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Intercalation of HF, HO and NH Clusters Within the Bilayers of Graphene and Graphene Oxide: Predictions from Coronene-based Model Systems Rohini Krishnakumar, Muthiah Ravinson Daniel Sylvinson, and Rotti Srinivasamurthy Swathi J. Phys. Chem. A, Just Accepted Manuscript • DOI: 10.1021/acs.jpca.5b05702 • Publication Date (Web): 15 Oct 2015 Downloaded from http://pubs.acs.org on October 20, 2015

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The Journal of Physical Chemistry

Intercalation of HF, H2O and NH3 Clusters within the Bilayers of Graphene and Graphene Oxide: Predictions from Coronene-Based Model Systems Rohini K, M. R. Daniel Sylvinson and R. S. Swathi* School of Chemistry, Indian Institute of Science Education and ResearchThiruvananthapuram, Kerala, India – 695016 E-mail: [email protected]

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ACS Paragon Plus Environment


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ABSTRACT Understanding molecular interactions with monolayers and bilayers of graphene and its derivatized forms is very important because of their fundamental role in gas sensing and separation, gas storage, catalysis, etc. Herein, motivated by the recent realization of graphene-based sensors for the detection of single gas molecules, we use density functional theory to study the non-covalent interactions of molecules and molecular clusters with graphene, graphene oxide and graphane, which are represented by coronene-based molecular model systems, C24H12 (coronene), C24OH12 (coroepoxide) and C24H36 (perhydrocoronene) respectively. The objective is to understand the structural and energetic changes that occur as a result of adsorption on monolayers and intercalation within bilayers. To begin with, the interactions of coronene, coroepoxide and perhydrocoronene with a variety of small molecules like HF, HCl, HBr, H2O, H2S, NH3 and CH4 are studied. Subsequently, the binding of coronene and coroepoxide substrates with molecular clusters of HF, H2O and NH3 is studied to understand the strength of adsorption on the substrates and the effect of substrates on hydrogen bonding interactions within the molecular clusters. Further, bilayers of the model systems, namely, coronene-coronene, coronene-coroepoxide and two configurations of coroepoxide-coroepoxide (one in which the oxygen atoms are facing each other and the other in which they do not face each other) are generated. The energetics for the nanoscale confinement or intercalation of the clusters within the bilayers along with the impact of the intercalation on the intermolecular hydrogen bonding interactions are investigated. Our coronene-based model systems can provide a simple way of describing the rather complex events that occur in representative regions of graphene-based heterogeneous substrates.

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KEYWORDS: coronene, perhydrocoronene, circumcoronene, graphene, graphene oxide, graphane, molecular clusters, hydrogen bonding, bilayers, intercalation.

INTRODUCTION Successful synthesis of graphene, a one atom thick, single sheet of carbon atoms arranged in a honeycomb lattice in the year 2004 has led to the emergence of its exciting features including giant charge carrier mobility, experimental observation of Dirac-like electronic energy band structure, room temperature quantum Hall effect and high thermal conductivity.1-5 Owing to its extraordinary properties, graphene has also attracted immense interest in a variety of areas ranging from electronics, single molecule gas detection to medicine.6-9 The last decade witnessed the development of synthetic methodologies for the covalent and the non-covalent functionalization of graphene.10 Immense conductivity of pristine graphene poses serious problems for its applications. Tuning the electronic properties by doping, derivatization, functionalization, adsorption and intercalation has emerged as a useful strategy for exploring the full potential of this wonder material, graphene.11,12 Derivatised forms of graphene like graphene oxide, graphone, graphane and fluorographene are currently being explored for novel applications.10 Graphene oxide (GO) is a single graphitic layer containing aromatic regions as well as oxygenated aliphatic regions with epoxy, hydroxyl, carbonyl and carboxyl functional groups.13-16 Graphene oxide exhibits a remarkable hydrophilic character due to the presence of oxygenated groups. Coating of graphite oxide with tetrabutyl ammonium ions is employed as a strategy to fabricate mosaic-like monolayers of GO. The coating reduces electrostatic repulsions and hydrogen bonding interactions to form monolayers.17,18 Graphone is a partially hydrogenated form of graphene in which half of the carbon atoms in graphene lattice are 3



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hydrogenated.19,20 Graphane, the fully hydrogenated form of graphene was initially proposed theoretically, subsequent to which experimental synthesis was reported by exposing graphene to hydrogen plasma discharge.21-23 Transformation from graphene to graphane leads to a complete change of the electronic properties from that of a highly conducting semimetallic behavior to an insulator. Fluorographene is a fully fluorinated form of graphene and is a 2D analogue of Teflon.24,25 Graphene and derivatized forms of graphene offer applications as gas sensors.6, 26, 27 Geim et al. studied the detection of individual gas molecules adsorbed on graphene surface6 by observing the changes in electrical conductivity on adsorption of gas molecules on the graphene surface. There have been several reports related to adsorption of small molecules on the surface of graphene.6,28-41 Leenaerts and group performed first-principles calculations to study the adsorption of molecules like H2O, CO, NO2 and NH3 on graphene surface.29 Garcia-Fernandez and coworkers studied the interaction of NO on the face as well as the edges of perfect and defective graphene sheets. The interaction on face leads to physisorption, while at the edges of defective clusters leads to CN chemical bond formation.42 The effect of electric field on the adsorption of CO on pristine as well as defective graphene lattice has also been investigated recently.28 Studies have also been performed on few layers of graphene and its derivatives to explore the mode of interaction between the layers.43-47 Further, investigations focused on understanding the effect of confinement of molecules within the bilayers of graphene have also been undertaken. It has been found that the intercalated structures of the target molecules placed between two coronene layers are about two times more stabilised than in the presence of a single substrate.48 The geometries of intercalated structures obtained by incorporating melamine tetramers in between two graphene layers reveal that the graphene layers separate from each other during intercalation and the intercalated melamine tetramer changes from a 3D to a 2D 4


