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Minerals
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Recent Advances in Molecular Modeling of Clay Minerals Interfaces
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Recent Advances in Molecular Modeling of Clay Minerals Interfaces

A special issue of Minerals (ISSN 2075-163X). This special issue belongs to the section "Clays and Engineered Mineral Materials".

Deadline for manuscript submissions: closed (9 April 2021) | Viewed by 18082

Special Issue Editors

Prof. Dr. Daniel Tunega

E-Mail Website
Guest Editor
Institute for Soil Research, University of Natural Resources and Life Sciences, 1180 Vienna, Austria
Interests: application of molecular modelling methods (from force-field based to quantum chemical) in fields of material chemistry; environmental chemistry; soil chemistry and geochemistry
Dr. Edgar Galicia-Andrés

E-Mail Website
Co-Guest Editor
Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences, Vienna, 1190 Wien, Austria
Interests: the behavior of complex fluids with interfacial and biological activity with potential application to material science; soil chemistry; geochemistry and environmental chemistry fields using computer simulation techniques; from atomistic to coarse-grained models
Dr. Peter Grancic

E-Mail Website
Co-Guest Editor
Institute for Soil Research, University of Natural Resources and Life Sciences, Vienna, 1180 Wien, Austria
Interests: computer simulations of materials chemistry and nanoparticles

Special Issue Information

Dear Colleagues,

Clays and clay minerals, a rich family of hydrous aluminosilicates, represent very useful materials for numerous applications in diverse industrial and environmental fields due to their low cost, natural availability, and ecofriendly character. Therefore, there is a paramount need to understand and predict the structure, physical properties, and reactivity of surfaces and interfaces of clay mineral particles at a molecular scale. To this end, molecular modelling studies play an important role. This Special Issue is focused on the most recent advances and achievements in molecular simulations of clay mineral surfaces and interfaces. Full papers, including reviews, covering the current trends and applications of a broad range of molecular simulation methods in this field are all welcome. The submission of papers addressing the topics listed below is particularly encouraged.

Prof. Dr. Daniel Tunega
Dr. Edgar Galicia-Andrés
Dr. Peter Grancic
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Minerals is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2400 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • clay minerals surfaces and interfaces
  • surface structure, reactivity, and physical–chemical properties
  • confined systems
  • clay nanoparticles
  • organoclay complex systems and hybrid materials
  • adsorption and surface complexation
  • classical molecular dynamics and Monte Carlo
  • large-scale and multiscale simulations
  • first principles methods

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Published Papers (6 papers)

