The absorption spectrum of dissolved organic matter (DOM) is a topic of interest to environmental scientists and engineers as it can be used to assess both the concentration and physicochemical properties of DOM. In this study, the UV–vis spectra for DOM model compounds were calculated using time-dependent density functional theory. Summing these individual spectra, it was possible to re-create the observed exponential shape of the DOM absorption spectra. Additionally, by predicting the effects of sodium borohydride reduction on the model compounds and then calculating the UV–vis absorbance spectra of the reduced compounds, it was also possible to correctly predict the effects of borohydride reduction on DOM absorbance spectra with a relatively larger decrease in absorbance at longer wavelengths. The contribution of charge-transfer (CT) interactions to DOM absorption was also evaluated, and the calculations showed that intra-molecular CT interactions could take place, while inter-molecular CT interactions were proposed to be less likely to contribute.

The three-dimensional configuration of dissolved organic matter (DOM) is an important factor in determining the role of DOM in natural and engineered systems, yet there is still considerable uncertainty regarding the formation and potential stability of molecular aggregates within DOM. In this paper, we describe a computational assessment of the three-dimensional configuration of DOM. Specifically, we were interested in evaluating the hypothesis that DOM forms thermodynamically stable molecular aggregates that as a result were potentially shielded from water solvent molecules. Molecular dynamics simulations of DOM model compounds carefully selected based on ultrahigh-resolution mass spectrometry data revealed that, while DOM does indeed form molecular aggregates, the large majority of molecules (especially, O-atom bearing molecules) are solvent accessible. Additionally, these computations revealed that molecular aggregates are weak and dissociate when placed in organic solvents (tetrahydrofuran, methyl tert-butyl ether). Time-dependent density functional theory calculations demonstrated long-wavelength absorbance for both model DOM chromophores and their molecular aggregates. This study has important implications for determining the origin of DOM optical properties and for enhancing our collective understanding of DOM three-dimensional structures.

Environmental contextThe correlation of physicochemical characteristics of humic substances with their function is crucial to our understanding of how environmental pollutants interact with humic substances. We have developed an approach that models emergent functions of fulvic and humic acids depending on sample characteristics. The results will be useful for predicting the sequestration of organic contaminants in soil under various conditions. AbstractThe structural organisation of humic substances (HS) has been a central question of earth sciences for several decades. The latest experimental results have led to the recognition of HS as complex mixtures of small molecules and oligomers. We investigate the correlation between the chemical composition of HS, perceived as labile aggregates, and the emergent functions. Computational modelling was used to help to understand the processes and mechanisms on the molecular scale that occur in different fractions of the HS, fulvic acids (FA) and humic acids (HA), as they interact with metal ions and organic pollutants. The importance of non-covalent interactions in the emergent functions of HS is highlighted. H-bonding, hydrophilic/hydrophobic surface areas and π-stacking interactions play a significant role in aggregation processes as well as in the sorption of environmental pollutants. In a highly hydrophilic system with small molecules (the SRFA-22 model), H-bonding is the main force that drives the aggregation process. However, in a highly aromatic and hydrophobic model with larger molecular fragments (SRHA-6), hydrophobic and π-stacking interactions dominate in the aggregation process. The chemical properties of contaminants significantly affect their mechanisms of sorption by HS. The interaction of a polar pollutant, phenol, with HS occurs through H-bonding, whereas non-polar benzene interacts through hydrophobic and π-stacking interactions. The non-polar pollutant results in a much stronger sorption by HS and causes an additional structural rearrangement of the aggregates, which make it more stable in the environment.

