Molecular Simulation of Naphthalene, Phenanthrene, and Pyrene Adsorption on MCM-41

International Journal of Molecular Sciences

Article Molecular Simulation of Naphthalene, Phenanthrene, and Pyrene Adsorption on MCM-41

Xiong Yang 1,2,† , Chuanzhao Zhang 3,†, Lijun Jiang 1,†, Ziyi Li 1,2,*, Yingshu Liu 1,2, Haoyu Wang 3, Yi Xing 1,2 and Ralph T. Yang 4

1 School of Energy and Environmental Engineering, University of Science and Technology Beijing, Beijing 100083, China; [email protected] (X.Y.); [email protected] (L.J.); [email protected] (Y.L.); [email protected] (Y.X.) 2 Beijing Higher Institution Engineering Research Center of Energy Conservation and Environmental Protection, Beijing 100083, China 3 College of Biochemical Engineering, Beijing Union University, Beijing 100023, China; [email protected] (C.Z.); [email protected] (H.W.) 4 Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109, USA; [email protected] * Correspondence: [email protected]; Tel.: +86-10-62332743 † These authors contributed equally to this work.

Received: 28 December 2018; Accepted: 31 January 2019; Published: 3 February 2019

Abstract: The adsorption of three typical polycyclic aromatic hydrocarbons (PAHs), naphthalene, phenanthrene, and pyrene with different ring numbers, on a common mesoporous material (MCM-41) was simulated based on a well-validated model. The adsorption equilibriums (isotherms), states (angle distributions and density profiles), and interactions (radial distribution functions) of three PAHs within the mesopores were studied in detail. The results show that the simulated isotherms agreed with previous experimental results. Each of the PAHs with flat molecules showed an adsorption configuration that was parallel to the surface of the pore, in the following order according to the degree of arrangement: pyrene (Pyr) > phenanthrene (Phe) > naphthalene (Nap). In terms of the interaction forces, there were no hydrogen bonds or other strong polar forces between the PAHs and MCM-41, and the O–H bond on the adsorbent surface had a unique angle in relation to the PAH molecular plane. The polarities of different H atoms on the PAHs were roughly the same, while those of the C atoms on the PAHs decreased from the molecular centers to the edges. The increasing area of the π-electron plane on the PAHs with the increasing ring number could lead to stronger adsorption interactions, and thus a shorter distance between the adsorbate and the adsorbent.

Keywords: polycyclic aromatic hydrocarbons (PAHs); molecular simulation; grand canonical Monte Carlo (GCMC); adsorption; mesoporous material

1. Introduction Polycyclic aromatic hydrocarbons (PAHs) generally refer to hydrocarbons that have two or more benzene rings [1,2]. PAHs, commonly known as carcinogens, mutagens, teratogens, and bioaccumulators, can cause great damage in humans and the environment [3–8]. They are also a part of the atmospheric particulate pollutant PM2.5 [9]. In 1976, the United States Environmental Protection Agency (EPA)’s list of 129 “priority pollutants” included 16 types of PAH compounds [10]. Low-ring PAHs such as naphthalene (Nap), phenanthrene (Phe) and pyrene (Pyr) are the main components in the atmosphere [11]. The adsorption method has become one of the important ways to purify PAHs due to its high efﬁciency and low energy consumption [12–14]. Ordered mesoporous adsorbents have shown high adsorption capacities for their tailorable pore systems, especially in the

Int. J. Mol. Sci. 2019, 20, 665; doi:10.3390/ijms20030665 www.mdpi.com/journal/ijms Int. J. Mol. Sci. 2019, 20, 665 2 of 13 adsorption of molecules such as PAHs [15,16]. Mastering the adsorption mechanism of PAHs on mesoporous materials is critical to optimize the material’s performance. Molecular simulation has obvious benefits in the adsorption isotherm calculation and adsorption state analysis of adsorption molecules. It can analyze the adsorption mechanism [17,18] and the nature of action in depth, and it has been widely used in adsorbent selection and design [19,20]. MCM-41 [21–23] is a typically ordered mesoporous adsorbent from a family of silicate and alumosilicate solids that has been employed to investigate the adsorption phenomena on various gases [24,25]. Since the emergence of MCM-41, a large number of adsorption-related material structures and physical and chemical properties have been analyzed [23,26]. Molecular simulations with MCM-41 have been conducted with the Monte Carlo (MC) method to calculate the various gas adsorption conditions [27–31]. The MCM-41 model evolved from earlier simple models [32–36] (e.g., single-layer cylindrical atomic wall, and the rough model of simple potential function), to later all-atom models [37,38] (e.g., carving out models in amorphous silica, and ensuring the bonding relationship between silicon and oxygen atoms), and recent templated synthesis models for restoring real synthetic conditions [39,40]. Among them, the carving-out modeling method is easier to implement, and calculations based on this model have been widely used for gas adsorption because of the good agreement with experimental results. Jing et al. [41] discussed the adsorption effects of two structural forms of unit cell models, and provided ideas for improving computational efficiency. Ugliengo et al. [42] optimized the MCM-41 structure by the density functional method. Pajzderska et al. [27] and Coasne et al. [43] studied the surface roughness, pore shape, and surface undulation of mesoporous channels, and made corresponding structural improvements. The above works have important significance in the improvement of the overall structure, surface morphology, and adsorption sites of the MCM-41 model. With the development of molecular simulation technology, MCM-41 has made great progress in the field of adsorption separation as a typical mesoporous molecular sieve [28,29,44,45]. With regard to small molecule gas adsorption, Bonnaud et al. [46] characterized and analyzed the adsorption state and the diffusion phenomenon of water molecules in the pores of MCM-41 [46]. In the adsorption simulation of low-volatility compounds and macromolecular organics such as drugs, the adsorption characteristics of ibuprofen [47], tert-butanol [48], and neopentane [49] have been studied, as well as the influence of water molecules on adsorption [50,51]. Coasne et al. [30,31,52] studied the role of organic molecules such as benzene and toluene in the pores based on the combination of the angle of the benzene ring plane and the density profile. Compared with common small molecular gases, macromolecular organic compounds have more obvious molecular structures such as prominent geometric skeletons, polypolar sites, and deformations. It is beneficial to grasp the distribution of these properties in a spatial capacity to judge the state of the molecules in the pores and analyze the adsorption mechanism. At present, there are few simulation studies on the adsorption of PAHs. Analyses of the adsorption states and the adsorption mechanism are relatively lacking. Studying the adsorption of typical PAHs such as Nap, Phe, and Pyr on mesoporous adsorbents is helpful to understand the adsorption mechanism and its application in the removal of PAHs. Analysis of the state of molecules inside the adsorbent is extremely important for research and the improvement of adsorption efficiency. In this paper, adsorption of the three PAHs Nap, Phe, and Pyr will be simulated based on the grand canonical Monte Carlo (GCMC) method. The potential adsorption mechanism will be discussed based on the adsorption states of the three molecules in the pores.

