electron optics instrumentation A CS Corrected HRTEM: Volume 37E Number 1 July 20, 2002 Initial Applications in Materials Science
Contents
A Cs Corrected HRTEM: Initial Applications in Materials Science...... 2 Quantitative Environmental Cell - Transmission Electron Microscopy: Studies of Microbial Cr(VI) and Fe(III) Reduction...... 6 Simulations of Kikuchi Patterns and John L. Hutchison†, John M. Titchmarsh†, David J. H. Cockayne†, Comparison with † † † Experimental Patterns...... 14 Guenter Möbus , Crispin J. D. Hetherington , Ron C. Doole , Experimental Atomically Resolved Fumio Hosokawa††, Peter Hartel††† and Max Haider††† HAADF-STEM Imaging -A Parametric Study ...... 22 †Department of Materials, Oxford University Observation of Waterborne Protozoan †† Oocysts Using Electron Optics Division, JEOL Ltd. ††† a Low-Vacuum SEM...... 26 CEOS GmbH A Possible Efficient Assay: Low-Vacuum SEM Freeze Drying and Its Application for Assaying Bacillus thuringiensis Formulations Quality...... 29 Observations of Algae and Their Floc in A new aberration-corrected TEM/STEM is being designed for applications in Water Using Low-Vacuum SEM and materials science. Here we describe preliminary tests of the objective lens CS EDS...... 34 corrector, and present images showing some of the advantages in applications Development of Nano-Analysis Electron of CS corrected HREM in the study of advanced materials. Microscope JEM-2500SE ...... 40 Development of JSM-7400F; New Secondary Electron Detection Systems Permit Observation of Introduction and energy-filtered imaging, EDS and hologra- Non-Conductive Materials ...... 44 phy. A wide objective lens pole-piece gap is Applications of Image Processing Since the invention of the electron micro- possible because of the CS correction and Technology in Electron Probe scope over 60 years ago the effects of aberra- allows a large range of specimen tilt while Microanalyzer...... 48 tions in round electromagnetic lenses have retaining HREM imaging capability. In order Technology of Measuring Contact Holes imposed fundamental limits on their perform- to minimise interference and to maximise ther- Using Electric Charge in a Specimen ..54 ance. In the case of HREM, spherical aberra- mal stability, the microscope column, power Organic EL Display Production Systems supplies and operating consoles will all be -ELVESS Series-...... 59 tion was shown by Scherzer [1] to limit inter- In-Situ Observation of Freeze Fractured pretable resolution, although special tech- installed in separate, adjacent rooms within a Red Blood Cell with High-Vacuum niques have been devised to get around this, purpose-built laboratory, now under construc- Low-Temperature Atomic Force such as “aberration-free focus” for particular tion. Components of the new instrument are Microscope ...... 62 crystal structures [2]. Small-probe techniques, being independently developed and tested Peak Deconvolution of Analysis in and in particular STEM, are similarly limited prior to final assembly. Auger Electron Spectroscopy...... 66 by spherical aberration in the probe-forming JEOL's Challenge to Nanotechnology ....70 lenses. The need for a small, well-defined Assessment and Preliminary Progress in Development of High-Density probe with a high current remains a pressing Applications of CS Corrected Reactive Ion Plating ...... 74 need here. The recent successful development Applications of High-Power Built-in of aberration correctors for electromagnetic Objective Lens Plasma Gun...... 78 lenses [3, 4] will radically change this situa- The objective lens CS corrector [5] has now Introduction of New Products...... 81 tion, as they offers dramatic improvements for been developed and tested on a separate JEM- direct interpretation of image contrast as well 2010F instrument and we illustrate here some as for microanalysis with improved spatial res- of the initial results. Tests have confirmed the Cover micrograph olution and sensitivity in materials science stability of the corrector over lengthy periods. Experimental Kikuchi pattern (left) and simu- applications. This corrector is based on the design concept lated Kikuchi pattern (right) of MgO [100]. of Rose [6], and consist of a series of two (See pages 14 to 21) A New Aberration-Corrected hexapole and two transfer lenses doublets Microscope (round lenses) located between the objective Courtesy of Professor Emeritus Michiyoshi and first intermediate lenses in the microscope Tanaka, Institute of Multidisciplinary Research In order to exploit these benefits a new column. This is shown in Fig. 1. The col- for Advanced Materials, Tohoku University. TEM with aberration correction of both con- umn height is increased by some 24 cm. The denser and objective lenses is now being successful operation of the corrector depends developed for installation at Oxford University. upon accurate measurement of the main aber- This instrument is based on the JEM-2010FEF rations present, and this is done by acquiring instrument with a Schottky field emission images of an amorphous film and measuring source and aims to provide an HREM informa- relative changes in two-fold astigmatism and tion limit and HAADF resolution close to 0.1 defocus with changes in incident beam tilt. nm. Analytical features will include EELS This in turn is achieved by calculating Fourier transforms of the images, and displaying these †Parks Road, Oxford, OX1 3PH, UK as a tableau showing the variations as a func- Serving Advanced Technology †E-mail: john. [email protected] tion of beam tilt and azimuthal orientation.
( 2) JEOL News Vol. 37E No.1 2 (2002) very close to zero. A more detailed compari- son of this image with those obtained using other techniques will be presented elsewhere [10]. It has been noted that while direct inter- pretation of aberration-corrected images prom- ises to be more accurate in many applications, image simulation will still be required [11]. Suppression of phase contrast A new area in which aberration correction will provide further significant benefits is the characterization of nanometer-sized particles. Important parameters are microstructure, shape and size, all of which are difficult to determine accurately by conventional HREM imaging. First, in conventional HREM imaging, i.e. at Scherzer focus, the presence of a prominent Fresnel fringe around the edge of a small parti- cle will make precise size measurement diffi- cult. Second, delocalised contrast (see above) gives rise to “ghost images”, particularly in a FEG instrument. Third, free-standing nanoparticles must be supported, usually on amorphous substrates for plan-view imaging. The immediate advantages of CS-corrected imaging are clearly illustrated in Fig. 5. This shows an image of a small (~ 4 nm) CdSe quantum dot on an amorphous carbon support film. In an uncorrected image of such a small particle recorded at Scherzer defocus, the pres- ence of strong Fresnel fringes and “ghost” images would obscure the fine scale structural features, which are further upset by strong phase contrast arising from the carbon film. The image recorded in the aberration-corrected state provides the following immediate advan- tages: the image is recorded at very close to Gaussian focus so that there is no Fresnel fringe around the edges of the particle; there are no ghost images present and the phase con- trast from the amorphous support film has been almost completely suppressed. Under these conditions the amplitude contrast contri- bution is optimised, and the contribution from
Fig. 1. Column of JEM-2010F microscope with CS corrector installed. the more strongly scattering Cd and Se is enhanced. The size, shape and internal struc- ture of the crystallite, only 2 nm in size, are thus revealed with much improved clarity [12]. This method was first described by Zemlin and (0.8 eV) and objective lens chromatic aberra- co-workers as a way of determining coma-free tion coefficient of 1.2 mm for the URP pole- Atomic resolution imaging of alignment conditions for HREM [7]. Figure 2 piece operating at 200 keV. complex oxide structures shows a tableau of diffractograms from a spec- Although high resolution images of com- imen of amorphous Ge imaged in an uncor- Applications of CS Corrected plex oxide structures have been widely studied rected state: here the electron beam has been for many years the resolution of contrast at aligned approximately to the voltage axis, and HREM in Materials Science oxygen sub-lattice sites remains a serious chal- two-fold astigmatism has been corrected. The Localised contrast at boundaries lenge. High-voltage HREM has been used inner four off-axis diffractograms represent a [13], and more recently image restoration tech- beam tilt of 9 mrad, the outer twelve a tilt of One of the major limitations in the current niques have been successfully developed to 18 mrad. The strong effects of axial coma, 3- generation of field-emission-gun HREM achieve this [14]. It is now clear that the fold astigmatism and spherical aberration are instruments is the delocalisation of contrast at enhanced high resolution capability afforded all evident; the tableau is evidently non-centro- boundaries and interfaces [9]. This effect by CS correction can produce resolution close symmetric. Measured aberration values are as arises from the width of the aberration discs to 0.1 nm, particularly when electron beam follows: CS: 0.59 mm, 3-fold astigmatism: 630 belonging to individual diffracted electron energy spread is reduced. Figure 6 shows an µm, coma: 1.5 µm. The aberration corrector beams, the diameter of which increases with image of a novel niobium oxide structure, is then used to compensate these effects, and a CS. This may produce bands of spurious con- where all the projected cation sites are tableau corresponding to the corrected state is trast up to several nm. in width, making quan- revealed, along with visible contrast at the presented in Fig. 3. Here there are almost no titative interpretation of image contrast diffi- anion sites. We can expect even further changes between the diffractograms for tilted cult. When CS is fully corrected, this phenom- improvements when the effects of chromatic illumination; 2-fold and 3-fold astigmatism, enon disappears, and interfaces or boundaries aberration are reduced by reducing the energy coma and spherical aberration have all been appear atomically sharp. spread in the incident electron beam. corrected. These results demonstrate an infor- The imaging of a grain boundary in a <111> mation limit, in the corrected state, between Au foil after aberration correction (Fig. 4) 0.12 and 0.13 nm, verified by measurement of demonstrates the effective removal of delo- Conclusions Young’s fringes [8]. This value is consistent calised phase contrast. This micrograph was A CS - corrected HREM has been built and with the energy spread in the electron beam recorded at close to Gaussian focus, with CS its performance assessed as part of a major
JEOL News Vol. 37E No.1 3 (2002) ( 3) Fig. 2. Diffractogram tableau for uncorrected microscope. Outer diffractograms correspond to a beam of 18 mrad.
