Chemical Physics Letters 515 (2011) 102–108

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Chemical Physics Letters

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First Molecular Dynamics simulation insight into the mechanism of organicsadsorption from aqueous solutions on microporous carbons

Artur P. Terzyk ⇑, Piotr A. Gauden, Wojciech Zielinski, Sylwester Furmaniak, Radosław P. Wesołowski,Kamil K. KlimekN. Copernicus University, Department of Chemistry, Physicochemistry of Carbon Materials Research Group, Gagarin St. 7, 87-100 Torun, Poland

a r t i c l e i n f o a b s t r a c t

Article history:Received 9 May 2011In final form 31 August 2011Available online 3 September 2011

0009-2614/$ - see front matter � 2011 Elsevier B.V. Adoi:10.1016/j.cplett.2011.08.093

⇑ Corresponding author. Fax: +48 056 654 24 77.E-mail address: aterzyk@chem.uni.torun.pl (A.P. TURL: http://www.chem.uni.torun.pl/~aterzyk/ (A.P

The results of 84 MD simulations showing the influence of porosity and carbon surface oxidation onadsorption of three organic compounds from aqueous solutions on carbons are reported. Based on amodel of ‘soft’ activated carbon, three carbon structures with gradually changed microporosity were cre-ated. Next, different number of surface oxygen groups was introduced. We observe quantitative agree-ment between simulation and experiment i.e. the decrease in adsorption from benzene down toparacetamol. Simulation results clearly demonstrate that the balance between porosity and carbon sur-face chemical composition in organics adsorption on carbons, and the pore blocking determine adsorp-tion properties of carbons.

� 2011 Elsevier B.V. All rights reserved.

1. Introduction

It is well known that among practical application of activatedcarbons, adsorption of organics from aqueous solutions plays prob-ably a major role. It is also obvious that two factors determineadsorption properties of activated carbons, namely chemical com-position of carbon surface layer and the pore size distribution [1].However, in adsorption from aqueous solutions on carbons chem-ical composition of carbon surface layer is the crucial factor deter-mining adsorption. Here the following problems arise: we still donot know the method providing a realistic pore size distributionfunction for activated carbons; and this is usually calculated usinglocal isotherms simulated for a slit-like model of pores as a kernelin the global adsorption isotherm equation. On the other hand, foractivated carbons also the chemical composition of surface layer isnot easy for evaluation. Therefore, it is difficult to determine themechanisms of adsorption in a real experiment.

In this Letter we use the method presented previously [2],namely we present the results of systematic Molecular Dynamicssimulations of adsorption of three organic compounds on so calledVirtual Porous Carbon (VPC) models of activated carbons.

Systematic and complex study make it possible to determinethe mechanisms of adsorption from solutions on molecular leveland this Letter is the first attempt of explanation of the relation be-tween carbon porosity and carbon surface composition in adsorp-tion from solutions.

ll rights reserved.

erzyk).. Terzyk).

2. VPC models

We study Virtual Porous Carbon (VPC) model of so called ‘soft’(i.e. graphitized) activated carbon containing a system of slit-likepores. The same model was considered in our previous paperwhere we studied the effect of surface oxygen functionalities onthe enthalpy of carbon immersion in water [3]. It is widely ac-cepted that this type of activated carbon is composed of microcrys-tallites [4–9]. Therefore the procedure applied in this study insertsrandomly double and triple layered graphene microcrystallites(shown at the bottom of Figure 1) into simulation box in such away, that a microporous carbon model is created. Carbon–carbonbond length was assumed as equal to 0.142 nm and the interlayerspacing between layers was fixed as equal to 0.335 nm (since wetry to prepare the model of ‘soft’ carbon both values are the sameas observed for graphite). Also like in graphite the centres of ben-zene rings in each layer are shifted by 1/3 (we assumed ABC stack-ing of graphene layers). Figure 1 shows applied basis ofmicrocrystallites (the notation mxyz is used, where x and y denotethe number of benzene rings in a layer in respective directions, andz is the number of layers). The program generating carbon struc-ture randomly uses one of 10 microcrystallites and introduces it in-side the simulation box at random position and with randomangular orientation. This insertion is accepted if there are no over-laps between fragments (i.e. the distance between any carbonatom of the inserted fragment and the fragments just present inthe box is not smaller than 0.34 nm). To perform molecular simu-lations one arbitrarily chosen structure (created using this method)was used. This structure has the radius equal to 2.3 nm (it meansthat all 1844 carbon atoms forming this structure are closed in asphere having this radius) and contains 24 microcrystallites

Figure 1. Studied molecules (benzene, phenol, paracetamol, and water) and applied methodology of representative structures creation together with nomenclature used(note that the frames are not simulation boxes but are only guide to the eye). Initial structure was oxidised (chemical modification), moreover the groups were distributed ina different way. Upper structures were obtained by shifting of carbon fragments to change the porosity.

