APS Science 2009

Advanced Photon Source ANL-10/06 ISSN 1931-5015 Argonne National Laboratory May 2010 9700 South Cass Avenue Argonne, IL 60439 USA

May 2010 www.anl.gov www.aps.anl.gov APS Science 2009 Argonne National Laboratory National Argonne

ANL-10/06 ISSN 1931-5007 ANL-10/06 ISSN Research and Engineering Highlights from the Advanced Photon Source at Argonne National Laboratory

U.S. DEPARTMENT OF ENERGY Argonne National Laboratory is a U.S. Department of Energy laboratory managed by UChicago Argonne, LLC ANL-10/06 ISSN 1931-5015 May 2010

The Advanced Photon Source at Argonne National Laboratory is supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, under Contract No. DE-ACO2-06CH11357

About Argonne National Laboratory Argonne is a U.S. Department of Energy laboratory managed by UChicago Argonne, LLC under contract DE-ACO2-06CH11357. The Laboratory’s main facility is outside Chicago, at 9700 South Cass Avenue, Argonne, Illinois 60439. For information about Argonne and its pioneering science and technology programs, see www.anl.gov.

Availability of This Report This report is available, at no cost, at http://www.osti.gov/bridge. It is also available on paper to the U.S. Department of Energy and its contractors, for a processing fee, from: U.S. Department of Energy Office of Scientific and Technical Information P.O. Box 62 Oak Ridge, TN 37831-0062 phone (865) 576-8401 fax (865) 576-5728 [email protected]

Disclaimer This report was prepared as an account of work sponsored by an agency of the United States Government. Neither the United States Government nor any agency thereof, nor UChicago Argonne, LLC, nor any of their employees or officers, makes any warranty, express or implied, or assumes any legal liability or responsibility for the accuracy, completeness, or usefulness of any information, apparatus, product, or process disclosed, or represents that its use would not infringe privately owned rights. Reference herein to any specific commercial product, process, or service by trade name, trademark, manufacturer, or otherwise, does not necessarily constitute or imply its endorsement, recommendation, or favoring by the United States Government or any agency thereof. The views and opinions of document authors expressed herein do not necessarily state or reflect those of the United States Government or any agency thereof, Argonne National Laboratory, or UChicago Argonne, LLC. ANL-10/06 ISSN 1931-5015 May 2010

APS Science 2009

The Annual Science Report of the Advanced Photon Source at Argonne National Laboratory

Argonne is a U.S. Department of Energy laboratory managed by UChicago Argonne, LLC The Advanced Photon Source is funded by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences

The Advanced Photon Source Annual Science Report 2009 1 Welcome from the Director

It is my pleasure to introduce the 2009 annual report of the Advanced Photon Source. This was a very good year for us. We operated with high reliability and availability, despite growing problems with obsolete systems, and our users produced a record output of publications. The number of user experiments increased by 14% from 2008 to more than 3600. We congratulate the recipients of the 2009 Nobel Prize in Chemistry—Venkatraman Ramakrishnan (Cambridge Institute for Medical Research), Thomas Steitz (Yale University), and Ada Yonath (Weizmann Institute) - who did a substantial amount of this work at APS beamlines.

Murray Gibson Thanks to the efforts of our users and staff, and the ongoing counsel (left), Argonne of the APS Scientific Advisory Committee, we made major progress in Associate advancing our planning for the upgrade of the APS (APS-U), producing a Laboratory proposal that was positively reviewed. We hope to get formal approval in Director for 2010 to begin the upgrade. With advocacy from our users and the support Photon Sciences, of our sponsor, the Office of Basic Energy Sciences in the Department of and X-ray Energy (DOE) Office of Science, our operating budgets have grown to Science Division the level needed to more adequately staff our beamlines. We were also Director Linda extremely fortunate to have received $7.9 M in American Recovery and Young in the Reinvestment Act (“stimulus”) funding to acquire new detectors and 7-ID research improve several of our beamlines. The success of the new Linac Coherent station on the Light Source at Stanford, the world’s first x-ray free-electron laser, made APS experiment us particularly proud since the undulators were designed and built by hall floor. the APS.

Among other highlights, we note that more than one-quarter of the 46 Energy Frontier Research Centers, funded competitively across the U.S. in 2009 by the DOE, included the Advanced Photon Source in their proposed work, which shows that synchrotron radiation, and the APS in particular, are central to energy research. While APS research covers everything from fundamental to applied science (reflected by the highlights in this report), the challenge of sustainable energy provides an opportunity for expanded involvement with industrial research.

We were privileged to recruit several outstanding new leaders at the APS. Linda Young, from Argonne’s Chemical Sciences Division, became the new Director of the X-ray Science Division (XSD). Chris Jacobsen (from Stony Brook University) has been added to Linda’s team as an XSD Associate Division Director, joining George Srajer. Alexander (Sasha) Zholents (formerly of Berkeley Lab) became Director of the Accelerator Systems Division. Sasha is the inventor of the short-pulse x-ray scheme that we plan to implement in the APS-U to obtain very high average brightness, broadband, 1-ps x-ray pulses. Walter Lowe (formerly of Howard University) has taken a new position as senior advisor for outreach and development of the user community. Walter’s role is to increase the diversity of the user community (with diversity read broadly to include

2 A rgonne National Laboratory users, institutions, and technical disciplines that are underrepresented at APS). Walter is also leading an effort to increase access for industrial users. I am confident that we have in place a great team to help our users and the APS take fullest advantage of the APS-U opportunity.

In planning with users for the proposed APS-U, we focused on the need to study “real materials under real conditions in real time” on spatial and temporal scales unavailable today. Only by studying materials as they are made—or as they perform—in difficult environments can we solve the grand challenge of higher-performance, sustainable materials for energy and health. The proposed APS-U will improve the brightness of penetrating x-rays produced by the APS over 100 times, and support our efforts in developing state-of-the-art instruments to address these challenges. Take a look at the potential impact of the APS-U as spelled out in our “Proposal for approval of Conceptual Design” (http://www.aps. anl.gov/Upgrade/Documents/aps_cdzero.pdf). The next few years promise to be an exciting time.

J. Murray Gibson ([email protected])

The APS Scientific Advisory Committee Photographed at the APS January 21, 2010

Front row: Seated in chairs (left to right): Miles V. Klein (University of Illinois at Urbana-Champaign), William Stirling, Chair (European Synchrotron Radiation Facility), J. Murray Gibson (Argonne National Laboratory). Second row: Seated on chair arms (left to right): Soichi Wakatsuki (High Energy Accelerator Research Organization), Janos Kirz (Lawrence Berkeley National Laboratory), Louise N. Johnson, DBE, (University of Oxford Laboratory of Molecular Biophysics), Ka Yee C. Lee (The University of Chicago). Third row: Standing (left to right): Glenn Waychunas (Lawrence Berkeley), John Corlett (Lawrence Berkeley National Laboratory), Tom Irving, PUC Chair, ex officio (Illinois Institute of Technology), Roger A. Leach (E.I. DuPont de Nemours & Company), Philip H. Bucksbaum (Stanford University), Howard M. Einspahr (Bristol-Myers Squibb, retired), Dan Neumann (National Institute of Standards and Technology), Paul Fuoss, APSUO Chair, ex officio (Argonne National Laboratory), Britt Hedman (Stanford Synchrotron Radiation Lightsource). Not pictured: J. Friso Van der Veen (Paul Scherrer Institut).

The Advanced Photon Source Annual Science Report 2009 3 The APS Upgrade – A Report from the Upgrade Steering Committee

The Path to Becoming a DOE Project A considerable amount of effort has gone into the development and refinement of a plan to enhance and expand the capabilities of the Advanced Photon Source since the last issue of APS Science (2008), including a name change for this effort. This project, originally called the APS Renewal, is now known as the APS Upgrade Project, or APS-U for short. The APS submitted a white paper to the Department of Energy (DOE) Office of Basic Energy Sciences (BES) in November 2008 making the broad case for investment in the facility to maintain its leadership capabilities for the next decade and beyond. Working closely with the DOE, the APS then developed a "Proposal for Approval of Conceptual Design (CD-0)" in May 2009 (http://www.aps.anl.gov/Upgrade/Documents/aps_cdzero. pdf). That document was organized around two themes ideally suited for study with the upgraded APS: “Mastering Hierarchical Structures through Imaging” and “Real Materials under Real Conditions in Real Time.” A BES- conducted peer evaluation of the proposal for the APS-U provided strong support for the decision to proceed toward Critical Decision Zero–Approval of Mission Need (CD-0). To further develop the case for Mission Need, BES assembled an integrated project team from Argonne, the DOE Office of Science, and the DOE Argonne Site Office. The APS Scientific Advisory Committee (SAC) met at the APS in October 2009 to hone the scientific case for the APS-U and provide guidance on project scope (i.e., identify the “flagship” beamlines) for the CD-0. Their advice was folded into a briefing book that provided more detailed information regarding our upgrade plans to assist the DOE in their planning process.

The APS Upgrade Steering Committee "Strawman" Beamline Configuration Map Photographed at the APS April 5, 2010 In addition to providing information to the DOE as described above, the APS began to formulate Left to right: Michael Borland, Bob Fischetti, Paul Fuoss, a beamline configuration map that captured the Denny Mills, John Maclean, George Srajer, and Rod Gerig. essence of the upgrade plans. The Upgrade Steering Not pictured: Tom Irving, Dan Neumann. Committee felt that it would be important to get a draft, or “strawman,” version of the roadmap out to the user community for comment before it would be discussed at the next APS SAC meeting scheduled for January 19-21, 2010. Unfortunately, even in late December 2009, it was not clear which of the various configurations for distribution of long straight sections (LLSs) would be possible from an accelerator operations point of view. In fact, APS accelerator physicists arranged to get access to Argonne supercomputers over the 2009-2010 holiday break to work on this problem; only at the beginning of January 2010 was a clearer picture emerging as to which LLS configurations might be feasible. Therefore, the strawman beamline configuration that was developed had to be done in a very short time by a small group of APS staff to allow for distribution of a plan to the community before the SAC meeting. The purpose in developing and releasing the roadmap was twofold: (1) to lay out a single possible beamline arrangement that would accommodate the flagship upgrades called out in previous documents, and (2) to stimulate engagement of the APS user community through comment and discussion of the strawman beamline configuration.

4 A rgonne National Laboratory The APS Upgrade – A Report from the Upgrade Steering Committee

The Next Steps At the time of this writing (March 2010) we are planning—in anticipation of a positive CD-0 determination by the DOE—the process for the next very important step in the proposed APS Upgrade: development of a Conceptual Design Report (CDR). In the conceptual design we will describe the capabilities that we propose to build, showing that these choices flow from the scientific vision we have articulated in our proposal. The CDR is one of the most important components needed to reach Real Materials under Real Conditions in Critical Decision 1 and proceed with the preliminary engineering design Real Time: The complex process of charge phase of the project. The CDR will connect more explicitly the proposed transfer and storage in batteries limits instrumentation to the science drivers for each of the six beamline areas performance. Improvements are expected we identified: by observing the electrochemistry in action Imaging and Coherence; Extreme Conditions; Ultrafast Dynamics; with hard x-rays. Interfaces in Complex Systems; High-Resolution Spectroscopy; Proteins to Organisms. During development of the CDR it will not be practical or necessary to For up-to-date information go to the APS-U Web site at: identify the location of each of the possible beamline upgrades that are proposed. However, the APS is planning to meet with all the user groups http://www.aps.anl.gov/Upgrade/ who have expressed concern about this draft roadmap and work to optimize the map further in 2010. We need such a roadmap soon in order APS Upgrade Contacts to make more precise resource and schedule estimates, and get as close as reasonably possible to the final configuration at the time we submit the Contact Denny Mills, Chair, ANL-PSC CDR. Much of this will be presented and discussed at the next APS User (APS, [email protected]), or any of the other APS Steering Committee Meeting in May 2010, where the focus of the meeting will be the upgrade. members (listed below) if you have comments, suggestions, or concerns regarding the APS Upgrade process.

Michael Borland, ANL-ASD (APS, [email protected]) The Role of the Steering Committee Bob Fischetti, GM/CA-CAT and ANL-BIO (APS Life Sciences Council Since this message is from the APS Upgrade Steering Committee, Representative, [email protected]) you might ask, “What is the role of this committee?” The APS Upgrade Steering Committee was chartered by APS Director Murray Gibson to Paul Fuoss, ANL-MSD (APS Users provide the upgrade project team with: Organization Representative, [email protected]) • Guidance and advice on strategic direction for the project; Rod Gerig, ANL-PSC • Input from the APS user communities; (APS, [email protected]) • Support in the development of workshops, meetings, etc., regarding Tom Irving, IIT and Bio-CAT (APS the APS Upgrade; and Partner User Council Representative, • Feedback on draft proposals, plans, designs, etc. [email protected]) The members of the Steering Committee, which meets weekly, are John Maclean, ANL-AES advocates for the APS user community, providing advice to the upgrade (APS, [email protected]) team on the process for insuring that user ideas and comments are heard, Dan Neumann, NIST guidance and suggestions for forums and meetings where information (APS Scientific Advisory Committee regarding the upgrade can be exchanged, and comments on various Member, [email protected]) documents developed by the upgrade team. George Srajer, ANL-XSD (APS, [email protected])

The Advanced Photon Source Annual Science Report 2009 5 The Advanced Photon Source Facility at Argonne National Laboratory

The APS occupies an 80-acre site on the Argonne campus, about 25 miles from downtown Chicago, Illinois. For directions to Argonne, see www.anl.gov/Administration/visit.html.

Access to Beam Time at the APS Beam time at the APS can be obtained either as a general user (a researcher not associated with a particular beamline) or as a partner user: a member of a collaborative access team [CAT], a partner user proposer, or a member of a collaborative development team. If you are a CAT member, contact your CAT for instructions on applying for CAT beam time. At minimum, 25% of the time at all operating beamlines is available to general users, but many offer considerably more general user time—up to 80% on X-ray Operations and Research beamlines, for example. APS general users get more than 50% of all the available beam time at the APS.

How General Users Can Apply for Beam Time at the APS 1) First-time users should read the information for new users found on our Web site at http://www.aps.anl.gov/Users/ Prospective/ before applying for beam time. Also, certain administrative requirements must be completed. In particular, a user agreement between the APS and each research-sponsoring institution must be in place.

2) To choose the appropriate technique(s) and beamline(s), see the beamlines directory in the “Data” section of this volume or at https://beam.aps.anl.gov/pls/apsweb/beamline_display_pkg.beamline_dir.

3) Submit a proposal via the Web-based system. Proposals are evaluated before each user run. For more information see the proposal system overview at: www.aps.anl.gov/Users/Scientific_Access/General_User/General_User_Proposal/Instructions/Proposer/.

Contact Us For more information about the Advanced Photon Source or to order additional copies of this, or previous, issues of APS Science, send an e-mail to [email protected], or write to APS info, Bldg. 401, Rm. A4115, Argonne National Laboratory, 9700 S. Cass Ave., Argonne, IL 60439. Visit the APS on the Web at www.aps.anl.gov.

6 A rgonne National Laboratory Table of Contents

Welcome from the Director...... 2 The APS Upgrade...... 4 Research Highlights Electronic & Magnetic Materials...... 10 Engineering Materials & Applications...... 26 Soft Materials & Liquids...... 32 Chemical Science...... 46 Life Science...... 52 Structural Biology...... 62 Environmental & Geological Science...... 96 Nanoscience...... 110 Structural Studies...... 122 Novel X-ray Techniques & Instrumentation...... 132 Reports from the APS X-ray Science Division ...... 140 Accelerator Systems Division...... 148 APS Engineering Support Division...... 156 Other Reports...... 165 APS Organization Chart, Staffing, & Funding ...... 168 Acknowledgments...... 169

The Advanced Photon Source Annual Science Report 2009 7 The Advanced Photon Source (APS), a national APS Sectors synchrotron radiation research facility at the U.S. Department of Energy’s (DOE’s) Argonne National Sectors 1-4: XOR 1-4 Laboratory in Illinois, provides this nation’s brightest X-ray Operations and Research (XOR) x-ray beams for science. Research by APS users extends from the center of the Earth to outer space, Sector 5: DND-CAT from new information on combustion engines and DuPont-Northwestern-Dow Collaborative Access Team (CAT) microcircuits to new drugs and nanotechnologies whose scale is measured in billionths of a meter. The Sector 6: MU/XOR APS, which is funded by the DOE Office of Science, Midwest Universities/XOR Office of Basic Energy Sciences, enhances America’s competitiveness in such areas as superconductors, Sector 7: XOR 7 semiconductors, pharmaceuticals, polymers, and Sector 8: XOR 8 catalysts, and promises to have far-reaching impact on our technology, economy, health, and fundamental Sector 9: XOR/CMC knowledge of the materials that make up our world. XOR/Complex Materials Consortium At the APS, a “sector” comprises the radiation sources Sector 10: MR-CAT (potentially one of the two bending magnets, and one Materials Research CAT insertion device, although the number of insertion devices in the straight sections of the storage ring can vary), and Sectors 11 and 12: XOR/BESSRC XOR/Basic Energy Sciences Synchrotron Radiation Center the beamlines, enclosures, and instrumentation that are associated with a particular storage ring sector. The APS Sectors 13 through 15: CARS has 35 sectors, 34 of which are dedicated to user science Center for Advanced Radiation Sources: and experimental apparatus. The 35th has limited space > GeoSoilEnviroCARS—sector 13 for instrumentation and is used primarily for accelerator- > BioCARS—sector 14 related studies. > ChemMatCARS—sector 15 X-ray Operations and Research (XOR) sectors Sector 16: HP-CAT comprise those beamlines operated by the APS. Some High Pressure CAT XOR sectors have historic CAT origins, e.g., XOR/PNC. Sector 17: IMCA-CAT Industrial Macromolecular Crystallography Association CAT Collaborative Access Team (CAT) sectors comprise beamlines operated by independent groups made up Sector 18: Bio-CAT of scientists from universities, industry, and/or research Biophysics CAT laboratories.

Sector 19: SBC-CAT To access the APS as general users (GUs), researchers Structural Biology Center CAT submit proposals that can be active for up to two years. These proposals are reviewed and rated by one of nine Sector 20: XOR/PNC XOR/Pacific Northwest Consortium proposal review panels comprising scientific peers, generally not affiliated with the APS. Beam time is then Sector 21: LS-CAT allocated by either of two APS Beam Time Allocation Life Sciences CAT Committees.

Sector 22: SER-CAT Those users who propose to carry out research programs Southeast Regional CAT beyond the scope of the GU program may apply to become partner users on any beamline operated by Sector 23: GM/CA-CAT the APS. Prospective Partner User Proposals are peer General Medicine and Cancer Institutes CAT reviewed by a subset of the APS Scientific Advisory Sector 24: NE-CAT Committee. Final decisions on the appointment of partner Northeastern CAT users are made by APS management.

Sector 26: CNM/XOR Center for Nanoscale Materials/XOR

Sector 30: XOR/IXS Beamlines, sector designations, disciplines, XOR/Inelastic X-ray Scattering techniques, radiation sources, and general-user status for particular beamlines are displayed with Sector 31: LRL-CAT the science highlights that follow. Lilly Research Laboratories This information can be viewed in whole at: Sector 32: XOR 32 http://beam.aps.anl.gov/pls/apsweb/beamline_ display_pkg.beamline_dir. Sectors 33 and 34: XOR/UNI XOR/University-National Laboratory-Industry

8 A rgonne National Laboratory APS Sector Allocations & Disciplines – Source Configuration

HP-CAT 16-BM-B • 16-BM-D ChemMatCARS 15-ID-B,C,D 16-ID-B • 16-ID-D BioCARS 14-BM-C IMCA-CAT 17-BM-B 14-ID-B 17-ID-B GSECARS 13-BM-C • 13-BM-D Bio-CAT 18-ID-D 13-ID-C,D 435 434 SBC-CAT 19-BM-D 19-ID-D XOR/BESSRC 12-BM-B 12-ID-B,C,D 18 19 20 XOR/PNC 20-BM-B 17 21 20-ID-B,C XOR/BESSRC 11-BM-B 16 22 LS-CAT 21-ID-D • 21-ID-F • 21-ID-G 11-ID-B • 11-ID-C • 11-ID-D 15 23 SER-CAT 22-BM-D MR-CAT 10-ID-B 14 436 22-ID-D Undulator/period 24 433 GM/CA-CAT 23-BM-B XOR/CMC 9-BM-B,C 13 2.3-cm 9-ID-B,C 23-ID-B • 23-ID-D 2.7-cm 12 Materials Science 26 Biological & Life Science 3.0-cm Canted undulator XOR 8-ID-E • 8-ID-I Geo/Soil Science configuration NE-CAT 24-ID-C • 24-ID-E 11 Environmental Science 3.3-cm Chemistry Tandem 3.5-cm XOR 7-ID-B,C,D Physics undulators 10 Polymers 5.5-cm CNM/XOR 26-ID-C MU/XOR 6-ID-B,C • 6-ID-D CPU 432 9

DND-CAT 5-BM-C • 5-BM-D 5-ID-B,C,D 8 30

7 XOR 4-ID-C • 4-ID-D 31

6 IEX-CDT 29-ID XOR 3-ID-B,C,D 32

5 437 XOR 2-BM-B 33 XOR/IXS 30-ID-B,C 2-ID-B • 2-ID-D • 2-ID-E 431 4 34 LRL-CAT 31-ID-D XOR 1-BM-B,C 3 1-ID-C 2 1 XOR 32-ID-B,C

XOR/UNI 33-BM-C 438 33-ID-D,E XOR/UNI 34-ID-C,E

The Advanced Photon Source Annual Science Report 2009 9 Electronic & Magnetic Materials

Giving Silicon a Longer-Lasting Memory

low temperature. X-ray diffraction IN SHORT > Silicon has one major drawback when it comes studies carried out beamline 33-BM to storing the 1s and 0s of computer memory. Without a confirmed that in extremely thin constant source of power, silicon quickly loses its electric films of the material, consisting of charge. A research team used the XOR/UNI 33-BM beamline alternating layers of strontium and titanium, the strontium atoms had at the APS to help them figure out how to give silicon a better squeezed themselves together to memory by coating it in a thin film of strontium titanate. match the pattern of silicon atoms. The team’s x-ray studies confirmed that the atoms of the In films that were five strontium strontium titanate become slightly compressed in the process, layers thick, the strontium atoms had which gives them the property of ferroelectricity—the same squeezed themselves from their usual property that allows modern subway and bus fare cards to spacing of 3.90 Å to a tighter spacing of 3.84 Å. In thicker films made of store information without drawing power. With any luck, 20 strontium layers, the atoms had the material, or something like, it could be used to make adopted their usual spacing. computers that start up much faster after being switched off. The researchers then used an atomic force microscope, which applies a small electric voltage to one or a few atoms at a time, to create a set of microscopic polarized patches in the strontium titanate MORE > In the standard random A research team including films. Consistent with the x-ray access memory (RAM) found in members from Cornell University; findings, all of the samples except home computers, microscopic zones the University of Pittsburgh; the the thickest one were able to support of silicon represent 1 or 0 depending National Institute of Standards and polarization. In the best performing on whether they are full of electrons Technology; Pennsylvania State film—six atomic layers thick—the or not. Because these zones rapidly University; Northwestern University; patches remained polarized for 72 h leak electrons, the memory has to Motorola, Inc.; Ames Laboratory; at room temperature. be constantly refreshed, which uses Intel Corporation; and TricornTech The researchers say it might power. If the computer is rebooted, wanted to see if they could create a be hard to turn their material into it needs time to reload the RAM ferroelectric material from strontium the kind of device found in real from the hard drive. Ferroelectric titanate, which is related to materials computer memory, where the silicon materials are better suited to used in ferroelectric fare cards, itself would deliver the voltage to storing information because they by applying it directly to silicon. switch the polarization of strontium are polarized, meaning they have Although strontium titanate is not titanate. But the payoff would a slight positive charge on one end itself ferroelectric, prior calculations be significant. By doing away and a negative charge on the other. indicated that if the two materials with the insulating layer used in By applying a voltage to a patch of came together gently enough, the previous designs, a smaller electric ferroelectric material, its polarization atoms making up strontium titanate voltage would accomplish the same can be flipped like a switch. The would squeeze together to fit with switching, which could save not trick is how to incorporate silicon, the more closely spaced silicon only precious time spent waiting the workhorse of modern electronics. atoms (see Fig. 1), thus becoming for the computer to power up, but In the past, researchers have placed ferroelectric in the process. energy, too. layers of ferroelectric material on To fuse the materials cleanly, silicon, but these devices have all the group developed a method of — JR Minkel required a separate insulating layer spray-painting strontium, titanium, in between the ferroelectric and and oxygen atoms (the ingredients the silicon. of strontium titanate) onto silicon at

10 A rgonne National Laboratory Electronic & Magnetic Materials

< Fig. 1 The atomic structure of a film of strontium titanate fused with silicon, shown schematically (left) and as measured by atomic force microscopy (below). Strontium titanate consists of alternating layers of strontium atoms (left; green) and titanium atoms (black), with oxygen (red) mixed in. Researchers found that when they carefully deposited these atoms onto silicon (pink), the strontium atoms squeezed together closer than usual, resulting in ferroelectricity.

See > Maitri P. Warusawithana1, Cheng Cen2, Charles R. Sleasman2, Joseph C. Woicik3, Yulan Li4, Lena Fitting Kourkoutis1, Jeffrey A. Klug5, Hao Li6, Philip Ryan7, Li-Peng Wang8,9, Michael Bedzyk5, David A. Muller1, Long-Qing Chen4, Jeremy Levy2, Darrell G. Schlom1*, “A Ferroelectric Oxide Made Directly on Silicon,” Science 324(17), 367 (April 2009). DOI: 10.1126/ science.1169678

Author affiliations > 1Cornell University, 2University > This work was supported by Office of Naval Research grant N00014-04-1-0426 of Pittsburgh, 3National Institute (M.P.W., L.F.K., D.A.M., and D.G.S.), > 33-BM • XOR/UNI • Materials of Standards and Technology, National Science Foundation grants DMR- science, physics, chemistry 4Pennsylvania State University, 0507146 and DMR-0704022, Materials • Anomalous and resonant 5 Research Science and Engineering scattering (hard x-ray), diffuse Northwestern University, Center program grants DMR-0520404, 6Motorola Inc., 7Ames Laboratory, x-ray scattering, powder diffraction, DMR-0520513, and DMR-0820404. Use x-ray reflectivity, general 8 9 Intel Corporation, TricornTech of the Advanced Photon Source was diffraction, grazing incidence supported by the U.S. Department of diffraction • Bending magnet Energy, Office of Science, Office of Basic • Accepting general users Correspondence > Energy Sciences, under Contract No. No. *[email protected] DE-AC02-06CH11357.

The Advanced Photon Source Annual Science Report 2009 11 Electronic & Magnetic Materials

The Importance of Magnetism and Structural Distortions in Arsenide Superconductors

weak AFM order (Fig. 2). In their IN SHORT > Iron pnictide compounds—which are based experiments, the scientists from Iowa State University were able to on conducting layers of iron (Fe) and arsenic (As)—were verify that the AFM and O transitions discovered in 2008 to possess superconducting properties separated, and were able to identify while under pressure and also upon doping. A subset of the structural and magnetic phases these iron-based superconductors, called 122 iron arsenides, in the underdoped region. A first- became important to condensed-matter physicists because order transition from a tetragonal relatively large and high-quality single crystals can be phase to a orthorhombic phase occurs for Ba(Fe Co ) As at grown. To learn more about the properties of these 122 iron 0.953 0.047 2 2 the structural transition temperature arsenides, researchers using the MU/XOR 6-ID-D beamline (TS) = 60K, and a second-order at the APS studied the magnetic and structural properties transition to an AFM state takes of the compound BaFe2As2 doped with cobalt (Co). Their place at the magnetic ordering research will help science gain a further understanding of how (Néel) temperature (TN) = 47K. superconductivity arises in high-temperature superconductor In the process, they succeeded in (high-T ) materials, and may help point the way to a yet-to-be making microscopic observations c of this transition, showing for the established high-Tc theory. first time the specific structural and magnetic changes taking place. The x-ray diffraction studies carried out at the 6-ID-D high-energy beamline at the APS verified that a single- phase orthorhombic structure existed MORE > The 122 iron arsenides before the antiferromagnetic (AFM) throughout the crystal, verifying the AFe2As2, where “A” denotes transition while cooling (Fig. 1). neutron scattering measurements the alkaline-earth metals of the In addition, superconductivity performed at the High Flux Isotope elements barium (Ba), calcium appears as the transition to the O Reactor at Oak Ridge National (Ca), or strontium (Sr), display and AFM phases is increasingly Laboratory. complicated structural, magnetic, suppressed with additional doping. As Co doping suppressed and superconducting properties in The researchers made first-ever both the O and AFM phases, a and around the boundary between microscopic observations that superconducting state evolved. In an antiferromagnetic (AFM) phase confirmed both the structural and fact, superconductivity occurred and a superconductivity (SC) magnetic changes taking place at within the orthorhombic and phase. The experiment with these each transition. antiferromagnetic state below 122 iron arsenides led the research X-ray diffraction and the superconducting transition group to discover that, instead of a neutron scattering analyses were temperature (Tc) = 17K. Below simultaneous first-order transition performed on the 122 iron arsenide the superconducting temperatures from a tetragonal (T) phase into superconductor based on single at 17K, the researchers found a an antiferromagnetic ordered crystals of the composition substantial reduction in magnetic orthorhombic (AFM-O) phase, which Ba(Fe1-x Cox)2As2. The experiment moments, along with a gap in low- occurs without doping, Co-doping was focused on a Co-doped energy spin excitations. With the causes the single simultaneous composition of 4.7% (x = 0.047), observed redistribution of spin transition to split into two called an underdoped composition, excitations and reduced magnetic transitions, with the transition to the where an emergent superconducting moment under these temperatures, orthorhombic (O) phase occurring phase coexists with a state of it is clear that competition occurs

12 A rgonne National Laboratory

Electronic & Magnetic Materials < < High-energy x-ray diffraction at 6ID-D: Fig. 1 X-ray and neutron diffraction data on a single crystal of 2.02 2.02

Ba(Fe1-xCox)2As2. The upper panels show x-ray diffraction K K data measured on MU/XOR beamline 6-ID-D on a single 2.00 crystal with x = 3.8%. At low temperatures (T = 7K, below 2.00

TS), the (220) nuclear Bragg peak is split by the orthorhombic

distortion. At 80K (above TS), the single (220) peak indicates T = 7 K T = 80 K 1.98 the tetragonal structure. The lower panel shows neutron 1.98 1.98 2.00 2.02 1.98 2.00 2.02 H scattering data on a single crystal with x = 4.7%. The H structural transition is indicated by the change of intensity of the (220) nuclear reflection. The magnetic Bragg peak Neutron diffraction at HB1A:

at (1/2 1/2 1) appears as TN < TS. Below TC, the magnetic Bragg peak is suppressed.

between the co-existing AFM and SC states. Such actions emphasize the important interrelationship between magnetism, structural distortions, and superconductivity within the iron arsenides.

