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DOE OSTI2025

Comparison of Ce( iv )/Th( iv )-alkynyl complexes and observation of a trans -influence ligand series for Ce( iv )

Organometallic cerium(iv) complexes have been challenging to isolate and characterize due to the strongly oxidizing nature of the cerium(iv) cation. Herein, we report two cerium(iv) alkynyl complexes, [Ce(TriNOx)(C[triple bond, length as m-dash]C-SiMe3)] (1-CeTMS) and [Ce(TriNOx)(C[triple bond, length as m-dash]C-Ph)] (1-CePh) (TriNOx3- = tris(2-tert-butylhydroxylaminato)benzylamine), that include terminal alkyne moieties. The isostructural thorium analogue [Th(TriNOx)(C[triple bond, length as m-dash]C-SiMe3)] (1-ThTMS) was also synthesized and compared with 1-CeTMS in bond distance, 13C-NMR spectra, vibrational spectra and electronic structure. The Ce-C bond distances were 2.501(3) Å for 1-CePh and 2.513(5) Å for 1-CeTMS on the shorter end of the few reported CeIV-C single bonds (2.478(3)-2.705(2) Å), possibly indicating significant Ce 5d- and 4f-orbital involvement. 13C-NMR spectroscopy was also consistent with Ce-C covalency, with significantly deshielded resonances ranging from 185-213 ppm. Such 13C-NMR shifts demonstrate a strong influence from spin-orbit coupling (SOC) effects, corroborated by computational studies. Raman analysis showed ν C[triple bond, length as m-dash]C stretching frequencies of 2000 cm-1 (1-CeTMS) and 2052 cm-1 (1-CePh), indicating the cerium(iv)-alkynyl interaction, compared to the parent HC[triple bond, length as m-dash]CPh (IR = 2105 cm-1 and Raman = 2104 cm-1). L3-edge X-ray absorption measurements revealed a predominant Ce(iv) electronic configuration, and magnetic measurements revealed temperature-independent paramagnetism. Electrochemical studies similarly revealed the electron donating ability of the alkynyl ligands, stronger than either fluoride or imido ligands for the Ce(iv)(TriNOx)-framework, with a cerium(iv/iii) reduction potential of E pc = -1.58 to -1.66 V vs. Fc/Fc+. Evidence for a trans-influence has been observed by evaluating a series including previously reported [CeIV(TriNOx)X]+/0 complexes with axial ligands X = THF, I-, Br-, Cl-, F-, -C[triple bond, length as m-dash]C-Ph, -C[triple bond, length as m-dash]C-SiMe3, -NH(3,5-(CF3)2-Ar), -OSiPh3, -N(M(L))(3,5-(CF3)2-Ar) [M(L) = Li(TMEDA), K(DME)2 or Cs(2,2,2-crypt)]. These data stand in contrast with previous reports of an inverse trans-influence at cerium(iv) and point to differences in involvement of cerium 4f- versus 5d-orbitals in the electronic structures of the complexes.

Yang, Qiaomu↗

DOE OSTI2023

An in-silico NMR laboratory for nuclear magnetic shieldings computed via finite fields: Exploring nucleus-specific renormalizations of MP2 and MP3

Here we developed and implemented a method-independent, fully numerical, finite difference approach to calculating nuclear magnetic resonance shieldings, using gauge-including atomic orbitals. The resulting capability can be used to explore non-standard methods, given only the energy as a function of finite-applied magnetic fields and nuclear spins. For example, standard second-order Møller-Plesset theory (MP2) has well-known efficacy for 1H and 13C shieldings and known limitations for other nuclei such as 15N and 17O. It is, therefore, interesting to seek methods that offer good accuracy for 15N and 17O shieldings without greatly increased compute costs, as well as exploring whether such methods can further improve 1H and 13C shieldings. Using a small molecule test set of 28 species, we assessed two alternatives: κ regularized MP2 (κ-MP2), which provides energy-dependent damping of large amplitudes, and MP2.X, which includes a variable fraction, X, of third-order correlation (MP3). The aug-cc-pVTZ basis was used, and coupled cluster with singles and doubles and perturbative triples [CCSD(T)] results were taken as reference values. Our κ-MP2 results reveal significant improvements over MP2 for 13C and 15N, with the optimal κ value being element-specific. κ-MP2 with κ = 2 offers a 30% rms error reduction over MP2. For 15N, κ-MP2 with κ = 1.1 provides a 90% error reduction vs MP2 and a 60% error reduction vs CCSD. On the other hand, MP2.X with a scaling factor of 0.6 outperformed CCSD for all heavy nuclei. These results can be understood as providing renormalization of doubles amplitudes to partially account for neglected triple and higher substitutions and offer promising opportunities for future applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