2. Results and Discussion

2.1. Adsorption Equlibrium Figure1 provides the GCMC simulation and experimental results [ 53,54] of the adsorption isotherms of Nap, Phe, and Pyr on MCM-41 at 398 K (normal flue gas temperature). The isotherms Int. J. Mol. Sci. 2019, 20, 665 3 of 13 from the simulation calculation were in good agreement with the experimental values, with the Int. J. Mol. Sci. 2019, 20, x FOR PEER REVIEW 3 of 13 following order according to the adsorption capacity: Pyr > Phe > Nap, corresponding to the inverse sequencesequence ofof thethe volatilityvolatility ofof thethe PAHPAH molecules. molecules. TheThe resultsresults indicateindicate thatthat thethe currentcurrent MCM-41MCM-41 unitunit cellcell modelmodel withwith thethe calculationcalculation conditioncondition waswas reasonablereasonable andand cancan trulytruly reflectreflect thethe adsorptionadsorption ofof PAHsPAHs atat lowlow concentrations.concentrations. TheThe threethree isothermsisotherms ofof thethe PAHsPAHs belongedbelonged toto TypeType II accordingaccording toto thethe IUPICIUPIC classificationclassification [[55].55]. BecauseBecause thethe PAHPAH concentrationsconcentrations werewere low,low, allall ofof thethe isothermsisotherms diddid notnot reachreach thethe −1 saturatedsaturated adsorptionadsorption capacity. Th Thee adsorption adsorption capacity capacity Q Q (mmmol·kg (mmmol·kg−1) can) can be bedetermined determined with with the theformula: formula: Q = 1000 ∗ NPAH/Madsorbent, (1) 𝑄 = 1000 ∗𝑁 /𝑀, (1) −1 where NPAH is the number of PAHs in the pores of MCM-41 and Madsorbent (g·mol ) is the molar mass 𝑁 𝑀 −1 ofwhere the adsorbent. is the number of PAHs in the pores of MCM-41 and (g·mol ) is the molar mass of the adsorbent.

FigureFigure 1.1. Adsorption isotherms for Nap,Nap, Phe,Phe, andand PyrPyr onon thethe MCM-41MCM-41 modelmodel comparedcompared withwith experimentexperiment resultsresults at at 398K.398K. ((aa)) Nap; Nap; ((bb)) Phe;Phe; ((cc)) Pyr;Pyr; Key:Key: red,red, grandgrand canonicalcanonical MonteMonte CarloCarlo (GCMC);(GCMC); black,black, experiment.experiment.

FigureFigure2 presents2 presents a diagram a diagram of PAH of adsorptionPAH adsorption as an instantaneous as an instantaneous map under map different under pressures, different andpressures, it reﬂects and the it reflects overall the distribution overall distribution state of PAH state molecule of PAH adsorptionmolecule adsorption in the cylindrical in the cylindrical channel. PAHchannel. pore PAH adsorption pore adsorption was mainly was based mainly on based single-layer on single-layer adsorption, adsorption, and this alsoand indicatedthis also indicated that the isothermthat the isotherm belonged belonged to Type I. Itto can Type also I. beIt can observed also be that observed the PAHs that were the adsorbed PAHs were on the adsorbed surface on of thethe mesoporoussurface of the channel mesoporous in a tiled channel manner. in a This tiled will manner. be discussed This will in be the discussed following in section. the following section. 2.2. Adsorption State

2.2.1. Angle Distribution It was important to explore the angular distribution of PAH adsorption in the pores since the PAHs exhibited a planar molecular structure. Thus, the adsorption state and conﬁguration of PAHs on the pore surfaces was statistically obtained. Here, the angle between the plane normal vector of the adsorbed PAHs and the axis direction of the cylindrical channel was deﬁned as θ (theta). Figure3 provides the angle distributions of Nap, Phe, and Pyr adsorption on MCM-41. The θ of the three PAH molecules as they adsorbed in the pore was mainly distributed between 80 and 90 degrees, and the probability of θ between 0 and 15 degrees was close to zero. This indicates that there are no PAHs perpendicular to the axial direction of the channel; that is to say, the PAHs are mainly adsorbed on the surface of the mesoporous channel in a tiled manner, which is consistent with Figure3. The degree of the parallel distribution (θ tends to 90◦) of adsorbate over the channel surface increased with increasing PAH weight, indicating a more stable interaction between the adsorbate and adsorbent.

Int. J. Mol. Sci. 2019, 20, 665 4 of 13 Int. J. Mol. Sci. 2019, 20, x FOR PEER REVIEW 4 of 13

(a) (b) (c)

Figure 2. Typical configurations conﬁgurations of Nap, Phe and Pyr adsorbed at 398K in the cylindrical nanopore of the model MCM-41. ( a) Nap; ( b) Phe; ( c) Pyr, Key:Key: Si, yellow; O, red; H,H, white;white; C,C, grey.grey.

2.2. AdsorptionIn order to State explain the orientation of the adsorbate molecules in the pores of MCM-41, an order index, S, was deﬁned as follows [30]: 2.2.1. Angle Distribution 3 1 S = cos2 θ − (2) It was important to explore the angular distribution2 2 of PAH adsorption in the pores since the PAHs exhibited a planar molecular structure. Thus, the adsorption state and configuration of PAHs − whereon the Spore tended surfaces to be was0.5 statistically when the adsorbateobtained. moleculesHere, the angle tended between to be parallel the plane to the normal surface, vector and of S thetended adsorbed to be 1 PAHs when and the adsorbatethe axis direction molecules of tendedthe cylindrical to be perpendicular channel was to defined the surface. as θ (theta). The statistical Figure 3results provides of the the S valuesangle distributions of the three PAHs of Nap, are Phe, shown and in Pyr Table adsorption1. The S values on MCM-41. of Phe and The Pyr θ of were the closethree − PAHto 0.4, molecules indicating as they that theadsorbed two molecular in the pore planes was mainly were close distributed to being between parallel to80 theand axial 90 degrees, direction and of the probability of θ between 0 and 15 degrees was close to zero. This indicates that there are no PAHs

Int. J. Mol. Sci. 2019, 20, 665 5 of 13 the channel. The S value of Nap was only −0.2, indicating that the tiling property of the adsorption conﬁguration on the surface was weak, and there was less molecular arrangement order compared to that of Phe and Pyr. The S values of the three PAHs did not reach the ideal value of −0.5, probably Int.because J. Mol. theSci. 2019 thermal, 20, x motionFOR PEER of REVIEW the molecule at a higher temperature of 398 K caused local perturbations 5 of 13 of the molecule at the adsorbed position. In this study, the adsorbates were at low gas concentrations, perpendicularand monolayer to adsorption the axial direction dominated. of the Three channel; non-polar that is PAHto say, molecules the PAHs exhibited are mainly relatively adsorbed weak on thephysical surface adsorption of the mesoporous properties channel on the surface.in a tiled Therefore,manner, which the angle is consistent and position with Figure of their 3. distribution The degree ofmay the also parallel be disturbed distribution by the (θ interaction tends to 90°) of the of surrounding adsorbate over adsorbate the channel molecules. surface increased with increasing PAH weight, indicating a more stable interaction between the adsorbate and adsorbent.

