Alexander
Markevich
a,
Simon
Kurasch
b,
Ossi
Lehtinen
b,
Oliver
Reimer
c,
Xinliang
Feng
d,
Klaus
Müllen
d,
Andrey
Turchanin
e,
Andrei N.
Khlobystov
a,
Ute
Kaiser
b and
Elena
Besley
*a
aSchool of Chemistry, University of Nottingham, NG7 2RD Nottingham, UK. E-mail: elena.besley@nottingham.ac.uk
bElectron Microscopy Department of Material Sciences, University of Ulm, 89081 Ulm, Germany
cFaculty of Physics, University of Bielefeld, 33615 Bielefeld, Germany
dMax Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
eInstitute of Physical Chemistry, Friedrich Schiller University Jena, Lessingstraße 10, D-07743 Jena, Germany
First published on 4th January 2016
The electron beam induced functionalization of graphene through the formation of covalent bonds between free radicals of polyaromatic molecules and CC bonds of pristine graphene surface has been explored using first principles calculations and high-resolution transmission electron microscopy. We show that the energetically strongest attachment of the radicals occurs along the armchair direction in graphene to carbon atoms residing in different graphene sub-lattices. The radicals tend to assume vertical position on graphene substrate irrespective of direction of the bonding and the initial configuration. The “standing up” molecules, covalently anchored to graphene, exhibit two types of oscillatory motion – bending and twisting – caused by the presence of acoustic phonons in graphene and dispersion attraction to the substrate. The theoretically derived mechanisms are confirmed by near atomic resolution imaging of individual perchlorocoronene (C24Cl12) molecules on graphene. Our results facilitate the understanding of controlled functionalization of graphene employing electron irradiation as well as mechanisms of attachment of impurities via the processing of graphene nanoelectronic devices by electron beam lithography.
It is also worth noting that the purity of graphene is naturally, and very easily, affected by the environment. Organic residues, charged impurities, surface contaminants, even atmospheric oxygen, all contribute to local doping of graphene. Contaminants have an adverse effect on production and reliable synthesis of large-scale, high-quality pure graphene, which remains key to its successful applications. Adsorption of contaminants on graphene surface and unintentional doping may lead not only to its structural deformation but also to an inhomogeneous charge density and a shift in Dirac voltage.8–12 In general, contaminant molecules act as external scattering centers and modify the properties of graphene, with the covalently attached contaminants having the strongest effect.13–17 While smart choices of solvents and chemicals are required to limit contamination in graphene-based electronics, organic residues from fabrication are inherent in any graphene processing and in particular by electron beam lithography.
In this paper, we explore functionalization reactions of graphene through the formation of covalent bond(s) between free radicals and CC bonds of pristine graphene surface using first principles calculations and high-resolution transmission electron microscopy (HRTEM). Graphene displays particularly high affinity to the so-called hydrocarbon contamination18 dominated by π–π interactions to the flat surface19 thus making polycyclic aromatic hydrocarbons (PAHs) one of the most common organic contaminants of graphene. The hydrophobic properties and molecular sizes of PAHs affect their adsorption on graphene. The HRTEM images20 reveal that after loading with PAHs, the potential adsorption sites of graphene can be altered during the imaging process. However, the detailed HRTEM study of the adsorption behaviors of PAHs on graphene at a molecular level is hindered by electron irradiation damage during imaging. The imaging electron beam (e-beam) breaks readily the C–H bond and destroys individual small PAH molecules over time. The prime example is a coronene molecule, which has been observed to decompose very fast in the HRTEM at energies of 80–120 keV.21 A simple and elegant solution to increase stability of organic molecules under the e-beam has been proposed recently22 through substitution of protium isotope of hydrogen for deuterium. Isotopic substitution has no effect on the molecular structure but