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structure.49 Qian and Wei have studied the phase diagram of water between two graphene sheets in the presence of an electric field.50 Based on the electric field strength, water confined between the layers can form amorphous, hexagonal or rhombic bilayer ice at low temperature. Recent activities in this area are directed towards utilizing graphene oxide for gas sensing applications.51-53 The presence of oxygen containing groups on the surface is expected to enhance the interaction energies and charge transfer processes. A comparative study of the non-covalent interactions of an organic pollutant on the surface of graphene oxide in the presence and absence of oxidative debris has been reported recently.54 Motion of water molecules through graphene oxide layers has also been studied.55-58 A recent work by Kim and co-workers probed the intercalation of gas molecules like CO2, CH4, N2 and H2 between graphene oxide interlayers.59 They have studied the interactions using graphene oxide interlayers which are swelled with water as well as dried ones. Herein, we first study the adsorption of a set of molecules, HF, HCl, HBr, H2O, H2S, NH3 and CH4 on the three electronically different substrates, graphene, graphene oxide and graphane that are represented by coronene-based model systems. In graphene, all the carbon atoms are in sp2 hybridised state, while in graphane, they are all sp3 hybridised. In graphene oxide, sp2 hybridised aromatic regions are interspersed with sp3 hybridized oxygenated carbon atoms. Based on the results from the initial studies, HF, H2O and NH3 are chosen for further detailed investigation of the concentration effects of these molecules on the adsorption on monolayers and intercalation within bilayers of graphene and graphene oxide. The study of agglomeration of molecules in confined nanoscale environments is a subject of great interest.60 To the best of our knowledge, this study is the first report on confinement effects on hydrogen-bonded molecular clusters intercalated within the bilayers of graphene and

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graphene oxide. Understanding molecular interactions at the interfaces is very important for applications in catalysis, energy storage and sensing applications.

COMPUTATIONAL METHODOLOGIES

All the computations reported in this manuscript are performed using the dispersionincluding density functional theory with the M06-2X functional at M06-2X/6311+G(d,p)//M06-2X/6-31G(d,p) level. This hybrid meta exchange-correlation functional has earlier been employed for modeling non-covalent interactions, particularly those involving graphene-based systems.28,

61

The interaction energies corresponding to the adsorption of

single molecules on the monolayers are evaluated using Eint = Ecomplex - Emonolayer - Emol,

(1)

where Ecomplex, Emonolayer and Emol are the energies of the complex, monolayer substrate and the molecule respectively. The total interaction energy associated with the adsorption of n molecules (where n=2, 3, 4 and 5) on a monolayer substrate is calculated using Eint = Ecomplex - Emonolayer - nEmol.

(2)

When molecule(s) is (are) intercalated within the bilayers, the interaction energies are evaluated using Eint = Ecomplex - Elayer1 - Elayer2 - nEmol,

(3)

where Ecomplex is the energy of the bilayer-molecule(s) system while Elayer1 and Elayer2 are the energies of the two monolayer substrates that make up the bilayer. Emol refers to the energy of the molecule. The interaction energies (Eint) defined so far for the adsorption or intercalation of molecular clusters (n=2, 3, 4 and 5) account for all the non-covalent interactions including 6


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substrate-cluster interactions (i.e. interactions between the molecular clusters and the monolayer/bilayer substrates) and the hydrogen bonding (H-bonding) interactions within the molecular clusters. The interaction energies solely due to the substrate-cluster interactions are therefore calculated as follows: Esub-cluster = Ecomplex - Emonolayer/bilayer - Ecluster,

(4)

where Emonolayer/bilayer and Ecluster are the single point energies of the monolayer/bilayer substrate and the molecular cluster respectively in the geometry of the complex. The numerical values of Esub-cluster are indicative of the strengths of adsorption on monolayer substrates and intercalation within bilayer substrates. The energies associated with the stabilization of bare molecular clusters (i.e. clusters not bound to any substrate) by means of intermolecular interactions are evaluated using Ebare cluster= Ecluster - nEmol,

(5)

where Ecluster refers to the energy of the hydrogen-bonded molecular cluster at its optimized geometry. The energy of interaction between the two monolayers in a bilayer complex (without any intercalated molecules), Elayer1-layer2 is calculated using Elayer1-layer2 = Ebilayer - Elayer1 - Elayer2.