Figure 3. Angle distribution of Nap, Phe, and Pyr on the MCM-41 model. Key: black, black, Nap; Nap; red, red, Phe; Phe; blue, Pyr. Table 1. Order parameter (S) for the molecular direction of Nap, Phe, and Pyr. In order to explain the orientation of the adsorbate molecules in the pores of MCM-41, an order index, S, was defined as followsAdsorbate [30]: S S Values Corresponding States 3 1 NapS= −cos0.1843 𝜃− 0 disordered(2) Phe 2−0.3568 2 1 vertical where S tended to be −0.5 whenPyr the adsorbate−0.3629 molecules−0.5 tended parallel to be parallel to the surface, and S tended to be 1 when the adsorbate molecules tended to be perpendicular to the surface. The statistical results2.2.2. Density of the S Profile values of the three PAHs are shown in Table 1. The S values of Phe and Pyr were close to −0.4, indicating that the two molecular planes were close to being parallel to the axial direction of the channel.The density The profileS value can of Nap be used was to only infer −0.2, the averageindicating spatial that positionthe tiling of property the molecules of the inadsorption the pores configurationby overlapping on the the profiles surface of was the weak, single-peak and there type, was symmetric less molecular double-peak arrangement type, and order irregular compared type, whichto that canof Phe be usedand Pyr. to further The S analyzevalues of the th adsorption.e three PAHs Figure did 4not shows reach plots the ideal of the value central of density−0.5, probably profile becauseof the three the PAHs thermal adsorbed motion on MCM-41.of the molecule The abscissa at a indicated higher temperature the radial direction of 398 of K the caused mesoporous local perturbationscylindrical channel, of the molecule and the origin at the representedadsorbed position. the center In this of thestudy, channel. the adsorbates The maximum were at distancelow gas wasconcentrations, almost equal and to monolayer the radius ofadsorption the pores domina in the MCM-41ted. Three model non-polar (around PAH 19 Å)molecules in our simulation; exhibited relativelythe further weak away physical the molecule adsorption was from properties the center on the of thesurface. pores, Therefore, the closer the it wasangle to and the edgeposition of the of theirpores. distribution For the special may structurealso be di ofsturbed the three by the PAHs interaction (two or moreof the benzene surrounding ring structures), adsorbate molecules. the density distributions of different geometric centers on Nap, Phe, and Pyr, as shown in Figure5, were refined to Table 1. Order parameter (S) for the molecular direction of Nap, Phe, and Pyr. furtherInt. J. Mol. gauge Sci. 2019 the, 20 state, x FOR of PEER adsorbed REVIEW molecules. 6 of 13

Adsorbate S S Values Corresponding States Nap −0.1843 0 disordered Phe −0.3568 1 vertical Pyr −0.3629 −0.5 parallel

2.2.2. Density Profile The density profile can be used to infer the average spatial position of the molecules in the pores by overlapping the profiles of the single-peak type, symmetric double-peak type, and irregular type, which can be used to further analyze the adsorption. Figure 4 shows plots of the central density profileFigure of the 4.4. DensityDensitythree PAHs proﬁlesprofiles adsorbed for for difﬁdent diffident on centers MCM-41. centers in (ina) Nap;(Tha) eNap; (abscissab) Phe;(b) Phe; (c )indicated Pyr (c) at Pyr 398K atthe on398K radial the on MCM-41 thedirection MCM-41 model. of the mesoporousmodel. cylindrical channel, and the origin represented the center of the channel. The maximum distance was almost equal to the radius of the pores in the MCM-41 model (around 19 Å) in our simulation; the further away the molecule was from the center of the pores, the closer it was to the edge of the pores. For the special structure of the three PAHs (two or more benzene ring structures), the density distributions of different geometric centers on Nap, Phe, and Pyr, as shown in Figure 5, were refined to further gauge the state of adsorbed molecules.

Figure 5. Graphical site description of polycyclic aromatic hydrocarbon (PAH) molecules. (a) naphthalene; (b) phenanthrene; (c) pyrene; Key: CoreX, the benzene ring center (X is the number); yellow, symbol of different atoms.

The molecules of Nap, Phe, and Pyr are stable planar molecules, and there are three special states in the adsorption process [49], which are in parallel with the molecular plane, perpendicular to the surface of the molecular sieve, and exist at a unique angle to the surface. These three different states correspond to three different interactions: the weak interaction between the surface of the adsorbent and the molecular plane, the strong interaction between the surface of the adsorbent and the polar edges of the molecules, and the combination of the two effects. Figure 4 shows that the density distributions of all centers did not exhibit obvious symmetrical bimodal phenomena. The larger the molecular radius, the farther the distance of the density distribution peak corresponding to the center of the pore (the corresponding distances from the center of benzene rings to the central axis of the pore were 14.35 Å, 14.65 Å, and 14.75 Å), and the stronger the interaction between the molecule and the surface. The peak position relationship of the density profile between the adsorbate molecules Core and CoreX illustrates the following three points. First, with increasing adsorbate molecular size, there was a greater coincidence that the peak position of the density was located between the centers of the benzene ring and the center of the molecule. This corresponded to an increase in the stability of the molecular plane with the edge of the PAHs likely to be deflected by the surface polarity interaction. Second, the two sub-centers of the Nap molecule were partially offset from the peak position of the density at the center, indicating that there was a significant tilt angle between the Nap molecule and the surface of the pore. Third, the difference between the density peak positions of the centers of the benzene ring and the center of the Phe and Pyr molecules was small. It can be concluded from the statistical results of the previous angle distributions that the parallelism between the molecular planes and the surface of the pore was satisfactory.

2.3. Adsorption Interactions The radial distribution function (RDF, g(r)) is a function of the distance between different particles (molecules or atoms). It is the ratio of the local density to the average density, which indicates the density variation of the particle in space. The RDF method was employed to further analyze the distribution distance between the adsorption sites of the PAHs (rings or atoms) and the

Int. J. Mol. Sci. 2019, 20, x FOR PEER REVIEW 6 of 13

Int. J. Mol.Figure Sci. 4.2019 Density, 20, 665 profiles for diffident centers in (a) Nap; (b) Phe; (c) Pyr at 398K on the MCM-416 of 13 model.

Figure 5.5.Graphical Graphical site site description description of polycyclic of polycyclic aromatic aromatic hydrocarbon hydrocarbon (PAH) molecules. (PAH) (molecules.a) naphthalene (a); (naphthalene;b) phenanthrene; (b) phenanthrene; (c) pyrene; Key: (c CoreX,) pyrene; the Key: benzene CoreX, ring the center benzene (X is thering number); center (X yellow, is the symbolnumber); of differentyellow, symbol atoms. of different atoms.

