The three-dimensional structure of humic substances and soil organic matter studied by computational analytical chemistry

A novel three-dimensional structural concept for humic substances and soil organic matter (SOM) is proposed which is based on previously published, comprehensive investigations combining geochemical, wetchemical, biochemical, spectroscopic, agricultural and ecological data with analytical pyrolysis. Direct, temperature-programmed pyrolysis in the ion-source of the mass spectrometer and soft ionization in very high electric fields (Py-FIMS) and Curie-point pyrolysis-gas chromatography/mass spectrometry (Py-GC/MS) were the main applied thermal methods. Emphasis is laid on molecular modelling and geometry optimization of complex, polydisperse structures of biomacromolecules using modern PC software (HyperChem^®). Trapping and binding of atrazine in an organo-mineral complex is introduced as a first example of simulation experiments for soil processes at atomic level (nanochemistry). Future applications of semi-empirical calculations and molecular dynamics in pyrolysis studies are outlined.Dedicated to Professor Dr. Dieter Klockow on the occasion of his 60th birthday     

Non-bonded organo-mineral interactions and sorption of organic compounds on soil surfaces: a model approach

Molecular mechanics and molecular dynamics calculations have been performed on organo-mineral composites that model the sorption of high-molecular-weight humic polymers on mineral surfaces and the sorption of low-molecular-weight organic contaminants on both mineral and organic surfaces in soil. Muscovite mica was chosen as a mineral model; an oxidized topological lignin-carbohydrate complex was chosen as a humic model; benzene, sodium benzoate, atrazine, and DDT represent different classes of contaminants. Sorption energies were estimated based on molecular mechanics calculations. Flexible linear polymers undergo drastic conformational changes when approaching the mineral surface, to ensure a gain in the interaction energy that outweighs a loss in the conformational energy proper. Therefore, the gas-phase conformation composi tion of environmental organic polymers is not directly related to their spatial organization in soil composites. Molecular dynamics simulation suggests high stability of the organic polymer coatings of mineral surfaces in the environment. Low-molecular-weight organic molecules demonstrate much less affinity for the mineral surface, which implies unhindered exchanges between the surface and its near environment. Ionizable compounds, e.g. salts of organic acids, are different, because they can form strong associations with a mineral surface through cation bridges. Sorption energies are compound-specific and depend on the sorbate-sorbent orientation. The calculations suggest some preference for the edges of a model muscovite sheet in comparison with the basal oxygen surface as a sorption site. Coating of mineral surfaces with organic polymers does not hinder the sorption of organic molecules except in the special case of organic ions.     

Ultra‐high performance supercritical fluid chromatography of lignin‐derived phenols from alkaline cupric oxide oxidation

Traditional chromatographic methods for the analysis of lignin‐derived phenolic compounds in environmental samples are generally time consuming. In this work, an ultra‐high performance supercritical fluid chromatography method with a diode array detector for the analysis of major lignin‐derived phenolic compounds produced by alkaline cupric oxide oxidation was developed. In an analysis of a collection of 11 representative monomeric lignin phenolic compounds, all compounds were clearly separated within 6 min with excellent peak shapes, with a limit of detection of 0.5–2.5 μM, a limit of quantification of 2.5–5.0 μM, and a dynamic range of 5.0–2.0 mM (R² > 0.997). The new ultra‐high performance supercritical fluid chromatography method was also applied for the qualitative and quantitative analysis of lignin‐derived phenolic compounds obtained upon alkaline cupric oxide oxidation of a commercial humic acid. Ten out of the previous eleven model compounds could be quantified in the oxidized humic acid sample. The high separation power and short analysis time obtained demonstrate for the first time that supercritical fluid chromatography is a fast and reliable technique for the analysis of lignin‐derived phenols in complex environmental samples.     

Copper-induced oligomerization of peptides: a model study

In this work, copper-binding of the tetraglycine peptide (Gly-Gly-Gly-Gly) was studied by electrospray ionization mass spectrometry. Experiments were performed under alkaline conditions, in the presence of ethanolamine (pH 10.95). We observed that the presence of copper(II) ions induces the aggregation of the peptide and the formation of copper-bound complexes with higher molecular mass is favored, such as the oligomer complexes [3M+2Cu-3H](+) and [4M+3Cu-5H](+). At 1:1 peptide-copper(II) ion ratio, the singly charged [3M+2Cu-3H](+) oligomer complex is the base peak in the mass spectrum. Metal ion-induced oligomer-ization of neurotoxic peptides is well known in the literature; however, there are very few examples in which such oligomerization was directly observed by mass spectrometry. Our results show that application of short peptides can be useful to study the -mechanism of metal ion binding and metal ion-induced oligomerization of peptides.     

