Density Functional Theory and Molecular Dynamics insights into the site-dependent adsorption of hydrogen fluoride on kaolinite

Journal Pre-proof Density Functional Theory and Molecular Dynamics insights into the site-dependent adsorption of hydrogen fluoride on kaolinite

Bibek Dash, Swagat S. Rath PII:

S0167-7322(19)35857-X

DOI:

https://doi.org/10.1016/j.molliq.2019.112265

Reference:

MOLLIQ 112265

To appear in:

Journal of Molecular Liquids

Received date:

22 October 2019

Accepted date:

4 December 2019

Please cite this article as: B. Dash and S.S. Rath, Density Functional Theory and Molecular Dynamics insights into the site-dependent adsorption of hydrogen fluoride on kaolinite, Journal of Molecular Liquids(2019), https://doi.org/10.1016/j.molliq.2019.112265

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© 2019 Published by Elsevier.

Journal Pre-proof

Density Functional Theory and Molecular Dynamics Insights into the Site-Dependent Adsorption of Hydrogen Fluoride on Kaolinite Bibek Dasha,b, Swagat S. Rathb,* aAcademy

of Scientific and Innovative Research, CSIR-Institute of Minerals and

Materials Technology, Bhubaneswar, India of Minerals and Materials Technology, Bhubaneswar, India

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bCSIR-Institute

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Abstract

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The removal of fluoride from water using adsorption on a low-cost mineral such as

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kaolinite is an important research topic. The present communication uses Density

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Functional Theory (DFT) and Molecular Dynamics (MD) based simulations to

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comprehensively investigate the adsorption behaviour of HF, one of the most predominant species of fluoride in the aqueous solutions, on the (0 0 1) surface of

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kaolinite. The optimum geometric configurations of adsorption of HF on different

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possible sites on the mineral surface have been established, and the corresponding adsorption energies, bond distances, Partial Density of States (PDOS), Mulliken charges and electron density difference plots have been analyzed to understand the interaction at each site. To explore the site-dependent adsorption behaviour, the interaction of HF has been investigated on different sites such as aluminium centres, surface oxygen atoms (both lying and upright) and cavity site (void space encircled by six aluminium centres). The analysis shows that the F atom has a strong tendency to form hydrogen bonds with the surface H atom on kaolinite. Among the three

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Journal Pre-proof aforementioned types of adsorption sites considered, the ―cavity‖ site is found to offer the greatest adsorption strength. Further, MD simulations have been undertaken to explain the effect of water on the adsorption and substantiate the bonding mechanism.

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Keywords: Hydrogen fluoride, kaolinite, adsorption, Density Functional Theory, Partial Density of States, Molecular Dynamics

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*Corresponding author: Email ID: [email protected]; Phone: +91-674-2379147 1. Introduction Fluoride in drinking water is a menace that needs serious measures for its remediation [1]. Fluorine is estimated to be the 13th most abundant element in the earth's crust and is widely dispersed in nature in the form of fluorides. Fluorides are

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typically colourless and odourless when dissolved in water that makes the physical

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determination of fluorides difficult in aqueous systems [2]. World Health

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Organization (WHO) has set the upper limit of F - at 1.5 mg/l in drinking water as

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suitable for human consumption [3, 4]. The Bureau of Indian Standards (BIS) has,

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therefore, laid down Indian standard drinking water specification from 1.5 mg/l as a maximum permissible limit of fluoride and highest desirable limit to 1.0 mg/l with

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further remarks as ‗lesser the better‘ [5]. Consumption of water with fluoride below

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or above the prescribed range is harmful and injurious to human health. Several serious diseases such as osteoporosis, brittle bones, skeletal deformities, arthritis,

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cancer, infertility, thyroid disorder and Alzheimer‘s disease are caused due to excess intake of fluoride in drinking water [6]. Globally, countries like Afghanistan, China, India, Japan, Iraq, Iran, Turkey etc are facing a significant problem of fluorosis, and other fluorine related health hazards. In India alone, more than 62 million people in twenty states are affected due to fluoride pollution [7]. Various statistical modelling tools are employed regularly to map the groundwater fluoride contamination and estimate the impact on human health in fluoride affected areas [8,9].

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Journal Pre-proof The techniques that are available for defluoridation are coagulation/precipitation, membrane separation, ion-exchange, deionization, electrodialysis and adsorption [10,11]. The adsorption process is suitable for the removal of fluoride with low concentrations and is considered suitable among all because of its advantages such as low cost, high efficiency, greater accessibility of low-cost adsorbents, low energy

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consumption and regenerative capability of raw materials [12–17].