Fig. 3. Diffractogram tableau for aberration- uncorrected state.
( 4) JEOL News Vol. 37E No.1 4 (2002) project to develop a “next generation” TEM/ STEM. This unique instrument will be installed in a specially built laboratory at Oxford University’s Department of Materials. We have demonstrated that the main objective lens aberrations may be fully corrected, and present examples of the main benefits to be gained by the use of CS corrected HREM in materials science. Acknowledgements This project is supported by a major JIF grant from HEFCE and EPSRC. We are also grateful to JEOL Ltd. and to JEOL (UK) Ltd. for their ongoing support. References 1. Scherzer O.: J. Appl. Phys. 20 20 (1949). 2. Hashimoto H.: Chemica Scripta 14 23 (1978-79) 3. Haider M., Rose H., Uhlemann S., Schwan E., Kabius B. and Urban K.: Ultramicroscopy 75, 53 (1998). 4. Krivanek O. L., Delby N. and Lupini A. R. Ultramicroscopy 78, 1 (1999). 5. Haider M., Braunshausen G. and Schwan E.: Optik 99, 167 (1995). 6. Rose H., Optik 85 19 (1990). 2 nm 7. Zemlin F., Weiss P., Schiske P., Kunath W. and Herrmann K.H.: Ultramicroscopy 49, 3 (1977). Fig. 4. ∑ 3 boundary in <111> gold foil, showing localised contrast. 8. Frank J.: Optik 30, 171 (1969). 9. Thust A., Coene M., Op de Beek M. and Van Dyck D.: Ultramicroscopy 64, 211 (1996). 10. Hetherington C J D et al. Proceedings of ICEM 15 (Durban) 2002. 11. Möbus G., Titchmarsh J. M., Hutchison J. L., Hetherington C. J. D., Doole R. C. and 2 nm Cockayne D. J. H.: Inst. Phys. Conf. Series No. 168, 27 (2001) 12. Allsop N. A., Hutchison J. L. and Dobson P. J.: Proceedings of ICEM 15 (Durban) 2002. 13. Horiuchi S. and Matsui Y.: Jpn. J. Appl. Phys. 31, L283 (1992) 14. Kirkland A. I., Meyer R. R., Saxton O. W., Hutchison J. L. and Dunin-Borkowski R. E.: Inst. Phys. Conf. Series No. 161, 291 (1999).
2 nm
Fig. 5. Nanocrystal of CdSe, with sup- pressed phase contrast of support- ing carbon substrate.
Fig. 6. Aberration-corrected image of a nio- bium oxide crystal, showing con- trast at both cation and anion lat- tice sites.
JEOL News Vol. 37E No.1 5 (2002) ( 5) Quantitative Environmental Cell - Transmission Electron Microscopy: Studies of Microbial Cr(VI) and Fe(III) Reduction
Tyrone L. Daulton†, Brenda J. Little††, Jin W. Kim†, Steven Newell†, Kristine Lowe†††, Yoko Furukawa†, Joanne Jones-Meehan††† and Dawn L. Lavoie†
†Marine Geosciences Division, Naval Research Laboratory ††Oceanography Division, Naval Research laboratory †††Chemistry Division, Naval Research Laboratory
Several applications of environmental cell (EC)-transmission electron microscopy (TEM) to microbial metal reduction studies are reviewed. Electron energy loss spectroscopy (EELS) techniques were used to determine oxidation state, at high spatial resolution, of Cr associated with the metal-reducing bacteria, Shewanella oneiden- 2- sis, in anaerobic cultures containing Cr(VI)O4 . These techniques were applied to fixed cells examined in thin section by conventional TEM and unfixed, hydrated bacteria examined by EC-TEM. Measurements by EELS demonstrated that cell boundaries became saturated with low concentrations of Cr and the precipitates encrust- ing bacterial cells contained a reduced form of Cr in oxidation state +3 or lower. In addition, reduction by S. oneidensis of structural Fe(III) in nontronite, an expandable clay, was studied under anaerobic conditions. Direct observations by EC-TEM yield unambiguous measurement of layer spacings and the contraction of hydrated, clay layers upon reduction of structural Fe(III). In particular, nonreduced and Fe(III)-reduced nontronite, observed by EC-TEM, exhibit mean (001) spacings of 1.50 nm and 1.26 nm, respectively.
Introduction of microbial metal reduction mechanisms and Both TEM and scanning electron their alteration products; two studies are microscopy (SEM) have sufficient resolution Conventional transmission electron reviewed. to study the spatial relationship between cells microscopy (TEM) studies of microbial reduc- and reduction products, as well as their chem- tion of metals have provided important infor- Microbial reduction of Cr(VI) istry. For example, energy-dispersive X-ray mation. However, they are limited because Hexavalent chromium species are strong spectroscopy (EDXS) has been used to identi- the techniques of fixation, embedding, and oxidants which act as carcinogens, mutagens, fy elements present in reduction products asso- microtoming, necessary to prepare thin speci- and teratogens in biological systems [1]. The ciated with bacteria [3-8] and wetland plants mens, are known to alter delicate cellular and high solubility, bioavailability, and toxicity of [9]. However, EDXS is insensitive to oxida- abiotic microstructures. Fixation and dehy- Cr(VI) make it a particular environmental con- tion state. Electron energy loss spectroscopy dration preserve some cellular structure, but cern. Microbial mechanisms for Cr(VI) (EELS) by TEM is a direct probe of the elec- buffer and organic solvent washes remove reduction are of particular technological and tron configuration around atoms, and can extracellular polymers. In addition, soluble biological importance because they convert a determine the oxidation state of 3d and 4d ions from extracellular and intracellular toxic, mobile element into a less toxic, immo- transition metals at high spatial resolution [10, sources, such as soluble reduction intermedi- bile form. The study of microbial Cr(VI) 11]. Furthermore, EELS techniques have ates, can be lost. Reduction intermediates are reduction, such as the identification of reduc- been used to produce oxidation state maps unstable with intermediate valence state tion intermediates, has been hindered by the using energy filtered imaging [12]. between the valances of the stable end mem- lack of an analytical technique that can deter- Determination of oxidation state by EELS is bers of the reduction process. Dehydration mine the oxidation state of Cr at subcellular accomplished by analyzing valence induced causes basal layer spacings in expandable clay spatial resolution. The most widely used differences in fine structure of L2 and L3 (or minerals to contract and the extracellular method for following Cr(VI) reduction is the collectively L2, 3) absorption edges by compari- biopolymers produced by bacteria associated diphenylcarbazide colorimetric method [2]. son of unknowns to standards of known oxida- with clays to collapse into a filamentous, web- Other methods used to determine oxidation tion state. The L2, 3 absorption edges arise like network. In contrast, environmental cell state in bacterial cultures include electron spin from transitions to unoccupied d levels from (EC)-TEM is a powerful technique in which resonance (ESR) (also called electron para- two spin-orbit split levels, 2p1/2 level (produc- hydrated specimens can be examined at high magnetic resonance (EPR) and electron mag- ing the L2 edge) and the 2p3/2 level (producing spatial resolution in more or less their natural netic resonance (EMR)) spectroscopy, and X- the L3 edge). The valence of a transition state. The purpose of this paper is to demon- ray photoemission spectroscopy (XPS). metal is related to the number of holes in the d strate the application of EC-TEM for the study These bulk techniques cannot provide detailed level (i.e. the 3dn or 4dn) configuration. For information at the subcellular (submicron) example, tetrahedral Cr(VI) has an empty d †Stennis Space Center, MS, 39529 USA level necessary for understanding microbial orbital (3d0 configuration) and octahedral † 3 E-mail : [email protected] reduction processes. Cr(III) has a 3d configuration. Since L2, 3