Electrospray ionization mass spectrometry of terrestrial humic substances and their size fractions

Electrospray ionization mass spectrometry (ESI-MS) was used to evaluate the average molecular mass of terrestrial humic substances, such as humic (HA) and fulvic (FA) acids from a soil, and humic acid from a lignite (NDL). Their ESI mass spectra, by direct infusion, gave average molecular masses comparable to those previously obtained for aquatic humic materials. The soil HA and FA were further separated in size-fractions by preparative high performance size exclusion chromatography (HPSEC) and analyzed with ESI-MS by both direct infusion and a further on-line analytical HPSEC. Unexpectedly, their average molecular mass was only slightly less than for the bulk sample and, despite different nominal molecular size, did not substantially vary among size-fractions. The values increased significantly (up to around 1200 Da) after on-line analytical HPSEC for the HA bulk sample, at both pH 8 and 4, and for the HA size-fractions when pH was reduced from 8 to 4. It was noticed that HA size-fractions at pH 8 were separated by on-line HPSEC in further peaks showing average masses which progressively increased with elution volume. Furthermore, when the HA and NDL bulk samples were sequentially ultracentrifuged at increasing rotational speed, their supernatants showed mass values which were larger than bulk samples and increased with rotational speed. These variations in mass values indicate that the electrospray ionization is dependent on the composition of the humic molecular mixtures and increases when their heterogeneity is progressively reduced. It is suggested that the dominance of hydrophobic compounds in humic supramolecular associations may inhibit the electrospray ionization of hydrophilic components. Our results show that ESI-MS is reasonably applicable to humic substances only after an extensive reduction of their chemical complexity.     

[14C]-Cellulase-humic complexes that are stable in soil

[¹⁴C]-Cellulase was extracted from the culture medium ofTrichoderma viride and an attempt made to complex it with humic acid by adsorption. The result showed that the humic acid extracted from soil does not form a stable complex with [¹⁴C]-cellulase. In contrast, the flocculation of humic acid by 0.025M Ca²⁺ in the presence of the cellulase resulted in the formation of stable humic-cellulase complexes. DEAE cellulose chromatography of cellulase-humic complex revealed that cellulase could not be separated from the humic acid. Enzyme activity was only eluted along with humic acid upon increasing gradient concentration from 1.0 to 1.5M NaCl. Furthermore, in order to test its stability, the enzyme-humic complex was incorporated into fresh soil for 90 d. During this period the enzyme-humic complex remained stable. The cellulase-humic complex was then extracted from soil. Fractionation of the extract on DEAE cellulose and G100 sephadex revealed that cellulase activity could not be separated from humic acid and was again eluted in the form of enzyme-humic complex. This confirmed the stability of cellulase-humic complex in soil.     

Complexation Properties of Typical Soil and Peat Humic Acids with Copper(II) and Cadmium(II)

Abstract

Potentiometric titration with ion-selective electrodes was applied to determine characteristic parameters like the degree of complexation and the approximate molecular weight of humic acids from theoretical considerations and conditional stability constants for the complexes of Cu(II) and Cd(II) with humic acids obtained from sources such as garden soil, peat prepared by decomposing water hyacinth in soil and humified water hyacinth. Double-reciprocal and Scatchard plots were constructed to determine the conditional stability constants of the complexes formed. Cu(II) was found to have more affinity for the humic acids than Cd(II) and the stability of the metal complexes in aqueous medium was found to increase with increasing pH. The order of stability of the complexes was M-HA (soil)>M-HA (peat)>M-HA (humified water hyacinth), where M and HA represent metal and humic acids, respectively.     

