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 WA44AD,United Kingdom
?Institute for Materials Research,SPEME,University of Leeds,Leeds LS29JT,United Kingdom
§School of Physics and Astronomy and ∥School of Materials,University of Manchester,Manchester,M139PL,United Kingdom *Supporting Information
he successful implementation of aberration correctors in electron microscopy has heralded a new era in materials science and nanoscience.In particular,the tremendous ?exibility 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.1These developments have been particularly bene ?cial in the ?eld of two-dimensional materials such as graphene.2Because minute structural variations may have tremendous e ?ects on their electronic con ?guration,and therefore on their properties,3?7it 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 identi ?ed with annular dark-?eld (ADF)imaging,8,9while single atom impurities or defects can also be chemically ?ngerprinted using either electron energy loss spectroscopy (EELS)10?13or energy-dispersive X-ray spectros-copy (EDXS).14,15Having 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 di ?erences a ?ect their electronic con ?guration?Studying the ?ne 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 two-dimensional materials exhibits unique features depending on
local bonding di ?erences 16,17or determine the valence state of single dopant atoms.11Here we combine experimental EEL
spectra and ab initio calculations to distinguish unambiguously
between two di ?erent 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 UltraSTEM100dedicated scanning transmission electron microscope equipped with a cold ?eld emission gun operated at 60keV to prevent knock-on damage to the graphene samples.This instrument has an ultrahigh-vacuum (UHV)design throughout,allowing pressures at the sample of below 5×10?9Torr for contamination-free observation.1The beam was set up to a convergence semiangle of 30mrad with a beam current of 31pA 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?.The semiangular ranges for the high and medium angle annular dark-?eld (HAADF or MAADF)
detectors used to record the images are 86?190and 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.18Electron energy loss spectra were recorded on a Gatan En ?na spectrometer with an acquisition time of 1s per spectrum.The spectrometer acceptance semiangle was calibrated at 35mrad.Received:November 13,2012
Revised:December 18,2012
Although the native energy spread of this instrument is 0.35eV,the spectrometer dispersion was chosen to allow for the simultaneous visualization of the Si L 2,3and carbon K EELS edges,resulting in an energy resolution of 0.9eV (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.19These 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 ?lm growth on the Cu substrate,or during the screening of the membranes after transfer to an oxidized Si wafer.20The CVD-grown membrane was then transferred onto a lacey carbon support ?lm using a standard wet chemistry method-ology.20,21The 3-fold coordinated Si defects,such as that depicted in Figure 1a,were systematically found in otherwise pristine areas of the graphene sheets,and were quite stable under the beam,allowing for repeated spectroscopic acquis-itions.13By contrast,the 4-fold con ?guration often occurred in 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 defects 22)are clearly seen in the few nm 2surrounding the substitutional atom itself.Frequent atomic rearrangement was observed in these areas;although the 60keV primary energy of the beam is below the knock-on threshold for carbon,23,24this damage formation energy can be lowered by the presence of
defects or at the edges of holes.25Lattice rearrangements can
then occur during the observation if a carbon atom is ejected from the lattice followed by bond rotation.26,27It was therefore essential in this case to monitor the defect coordination throughout the spectroscopic acquisition.Quantitative image intensity analysis can be used to con ?rm the substitutional nature of the observed defects.After processing the images with a maximum-entropy-based probe deconvolution algorithm in
order to remove the in ?uence of probe tails (Supporting Information,Figure S1),28the intensity ratio between the single bright defect and the carbon sites is 4.44for the defect in Figure 1a and 4.07for the defect in Figure 1b.These values correspond to a ～Z 1.7dependence 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.8,29We 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.13,30,31However,in order to obtain EELS data of high enough quality (non noise-limited)to reliably interpret the observed ?ne structure in terms of electronic structure and atomic bonding,it was necessary to employ a technique initially devised for the demonstration of single atom identi ?cation using energy dispersive X-ray spectroscopy.14Once a suitable Si defect is located,a small subscan window is de ?ned 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?×2.5?.