( 6) JEOL News Vol. 37E No.1 6 (2002) absorption edges are inherently dependent on However, the expected contraction in clay from Uley graphite mine, South Australia the number of unoccupied d levels in 3d and (001) layer spacing was not found. A constant (Clay Mineral Society standard (NAu-1) [30]) 4d transition metals, they are sensitive to layer spacing of 1.26 nm was observed in both was used as the sole terminal electron accep- valence state. In general, oxidation state can oxidized and reduced smectite. This measure- tor. Samples (diameters < 2.0 µm) were ster- affect the position, shape and relative intensity ment is in conflict with the earlier in-situ pres- ilized by exposure to microwave radiation (5 of L2, 3 absorption edges. Techniques used to sure-cell X-ray diffraction work of Wu et al. min), and sterility was confirmed from lack of determine mixed/single valence states involve [23] which demonstrated a decrease in mean bacterial growth on Luria-Bertani (LB) agar analysis of the following: (a) the position of interlayer distance upon reduction of Fe(III) in after 2 days. Cells were grown anaerobically the L2, 3 absorption edges [10], (b) the ratio of bulk Na-nontronite. However, the effects of with nontronite for 4 days, then examined by the I(L3)/I(L2) integrated-peak intensity (hence- resin infiltration on the interlayer spacing are EC-TEM at 10 - 100 Torr of air (saturated with forth abbreviated L3/L2) [10, 11], and (c) least uncertain and, therefore, the homogeneous water vapor) circulating through the EC at a squares fits of summed spectra of standards or layer spacing observed by Stuki and Tessier rate of 2 Torr L min-1. calculations to the shape of L2, 3 absorption [24] may be due to artifacts induced by resin edges [13]. infiltration. We recently demonstrated the Transmission electron microscopy Because of difficulties in the application of application of EC-TEM to study the collapse A JEOL JEM-3010 transmission electron EELS techniques to actual microcharacteriza- of basal spacing in ferruginous-expandable microscope operating at 300 keV with a LaB6 tion of mineral oxidation state, these tech- clays induced by microbial Fe(III) reduction filament was used in these studies. This niques have been under utilized. For exam- [25]. The effects of anaerobic respiration instrument is equipped with an EDXS system, ple, despite the detailed, submicron-scale (Fe(III) reduction) by S. oneidensis on non- a Gatan imaging filter (GIF200) capable of information EELS techniques can provide, to tronite were examined. In particular, differ- EELS, and a JEOL EC system. The EC-TEM our knowledge, they have never been applied ences in layer spacings between nonreduced system is of the closed cell type [31] where in microbial reduction studies. In fact, previ- and reduced nontronite, in their ‘native’ confinement of a pressurized environment is ous TEM studies assumed microbial Cr(VI) hydrated state, were characterized using EC- achieved with electron-transparent windows. reduction products were Cr(III) [6, 8]. Since TEM. The microscope is equipped with two inter- Cr(III) is a stable and insoluble reduced form, changeable JEOL EC specimen holders (a this assumption is likely correct. However, Cultures, Methods, and two-line gas EC and a four-line gas/liquid EC) the oxidization state of the Cr associated with Techniques that are connected to the EC system by flexi- bacteria has not yet been determined by direct ble, stainless steel lines. Both in-situ EC- measurement. We recently demonstrated the Cultures TEM specimen holders are capable of circulat- application of EELS techniques for the deter- S. oneidensis [15] was originally isolated ing dry or water-saturated gas (using two lines) mination of oxidation state of metals associat- from the anaerobic zone of Mn-rich sediments at flow rates of 0 - 15 Torr L min-1 through the ed with hydrated bacteria [14]. In particular, in Oneida Lake, NY [26]. S. oneidensis specimen chamber at l0-3 to > 200 Torr pres- Cr(VI) reduction by Shewanella oneidensis (ATCC RF50108) is a Gram-negative bacteri- sure. The four-line holder has two additional [15] was studied. um capable of respiring aerobically and anaer- service lines which can be used to independ- Basal layer contraction obically using a variety of terminal electron ently inject several microliters of liquids from acceptors, including: O2, Fe(III), Mn(IV), different reservoirs. Each EC holder consists of expandable clays induced by - - 2- nitrite (NO2 ), nitrate (NO3 ), sulfite (SO3 ), of a small cylindrical cell sealed by two elec- 2- 2- Fe(III) reduction thiosulfate (S2O3 ), tetrathionate (S4O6 ), tron transparent windows on the top and bot- Bacteria have been shown to effectively trimethylamine N-oxide, fumarate, glycine, tom (see Fig.1 for the 4-line cell used in this reduce octahedral Fe(III) in clays [16, 17]. Cr(VI), U(VI), and Tc(VII) [27-29]. Complete study). The windows are 15 - 20 nm thick The importance of the role of redox driven details on the cultures and reduction experi- amorphous carbon (a-C) films covering seven interactions between ferruginous clays and ments can be found in [14, 25], and are sum- hexagonally arrayed, 0.15 mm apertures on a bacteria in the alteration of clays has been marized below. 3.5 mm diameter Cu disk (Fig. 1). Prior to receiving increasingly more attention. For For conventional-TEM studies of Cr(VI) use, the windowed grids were tested to with- example, swelling pressures of ferruginous reduction, cells were grown anaerobically for stand a pressure differential of 250 Torr for 2- clays are related to basal layer spacing [18], 30 days with 100 µM CrO4 as the sole termi- one minute. A computer controls the EC sys- which depends on the oxidation state of octa- nal electron acceptor. Samples (1 mL) were tem and facilitates the operation of inserting, hedral Fe [19]. Furthermore, reduction of pelleted by centrifugation, fixed in 1 mL of a and removing the EC holders from the micro- Fe(III) in ferruginous clays produces decreased 5% aqueous solution of glutaraldehyde scope column without breaching the delicate swelling pressures [20], increased cation fixa- overnight at room temperature, and embedded windows (Fig. 2). Higher sensitivity leak tion [21], smaller specific surface area [22], in Spurr’s resin. The embedded specimen checks of the EC windows are performed auto- and a decrease in mean layer spacing [23]. was sectioned to 80 nm thickness by micro- matically during the specimen insertion Interlayer force is believed produced by the tome, and mounted on amorphous carbon sequence prior to full insertion into the col- mutual attraction to interlayer cations by the (a-C) coated Cu TEM grids (see [14] for full umn. Specimens are supported on the lower net-negative charge of phyllosilicate layer sur- description). a-C film window. In conventional TEM, faces which balances the total charge of the For EC-TEM studies of Cr(VI) reduction, many specimens are supported on a-C films, in clay. Therefore these studies suggest, cells were grown anaerobically with 100 µM this sense, there is only one additional a-C film 2- increased interlayer force may be driven by CrO4 as the sole terminal electron acceptor. the electron beam must past through using EC- reduction-induced changes in the surface layer A total of 0.275 moles K2CrO4 was added to TEM. Resolution tests of graphite in the EC charge. However, this theory cannot be fully the culture over a 51-day incubation. In con- show lattice resolution of at least 0.38 nm at 60 evaluated because of the lack of direct meas- trast to conventionally prepared TEM speci- Torr of hydrated room air. It should be noted urements. Nearly all structural data have been mens, EC-TEM specimen preparation was that the EDXS system cannot be used with obtained by bulk techniques, and data avail- minimal: culture was centrifuged, supernatant EC-TEM because there is no direct line of able by direct measurements are inconclusive, removed, and the pellet rinsed with distilled sight between the specimen and the EDXS e.g. [24]. water to remove trace salts. An aliquot (sev- detector. Stuki and Tessier [24] examined chemically eral µL) of the resuspended pellet was quickly Unlike EC systems based on the principle of reduced Fe-rich smectite by high resolution loaded into the EC-specimen holder. differential pumping, closed-cell EC systems (HR)-TEM. Specimens were prepared by thin Removal of trace salts from the culture cir- require absolutely no modification to the col- section after water exchange with embedding cumvented salt precipitation on the EC win- umn and the transmission electron microscope resin. Using selected area electron diffraction dow as the bulk of the aliquot evaporated, can still be used for conventional TEM without (SAED), they showed the crystal stacking leaving a thin hydrated layer. The specimen compromising resolution and analytical capa- changed from turbostratic to a more ordered was examined at 100 Torr of air (saturated bilities. The microscope was also equipped structure in the reduced state, indicating an with water vapor) circulating through the EC with conventional single- and double-tilt speci- increase of interlayer attraction due to the at a rate of 2 Torr L min-1. men holders for conventional TEM. The sin- structural reduction of Fe(III) to Fe(II). For studies of clay reduction, nontronite gle-tilt holder has an adapter which accepts
