Probing the Bonding and Electronic Structure of Single Atom Dopants

Dec 21, 2012 - A combination of scanning transmission electron microscopy, electron energy loss spectroscopy, and ab initio calculations reveal striki...
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Probing the Bonding and Electronic Structure of Single Atom Dopants in Graphene with Electron Energy Loss Spectroscopy Quentin M. Ramasse,*,† Che R. Seabourne,‡ Despoina-Maria Kepaptsoglou,† Recep Zan,§,∥ Ursel Bangert,∥ and Andrew J. Scott‡ †

SuperSTEM Laboratory, STFC Daresbury Campus, Daresbury WA4 4AD, United Kingdom Institute for Materials Research, SPEME, University of Leeds, Leeds LS2 9JT, United Kingdom § School of Physics and Astronomy and ∥School of Materials, University of Manchester, Manchester, M13 9PL, United Kingdom ‡

S Supporting Information *

ABSTRACT: A combination of scanning transmission electron microscopy, electron energy loss spectroscopy, and ab initio calculations reveal striking electronic structure differences between two distinct single substitutional Si defect geometries in graphene. Optimised acquisition conditions allow for exceptional signal-tonoise levels in the spectroscopic data. The near-edge fine structure can be compared with great accuracy to simulations and reveal either an sp3-like configuration for a trivalent Si or a more complicated hybridized structure for a tetravalent Si impurity.

KEYWORDS: Graphene, doping, bonding, electronic structure, EELS, STEM

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spectra and ab initio calculations to distinguish unambiguously between two different electronic structures of single Si substitutional defects in single-layer graphene, depending on the number of direct bonds they form with the host lattice. All experimental data were acquired at the SuperSTEM Laboratory on a Nion UltraSTEM100 dedicated scanning transmission electron microscope equipped with a cold field emission gun operated at 60 keV to prevent knock-on damage to the graphene samples. This instrument has an ultrahighvacuum (UHV) design throughout, allowing pressures at the sample of below 5 × 10−9 Torr for contamination-free observation.1 The beam was set up to a convergence semiangle of 30 mrad with a beam current of 31 pA at the sample measured immediately prior to the spectrum acquisition. In these operating conditions the estimated probe size (full width at half-maximum) is 1.2 Å. The semiangular ranges for the high and medium angle annular dark-field (HAADF or MAADF) detectors used to record the images are 86−190 and 50−86 mrad respectively; the intensity recorded by the HAADF detector (used unless otherwise stated) with the probe positioned on an atomic site is approximately proportional to the square of the average atomic number Z of this site.18 Electron energy loss spectra were recorded on a Gatan Enfina spectrometer with an acquisition time of 1 s per spectrum. The spectrometer acceptance semiangle was calibrated at 35 mrad.

he successful implementation of aberration correctors in electron microscopy has heralded a new era in materials science and nanoscience. In particular, the tremendous flexibility of probe-corrected scanning transmission electron microscopes (STEM) now routinely allows researchers to study sensitive materials at true atomic resolution but using primary beam energies below their knock-on damage threshold.1 These developments have been particularly beneficial in the field of two-dimensional materials such as graphene.2 Because minute structural variations may have tremendous effects on their electronic configuration, and therefore on their properties,3−7 it is essential to study these materials quite literally one atom at a time. Recent studies have thus demonstrated that every atom within the structure of these remarkable systems can be quantitatively identified with annular dark-field (ADF) imaging,8,9 while single atom impurities or defects can also be chemically fingerprinted using either electron energy loss spectroscopy (EELS)10−13 or energy-dispersive X-ray spectroscopy (EDXS).14,15 Having shown what atomic species are present and where they are located, some fundamental questions remain: how exactly are these atoms bonded to one another and how do structural differences affect their electronic configuration? Studying the fine structure of electron energy loss spectra can provide answers to these questions at the single atom level and reveal for instance how the electronic structure of individual atoms at edges or point defects in twodimensional materials exhibits unique features depending on local bonding differences16,17 or determine the valence state of single dopant atoms.11 Here we combine experimental EEL © XXXX American Chemical Society

