Insights into the role of methionine synthase in the universal 13 C depletion in O - and N -methyl groups of natural products

Fingerprinting Organofluorine Molecules via Position-Specific Isotope Analysis

Organofluorine substances are found in a wide range of materials and solvents commonly used in industry and homes, as well as pharmaceuticals and pesticides. In the environment, organofluorine molecules are now recognized as an important class of anthropogenic pollutants. Fingerprinting organofluorine compounds via their carbon isotope ratios (13C/12C) is crucial for correlating molecules with their source. Here we apply a 19F nuclear magnetic resonance spectroscopy (NMR) technique to obtain the first position-specific carbon isotope ratios for a diverse set of organofluorine molecules. In contrast to traditional isotope ratio mass spectrometry, the 19F NMR method provides 13C/12C isotope ratios at each carbon position where a C-F bond is present, and does not require fragmentation or combustion to CO2, overcoming challenges posed by the robust C-F covalent bonds. The method was validated with 2,2,2-trifluoroethanol, and applied to analyze heptafluorobutanoic acid, 5-fluorouracil and fipronil. Results reveal distinct intramolecular carbon isotope distributions, enabling differentiation of chemically identical molecules. Notably, the NMR method accurately analyzes carbon isotopes within target molecules despite impurities. Potential applications include the detection of counterfeit products and drugs, and ultimately pollution tracking in the environment.

Position-specific carbon stable isotope analysis of glyphosate: isotope fingerprinting of molecules within a mixture

Glyphosate [N-(phosphonomethyl) glycine] is a widely used herbicide and a molecule of interest in the environmental sciences, due to its global use in agriculture and its potential impact on ecosystems. This study presents the first position-specific carbon isotope (13C/12C) analyses of glyphosates from multiple sources. In contrast to traditional isotope ratio mass spectrometry (IRMS), position-specific analysis provides 13C/12C ratios at individual carbon atom positions within a molecule, rather than an average carbon isotope ratio across a mixture or a specific compound. In this work, glyphosate in commercial herbicides was analyzed with only minimal purification, using a nuclear magnetic resonance (NMR) spectroscopy method that detects 1H nuclei with bonds to either 13C or 12C, and isolates the signals of interest from other signals in the mixture. Results demonstrate that glyphosate from different sources can have significantly different intramolecular 13C/12C distributions, which were found to be spread over a wide range, with δ13C Vienna Peedee Belemnite (VPDB) values of -28.7 to -57.9‰. In each glyphosate, the carbon with a bond to the phosphorus atom was found to be depleted in 13C compared to the carbon at the C2 position, by 4 to 10‰. Aminomethylphosphonic acid (AMPA) was analyzed for method validation; AMPA contains only a single carbon position, so the 13C/12C results provided by the NMR method could be directly compared with traditional isotope ratio mass spectrometry. The glyphosate mixtures were also analyzed by IRMS to obtain their average 13C/12C ratios, for comparison with our position-specific results. This comparison revealed that the IRMS results significantly disguise the intramolecular isotope distribution. Finally, we introduce a 31P NMR method that can provide a position-specific 13C/12C ratio for carbon positions with a C-P chemical bond, and the results obtained by 1H and 31P for C3 carbon agree with one another within their analytical uncertainty. These analytical tools for position-specific carbon isotope analysis permit the isotopic fingerprinting of target molecules within a mixture, with potential applications in a range of fields, including the environmental sciences and chemical forensics.

Novel Nuclear Magnetic Resonance Method for Position-Specific Carbon Isotope Analysis of Organic Molecules with Significant Impurities

We introduce a novel nuclear magnetic resonance (NMR) tool for determining position-specific carbon (¹³C/¹²C) isotope ratios within complex organic molecules. This analytical advancement allows us to measure position-specific isotope ratios of samples that contain impurities with NMR peaks that overlap with the signals of interest. The method involves collecting a series of alternating ¹³C-coupled and ¹³C-decoupled ¹H NMR spectra using an NMR pulse sequence designed to optimize temperature stability, followed by a data reduction scheme that allows the signals of interest to be isolated from signals of impurities. The method was validated using glycine reference materials with known ¹³C/¹²C ratios from the US Geological Survey (USGS) into which impurities typically found in amino acid samples were intentionally introduced. Following validation, the method was used to determine position-specific ¹³C/¹²C ratios in a set of USGS l-valine materials (USGS73, -74, -75) that contain significant impurities associated with their biological origin. The l-valines were found to contain distinct intramolecular isotope variability, and the ¹³Cα isotope spikes in USGS74 and USGS75 were clearly detected, where they preserve carbon isotope ratios of -4.8 ± 0.9‰ and +11.5 ± 0.8‰, respectively. Carbon isotope abundance at the beta and gamma positions indicates that the USGS73 l-valine was obtained from a different source than USGS74 and -75. This analytical approach is a significant step forward in the field of position-specific isotope analysis at natural abundance via NMR because it enables the investigation of samples that contain impurities which are typically present in samples derived from natural sources.