JEOL News Vol. 37E No.1 7 (2002) ( 7) windowed EC grids for analysis following Results of both techniques are used in combi- and TEM conditions: an illumination angle their use in the EC holder. nation to yield higher confidence and accura- 2 = 4 - 10 mrad, a collection angle of 2 = cy. In contrast, previous EELS studies have 10.8 mrad, a 2 mm entrance aperture, and an EELS techniques for oxidation focused on demonstrating the capability of one energy dispersion of 0.1 eV/channel. Low- state determination technique, rather than applying techniques in loss spectra were acquired with an integration Two EELS techniques were used to identify combination to actual microcharacterization in time of 0.128 s and core-loss spectra between oxidation state of Cr associated with bacteria. physical/biological systems. 0.512 and 1.02 s. For each acquisition, 10 Oxidation state was determined by both the (EC-TEM) or 25 (conventional TEM) spectra EELS experimental parameters chemical shift of L2, 3 edges and the ratio of were summed. Spectra were collected in dif- L3/L2, integrated-peak intensities, the two most The following conditions were used during fraction mode of the transmission electron sensitive and straightforward techniques. collection of EELS spectra under EC-TEM microscope (i.e. image coupling to the EELS
Fig. 3. Shewanella oneidensis imaged by EC-TEM at 100 Torr: (a) bacteria exhibit- ing low contrast in bright-field imaging and (b) bacteria encrusted with elec- tron dense particulate. The arrowhead in panel (b) points to a low contrast Fig. 1. Schematic illustration of the speci- bacterium in the same field of view as a bacterium with electron dense par- men chamber for the four-line EC ticulate, illustrating the dramatic contrast difference. specimen holder.
Fig. 2. Schematic illustration of the EC control system.
( 8) JEOL News Vol. 37E No.1 8 (2002) Fig. 6. A comparison of the core-loss EELS spectra of encrusted Shewanella Fig. 4. Shewanella oneidensis imaged by Fig. 5. Shewanella oneidensis imaged by oneidensis in the EC at 100 Torr and EC-TEM at 100 Torr: (a) cell is conventional TEM in 80 nm thick, Cr standards of known oxidation encrusted with electron dense par- thin section: (a) cell is encrusted state. Spectra were normalized to ticulate. (b) EC-TEM EELS spec- with electron dense particulate. the intensity of the L3 peak and off- trum from the bacterium demon- The field of view displays several set from one another. The spectra strates the presence of Cr. Both the bacterial cells in random, oblique shown for the Cr standards repre- low-loss spectrum containing the cross-section. Cross-sectional sent the sum of twenty individual zero-loss peak (ZLP) and the core- images show precipitates occur on spectra. The error bars shown for loss spectrum of the O-K and Cr-L the outer cell surface and no evi- S. oneidensis represent the error in absorption edges are shown. The dence of intracellular precipitates is energy loss calibration for that spec- full width at half maximum of the observed. (b) EELS spectra from trum only. For the errors associat- ZLP is a measure of the instrumen- the isolated precipitates demon- ed with other spectra, see Table 1. tal resolution, which under these strates the presence of Cr. The ana- EC-TEM conditions is 1 eV. As lyzed precipitates are labeled and indicated by vertical arrows, the top the diameter of the circle corre- abscissa corresponds to the low-loss sponds to the electron probe diame- spectrum and the bottom abscissa ter. corresponds to the core-loss spec- trum.
spectrometer) and were corrected for dark cur- ing was removed by Fourier deconvolution Cells remained hydrated and intact while rent and channel-to-channel gain variation of methods [32]. extracellular polymers surrounding the cells the charge coupled device (CCD) detector. Chromium standards were analyzed by con- retained moisture. In comparison, unfixed Energy calibration of the core-loss regime ventional TEM. Standards were produced by cells deposited on a holy a-C film and exam- and measurement of energy drift during data placing high purity Cr(II)F2, Cr(II)Se, ined under high vacuum by conventional TEM acquisition were performed by collecting zero- Cr(III)Cl3, Cr(III)2O3, KCr(III)(SO4)2¥12H2O, (not shown), exhibited ruptured cell mem- loss spectra before and following collection of and K2Cr(VI)O4 powders directly on Cu TEM branes, as well as loss of both cell and extra- core-loss spectra. Energy of core-loss spectra grids coated with holey a-C. Once the stan- cellular polymer mass through dehydration. was calibrated using the average position of dard was prepared, it was examined immedi- Direct imaging revealed two distinct popu- the two zero-loss peaks. The error in the ener- ately. For each standard, 20 individual grains lations of S. oneidensis in the cultures: bacteria gy calibration corresponded to the energy drift were analyzed by EELS. Results were aver- exhibiting low image contrast (Fig. 3a) and of the zero-loss peaks. In addition, a C-K aged and reported with the statistical standard bacteria exhibiting electron dense, high-con- edge spectrum was acquired immediately fol- error. trast cell boundaries often encrusted with high- lowing spectrum collection from the O-K / Cr- contrast precipitates (Fig. 3b). Cross section- L core-loss regime. The measured position Results al images of bacteria by conventional TEM of the C-K (1s) peak at 284.9 eV (arising from showed no evidence of intracellular precipi- Direct imaging of Cr(VI) cultures transitions to the π* molecular orbital) from tates, suggesting precipitates are restricted to the TEM a-C support film was used to evalu- Examination of S. oneidensis in Cr(VI) cul- the outer surface of the bacteria. Precipitates ate the energy calibration. Either the pre-O-K tures by EC-TEM, showed the rod-shaped ranged in size between 10 - 200 nm, and edge background or the pre-Cr-L edge back- morphology typical of the species (Fig. 3). SAED indicated that the grains were predomi- ground (depending on the analysis to be per- The micrographs demonstrate that bacterial nantly amorphous perhaps due to a high formed) was subtracted from core-loss spectra membranes were intact and did not show evi- degree of hydration. Often the cells exhibited using a power law and plural inelastic scatter- dence of rupture from partial decompression. a 30 - 49 nm thick, high contrast perimeter,