Received: November 13, 2012 Revised: December 18, 2012

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regions of the graphene sheet already comprising a high density of structural defects, as observed in Figure 1b where combinations of 5- and 7-member rings (Stone-Wales-like defects22) are clearly seen in the few nm2 surrounding the substitutional atom itself. Frequent atomic rearrangement was observed in these areas; although the 60 keV primary energy of the beam is below the knock-on threshold for carbon,23,24 this damage formation energy can be lowered by the presence of defects or at the edges of holes.25 Lattice rearrangements can then occur during the observation if a carbon atom is ejected from the lattice followed by bond rotation.26,27 It was therefore essential in this case to monitor the defect coordination throughout the spectroscopic acquisition. Quantitative image intensity analysis can be used to confirm the substitutional nature of the observed defects. After processing the images with a maximum-entropy-based probe deconvolution algorithm in order to remove the influence of probe tails (Supporting Information, Figure S1),28 the intensity ratio between the single bright defect and the carbon sites is 4.44 for the defect in Figure 1a and 4.07 for the defect in Figure 1b. These values correspond to a ∼Z1.7 dependence of the HAADF contrast on the atomic number Z of C (Z = 6) and Si (Z = 14), which is in excellent agreement with previous quantitative contrast analyses carried out on other systems in extremely similar experimental conditions.8,29 We note that these initial images were deliberately acquired with relatively short probe dwell times and without recentring the defect in order to minimize the exposure to the beam prior to the crucial spectroscopic acquisition. There have been previous reports of electron energy loss spectroscopic data acquired from single impurity atoms within a graphene sample.13,30,31 However, in order to obtain EELS data of high enough quality (non noise-limited) to reliably interpret the observed fine structure in terms of electronic structure and atomic bonding, it was necessary to employ a technique initially devised for the demonstration of single atom identification using energy dispersive X-ray spectroscopy.14 Once a suitable Si defect is located, a small subscan window is defined around the substitutional atom of interest. The size of the window is adjusted so that it contains the impurity’s nearest neighbors only, thus covering an area of approximately 2.5 Å × 2.5 Å. This

Although the native energy spread of this instrument is 0.35 eV, the spectrometer dispersion was chosen to allow for the simultaneous visualization of the Si L2,3 and carbon K EELS edges, resulting in an energy resolution of 0.9 eV (as estimated by the full width at half-maximum of the zero-loss peak), limited by the point-spread function of the detector. Two types of single Si atom substitutional defects are typically observed within single-layer graphene sheets with the impurity substituting either for a single C atom or for a C−C pair, resulting in either 3-fold or 4-fold coordinated Si defects.19 These substitutional defects are thought to originate from the chemical vapor deposition process used to grow the graphene sample used here, whereby Si impurities are captured during the film growth on the Cu substrate, or during the screening of the membranes after transfer to an oxidized Si wafer.20 The CVD-grown membrane was then transferred onto a lacey carbon support film using a standard wet chemistry methodology.20,21 The 3-fold coordinated Si defects, such as that depicted in Figure 1a, were systematically found in otherwise

Figure 1. HAADF images (raw data) of Si atoms substituted within a single layer graphene sheet. While the atom in (a) is in an otherwise pristine area of graphene, the atom in (b) is close to a highly defected region comprising 5-and 7-member C rings. The yellow boxes show the subregion over which the probe was scanned repeatedly to acquire high signal-to-noise EEL spectra.

pristine areas of the graphene sheets, and were quite stable under the beam, allowing for repeated spectroscopic acquisitions.13 By contrast, the 4-fold configuration often occurred in