Stimulation of Dissimilatory Sulfate Reduction in Response to Sulfate in Microcosm Incubations from Two Contrasting Temperate Peatlands near Ithaca, NY, USA

Abstract Peatlands are responsible for over half of wetland methane emissions, yet major uncertainties remain regarding carbon flow, especially when increased availability of electron acceptors stimulate competing physiologies. We used microcosm incubations to study the effects of sulfate on microorganisms in two temperate peatlands, one bog and one fen. Three different electron donor treatments were used (13C-acetate, 13C-formate, and a mixture of 12C short-chain fatty acids) to elucidate the responses of sulfate-reducing bacteria (SRB) and methanogens to sulfate stimulation. Methane production was measured and metagenomic sequencing was performed, with only the heavy DNA fraction sequenced from treatments receiving 13C electron donors. Our data demonstrate stimulation of dissimilatory sulfate reduction in both sites, with contrasting community responses. In McLean Bog (MB), hydrogenotrophic Deltaproteobacteria and acetotrophic Peptococcaceae lineages of SRB were stimulated, as were lineages with unclassified dissimilatory sulfite reductases. In Michigan Hollow Fen (MHF), there was little stimulation of Peptococcaceae populations, and a small stimulation of Deltaproteobacteria SRB populations only in the presence of formate as electron donor. Sulfate stimulated an increase in relative abundance of reads for both oxidative and reductive sulfite reductases, suggesting stimulation of an internal sulfur cycle. Together, these data indicate a stimulation of SRB activity in response to sulfate in both sites, with a stronger growth response in MB than MHF. This study provides valuable insights into microbial community responses to sulfate in temperate peatlands and is an important first step to understanding how SRB and methanogens compete to regulate carbon flow in these systems.

Microbiology↗

DOE OSTI2024

Two-dimensional heteronuclear single quantum coherence (HSQC) NMR spectra of lignin isolated from Populus trichocarpa residues after CELF pretreatment and CBP fermentation

Here we present a curated dataset of a series of two-dimensional heteronuclear single quantum coherence (HSQC) nuclear magnetic resonance (NMR) spectra of lignin isolated from a woody energy crop (Populus trichocarpa) residues after co-solvent enhanced lignocellulosic fractionation (CELF) pretreatment and consolidated bioprocessing (CBP) process. The natural poplar variant GW-9947 from the Center for Bioenergy Innovation (CBI) was used. The poplar was knife milled and passed through a 1 mm sieve. The CELF pretreatment was performed in a Parr autoclave reactor with 7.5 wt % solids loading, 0.5 wt% H2SO4 as catalyst at 150°C with 15, 25 and 30 minutes, respectively. Tetrahydrofuran was added in a 1:1 mass ratio with water as the pretreatment solvent. The residues from CELF pretreatment were then subjected to CBP using the bacterium C. thermocellum DSM 1313. CBP fermentations were performed at 60 °C in a shaker at 50 grams/L solids loadings. Lignin was isolated from the pretreated samples after ball-milling in a porcelain jar with ceramic balls via Retsch PM 200 at 580 rpm for 2.5 h followed by enzymatic hydrolysis in acetate buffer (pH 4.8, 50 °C) for 48 h. The lignin samples were characterized using 13C–1H HSQC experiments which were performed in a Bruker Avance III HD 500 MHz NMR spectrometer operating at a frequency of 125.12 MHz for the 13C nucleus. A standard Bruker pulse sequence was used on a Prodigy platform cryoprobe. The dry lignin samples were dissolved in deuterated dimethylsulfoxide for HSQC experiments. The spectra were acquired under the following acquisition conditions: 210 ppm spectral width in F1 (13C) dimension with 256 data points and 11 ppm spectral width in F2 (1H) dimension with 1024 data points, a 90° pulse, a one bond C–H coupling constant of 145 Hz, a 1.0 s pulse delay, and 64 scans. All the data was processed using the TopSpin 3.6 software (Bruker BioSpin). The NMR spectra provides structural characteristics information about lignin remaining in solids after CELF (150 °C with 15, 25 and 30 minutes) process and C. thermocellum CBP.