— William Arthur Atkins and Patricia Panatier

See > Daniel Keith Pratt, W. Tian, A. Kreyssig, J.L. Zarestky, < Fig. 2 Phase diagram for

S. Nandi, N. Ni, S.L. Bud’ko, P.C. Ba(Fe1-xCox)2As2 showing Canfield, A.I. Goldman, and Robert paramagnetic tetragonal (T), John McQueeney*, “Coexistence paramagnetic orthorhombic (O), of Competing Antiferromagnetic AFM ordered orthorhombic and Superconducting Phases in the (AFM O), and superconducting

Underdoped Ba(FE0.953Co0.047)2As2 (SC). AFM O and SC phases Compound Using X-ray and coexist between x = 4% and Neutron Scattering Techniques,” 6%. The vertical line shows the Phys. Rev. Lett. 103, 087001 (2009). position of the x = 4.7% sample DOI:10.1103/PhysRevLett. studied here. 103.087001 Note: similar results have been described by Christianson et al., > Work at the Ames Laboratory and Phys. Rev. Lett. 103, 087002 (2009). the MU/XOR is supported by the U.S. > 6-ID-D • MU/XOR • Materials Department of Energy Office of Science science, physics • High-energy under Contract No. DE-AC02 07CH11358. Author affiliation > x-ray diffraction, magnetic x-ray Use of the Advanced Photon Source scattering, pair distribution Iowa State University at Argonne National Laboratory was function, powder diffraction • supported by the U.S. Department of 3.3-cm Undulator A • Accepting Energy, Office of Science, Office of Basic general users Correspondence > Energy Sciences, under Contract No. *[email protected] DE-AC02-06CH11357.

The Advanced Photon Source Annual Science Report 2009 13 Electronic & Magnetic Materials

Charge Excitation from Stripes in Nickelate and Superconducting Cuprates

was performed at a temperature of IN SHORT > Within high-temperature superconductor 10K, using the MERIX spectrometer installed on the XOR/IXS 30-ID (HTS) compounds of cuprates, charge stripe order appears beamline at the APS. Likewise, when holes are doped because of strong repulsive electron- the cuprate measurements were electron correlations. For a better understanding of the performed at 8K with an inelastic charge dynamics within stripes, researchers using an APS x-ray spectrometer installed on the beamline observed, for the first time, charge excitations BL11XU beamline at the SPring-8 light source in Japan. occurring from the charge stripe-ordered state in 214-type The researchers prepared single nickelate and cuprate superconductors. This research advances crystals of the nickelate LSNO our understanding of strongly correlated electron systems, with x = 1/3, and the cuprates LBCO including the high-temperature superconductor compounds, with x = 0.125, LBCO with x = 0.08, and helps scientists better understand the behavior of and LSCO with x = 0.12. LSNO collective electrons under strong correlations, which has and LBCO (x = 0.125) produced strong charge stripe order below been a long-standing puzzle. 180K and 55K, respectively (Fig. 1). LBCO (x = 0.08) did not result in charge stripe order, and the researchers could not verify charge stripe order in LSCO. They observed three peaks from MORE > Charge stripes are LSCO, respectively). For their the RIXS spectra at all but one defined as doped holes —separated experiments, the researchers used [qs = (4π/3, 2π/3)] of the different by insulated regions not containing hard x-ray resonant inelastic x-ray momentum transfer positions for holes—that are confined to parallel scattering (RIXS) to measure charge LSNO. The three peaks consisted lines of copper atoms in copper- excitation within these compounds. of an “elastic” peak at zero energy oxygen planes. And, importantly, a The method permits the probing of transfer (0 eV), an “in-gap” peak dynamical collective motion of these a stripe possessing a characteristic at ~1.5 eV, and a “CT” peak stripes is thought by scientists to help momentum transfer (qs) that measures at ~4.5 eV (where CT refers to bring about superconductivity. its spatial period. Their measurements charge transfer, involving the charge For their study of charge show an approximate 1-eV charge excitation across the CT gap). excitation from stripes, the scientists excitation for both the nickelate RIXS data from LBCO found from the Japan Atomic Energy stripes, which propagate diagonally that all spectra contained two peaks: Agency, Tohoku University, the along the plane containing the the elastic peak and the CT peak

Advanced Institute for Materials NiO2 square lattice, and the cuprate at ~4 eV. However, the cuprates Research, and Argonne researched the stripes, which propagate vertically or did not show a defined in-gap peak

nickelate compound La5/3Sr1/3NiO4 horizontally along the CuO2 plane. below the CT gap energy, while the —part of the 214 nickelate family: Hard x-rays were used for nickelate did, because the cuprates La2-xSrxNiO4(LSNO). They also this RIXS study in order to excite are not insulators like the nickelate. studied the superconducting cuprate electrons from the 1s orbital to the According to this study, compounds La15/8Ba1/8CuO4, 4pπ orbital, with a specific incident the charge stripe state results in La1.92Ba0.08CuO4 , and La1.88Sr0.12CuO4 photon energy of 8,347 eV for the additional RIXS signals at energy —part of the 214 cuprate family nickelate and 8,993 eV for the three transfer 1 eV and characteristic La2-x(Ba or Sr)xCuO4 (LBCO and cuprates. The nickelate measurement momentum transfer, regardless of

14 A rgonne National Laboratory Electronic & Magnetic Materials

See > Shuichi Wakimoto1* H. Kimura2, K. Ishii3, K. Ikeuchi3, T. Adachi4, M. Fujita5, K. Kakurai1, Y. Koike4, J. Mizuki3, Y. Noda2, K. Yamada5,6, A.H. Said7, and Yu. Shvyd’ko7, “Charge Excitations in

the Stripe-Ordered La5/3Sr1/3NiO4 and La2-x(Ba, Sr)xCuO4 Superconducting Compounds,” Phys. Rev. Lett. 102, 157001 (2009). DOI:10.1103/ PhysRevLett.102.157001

Author affiliations > 1Japan Atomic Energy Agency, 2Tohoku University, 3Japan Atomic < 4 Fig. 1 Upper panels show charge stripe ordered states for La15/8Ba1/8CuO4 and La5/3Sr1/3NiO4 Energy Agency, Tohoku University, on planes consisting of Cu (or Ni) and oxygen atoms. Arrows show spins of electrons 5Tohoku University, 6Advanced and red circles show doped holes that extinguish spins. Lower panels show comparison Institute for Materials Research, 7 between scattered x-ray intensity with momentum transfer qs corresponding to the Argonne National Laboratory

spatial period of charge stripes (blue data) and that without qs (red data). An additional signal of charge excitation from the stripe state is observed around the energy transfer Correspondence >

of 1 eV in the scattering x-ray intensity with qs in both materials, regardless of the *[email protected] geometry of the stripes.

> This work is supported by a Grant-In-Aid from the Ministry of Education, Culture, Sports, Science, and Technology, Japan. the stripe geometry. The charge of the striped system. That is, the The synchrotron radiation experiments stripe excitations appear in all of at SPring-8 were performed under the anomaly may result from softening Common-Use Facility Programme of the diagonal nickelate stripes and in the charge excitonic modes of the JAEA. Use of the Advanced Photon the vertical cuprate stripes. The in-gap states. Source at Argonne National Laboratory researchers state that because the was supported by the U.S. Department of Energy, Office of Science, Office of Basic charge stripe excitations appear — William Arthur Atkins Energy Sciences, under Contract No. even in the insulating LSNO, DE-AC02-06CH11357. they may not be directly related to superconductivity, although they may be necessary for the superconductivity—that is, they could be interpreted as collective > 30-ID • XOR/IXS • Geoscience • life science • materials science • stripe excitations. In another physics • Inelastic x-ray scattering possibility, the observed anomaly at • 3.0 undulator (US), 3.0 undulator the characteristic momentum transfer (DS) • Accepting general users might be caused by the in-gap state

The Advanced Photon Source Annual Science Report 2009 15 Electronic & Magnetic Materials

Putting the Squeeze on Magnetic Semiconductors

could potentially raise the value IN SHORT > The interest in spintronic devices has of Tc beyond the value of the electron-delocalization limit in fueled many directions in materials research, in particular bulk EuO. research into the properties of ferromagnetic-semiconductor The group exploited the EuX monochalcogenides. Their ferromagnetic ordering element and orbital selectivity of temperature (Tc) can be increased from 70K to values near Eu L-edge x-ray absorption in the room temperature by subjecting them to hydrostatic pressure, electric dipole (2p to 5d) and electric thereby opening the door for many potential bulk applications. quadrupole (2p to 4f) channels to But a detailed understanding of the way pressure compresses probe the spin polarization of the valence (4f) and conduction (5d) the lattice isotropically, changes the electronic structure, states of the EuX lattice as pressure and strengthens the ferromagnetism in these materials was applied in a diamond anvil cell. remains elusive. Researchers using the APS obtained direct The results they obtained on the spectroscopic evidence that electronic mixing in a particular Eu 4f-5d mixing were supported monochalcogenide is significantly enhanced by the application by density functional theory of external pressure, the first measurements to establish the calculations. The researchers also definite, key role played by this orbital mixing in increasing investigated the effect of anion substitution and found that while the ferromagnetic ordering temperature. such a substitution gives rise to a lattice contraction much larger than the one obtained by the application of hydrostatic pressure, the concomitant enhancement of ferromagnetism was not as significant. At the onset MORE > Most models circular dichroism (XMCD) of absorption, theory suggests the that have been suggested for experiments, and obtained direct photoexcitation process is dominated monochalcogenides EuX (where spectroscopic evidence that Eu 4f- by the weak quadrupolar (2p to X can denote either Te, Se, S, or 5d electronic mixing is significantly 4f) interaction, while the dipolar O) hinge on f-d, s-f, or p-f orbital enhanced by the application of contributions (2p to 5d) take over mixing, and there is significant external pressure. as the absorbed energies become experimental evidence pointing to This initial direct evidence is higher. Indeed, the spectral weight the fact that Eu 4f-5d mixing plays tantalizing, and could potentially transfer from high to low energies a key role in the ferromagnetic affect future experimental work is observed in both XMCD and enhancement. Researchers from aimed at investigating other XANES data, indicating charge Argonne, Northwestern University, mechanisms that have also been transfer from the Eu 4f to the Eu and the Commissariat à l'énergie found to enhance ferromagnetic 5d states. Density functional theory atomique, working at XOR beamline ordering, such as interfacial strain band structure calculations indicate 4-ID-D at the APS, carried out both in epitaxial films, or chemical that empty 4f states come from x-ray absorption near edge structure substitution. The former is of predominantly spin-up states that (XANES) and x-ray magnetic particular interest because, while lie slightly below the Fermi level it is true that biaxial strain is less at atmospheric pressure, but they effective than hydrostatic pressure become chemically active through at raising Tc, symmetry breaking hybridization with empty 5d states in at the interfaces of strained films the conduction band as the lattice is

16 A rgonne National Laboratory Electronic & Magnetic Materials

See > Narcizo M. Souza-Neto*1, Daniel Haskel**1, Yuan-Chieh Tseng2,1, and Gerard Lapertot3, “Pressure-Induced Electronic Mixing and Enhancement of Ferromagnetic Ordering in EuX (X = Te, Se, S, O) Magnetic Semiconductors,” Phys. Rev. Lett. 102, 057206 (6 February 2009). DOI:10.1103/ PhysRevLett.102.057206

Author affiliations > 1Argonne National Laboratory, 2Northwestern University, 3Institut Nanosciences et Cryogénie

Correspondence > *[email protected] < Fig. 1 Mixing fraction, (A-B)/C, as a function of the lattice parameter. A is the area to the **[email protected] left, and B to the right of the peak amplitude C. The strong correlation between the Mixing fraction (dots) and the Ferromagnetic ordering temperature (boxes) is readily apparent. (Copyright © 2009 The American Physical Society) > Use of the Advanced Photon Source at Argonne National Laboratory was supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, under Contract No. DE-AC02-06CH11357. contracted by the applied pressure. contracted lattices as 4f levels cross To quantify this enhancement of the Fermi level, and that a strong quadrupolar contributions (and correlation exists between the mixing hence the reduction of the dipolar fraction and the value of Tc in these > 4-ID-D • XOR • Physics, materials contribution) in the absorption as compounds, again demonstrating that science • Anomalous and resonant scattering (hard x-ray), magnetic a result of the lattice contraction, f-d mixing is the primary cause of Tc x-ray scattering, magnetic circular the mixing fraction was calculated, enhancement under pressure. dichroism (hard x-ray) • 3.5-cm as shown in Fig. 1. It can be seen undulator • Accepting general users that the mixing fraction grows for — Luis Nasser

The Advanced Photon Source Annual Science Report 2009 17 Electronic & Magnetic Materials

Better Switching through Chemistry in Thin Ferroelectrics

< < Fig. 1 Hysteresis in L scans through the IN SHORT > Because the atomic structure and polarity of 304 Bragg peak of a 10-nm PbTiO3 film at 644K, at various oxygen partial ferroelectric materials respond dramatically to an applied pressures pO2. Plots (a) and (b) are

electric field, they have found increasing application in such for pO2 decreasing from a high value areas as electromechanical actuators, nonvolatile computer and increasing from a low value, memories, and advanced radio-frequency electronics. respectively. Redder hues indicate But what if there were another way to make ferroelectric higher intensity (log scale). Plots (c) and (d) show peak position and materials do their thing—not electrically by applying intensity; closed and open symbols a voltage, but through another mechanism? A group of are for decreasing and increasing

experimenters from Argonne, the University of Pennsylvania, pO2, respectively. To fully switch and Northern Illinois University has managed to do just the sample at low pO2 (not shown), that, proving that not just electricity but also a little bit oxygen flow was set to zero, resulting in pO < 10-7 mbar. (Copyright © 2009 of chemistry can flip the structure and thus the polarity of 2 The American Physical Society) a ferroelectric film.

MORE > The researchers studied different pO2. At a high pO2, their important, but so is the chemistry: very thin lead titanate (PbTiO3) films, polarization pointed up. By changing whether there are extra ions of one 2 to 21 nm in thickness, grown on to low pO2, it could be switched and sign or another. SrRuO3 films on SrTiO3 substrates. made to point down. The switching The changes in the PbTiO3 While varying the oxygen partial was reversible and could be cycled surface resulting from equilibration

pressure (pO2) on the top surface of back and forth repeatedly. During with the atmosphere were confirmed the lead titanate film at temperatures the polarization switching process, by x-ray experiments showing a from 550K to 950K, the team used scattering interference patterns new surface structure and by synchrotron x-ray scattering at the showed that domains of both ab initio calculations based on XOR/BESSRC 12-1D beamline at directions were present. density functional theory. The team the APS. By using 28-keV x-rays to The team’s finding—that the thinks that the outermost atomic penetrate the reactive atmosphere chemically-induced polarization layer is losing 1 out of every 4 and chamber walls, the structural switching could be reproduced and oxygens at low oxygen pressure. changes in the thin films could be repeated under control—is quite That discovery has implications monitored in situ as they occurred, significant because it indicates that both for the future design of devices providing more direct information the chemical environment in which based on these film structures than had been available (Fig.1). these ultrathin ferroelectrics operate and for the development of new

As the pO2 was altered, is more important and influential applications. Although the team hysteresis was evident in the film than previously believed. It is a emphasizes that they are still at the structure, indicating polarization phenomenon that needs to be taken fundamental research stage, and so changes. All of the unit cells in the into account as these materials are the applications are not very certain lead titanate changed their structure created and used. Not only are the or direct, the researchers speculate when the surface was exposed to a electronic properties of the interface that this awareness of chemical

18 A rgonne National Laboratory Electronic & Magnetic Materials

See > R.V. Wang1§, D.D. Fong1, F. Jiang1§§, M.J. Highland1, P.H. Fuoss1, Carol Thompson2, A.M. Kolpak3§§§, J.A. Eastman1, S.K. Streiffer1, A.M. Rappe2, and G.B. Stephenson1*, “Reversible Chemical Switching of a Ferroelectric Film,” Phys. Rev. Lett. 102, 047601 (2009). DOI: 10.1103/ PhysRevLett.102.047601

Author affiliations > 1Argonne National Laboratory, 2Northern Illinois University, 3University of Pennsylvania §Present address: Numonyx Corp., §§Present address: Ohio University, §§§Present address: Yale University

Correspondence > *[email protected]

> This work was supported under Contract No. DEAC02-06CH11357 between UChicago Argonne LLC and the Department of Energy. A. M. K. and A. M. R. acknowledge the support of the Department of Energy under Grant DE-FG02-07ER15920, the Air Force Office of Scientific Research under Grant FA9550-07-1-0397, and a Challenge Grant from the HPCMO of the Department of Defense. Use of the Advanced Photon Source at Argonne National Laboratory was supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, under Contract No. DE-AC02-06CH11357. ferroelectric switching and the ability switching chemically rather than to manipulate it could lead to new electrically is a new capability, types of catalysts and chemical opening fascinating possibilities actuators for nanoelectronics. for the study of new basic scientific > 12-ID • XOR/BESSRC • Chemistry, For now, the team plans to phenomena. physics, materials science • Small- continue to investigate chemical angle x-ray scattering, wide-angle x-ray scattering, grazing incidence ferroelectric switching, including the — Mark Wolverton small-angle scattering, surface use of different chemistries and the diffraction • 3.3-cm Undulator A precise details of the mechanisms • Accepting general users involved. Achieving ferroelectric

The Advanced Photon Source Annual Science Report 2009 19 Electronic & Magnetic Materials

Avoiding Short Circuits by a Whisker

MORE > Researchers from position. Finally, the local stresses IN SHORT > Whiskers Germany’s Max Planck Institute of each probed position were are generally associated for Metals Research, Robert derived directly from the measured with shaving cream Bosch GmbH, Oak Ridge National Laue patterns. Laboratory, and Argonne used the Previous work on whisker commercials and XOR/UNI 34ID-E beamline at the formation in Sn coatings on Cu grizzled old prospectors APS to study how differences in surfaces had shown that compressive from western movies. mechanical stress in an Sn plating stress in the Sn layer plays an But when whiskers cause the whiskers to form. Using important role, but the experimenters of tin (Sn) form on a technique known as white-beam in this study revealed for the first time that this is not a necessary condition coatings of that metal micro-Laue diffraction, they were able to measure extremely fine for whisker formation. Based on state- when it is used to plate differences in stress distribution of-the-art laboratory and synchrotron and solder copper around the whisker root during x-ray diffraction stress investigations (Cu) microelectronic ongoing growth, revealing the forces of unprecedented accuracy during components, the driving the growth for the first time. whisker growth, the researchers whiskers can grow The experimenters have shown that a negative nature electrodeposited pure Sn thin films of the stress gradients viewed from and create electrical with an approximate thickness of the whisker root, not a possibly connections where 3 µm onto pure Cu substrates, and compressive nature of the stress, is none are meant to be, aged them at room temperature. decisive for whisker formation. causing short circuits About four days later, the first Thus, the following model for that damage and destroy Sn whiskers began to form. whisker formation emerges: During (For comparison purposes, some room-temperature ageing, Cu atoms delicate equipment. whisker-free specimens were also from the substrate diffuse into the Sn It has happened in prepared by annealing the Sn films film above and form the intermetallic satellites, computers, at 150° C for 1 h.) The researchers compound Cu6Sn5 along Sn grain even pacemakers, first determined the stress differences boundaries at the Cu/Sn interface. wreaking great havoc, between the base and the surface Due to this compound formation, of the tin film by performing x-ray compressive stress is generated at the and all caused by a diffraction measurements in the whisker of tin that laboratory. Then, in order to precisely might be only a few measure and spatially resolve the 13 days 10μm micrometers thick by a stress distribution in the surface plane couple of millimeters around a growing whisker, they used the micro-Laue diffraction method long. Even after 50 years at the APS (Fig. 1). A very fine x-ray of research, a definite beam with a diameter of about 300 explanation for the nm was used to scan in 0.5-µm steps 18 days cause of the whiskers the region around the whisker root. has proven maddeningly In combination with a very-high- resolution charge-coupled device elusive. Now, a team of detector, Laue diffraction patterns researchers used an APS were captured from each probed 54 days beamline to achieved a 25 days 33 days crucial new insight into how and why these tin

whiskers form and grow. < Scanning electron micrographs of the same Sn whisker taken at different ageing times at room temperature.

20 A rgonne National Laboratory Electronic & Magnetic Materials interface, and tensile stress forms continues as long as the stress is likely due to the anisotropy of at the surface of the Sn film. At gradients persist. physical properties (as the diffusion the locations where this compound In essence, Sn atoms are forced coefficients) of Sn. formation is most significant at the toward the whisker root by the nature The next step will be to find interface with the substrate, tensile of the surrounding stress field, much ways to prevent the formation stress is also most significant at as pressure on the end of a toothpaste and propagation of these negative the Sn surface. Consequently, both tube forces toothpaste out the other stress gradients that lead to whisker negative out-of-plane stress gradients end. This model is confirmed by formation and growth in Sn/Cu films. from the Sn surface to the interface examination of the whisker-free That will be the key to solving the region and negative in-plane stress samples, which showed none of the hairy problem of metallic whisker gradients from the site of the forming in-plane or out-of-plane negative formation in microelectronic circuits. whisker toward its surrounding area stress gradients in the Sn layer. develop. These stress gradients move Interestingly, the experimenters — Mark Wolverton Sn atoms to the whisker formation found that whiskers do not form site, and the whisker continues to at every location with a significant 1,2 grow outward as more Sn atoms are amount of Cu6Sn5 beneath the Sn See > M. Sobiech *, added to the base. Whisker growth surface. They speculate that this M. Wohlschlögel1, U. Welzel1, E.J. Mittemeijer1**, W. Hügel2, A. Seekamp2, W. Liu3***, and G.E. Ice4, “Local, submicron, strain gradients as the cause of Sn whisker growth,” Appl. Phys. Lett. 94, 221901(2009). DOI: 10.1063/1.3147864

Author affiliations > 1Max Planck Institute for Metals Research, 2Robert Bosch GmbH, 3Argonne National Laboratory, 4Oak Ridge National Laboratory

Correspondence > *[email protected] **[email protected] ***[email protected]

> The authors are much obliged to the company Hans Heimerdinger Oberflächentechnik in Pforzheim, Germany, for specimen preparation. G.E.I. was supported by the U.S. Department of Energy Division of Material Sciences and Engineering, Office of Basic < Fig. 1 Two-dimensional micro-diffraction (area of ~20 × 20 × µm2) data taken around Energy Sciences. Use of the Advanced the root (white dotted circle) of a growing Sn whisker. The regions colored black Photon Source was supported by the U.S. Department of Energy, Office of Science, correspond to non-indexed data points. (a) The orientation image displays the Office of Basic Energy Sciences, under corresponding (RGB) color-coded crystallographic orientations of the [001] axis of Contract No. DEAC02-06CH11357. the Sn grains with respect to the [001] pole (which has the white color code). [(b)–(d)]

Color-coded diagonal (deviatoric) strain tensor components εxx, εyy, and εzz (see the illustration of the beamline setup and indication of the specimen frame of reference at the bottom of the figure). The scale bar displays the color-coded deviatoric strains. > 34-ID • XOR/UNI • Materials (e) Radially, in the plane of the surface, averaged values of all diagonal (deviatoric) science, physics • Coherent x-ray strain tensor components (εxx, εyy, and εzz)as a function of the distance from the scattering, microdiffraction

whisker root. (f) Radially averaged inplane strain ε|| as function of the distance from • 3.3-cm Undulator A • Accepting −1 general users the whisker root in comparison with the radially averaged values of ε||2ν(1−ν)

and −εzz. (Copyright © 2009 American Institute of Physics)

The Advanced Photon Source Annual Science Report 2009 21 Electronic & Magnetic Materials

Accentuating the Positive by Cation Ordering in Manganite Superlattices

the effects of cation-site order on randomly-oriented La / Sr / MnO IN SHORT > Heterostructures are indispensable in the 1 3 2 3 3 films and (SMO) -(LMO) manufacture of semiconductor devices and other critical 2 1 superlattices that were grown under applications, and the quest to improve their capabilities similar conditions (Fig. 1). and characteristics is of great importance. One approach Neutron scattering studies show is to attain greater control over the creation of these that both types of films displayed structures, ideally down to the level of a single unit-cell. A-type antiferromagnetism, with Such capabilities could allow control over useful properties in-plane, double-exchange-mediated, ferromagnetic sheets coupled in such as the ferromagnetic (or antiferromagnetic) ordering the out-of-plane direction along of a material by altering the atomic structures in ways the c axis antiferromagnetically. that would adjust its Curie or Néel temperatures. Argonne In the superlattices, the A-type AF researchers at the Materials Science Division (MSD), Center order propagates coherently in for Nanoscale Materials (CNM) and the APS, using the the direction of growth, with the MU/XOR 6-ID-B,C and XOR/UNI 33-BM beamlines at the m = 1 superlattices maintaining long-range order up to a temperature APS and neutron scattering at Oak Ridge National Laboratory, of 320K, and the m = 2 superlattices have demonstrated just such a capability. up to 285K. This amounts to a Néel temperature approximately 70K higher than seen in the

La1/3Sr2/3MnO3 films. X-ray scattering shows that this is the result of an in-plane structural MORE > Using molecular beam disorder can affect the ferromagnetic modulation in the superlattices. epitaxy approaches similar to those characteristics of complex oxides, The cation ordering drives this used for semiconductors, researchers but the effects of disorder on modulation to longer wavelengths, from Argonne and the University antiferromagnetism remain largely improving charge itinerancy and of Illinois at Urbana-Champaign unexplored. Because the various the ordering temperature, and thus were able to interweave single unit- order parameters—such as charge, increasing the Néel temperature. cell layers of undoped LaMnO3 spin, orbitals, etc.—in these The ability to increase the and SrMnO3 in a superlattice materials can be closely coupled to Néel temperature of complex structure, thus eliminating disorder one another, altering one parameter oxides to above room temperature at La/Sr cation sites. With this via doping can affect others, displayed in this work opens up method, which the researchers sometimes creating potentially some intriguing possibilities for call “digital synthesis,” they were useful effects. The researchers the design and development of able to adjust the Néel temperature created (LMO)m(SMO)2m structures various similar materials. The digital (TN) of the films. Compared to in superlattices in which La/Sr synthesis process demonstrated a compositionally-equivalent, cations were arranged in ordered here can be used with many other randomly-doped manganese film, two-dimensional layers while still oxides, promising new materials

La1/3Sr2/3MnO3, the team enhanced preserving the La/Sr ratio found with enhanced characteristics for the TN by approximately 70K, a in similar random alloys. They a wide range of applications. substantial increase. used x-ray diffraction at the APS Previous experimental work beamlines neutron scattering at Oak — Mark Wolverton had already demonstrated that lattice Ridge National Laboratory to probe

22 A rgonne National Laboratory Electronic & Magnetic Materials

< Fig. 1 (a) Antiferromagnetic La2/3Sr1/3MnO3 with random La/Sr cations and ordered La/Sr

cations in (LaMnO3)m (SrMnO3)2m superlattices. The magnetic moment on the Mn atoms align antiferromagnetically (blue arrows) at low temperatures (b) The magnetic order, as measured with neutron scattering, is lost upon warming up above the Néel

temperature TN, which is 70K higher when the cations are ordered (c) Superlattice fringes about the main (22d) peak indicate a periodic in-plane modulation in the lattice that is strongest in the material with the randomly arranged La/Sr cations, which also 1 2 has the lowest TN. The modulation shifts to longer wavelengths as TN increases. See > S.J. May , P.J. Ryan , J.L. Robertson3, J.-W. Kim1, T.S. Santos1, E. Karapetrova1, J.L. Zarestky4, X. Zhai5, S.G.E. te Velthuis1, J.N. Eckstein5, S.D. Bader1, and A. Bhattacharya1*, (a) (b) “Enhanced ordering temperatures in antiferromagnetic manganite superlattices,” Nat. Mater. 8, 892 (November 2009). DOI:10.1038/ NMAT2557

Author affiliations > 1Argonne National Laboratory, 2Ames Laboratory, 3Oak Ridge National Laboratory, 4Ames Laboratory and Iowa State University, 5University of Illinois at Urbana-Champaign (c) Correspondence > *[email protected]

> 6-ID-B,C • MU/XOR • Materials science, physics • Anomalous and resonant scattering (hard x-ray), general diffraction, grazing incidence diffraction, liquid scattering, magnetic x-ray scattering, surface diffraction (UHV) • 3.3-cm Undulator A • Accepting general users

> Work at Argonne, including use of the > 33-BM • XOR/UNI • Materials Advanced Photon Source and the Center science, physics, chemistry for Nanoscale Materials, was supported • Anomalous and resonant by the U.S. Department of Energy, scattering (hard x-ray), diffuse Office of Science, Office of Basic Energy x-ray scattering, powder diffraction, Sciences, under contract No DE-AC02- x-ray reflectivity, general 06CH11357. Work at Oak Ridge National diffraction, grazing incidence Laboratory’s High Flux Isotope Reactor diffraction • Bending magnet was sponsored by the Scientific User • Accepting general users Facilities Division, Office of Basic Energy Sciences, U.S. Department of Energy.