This 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.Figure 2.High signal-to-noise EEL spectrum acquired by accumulating 1s exposures while scanning repeatedly the area indicated by the yellow box shown on (a)Figure 1a and (b)Figure 1b for 200s.The insets present a 50frame 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.
small window is then scanned repeatedly at a really high frame rate(50ms per frame or faster)over a200s total acquisition time per spectrum,adjusting the position of the window to account for simple sample drift(typically less than1?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 con?guration of the defect.All these subscan images are however saved as an“image stack”,thus keeping a continuous record of the defect atomic con?guration 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 di?erent electronic https://www.doczj.com/doc/b44154336.html,ing this“atom-tracking”technique,it was possible to acquire high-signal-to-noise electron energy loss spectra by accumulating over200consecutive1s exposures.Figure2a shows the resulting spectrum for the Si L2,3edge obtained from a3-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 demon-strates that the bright impurity is establishing direct bonds with its three nearest neighbors.It is therefore tempting to postulate that such a3-fold coordinated Si substitutional impurity where the foreign atom replaces exactly one of the host matrix atoms takes the same electronic con?guration,resulting in an sp2 bonded Si atom,a con?guration not usually observed.As the Si atom occupies approximately10%of the subscan window,the 1.2?probe thus spent approximately20s over the Si atom to generate this spectrum,corresponding in the experimental conditions to an irradiation of the substitutional Si atom by approximately4×109electrons.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 Figure2a shows indeed only0.8%noise r.m.s.:the net Si count rate around the edge maximum at129eV is4.4×104electrons/eV after subtraction of a decaying power law background.Figure 2b shows a data set acquired in identical conditions,but on a4-fold 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?ne structure,which is strikingly di?erent from the3-fold coordinated case.
It is interesting to note that assuming a combined cross-section for the Si L2and L3edges of3.2×10?3?232(neglecting the Si L1edge),the theoretical count rate for the Si edge would be4.3electrons/s,given a31pA current contained in a1.2?diameter probe.14Considering the uncertainties,this is in extremely good agreement with the experimental count rate of 2.5electrons/s,which can be derived by integrating the signal under the curve in the spectra of Figure2a,b over a100eV window(capturing approximately60%of the total energy loss electrons)and assuming that in the collection geometry used,about90%of the Si L2,3loss electrons are detected.These results not only con?rm that quantitative spectroscopy should now be possible at the one atom level but also demonstrate that single atom?ne structure analysis can be carried out without being noise-limited.
Indeed,the two experimental spectra exhibit very stark and clear di?erences,suggesting a completely di?erent electronic structure.The L2,3peak for the trivalent atom has a sharp and intense?rst maximum at～102.5eV,preceded by a well-resolved,less intense,shoulder starting at the edge onset at99 eV.The secondary peak is broad,centered at130eV,and its intensity is of similar magnitude to the?rst peak.By contrast,in the case of the4-fold coordinated Si atom,the peak onset is shifted to100eV with a much weaker initial sharp peak.This sharp onset is followed by an unusual peak doublet at105and 108eV before the secondary broader peak with maximum at 127eV.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 however3times more intense than the?rst 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 a4H-SiC crystal oriented down its?0001?zone axis(Supporting Information,Figure S3).For obvious reasons, the bulk SiC sample was far thicker(approximately20nm 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 a?ected by plural scattering events,do not match any of the features observed for either substitutional Si atom.Here,the edge onset lies at99eV and its broader initial peak at103eV is neither followed by the peak doublet of the4-fold coordinated Si,nor the plateau observed in the3-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 substitu-tional 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 basis-set size(as de?ned by the kinetic energy cuto?)and the density of sampling(k)points in reciprocal space.For experiments involving geometry optimization,the kinetic energy cuto?value was converged against the overall system energy.The parameter was sampled in20eV intervals,until the overall system energy varied by less than0.0001eV.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 from12×12×4to24×24×8the system energy changed by less than0.005eV,which was considered an acceptable balance of precision and feasibility of computing the results.This represented an average k-point separation in reciprocal space of0.019??1.These parameters were used for all further calculations involving structural minimization.The speci?c geometry optimization scheme utilized to obtain the
?nal,stable,models of the trivalent and tetravalent Si substitutional structures was the BFGS methodology.34?38Parallel convergence tests for the Si L 2,3EELS edge calculations were also carried out.A value of 800eV for the kinetic energy cuto ?was considered acceptable.Upon doubling the value from 400to 800eV 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 6×6×2to 12×12×4there was a negligible di ?erence in the predicted spectrum after application of a lifetime-based broadening scheme to re ?ect the instrumental resolution of 0.9eV.These k -point spacings were therefore used for any EELS calculation shown.Previous analogous work 7suggested that a layer separation of 25?would be enough to fully decouple the layers and realistically simulate graphene.This value was however doubled to 50?for the simple model system in order to con ?rm 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 2×2×1supercell and a 4×4×1supercell,both with 25?of vacuum in the c direction,initially with a trivalent Si substitutional atom.A relaxed 4×4×1cell is shown in Figure 3a.For the Si L 2,3edge,it was shown that upon changing the lateral expansion of the cells the predicted result varied minimally,so this size of cell,4×4×1with 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 0.05eV/?;(2)the maximum change in position for all atoms between BFGS steps was less than 2×10?3?;(3)the maximum change in the total system enthalpy between BFGS steps was less than 2×10?5eV 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 e ?ectively puckering out-of-plane.This suggestion arises from the fact that when enforcing a ?at geometry,all atoms being constrained to the horizontal plane,the Si ?C bond lengths in the 3-fold optimized model are signi ?cantly stretched (1.676?)compared to bulk graphene (1.420?);see Figure 3a.
