Atrazine Desorption Mechanism from an Hydrated Calcium Montmorillonite-A DFT Molecular Dynamics Study.

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.

Interaction of Metamitron and Fenhexamid with Ca2+ -Montmorillonite Clay Surfaces: A Density Functional Theory Molecular Dynamics Study.

Metamitron (Meta), an herbicide, and fenhexamid (Fen), a fungicide, are authorized by the European Union to be used in agriculture. This article reports theoretical calculations about Meta and Fen in interaction with a clay surface: a Ca-montmorillonite (Mont). Conformational searches have been performed thanks to Car-Parrinello molecular dynamics simulations from which geometries have been extracted. Interaction and adsorption energies have been calculated for isomers of Meta or Fen in interaction with Mont to understand the relative stability of various kinds of complexation. Substantial adsorption energies are comparable for Meta and Fen: around -40 kcal/mol. For Fen-Mont, the CO monodentate family is surprisingly the lowest in energy. Moreover, the 10 lowest-energy isomers involve complexation on Fen carbonyl oxygens. The Meta-Mont lowest-energy family, N-N, does not involve π delocalization breaking within Meta. At the same time, the stronger the interaction energy is, the larger the structural modifications within Mont are, particularly concerning the interacting cation distance to the surface. The non-negligible charge transfer and the magnitude of the adsorption energy speak in favor of the chemisorption of the pesticide on the surface. © 2019 Wiley Periodicals, Inc.

Theoretical study of the atrazine pesticide interaction with pyrophyllite and Ca(2+) -montmorillonite clay surfaces.

Atrazine, a pesticide belonging to the s-triazine family, is one of the most employed pesticides. Due to its negative impact on the environment, it has been forbidden within the European Union since 2004 but remains abundant in soils. For these reasons, its behavior in soils and water at the atomic scale is of great interest. In this article, we have investigated, using DFT, the adsorption of atrazine onto two different clay surfaces: a pyrophyllite clay and an Mg-substituted clay named montmorillonite, with Ca2+ compensating cations on its surface. The calculations show that the atrazine molecule is physisorbed on the pyrophyllite surface, evidencing the necessity to use dispersion-corrected computational methods. The adsorption energies of atrazine on montmorillonite are two to three times larger than on pyrophyllite, depending on the adsorption pattern. The computed adsorption energy is of about -30 kcal mol-1 for the two most stable montmorillonite-atrazine studied isomers. For these complexes, the large adsorption energy is related to the strong interaction between the chlorine atom of the atrazine molecule and one of the Ca2+ compensating cations of the clay surface. The structural modifications induced by the adsorption are localized: for the surface, close to substitutions and particularly below the Ca2+ cations; in the molecule, around the chlorine atom when Ca2+ interacts strongly with this basic site in a monodentate mode. This study shows the important role of the alkaline earth cations on the adsorption of atrazine on clays, suggesting that the atrazine pesticide retention will be significant in Ca2+ -montmorillonite clays. © 2016 Wiley Periodicals, Inc.

Prediction of the Fate of Organic Compounds in the Environment From Their Molecular Properties: A Review.

A comprehensive review of quantitative structure-activity relationships (QSAR) allowing the prediction of the fate of organic compounds in the environment from their molecular properties was done. The considered processes were water dissolution, dissociation, volatilization, retention on soils and sediments (mainly adsorption and desorption), degradation (biotic and abiotic), and absorption by plants. A total of 790 equations involving 686 structural molecular descriptors are reported to estimate 90 environmental parameters related to these processes. A significant number of equations was found for dissociation process (pKa), water dissolution or hydrophobic behavior (especially through the KOW parameter), adsorption to soils and biodegradation. A lack of QSAR was observed to estimate desorption or potential of transfer to water. Among the 686 molecular descriptors, five were found to be dominant in the 790 collected equations and the most generic ones: four quantum-chemical descriptors, the energy of the highest occupied molecular orbital (EHOMO) and the energy of the lowest unoccupied molecular orbital (ELUMO), polarizability (α) and dipole moment (µ), and one constitutional descriptor, the molecular weight. Keeping in mind that the combination of descriptors belonging to different categories (constitutional, topological, quantum-chemical) led to improve QSAR performances, these descriptors should be considered for the development of new QSAR, for further predictions of environmental parameters. This review also allows finding of the relevant QSAR equations to predict the fate of a wide diversity of compounds in the environment.

Direct selected multireference configuration interaction calculations for large systems using localized orbitals.