Effects of sample properties and mass spectroscopic parameters on electrospray ionization mass spectra of size-fractions from a soil humic acid

Size-fractions from a soil humic acid were separated by preparative size-exclusion chromatography (SEC), desalted, and concentrated by ultrafiltration and vacuum centrifugation without being subjected to any freeze-drying process. After having assessed the lack of formation of any multiple-charged ions by high-resolution Fourier transform ion cyclotron resonance electrospray ionization (ESI) mass spectrometry (MS), the size-fractions were used by direct infusion to compare the molecular ion distribution by both atmospheric pressure chemical ionization (APCI)- and ESI-MS in negative mode. The weight- (Mw) and number-averaged (Mn) molecular weight obtained by ESI-MS were invariably larger than by APCI-MS for all size-fractions, thereby indicating that ESI is more efficient than APCI to evaluate the molecular mass distribution of humic samples. No substantial difference was observed when concentration and pH of unfreeze-dried humic size-fractions were varied. The negative mode was applied to assess the effect of cone voltage from −20 to −60 V on ESI of the humic size-fractions further separated through an on-line SEC column. The resulting mass spectra and Mw and Mn values suggested that the variation of cone voltage in ESI-MS affects the ionization potential of associated humic molecules more in solution rather than their fragmentation. These findings agree with previous observations which indicated a limitation of ESI in providing consistent mass detection for a complex mixture of heterogeneous humic molecules, especially when they are aggregated by a freeze-drying process.     

Limitations of electrospray ionization in the analysis of a heterogeneous mixture of naturally occurring hydrophilic and hydrophobic compounds

A model heterogeneous mixture of a hydrophilic tripeptide (phenylalanine-glycine-glycine, PGG) and hydrophobic organic acids ((12)C- and (13)C-octanoic acid and pentadecanoic acid) was subjected to electrospray ionization mass spectrometry (ESI-MS). The objective was to verify the previously noted inconsistencies in ESI-MS of complex environmental samples such as humic materials from either aquatic or terrestrial origins. The hydrophobic organic acids, either alone or together, reduced significantly the ESI-MS detection of the tripeptide molecular and self-associated ions at a concentration that was an order of magnitude lower than that of PGG. The most intense peaks were invariably those of the octanoic acid as either deprotonated, self-associated, or acetate-clustered molecules. The presence of equimolar amounts of PGG and organic acids yielded similar results, but with a significant increased detection of PDA and a smaller depression of the PGG signals. This behaviour is attributed to a different electrospray ionization of the mixture compounds depending on their most probable positioning at the surface of the evaporating droplet. The most favoured positioning of hydrophobic molecules at the aqueous-gas interphase allows preferential evaporation of hydrophobic ions whereas the hydrophilic molecules are retained in the droplet interior, and, their ESI-MS detection depressed. These findings suggest that the electrospray ionization of different molecules present in complex heterogeneous mixtures of environmental significance such as humic substances is limited by their concentration and reciprocal attracting forces.     

Enzymatic degradation of Lignin-Carbohydrate complex (part I)

Initial steps in an early metabolic pathway of biodegradation of lignin by white-rot fungus are very important for application of biotechnology to the utilization of biomass; for example, enzymatic pretreatment for ethanol production from plant resources and biological pulping. Lignins in woody plants exist as giant high molecular weight compounds bounded with carbohydrates, mainly hemicelluloses at middle lamella and in secondary cell wall, and show resistance against the invasion of general microorganisms other than wood-rotting fungi and also against enzymatic digestion of cellulose. We assumed that white-rot fungi first attack the lignin-carbohydrate complex (LCC) and then decompose to some degree into oligomers of lignin and hemicellulose by an unknown enzymatic reaction. The study began with a screening of the fungus, which grew well on the LCC medium. LCCs were prepared from wood meal ofPicea jezoensis that had been extracted MWL, by the method of Koshijima (1). Six fungi (2) that grew well on the media containing decayed lignin were inoculated on agar media of LCC. After 3 d cultivation, the fungiGanoderma sp. andPoria subacida showed most growth on the medium. Crude enzyme preparations were made from decayed wood meal media with each fungus. Chromatographic detection of decomposed compounds from LCC, which is soluble in hot water, by each enzyme and Meicelase fromTricoderma viride, suggest that the wood-rotting fungus may contain another enzyme able to liberate a phenolic compound from LCC besides the enzymes ofTricoderma viride.     