Lignin structure, HSQC, poplar, CELF, CBP, CBI↗

DOE OSTI2024

Two-dimensional heteronuclear single quantum coherence (HSQC) NMR spectra of lignin isolated from field grown transgenic poplar

Here we present a curated dataset of a series of two-dimensional heteronuclear single quantum coherence (HSQC) nuclear magnetic resonance (NMR) spectra of lignin isolated from a field grown transgenic poplar engineered with a monolignol 4-O-methyltransferase (MOMT4). The poplar was collected from a 2-year-old rotation trees within a three-year field trial experiment. The poplar was Soxhlet-extracted with toluene/ethanol and the extractives-free poplar was then ball-milled in a Retsch PM100 planetary ball mill using a porcelain jar with ceramic balls at 600 rpm for 2 h (in 5 min on and 5 min off cycles to avoid excessive sample heating). The ball-milled materials were then subjected to enzymatic hydrolysis for 48 h followed by centrifugation and washing with deionized water. The solid residue was extracted twice with 96:4 (v/v) 1,4-dioxane/water mixture at room temperature overnight. The extracts were combined, rotary evaporated, and freeze-dried to recover the lignin. The dry lignin samples were dissolved in deuterated dimethyl sulfoxide for NMR experiments. 13C–1H HSQC experiments were performed in a Bruker Avance III HD 500 MHz NMR spectrometer operating at a frequency of 125.12 MHz for the 13C nucleus using a standard Bruker pulse sequence (hsqcetgpsisp2.2) on a Prodigy platform cryoprobe. The NMR spectra were acquired under the following acquisition conditions: 220 ppm spectral width in F1 (13C) dimension with 256 data points and 12 ppm spectral width in F2 (1H) dimension with 1024 data points, a 90° pulse, a one bond C–H coupling constant of 145 Hz, a 1.0 s pulse delay, and 64 scans. All the data was processed using the Bruker’s TopSpin 3.6 software. The NMR spectra provides structural characteristics information about lignin in field grown transgenic MOMT4 poplar. Additional meta data is embedded in the raw spectra figures.

Lignin structure, HSQC, poplar, field trial, MOMT4↗

DOE OSTI2024

HSQC spectra of lignin isolated from poplar stems

Here we present a curated dataset of two-dimensional heteronuclear single quantum coherence (HSQC) nuclear magnetic resonance (NMR) spectra of lignin isolated from stems of genetically engineered poplar through auxin signaling gene modification. The plants were grown in greenhouse with temperatures between 21 and 23 °C. Plants were harvested and the aboveground stems were cut off an approximately five-inch-long segment from the bottom end of the plant stem, debarked and air-dried for three weeks. The dried stem samples were Wiley milled (mesh size 20), Soxhlet-extracted with toluene/ethanol for 24 h to remove extractives. The extracted biomass was ball-milled in a Retsch PM100 planetary ball mill using a porcelain jar with ceramic balls at 600 rpm for 2 h (in 5 min on and 5 min off cycles to avoid excessive sample heating). The ball-milled materials were then subjected to enzymatic hydrolysis for 48 h followed by centrifugation and washing with deionized water. The solid residue was freeze-dried to recover the lignin. The dry stem lignin samples were dissolved in deuterated dimethyl sulfoxide (d6) and transferred into a 5 mm tube. 13C–1H HSQC experiments were performed in a Bruker Avance III HD 500 MHz NMR spectrometer operating at a frequency of 125.12 MHz for the 13C nucleus using a standard Bruker pulse sequence on a Prodigy platform cryoprobe. The NMR spectra were acquired under the following acquisition conditions: 230 ppm spectral width in F1 (13C) dimension with 256 data points and 12 ppm spectral width in F2 (1H) dimension with 2048 data points, a 90° pulse, a one bond C–H coupling constant of 145 Hz, a 1.0 s pulse delay, and 64 scans. Spectra were processed using the Bruker TopSpin 3.6 software. Additional meta data is embedded in the raw spectra figures.