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There are reports of adsorption of fluoride using different materials like alumina/aluminium-based materials, clays and soils, calcium-based minerals,

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synthetic compounds and carbon-based materials [18]. Among these materials,

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natural clay minerals with high surface area, layered molecular structure, chemical

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and mechanical stability along with the variety of surface properties that provide

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active sites for adsorption have proven to be very useful adsorbent materials [19,20]. Kaolinite, one of the most abundant and cheap clay minerals, has been extensively

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used in adsorption studies owing to its unique physicochemical properties and

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numerous reports can be found in the literature dealing with adsorption of both organic compounds and inorganic ions on kaolinite surface [21–27]. Although several studies concerning kaolinite being used to remove fluoride from aqueous solution have been reported [10,28–33], the atomic level adsorption mechanism of fluoride ions on the clay mineral surface is still unclear. Computer-based simulation methods have proven to be reliable tools to understand the structural and chemical mechanism of molecules on solid interfaces. Molecular modeling studies involving Density Functional Theory (DFT) which is a method to

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Journal Pre-proof determine electronic structures and properties of materials, and molecular dynamics (MD) which is a method for determining time evolution of molecular system based on numerical solution of Newton's laws of motion have opened a new door towards the understanding of the underlying phenomena and fundamentals of adsorption processes on mineral surfaces. First-principle studies using DFT for examining

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kaolinite structure and adsorption of various metal ions and organic materials on

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kaolinite surfaces and MD studies on mineral surfaces are reported in the literature [34–37]. However, to the best of the authors‘ knowledge, no systematic molecular

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modelling studies have been carried out on adsorption of HF on kaolinite surfaces.

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In this communication, a density functional study of the adsorption of HF at the

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basal (001) surface of kaolinite using periodic slab model is being presented. The

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surface complexation of hydrogen fluoride at different possible adsorption sites of kaolinite (0 0 1) has been examined, and corresponding adsorption energies have

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been estimated. The possible adsorption structures and thereby, the adsorption

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mechanism of adsorbates have been presented based on DFT simulations involving charge transfer analysis, electron density difference plots and partial density of states (PDOS) calculations. Further, MD simulations have been carried out to understand the effect of the aqueous environment on the adsorption of HF at the mineral surface. 2. Materials and methods 2.1 Sample characterization To supplement the simulation results, some characterization studies were

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Journal Pre-proof undertaken on pure kaolinite samples handpicked from one of the mines of Odisha, India. X-ray diffraction study (XRD) was carried out by Phillips X-ray diffractometer to investigate the predominant planes present in the powdered kaolinite sample. Fourier Transform Infra-Red (FTIR) spectra of the kaolinite sample were recorded in the range of 400-4000 cm-1 over KBr disc pellet using a Shimadzu make instrument.

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A pellet made of a mixture of around 2 mg of sample with 100 mg KBr was prepared

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for FTIR studies. The FTIR spectra were recorded for the kaolinite sample before and after being treated with fluoride. All the relevant discussions related to these tests

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have been incorporated in the appropriate sections.

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2.2 Computational methodology

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All plane-wave dispersion-corrected density functional calculations (DFT-D) were

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performed using the Cambridge Sequential Total Energy Package (CASTEP) module of Biovia Materials Studio 7.0 [38]. The dispersion correction scheme proposed by

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Grimme was used together with the generalized gradient approximation (GGA).

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Perdew-Burke-Ernzerhof (PBE) exchange-correlation functional [39] [40] was considered for the calculations because of its high accuracy in describing the interactions between molecules, metal surfaces and hydrogen bond [40]. The core electrons and the nuclei of the atoms were described using Vanderbilt ultrasoft pseudopotential [41] with cut-off energy of 380 eV. The atomic positions were optimized using the Broyden-Fletcher-Goldfarb-Shanno (BFGS) scheme [42]. The wave functions were converged to 10-5 eV/atom with maximum force and stress at 0.05 eV/Å and 0.1 GPa respectively. Electronic minimization during optimization

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Journal Pre-proof was carried out using the Pulay density mixing scheme [43]. The self-consistent field (SCF) convergence was set to 2×10-6 eV/atom. A 2x2x2 Monkhorst-Pack k-point grid was used to model the first Brillouin zone [44]. The bulk kaolinite unit cell was subjected to geometry optimization using the settings as given above, and the parameters calculated for the triclinic primitive cell were: a=5.21Å, b=9.00Å, c=7.48

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Å, and α=91.9°, β= 105.0°, γ=89.79°. The results were found to compare very well with the experimental results [45].

