to the discovery of two previously unreported decomposition products (CHO and HNCO), which were confirmed through hydrogen labelling utilizing deuterium isotopes. These results provide detailed speciation trends of gaseous products during LLM-105 decomposition, offering new insights into reaction pathways. Experimental data reported here will support the development of a detailed chemical kinetics model for LLM-105, essential for the safe handling of high explosives.
Chemistry - Chemical explosives↗
Mercury Methylation and Soil Organic Matter Degradation in Incubations with Added Acetate, Isotope-Labeled Mercury, and Selective Microbial Inhibitors, Teller and Council Sites, Seward Peninsula, 2018-2019
This dataset provides the results of laboratory soil microcosm incubation experiments conducted under anaerobic conditions with added acetate, isotope-labeled mercury, and selective microbial inhibitors (2-bromoethanesulfonate and sodium molybdate). The microcosms contained soil collected in August 2018 from the NGEE Arctic Teller Road Site at mile marker 27 (TL_MM27) near Intensive Site 9 (TL_IS_9) and from the Council Road Site (CN_MM71). Incubations were conducted at 8°C for 180 days (Teller incubations) or 60 days (Council incubations). The microcosm headspace was sampled at designated intervals for greenhouse gas concentrations, then destructively harvested and extracted using ultrapure water and 0.1 M KCl for analysis of the porewater geochemistry. This dataset contains one pdf, two csv data files, and one zipped file with raw data.The Next-Generation Ecosystem Experiments: Arctic (NGEE Arctic), was a research effort to reduce uncertainty in Earth System Models by developing a predictive understanding of carbon-rich Arctic ecosystems and feedbacks to climate. NGEE Arctic was supported by the Department of Energy's Office of Biological and Environmental Research.The NGEE Arctic project had two field research sites: 1) located within the Arctic polygonal tundra coastal region on the Barrow Environmental Observatory (BEO) and the North Slope near Utqiagvik (Barrow), Alaska and 2) multiple areas on the discontinuous permafrost region of the Seward Peninsula north of Nome, Alaska.Through observations, experiments, and synthesis with existing datasets, NGEE Arctic provided an enhanced knowledge base for multi-scale modeling and contributed to improved process representation at global pan-Arctic scales within the Department of Energy's Earth system Model (the Energy Exascale Earth System Model, or E3SM), and specifically within the E3SM Land Model component (ELM).
54 ENVIRONMENTAL SCIENCES↗
Shotgun proteomics of cell lysates and absolute quantification of E. coli, Z. mobilis, C. thermocellum glycolytic proteins
For E. coli, C. thermocellum, Z. mobilis: shotgun proteomics analyses of tryptic digests of cell lysates; direct infusion of cell lysates spiked with isotopically labelled peptides to perform absolute quantification of specific proteins of interest, primarily related to glycolysis
absolute quantification↗
LC/MS Method for the Determination of Stable Isotope Labeled Promethazine in Human Plasma
Promethazine (PMZ) is taken by astronauts orally (PO), intramuscularly (IM) or rectally (PR) for space motion sickness. LC/MS method was developed with off-line solid phase extraction to measure plasma concentrations of PMZ given as stable isotope-labeled (SIL) formulations by the three different routes of administration simultaneously. Samples (0.5ml) were loaded on to Waters Oasis HLB co-polymer cartridges and eluted with 1.0 mL methanol. HPLC separation of the eluted sample was performed using an Agilent Zorbax SB-CN column (50 x 2.1 mm) at a flow rate of 0.2 mL/min for 6 min. Acetonitrile/ ammonium acetate (30 mM) in water (3:2, v/v), pH 5.6 plus or minus 0.1, was used as the mobile phase for separation. Concentrations of PMZ, PMZ-d4 and PMZ-d7 and chlorpromazine (internal standard) were determined using a Micromass ZMD single quadrupole mass spectrometer with Electrospray Ionization (ESI). ESI mass spectra were acquired in positive ion mode with selected ion monitoring of [M+ H]dot plus. The method is rapid, reproducible and the assay specific parameters are listed in a table. A novel, sensitive and specific method for the measurement of PMZ and SIL PMZ in human plasma is reported.