HSQC, lignin, poplar, stems, CBI↗

DOE OSTI2024

HSQC spectra of lignin isolated from poplar roots

Here we present a curated dataset of two-dimensional heteronuclear single quantum coherence (HSQC) nuclear magnetic resonance (NMR) spectra of lignin isolated from roots of a greenhouse grown natural population of an energy crop poplar (Populus trichocarpa). Dormant cuttings of field-grown poplar were grown in 6-liter pots in a peat-based media containing bark, perlite, vermiculite, dolomite lime and a wetting agent in an environmentally controlled greenhouse. Temperatures were between 21 and 23 °C, with supplemental lighting to support a 16-h day length using 1000-watt high-pressure sodium lights in greenhouse. Once established, all plants were cut-back, allowed to regrow and harvested at the same time following an eight-month long growth period. Plants were harvested and the belowground roots were washed off soils, blotted, dried in an oven at 70 °C for 3 days, and Wiley milled (mesh size 20). The roots were Soxhlet-extracted with toluene/ethanol for 24 h to remove extractives. The extracted roots were ball-milled in a Retsch PM100 planetary ball mill using a porcelain jar with ceramic balls at 600 rpm for 2 h (in 5 min on and 5 min off cycles to avoid excessive sample heating). The ball-milled materials were then subjected to enzymatic hydrolysis for 48 h followed by centrifugation and washing with deionized water. The solid residue was extracted twice with 96% (v/v) 1,4-dioxane/water mixture at room temperature overnight. The extracts were combined, rotary evaporated, and freeze-dried to recover lignin. The dry lignin samples were dissolved in deuterated dimethyl sulfoxide (d6) and transferred into a 5 mm tube. 13C–1H HSQC experiments were performed in a Bruker Avance III HD 500 MHz NMR spectrometer operating at a frequency of 125.12 MHz for the 13C nucleus using a standard Bruker pulse sequence on a Prodigy platform cryoprobe. The NMR spectra were acquired under the following acquisition conditions: 220 ppm spectral width in F1 (13C) dimension with 256 data points and 12 ppm spectral width in F2 (1H) dimension with 1024 data points, a 90° pulse, a one bond C–H coupling constant of 145 Hz, a 1.0 s pulse delay, and 64 scans. Spectra were processed using the Bruker TopSpin software. Additional meta data is embedded in the raw spectra figures.

HSQC, lignin, poplar, roots, CBI↗

DOE OSTI2026

Dataset_for_Molecular_Motion_Below_the_Glass_Transition_A_Solid-State_NMR_Study_of_Siloxane_Polymer_Dynamics Study

This dataset contains solid-state 1H and 13C NMR relaxometry data, differential scanning calorimetry (DSC) data, and size exclusion chromatography (SEC/GPC) data supporting the study of sub-glass-transition (sub-Tg) molecular dynamics in a composition- and sequence-controlled series of diphenyl-substituted polysiloxanes (PDMS, 14Ph, 33Ph, 50Ph, 67Ph, and 100Ph; 0–100% diphenylsiloxane content by mole).All solid-state NMR data were acquired on a 200 MHz Bruker Avance III HD spectrometer using a static 7 mm HX probe or a 4 mm HX probe under 4 kHz magic-angle spinning. Raw Bruker TopSpin experiment folders are included for: (1) variable-temperature 1H lineshape measurements used to determine linewidth (FWHM) as a function of temperature across the glass transition; (2) 1H T1 (saturation recovery with solid-echo detection), probing nanosecond-scale dynamics near the 1H Larmor frequency; (3) 1H T1rho (direct spin-lock, 62.5 kHz), probing microsecond-scale segmental dynamics; (4) 13C-detected Lee–Goldburg cross-polarization 1H T1rho (LGCPH T1rho) for 33Ph and 50Ph, resolving aromatic and aliphatic proton environments; and (5) 13C T1 relaxation for 33Ph and 50Ph. Differential scanning calorimetry data (TA Instruments DSC 25, −150 to +120 °C, up to +300 °C for 100Ph, 10 °C/min) are included for all six compositions and support the glass-transition temperatures in Table 1 and Figure 1. Size exclusion chromatography data (Agilent 1200 Series, PL-Gel 300 mixed-C column, THF mobile phase, polystyrene calibration standards) are included for the three synthesized copolymers (33Ph, 50Ph, 67Ph) and support the number-average molecular weights in Table 1. Processed data include per-composition relaxation-time summaries (Excel), curve-fitting and Bloembergen-Purcell-Pound (BPP) model analysis notebooks (Jupyter/Python), and Igor Pro (.pxp) master files used to generate the manuscript's figures.