increases the atomic weight of the hydrogen atoms by 100%, which drastically improves the stability of organic molecules (or crystals) in the HRTEM, thus allowing imaging of individual species. Another effective approach to enhance the stability of organic molecules in HRTEM is halogenation, although substitution of hydrogen with halogens alters the original chemical properties of the molecules. It has been observed23,24 that halogenated substituents of benzene, benzoquinone and phthalocyanine, where all hydrogen atoms are replaced for much heavier atoms, exhibit greater durability against electron irradiation. A HRTEM study of perchlorocoronene, C24Cl12, suggests its high stability against the e-beam.25 The damaging mechanisms for disintegration of crystalline C24Cl12 during electron radiation have been previously studied using HRTEM, electron diffraction, and electron energy-loss spectroscopy.26
It is well known that hydrocarbons adsorbed on graphene diffuse along its surface towards the edge of the irradiated area or towards large structural defects (typically extended vacancy lines or holes) where they are immobilized by forming covalent bonds with carbon atoms at the edge of the defected area.18 An alternative example of chemical functionalization of the graphene surface is an addition of organic free radicals to sp2 carbon atoms of pristine graphene. The free radical addition method has been recently tested27 to achieve the reaction of benzoyl peroxide with graphene sheets, which was induced photochemically (using focused Ar-ion laser beam). The attachment of the phenyl groups was directly indicated by the appearance of a strong D-band at 1343 cm−1 in the Raman spectrum, which is due to the formation of sp3 carbon atoms in the basal plane of graphene by covalent attachment of phenyl groups. In this case, the covalent addition of phenyl groups to graphene led to a significant decrease in conductivity due to disruption of the aromatic system via transformation of carbon atoms from sp2 to sp3 hybridization.
In the present work we demonstrate the creation of free radicals of small organic molecules and their covalent chemical attachment to graphene during HRTEM imaging. The radicals strongly anchored to graphene are amenable to HRTEM imaging, unlike highly mobile physisorbed molecules. Since imaging of PAHs on graphene by HRTEM is not currently possible, we have deposited perchlorocoronene, C24Cl12, molecules on graphene and observed in HRTEM structural transformations induced by the e-beam in real time with near-atomic resolution. We find that perchlorocoronene radicals are preferably aligned along the armchair direction in graphene, which is consistent with our theoretical predictions for PAHs. Time series of HRTEM imaging clearly demonstrate switching between the vertical (“stand up”) and near horizontal (“lie down”) positions of perchlorocoronene radical. This can be understood by the interplay between the strain in covalent bonds formed between the radicals and graphene and the van der Waals attraction, as demonstrated by classical molecular dynamics (MD) simulations. The comparison between theoretically predicted behavior of PAH radicals anchored to graphene and stable halogenated PAH radicals on graphene observed in HRTEM reveals common dynamic behavior and chemical transformations of small radicals on graphene and enables capturing the atomistic mechanisms of the chemical bond formation.
Molecule | C6H6 | C10H8 | C14H10 | C14H10 | C24H12 |
---|---|---|---|---|---|
E b, eV | 0.38 | 0.60 | 0.81 | 0.82 | 1.33 |
Radical | C6H5 | C10H6 | C14H6 | C14H7 | — |
---|---|---|---|---|---|
E b, eV | 0.36 | 0.56 | 0.74 | 0.76 | — |