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2.3 Surface models

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Kaolinite mineral (Al2Si2O5(OH)4) has an almost perfect 1:1 layer structure consisting

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of two different aluminosilicate layers. One layer is composed of two sub-layers

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where one side has a gibbsite-type sheet with Al atoms coordinated octahedrally by

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oxygen atoms, and the other consists of a silica sheet having Si atoms tetrahedrally coordinated with oxygen atoms. These sheets are connected by the Van der Waals

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forces and hydrogen bonds formed between the hydroxyl groups of the Al layer and

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the oxygen atoms of the Si layer [46–48]. The predominant cleavage planes of kaolinite are the hydroxylated Al surface (0 0 1) and the (0 0 -1) surface terminating with silicoxane. While the tetrahedral Si surface is saturated and hydrophobic, the hydroxylated octahedral Al surface is hydrophilic. Therefore, the kaolinite (0 0 1) surface is of primary interest in adsorption studies [49, 50]. To determine the most exposed cleavage plane, the XRD studies of a natural kaolinite sample was carried out, and the pattern is shown in Fig. 1. The pattern is found to be mostly dominated by the kaolinite peaks indicating that it has minimal presence of other phases. The (0

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Journal Pre-proof 0 1) plane having a d value of 7.116 Å is represented by the peak having the highest intensity and hence, is the most exposed surface of kaolinite. Considering the surface (0 0 1) to be the most predominant plane as per published literature as well as the XRD pattern (Fig. 1), all the DFT and MD calculations of adsorption were

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done on this plane.

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Fig. 1. XRD pattern of natural kaolinite mineral (K: Kaolinite) In the present work, the surface model of kaolinite was constructed using a onelayer thick (2x1) slab consisting of six atomic sub-layers of ―O-Si-O-Al-O-H‖ exposing the (0 0 1) Al surface (Fig. 2a). The interlayer spacing was set to 15 Å. The periodic computational box for the kaolinite supercell used for all DFT simulations had a size of 10.43x9.00x20.28 Å. The periodic boundary conditions were applied in all directions.

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Fig. 2. (a) Side view of single layer kaolinite structure; (b) top view of kaolinite

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surface with sites for adsorption. The Al, O, Si and H atoms in kaolinite structure are

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indicated by purple, red, yellow and white colour respectively.

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Different possible adsorption sites on the kaolinite surfaces were considered for the study. The surface model, as shown in Fig. 2 (b) indicates the presence of a repeating unit constituting 6 Al atoms bonded to each other by O atoms. H atoms are bonded to the O atoms in two different fashions resulting in upright OH groups (O u) oriented primarily perpendicular to the surface plane and lying OH groups (O l) that are positioned parallel to the surface plane. The surface aluminium centres (Al centre) are arranged in two different crystallographic schemes. In one scheme, Al is connected to two Ou‘s and one Ol while the other one is characterized by the Al

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Journal Pre-proof atom bonded to two Ol‘s and one Ou. Therefore, some of the input configurations were formed taking in to account the possible interaction of the fluoride species with these two types of Al centres namely, Al 1 and Al 2, and two O l‘s and one Ou as indicated in Fig. 2 b. Other than these sites, the kaolinite surface has free spaces or cavities surrounded by six neighbouring Al atoms. This cavity site could also be a

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potential adsorption site for fluoride, considering it is surrounded by many surface

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functional groups and devoid of any steric hindrance. Therefore, in addition to the sites as mentioned above, the cavity was also considered as an adsorption site on

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kaolinite (0 0 1) surface (Fig. 2b).

) for the fluoride-kaolinite interaction was

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The total adsorption energy (

(1),

refers to the total energy of the geometry optimized adsorption

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where

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calculated using the following expression:

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configuration, whereas

and

refer to the total energy of the

adsorbate (HF) and the bare kaolinite surface, respectively. Negative adsorption energy implies more exothermic adsorption and stronger interaction of HF on the mineral surface. In addition to the determination of total energy difference, the interaction patterns of the sorbate on the mineral surface were also analyzed using the partial density of states, charge distribution calculation and electron density difference plots. It is to be noted that the density of states calculations give an

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Journal Pre-proof overview of the orbital overlapping while electronic charge distributions indicate the strength of the electrostatic interactions between two species. Mulliken charge analysis, in this work, was carried out to determine the electronic charge distributions while electron density difference plots helped in the visual interpretation of charge transfer.