Bloembergen-Purcell-Pound theory↗

DOE OSTI2022

Light-Dependence of Formate (C1) and Acetate (C2) Transport and Oxidation in Poplar Trees

Although apparent light inhibition of leaf day respiration is a widespread reported phenomenon, the mechanisms involved, including utilization of alternate respiratory pathways and substrates and light inhibition of TCA cycle enzymes are under active investigation. Recently, acetate fermentation was highlighted as a key drought survival strategy mediated through protein acetylation and jasmonate signaling. Here, we evaluate the light-dependence of acetate transport and assimilation in Populus trichocarpa trees using the dynamic xylem solution injection (DXSI) method developed here for continuous studies of C1 and C2 organic acid transport and light-dependent metabolism. Over 7 days, 1.0 L of [13C]formate and [13C2]acetate solutions were delivered to the stem base of 2-year old potted poplar trees, while continuous diurnal observations were made in the canopy of CO2, H2O, and isoprene gas exchange together with δ13CO2. Stem base injection of 10 mM [13C2]acetate induced an overall pattern of canopy branch headspace 13CO2 enrichment (δ13CO2 +27‰) with a diurnal structure in δ13CO2 reaching a mid-day minimum followed by a maximum shortly after darkening where δ13CO2 values rapidly increased up to +12‰. In contrast, 50 mM injections of [13C]formate were required to reach similar δ13CO2 enrichment levels in the canopy with δ13CO2 following diurnal patterns of transpiration. Illuminated leaves of detached poplar branches pretreated with 10 mM [13C2]acetate showed lower δ13CO2 (+20‰) compared to leaves treated with 10 mM [13C]formate (+320‰), the opposite pattern observed at the whole plant scale. Following dark/light cycles at the leaf-scale, rapid, strong, and reversible enhancements in headspace δ13CO2 by up to +60‰ were observed in [13C2]acetate-treated leaves which showed enhanced dihydrojasmonic acid and TCA cycle intermediate concentrations. The results are consistent with acetate in the transpiration stream as an effective activator of the jasmonate signaling pathway and respiratory substrate. The shorter lifetime of formate relative to acetate in the transpiration stream suggests rapid formate oxidation to CO2 during transport to the canopy. In contrast, acetate is efficiently transported to the canopy where an increased allocation towards mitochondrial dark respiration occurs at night. The results highlight the potential for an effective integration of acetate into glyoxylate and TCA cycles and the light-inhibition of citrate synthase as a potential regulatory mechanism controlling the diurnal allocation of acetate between anabolic and catabolic processes.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Root carbon interation with soil minerals is dynamic, leaving a legacy of microbially derived residues

Minerals preserve the oldest most persistent soil carbon, and mineral characteristics appear to play a critical role in the formation of soil organic matter (SOM) associations. To test the hypothesis that carbon source and soil microorganisms also influence mineral-SOM associations, we incubated permeable minerals bags in soil microcosms with and without plants, in a 13CO2 labelling chamber. Mineral bags contained quartz, ferrihydrite, kaolinite, or native soil minerals isolated via density separation. Using 13C-NMR, FTICR-MS, and lipidomics, we traced plant-derived carbon onto minerals harvested from microcosms at three plant growth stages, characterizing total carbon, 13C enrichment, and SOM chemistry. While C accumulation was rapid and mineral-dependent, the accumulated amount was not significantly affected by the presence of plant roots. However, the rhizosphere did shape the chemistry of mineral-associated SOM. Minerals incubated in the rhizosphere were associated with a more diverse array of compounds with different C functional groups (carbonyl, aromatics, carbohydrates, lipids) than minerals incubated in a bulk soil control. These diverse rhizosphere-derived compounds may represent a “transient fraction” of mineral SOM, rapidly exchanging with mineral surfaces. Our results also suggest that many of the lipids which persist on minerals are microbially-derived with a large fraction of fungal lipids.

