scanning tunnelling microscopy: a powerful probe of unusual

Scanning Tunnelling Microscopy: a powerful probe of unusual electronic phenomena and structural features in molecular electronic materials and photosynthetic proteins

Philip Lukins

Verdico Pty Ltd, PO Box 593 Gordon NSW, Australia. [email protected]

Scanning tunnelling microscopy and spectroscopy allow atomic-resolution surface imaging and electronic spectroscopy at the atomic level and full electronic spectroscopic imaging of conductive and semiconductive materials. The power and unique capabilities of this technique will be demonstrated using 5 unusual application examples in molecular, biomolecular and device imaging and spectroscopy from recent work in our laboratory: single-molecule donor-acceptor molecular electronic diode device structures, hybrid organic/nanoparticle devices, coherent electron conduction in photosynthetic reaction centres, surface conduction and internal structure of chlorosomes, and protein and supramolecular structure determination of algal light-harvesting complexes and linker proteins.

Keywords scanning tunnelling microscopy; electron conduction; photosynthetic protein structure; molecular electronics

1. Introduction

Scanning tunnelling microscopy (STM) was first discovered in 1981 by Binnig and Rohrer [1]. STM was the first scanning probe microscopic technique and remains perhaps the highest resolution microscopy available with ultimate axial and lateral resolutions of ~ 1 pm and ~ 10 pm, respectively. Although other scanning probe techniques such as atomic force microscopy (AFM) are now far more easily and widely used, STM has remained the technique of choice in particular niche areas and applications such as ultrahigh-resolution imaging of atomically-flat systems, manipulation of atoms or molecules on surfaces, inorganic semiconductor nanodevices, molecular conductors and semiconductors, and electrochemistry. Furthermore, the interaction mechanism in STM lends itself to electronic spectroscopy of surfaces with high spatial resolution and ultimately scanning tunnelling spectroscopy (STS) and STM/STS in which full spectroscopic imaging is achieved. Here, we will show that STM/STS are useful techniques not only in their traditional areas but also in a diverse range of unexpected areas including biomolecular and protein structure, biological organelles and organic molecular electronic systems and devices. We will also see that STM of real systems, comprising a specimen on a substrate, naturally involves transmolecular tunnelling or transmolecular conduction whether this be within the specimen or the substrate. Therefore, STM is not simply a surface technique, as is often thought, but involves bulk tunnelling or conduction. This leads to the possibility of obtaining microscopic information in the axial direction using STM and perhaps even a pseudo-3D imaging capability that could have many important applications for thin samples. The scope of STM has even extended to materials generally considered to be insulators, such as diamond and mica, where tunnelling and conduction are supported through the presence of defects or hydrated regions [2].

2. The techniques

STM is based on quantum mechanical tunnelling between an atomically-sharp metal probe tip and the surface atoms of the specimen when the tip approaches the surface to within an atomic dimension. The tunnelling current depends on the Fermi functions f(E), transmission function T(E,V) and the potentials µ, µ′ for each side of the tunnelling junction, I = (2e/h) ∫T(E,V)[f(E-µ) – f(E-µ′)]dE (1) where e is the electronic charge, h is Plank’s constant, E is energy and V is voltage. The current has an exponential dependence on tip-sample separation consistent with tunnelling as the contrast mechanism. The external circuit between the tip input and the substrate output contains a feedback system to maintain either constant tip-sample distance (constant height mode) or constant tunnelling current (constant current mode). A detailed description of the theoretical and instrumental aspects of STM is beyond the scope of this chapter and can be found elsewhere [3-5]. We used a variety of STM systems including Park Autoprobe, Burleigh and Nanosurf EasyScan systems. Image Metrology SPIP was used for image processing, display and tip characterisation. All of the STMs could be operated in the standard constant-height or constant-current modes. Each instrument was modified to operate in the new quasi-constant-height and quasi-constant-current modes which we have developed specifically for biological STM imaging and imaging weakly conductive samples [6,7]. In these later modes, a degree of height and current variation, respectively, is allowed in order to maintain optimal imaging for atomically-rough surfaces. For the biological, protein

Current Microscopy Contributions to Advances in Science and Technology (A. Méndez-Vilas, Ed.)

© 2012 FORMATEX 930

and biomolecular imaging work described here, we used cut tips only made from Pt:Ir wire (80:20 Pt:Ir) of ~ 0.2 mm diameter and ~ 2.5 mm length cut at an angle of ~ 300 which we have found to be optimal for biological imaging. For specimens where there are substantial topographic variations, tip characterisation using SPIP was performed which typically gave tip apex angles of ~ 1100.