JEOL News Vol. 37E No.1 9 (2002) ( 9) indicating that the cell boundary became satu- rated with elements of heavy mass. Table 1 Chemical analysis by EELS of Cr-L3 (2p3/2) and Cr-L2 (2p1/2) Adsorption-Edges Cr(VI) cultures XPS-binding energies, EELS L edge peak positions Compound Formal Cr-L3 (2p3/2) Cr-L2 (2p1/2) Technique Reference Figure 4 shows EELS low-loss and core- Valence (eV) (eV) loss spectra collected from an encrusted bac- Cr 0 573.8 583.0 XPS [40] terium examined by EC-TEM. The dominant 574.0 583.4 XPS [41]a feature in the low-loss spectrum is the zero- loss peak corresponding to electrons which 574.1 XPS [42]b escaped inelastic collisions. The width of the 574.3 582.8 EELS [43]c zero-loss peak is a measure of the energy dis- 576.5 ± 1.0 585.0 ± 1.0 EELS [38]d tribution of the incident beam and corresponds CrP 0 574.2 XPS [42] to the best energy resolution of the spectrome- Cr(CO)6 0 577.6 586.3 XPS [40] ter (energy resolution typically decreases with CrF2 II 574.2 ± 0.1 583.5 ± 0.1 EELS This study increasing energy loss). The narrow zero- CrSe II 574.2 ± 0.1 583.1 ± 0.1 EELS This study loss peak (Fig. 4) shows energy resolution is CrCl3 III 574.9 ± 0.1 583.4 ± 0.1 EELS This study not significantly affected by transmission 576.4 587.4 XPS [40] through the hydrated, pressurized environment CrP04•4H20 III 576.4 ± 0.2 XPS [44]b of the EC. The broad feature around 25 eV in CuCr02 III 576.4 ± 0.2 586.2 ± 0.2 XPS [40] [45]e the low-loss spectrum corresponds to plasmon Cr3(OH)2(OOCCH3)7 III 576.5 ± 0.2 XPS [44]b excitations (i.e., collective excitations of NaCr0 III 577.0 ± 0.2 586.9 ± 0.2 XPS [40] [45]e valence electrons). The ratio of the integrated 2 Cr 0 III 575.9 ± 0.1 584.3 ± 0.1 EELS This study intensity under the zero-loss and plasmon 2 3 peaks is related to specimen thickness. The 576.4 585.9 XPS [41]a relative height of the two peaks illustrates that 576.6 - 576.8 XPS [42] multiple scattering is not severe in the EC. 576.8 ± 0.2 586.2 ± 0.2 XPS [40] [45]e The total thickness traversed by the electron 576.8 584.8 EELS [46] beam, estimated by the log-ratio technique 576.8 586.7 XPS [47] [32], is 1.13 , where is the total mean free 577.9 ± 1.0 585.8 ± 1.0 EELS [38]d path for inelastic scattering through the EC FeCr204 III 576.0 584.0 XPS [48]f windows and specimen. The low-loss spec- KCr(S04)2•12H20 III 576.0 ± 0.1 584.5 ± 0.1 EELS This study trum also exhibits a sharp feature at 13.2 eV 581.0 590.5 XPS [40] [45]e that is only observed in EELS spectra collected LaCr03 III 576.1 ± 0.09 585.8 ± 0.05 XPS [49] in the EC. It is consistent with the EELS K- LiCr02 III 577.0 ± 0.2 586.8 ± 0.2 XPS [40] [45]e edge of hydrogen [33] which can be produced CrOOH III 577.0 586.9 XPS [47] by electron beam radiolysis of water in the Cr(OH) •0.4H 0 III 576.9 586.3 XPS [41]a hydrated specimen. For example, similar 3 2 577.1 XPS [42] EELS edges at 13 eV have also been observed concurrently with electron-beam-induced bub- CrP III 577.4 XPS [42] ble formation from frozen-hydrated biological CrCl3•6H20 III 577.5 XPS [42] specimens and were attributed to hydrogen CrP04 III 577.8 XPS [42] formation [34]. CrB03 III 578.0 XPS [42] In the core-loss spectrum of encrusted S. Cr2(S04)•15H20 III 578.6 XPS [42] oneidensis examined by EC-TEM, a strong O- Cr02 IV 576.3 586.0 XPS [47] K (1s) edge signal was observed at 537.1 ± 0.5 LaCr04 V 578.8 ± 0.21 588.0 ± 0.22 XPS [49] eV due to H2O in the hydrated bacterium and Cr03 VI 578.3 ± 0.2 587.0 ± 0.02 XPS [45]e extracellular substances. A less intense fea- 579.0 588.2 XPS [41]a ture at 529.2 ± 0.5 eV can be attributed to oxy- CaCr04 VI 578.9 ± 0.2 588.1 ± 0.2 XPS [40] [45]e gen 2p hybridization with the Cr 3d band, BaCr04 VI 579.1 ± 0.2 588.4 ± 0.2 XPS [40] [45le while the broad feature at 558 eV can be attrib- K2Cr207 VI 579.4 ± 0.2 588.8 ± 0.2 XPS [40] [45]e uted to plural (O-K core-loss plus plasmon) 579.8 589.1 XPS [47] scattering. The characteristic pair of Cr-L2 Na2Cr207 VI 579.4 ± 0.2 588.5 ± 0.2 XPS [40] [45]e and Cr-L3 edges in the EELS spectrum indi- cates that the precipitates are Cr-rich. Rb2Cr207 VI 579.4 ± 0.2 588.7 ± 0.2 XPS [40] [45]e Bacterial cultures were also examined in Cs2Cr207 VI 579.5 ± 0.2 588.7 ± 0.2 XPS [40] [45]e cross-section by conventional TEM. Spectra SrCr04 VI 579.6 ± 0.2 588.6 ± 0.2 XPS [40] [45]e collected from individual precipitates encrust- K2Cr04 VI 578.6 ± 0.1 587.2 ± 0.1 EELS This study ing the outer cell boundary of S. oneidensis 579.6 ± 0.2 588.9 ± 0.2 XPS [40] [45]e (Fig. 5) showed characteristic Cr-L2, 3 edges. PbCr04 VI 578.6 587.2 XPS [48]f The sectioned precipitates selected for analysis 580.9 587.8 - 589.5 EELS [50] were those loosely attached to the bacterial Cs2Cr04 VI 579.8 ± 0.2 588.8 ± 0.2 XPS [40] [45]e outer surface where spectra could be collected Li2Cr04 VI 579.8 ± 0.2 589.0 ± 0.2 XPS [40] [45]e without contributions from the bacterial cell. Na2CrO4 VI 579.8 ± 0.2 589.1 ± 0.2 XPS [40] [45]e In addition, the electron-dense cell boundary of S. oneidensis cells that lacked precipitates XPS studies used the Au 4Ä7/2 Iine at 84.0 eV for energy calibration unless otherwise stated. a) After recalibrating the XPS Au 4Ä7/2 Iine to 84.0 eV from 84.07 eV. encrusting the surface was examined by EELS b) Reported as calibrated to XPS Au 4Ä7/2 Iine at 84.0 eV and C (1s) at 284.8 eV. in cross section. Spectra from the cell bound- c) As reported in reference as binding energies. ary revealed characteristic Cr-L2, 3 edges indi- d) EELS L-edge onsets reported in reference, however L-peak positions are shown here. cating the cell boundary was saturated with Cr e) After recalibrating the XPS Au 4Ä7/2 Iine to 84.0 eV from 82.8 eV. at concentrations likely too low to be detected f) Energy calibration not reported. by EDXS. A comparison of core-loss spectra from encrusted, hydrated S. oneidensis (collected by EC-TEM) and Cr standards of known oxida-
(10) JEOL News Vol. 37E No.1 10 (2002) ly following the Cr-L2 peak, in the edge tail, prior to the post-edge feature. Once the background was subtracted using either of the two methods, the Cr-L peaks were integrated over a 5 eV window. The L3/L2 peak ratios for the Cr standards are summa- rized in Table 2. The flat, two-step back- ground subtraction method yielded the lower values, however, less relative scatter in the data. The core-loss spectra for K2CrO4 exhib- ited almost no post L2 edge features and this may account for the close similarity in L3/L2 peak ratios determined using the two back- ground subtraction methods (Table 2). The correlation between measured L3/L2 integrated- peak intensity ratios and L3 peak positions for the Cr oxidation-state standards is shown in Fig. 7. Core-loss EELS spectrum for Fig. 8a. Measurements of the standards K2CrO4 illustrating the back- demonstrate that Cr oxidation states fall within ground subtraction used in well-separated regions in the correlation plot. method I. The step function Since the local electronic structure of the atom (bold line) used to subtract the is responsible for the fine structure of absorp- background from the L2. 3 edges tion edges, other factors in addition to valence and the areas integrated to yield state influence L2, 3 fine structure. These fac- peak intensities (shaded regions) tors include atom coordination, spin-orbit are shown. The fitting parame- interactions, crystal field splitting, atomic ters a, b, s, and m are: the L3 coulomb repulsion, and exchange effects. For maximum, the L2 maximum, the slope of the linear function fitted example, within a given oxidation state in Fig. 8a, spectra for the individual standards fall to the 20 eV post L2 edge region (600 - 620 eV), and the intercept within separate groupings reflecting possible Fig. 8. The correlation between measured L3/L2 of the linear function. The differences from these factors which must be integrated-peak intensity ratios and L3 parameter m’ is given by m’ = (2 considered to correctly interpret fine structure peak positions for a) the Cr oxidation- m-as)/3. of absorption edges. The correlation plot rep- state standards, b) bacteria and precipi- resents a map of the possible range in fine tates. Plotted L3/L2 ratios were deter- mined using background subtraction structure (including influences from factors method II. The different Cr oxidation other than valence) that a particular Cr oxida- states fall within separate regions in the tion state can display. plot and are labeled II, III, and VI. The solid data points represent the mean of EELS oxidation state analysis of the data for a particular Cr standard. Cr(VI) cultures The EELS measurements of the bacterium examined by EC-TEM and precipitates exam- ined in thin section by conventional TEM are tion state (collected by conventional TEM) is over a 20 eV window (extending from 600 to summarized in Table 3. The error reported shown in Fig. 6. The spectrum of KCr(SO4)2¥ 620 eV). A linear step function was inserted for the precipitates represents the standard 