Position-specific carbon isotope analysis of serine by gas chromatography/Orbitrap mass spectrometry, and an application to plant metabolism

RATIONALE

Position-specific ¹³ C/¹² C ratios within amino acids remain largely unexplored in environmental samples due to methodological limitations. We hypothesized that natural-abundance isotope patterns in serine may serve as a proxy for plant metabolic fluxes including photorespiration. Here we describe an Orbitrap method optimized for the position-specific carbon isotope analysis of serine to test our hypothesis and discuss the generalizability of this method to other amino acids.

METHODS

Position-specific carbon isotope ratios of serine were measured using a Thermo Scientific™ Q Exactive™ GC Orbitrap™. Amino acids were hydrolyzed from Arabidopsis biomass, purified from potential matrix interferences, and derivatized alongside standards. Derivatized serine (N,O-bis(trifluoroacetyl)methyl ester) was isolated using gas chromatography, trapped in a reservoir, and purged into the electron ionization source over tens of minutes, producing fragment ions containing different combinations of atoms from the serine-derivative molecule. The ¹³ C/¹² C ratios of fragments with monoisotopic masses of 110.0217, 138.0166, and 165.0037 Da were monitored in the mass analyzer and used to calculate position-specific δ¹³ C values relative to a working standard.

RESULTS

This methodology constrains position-specific δ¹³ C values for nanomole amounts of serine isolated from chemically complex mixtures. The δ¹³ C values of fragment ions of serine were characterized with ≤1‰ precisions, leading to propagated standard errors of 0.7-5‰ for each carbon position. Position-specific δ¹³ C values differed by up to ca 28 ± 5‰ between serine molecules hydrolyzed from plants grown under contrasting pCO₂ , selected to promote different fluxes through photosynthesis and photorespiration. The method was validated using pure serine standards characterized offline.

CONCLUSIONS

This study presents the first Orbitrap-based measurements of natural-abundance, position-specific carbon isotope variation in an amino acid isolated from a biological matrix. We present a method for the precise characterization of isotope ratios in serine and propose applications probing metabolism in plants. We discuss the potential for extending these approaches to other amino acids, paving the way for novel applications.

Insights Into the Known 13C Depletion of Methane-Contribution of the Kinetic Isotope Effects on the Serine Hydroxymethyltransferase Reaction

We determined the kinetic isotope effect on the serine hydroxymethyltransferase reaction (SHMT), which provides important C₁ metabolites that are essential for the biosynthesis of DNA bases, O-methyl groups of lignin and methane. An isotope effect on the SHMT reaction was suggested being responsible for the well-known isotopic depletion of methane. Using the cytosolic SHMT from pig liver, we measured the natural carbon isotope ratios of both atoms involved in the bond splitting by chemical degradation of the remaining serine before and after partial turnover. The kinetic isotope effect ¹³(V_Max/K_m) was 0.994 0.006 and 0.995 0.007 on position C-3 and C-2, respectively. The results indicated that the SHMT reaction does not contribute to the ¹³C depletion observed for methyl groups in natural products and methane. However, from the isotopic pattern of caffeine, isotope effects on the methionine synthetase reaction and on reactions forming Grignard compounds, the involved formation and fission of metal organic bonds are likely responsible for the observed general depletion of “activated” methyl groups. As metal organic bond formations in methyl transferases are also rate limiting in the formation of methane, they may likely be the origin of the known ¹³C depletion in methane.

Intramolecular distribution of 13C/12C isotopes in amino acids of diverse origins