Zuwei, Wang↗
Elevated Temperature Effects on Protein Turnover Dynamics in Arabidopsis thaliana Seedlings Revealed by 15 N-Stable Isotope Labeling and ProteinTurnover Algorithm
Global warming poses a threat to plant survival, impacting growth and agricultural yield. Protein turnover, a critical regulatory mechanism balancing protein synthesis and degradation, is crucial for the cellular response to environmental changes. We investigated the effects of elevated temperature on proteome dynamics in Arabidopsis thaliana seedlings using 15 N-stable isotope labeling and ultra-performance liquid chromatography-high resolution mass spectrometry, coupled with the ProteinTurnover algorithm. Analyzing different cellular fractions from plants grown under 22 °C and 30 °C growth conditions, we found significant changes in the turnover rates of 571 proteins, with a median 1.4-fold increase, indicating accelerated protein dynamics under thermal stress. Notably, soluble root fraction proteins exhibited smaller turnover changes, suggesting tissue-specific adaptations. Significant turnover alterations occurred with redox signaling, stress response, protein folding, secondary metabolism, and photorespiration, indicating complex responses enhancing plant thermal resilience. Conversely, proteins involved in carbohydrate metabolism and mitochondrial ATP synthesis showed minimal changes, highlighting their stability. This analysis highlights the intricate balance between proteome stability and adaptability, advancing our understanding of plant responses to heat stress and supporting the development of improved thermotolerant crops.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Coordination-Induced N–H Bond Weakening in a Molybdenum Pyrrolidine Complex: Isotopic Labeling Provides Insight into the Pathway for H 2 Evolution
The synthesis and characterization of a cationic molybdenum pyrrolidine complex is described that exhibits significant coordination-induced N–H bond weakening. Here, the N–H bond dissociation free energy (BDFE) of the coordinated pyrrolidine in [( Ph Tpy)(PPh 2 Me) 2 Mo(NH(pyrr))][BArF 24 ] ([1-NH(pyrr)] + ; PhTpy = 4'-Ph-2,2',6',2''-terpyridine, NH(pyrr) = pyrrolidine, ArF 24 = [C 6 H 3 -3,5-(CF 3 ) 2 ] 4 ) was determined to be between 41–51 kcal mol -1 by thermochemical analysis and supported by a density functional theory (DFT) computed value of 48 kcal mol -1 . The complex [1-NH(pyrr)] + underwent proton-coupled electron transfer (PCET) to 2,4,6-tri-tert-butylphenoxyl radical, as well as spontaneous H 2 evolution upon gentle heating to furnish the corresponding molybdenum pyrrolidide complex, [( Ph Tpy)(PPh 2 Me) 2 Mo(N(pyrr))][BArF 24 ] ([1-N(pyrr)] + ). Thermolysis of the deuterated isotopolog, [1-ND(pyrr)] + still produced H 2 with concomitant incorporation of the isotopic label into the pyrrolidide ligand in the product [(1-N(pyrr-d n )] + (n = 0–2), consistent with an H 2 evolution pathway involving intramolecular H–H bond formation followed by an intermolecular product-forming PCET step. These observations provide context for understanding H 2 evolution in the nonclassical ammine complex [( Ph Tpy)(PPh 2 Me) 2 Mo(NH 3 )][BArF 24 ] ([1-NH 3 ] + ) and are supported by DFT-computed reaction thermochemistry. Overall, these studies offer rare insight into the H 2 formation pathway in nonclassical amine complexes with N–H BDFEs below the thermodynamic threshold for H 2 evolution and inform the development of well-defined, thermody-namically potent PCET reagents.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Syntheses and characterization of isotopically labeled 1,3,5-triamino-2,4,6-trinitrobenzene (TATB)
Synthesis and characterization of chemical analogues of TATB, where specific atoms in the structure have been isotopically substituted, are reported. 15 N, 2 H, and 18 O have replaced the naturally occurring isotope distributions in the amino and/or the nitro attendant sites and 13 C has replaced the carbon in the ring structure. A modified wet-amination method was used to produce the analogues, and the isotopic replacements were performed by selective choice of labeled precursors. Four 15 N-labeled compounds (N replaced in the amino and nitro positions), two deuterium-labeled compounds (hydrogens replaced on the amino groups), and one 13 C-labeled compound (C in the ring substituted) were synthesized of high isotopic and chemical purity. One partially labeled 18 O-labeled compound (O in the nitro position) was a result of incomplete labeling due to exchange reactions during synthesis. The compounds were characterized by various spectroscopic methods – mass spectrometry (MS), solid-state nuclear magnetic resonance (SS-NMR), infrared (FTIR), powder x-ray diffraction (PXRD), and differential scanning calorimetry (DSC), depending upon the substitution. In conclusion, these compounds have been critical to the efforts in understanding the decomposition pathways of TATB when exposed to abnormal thermal environments.
36 MATERIALS SCIENCE↗
Investigating intermolecular interactions among CO 2 , water and PEEK-ionene membrane using cryo ToF-SIMS and isotopic labeling
Cryogenic time-of-flight secondary ion mass spectrometry (cryo ToF-SIMS) has emerged as a powerful tool for investigating molecular interactions, speciation, and dynamics in materials for CO 2 capture. In this study, we apply cryo ToF-SIMS to probe interactions between CO 2 , water, and PEEK-ionene membranes—a promising material for direct CO 2 capture due to its selectivity, durability, and efficiency. Despite this potential, the mechanisms governing CO 2 diffusion and the influence of water vapor on CO 2 behavior remain unclear. To address this, we loaded PEEK-ionene membranes with 13 CO 2 and D 2 O and employed cryo ToF-SIMS to visualize the 3D distribution of CO 2 and water within the membrane. While prior studies suggest that 13 CO 2 is absorbed under ambient conditions, our cryo ToF-SIMS analysis revealed no enhancement of the 13 C/ 12 C ratio, suggesting weak CO 2 -membrane interactions. As a result, CO 2 vaporizes even at low temperatures (−140°C) under vacuum conditions. In contrast, D 2 O displayed a relatively homogeneous distribution in the membrane, suggesting stronger water-membrane interactions via hydrogen bonding (18–20 kJ/mol). Interestingly, CO 2 was not detected in D 2 O-loaded membranes, indicating minimal interference from water vapor on CO 2 diffusion. As a comparison, the cryo ToF-SIMS data show that 13 CO 2 can readily react with a basic Na 2 CO 3 aqueous solution to form NaH 13 CO 3 . These findings demonstrate cryo ToF-SIMS as a critical technique for understanding gas-water-membrane interactions, offering insights for membrane functionalization to improve CO 2 capture efficiency.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Raw LC–MS mzML files for isotopic labeling experiment in Aconitum plicatum callus cultures
Raw LC–MS data files in mzML format obtained from isotopic feeding experiments in Aconitum plicatum callus cultures. Samples fed with L-serine (2,3,3-D3,¹⁵N) were acquired at a resolution of 500,000 to allow resolution of the nitrogen isotopologue. Control samples were re-acquired at the same resolution for comparison.
biosynthesis↗