A.P. Terzyk et al. / Chemical Physics Letters 515 (2011) 102–108 103

(14 of m332, 2 of m333, 2 of m432, 1 of m433, 4 of m442 and 1 ofm543, respectively).

To check the influence of carbon surface oxidation on adsorp-tion of organic compounds we used the procedure of so called ‘vir-tual oxidation’ proposed previously [2,10–12], introducingcarbonyl surface groups into the initial structure. To do this thetwo-bonded carbon atoms (potential sites for bonding) in thestructure are detected, and next (in a random way) 240 carbonylgroups (14.8% – mass percentage of oxygen) are attached (thegroup is located in a way excluding overlaps). The direction of abond between a carbon atom in the structure and an oxygen atom(having length 0.1233 nm [13]) in the carbonyl groups is deter-mined by the secant of an angle C–C–C (the middle C denotes anatom where the group is bonding; the remaining atoms are thosein the structure and bonded with this carbon). Obtained structureis labelled as S1_240. Structure S2_240 is also obtained by a ran-dom creation of carbonyl groups. This is due to check the influenceof surface group location on enthalpy of immersion. Contrary, inthe case of S3_240 the groups were also attached randomly butonly to the carbon atoms located at the edges of microcrystallites

(the groups were not introduced into the central part of VPC modeli.e. into the central part closed in a sphere having radius 1.25 nm).From oxidised structures (S1_240, S2_240 and S3_240) containingmaximum number of carbonyl groups the structures with system-atically decreasing number of carbonyls were prepared by a ran-dom deleting of 1/4 of initial number of groups. In this way weobtained three series of structures containing 180, 120 and 60 car-bonyl functionalities, respectively.

To study the influence of carbon porosity on adsorption thestructures with shifted fragments were prepared from the modelsof Series 1. Those VPCs were obtained by the proportional displace-ment of the centres of microcrystallites (by the factor 1.125, 1.25and 1.5) forming the initial structure.

To determine the pore size distribution (PSD) of all VPCs we ap-plied the method proposed by Bhattacharya and Gubbins [14]using the procedure described in detail previously [10]. In thismethod a uniform grid of points is generated in the simulationbox (for studied structures 200 � 200 � 200) and for each suchpoint (located in a pore) the largest sphere containing this point(and situated in the pore) is found. The diameter of this sphere is

104 A.P. Terzyk et al. / Chemical Physics Letters 515 (2011) 102–108

equal to the diameter of the pore and the collection of histogramsof the diameters of pores for each such a point of the grid makes itpossible to plot the histogram of the pore diameters (related to thePSD curve – see equation in Figure 2 captions). This method leadsto the PSD function of any structure placed in a simulation box.Since we use periodic boundary conditions in all three directionsthere are also larger pores (mesopores) present between imagesof the structure. In the current studies we limited considerationsonly to micropores.

In our previous study we proposed a modification of the BGmethod [2]. It was proposed to use mass centers of adsorbed mol-ecules to determine the pore size distribution. In this case thenodes in the structures are replaced by the centers of benzene ringsof adsorbed molecules in equilibrated simulation boxes (inset inFigure 4). PSD curves obtained in this way provide informationabout diameters of pores (D) filled by adsorbed molecules, and al-low to conclude what is the influence of porosity as well as of oxi-dation on the distribution of adsorbed molecules among poreswith different diameters.

Summing up: Series 1, 2 and 3 should have different distribu-tion of carbonyl groups (in Series 1 and 2 the groups are distributedrandomly, in Series 3 they are bounded to the edges of crystallites).Next 3 series (with different porosity) are obtained from Series 1by displacement of microcrystallites. Using those VPCs in connec-tion with MD simulation technique after equilibration of the sys-tem one can calculate the distribution of adsorbed moleculesamong pores and in this way, to study the effect of porosity andchemical composition of carbon surface on the changes inadsorption.

3. Molecular Dynamics simulation

All simulations were performed using Gromacs MolecularDynamics package [15]. Water was modelled using the TIP4P mod-el [16] and the Lennard-Jones potential parameters for carbonwere taken from [3,17] (carbon structures are treated as rigid

Figure 2. Histogram of pore size distribution (deff is the effective pore diameter) obtainedistribution of surface oxygen groups) and 1 � 1.500 (i.e. series where we analyse the effArrow shows the changes from the initial structure up to the structure with maximum

during simulations). Simulations were performed in the isobaric-isothermal Ensemble with Berendsen thermostat and barostat(298.15 K, 1 atm). The density of water far from the structure aftersimulations is always close to 0.997 g/cm3. Periodic boundary con-ditions were applied in all three directions, cut-offs for electrostat-ics and van der Waals interactions were located at 0.90 nm. Theparameters for organic molecules were taken from the OPLSAAforce field projected for simulation of condensed phases (we dis-cuss those parameters in our previous study – see [18]) [19–21].Simulations were performed for the time range 12.5–30 nsdepending on the studied system. The number of organic mole-cules was equal to 50 per box. Equilibrium was checked by plottingkinetic curves. For this purpose we checked the number of ad-sorbed molecules, moreover, we also monitored the number ofmolecules adsorbed in the internal part of a simulation box to en-sure that there is no diffusion flow after adsorption. All equilibriumproperties (including BG pore size distribution for adsorbed phe-nol) were calculated from last 0.5 ns. We performed 84 simulationsin this study.