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2.4 Molecular dynamics simulations Classical MD simulations were carried out using the Forcite module of Materials

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Studio 7.0. The Universal force field [51] and the single point charge (SPC) water

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model [52] were chosen for the simulations. The model consisted of a periodic

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(4x2x1) supercell having 8 unit cells of kaolinite with a total of 272 number of atoms.

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An amorphous orthorhombic cell containing 250 water molecules with a density of 1

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g/cm3 was constructed. The kaolinite-HF-H2O water system was obtained by packing these two systems using the layer building module followed by UFF based

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geometric optimization before carrying out the MD simulations. The simulation box

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generated had the dimensions: a= 20.86Å, b= 18.12Å and c= 31.80Å. MD simulations were performed under NVE ensemble for 200 ps. In MD, Newton's equations of motion were numerically integrated using the Verlet velocity algorithm [53] with a time step of 1.0 fs. The trajectory frame was recorded every 20 fs. The long-range electronic interactions were calculated by the Ewald summation method [54], and the atomic charges were assigned using the charge equilibration method [55]. All atoms were allowed to move freely during the simulations.

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Journal Pre-proof 3. Results and discussion 3.1 Mechanism of HF-kaolinite interaction Possible input complexes of HF on different sites of kaolinite (0 0 1) as shown in Fig. 2 b were subjected to geometric optimization. The corresponding adsorption energies were calculated using Eq. (1), and given in Table 1. All the values of the

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adsorption energies being negative, it is implied that the adsorption structures are stable, and the process is exothermic. The adsorption of HF on kaolinite (001)

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surface, as shown in Figure 3, was examined in six configurations such as (1) HF on

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Al centre 1 (complex A); (2) HF on Al centre 2 (complex B); (3) HF on O l1 (complex

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C); (4) HF on Ol2 (complex D); (5) HF on Ou1 (complex E) and (6) HF on cavity

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(complex F). The adsorption energies for the complexes where HF approaches Al

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centres or Ol are more or less the same (-19.5 to -20.7 kcal/mol). The interaction of HF at the cavity is found to be the strongest with an adsorption energy value of -

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22.183 kcal/mol. The HF molecule is found to be placed inside the cavity of the

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kaolinite surface while forming three hydrogen bonds resulting in a very stable configuration (Fig. 3 f). In contrast, the adsorption on Ou (Fig. 3e) is the weakest considering the total energy difference is only -3.71 kcal/mol. The overall bonding pattern, as observed in the complexes shown in Figure 3, is dominated by the hydrogen bonds (marked by dashed lines). In the case of the complex F, which deals with the most potent interaction of HF and kaolinite (0 0 1), HF is positioned in the cavity with the H atom of HF bonded to the surface O atom via one hydrogen bond, and the F atom of HF is bonded with surface H atoms

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Journal Pre-proof through two hydrogen bonds. Thus, the complex F is marked by three strong hydrogen bonds such as two F-H bonds having lengths of 1.667Å and 1.657Å, and one O-H bond of 1.276Å. The bond lengths are found to be comparable with the lengths reported in the literature for the adsorption of uranyl on kaolinite Al Octahedral (001) surface [56]. Similarly, the least favourable site for adsorption is

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found to be the upright OH on the kaolinite surface, where HF adsorption energy is

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the lowest among all the sites considered (Table 1). The corresponding configuration has two F-H hydrogen bonds having bond lengths of 1.873Å and 3.447Å and no H-O

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type hydrogen bond explaining a weak interaction.