Rhizosphere, soil organic matter, grassland, 13C-N↗

DOE OSTI2023

A High-Quality Genome-Scale Model for Rhodococcus opacus Metabolism

Rhodococcus opacus is a bacterium that has a high tolerance to aromatic compounds and can produce significant amounts of triacylglycerol (TAG). Here, we present iGR1773, the first genome-scale model (GSM) of R. opacus PD630 metabolism based on its genomic sequence and associated data. The model includes 1773 genes, 3025 reactions, and 1956 metabolites, was developed in a reproducible manner using CarveMe, and was evaluated through Metabolic Model tests (MEMOTE). We combine the model with two Constraint-Based Reconstruction and Analysis (COBRA) methods that use transcriptomics data to predict growth rates and fluxes: E-Flux2 and SPOT (Simplified Pearson Correlation with Transcriptomic data). Growth rates are best predicted by E-Flux2. Flux profiles are more accurately predicted by E-Flux2 than flux balance analysis (FBA) and parsimonious FBA (pFBA), when compared to 44 central carbon fluxes measured by 13C-Metabolic Flux Analysis (13C-MFA). Under glucose-fed conditions, E-Flux2 presents an R2 value of 0.54, while predictions based on pFBA had an inferior R2 of 0.28. We attribute this improved performance to the extra activity information provided by the transcriptomics data. For phenol-fed metabolism, in which the substrate first enters the TCA cycle, E-Flux2’s flux predictions display a high R2 of 0.96 while pFBA showed an R2 of 0.93. We also show that glucose metabolism and phenol metabolism function with similar relative ATP maintenance costs. These findings demonstrate that iGR1773 can help the metabolic engineering community predict aromatic substrate utilization patterns and perform computational strain design.

Roell, Garrett W.↗

DOE OSTI2025

A Thorough Characterization of the Tellurocyanate Anion

Tellurocyanate, [TeCN] − , is the heaviest group 16 congener of the cyanate anion, [OCN] − . Due to the relative instability of the C─Te bond, tellurocyanate chemistry has seen only scarce attention. Here, we present the facile synthesis and thorough characterization of [K@crypt-222][TeCN]. The anion is essentially linear with interatomic distances C─N = 1.150(6)Å and C─Te = 2.051(4)Å, thus approximating a C≡N triple bond and for C─Te a bond order between 1 and 2. Fully 13 C and 15 N labeled [Te 13 C 15 N] − allowed for the extraction of chemical shifts and all possible coupling constants ( 13 C = 77.8 ppm, 15 N = 285.7 ppm, 125 Te = −566 ppm, 1 J 13C-15N = 8 Hz, 1 J 13C-125Te = 748 Hz, 2 J1 5N-125Te = 55 Hz), which were also determined independently by quantum chemical calculations. In the series [ChCN] − (Ch = O─Te), [TeCN] − shows the strongest spin-orbit coupling (SOC) induced heavy-atom effect on the light-atom shielding (SO-HALA-effect). In contrast, 15 N shifts are also well described without considering relativistic effects and/or SOC. Negative-ion photoelectron spectroscopy was used to extract the electron affinity (EA = 3.034 eV) and spin-orbit splitting (3807 cm −1 ) of [TeCN] • . These values continue the trends of falling EA and rising SOC in the series [ChCN] • .