Figure 2. High signal-to-noise EEL spectrum acquired by accumulating 1 s exposures while scanning repeatedly the area indicated by the yellow box shown on (a) Figure 1a and (b) Figure 1b for 200 s. The insets present a 50 frame average in false color from the stacks of images created during the acquisitions, showing clear 3-fold coordination (a) or 4-fold coordination (b) of the Si atom. B

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about 90% of the Si L2,3 loss electrons are detected. These results not only confirm that quantitative spectroscopy should now be possible at the one atom level but also demonstrate that single atom fine structure analysis can be carried out without being noise-limited. Indeed, the two experimental spectra exhibit very stark and clear differences, suggesting a completely different electronic structure. The L2,3 peak for the trivalent atom has a sharp and intense first maximum at ∼102.5 eV, preceded by a wellresolved, less intense, shoulder starting at the edge onset at 99 eV. The secondary peak is broad, centered at 130 eV, and its intensity is of similar magnitude to the first peak. By contrast, in the case of the 4-fold coordinated Si atom, the peak onset is shifted to 100 eV with a much weaker initial sharp peak. This sharp onset is followed by an unusual peak doublet at 105 and 108 eV before the secondary broader peak with maximum at 127 eV. This secondary peak is narrower than in the case of the 3-fold coordinated atom but has similar intensity in terms of absolute electron counts. It is however 3 times more intense than the first peak. As only Si and C are present, it is interesting to compare these spectra to an experimental SiC reference, obtained with identical acquisition parameters and using the subscan average technique, on a 4H-SiC crystal oriented down its ⟨0001⟩ zone axis (Supporting Information, Figure S3). For obvious reasons, the bulk SiC sample was far thicker (approximately 20 nm in the region considered, as evaluated from a low loss spectrum) and the spectra are not directly comparable. Qualitatively, however, it is striking that the SiC spectrum features, especially those close to the edge onset and thus not affected by plural scattering events, do not match any of the features observed for either substitutional Si atom. Here, the edge onset lies at 99 eV and its broader initial peak at 103 eV is neither followed by the peak doublet of the 4-fold coordinated Si, nor the plateau observed in the 3-fold coordinated atom. It is thus clear that the substitutional arrangements result in quite unique electronic structures. Ab initio calculations were therefore carried out in order to understand these experimental features and relate them to the precise electronic arrangement of the substitutional defects. Calculations were performed in the ground electronic state using the CASTEP density functional theory (DFT) code.33 Prior to optimizing the atomic positions of the two substitutional arrangements, a model system consisting of a standard graphite unit cell with a single silicon atom in place of one of the carbon atoms was chosen for convergence experiments. The two key DFT code parameters to converge are the basisset size (as defined by the kinetic energy cutoff) and the density of sampling (k) points in reciprocal space. For experiments involving geometry optimization, the kinetic energy cutoff value was converged against the overall system energy. The parameter was sampled in 20 eV intervals, until the overall system energy varied by less than 0.0001 eV. In terms of converging k-points in reciprocal space, sequential steps were used whereby the number of k-points in each dimension was doubled, and the change in system energy determined. Upon changing the grid from 12 × 12 × 4 to 24 × 24 × 8 the system energy changed by less than 0.005 eV, which was considered an acceptable balance of precision and feasibility of computing the results. This represented an average k-point separation in reciprocal space of 0.019 Å−1. These parameters were used for all further calculations involving structural minimization. The specific geometry optimization scheme utilized to obtain the