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Research

16 pages, 4423 KiB  
Article
On the Adsorption Mechanism of Humic Substances on Kaolinite and Their Microscopic Structure
by Edgar Galicia-Andrés, Chris Oostenbrink, Martin H. Gerzabek and Daniel Tunega
Minerals 2021, 11(10), 1138; https://doi.org/10.3390/min11101138 - 17 Oct 2021
Cited by 8 | Viewed by 2537
Abstract
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 [...] Read more.
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. Full article
(This article belongs to the Special Issue Recent Advances in Molecular Modeling of Clay Minerals Interfaces)
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11 pages, 11044 KiB  
Article
Hydrophobicity and Charge Distribution Effects in the Formation of Bioorganoclays
by Peter Grančič and Daniel Tunega
Minerals 2021, 11(10), 1102; https://doi.org/10.3390/min11101102 - 8 Oct 2021
Cited by 3 | Viewed by 1608
Abstract
Interactions of bioorganic moieties with clay minerals have attracted attention not only from the perspective of novel bioclay materials but also because they play a crucial role in our understanding of physical and chemical processes in soils. The aim of the present article [...] Read more.
Interactions of bioorganic moieties with clay minerals have attracted attention not only from the perspective of novel bioclay materials but also because they play a crucial role in our understanding of physical and chemical processes in soils. The aim of the present article is to explore the interactions responsible for the formation of a phosphatidylcholine-kaolinite bioclay by employing a series of classical molecular dynamic simulations. Detailed analysis of the structure and energies of the resulting bioclays reveals that the phosphatidylcholine molecules bind to the kaolinite surface either via their zwitterionic heads or hydrophobic aliphatic tails, depending on the kaolinite surface characteristics and the density of organic coating. The phosphatidylcholine molecules have a tendency to form irregular layers with a preferred parallel orientation of molecules with respect to the kaolinite surface. The tails exhibit varying degrees of flexibility and disorder depending on their distance from the surface and the density of surface coating. Significant differences in the binding can be spotted with respect to the two types of kaolinite basal surfaces, i.e., the hydrophobic siloxane surface, which possesses a considerable dispersion character, and the hydrophilic alumina surface, polarized by the surface hydroxyl groups. Full article
(This article belongs to the Special Issue Recent Advances in Molecular Modeling of Clay Minerals Interfaces)
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20 pages, 8730 KiB  
Article
Stability of Atrazine–Smectite Intercalates: Density Functional Theory and Experimental Study
by Daniel Moreno-Rodríguez, Ľuboš Jankovič, Eva Scholtzová and Daniel Tunega
Minerals 2021, 11(6), 554; https://doi.org/10.3390/min11060554 - 24 May 2021
Cited by 12 | Viewed by 2822
Abstract
Atrazine (A) is one of the most applied herbicides and has a negative impact on the environment and health. Density functional theory (DFT) and experimental methods were used in the study of the immobilization of atrazine in two smectites, montmorillonite (Mt) and beidellite [...] Read more.
Atrazine (A) is one of the most applied herbicides and has a negative impact on the environment and health. Density functional theory (DFT) and experimental methods were used in the study of the immobilization of atrazine in two smectites, montmorillonite (Mt) and beidellite (Bd), as well as in their organically modified structures. Four systems were examined: A-Mt and A-Bd, as well as the structures modified by tetramethylphosphonium cation (TMP), A-TMP-Mt and A-TMP-Bd. The calculations revealed a flat arrangement of the atrazine in the interlayer space of both smectites with higher stability of beidellite structures. The presence of the TMP cation increased the fixation of atrazine in both organically modified smectites. The calculated vibrational spectra allowed a detailed analysis of the overlapping bands observed in the experimental FTIR spectra and their correct assignment. Further, selected FTIR bands unambiguously assigned to atrazine and both smectites served for the estimation of the adsorbed amount of atrazine. It was shown that the adsorption capacity of both TMP-modified smectites did not increase in comparison to the adsorption capacity of unmodified smectite samples. Full article
(This article belongs to the Special Issue Recent Advances in Molecular Modeling of Clay Minerals Interfaces)
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11 pages, 1859 KiB  
Article
Insight into the Structure of TMA-Hectorite: A Theoretical Approach
by Eva Scholtzová
Minerals 2021, 11(5), 505; https://doi.org/10.3390/min11050505 - 11 May 2021
Cited by 2 | Viewed by 1860
Abstract
An ab initio density functional theory method (DFT) with D3 dispersion corrections (DFT-D3) was employed to study the 64 possible models of the structure of hectorite intercalated with tetramethylammonium (TMA) cations with the aim to find the additional information about the structure for [...] Read more.