The molecules of Nap, Phe, and Pyr are stable plan planarar molecules, and there are three special states in the adsorptionadsorption process [[49],49], which are inin parallelparallel withwith thethe molecularmolecular plane,plane, perpendicularperpendicular to the surface of the molecular sieve, and exist at a unique angle to the surface. These three different states correspond to three different interactions: the weak interaction between the surface of the adsorbent and the molecular plane, the strong interaction betweenbetween the surface of the adsorbent and the polar edges of the molecules, and the combination ofof thethe twotwo effects.effects. Figure4 4 shows shows thatthat thethe densitydensity distributionsdistributions ofof allall centerscenters diddid notnot exhibitexhibit obviousobvious symmetricalsymmetrical bimodal phenomena. The The larger larger the the molecular molecular ra radius,dius, the the farther farther the the distance distance of the density distribution peak peak corresponding corresponding to to the the center center of th ofe thepore pore (the corresponding (the corresponding distances distances from the from center the centerof benzene of benzene rings to rings the central to the centralaxis of the axis pore of the we porere 14.35 were Å, 14.3514.65 Å,Å, 14.65and 14.75 Å, and Å), 14.75 and the Å), stronger and the strongerthe interaction the interaction between betweenthe molecule the molecule and the surface. and the surface.The peak The position peak positionrelationship relationship of the density of the densityprofile between profile between the adsorbate the adsorbate molecules molecules Core and Core Co andreX CoreXillustrates illustrates the following the following three points. three points. First, First,with increasing with increasing adsorbate adsorbate molecular molecular size, size,there there was wasa greater a greater coincidence coincidence that that the thepeak peak position position of ofthe the density density was was located located between between the thecenters centers of the of benzene the benzene ring ringand the and center the center of the of molecule. the molecule. This Thiscorresponded corresponded to an to increase an increase in the in thestability stability of the of the molecular molecular plane plane with with the the edge edge of of the the PAHs PAHs likely to be deflecteddeflected byby thethe surfacesurface polaritypolarity interaction.interaction. Second, the two sub-centers of the Nap molecule were partially offset from the peak position of thethe density at the center, indicating that there was a significantsignificant tilt angle between the Nap moleculemolecule andand thethe surfacesurface ofof thethe pore.pore. Third, the difference between thethe densitydensity peakpeak positions positions of of the the centers centers of of the the benzene benzene ring ring and and the the center center of the of the Phe Phe and and Pyr moleculesPyr molecules was small.was small. It can beIt concludedcan be concluded from the from statistical the resultsstatistical of theresults previous of the angle previous distributions angle thatdistributions the parallelism that the between parallelism the molecular between planesthe molecular and the surfaceplanes ofand the the pore surface was satisfactory. of the pore was satisfactory. 2.3. Adsorption Interactions 2.3. AdsorptionThe radial Interactions distribution function (RDF, g(r)) is a function of the distance between different particles (molecules or atoms). It is the ratio of the local density to the average density, which indicates the The radial distribution function (RDF, g(r)) is a function of the distance between different density variation of the particle in space. The RDF method was employed to further analyze the particles (molecules or atoms). It is the ratio of the local density to the average density, which distribution distance between the adsorption sites of the PAHs (rings or atoms) and the active atoms indicates the density variation of the particle in space. The RDF method was employed to further on the adsorbent surface, such as O and H. The RDF between the PAH molecules and different sites analyze the distribution distance between the adsorption sites of the PAHs (rings or atoms) and the of the mesoporous surface is shown in Figure6. The distances corresponding to the RDF peaks are summarized in Table2. Int. J. Mol. Sci. 2019, 20, x FOR PEER REVIEW 7 of 13

active atoms on the adsorbent surface, such as O and H. The RDF between the PAH molecules and Int. J. Mol. Sci. 2019, 20, 665 7 of 13 different sites of the mesoporous surface is shown in Figure 6. The distances corresponding to the RDF peaks are summarized in Table 2.

(1)

(2)

(3)

(4)

FigureFigure 6. 6.Radius Radius distribution distribution function function for for ( a(a)) Nap, Nap, ( b(b)) Phe, Phe, and and ( c(c)) Pyr. Pyr. ((11)) OO atomsatoms onon MCM-41MCM-41 andand H atomsH atoms on PAHs, on PAHs, (2) H (2 atoms) H atoms on MCM-41 on MCM-41 and Cand atoms C atoms on PAHs, on PAHs, (3) H ( atoms3) H atoms on MCM-41 on MCM-41 and centers and oncenters PAHs, on and PAHs, (4) O and atoms (4) O on atoms MCM-41 on MCM-41 and centers and oncenters PAHs. on PAHs.

TableTable 2. Distances 2. Distances between between the theH or H O or atom O atom of MC ofM41 MCM41 model model and CoreX and CoreX of the of three the threePAHs. PAHs.

Distance (Å) Type Distance (Å) Type NapNap Phe Phe Py Pyrr

OOMCM41MCM41–H–HPAHsPAHs 3.433.43 3.63 3.63 3.53 3.53 HHMCM41MCM41–Core–CorePAHsPAHs 4.484.48 4.43 4.43 4.38 4.38 OOMCM41MCM41–Core–CorePAHsPAHs 4.924.92 4.83 4.83 4.83 4.83 OMCM41–HMCM41 0.94 OMCM41–HMCM41 0.94

Figure6(1) shows that the H atoms on the PAHs at different positions were the same distance from the O atoms on the surface of MCM-41. This indicated that the H atoms in the same PAH molecule had similar weak activities. The peaks of the RDF distances corresponding to Nap, Phe, and Pyr were Int. J. Mol. Sci. 2019, 20, x FOR PEER REVIEW 8 of 13