Pyrolysis and soft ionization mass spectrometry of aquatic/terrestrial humic substances and soils

The rapid, reproducible, chemical characterization of complex environmental materials such as plants, humic substances and whole soil can be performed by controlled thermal degradation. Except for drying and milling no pre-treatment of the samples is required. Biomacromolecular cleavage during a short degradation step directly in the ion source of a mass spectrometer results in the production of high-mass chemical subunits. Short reaction times and small amounts of sample favour the generation of large, thermal fragments, i.e., chemical building blocks, which can be identified and correlated with the structure of the polymeric biomaterials investigated. The principal aim is to monitor the primary, thermal fragmentation by high molecular ion intensities of the pyrolyzates and to avoid consecutive, mass spectrometric fragmentation as far as possible.For the detection and identification of the pyrolysis (Py) products, a combination with time-/temperature-controlled mass spectrometry (MS) is used. Typical heating rates are 0.2–10°C/s and the temperature range is 50–800°C. Soft ionization techniques such as field ionization (FI), field desorption, chemical ionization (CI) and, to some extent, fast atom bombardment are employed in the positive and negative modes. The results of direct Py-MS are supported by high-resolution mass measurements using electric or photographic detection and Curie-point pyrolysis in combination with gas chromatography-electron ionization/FI/CIMS and library searches for the identification of the pyrolysis products.Fingerprinting and time-resolved Py-MS of aquatic and terrestrial humic substances are reported. The methodology for the investigations of dynamic processes during the volatilization and thermal decomposition of these complex biomaterials is illustrated. Weight loss curves and the temperature function of accurate molecular weight averages for aquatic fulvic and humic acid are derived from the Py-FIMS data. Initial results on the differentiation of soil horizons in a moder profile by Py-FIMS and pattern recognition are presented. In particular, the chemometric evaluation appears promising for future Py-MS studies of humic substances and whole soils, but also for fossil fuels, synthetic polymers and food. In an integrated approach, the linking of conventional chemical and spectroscopic data with the high-mass signals in pyrolysis-mass spectra will be the focus of forthcoming work. Preliminary results for combining wet-chemical data with those of ¹³C nuclear magnetic resonance, Fourier transform infrared and electron spin resonance spectroscopy are put forward in this survey. Finally, initial results of pilot studies to detect biocides such as atrazine directly in soils using Py-FIMS are demonstrated.     

Aerobic oxidation reactions catalyzed by vanadium complexes of bis(phenolate) ligands

Vanadium(V) complexes of the tridentate bis(phenolate)pyridine ligand H(2)BPP (H(2)BPP = 2,6-(HOC(6)H(2)-2,4-(t)Bu(2))(2)NC(5)H(3)) and the bis(phenolate)amine ligand H(2)BPA (H(2)BPA = N,N-bis(2-hydroxy-4,5-dimethylbenzyl)propylamine) have been synthesized and characterized. The ability of the complexes to mediate the oxidative C-C bond cleavage of pinacol was tested. Reaction of the complex (BPP)V(V)(O)(O(i)Pr) (4) with pinacol afforded the monomeric vanadium(IV) product (BPP)V(IV)(O)(HO(i)Pr) (6) and acetone. Vanadium(IV) complex 6 was oxidized rapidly by air at room temperature in the presence of NEt(3), yielding the vanadium(V) cis-dioxo complex [(BPP)V(V)(O)(2)]HNEt(3). Complex (BPA)V(V)(O)(O(i)Pr) (5) reacted with pinacol at room temperature, to afford acetone and the vanadium(IV) dimer [(BPA)V(IV)(O)(HO(i)Pr)](2). Complexes 4 and 5 were evaluated as catalysts for the aerobic oxidation of 4-methoxybenzyl alcohol and arylglycerol β-aryl ether lignin model compounds. Although both 4 and 5 catalyzed the aerobic oxidation of 4-methoxybenzyl alcohol, complex 4 was found to be a more active and robust catalyst for oxidation of the lignin model compounds. The catalytic activities and selectivities of the bis(phenolate) complexes are compared to previously reported catalysts.     