small window is then scanned repeatedly at a really high frame rate (50 ms per frame or faster) over a 200 s total acquisition time per spectrum, adjusting the position of the window to account for simple sample drift (typically less than 1 Å over the entire acquisition in the conditions used) or occasional atomic jumps of the impurity to a neighboring site. Such jumps suggest that although relatively stable, the impurities contribute to lowering locally the defect formation energy. Despite the low primary energy used, the electron beam may be energetic enough to alter the bonding and temporarily change the structure and electronic configuration of the defect. All these subscan images are however saved as an “image stack”, thus keeping a continuous record of the defect atomic configuration throughout the acquisition, which demonstrates that atomic jumps are quite rare. During the overwhelming majority of the long acquisition times used here, the Si impurities are in the depicted trivalent or tetravalent geometries and not in an intermediate state which could imply a different electronic structure. Using this “atom-tracking” technique, it was possible to acquire high-signal-to-noise electron energy loss spectra by accumulating over 200 consecutive 1 s exposures. Figure 2a shows the resulting spectrum for the Si L2,3 edge obtained from a 3-fold coordinated impurity with an inset corresponding to a 50-frame average extracted from the atom-tracking stack (larger versions of the insets are provided in the Supporting Information, Figure S2). The tracking image clearly demonstrates that the bright impurity is establishing direct bonds with its three nearest neighbors. It is therefore tempting to postulate that such a 3-fold coordinated Si substitutional impurity where the foreign atom replaces exactly one of the host matrix atoms takes the same electronic configuration, resulting in an sp2 bonded Si atom, a configuration not usually observed. As the Si atom occupies approximately 10% of the subscan window, the 1.2 Å probe thus spent approximately 20 s over the Si atom to generate this spectrum, corresponding in the experimental conditions to an irradiation of the substitutional Si atom by approximately 4 × 109 electrons. Special care was also paid to the raw data processing: in particular, long, averaged, “dark current” images were used instead of the automatic dark count subtraction in order to ensure the noise levels were as close as possible to their shot-noise fundamental limit. With these optimized acquisition parameters, the spectrum in Figure 2a shows indeed only 0.8% noise r.m.s.: the net Si count rate around the edge maximum at 129 eV is 4.4 × 104 electrons/eV after subtraction of a decaying power law background. Figure 2b shows a data set acquired in identical conditions, but on a 4fold coordinated Si substitutional atom: four neighboring C atoms are clearly seen in the averaged image obtained from the tracking image stack, inset. Here again, thanks to the long acquisition times, the r.m.s. noise in the spectrum is kept below 1% after background subtraction, providing excellent statistics for a detailed interpretation of the fine structure, which is strikingly different from the 3-fold coordinated case. It is interesting to note that assuming a combined crosssection for the Si L2 and L3 edges of 3.2 × 10−3 Å232 (neglecting the Si L1 edge), the theoretical count rate for the Si edge would be 4.3 electrons/s, given a 31 pA current contained in a 1.2 Å diameter probe.14 Considering the uncertainties, this is in extremely good agreement with the experimental count rate of 2.5 electrons/s, which can be derived by integrating the signal under the curve in the spectra of Figure 2a,b over a 100 eV window (capturing approximately 60% of the total energy loss electrons) and assuming that in the collection geometry used, C

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Figure 3. (a) Models of tetravalent and trivalent substitutional Si atoms within a single-layer graphene sheet. The atomic positions were optimized using DFT calculations: note the lengthening of the Si−C bonds in the planar trivalent case, middle. The structure was allowed to relax out of plane in the bottom model. (b) Comparison between the experimental spectra (solid lines) after background subtraction using a decaying power law, and the spectra calculated by DFT using the models shown in (a) (shaded areas).

final, stable, models of the trivalent and tetravalent Si substitutional structures was the BFGS methodology.34−38 Parallel convergence tests for the Si L2,3 EELS edge calculations were also carried out. A value of 800 eV for the kinetic energy cutoff was considered acceptable. Upon doubling the value from 400 to 800 eV the predicted edge was virtually identical, which demonstrated the viability of this choice. In terms of k-point sampling, upon doubling the EELS-step grid from 6 × 6 × 2 to 12 × 12 × 4 there was a negligible difference in the predicted spectrum after application of a lifetime-based broadening scheme to reflect the instrumental resolution of 0.9 eV. These k-point spacings were therefore used for any EELS calculation shown. Previous analogous work7 suggested that a layer separation of 25 Å would be enough to fully decouple the layers and realistically simulate graphene. This value was however doubled to 50 Å for the simple model system in order to confirm this assumption. Again, it was shown the change to the predicted EELS spectrum was minimal. It was also necessary to consider the requisite expansion of the cell in the a/b direction Therefore, two systems were initially compared, a 2 × 2 × 1 supercell and a 4 × 4 × 1 supercell,