3. Results and discussion

3.1 TTF-TCNQ single-molecule diodes

The donor-acceptor (D-A) complex TTF-TCNQ formed between tetrathiofulvalene (TTF) and tetracyano-quinonedimethane (TCNQ) is a classic organic molecular semiconductor [8] which has been studied in various physical states. So far, however, studies of the single-molecule complexes have been rare because of the obvious difficulties in isolation, stabilisation and characterisation of single complexes. We prepared TTF-TCNQ complexes using standard procedures [9] and then deposited single complexes onto freshly-cleaved single-crystal graphite from dilute solutions followed by STM manipulation to achieve oriented TTF-TCNQ where the molecular axis of the complex is (80 ± 20)0 to the substrate surface as inferred from the single-molecule STM images. The current-voltage behaviour of these TTF-TCNQ complexes can be analysed using a relation of the form I = I0[exp(e(V-IRs)/qkT) - 1] + (V-IRs)/Rsh (2) where I is the current, I0 the reverse saturation current, e the electronic charge, V the voltage, q the diode quality factor, k Boltzmanns constant, T temperature and Rs and Rsh the series and shunt resistances, respectively. When the tip-D-A-substrate junction formed is studied by STS, we observe clear diode-like behaviour with a bandgap of ~ 0.8 eV (Fig. 1). Fitting eqn 2 to this data yields q~ 8.0. In comparison, doped silicon shows a sharper rectification characteristic at a lower bandgap of ~ 0.6 eV. The TTF-TCNQ I-V characteristic is not as sharp or desirable as that for doped silicon. The single-molecule TTF-TCNQ diode has many advantages particularly as a molecular diode buiilding block with very small device sizes ~ 1 nm3 which is important in ultra-high density circuits. The molecular nature of the diode has advantages for direct molecular coupling to molecular sensors such as biosensors. We foresee applications for these TTF-TCNQ diode structures as components in molecular electronic devices, as rectifying linkers and in organic photovoltaics. However, realisation of this potential requires solving some of the problems associated with these devices including the relatively large q, the orientational dependence of their electronic properties and the perturbations due to intermolecular interactions with surrounding molecules. STM is the ideal platform for such studies because specimen preparation and placement, device imaging and structure determination, and device electronic spectroscopy and characterisation by STS are all achieved very elegantly under ambient conditions in the one instrument.

Fig. 1 Current-voltage curve for single TTF-TCNQ complexes on graphite. The curves for doped silicon and single-crystal graphite are included for comparison.



3.2 Hybrid organic-nanoparticle devices

An interesting new approach to semiconductor design is the use of metal nanoparticles functionalized by coatings of organic molecular electronic materials, a method which not only exploits the unusual electronic properties of both the nanoparticles and the molecular coating but the nanoparticles also act as a scaffold supporting the overall structure. We prepared a range of silver or gold nanoparticles (10 nm or 15 nm diameter) coated with the electron donor tetramethyl-phenylenediamine (TMPD) or the electron acceptor tetracyanoquinonedimethane (TCNQ) using spin-coating techniques [10]. SEM shows that these coated nanoparticles are typically ~ 80 nm in size and aggregate to form a disordered but connected film (Fig. 2). Using STS, the current and differential conductance curves were measured for donor-acceptor bilayer structures comprising various combinations of metal, nanoparticle size, molecular coating type and coating thickness. An example of the curves for one such combination oriented as both A-D and D-A configurations is shown in Fig. 3. The density of states (DOS) available for tunnelling is related to the normalised differential conductance, DOS ~ (V/I) dI/dV. (3) For the example in Fig. 3, the device has a high DOS for V < 0 and is insulating for V > 0 in the D-A configuration while in the A-D configuration the device has a moderate DOS for V > -100 mV and is insulating for V < - 100 mV. These unusual I-V and (dI/dV)-V curves are partly due to the very different conduction mechanisms for the nanoparticles and for the organic coatings. Both D and A layers comprise multi-juction structures as each coated nanoparticle forms many randomly-oriented junctions.

Fig. 3 STS of hybrid organic/nanoparticle D-A bilayer junctions on graphite. Current-voltage (a) and differential conductance-voltage (b) curves for D-A junctions formed using ~ 10 nm silver nanoparticles coated with TMPD (D) and TCNQ (A) [10].

