13C NMR data for the five dissolved organic matter
Cite this dataset
Li, Siyu et al. (2025). 13C NMR data for the five dissolved organic matter [Dataset]. Dryad. https://doi.org/10.5061/dryad.jsxksn0hr
Abstract
Dissolved organic matter (DOM) is one of the most complex, dynamic, and abundant sources of organic carbon, but its chemical reactivity remains uncertain. Greater insights into DOM structural features could facilitate understanding its synthesis, turnover, and processing in the global carbon cycle. Here we use complementary multiplicity-edited 13C NMR spectra to quantify key substructures assembling the carbon skeletons of DOM from four main Amazon rivers and two mid-size Swedish boreal lakes. We find that one type of reaction mechanism, oxidative dearomatization (ODA), widely used in organic synthesic chemistry to create natural product scaffolds, is likely a key driver for generating structural diversity during processing of DOM that are rich in suitable polyphenolic precursor molecules. Our data suggest a high abundance of tetrahedral quaternary carbons bound to one oxygen and three carbon atoms (OCqC3 units). These units are rare in common biomolecules but could be readily produced by ODA of lignin and tannin derived polyphenols. Tautomerization of (poly)phenols by ODA creates non-planar cyclohexadienones which are subject to immediate and parallel cycloadditions. This combination amounts to a proliferation of structural diversity of DOM compounds from early stages of DOM processing, with an increase in oxygenated aliphatic structures. Overall, we propose that ODA is a key reaction mechanism for complexity acceleration in the processing of DOM molecules, creation of novel oxygenated aliphatic molecules, and that it could be prevalent in nature.
README: 13C NMR data for the five dissolved organic matter
https://doi.org/10.5061/dryad.jsxksn0hr
Five *.pdf files with the 13C NMR data for the five dissolved organic matter investigated. N-DOM (DOM in the Negro River), S-DOM (DOM in the Solimões River), A-DOM (DOM in the Amazonas River), T-DOM (DOM in the Tapajós River), B-DOM (DOM in the boreal lakes).
Description of the data and file structure
These files comprise 13C NMR section integrals for the five DOM, divided into buckets of 0.1 ppm width, and ranging from δC = 0 – 235 ppm. The total integral of these 13C NMR spectra is area normalized to Call = 100% for all five DOM, and to CH0123 according to its proportions. The 13C NMR section integral from δC = 47 - 51 ppm is set to zero for all five 13C NMR spectra of DOM, because of interference from the solvent 12CD3OD, which resonates at δC = 49.0 ppm.
Methods Overview
A Bruker Avance III spectrometer and TopSpin 3.6/PL6 software were used to acquire 13C nuclear magnetic resonance (NMR) spectra of re-dissolved DOM (10-40 mg solid SPE-DOM in typically 75-135 µL CD3OD (99.95 % 2H; 13C-depleted 12CD3OD, Aldrich, Steinheim, Germany). Briefly, the re-dissolved DOM were transferred to 2.5-3.0 mm Bruker Match tubes and sealed. A cryogenic classical geometry 5 mm z-gradient 13C, 1H probe (B0 = 11.7 T) was used for acquisition of 13C NMR spectra. Transmitter pulses were at ~10 µs for 1H and 13C, and calibrated 90/180-degree pulses were employed for each sample.
We used inverse-gated 1H decoupling for 13C NMR spectra to eliminate nOe effects (nuclear Overhauser effects), and (acquisition-time adjusted) linear combinations of the 13C DEPT-45, -135 and -90 NMR spectra (1JCH: 150 Hz) to compute the individual traces of CH (13C DEPT-90 NMR spectrum), CH2 (13C DEPT-45 minus 13C DEPT-135) and CH3 ([13C DEPT-45 plus 13C DEPT-135] minus 13C DEPT-90). We corrected the 13C DEPT-90 NMR spectrum by subtracting an appropriate amount (commonly ~2-3%) of the 13C DEPT-45 NMR spectrum to attenuate leakage of CH3 and CH2 into the 13C DEPT-90 NMR spectrum (methine carbon (CH) in DOM does not show appreciable 13C NMR resonances at δC < 20 ppm) that arises from the unavoidable variance in 1JCH of DOM. Then we determined the relative contributions of the individual spectra (CH3, CH2, CH1) to the sum CH123 as observed in 13C DEPT-45 NMR spectra with recognition of the individual transfer amplitudes which were as follows (CH3 = 1.06; CH2 = 1.0; CH = 0.707). The proportions of quaternary carbon atoms Cq in DOM were computed from comparison of 13C DEPT-45, 13C QUAT, and single pulse 13C NMR spectra.
13C NMR overlay figures were computed using the Bruker AMIX software (version 3.9.4) from area normalized spectra with 0.1 ppm buckets and 100% total NMR integral area from δC: 0-235 ppm, with exclusion of the solvent 12CD3OD, which resonates at δC = 49.0 ppm.
Methods
These files comprise 13C NMR section integrals for the five DOM, divided into buckets of 0.1 ppm width, and ranging from dC = 0 – 235 ppm. The total integral of these 13C NMR spectra is area normalized to Call = 100% for all five DOM, and to CH0123 according to its proportions. The 13C NMR section integral from dC = 47 - 51 ppm is set to zero for all five 13C NMR spectra of DOM, because of interference from the solvent 12CD3OD, which resonates at dC = 49.0 ppm.
Funding
Alexander von Humboldt Foundation
Swedish Research Council for Environment Agricultural Sciences and Spatial Planning, Award: 2021-0242
Swedish Research Council, Award: 2012-00048
European Research Council, Award: 725546
Ministry of Education of the People's Republic of China, Award: 201806360268
Coordenação de Aperfeicoamento de Pessoal de Nível Superior
Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro
National Council for Scientific and Technological Development, Award: 290004/2014-4