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 61 62 63 64 65

Theoretical study on the adsorption of pyridinederivatives on graphene

E. N. Voloshina!, D.Mollenhauer, L. Chiappisi, B. Paulus

Institut fur Chemie und Biochemie – Physikalische und Theoretische Chemie,Freie Universitat Berlin, Takustraße 3, 14195 Berlin, Germany

Abstract

The adsorption of pyridine and its derivatives on the graphene surface has

been studied using density functional theory (DFT). Adsorption geometries

and energies as well as nature of binding have been analyzed. Dispersion

e!ects have been taken into account via a semiempirical DFT-D2 method.

Influence of electron-donor and electron-acceptor substituents in 4-position of

the heterocyclic ring, e!ect of substrate and adsorbate’s concentration on the

interaction energy have been investigated. Impact of the pyridine adsorption

on the electronic band structure of graphene has been studied.

Keywords: Graphene; Adsorbates on surfaces; Electronic structure

calculations; First-principles calculations

Graphene, a recently discovered two-dimensional form of carbon, has at-

tracted unrivaled attention due to its unique physical properties and poten-

tial applications in electronics [1]. However, not less important is its ability

to passivate metal surfaces [2–5]. In combination with its intrinsic strength

and weak interaction with gold, silver and copper [6–9], this property of

!Corresponding authorEmail address: elena.voloshina@fu-berlin.de (E. N. Voloshina)

Preprint submitted to cplett April 25, 2011

*The ManuscriptClick here to view linked References

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 61 62 63 64 65

graphene can be used to improve stability of noble metal nanoparticles (see

e.g. Ref. [10]).

Metal nanoparticles have been identified as critical components in the de-

velopment of next-generation medical applications (for a Review, see Ref. [11]),

including cancer-destroying technologies, novel diagnostic devices, and new

controlled drug-delivery methods. Considering pyridine as a precursor to

pharmaceuticals [12], it is important to investigate the binding mechanism

of this molecule with nanoparticles. During such a study the substrate can

be modeled by one or several graphene monolayers: Since graphene is known

to be physisorbed on Au, Ag, and Cu [9], influence of metal filling on the

substrate-adsorbate binding energy is negligible.

Although interaction of pyridine with noble metal surfaces has been stud-

ied theoretically rather intensively [13–16], that is not the case when consid-

ering graphene-like substrates (The only publication related to the subject

of the present study we have found deals with adsorption of aminotriazines

on graphene [17]). This is not surprising, since one may expect significant

contribution of van der Waals e!ects in the latter case. Though satisfactory

for many applications, a standard density functional theory (DFT) approach

becomes inadequate if adsorption is caused by dispersion forces, that is a

consequence of local character of the most commonly employed exchange-

correlation functionals. However, a variety of practical methods have been

proposed in the past few years to make DFT calculations able to reproduce

well van der Waals e!ects (for a Review, see Ref. [18]).

In the present study we focus on the bonding of a single pyridine molecule

adsorbed on a graphene surface. The peculiar feature of this molecule is the

2

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 61 62 63 64 65

N N

par perp

Figure 1: (Color online) The pyridine-graphene arrangements are defined by the position

of N atom above the six-membered carbon ring (T/C) and the orientation of the pyridine

plane regarding the graphene surface: either parallel (par) or perpendicular (perp).

possibility to interact with the substrate: (i) via its planar aromatic !-like

molecular orbitals or/and (ii) through its nitrogen lone-pair electrons. In the

first case the pyridine adsorbs with its molecular plane parallel to surface,

while in the second case the heterocyclic ring is perpendicular to surface

(Fig. 1). At low coverage, the competition between these two adsorption

mechanisms might lead to tilted binding geometries as well.

The DFT calculations were carried out using the projector augmented

wave method [19], a plane wave basis set and the generalized gradient ap-

proximation as parameterized by Perdew et al. (PBE [20]), as implemented

in the VASP program [21]. The plane wave kinetic energy cuto! was 400 eV.

The calculations are performed with the experimental graphene lattice con-

stant of 2.464 A using a (4 ! 4) surface periodicity, that corresponds to an

3

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 61 62 63 64 65

Table 1: Adsorption energies (Eads in meV) and equilibrium distances (d0 in A) as

obtained for the 4-substituted pyridines. d0 is defined as a distance between nitrogen

atom of the heterocyclic ring and the graphene surface.

