Editorial: Molecular modelling in soil research

Gerzabek, Martin H.; Haberhauer, Georg; Totsche, Kai Uwe; Tunega, Daniel

doi:10.1111/j.1365-2389.2007.00918.x

Cited by 3 publications

(2 citation statements)

References 19 publications

(15 reference statements)

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“…Their sorption is strongly affected by pH and ionic strength (Ter Laak et al, 2006;Gao and Pedersen, 2005;Kurwadkar et al, 2007). Since adsorption experiments yield information that can only be correlated statistically to soil properties, combination of molecular modeling and computational chemistry is a complementary promising approach to develop an atomistic understanding of the binding of pollutants to soil (Gerzabek et al, 2001;Schaumann and Thiele-Bruhn, 2011).…”

Section: Introductionmentioning

confidence: 99%

Interaction of polar and nonpolar organic pollutants with soil organic matter: Sorption experiments and molecular dynamics simulation

Ahmed

Thiele‐Bruhn

Aziz

et al. 2015

Science of The Total Environment

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The fate of organic pollutants in the environment is influenced by several factors including the type and strength of their interactions with soil components especially SOM. However, a molecular level answer to the question "How organic pollutants interact with SOM?" is lacking. In order to explore mechanisms of this interaction, we have developed a new SOM model followed by carrying out molecular dynamics (MD) simulations in parallel with sorption experiments. The new SOM model comprises free SOM functional groups (carboxylic acid and naphthalene) as well as SOM cavities (with two different sizes), representing the soil voids, containing the same SOM functional groups. To examine the effect of the hydrophobicity on the interaction, the organic pollutants hexachlorobenzene (HCB, non-polar) and sulfanilamide (SAA, polar) were considered. The experimental and the theoretical outcomes explored four major points regarding sorption of SAA and HCB on soil. 1-The interaction depends on the SOM chemical composition more than the SOM content. 2-The interaction causes a site-specific adsorption on the soil surfaces. 3-Sorption hysteresis occurs, which can be explained by inclusion of these pollutants inside soil voids. 4-It was observed that the hydrophobic HCB is adsorbed on soil stronger than the hydrophilic SAA.Moreover, the theoretical results showed that HCB forms stable complexes with all SOM models in the aqueous solution while most of SAA complexes are accompanied by dissociation. The SOMcavity modeling showed a significant effect on binding of organic pollutants to SOM. Both HCB and SAA bind to the SOM models in the order of models with a small cavity > models with a large cavity > models without a cavity. Although HCB binds to all SOM models stronger than SAA, the latter is more affected by presence of the cavity. Finally, HCB and SAA bind to the hydrophobic functional group (naphthalene) stronger than to the hydrophilic one (carboxylic acid) for all SOM models containing cavity. For models without a cavity, SAA binds to carboxylic acid stronger than to naphthalene. 4

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Section: Introductionmentioning

confidence: 99%

Interaction of polar and nonpolar organic pollutants with soil organic matter: Sorption experiments and molecular dynamics simulation

Ahmed

Thiele‐Bruhn

Aziz

et al. 2015

Science of The Total Environment

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“…Single molecules of humic substances can only be an example for this divergent group of substances (e.g. Gerzabek et al , 2001). Humic acids contain several relevant functional groups, mainly carboxyl, carbonyl, alcoholic and phenolic units (Schulten, 1994), which play a major role in binding of polar molecules from a polar solvent environment.…”

Section: Introductionmentioning

confidence: 99%

Interaction of the 2,4‐dichlorophenoxyacetic acid herbicide with soil organic matter moieties: a theoretical study

Aquino

Tunega

Haberhauer

et al. 2007

European J Soil Science

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The determination of the structure of humic substances from soils and natural waters is an intriguing problem in soil science. Humic substances consist of molecules covering a broad distribution of molecular size and involving different functional groups. Taking this into account, we have chosen smaller model systems with functional groups typically present in humic substances. We investigated theoretically, by quantum chemical calculations, the environmental effects on the complexes formed from the interaction of 2,4-dichlorophenoxyacetic acid and its anion with acetaldehyde, methanol, methylamine, protonated methylamine, acetic acid and water. The important case of a cation bridge mechanism, with Ca 2þ as the bridging cation, is also included into the set of model reactions. It is found that this cation bridge belongs to one of the most stable mechanisms of fixation of organic compounds in soils. According to our calculations the hydroxyl group forms the most stable complexes with 2,4-D in a polar solvent environment.

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Biogeochemical interfaces in soil: The interdisciplinary challenge for soil science

Totsche

Rennert

Gerzabek

et al. 2010

Z. Pflanzenernähr. Bodenk.

160

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Soil, the “Earth's thin skin” serves as the delicate interface between the biosphere, hydrosphere, atmosphere, and lithosphere. It is a dynamic and hierarchically organized system of various organic and inorganic constituents and organisms, the spatial structure of which defines a large, complex, and heterogeneous interface. Biogeochemical processes at soil interfaces are fundamental for the overall soil development, and they are the primary driving force for key ecosystem functions such as plant productivity and water quality. Ultimately, these processes control the fate and transport of contaminants and nutrients into the vadose zone and as such their biogeochemical cycling. The definite objective in biogeochemical‐interface research is to gain a mechanistic understanding of the architecture of these biogeochemical interfaces in soils and of the complex interplay and interdependencies of the physical, chemical, and biological processes acting at and within these dynamic interfaces in soil. The major challenges are (1) to identify the factors controlling the architecture of biogeochemical interfaces, (2) to link the processes operative at the individual molecular and/or organism scale to the phenomena active at the aggregate scale in a mechanistic way, and (3) to explain the behavior of organic chemicals in soil within a general mechanistic framework. To put this in action, integration of soil physical, chemical, and biological disciplines is mandatory. Indispensably, it requires the adaption and development of characterization and probing techniques adapted from the neighboring fields of molecular biology, analytical and computational chemistry as well as materials and nano‐sciences. To shape this field of fundamental soil research, the German Research Foundation (DFG) has granted the Priority Program “Biogeochemical Interfaces in Soil”, in which 22 individual research projects are involved.

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Editorial: Molecular modelling in soil research

Cited by 3 publications

References 19 publications

Interaction of polar and nonpolar organic pollutants with soil organic matter: Sorption experiments and molecular dynamics simulation

Interaction of polar and nonpolar organic pollutants with soil organic matter: Sorption experiments and molecular dynamics simulation

Interaction of the 2,4‐dichlorophenoxyacetic acid herbicide with soil organic matter moieties: a theoretical study

Biogeochemical interfaces in soil: The interdisciplinary challenge for soil science

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