Figure 6(1) shows that the H atoms on the PAHs at different positions were the same distance Int. J. Mol. Sci. 2019, 20, 665 8 of 13 from the O atoms on the surface of MCM-41. This indicated that the H atoms in the same PAH molecule had similar weak activities. The peaks of the RDF distances corresponding to Nap, Phe, and 3.43Pyr Å,were 3.63 3.43 Å, andÅ, 3.63 3.53 Å, Å, and respectively 3.53 Å, respectively (see Table2 (see), which Table were 2), which all larger were than all thelarger common than the hydrogen common bondhydrogen length bond (≤3.10 length Å). This(≤3.10 indicated Å). This thatindicated there that could there be limited could be hydrogen limited hydrogen bonds produced bonds produced between PAHbetween molecules PAH molecules and surface and silanol surface groups silanol (Si–OH). groups (Si–OH). FigureFigure6 (2)6(2) shows shows there there were were large large differences differences in thein the distances distances between between the the H atomsH atoms on MCM-41on MCM- and41 and C atoms C atoms (HMCM41 (HMCM41–C–orePAHsCorePAHs)) at at different different positions positions on on the the PAHs. PAHs. The The C C atoms atoms of of the the C–H C–H bonds bonds onon the the PAH PAH were were close close to to H H atoms atoms on on MCM-41, MCM-41, and and C C atoms atoms near near the the centercenter ofof thethe PAHPAH were were spaced spaced apartapart fromfrom thethe H H atoms atoms on on MCM-41. MCM-41. ThisThis distributiondistribution andand actionaction waswas aa resultresult ofof thethe positive positive andand negativenegative chargescharges ofof thethe molecule.molecule. TheThe HH andand OO atomsatoms onon thethe PAHsPAHs or or the the surface surface of of MCM-41 MCM-41 had had positivepositive potential potential and and negative negative potential potential electrical electrical properties, properties, respectively, respectively, while the while electrical the propertyelectrical ofproperty C atoms of on C theatoms PAHs on wasthe PAHs dependent was dependent on the positions. on the positions. The central The C atomcentral was C atom positively was positively charged whilecharged the while outer Cthe atom outer was C atom negatively was negatively charged. charged. TableTable2 2shows shows that that the the difference difference in in the the distance distance between between H H and and O O atoms atoms on on MCM-41 MCM-41 and and the the RDFRDF peak peak of of the the PAH PAH centers centers was was 0.44 0.44 Å Å (Nap), (Nap), 0.4 0.4 Å Å (Phe), (Phe), and and 0.45 0.45 Å Å (Pyr). (Pyr). They They were were smaller smaller than than thethe average average distancedistance betweenbetween H and and O O atoms atoms in in the the surface surface silanol silanol group group (0.94 (0.94 Å), Å), indicating indicating that that the themolecular molecular planes planes of ofthe the O– O–HH bond bond and and the the PAHs PAHs were were not not perpen perpendicular,dicular, but existedexisted atat aa uniqueunique angle.angle. The The spacing spacing between between the the central central PAH PAH ring ring and and the the H H and and O O atomsatoms ofof thethe PAHsPAHs decreased decreased with with increasingincreasing PAHPAH molecular molecular size. size. TheThe CC atomsatoms nearnear thethe centercenter ofof thethe PAHs,PAHs, which which were were negatively negatively charged,charged, attractedattracted SiSi andand HH atomsatoms thatthat werewere positivelypositively charged,charged, andand thisthis ledled toto aa decreasedecrease inin thethe distancedistance between between the the PAHs PAHs and and the the inner inner surface surface of theof the adsorbent. adsorbent. This This result result was was consistent consistent with with the densitythe density peak peak position position results results shown shown in Figure in Figure4. 4. ItIt can can be be concluded concluded from from the the angular angular distribution distribution and and density density peak peak position position analysis analysis that that the the threethree PAH PAH molecules molecules were were adsorbed adsorbed in in a a flat flat position position onon thethe innerinner surfacesurface ofof thethe adsorbentadsorbent tunnel.tunnel. TheThe adsorbates adsorbates possessed possessed aa stable stable planarplanar structurestructure withwith HH atoms atoms on on the the molecular molecular edge, edge, and and there there waswas no no strong strong polar polar force force generated generated during during the the adsorption adsorption process process that that can can result result in in the the severe severe tilt tilt or or deflectiondeflection of of the the molecular molecular plane. plane. TheseThese findingsfindings werewere provedproved byby RDF RDF results, results, where where the the hydrogen hydrogen bondingbonding was was weak weak at at the the edge edge of of the the PAHs PAHs from from the the large large distance distance between between H atomsH atoms on on PAHs PAHs and and O atomsO atoms on MCM-41.on MCM-41. Additionally, Additionally, there wasthere no was unique no Hunique atom, H and atom, the surface and the generated surface agenerated prominent a forceprominent that tilted force the that PAH tilted plane the for PAH the plane same activityfor the sa ofme H atomsactivity at of the H edgeatoms of at the the PAHs. edge Asof the we know,PAHs. theAs currentwe know, PAHs the current were formed PAHs bywere the formed combination by the ofcombination benzene rings, of benzene and large rings,π bonds and large easily π bonds form throughouteasily form the throughout molecule. the The molecule. potential The and potential charge density and charge distributions density ofdistributions Nap, Phe, and of Nap, Pyr obtained Phe, and byPyr the obtained DFT simulations, by the DFT shown simulations, in Figure shown7, illustrated in Figure that 7, illustrated the center that of the the ring center on of both the sidesring on of theboth PAHsides molecular of the PAH plane molecular was negatively plane chargedwas negatively (red part charged in Figure (red7), which part isin aFigure neighboring 7), whichπ bond, is a andneighboring the area of π action bond, of and the theπ-electron area of plane action increased of the π when-electron the numberplane increased of rings increased.when the Thisnumber led toof enhanced,rings increased. or stronger, This adsorptionled to enhanced, when the or adsorption stronger, processadsorption was when governed the byadsorption dispersion process forces [56was]. Hence,governed the by heavier dispersion the molecular forces [56]. weight Hence, of the heav PAHs,ier the thestronger molecular the weight interaction of the withPAHs, the the surface stronger of thethe pore interaction and the with shorter the thesurface distance of the between pore and the the adsorbate shorter and the adsorbent.distance between the adsorbate and adsorbent.

FigureFigure 7.7. ElectrostaticElectrostatic potential potential and and charge charge density density dist distributionribution results results of Nap, of Nap, PhePhe and andPyr. Pyr.The Theelectrostatic electrostatic potential potential distribution distribution ranged ranged from from −0.03−0.03 to 0.03, to 0.03, with with the theblue blue portion portion representing representing the thepositive positive potential potential and and the the red red portion portion representing representing the the negative negative potential. potential.

Int. J. Mol. Sci. 2019, 20, 665 9 of 13

Int. J. Mol. Sci. 2019, 20, x FOR PEER REVIEW 9 of 13 3.Int. Methods J. Mol. Sci. 2019 and, 20 Parameters, x FOR PEER REVIEW 9 of 13 3. Methods and Parameters 3.1.3. Methods Model Structures and Parameters 3.1. Model Structures 3.1. ModelAn all-atom Structures model of MCM-41 was established with the carving-out method [36,37] based on the rhombohedralAn all-atom model cell model of MCM-41 [57], as shownwas established in Figure8 wi. Theth the main carving-out mesoporous method structure [36,37] of the based model on consistedthe rhombohedralAn all-atom of excavated model cell model cylindrical of MCM-41 [57], as holes shownwas inestablished in amorphous Figure 8.wi Theth silica. the main carving-out Each mesoporous unit contained method structure [36,37] four of cylindrical the based model on channels.consistedthe rhombohedral of The excavated atomic cell bondsmodel cylindrical [57], in the as holes whole shown in unit inamorphous Figu cellre were 8. The silica. saturated main Each mesoporous by unit the contained connection structure four of of thecylindrical the oxygen model (O)channels.consisted and hydrogen Theof excavated atomic (H) bonds atomscylindrical in to the the whole holes unsaturated unitin amorphous cell bondswere saturated fromsilica. silicon Each by the unit (Si) connection andcontained O atoms of four the (the oxygencylindrical Si atoms (O) withandchannels. hydrogen three The OH atomic(H) atoms atoms bonds were to removed).inthe the unsaturated whole The unit model bonds cell were was from optimizedsaturated silicon (Si) by and theand relaxed connection O atoms based (the of onthe Si interactions atomsoxygen with (O) describedthreeand hydrogen OH byatoms the (H) Dreidingwere atoms removed). to force the ﬁeld.unsaturated The The model ESP bonds charges was fr optimizedom were silicon calculated (Si)and andrelaxed according O atoms based to (the the on Si method interactionsatoms fromwith Zhuodescribedthree etOH al. byatoms [44 the] to Dreiding were ﬁnalize removed). force the structure field. The The ofmodel ESP MCM-41. char wasges optimized The were model calculated and structure relaxed according parameters based to the on aremethod interactions shown from in TableZhuodescribed S1,et al. and by [44] the comparisons to Dreiding finalize force ofthe the structure field. characterization The of ESP MC charM-41. resultsges The were with model calculated experimental structure according parameters values to [the52] aremethod are shown from in FigureTableZhuo S1,et S1 al. and in [44] the comparisons Supplementaryto finalize theof the structure Material. characterization of MCM-41. results The with model experimental structure parameters values [52] areare shown in FigureTable S1, S1 andin the comparisons Supplementary of the Material. characterization results with experimental values [52] are shown in Figure S1 in the Supplementary Material.