A selected multireference configuration interaction (CI) method and the corresponding code are presented. It is based on a procedure of localization that permits to obtain well localized occupied and virtual orbitals. Due to the local character of the electron correlation, using local orbitals allows one to neglect long range interactions. In a first step, three topological matrices are constructed, which determine whether two orbitals must be considered as interacting or not. Two of them concern the truncation of the determinant basis, one for occupied/virtual, the second one for dispersive interactions. The third one concerns the truncation of the list of two electron integrals. This approach permits a fine analysis of each kind of approximation and induces a huge reduction of the CI size and of the computational time. The procedure is tested on linear polyene aldehyde chains, dissociation potential energy curve, and reaction energy of a pesticide-Ca(2+) complex and finally on transition energies of a large iron system presenting a light-induced excited spin-state trapping effect.

C-H bond activation of benzene by unsaturated η2-cyclopropene and η2-benzyne complexes of niobium.

We report the synthesis of a niobium cyclopropyl complex, Tp(Me2)NbMe(c-C(3)H(5))(MeCCMe), and show that thermal loss of methane from this compound generates an intermediate that is capable of activating both aliphatic and aromatic C-H bonds. Isotopic labeling, trapping studies, a detailed kinetic analysis, and density functional theory all suggest that the active intermediate is an η(2)-cyclopropene complex formed via ß-hydrogen abstraction rather than an isomeric cyclopropylidene species. C-H activation chemistry of this type represents a rather unusual reactivity pattern for η(2)-alkene complexes but is favored in this case by the strain in the C(3) ring which prevents the decomposition of the key intermediate via loss of cyclopropene.

DFT modeling of reactivity in an ionic liquid: How many ion pairs?

The modeling of reactivity in an ionic liquid is examined with DFT and DFT/MM calculations on the S(N)2 intramolecular rearrangement of the Z-phenylhydrazone of 3-benzoyl-5-phenyl-1,2,4-oxadiazole into 4-benzoylamino-2,5-diphenyl-1,2,3-triazole induced by amines. Experimental research has shown that the reaction occurs in 1-butyl-3-methylimidazolium tetrafluoroborate, and in conventional organic solvents such as acetonitrile with comparable rates. The structure for the reactants, transition states and products for the rate-determining step are optimized, and the energy barrier is computed in three different environments: gas phase, water solvent, and ionic liquid. The results are encouraging in describing the energy barrier in the ionic liquid. A simple model is formulated to explain the effect of the solvent in this particular process, and a procedure to study theoretically the reactivity in an ionic liquid is proposed.

Categorizing chlordecone potential degradation products to explore their environmental fate.

Chlordecone (C10Cl10O; CAS number 143-50-0) has been used extensively as an organochlorine insecticide but is nowadays banned and listed on annex A in The Stockholm Convention on Persistent Organic Pollutants (POPs). Although experimental evidences of biodegradation of this compound are scarce, several dechlorination products have been proposed by Dolfing et al. (2012) using Gibbs free energy calculations to explore different potential transformation routes. We here present the results of an in silico classification (TyPol - Typology of Pollutants) of chlordecone transformation products (TPs) based on statistical analyses combining several environmental endpoints and structural molecular descriptors. Starting from the list of putative chlordecone TPs and considering available data on degradation routes of other organochlorine compounds, we used different clustering strategies to explore the potential environmental behaviour of putative chlordecone TPs from the knowledge on their molecular descriptors. The method offers the possibility to focus on TPs present in different classes and to infer their environmental fate. Thus, we have deduced some hypothetical trends for the environmental behaviour of TPs of chlordecone assuming that TPs, which were clustered away from chlordecone, would have different environmental fate and ecotoxicological impact compared to chlordecone. Our findings suggest that mono- and di-hydrochlordecone, which are TPs of chlordecone often found in contaminated soils, may have similar environmental behaviour in terms of persistence.

TyPol - a new methodology for organic compounds clustering based on their molecular characteristics and environmental behavior.