12H2O exhibited a peak at 535.7 eV similar to at the L2 maximum and a straight line (of the error of the mean of 10 measurements. The the stronger feature observed in the spectrum same slope as that fitted to the Cr-L2 post-edge errors reported for the encrusted bacteria repre- from hydrated S. oneidensis, and likely corre- region) was extrapolated into the L3 threshold. sent the drift in energy calibration of the spec- sponds to H2O bound in the structure. More A second step function was inserted at the L3 trometer (L3 position) and an estimate based on importantly, systematic differences in Cr-L2, 3 maximum and set to zero below the L3 maxi- counting statistics (L3/L2 ratio). fine structure are apparent in the spectra of mum. The ratio for the step heights was set at standards (Fig. 6). For example, the Cr-L2, 3 2:1, consistent with the multiplicity of the ini- Direct imaging of nontronite lines for the standards show a systematic shift tial states, that of four 2p3/2 electrons and two cultures in edge-peak energy and variation in relative 2p1/2 electrons. It should be noted that the Clay-layer structures in their hydrated state intensity with oxidation state (Fig. 6). In ratios of L3 to L2 intensities do not follow the are beam sensitive. Therefore, standard pro- addition, the Cr-L2, 3 lines of the K2CrO4 peaks expected 2:1 ratio for early 3d transition met- cedures for imaging beam sensitive specimens are further differentiated in that they appear als [36]. These anomalous ratios can be par- were employed. Representative examples of asymmetric because each is split into two sep- tially explained by atomic multiplet effects high resolution lattice images of nontronite arate peaks separated by ~ 2 eV. producing overlapping transitions from 2p3/2 basal layers taken by EC-TEM are shown in and 2p1/2 states [37]. Nonetheless, an approx- Fig. 9. The EC-TEM measured distributions EELS oxidation state analysis of imation of 2:1 is sufficient for this work. of (001) layer spacings in nonreduced and standards Although the first subtraction method microbially reduced nontronite are shown in Oxidation state was identified by both the approximates the decreasing background, the Fig. 10. Each data point in the distribution L3 peak positions and the ratio of L3/L2 inte- fit of Cr-L2 post-edge region was often affect- represents the mean (001) spacing of a packet grated-peak intensities. Measurement of the ed by a broad post-edge feature, containing of fringes within individual clay grains. L3 peak positions is straightforward and the plural scattering effects not completely Nonreduced nontronite has mean (001) spac- results for Cr standards are summarized in removed from the spectra. The post-edge fea- ing of 1.50 ± 0.08 nm and the microbially Table 1. For measurement of the ratio of ture varied with each spectrum, introducing Fe(III) reduced form has mean (001) spacing L3/L2 integrated-peak intensities, two methods scatter in the L3/L2 peak ratios. To provide a of 1.26 ± 0.10 nm (the errors represent the of background subtraction were used. The more consistent background subtraction for all standard deviation of the population). It is first method, illustrated in Fig. 7, is similar to spectra, a second method using a flat, two-step clear from Fig. 10 that the distributions differ the double step function used by [35]. In this function was applied. The second background and a standard statistical T-test for unpaired method, the Cr-L3 pre-absorption edge was fit fitting procedure is identical to the first except data with unequal variance confirms the differ- to a power law and subtracted. A linear func- the slope of the linear function is set to zero ence in means is significant. Reduction of tion was then fit to the Cr-L2 post-edge region and it is fit to a 2 eV wide window immediate- Fe(III) in nontronite over 4 days by S. oneiden-
JEOL News Vol. 37E No.1 11 (2002)(11) sis produced a 0.24 nm contraction in mean (001) layer spacing. Table 2 Discussion Cr-L Adsorption Edge Ratios Oxidation state determination Compound Formal L3/L2 Integrated Ratio It is difficult to explicitly deconvolve the Valence Background Method I Background Method II influences of atom coordination, spin-orbit Pearson et al. (1993) Flat Two Step interactions, and crystal field splitting on fine CrF2 II 2.97 ± 0.07 2.37 ± 0.03 structure from those of valence state. CrSe II 2.60 ± 0.06 2.04 ± 0.02 Nonetheless, the mean oxidation state of an CrCl3 III 1.75 ± 0.03 1.68 ± 0.01 unknown can be determined by plotting its L3 Cr203 III 1.81 ± 0.01 1.70 ± 0.01 peak position and L3/L2 integrated-peak inten- KCr(S04)2•12H20 III 1.77 ± 0.02 1.60 ± 0.01 sity ratio in a correlation plot of oxidation state K2Cr04 VI 1.42 ± 0.01 1.44 ± 0.01 standards (see Fig. 8a). However, it is impor- tant that the correlation plot contain the broad- est collection of standards feasible to map the Table 3 full range in fine structure that a particular oxi- Cr-L3 (2p3/2), Cr-L2 (2p1/2) Adsorption-Edges and L3/L2 Integrated Ratios dation state can display. The better these Specimen Cr-L3 (2p3/2) Cr-L/2 (2p1/2)L3/L2 Integrated Ratio ranges are known, the more confidence can be (eV) (eV) Background Background placed in the oxidation state determination. In Method I Method II this regard, the data in Table 1 supplement that Encrusted S. oneidensis 575.7 ± 0.5 584.5 v 0.5 2.75 ± 0.30 1.90 ± 0.30 of Fig. 8a. Table 1 includes published L2, 3 Isolated precipitates 575.7 ± 0.1 584.3 ± 0.1 1.72 ± 0.02 1.85 ± 0.02 peak positions (absorption edge maximums) 576.3 ± 0.1 584.7 ± 0.1 1.77 ± 0.02 1.91 ± 0.02 from previous EELS studies as well as core- level (or inner-shell) binding energies meas- ured from XPS studies. In XPS, a bulk speci- men is illuminated with monochromatic X- rays and the kinetic energies of ejected photo- electrons are measured. The EELS edge onset, the sudden rise in intensity preceding each of the L2, 3 peaks, represents the ionization threshold which approximately corresponds to the inner-shell binding energy measured by XPS. The difference in chemical shift meas- ured by EELS and XPS for oxides has been suggested to be on the order of the band-gap energy [38], and may arise from many-body relaxation effects (more dominant in XPS) in which nearby electron orbitals are pulled towards a core hole [32]. Table 1 gives an indication of the range of L2. 3 peak positions expected for each Cr oxidation state and their relative overlap. It is important to note that XPS values are reported as binding energies, not edge maxima. Furthermore, charging of insulating materials in XPS requires the refer- encing of binding energies to allow compara- bility of results from different specimens. However, various methods are used for this Fig. 9. High resolution lattice images of basal layers of nontronite imaged by EC- referencing which lead to binding energy dif- TEM at l0 - 100 Torr: (a) nonreduced control and (b) microbial Fe(III) ferences of up to 0.5 eV [39]. Therefore, the reduced form. The bar illustrates five consecutive basal layer fringes and XPS binding energies in Table 1 should be their average (00l) spacing is indicated. There is a range of (00l) layer fringe compared qualitatively. spacings in any one nontronite image. However, the mean spacing is gener- The EELS measurements of the bacteria ally smaller for Fe(III)-reduced nontronite than the nonreduced nontronite examined by EC-TEM and precipitates exam- control (see Fig. 10). The layer fringes annotated by the bars were chosen to ined in thin section by conventional TEM are contrast the difference in (001) spacings for fringes near the means of the dis- plotted in Fig. 8b. The correlation plot (Fig. tributions shown in Fig. 10. 8b) indicates that Cr associated with S. onei- densis is most consistent with a mean oxida- tion state of +3 or lower. Measurements of hydrated bacteria in the EC are in good agree- ment with the analysis of isolated precipitates measured in cross section by conventional TEM. These results illustrate EELS tech- niques yield accurate data even under the more onerous experimental conditions of the EC.