Fig. 3. Optimized adsorption configurations of HF adsorption at different adsorption sites (a) and (b) Al centres, (c) and (d) O lying, (e) O upright and (f)

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Journal Pre-proof cavity site of kaolinite. Atoms of Al, O, H and F are shown in purple, red, white and light green respectively. Table 1. The adsorption energies (in kcal/mol), number of F-H/O-H hydrogen bonds and bond length (in Å) for different adsorption configurations of HF on the surface of kaolinite

O lying O lying O upright

2 1 2

2.132, 1.868 1.997, 2.010 1.873, 3.447

F

Cavity

2

1.667, 1.657

Adsorption Energy Ead(kcal/mol) -20.576 -19.504

1 1 0

1.380 1.391

-20.170 -20.767 -3.719

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1.276

-22.183

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3.2 Mulliken charge analysis

1.410 1.481

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C D E

1.975 1.949

O-H bond length (Å)

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A B

Number of H-O hydrogen bonds (nHO) 1 1

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F-H bond length (Å)

Al centre Al centre

Number of F-H hydrogen bonds (nFH) 1 1

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Adsorption site

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Complex Name

Charge transfer is one of the major contributors to the formation of hydrogen bond

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[57]. Therefore, Mulliken population analysis [58] was carried out to calculate the

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charges of each atom of the adsorbate and the (0 0 1) surface of kaolinite before and after adsorption, and the results are listed in Table 2. The comparison of original Mulliken charges of Al, O and H atoms of the bare kaolinite surface along with the isolated molecule of HF with that of the adsorbed complex gives an account of the charge transfer that happened during the interaction. The charge transfer of individual atoms (

), during the process of adsorption, was estimated using the

following equation. (2),

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where

and

denote the charges of

the Al, O and H surface atoms of kaolinite with fluoride adsorption and in the bare kaolinite, respectively. The charges of atoms in the isolated HF molecule and in adsorbed complexes were also evaluated. A positive value of charge transfer indicates a gain of electrons and a negative value denotes a loss of electrons during

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adsorption.

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Table 2. Mulliken charges of atoms before and after HF adsorption on kaolinite

Kaolinite surface atoms

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Fluoride species HF in adsorption complex

Center Al

Neighbori ng Al

Center Al connecting O O=-0.980 O=-1.060 O=-1.060 O=-0.980 O=-1.030 O=-1.060 O=-0.960 O=-1.060 O=-1.040 O=-0.980 O=-1.060 O=-1.070 O=-1.060 O=-1.040 O=-1.060

H=0.500 F=-0.660

Al=1.810

Al=1.830 Al=1.800

B

H=0.510 F=-0.640

Al=1.820

C

H=0.500 F=-0.640

Al=1.800

Al=1.810 Al=1.790 Al=1.820 Al=1.820 Al=1.810

D

H=0.490 F=-0.650

Al=1.820

Al=1.830 Al=1.810

E

H=0.640 F=-0.610

Al=1.800

Al=1.820 Al=1.820

F

H=0.480 F=-0.610

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A

Al=1.820 Al=1.810 Al=1.810 Al=1.810 Al=1.810

Neighboring Al connecting O O=-1.060 O=-1.070 O=-1.070 O=-1.040 O=-1.070 O=-1.060 O=-1.080

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Complex

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surfaces and charge transfer of surface atoms and fluoride species

O=-1.070 O=-1.070 O=-1.040

O=-0.960 O=-1.040 O=-1.070 O=-1.070 O=-1.050

Center Al connecting H H=0.450 H=0.460 H=0.470 H=0.460 H=0.430 H=0.420 H=0.430 H=0.460 H=0.430 H=0.450 H=0.460 H=0.460 H=0.450 H=0.420 H=0.450

Charge Transfer

Neighbo ring Al connecti ng H H=0.470 H=0.460 H=0.440 H=0.440 H=0.430 H=0.470 H=0.460

Fluoride species

Kaolinite surface atoms

ΔH=-0.14 ΔF=-0.02

H=0.430 H=0.460

ΔH=-0.15 ΔF=-0.01

H=0.410

ΔH=0.0 ΔF=0.03

H=0.470 H=0.430 H=0.450 H=0.440 H=0.460

ΔH=-0.16 ΔF=0.04

ΔAl=-0.01 ΔO=0.08 ΔH=0.07 ΔAl=-0.04 ΔO=0.1 ΔH=-0.03 ΔAl=-0.03 ΔO=0.07 ΔH=0.02 ΔAl=0.01 ΔO=0.05 ΔH=0.05 ΔAl=-0.01 ΔO=0.00 ΔH=-0.03 ΔAl=-0.03 ΔO=-0.03 ΔH=0.03