Stability and Mobility of Metal-Humic Complexes Isolated from Different Soils

The contamination of potable water aquifers by heavy metals is one of the most severe environmental threats. For the transport of heavy metals from various types of contaminated sites into the ground water and also into surface water aquifers, humic substances (HS) are recognized to be of main importance. Dissolved in natural waters humic substances are readily complexed with a variety of metal ions. Therefore, humic substances are of cardinal importance for the migration and, consequently, the pollution of ground waters with heavy metals. Our paper presents the results of a comprehensive comparison of several isolated humic acids of soils of different origin (different geochemical milieu) and their metal complexes. Two polluted sites in Germany, which differ in their geochemical milieu (pH-value) were selected. The aim of our experiments was to describe the properties of terrestrial humic substances depending on their origin and genesis as well as the effects of the transport of humic substance-bound metals into the water-unsaturated soil zone. After determination of heavy metals in the soils by photon activation analysis the activated soil was used as an inherent tracer in batch experiments with the isolated humic acid. After adsorption of the loaded humic acid on an XAD-8 resin column, the partition of metals mobilized by humic acids could be quantified. There are correlations of the formation of metal-humic complexes with the soil pedogenes, with the pH-value as well as with the humic acid concentration.     

Molecular features of organic matter in diagnostic horizons from andosols as seen by analytical pyrolysis

Andosols are usually formed from volcanic substrates, with thick A horizons high in organic carbon mainly in the form of stabilized humic fractions. The peculiar properties of these soils are, to large extent, affected by poorly crystalline materials like allophanes, imogolite and other Fe and Al oxyhydroxides that induce intense organo-mineral interactions which are considered to play a relevant role in OM protection against biodegradation as regards other soils developed under similar climatic conditions. Little is known about the molecular composition of this stabilized OM in a soil scenario often considered as an efficient C-sink in terms of C sequestration processes.

Whole soil samples in addition to isolated humic and fulvic acids from organic A horizons of three soils with andic properties and one non-andic soil (Sodic Cambisol) from the island of Tenerife (Canary Islands, Spain) were analysed by double shot pyrolysis-gas chromatography–mass spectrometry (Py-GC/MS) in order to get some insight on the molecular composition of different structural domains of progressive structural stability.

Clear differences were found between soils, both in thermal desorption and pyrolysis behaviour of humic substances. In general the results suggest large yields of aliphatic (both alkyl and carbohydrate-derived pyrolysis compounds) pointing to high-performance processes of incorporation of aliphatic humic constituents in andosols probably favoured by interactions with amorphous minerals, whereas in non-andic soils the latter are comparatively less stabilized and are removed in early pyrolysis stages as if they occurred as loosely joined, thermoevaporation-released products.

In fact, compared to Cambisol, humic and fulvic acids from andic soils led to comparatively richer pyrograms and compound assemblages. The lack of similar amounts of these loosely joined, mainly aliphatic structures after thermal desorption of the whole andic soils indicate an origin for humic substances based on rapid sequestration of C-forms of recent (litter or microbial) origin.     

Molecular features of organic matter in diagnostic horizons from andosols as seen by analytical pyrolysis

Andosols are usually formed from volcanic substrates, with thick A horizons high in organic carbon mainly in the form of stabilized humic fractions. The peculiar properties of these soils are, to large extent, affected by poorly crystalline materials like allophanes, imogolite and other Fe and Al oxyhydroxides that induce intense organo-mineral interactions which are considered to play a relevant role in OM protection against biodegradation as regards other soils developed under similar climatic conditions. Little is known about the molecular composition of this stabilized OM in a soil scenario often considered as an efficient C-sink in terms of C sequestration processes.Whole soil samples in addition to isolated humic and fulvic acids from organic A horizons of three soils with andic properties and one non-andic soil (Sodic Cambisol) from the island of Tenerife (Canary Islands, Spain) were analysed by double shot pyrolysis-gas chromatography–mass spectrometry (Py-GC/MS) in order to get some insight on the molecular composition of different structural domains of progressive structural stability.Clear differences were found between soils, both in thermal desorption and pyrolysis behaviour of humic substances. In general the results suggest large yields of aliphatic (both alkyl and carbohydrate-derived pyrolysis compounds) pointing to high-performance processes of incorporation of aliphatic humic constituents in andosols probably favoured by interactions with amorphous minerals, whereas in non-andic soils the latter are comparatively less stabilized and are removed in early pyrolysis stages as if they occurred as loosely joined, thermoevaporation-released products.In fact, compared to Cambisol, humic and fulvic acids from andic soils led to comparatively richer pyrograms and compound assemblages. The lack of similar amounts of these loosely joined, mainly aliphatic structures after thermal desorption of the whole andic soils indicate an origin for humic substances based on rapid sequestration of C-forms of recent (litter or microbial) origin.     

