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Molecular and Chemical Studies of Organic Compound Behavior in Soils
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Molecular and Chemical Studies of Organic Compound Behavior in Soils

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Physical Chemistry and Chemical Physics".

Deadline for manuscript submissions: closed (10 July 2024) | Viewed by 2568

Special Issue Editors

Dr. Fabienne Bessac

E-Mail Website
Guest Editor
1. Laboratoire de Chimie et Physique Quantiques (LCPQ), 31062 Toulouse, France
2. Ecole d’Ingénieurs de Purpan, 31076 Toulouse, France
Interests: molecular simulations (MD, ab initio, DFT, DFTB); interaction and complexation energies; solvation; pesticides; soil mineral matter (clays)
Dr. Sophie Hoyau

E-Mail Website
Guest Editor
Laboratoire de Chimie et Physique Quantiques (LCPQ), 31062 Toulouse, France
Interests: development of multi-reference methods using localized orbitals; theoretical study of cation–molecule interaction; molecule solvation and pesticide interaction with soil mineral matter

Special Issue Information

Dear Colleagues,

Soil science is an interdisciplinary science that is confronted today and for several decades with major societal, environmental, and human health issues. It has at its disposal a wide range of experimental and modeling techniques to address the issues at different scales of time and space. Its challenges concern, for example, the knowledge and control of pollution risks by contaminant molecules such as pesticides, drugs, pharmaceuticals, etc. The soil is a compartment of the ecosystem that significantly contributes to the global cycle of pollutants. In most cases, it serves as the major sink capacity and transformation reactor. The rapid progress in computer technology and in the development of computational methods in theoretical chemistry has allowed us to access to analyze complex systems such as soil and solvated contaminant systems and their interactions within biogeochemical interfaces.

In this Special Issue, we welcome contributions from all fields of computational and theoretical chemistry, including reviews and original works, demonstrating the key role of soil, as an ecosystem compartment, in the global pollutant cycle.

Dr. Fabienne Bessac
Dr. Sophie Hoyau
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. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

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Keywords

  • molecular simulation

  • molecular dynamics
  • Monte Carlo method
  • ab initio methods
  • density functional theory
  • molecular mechanics
  • pesticides
  • contaminant
  • organic molecule
  • soil
  • clay
  • organic matter
  • hydration
  • degradation
  • adsorption
  • dissolution

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Published Papers (2 papers)

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Research

15 pages, 71173 KiB  
Article
Atrazine Desorption Mechanism from an Hydrated Calcium Montmorillonite—A DFT Molecular Dynamics Study
by Quentin Desdion, Fabienne Bessac and Sophie Hoyau
Int. J. Mol. Sci. 2024, 25(3), 1604; https://doi.org/10.3390/ijms25031604 - 27 Jan 2024
Cited by 1 | Viewed by 999
Abstract
Atrazine is one of the most widely used herbicide molecules in the triazine family. Despite its interdiction in the European Union in 2004, atrazine and its main degradation products remain among the most frequently found molecules in freshwater reservoirs in many European Union [...] Read more.
Atrazine is one of the most widely used herbicide molecules in the triazine family. Despite its interdiction in the European Union in 2004, atrazine and its main degradation products remain among the most frequently found molecules in freshwater reservoirs in many European Union countries. Our study aims in obtaining insight into the desorption process of atrazine from the main soil absorbent material: clay. Constrained Molecular Dynamics simulations within the Density Functional Theory framework allow us to obtain a free energy desorption profile of atrazine from a Ca2+-montmorillonite surface. The results are interpreted in terms of atrazine inclination to the clay surface and moreover, in terms of hydration states of the cations present in the clay interlayer as well as the hydration state of the atrazine. The desorption mechanism is driven by atrazine alkyl groups and their sizes because of dispersion stabilizing effects. The highest barrier corresponds to the loss of the isopropyl interaction with the surface. Full article
(This article belongs to the Special Issue Molecular and Chemical Studies of Organic Compound Behavior in Soils)
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14 pages, 2511 KiB  
Article
Selective Adsorption of Organic Micro-Pollutants by Smectite Clays Revealed from Atomistic Simulations
by Mathieu Cancade, Thomas Thiebault and Pierre Mignon
Int. J. Mol. Sci. 2023, 24(19), 14781; https://doi.org/10.3390/ijms241914781 - 30 Sep 2023
Viewed by 942
Abstract
In this study, atomistic simulations were carried out to study the difference in the adsorption process between two similar molecules, diazepam and oxazepam, on Na+-montmorillonite. Kinetic and XRD measurements showed a contrasting adsorption mechanism of these two molecules, differing only by [...] Read more.
In this study, atomistic simulations were carried out to study the difference in the adsorption process between two similar molecules, diazepam and oxazepam, on Na+-montmorillonite. Kinetic and XRD measurements showed a contrasting adsorption mechanism of these two molecules, differing only by the presence/absence of methyl and hydroxyl groups, with a larger adsorption amount and intercalation for the oxazepam. The structural characterization of these molecules was investigated through DFT calculations and showed the vicinity of hydroxyl and carbonyl groups for only the chair conformation of oxazepam compared to the boat conformation. Classical molecular dynamics simulations of diazepam and the two forms of oxazepam on the external surface of Na+-montmorillonite highlighted the better coordination of the oxazepam-chair conformation, compared to its boat counterpart and diazepam. This has been confirmed through DFT calculations, from which a coordination energy that is greater by 10 kcal·mol−1 is observed. This strongly suggests that the experimentally observed intercalation of oxazepam occurs only in the chair form because of the strong coordination with the Na+ cation present in the Na-Mt interlayer. Classical MD simulations of the intercalated oxazepam chair molecule in the Na-Mt interlayer allowed the evaluation of the interlayer spacing d001, which was in very good agreement with the experimental XRD measurement. Full article
(This article belongs to the Special Issue Molecular and Chemical Studies of Organic Compound Behavior in Soils)
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