Competitive formation of molecular inclusion complexes of chlordecone and β- hexachlorocyclohexane with natural cyclodextrins: DFT and Molecular Dynamics study

doi:10.21203/rs.3.rs-1982299/v1

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Competitive formation of molecular inclusion complexes of chlordecone and β- hexachlorocyclohexane with natural cyclodextrins: DFT and Molecular Dynamics study

https://doi.org/10.21203/rs.3.rs-1982299/v1

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published 02 Jun, 2023

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The chlordecone (CLD) and β-hexachlorocyclohexane (β-HCH) are chlorinated pesticides that coexist as persistent organic pollutants in the groundwater of several countries in the Caribbean, being an environmental issue. This work theoretically evaluates the competitive formation of host-guest complexes pesticides@cyclodextrines (CDs) as an alternative for water purification and selective separation of pesticides. Quantum mechanical calculations based on Density Functional Theory (DFT) and classical molecular dynamics (MD) simulations were used to achieve information on geometries, energies, structure, and dynamics of guest-host complexes in the gas phase, implicit solvent medium, and in aqueous solutions. DFT studies showed that interactions of both pesticides with CDs are mediated by steric factors and guided by maximization of the hydrophobic interactions either with the other pesticide or with the CD cavity’s inner atoms. MD results corroborate the formation of stable complexes of both pesticides with the studied CDs. α-CD exhibited a preference for the smaller β-HCH molecule over the CLD that could not perturb the formed complex. The simulation of competitive formation with γ-CD illustrated that this molecule could accommodate both pesticides inside its cavity. These results suggest that CDs with smaller cavity sizes such as α-CD could be used for selective separation of β-HCH from CLD in water bodies while γ-CD could be used for methods that aim to remove both pesticides at the same time.

molecular inclusion complexes

pesticides

cyclodextrins

DFT

Molecular Dynamics

Persistent organic pollutants (POPs) are toxic substances that present a serious threat to the environment and human health. They have an elevated time of residence in the environment due to their high resistance to chemical and/or biological degradation and to the fact that they were disposed in an amount that outcome the capacity of the natural media to degrade them. These compounds could be found in all environmental compartments i.e., soil, air, water, and biota (Jones &de Voogt 1999). It should be mentioned that, among the 22 currently POPs listed by the Stockholm Convention (Anonymous 2011), 15 of them are pesticides. This has promoted the search for alternatives for removing of these types of compounds that, despite the prohibition of their utilization for more than 20 years, are still present all over the world.

Two of them, chlordecone (CLD, C₁₀Cl₁₀O, CAS: 143-50-5) and β-hexachlorocyclohexane (β-HCH, C₆H₆Cl₆, CAS 319-85-7) had been the focus of several investigations due to their presence in polluted areas of several islands of the Caribbean like Guadalupe and Martinique (Della Rossa et al. 2017, Robert 2012) and in minor extension Cuba (Alonso-Hernandez et al. 2012, Alonso-Hernandez et al. 2014, Dierksmeier 1996, Tolosa et al. 2010). Figure 1 shows a representation of these pollutants. CLD and β-HCH are generally detected in surface waters of the south of Basse-Terre (Guadeloupe), where banana plantations are generally located (Della Rossa et al. 2017). These molecules have a great affinity for the soils rich in organic material, which is evidenced by their octanol-water partition coefficients (log K_oc ≈ 4.2 and 3.57, respectively (Phillips et al. 2005)). These pollutants have a marked tendency to bioaccumulation and biomagnification through different environmental compartments (Willett et al. 1998, Xiao et al. 2004). Both pesticides cause severe affectations to human health, being carcinogenic, acting as neuroendocrine disruptors, among other pathologies (De Proft et al. 2007, Newhouse et al. 2009). Therefore, several alternatives for removing these pesticides from the environment have been studied employing different processes like adsorption and advanced oxidation (Cruz-Gonzalez et al. 2018, Durimel et al. 2015, Gamboa-Carballo et al. 2016). An improvement in the efficiency of these methods is, however, still necessary.