The Advanced Photon Source Annual Science Report 2009 23 Electronic & Magnetic Materials

Linking Surface Structure and Magnetism

surface bilayer. The most significant IN SHORT > Manganites have been extensively studied for change was in the spacing between many years because of their rich array of intriguing electronic, manganese and the top/bottom magnetic, and structural properties arising from strongly oxygen, designated as Mn-O(II). The other two Mn-O spacings basically competing internal interactions that can lead to unexpected keep their bulk values. The reduction ground states. For example, the broken translational symmetry of Mn-O(II) is consistent with a at the surface of such a material can be enough to produce change in orbital occu­pancy and, distinct functionality there due to the changing balance of consequently, the magnetic order at charge, lattice, orbital, and spin degrees of freedom. With the the surface. Specifically, the surface help of the XOR 4-ID-C beamline at the APS, researchers relaxation was seen to produce a from Louisiana State University, Northwestern University, collapse in the c axis, decreasing the Jahn-Teller lattice distortion. the University of Tennessee, Oak Ridge National Laboratory, Bulk theoretical calculations the Royal Institute of Technology, Charles University, and revealed that, even at fixed doping Argonne investigated the origin of a nonferromagnetic phase level, the relaxation of the

present at the surface of La2–2xSr1+2xMn2O7 manganites with Jahn-Teller distortion at the surface hole doping levels corresponding to bulk ferromagnetic order is consistent with the stabilization (x = 0.36 and 0.40), using a combined experimental and of an A-type state with moments aligned ferromagnetically within theoretical analysis. the layer and antiparallel between the double layers. This theoretical finding was supported by directly measuring the magnetic state at the surface using x-ray resonant magnetic MORE > A quantitative study of at the surface must not be due to scattering (XRMS) on XOR surface structure was undertaken a change of symmetry, but could beamline 4-ID-C at the APS using low-energy electron diffraction be due to a change of lattice (Fig. 1a). The key observation from (LEED) to determine geometric parameters at the surface. This the XRMS mea­surements is that a and chemical ordering, and the finding was consistent with a change of sign of the XRMS signal full-potential linearized augmented detailed comparison of the electronic occurs and can be connected to a plane-wave (FLAPW) theoretical properties of manganese at the single surface bilayer that displays approach was employed in surface and in the bulk material no net magnetism and is therefore calculating the electronic structure using x‑ray absorption spectroscopy, not ferromagnetic (Fig. 1b). Such

of the La2–2xSr1+2xMn2O7 system for showing that the surface had a sign change would be absent if the two doping levels. Electronic the same composition as the ferromagnetism was present in the and magnetic characterizations of bulk material. surface bilayer. in situ cleaved (001) surfaces were To probe the details of the also performed using x-ray resonant surface structure, a quantitative — Vic Comello magnetic scattering. analysis of the experimental and The LEED structural analyses theo ­retical LEED I(V) curves was revealed a LaSrO rocksalt­- conducted, showing that the main terminated surface that showed structural changes at the (001) no sign of surface reconstruction surface pertain to three different (Fig. 1c). This indicates that the manganese-oxygen (Mn‑O) changes in the physical properties distances in the top half of the

24 A rgonne National Laboratory Electronic & Magnetic Materials

(b)

< Fig. 1 (a) Schematic representation of the XRMS experiment on the (001) surface of the La/Sr bilayered manganites. (b) Obtained results indicate that the top bilayer presents no magnetic ordering. (c) LEED pattern collected at 150 eV, which shows no evidence for changes in symmetry at the surface.

(a)

See > V.B. Nascimento1*, J.W. Freeland2, R. Saniz3,§, R.G. Moore4, D. Mazur2, 150 eV H. Liu4, M.H. Pan5, J. Rundgren6, K.E. Gray2, R.A. Rosenberg2, H. Zheng2, J.F. Mitchell2, (c) A.J. Freeman3, K. Veltruska7, and E.W. Plummer1,4, “Surface-Stabilized Nonferromagnetic Ordering of a Layered Ferromagnetic Manganite,” Phys. Rev. Lett. 103, 227201 (27 November 2009). DOI: 10.1103/ PhysRevLett.103.227201 > Work at Argonne, including the Advanced Photon Source, was supported by the U.S. Department of Energy (DOE), Author affiliations > Office of Science, Office of Basic Energy 1Louisiana State University, Sciences under Contract No. DE-AC02- 2Argonne National Laboratory, 06CH11357. Work at Northwestern > 4-ID-C • XOR • Materials University was supported by the DOE 3Northwestern University, science, physics • Anomalous and under Grant No. DE-FG02-88ER45372 resonant scattering (soft x-ray), 4 University of Tennessee, and a grant of computer time at the magnetic circular dichroism (soft 5Oak Ridge National Laboratory, National Energy Research Scientific x-ray), magnetic x-ray scattering, 6Royal Institute of Technology, Computing Center. V.B.N. acknowledges x-ray photoemission electron support from the Distinguished Scientist 7Charles University §Present address microscopy, x-ray photoemission Program at UTK-ORNL (E.W.P.). The part spectroscopy, x-ray magnetic Universiteit Antwerpen of this work performed at the University linear dichroism • Circularly of Tennessee and ORNL received polarized undulator • Accepting support from the National Science general users Correspondence > Foundation and DOE (DMS&E) Grant No. *[email protected] NSF-DMR-0451163.

The Advanced Photon Source Annual Science Report 2009 25 Engineering Materials & Applications

Stressing Out the Twins in Magnesium

The researchers identified IN SHORT > The way a material reacts under stress is a three grains that, because of their question of critical relevance, especially when considering orientation, were good candidates for that material’s strength and versatility for various uses. twinning, along with another grain in a completely different orientation Under stress, hexagonal-close-packed (HCP) metals are for use as a control reference. They known to undergo crystallographic twinning, when parts monitored these grains during the of a grain abruptly flip and create mirror-image copies of experimental runs as stress was themselves. Because twinning also results in new reoriented applied. Because the team found grain domains and shear patterns that can affect the that the overlapping of diffraction mechanical qualities of a metal, a detailed understanding spots increased with stress, usable and precise characterization of such behavior is essential for signal was no longer generated by two of the grains after a certain the development and use of predictive models. Working at point, but the remaining grain the XOR 1-ID beamline at the APS, a team of researchers displayed a good degree of twinning has pioneered a method of using three-dimensional x-ray before it was also overlapped diffraction (3DXRD) to study the twinning process in low- by diffraction spot signals at about symmetry materials and its evolution in situ on the level of 90 MPa. individual grains, while also allowing the full stress tensor to When the orientation of the parent grain is known, it is possible be measured. to calculate the positions of the diffraction spots of the twins, and their subsequent appearance in the predicted locations indicates the presence of that particular twin variant. The grain displayed MORE > The experimenters— Data from the diffraction spots were variants 2 and 5 of the 6 variants from the Los Alamos, Lawrence analyzed by computer to identify in the {1012}<1011> twinning Livermore, and Argonne national grains in twinning orientations. system (as numbered clockwise laboratories—examined cylindrical Magnesium was chosen as an around the c axis of the hexagonal samples of the magnesium alloy experimental material because its unit cell), beginning at 40-MPa AZ31 on the 1-ID beamline, using hexagonal structure allows twinning of compression. Although all six 3DXRD with a 200-µm × 200-µm to be easily induced under stress. variants are possible, in general, only synchrotron x-ray beam at Previous neutron diffraction one is actually generated, and that 80.7 keV. Compression stress at studies of AZ31 clarified the need is the one for which the resolved 20-MPa increments was applied for obtaining data at a finer level shear stress on the twin system is the perpendicular to the axis of the of precision than is possible with highest. If two of them have a high x-ray beam while the sample was that method. The researchers were value of the resolved shear stress, rotated over 120° along the loading looking for experimental input for then you one have two. It all depends axis. Bragg reflections (diffraction some of their modeling efforts, to see on the orientation of the parent grain. spots) from various grains were how twinning influences deformation The researchers were able to picked up by an area detector in of materials in general. While determine the three-dimensional several crystallographic planes. neutron diffraction provides excellent stress tensors of the parent grain statistical data, it cannot delineate the and its twin variants at every stage individual twinning process in single of evolution with greater precision grains, unlike the 3DXRD technique than previously achieved with the used in the current work. 3DXRD technique (Fig. 1).

26 A rgonne National Laboratory Engineering Materials & Applications

See > C.C. Aydıner1*, J.V. Bernier2, B. Clausen1**, U. Lienert3, C.N. Tomé1, and D.W. Brown1, “Evolution of stress in individual grains and twins in a magnesium alloy aggregate,” Phys. Rev. B 80, 024113 (2009). DOI: 10.1103/ PhysRevB.80.024113

Author affiliations > 1Los Alamos National Laboratory, 2Lawrence < Fig. 1 Resolved shear stress on the twin system as a function of applied stress; once Livermore National Laboratory, the twinning occurs, the resolved shear stress in the parent saturates, and more 3Argonne National Laboratory importantly, the shear stress in the twin(s) is initially of the opposite sign than in the parent. This illustrates the significant stress relaxation associated with twinning. Correspondence > *[email protected] **[email protected]

The team hopes to use the hexagonal systems, including present data to refine their current magnesium, zirconium, and models to predict how various titanium. The process of twinning > This work was supported by the U.S. Department of Energy Office of Basic low-symmetry materials will is very similar to martensitic Energy Science through Project No. behave. A future question is how transformations, so the same FWP 06SCPE401. Use of the Advanced the surrounding grains affect the techniques could be used for looking Photon Source was supported by the U.S. Department of Energy, Office of Science, stresses on the twinning grain. at domain switching in ferroelectrics Office of Basic Energy Sciences, under Statistically, the grains around the and martensitic phase transformation Contract No. DE-AC02-06CH11357. parent grain that is twinning will also in shape memory alloys. have some influence. In the future, the researchers would like to take — Mark Wolverton into account all the actual grains > 1-ID • XOR • Materials science, around, because they are themselves physics, chemistry • High-energy anisotropic. x-ray diffraction • 3.3-cm Undulator A The models could also • Accepting general users eventually be applicable to other

The Advanced Photon Source Annual Science Report 2009 27 Engineering Materials & Applications

High-Pressure “Alchemy”

between strong and weak magnetism IN SHORT > The properties of magnetic materials continue that are associated with normal to spark great scientific and practical interest. One of the most Invar behavior. Up to this point, the well-known magnetism-related phenomenon is the so-called researchers had been unaware that the material might be capable of the Invar effect, in which Invar alloys maintain nearly constant Invar effect. size over a wide range of temperatures. This makes them To confirm the predicted ideal for use in watches, toasters, light bulbs, engine parts, change in electronic states, the satellites, lasers, scientific instruments, and even computer researchers conducted a nuclear and television screens. While it has long been known that forward scattering (NFS) experiment on HP-CAT beamline 16-ID-D at the the chemical makeup of the alloys is responsible for Invar APS to gain a direct measure of the behavior by creating unusual electronic configurations that magnetic state of the material under constrain lattice expansion, the Invar effect remains one of pressure. NFS spectra from Pd3Fe the oldest and most-studied unresolved problems in materials showed quantum beats at lower research. With the aid of a beamline at the APS, researchers pressures, indicating that the material was magnetically ordered, but the have helped unify our understanding of Invar behavior. beats decreased significantly in amplitude at 12.3 GPa and vanished altogether at higher pressures (Fig. 1). This result is consistent with a first-order phase transition in which pressure causes a shift MORE > Studies carried out Initial testing at the National from a high magnetization state to a by researchers from Caltech, The Synchrotron Light Source (NSLS) low magnetization state. As a final University of Chicago, and the at Brookhaven National Laboratory, check on the calculated result, the

Carnegie Institution of Washington using energy-dispersive x-ray researchers heated a sample of Pd3Fe show that Pd3Fe, a ferromagnetic diffraction at room temperature and under a pressure of 7 GPa and found material that does not exhibit Invar pressures up to 33 GPa, showed that negligible thermal expansion from behavior at ambient pressure, Pd3Fe suffered a significant volume 300K to 523K, demonstrating Invar does show Invar characteristics collapse between approximately behavior. These studies identified when placed under great pressure, 10 GPa and 15 GPa, and that the the necessary condition for Invar indicating the possibility of a kind material stiffened by an unexpectedly behavior as having an alloy at the of alchemy in which pressure large amount above 15 GPa. edge of the transition from strong to makes electrons behave as if they To understand why, the weak ferromagnetism. were in a material of different scientists simulated the quantum chemical composition. The ability mechanical behavior of the — Vic Comello to use pressure to force a material’s electrons in the alloy under pressure electrons into new states points using density functional theory to new directions in materials calculations. The simulations chemistry in which novel properties suggested that the electrons in the may be found, at least for magnetic alloy shifted under pressure into materials. the special electronic energy levels

28 A rgonne National Laboratory Engineering Materials & Applications

See > Michael L. Winterrose1, Matthew S. Lucas1, Alan F. Yue1, GPa Itzhak Halevy1, Lisa Mauger1, Jorge A. Muñoz1, Jingzhu Hu2, 25.3 Michael Lerche3, and Brent Fultz1*, “Pressure-Induced Invar Behavior

in Pd3Fe,” Phys. Rev. Lett. 102, 19.0 237202 (12 June 2009). DOI:10.1103/PhysRevLett. 102.237202

15.1 Author affiliations > 1California Institute of Technology,

2The University of Chicago, 13.4 3Carnegie Institution of Washington

Correspondence > 12.3 *[email protected] Log Intensity

> This work was supported by the Carnegie-U.S. Department of Energy 8.9 (DOE) Alliance Center and was funded by the DOE through the Stewardship Sciences Aca­demic Alliance of the National Nuclear Security Administration 7.5 (NNSA). HP-CAT was supported by DOE- Basic Energy Sciences (DOE-BES), DOE- National Nuclear Security Administration, the National Science Foundation (NSF), and the W. M. Keck Foundation. Use 4.7 of the NSLS was supported by DOE- BES under Contract No. DE-AC02- 98CH10886. Beamline X17C at NSLS was supported by the Consortium for 0.0 Materials Properties Research in Earth Sciences (COMPRES) of the NSF. Use of 25 40 55 70 85 100 115 the Advanced Photon Source at Argonne National Laboratory was sup­ported by Time (ns) the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, under Contract No. DE-AC02­06CH11357. < Fig. 1 Nuclear forward scattering spectra > 16-ID-D • HP-CAT • Materials 57 science, geoscience, physics from chemically ordered Pd3 Fe • Nuclear resonant scattering, showing a sudden decrease of the inelastic x-ray scattering, x-ray hyperfine magnetic fields in the Raman scattering, x-ray emission material at around 12 GPa. spectroscopy • 3.3-cm Undulator A • Accepting general users

The Advanced Photon Source Annual Science Report 2009 29 Engineering Materials & Applications

Revealing Degradation Mechanisms in Solid-Oxide Fuel Cells

Researchers have attempted IN SHORT > Technologists anticipate that solid-oxide fuel to develop coatings to prevent chromium diffusion to the cathode, cells will play an important role in high-efficiency power but a long-term solution is yet to plants and clean-coal technology, but these future energy be found, which threatens to stifle devices are not without problems. Solid-oxide fuel cells, the development of SOFCs. Part of SOFCs, produce electricity by electro-chemically oxidizing the problem is that researchers do a fuel, such as hydrogen or carbon monoxide, to water not have a complete picture of the chromium migration process despite or CO2. Like all fuel cells they have an ion-conducting various studies using elemental electrolyte that divides two electrodes, anode and cathode, analysis, surface x-ray scattering, which are fed by fuel gas and air, respectively. The electric scanning electron microscopy, and current starts to flow when the electrodes are connected transmission electron microscopy. with the external load while charged ions, produced These conventional techniques electrochemically, are transported through electrolyte inside have all failed so far to provide a of the fuel cells. In a polymer electrolyte fuel cell, a polymer comprehensive picture of the nature membrane carries hydrogen ions (protons) from the cell’s and distribution of the chromium contaminants, as well as changes in anode to its cathode. In a SOFC, the membrane is replaced the cell’s physical properties that by a solid-oxide electrolyte that carries negative oxygen they may induce. ions from the cathode to the anode. Experiments carried The Argonne researchers out by Argonne scientists using the XOR 1-ID beamline at turned to recently developed high the APS revealed important facets of the cells’ construction energy microbeam synchrotron and operation, and could lead to improved performance x-ray diffraction and radiographic techniques to investigate the layer and longer lifetimes for these devices. composition and internal strain inside of SOFC layers with unprecedented spatial resolution (Fig. 1). They conducted the first accurate measurement of two-dimensional (2-D) Cr species distributions and MORE > All types of fuel cell So-called planar SOFCs use revealed the presence of manganese- device have their own advantages inexpensive metallic interconnects chromium spinel and chromium(III) and challenges. SOFCs typically made from ferritic stainless steels oxide as the main contaminants in operate at a temperature range of to draw the electric current produced the chromium poisoned SOFCs. The 600° C to 1000° C, producing power at the electrodes. These materials accumulation of these two materials outputs from less than 100 W to are cheaper than the alternatives, at the cathode catalyst and electrolyte better than megawatts with a putative but contain high levels of chromium interface prevents the normal flow efficiency of more than 60%. The (Cr). Under operating conditions, of fuel gas, damages the cathode’s high-temperature operation also chromium forms various kinds of structural integrity, and ultimately makes it feasible to recover the waste oxides, which segregate from the deactivates the SOFC. heat produced from SOFCs to drive interconnects and accumulate on the An additional important point gas turbines for secondary power cathode through diffusion, leading emerges from this study. Earlier generation, therefore further boosting to degradation and failure of the work by others had suggested that the total efficiency. SOFC—a phenomenon known as chromium might be transported chromium poisoning. through gas diffusion to the cathode.

30 A rgonne National Laboratory Engineering Materials & Applications

(a)

(b)

Incident 81-keV X-ray (c) 2(V) × 50(H) microns2

The present work confirms that volatile chromium species, such as chromium oxyhydroxide—

CrO2(OH)2,—and chromium(VI) oxide—CrO3,—are generated on the < surface of the metallic interconnects Fig. 1 Schematic showing the high-energy microbeam synchrotron x-ray diffraction and and permeated through the porous radiographic technique with a typical diffraction pattern along with 2-D distributions layers of the cathode. As soon as of (a) Cr2O3 weight fraction, (b) porosity and (c) deviatoric strain in the YSZ phase. these high-valance-state, volatile species come into contact with the electrolyte and catalyst, they are reduced to low-valance oxides and deposited inside the most active See > Di-Jia Liu* and Jonathan > This study was supported by the U.S. region of the cathode. The process Almer, “Phase and strain Department of Energy offices of Basic Energy Sciences and Fossil Energy. Use continues until the SOFC fails. distributions associated with of the Advanced Photon Source was The Argonne researchers reactive contaminants inside of a supported by the Office of Science, Office add that it is the strong penetrating solid oxide fuel cell,” Appl. Phys. of Basic Energy Science, under Contract power of the APS high-energy x-rays Lett. 94, 224106 (2009). DOI: No. DE-AC02-06CH11357. and high spatial resolution of the 10.1063/1.3148362 technique that make up a powerful tool for investigating SOFCs and Author affiliation > other layered electrochemical devices Argonne National Laboratory > 1-ID • XOR • Materials science, physics, chemistry • High-energy under actual operating conditions. x-ray diffraction • 3.3-cm Undulator A Correspondence > • Accepting general users — David Bradley *[email protected]

The Advanced Photon Source Annual Science Report 2009 31 Soft Materials & Liquids

Ordering the “Nano” World

aggregates rearrange to form IN SHORT > A variety of novel technologies, including well-ordered, larger (micrometer- drug delivery systems, photovoltaic cells, and computer size) crystal structures. microprocessors, depend on the use of nanotechnology, The researchers also examined the effects of various which makes use of the submicroscopic particles called environmental parameters on the nanoparticles. The assembly of nanoparticles into uniformly- assembly process. For example, ordered materials is critical for the reliable functioning of higher temperatures are necessary nanotechnology. More than a decade ago, researchers at to achieve the greatest extent of Northwestern University developed a process that used small ordering among the structures, whereas at room temperature, no strands of DNA attached to gold nanoparticles to direct crystallinity is observed in the nanoparticle assembly. DNA consists of building blocks called aggregates. In addition, DNA length nucleotides that pair together in a predictable manner, and the has a significant impact on the process is used to assemble nanoparticles by programming timescale of the assembly process, specific nucleotide sequences. In 2008, the research team with longer DNA linkers forming crystals at a slower rate. The group further expanded this method of assembly to create highly also determined that the assembly ordered, three-dimensional (3-D) nanoparticle architectures. process affected the final structure In the current study, these researchers and colleagues from of crystals obtained. Distinct Argonne used two x-ray beamlines at the APS to characterize crystal types were obtained the way in which these 3-D crystal structures are formed as a depending on whether a single self-complementary strand of DNA path to creating ordered crystal structures that can be used to (i.e., a one-component system) or extend the useful applications of this technology. a more complex (two-component) system was used. They also characterized the timing of the assembly depending on whether a one- or two-component system was used. MORE > Nanoparticles are process at the DND-CAT 5-ID By understanding these typically about 100 nm or less beamline and the XOR/BESSRC processes and the manner in which in size, smaller than most cells, 12-ID beamline at the APS to DNA can be used to create ordered or about the size of a large virus. characterize the three-phase process crystal structures, it is possible to Nanomaterials often exhibit unique in which DNA-functionalized gold design more effective and efficient properties due to their extremely nanoparticles assemble into well- methods and procedures for creating small size and large surface ordered crystal structures (Fig. 1). gold nanoparticle crystal systems area-to-volume ratio. For example, They found that when the used in nanotechnology, thereby a solution of gold nanoparticles, appropriate DNA linkers are added extending the useful applications appears red in color, as opposed to a solution of DNA-functionalized of this technology. to the shiny yellow of bulk gold. nanoparticles, they first form small, Well-ordered 3-D structures are disordered clusters consisting of — Emma Hitt necessary for creating consistent just a few nanoparticles. In a second physical properties in the materials step, these clusters simultaneously used in nanotechnology. The reorganize into ordered crystals researchers in this study used small and aggregate to form larger angle x-ray scattering measurements cluster-cluster aggregates. In a third carried out during the crystallization and final step, the cluster-cluster

32 A rgonne National Laboratory Soft Materials & Liquids

(a) (b) (c) < References > C.A. Mirkin, Fig. 1 Top: Programmable DNA interactions assemble nanoparticles into ordered 3-D R.L Letsinger, R.C. Mucic, structures via a process of a) small, disordered cluster formation, b) simultaneous and J.J. Storhoff, “A DNA-Based cluster reorganization and cluster-cluster aggregation, and c) reorganization of Method for Rationally cluster-cluster aggregates into ordered crystals. Bottom left: Small-angle x-ray Assembling Nanoparticles into scattering patterns demonstrating the transition from a disordered aggregate to an Macroscopic Materials,” ordered crystal. Bottom right: A face-centered cubic unit cell, demonstrating the Nature 382(6592), 607 (1996). final arrangement of nanoparticles within the 3-D lattice. S.Y. Park et al., DNA-Programmable Nanoparticle Crystallization,” Nature 451(7178), 553 (2008).

> This work was supported by the See > Robert J. Macfarlane1, National Science Foundation > 5-ID • DND-CAT • Materials 2 1 Byeongdu Lee , Haley D. Hill , Nanoscience and Engineering Center, science, polymer science • Powder Andrew J. Senesi1, Soenke Seifert2, the Air Force Office of Scientific diffraction, small-angle x-ray and Chad A. Mirkin1*, “Assembly Research, the National Cancer Institute scattering, surface diffraction, and organization processes in DNA- Center for Cancer Nanotechnology wide-angle x-ray scattering, x-ray Excellence, and a National Institutes optics development/techniques, directed colloidal crystallization,” of Health Director’s Pioneer Award x-ray reflectivity, x-ray standing Proc. Nat. Acad. Sci. USA 106(26), (to C.A.M.); and a U.S. Department of waves • 3.3-cm Undulator A 10493 (2009). DOI:10.1073/ Homeland Security Graduate Fellowship • Accepting general users pnas.0900630106 under the DHS Scholarship and Fellowship Program (to H.D.H.). The > 12-ID • XOR/BESSRC DND-CAT is supported by E. I. DuPont • Chemistry, materials science, Author affiliations > de Nemours & Co., The Dow Chemical physics • Grazing incidence small- 1Northwestern University, Company, and the State of Illinois. angle scattering, small-angle x-ray scattering, surface diffraction, 2Argonne National Laboratory Use of the Advanced Photon Source was supported by U.S. Department of wide-angle x-ray scattering Energy, Office of Science, Office of • 3.3-cm Undulator A • Accepting Correspondence > Basic Energy Sciences, under Contract general users *[email protected] DE-AC02-06CH11357.

The Advanced Photon Source Annual Science Report 2009 33 Soft Materials & Liquids

Exploring the Constructs of Bird Feather Color

growth. However, a contrasting way in which color can be created is IN SHORT > Bird feathers are adorned with some of the through the undirected self-assembly richest, deepest colors in the animal kingdom. Many of these of crystal-like particles. The Yale colors are formed not from pigment, but from the scattering group hypothesized that photonic of light by extremely small, ordered structures within the nanostructures in bird feathers self- cells of the bird feathers. These “nanostructures,” which assemble, and sought to elucidate cause light to scatter and make color, are made of beta-keratin the way in which this occurs. (not to be confused with β-carotene, or vitamin A). Beta- Feathers consist almost entirely of beta-keratins that keratin is a protein found in the feathers and skin of birds and self-assemble into strands called reptiles that confers waterproofing and prevents desiccation. filaments. Two types of these Bird feathers and their colors play an important role in social nanostructures have been identified and sexual communication among birds, so the way in which based on their structure. One type is the shape and form of these nanostructures translate into referred to as a “channel” type that has a twisted, string-like appearance. projecting various colors is of interest. To find out more This channel type nanostructure is about this process, researchers from Yale University used the found in the blue back plumage of XOR 8-ID-I beamline at the APS in their investigations into the Eastern Bluebird. The other type precisely how these nanostructures develop. Their findings of nanostructure is referred to as may provide additional information about the way in which “spherical” and is the type found in the vivid turquoise-blue plumage of other photonic (i.e., light sensing, detecting, and emitting) the Plum-Throated Cotinga bird. It nanostructures can be synthesized. appears that channel and spherical types of nanostructures have evolved independently in birds. The researchers compared the optical light scattering properties between the Eastern Bluebird and MORE > The field of photonics In their study, the Yale researchers the Plum-Throated Cotinga using incorporates many applications, sought to understand more about small-angle x-ray scattering. They including laser manufacturing, the function and evolution of the found several differences between biological and chemical sensing, coloration of bird feathers and how the optical properties of the feathers medical diagnostics and therapy, photonic nanostructures form during of these two birds. One difference and display technology. By bird development. was that the light emitted by the understanding more about photonics, According to the researchers, Plum-Throated Cotinga was about it may be possible to advance the colors vary according to eight times that emitted by the understanding of the field and differences in the size and shape of feathers of the Eastern Bluebird. develop new and useful applications. nanostructures. Given the role of On the basis of their colors and their appearance in bird observations, the researchers social and sexual communication, conclude that birds develop color- it is important that the growth producing nanostructures by of these nanostructures is tightly arresting structural formation during controlled during development development. Structures vary due to by “templates” that direct cellular the rate of beta-keratin expression;

34 A rgonne National Laboratory Soft Materials & Liquids

< (a) Photograph of crown feathers from L. coronata: the field of view is 1 cm.(b) TEM image of air spheres in beta-keratin from L. coronata: the field of view is 5.5 µm.