(a) (b) (a) (b) FigureFigure8. 8. TheThe final ﬁnal structure structure of of the MCM-41 model. ( a)) Ball-and-stick model; ( b) CPK model; silicon (Si),Figure8. yellow; The oxygen final structure (O), red;red; of hydrogenhydrogen the MCM-41 (H),(H), white.white.model. (a) Ball-and-stick model; (b) CPK model; silicon (Si), yellow; oxygen (O), red; hydrogen (H), white. Nap, Phe,Phe, andand Pyr Pyr are are typical typical benzene-ring benzene-ring structures, structures, as shown as shown in Figure in Figure9. The molecular9. The molecular models ofmodels theNap, three of thePhe, PAHs three and were PAHs Pyr determined are were typical determined withbenzene-ring the with density th strue functiondensityctures, function theoryas shown (DFT) theory in method,Figure (DFT) 9.method, with The all-electron molecular with all- atomicelectronmodels chargesof atomic the three obtainedcharges PAHs byobtained were the determined ESP by method. the ESP with In me the ththod.e DFT density In calculation, the function DFT thecalculation,theory Perdew–Wang (DFT) the method, Perdew–Wang method with was all- employedmethodelectron wasatomic to exchangeemployed charges correlation to obtained exchange functionsby correlation the ESP in theme func calculation,thod.tions In inthe the where DFT calculation, thecalculation, base groupwhere the used thePerdew–Wang wasbase doublegroup numericalusedmethod was was double plus employed polarization numerical to exchange plus (DNP). polarization Thecorrelation distribution (DNP). functions The of the distributionin electrostaticthe calculation, of the potentials electrostaticwhere onthe thebase potentials electron group isopycniconused the was electron surfacedouble isopycnic ofnumerical the three surface plus PAHs ofpolarization th ise shown three PAHs in (DNP). Figure is shownThe7. distribution in Figure 7.of the electrostatic potentials on the electron isopycnic surface of the three PAHs is shown in Figure 7.

Figure 9. The structures of naphthalene (Nap), phenanthrene (Phe), and pyrene (Pyr) with ESP Figurecharges. 9.9. ( aTheThe) Nap; structures structures (b) Phe; of (of naphthalenec) Pyr;naphthalene Key: carbon (Nap), (Nap), phenanthrene(C), phenangrey; H,threne white; (Phe), (Phe), charges, and pyrene and yellow. pyrene (Pyr) with (Pyr) ESP with charges. ESP (charges.a) Nap; ((ba) Phe;Nap; ((cb)) Pyr; Phe; Key: (c) Pyr; carbon Key: (C), carbon grey; (C), H, white;grey; H, charges, white; yellow.charges, yellow. 3.2. Calculation Method 3.2. Calculation Method In the GCMC simulation, the adsorption temperature was fixed at 398 K, and the adsorbate In the GCMC simulation, the adsorption temperature was fixed at 398 K, and the adsorbate moleculesIn the were GCMC regarded simulation, as rigid the molecules. adsorption The temperature Dreiding force was field fixed was at used 398 toK, describe and the theadsorbate energy molecules were regarded as rigid molecules. The Dreiding force field was used to describe the energy formsmolecules of the were adsorbent–adsorbate regarded as rigid molecules. and adsorbate–adso The Dreidingrbate force interactions. field was Theused atomic to describe force thefield energy form forms of the adsorbent–adsorbate and adsorbate–adsorbate interactions. The atomic force field form andforms interaction of the adsorbent–adsorbate parameters are shown and adsorbate–adsoin Table S2. Electrostaticrbate interactions. interactions The areatomic described force field in Ewald form formatand interaction with an parametersaccuracy of are10− 4shown kcal mol in −Table1. The S2.cutoff Electrostatic radii for theinteractions van der Waalsare described interactions in Ewald and hydrogenformat with bonds an accuracy were 15.5 of Å 10 and−4 kcal 4.5 Å,mol respectively.−1. The cutoff The radii total for step the number van der was Waals 1 × 10interactions7, in which and the hydrogen bonds were 15.5 Å and 4.5 Å, respectively. The total step number was 1 × 107, in which the

Int. J. Mol. Sci. 2019, 20, 665 10 of 13 and interaction parameters are shown in Table S2. Electrostatic interactions are described in Ewald format with an accuracy of 10−4 kcal mol−1. The cutoff radii for the van der Waals interactions and hydrogen bonds were 15.5 Å and 4.5 Å, respectively. The total step number was 1 × 107, in which the ﬁrst 5 × 106 steps were used to balance the adsorption state, and the next 5 × 106 steps were used to calculate the state average of the entire ensemble. The PAHs’ gas partial pressure in the simulation was set at a lower level (~100 ppm) according to the common concentration ranges of PAHs in actual situations [58]. The fugacity value required in the calculation process was obtained by converting the pressure into the physical parameters of Nap, Phe, and Pyr by the Peng–Robinson equation. The parameters such as critical temperature, critical pressure, and the eccentricity factor are shown in Table S3. The adsorption model results under the pressure of 0.8 Pmax were used to further analyze the adsorption state of the three PAH molecules in the main channel of MCM-41. The adsorption states including the angle distribution and the density peak were analyzed. The radius radial distribution function representative of adsorbate–adsorbent mutual force was ﬁnally discussed.

4. Conclusions Based on the GCMC simulation, the MCM-41 model was established, and the adsorption of Nap, Phe, and Pyr on MCM-41 was simulated. The adsorption model was validated by use of experimental adsorption isotherms. During the adsorption, no perpendicular state between the PAH molecular plane and the central axis of the adsorbent channel was observed. The order according to the degree of adsorption was: Pyr > Phe > Nap. The three PAHs were adsorbed in a ﬂat position on the surface of the pore, and the conﬁguration planes of Phe and Pyr were more parallel to the surface compared to Nap. The RDF curves indicated that there was no hydrogen bonding produced during the adsorption process. The H atoms in the same PAHs had the same activity, but the adsorption activity of the C atoms decreased from the central position, and the O–H bond on the adsorbent surface had a unique angle with the plane of the PAHs. The area of action of the π-electron plane increased when the number of rings increased, leading to enhanced, stronger adsorption, and thus, a shorter distance between the adsorbate and adsorbent.

Supplementary Materials: Supplementary materials can be found at http://www.mdpi.com/1422-0067/20/3/ 665/s1. Author Contributions: Conceptualization, X.Y., Z.L. and R.T.Y.; methodology, C.Z., L.J. and Z.L.; writing, X.Y., L.J. and H.W.; project administration, Y.L. and Y.X. Funding: This research was funded by National Natural Science Foundation of China (51604016, 51478083, 21676025), Beijing Natural Science Foundation (No. 8182019, 8174064), National Key R&D Program of China (No. 2017YFC0210302), the National Postdoctoral Program for Innovative Talents (No. BX201700029), the China Postdoctoral Science Foundation (No. 2018M630075), the Fundamental Research Funds for the Central Universities (No. FRF-TP-17-063A1, FRF-BD-18-015A). Conﬂicts of Interest: The authors declare no conﬂict of interest.

Abbreviations

Nap Naphthalene Phe Phenanthrene Pyr Pyrene GCMC Grand Canonical Monte Carlo

References

1. Casarett, L.J.; Doull, J. Toxicology: The Basic Science of Poisons; McGraw-Hill: New York, NY, USA, 1996. 2. Li, Z.; Liu, Y.; Yang, X.; Xing, Y.; Wang, Z.; Yang, Q.; Yang, R.T. Desorption kinetics of naphthalene and acenaphthene over two activated carbons via thermogravimetric analysis. Energy Fuels 2015, 29, 5303–5310. [CrossRef] Int. J. Mol. Sci. 2019, 20, 665 11 of 13