Molecular inclusion complexes are a type of supramolecular structures that have gained popularity due to their application in several areas (Lee et al. 2020, Oliveri &Vecchio 2018). Among the most popular host molecules are the natural occurring cyclodextrins (CDs), a family of cyclic oligosaccharides formed from 6–8 α-D-glucopyranose units (α-CD, β-CD, and γ-CD respectively) linked by (1\(\to\)4) glycosidic bonds (Fig. 1c). Because of the chair conformation of glucopyranose units, these compounds have a truncated cone shape, with the primary hydroxyls groups delimiting the narrower ring and the secondary hydroxyls the broader one. That particular tridimensional structure of CDs makes them very attractive as host molecules thanks to the combination of a capacity to encapsulate lipophilic molecules of a certain size inside their cavities and their solubility in water (Crini 2014). The topological nature of these complexes implicates that their stoichiometry (i.e., host-guest molecules ratio) and the type of occlusion of the guest molecules depend to a great extent on its morphology (Bouhadiba et al. 2020).

These complexes present applications for many sectors like agriculture and the environment (Bilensoy 2011, Duca &Boldescu 2008). Notably, in the past few years, our group have been studying, through experimental (Ferino-Pérez et al. 2019, Rana et al. 2016) and theoretical (Ferino-Pérez et al. 2019, Gamboa-Carballo et al. 2020, Jáuregui-Haza et al. 2020) works, the possibility of using CDs for the removal of CLD and β-HCH from polluted water. Since these two compounds coexist in water bodies (Robert 2012), it arises the necessity of understanding the competitive formation of those complexes and how it affects the whole process when both pesticides are present, as both form independently highly stable complexes with CDs (Ferino-Pérez et al. 2019, Gamboa-Carballo et al. 2020, Jáuregui-Haza et al. 2020, Rana et al. 2016).

Additionally, computational methods allow a better understanding of chemical phenomena to optimize time and resources, which have additional importance when working with noxious compounds such as pesticides. Quantum calculations based on Density Functional Theory have demonstrated the capability to perform precise estimations about the geometry and energies of a wide range of molecules. The computational cost of these quantum calculations is acceptable even for relatively large systems of over 100 atoms. On the other hand, it should be considered that the competitive formation of studied complexes is a dynamic process, and in spite that DFT calculations could give useful information about their structure, time-dependent calculations are still necessary. However, quantum mechanical calculations such as DFT-based calculations can estimate the geometry and energies of molecules in the complexes both in the gas phase and in implicit solvent but unable to give detailed information on the dynamical behavior of molecules and complexes. In order to tackle this problem and achieve dynamical information about the process of complex formation in aqueous solutions, the powerful method of classical molecular dynamics simulations is very useful. Computational modeling methods such as MD simulations can give us valuable information on the dynamics and mechanism of the host-guest process and complex formation of CD with different molecules such as above mentioned pesticide molecules where interactions and the dynamic properties of inclusion complexes can be studied at the molecular level. Besides, MD simulations can reveal the possible, preferable complexes and suggest the nature of the interactions involved in the formation of inclusion complexes of cyclodextrins with persistent organic pollutants. Molecular dynamics simulations have the capability to give structural and dynamical information to study the cyclodextrins persistent organic pollutant, guest- host complexes. Moreover, as the QM, calculations give geometry and energies precisely to the complex. Thus further investigation by application of MD simulations, detailed information on the dynamical molecular behavior of the complexes of persistent organic pollutants with cyclodextrins in aqueous solutions will be achieved.

This work aims to theoretically evaluate the competitive formation of host-guest complexes pesticides@CDs, in a mixture containing both CLD and HCH by DFT-based quantum mechanical calculations and classical molecular dynamics simulations to achieve information on geometries, energies, structure, and dynamics of guest-host complexes in the gas phase, implicit solvent medium and aqueous solutions.