(a) (b)

the rate of polymerization See > Eric R. Dufresne*, > This work was supported with seed (i.e., joining together) of the Heeso Noh, Vinodkumar Saranathan, funding from the Yale NSF-MRSEC (DMR-0520495) and National Science beta-keratin subunits; and the rate Simon G.J. Mochrie, Hui Cao, Foundation grants to E.R.D. (CBET), of cross-linking of beta-keratin and Richard O. Prum**, S.G.J.M. (DMR), H.C. (EECS), and R.O.P. (DBI). Use of the Advanced Photon strands. In addition, the group also “Self-assembly of amorphous Source at Argonne National Laboratory determined that beta-keratins appear biophotonic nanostructures by phase was supported by the U.S. Department of Energy, Office of Science, Office of Basic to self-assemble during a process separation,” Soft Matter 5(9), 1792 Energy Sciences, under Contract No. called phase-separation in (2009). DOI:10.1039/b902775k DE-AC02-06CH11357. which beta-keratins separate from other components within Author affiliation > the cellular cytoplasm. Yale University > 8-ID-I • XOR • Materials science, By mimicking this process physics, polymer science • with other biological substances, it Intensity fluctuation spectroscopy, Correspondence > small-angle x-ray scattering, x-ray may be possible to create new ways *[email protected] photon correlation spectroscopy to develop photonic nanostructures. **[email protected] • 3.3-cm Undulator A • Accepting general users — Emma Hitt

The Advanced Photon Source Annual Science Report 2009 35 Soft Materials & Liquids

Two Ways of Laying Down the Lipids

LBS deposition (Fig. 1), the IN SHORT > Lipid monolayer and bilayer structures are experimenters found that while interesting not only because they can be studied as a working both have highly similar structures, model of cellular membranes, but also because the ability to the bilayers formed by vesicular fusion show asymmetric electron better understand and create them could lead to the development density distribution between their of new medical applications and treatments. Generally, the two leaflets, with the inner leaflet extreme thinness and delicacy of these bilayers makes them showing a higher than expected notoriously difficult to examine in precise detail. A research electron density. This seems to be team from the University of California, Davis; and Los Alamos due to greater disorder in the inner leaflet caused by the vesicular fusion National Laboratory employed the MU/XOR 6-ID-B,C process. The bilayers formed by beamline at the APS to carry out experiments comparing two vesicular fusion are also in general different methods for artificially forming lipid bilayers, using about 5% thicker than bilayers x-ray reflectivity and grazing incidence diffraction (GIXD) to prepared by LBS. characterize and measure the formation and structure of lipid Scattering intensity, as shown by GIXD, displayed distorted bilayers with unprecedented clarity. hexagonal lattices similar to DPPC multilayers. Bragg rod analysis showed that despite being deposited independently of one another, the lipid tails in opposing leaflets quickly self-organized and coupled, MORE > The experimenters observations were performed at and scattered accordingly as a studied membranes formed from HASYLAB’s BW1 undulator single entity. Modeling using the dipalmitoyl-phosphatidylcholine beamline in Hamburg, Germany; intensity distribution bilayer Bragg (DPPC). DPPC is one of the most the bilayer observations were done data suggested the existence of common phospholipids, a class of at the 6-ID-B,C beamline. orientational texture of the lipid molecules with “heads” that attract Aside from comparing the tilt directions. The observed water (hydrophilia) and “tails” that two bilayer preparation techniques, Bragg peaks also suggested that repel it (hydrophobia), causing these the team also sought to determine the substrate has no appreciable molecules to spontaneously arrange the role of the solid substrate on effect on the bilayer structure. themselves when in water into a the membrane structure and the The major difference between the two-molecule-thick bilayer with the qualities of any ordered domains that LBS and the vesicular bilayers is hydrophilic heads facing out and might form within the layers. LBS the greater disorder within the the hydrophobic tails inward. For DPPC bilayers were formed by the inner leaflet of the bilayers formed this study, bilayers were created on deposition of DPPC monolayers in by vesicular fusion. a solid quartz substrate either by a Langmuir trough, while vesicular The ability to measure and vesicular fusion, the most popular fusion samples were prepared characterize in high resolution these bilayer preparation method, or via from unilamellar vesicles of about relatively stable, supported bilayer the Langmuir-Blodgett-Schaeffer 500-Å diameter made with a tip molecular films opens up new (LBS) deposition technique. probe sonicator. A very thin water avenues of research for even more The team’s goal was to determine cushion was present between the precise characterization and perhaps which method yielded the most inner leaflet of the bilayers and the even control of their formation. complete, well-packed, and easily substrate support. Aside from the obvious value of reproducible membranes, among In comparing the samples acquiring a greater understanding of other questions. Monolayer prepared by vesicle fusion and lipid bilayers in living cells, these

36 A rgonne National Laboratory Soft Materials & Liquids

< < Fig. 1 Electron density profile,r (z), for DPPC bilayers deposited by LBS and vesicle fusion at the quartz-H2O interface. The thick green curve demonstrates the bilayer structural variation for the LBS bilayer preparation over approximately a dozen measurements and four sample preparations. The dotted curves encompass the variation of vesicle fusion bilayers and show a larger variation in structure than the LBS bilayers. The largest differences between the two sample preparation methods occur in the inner leaflet, adjacent to the quartz substrate. The dark blue curve corresponds to a representative LBS DPPC bilayer. 0 Å denotes the center of the bilayer. A volume-constrained model for each lipid leaflet was constructed for the representative LBS bilayer; these are shown in dotted red. The solid red line is the lipid contribution to the total electron density. The light blue curves denote the contribution of water to the total electron density and gives a quantified amount of hydration between the bilayers and the quartz substrate.

possibilities include the development of sophisticated biosensors and more advanced liposomes for targeted drug delivery within the body.

— Mark Wolverton

See > E.B. Watkins1,2, C.E. Miller2*, D.J. Mulder1, T.L. Kuhl1, and J. Majewski2, “Structure and Orientational Texture of Self- Organizing Lipid Bilayers,” Phys. Rev. Lett. 102, 238101 (12 June 2009). DOI: 10.1103/ > 6-ID-B,C • MU/XOR • Materials PhysRevLett.102.238101 > This work was supported by the science, physics • Anomalous and Department of Energy, Office of Science, resonant scattering (hard x-ray), Office of Basic Energy Sciences through general diffraction, grazing Author affiliations > Grant No. 46340 and Los Alamos National 1 incidence diffraction, liquid University of California, Davis; Laboratory under DOE Contract No. scattering, magnetic x-ray 2 W7405-ENG-36. Use of the Advanced Los Alamos National Laboratory scattering, surface diffraction Photon Source is supported by the U.S. (UHV) • 3.3-cm Undulator A Department of Energy, Office of Science, • Accepting general users Correspondence > Office of Basic Energy Sciences, under *[email protected] Contract No. DE-AC02-06CH11357.

The Advanced Photon Source Annual Science Report 2009 37 Soft Materials & Liquids

Tracking Polymer Melt Dynamics at the Nanometer Scale

beamline 8-ID-I of the APS, a highly IN SHORT > Disordered, glassy materials are ubiquitous intense beam of monochromatic, coherent x-rays was aimed at the in nature. Often, the microscopic constituents of these samples. The scattered x-rays materials can move exceedingly slowly, and one of the major produced a pattern of “speckles,” challenges for materials scientists is to gain direct information which are variations in x-ray about the nature of this motion at the relevant small length intensity from one spot to another scales and long time intervals. By applying x-ray photon within the scattering pattern that occur when coherent light impinges correlation spectroscopy (XPCS) to track the mobility of on a disordered material. Over time, tiny gold nanoparticles suspended in polymer liquids as they the motion of the gold nanoparticles are cooled into glass, a team of researchers has succeeded altered the pattern of speckles, in elucidating the motion in the polymers at the nanometer and recording and analyzing this scale (i.e., one billionth of a meter). A surprising observation evolution enabled the researchers to determine a statistical average in the experiments was the increasing prevalence of slow, of the particle motion. heterogeneous flow in the polymers as they were cooled closer Among the key outputs of and closer to the glass state. The apparently universal nature the XPCS measurement was a of that complex, low-temperature flow indicates a generic set of characteristic times that origin that any microscopic theory for glassy materials will described the duration required for the particles to move on average need to confront. different distances. More precisely, these times were measured at different scattering wave vectors (wave vectors represent waves in vector form; they find use in the characterization of groups of MORE > At higher temperature, To capture the behavior of the coherent waves moving in the same where the liquids have a lower nanoparticles in isolation within the direction, such as from an x-ray viscosity, the observed motion of the polymer, without undue influence beam derived from the APS). At nanoparticles was diffusive; that is, from neighboring particles, the temperatures well above the glass the particles exhibited random walks researchers—from Johns Hopkins transition temperature Tg of the as a consequence of their constant University, McGill University,and polymer, the characteristic times bombardment by surrounding the University of Ottawa—kept were observed to vary inversely polymer molecules. At lower the concentration of gold very with the square of the wave vector; temperature, however, this diffusion low (between 0.04% to 0.1% by i.e., when plotted against the wave was superseded by a second process volume) and the sizes of the gold vector on a log-log scale, the times that suggested the particles became nanoparticles quite small as well followed a line with a slope of caught up in complicated flow that (diameters of either 2 nm or negative two, as shown in Fig.1. appeared in the polymer when it was 3 nm). To prevent the particles This behavior is a signature of cooled. The emergence of this flow from clumping, the researchers diffusion, where the random-walk bears strong resemblance to similar attached to the surfaces a dense motions cover distances that on behavior seen in other disordered layer of polymer molecules that average increase as the square-root materials in which the microscopic were chemically identical to the of the elapsed time. However, as the constituents move slowly, such surrounding material. In the XPCS polymer’s temperature approached as gels. experiments, carried out at XOR the glass transition—at around

38 A rgonne National Laboratory Soft Materials & Liquids < 1.1Tg—the characteristic times disordered, glassy materials, and Fig. 1 Left: Schematic of a nanoparticle in adopted a different trend, varying presents a significant new challenge a polymer melt. Right: Characteristic inversely with a linear power of to materials scientists attempting to times vs wave vector measured by the wave vector. This linear understand their properties. XPCS for nanoparticle motion in relationship implied that the particles polymer melts. on average traveled a distance in — Philip Koth direct proportion to the time elapsed, as if they had a characteristic velocity. The magnitude of these velocities was exceedingly small, less than a tenth of a nanometer See > Hongyu Guo1, Gilles > Funding for this research was provided per second, illustrating the power Bourret2, Muriel K. Corbierre2, by the Petroleum Research Fund and 2 the Natural Sciences and Engineering of XPCS to monitor small motions Simona Rucareanu , R. Bruce Research Council of Canada. Use of the occurring over long durations; Lennox2, Khalid Laaziri3, Luc Advanced Photon Source at Argonne nevertheless, those seemingly Piche2, Mark Sutton2, James L. National Laboratory was supported by minute velocities were still much Harden3, and Robert L. Leheny1*, the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, faster than any diffusion that “Nanoparticle Motion within Glassy under Contract No. DE-AC02-06CH11357. occurred within the highly viscous Polymer Melts,” Phys. Rev. Lett. polymer at low temperatures. 102, 075702 (2009). DOI: 10.1103/ The researchers interpreted this PhysRevLett.102.075702 motion as the velocity of slow, > 8-ID-I • XOR • Materials science, heterogeneous flow in the polymer Author affiliations > physics, polymer science • 1 2 Intensity fluctuation spectroscopy, that appears as a consequence of Johns Hopkins University, McGill small-angle x-ray scattering, x-ray the deep cooling. The observation University, 3University of Ottawa photon correlation spectroscopy of this complex flow adds a new • 3.3-cm Undulator A • Accepting piece to the overall picture of the Correspondence > general users internal dynamics occurring within *[email protected]

The Advanced Photon Source Annual Science Report 2009 39 Soft Materials & Liquids

Mixing and Matching Detergents for NMR Membrane Protein Structure Determinations

peaks were not observed in FC-10 IN SHORT > Membrane proteins make up about 25% of the and DDM because of extensive line broadening. proteins in a cell and are crucial for transport and signaling EPR was used to investigate across cell membranes. Yet these important proteins account the physical origin of the line for less than 1% of the known protein structures. One broadening by studying the structure reason is the difficulty of selecting a detergent that mimics and dynamics of TM0026 under the native lipid bilayer comprising the cell membrane; different detergent conditions. The suitable detergents must stabilize protein folding while data demonstrated that the structure of TM0026 was perturbed by FC-10 solubilizing membrane proteins for structural and functional and DDM. investigations. The problem is that detergents are unlike To understand how the lipid bilayer sheets in that they form micelles that have detergents influence TM0026 different shapes and sizes depending on their chemical structure, SAXS was used to structure. Currently, detergents are selected by exhaustive investigate the sizes and shapes of screening because the effects of protein-detergent interactions the micelles formed by the different detergents. The researchers, from the on protein structure are poorly understood. Researchers University of Virginia, The Scripps addressed this problem by investigating how different Research Institute, and Stanford detergents and detergent mixtures affect the structure and University found that the detergents dynamics of the membrane protein TM0026, using small- for which poor NMR spectra were angle x-ray scattering (SAXS) at the XOR/BESSRC 12-ID observed form micelles that were beamline at the APS in conjunction with nuclear magnetic either smaller and thinner (FC-10), resonance (NMR) and electron paramagnetic resonance or larger and thicker (DDM) than the micelles formed by DM and (EPR) spectroscopy. The results suggest that matching FC-12 (Fig. 1). The researchers micelle dimensions to the protein’s hydrophobic surface then investigated whether mixing combats the line broadening that reduces the completeness detergents at different ratios might be of NMR observations. The finding possibly provides a a way to systematically change the basis for the rational design of mixed micelles that may size and shape of detergent micelles. advance membrane protein structure determinations Toward this end, SAXS data were obtained for a comprehensive set of by NMR. mixed micelles. The researchers found that the thickness of mixed micelles depends linearly on the mixing ratio for a significant range of detergent mixtures and that this thickness MORE > TM0026 was found to decylphosphocholine (FC-10), and appears to correlate strongly with the produce NMR spectra that were dodecylphosphocholine (FC-12). quality of NMR observations. The drastically different as assessed For the detergents DM and FC- generality of this result is difficult by 15N, 1H-TROSY (transverse 12, 51 of 66 expected cross peaks to assess; however, the observations relaxation-optimized spectroscopy) were observed, while only 32 and are in qualitative agreement with with respect to four different 36 cross peaks were observed for previous findings. Future work will detergents: decyl maltoside the detergents FC-10 and DDM, explore whether similar relationships (DM), dodecyl maltoside (DDM), respectively. The expected cross can be observed for different

40 A rgonne National Laboratory Soft Materials & Liquids

L=34Å < Fig. 1 Model demonstrating hydrophobic matching between the hydrophobic dimensions of the protein (hydrophobic length of the α-helices is ≈32 Å) and the detergent alkyl chains. The interior of the DM micelle is colored yellow. The protein residues for which nuclear Overhauser effects (NOEs) between the amide proton and the alkyl chain of detergent molecules were observed are colored red, and the residues that were unassigned or lacked NOEs with the detergent are colored gray. The nitroxide side chain at residue 13 is rendered as blue sticks. The dominant head group separation (L) is labeled. > Support for this research was provided by National Institutes of Health Grants 1F32GM068286 and The Jeffress Memorial Trust (L.C.) PO1 GM0066275 (S.D.), and Protein Structure Initiative 1,2 membrane proteins varying in size, See > Linda Columbus *, Grants P50 GM62411 and U54 GM074898 fold, and origin. Other micelle Jan Lipfert3, Kalyani Jambunathan1, (S.L.). A.Y.L.S. is supported by A*STAR. properties (such as the total micelle Daniel A. Fox1, Adelene Y.L. Sim3, Use of the Advanced Photon Source volume) will likely have to be taken Sebastian Doniach3, and Scott A. was supported by the U.S. Department of Energy, Office of Science, Office of 2 into account to fully understand Lesley , “Mixing and Matching Basic Energy Sciences, under Contract protein-detergent interactions. Detergents for Membrane Protein DE-AC02-06CH11357. Nonetheless, the data suggest that, NMR Structure Determination,” rather than exhaustively screening J. Am. Chem. Soc. 131, 7320 (2009). a multitude of detergents, it might DOI:10.1021/ja808776j be possible to rationally engineer > 12-ID • XOR/BESSRC • appropriate mixed micelles for NMR Author affiliations > Chemistry, physics, materials structure determinations following 1University of Virginia, science • Small-angle x-ray scattering, wide-angle x-ray 2 simple principles and using a limited Scripps Research Institute, scattering, grazing incidence set of detergents. 3Stanford University small-angle scattering, surface diffraction • 3.3-cm Undulator A • Accepting general users — Vic Comello Correspondence > *[email protected]

The Advanced Photon Source Annual Science Report 2009 41 Soft Materials & Liquids

Development of Icosahedral Short-Range Order Confirmed in Glass Transition

< < Fig. 1 (a) The scaled number of IN SHORT > Much remains to be discovered about how quasicrystal grains as a function metallic glasses form from the liquid state upon cooling, which of scaled annealing time; N is the number per unit volume, Is is the should not be surprising given that the glass transition in steady-state nucleation rate, and general is one of the most significant­ outstanding problems in t is the transient time. (b) Left, condensed matter physics. While there is general agreement that electrostatic levitation facility used the dynamics of the transition involve the development­ of local for the x-ray diffraction studies; and perhaps intermediate-range order in the metastable liquid, right, levitated liquid sample. (c) The the nature of this order has remained controversial.­ Icosahedral pair correlation function computed short-range order (ISRO) has been frequently argued to from the experimental scattering data (circles) and Reverse Monte dominate the local structures­ of supercooled metallic liquids Carlo fits (solid lines); the data were and glasses, but definitive experimental confirmation of a link sparsely plotted to show the quality between developing ISRO and the glass transition has been of the fits. (d) The intensity of the lacking, until now. Researchers from Washington University 1551 Honeycutt-Andersen index made the first quantitative measurements of the time-dependent (characteristic of icosahedral short- nucleation rate in a metallic glass, studying the crystallization range order) as a function of liquid temperature. The dashed line is a of a Zr59Ti3Cu20Ni8Al10 bulk metallic glass to an icosahedral quasicrystal of the same chemical composition. The researchers polynomial fit; gT indicates the glass transition temperature. then obtained direct measurements of the evolution of the local structure of the liquid in the deeply supercooled and amorphous states based on a reverse Monte Carlo (RMC) analysis of liquid studies confirmed that only the diffraction data obtained at the APS. The results from the two icosahedral quasicrystal phase was very different experiments provide the strongest experimental formed during these anneals. The demonstration to date that ISRO dominates the structures of number of icosahedral quasicrystal both the liquid and the glass and strongly supports an ISRO- phase grains produced after the nucleation and growth treatments based frustration model for the glass transition in this and were counted manu­ally from TEM possibly other zirconium-based metallic glasses. images. A detailed analysis of these data revealed an extremely small value for the interfacial free energy between the amorphous and icosahedral quasicrystal phase. Such a small interfacial free

MORE > According to classical Zr59Ti3Cu20Ni8Al10 at a range of energy—almost an order of nucleation theory, random nucleation temperatures and anneal magnitude smaller than the values fluctuations in a liquid produce an times to produce populations of obtained between a supercooled ensemble of small clusters having nuclei. Subsequent 2-min anneals liquid and a quasicrystal—implies the structure of the ordered phase. at the higher temperature of very strong ISRO in the glass. How­ever, only those clusters 430° C allowed these nuclei to This conclusion was further exceeding a critical size can nucleate grow to observ­able size. X-ray supported by x-ray diffraction and grow. The researchers first diffraction and transmission measure ­ments made at the annealed ribbons of amorphous electron microscopy (TEM) MU/XOR 6-ID-D beamline at the

42 A rgonne National Laboratory Soft Materials & Liquids

APS on electrostatically levitated, and increases the viscosity of the nearly spherical droplets of the liquid, making it easier to form supercooled liquid and glass the glass. > The work at Washington University on. Structural models for the was partially sup­ported by the National liquids were obtained from RMC — Vic Comello Science Foundation under Grant No. DMR-0606065 and by NASA under simulations, and the topologies Contract No. NNM04AA016. MU/XOR of the RMC-generated structures is supported by the U.S. Department of were then analyzed. ISRO was See > Y.T. Shen, T.H. Kim, Energy, Office of Science, Office of Basic found to increase dramatically with A.K. Gangopadhyay, and Energy Sciences. Use of the Advanced super ­cooling to the glass transition K.F. Kelton*, “Icosahedral Order, Photon Source is supported by the U.S. Department of Energy, Office of Science, (Fig. 1). These two results provide Frustration, and the Glass Transition: Office of Basic Energy Sciences under the strongest experimental evidence Evidence from Time-Dependent Contract No. DE-AC02-06CH11357. to date of the connection between Nucleation and Supercooled Liquid ISRO and the topological frustration Structure Studies,” Phys. Rev. underlying the glass transition in Lett. 102, 057801. DOI:10.1103/ this and related glasses. Further, PhysRevLett.102.057801 > 6-ID-D • MU/XOR • Materials they indicate that ISRO can play a science, physics • High-energy x-ray diffraction, magnetic x-ray central role in glass formation in Author affiliation > scattering, pair distribution Zr-based bulk metallic glasses. The Washington University function, powder diffraction • growth of ISRO in the supercooled 3.3-cm Undulator A • Accepting liquid raises the nucleation barrier Correspondence > general users for the formation of crystal phases *[email protected]

The Advanced Photon Source Annual Science Report 2009 43 Soft Materials & Liquids

Nano-Layered Organic/Inorganic Structures Make Better Photoconductors

their conductivity. Adding organic dyes might improve conduction IN SHORT > For reasons ranging from cheaper solar cells by reducing edge disruption. For to reducing the use of toxic metals, researchers want to the best performance, however, the find materials for light harvesters that are different than the organic and inorganic materials need semiconductors used today. Although the photodetectors to be intimately connected in an now in use are very efficient, they are based on the same organized way. single-crystal silicon used for computer chips (which The Northwestern group made is expensive) or compounds made with cadmium, lead, a nano-ordered, self-assembled hybrid of inorganic semiconductor mercury, or arsenic (which are toxic). A less-expensive, less- zinc oxide and thiophene, using hazardous photodetector that, ideally, can also be tuned to electrodeposition to grow plate- detect different wavelengths could enable new applications like structures from solution on that need these properties as well as flexibility and light an electrode. The thiophene-based weight. Researchers from Northwestern University created small molecules are electrically active conjugated surfactants. The a nano-engineered, self-assembling photodetecting material parts of the molecules that share that they studied with a variety of methods, including x-ray electrons control assembly and absorption spectroscopy (XAS), at the DND-CAT 5-BM-D enhance long-range ordering. As beamline at the APS. The researchers found this material grown, the inorganic layers didn’t to be very efficient compared to similar technologies, and show a response to light, but after they researchers hope that the new, environmentally-benign heating to 150° C, the conductivity increased dramatically. material could provide low-power, flexible light detectors. To see what, exactly, they had made, the researchers used several imaging methods. Images of the material show tiny plates 1-nm thick made of crystalline zinc oxide layered on 2- or 3-nm thick MORE > Organic materials are is that they degrade quickly, usually layers of organic molecules. The less expensive than inorganics, and due to chemical changes that occur XAS measurements carried out at more flexible. By manipulating when electrical charges are trapped beamline 5-BM-D determined the the molecular structure of these or the materials react with oxygen. identity of the inorganic phase at materials, organic dyes allow users Another approach is to specific temperatures. When they to “tune” a photodetector to a combine organic and inorganic looked at the K absorption near-edge specific wavelength, and the wide materials in ways that use the structure of the inorganic before range of available molecules allows strengths of each. Ideally, organic annealing, the results looked like control over the lifetime of charge- and inorganic materials would work insulating Zn(OH)2. After annealing, trapping states. A major drawback together to trap photons, generate the structure suggested the material of organic photodetectors, however, charge-carriers, and conduct the had changed to tetrahedral ZnO separated charges to the appropriate crystallites smaller than a nanometer electrodes. Previous work by other in diameter. The nanocrystalline researchers showed that fused ZnO matrix conducts charges well. nanoparticles could be very sensitive The group used a variety of light detectors if the trap states at thiophene molecules, and found the edges of crystals didn’t disrupt that by designing a surfactant that

4 4 A rgonne National Laboratory Soft Materials & Liquids

< Fig. 1 Schematic diagram of lamellar ordering composed of inorganic Zn-rich regions (dark blue) and bilayers of 1-pyrenebutyric acid (PyBA). (Copyright © 2010 Nature Publishing Group, a division of Macmillan Publishers Limited.)

1.5

1.0

Zn(OH) 0.5 2 RT

0.0 -40 0 40 80 E (eV)

1.5

1.0 absorbs light at energies below the ZnO bandgap (which created fiber- like, rather than plate-like structures, 0.5 ZnO 150 oC but retained the layering), they could 350 oC engineer a system where light is 0.0 absorbed by the organic, which then transfers electrons to the ZnO, which -40 0 40 80 efficiently shepherds the charges to E (eV) the electrode. < — Yvonne Carts-Powell Fig. 2 XANES (x-ray absorption near edge structure) spectra of hybrid films deposited with PyBA as a function of heat treatment (pre- See > Marina Sofos, Joshua anneal, 150° C and 350° C) and

Goldberger, David A. Stone, of Zn(OH)2 and ZnO standards. Jonathan E. Allen, Qing Ma, > This work was supported by the U.S. XANES proved that the initial hybrid David J. Herman, Wei-Wen Tsai, Department of Energy under Award film had Zn(OH)2 as the inorganic Lincoln J. Lauhon, and Samuel I. DE-FG02-00ER54810 and the National phase, which converted to ZnO upon Science Foundation under award DMR annealing. Stupp*, “A synergistic assembly of 0605427. DND-CAT is supported by the nanoscale lamellar photoconductor E.I. DuPont de Nemours & Co., The Dow hybrids,” Nat. Mater. 8, 68 (2009). Chemical Company, the U.S. National DOI: 10.1038/NMAT2336 Science Foundation through Grant DMR-9304725, and the State of Illinois through the Department of Commerce and Author affiliation > > 5-BM-D • DND-CAT • Materials Board of Higher Education Grant IBHE science, polymer science • Northwestern University HECA NWU 96. Use of the Advanced High-energy x-ray diffraction, x-ray Photon Source was supported by the U.S. absorption fine structure • Bending Department of Energy, Office of Science, magnet • Accepting general users Correspondence > Office of Basic Energy Sciences, under *[email protected] Contract No. DE-AC02-06CH11357.

The Advanced Photon Source Annual Science Report 2009 45 Chemical Science

Perfecting Catalytic Arrays

microscopy at the EMC and IN SHORT > Catalysts speed up chemical reactions and synchrotron x-ray scattering at the remain largely unchanged themselves at the end of the APS (Fig. 1). They found that they process. This apparently simple statement harbors a chemical could produce nanoparticles in a small size range from 30 nm to 40 nm secret: catalysts are much more complicated than that. Now, by annealing at a temperature of work carried out on beamline 11-ID-D at the APS, as well as 1450K under a flow of the relatively at the Argonne Center for Nanoscale Materials (CNM) and unreactive gas, nitrogen. Electron Microscopy Center for Materials Research (EMC), The team demonstrated that could improve our understanding of at least one class of each array on the strontium titanate surface contains 75 million particles industrially important catalyst: metal nanoparticle catalysts. in a square lattice, with a spacing of 200 nm between the particles. The x-ray diffraction measurements suggest that the particles lock on to the crystal structure of the substrate and are shaped like a cuboctahedron MORE > Chemists can disperse if it were possible to constrain the cut in half. metal nanoparticles on high-surface- sizes of the nanoparticles to a tighter The researchers once more area support materials to produce range of diameters, then the catalytic used DFT calculations to explain how an enormous area of catalyst to process would be more consistent. It this particular shape arises during interact with the starting materials might also be possible to optimize the the process and suggest that it is due in a reaction mixture. This allows nanoparticle size and shape as well to the partial “wetting” of platinum those materials to come together as the detailed nature of their surface on the strontium titanate during very readily, to then react and structure to improve industrial annealing. They add that wide-angle transformation into large quantities catalytic reactions. reflectivity scans showed that only of product with little waste. The researchers have used a negligible few of the platinum The added advantage of this density functional theory (DFT) nanoparticles are misoriented on type of catalyst is that it can reduce calculations to guide their studies the surface. the need for energy-intensive on arrays of nanoparticles made Having produced such perfect pressurization or high temperatures. from platinum. Their calculations platinum nanoparticle arrays, the In other words, it can make a allowed them to control the growth team then carried out some bulk process that would be otherwise of identical platinum nanoparticles, tests of their catalytic prowess. environmentally unfriendly into which form arrays on a strontium Oxygen-reduction electrocatalytic a greener way to manufacture a titanate (STO) substrate, using activity was used to test each of the chemical product. The same principle electron beam lithography at the three arrays produced on different applies whether that chemical is a CNM. The team points out that they crystal forms of strontium titanate pharmaceutical drug, a technological can produce three distinct shapes of with good results. This catalytic test, material, or an agrochemical, such nanoparticle. These can be produced the researchers say, is one of the as a pesticide or herbicide. selectively simply by changing the most important ways of evaluating Researchers from Safarik crystallographic surface features electrocatalytic activity. University, Argonne, and the of the strontium titanate substrate Intriguingly, the crystallographic Paul Scherrer Institut investigated on which they form and the physical surface form of the nanoparticles how metal nanoparticle catalysts conditions used to anneal, or fix, the displayed activity opposite to what might themselves be produced nanoparticles to that surface. is seen with conventional non- more consistently. They reasoned In order to characterize the nanoscopic platinum catalysts that various factors could further resulting nanoparticle arrays, the traditionally modeled with single improve these catalysts For instance, team turned to scanning electron crystal extended surfaces. The one

46 A rgonne National Laboratory Chemical Science

< Fig. 1 Left: Truncated crystal truncation rods of (111) facets (top) and hex reconstruction peaks from (100) nanofacets (bottom). Right: Successively zoomed images of nanoparticles. The top image shows clearly a cuboctahedron; one (100) facet at the center and four adjacent (111) facets.