3. Cheng, X.; Kan, A.T.; Tomson, M.B. Naphthalene adsorption and desorption from aqueous C60 fullerene. J. Chem. Eng. Data 2004, 49, 675–683. [CrossRef] 4. Yang, K.U.N.; Wu, W.; Jing, Q.; Zhu, L. Aqueous adsorption of aniline, phenol, and their substitutes by multi-walled carbon nanotubes. Environ. Sci. Technol. 2008, 42, 7931–7936. [CrossRef][PubMed] 5. Owabor, C.N.; Ogbeide, S.E.; Susu, A.A. Adsorption and desorption kinetics of naphthalene, anthracene, and pyrene in soil matrix. Pet. Sci. Technol. 2010, 28, 504. [CrossRef] 6. Long, A.S.; Lemieux, C.L.; Gagné, R.; Lambert, I.B.; White, P.A. Genetic Toxicity of Complex Mixtures of Polycyclic Aromatic Hydrocarbons: Evaluating Dose-Additivity in a Transgenic Mouse Model. Environ. Sci. Technol. 2017, 51, 8138–8148. [CrossRef][PubMed] 7. Liamin, M.; Le Mentec, H.; Evrard, B.; Huc, L.; Chalmel, F.; Boutet-Robinet, E.; Le Ferrec, E.; Sparfel, L. Genome-Wide Transcriptional and Functional Analysis of Human T Lymphocytes Treated with Benzo [α] pyrene. Int. J. Mol. Sci. 2018, 19, 3626. [CrossRef] 8. Libalova, H.; Rossner, P.; Vrbova, K.; Brzicova, T.; Sikorova, J.; Vojtisek-Lom, M.; Beranek, V.; Klema, J.; Ciganek, M.; Neca, J.; et al. Comparative analysis of toxic responses of organic extracts from diesel and selected alternative fuels engine emissions in human lung BEAS-2B cells. Int. J. Mol. Sci. 2016, 17, 1833. [CrossRef] 9. Mastral, A.M.; Callen, M.S. A review on polycyclic aromatic hydrocarbon (PAH) emissions from energy generation. Environ. Sci. Technol. 2000, 34, 3051–3057. [CrossRef] 10. Keith, L.; Telliard, W. ES&T special report: Priority pollutants: Ia perspective view. Environ. Sci. Technol. 1979, 13, 416–423. 11. Albuquerque, M.; Coutinho, M.; Borrego, C. Long-term monitoring and seasonal analysis of polycyclic aromatic hydrocarbons (PAHs) measured over a decade in the ambient air of Porto, Portugal. Sci. Total Environ. 2016, 543, 439–448. [CrossRef] 12. Dowaidar, A.M.; El-Shahawi, M.S.; Ashour, I. Adsorption of Polycyclic Aromatic Hydrocarbons onto Activated Carbon from Non-Aqueous Media: 1. The Influence of the Organic Solvent Polarity. Sep. Sci. Technol. 2007, 42, 3609–3622. [CrossRef] 13. Mastral, A.M.; Callen, M.; Murillo, R. Assessment of PAH emissions as a function of coal combustion variables. Fuel 1996, 75, 1533–1536. [CrossRef] 14. Zhou, H.C.; Zhong, Z.P.; Jin, B.S.; Huang, Y.J.; Xiao, R. Experimental study on the removal of PAHs using in-duct activated carbon injection. Chemosphere 2005, 59, 861–869. [CrossRef][PubMed] 15. Li, Z.; Liu, Y.; Yang, X.; Xing, Y.; Tsai, C.; Wang, Z.; Yang, Q.; Yang, R.T. Desorption of polycyclic aromatic hydrocarbons on mesoporous sorbents: Thermogravimetric experiments and kinetics study. Ind. Eng. Chem. Res. 2016, 55, 1183–1191. [CrossRef] 16. Araújo, R.S.; Azevedo, D.C.S.; Cavalcante, C.L., Jr.; Jiménez-López, A.; Rodríguez-Castellón, E. Adsorption of polycyclic aromatic hydrocarbons (PAHs) from isooctane solutions by mesoporous molecular sieves: Influence of the surface acidity. Microporous Mesoporous Mater. 2008, 108, 213–222. [CrossRef] 17. Shang, J.; Li, G.; Singh, R.; Gu, Q.; Nairn, K.M.; Bastow, T.J.; Medhekar, N.; Doherty, C.M.; Hill, A.J.; Liu, J.Z.; et al. Discriminative separation of gases by a “molecular trapdoor” mechanism in chabazite zeolites. J. Am. Chem. Soc. 2012, 134, 19246–19253. [CrossRef][PubMed] 18. Shang, J.; Li, G.; Webley, P.A.; Liu, J.Z. A density functional theory study for the adsorption of various gases on a caesium-exchanged trapdoor chabazite. Comput. Mater. Sci. 2016, 122, 307–313. [CrossRef] 19. Li, Z.; Liu, Y.; Zhang, C.; Yang, X.; Ren, J.; Jiang, L. Methane recovery from coal bed gas using modified activated carbons: A combined method for assessing the role of functional groups. Energy Fuels 2015, 29, 6858–6865. [CrossRef] 20. Li, G.K.; Shang, J.; Gu, Q.; Awati, R.V.; Jensen, N.; Grant, A.; Zhang, X.; Sholl, D.S.; Liu, J.Z.; Webley, P.A.; et al. Temperature-regulated guest admission and release in microporous materials. Nat. Commun. 2017, 8, 15777. [CrossRef][PubMed] 21. Beck, J.S.; Vartuli, J.C.; Roth, W.J.; Leonowicz, M.E.; Kresge, C.T.; Schmitt, K.D.; Chu, C.T.W.; Olson, D.H.; Sheppard, E.W.; McCullen, S.B.; et al. A new family of mesoporous molecular sieves prepared with liquid crystal templates. J. Am. Chem. Soc. 1992, 114, 10834–10843. [CrossRef] 22. Kresge, C.T.; Leonowicz, M.E.; Roth, W.J.; Vartuli, J.C.; Beck, J.S. Ordered mesoporous molecular sieves synthesized by a liquid-crystal template mechanism. Nature 1992, 359, 710. [CrossRef] Int. J. Mol. Sci. 2019, 20, 665 12 of 13