4. Results and discussion

Typical BG pore size distributions collected in Figure 2 confirmthat applied procedure of virtual oxidation practically does notchange the geometric PSD of carbons from Series 1–3 (note thatthe same results were obtained for other VPC series studied in thisLetter). The rise in distance between microcrystallites leads to therise in the average micropore diameters, therefore the largestmicropores are observed for the Series 1 � 1.500 (Figure 2). Ob-tained results of the probability of finding molecules in pores canbe divided into two groups. Since large amount of data has beencollected in this Letter we present only representative and sum-mary results (the results for all system follow the general regular-ities). Those obtained for Series 1–3 (i.e. the series having differentdistribution of surface carbonyls, see Figures 3 and 4) generallyshow, that the probability of adsorption of all three molecules in

d from the BG method for the Series 1–3 (i.e. series where we analyse the effect ofect of porosity). Upper panel shows the integral PSD curves (fintðdeff Þ ¼

Pd06deff

Pðd0Þ).number (240) of surface carbonyls.

Figure 4. The probability of adsorption of all three molecules in the pores of Series 2.

Figure 3. Histogram of pore size distributions calculated for adsorbed molecules (D is the effective pore diameter where molecule are adsorbed) obtained from the BGmethod for the Series 1. Upper panel shows the integral PSD curves (fintðDÞ ¼

Pd06DPðd0Þ). Inset shows a schematic representation of the modification of BG method applied in

this study. This method allows calculate the pore size distributions from equilibrium MD configurations of adsorbed molecules.

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small pores decreases with the rise in the number of surfacegroups. One can also see that among studied molecules the proba-bility of adsorption inside micropores decreases from benzenedown to paracetamol.

We can compare the results for Series 1 and 2 since both pos-sess randomly placed carbonyl groups. It was recently concluded(from previous MD simulation results) that the location of groupspractically does not change the value of the enthalpy of carbonimmersion in water [3]. However, one can see that the locationof groups has influence on adsorption of studied molecules. Thisis visible especially for larger oxygen contents, and this is impor-

tant observation (see Figure 4). Moreover, one can also see thatfor all three molecules the introduction of small amount of oxygenalmost does not change accessibility to the smallest pores. Stronglymarked influence is observed for carbons containing larger numberof groups than ca. 11.5%. It is also interesting, that in spite of differ-ences in diameters of phenol and paracetamol, both moleculeshave almost similar accessibility to the smallest pores (see, forexample Figure 4).

The comparison of the results obtained for Series 1 and 2 withthe results obtained for Series 3 (where the groups are locatedon the edges of structure) show almost no influence of location

Figure 5. The comparative results showing correlation between the probability of adsorption in micropores and the contents of oxygen.

Figure 6. The correlation between average micropore diameters calculated from application of the BG method for adsorbed molecules and from typical BG method applied

for structures (Figure 2). Average effective micropore diameters from BG method were calculated using Dmi;av ¼P

D62nmD�PðDÞ

PD62nm

PðDÞor deff;mi;av ¼

Pdeff 62nm

deff �Pðdeff ÞP

deff62nmPðdeff Þ

.

106 A.P. Terzyk et al. / Chemical Physics Letters 515 (2011) 102–108

Figure 7. A correlation between the number of water molecules displaced per oneorganics molecule (r) and the contents of oxygen for a series 1 � 1.250.

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of surface groups on benzene accessibility to small micropores(this can bee seen only for large number of groups), and a decreasein adsorption after surface oxidation observed for the two remain-ing molecules. Thus, the most important conclusions from this partof our study is that for the initial carbon (i.e. does not containingoxygen) adsorption decreases from benzene down to paracetamol(in accordance with experimental data – see [22,23]) and the loca-tion of surface groups has the influence on accessibility of mole-cules to the smallest pores, whereas this effect is the moststrongly pronounced for phenol and paracetamol only if carboncontains larger amount of surface oxygen.