Substi- T-par C-par T-perp C-perp

tuent Eads d0 Eads d0 Eads d0 Eads d0

–H "357 3.37 "412 3.20 "218 3.05 "250 2.89

–F "382 3.39 "447 3.22 "209 3.13 "247 2.88

–Cl "412 3.36 "479 3.20 "210 3.14 "248 2.95

–Br "445 3.34 "510 3.16 "206 3.21 "232 3.14

–OH "400 3.38 "470 3.20 "212 3.12 "237 3.15

–NH2 "412 3.36 "489 3.19 "212 3.13 "257 2.88

–NO2 "472 3.33 "530 3.22 "209 3.08 "248 2.95

–OCH3 "472 3.37 "546 3.19 "215 3.15 "252 2.97

adsorbate concentration of approximately 1.2 · 10"2 A"2. In the total energy

calculations and during the structural relaxations (graphene geometry is kept

fixed and the molecular degrees of freedom are allowed to relax until atomic

forces are lower than 0.005 eV/A) the k-meshes for sampling of the supercell

Brillouin zone were chosen to be as dense as 24 ! 24 and 12 ! 12 k-mesh,

respectively, when folded up to the simple graphene unit cell. The vacuum

region between graphene layers was set to ca. 18 A. The relevance of long-

range van der Waals interactions on the molecule-surface adsorption process

was investigated by means of a semiempirical DFT-D2 approach proposed by

Grimme [22]. Cluster calculations are performed with the program package

MOLPRO [23].

The relative stability of the adsorption geometries can be assessed from

the calculated adsorption energy Eads defined as Eads = ES+M " ES " EM,

4

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 61 62 63 64 65

!"# !"$ %"# %"$ $"# $"$ &"#

'%##

'!##

'(##

')##

#

)##

*'+,-./012/012'3(

*'+4-+./012/012'3(

/

/

Adsorption energy (meV)

Pyridine­graphene distance (A)°

!"# !"$ %"# %"$ $"# $"$ &"#

'%##

'!##

'(##

')##

#

)##

*'+,-./012/012'3(

*'+4-+./012/012'3(

/

/

Adsorption energy (meV)

Pyridine­graphene distance (A)°

Figure 2: (Color online) Pyridine-graphene interaction energy as a function of substrate-

adsorbate distance as obtained with or without accounting for dispersion e!ects for the

four considered geometries. Pyridine-graphene distance is defined as a distance between

nitrogen atom of the heterocyclic ring and the graphene surface.

5

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 61 62 63 64 65

where ES+M represents the total energy of the relaxed pyridine-substrate

system, ES is the total energy of the isolated substrate, and EM is the total

energy of the isolated pyridine molecule, respectively.

When considering the pyridine/graphene system, the dispersion correc-

tion term represents the dominant contribution to the binding energy. The

interaction energies evaluated with the standard PBE functional are severely

underestimated. The corresponding equilibrium distances are very large and

energy minima are shallow (Fig. 2). The relaxed geometry of the pyridine

molecule obtained with the inclusion of the van der Waals forces is basically

the same as without considering these forces, the main geometrical e!ect is

reduction of the equilibrium distance between adsorbate and substrate, d0,

by ca. 17%, when employing the DFT-D2 scheme. Consequently, adsorp-

tion energies are increased in 10 or 15 times for the normal or flat adsorption,

respectively.

PBE-D2 predicts the adsorption of pyridine in parallel conformation to

be approximately 1.5 times stronger as compared to the case when pyridine

is normal to the graphene plane, with a small preference towards hollow

(C) adsorption site. That is not surprising, taking into account the fact

that the interaction between graphene and pyridine are mainly of dispersive

nature, therefore stronger for the parallel configuration, where substrate and

adsorbate have the larger contact area. Since pyridine and graphene rings are

geometrically fairly similar, the packing in a graphite-like manner is expected

to be energetically more favourable.

The equilibrium distances and adsorption energies computed for the se-

ries of 4-substituted pyridine derivatives are summarized in Tab. 1. When

6

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 61 62 63 64 65

! " #! #" $! $" %! %"

&$$"

&%!!

&%'"

&("!

&"$"

)*&+,-)).&+,-)*&+/-+).&+/-+

)

01/23)45-/6/)6789+-7:;<

=>2?/-)7@)/A/B9-76:)86)9C/):>?:989>/69

Figure 3: (Color online) Adsorption energy as a function of the number of electrons in the

substituents as obtained for the four considered geometries. Dashed lines are linear fits

performed for the data-points in order to visualize the general trend.

considering flat-adsorption, one observes rather strong enhancement of bind-

ing strength due to the H-substitution by up to 134meV (in the case of

4-methoxypyridine adsorbed at the hollow site) accompanied by insignif-

icant change in d0 of about 1%. The situation is controversial for the

normal adsorption: very small change in Eads as compared to the parent

molecule at substantial deviation in equilibrium distance by up to 9% if

4-hydroxypyridine occupies the hollow site.