Collapse of nontronite layers by Fig. 10. Distribution of (001) layer Fe(III) reduction spacings in nonreduced and We report the first accurate TEM measure- microbially reduced non- ments of nontronite layer contraction induced tronite as measured by EC- by the reduction of structural Fe(III). A con- TEM. The horizontal bar traction of 0.24 nm in mean (00l) layer spacing represents the mean of the was observed. Our measurement is consistent distribution. with previous in-situ X-ray diffraction studies
(12) JEOL News Vol. 37E No.1 12 (2002) which observed an interlayer contraction of References 28. Lovley, D. R., Phillips, E. J. P., Gorby, Y. 0.28 ± 0.04 nm in Na-nontronite after 85% A., and Landa, E. R., Nature, 350, 413 of the Fe(III) was reduced (based on Fig. 8 of 1. Cieslak-Golonka, M., Polyhedron, 15, (1991). [23]). Our TEM measurement was possible 3667 (1995). 29. Llyod, J. R. and Macaskie, L. E., Appl. because clays were examined in their ‘native’ 2. Clesceri, L. S., Greenberg, A. E., and Environ. Microbiol., 62, 578 ( 1996). hydrated state in an EC. Previous TEM Eaton, A. D. (Eds) Standard Methods for 30. Keeling, J. L., Raven, and M. D., Gates, reduction studies used water exchange with the Examination of Water and Wastewater, W. P, Clays and Clay Minerals, 48. 537 methanol and infiltration with L.R. White American Public Health Association, (2000). resin in attempts to preserve the layer spacings Washington, DC (1999). 31. Fukami, A., Fukushima, K., and Kohyama, of hydrated clay [24]. However, our EC-TEM 3. Hill R. R. H. and Cowley H. M., S. Afr. J. N., In: Bennett R. H., Bryant W. R. and results suggest the homogeneous layer spacing Sci., 82, 595 ( 1986). Hulbert M. H. (Eds.), Microstructure of observed in both reduced and oxidized smec- 4. Fude, L., Harris, B., Urrutia, M. M., and Fine-grained Sediments from Mud to tite by Stuki and Tessier [24] results from the Beveridge. T. J., Appl. Environ. Shale, Springer-Verlag, New York, pp. interaction between the non-polar methanol Microbiol., 60, 1525 (I 994). 321 (1991). and clay interlayer surfaces. In comparison to 5. Badar, U., Ahmed, N., Beswick, A. J., 32. Egerton, R. F., Electron Energy-loss EC-TEM results, the observation that a homo- Pattanapipitpaisal, P., and Macaskie, L. E., Spectroscopy in the Electron Microscope, geneous 1.26 nm (001) layer spacing is pro- Biotech. Let., 22, 829 (2000). Plenum, New York (1996). duced in the methanol-clay system regardless 6. McLean, J. S., Beveridge, T. J., and 33. Geiger, J., Schmoranzer, H., J. Mol. of Fe(III)/Fe(II) content [24] suggest interlayer Phipps, D., Environ. Microbiol., 2, 611 Spectrosc., 32, 39 (1969). forces are effected by the presence or lack of (2000). 34. Leapman. R. D. and Sun, S., polar water molecules. 7. Smith, W. L. and Gadd G. M., J. Appl. Ultramicroscopy, 59, 71 (1995). We show that established embedding tech- Microbiol., 88, 983 (2000). 35. Pearson, D. H., Ahn, C. C., and Fultz, B, niques used to study clay reduction do not 8. McLean, J. and Beveridge, T. J., Appl. Phys. Rev. B, 47, 8471 (1993 ). accurately preserve basal spacings of expand- Environ. Microbiol., 67, 1076 (2001 ). 36. Leapman, R. D. and Grunes, LA., Phys. able clays. At least for L. R. White, solvent 9. Lytle, C. M., Lytie, F. W., Yang, N., Qian. Rev. Lett., 45, 397 ( 1 980). exchange and resin infiltration contract layer J. H., Hansen, D., Zayed. A., and Terry, 37. Zaanen, J., Sawatzky, G. A., Fink, J., spacings, and therefore cannot be used to N., Environ. Sci. Technol., 32, 3087 Speier, W., and Fuggle, J. C., Phys. Rev. B, study, for example, the correlation between (1998). 32, 4905 (1985). layer spacing and local Fe(III)/Fe(II) composi- 10. Paterson, J. H., Krivanek, O. L., 38. Leapman. R. D., Grunes, LA., and Fejes, tion. In fact, conventional TEM has been Ultramicroscopy, 32, 319, (1990). P.L., Phys. Rev., B, 26. 614 (1982). unable to even image conclusively the contrac- 11. van Aken, P. A., Liebscher, and B., Styrsa, 39. Swift, P., Surf. Interface Anal., 4, tion of clay layers induced by Fe(III) reduc- V. J., Phys. Chem. Min., 25, 323 (1998). 47(1982). tion. As demonstrated here, conventional 12. Wang, Z. L., Bentley, J., and Evans, N.D., 40. Allen, G.C. and Tucker, P.M., Inorg. J. Phys. Chem. B, 103, 751 (1999). TEM specimen preparation artifacts such as Chim. Acta., 16, 41 (1976). clay layer contraction arising from solvent 13. Cressey, G., Henderson, C. M. B., and van 41. Asami, K. and Hashimoto, K., Corrosion exchange, dehydration, and resin infiltration der Laan, G., Phys. Chem. Miner., 20, 111 Science, 17, 559 (1977). are avoided by using EC-TEM. (1993). 42. Moffat, T. P., Latanision, R. M., and Ruf, 14. Daulton T. L., Little B. J., Lowe K., and R. R., Electrochim. Acta, 40, 1723 (1995). Summary Jones-Meehan J., Journal of 43. Fink, J., Mtiller-Heinzerling, T., Scheerer, Microbiological Methods, in press (2002). B., Speier, W., Hillebrecht, F. U., Fuggle, We demonstrate quantitative EELS oxida- 15. Venkateswaran, K., Moser, D. P., tion state measurements can be performed J. C., Zaanen, J., and Sawatzky, G. A., Doilhopf, M. E., Lies, D. P., Saffarini, D. Phys. Rev. B, 32, 4899 (1985). using EC-TEM which could provide data lost A., MacGregor, B. J., Ringelberg, D. B., by conventional specimen preparation. To 44. Neal, A. L., Lowe, K., Daulton, T. L., White, D. C., Nishijima. M., Sano, H., Jones-Meehan, J., and Little B. J., Journal our knowledge, this is the first demonstration Burghardt, J., Stackebrandt, E., and of EELS microanalysis by EC-TEM. We fur- of Applied Surface Science. submitted Nealson, K. H., Int. J. Syst. Bacteriol., 49, (2002) . ther demonstrate, for the first time using TEM, 705 ( 1 999). the collapse of (001) layers of nontronite 45. Allen, G. C., Curtis, M. T., Hooper, A. J., 16. Stucki, J. W., Komadel, P., and Wilkinson, and Tucker, P. M., J. Chem. Soc., Dalton induced by Fe(III) reduction. This is possible H. T., Soil Science Society of America because the clays were examined in their Trans., 16, 1675 ( 1973). Journal, 51, l 663 ( 1987). 46. Krivanek, O. L. and Paterson, J. H., ‘native’ hydrated state using an EC. The tech- 17. Kostka, J. E., Stucki, J. W., Nealson, K. nique of EC-TEM, especially together with Ultramicroscopy. 32, 313 (1990). H., and Wu, J., Clays & Clay Minerals, 44, 47. Ikemoto, I., Ishii, K., Kinoshita, S., EELS, can provide data on mineralogy, spatial 522 ( 1 996). distribution, and speciation of metals, neces- Kuroda, H., Alario-Franco, M. A., and 18. Ravina, I. and Low, P. F., Clay & Clay Thomas, J. M., J. Solid State Chem., 17, sary for determining the mechanism (s) of Minerals, 20, 109 (1972). microbial metal reduction/oxidation. 425 ( 1976). 19. Kohyama, N., Shimoda, S., and Sudo, T., 48. Kendelewicz, T., Liu, P., Doyle, C. S., Acknowledgements Clay &. Clay Minerals, 21, 229 (1973). Brown, G. E., Nelson, E. J., and 20. Stucki, J. W., Low, P. F., Roth, C. B., and Chambers, S. A., Surf. Sci., 424, 219 This work was supported by ONR program Golden, D. C., Clays & Clay Minerals, 32, (1999). element 0602233N, NRL/ONR Core 6.1 357 (1984) . 49. Konno, H., Tachikawa, H., Furusaki, A., Funding, CORE/NRL Postdoctoral Fellowship 21. Chen, S. Z., Low, P. F., and Roth, C. B., and Furuichi, R., Anal. Sci., 8, 641 (1992). (J. Kim), and ONR-ASEE Postdoctoral Soil Sci. Soc. Amer. J., 51, 82 (1987). 50. Brydson. R., Garvie, L. A. J., Craven, A. Fellowship (K. Lowe). We thank Dr. K. 22. Shen, S., Stucki, J. W., and Boast, C. W., J., Sauer, H., Hofer, F., and Cressey, G., Nealson (University of Southern California) Clays & Clay Minerals, 40, 381 (1992). J. Phys.: Condens. Matter, 5 , 9379 ( and Dr. J. Kostka (Florida State University) for 23. Wu, J., Low, P. F., and Roth, C. B., Clays 1993). kindly providing specimens of S. oneidensis. & Clay Minerals., 37, 211 (1989). We thank Dr. W. Straube (Geo-Centers, Inc.) 24. Stucki, J. W. and Tessier, D., Clays & for fixing and embedding Cr-cultures for TEM Clay Minerals, 39, 137 (199l). analysis. We thank Dr. A. Neal (Montana 25. Kim, J., Daulton, T., Furukawa, Y., State University) for comments. Lavoie, D., and Newell, S., Geology, sub- mitted (2002). 26. Myers. C. R. and Nealson, K. H., Geochim. Cosmochim. Acta, 52, 2727 (1988b). 27. Myers, C. R. and Nealson, K. H., Science, 240, 1319 (1988a).