(6)

Although the M06-2X functional has been extensively used for graphene-based systems, further validation of the methodology is done by performing calculations for the adsorption and intercalation of pentameric molecular clusters using a dispersion-corrected density functional, ωB97X-D at the ωB97X-D/6-311+G(d,p)//ωB97X-D/6-31G(d,p) level.62 The computations reported herein are all carried out using the Gaussian-09 suite of programs.63 Additionally, Quantum Theory of Atoms in Molecules (QTAIM) calculations have been performed to assess the strength of H-bonding interactions. These calculations are implemented using the AIMAll package.64 7



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RESULTS AND DISCUSSION The main objective of this work is to understand the structures and energetics of the complexes of molecules and molecular clusters with monolayers and bilayers of graphene and derivatized forms of graphene, namely graphene oxide and graphane. The three electronically different substrates are used to understand non-covalent interactions in confined hydrophobic vs hydrophilic regions. Coronene-based model systems, namely coronene (C24H12), coroepoxide (C24OH12) and perhydrocoronene (C24H36) are chosen as models for the three electronically different substrates, graphene, graphene oxide and graphane respectively. Coronene has earlier been used as a model for graphene in numerous theoretical studies.30,32 As a model for graphene oxide, we use a structure obtained by introducing an epoxide linkage at a C-C bond on the central ring in coronene and refer to it as coroepoxide. The choice of this model system is motivated by the fact that under oxygen-rich conditions, graphene is found to have numerous epoxy linkages. The fully hydrogenated form of coronene, perhydrocoronene (C24H36) is used as a model for graphane. One would expect the energetics of adsorption of various molecules on each of the substrates to be different because of the difference in their electronic structure. Coronene has a π-electron cloud, while in coroepoxide, the π-cloud is distorted due to the epoxide functionalisation. Perhydrocoronene is a fully saturated hydrocarbon lacking π-electrons. The optimized geometries of these model systems are shown in Figure 1. The C-O distance in coroepoxide is found to be 1.41 Å, which is similar to the C-O distance in graphene oxide reported earlier.16 The initial geometries for the adsorption of a set of molecules, HF, HCl, HBr, H2O, H2S, NH3 and CH4 on the model systems are generated by placing the molecules in their optimized geometries at a distance of ~2.5 Å from the substrates and full geometry optimizations are performed. The geometries of the resultant lowest energy adsorbate-substrate complexes 8


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along with the interaction energies (Eint) are given in Figure 2. Eint is evaluated using equation (1) of the computational methodologies section. The average distances between the centre of mass of the adsorbate and that of the substrate are shown in Table 1. The mode of interaction in the case of adsorption of molecules on coroepoxide systems is largely dominated by hydrogen bonding interactions with the epoxide oxygen. The primary modes of interaction of adsorbates with the coronene and perhydrocoronene systems are polar-π and dispersion interactions respectively. Consequently, the binding energies are the largest for coroepoxide systems and the lowest for perhydrocoronene systems. An exception to this is the case of adsorption of CH4, wherein strongest binding is found for coronene. This anomaly is a consequence of the non-polar nature of CH4 which prevents the formation of strong Hbonding interactions with the epoxide oxygen of coroepoxide. Additionally, the interaction of CH4 with the extended π cloud of coronene is more effective than with the distorted π cloud of coroepoxide. From the adsorption geometries, it is clear that the electron deficient ends of molecules face the π-electron cloud for adsorption on coronene. The complexes of coroepoxide are characterized by short O…H-X distances (with X=F, Cl, Br, O, S, N and C) listed in Table 1, indicative of the existence of H-bonding interactions that ultimately lead to large binding energies. Previous calculations on the adsorption of a H2O molecule on coronene substrate with the same functional reported an interaction energy of -4.63 kcal/mol and intermolecular distance of 3.20 Å which are in good agreement with our findings.31 Another study on adsorption of H2O, NH3 and CH4 molecules on the coronene substrate reported interaction energies of 3.55, -3.33 and -2.79 kcal/mol respectively.33 A previous work on adsorption and dissociation of NH3 on graphene oxide reported an interaction energy of -7.10 kcal/mol and intermolecular separation (O…H distance) of 2.11 Å.52 A similar work by Peng and Li aimed at studying the adsorption of NH3 on graphene oxide reported -3.29 kcal/mol as the 9



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interaction energy.32 Our calculation gives an interaction energy of -4.79 kcal/mol and an intermolecular separation (O…H distance) of 2.29 Å for the binding of NH3 on coroepoxide. In Table 2, we provide a comparison of the coronene-H2O, coronene-NH3 and coronene-CH4 interaction energies obtained using DFT/CC, MP2 and DFT-D approaches. This includes our own results using the M06-2X and ωB97X-D methodologies as well as other reports from the literature.

Coronene

Coroepoxide

Perhydrocoronene

Figure 1. Optimized geometries of the three model systems used in this study for representing graphene, graphene oxide and graphane. Due to their strong binding with various molecules, coronene and coroepoxide are chosen as the substrates for further studies on molecular adsorption. Based on the fact that the difference in electronegativity between hydrogen and fluorine, oxygen or nitrogen is large, HF, H2O and NH3 molecules are chosen as representatives for monohalides, dihydrides and trihydrides in order to study the concentration effects on adsorption. HF, H2O and NH3 are capable of forming strong hydrogen-bonded molecular clusters. Further, it is clear from Figure 2 that the binding energies are very high for the adsorption of these three molecules on various substrates. The initial geometries of the dimeric, trimeric, tetrameric and pentameric molecular clusters of HF, H2O and NH3 are created so as to have favorable intermolecular Hbonding interactions and full geometry optimizations are performed at the same level of theory as earlier (M06-2X/6-311+G(d,p)//M06-2X/6-31G(d,p)). The optimized geometries of the bare molecular clusters, along with the interaction energies (evaluated using equation (5) 10