硫酸盐法制浆黑液中主要有机组分的热解特性研究

采用管式炉对硫酸盐法竹子、阔叶木混合制浆黑液固形物(BLS)及其三种主要组分碱木素(AL)、多糖(PLS)和木素-碳水化合物复合体(LCC),在400~800℃进行热解,全面分析了各相热解产物组成与分布规律。结果表明,BLS及其三种主要组分的热解产物组成与分布规律存在明显差异。AL、PLS和LCC对BLS热解产生H₂和CO的产率影响不大,PLS热解生成CO₂的能力明显高于BLS、AL和LCC。BLS热解液相产物中的酚类和醚类主要是来自AL和LCC;酮类和酸类是由AL、PLS和LCC共同贡献的。BLS、AL、PLS和LCC热解半焦表面形貌存在明显差异。在BLS热解过程中,AL、PLS和LCC会相互影响、相互制约,共同决定着BLS的热解特性。     

A new approach to study cadmium complexes with oxalic acid in soil solution

This study presents a new analytical approach for the determination of heavy metals complexed to low-molecular-weight-organic acids in soil solutions, which combines the sensitivity of differential pulse anodic stripping voltammetry (DPASV) with the molecular insight gained by electrospray ionization mass spectrometry (ESI-MS). The combination of these analytical methods allows the investigation of such complexes in complex matrixes. On the voltammograms of the soil solutions, in addition to the expected complexes of oxalic acid with cadmium and lead, respectively, also peaks belonging to mixed complexes of cadmium, lead, and oxalic acid (OAH(2)) were observed. In order to verify the possible formation of complexes with OAH(2), aqueous solutions of OAH(2) with traces of Cd(II) were investigated as model systems. Signals corresponding to several distinct molecular complexes between cadmium and oxalic acid were detected in the model solutions using negative-ion ESI-MS, which follow the general formula [Cd(n)(X,Y)((2n+1))](-), where n is the number of cadmium atoms, X=Cl(-), and Y=OAH(-). Some of these complexes were also identified in the ESI mass spectra taken from the soil solutions.     

Application of Differential UV Spectroscopy to the Determination of Lignin Substances in Polluted Water

The absorption spectra of Bjorkman lignin, lignin sulfate, lignosulfonates, and humic substances in neutral and alkaline media are considered. It was found that the difference spectra of lignins (an alkaline solution with reference to a neutral solution) exhibited several intense bands, whereas humic substances exhibited equal shifts of the spectra over the entire spectral range. This distinctive property of the difference spectra of lignin substances, as compared to the spectra of humic substances, can be used for determining lignins in polluted water.     

Modeling sorption of soil organic matter on mineral surfaces: wood-derived polymers on mica

Molecular mechanics and molecular dynamics calculations were carried out on model organo–mineral composites typical of both paper products and soil. Sorption energy of neutral model linear chains of lignin, carbohydrate, and humic substances on muscovite mica depends on the mutual orientation of organic and mineral components, spatial organization and functionality of the organic chain, and the presence of metal cations. Carbohydrates are characterized by their higher affinity towards the mineral surface than the more flexible helical aromatic polymers. In the model calculations, sorption energies are twice as high. Oxidation of lignin into respective humic acids does not lead to better sorption. Unlike metal cations, water molecules interlacing between organic and mineral surfaces do not act as bridges and sharply decrease sorption energy. Flexible linear polymers may undergo drastic conformational changes when approaching the mineral surface, to ensure a gain in the interaction energy that more than compensates a loss in the conformational energy proper.     

Stable associates of polyether oligomers with chlorine anion as revealed by the data of electrospray mass spectrometry and molecular dynamics

Stable complexes of oligomers of polyether (oxyethylated glycerol derivatives) with a chlorine anion have first been registered in negative-ion electrospray ionization mass spectra. The results of molecular dynamics simulation demonstrate that the stabilization of such complexes in the gas phase can be due to the formation of a quasicyclic structure of the polymer chain around the chlorine anion and its coordination by CH₂- and OH- groups of the oligomer. This structure is inverted towards the known quasicyclic structure of polyethers, in which metal cations are coordinated by oxygen atoms of ether groups.