Following legislation, the assessment of the environmental risks of 30000-100000 chemical substances is required for their registration dossiers. However, their behavior in the environment and their transfer to environmental components such as water or atmosphere are studied for only a very small proportion of the chemical in laboratory tests or monitoring studies because it is time-consuming and/or cost prohibitive. Therefore, the objective of this work was to develop a new methodology, TyPol, to classify organic compounds, and their degradation products, according to both their behavior in the environment and their molecular properties. The strategy relies on partial least squares analysis and hierarchical clustering. The calculation of molecular descriptors is based on an in silico approach, and the environmental endpoints (i.e. environmental parameters) are extracted from several available databases and literature. The classification of 215 organic compounds inputted in TyPol for this proof-of-concept study showed that the combination of some specific molecular descriptors could be related to a particular behavior in the environment. TyPol also provided an analysis of similarities (or dissimilarities) between organic compounds and their degradation products. Among the 24 degradation products that were inputted, 58% were found in the same cluster as their parents. The robustness of the method was tested and shown to be good. TyPol could help to predict the environmental behavior of a "new" compound (parent compound or degradation product) from its affiliation to one cluster, but also to select representative substances from a large data set in order to answer some specific questions regarding their behavior in the environment.

Chemical bonding in phosphane and amine complexes of main group elements and transition metals.

The geometries and bond dissociation energies of the main group complexes X3B-NX3, X3B-PX3, X3Al-NX3, and X3Al-PX3 (X = H, Me, Cl) and the transition metal complexes (CO)5M-NX3 and (CO)5M-PX3 (M = Cr, Mo, W) have been calculated using gradient-corrected density functional theory at the BP86/TZ2P level. The nature of the donor-acceptor bonds was investigated with an energy decomposition analysis. It is found that the bond dissociation energy is not a good measure for the intrinsic strength of Lewis acidity and basicity because the preparation energies of the fragments may significantly change the trend of the bond strength. The interaction energies between the frozen fragments of the borane complexes are in most cases larger than the interaction energies of the alane complexes. The bond dissociation energy of the alane complexes is sometimes higher than that of the borane analogues because the energy for distorting the planar equilibrium geometry of BX3 to the pyramidal from in the complexes is higher than for AlX3. Inspection of the three energy terms, DeltaE(Pauli), DeltaE(orb), and DeltaE(elstat), shows that all three of them must be considered to understand the trends of the Lewis acid and base strength. The orbital term of the donor-acceptor bonds with the Lewis bases NCl3 and PCl3 have a higher pi character than the bonds of EH3 and EMe3, but NCl3 and PCl3 are weaker Lewis bases because the lone-pair orbital at the donor atoms N and P has a high percent s character. The calculated DeltaE(int) values suggest that the trends of the intrinsic Lewis bases' strengths in the main-group complexes with BX3 and AlX3 are NMe3 > NH3 > NCl3 and PMe3 > PH3 > PCl3. The transition metal complexes exhibit a somewhat different order with NH3 > NMe3 > NCl3 and PMe3 > PH3 > PCl3. The slightly weaker bonding of NMe3 than that of NH3 comes from stronger Pauli repulsion. The bond length does not always correlate with the bond dissociation energy, nor does it always correlate with the intrinsic interaction energy.

Large systems at ab initio multireference level: a cheap treatment thanks to a division into fragments.

Thanks to the use of localized orbitals and the subsequent possibility of neglecting long-range interactions, the linear-scaling methods have allowed to treat large systems at ab initio level. However, the limitation of the number of active orbitals in a complete active space self consistent-field (CASSCF) calculation remains unchanged. The method presented in this paper suggests to divide the system into fragments containing only a small number of active orbitals. Starting from a guess wave function, each orbital is optimized in its corresponding fragment, in the presence of the other fragments. Once all the fragments have been treated, a new set of orbitals is obtained. The process is iterated until convergence. At the end of the calculation, a set of active orbitals is obtained, which is close to the exact CASSCF solution, and an accurate CASSCF energy can be estimated.

Why is BCl3 a stronger Lewis acid with respect to strong bases than BF3?

Geometries and bond dissociation energies of the complexes Cl(3)B[bond]NH(3) and F(3)B[bond]NH(3) have been calculated using DFT (PW91) and ab initio methods at the MP2 and CCSD(T) levels using large basis sets. The calculations give a larger bond dissociation energy for Cl(3)B[bond]NH(3) than for F(3)B[bond]NH(3). Calculations of the deformation energy of the bonded fragments reveal that the distortion of BCl(3) and BF(3) from the equilibrium geometry to the pyramidal form in the complexes requires nearly the same energy. The higher Lewis acid strength of BCl(3) in X(3)B[bond]H(3) compared with BF(3) is an intrinsic property of the molecule. The energy partitioning analysis of Cl(3)B[bond]NH(3) and F(3)B[bond]NH(3) shows that the stronger bond in the former complex comes from enhanced covalent interactions between the Lewis acid and the Lewis base which can be explained with the energetically lower lying LUMO of BCl(3).