Bonding analysis↗

DOE OSTI2021

Differential effects of redox conditions on the decomposition of litter and soil organic matter

Soil redox conditions exert substantial influence on biogeochemical processes in terrestrial ecosystems. Humid tropical forests are often characterized by fluctuating redox dynamics, yet how redox fluctuations affect patterns in soil versus litter decomposition and associated CO2 fluxes are not well understood in these ecosystems. We used a 13C-labeled litter addition to explicitly follow the decomposition of litter-derived vs. native soil-derived organic matter in response to four different soil redox regimes—static oxic or anoxic, and two oscillating treatments—in soil from the Luquillo Experimental Forest, Puerto Rico. We coupled this incubation experiment with high-resolution mass spectrometry analysis to characterize the preferential decomposition of specific classes of organic molecules. CO2 production from litter and soil organic matter (SOM) showed distinctly different responses to redox manipulation. The cumulative production of SOM-derived CO2 was positively correlated with the length of soil exposure to an oxic headspace (r = 0.89, n = 20), whereas cumulative 13C-litter-derived CO2 production was not linked to oxygen availability. The CO2 production rate from litter was highest under static anoxic conditions in the first half of the incubation period, and later dropped to the lowest among all redox treatments. In the consistently anoxic soils, we observed the depletion of more oxidized water-extractable organic matter (especially amino sugars, carbohydrates, and proteins) over time, suggesting that under anaerobic conditions, microbes preferentially used more oxidized litter-derived compounds during the early stages of decomposition. Results from kinetic modeling showed that more frequent anoxic exposure limited the decomposition of a slow-cycling C pool, but not a fast-cycling pool. Overall, our results demonstrate that substrate source—freshly added litter vs. native organic matter—plays an important role in the redox sensitivity of organic matter decomposition. In soil environments that regularly experience redox fluctuations, anaerobic heterotrophs can be surprisingly effective in degrading fresh plant litter.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

High-dimensional isotomics, part 2: Observations of over 100 constraints on methionine's isotome

The abundances of different isotopic forms of a compound, or isotopologues, will vary based on its physical and chemical history. The number of isotopologues increases combinatorically with the size of a molecule, and even small molecules such as amino acids have thousands of potentially observable isotopic variants. However, due to the analytical challenges of separating and observing isotopologues, only a few dimensions of isotopic diversity are routinely measured. Overcoming these challenges requires both an experimental method to observe many isotopic properties and a theoretical framework for interpreting these experiments. In Part 1, we presented such a theoretical framework; here, we demonstrate an experimental method, which we apply to methionine. Our approach uses a Q Exactive HF Orbitrap to perform several “M + N experiments”, where a sample is ionized, a subset of its isotopologues with cardinal mass N daltons greater than the unsubstituted isotopologue is selected and fragmented, and the proportions of all detectable isotopic forms of those fragment ions are quantified. We perform M + 1, M + 2, M + 3, and M + 4 experiments of a methionine sample and standard where the sample has a 100 ‰ enrichment of 13C at the methyl carbon relative to the natural 13C abundance at that position in the standard, and is otherwise identical to the standard. We observe isotopic forms of 8 fragment ion species for each version of the M + N experiment. With the assistance of a forward model of expected mass spectra, we identify isotopic peaks for each fragment ion based on observed mass and abundance, screen these for data quality, and quantify abundances for 146 unique isotopic peaks at precisions of ≈ 0.3–3 ‰. We present our direct observations and use them to reconstruct the concentrations of 19 individual singly, doubly, and triply-substituted isotopologues; doing so gives fewer constraints and broader error bars than working with the direct observations, but may be more interpretable for some applications. We also examine possibilities for measuring additional peaks, which are primarily limited by the detection limit of the Orbitrap-IRMS method. We then suggest some possible uses of our direct measurements for chemical forensics and hypothesis testing. Furthermore, our results demonstrate the diversity of isotopic constraints currently observable and interpretable for organic molecules.

58 GEOSCIENCES↗

DOE OSTI2020

A Study of the Conformational Isomerism of n-Propyl Nitrate by Microwave Spectroscopy

The rotational spectrum of n-propyl nitrate was measured in the frequency range between 6 to 18 GHz using a Balle-Flygare Fourier transform microwave jet/cavity spectrometer. Parent, 13C and 15N isotopologue transitions for the lower-energy anti-gauche (AG) conformer were found using this instrument. The search for spectra from other conformers was performed using a broadband chirped-pulse jet spectrometer. Transitions from the anti-anti (AA) conformer were observed in this manner. Parent, 13C and 15N isotopologue transitions for the AA conformer were rescanned using the cavity instrument to improve resolution and the signal-to-noise ratio. Rotational, centrifugal distortion, and nuclear electric quadrupole coupling constants for all conformers/isotopologues were fit using Pickett’s SPFIT program. The structure of n-propyl nitrate is discussed considering these results.