An ab initio density functional theory method (DFT) with D3 dispersion corrections (DFT-D3) was employed to study the 64 possible models of the structure of hectorite intercalated with tetramethylammonium (TMA) cations with the aim to find the additional information about the structure for the energetically most suitable mutual arrangement of the TMA cations. The complex analysis of total energies showed small differences among the structural models with the lowest (L model) and the highest (H model) total energy (~50 kJ/mol). The analysis of the calculated vibrational spectrum of the L model of the TMA-H structure was conducted in detail. Full article
(This article belongs to the Special Issue Recent Advances in Molecular Modeling of Clay Minerals Interfaces)
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18 pages, 4979 KiB  
Article
The Binding of Phosphorus Species at Goethite: A Joint Experimental and Theoretical Study
by Prasanth B. Ganta, Mohsen Morshedizad, Oliver Kühn, Peter Leinweber and Ashour A. Ahmed
Minerals 2021, 11(3), 323; https://doi.org/10.3390/min11030323 - 20 Mar 2021
Cited by 12 | Viewed by 4694
Abstract
Knowledge of the interaction between inorganic and organic phosphates with soil minerals is vital for improving soil P-fertility. To achieve an in-depth understanding, we combined adsorption experiments and hybrid ab initio molecular dynamics simulations to analyze the adsorption of common phosphates, i.e., orthophosphate [...] Read more.
Knowledge of the interaction between inorganic and organic phosphates with soil minerals is vital for improving soil P-fertility. To achieve an in-depth understanding, we combined adsorption experiments and hybrid ab initio molecular dynamics simulations to analyze the adsorption of common phosphates, i.e., orthophosphate (OP), glycerolphosphate (GP) and inositolhexaphosphate (IHP), onto the 100 surface plane of goethite. Experimental adsorption data per mol P-molecule basis fitted to the Freundlich model show the adsorption strength increases in the order GP < OP < IHP, and IHP adsorption being saturated faster followed by GP and OP. Modeling results show that OP and GP form stable monodentate (M) and binuclear bidentate (B) motifs, with B being more stable than M, whereas IHP forms stable M and 3M motifs. Interfacial water plays an important role through hydrogen bonds and proton transfers with OP/GP/IHP and goethite. It also controls the binding motifs of phosphates with goethite. Combining both experimental and modeling results, we propose that the B motif dominates for OP, whereas GP forms M and IHP forms a combination of M and 3M motifs. The joint approach plausibly explains why IHP is the predominant organically bound P form in soil. This study could be considered as a preliminary step for further studies for understanding the mechanisms of how microbes and plants overcome strong IHP–mineral binding to implement the phosphate groups into their metabolism. Full article
(This article belongs to the Special Issue Recent Advances in Molecular Modeling of Clay Minerals Interfaces)
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12 pages, 3526 KiB  
Article
Adsorption of Pharmaceuticals onto Smectite Clay Minerals: A Combined Experimental and Theoretical Study
by Gwenaëlle Corbin, Emmanuelle Vulliet, Bruno Lanson, Albert Rimola and Pierre Mignon
Minerals 2021, 11(1), 62; https://doi.org/10.3390/min11010062 - 11 Jan 2021
Cited by 18 | Viewed by 3343
Abstract
The adsorption of two pharmaceuticals, carbamazepine and paracetamol, onto the expandable clay mineral saponite has been studied through the combination of kinetic experiments, X-ray diffraction, and theoretical modeling. Kinetic experiments indicate low adsorption for carbamazepine and paracetamol on expandable smectite clay. Accordingly, X-ray [...] Read more.
The adsorption of two pharmaceuticals, carbamazepine and paracetamol, onto the expandable clay mineral saponite has been studied through the combination of kinetic experiments, X-ray diffraction, and theoretical modeling. Kinetic experiments indicate low adsorption for carbamazepine and paracetamol on expandable smectite clay. Accordingly, X-ray diffraction experiments show that neither compound enters smectite interlayer space. Molecular dynamics simulations were carried out to understand the interactions between the two pharmaceuticals and the saponite basal surface in the presence of Na+ cations. Calculations reveal that paracetamol almost does not coordinate solution cations, whereas a rather low coordination to cation is observed for carbamazepine. As a result, the adsorption onto the clay surface results mainly from van der Waals interactions for both pharmaceuticals. Carbamazepine does adsorb the surface via two configurations, one involving cation coordination, which corresponds to a rather stable adsorption compared to paracetamol. This is confirmed by structural analyses completed with desorption free energy profile. Full article
(This article belongs to the Special Issue Recent Advances in Molecular Modeling of Clay Minerals Interfaces)
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