2.1. System under study

For the study of the competitive formation of molecular inclusion complexes of CLD and β-HCH with CD, initial positions of the molecules involved were taken, as depicted in Fig. 2. The four initial positions, in the first row of Fig. 2, were chosen to evaluate the simultaneous interaction of both pesticides with the host molecule in the cases where each pesticide interacts from different sides of the cavity (the two at the left, first row of Fig. 2) and when both pesticides interact by the same side of the CD (the two at the right, first row of Fig. 2). In the second row of Fig. 2, the other four initial positions, were evaluated to explore the interaction of one of the pesticides when a complex is already formed with the other one. Geometries of the formed complexes in the case of partial occlusion of the pollutants were obtained from the works of Gamboa-Carballo et al. (Gamboa-Carballo et al. 2020) and Ferino-Pérez et al. (Ferino-Pérez et al. 2019) for the CLD@α-CDs and β-HCH@α-CDs complexes, respectively. Furthermore, since these previously mentioned studies showed that the CD cavity’s size influences the occlusion process, α-CD and γ-CD were both evaluated as host molecules. It should be pointed out that α-CD only presents partial occlusion of the pesticide (Ferino-Pérez et al. 2019, Gamboa-Carballo et al. 2020), the one that is going to interact with the formed complex is placed on the other side of the cavity. For interactions with γ-CD complexes, it was considered that total occlusion of one of the pesticides had occurred, and then the other was placed on both sides of the cavity. This gives 14 systems, 6 for the pesticides@α-CD and 8 for the pesticides@γ-CD.

To understand the mechanism and dynamics of guest-host complex formation, the interactions between CLD and β-HCH with CD have been studied at the molecular level using classical molecular dynamics (MD) simulations. MD simulations of CLD and β-HCH with CD in aqueous solutions has been performed using the General Amber Force Field (GAFF) (Case et al. 2004) for organic molecules, and GLYCAM (Kirschner et al. 2008) amber compatible force field for CD molecules.

3.1. DFT calculations

Representative structures (i.e., different geometries of CD-pollutants complexes) were optimized using DFT (Hohenberg &Kohn 1964, Kohn &Sham 1965). For this optimization, M06-2X (Johnson et al. 2009, Zhao &Truhlar 2008) functional was employed (along with the 6-31G(d,p) basis set). It has been reported that this combination correctly describes the interactions found in non-covalent bonded dimers (Johnson et al. 2009), particularly in the case of the van der Waals interactions present on the studied systems. DFT-D3 dispersive corrections (Grimme et al. 2011) were applied to all DFT calculations. The solvent effects were taken into account using the solvent implicit model SMD (Marenich et al. 2009) using water as solvent. Thus, hereafter the D3 and SMD parts in SMD/M06-2X-D3 calculation scheme will be omitted for simplicity and readability. All the calculations were performed using the software package Gaussian09 (Frisch et al. 2009).