23. Selvam, P.; Bhatia, S.K.; Sonwane, C.G. Recent advances in processing and characterization of periodic mesoporous MCM-41 silicate molecular sieves. Ind. Eng. Chem. Res. 2001, 40, 3237–3261. [CrossRef] 24. Corma, A. From microporous to mesoporous molecular sieve materials and their use in catalysis. Chem. Rev. 1997, 97, 2373–2420. [CrossRef][PubMed] 25. Ciesla, U.; Schüth, F. Ordered mesoporous materials. Microporous Mesoporous Mater. 1999, 27, 131–149. [CrossRef] 26. Rimola, A.; Costa, D.; Sodupe, M.; Lambert, J.F.; Ugliengo, P. Silica surface features and their role in the adsorption of biomolecules: Computational modeling and experiments. Chem. Rev. 2013, 113, 4216–4313. [CrossRef] 27. Pajzderska, A.; Gonzalez, M.A.; Mielcarek, J.; W ˛asicki,J. Water behavior in MCM-41 as a function of pore filling and temperature studied by NMR and molecular dynamics simulations. J. Phys. Chem. C 2014, 118, 23701–23710. [CrossRef] 28. Coasne, B.; Galarneau, A.; Di Renzo, F.; Pellenq, R.J. Molecular simulation of nitrogen adsorption in nanoporous silica. Langmuir 2010, 26, 10872–10881. [CrossRef] 29. Chang, S.C.; Chien, S.Y.; Chen, C.L. Analyzing adsorption characteristics of CO2, N2 and H2O in MCM-41 silica by molecular simulation. Appl. Surf. Sci. 2015, 331, 225–233. [CrossRef] 30. Coasne, B.; Galarneau, A.; Pellenq, R.J.M.; di Renzo, F. Adsorption, intrusion and freezing in porous silica: The view from the nanoscale. Chem. Soc. Rev. 2013, 42, 4141–4171. [CrossRef] 31. Coasne, B.; Alba-Simionesco, C.; Audonnet, F.; Dosseh, G.; Gubbins, K.E. Adsorption and structure of benzene on silica surfaces and in nanopores. Langmuir 2009, 25, 10648–10659. [CrossRef] 32. Ravikovitch, P.I.; Domhnaill, S.C.Ó.; Neimark, A.V.; Schueth, F.; Unger, K.K. Capillary hysteresis in nanopores: Theoretical and experimental studies of nitrogen adsorption on MCM-41. Langmuir 1995, 11, 4765–4772. [CrossRef] 33. Maddox, M.W.; Gubbins, K.E. Molecular simulation of fluid adsorption in buckytubes and MCM-41. Int. J. Thermophys. 1994, 15, 1115–1123. [CrossRef] 34. Maddox, M.W.; Olivier, J.P.; Gubbins, K.E. Characterization of MCM-41 using molecular simulation: Heterogeneity effects. Langmuir 1997, 13, 1737–1745. [CrossRef] 35. Koh, C.A.; Montanari, T.; Nooney, R.I.; Tahir, S.F.; Westacott, R.E. Experimental and computer simulation studies of the removal of carbon dioxide from mixtures with methane using AlPO4-5 and MCM-41. Langmuir 1999, 15, 6043–6049. [CrossRef] 36. He, Y.; Seaton, N.A. Heats of adsorption and adsorption heterogeneity for methane, ethane, and carbon dioxide in MCM-41. Langmuir 2006, 22, 1150–1155. [CrossRef][PubMed] 37. Brodka, A.; Zerda, T.W. Properties of liquid acetone in silica pores: Molecular dynamics simulation. J. Chem. Phys. 1996, 104, 6319–6326. [CrossRef] 38. Pellenq RJ, M.; Levitz, P.E. Capillary condensation in a disordered mesoporous medium: A grand canonical Monte Carlo study. Mol. Phys. 2002, 100, 2059–2077. [CrossRef] 39. Gelb, L.D.; Gubbins, K.E. Characterization of porous glasses: Simulation models, adsorption isotherms, and the Brunauer–Emmett–Teller analysis method. Langmuir 1998, 14, 2097–2111. [CrossRef] 40. Pérez-Sánchez, G.; Gomes, J.R.B.; Jorge, M. Modeling self-assembly of silica/surfactant mesostructures in the templated synthesis of nanoporous solids. Langmuir 2013, 29, 2387–2396. [CrossRef] 41. Jing, Y.; Wei, L.; Wang, Y.; Yu, Y. Molecular simulation of MCM-41: Structural properties and adsorption of CO2, N2 and flue gas. Chem. Eng. J. 2013, 220, 264–275. [CrossRef] 42. Ugliengo, P.; Sodupe, M.; Musso, F.; Bush, I.J.; Orlando, R.; Dovesi, R. Realistic models of hydroxylated amorphous silica surfaces and MCM-41 mesoporous material simulated by large-scale periodic B3LYP calculations. Adv. Mater. 2008, 20, 4579–4583. [CrossRef] 43. Coasne, B.; Pellenq, R.J.M. Grand canonical Monte Carlo simulation of argon adsorption at the surface of silica nanopores: Effect of pore size, pore morphology, and surface roughness. J. Chem. Phys. 2004, 120, 2913–2922. [CrossRef][PubMed]

44. Zhuo, S.; Huang, Y.; Hu, J.; Liu, H.; Hu, Y.; Jiang, J. Computer simulation for adsorption of CO2,N2 and ﬂue gas in a mimetic MCM-41. J. Phys. Chem. C 2008, 112, 11295–11300. [CrossRef] 45. Zhang, X.; Shao, X.; Wang, W.; Cao, D. Molecular modeling of selectivity of single-walled carbon nanotube and MCM-41 for separation of methane and carbon dioxide. Sep. Purif. Technol. 2010, 74, 280–287. [CrossRef] Int. J. Mol. Sci. 2019, 20, 665 13 of 13

46. Bonnaud, P.A.; Coasne, B.; Pellenq, R.J.M. Molecular simulation of water confined in nanoporous silica. J. Phys. Condens. Matter 2010, 22, 284110. [CrossRef][PubMed] 47. Brás, A.R.; Fonseca, I.M.; Dionísio, M.; Schönhals, A.; Affouard, F.; Correia, N.T. Influence of nanoscale confinement on the molecular mobility of ibuprofen. J. Phys. Chem. C 2014, 118, 13857–13868. [CrossRef] 48. Ghoufi, A.; Hureau, I.; Lefort, R.; Morineau, D. Hydrogen-bond-induced supermolecular assemblies in a nanoconfined tertiary alcohol. J. Phys. Chem. C 2011, 115, 17761–17767. [CrossRef] 49. Herdes, C.; Ferreiro-Rangel, C.A.; Duren, T. Predicting neopentane isosteric enthalpy of adsorption at zero coverage in MCM-41. Langmuir 2011, 27, 6738–6743. [CrossRef] 50. Lerbret, A.; Lelong, G.; Mason, P.E.; Saboungi, M.L.; Brady, J.W. Molecular dynamics and neutron scattering study of glucose solutions confined in MCM-41. J. Phys. Chem. B 2011, 115, 910–918. [CrossRef] 51. Huang, J.; Meagher, M.M. Pervaporative recovery of n-butanol from aqueous solutions and ABE fermentation broth using thin-film silicalite-filled silicone composite membranes. J. Membr. Sci. 2001, 192, 231–242. [CrossRef] 52. Coasne, B.; Fourkas, J.T. Structure and dynamics of benzene confined in silica nanopores. J. Phys. Chem. C 2011, 115, 15471–15479. [CrossRef] 53. Li, Z.; Liu, Y.; Yang, X.; Xing, Y.; Yang, Q.; Yang, R.T. Adsorption thermodynamics and desorption properties of gaseous polycyclic aromatic hydrocarbons on mesoporous adsorbents. Adsorption 2017, 23, 361–371. [CrossRef] 54. Li, Z.; Liu, Y.; Yang, X.; Xing, Y.; Tsai, C.J.; Meng, M.; Yang, R.T. Performance of mesoporous silicas and carbon in adsorptive removal of phenanthrene as a typical gaseous polycyclic aromatic hydrocarbon. Microporous Mesoporous Mater. 2017, 239, 9–18. [CrossRef] 55. Yang, R.T. Gas Separation by Adsorption Processes; Butterworth-Heinemann: Oxford, UK, 2013. 56. Moreno-Castilla, C. Adsorption of organic molecules from aqueous solutions on carbon materials. Carbon 2004, 42, 83–94. [CrossRef] 57. Siperstein, F.R.; Gubbins, K.E. Synthesis and characterization of templated mesoporous materials using molecular simulation. Mol. Simul. 2001, 27, 339–352. [CrossRef] 58. Liu, Y.; Li, Z.; Yang, X.; Xing, Y.; Tsai, C.; Yang, Q.; Wang, Z.; Yang, R.T. Performance of mesoporous silicas (MCM-41 and SBA-15) and carbon (CMK-3) in the removal of gas-phase naphthalene: Adsorption capacity, rate and regenerability. RSC Adv. 2016, 6, 21193–21203. [CrossRef]

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