See > Vladimir Komanicky1,2*, Hakim Iddir2, Kee-Chul Chang2, Andreas Menzel2,3, Goran Karapetrov2, Daniel Hennessy2, Peter Zapol2, and Hoydoo You2**, that would conventionally be most scattering experiments to be “Shape-Dependent Activity of reactive turned out to be the least performed, but with millions of Platinum Array Catalyst,” J. Am. catalytically active form, and vice nanoparticles. Chem. Soc. 131, 5732 (2009). versa. The researchers suggest The team concedes that DOI: 10.1021/ja900459w that this is due to a “division of electron beam lithography, being labor” effect arising through the a serial, or sequential, rather than Author affiliations > 1Safarik close proximity of the facets of the parallel technique, limits how University, 2Argonne National divided cuboctahedrons, which much surface can be covered with Laboratory, 3Paul Scherrer Institut allows oxygen to be adsorbed on catalytic nanoparticles in a given time to the conventionally less catalytic However, they also point out that Correspondence > surface more effectively than it parallel nanofabrication techniques *[email protected] would otherwise be. are being developed and could **[email protected] Such insights regarding the soon overcome such a limitation, behavior of catalysts is allowing allowing the approach to be extended researchers to lay bare the simplistic for the production of optimized > This work and use of the Advanced notion that catalysts simply speed metal catalysts for use in the Photon Source, the Center for Nanoscale Materials, and the Electron Microscopy up reactions and so is helping chemical industry. Center for Materials Research were them developing novel materials According to the team, the supported by the U.S. Department of with a wide range of potential APS played a crucial role in the Energy, Office of Science, Office of Basic applications. characterization of the arrays Energy Sciences, under Contract No. DE-AC02-06CH11357. This work demonstrates, for produced. Since the coverage the first time, full control over all of platinum catalyst on the STO possible variables connected with substrate is relatively low, use high surface area catalysts, such of a high-brilliance x-ray source > 11-ID-D • XOR/BESSRC • as size, shape, number, and even was necessary for confident Chemistry, geoscience, materials the orientation of particles. From characterization of epitaxial relation science • General diffraction, the standpoint of x-ray scientists, between the catalyst particles and time-resolved x-ray absorption control over spatial orientation fine structure, x-ray absorption the substrate and detection of fine structure • 3.3-cm Undulator A of particles and their arrangement misoriented particles. (US), 2.3-cm undulator (DS) in a relatively perfect square lattice • Accepting general users would allow single nanoparticle — David Bradley

The Advanced Photon Source Annual Science Report 2009 47 Chemical Science

Storing Hydrogen

> Fig. 1 The phase diagram of bulk and IN SHORT > Researchers have been studying mesoporous nanophase ammonia borane. materials for almost two decades with a view to using them as When heated, bulk ammonia hosts for small molecules and scaffolds for molding organic borane undergoes an orthorhombic compounds into new hybrid materials and nanoparticles. to tetragonal phase transition at 225K and becomes amorphous Their use as potential storage systems for large quantities above 343K. However, confined of hydrogen has also been mooted. Such systems that might nanophase ammonia borane does hold large quantities of hydrogen safely and in a very compact not undergo the phase transition volume would have enormous potential for powering fuel cell at 225K. Instead, it remains in the vehicles, for instance. A sponge-like form of silicon dioxide, tetragonal phase from 110K to the stuff of sand particles and computer chips, can soak up 240K. Amorphization of nanophase ammonia borane occurs at a much and store other compounds including hydrogen. Studies lower temperature, 240K, than bulk carried out at the XOR/BESSRC 11-ID-B beamline at the APS ammonia borane. have revealed that the nanoscopic properties of the hydrogen- rich compound ammonia borane help it store hydrogen more efficiently than usual. The material may have potential for addressing the storage issues associated with a future a porous structure. Instead, the molecular crystals retain their hydrogen economy. tetragonal phase over a wide temperature range of temperatures from 110K to 240K. The data suggest that trapping ammonia borane in MCM-41 destabilizes the molecular crystal MORE > Researchers from silica could have a synergetic effect at temperatures above 240K and Los Alamos National Laboratory, on the storage properties. stabilizes its high-temperature the Pacific Northwest National The researchers obtained disordered tetragonal phase even Laboratory, and Argonne carried diffraction patterns for ammonia at much lower temperatures than out synchrotron x-ray powder borane embedded in the mesoporous would be expected. The PDF diffraction experiments at the silica, MCM-41, across a temperature analyses of the data, coupled 11-ID-B beamline. The team range from 80K to 300K. They then with previously available results sought to uncover the properties used an analytical technique known of xenon-129 nuclear magnetic and structure of the nanophase as atomic pair distribution function resonance spectroscopy, hints at of ammonia borane held within (PDF) to unravel the x-ray data. how this might work to improve the mesoporous silica, in which the The key finding from their hydrogen storage capacity of porous pore diameters are 2 to 50 nm, which research is that the nanophase silica composite materials containing is midway between microporous ammonia borane held within ammonia borane. (less than 2 nm) and macroporous the confined spaces of the The research not only (greater than 50 nm). Ammonia mesoporous silica begin to lose provides useful information about borane itself, with the formula their crystalline character at much the nanophase of ammonia borane NH3BH3, is loaded with hydrogen lower temperatures, above 240K, confined in mesoporous silica, and has been the focus of hydrogen and surprisingly do not undergo the but also demonstrates the prowess storage aspirations for some time. expected structural phase change of PDF analysis of x-ray powder It forms stable molecular crystals at 225K (Fig. 1). This transition diffraction data for the determination that hook together via dihydrogen is observed for bulk crystals of of soft materials—compounds bonds. Packing it into mesoporous ammonia borane not confined in containing light elements—trapped

48 A rgonne National Laboratory Chemical Science

See > Hyunjeong Kim1*, Abhi Karkamkar2, Tom Autrey2**, Peter Chupas3, and Thomas Proffen1, “Determination of Structure and Phase Transition of Light Element Nanocomposites in Mesoporous Silica: Case study of NH3BH3 in MCM-41,” J. Am. Chem. Soc. 131, 13749 (2009). DOI: 1021/ja904901d

Author affiliations > 1Los Alamos National Laboratory, 2Pacific Northwest National Laboratory, 3Argonne National Laboratory

Correspondence > *[email protected] **[email protected] within heavy mesoporous materials. The team concludes that Conventional crystallographic their analytical technique could be diffraction techniques are insufficient broadly applied to any number of to characterize such guest species encapsulated materials as well as to > H.K. and T.P. acknowledge support from the Lujan Neutron Scattering Center, with limited long-range order. organic functional groups supported funded by the U.S. Department of Energy Below 240K, nanophase ammonia on mesoporous surfaces. This will Office of Basic Energy Sciences. Los borane inside MCM-41 pores has a allow researchers to study the Alamos National Laboratory is operated by Los Alamos National Security LLC tetragonal structure. However, the chemical and physical properties of under Contract DE-AC52-06NA25396. structural correlation only persists such systems in a way that was not T.A. and A.K. acknowledge support from up to 40 Å because it is confined previously possible. the U.S. Department of Energy, Office in 40-Å-diameter pores. Therefore, of Basic Energy Sciences, Division of Chemical Sciences, Biosciences, and below 240K, nanophase ammonia — David Bradley Geosciences. Pacific Northwest National borane has medium-range structural Laboratory is operated by Battelle for the order, which usually does not give U.S. Department of Energy. Use of the Advanced Photon Source is supported by well defined, sharp Bragg peaks. the U.S. Department of Energy, Office of Currently available high-flux Science, Office of Basic Energy Sciences, synchrotron x-ray sources, such as under Contract No. DE-AC02-6CH11357. those offered by the APS, together with area-detector technology allow researchers to obtain data even from very small amounts of sample and > 11-ID-B • XOR/BESSRC • in a relatively short time, which can Chemistry, environmental science, then be analyzed using PDF, for materials science • Pair distribution instance, to differentiate between the function • 2.3-cm undulator • light guest molecules and the heavy Accepting general users host material.

The Advanced Photon Source Annual Science Report 2009 49 Chemical Science

A Stable Open Framework with Wide Open Spaces

three-dimensional arrangement of IN SHORT > Porous materials frameworks with open cuboctahedra, with a well-defined crystal structure, that the researchers structures, containing substantial numbers of cavities and call a porous coordinated network extended internal surfaces where smaller guest molecules can (PCN). Use of the smaller ligand attach, are potentially useful for a wide range of applications, produces a structure in which such as gas storage, catalysis, and drug delivery. One class of the cuboctahedra pack together such open-framework materials is metal-organic frameworks leading to cavities of two distinct sizes arranged in a regular way. (MOFs), with metal ions or clusters of ions fixed in a scaffold X-ray diffraction studies of this of organic linkers. The more porous these frameworks are, with crystalline solid, dubbed PCN-61, bigger open spaces, the more fragile they tend to become. reveals that the smaller of the two Now, researchers have made a MOF that is remarkably open cavities (yellow in the accompanying but also stable through the incorporation of cavities that are diagram) are 15 Å across, while the larger are 23 Å. PCN-66, larger than 20 Å (mesocavities) but with openings less than the metal-organic framework 20 Å (microwindows), a strategy demonstrated by x-ray formed using the larger ligand has diffraction studies at the ChemMatCARS beamline 15-ID the same cuboctahedra packed at the APS. This new synthetic strategy may serve as a general similarly, leading to slightly larger approach toward stable MOFs with even higher surface areas, cavities, measuring 16 Å and 26 Å, respectively. eventually leading to even greater practical applications. X-ray diffraction measurements also show that the two PCN structures do not change when small molecules adsorbed in their interior cavities are removed. That is in contrast to some other large-pored MORE > A standard way to Researchers at Texas metal-organic frameworks, whose construct MOFs is to connect metal A&M University and Shandong cavities have been found to collapse ions using organic linking molecules, University in China chose as their when they are empty. The stability or ligands. Solvothermal reactions, building blocks copper-containing of the large mesoscale cavities in which are carried out in organic cuboctahedra, well-known structures the PCN comes about because their solvents under high temperature, that have 6 square faces and surfaces are formed from the rigid are used to form bonds between the 8 triangular faces enclosing a ligands and the relatively small linkers and the metal ions. Increasing cavity about 13 Å (1.3 nm) across. faces of the cuboctahedra, which the size of the ligands will expose To incorporate the cuboctahedra control the size of the openings of otherwise hidden edges of these within MOFs in a novel way, the the cavities and give stability to the molecules, leading to higher surface researchers designed two new overall structure. area. However, the frameworks ligands, each one a planar molecule The cuboctahedra faces act tend to be “fragile,” reducing their with three arms extending out at as “microwindows” opening to the practical value. 120° from each other. The ligands interior of the mesocavities. The are similar in molecular form, with PCN structure is akin to a building one having slightly longer arms that has many large rooms with than the other. small doors and narrow hallways Solvothermal reactions of the connecting them. A large number of ligands with copper salts formed a people could fit into the rooms, but

50 A rgonne National Laboratory Chemical Science

See > Dan Zhao1, Daqiang Yuan1, Daofeng Sun2, and Hong-Cai Zhou1*, “Stabilization of Metal- Organic Frameworks with High Surface Areas by the Incorporation of Mesocavities with Microwindows,” J. Am. Chem. Soc. 131, 9186 (2009). DOI: 10.1021/ja901109t

Author affiliations > 1Texas A&M University, 2Shandong University

Correspondence > *[email protected]

> This work was supported by the U.S. Department of Energy (DE-FC36- 07GO17033), the U.S. Defense Logistics Agency (N00164-07-P-1300), and the < Fig. 1 In this depiction of the structure of PCN-61, a metal-organic framework, copper U.S. National Science Foundation atoms (blue) sit in “paddlewheel” structures with oxygen (red) and carbon (black) (CHE-0449634). The microcrystal diffraction was carried out with the kind atoms. The paddlewheels link together to form cuboctahedra enclosing volumes assistance of Yu-Sheng Chen at Argonne about 13 Å across (large red spheres). Three-armed ligand molecules then connect National Laboratory (CHE-0535644, the cuboctahedra into a larger structure enclosing cavities 15 Å (yellow spheres) DEAC02-06CH11357).

and 23 Å (blue) across. (Credit: Zhou et al.) Use of the Advanced Photon Source at Argonne National Laboratory was supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences (DOE-BES), under the small doors control how fast they the surface area is from 4,000 to Contract No. DE-AC02-06CH11357. could move in and out. Similarly, 4,600 m2 per gram—among the the PCNs can store large amounts of highest values ever found for metal- gas inside the cavities, but the rate organic frameworks. Zhou and of gas molecules going in and out is his colleagues are now working to controlled by the microwindows. employ the techniques demonstrated > 15-ID • ChemMatCARS • These porous molecules with these two frameworks to build Chemistry, materials science • Anomalous and resonant have large internal surfaces on framework structures with still larger scattering (hard x-ray), liquid which smaller molecules may be pores and surface areas. scattering, microdiffraction, single- adsorbed. For PCN-61, the surface crystal diffraction, small-angle area amounts to 3,000 to 3,500 — David Lindley x-ray scattering, surface diffraction, wide-angle x-ray scattering • 2 m per gram, depending on how 3.3-cm Undulator A • Accepting it is estimated, while for PCN-66, general users constructed with the larger ligands,

The Advanced Photon Source Annual Science Report 2009 51 Life Science

Tracing Selenium with XFM

developmental stages. Using IN SHORT > Sometimes even a tiny amount of something immunostaining of testis tissue can make a big difference. An example can be found within with GPx4 and TGR antibodies, the our own bodies, in which a number of trace elements, in researchers confirmed that the later spite of their small quantity, can play important roles in stage spermatids had a sharp increase in mGPx4 expression, indicating that keeping the body healthy and functioning. Selenium (Se) is this particular selenoprotein form is one of these, an essential element of various proteins needed chiefly responsible for the increased for some cellular and developmental processes, such as the Se distribution in these cells. generation of sperm cells. But imaging selenium and other Examining tissue sections such trace elements within the body with enough resolution from knockout mice subjects with and sensitivity to map their distribution and activity has been deficiencies in certain selenoproteins (Fig. 1), the researchers found that a challenge, making it difficult to determine their precise role while a lack of nGPx4 had no effect and functions. Using XFM (x-ray fluorescence microscopy) on Se content in the testis, knockout at the XOR beamline 2-ID-E at the APS, researchers have of mGPx4 and SelP selenoproteins now managed for the first time to both identify and quantify did result in a marked decrease in Se at high resolution in its native environment within the overall Se distribution. This confirms body, in the process revealing fresh insight into the role of Se the crucial role of SelP, which is made in the liver and delivers Se in spermatogenesis. to testes, and of mGPx4, the main Se user in spermatids, during the spermatogenesis process.

MORE > Scientists from Argonne, be involved in spermatogenesis are > Fig. 1 XFM scan of a mouse seminiferous the University of Nebraska, and SelP (Selenoprotein P) and TGR tubule. (a) A paraffin embedded the National Cancer Institute (thioredoxin-glutathione reductase). testis section (5 µm) of a C57BL/6J focused on selenium in mammalian The use of synchrotron XFM wild-type mouse was mounted on spermatogenesis, examining at a third-generation, high-brilliance a silicon nitride window and both tissue and sperm samples from x-ray facility such as the APS lends light microscope and XFM images mice under XFM at the 2-ID-E itself especially well to this type of were obtained. The corresponding beamline. Although it was known work because of its ability to map element and its maximum and that Se generally took the form of trace elements at submicrometer minimum threshold values in ng/cm2 selenocysteine (Sec) within proteins resolution. For the first time, the are given above each image. The and is important in spermatogenesis, team was able to identify and scan was obtained by using 12-keV its exact distribution and functions quantify the distribution of Se (and incident energy with a dwell time within the body tissues have been other trace elements), obtaining of 1.3-s per pixel and 1-µm steps mystery. Different selenoproteins high-quality, high-resolution through the sample. The upper left have been identified, including images within tissue slices from panel shows a phase contrast image, GPx4 (glutathione peroxidase seminiferous tubules and dried with the red rectangle indicating 4), present in most cell types sperm cells. the area of fine elemental scan. in some form and, within the Under XFM, the mouse (b) Overlays of P, Se, and Zn maps. testes, especially predominant seminiferous tubule tissues in mitochondrial (mGPx4) and displayed a marked increase in nuclear (nGPx4) type. Other Se within spermatids, compared important selenoproteins known to to spermatogenic cells at earlier

52 A rgonne National Laboratory Life Science

In addition, Se was observed such correlation. However, Se only a first step. The experimenters to concentrate in the midpiece of co-localized with copper in the envision the extension of these mature sperm cells and to a lesser midpiece of sperm cells. methods to studying the role of Se degree in sperm cell heads. The The research team’s work and other trace elements in other XFM technique also revealed marks the first time that Se has mammalian physiological functions, the presence of significant trace ever been imaged at cellular or a great potential that will only be amounts of zinc, phosphorus, subcellular levels at high spatial enhanced as XFM methods grow in iron, copper, and sulfur during resolution, and visualized, localized, sensitivity and sophistication. spermatogenesis. The greatest and quantified in sperm. Still, this amount of Se was associated with demonstration of the power of XFM — Mark Wolverton decreased phosphorus levels, techniques to accurately measure while zinc levels showed no and image Se in tissues and cells is

See > Sebastian Kehr1, Mikalai Malinouski1, Lydia Finney2, Stefan Vogt2, Vyacheslav M. Labunskyy1, Marina V. Kasaikina1, (a) Bradley A. Carlson3, You Zhou1, Dolph L. Hatfield3, and Vadim N. Gladyshev1*, “X-Ray Fluorescence Microscopy Reveals the Role of Selenium in Spermatogenesis,” J. Mol. Biol. 389, 808 (2009). DOI:10.1016/j.jmb.2009.04.024

Author affiliations > 1University of Nebraska-Lincoln, 2Argonne National Laboratory, 3National Cancer Institute

Correspondence > *[email protected]

> This study was supported by National Institutes of Health Grant GM065204 (to V.N.G.) and the Intramural Research (b) Program of the Center for Cancer Research, National Cancer Institute, National Institutes of Health (to D.L.H.). Use of the Advanced Photon Source was supported by the Department of Energy, Office of Science, Office of Basic Energy

> 2-ID-E • XOR • Life science, materials science, environmental science • Microfluorescence (hard x-ray • 3.3-cm Undulator A • Accepting general users

The Advanced Photon Source Annual Science Report 2009 53 Life Science

Frozen Fruit Flies

organism Drosophila melanogaster IN SHORT > The larvae of the common fruit fly, with do not survive freezing, whereas which we share more than 70% of our genes, cannot survive their Canadian cousins Chymomyza freezing, whereas a distant cousin can do so. But an x-ray amoena, another type of fruit fly study carried out by researchers using the XOR 32-ID can survive ice. Synchrotron x-ray phase- beamline at the APS suggests that there is little difference contrast imaging has emerged as between how freezing takes place in both the survivors and a useful tool for studying internal those killed by the big chill. This work is the first to use processes in insects, including phase-contrast synchrotron x-ray imaging to visualize ice respiratory tracheal compression and formation in intact, freeze-surviving insects. Understanding internal fluid dynamics of digestion the underlying process of ice formation in these insects, and and circulation because the technique is just as amenable to observing the extent to which these processes differ among insects that the water-to-ice phase transition at do and do not survive freezing, plays an important role in high resolution. understanding the freezing process. The work suggests that The researchers in this study, key adaptations taking place during the freezing process from The University of Western occur at the cellular, molecular, and biochemical levels and Ontario, the University of Nevada- might eventually lead to frozen storage of fruit flies that are Las Vegas, Argonne, and Virginia Polytechnic Institute and State so widely used in important studies of genetics, development, University, used a two-dimension evolution, and ageing. synchrotron x-ray technique to observe ice forming, for the first time, within intact insect larvae of the two fruit fly species in real time (Fig. 1). The chamber containing the larvae was placed on a translation MORE > Some insects can be Carbohydrates, for instance, are stage in the path of the x-ray frozen solid and survive at very low thought to protect cell membranes at beamline 32-ID. The initial temperatures, while chilling others and proteins as water in an insect’s hypothesis was that there would be to a few degrees below freezing kills body expands and freezes and the visible differences in the pattern of them. Scientists have known about cells undergo dehydration. There ice formation and its interaction with biological antifreeze compounds are also ice nucleators that control the insect’s tissues between the larvae in some species of insect for many the freezing processes, while that do and do not survive freezing. years. However, even synchrotron antifreeze proteins control the shape The team says that the x-ray studies could not spot the and structure of the ice as it forms. prolonged exposure to x-rays difference between the formation of However, none of the protection caused a slight rise in temperature ice crystals in insects during lethal mechanisms seems to be necessary of all larvae studied and ultimately and non-lethal freezing. Our limited or sufficient to allow an insect to killed the insects. However, control understanding of insect freezing survive the big freeze. experiments in which larvae of survival points to the existence of Other researchers have each species were frozen under various protection mechanisms. turned to light microscopy, thermal similar conditions, but without the imaging, magnetic resonance x-ray exposure, allowed the team imaging, x-ray spectroscopy, and to confirm which species survived other techniques in an effort to and which didn’t. Although home in on the fundamentals of the C. amoena froze and survived down ice protection racket. Particularly to −14° C, the freezing processes poignant is that larvae of the model were remarkably similar to those in

5 4 A rgonne National Laboratory Life Science

TC < Fig. 1 Ice formation in gut during freezing. Apparent gut freezing in a non-diapausing C. amoena larva. Left image is the x-ray image, right is a composite of subtraction images of the frames where the gut appeared to freeze (orange) and the initial freezing frame (green), which shows the locations of the cuticle and tracheal landmarks. The individual froze at −3.0° C, and the gut froze 67.6 s after the initiation of freezing; inset shows exotherm from this individual, note the lack of a double exotherm. “Ant.’ indicates the anterior of the animal, TC indicates the thermocouple.

D. melanogaster, which was killed See > Brent J. Sinclair1*, Allen by the low-temperature exposure. G. Gibbs2, Wah-Keat Lee3, Arun This, the team says, implies that the Rajamohan1§, Stephen P. Roberts2§§, physical ice formation process itself John J. Socha4, “Synchrotron X-Ray does not differ between different Visualisation of Ice Formation in > This work was supported by grant larval species regardless of whether Insects during Lethal and Non-Lethal number RR022885 from the National Center for Research Resources, a they survive freezing. Freezing,” PLoS ONE 4(12), e8259 component of the National Institutes of The team did notice that the (December 2009). Health; an NSERC Discovery Grant; and body of the freeze-tolerant species grants from the Canada Foundation for Innovation and the Ontario Research Fund wasn’t stretched as much during Author affiliations > to B.J.S. Use of the Advanced Photon ice formation as D. melanogaster, 1The University of Western Ontario, Source at Argonne National Laboratory and that freezing seemed to happen 2University of Nevada-Las Vegas, was supported by the U.S. Department of Energy, Office of Science, Office of Basic 3 at a more reliable temperature Argonne National Laboratory, Energy Sciences, under Contract No. in C. costata. This suggests that 4Virginia Polytechnic Institute and DE-AC02-06CH11357. insects that survive freezing have State University §Present address: some control over ice formation, North Dakota State University, but the overall differences were §§Present address: Central Michigan not striking. The research suggests University that studies might glean more about > 32-ID • XOR • Materials science, cryoprotection in fruit flies by Correspondence > life science • Phase-contrast focusing on differences at the cellular imaging, ultra-small-angle x-ray *[email protected] scattering, radiography • 3.3-cm and biochemical level. Undulator A • Accepting general users — David Bradley

The Advanced Photon Source Annual Science Report 2009 55 Life Science

A New Way to Peer in a Grasshopper

finer physiologic details. As a result, > Fig. 1 A still x-ray image, taken from IN SHORT > Until now, certain questions regarding small a video, shows a side view of the directly viewing the animal physiology—for example the grasshopper heart (edges are flow of blood in living, precise movement of insect blood— outlined in red). The dashed blue remain poorly understood. line is the ventral diaphragm and opaque insects—such Although current non-imaging the solid blue line near the top as the grasshopper—has techniques can be used to indirectly indicates the dorsal surface (back) not been possible due to infer movement of the heart and of the grasshopper. Microbubbles the lack of an effective insect blood flow, these methods can be seen on the upper edge of imaging technique. cannot reveal the finer details of the heart tube. Two large side air the beating heart or blood flow sacs (outlined in green) can be seen. Researchers using the patterns. Obstacles include a lack The field of view is about 1.3 mm XOR 32-ID beamline of contrast between blood vessels horizontal by 0.9 mm vertical. at the APS to study and the surrounding tissue, as well grasshoppers have as resolution too low to observe produced the first images most physiological processes. To overcome these hurdles, researchers of the air sacs and tracheae, and a with certain details of from Virginia Polytechnic Institute main longitudinal tracheal trunk insect blood flow, flow and State University, and Argonne running alongside the heart (Fig. 1). patterns within the heart, borrowed a trick from ultrasound The researchers were also able to and the relationship imaging in order to enhance what visualize the contraction of the heart between respiratory and could already be seen with real-time and ascertain details about blood synchrotron x-ray phase-contrast flow within the heart. circulatory systems. The imaging carried out at the 32-ID They concluded that insect ability to directly view beamline. blood transport may be more basic functions of blood The real-time synchrotron complicated than the simple flow in living insects x-ray phase-contrast imaging peristaltic motion previously promises to advance our technique has the necessary assumed to take place. In addition, resolution to visualize small-insect they determined that the respiratory knowledge of circulation physiology, but lacks the ability to structures contracted in ways in small animals. distinguish blood from other soft that were both synchronous and tissue because the densities of blood asynchronous to the local heartbeat, and soft tissue are nearly the same. which was previously unknown. The The researchers adapted this imaging researchers were also able to image technique to include microbubble individual microbubbles, which injection, a procedure used in range in size from 10–150-μm in MORE > In studies of insect patients undergoing ultrasound diameter, enabling them to quantify physiology, it is necessary to imaging. When used to enhance the speed of flow and to map measure events that occur in ultrasound images, microbubbles are complex details, which would not be less than 0.1 sec and to visualize administered intravenously to the possible using any other technique. structures smaller than 50 μm. systemic circulation. By combining The application of this Current imaging methods such synchrotron x-ray phase-contrast combined technique has produced as magnetic resonance imaging, imaging with microbubble injection, the first measurements of blood-flow ultrasound, and visible light probes sufficient resolution—as well as rates and patterns within an insect are limited in their ability to view the necessary image contrast—was heart. Being able to directly view fine and moving structures in opaque achieved. It was possible to clearly the basic physiological functions of insects and to elucidate some of the visualize the respiratory structures blood flow in living insects will help

56 A rgonne National Laboratory Life Science

answer many long-standing questions See > Wah-Keat Lee1* and John about circulation, which extends to J. Socha2**, “Direct visualization > Use of the Advanced Photon Source subjects such as insect retrograde of hemolymph flow in the heart at Argonne National Laboratory was heart flow and the development of of a grasshopper (Schistocerca supported by the U.S. Department of Energy, Office of Science, Office of Basic blood flow in embryonic vertebrates. americana),” BMC Physiology 2009, Energy Sciences, under Contract No. 9:2. DOI: 10.1186/1472-6793-9-2 DE-AC02-06CH11357. — Emma Hitt Author affiliations > 1Argonne National Laboratory, 2Virginia Polytechnic Institute > 32-ID • XOR • Materials science, and State University life science • Phase-contrast imaging, ultra-small-angle x-ray scattering, radiography • 3.3-cm Correspondence > Undulator A • Accepting *[email protected] general users **[email protected]

The Advanced Photon Source Annual Science Report 2009 57 Life Science biocat_biochemus_48_6072 REV.doc