3.2. Molecular dynamics simulations

The partial charges of CLD and β-HCH molecules were calculated by Restrained Electrostatic Potential (RESP) fitting scheme (Bayly et al. 1993) using the Antechamber program (Wang et al. 2006) for the geometrically optimized structures while GLYCAM force field charges where used for CD molecules. For the preparation of the systems, one molecule of CD, one molecule of CLD, or one molecule of β-HCH was solvated in simulation boxes by water molecules. For competitive interaction of CLD and β-HCH with CD molecule a system, containing one molecule of CD, one molecule of CLD, and one molecule of β-HCH were solvated in the simulation box with water. The molecules of CD, CLD, β-HCH in all simulation boxes were randomly distributed by Packmol package (Martínez &Martínez 2003, Martínez et al. 2009). As CD, CLD, β-HCH molecules, and latter water molecules were randomly added to the simulations boxes. The steepest descent minimization procedure was needed to eliminate unfavorable interactions in the systems. After minimization, all systems were equilibrated for 500 ps NVT (Canonical ensemble) followed by 500 ps NPT (isothermal–isobaric ensemble) simulations. After equilibration, the production runs were performed with the linear constraint solver (LINCS) algorithm (Hess et al. 1997) employed for all bonds involving hydrogen atoms. The cut-off of the short-range nonbonded interactions was set to 1.2 nm. The long-range electrostatic interactions were treated by the particle mesh Ewald method (PME) (Darden et al. 1993). Initial velocities for all particles in the simulations were produced by Maxwell–Boltzmann distribution at 300K. V-rescale coupling algorithm (Bussi et al. 2007) with the coupling constant of 0.1 ps was used to maintain constant temperature and pressure during the simulations. The production runs for analysis were performed in NPT ensemble for 50 ns at 300 K with 2 fs time step. Gromacs 4.6.5 program package was used for performing MD simulations (Berendsen et al. 2005, Berendsen et al. 1995, Lindahl et al. 2001) while Visual Molecular Dynamics (VMD) was used for visualizations and preparation of snapshots (Humphrey et al. 1996).

4.1. DFT calculations results

The geometries of the 14 ensembles of molecules used for describing the system under study were optimized using DFT calculations. This was performed to explore the possible stable minima when the two compounds of interest interact at the same time with the CDs. Figure 3 shows the minima obtained when both pesticides interact by the same side of the CDs cavity. These minima suggest that when this phenomenon occurs, the system’s stabilization goes through hydrophobic interactions between the two pesticides. There is not a preferential interaction of the cavity with none of the two pesticides. Figure 3 illustrates that this happens despite CD cavity’s size of the as similar geometries were obtained for complexes with γ-CD.

On the other hand, when the CLD and β-HCH were placed on opposite sides of the CDs cavity, the minima appear when a partial occlusion of the pesticides into the CD cavity takes place (Fig. 4). In the cases where α-CD is the host molecule, the occlusion did not occur to a great extent by any of the two sides of the α-CD cavity. In those cases, system’s stabilization is achieved by means of the interactions of both compounds with the outer atoms of the cavity. Meanwhile, when γ-CD is the host molecule, a greater occlusion grade of both pesticides is observed in the obtained minima (Fig. 4b). These results suggest that complexes of where both pesticides partially occlude into the CD cavity could be thermodynamically stable. However, dynamic studies are needed for determining if the formation of complexes with one of the guest molecules is preferred.

Figure 5 presents the final geometries for the systems where one of the pesticides was settled to interact with a previously formed nanoaggregate. It could be seen that in all the cases, the presence of a second pollutant does not affect the formed complex considerably. For both CLD@CD and β-HCH@CD complexes, the “foreigner” pollutant, initially situated in the cavity axis, ends interacting with atoms at the border of cyclodextrins cavity. This confirms the results of previous works (Ferino-Pérez et al. 2019, Gamboa-Carballo et al. 2020) about the high stability of these inclusion complexes.

It is crucial to notice that all these calculations have a static nature and, therefore, only depicted minima of the potential energy surface that characterized the studied systems. As previously stated, the competitive formation is a dynamic process and, therefore, the calculations of molecular dynamics should be performed to confirm these results.

4.2. MD simulations results

α-CD and γ-CD molecules have different cavity sizes. Therefore, their affinities to accommodate β-HCH and CLD molecules must be different due to the size of β-HCH and CLD. To quantify the process of guest-host complex formation of CDs with β-HCH and CLD and their interactions, the distances between the center of mass of CDs with guest molecules were calculated in the solutions containing either only one of the guest molecules (CLD/β-HCH) or both of them. Figure 6 shows the distance of the center of mass of α-CD to the center of mass of CLD in the solutions containing one CLD and one α-CD molecule.