Formation of covalent bonds between free radicals and graphene can be either thermodynamically driven or promoted by collisions with high-energy electrons of the imaging beam. The outcome of functionalization depends on the structure of a newly formed reactive carbon edge (armchair or zigzag) and the relative position of the radical edge with respect to the graphene substrate. For the smallest member of the studied family – benzene molecule – four possible chemisorption configurations on graphene are considered, as depicted in Fig. 1a–d, which are labeled to distinguish between different bonding sites within a hexagon in the graphene lattice. Mono-radical of benzene C6H5 (phenyl radical), shown in Fig. 1a, exhibits the binding energy of Eb = 0.99 eV and the magnetic moment of M = 1μB. In contrast, benzene bi-radical demonstrates different bonding modes on graphene, which are denoted as the 1,2-bonding (Fig. 1b), the 1,3-bonding (Fig. 1c), and the 1,4-bonding (Fig. 1d) positions. In the 1,2- and 1,4-bonding positions, the bi-radical is attached to graphene carbon atoms residing in different sub-lattices (shown in Fig. 1e in different color: yellow and blue), and it is aligned along the armchair direction in graphene. The binding energies of the 1,2- and 1,4-bonding positions are found to be very similar, namely Eb = 1.15 eV for the 1,2-bonding and Eb = 1.13 eV for the 1,4-bonding, and both configurations have zero magnetic moment. In a metastable 1,3-bonding position, the bi-radical of benzene is bound to carbon atoms in the same graphene sub-lattice, and it is aligned along the zigzag direction in graphene. The calculated binding energy for the 1,3-bonding position is only Eb = 0.29 eV, which is even smaller than a typical physisorption binding energy for benzene radicals. The magnetic moment M = 2μB of the 1,3-bonding position indicates that the lack of stability is related to the fact that the 1,3-bonding to graphene leads to a structure with open electronic shell (two topologically isolated unpaired electrons which cannot recombine). As a result the 1,2- and 1,4-bonding structures are both much more stable than the 1,3-bonding structure, even though they are more sterically strained. The lengths of the C–C bonds formed between the radicals and graphene vary between 1.54 Å for the case of 1,2-bonding of the C6H4 radical (Fig. 1b) and 1.59 Å for the C6H5 radical (Fig. 1a) indicating that in all cases chemical bonds between the radicals and graphene are formed. The table showing the calculated binding energies and magnetic moments for all studied radicals can be found in ESI (Table S1†).
Similar chemisorption behavior has been predicted for the 1,8-C10H6 bi-radical of naphthalene molecule. When the 1,8-C10H6 radical is bound to graphene carbon atoms in different sub-lattices (shown in Fig. 1f and h), the corresponding binding energies are very similar: Eb = 2.95 eV for the 1,2-bonding position and Eb = 2.80 eV for the 1,4-bonding position. In the 1,3-bonding position (Fig. 1g), the bi-radical 1,8-C10H6 is bound to carbon atoms in the same graphene sub-lattice showing a significantly lower binding energy of Eb = 1.94 eV. A general trend has been observed where benzene and naphthalene bi-radicals chemisorbed on graphene along the armchair direction have the total magnetic moment of M = 0, while in the case of chemisorption along the zigzag direction M = 2μB. The same conclusions have been previously reached for chemisorption of atomic hydrogen on graphene layer36,37 showing that if a pair of hydrogen atoms are bound to different graphene sub-lattices the total magnetic moment of the system is zero. However, if all hydrogen atoms are bound to the same graphene sub-lattice the magnetic moment of the system is equal to the number of covalent bonds formed.
Larger molecules form more complicated chemisorption patterns on graphene but they follow similar structural and energetic trends. For example, anthracene tri-radical, 1,8,9-C14H7, tends to align along the 1,4-bonding armchair direction in graphene (Fig. 2a) with the binding energy of Eb = 4.46 eV, which is about 1.5 eV more favorable than chemisorption along the 1,3-bonding zigzag direction (Fig. 2b). Fig. 2c and d show phenanthrene tetra-radical, 3,4,5,6-C14H6, aligned along the 1,2- and 1,4-bonding armchair direction in graphene. In the alignment along the 1,4-bonding armchair direction a significant deformation of graphene substrate layer occurs, however, this configuration remains energetically more favorable than the 1,2-bonding case. Regardless of the radical structure, all chemisorbed molecules are preferably bound to graphene carbon atoms residing in different sub-lattices and aligned along the armchair direction in graphene. This result agrees with a general conclusion38 that chemisorption of atoms as well as functional groups on two different graphene sub-lattices is energetically more favorable than chemisorption on the same sub-lattice.