both with 25 Å of vacuum in the c direction, initially with a trivalent Si substitutional atom. A relaxed 4 × 4 × 1 cell is shown in Figure 3a. For the Si L2,3 edge, it was shown that upon changing the lateral expansion of the cells the predicted result varied minimally, so this size of cell, 4 × 4 × 1 with a large vacuum gap along the out-of-plane c direction, was considered acceptable, and the spectra converged. For both the trivalent and tetravalent models, BFGS geometry optimization was carried out using previously described parameters with the following tolerances: (1) the maximum force on all atoms was less than 0.05 eV/Å; (2) the maximum change in position for all atoms between BFGS steps was less than 2 × 10−3 Å; (3) the maximum change in the total system enthalpy between BFGS steps was less than 2 × 10−5 eV per atom. It is arguable for the trivalent case that the Si atom might be slightly displaced in c from the other atoms, the defect effectively puckering out-of-plane. This suggestion arises from the fact that when enforcing a flat geometry, all atoms being constrained to the horizontal plane, the Si−C bond lengths in the 3-fold optimized model are significantly stretched (1.676 Å) compared to bulk graphene (1.420 Å); see Figure 3a. In D

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Figure 4. (a) Total electron density map for the tetravalent Si impurity. A line profile across the Si−C bond is indicated. (b) Orbital isosurface, showing the localization of all orbitals contributing to the electron density. Orbitals are clearly “bridging” across the honeycomb holes, indicating the likely presence of d-band hybridization. For clarity, two supercells are repeated periodically in these figures, a ball and stick model being overlaid on the bottom-left repeat unit.

the relative peak intensities are reproduced faithfully by the simulations. In the planar geometry, however, a small feature 20 eV above the edge onset appears in the simulation instead of the relatively feature-less plateau observed experimentally. The 3D distorted configuration provides by contrast an almost perfect match to the experiment and confirms the initial suggestion that the trivalent structure in fact sticks out-of-plane to accommodate the longer Si−C bonds. The distorted trivalent model predicts 1.740 Å bonds, the Si atom sitting 0.950 Å above the horizontal plane, with neighboring C atoms also displaced upward from the graphene plane; see Figure 3a. The sp2 network of graphene clearly distorts and buckles to integrate this larger atom, tending locally toward a structure more akin to sp3 bonding (the predicted Si−C bond angles are indeed 107.3 degrees), as would be expected for Si−C bonds. These results therefore show that with such low noise levels the EELS fine structure can be used not only to distinguish unambiguously between a trivalent and a tetravalent single atom impurity, but also to fingerprint sub-Å distortions around point defects and understand the precise bonding environment of the defects. The broader appearance of the tetravalent spectrum, which comprises a larger number of subfeatures than the very sharply peaked trivalent case, is consistent with a complex electronic density redistribution possibly due to some degree of d-orbital hybridization. This suggestion is further supported by examining the calculated total electron density around the substitutional atom in Figure 4a. In addition to the obvious symmetry break due to the addition of a tetravalent atom in the

