Molecular Models of Cation and Water Molecule Bridges in Humic Substances

Tunega, Daniel; Aquino, Adélia J. A.; Haberhauer, Georg; Lischka, Hans; Schaumann, Gabriele E.; Gerzabek, Martin H.

doi:10.1007/978-3-319-04084-4_11

Cited by 5 publications

(8 citation statements)

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“…Our own previous works aimed at QC modeling of complex HS species using mainly the DFT approach. These studies were focused on typical features of SOM, such as polar functional groups (e.g., carboxyl), nonpolar domains, hydrogen bonding, pH effects, the role of cations and water bridges in the formation of supramolecular structures of SOM, and interactions with small organic molecules such as naphthalene (Aquino et al, 2009(Aquino et al, , 2014Aquino, Tunega, Pasalic et al 2011;Aquino, Tuniga, Schaumann et al, 2011;Kunhi Mouvenchery et al, 2013;Schaumann & Bertmer, 2008;Tunega et al, 2014Tunega et al, , 2020.…”

Section: Modeling Of Som Its Interactions In Soils and Associated Cha...mentioning

confidence: 99%

“…These studies were focused on typical features of SOM, such as polar functional groups (e.g., carboxyl), nonpolar domains, hydrogen bonding, pH effects, the role of cations and water bridges in the formation of supramolecular structures of SOM, and interactions with small organic molecules such as naphthalene (Aquino et al., 2009, 2014; Aquino, Tunega, Pasalic et al. 2011; Aquino, Tuniga, Schaumann et al., 2011; Kunhi Mouvenchery et al., 2013; Schaumann & Bertmer, 2008; Tunega et al., 2014, 2020). The models used in these investigations spanned from small models representing polar functional groups to larger fragment species such as fatty acid chains to model hydrophillic/hydrophobic domains typical for SOM (Figure 2).…”

Section: Introductionmentioning

confidence: 99%

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A contribution of molecular modeling to supramolecular structures in soil organic matter^#

Gerzabek

Aquino

Balboa

et al. 2022

J. Plant Nutr. Soil Sci.

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Background Knowledge of the stabilizing mechanisms of soil organic matter (SOM) is extremely important for numerous soil functions. For this, insight into the nature of organic matter through appropriate model concepts are crucial. Aims For several years, a heated debate has emerged on the transformation and stabilization of SOM. In the present work, we try to contribute to this debate using molecular modeling and providing a comprehensive overview of the history of application of molecular modeling tools and developing structural concepts of SOM. Methods Molecular modeling methods based on quantum and/or classical mechanics were used to model SOM and related properties including interactions with reactive surfaces of soil minerals. Results Modeling of SOM aggregates revealed that hydrogen bonds and cation bridges are the main stabilizing factors in soil solution, whereas pH modifies the stability. The modeled supramolecular SOM aggregates exhibit physicochemical properties, similar to those of humic substances (HS) described in literature. The interactions of the HS models with surfaces in kaolinite nanopores led to a partial disintegration of the aggregates into individual molecules and/or smaller subaggregates. Conclusions From the molecular modeling point of view, supramolecular microaggregate models that exhibit the properties of HS are stable in the soil solution. However, their binding to reactive mineral soil constituents can be also in the form of individual molecules or subaggregates. Thus, HS microaggregate stability is relative, depending on the interacting environment. This reconciles two points of view of HS: either as small molecules and/or supramolecular structures.

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Section: Modeling Of Som Its Interactions In Soils and Associated Cha...mentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

A contribution of molecular modeling to supramolecular structures in soil organic matter^#

Gerzabek

Aquino

Balboa

et al. 2022

J. Plant Nutr. Soil Sci.

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“…The negative charge of carboxylate groups was neutralized by calcium cations (Ca 2+ ) embedded in the aggregate model. These cations are essential for keeping the molecular rigidity of the HA models through cation bridges (CaB) [13,15,16,19,20,40,41].…”

Section: Initial Configurationmentioning

confidence: 99%

“…There is an intensive experimental effort to quantify and understand organic matter-mineral interface from classical experimental techniques (e.g., batch sorption experiments or calorimetry) to advanced techniques such as atomic force spectroscopy [12]. In the formation of SOM and/or SOM-mineral aggregates, an important role is attributed to soil solutions, particularly to water and its ability to from water hydrogen bond bridges, and/or inorganic cations naturally occurring in soil solutions (e.g., Na + , K + , Mg 2+ , or Ca 2+ ) and their ability to form cation cross-linking bridges among sites of aggregate components [4,[13][14][15][16][17][18][19][20]. Water and cations serve as a glue that, depending on water and cation content, can either enhance or weaken structural stability and resistance of the SOM itself and SOM-mineral aggregates.…”