The dynamical behaviour of chemisorbed PAH radicals on graphene substrate has been studied using classical molecular dynamics with the AIREBO39 potential. The C24H10 radical of coronene molecule has been modelled in the 1,2- and 1,4-bonding configurations. Two different initial geometries corresponding to the chemisorbed molecule either lying or standing on graphene substrate have been considered. The size of the considered molecule implies that the dispersion attraction to the substrate will make a significant contribution to the total binding energy. The physisorption energies calculated with the AIREBO potential were found to be Eb = 0.42 eV for C6H6, Eb = 1.41 eV for C24H12 and Eb = 2.97 eV for C54H18, in a good agreement with theoretical (DFT) and experimental results (see Table 1 and the accompanying text) thus suggesting that the AIREBO potential provides a realistic description of dispersion interactions. The MD simulations have shown that the C24H10 radical tends to assume vertical position on the graphene substrate irrespective of bonding direction and initial configuration. The “standing up” molecule exhibits two types of oscillating motion – bending (Fig. 3a) and twisting (Fig. 3b) – caused by the presence of acoustic phonons in graphene.
A very different behaviour has been observed for the larger C54H15 radical in the 1,4-bonding configuration. If the chemisorbed radical is initially lying on the graphene surface it remains in the same configuration for the whole time of the MD simulation (Fig. 3c). In this case, the binding energy due to the dispersion interactions between the radical and graphene is higher than the strain energy caused by the bending of sp2 carbon bonds. However, if the initial configuration is a standing radical it does not lie down during simulation and the oscillations of the molecule are less pronounced than in the case of the C24H10 radical. Stabilization of the radical in this configuration can be explained by the fact that dispersion interactions are significantly reduced compared to the case of the lying molecule and contribute only 0.4 eV to the binding energy. Formation of three covalent bonds also makes the radical more stable with regards to the oscillations compared to the chemisorbed C24H10 radical in which only two covalent bonds are formed.
It is not possible to observe directly the dynamic behavior and chemical transformations of standard PAH molecules on graphene due to the rapid onset of knock-on damage caused by the fast electrons of the e-beam during HRTEM imaging.22 The structure of PAH molecule would need to be modified to prolong its lifetime under the e-beam exposure and to slow down the dynamics to the timescale of HRTEM imaging (e.g. few seconds). To achieve this, we have substituted all hydrogen atoms in coronene with chlorine atoms to form a perchlorocoronene molecule (C24Cl12) that exhibits a greater stability against electron irradiation. C24Cl12 molecules were then deposited onto graphene sheets suspended on HRTEM grids via physical vapor deposition at ultra-high vacuum conditions (see ESI† for details). The X-ray photoelectron spectroscopy (XPS) characterization of samples prepared at similar conditions on highly oriented pyrolytic graphite substrates demonstrates the adsorption of C24Cl12 molecules by appearance of the characteristic Cl 2s and Cl 2p3/2,1/2 peaks (see ESI†). The estimated coverage corresponds to ∼1% of a monolayer. If the mechanism of chemical bond formation to graphene is similar for small hydrogenated and halogenated aromatic molecules, it is expected that once two or more chemical bonds are formed between graphene and radicals (produced from C24Cl12 damaged by the e-beam), these molecules can also rotate into a vertical position and align along the preferential armchair direction, as theoretically predicted for PAHs.
The higher stability of C24Cl12 molecule in the e-beam enabled experimental investigation of the predicted mechanisms by aberration-corrected HRTEM imaging. The heavier chlorine atoms at the molecular edge produce a stronger contrast compared to lighter C atoms in the center, so the molecules are expected to have a ring-like appearance in HRTEM images as predicted by image simulation shown in Fig. 4b. Areas of graphene as large as tens to hundreds of nm in diameter were observed, which were free from contamination, similar to the case of imaging graphene with no deposition treatment but after pre-imaging cleaning.40
Additionally, a large number of circles of dark contrast were observed on the otherwise clean area of graphene, as marked by the arrows in Fig. 4d. At higher magnification most of these features appeared to be ring-like structures of about 1 nm in diameter as shown in Fig. 4c and e. The shape and size of the observed structures and experimental conditions of the samples preparation indicate that the rings of dark contrast correspond to the 2D projection of the deposited C24Cl12 molecules. The molecules undergo a constant motion on the graphene surface (Fig. 4e) caused by thermal effects and electron irradiation so that the individual chlorine atoms cannot be resolved.