Carbon stable isotope analysis can provide information about the origin and synthetic pathways that produce organic molecules, with applications in chemical, medical and (bio)geochemical sciences. The ¹³C/¹²C isotope ratios of organics such as amino acids are most commonly obtained as whole molecule averages. In this study, we apply proton nuclear magnetic resonance spectroscopy to conduct position-specific carbon isotope analyses of L-/D-alanine, L-threonine and L-histidine from different sources, in addition to molecule average stable isotope analyses obtained via mass spectrometry. Our results demonstrate that carbon isotope ratios can vary significantly between the individual carbon positions within an amino acid. For example, the β- and γ- carbons of L-threonine can differ in ¹³C/¹²C ratio by > 20 ‰. Comparisons of the position-specific and whole molecule average stable isotope abundances show that whole molecule analyses can mask the intramolecular isotope variation. These results provide the first experimentally measured position-specific isotope ratios for alpha and side chain carbons of alanine, threonine and histidine. Comparison with previous ab initio calculations of intramolecular equilibrium fractionation shows that the carbon isotope distributions are not at equilibrium, thus kinetic isotope effects play a significant role in amino acid synthesis. We hypothesize that position-specific ¹³C/¹²C isotope ratios provide an "isotopic fingerprint" that can give insight into the origin or synthesis pathway that formed an amino acid, and that this emerging analytical field will be a valuable addition to traditional stable isotope analysis.

Position-Specific Carbon Stable Isotope Ratios by Proton NMR Spectroscopy

Carbon stable isotopes provide insights into the origin and synthesis pathway of an organic molecule, and hence, contribute information that is fundamental to understanding chemical, physiological, and ecological processes. Organic carbon ¹³C/¹²C isotope ratios are commonly obtained as whole-molecule averages or as measurements of bulk samples. In contrast, position-specific isotope analysis (PSIA) provides isotope ratios for the individual carbons within a molecule, providing additional information that is masked by traditional analytical techniques. Here we introduce a ¹H NMR method for determining position-specific ¹³C/¹²C ratios within organic molecules. A peak shape superposition procedure is used to bypass the need for traditional peak integration, by exploiting relationships among the shapes of ¹H and ¹³C satellite peaks in ¹H NMR spectra. The method also has a significant sensitivity advantage over NMR methods that utilize direct detection of ¹³C. Furthermore, we demonstrate that isotope standard materials (such as those obtainable from U.S. Geological Survey) are indispensable in calibrating an NMR instrument, in order to obtain accurate isotope ratio results. Our analytical approach was applied to organic molecules of different complexity and origin, including ethanols, propionic acids, and thymidine. Results verify that chemically identical molecules from different sources can have different intramolecular isotope distributions; hence position-specific ¹³C/¹²C ratios provide an isotopic fingerprint of an organic molecule. Position-specific information for the nucleoside thymidine, where five of eight carbon positions were measured, is significant because its complexity would make it a difficult target for PSIA by mass spectrometry. The ¹H NMR method is complementary to other methods of PSIA, and will make ¹³C/¹²C PSIA employable to a wider range of organic molecules.

Methyl sulfates as methoxy isotopic reference materials for δ13 C and δ2 H measurements

RATIONALE

Stable hydrogen and carbon isotope ratios of methoxy groups (OCH₃ ) of plant organic matter have many potential applications in biogeochemical, atmospheric and food research. So far, most of the analyses of plant methoxy groups by isotope ratio mass spectrometry have employed liquid iodomethane (CH₃ I) as the reference material to normalise stable isotope measurements of these moieties to isotope-δ scales. However, comparisons of measurements of stable hydrogen and carbon isotopes of plant methoxy groups are still hindered by the lack of suitable reference materials.

METHODS

We have investigated two methyl sulfate salts (HUBG1 and HUBG2), which exclusively contain carbon and hydrogen from one methoxy group, for their suitability as methoxy reference materials. Firstly, the stable hydrogen and carbon isotope values of the bulk compounds were calibrated against international reference substances by high-temperature conversion- and elemental analyser isotope ratio mass spectrometry (HTC- and EA-IRMS). In a second step these values were compared with values obtained by measurements using gas chromatography/isotope ratio mass spectrometry (GC/IRMS) where prior to analysis the methoxy groups were converted into gaseous iodomethane.

RESULTS

The ² H- and ¹³ C isotopic abundances of HUBG1 measured by HTC- and EA-IRMS and expressed as δ-values on the usual international scales are -144.5 ± 1.2 mUr (n = 30) and -50.31 ± 0.16 mUr (n = 14), respectively. For HUBG2 we obtained -102.0 ± 1.3 mUr (n = 32) and +1.60 ± 0.12 mUr (n = 16). Furthermore, the values obtained by GC/IRMS were in good agreement with the HTC- and EA-IRMS values.

CONCLUSIONS

We suggest that both methyl sulfates are suitable reference materials for normalisation of isotope measurements of carbon of plant methoxy groups to isotope-δ scales and for inter-laboratory calibration. For stable hydrogen isotope measurements, we suggest that in addition to HUBG1 and HUBG2 additional reference materials are required to cover the full range of plant methoxy groups reported so far.