Protein Assembly and Disease

indicated that they are put together IN SHORT > For some time now, proteins known as amyloids differently and had a smaller average have been implicated in the onset and advance of Alzheimer’s diameter when compared to the and other diseases, such as type 2 diabetes. One of the curious normal fibrils. In perhaps the most exciting aspects of linking these proteins to diseases is that it seems to of the new findings presented by be primarily unusual protein folding and assembly that leads the investigators, a majority of the to disease. This is especially so in the case of Alzheimer’s and mutant fibrils exhibited a structure cerebral amyloid angiopathy, where mutations such as the Iowa consistent with antiparallel β-sheets mutant are associated with familial inheritance and early onset and are thus assembled quite of the disease. Patients carrying the mutation develop neuritic differently from the parallel β-sheet of the normal protein. This clear plaques and large deposits of the mutant protein in cerebral difference in orientation between blood vessels. Exactly how the protein does so much damage the mutant and normal molecules has been the subject of intense recent research, including represents one of the first truly these findings by researchers from The University of Chicago, distinguishing characteristics the National Institutes of Health, and the Illinois Institute of of the mutant protein and will Technology. With the help of the Bio-CAT 18-ID beamline at certainly lead to better ways of detecting and treating the resulting the APS, the team used x-ray diffraction, electron microscopy, disease states. and nuclear magnetic resonance (NMR) spectroscopy to show Using these new data, the how the mutant and normal proteins differ with respect to research team proposed a link folding and assembly. What the research group found goes between aberrant assembly and a long way toward explaining how the mutant protein is able tissue pathology of the patients to create so much havoc in tissues and how b-amyloids relate carrying the mutation for D23N- Aβ40 (Fig. 1). Further work is to disease. planned to answer questions about how exactly the mutant protein assembles to produce some molecules that look like the normal protein, even though most of them do not. Previous work by the research MORE > The researchers focused team found that it occurs in more group showed that examining the on the β-amyloid coded by the Iowa than one morphotype (organisms mechanisms for bends or folds mutation, which differs from the that are classified together on the between sheets holds promise for normal protein by only one amino basis of similar physical features explaining these differences and acid. They found that the mutant without knowledge of their genetic allowed them to construct a model protein, known as D23N-Aβ40, relationship). consistent with their current results. forms fibrils much more rapidly Further investigations using Additional questions include how the than the normal protein and does NMR spectroscopy showed that substitution of a single amino acid so without first undergoing the only a minority of the mutant in the mutant protein allows it to lag phase observed for the normal protein fibrils looked like the typical form the very different anti-parallel protein. X-ray diffraction patterns β-amyloid protein fibrils, which β-sheet structure. And the large from the mutant protein showed exhibit a parallel β-sheet structure. protein deposits characteristic of cross-β patterns and other attributes Thus, a majority of the mutant the disease in patients carrying that differed from the normal protein. protein fibrils looked quite different the Iowa mutation, as well as the Observing the mutant protein from the normal fibrils. Further frequency with which β-amyloid using electron microscopy, the examination of the mutant fibrils protein is transported into the

58 A rgonne National Laboratory biocat_biochemus_48_6072 REV.doc Life Science

< Fig. 1 Protein shape changes in wild type and mutant β-amyloids related to classic Alzheimer’s disease and hemorrhagic stroke.

blood vessel wall, may also be related to how and when the fibrils > This work benefited from the support are assembled. of the NSF Research Collaborative The work reported by the See > Robert Tycko1, Kimberly L. Network, “Fibernet” (MCB-0234001). 2 3 Use of the Advanced Photon Source was research team points to two Sciarretta , Joseph P.R.O. Orgel , and supported by the U.S. Department of characteristics of proteins that Stephen C. Meredith2*, “Evidence Energy, Office of Science, Office of Basic can never be ignored: the amino for Novel β-Sheet Structures in Energy Sciences, under Contract No. acid sequence and how the protein Iowa Mutant β-Amyloid Fibrils,” DE-AC02-06CH11357 is assembled. In the case of the Biochemistry-US 48, 6072 (2009). β-amyloid proteins, changing one DOI: 10.1021/bi9002666 amino acid creates a mutant protein > 18-ID • Bio-CAT • Life science • that can assemble quite differently Author affiliations > Fiber diffraction, microdiffraction, and lead to diseases such as 1National Institutes of Health, microfluorescence (hard x-ray), Alzheimer’s, an understanding of 2The University of Chicago, micro x-ray absorption fine which may lead to the development 3Illinois Institute of Technology structure, small-angle x-ray scattering, time-resolved x-ray of new therapeutic options. scattering • 3.3-cm Undulator A • Correspondence > Accepting general users — Mona Mort *[email protected]

The Advanced Photon Source Annual Science Report 2009 59 Life Science

The Power of Proteins: Prion Diseases Demystified

> Fig. 1 Diffraction from natural and IN SHORT > It is hard to believe that a single protein recombinant prions: the observed x-ray diffraction pattern from can be responsible for the damage inflicted by diseases (A) natural prions best fits the calculated such as human Creutzfeldt-Jakob and bovine spongiform pattern (B) from a 3-protofilament encephalopathy (Mad Cow Disease). Yet the implicated helical model (C); the observed protein, known as a prion and only about 200 amino acids x-ray diffraction pattern (D) from long, can initiate and propagate a disease cycle just by recombinant prions best fits the changing its shape. Studying the prion diseases has required calculated pattern (E) from a stacked β-sheet model (F). (From patience because of the disorder and insolubility of the H. Wille et al., Proc. Nat. Acad. prion samples. Aided by beamlines at the APS, the Stanford Sci. USA 106[40], 16990 [2009], Synchrotron Radiation Lightsource (SSRL), and the Advanced (Copyright © 2009 National Academy Light Source, a collaborative research team of scientists of Sciences, U.S.A.) from Vanderbilt University and the University of California, San Francisco, have achieved a significant advance in our understanding of the infectious power of the prion protein. For many years, researchers had proposed that the prion structure was a cross-b structure, and the most convincing models from collaborators and other groups all incorporated this feature. However, it MORE > Prions are amyloids, with diffraction patterns from took many years to prove this, until which are misfolded proteins now genetically engineered prions, and this study. Recent work is showing implicated in numerous diseases. discovered important differences, that biologically significant amyloids Prions and other misfolded proteins, both in structure, as determined come in a variety of structures, such as those associated with by diffraction studies, and in all cross-b, but with the b-strands Alzheimer’s disease, represent both heterogeneity, as determined by connected in very different ways. a fascinating problem in protein electron microscopy (Fig. 1). Both On an interesting side note, folding and an excellent application types of samples exhibit cross-b the research team found that the of fiber diffraction. Previous work diffraction, which is indicative synthetic prions recovered from had definitively shown that a of amyloid structure. The most mice inoculated with recombinant particular conformation, or isoform, prominent difference was equatorial prions were more like the naturally of the mammalian prion protein was intensity indicative of stacked occurring prion proteins than the responsible for causing the central b-sheets, which is present in the recombinant ones. The investigators nervous system (CNS) diseases now recombinant samples but missing put forth several hypotheses known as prion diseases: Creutzfeldt- from the brain-derived prions. Some that would explain the observed Jakob, bovine spongiform of the patterns from infectious structural differences, including the encephalopathy, ovine scrapie, and prions produced data consistent intriguing idea that only some of the other mammalian CNS disorders. with a repeating unit of 4 b strands, recombinant prion proteins have a The research team used the which is consistent with the group’s conformation that would make them BioCARS beamline 14-ID-B at earlier model derived from electron infectious or that some difference in the APS and an SSRL beamline crystallography. the recombinant protein is inhibiting to obtain diffraction patterns from Discovering that the structure its transformation to an infectious infectious prions, compared them was cross-b was not surprising. conformation.

60 A rgonne National Laboratory Life Science

> This work was supported by National Institutes of Health (NIH) grants NS064, AG010770, and AG02132; the Fairchild Foundation; the G. Harold and Leila Though more work needs See > Holger Wille,1, Wen Bian2, Y. Mathers Foundation; and a Jane to be done to pinpoint the exact Michele McDonald2, Amy Kendall2, Coffin Childs postdoctoral fellowship (to David W. Colby1, Lillian Bloch1, D.W.C). Diffraction data were collected at structural changes that make the BioCARS under the Bio-CAT/BioCARS 1§ prion infectious, the present work Julian Ollesch , Alexander L. collaborative agreement; preliminary sets the stage for that next set of Borovinskiy2§§, Fred E. Cohen1, data were collected at beamline 12.3.1 experiments. The team is particularly Stanley B. Prusiner1, and Gerald at the Advanced Light Source, Lawrence Berkeley National Laboratory. The SSRL 2 interested in looking at strains Stubbs *, “Natural and synthetic and ALS are supported by the U.S. of prions in which the molecules prion structure from X-ray fiber Department of Energy; beamlines 4-2, are slightly differently folded, diffraction,” Proc. Nat. Acad. Sci. BioCAT, and BioCARS are also supported by the NIH National Center for Research with significant consequences USA 106(40), 16990 (2009). Resources. Use of the Advanced Photon for infectivity, symptoms, and DOI: 10.1073_pnas.0909006106 Source was supported by the U.S. even in rare cases the ability to be Department of Energy, Office of Science, transmitted from one species to Author affiliations > Office of Basic Energy Sciences, under Contract No. DE-AC02-06CH11357. 1 another. Transmission across species University of California, San The Stanford Synchrotron Radiation is what makes the question of strain Francisco; 2Vanderbilt University Lightsource is a national user facility structure one of the most interesting §Present address: Max-Planck- operated by Stanford University on behalf of the U.S. Department of Energy, Office in prion research at present. Forschungsstelle für Enzymologie of Basic Energy Sciences. By elucidating and under- der Proteinfaltung, Martin-Luther scoring the differences between the Universität Halle-Wittenberg, §§ brain-derived infectious form and Present address: Genesys > 14-ID-B • BioCARS • Life the recombinant forms of the prion Telecommunications Laboratory sciences • Anomalous diffraction proteins, the present work provides (MAD/SAD), biohazards at the Correspondence > BSL2/3 level, Laue crystallography, bright beacons on the path to macromolecular crystallography, understanding the infectious power *[email protected] time-resolved x-ray scattering • of the prion protein. 2.7-cm undulator, 2.3-cm undulator • Accepting general users — Mona Mort

The Advanced Photon Source Annual Science Report 2009 61 Structural Biology

Receptor Structure, Caffeine, and Preventing Disease

> Fig. 1 The three-dimensional structure of IN SHORT > Coffee drinkers tend to have a lower risk the human adenosine A2A receptor (red) in a neuron. of developing Parkinson’s disease. Since these data have come to the fore, much effort has been expended on finding the underlying mechanism for this effect. Once the exact mechanism is known, drugs and therapies can be designed what particular structural changes that would help treat the disease. Earlier studies showed occur when adenosine A2A binds to that caffeine interacts with an adenosine receptor that, in an antagonist. The researchers found association with dopamine and glutamate receptors, controls that, when binding the antagonist,

locomotor behavior. If more selective compounds could be the adenosine A2A receptor forms designed for interaction with the various adenosine receptor a pocket that is different than that subtypes, the result would be better therapies not only for found in previously determined Parkinson’s, but also for related neurological diseases, such as GPCR structures. The pocket is pain, Huntington’s disease, asthma, and seizures. With an eye formed by four disulfide bridges in the extracellular domain, toward obtaining fine detail on adenosine receptor structure, along with a repacking of and aided by the GM/CA-CAT beamline 23-ID-D at the APS, transmembrane helices relative to researchers determined the crystal structure of the human associated receptor structures. This

adenosine A2A receptor. Their data provide, in exquisite detail, arrangement, in addition to being important structural information that can now be used in previously undetected in GPCRs, is interesting because it allows the improving therapies for diseases in which adenosine receptors antagonist to bind in an extended play an important role. conformation perpendicular to the membrane plane. The data also show that there is not really a conserved structure among pockets of the receptor subtypes. With a conserved structure, specificity could be MORE > The research team, (Figs. 1 and 2). The adenosine achieved by varying only the side from the Scripps Research Institute A2A receptor had already been chains. Rather, the structure of the and the Leiden/Amsterdam Center shown to have its action blocked, entire pocket varies significantly for Drug Research, studied the or antagonized, by caffeine. The among the receptor subtypes,

adenosine A2A receptor from a class researchers characterized the crystal suggesting that specificity comes of receptors known as GPCRs structure of the A2A adenosine from varying the pocket’s position (G Protein-Coupled Receptors). The receptor, to a resolution of 2.6 Å, and orientation. These last pieces receptor family is the largest single when the receptor was in complex of information will be especially protein family in the human genome with a high-affinity subtype-selective important in future drug design. and binds to G proteins (guanine antagonist to treat Parkinson’s Additional findings about nucleotide-binding proteins). Of the disease known as ZM241385. By the adenosine A2A receptor-binding four adenosine-receptor subtypes choosing to study the adenosine site suggest important roles for the

(A1, A2A, A2B, and A3), the A2A structure, in complex with an extracellular loops and helical core A2A subtype is the one that is antagonist for which the receptor in recognizing binding molecules linked to caffeine and lowered had high specificity, the research and also point to telling details risk of Parkinson’s disease team was able to clearly focus on about binding and subsequent shape

62 A rgonne National Laboratory Structural Biology

changes. All of these results were data, the research team can now unexpected based on previously paint a very clear picture of how the

determined GPCR structures and adenosine A2A receptor functions highlighted in a community-wide in binding an antagonist such as assessment that was conducted to caffeine. And now that the research evaluate where the field is at in team has provided a structure for GPCR modeling and docking for another human GPCR, structural drug discovery [1]. differences can be analyzed for their By diligently collecting details relevance to pharmacology, ligand about ZM241385 and its specificity recognition, and receptor activation

for the adenosine A2A receptor, and for other receptors. combining these observations with previously reported mutagenesis — Mona Mort

Reference > [1] M. Michino; > This work was supported by the E. Abola; C.L. Brooks, 3rd; J.S. National Institutes of Health Roadmap Dixon; J. Moult; and R.C. Stevens, Initiative grant P50 GM073197 for technology development, Protein “Community-wide assessment of Structure Initiative grant U54 GM074961 GPCR structure modeling and ligand for target processing, and Pfizer (R.C.S.). docking: GPCR Dock 2008,” Nat. A.P.IJ. and J.R.L. thank the Dutch Top Institute Pharma for financial support Rev. Drug Discov. 8, 455 (June through the GPCR forum program 2009). DOI:10.1038/nrd2877 (D1-105). The GM/CA-CAT beamline (23-ID) is supported by the National See > V.P. Jaakola1, M.T. Griffith1, Cancer Institute (Y1-CO-1020) and the National Institute of General Medical 1 1 M.A. Hanson , V. Cherezov , E.Y. Sciences (Y1-GM-1104). Use of the Chien1, J.R. Lane2, A.P. IJzerman2, Advanced Photon Source at Argonne and R. C. Stevens1*, “The 2.6 National Laboratory was supported Angstrom Crystal Structure of a by the U.S. Department of Energy, Office of Science, Office of Basic Human A2A Adenosine Receptor Energy Sciences, under Contract No. Bound to an Antagonist,” DE-AC02-06CH11357. Science 322(5905), 1211 (21 November 2008). DOI: 10.1126/ science.1164772

< > 23-ID-D • GM/CA-CAT • Fig. 2 The three-dimensional structure Author affiliations > Life science • Macromolecular 1 of the human adenosine A2A receptor The Scripps Research Institute, crystallography, microbeam, and caffeine molecules floating 2Leiden/Amsterdam Center for microdiffraction, anomalous diffraction (MAD/SAD), subatomic above a cup of coffee; the adenosine Drug Research (<0.85 Å) resolution • 3.0-cm A2A receptor is the molecule in the undulator • Accepting general human body that recognizes the Correspondence > users caffeine that we consume. *[email protected]

The Advanced Photon Source Annual Science Report 2009 63 Structural Biology

Molecular Mechanisms and Drug-Resistant Cancers

> Fig. 1 A surface model of the IN SHORT > When cells need a vacuum cleaner, it’s good inward-facing conformation of the multidrug transporter P-gp. to have one that cleans up all sorts of molecules that are not (Image created by Graham Johnson wanted or are potentially toxic. The P-glycoprotein (P-gp) is of www.grahamj.com and TSRI.) a great candidate for this activity because it can tidy up cells by expelling many different kinds of toxins. Under normal circumstances, this substrate promiscuity would make P-gp the ideal vacuum cleaner. But in cancer treatment, P-gp compounds, the research team produced structures at a resolution of activity can present a problem. If all of the drugs used are 3.8 Å, which then allowed them to exported by P-gp before they can perform their therapeutic model the molecular basis for P-gp’s functions, the result is multidrug resistance (MDR). Because poly-specificity. P-gp is implicated in MDR cancers, knowing how the protein The researchers found an structure results in binding so many types of drugs is critical architecturally and biochemically to designing anticancer drugs and MDR inhibitors. With interesting x-ray structure for P-gp (Fig. 1). The overall structure is the goal of learning the underpinnings of polyspecific drug inward facing and arranged as two binding in the P-glycoprotein, a research team used two GM/ symmetrical halves. An internal CAT-CAT 23-ID beamlines at the APS, two beamlines at cavity of about 6000 Å, which the Stanford Synchrotron Radiation Lightsource, and two is large enough to hold at least beamlines at the Advanced Light Source to produce detailed two molecules simultaneously, structures of P-gp in both its free state and drug-bound. Their contains two nucleotide-binding domains separated by 30 Å. There work provides new, important insight on how P-gp operates are chemical differences between and advances the search for understanding of MDR cancers. the upper and lower halves of the drug-binding pocket that would allow for spatial heterogeneity in terms of what types of molecules bind: the upper half contains more hydrophobic and aromatic residues MORE > The P-gp is the most the membrane and exports them, while the lower half has more prevalent of three molecular resulting in MDR. Previous work polar and charged residues. Both “pumps” that transport drugs out had yielded low-resolution structural unbound and drug-bound P-gp of cells. And P-gp appears to have data. Recognizing the clinical value structures have two portals that are the broadest range of compounds of high-resolution structural data, open to the cytoplasm and to the that it taps for export; the size range the researchers, from the Scripps inner lipid bilayer, allowing entry of of the expelled compounds ranges Research Institute and Texas Tech hydrophobic molecules directly from from 330 to 4000 daltons. Because University, set out to produce an the membrane. most of the compounds that P-gp x-ray structure of P-gp. They used Because the inward- binds are hydrophobic, and thus are mouse P-gp, which has high (87%) facing structure would not allow found in the lipid bilayer of the cell sequence similarity to human P-gp molecules to enter from the outer membrane, P-gp has been called and studied the glycoprotein both cell membrane or from outside a “hydrophobic vacuum cleaner.” with and without bound drugs. the cell, the researchers propose P-gp removes molecules from By carefully choosing the bound that this structure depicts P-gp in

6 4 A rgonne National Laboratory Structural Biology

> This work was supported by grants from the U.S. Army (W81XWH-05-1-0316), National Institutes of Health (GM61905, GM078914, and GM073197), the Beckman Foundation, the Skaggs Chemical Biology Foundation, Jasper L. and Jack Denton Wilson Foundation, the Southwest Cancer and Treatment Center, and the Norton B. Gilula Fellowship. Use of the Advanced Photon Source at Argonne National Laboratory was supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, under Contract No. a pre-transport state, when it binds See > Stephen G. Aller1, Jodie DE-AC02-06CH11357. molecules inside the cell and readies Yu1, Andrew Ward1, Yue Weng1,3, them for eviction. Then, binding of Srinivas Chittaboina1, Rupeng Zhuo2, ATP and the resulting catalytic cycle Patina M. Harrell2, Yenphuong would change P-gp to its outward- T. Trinh2, Qinghai Zhang1, Ina L. > 23-ID-B • GM/CA-CAT • 2 1 facing conformation and allow it to Urbatsch , and Geoffrey Chang *, Life science • Microbeam, escort molecules outside the cell. “Structure of P-Glycoprotein Reveals macromolecular crystallography, After the ATP is released, the P-gp a Molecular Basis for Poly-Specific microdiffraction, anomalous molecule would return to its inward- Drug Binding,” Science 323, 1718 diffraction (MAD/SAD), subatomic (<0.85 Å) resolution • 3.3-cm facing structure, ready to bind the (27 March 2009). DOI: 10.1126/ Undulator A • Accepting general next molecule that is to be expelled science.1168750 users from the cell. > 23-ID-D • GM/CA-CAT • Author affiliations > Life science • Macromolecular — Mona Mort 1The Scripps Research Institute, crystallography, microbeam, 2Texas Tech University Health microdiffraction, anomalous 3 diffraction (MAD/SAD), subatomic Sciences Center, Wuhan University (<0.85 Å) resolution • 3.0-cm undulator • Accepting general Correspondence > users *[email protected]

The Advanced Photon Source Annual Science Report 2009 65 Structural Biology biocat_biomacro_10_302_DRFT.doc

Getting to Know Cellulose

focused more on visualizing the IN SHORT > As humans continue to deplete the Earth’s structure and ways of producing supply of fossil fuels, finding new sources of energy becomes cellulose III, the form that would a priority. Biomass, such as cornhusks left after harvest, is one be most advantageous for biofuels such alternative energy source. Before efficient use can be production. made of such materials, understanding how to break down The investigators had previously reported the first cellulose—the fiber in human nutrition and the main high-resolution x-ray data for a component of much biomass waste—is crucial. With the help crystalline form of cellulose III

of the NE-CAT and Bio-CAT beamlines at the APS and the (IIIII) that they produced by treating SPring-8 (Japan) beamline BL38B1, an international research cellulose II with ammonia. The team from Los Alamos National Laboratory, the University of team now extended the emerging Tokyo, and the University of Grenoble has identified important picture by using crystallography new features of cellulose structure. Their work provides and spectroscopy to determine a new crystal structure for cellulose important new details that could be used in designing more IIIII. Their data reveal diffuse efficient treatments for cellulosic biomass. patterns in cellulose III that indicate a relatively high level of disorder when compared to naturally occurring cellulose chains (Fig. 1). Not only does the cellulose III show more disorder, it also is present in MORE > Cellulose is a intermediate crystalline amine- three different types of molecular complicated macromolecule and cellulose I complexes and then, conformation. The data also led the only a few living things, including when the amines were removed, researchers to propose a new crystal the microbes inhabiting the stomachs into a form called cellulose III that structure for cellulose, a structure of cows and other ruminates, have happens to be in an activated state that would be consistent with an figured out how to metabolize it. for hydrolysis by cellulases. This aggregated microdomain structure

Yet biochemists and biophysicists latter finding is good news if the for cellulose IIIII. Further work have made significant progress goal is to make cellulose easier to will help determine if modifying in learning how cellulose is put turn into biofuels. The researchers the amine treatment of cellulose II together and how to break it apart. were also able to find conditions will result in a more ordered Among the most promising research under which they could turn the cellulose III, or whether statistical in this area is the work done with cellulose III back into cellulose I, disorder is an inherent property of compounds called amines, which important information for those cellulose III. are used in the processing of who want to clearly understand the cellulose and cellulosic biomass. process and how to control it. — Mona Mort The amines swell the cellulose fibers To add further intrigue to and make them more susceptible the story, cellulose I can also to the cellulase enzymes used in be irreversibly converted to a converting biomass to biofuels. The form called cellulose II, which researchers had already studied how has improved properties for use amines affect the naturally occurring in textiles. It turns out that, like crystal forms of cellulose, called cellulose I, cellulose II can also cellulose I. During the course of be converted into cellulose III their studies, the team found that by treatment with amines. As the the amines turned the cellulose into plot thickened, the research group

66 A rgonne National Laboratory biocat_biomacro_10_302_DRFT.doc Structural Biology

> M.W. was supported by a Grant-in-Aid for Scientific Research (18780131). This study was partly funded by the French Agence Nationale de la Recherche. P.L. was supported in part by the Office of Biological and Environmental Research of the Department of Energy, a grant from the National Institute of Medical Sciences of the National Institutes of Health (1R01GM071939-01), and a Laboratory Directed Research and Development grant from Los Alamos National Laboratory (20080001DR).

Use of the Advanced Photon Source is supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, under Contract No. DE-AC02-06CH11357. < Fig. 1 Color palette figure showing See > Masahisa Wada1, Laurent x-ray data collected at the NE-CAT Heux2, Yoshiharu Nishiyama2, beamline from fiber samples of and Paul Langan3*, “X-ray cellulose that have been converted Crystallographic, Scanning > 18-ID • Bio-CAT • Life science •

into cellulose IIIII. Microprobe X-ray Diffraction, Fiber diffraction, microdiffraction, and Cross-Polarized/Magic Angle microfluorescence (hard x-ray), micro x-ray absorption fine Spinning 13C NMR Studies of structure, small-angle x-ray the Structure of Cellulose IIIII” scattering, time-resolved x-ray Biomacromolecules 10(2), 302 scattering • 3.3-cm Undulator A (2009). DOI: 10.1021/bm8010227 • Accepting general users > 24-ID-E • NE-CAT • Life science Author affiliations > • Macromolecular crystallography, 1The University of Tokyo, 2CNRS, microdiffraction, microbeam, single-crystal diffraction, single- 3 Los Alamos National Laboratory wavelength anomalous dispersion • 3.3-cm Undulator A • Accepting Correspondence > general users *[email protected]

The Advanced Photon Source Annual Science Report 2009 67 Structural Biology

Visualizing an ATP-Gated Ion Channel

> Fig. 1 Architecture of the P2X receptors IN SHORT > It is almost always referred to as ATP, not by its showing subunit folds and dolphin- complete name of adenosine triphosphate, and usually in the like shape, grey bars indicate inner context of carrying cellular energy. But ATP has of late been (in) and outer (out) leaflets of the popping up in other, seemingly unrelated contexts. One such membrane bilayer. case is that of extracellular signalling for sensory and vascular functions, where an ATP-gated receptor known as P2X has been identified. Though dysfunctional P2X receptors have Further structural details been implicated in cancer and inflammatory, cardiovascular, showed an hourglass shape for the and neuronal diseases, high-resolution structural data have transmembrane region, which is not been available until now. With the help of the NE-CAT made of six helices, two from each of the receptors subunits. Looking at beamline 24-ID-E at the APS, and Advanced Light Source how the subunits themselves beamlines 5.0.2, 8.2.1, and 8.2.2 at Lawrence Berkeley are constructed, the research team National Laboratory, researchers have produced, in exquisite found a dolphin-like shape, where detail, crystal structures for an ATP-gated P2X ion channel the transmembrane helices would in a closed, resting state. Their work shows how ATP could be the flukes and the extracellular help in opening a closed channel and provides important region analogous to the upper body new details about how a system malfunction could lead (Fig. 1). Attached to the body are the head region and three additional to disease. domains: the dorsal fin, left flipper, and right flipper. Extending the dolphin analogy, the team identified three major subunit interfaces: body-to-body, head-to-body, and MORE > The research team from that is shaped like a chalice and has left flipper-to-dorsal fin. These data the Vollum Institute and the Oregon three subunits. The ways in which led the researchers to postulate that Health and Science University the subunits are knit together is the subunit interactions, especially started out in somewhat unknown critical to proper functioning of head-to-body and left flipper-to- territory: P2X receptors are not the channel gates and receptor dorsal fin, are important in receptor related to other ion channel proteins assembly. Extracellular regions of function. Support for this hypothesis of known structure, so it was not the receptor, with their multiple comes from experiments on another

possible to predict either structural b-strands, provide acidic regions receptor (P2X3), where a single details or possible mechanisms that are important to attracting the mutation in the left flipper slowed for opening and closing of the ion right ions to the gate. In the pore the receptor desensitization rate. channel. Their studies focused on that crosses the cell membrane, Perhaps the most surprising obtaining crystal structures for the a gate-like area is formed with a aspect of the team’s results lies in

zebrafish P2X4 receptor in its closed, protein slab. And the fine level of predicting an unusual binding mode resting state. What they revealed is detail at which the team was able and function for ATP. By binding an architecturally beautiful structure to visualize the structure allowed where proposed—at three sites that them to identify three unusual would be look like an open jaw ATP-binding sites between the of the dolphin—ATP would play receptor’s subunits. The location of an important role in changing the the ATP binding sites suggests that molecular shape of the receptor ATP is important in mediating the and allowing the ion channel to rearrangement necessary for opening change state. If the proposed model the closed gate. is correct, the ATP molecule would

68 A rgonne National Laboratory Structural Biology

See > Toshimitsu Kawate1,2, Jennifer Carlisle Michel1,2, William T. Birdsong1,2, and Eric Gouaux1,2,3*, “Crystal structure of the ATP-gated P2X4 ion channel in the closed state,” Nature 460, 592 (30 July 2009). DOI:10.1038/nature08198

Author affiliations > 1Vollum Institute, 2Oregon Health and Science University, 3Howard Hughes Medical Institute

Correspondence > *[email protected]

See also > “Structural biology: Trimeric ion-channel design,” by Shai D. Silberberg and Kenton J. Swartz, Nature News and Views, Nature 460, 580 (30 July 2009). DOI:10.1038/460580a;

> This work was supported by the National Institutes of Health (NIH) and the American Asthma Foundation. E.G. is an investigator with the Howard Hughes Medical Institute. Use of the Advanced Photon Source at Argonne National Laboratory was supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, under Contract No. DE-AC02-06CH11357. cause the head, right flipper, and proposed model for how ATP, in an dorsal fin to close the jaws, and unusual role, can mediate opening by doing so, start the cascade of the channel. Their work provides > 24-ID-E • NE-CAT • Life science changes leading to the opening important foundations for continued • Macromolecular crystallography, of the gate. studied, especially when considering microdiffraction, microbeam, single-crystal diffraction, single- Along with a previously the role of dysfunctional P2X wavelength anomalous dispersion unknown structure for a P2X ion receptors in disease. • 3.3-cm Undulator A • Accepting channel, the research team has general users provided intriguing details and a — Mona Mort

The Advanced Photon Source Annual Science Report 2009 69 Structural Biology

Secrets of the Lacewing’s Silk

in protein folding. These misfolded IN SHORT > Green lacewings (Chrysopidae) are beneficial proteins can aggregate to form the insects well known to naturalists and scientists for their many amyloid plaques that characterize elegant solutions to life’s problems, such as how to eat without neurodegenerative diseases such as Alzheimer’s and Parkinson’s. being eaten. The larvae of many species adopt a wolf-in- Accordingly, cross-beta structures sheep’s-clothing strategy when feeding upon their major prey are of great interest to researchers item, aphids. They cover themselves with either the tufted wax in diverse fields. exudate or the spent carcasses of their prey in order to escape The CSIRO researchers detection by honeydew-feeding ants, which normally attack identified and sequenced two intruders in their aphid herds. The adult female protects silk genes, which they named her eggs from detection and predation (especially by ants) MalXB1 and MalXB2. These genes are expressed in adult female M. by suspending each egg at the end of a fine strand of silk signata only, not in males or larvae, (top figure, next page). Utilizing the high-flux ChemMatCARS confirming that the silk of lacewing 15-ID beamline at the APS, researchers from Australia’s cocoons is composed of different Commonwealth Scientific and Industrial Research Organisation proteins. Over 70% of each protein (CSIRO) recently completed studies that confirm the elegant is composed of repeating 16-residue and unique structure of the lacewing’s silken egg stalk. The motifs, suggesting a high level of crystallinity. Based on their data, the information they obtained suggests that lacewing silk may have CSIRO researchers propose that the potential value as a biomaterial. cross-beta structure is made up of 8-residue crystallite strands stacked perpendicular to the direction of the fiber. As the lacewing female draws the liquid silk into a strand, a network of cysteine cross links are MORE > Lacewing egg stalk silk that encode the silk proteins and created that result in rapid hardening is based on completely different developing a more detailed model of the stalk. design principles to the well-known of the structure. The cross-beta structure silks of domesticated silkworms The researchers used wide- accounts for the remarkable or spider webs. The lacewing angle x-ray scattering at the extensibility of the egg stalk silk, silk evolved to function as a rigid ChemMatCARS facility to obtain which can be stretched to nearly support column, rather than a long detailed information about the 500% of its length before breaking. flexible thread. Its protein sequence protein structure of a single silk Its bending rigidity, achieved by and structure are unique. fiber. Since the tiny egg stalks cysteine cross linking, is almost The scientists studied Mallada are only 3-mm long and 15 µm three times greater than that of signata, a species of green lacewing in diameter, they couldn’t have silkworm fibers. These properties, native to Australia. A half-century obtained clear data anywhere except along with reasonable tensile earlier, classic protein structural at a high-flux third-generation strength and the relative simplicity studies had reported on the unusual synchrotron source. of its production, suggest lacewing cross-beta sheet structure of the Functional proteins with a silk may have potential value as silk of another green lacewing cross-beta structure are rare in a biomaterial. species, Chrysopa flava. The CSIRO nature and appear to be limited to researchers were able to apply the extruded products such as arthropod — Carol Hart technological advances of recent silks. Within a cellular environment, decades to identifying the genes cross-beta structures occur as errors

70 A rgonne National Laboratory Structural Biology

See > Sarah Weisman1, Shoko Okada1, Stephen T. Mudie2, Mickey G. Huson2, Holly E. Trueman1, Alagacone Sriskantha1, Victoria S. Haritos1, and Tara D. Sutherland1*, “Fifty Years Later: The Sequence, Structure and Function of Lacewing Cross-Beta Silk,” J. Struct. Biol. 168, 467 (2009). DOI: 10.1016/j. jsb.2009.07.002

Author affiliations > 1CSIRO Entomology, 2CSIRO Material Science and Engineering

Correspondence > *[email protected]

> This work was financially supported by the Grains Research and Development Corporation. Use of ChemMatCARS Sector 15 at the Advanced Photon Source was supported by the Australian Synchrotron Research Program, which is funded by the Commonwealth of Australia under the Major National Research Facilities Program. ChemMatCARS Sector 15 is principally supported by the National Science Foundation/Department of Energy under Grant No. CHE-0535644.