Orellana, Will D.↗

DOE OSTI2020

Linking Internal Dosimetries of the Propyl Metabolic Series in Rats and Humans Using Physiologically Based Pharmacokinetic (PBPK) Modeling

The metabolic series approach has successfully linked internal dosimetries of metabolically related compounds reducing cost and time for chemical risk assessments. Here, we developed a physiologically based pharmacokinetic (PBPK) model in rats and humans for the propyl metabolic series including propyl acetate, 1-propanol, propionaldehyde, and propionic acid. Manufacturers use these compounds as organic solvents and intermediates during chemical synthesis. Public exposures can occur through using consumer products containing propyl compounds like cosmetics, aerosol sprays, or foods. To develop the PBPK model, we measured in vitro metabolism of propyl acetate in blood and liver S9 fractions. We measured concentrations of propyl compounds in blood following intravenous (iv) infusion of 13C-propanol or 13C-propionic acid and closed chamber inhalation exposures to propyl acetate or propanol in rats. Using these studies and other published data, we modified an existing PBPK model for the butyl metabolic series to simulate time course concentrations of propyl compounds in rats and humans. Consistent with measured in vitro and in vivo data, the optimized propyl series model predicts rapid clearance of propyl acetate, higher concentrations of propanol in blood from propyl acetate inhalation compared to propanol inhalation, and low concentrations of propionic acid in blood from exposures to propyl acetate or propanol. Regulators can use this model as a tool for propyl compound risk assessment by linking internal dosimetries under various exposure scenarios.

Smith, Jordan N.↗

DOE OSTI2023

Life history strategies among soil bacteria—dichotomy for few, continuum for many

Abstract Study of life history strategies may help predict the performance of microorganisms in nature by organizing the complexity of microbial communities into groups of organisms with similar strategies. Here, we tested the extent that one common application of life history theory, the copiotroph-oligotroph framework, could predict the relative population growth rate of bacterial taxa in soils from four different ecosystems. We measured the change of in situ relative growth rate to added glucose and ammonium using both 18O–H2O and 13C quantitative stable isotope probing to test whether bacterial taxa sorted into copiotrophic and oligotrophic groups. We saw considerable overlap in nutrient responses across most bacteria regardless of phyla, with many taxa growing slowly and few taxa that grew quickly. To define plausible life history boundaries based on in situ relative growth rates, we applied Gaussian mixture models to organisms’ joint 18O–13C signatures and found that across experimental replicates, few taxa could consistently be assigned as copiotrophs, despite their potential for fast growth. When life history classifications were assigned based on average relative growth rate at varying taxonomic levels, finer resolutions (e.g., genus level) were significantly more effective in capturing changes in nutrient response than broad taxonomic resolution (e.g., phylum level). Our results demonstrate the difficulty in generalizing bacterial life history strategies to broad lineages, and even to single organisms across a range of soils and experimental conditions. We conclude that there is a continued need for the direct measurement of microbial communities in soil to advance ecologically realistic frameworks.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2026

Conserved Macromolecular Architecture of Poplar Secondary Cell Walls Revealed by ssNMR and Atomistic Modeling

The macromolecular architecture of plant secondary cell walls governs wood's mechanical and biochemical properties, yet its natural intra-species variability remains poorly characterized. Here, we combined 13C solid-state NMR (ssNMR), multivariate statistical analysis, and molecular modeling to profile nanoscale structure across 13 genetically diverse Populus trichocarpa genotypes grown in 13C-enriched atmospheres. SsNMR-derived phenotypes spanning composition, structure, mobility, and inter-polymer proximities reveal a conserved architecture, with a subtle yet coordinated variation organizing into dominant structural and secondary mobility axes. A representative atomistic model captures these features and reproduces experimental metrics. Molecular dynamics simulations support a weak but consistent positive correlation between cellulose abundance and crystalline-like order, with interior cellulose chains enriched in tg (trans-gauche) conformations without expanding crystalline cores. Together, experiment and simulation reveal a genetically buffered, broadly conserved nanoscale architecture across genotypes, where subtle fine-tuning of cellulose bundling and matrix packing balances mechanical performance with biological function.

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