JEOL News Vol. 37E No.1 13 (2002) (13) Simulations of Kikuchi Patterns and Comparison with Experimental Patterns
Kazuya Omoto†, Kenji Tuda and Michiyoshi Tanaka
Institute of Multidisciplinary Research for Advanced Materials, Tohoku University
Introduction by Hall and Hirsch [4], the expression of tically in slice 2 of infinitely small thickness Rossouw and Bursill [5] is derived. This d and again scattered elastically in slice 3 of Since the energy filtering technique for expression is used here in computer simula- thickness (t Ð ). electron microscopy was established, it has tions of TDS intensity distributions (Kikuchi Let us consider only thermal diffuse scatter- already been a common sense that rocking patterns). We will show several results of the ing (TDS). When the atom vibrations are curves of diffraction patterns (CBED patterns) simulations for MgO and compare them with approximated by the Einstein model, the inten- formed by elastically scattered electrons are experimental results. sity of TDS electrons in direction p + G per a reproduced very well by the dynamical calcu- Before showing the simulation results of solid angle is expressed as lations of electron diffraction. It is high time to Kikuchi patterns, we briefly describe the theo- G study inelastic scattering quantitatively. There dIp ry of inelastic scattering and quote the impor- = t G p p ’ G 0 O O 0 ’ exist three major fundamental inelastic scatter- d tant equations, which are the basis of the pres- ’ ’ ’ exp[it p ’] – exp[it 0 ’] ing processes: plasmons (5 to 30eV), core- T ’ , ent calculations. it( – ) excitations (> 50eV) and phonons (thermal dif- p ’ 0 ’ fuse scattering, TDS) (< 0.1eV). The cross sec- Theoretical (5) tion of the core-excitations is small but that of where plasmons is very large. Inelastic scattering due A comprehensive expression of the scatter- ’ to plasmons is harmful to the quantitative ing amplitude for elastic and inelastic scatter- T ’ = p g g’ p ’ T(Q,Q’) h 0 0 ’ h’ , analysis of the rocking curves of the diffrac- ing of fast transmission electrons from a per- gh g’h’ Q=p+g–h, Q’=p+g’– h’ tion patterns. In order to remove the back- fect crystal is given as ground intensities of these inelastically scat- (6) ˆ * and and denote indices of tered electrons, various energy-filtering tech- ¿(t) = exp[itM] a0 O , (1) p ’ p p ’ ’ the Bloch states. T stands for inelastic scat- niques have been developed. We have devel- where a and O are the initial states of the ’ oped, in collaboration with JEOL, the JEM- 0 tering and other terms stand for elastic scatter- crystal and the incident plane wave of an elec- ing. T(Q,Q’) is the following function 2010FEF field-emission electron microscope tron, Mˆ is the elastic and inelastic scattering equipped with a new filter, which enables us T(Q,Q’) = 1 f (Q) f (Q’)exp[–i(Q – Q’)·r ] operator and t is the thickness of a specimen. V to remove the plasmon-loss and core-loss c The scattering amplitude in direction Ki + G intensities over the entire CBED patterns. to excite the crystal from the 0th state to the exp[–W (Q – Q’)] – exp[–W (Q) – W (Q’)] , However, inelastic (quasi-elastic) scattering ith state, where G is the reciprocal lattice vec- (7) due to phonons (TDS) is difficult and impracti- tor, is obtained by multiplying (1) by G ai which is the TDS scattering factor given by cal to remove at present. TDS is known as the from the left side. major origin of the anomalous absorption Hall and Hirsch. T(Q,Q’) for MgO is shown in ˆ . effect. In contrast to plasmon scattering, TDS G ai ¿(t) = G ai exp[itM] a0 O (2) Fig. 1(b) extends to large scattering angles and forms If we consider only elastic scattering (i = 0), Kikuchi bands and Kikuchi lines, which are In the limiting case t , only the terms eq.(2) is reduced to impedimental to the accurate analysis of the = ’ and = ’ remain, the TDS intensity or (0) ˆ eq.(5) becomes rocking curves of CBED patterns. G ai ¿(t) = G exp[itM00] O , (3) G Omoto et al. [1], derived a comprehensive 1 dIp 2 2 where the superscript (0) implies elastic scat- lim = G p T 0 O , t t theoretical expression for inelastic scattering tering. The expression (3) is exactly d of fast transmission electrons from a perfect Fujimoto’s equation. Thus, equation (1) (8) crystal. Their expression includes both elastic including inelastic scattering is regarded as a where and inelastic multiple scatterings and is regard- natural extension of Fujimoto’s equation. ’ ed as an extended form of Fujimoto’s expres- The amplitude of single inelastic scattering T =T ’= p g g’ p T(Q,Q’) h 0 0 h’ . gh g h sion for elastic scattering [2]. When the G a ¿(t) (1) is expressed in the following way, ’ ’ approximation of single inelastic scattering is i (9) (1) applied to the expression, it becomes equiva- G ai ¿(t) = This is equivalent to Takagi’s expression [6]. lent to the formula of Rez et al. [3]. When In this expression, the cross terms of the transi- t G i t– Mˆ id Mˆ i Mˆ O exp[ ( ) ] exp[ ] ii i0 00 . TDS is considered with the use of the Einstein tion probabilities (Fig. 1(c)) are omitted and 0 model or the scattering factor for TDS given 321 the absorption effect in the elastic scattering (4) process cannot be taken into account. As a 2-1-1 Katahira, Aoba-ku, Sendai 980-8577 Japan As illustrated in Fig. 1(a) on the right-side result, the thickness dependence, the asymme- E-mail:[email protected] page, the incident electron is scattered elasti- try features, the accurate intensity distribution †He now works for JEOL Ltd. cally in slice 1 of thickness , scattered inelas- along the band, the accurate incidence-orien-
(14) JEOL News Vol. 37E No.1 14 (2002) (a) MgO [100] 100kV
70nm70nm 50nm50nm
(b) T(Q,Q-G)
B(Mg):0.31Å2, B(O):0.34Å2 G 000 G 020 0.01 G 040 G 060
0.0 20nm20nm 60nm60nm
G 0100 0.01 G 080