Use of the Advanced Photon Source is supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, under Contract No. DE-AC02-06CH11357. < Fig. 1 Top: In laying her eggs, the female green lacewing first secretes a drop of liquid silk onto a stem or leaf, then stretches the silk out into a fine strand as she lifts her > 15-ID • ChemMatCARS • Chemistry, materials science • abdomen from the substrate. A few seconds later, she deposits an egg on the tip of Anomalous and resonant scattering the stalk. Then she repositions herself to repeat the process for subsequent eggs. (hard x-ray), liquid scattering, The eggs are effectively removed from the search paths of most likely predators. microdiffraction, single-crystal Moreover, the separation of the eggs reduces the risk of brood cannibalism, which diffraction, small-angle x-ray scattering, surface diffraction, can occur when eggs are deposited in clusters. Lacewing . Bottom: (Chrysopa perla) wide-angle x-ray scattering (Top image: the authors. Bottom image: Quartl, Wikimedia Commons, http://commons. • 3.3-cm Undulator A • Accepting wikimedia.org/wiki/File:Chrysopa_perla_Goldauge_seite.jpg) general users

The Advanced Photon Source Annual Science Report 2009 71 Structural Biology

Visualizing the HIV Capsid

forming three distinct interfaces IN SHORT > In mature infective human immunodeficiency with the domains of adjacent virus (HIV) particles, the capsid (CA) protein forms a shell proteins: the NTD-NTD interface that packages and organizes the virus replication complex. that creates the symmetric hexameric The capsid of HIV (and of retroviruses in general) is a rings, a CTD-CTD interface that self-assembling, highly variable lattice of hexagonal and links neighboring hexamers, and an intermolecular NTD-CTD interface pentagonal rings of CA protein. Previous work with electron that reinforces the hexamer. cryomicroscopy had established the lattice architecture of the The first three helices of capsid to a resolution of about 9 Å. Using x-ray beamlines CA make the symmetric 6-fold at two U.S. Department of Energy synchrotron light source NTD-NTD interactions, which form facilities, researchers succeeded in visualizing the hexagonal a loose barrel at the center of the units of the HIV capsid to the atomic level (2 Å). Their hexamer. Despite the presence of a findings may advance work on capsid assembly inhibitors as small hydrophobic core, much of this interface is mediated by interactions a new class of antiretroviral agents to augment existing highly with water molecules, with hydrogen active antiretroviral therapy regimens for treating HIV. bridge bonds between hydrophilic side chain and backbone atoms. Water interactions are also present in the NTD-CTD interface. Every helix in the NTD-CTD interface has a flexible side chain that extends MORE > The HIV capsid utilizes electron cryomicroscopy studies, to form a cap for a helix in the about 1,500 copies of CA protein the researchers in this study, from other domain. These caps may to form a variably curved cone made The Scripps Research Institute, serve as pivot points for producing up of six-sided rings (hexamers) the University of Utah School the varying degrees of surface with five-sided rings (pentamers) of Medicine, the Scripps Clinic, curvature of the conical capsid. The capping the two ends of the and University of Virginia Health water interactions at the NTD-NTD cone (Fig. 1). Each capsid has a System, engineered CA hexamers interface may facilitate alternate variable number of hexameric units that were stable enough to grow packing as pentamers rather (approximately 250) and exactly crystals. X-ray crystallography than hexamers. 12 pentamers, 7 at the broad end, at SER-CAT beamline 22-BM The atomic detail of their x-ray and 5 at the narrow end of the at the APS, and at the Stanford structures allowed the researchers conical structure. The CA protein Synchrotron Radiation Lightsource to analyze the precise mechanisms folds primarily into helices beamline 7-1 revealed that the and targets of two capsid assembly with two independent, flexibly CA hexamer is composed of two inhibitors currently in development, linked domains: an N-terminal concentric rings, with six NTDs the small molecules CAP-1 and domain (NTD) and a C-terminal forming a relatively rigid inner ring CA-I, both of which act at the domain (CTD). and with the CTDs arranged in a NTD-CTD interface. Knowing The flexible link between more mobile outer ring. The mobility the molecular structures of the two CA domains, coupled of this outer ring permits the variable the hexameric interfaces will with the natural variability in the curvature needed for the capsid to undoubtedly aid in the design of curvature of the capsids, made it assume its conical form. novel capsid assembly inhibitors, challenging to grow stable crystals The two CA domains maintain a new and potentially very valuable of a complete hexagonal array. their independence in the assembled class of HIV therapeutics. Guided by a model of the hexameric hexamer, interacting minimally CA lattice developed from their within the individual protein but — Carol Hart

72 A rgonne National Laboratory Structural Biology

> Fig. 1 A fullerene cone model for the HIV-1 capsid (in light purple). The inset shows one hexamer surrounded by six others, and illustrates the clear functional delineation of the NTD and CTD. The NTD (colored orange) forms the hexameric rings, and the CTD (purple) connects each ring to its six neighbors.

See > Owen Pornillos1,4, Barbie K. Ganser-Pornillos1,4, Brian N. Kelly2, Yuanzi Hua1, Frank G. Whitby2, C. David Stout1, Wesley I. Sundquist2, Christopher P. Hill2, and Mark Yeager1,3,4*, “X-Ray Structures of the Hexameric Building Block of the HIV Capsid,” Cell 137, 1282 (June 26, 2009). DOI:10.1016/j. cell.2009.04.063 > This study was funded by National Institute of Health grants R01-GM066087 Author affiliations > (M.Y.) and P50-GM082545 (M.Y., C.P.H., 1The Scripps Research Institute, and W.I.S.). B.G.-P. was supported 2 by a postdoctoral fellowship from the University of Utah School George E. Hewitt Foundation for Medical of Medicine, 3Scripps Clinic, Research. Use of the Advanced Photon > 22-BM • SER-CAT • Life science 4 University of Virginia Health System Source at Argonne National Laboratory • Macromolecular crystallography was supported by the U.S. Department of • Bending magnet • Accepting Energy, Office of Science, Office of Basic general users Correspondence > Energy Sciences, under Contract No. *[email protected] DE-AC02-06CH11357.

The Advanced Photon Source Annual Science Report 2009 73 Structural Biology

A Potent Antibody against Influenza

predominating in the stalk and the IN SHORT > The initial shortage of vaccine against the three globular HA1 subunits forming 2009 pandemic H1N1 swine flu highlights the difficulty the spike head. The globular HA1 of forecasting and combating influenza outbreaks. In the subunits are responsible for attaching last century, three influenza pandemics—the 1918 Spanish to the host cell membrane. The fusion mechanism resides in the flu (H1N1), the 1957 Asian flu (H2N2), and the 1968 Hong HA2 subunits, which each contain Kong flu (H3N2)—were responsible for an estimated 50 a large CD helix and a shorter A to 100 million deaths worldwide. Because the influenza A helix. Exposure to low pH following virus readily mutates to escape immune system recognition, endocytosis triggers a conformational prevention has relied on inactivated or attenuated virus change in HA that results in fusion of vaccines that must be reformulated annually based on the viral and cellular membranes. surveillance to predict the seasonally prevalent subtypes. Analysis of the crystals revealed three antibodies bound Now a team of researchers from the Scripps Research Institute to each HA trimer. CR6261 binds and the Dutch biopharmaceutical company Crucell have primarily to the short A helix of discovered a neutralizing antibody with broad efficacy against the HA2 stalk, close to the viral multiple strains of influenza virus. Antibody-antigen crystals membrane. Comparison of the two imaged at the GM/CA-CAT 23-ID-B beamline at the APS crystals confirmed that this site demonstrated that the antibody targets a highly conserved constitutes 70% of the epitope in portion of the influenza A virus. This discovery will guide both H1 and H5 HAs. Other binding contacts, including those to residues ongoing research to develop a long-lasting, cross-protective of the HA1 subunit, also play a role vaccine as well as new antibody-based therapies. in virus neutralization. Review of a large database of influenza HA sequences confirmed that the A helix is highly conserved in all influenza A viruses. The conservation of this epitope suggests MORE > Influenza A virus antibodies capable of neutralizing it plays a critical role in membrane evades immune system targeting recombinant H5 avian influenza fusion. The researchers propose that by accumulating point mutations virus. To determine the antibody’s epitope binding by CR6261 freezes in its two integral membrane epitope (binding site) on HA, the HA in its prefusion conformation, proteins, hemagglutinin (HA) and researchers crystallized the fragment thus preventing the pH-induced neuraminidase. There are at least 16 antigen–binding region (Fab) of the conformational changes in the HA subtypes, designated H1 through antibody in complex with HAs from endosomal compartments that allow H16. HA is responsible for host cell the human 1918 H1N1 pandemic the virus to infect the host cell. attachment and membrane fusion virus and from a highly pathogenic Most neutralizing antibodies and is the primary target (antigen) avian H5N1 virus. The crystals against influenza HA target the of neutralizing antibodies. However, were imaged to 2.2-Å and 2.7-Å hypervariable regions of the HA1 the variability of the protein means resolution, respectively. globular domain that surround the that new viral strains may not be Influenza HA has two subunits, receptor binding site. By targeting a recognized by antibodies to previous HA1 and HA2, and is assembled crucial, conserved region associated infections. as a trimer. The mature protein with the HA2 fusion machinery, The CR6261 antibody projects from the viral membrane CR6261 is able to neutralize the was identified by using phage in a spike-shaped structure, with viruses from about half of the 16 display technology to screen for the three helical HA2 subunits HA subtypes. Identification of the

74 A rgonne National Laboratory Structural Biology

< Fig. 1 Structure of the broadly neutralizing antibody CR6261 bound to an H5 avian influenza hemagglutinin. A trimeric hemagglutinin spike is represented as a molecular surface, with one HA1 subunit highlighted in magenta and an HA2 subunit highlighted in cyan. As depicted, the surface of the virus would be located at the bottom edge of the hemagglutinin, while attachment to a target cell would occur at the top. Antibody CR6261 (ribbon representation, colored red and blue) recognizes a conserved epitope in the bottom half of the hemagglutinin molecule, near the viral membrane, preventing membrane fusion.

CR6261 epitope provides a research lead of enormous importance for the development of a durable vaccine against influenza A and for the design of better antiviral agents.

— Carol Hart

See > Damian C. Ekiert1, Gira > This work was supported in part Bhabha1, Marc-André Elsliger1, Robert by National Institutes of Health grant 2 2 AI-058113 (I.A.W.) and a predoctoral H.E. Friesen , Mandy Jongeneelen , fellowship from the Achievement Rewards Mark Throsby2, Jaap Goudsmit2, and for College Scientists Foundation (D.C.E.) Ian A. Wilson1*, “Antibody Recognition and the Skaggs Institute. The Joint of a Highly Conserved Influenza Virus Center for Structural Genomics (JCSG) is supported by NIH National Institute Epitope,” Science 324, 246 (10 April of General Medical Sciences (NIGMS) 2009). DOI: 10.1126/science.1171491 (U54GM074898). The GM/CA CAT 23-ID- > 23-ID-B • GM/CA-CAT • B beamline is funded in whole or in part Life science • Microbeam, with federal funds from National Cancer macromolecular crystallography, Author affiliations > Institute (Y1-CO-1020) and NIGMS (Y1- 1 microdiffraction, anomalous The Scripps Research Institute, GM-1104). Use of the Advanced Photon diffraction (MAD/SAD), subatomic 2Crucell Holland BV Source at Argonne National Laboratory (<0.85 Å) resolution • 3.3-cm was supported by the U.S. Department of Undulator A • Accepting Energy, Office of Science, Office of Basic general users Correspondence > Energy Sciences, under Contract no. *[email protected] DE-AC02-06CH11357.

The Advanced Photon Source Annual Science Report 2009 75 Structural Biology

How Get3 Moves Tail-Anchored Proteins to Their Destination

are striking differences between IN SHORT > Within every cell, newly synthesized proteins the two configurations. In the closed state, Get3 displays an must be sorted and directed to the correct cellular destination. enormous hydrophobic groove Most membrane and secretory proteins are targeted to the (~30 × 15 × 15 Å), while in the endoplasmic reticulum (ER) early in the translation process open, unbound state, the groove’s by a cytosolic signal recognition particle (SRP) that binds to hydrophobic surfaces are buried. an identifying sequence near the N terminal of the protein as A single zinc ion within the interface it emerges from the ribosome. But some membrane proteins acts as a hinge to stabilize the two conformations. cannot be directed to the ER by SRP because their recognition TA protein recognition is site is at the C terminal tail and does not emerge from the TMD dependent: all the targeting ribosome until translation is complete. These proteins are information is contained within the characterized by a single transmembrane domain (TMD) near hydrophobic tail of these proteins. the C terminal that anchors them in the membrane, with the To enable efficient binding, the functional N terminal end positioned in the cytosol, and are recognition site would need to be hydrophobic as well (i.e., non-polar thereby known as tail-anchored (TA) membrane proteins. or neutral). Both the crystallographic Important members of the TA protein class include the SNARE analysis and functional studies of proteins, which traffic vesicles within the cell, and the Bcl-2 site-directed mutants indicate that the family of apoptosis regulators. The mechanism for targeting hydrophobic groove that is exposed TA proteins is not as well understood as the SRP pathway, in the ATP-bound state of Get3 forms but it is known to be powered by hydrolysis of the nucleotide the TMD binding site. The non-polar character of the groove is retained adenosine triphosphate (ATP). Recent studies identified in TRC40/Get3 homologues, as are TRC40/Get3, a highly conserved ATPase, as a central player two other key structures in the Get3 in transporting TA proteins from the cytosol to the ER. Using homodimer: 1) a 20-residue insertion the LS-CAT beamline 21-ID-G and GM/CA-CAT beamline in the α-helical subdomains that 23-ID-D at the APS, a team of researchers have investigated may function as a dynamic lid for crystal structures of this ATPase and proposed a coherent shielding the binding site, and 2) a switching mechanism within the ATP account of its function in TA protein recognition and transport. binding site. This switch is thought to relay structural changes induced by ATP binding and its subsequent hydrolysis to the dimer interface and the TA binding site. In the model developed by the MORE > Working with Get3, the (nucleotide free) and closed researchers, ATP binding drivesGet3 yeast homologue of mammalian (ADP x AIF4- bound), with the toward the closed conformation, TRC40, the researchers, from The latter simulating the ATP-bound facilitating recognition of newly University of Chicago, the National state (Fig. 1). In both states, synthesized TA membrane proteins Institutes of Health, the University Get3 forms a symmetric homodimer within the hydrophobic groove. The of Wroclaw, and Jagiellonian in which the monomers consist Get3-TA protein complex is then University crystallized the protein of a core ATPase subdomain and targeted to the ER by an interaction in two configurations: open an α-helical subdomain. But there with other members of the Get

76 A rgonne National Laboratory Structural Biology < Fig. 1 Structure of yeast Get3 in “open” (left) and “closed” (right; bound to ADP-AlF4-) dimer conformations. Each monomer comprises a core ATPase subdomain (blue, green) and an α-helical subdomain (magenta, yellow). Juxtaposition of the α-helical subdomains in the closed conformation (right) creates a large hydrophobic groove suitable for binding to a tail-anchored membrane protein substrate. > This work was supported by a grant from the Edward Mallinckrodt, Jr. Foundation (to R.J.K.) and by the Intramural Research Program of the National Institutes of Health (to R.S.H.). Use of the Advanced Photon Source at Argonne National family, the membrane-bound See > Agnieszka Mateja1, Anna Laboratory was supported by the U.S. Department of Energy, Office of Science, 1,3 1 Get1/2. After ATP hydrolysis, Szlachcic , Maureen E. Downing , Office of Basic Energy Sciences, under conformational changes in the Malgorzata Dobosz1,4, Malaiyalam Contract No. DE-AC02-06CH11357. conserved switching mechanism Mariappan2, Ramanujan S. Hegde2, destabilize the groove, releasing the and Robert J. Keenan1*, “The TA protein for membrane insertion. structural basis of tail-anchored Disruption of the closed dimer also membrane protein recognition releases Get3 from the membrane by Get3,” Nature 461, 361 (17 > 21-ID-G • LS-CAT • Life science and switches it to the open September 2009). DOI:10.1038/ • Macromolecular crystallography, anomalous diffraction (MAD/SAD) configuration, whereupon it returns nature08319 • U33S undulator • Accepting to the cytosol, ready for another general users round of TA protein targeting. Author affiliations > > 23-ID-D • GM/CA-CAT • 1 The University of Chicago, Life science • Macromolecular — Carol Hart 2National Institutes of Health, crystallography, microbeam, 3University of Wroclaw, microdiffraction, anomalous 4 diffraction (MAD/SAD), subatomic Jagiellonian University (<0.85 Å) resolution • 3.0-cm undulator • Accepting general Correspondence > users *[email protected]

The Advanced Photon Source Annual Science Report 2009 77 Structural Biology

Closing in on a Common Cancer Mutation

shift has not been reported in studies IN SHORT > Phosphoinositide 3-kinases (PI3Ks) are a of wortmannin binding to p110γ. family of signal transduction enzymes that participate in Although wortmannin itself is both regulating cellular proliferation and survival in all tissue unstable and toxic, derivatives are currently being investigated types. Mutational activation of PI3Ks is implicated in many as potential cancer therapeutics. cancers, including those of the breast, colon, uterus, stomach, The discovery of these distinct and ovary. The oncogene PIK3CA, which encodes the conformational changes may offer p110α subunit of PI3Kα, is one of the two most commonly new leads for the development of mutated genes in human tumors. Using data collected at more tolerable inhibitors that are specific to a PI3Kα isoform. the LRL-CAT 31-ID beamline at the APS, researchers from In the crystal structure of The Johns Hopkins University have uncovered the atomic the p85α-p110α, the N-terminal SH2 structure and probable mechanism of the most common domain of p85α serves as a broad oncogenic mutant of PIK3CA. Their research offers direction scaffold for the enzyme complex, to ongoing research efforts to design targeted PI3K inhibitors interacting with four distinct domains: the inter-SH2 domain of for the treatment of cancer. p85α, as well as three of p110α’s five domains: the C2, helical, and kinase domains (Fig. 1). The N-terminal SH2 domain is thus well positioned to transmit signals from bound phosphopeptides to other domains MORE > PI3Ks produce lipid domains that interact with other within the complex. Analysis of the secondary messengers that serve as signaling proteins, including two structure confirms the suspected membrane docking sites for effector SH2 domains, which typically oncogenic mechanism of two other proteins. They are heterodimers bind phosphopeptides. The region hotspot PIK3CA mutations that occur consisting of a p110 catalytic between these two SH2 domains, in the helical domain; by interfering subunit bound to a p85 regulatory called the inter-SH2 domain, with N-terminal SH2 binding to subunit. The mutation in p110α interacts with the catalytic p110 p110α, these mutations release the that was studied has an amino acid subunit. The researchers compared catalytic subunit from regulatory substitution in the kinase domain the crystal structures of wild-type inhibition by p85α. (an arginine for a histidine at residue and mutant p110α in complex with Oncogenic mutations in 1047) that results in a twofold the two interacting domains of p85α other kinases typically increase increase in lipid kinase activity. (the inter-SH2 and the N-terminal activity by locking the kinase Of over 1,500 known cancer- SH2), both free and bound to activation loop into an active related mutations in PIK3CA, wortmannin, a nonspecific PI3K conformation or by destabilizing the the His1047Arg mutation is the inhibitor. inactive conformation. However, the most common. Wortmannin binds the mutant Arg1047 is positioned further The regulatory p85 p110α kinase domain at the ATP from the activation loop than the subunit includes several modular binding site in a pocket that is His1047 of the wild-type enzyme. largely conserved between p110α Instead, Arg1047 points toward the and another well-studied isoform, cell membrane and causes two other p110γ. Upon binding to wortmannin, loops to change their conformation, the mutant p110α underwent a bringing them into contact with the conformational shift in a kinase membrane. The researchers therefore domain loop. This conformational propose that the His1047Arg

78 A rgonne National Laboratory Structural Biology

See > Diana Mandelker1, Sandra B. Gabelli2*, Oleg Schmidt-Kittler1, Jiuxiang Zhu1, Ian Cheong1, Chuan-Hsiang Huang2, Kenneth W. Kinzler1, Bert Vogelstein1, and L. Mario Amzel2, “A frequent kinase domain mutation that changes the interaction between PI3Kα and the membrane,” Proc. Nat. Acad. Sci. USA 106, 16996 (October 6, 2009). DOI:10.1073_pnas.0908444106

Author affiliations > 1Johns Hopkins Kimmel Cancer Center, 2Johns Hopkins University School of Medicine

Correspondence > *[email protected]

> Use of the LRL-CAT beamline was provided by Eli Lilly & Company, which

< operates the facility. Support for this Fig. 1 Effects of the oncogenic His1047Arg mutation on the structure of the PI3Kα. research was provided by the Virginia and Ribbon diagram of the inter-SH2 domain (gold, coiled coil) and the N-terminal D.K. Ludwig Fund for Cancer Research SH2 domain (gold, α plus β-fold) of the regulatory p85α subunit in complex with and National Institutes of Health Grants the five domains of p110α: the adaptor-binding domain (blue), the Ras-binding CA43460, GM07309, and GM07184. domain (red), the C2 domain (purple), the helical domain (green) and the catalytic Use of the Advanced Photon Source was supported by the U.S. Department of kinase domain (cyan). The two loops of the kinase domain (residues 864-874 Energy, Office of Science, Office of Basic and 1050-1062) that change conformation in the mutant enzyme and contact the Energy Sciences, under Contract No. cell membrane are at the forefront. DE-AC02-06CH11357.

> 31-ID • LRL-CAT • Life science • mutation changes the interaction mechanism for mutational activation Macromolecular crystallography, with the cell membrane in such a of a kinase that may well offer single-crystal diffraction, fiber diffraction, single-wavelength way as to increase substrate access further direction for the development anomalous dispersion • 3.3-cm to the kinase binding site, thereby of targeted therapeutics. Undulator A • Accepting general increasing the signaling along users oncogenic pathways. This is a novel — Carol Hart

The Advanced Photon Source Annual Science Report 2009 79 Structural Biology

Toxin-Spewing Bacteria Take a Page from Viruses

IN SHORT > New research performed at the APS confirms a suspected link between a virus that infects bacteria and a system many bacteria use to inject toxins into their host. Researchers solved the three-dimensional structure of a key protein in the type VI secretion system (T6SS) found in bacteria that cause cholera and other diseases. The finding confirms the suspicion that the protein shares the same needle- like structure as the tip complex of the virus T4, which uses the tip to puncture bacteria and infect them with its DNA. < MORE > Many infectious bacteria the T6SS and found corresponding Fig. 1 Schematic structure of the E. coli cause disease by secreting toxic genes in a full one-quarter of a VgrG-1 protein (left), part of a system proteins into or around the cells of group of pathogenic bacteria that for injecting toxin into host cells, their host. Before 2006, biologists includes Salmonella, E. coli, and next to the needle complex (right) of knew of five bacterial systems Pseudomonas aeruginosa, which T4 bacteriophage, a virus that infects for secreting proteins. That year, infects people with cystic fibrosis. bacteria. The close match implies researchers working in the lab of An analysis of the amino a common function: puncturing John Mekalanos, a microbiologist acid sequence of one of those host cells. and molecular geneticist at Harvard proteins, VgrG-1, immediately Medical School, discovered a sixth suggested a mechanism by which mechanism—the type six secretion T6SS might inject toxin into host system (T6SS)—in a strain of Vibrio cells. The sequence was similar to E. coli. At the base of T4’s cylindrical cholerae. The team identified 15 to 20 that of a protein complex found in body is a spike made of two proteins, protein-coding genes responsible for bacteriophage T4, a virus that infects gp5 and gp27, which the virus uses to

80 A rgonne National Laboratory Structural Biology pierce the outer membrane of a host it corresponds to a part of T4 that the T6SS suggests that bacteria cell and inject its DNA through an attaches to the needle-tip (Fig. 2), might have picked up tricks from opening in the needle tip. Similarly, suggesting that Hcp binds to VgrG-1. viruses, too. a bacterium wielding the T6SS might The researchers found that extend a spike into a host cell and when Hcp proteins are concentrated — JR Minkel inject toxin inside. in solution, they appear to stack To find out if the protein together into elongated tubes. They structures matched, the researchers propose that the T6SS pumps Hcp See > Petr G. Leiman1,§, Marek from Purdue University, the and VgrG proteins into the space Basler2, Udupi A. Ramagopa3, Harvard Medical School, the Albert between a bacterium’s two outer Jeffrey B. Bonanno3, J. Michael Einstein College of Medicine, the envelopes, where Hcp proteins stack Sauder4, Stefan Pukatzki5, Stephen K. University of Alberta, and SGX together into a tube with a VgrG Burley4, Steven C. Almo3, and Pharmaceuticals, Inc., isolated needle at the tip. This sharp tube John J. Mekalanos2,*, “Type VI VgrG-1 from an E. coli strain that would project through the outer secretion apparatus and phagetail- infects the urinary tract. Then they membrane of the bacterium and into associated protein complexes share crystallized it and measured its x-ray the host, perhaps driven by the force a common evolutionary origin,” diffraction pattern using the LRL- of Hcp donuts assembling together. Proc. Nat. Acad. Sci. USA CAT facility at APS sector 31-ID. The needle tip might be toxic itself, 106(11), 4154 (March 17, 2009). As predicted, the structure of VgrG-1 or the tube might serve as a conduit DOI:10.1073/pnas.0813360106 is nearly identical to that of the for other toxins. T4 gp5-gp27 complex (Fig. 1). The T6SS is not the first Author affiliations > In previous work, the group bacterial secretion system to have 1Purdue University; 2Harvard Medical solved the structure of a second T6SS seemingly been plucked from School; 3Albert Einstein College of protein called Hcp, isolated from another organism. Yersinia pestis, Medicine; 4SGX Pharmaceuticals, P. aeruginosa. The protein formed the bacterium that causes bubonic Inc.; 5University of Alberta a donut shape containing a hole big plague, injects toxin into host cells §Present address: École Polytechnique enough around for a stretched-out using protein machinery derived Fédérale de Lausanne protein to pass through. In the new from the flagellum, the whip-like study, the researchers took a second structure some bacteria use to propel Correspondence > look at the structure and found that themselves. The existence of *[email protected]

> Work in J.J.M.’s laboratory on Type VI secretion has been supported by Grant AI-18045 and AI-26289 from the National Institutes of Allergy and Infectious Disease. P.G.L.’s work in Michael Rossmann’s laboratory is supported by the National Science Foundation grant MCB-0443899. M.B. was supported by EMBO fellowship ALTF 350-2008. Use of the Advanced Photon Source at Argonne National Laboratory was supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, under Contract No. DE-AC02-06CH11357.