E!ect of substituents on the adsorption energy can be attributed to two

phenomena: (i) a change in the binding properties of the aromatic nitrogen

(should be more important for the normal adsorption) or (ii) stronger van

der Waals interactions due to an increased number of atoms (and electrons)

in the molecule (should be more important for the flat adsorption). The fact

7

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 61 62 63 64 65

that the e!ect of substituents on Eads in the perpendicular conformations

is very weak gives us a hint that the main e!ect on the adsorption energy

has to be ascribed to increased van der Waals interactions. Fig 3 shows

the adsorption energies plotted as a function of the number of electrons in

the substituent: a clear trend can be recognised for T-par and C-par, with

an averaged linear growth of adsorption energy with increasing number of

electrons in the substituents (regardless of their electron-donor or electron-

acceptor character). The independence of the adsorption energy from the

substituents in the case of T-perp and C-perp is confirmed by the very small

slope of the fitted straight line.

Our calculations for graphite modeled by two-layered structure show an

increase of Eads by approximately 3" 8%, depending on adsorption position

and orientation of the pyridine molecule (Tab. 2). This enhancement of

adsorption energy is accompanied by insignificant change in d0, that is 0.01 A

and 0.02 A for top (T) and hollow (C) adsorption sites, respectively. Further

graphene monolayers have nearly no e!ect on the both Eads and d0.

Adsorption energy calculated for the energetically most favourable ar-

rangement of pyridine relative to the graphite surface ("441meV) is in rea-

sonable agreement with experimental result ("433meV [24]). Small devi-

ation may be due to e.g. the concentration e!ect, if further experimental

details are not taking into account: An increase of the pyridine concentra-

tion in ca. 2 times (up to 2.1 · 10"2 A"2) yields adsorption energy lowering by

about 3%.

Keeping in mind the main motivation of our studies, it is interesting to

compare the presented results with the ones obtained for pyridine adsorp-

8

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 61 62 63 64 65

Table 2: Adsorption energies (in meV) as obtained for the four studied geometries when

increasing number of graphene monolayers.

Number of T-par C-par T-perp C-perp

layers

1 "357 "412 "218 "250

2 "384 "439 "225 "261

3 "388 "441 "229 "263

tion on noble metal substrates. In contrast to the data obtained in this

work, for all reported cases, those are Cu(111), Cu(110), Cu(100), Ag(110),

Au(111) [13–15], normal adsorption, involving the nitrogen lone-pair elec-

trons, is energetically more preferable, than the flat adsorption. In general,

interaction energy between pyridine and metal substrate is at least 30%

stronger, than Eads obtained in the present work, when energetically most

stable structures are compared. This can be viewed as an additional advan-

tage for the usage of graphene encapsulated metal nanoparticles for medical

applications.

In order to investigate the possibility of modeling an extended graphene

surface via finite fragments, we have used ring-like structures of increasing

number of carbons, where dangling bonds are substituted with H-atoms.

For the T-par geometry, convergence in adsorption energy was achieved for

the C96H25 cluster and the resulting Eads consists "339meV, when PBE

functional and basis set of valence double-" quality [25] are used. The va-

lence triple-" basis [25] estimate yields "351meV. The equilibrium graphene-

pyridine distance is 3.38 A. Good coincidence of the values obtained in this

work via periodic and cluster approach opens up a possibility to use post-

9

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 61 62 63 64 65

E­EF (eV)

­6

­4

­2

0

2

4

!

!"

­4

­2

0

2

4

rG/yP  )c(yP  )b(rG  )a(

­4

­2

0

2

4

# $ % # # $ % #

Figure 4: (Color online) (a) Band structure of single graphene (Gr) layer; (b) molecular

energy levels of gas-phase pyridine (Py); (c) band structure of Py/Gr (C-par geometry).

For the thicker lines, the carbon pz character is used as a weighting factor. The upward

shift of pyridine ! states is shown with thin dashed lines.

HF quantum-chemical methods, when extremely accurate result is required,

albeit for the price of inability to consider the unique band structure of

graphene.

Free-standing graphene is a semimetal (“zero-gap semiconductor”): its

conduction and valence bands touch in so-called conical or Dirac points and

the dispersion is essentially linear within ±1 eV of the Fermi energy [Fig. 4

(a)]. Adsorption of pyridine derivatives preserves this typical band structure

[see Fig. 4 (c)] due to relatively weak interaction between the molecule and the

substrate. One may note small upward shift of ! states of pyridine [compare

Fig. 4 (b) and (c)] caused by their interaction with mirror charge of graphene;

unchanged graphene states is the result of good charge screening.