ΔH=-0.13 ΔF=0.00 ΔH=-0.14 ΔF=0.0

The Mulliken charge on the H atom of the isolated HF molecule was 0.64, and that

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Journal Pre-proof on the F atom was -0.64. The data given in Table 2 suggest that the Mulliken charges of the H atom are 0.50, 0.51, 0.50, 0.49 and 0.48 in the optimized complexes A, B, C, D and F respectively, which are lesser than the charge of H atom in the isolated HF. In contrast, in the case of complex E where the upright oxygen of the kaolinite surface was chosen as the adsorption site, the Mulliken charge on the H atom is found to be

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0.64. This is equal to the charge of H in the isolated HF, which indicates that the

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corresponding H atom has not taken part in any bond formation. This is consistent with the data presented in Table 1. On the other hand, the maximum charge transfer

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(0.16) of H in the case of complex F, which deals with the adsorption on the cavity

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site, indicates a strong interaction which is also supported by the corresponding

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hydrogen bond data as given in Table 1. The charge on F atom post adsorption is

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found to be to -0.66, -0.64, -0.64, -0.65, -0.61, and -0.61 in complexes A, B, C D, E and F respectively. This is an indication of loss of electrons for F atom during adsorption.

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On analysing the Mulliken charges of surface Al, O and H atoms of kaolinite after

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adsorption, it is observed that the charge transfers for Al atoms are negative, which suggests that Al acts as an electron donor. The charge transfer of O atoms at the cavity site is slightly negative, which suggests O acts as an electron donor in complex F. In all other cases, the charge transfer of O and H atoms are positive, as they act as the electron acceptor. The change in charges of Al atoms was in the range of 0.0 to -0.03, and for O and H atoms, it was in the range of -0.03 to 0.1 and 0.02 to 0.07 respectively in all the adsorption complexes. These data suggest that the charge transfer in the case of Al is less compared to O and H. The O and H atoms of the

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Journal Pre-proof surface hydroxyl group of kaolinite are near HF that induces a great change in the charges thereby a strong interaction. On the contrary, the influence of HF on the Al atoms which are present in the 2 nd or 3rd layer of the mineral surface is relatively weaker. When HF gets adsorbed on the cavity site, which is the most favourable adsorption configuration, the Mulliken charge transfer values are -0.16, 0.04, -0.03, -

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0.03 and 0.03 for H, F of HF and Al, O and H of kaolinite respectively. The charge

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transfer values in the case of the cavity site are higher in comparison to other adsorption sites, which is in tune with the strongest adsorption energy value of -

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22.183 kcal/mol and shortest hydrogen bond lengths of 1.667Å, 1.657Å and 1.276Å

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(Table 1). The comprehensive examination of the charge transfer data for HF

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adsorption complexes on kaolinite surface suggest that HF molecule gets

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preferentially adsorbed on the kaolinite surface following the order: Cavity-site > Olying-site 1 > Al-center-site 1 &2 > O-lying-site 2 > O-upright-site.

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3.3 Electron density difference

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The electron transfer between HF and the various adsorption sites of kaolinite surface were also studied vide the electron density difference plots shown in Fig. 4. The yellow and blue areas, as indicated in the figure, correspond to the electron density consumption and aggregation, respectively. All the isosurfaces have been set at 0.01 electrons/Å3. The electron density difference plots for all conformations shown in Fig. 4 represent the charge accumulation/depletion around the surface atoms and HF depicting the respective interactions. It is observed that the electron transfer in the case of the HF-adsorbed cavity site (Fig. 4f) is the most significant

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Journal Pre-proof one. A substantial electron density transfer between F and two surfaces H is visible. A similar electron density transfer between the H of HF and one surface O is also notable. In contrast, in the case of adsorption on the Ou site (Fig. 4e), the transfer is minimal that validates the lowest adsorption energy as calculated using DFT.

(b)

(c)

F H

F H

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H F

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Fig. 4. Electron density difference of HF adsorption at different adsorption sites (a)

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Al center 1, (b) Al centre 2, (c) O lying 1, (d) O lying 2, (e) O upright and (f) cavity site of kaolinite surface. 3.4 PDOS analysis To further understand the electronic interactions between HF with kaolinite (001) surface, the PDOS of the surface atoms in the most stable adsorption configuration (cavity site) was calculated. It is observed from Fig.5 that the PDOS peaks of the isolated HF mainly consists of 2s and 2p orbitals for fluorine and 1s orbitals of

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Journal Pre-proof hydrogen. In the case of adsorption, the s and p orbitals of fluorine move to left indicating lowering of energy level. Further, the intensities of the shifted peaks are found to be smaller compared to that of the isolated HF molecule. This phenomenon justifies the fact that the concerned orbitals take part in the interaction and the lowering of the total energy hints the stabilization of the same in the adsorbed

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complex [59–62]. A similar observation of lowering and shifting of the 1s orbital of

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H, justifying the participation of H in the H-bond formation, is observed in Fig. 5 b.