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of the methodologies section) are reported in Figure 3. The average intermolecular Hbonding distances are also reported in Figure 3. In order to validate the methodology, cluster geometries were also optimized at the ωB97X-D/6-311+G(d,p)//ωB97X-D/6-31G(d,p) level. The interaction energies as well as the average hydrogen bond lengths of molecular clusters of HF, H2O and NH3 obtained with the MO6-2X and the ωB97X-D functional are plotted as a function of the cluster size in Figure 4. The numerical values of the interaction energies of the various molecular clusters of HF, H2O and NH3 are given in Table 3 along with the results from previous reports on such clusters.65-71 Molecule/ Substrate

Coroepoxide

Coronene

Perhydrocoronene

-9.61

-3.63

-7.54

-4.55

-6.63

-4.44

-2.17

-6.41

-4.53

-2.63

-6.09

-5.71

-3.02

-4.79

-4.59

HF -1.65

HCl -2.85

HBr

H2O

H2S

NH3 -2.80

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CH4 -2.94

-3.69

-1.44

Figure 2. The optimized geometries and the interaction energies (in kcal/mol) of the complexes of coronene, coroepoxide and perhydrocoronene with various molecules.

Table 1. The average intermolecular distances of the adsorbates from the substrates (in Å). Substrate/Molecule HF

HCl

HBr

H2O

H2 S

NH3

CH4

Coroepoxide

4.37a (1.80)b

3.43 (1.94)

3.79 (2.06)

3.97 (2.12)

4.36 (2.26)

4.65 (2.29)

4.49 (2.54)

Coronene

2.72

4.39

4.17

2.94

3.93

3.67

3.53

Perhydrocoronene

3.65

4.34

3.79

3.49

4.16

4.41

4.34

a

The distance between the centre of mass of the adsorbate and that of the substrate.

b

The shortest distance between the epoxide oxygen and the hydrogen atoms in the adsorbates.

Table 2. The interaction energies (in kcal/mol) for the adsorption of H2O, NH3 and CH4 on coronene obtained using various methodologies. H2O

NH3

CH4

-4.53 (M06-2X)a

-4.59 (M06-2X)a

-3.69 (M06-2X)a

-5.41 (ωB97X-D)a

-4.94 (ωB97X-D)a -4.23 (ωB97X-D)a

-4.63 (M05-2X)b

-3.62 (MP2)d

-3.75 (MP2)d

-3.62 (B97-D)c

-3.33 (DFT/CC)d

-3.96 (MP2)e

-3.37 (BLYP+D)c

-2.79 (DFT/CC)d

12


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-3.05 (DFT/SAPT)c

-2.85 (CCSD(T))e

-3.79 (MP2)d -3.55 (DFT/CC)d

a

This study. b Ref 31. c Ref 40. d Ref 33.e Ref 39.

Table 3. The interaction energies (in kcal/mol) of bare clusters of HF, H2O and NH3 obtained using various methodologies. (HF)2

(HF)3

(HF)4 -30.54 (M06-2X)a

(HF)5

-5.52 (M06-2X)a

-17.74 (M06-2X)a

-41.40 (M06-2X)a

-4.94 (ωB97X-D)a

-15.88 (ωB97X-D)a -33.29 (ωB97X-D)a -43.81 (ωB97X-D)a

-4.37 (MP2)b

-15.20 (B3LYP)c

-28.89 (B3LYP)c

-39.89 (B3LYP)c

-4.51 (B3LYP)c

-13.79 (B3PW91)c

-26.57 (B3PW91)c

-36.81 (B3PW91)c

(H2O)3

(H2O)4

(H2O)5

-3.87 (B3PW91)c -4.57 (CCSDT(Q))d (H2O)2 -6.46 (M06-2X)a

-20.04 (M06-2X)a

-6.33 (ωB97X-D)a


-4.54 (B3LYP)f

-14.21 (B3LYP)f

-24.39 (B3LYP)f

-36.31 (MP2)e

-3.97 (B3PW91)f

-12.81 (B3PW91)f

-23.78 (B3PW91)f

-36.01 (CCSD(T))e

-4.97 (MP2)e

-15.82 (MP2)e

-27.63 (MP2)e

-5.01 (CCSDT(Q))d -15.70 (CCSD(T))e (NH3)2

(NH3)3

-33.54 (M06-2X)a

-43.92 (M06-2X)a

-27.43 (CCSD(T))e (NH3)4 -19.94 (M06-2X)a

(NH3)5

-3.96 (M06-2X)a

-13.18 (M06-2X)a

-4.13 (ωB97X-D)a


-3.20 (MP2)g

-13.02 (MP2)h

-20.12 (MP2)h

-25.20 (M06-2X)a

-25.48 (MP2)h

-3.15 (CCSDT(Q))d

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a

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This study. b Ref 70. c Ref 71. d Ref 66. e Ref 65. f Ref 69. g Ref 68. h Ref 67.