3.3 Spatially-coherent transmolecular electron tunnelling

Photosystem II (PSII) is one of the two photosynthetic reaction centres in plants and algae that is responsible for the conversion of light energy into electrochemical energy for use in the organisms metabolic processes, and is therefore one of the most important proteins in nature and a basis for the existence of life on earth. Great advances have been

Fig. 2 SEM image of organic-coated silver nanoparticles of average diameter ~ 80 nm.



made in understanding the function of PSII and the structure of PSII is now well-understood from X-ray crystallography [11-13] as well as STM [6,14-16]. PSII core dimer complexes, prepared by the method of van Leeuwen et al. [17], were deposited by electrically-assisted Langmuir-Blodgget deposition [18] onto single-crystal graphite. The PSII form 2D crystalline arrays on the atomically-flat graphite with the crystals aligned along steps and edges on the substrate surface (Fig. 4a). At higher resolution, we see the dimeric supramolecular structure of the core complexes in a regular lattice (Fig. 4b). By carefully varying the current and voltage conditions, we were able to simultaneously observe the PSII at moderate resolution and the underlying graphite substrate with atomic resolution (~ 0.2 Å). Under these conditions, the PSII images appear as a convolution of the PSII structure and the hexagonal graphite surface structure (Fig. 4b). The 2D FFT (Fig. 4c) clearly shows the PSII signal at low frequency surrounded by 6 hexagonally-disposed graphite peaks at higher frequencies. This intriguing observation [19] can only be explained by spatially-coherent transmolecular electron tunnelling through the ~ 10 nm thick PSII into the atomically-flat graphite substrate below. We postulate that the mechanism for this phenomenon in PSII involves hopping conduction along the α-helices which span the protein, the semiconduction along the PSII reaction centre primary electron transport pathway and coherent interactions in the dimer complex. This unusual coherent tunnelling phenomenon, first seen in our laboratories, should also be observable in other highly-ordered biomolecular systems with interesting electronic or photonic properties.

Fig. 4 STM of 2D crystals of Photosystem II core complexes. The images are (a) a medium-resolution image of a section of a 2D PSII crystal at a step edge, (b) a high-resolution image of the 2D PSII crystal showing several PSII core dimer complexes (peanut-shaped objects) on a background of atomically-resolved single-crystal graphite, (c) the 2D FFT of the region of interest defined by the square box in image b [19].

3.4 Surface and internal structure of chlorosomes

The general structure of chlorosomes involves a lipid envelope enclosing bacterial chlorophyll (BChl) oligomer structures and incorporating a baseplate structure [20,21]. From electron microscopy studies, these oligomer structures are now thought to be either rod-like or lamellar in shape. The motivations of an STM study are not only to clarify the topographic features and dimensions of isolated chlorosome particles but also to study possible interactions of the internal oligomers with the lipid envelope. Chlorosomes were prepared by the method of Zhu et al. [22] and deposited from dilute buffer solutions onto freshly-cleaved graphite and air-dried. STM of a single chlorosome particle (Fig. 5) shows an ellipsoidal overall shape with lateral dimensions of 81 nm in length and 36 nm in width [23]. These dimensions are very similar to values of 99 nm and 31 nm obtained by Zhu et al. [22] using AFM but somewhat smaller than those reported by Martinez-Planells et al. [24] who obtained 166 nm and 97 nm, respectively. These differences probably reflect the differing preparation techniques and original organisms. The surface has many contours and irregular elevations, and associated with these features are many localised high-conductance regions seen as bright spots in the image. These high-conductance regions are typically ~ 2 – 3 nm in diameter, significantly larger than the resolution of < 0.5 nm. We believe that the high-conductance regions on the lipid surface indicate regions of protrusion of the BChl oligomers into the lipid layer. The distribution of these high-conductance regions then reflects the internal positioning of the BChl oligomers and may provide some indirect evidence regarding the oligmer structure itself. This idea is represented schematically in Fig. 6 where we see that for a generalised chlorosome (Fig. 6a) that the transmolecular conduction through the lipid layer, BChl oligomers, baseplate and substrtate will be greatest in those localised regions where the oligomer stacks cause deformations of the lipid envelope (Fig. 6b). The lipid layer acts as a conformal coating holding together the oligomer stacks into the chlorosome organelle.



A statistical analysis of the separation of these high-conductance regions indicates that the average separation is 2.1 ± 1.0 nm which is close to the characteristic dimension ~ 2.05 nm for the striations seen in various electron microscopy reports on chlorosomes. While not definitive, these results lend support to the lamellar model [25] for the structure of the BChl oligomers whereas these high-conductance regions are not adequately explained by the rod model.

Fig. 6 Internal structure of chlorosomes (a) showing BChl oligomers arranged inside the lipid envelope and the conduction pathways (b) observed for different overlap or protrusion of the BChl oligomers into the lipid layer.