Fig. 5. PDOS curves for HF adsorption on (001) surface of kaolinite (a) F-s and p

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Journal Pre-proof orbitals before and after adsorption; (b) H-s orbitals before and after adsorption. (For interpretation of the references to colour in this figure, the reader is referred to

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the web version of this article.)

Fig. 6. PDOS curves for HF adsorption on cavity site of (001) surface of kaolinite (a) surface Al-s and p orbitals before adsorption; (b) surface O-s and p orbitals before adsorption; (c) surface H-s orbitals before adsorption; (d) surface Al-s and p orbitals after adsorption; (e) surface O-s and p orbitals after adsorption; (f) surface H-s

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Journal Pre-proof orbitals after adsorption (For interpretation of the references to colour in this figure, the reader is referred to the web version of this article.) The plots of PDOS for surface Al, O and H atoms of kaolinite (0 0 1) surface before and after HF adsorption are depicted in Fig. 6. It is observed that the s and p orbitals of Al have moved to deeper energy with a slight decrease in the intensities of the

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peaks. However, the reduction in the intensities of the p orbitals of O and s orbitals

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of H is relatively more significant. These findings confirm that the surface O and H

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atoms of kaolinite are more involved in the interaction with HF if compared to the

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Al atoms. This is attributed to the fact that the O and H atoms are placed in the top

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layer enabling them to take part in the interaction. To further understand the bonding mechanism of fluoride species on the cavity site

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of the kaolinite surface, the PDOS curves were obtained for HF along with the

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corresponding interacting surface H and O atoms. Fig.7a and 7b show the PDOS

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curves of the H and F atoms of HF molecule interacting with the surface H and O atoms of kaolinite, respectively, in the adsorbed complex. From Fig.7a, it is observed that there is overlapping of 2p orbitals of F atom of HF and 1s orbitals of H atoms of kaolinite surface. Similarly, from Fig 7b, it is found that there is overlapping of H s orbital of HF and O p orbitals of kaolinite. These results indicate a strong hybridization of F 2p with surface H 1s orbitals, and surface O p orbitals with H 1s orbital explaining the formation of hydrogen bonds in the adsorbed complex.

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Journal Pre-proof The PDOS plots for all other adsorption conformations are given as supplementary

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data.

Fig. 7. PDOS curves for HF adsorption on (001) Al surface of kaolinite (a) F and neighbouring H-s and p orbitals in HF adsorbed on cavity site; (b) H and neighbouring O-s and p orbitals in HF adsorbed on cavity site (For interpretation of

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Journal Pre-proof the references to colour in this figure, the reader is referred to the web version of this article.) 3.5. Molecular Dynamics The gas-phase DFT simulations could explain the difference in the interactions of HF on several identified adsorption sites on the kaolinite (0 0 1) surface. However, to

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study the different possible conformations in an aqueous medium, MD simulations were carried out on three important sites on the kaolinite surface, namely;

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aluminium center site, oxygen site and cavity site. The water molecules were

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allowed to move freely to interact with HF molecule and the hydroxyls groups of

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kaolinite surface. The ultimate conformations of MD simulations for HF adsorption

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on Al center, oxygen and cavity site are shown in Fig. 8. It is observed that water

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molecules form two types of hydrogen bonds, among themselves and with the surface hydroxyl groups. Similarly, the fluorine atom of HF molecule formed two

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types of hydrogen bonds, one with surface H atoms and the other with H atoms of

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surrounding water molecules. The H-bonds formed between F atom of HF and H atom of the surface hydroxyl group, F atom of HF and H atom of water, and H atom of HF and O atom of water were termed as F-H(surface), F-H(water) and HO(water) respectively. The ultimate conformations on Al center, oxygen and cavity sites of kaolinite surfaces had the final energy values of -24673.85, -24723.01 and 26969.35 kcal/mol respectively. These simulation results demonstrate that on the (0 0 1) surface of kaolinite, HF molecules adsorb more preferentially at the cavity site than any other adsorption sites. Three hydrogen bonds of different types such as1 F-