From the Fig. 6, it can be concluded that the CLD molecule approaches the α-CD molecule and the distance of the center of mass of α-CD to the center of the mass of CLD is about 0.5 nm, which shows the CLD molecule gets close to the cavity of α-CD and finally the complex of α-CD and CLD forms. On the other hand, the figure shows that the process of complex formation and accommodation of CLD inside the cavity of α-CD starts from less than 5 ns time where the CLD gets close to the α-CD and later occupies the cavity and stays inside of it until the end of simulation at 50 ns.

Figure 7 shows that the β-HCH molecule approaches the α-CD molecule and the distance of its center of mass to the center of mass of β-HCH is about 0.5 nm. This means that the β-HCH gets to the cavity of α-CD. Also, the figure shows that the process of complex formation and accommodation of β-HCH inside the cavity of α-CD starts around 10 ns of simulation, where the β-HCH gets close to the α-CD and later occupies the cavity until the end of simulation at 50ns. When the dynamics of complex formation of CLD and β-HCH with α-CD is compared, it can be observed that the CLD molecule gets to the cavity of α-CD faster than that of β-HCH, but after the formation of complex, the guest molecules do not leave the cavity and make stable guest–host complexes.

In order to explore the competitive behavior of β-HCH and CLD molecules for occupying the cavity of α-CD, a solution containing one molecule of β-HCH, CLD, and one molecule of α-CD has been simulated. In the solution, both β-HCH and CLD can compete to occupy the cavity; therefore, the distance of the center of mass of each of the pesticide molecules with α-CD can show their competitive dynamics. Figure 8 shows the distance of the center of mass of α-CD to the center of mass of β-HCH and CLD in the solution containing one β-HCH, one CLD, and one α-CD molecule.

Figure 8 clearly shows a difference in the dynamics of β-HCH, CLD molecules and their tendency to occupy the cavity of the α-CD molecule where the β-HCH approaches the α-CD at the distance of about 0.5 nm, then the α-CD cavity is filled by β-HCH. Also, the figure shows that the process of complex formation and accommodation of β-HCH inside the cavity of α-CD starts from less than 5 ns time where the β-HCH gets close to the α-CD and later occupies the cavity and stays in the cavity until the end of simulation time of 50 ns. While the CLD molecule approaches the α-CD and makes some unstable interactions with α-CD, but it later leaves the α-CD molecule and solvates in aqueous solution.

To explore the effect of the cavity’s size on the dynamics and stability of guest-host complex formation of both β-HCH and CLD molecules, the γ-CD, a molecule with a bigger cavity than α-CD, has been used. MD simulations showed that the interaction and dynamics of β-HCH and CLD with γ-CD are different since the γ-CD molecule can accommodate both pesticides in the cavity from both sides of the molecule. Figure 9 clearly shows a difference in the dynamics of β-HCH and CLD when compared with the behavior showed in Fig. 8. With γ-CD, both pesticides tend to occupy the cavity of the host molecule.

Figure 9 shows that in the process of complex formation of β-HCH and CLD with γ-CD, first the smaller β-HCH molecule gets closer to the cavity of γ-CD and forms the complex within the first 5 ns of simulation time while the bigger CLD molecule enters the cavity after 25 ns of simulation time. Also, the graph shows that when the CLD molecule occupies the cavity, a rearrangement of the already formed β-HCH@γ-CD complex occurs. The β-HCH molecule gets further from the center of mass of γ-CD, allowing the second molecule to be accommodated inside the cavity of its cavity.

Moreover, MD simulations revealed that in the process of guest-host complex formation of α-CD or γ-CD with β-HCH and CLD molecules, mainly weak interactions such as van der Waals force or hydrogen bonds are involved where the later one is possible in the case of CLD molecule.

Figures 10 shows snapshots from MD simulations with host molecules accommodating either β-HCH, CLD, or both in the cavity. Also, the snapshots show the possible orientation of the CLD molecule in the cavity where the oxygen atom of CLD can form a hydrogen bond with –OH groups of CD molecule.