3.5 Structure of R-phycoerythrin and location of the γ-subunit

Cyanobacteria, red algae and cryptophytes use water-soluble phycobiliproteins (PBPs) with covalently-bound linear tetrapyrrole pigments to harvest sunlight for photosynthesis. High-resolution structures are available for many of these PBPs and in both cyanobacteria and red algae there is a basic (αβ)3 or (αβ)6 structure with a three-fold symmetry axis. In addition to the αβ units some PBPs are intimately associated with linker proteins with the 31-33 kDa γ-subunits of B-PE and R-PE being the subject of considerable biochemical investigation [26,27]. In general, the structure of these associated linker proteins is unknown since the three-fold symmetry causes the X-ray diffraction pattern to be averaged. However, in one case [28], some partial structural information could be obtained for the central region of R-PE. However, for R-PE from both Polysiphonia urceolata [29] and Griffithsisa monilis [30], the high-resolution structures not only showed electron density in the centre of the trimer of αβ subunits but that this was associated with an altered structure of a β-subunit chromophore. In the allophycocyanin–linker complex from Mastigocladus [28], the embedded linker does not protrude from either surface but probably alters the trimeric structure of the allophycocyanin so that successive trimers in the phycobilisome directly interact more favourably. To obtain more information on the

Fig.5 STM image of a single chlorosome from Chloroflexus Aurantiacus [23]. The curerent setpoint and tip bias are 3 nA and 20 mV, and the image size is 90 nm x 90 nm.



topography of the γ-subunit within R-PE of Griffithsia monilis and to resolve some of the above issues, we have used scanning tunnelling microscopy of single complexes of R-PE. The X-ray crystal structure of R-PE [30,31] shows that the complex contains an (αβ)6-hexamer in a structure with three-fold symmetry together with some signal arising from the centre of the complex, possibly due to the γ-subunit. The resolution of 1.9 Å over most of the structure allows determination of the structure of the (αβ)6-hexamer; however, there is a loss of resolution near the centre of the complex due, in part, to the C3 symmetry which causes an averaging of the diffracted intensity from this region. This problem leads to an ambiguity in the position, structure and function of the moiety at the centre of the complex. Samples of R-PE were prepared as described previously [31]. These samples were diluted to various concentrations, deposited as 2 μl droplets on freshly-cleaved pyrolytic graphite and air-dried for 10 mins. STM images were obtained using a Nanosurf EasyScan STM system. The STM images (Fig. 7) indicate that the isolated complex has a rounded triangular shape ~ 15 nm across and ~ 1.5 nm high with three distinct subunits arranged with three-fold axial symmetry together with a shallow depression in the central region of ~ 0.2 nm depth [32]. The topographic character of the image (Fig. 7a) was analysed by taking 16 profiles all through the centre of the complex, each separated by 22.5 0 and averaged to obtain the rotationally-averaged radial profile in Fig. 7b. From this profile, the volume of the R-PE complex is determined to be 143 ± 5 nm3. Since the γ-subunit is ~ 30 kDa and the whole complex is ~ 240 kDa, the volume of the γ-subunit is ~ 18 nm3 and the (αβ)6-hexamer is ~ 125 nm3.

Fig. 7 Topographic STM image (a) of a single R-PE complex showing the (αβ)6 hexamer and central γ-subunit, and the radial profile (b) obtained by rotationally-averaging 16 sections of equal angular spacing through the centre of the complex [32]. The maximum slope of the protein surface observed in the region of the central depression is tan θ = 0.14 ± 0.02 from which the maximum inclination angle θ can be calculated as (8.1 ± 1.1) 0. By comparison, the STM tip apex half-angle is ~ 57 0 so its inclination angle is ~ 33 0. Therefore, the STM tip is much sharper, by a factor 4, than the minimum sharpness required to follow the surface topography. This confirms that the profile in Fig. 7b is representative of the protein surface topology. The observed central depression in the R-PE complex is consistent with the γ-subunit being located in the centre of the complex. The fact that the γ-subunit does not protrude above the (αβ)6-hexamer suggests that it does not function, at least alone, as a linker but rather as a site for addition of other proteins, which may act as linkers, onto R-PE. The close agreement between the STM images and the overlayed X-ray structure (Fig. 8) indicates that the two techniques give consistent structures, any difference between the preparations are not structurally important and that the single-molecule and crystalline state structures are similar. We have showed that the region at the centre of the (αβ)6-hexamer complex is not a hollow structure but instead contains a subunit ~ 30 kDa which we assign to the γ-subunit. This subunit only partially fills the centre region with its surface lying ~ 0.2 nm below the surface of the (αβ)6-hexamer which indicates that additional linker complexes are involved in the binding of R-PE to other proteins in the natural state.



Fig. 8 Comparison of the STM image [32] of R-phycoerythrin with the overlayed X-ray crystal structure [30].

Acknowledgements I would like to thank several colleagues particularly Drs C.S. Barton, A.F. Collings, R.G. Hiller, T. Reda and M.H. Zareie. The financial support of the Australian Research Council is gratefully acknowledged. I also wish to thank The University of Sydney and Verdico Pty Ltd for supporting various parts of this work.

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scanning tunnelling microscopy: a powerful probe of unusual

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