Subsequently, the hydrogen-bonded molecular clusters in their optimized geometries are placed on the coronene and the coroepoxide substrates at a distance of ~2.5 Å and full geometry optimizations are performed. The optimized geometries and the interaction energies (Eint) of the entire assemblies are given in Figures 5 and 6 respectively. Eint is evaluated using equation (2) of the methodologies section. The Eint values reported include the contributions from the substrate-cluster interactions as well as the H-bonding interactions within the clusters. In order to separate out the binding energies of the molecular clusters to the substrates, we use equation (4) to calculate Esub-cluster values and these are reported in parentheses in Figures 5 and 6. In Figure 6, the shortest O…H distances (‘O’ refers to the epoxide oxygen) are also given.

Molecule/Cluster

Dimer

Trimer

Tetramer

Pentamer

HF -5.52 (1.82)

-17.74 (1.65) -30.54 (1.43) -41.40 (1.35)

H2O -6.46 (1.92)

-20.04 (1.85) -33.54 (1.70) -43.92 (1.67)

NH3 -3.96 (2.22)

-13.18 (2.11) -19.94 (2.03) -25.20 (2.03)

Figure 3. The optimized geometries of the dimeric, trimeric, tetrameric and pentameric molecular clusters of HF, H2O and NH3 along with their interaction energies (in kcal/mol) and the average intermolecular hydrogen bonding distances (in Å in parentheses). 14


HF @ M06-2X

0

H2O @ B97X-D NH3 @ M06-2X NH3 @ B97X-D

-15

HF @ M06-2X

3.0

HF @ B97X-D H2O @ M06-2X

Average bond length (Å)

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60


Interaction energy (kcal/mol)

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-30

-45

HF @ B97X-D H2O @ M06-2X H2O @ B97X-D

2.5

NH3 @ M06-2X NH3 @ B97X-D

2.0

1.5

1.0

2

3

4

5

2

3

4

Cluster size

Cluster size

(a)

(b)

5

Figure 4. (a) and (b) show a comparison of the interaction energies and the average hydrogen bond lengths of molecular clusters of HF, H2O and NH3 obtained using the M06-2X and the ωB97X-D methodologies. We now analyze the geometries and the binding strengths of the adsorbate-monolayer substrate complexes. For clusters bound to coronene and coroepoxide monolayers, the total interaction energy, Eint increases (in magnitude) from dimers to pentamers, on account of increasing number of interactions. The substrate-cluster binding energy (Esub-cluster) is intuitively expected to follow the same trend. However there is a slight deviation. In all cases except the H2O/coronene systems, Esub-cluster increases from trimers to pentamers (in magnitude) as a result of increasing number of substrate-cluster interactions. However, dimers show unusually higher values for Esub-cluster in comparison with the corresponding trimers (also tetramers and pentamers in some cases). The reason for this anomalous trend is that the open geometries of dimers allow the hydrogen atoms at the open ends (that are otherwise part of the inter-molecular hydrogen bonds in cyclic clusters) to reorient themselves for favorable interactions with the π-cloud in the case of coronene and epoxide 15



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oxygen in the case of coroepoxide as opposed to the closed geometries of trimers, tetramers and pentamers. The dimeric clusters bound to coroepoxide exhibit exceptionally higher values of Esub-cluster due to the strong H-bonding interactions between the epoxide oxygen and the hydrogen atoms at the open ends of the dimers. The H2O/coronene systems stand out as an exception to this anomalous trend because in the optimized geometry of the dimeric cluster of H2O adsorbed on coronene, the hydrogen atoms in the dimer of H2O are obliquely oriented towards the π-cloud, thereby reducing the extent of interaction with the substrate leading to a lower value of Esub-cluster for the dimer. From the numerical values of Eint and Esubcluster,

it is clear that the H2O clusters have the strongest binding with coronene and

coroepoxide substrates among the trimeric, tetrameric and pentameric complexes of HF, H2O and NH3. However, among the dimeric complexes, HF forms the strongest complexes with coronene and coroepoxide.

16


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Molecule /Cluster

Dimer

Trimer

Tetramer

Pentamer

-14.06a (-9.23)b

-22.72 (-6.17)

-35.39 (-8.03)

-47.62 (-10.13)

-13.45 (-8.23)

-28.82 (-10.24)

-43.84 (-12.11)

-56.11 (-14.58)

-9.95 (-8.86)

-20.62 (-7.93)

-29.46 (-10.09)

-34.53 (-10.58)

HF

H2O

NH3

Figure 5. The optimized geometries and the interaction energies (in kcal/mol) for the complexes of coronene with the molecular clusters of HF, H2O and NH3. aEint and bEsub-cluster values.

17



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Molecule /Cluster

Dimer

Page 18 of 41

Trimer

Tetramer

Pentamer

-23.71 (-7.83) 2.37

-36.82 (-9.77)

-51.75 (-14.56)

2.43

2.32

-35.02 (-10.32) 2.24

-42.25 (-12.71)

-54.58 (-14.69)

2.23

2.47

- 26.82 (-7.78) 2.34

-34.52 (-8.87)

-41.79 (-11.29) 2.55

HF

-18.69a (-15.66)b 1.61c

H2O

-17.08 (-13.22) 2.04

NH3

-11.62 (-9.24) 2.25

2.56

Figure 6. The optimized geometries and the interaction energies (in kcal/mol) for the complexes of coroepoxide with the molecular clusters of HF, H2O and NH3. aEint, bEsub-cluster and cshortest O…H distances (in Å). Note that ‘O’ refers to the epoxide oxygen.

