Computer simulation of benzene , toluene and p-xylene adsorption onto activated carbon

1 Program of Post Graduation in Chemical Engineering, Federal University of Para, Rua Augusto Corrêa S/N, Guamá, 66075-900 Belém, Pará, Brazil. 2 LABEX/FEA (Faculty of Food Engineering), Federal University of Para, Rua Augusto Corrêa S/N, Guamá, 66075-900 Belém, Pará, Brazil. 3 Molécules Thérapeutiques in Silico, Université Paris Diderot, INSERM UMR-S 973, Sorbonne Paris Cité, 75013, Paris, France. 4 IESAM (Faculty of Computer Engineering), Av. Gov. José Malcher, 1148 Nazaré, Belém PA, 66055-260, Brazil.


INTRODUCTION
Monoaromatic hydrocarbons are among the major contaminants of groundwater.These contaminants such as benzene, toluene and xylenes (ortho-, meta-, para-), also called BTX, are powerful depressants of the central nervous system, presenting chronic toxicity, even in small concentrations.BTX compounds contaminate water and groundwater through effluents from petrochemicals and related industries.Also, fuel leakage from underground storage tanks of gasoline in urban areas and accidents in the transportation of petroleum fuels cause the release of this kind of pollutants into the environment (Torabian et al., 2010;Chakraborty and Coates, 2004).
Among the various methods of these pollutants removal, adsorption with activated carbon is one of the most widely used, since it has the ideal physicochemical properties to adsorb organic components components of low molecular weight, such as BTX.Adsorption is a separation process that has been used in the recovery, *Corresponding author.E-mail: wanessa.almeida712@yahoo.com.br.Tel: +5591983977916.
Author(s) agree that this article remains permanently open access under the terms of the Creative Commons Attribution License 4.0 International License concentration, separation and purification of compounds that can present high value-added.It is a process of mass transfer in which one or more compounds present in a phase (liquid, vapor or gas), are adhered on the surface of a solid (Yang, 2003;Ghiaci et al., 2004;Ahmaruzzaman, 2008).
For this process, activated carbon remains one of the most important microporous adsorbents from the industrial point of view.It presents very complex surface characteristics (porosity and surface chemistry), with pore size ranging from micropores (diameter less than 2 nm) to macropores (diameter more than 50 nm).The volumes of micropores range from 0.15 to 0.6 cm 3 /g and exhibits a large variety of surface groups, impurities and irregularities.The surface characteristics of activated carbon depend on the raw material used and the mode of activation (Wibowo et al., 2007;Yalçın and Sevinc, 2000).
Simulation in computational environments allows researchers to be able to understand the behavior of matter on a scale that cannot be naturally observed.Computational modeling can be used in the fields of computational chemistry, drug design and computational biology.It offers not only ways to solve mathematical calculations, but also, and above all, the creation of virtual laboratories in which studies can be carried out very close to reality.Thus, the understanding and observing of a problem can be done reliably and effectively (Meller, 2001;Rangel-Vázquez, 2015;Ganesan et al., 2017).
In this context, since the experimental process of adsorption of BTX is well known (Wu et al., 2000;Shim and Kim, 2010), the present work proposed a practical approach of molecular modeling as a tool to study and confirm the relations between the structure and activity of the activated carbon under analysis, regarding mainly the adsorption process of the compounds: benzene, toluene and p-xylene on the activated carbon surface.

Design of the main structure of carbon
From the primary model created by Bourke et al. (2007), a new structure was generated by computer modeling, using the software MarvinSketch 6.0.0, which provided its two-dimensional structure.
This model was optimized by DFT calculation, at BELYP theory level and 6-31G base by the software Gaussian 09.The files obtained through optimization were used to generate the data of three-dimensional coordinates, topology, loads, angles, bonds and dihedral angles, using the FF99SB force field and the antechamber code of the package AMBER 13 (Lindorff-Larsen et al., 2010).The same procedure was performed for benzene, toluene and p-xylene structures.
From the unit cell generated, a complex formed by double layers of carbon together with the molecules of each pollutant was created.The pore size was equal to 8Å and the plate spacing was equal to 20Å, as suggested in the work of Lima et al. (2012).
da Costa et al. 1177 Solvation, minimization, heating and molecular dynamics In order to simulate a system that was as close as possible to the reality of an experimental adsorption test, the system was solvated with an octahedral TIP3P water box to simulate the aqueous environment (Mark and Nilsson, 2001).The package ambertools version 13 (Case et al., 2012) was used to construct the mesopore model and the adsorption system containing carbon and pollutants.
The system underwent a minimization process divided into 4 stages: the first one that minimizes the water molecules; the second that considers the hydrogens of the structure; the third that minimizes the hydrogens + water and the last one that minimizes all atoms (Case et al., 2005).
The heating stage simulated the temperature increase from 0 to 25°C and was divided into five stages with increment of 5°C and 500 ps (picoseconds) of simulation in each step, and its information was collected every 50 ps.The structure was then subjected to system equilibrium for 500 ps so that the dynamics process could start.