The competitive formation of guest-host complexes of two pesticides, CLD, and β-HCH, with two occurring natural CDs (α-CD and γ-CD) has been theoretically evaluated using classical and quantum calculations. DFT studies showed that interactions of both pesticides with CDs are mediated by steric factors and guided by maximization of the hydrophobic interactions either with the other pesticide or with the inner atoms of CD cavity (preferred). Furthermore, MD results corroborate the formation of stable complexes of both pesticides with the studied CDs. Additionally, when the competitive formation was tested, α-CD exhibited a preference for the smaller β-HCH molecule over the CLD molecule that was unable to perturb the formed complex. The simulation of competitive formation with γ-CD as a host molecule illustrated that this molecule could accommodate both pesticides inside its cavity. These results suggest that CDs with smaller cavity sizes such as α-CD could be used for selective separation of β-HCH from CLD in water bodies, while CDs such as γ-CD could be used for methods that aim to remove both pesticides at the same time.

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Availability of data and materials

Data sharing is not applicable to this article as no datasets were generated or analysed during the current study.

Competing interests

The authors declare that they have no competing interests

Funding

This work was supported by the project CIMPest (CBA-330810-2018-P-1, INTEC, Dominican Republic), the project DetDePest (CAPES, Guadeloupe), and project TATARCOP (InSTEC, Cuba).

Authors' contributions

Conceptualization [Anthuan Ferino-Pérez, Babak Minofar, Ulises J. Jaúregui-Haz]; Data curation [Anthuan Ferino-Pérez, Queiroz Portorreal, Juan J. Gamboa-Carballo, Babak Minofar]; Formal analysis [Anthuan Ferino-Pérez, Babak Minofar, Sarra Gaspard, Ulises J. Jaúregui-Haza]; Funding acquisition [Sarra Gaspard, Ulises J. Jaúregui-Haza]; Investigation [Anthuan Ferino-Pérez, Queiroz Portorreal, Juan J. Gamboa-Carballo, Babak Minofar]; Methodology[Anthuan Ferino-Pérez, Babak Minofar, Ulises J. Jaúregui-Haza]; Project administration [Ulises J. Jaúregui-Haza]; Resources[Babak Minofar, Sarra Gaspard, Ulises J. Jaúregui-Haza]; Software[Anthuan Ferino-Pérez, Juan J. Gamboa-Carballo, Babak Minofar]; Supervision [Babak Minofar, Sarra Gaspard, Ulises J. Jaúregui-Haza]; Visualization [Anthuan Ferino-Pérez, Babak Minofar]; Writing – original draft [Anthuan Ferino-Pérez, Babak Minofar, Ulises J. Jaúregui-Haza]; Writing – review & editing [Juan J. Gamboa-Carballo, Sarra Gaspard, Ulises J. Jaúregui-Haza]

Acknowledgements

Computational calculations were performed using Wahoo, the cluster of the Centre Commun de Calcul Intensif of the Université des Antilles, Guadeloupe, France. The authors wish to thank Raphael Pasquier, Jacques Laminie and Pascal Poullet for their support with the calculation facilities. The Informatics service of InSTEC at Havana, Cuba, is also gratefully acknowledged. Babak Minofar acknowledges the access to computational resources provided by the CESNET LM2015042 and the CERIT Scientific Cloud LM2015085, provided under the program “Projects of Large Research, Development, and Innovations Infrastructures”.

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No competing interests reported.

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published 02 Jun, 2023

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Competitive formation of molecular inclusion complexes of chlordecone and β- hexachlorocyclohexane with natural cyclodextrins: DFT and Molecular Dynamics study

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Journal Publication

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Abstract

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1. Introduction

2. Methods

2.1. System under study

3. Computational Details

3.1. DFT calculations

3.2. Molecular dynamics simulations

4. Results And Discussion

4.1. DFT calculations results

4.2. MD simulations results

5. Conclusions

Declarations

References

Additional Declarations

Status:

Journal Publication

Version 1