18


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-18.06 (3.3)

-19.19 (3.2)

-29.51 (3.0)

-22.94 (4.5)

-10.01 (3.8)

-17.82 (3.9)

-12.15 (4.5)

Figure 7. The optimized geometries and the interaction energies (in kcal/mol) of the homo and hetero-bilayers generated from the three substrates – coronene, coroepoxide and perhydrocoronene. Bilayer distances (center of mass distances in Å in parentheses) are also given. Table 4. The interaction energies (in kcal/mol) of coronene dimer and perhydrocoronene dimer obtained using various methodologies. (Coronene)2

(Perhydrocoronene)2

-18.06 (M06-2X)a

-12.15 (M06-2X)a

-17.91 (M06-2X)b

-13.45 (B3LYP-D3)c

-21.28 (B3LYP-D3)c

-9.18 (MP2)c

-23.45 (MP2)c

-13.55 (CCSD(T))c

-19.98 (CCSD(T))c

a

This study. bRef 46. cRef 43.

Further, we have obtained the optimized geometries of the homo and hetero-bilayers of coronene, coroepoxide and perhydrocoronene (see Figure 7). The coronene bilayers are stabilized by π-stacking while the perhydrocoronene bilayers are held by weak dispersion forces. In perhydrocoronene dimer, the hydrogens of one layer fill the cavity formed by the 19



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Page 20 of 41

cyclohexane building unit of the other layer. Two types of coroepoxide bilayers are initially chosen for geometry optimization, one of them where the epoxide oxygens face each other (coroepoxide-coroepoxide-face) and the other where the oxygens are far away (coroepoxidecoroepoxide-far). The structure with oxygen atoms far apart is found to be more stabilized due to lower repulsive interactions between the epoxide oxygens. The hetero-bilayers of the three substrates are also formed namely, coronene-coroepoxide, coronene-perhydrocoronene and perhydrocoronene-coroepoxide. In the coronene-perhydrocoronene structure, the C-H moieties of perhydrocoronene point to the π-cloud of coronene and is hence stabilized by CH/π interactions while the coronene-coroepoxide bilayer is stabilized largely by polar/π interactions. The interaction energies of the bilayers are evaluated using equation (6) of the methodologies section and are reported in Figure 7. Previous reports on coronene and perhydrocoronene bilayers with CCSD(T) level of calculations reported interaction energies of -19.98 and -13.55 kcal/mol respectively (given in Table 4).43 A similar study of coronene dimers using M06-2X reported an interaction energy of -17.91 kcal/mol.46 From our calculations we have obtained interaction energies (Elayer1layer2)

of -18.06 kcal/mol for coronene bilayer and -12.15 kcal/mol for perhydrocoronene

bilayer. The bilayers containing perhydrocoronene have been excluded from further studies as they interact weakly with the molecules. We have therefore considered coronenecoronene, coroepoxide-coroepoxide and coronene-coroepoxide bilayers for further studies on intercalation of HF, H2O and NH3 molecules and molecular clusters into the confined nanospaces in the region between the layers. Both the arrangements of coroepoxide bilayers (coroepoxide-coroepoxide-far and coroepoxide-coroepoxide-face) are taken as starting points to determine the optimal configurations with respect to intercalation. The optimized geometries of the complexes of the molecules and molecular clusters of HF, H2O and NH3 within the bilayers of coronene-coronene, coroepoxide-coronene and 20


Page 21 of 41

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coroepoxide-coroepoxide-far and coroepoxide-coroepoxide-face are given in Figures 8, 9, 10 and 11 respectively. Eint in this case (see equation (3) of the methodologies section) for the intercalation of dimeric, trimeric, tetrameric and pentameric clusters includes the interaction between the two layers of the bilayer, the interaction of the molecules within the molecular clusters as well as their interaction with the substrates. On the other hand, Esub-cluster accounts for the stabilization solely due to the interactions of the intercalated molecular clusters with the bilayers and are reported in parentheses in Figures 8, 9, 10 and 11. The separation between the two layers in the bilayer coronene was found to be 3.3 Å (see Figure 7). Upon intercalation of pentameric molecular clusters of HF, H2O and NH3 within the bilayer of coronene, the separation distance between the coronene layers increases to 5.7 Å, 6.0 Å and 6.7 Å respectively. The other bilayer complexes also show similar trends for the separation distance between the layers (i.e. NH3>H2O>HF). The Eint values in the case of HF, H2O and NH3 bound within coronene-coronene bilayers show an increasing trend from monomers to pentamers. An exception to this is the case of dimeric NH3 cluster. The calculations in this case do not yield an optimized geometry wherein the dimer is neatly intercalated within the bilayer. Esub-cluster also follows the same trend except for the HF dimeric cluster, for which in the optimized geometry, the hydrogen atom at the open end of the dimer is directed towards the π-electron cloud of coronene for better interaction, thereby accounting for a high value of Esub-cluster. Among HF, H2O and NH3, intercalation of H2O molecules within the bilayers leads to the strongest complexes. Note that the largest binding strengths are also found earlier for H2O adsorption on monolayer substrates. Eint values also increase from monomers to pentamers for coronene-coroepoxide bilayers with the exception of HF dimer where the substrate-substrate interactions are considerably high as is evident from the optimized structure which shows that both the 21