Molecular dynamics
The molecular dynamics stage simulated the state of the system in instants from 0 to 30 ns (nanoseconds) divided into five steps with increment of 2 ns in each.For this, the AMBER FF99SB force field was used.This step was performed with the module sander also included in the software AMBER 13 (Salomon-Ferrer et al., 2013), with information collected every 10 ps.The results, a threedimensional representation of the imposed conditions, are images obtained and rendered by the software VMD (Humphrey et al., 1996;Stone et al., 2001).Simulations of molecular dynamics provide information on molecular mobility at an atomic level (Case et al., 2005).Information of temperature, pressure and total energy of the system were obtained.

RESULTS AND DISCUSSION
Figure 1 shows the main structure and the minimized model of the carbon obtained from the model postulated by Bourke et al. (2007).Figure 2 shows the minimized structures of benzene, toluene and p-xylene.Geometric optimization alters the molecular geometry to decrease the energy of the system and produces a more stable conformation.The minimization of energy before the molecular dynamics, besides taking the structure to a minimum of energy, was performed with the intention of removing any "bad contact" created by solvation (due to ionic dissociation of water molecules) (Ivone et al., 2003;Jo et al., 2009).
Regarding the systems solvation, although there are other models, TIP3P is probably the most used because of the good dynamic and thermodynamic properties that it provides for most force fields (Jorgensen et al., 1983;Ganesan et al., 2017).The solvated model simulates the adsorption conditions in aqueous medium.
In Figure 3, comparing the initial (a) and the final state (b), it is possible to observe that there was interaction between the molecules of the pollutants and the surface of the carbon.According to Boehm (2007), functional groups and delocalized electrons are factors that determine the chemical character (acidic or basic) of the  activated carbon surface, since oxygen may be present in various forms.In the case of the carbon structure under analysis, the ether, carbonyl and lactone groups (Figure 4) are present, which make the structure more acidic, apolar and consequently, it ends up exhibiting a negative surface charge.According to Wibowo et al. (2007), carbons with few oxygenated surface groups have higher adsorption capacity.
The non-polar character of the surface of the activated carbon is a preponderant factor in the adsorption of nonpolar molecules, and can be increased by the appropriate modification of the chemical nature of the carbon surface (e.g.acid treatment).Due to its non-polarity and for having a larger volume of micropores, carbon adsorbs more strongly the apolar or weakly polar organic molecules, such as the pollutants benzene, toluene and p-xylene (Yang, 2003).With the tool xmgrace from AMBER 13 package (Zhang, 2009), the graphs of total energy vs. time, pressure vs. time and temperature vs. time were obtained from the data obtained in the dynamics files (Figures 5 and 6).
The graph energy vs. time (Figure 5) demonstrated that all adsorption processes analyzed are exothermic.This occur because when the molecule is attracted to the surface of the adsorbent, forming an intermolecular bond, there is a need to release the energy it had in the medium (Ruthven, 1984).Figure 5 also shows how the energy increases considerably during the equilibrium stage (beginning of the curve), then there is a slight decrease until its stabilization.This stabilization begins along with the dynamics process.The energy varies very little throughout this process.The mean values of energy of these processes were -57.62 x 10 3 Cal/mol for the benzene's system, -89.52 x 10 3 Cal/mol for the toluene's system and -82.35 x 10 3 Cal/mol for the p-xylene's system.
Just like in a real process conducted in normal conditions, the system was programmed so that the temperature and pressure remained constant throughout the dynamics process.Figure 6a and b shows the stability of these parameters.

Conclusion
Studies that focus on processes simulations are important to reduce costs, avoid problems, optimize and control changes in the system.The software used proved to be efficient at all stages of this work.Sometimes, the adsorption success is believed to be due only to the microporous structure of the activated carbon; however, this study showed that also, the ether, lactone and carbonyl groups present in the carbon structure under analysis are fundamental for adsorption of apolar compounds, as is the case of the pollutants: benzene, toluene and p-xylene.This study allowed a better    understanding of the phenomenon of BTX adsorption on activated carbon.

Figure 1 .
Figure 1.Two-dimensional (a) and minimized three-dimensional (b) models of activated carbon.

Figure 4 .
Figure 4. Functional groups found on the surface of the carbonether (a), carbonyl (b) and lactone (c).

Figure 5 .
Figure 5. Representation of energy variation over time for systems containing benzene (green line), toluene (black line) and p-xylene (red line) from the equilibrium step to the last dynamic process.

Figure 6 .
Figure 6.Representation of variation of pressure with time (a) and temperature with time (b) for all systems during the entire dynamics process.Benzene (green line), toluene (black line) and p-xylene (red line).