In
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).
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 ?ne structures can in speci ?c cases be related to picometer-sized three-dimensional atomic displacements.7Calculations in the trivalent case were therefore carried out for both a ?at and a three-dimensional structure corresponding to an out-of-plane distortion of the graphene sp 2bonding 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 di ?erent starting positions were used,both resulting in virtually identical ?nal structures.Following geometry optimization for the 4-fold and both ?at and distorted 3-fold coordinated arrangements,all of which satisfy the stability requirements described above and therefore represent plausible atomic con ?gurations (Figure 3a),ground state EELS calculations were carried out using previously described parameters.Figure 3b compares the experimental spectra after back-ground 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 the relative peak intensities are reproduced faithfully by the simulations.In the planar geometry,however,a small feature 20eV above the edge onset appears in the simulation instead of the relatively feature-less plateau observed experimentally.The 3D distorted con ?guration provides by contrast an almost perfect match to the experiment and con ?rms 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?bonds,the Si atom sitting 0.950?above the horizontal plane,with neighboring C atoms also displaced upward from the graphene plane;see Figure 3a.The sp 2network of graphene clearly distorts and buckles to integrate this larger atom,tending locally toward a structure more akin to sp 3bonding (the predicted Si ?C bond angles are indeed 107.3degrees),as would be expected for Si ?C bonds.These results therefore show that with such low noise levels the EELS ?ne structure can be used not only to distinguish unambiguously between a trivalent and a tetravalent single atom impurity,but also to ?ngerprint sub-?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
Figure 4.(a)Total electron density map for the tetravalent Si impurity.A line pro ?le 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 ?gures,a ball and stick model being overlaid on the bottom-left repeat unit.
honeycomb graphene lattice,the calculated electron density is lower at the tetravalent Si impurity and along the Si?C bonds (Figure4a).The bonding network is thus quite disrupted around the4-fold impurity and the orbital isosurface map (Figure4b),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.Di?erent geometry orbitals must be involved in the bonding con?g-uration and the deviation from pure sp2bonding 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 https://www.doczj.com/doc/b44154336.html,ing optimized acquisition procedures resulting in very high-signal-to-noise data,we were reliably able to reveal marked di?erences in the ?ne 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 di?erences observed experimentally and suggest that if3-fold coordinated a Si substitutional atom integrates by distorting the sp2structure 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 ?ngerprinted atom-by-atom,bonding di?erences between single atom impurities of the same species are now also distinguishable with energy loss spectroscopy,paving the way
toward single atom physical chemistry.
■ASSOCIATED CONTENT
*Supporting Information
Additional?gures are provided.These include probe-deconvoluted 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 https://www.doczj.com/doc/b44154336.html,.
■AUTHOR INFORMATION
Corresponding Author
*E-mail:qmramasse@https://www.doczj.com/doc/b44154336.html,.
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.39The authors declare no
competing?nancial interest.
■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 University of Leeds,which provided access to Accelrys Materials Studio to generate electron density?gures.40The authors gratefully acknowledge Professor Ondrej Krivanek for invaluable discussions and guidance.
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