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substrates are at reasonably close proximity to each other. Further, Esub-cluster values for the coronene-coroepoxide systems also increase from monomer to pentamer again with the exception of the HF dimeric case where the strong H-bonding interaction of the open hydrogen end with the epoxide oxygen ensures a value of Esub-cluster higher than the trimeric case. The strong H-bonding interaction of the dimer with the epoxide oxygen is also reflected in the corresponding short O…H distance reported in Figure 9. In the case of coroepoxide-coroepoxide-far bilayers, Eint and Esub-cluster values follow the expected trends for H2O and NH3 clusters. In the case of the HF clusters, Eint increases from the trimers to the pentamers as expected. However, the monomeric and the dimeric case exhibit higher Eint than the other complexes which can be attributed to the strong substratesubstrate interactions on account of both the substrates found quite close to each other in the optimized geometries. Esub-cluster values for the HF clusters, increase from monomer to pentamer with the exception of the dimer which exhibits a higher value of Esub-cluster than the trimeric and tetrameric complexes again due to the H-bonding interaction of the hydrogen atom at the open end of the dimer with the epoxide oxygen as in the case of HF dimers within coronene-coroepoxide bilayers. The coroepoxide-coroepoxide-face bilayers show an increasing trend in the case of Eint for the HF, H2O and NH3 clusters. Even the Esub-cluster values show similar trends for H2O and NH3 clusters. However, as earlier, we see some deviations in the case of HF clusters. The dimeric and trimeric clusters of HF have higher Esub-cluster values than the tetrameric case. The higher value of Esub-cluster for the dimeric case can again be attributed to strong H-bonding between the hydrogen atom at the open ends and the epoxide oxygen. It is interesting to note that the trimer bound within the coroepoxide-coroepoxide-face bilayer is not cyclic as in all the other cases, but open ended in the lowest energy structure for better H-bonding interactions with both the epoxide oxygens thereby accounting for the higher value of Esub22


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cluster.

The strong H-bonding interactions with epoxide oxygens in the case of both the dimeric

and trimeric HF clusters are also reflected in the short O…H distances reported in Figure 11.

-16.85a (-4.85)b

-21.25 (-11.88)

-29.00 (-10.91) -42.95 (-14.07)

-56.33 (-17.85)

-10.74 (-7.30)

-23.34 (-12.99)

-36.01 (-16.03) -53.35 (-19.59)

-67.23 (-24.98)

-28.41 (-15.80) -38.13 (-19.39)

-44.62 (-21.60)

-15.15 (-6.22)

- 33.09 (-7.37)

Figure 8. The optimized geometries and the interaction energies (in kcal/mol) of the intercalated structures of HF, H2O and NH3 in the coronene-coronene bilayers. aEint and bEsubcluster values.

-22.10a (-10.58)b -33.50 (-13.98) -31.49 (-11.43) -43.00 (-15.53) -59.51 (-21.39) 1.85c

-16.31 (-9.27) 2.30

1.84

2.47

2.42

2.33

-30.37 (-17.42) -37.78 (-18.81) -51.58 (-21.16) -65.55 (-23.87) 2.28

2.23

2.27

2.44

23



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-17.79 (-8.74) 2.49

Page 24 of 41

-18.46 (-14.74) -34.88 (-15.64) -43.31 (-17.80) -51.44 (-21.48) 2.35

2.35

2.53

2.56

Figure 9. The optimized geometries and the interaction energies (in kcal/mol) of the intercalated structures of HF, H2O and NH3 in the coronene-coroepoxide bilayers. aEint, bEsubcluster

and cshortest O…H distances (in Å) are given. Note that ‘O’ refers to the epoxide

oxygen.

-32.57a (-11.31)b -29.86 (-17.67) c

-29.37 (-13.74)

-47.15 (-16.41)

-60.55 (-22.43)

1.79

1.70

2.11

2.46

2.35

-29.69 (-8.90)

-41.85 (-18.20)

-52.67 (-19.08)

-55.74 (-23.53)

-68.09 (-27.54)

2.44

1.98

2.21

2.45

2.16

-30.15 (-10.04)

-32.49 (-16.76)

-36.62 (-18.19)

-44.14 (-19.99)

-50.47 (-20.62)

2.63

2.30

2.25

2.62

2.63

Figure 10. The optimized geometries and the interaction energies (in kcal/mol) of the intercalated structures of HF, H2O and NH3 in the coroepoxide-coroepoxide-far bilayers. aEint, b

Esub-cluster and cshortest O…H distances (in Å) are given. Note that ‘O’ refers to the epoxide

oxygen. 24


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-21.34a (-11.66)b -31.70 (-19.66) -39.42 (-23.70) -57.57 (-17.04) -69.14 (-25.81) 1.83c

-20.72 (-10.49) 2.13

-23.78 (-7.56) 2.38

1.79

1.57

2.33

2.29

-39.92 (-18.33) -47.44 (-18.64) -59.36 (-24.21) -71.12 (-24.75) 2.28

2.16

2.10

2.54

-28.08 (-12.54) -39.66 (-14.78) -49.11 (-17.72) -57.94 (-21.42) 2.21

2.33

2.53

2.57

Figure 11. The optimized geometries and the interaction energies (in kcal/mol) of the intercalated structures of HF, H2O and NH3 in the coroepoxide-coroepoxide-face bilayers. a