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Journal Pre-proof H (surface), 1 F-H (water) and 1 H-O (water) were formed for the conformation on Al center, which had the bond lengths of 2.377, 2.247 and 2.475 Å respectively. Similarly, on oxygen site, 3 F-H (surface) H-bonds of lengths 2.478, 2.404, 2.474 Å 3 F-H (water) H-bonds of lengths 2.228, 2.402, 2.246 Å and 1 H-O (water) H-bond with length 2.434 Å were formed. The cavity site displayed 3 F-H (surface) H-bonds of

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lengths 2.416, 2.148, 2.267 Å, 3 F-H (surface) H-bonds of lengths 2.193, 2.451, 2.323 Å,

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1 H-O (water) H-bond of length 2.391 Å. It is noticeable that the cavity site has more number of H-bonds with smaller bond lengths compared to other sites. Also, the

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visual inspection of the three systems (Fig. 8) leads to the conclusion that the layer of

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water molecules with HF over the cavity site is more ordered than its counterparts

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over Al center and surface O site. This behaviour is in agreement with the previous

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results of final energy values of the three systems calculated by the MD simulations. Overall, the MD simulation results of HF adsorption over kaolinite surface in the

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presence of water molecules indicate the cavity site to be the most stable adsorption

(a)

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site, which is in agreement with the DFT calculations. (b)

(c)

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Journal Pre-proof Fig. 8. The ultimate conformations of MD simulations for HF adsorption complexes of (a) Oxygen site (b) Al center site and (c) cavity site on (0 0 1) surface of kaolinite. 3.6 FTIR analysis To validate the fluoride adsorption on kaolinite, FTIR spectra of the kaolinite sample before and after being treated with fluoride were recorded and presented in Fig. 9.

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The spectra of the untreated sample depict the usual kaolinite bands at 3669-3673 cm-1 for inner Al-O-H stretching, 3645-3650 cm-1 for crystalline hydroxyl O-H

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stretching, 1105-1117 cm-1 for Si-O stretching in clay minerals, 784 cm-1 for OH

-p

deformations linked to Al, 542 cm-1 for Si-O-Al stretching, 475 cm-1 for Si-O

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vibrations, 465 cm-1 Si-O-Si bending [63]. The decrease in the peak intensities in the

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case of the fluoride-treated kaolinite especially in the band 3669-3675 cm-1 and 3645-

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3650 cm-1are visible. This finding suggests some possible involvement of the surface functional groups that has affected the Al-O-H and OH stretching, thereby

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confirming the adsorption of fluoride species on the kaolinite surface as revealed by

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the molecular modelling calculations.

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Journal Pre-proof Fig. 9 FTIR spectra of kaolinite before and after fluoride adsorption

4. Conclusion The mechanism of adsorption of fluoride on the basal kaolinite (0 0 1) surface was investigated using DFT simulations. The preferred adsorption configurations HF on different sites of kaolinite surface were determined through geometric optimization.

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The adsorption stability was found to be closely associated with the formation of

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hydrogen bonds, and electrostatic interactions between the surface O and H atoms,

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and fluoride. Through detailed analysis of PDOS projections, Mulliken populations,

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and electron density difference plots, it was obvious that fluorine atom and surface

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oxygen atoms of kaolinite act as the electron donors, whereas the surface hydrogen and aluminium atoms of kaolinite accept electrons during the adsorption process. F

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2p-H 1s orbital hybridization acted as the primary contributor for the formation of

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strong hydrogen bonds between F and H atoms. The cavity sites surrounded by six

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aluminium centres were found to be the most dominant adsorption site. Further, the adsorption behaviour in an aqueous environment was investigated using MD simulation. The bonding patterns of HF with water as well as the kaolinite surface were established. Notes The authors declare no competing financial interests.

Acknowledgements The study has been financially supported by CSIR-Institute of Minerals & Materials

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Journal Pre-proof Technology, Bhubaneswar. The authors are also thankful to the Director of the Institute for giving his consent to publish this article.

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Journal Pre-proof Highlights

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● Adsorption of HF on the kaolinite (0 0 1) surface was investigated by DFT-D simulation. ● Optimum adsorption configurations of HF on different possible sites are established. ● MD simulations reveal effect of solvent on the behaviour of HF adsorption. ● Complex structure, preferred adsorption position and adsorption bonding pattern were solved. ● Among all the adsorption sites considered, the ―cavity‖ site is found to offer the greatest adsorption strength.

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