Figures 5 and 6 show the summary of the results presented inthe form shown in Figures 2–4. We plotted here the comparativeresults of probability of adsorption (in micropores i.e. in pores withdiameter (deff and/or D) smaller than 2 nm) vs. oxygen contents,and average micropore diameters. Considering the changes in por-ous structure due to rise in a distance between the microcrystal-lites (i.e. the rise in micropore diameter) a progressive decreasein adsorption is observed with the rise in a distance betweenmicrorystallites forming carbon structure. Also a progressive

Figure 8. Selected snapshots showing adsorbed molecules in a slice cut from the

change in a shape of distribution curve occurs (from the type ob-served in Figures 3 and 4 to the s-shaped curve). Moreover, onecan also see that the effect of carbon surface chemical groups van-ishes with the rise in micropore diameters, however it is still ob-served, especially for phenol and paracetamol adsorbed oncarbons of Series 1 � 1.500 (possessing 180 and 240 carbonylgroups). Generally it can be concluded that a progressive rise inmicropore diameter (for carbons without oxygen) has small influ-ence on probability of benzene adsorption (see Figure 5). In thiscase, the strongly marked decrease in adsorption is observed forthe Series 1 � 1.500 having the largest micropore diameter. How-ever, if we consider the series containing oxygen the decrease inbenzene adsorption is strongly pronounced if the number ofgroups increases. Similar situation occurs for the two remainingmolecules.

In Figure 5 one can also see a decrease in adsorption with a risein the number of surface oxygen groups. Therefore, we see niceinterrelation between two effects, i.e. pore accessibility stronglydepends on the concentration of surface groups, however this ef-fect vanishes for larger micropores (see the results for Series1 � 1.500 in Figure 5). In this case probability of adsorption of allmolecules is almost the same and surface oxygen almost doesnot play a role in adsorption.

The average micropore diameter calculated from BG method foradsorbed molecules is correlated with the BG pore diameter calcu-lated for the structures (Figure 6). We observe that the averagemicropore diameter calculated for adsorbed molecules is similarfor all three adsorbates. For the structure without oxygen groupswe observe that the smallest pores are accessible for benzeneand this is in agreement with Gurvitch’s rule. Moreover one canalso clearly observe how the distribution of surface groups influ-ences accessibility of molecules to pores (see for example the dif-ferences in diameters of pores accessible for benzene for thestructures containing 240 groups). It is interesting that for thestructure with larger micropores those differences in accessibilityvanish and we observe the same accessibility for all three mole-cules and for each oxygen contents. This result in our opinionclearly demonstrates, that for larger micropores the differencesin adsorption are not caused by the collision diameters of adsorbedmolecules but that those differences in accessibility to microporesare resulted by the pore blocking effect.

We were interested in the calculation of the number of watermolecules displaced by a single adsorbed molecule. This ratio (r)is usually calculated as the ratio of molar volumes of solute andwater. In our previous study [24] calculated in this way ratio forphenol–water system was equal to 4.91 and for paracetamol–water to 5.81. Obtained from simulation results are shown in

internal part of the simulation box containing two representative structures.

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Figure 7. We have chosen structure where water has full accessibil-ity to the internal part of carbon model. As one can observe, r valueincreases with the rise in molar volume of a solute molecule.However primarily results showed in Figure 7 clearly indicate thatr depends on the chemical composition of carbon layer. This prob-lem will be studied in next papers because as it is shown in Figure 8(showing selected snapshots in the thin slice cut from the internalpart of simulation box for one of studied structures) the number ofwater molecules inside a simulation box depends on the porosityand chemical composition of carbon surface layer.

5. Conclusions

We present the first MD simulation results of organics adsorp-tion on microporous carbon model. Our complex study (84 systemsaltogether) are in agreement with experimental data showing that:

(1) Adsorption in small micropores (ca. 0.7 nm) of carbons donot possessing surface oxygen groups depends on the colli-sion diameter of molecules (Gurvitch’s rule) and decreasesfrom benzene down to paracetamol.

(2) The presence of carbon surface oxides decreases adsorption,and this effect is the strongly pronounced for phenol andparacetamol, i.e. for polar molecules, this effect also dependson the porosity of carbon, i.e. it almost vanishes for largemicropores, for carbons with small micropore diameteradsorption depends on location of surface groups in struc-ture. This observation makes it possible to explain experi-mental results reporting differences in adsorption forcarbons having similar pore size distributions and similarcontent of oxygen functionalities.

(3) The assumption that the number of water molecules dis-placed by a solute molecule calculated from the ratio ofmolar volumes is a rough approximation.

Summing up, pore blocking effect dominates but the power ofthis effect depends on pore diameter. The details of the pore block-ing mechanism will be reported in the next paper of this series.

Acknowledgments

Authors acknowledge the use of the computer cluster at Torun(the Information and Communication Technology Centre of the

Nicolaus Copernicus University, Poland) and at Poznan (PoznanSupercomputing and Networking Centre). S.F. gratefully acknowl-edges the financial support from the Foundation for Polish Science.The paper was supported by Grant No. N204 288634 (P.G.).

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