Eint, bEsub-cluster and cshortest O…H distances (in Å) are given. Note that ‘O’ refers to the

epoxide oxygen. From the analysis thus far in terms of the numerical values of Eint and Esub-cluster, it is clear that the interaction of molecular clusters with the bilayers is stronger than with the monolayers. The binding of various molecular clusters with the monolayers and bilayers of coroepoxide and also the mixed coronene-coroepoxide bilayers is strongly affected by the hydrogen-bonding interactions between the molecular cluster and the epoxide oxygen atoms. From the values of Esub-cluster reported in Figures 8-11, we can infer that among the three types of intercalated molecular clusters, H2O clusters bind the strongest with the coronenecoronene, coronene-coroepoxide and coroepoxide-coroepoxide-far bilayers. However, when 25



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Page 26 of 41

clusters are intercalated into coroepoxide-coroepoxide-face bilayers, we find that in majority of cases, HF clusters bind more strongly with the bilayers than H2O clusters. In order to ascertain the role of structural models used to represent graphene and graphene oxide, we also considered circumcoronene (C54H18) and the corresponding epoxide functionalized form (C54H18O) as the model systems for graphene and graphene oxide respectively. Further, calculations are also performed using a dispersion-corrected density functional, ωB97X-D to analyze the role of computational methodology. Considering the computational costs associated with such model systems, we restrict our analysis to the adsorption and intercalation of the pentameric clusters of HF, H2O and NH3. Calculations for adsorption on monolayers were performed using both the functionals (M06-2X and ωB97XD), while those for intercalation within the bilayers were performed using the M06-2X functional. A detailed comparison of the results for the coronene-based model systems and the circumcoronene-based model systems is shown in Figures S1-S7. As can be seen from the figures, edge effects become more important for NH3 clusters, while they are less significant for HF and H2O clusters. This is to be expected because of the large size of the pentameric NH3 cluster. Finally, we assess the variation in the strength of the inter-molecular H-bonds that hold the cyclic molecular clusters together in the presence and absence of monolayer and bilayer substrates from two perspectives: structural and topological. The average value of the bondlengths of all the intermolecular H-bonds within the cluster (davg) is used as a structural parameter to assess the strength of the H-bonds that hold the cluster together with lower values of davg corresponding to stronger bonds. The average value of the QTAIM electron density at all bond critical points (BCPs) associated with the intermolecular H-bonds within the cluster (ρavg) is used for the assessment of the strength of intermolecular H-bonds with higher ρavg values indicating stronger bonds. It is evident from both the perspectives (Figure 26


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12) that, in all cases, the inter-molecular H-bonds associated with the molecular clusters indeed behave cooperatively with trimers having the longest H-bonds and the lowest ρavg values while pentamers have the shortest H-bonds and the highest ρavg values. In the case of HF clusters, the bare clusters (i.e. clusters not bound to any substrate) are found to possess the strongest H-bonds across all cyclic clusters (from trimers to pentamers) followed by clusters bound to monolayer coronene, coronene-coronene, coroepoxidecoroepoxide-far,

monolayer

coroepoxide,

coronene-coroepoxide

and

coroepoxide-

coroepoxide-face in the order of decreasing strengths. The interactions of the clusters with the epoxide oxygen of coroepoxide seem to weaken the intermolecular H-bonds within the cluster. This can be attributed to repulsions between the electronegative fluorine atoms within the ring and the epoxide oxygen of coroepoxide resulting in an expansion of the cyclic ring thereby weakening the H-bonds. This effect is the strongest in the case of coroepoxidecoroepoxide-face bilayer which has 2 epoxide oxygen atoms pointed towards the cyclic ring thereby resulting in the weakest H-bonds among all the substrates. The cyclic water clusters also exhibit similar trends with the surprising exception of the pentameric cluster of H2O adsorbed on monolayer coronene and intercalated within bilayer of coronene having marginally stronger H-bonds than the bare pentameric clusters. As in the case of HF clusters, all the coroepoxide systems exhibit weaker inter-molecular H-bonds due to repulsions between the oxygen atoms within the cyclic ring and the epoxide oxygen. On similar lines, the cyclic clusters of NH3 bound to the coroepoxide systems again exhibit weaker intermolecular H-bonds on account of the aforementioned repulsive interactions. However, the tetrameric and the pentameric clusters of NH3 bound to coronene monolayer and bilayer are found to have stronger H-bonds than those of the corresponding tetrameric and pentameric bare clusters.

27



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The exact reason for the anomalous strengthening of the inter-molecular H-bonds in the case of the pentamer of H2O and the tetramer and the pentamer of NH3 bound to coronene monolayer and bilayer over that of the corresponding bare clusters is elusive at this stage. However, the extra strengthening could be an effect of the interaction of the clusters with the π cloud of the coronene substrates. In the case of the pentamer of H2O bound to coronene bilayer, there are five hydrogen atoms oriented towards the π clouds of the coronene substrates for favorable polar-π interactions and the combined effect of these interactions could result in an anomalous strengthening of the inter-molecular H-bonds. Although, such polar/π interactions are also present in the lower order clusters (trimer and tetramer) of H2O bound to coronene bilayer and coronene monolayer, the number of such interactions (

Predictions from Coronene-Based Model Systems - ACS Publications

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