contrast, measurements of the Si−C distances in the images (Supporting Information, Figure S4), in particular using averaged image stacks, do not reveal any marked bond stretching (or a much smaller stretching), thus lending credibility to an out-of-plane buckling geometry observed in projection. It has been recently shown that EELS fine structures can in specific cases be related to picometer-sized threedimensional atomic displacements.7 Calculations in the trivalent case were therefore carried out for both a flat and a three-dimensional structure corresponding to an out-of-plane distortion of the graphene sp2 bonding network. The optimization for the latter was performed by allowing the atoms to relax in the vertical direction, the Si atom being initially positioned at a nonzero height. Two different starting positions were used, both resulting in virtually identical final structures. Following geometry optimization for the 4-fold and both flat and distorted 3-fold coordinated arrangements, all of which satisfy the stability requirements described above and therefore represent plausible atomic configurations (Figure 3a), ground state EELS calculations were carried out using previously described parameters. Figure 3b compares the experimental spectra after background subtraction (solid lines) and the simulated spectra obtained from the optimized calculated structures (shaded areas), revealing a remarkable match. In the case of the 4-fold coordinated structure, the weaker initial onset and the subsequent peak doublet are reproduced perfectly, while overall peak positions agree extremely well. Similarly for both 3-fold structures, the initial shoulder, the sharp and intense onset, and E

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University of Leeds, which provided access to Accelrys Materials Studio to generate electron density figures.40 The authors gratefully acknowledge Professor Ondrej Krivanek for invaluable discussions and guidance.

honeycomb graphene lattice, the calculated electron density is lower at the tetravalent Si impurity and along the Si−C bonds (Figure 4a). The bonding network is thus quite disrupted around the 4-fold impurity and the orbital isosurface map (Figure 4b), which depicts the spatial distribution of all orbitals contributing to the electron density, shows how the orbitals seem to bridge across the “holes” in the lattice. Different geometry orbitals must be involved in the bonding configuration and the deviation from pure sp2 bonding is likely due to a certain amount of d-band hybridization. By contrast in the distorted trivalent model the honeycomb structure of the orbital iso-surface map remains largely undisturbed although the lattice is distorted (Supporting Information, Figure S5). This suggests that in the trivalent case the Si impurity acts as a good chemical replacement for a single carbon atom despite the out-of-plane distortions necessary to accommodate the longer bonds and silicon’s propensity for sp3-like bonding. In conclusion, we have shown that electron energy loss spectroscopy can now yield precise electronic structure information at the single atom level. Using optimized acquisition procedures resulting in very high-signal-to-noise data, we were reliably able to reveal marked differences in the fine structure of spectra from a single Si impurity in single-layer graphene, depending on the number of bonds the atom establishes with its host lattice. Ab initio simulations reproduce faithfully the differences observed experimentally and suggest that if 3-fold coordinated a Si substitutional atom integrates by distorting the sp2 structure so that the Si atom and its neighbors pucker slightly out of the graphene plane to accommodate the longer Si−C bonds. By contrast, a tetravalent substitutional Si atom acts as a “true impurity” and generates a noticeable disruption to the electronic density possibly due to a degree of d-band hybridization. Not only can foreign species be fingerprinted atom-by-atom, bonding differences between single atom impurities of the same species are now also distinguishable with energy loss spectroscopy, paving the way toward single atom physical chemistry.

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ASSOCIATED CONTENT

S Supporting Information *

Additional figures are provided. These include probedeconvoluted micrographs and image simulations, a reference experimental spectra from bulk SiC, and orbital isosurface plots for the trivalent model. This material is available free of charge via the Internet at http://pubs.acs.org.

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REFERENCES

AUTHOR INFORMATION

Corresponding Author

*E-mail: [email protected]. Notes

During the review of this work, it has come to our attention that W. Zhou et al. have recently and independently reported electron energy loss spectroscopy results also allowing them to distinguish between trivalent and tetravalent Si substitutional impurities in single-layer graphene.39 The authors declare no competing financial interest.

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ACKNOWLEDGMENTS This work and the SuperSTEM Laboratory were supported by the U.K. Engineering and Physical Sciences Research Council (EPSRC). Computational work was undertaken using the advanced research computing (ARC1) HPC facilities at The F

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