Carbon (1s) NEXAFS Spectroscopy of Biogeochemically Relevant Reference Organic Compounds

Abstract

Natural organic matter (NOM) is a highly active component of soils and sediments, and plays an important role in global C cycling. However, NOM has defied molecular‐level structural characterization, owing to variations along the decomposition continuum and its existence as highly functionalized polyelectrolytes. We conducted a comprehensive systematic overview of spectral signatures and peak positions of major organic molecules that occur as part of NOM using near‐edge x‐ray absorption fine structure (NEXAFS) spectroscopy. The spectra of carbohydrates and amino sugars show resonances between 289.10 and 289.59 eV, attributed to 1s‐3p/σ* transitions of O‐alkyl (C‐OH) moieties. They also exhibited distinct peaks between 288.42 and 288.74 eV, representing C 1s–π*C = O transition from COOH functionalities. Amino acids produced a strong signal around 288.70 eV, which can be identified as a C 1s–π*C=O transition of carboxyl/carbonyl (COOH/COO‐) structures. Spectral features near 285.29 eV were ascribed to C 1s–π*C=C transition of ring structure of aromatic amino acids, while spectra between 287.14 and 287.86 eV were attributed to C 1s–π*C‐H and C 1s–σ*C‐H/3p Rydberg‐like excitations from CH and CH2 groups. Phenols and benzoquinone produced strong resonances between 285.08 and 285.37 eV, attributed to the π* orbital of C (C 1s–π*C=C) atoms connected to either C or H (C–H) in the aromatic ring. The next higher excitation common to both phenols and quinone appeared between 286.05 and 286.35 eV, and could be associated with C 1s–π*C=C transitions of aromatic C bonded to O atom in phenols, and to C 1s–π*C=O transitions from aromatic C connected to O atom (C‐OH) in phenols or to a C=O in p‐benzoquinone and some phenols with carbonyl structures, respectively. Nucleobases exhibited complex spectral features with pronounced resonances between 286.02 and 286.84 eV and between 288.01 and 288.70 eV. Molecular markers for black C (benzenecarboxylic acid and biphenyl‐4,4′‐dicarboxylic acid) exhibit sharp absorption bands between 285.01 and at 285.43 eV, possibly from C 1s–π*C=C transition characteristic of C‐H sites or unsaturated C (C=C) on aromatic ring structures. These aromatic carboxylic acids also exhibit broad peaks between 288.35 and 288.48 eV, reflecting C 1s–π*C=O transition of carboxyl functional groups bonded to unsaturated C. This investigation provides a more comprehensive NEXAFS spectral library of biogeochemically relevant organic C compounds. The spectra of these reference organic compounds reveal distinct spectral features and peak positions at the C K‐edge that are characteristic of the molecular orbitals bonding C atoms. Detailed structural information can be derived from these distinctive spectral features that could be used to build robust peak assignment criteria to exploit the chemical sensitivity of NEXAFS spectroscopy for in situ molecular‐level spatial investigation and fingerprinting of complex organic C compounds in environmental samples.

Characterization of refractory organic substances by NEXAFS using a compact X-ray source

“…The spectra are comparable to those achieved with synchrotron radiation (Solomon et al 2005(Solomon et al , 2009Schumacher et al 2005), as they exhibit the expected peaks at the characteristic positions. This could provide the possibility to perform test experiments with samples, which are later studied in more detail with X-rays generated by a storage ring and might as well give an impulse on the broader spread of the Table 1, and the peak assignments for luvisol are also collated in Table 2 application of NEXAFS spectroscopy.…”

“…2 with the assignments of the peaks depicted in more detail. The relation of the peak heights within the spectrum is characteristic for this sample, as the comparison with HA in the following paragraph and from literature (Solomon et al 2005(Solomon et al , 2009 shows. The inset shows the second derivative of the absorption with respect to the energy.…”

“…2 and the inset. Secondly, we took advantage of the fact that published NEXAFS-spectra of many chemical compounds already exist, e.g., (Smith et al 2001;Hitchcock et al 2005;Dhez et al 2003;Shober et al 2006;Hitchcock 2009;Ishii and Hitchcock 1988;Cooney and Urquhart 2004;Solomon et al 2005Solomon et al , 2009. We compared these with the positions gained from the derivatives.…”

“…However, as seen from NEXAFS spectra of small, well-understood molecules Hitchcock 1987, 1988;Sham et al 1989;Cooney and Urquhart 2004;Kolczewski et al 2006;Bâldea et al 2007;Solomon et al 2009), shifts of peak positions and absorption edges occur, depending on, e.g., the chemical environment, the substrate, or the state of aggregation. Furthermore, the functional and other subgroups in such large compositions are regarded as independent units.…”

“…Soon, more complex samples from polymer science were investigated using NEXAFS spectroscopy, see for example Kikuma and Tonner (1996); Urquhart and Ade (2002). Over the recent years, more and more complex heterogeneous samples from biomolecular (Boese et al 1997;Hitchcock et al 2005;Benzerara et al 2006) or environmental (Cody et al 1998;Braun 2005;Solomon et al 2009) origin were studied. Especially natural organic matter and soils Schumacher et al 2005;Lehmann et al 2007;Thieme et al 2010), or particulate matter (Braun et al , 2007 were subject to such studies, by which valuable information about the chemical composition and functional groups and also their change due to photolysis, temperature, and so on could be gained.…”