Section: Introductionmentioning

confidence: 99%

On the Adsorption Mechanism of Humic Substances on Kaolinite and Their Microscopic Structure

et al. 2021

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Soil organic matter (SOM) and various inorganic minerals represent key components of soils. During pedogenesis and due to biological activity these species interact, having a crucial impact on the formation of an aggregated soil structure with a hierarchical arrangement from nano to macro scale. In this process, the formation of organo–mineral microaggregates represents a dominant factor affecting soil functions and properties. This study focuses on the interactions between humic substances (HSs) and the mineral kaolinite as typical representatives of SOM and soil minerals. By performing classical molecular dynamics (MD) simulations on models of HSs and kaolinite, we demonstrate how two dominant but chemically different kaolinite surfaces affect the stability of HSs microaggregates. By analyzing volumetric, structural, and energetic properties of SOM–kaolinite models, we explain possible mechanisms of the formation of stable SOM–clay aggregates and show how a polarized environment affects the electrostatic interactions, stabilizing the microscopic structure of SOM–mineral aggregates. Our results showed that when stable aggregates of HSs are confined in kaolinite nanopores, their interactions with kaolinite surfaces disintegrate them into smaller subaggregates. These subaggregates are adsorbed more strongly on the polar aluminol surface of kaolinite compared to less the active hydrophobic siloxane surface.

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“…In the 1990s, new evidence concerning the "supramolecular" concept of humic substances as aggregates of small molecules stabilized by weak interactions was introduced. The results came from changes on HPSEC chromatograms of humic acids treated to specific pH with various organic and inorganic acids (Piccolo et al 1996;Piccolo 2001;Sposito 2008;Tunega et al 2014). Accordingly, humic substances formed during humification processes are composed of different molecules mixture, which results in their different properties.…”

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confidence: 99%

Differences in humic acids structure of various soil types studied by DRIFT spectroscopy

Pavlů¹,

Mühlhanselová²

2018

Soil & Water Res.

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Pavlů L., Mühlhanselová M. (2018): Differences in humic acids structure of various soil types studied by DRIFT spectroscopy. Soil & Water Res., 13: 29−35.The method of diffuse reflectance infrared spectroscopy (DRIFT) proved to be useful for studying the soil organic matter structure. The aim of this study was to compare DRIFT spectra of humic acids (HAs) separated from various soils and to identify their specific nature. Samples of agricultural soils (Dystric Cambisol, Haplic Chernozem, Greyic Phaeozem, and Haplic Luvisol) were collected from humic (A) horizons. Soil samples of reclaimed dumpsites (Haplic Technosol (molic) and (calcic)) were taken from the upper part of the soil profile. Samples of forest soils were collected from surface organic (H) horizons of Cambisols in spruce (Picea abies L. Karst.) and beech (Fagus silvatica L.) forests. The selected soil types differ in pH, carbon content, texture, and humus quality. An extraction of HAs was performed using a mixture of 0.5 M NaOH and 0.1 M Na 4 P 2 O 7 . The separated HAs were freeze-dried and analyzed using a DRIFT spectrometer (Thermo Nicolet Nexus) without KBr dilution. There were found differences in relative aromaticity among the agricultural soils HAs. The most aromatic character was observed in HAs from Chernozems and the least in Cambisols. Preservation of the natural structure of Chernozem HAs during the reclamation process was documented on the HAs spectra from Haplic Technosols (molic). By using the DRIFT spectra of HAs of forest H horizons, it is possible to identify the fragments of decomposed material (gymnosperms or angiosperms). HAs isolated from these horizons represent a certain interstage between lignin and the matured soil humic acids.

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Molecular Models of Cation and Water Molecule Bridges in Humic Substances

Cited by 5 publications

References 28 publications

A contribution of molecular modeling to supramolecular structures in soil organic matter^#

A contribution of molecular modeling to supramolecular structures in soil organic matter^#

On the Adsorption Mechanism of Humic Substances on Kaolinite and Their Microscopic Structure

Differences in humic acids structure of various soil types studied by DRIFT spectroscopy

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Molecular Models of Cation and Water Molecule Bridges in Humic Substances

Cited by 5 publications

References 28 publications

A contribution of molecular modeling to supramolecular structures in soil organic matter#

A contribution of molecular modeling to supramolecular structures in soil organic matter#

On the Adsorption Mechanism of Humic Substances on Kaolinite and Their Microscopic Structure

Differences in humic acids structure of various soil types studied by DRIFT spectroscopy

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A contribution of molecular modeling to supramolecular structures in soil organic matter^#

A contribution of molecular modeling to supramolecular structures in soil organic matter^#