Environmental contextThe fundamental basis for the high flexibility of humic substances is still unclear, though it is crucial for the understanding of metal bioavailability and toxicity in soil and aqueous environments. We show at the molecular level how characteristics of organic matter affect metal binding depending on the environmental conditions. Such understanding will help in the modulation of metal availability in soil and water in changing environmental situations. AbstractIn this work, we explore the hypothesis that humic substances (HS) can be perceived as labile supramolecular assemblages, the functioning of which is mainly determined by chemical composition and characteristics, the size of molecular units and weak intermolecular forces, rather than the exact primary structure of molecular moieties and their spatial configuration. To test the hypothesis, 72 computational models of three different organic mixtures were composed. The formation of inner and outer sphere metal–ligand complexes, metal binding sites, complex configurations, binding energies and aggregation/dissolution as emergent properties of HS were determined under various conditions. The results of computational modelling revealed that: (i) the highest Cu2+ binding (55.6%) was by the SRFA-22 organic model, which represents low-molecular-weight fulvic acids. In contrast, the highest amount of inner-sphere Mg–organic matter complex (63.4%) was formed in SRHA-6, which has higher-molecular-weight constituents. Therefore, a correlation between the type of cation, the system aromaticity and the extent of metal complexation is proposed. (ii) Increase of metal ion concentration and decrease of water content resulted in an increase in the number of hydrogen bonds and more compact and stable aggregates with lower hydrophilic and higher hydrophobic surface areas in SRFA-22. However, in SRHA-6, the results varied owing to the competition between metal binding, H-bonding and non-polar interactions in the structural arrangement of the aggregates. In general, the aggregation process, driven by metal complexation and water removal, resulted in the formation of more stable conformers, with lower potential energy, with the only exception of SRHA-6–Cu.

Vialykh, E. A., Ilarionov, S. A., Abdelrahman, H. M. and Vialykh, I. A. 2014. Changes in amino acids content of humic acids sequentially extracted from peat and sod Á Podzolic soil. Can. J. Soil Sci. 94: 575Á583. Amino acids (AA) and peptides are thought to be part of humic acids (HA), but debate whether they are an integral part of the HA is still going. Humic acids sequentially extracted from peat and sod-podzolic soil were analyzed for their AA content, elemental composition and by Fourier transform infrared spectroscopy. Extracted HA were hydrolyzed in 6 M HCl for 16 h for AA release, which was detected by a capillary electrophoresis system. Alanine, arginine, sum of aspartic acid and asparagine, sum of cysteic acid and cysteine, sum of glutamic acid and glutamine, glycine, histidine, leucine and isoleucine, lysine, methionine, phenylalanine, proline, serine, threonine, tyrosine, valine were identified. The total content of hydrolyzable AA in sod-Podzol HA increased by 6.2Á8.2% with increasing the extraction cycles while an inverse tendency was observed for AA released from peat HA. Moreover, individual AA expressed as percentages of total AA were constant values with coefficients of variation lower than 20% for the studied HA.Vialykh, E. A., Ilarionov, S. A., Abdelrahman, HJ. M. et Vialykh, I. A. 2014. Modification de la proportion d'acides amine´s dans les acides humiques extraits de fac¸on se´quentielle de la mousse de sphaigne et d'un podzol gazonne´. Can. J. Soil Sci. 94: 575Á583. On pense que les acides amine´s (AA) et les peptides entrent dans la composition des acides humiques (AH), mais la controverse sur le fait qu'ils en font partie inte´grante continue de faire rage. Les auteurs ont analyse´les acides humiques extraits successivement de la mousse de sphaigne et d'un podzol gazonne´en vue d'e´tablir leur teneur en AA, les e´le´ments les composant et leur spectroscopie IRTF. Les AH extraits ont e´te´hydrolyse´s dans du HCl 6 M pendant 16 h pour permettre la libe´ration des AA, lesquels ont e´te´de´tecte´s par un syste`me d'e´lectrophore`se capillaire. On a ainsi identifieĺ 'alanine, l'arginine, le me´lange d'acide aspartique et d'asparagine, le me´lange d'acide cyste´ique et de cyste´ine, le me´lange d'acide glutamique et de glutamine, la glycine, l'histidine, la leucine et l'isoleucine, la lysine, la me´thionine, la phe´nylalanine, la proline, la se´rine, la thre´onine, la tyrosine et la valine. La concentration totale d'AA hydrolysables dans les AH du podzol gazonne´augmente de 6,2 a`8,2 % avec la hausse du nombre de cycles d'extraction, les AA libe´re´s par les AH de la mousse de sphaigne suivant une tendance inverse. Par ailleurs, quand ils sont exprime´s sous forme de pourcentage des AA totaux, les AA individuels constituent une valeur stable dont le coefficient de variation est infe´rieur a2 0 % chez les AH examine´s.Abbreviations: DBE, double bond equivalents; HA, humic acid; AA, amino acid; FTIR, Fourier transform infraredCan.