In conclusion, we performed a DFT study for the adsorption of the pyri-

dine molecule on graphene in conjugation with the semiempirical C6R"6 ap-

proach in order to account for dispersive forces, those are shown to be very

important for the studied system since bring about 90% to Eads. It has been

10

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 61 62 63 64 65

demonstrated, that the flat orientation of the adsorbate is more favourable

than the normal one. Hollow adsorption site is preferred by pyridine and the

most stable structure is characterized by an adsorption energy of "412meV.

Substitution of hydrogen in the 4-position of pyridine yields increasing Eads

by up to 134meV. Even then, this is significantly weaker binding, than the

one obtained for the noble metal substrates [13–16, 26]. Besides the improved

stability of the metal nanoparticles because of the graphene encapsulation,

this can be considered as an additional advantage for their medical appli-

cation in the assisted delivery of drugs. Due to relatively weak interaction

between studied pyridine derivatives with the substrate, caused mainly by

van der Waals forces, conical band structure of graphene stays unchanged

upon adsorption.

We appreciate the support from the German Research Foundation (DFG)

through the Collaborative Research Center (SFB) 765. The computing facili-

ties (ZEDAT) of the Freie Universitat Berlin are acknowledged for computer

time. The authors thank Dr. Yu. S. Dedkov (Technische Universitat Dres-

den) for useful discussions.

References

[1] A. K. Geim, Science 324 (2009) 1530.

[2] Yu. S. Dedkov, M. Fonin, U. Rudiger et al., Appl. Phys. Lett. 93 (2008)

022509.

[3] Yu. S. Dedkov, M. Fonin, and C. Laubschat, Appl. Phys. Lett. 92 (2008)

052506.

11

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 61 62 63 64 65

[4] E. Sutter, P. Albrechet, F. E. Camino et al., Carbon 48 (2010) 4414.

[5] S. Bottcher, M. Weser, Yu. S. Dedkov et al., Nanoscale Res. Lett. 6

(2011) 214.

[6] Yu. S. Dedkov, A. M. Shikin, V. K. Adamchuk et al.,, Phys. Rev. B 64

(2001) 035405.

[7] D. Faras, A. M. Shikin, K.-H. Rieder et al., J. Phys.: Condens. Matter

11 (1999) 8453.

[8] A. M. Shikin, G. V. Prudnikova, V. K. Adamchuk et al.,, Phys. Rev. B

62 (2000) 13202.

[9] G. Giovannetti, P. A. Khomyakov, G. Brocks, V. M. Karpan, J. van den

Brink, P. J. Kelly, Phys. Rev. Lett. 101 (2008) 026803.

[10] N. A. Luechinger, E. K. Athanassiou, and W. J. Stark, Nanotechnology

19 (2008) 445201.

[11] O. V. Salata, J. Nanobiotechnology 2 (2004) 3.

[12] G.D. Henry, Tetrahedron 60 (2004) 6043.

[13] H. Lesnard, N. Lorente, and M.-L. Bocquet, J. Phys.: Condens. Matter

20 (2008) 224012.

[14] N. Atodiresei, V. Caciuc, J.-H. Franke et al., Phys. Rev. B 78 (2008)

045411.

[15] K. Tonigold and A. Groß, J. Chem. Phys. 132, 224701 (2010).

12

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 61 62 63 64 65

[16] A. Bilic, J. R. Reimers, N. S. Hush, J. Phys. Chem. B 106 (2002) 6740.

[17] J. D. Wuest and A. Rochefort, Chem. Commun. 46 (2010) 2923.

[18] K. E. Riley, M. Pitonak, P. Jurecka et al., Chem. Rev. 110 (2010) 5023.

[19] P. E. Blochl, Phys. Rev. B 50 (1994) 17953.

[20] J. P. Perdew, K. Burke, and M. Ernzerhof, Phys. Rev. Lett. 77 (1996)

3865.

[21] G. Kresse and J. Hafner, J. Phys.: Condens. Matter 6 (1994) 8245.

[22] S. Grimme, J. Comput. Chem. 27 (2006) 1787.

[23] MOLPRO, version 2006.2, a package of ab initio programs, H.-J.

Werner, P. J. Knowles, F. R. Manby, M. Schtz, and others, see

http://www.molpro.net.

[24] E. M. Arnett, B. J. Hutchinson, M. H. Healy, J. Am. Chem. Soc. 110

(1988) 5255.

[25] T. H. Dunning, Jr. J. Chem. Phys. 90 (1989) 1007.

[26] D. Mollenhauer et al., unpublished.

13