It has been observed that many of the adsorbed molecules occasionally undergo a reversible transformation between circular and linear projections. An example of such transformation is shown as a time series of HRTEM images in Fig. 5a. The time between the molecular transformations varies from few to hundred seconds at the dose rates used in experiment that range from 2 × 106 e nm−2 s−1 to 13 × 106 e nm−2 s−1. Often, just before the transformation to the linear projection, the molecule exhibits a crescent-like shape with diminishing contrast at one edge indicating the loss of Cl atoms and formation of a molecular radical. We suggest that the e-beam damages the initial structure of the molecule and promotes formation of covalent bonds between the radical and the graphene substrate, which induces the rotation of the radical by 90° with respect to the graphene plane, as theoretically predicted for PAHs. In such configuration the projection of the radical has nearly a linear shape. The reversible switching between two configurations suggests that under the e-beam irradiation conditions both formation and breaking of covalent bonds between the molecular radicals and graphene occurs.
The molecules, when covalently attached to graphene, show remarkably consistent behaviour in terms of their orientation relative to the substrate. In full agreement with the computational predictions (both for the dynamics and stability), the molecules align along the armchair direction of graphene with no observed exceptions in our experiment. The sequences of images in Fig. 5 have the nearest armchair direction of graphene marked by the dashed lines whenever the molecule is in the ‘stand-up’ position. We note that the structure of the reactive edge and the binding configuration of the radicals on graphene cannot be determined from the TEM images. However, the fact “standing up” radicals are strictly aligned along the armchair direction of graphene and are stable in this configuration for extended period of time suggests that at least two covalent bonds have to be formed between the radical and graphene to promote rotation of the radical into the vertical position. Closer examination indicates that the size of the molecules tend to get smaller during imaging indicating gradual fragmentation and removal of atoms by the electron beam. Eventually the molecules are getting detached from the substrate, and either re-attach at, e.g., nearby contamination, or disappear completely.
The sharp line observed in TEM images for the “stand up” state of a radical of the C24Cl12 molecule suggests that no significant oscillations of the radical occur. This is in contrast with the strong oscillating motion predicted by MD simulations for the C24H10 radical chemisorbed on graphene (see Fig. 3). It should be noted, however, that in the case of the C24Cl12 molecule the chlorine atoms constitute about 75% of the molecular mass. Therefore, the heavy edge of the molecule will strongly suppress the oscillatory motion of the lighter C skeleton caused by the presence of phonons in graphene.
The dynamic behaviour of the C24H10 and C54H15 radicals covalently bonded to graphene substrate has been investigated using classical MD calculations with the AIREBO potential.39 The calculations have been carried out using LAMMPS molecular dynamics simulator.44 The graphene layer has been represented with 680 carbon atoms and periodic boundary conditions have been employed. All structures have been initially optimized using the conjugate gradient energy minimization scheme and then equilibrated at temperature 300 K over 10 ns. The dynamic behavior of the radicals was studied in the subsequent NVE simulation for another 10 ns.
The image simulations were conducted with the QSTEM software45 using a spherical aberration value of 20 μm, focal spread of 6 nm and Scherzer focus. The value of the electron dose was taken to be 107 e nm−2. The experimentally measured modulation transfer function (MTF) of a CCD camera46 at an 80 kV accelerating voltage was then applied to obtain an accurate signal to noise ratio.
The samples were characterized by aberration-corrected high-resolution transmission electron microscopy using an FEI Titan 80–300 microscope, equipped with an image-side spherical aberration corrector. The microscope was operated at 80 kV, and the extraction voltage of the field emission gun was set to 2 kV to reduce the energy spread of the electron beam. The spherical aberration coefficient was tuned to <20 μm and the imaging was conducted at under focus resulting in atoms appearing as dark spots in the images. The electron dose rate was (2–13) × 106 e nm−2 s−1.
Footnote |
† Electronic supplementary information (ESI) available: A table showing the calculated binding energies and magnetic moments for all studied molecular radicals; details of samples preparation and characterization; time series of TEM images showing transformations of a C24Cl12 molecule on graphene under electron irradiation. See DOI: 10.1039/c5nr07539d |
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