> 31-ID • LRL-CAT • Life science • Macromolecular crystallography, single-crystal diffraction, fiber diffraction, single-wavelength < Fig. 2 Structure of the toxin secretion protein Hcp1 (red and blue) superimposed on the anomalous dispersion • 3.3-cm gp27 protein (light blue) of T4 virus. Hcp1 corresponds to the so-called tube-like Undulator A • Accepting general users domain of gp27, which is structurally similar to a second T4 protein that composes the virus’s tube, suggesting that Hcp1 has the potential to form tubes.

The Advanced Photon Source Annual Science Report 2009 81 Structural Biology

How a Gate, Latch, and Lock Activate a Plant Hormone

The hormone is useless without a like before and after photos, the IN SHORT > Researchers receptor to recognize it and transfer researchers used these two structures have figured out the its message to the rest of the cell. to determine what happens after structure of a protein The importance of this process is the receptor binds to its hormone. that allows a key plant such that, of 14 ABA receptors According to the group’s report, the hormone to regulate isolated from the same species receptor forms a pocket shaped such growth and development. of plant, all of them share certain that ABA can enter inside. When The hormone, called amino acids, which implies they all that happens, a pair of protein wings abscisic acid (ABA), work in the same way in a highly flanking the entrance close together redundant manner. In the study, like a gate and latch (Fig. 1). These triggers a cascade of based on research at the LS-CAT wings are made of nearly identical chemical reactions that 21-ID-D and 21-ID-F beamlines, amino acids in other receptors, which allows plants to adapt to the researchers from the Van Andel suggest they all work the same way. conditions of drought, Research Institute; the National cold, and high salt. Less University of Singapore; the clear were the molecular University of California, Riverside; details that allow ABA to the Medical College of Wisconsin;

King Abdullah University of Science < Fig. 1 Image of the receptor PYL2 exert its effects. In a study and Technology; and the National (turquoise) bound to abscisic acid derived from work on two Center for Plant Gene Research (white and red) and to the enzyme LS-CAT beamlines at the (China) purified a receptor called HAB1 (yellow-green). The gate loop APS, researchers reported PYL2 from the lab plant Arabidopsis (pink) and latch loop (gold) regions the first three-dimensional that was amenable to crystallization, of PYL2 enclose abscisic acid and structure of ABA bound and therefore x-ray crystallography, present a face to which HAB1 can to determine the plant’s atomic bind. (Purple spheres represent to a so-called “receptor structure. magnesium ions.) HAB1 extends molecule.” The structures The researchers first prepared part of the amino acid tryptophan show a “gate-and-latch” two samples of PYL2, one by itself (white and blue) into the gate and mechanism, by which the and one bound to ABA. Much latch mechanism of PYL2. receptor protein encloses itself around the hormone, and which appears to be widespread in the plant kingdom.

MORE > Like any organism, when a plant is faced with a stressful environment, it activates counter-measures to minimize the stress, starting with abscisic acid.

82 A rgonne National Laboratory Structural Biology

> Fig. 2 Close-up of the interface between absisic acid-bound PYL2 (shown as surface) and the HAB1 phosphatase (gold). The amino acid tryptophan inserts into the PYL2 cavity between the gate and latch regions.

The team next prepared a complex of ABA, PYL2, and HAB1, a so-called phosphatase, which maintains calm in the cell by removing bulky phosphate groups (phosphorous and oxygen) from other proteins in the cell. Together the ABA and its receptor form a new molecular surface capable of binding to HAB1 and inhibiting it, which activates genes that help the plant cope with stress. The team found that HAB1 inserts an amino acid into the gate and latch of PYL2 (Fig. 2), which would stabilize the structure so that it doesn’t easily come apart. In other words, HAB1 locks the receptor and hormone together like a See > Karsten Melcher1, Ley-Moy > This work was supported by the Jay key inserted in a lock. Ng1,2, X. Edward Zhou1, Fen-Fen and Betty Van Andel Foundation (H.E.X.), 1,2 1 the National Institutes of Health (H.E.X., As confirmation of the Soon , Yong Xu , Kelly M. Suino- B.F.V., and J-K. Z.), and the National importance of these structural Powell1, Sang-Youl Park3, Joshua J. Science Foundation (S.R.C.). L.-M.N. details, the researchers conducted Weiner4, Hiroaki Fujii3,5, Viswanathan and F.-F.S. were supported by an 3,5 1 overseas Ph.D. scholarship from the experiments to change key amino Chinnusamy , Amanda Kovach , NUS Graduate School for Integrative 1,2 6 acids in the gate, latch, and lock Jun Li , Yonghong Wang , Jiayang Sciences & Engineering (NGS). areas to see what effect it had on the Li6, Francis C. Peterson4, Davin R. LS-CAT is in part funded by the Michigan Jensen4, Eu-Leong Yong2, Brian F. Economic Development Corporation and phosphatase. As would be predicted the Michigan Technology Tri-Corridor. 4 3 if the amino acids were keeping the Volkman , Sean R. Cutler , Jian-Kang Use of the Advanced Photon Source structure together, changing them Zhu3,5, and H. Eric Xu1*, “Agate– at Argonne National Laboratory was led to a reduction in inhibition of the latch–lock mechanism for hormone supported by the U.S. Department of Energy, Office of Science, Office of Basic phosphatase enzyme. The researchers signalling by abscisic acid receptors,” Energy Sciences, under Contract No. also introduced a second protein Nature 462, 602 (3 December 2009). DE-AC02-06CH11357. to see if it would compete for the DOI:10.1038/nature08613 space on the phosphatase where the receptor and ABA bind. The Author affiliations > 1Van Andel 2 other protein caused an increase in Research Institute; National > 21-ID-D • LS-CAT • Life science phosphatase activity, suggesting that University of Singapore; 3University • Macromolecular crystallography, the ABA receptor competes for space of California, Riverside; 4Medical anomalous diffraction (MAD/SAD) • U33S undulator • Accepting 5 on the phosphatase but doesn’t bind College of Wisconsin; King general users to it irreversibly. Abdullah University of Science Together, these results indicate and Technology; 6National Center > 21-ID-F • LS-CAT • Life science • Anomalous diffraction (MAD/SAD), the gate-latch-lock mechanism is for Plant Gene Research macromolecular crystallography widespread in the plant kingdom. • 3.0-cm undulator • Accepting Correspondence > general users — JR Minkel *[email protected]

The Advanced Photon Source Annual Science Report 2009 83 Structural Biology

Breaking a Carbon-Carbon Bond

IN SHORT > Researchers have figured out how a simple bacterium is able to perform a chemical reaction that has never before been seen in the living world. The group, from

the University of Illinois at Urbana-Champaign, used the < Fig. 1 Structure of the HEPD enzyme, LS-CAT beamlines 21-ID-D and 21-ID-F at the APS to solve which uses an iron atom to break the three-dimensional structure of a bacterial enzyme that carbon-carbon bonds. The iron atom breaks apart chemical bonds between two carbon atoms. in this structure has been replaced Unlike other known reactions in enzymes, the bond between with cadmium (red). the carbon atoms has no preexisting activation to get the reaction started. The results might help in the design of new antibiotics.

MORE > Many of today’s electrically charged than the other, spontaneously jump to make bonds antibiotics were originally it may hog the electrons, making with other atoms in the molecule. discovered in bacteria. The micro- it easy for the bond to break apart. To confirm the details of the organisms have special enzymes In the chemical reaction during the reaction, the team used a common for making these antibiotics out of biosynthesis of phosphinothricin, technique of placing an atom of raw materials. In this new study, the two carbon atoms being broken deuterium, a heavier isotope of the researchers were interested up shared two electrons equally. hydrogen, on each of the two in a reaction that occurs in two In this reaction, an enzyme called carbons that would be split apart. bacterial species of the group HEPD chews up a two-carbon After the reaction, the group Streptomyces. Prior research had molecule and spits out a pair of used mass spectrometry, a tool found that when the bacteria made one-carbon molecules. for analyzing the structure of a the antibiotic phosphinothricin, one The researchers performed molecule by breaking it into smaller of the chemical reactions involved x-ray crystallography on the pieces. They saw two molecules splitting apart two carbon atoms in HEPD enzyme to get clues to how containing deuterium, corresponding an unprecedented way. it worked. (Fig. 1) The enzyme to the two single-carbon molecules In a chemical bond, two atoms requires iron atoms to carry out the generated by the HEPD enzyme. share a pair (or more) of electrons. reaction on the starting material, The researchers say the ability If one of the atoms is more a molecule called HEP. Based to break carbon-carbon bonds on the structure of the enzyme, may prove useful in making new derived from work on the LS-CAT antibiotics. Researchers could beamlines, the group came up with engineer other bacteria to express a specific sequence of events to the HEPD enzyme, changing the explain the reaction. An iron atom structures of carbon molecules latches on to a phosphonate group in new ways. (phosphorous and oxygen atoms) in the two-carbon HEP molecule. — JR Minkel After oxygen reacts with the iron, electrons in the carbon-carbon bond

84 A rgonne National Laboratory Structural Biology

> This work was supported by grants from the National Institutes of Health (PO1 GM077596 to W.W.M., W.A.v.d.D. and S.K.N., and NIH RO1 GM59334 to W.W.M.), and by the University of Illinois. Use of the Advanced Photon Source at Argonne National Laboratory was supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, under Contract No. DE-AC02-06CH11357.

See > Robert M. Cicchillo, Author affiliation > > 21-ID-D • LS-CAT • Life science Houjin Zhang, Joshua A.V. Blodgett, University of Illinois at • Macromolecular crystallography, John T. Whitteck, Gongyong Li, Urbana-Champaign anomalous diffraction (MAD/SAD) • U33S undulator • Accepting Satish K. Nair*, Wilfred A. van general users der Donk**, and William W. Correspondence > Metcalf***, “An unusual carbon– *[email protected] > 21-ID-F • LS-CAT • Life science • Anomalous diffraction (MAD/SAD), carbon bond cleavage reaction during **[email protected] macromolecular crystallography phosphinothricin biosynthesis,” ***[email protected] • 3.0-cm undulator A • Accepting Nature 459, 871 (11 June 2009). general users DOI:10.1038/nature07972

The Advanced Photon Source Annual Science Report 2009 85 Structural Biology

Holding Steady to Form the First Peptide Bond

In their 2009 study, Steitz and his colleagues discovered how IN SHORT > Researchers using U.S. Department of Energy EF-P, the ribosome, and the initiator synchrotron light sources at Argonne and at Brookhaven transfer RNA fit together. Using National Laboratory are putting the finishing touches on a x-ray data obtained on NE-CAT 30-year scientific story that garnered three biologists the beamline 24-ID-C at the APS, and 2009 Nobel Prize in Chemistry, awarded for uncovering the National Synchrotron Light Source atomic structure of the ribosome, the molecular factory that beamline X29, they reconstructed synthesizes the thousands of proteins that make up every the atomic structure of a bacterial ribosome in complex with EF-P living cell. A study carried out by researchers from Yale and initiator transfer RNA (Fig. 1). University using two U.S. Department of Energy synchrotron Their findings indicate that EF-P light sources reported the three-dimensional structure of a works by steadying the transfer bacterial ribosome bound to a helper protein called elongation RNA so that it doesn’t wiggle and factor P (EF-P). The structural details make it clearer how dislodge itself from the P site before the ribosome takes the first step in protein synthesis; the the ribosome can transfer methionine to the next amino acid. fusing of two amino acids into a single molecule. The structure shows EF-P pressed against the transfer RNA on one side and a mobile, finger-like projection of the ribosome, called the L1 stalk, on the other. The surface of EF-P exposed to the L1 MORE > Since the 1960s, halves, paving the way for their stalk is negatively charged, which researchers have known that the job shared Nobel Prize nine years later. fits nicely into a positively charged of the ribosome is to fuse together One of the mysteries Steitz’s pocket on L1. EF-P also touches amino acids in a specific order under lab has been working on since then a separate piece of RNA contained the direction of a molecule called is how a specially modified version in the ribosome that is thought messenger RNA, which carries of the amino acid methionine to help hold the transfer RNA in an edited version of information triggers the start of protein synthesis the correct position for peptide encoded in DNA. What took decades in bacteria. Like other amino acids, bond formation. to figure out was how the structure this initiator methionine comes In non-bacterial cells, a protein of the ribosome allows it to carry to the ribosome attached to an called eIF5A takes the place of out the chemical steps required to L-shaped molecule called transfer EF-P. Using the new structure to form a chemical bond between two RNA. The first peptide bond is model that of eIF5A, the researchers amino acids, called a peptide bond. ready to be formed as soon as this find that the two proteins might In 2000, three researchers—Steitz; so-called “initiator transfer RNA” make a similar but slightly different Venkatraman Ramakrishnan of the becomes lodged in a pocket on the fit with the ribosome and transfer M.R.C. Laboratory of Molecular ribosome called the “P site.” The RNA, for the same end result: two Biology in Cambridge, England; ribosome then draws in a second amino acids become one molecule. and Ada E. Yonath of the Weizmann amino acid and fuses methionine Institute of Science in Rehovot, to it. The EF-P protein speeds up — JR Minkel Israel—simultaneously published the formation of the initial peptide the first atomically detailed bond by making contact with the structures of the ribosome’s two ribosome.

86 A rgonne National Laboratory Structural Biology

See > Gregor Blaha, Robin E. Stanley, and Thomas A. Steitz*, “Formation of the First Peptide Bond: The Structure of EF-P Bound to the 70S Ribosome,” Science 325, 966 (21 August 2009). DOI:10.1126/ science.1175800

Author affiliation > Yale University

Correspondence > *[email protected]

> This work was supported by National Institutes of Health grant GM22778 (to T.A.S.). Use of the Advanced Photon Source at Argonne National Laboratory was supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, under Contract No. DE-AC02-06CH11357. < Fig. 1 In this structure, the ribosome of Thermus thermophilus, a bacterium that thrives in high temperatures, is poised to take the first step of protein synthesis. Researchers > 24-ID-C • NE-CAT • Life science • Anomalous diffraction believe the EF-P protein (pink) serves to maintain the proper orientation of initiator (MAD/SAD), MAD phasing, transfer RNA (green), which delivers the first amino acid to the ribosome. Helping macromolecular crystallography, to hold EF-P in place is a flexible part of the ribosome called the microdiffraction, microbeam, L1 stalk (gold). single-crystal diffraction, single- wavelength anomalous dispersion • 3.3-cm Undulator A • Accepting general users

The Advanced Photon Source Annual Science Report 2009 87 Structural Biology

Some Self-Assembly Required

< < Fig. 1 Model of bacteriophage f29 IN SHORT > Acting like microscopic lunar landers, structures approaching their bacteriophages, the viruses that infect bacteria, recognize bacterial host, Bacillus subtilis. and bind to specific molecules on the surface of their bacterial Shown are fully assembled hosts. In an infection cycle very similar to that of the viruses particles, in white and purple, that infect humans, once they are bound to the surface of and multicolored particles showing bacteriophage with tail the bacterial cell, bacteriophages break through the bacterial spike assemblies, showing the cell wall, inject their genomes, and proceed to take over the autochaperone structure before internal machinery of the cell. Within a short time, bacterial and after autocatalytic processing. molecules have been hijacked to manufacture the proteins encoded by the viral genome. Once the viral proteins are made, the viruses go through a complex process of self- molecule is crucial for guiding the assembly, becoming particles that are ready to leave the cell formation of the trimer by shielding to find new victims to infect. A deeper understanding of these certain water-insoluble amino acids (that will reside within the interior complex infection processes is vital to designing treatments of the structure) from the watery against viral infections in people. milieu of the bacterial cytosol. If the base portion of the molecule is deleted, for example, the trimeric structure does not coil properly and results in an improperly folded, non-functional protein. Once MORE > Structural studies of one of the trimeric appendages of self-assembly has completed, the the tailed bacteriophage, f29, the tail spike showed that the f29 chaperone base moves neatly over have shed light on two steps in tail spike is assembled by a process a portion of the coiled domain onto this infection cycle. The work, involving a special autochaperone a putative proteolytic site, where it performed at the BioCARS 14-ID, “base” region at the C-terminal end is cleaved and then released with SER-CAT 22-ID, and GM/CA-CAT of the protein sequence that aids in the hydrolysis of a molecule of 23-ID-D beamlines at the APS, has formation of the gp12 trimer. Then, ATP. The researchers were able to revealed the mechanism by which once its work is done, it neatly identify and test possible amino the tail spike of this bacteriophage removes itself in an autocatalytic acids in the structure to confirm is assembled in the host cell and step that involves ATP hydrolysis. that both the removal of the base provided clues to how it binds its The researchers in this portion by autocatalytic cleavage host. Bacteriophage f29 uses a study, from Purdue University and the ATP hydrolysis could be 12-appendage tail spike to recognize and the University of Minnesota, accounted for by elements of the glycopolymers on the cell wall of its first generated crystals of the viral protein structure rather than bacterial host, Bacillus subtilis. Each gp12 protein before and after the external elements. This fascinating of the 12 appendages consists of autochaperone region had been self-assembly and processing three copies of a protein called gp12 removed, and then solved the sequence appears to be conserved that assemble to form a trimeric structure of the protein using single among other viruses that contain coil containing the recognition sites anomalous dispersion phasing bacterial tail spikes similar to that for the B. subtilis cell wall. This to a resolution of 2.0 Å (Fig. 1). of f29 and may provide insight into complex structure is assembled The full-length structure reveals a how self-assembly of viruses could inside the bacterium during infection coiled-coil trimeric domain with be blocked. and incorporated into new viral a globular trimeric base at one particles that are released from the end. During assembly within the The structure also revealed cell. Elucidation of the structure of host cell, this base portion of the information about the ability of

88 A rgonne National Laboratory Structural Biology

See > Ye Xiang1, Petr G. Leiman1,§, Long Li1, Shelley Grimes2, Dwight L. Anderson2, and Michael G. Rossmann1*, “Crystallographic Landing of a dsDNA Insights into the Autocatalytic Assembly Mechanism of a Bacteriophage Bacteriophage Tail Spike,” Mol. Cell 34, 375 (May 15, 2009). DOl:10.1 016/j.molceI.2009.04.009

Author affiliations > 1Purdue University, 2University of Minnesota §Present address: École Polytechnique Fédérale de Lausanne

Correspondence > *[email protected]

> This work was supported by National Science Foundation Grant MCB-0443899 to M.G.R. and National Institutes of Health Grant DE003606 to D.LA, S.G., and M.G.R. Use of the Advanced Photon Source at Argonne National Laboratory was supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, under Contract No. DE-AC02-06CH11357.

> 14-ID • BioCARS • Life sciences • Anomalous diffraction (MAD/ SAD), biohazards at the BSL2/3 level, Laue crystallography, macromolecular crystallography, time-resolved x-ray scattering • 2.7 undulator, 2.3 Undulator • Accepting general users

> 22-ID • SER-CAT • Life science • Macromolecular crystallography, the f29 tail spike to recognize host 12 appendages binds the host cell multiwavelength anomalous cell-wall molecules. In experiments wall in succession to drive the dispersion • 3.3-cm Undulator A where bacterial cell-wall analogs virus through the bacterial cell • Accepting general users were bound to the gp12 trimeric wall, will be the subject of future > 23-ID-D • GM/CA-CAT • structure, the researchers were able investigations. Life science • Macromolecular to show which specific regions of crystallography, microbeam, microdiffraction, anomalous gp12 bind to the host, and that this — Sandy Field diffraction (MAD/SAD), subatomic interaction is dependent on metal (<0.85 Å) resolution • 3.0-cm ions in the viral protein structure. undulator • Accepting general users Their hypothesis, that each of the

The Advanced Photon Source Annual Science Report 2009 89 Structural Biology

Inhibiting Estrogen-Dependent Breast Cancer at the Source

> Fig. 1 A view of the human placental IN SHORT > Recent developments in breast cancer research aromatase active site showing the have revealed that there are a number of different mechanisms bound androgen molecule within its unbiased electron density surface by which this cancer may form. One of these is through contoured at 4.5 times the standard inappropriate activation of cancer cell growth by naturally deviation. Amino acid side chains, occurring estrogen in a woman’s body. This knowledge has the heme group, and bound water provided two possible targets for treatment: through inhibition molecules that snugly enclose of the binding of estrogen to the estrogen receptor or through the bound substrate are shown. inhibition of natural estrogen synthesis in the patient. Element colors are: C: gray, N: blue, O: red, S: yellow, Fe: firebrick, and Research at the SBC-CAT beamline 19-ID at the APS solved H: orange. The C atoms of androgen the structure of the enzyme aromatase to 2.9-Å resolution. are colored in light blue. This work provides important insights into the mechanism of action of aromatase, the specificity of its androgen binding cleft, and its membrane localization that will enable when one lines up their amino researchers to improve the existing inhibitors of this unique acid sequences. cytochrome P450-family enzyme. The next step toward understanding how to design a better aromatase inhibitor was to create a model of the structure of aromatase with one of the inhibitors bound to the active site of the enzyme. MORE > Estrogens are that aromatase has a unique By using the information they synthesized in the body by an specificity among these enzymes had gained from the structure and enzyme called aromatase cytochrome and that the current inhibitors proposed catalytic mechanism of P450 from their cellular precursors, cross-react with other cytochrome aromatase bound to androgen, the androgens. Inhibition of this enzyme, P450 family members causing research team was able to model therefore, has provided a target side effects. an aromatase inhibitor, exemestane, for small molecules that might Now, with solution of the into the active site of aromatase. inhibit its synthetic activity. Three crystal structure by researchers from Analysis of the differences between of these aromatase inhibitors have the Hauptman-Woodward Medical the way androgens bind aromatase been approved by the Food and Research Institute and the Roswell and the way the inhibitor binds Drug Administration for treatment Park Cancer Institute, the molecular showed that exemestane can bind of estrogen-dependent breast basis for the specificity of aromatase to the active site but does not have cancer. However, these molecules has been revealed (Fig.1). Within the chemical group available for have all been developed without the binding cleft for androgen, there catalysis and therefore remains specific structural knowledge of is a unique amino acid, proline 308, tightly bound, blocking any further the aromatase enzyme’s androgen which changes the structure of the androgen access to the catalytic cleft. binding site or catalytic mechanism pocket to accommodate androgen The researchers are continuing to of action. Aromatase belongs to a perfectly. This confirms earlier work on the structure of aromatase large family of membrane-bound studies showing that proline 308 bound to the other inhibitors and cytochrome P450 enzymes that plays a crucial role in aromatase have already made important strides play important roles in cellular activity and that it is unique towards the design of more specific metabolism. Research has shown among cytochrome P450 enzymes aromatase inhibitors.

90 A rgonne National Laboratory Structural Biology

See > Debashis Ghosh1,2*, Jennifer Griswold1, Mary Erman1, and Walter Pangborn1, “Structural basis for androgen specificity and oestrogen synthesis in human aromatase,” Nature 457, 219 (8 January 2009). DOI:10.1038/nature07614.

Author affiliations > 1Hauptman-Woodward Medical Research Institute, 2Roswell Park Cancer Institute

Correspondence > *[email protected]

See also > “Structural biology: Anticancer drug target Another important aspect a clue to the reason for the crucial pictured,” by Michael R. Waterman, of cytochrome P450 enzymes is membrane integration requirement Nature News and Views, Nature that they are bound to cellular of aromatase and other cytochrome 457, 159 (8 January 2009). membranes and catalyze reactions P450 enzymes. DOI:10.1038/457159a involving molecules that prefer a For the future, the researchers lipid environment to the watery plan to focus on the design of more environment of the cytosol. specific inhibitors for aromatase > This research is supported in part by Analysis of the membrane-binding and to gain a more complete grants GM62794 and GM59450 (to D.G.) from the National Institutes of Health. portions of aromatase allowed the understanding of the mechanism Use of the Advanced Photon Source researchers to hypothesize about of aromatase’s unique catalytic at Argonne National Laboratory was how the orientation of the enzyme chemistry. supported by the U.S. Department of Energy, Office of Science, Office of Basic in the cellular membrane affects Energy Sciences, under Contract No. its interaction with its lipid-loving — Sandy Field DE-AC02-06CH11357. steroidal substrates. The analysis showed that the membrane binding portions of the enzyme bring the active site cleft of the enzyme into > 19-ID • SBC-CAT • Life science • close proximity to the membrane, Anomalous diffraction (MAD/SAD), subatomic (<0.85 Å) resolution, providing a channel for androgens ultra-low-temperature (15K) • and estrogens to get in and out of 3.3-cm Undulator A • Accepting the enzyme through the lipid bilayer. general users This fascinating discovery provides

The Advanced Photon Source Annual Science Report 2009 91 Structural Biology

Ensuring that Proteins Reach Their Proper Destinations

contain an amino acid sequence acid domain. However, when the that “tags” them for import into or researchers in this study looked at IN SHORT > In export out of the nucleus. Special the structure, they observed that eukaryotes (organisms transporters recognize these nuclear a sequence in the N-terminus of with a cell nucleus), localization signals (NLS) or SNUPN responsible for CRM1 proteins are made by leucine-rich nuclear export signals recognition did actually contain the transcribing DNA into (NES), and guide them through consensus for a leucine-rich NES. messenger RNA (mRNA), pores in the nuclear membrane to The leucine-rich NES nestles into which is then translated their destinations. One of these a groove between two a-helices in transporter proteins is called CRM1 ring-shaped CRM1 that provides a to build proteins from (exportin-1) and it is responsible hydrophobic environment for the amino acids. DNA is for the transport of hundreds of interaction (Fig. 1). Alteration of in the nucleus, and proteins out of the nucleus. One of hydrophobic amino acids in the protein synthesis occurs the CRM1 cargo proteins is called leucine-rich NES or the hydrophobic outside the nucleus in snurportin (SNUPN), which moves NES-binding groove of CRM1 the cytoplasm. However, ribonucleoproteins into the nucleus interrupted the binding of CRM1 to and then must be recycled back SNUPN, proving that the N-terminus many newly made proteins out. Although amino acid sequence of SNUPN is a true NES and its “work” in the nucleus and “tags” have been identified for binding site on CRM1 is the bona have to be transported many proteins that are imported into fide NES-binding site. there after they are and out of the nucleus, many other Leucine-rich NESs made. The details of this proteins with similar sequences are known to be short stretches transportation process are are, in fact, not transported. This of hydrophobic amino acids suggests that these signals are interspersed with other amino a mystery investigated not the only determinant for this acids. The interactions mediated by by researchers from process. This study has provided these regions are usually weak and the University of Texas some answers to this mystery: The these sequences are often found in Southwestern Medical structure of CRM1 in complex with proteins that are not exported from Center at Dallas, using the SNUPN at 2.9-Å resolution, solved the nucleus. This led to the notion SBC-CAT 19-ID beamline by multiwave-length anomalous that there must be other factors dispersion at the 19-ID beamline, involved in the specificity of nuclear at the APS. has shown how CRM1 recognizes export recognition. As predicted, the SNUPN leucine-rich NES and an the CRM1/ SNUPN structure shows additional binding surface between that SNUPN contains a basic region these proteins, and has revealed that interacts with a complementary how the drug Leptomycin B inhibits acidic surface on CRM1 adjacent to nuclear export by CRM1. where it binds the SNUPN leucine- MORE > Separation of nuclear The first mystery solved rich NES (Fig. 1). This interaction activities from cytoplasmic by elucidation of the structure was stabilizes the interaction with activities is tightly regulated, so the location of the leucine-rich SNUPN and is likely to be present in a complex but efficient system of NES on SNUPN. Investigators other CRM1 cargoes. Interestingly, moving cellular components into had previously reported that this model of bipartite binding of and out of the nucleus has evolved. SNUPN didn’t have a leucine-rich nuclear export receptor to its cargo This transport process involves a NES, but is an atypical cargo that is similar to one observed earlier postal-like system wherein proteins bound CRM1 using a 300-amino for nuclear import processes and

92 A rgonne National Laboratory Structural Biology < Fig. 1 Overall structure of the CRM1–SNUPN complex. CRM1 is shown in pink and SNUPN is shown in blue. SNUPN binds CRM1 through its leucine-rich NES (labeled) and its basic nucleotide binding domain (shown as surface representation).

suggests that these two processes See > Xiuhua Dong, Anindita are more similar than previously Biswas, Katherine E. Süel, appreciated. Laurie K. Jackson, Rita Martinez, Finally, the CRM1/SNUPN Hongmei Gu, and Yuh Min Chook*, structure was used to answer another “Structural basis for leucine-rich > This work is funded by National outstanding question. Leptomycin B nuclear export signal recognition Institutes of Health grants R01GM069909, R01GM069909-03S1, and 5-T32- is an anti-fungal anti-bacterial agent by CRM1,” Nature 458, GM008297; Welch Foundation grant that is known to inhibit nuclear 1136 (30 April 2009). I-1532; and the UT Southwestern export by binding to cysteine 528 DOI:10.1038/nature07975 Endowed Scholars Program. Use of the of CRM1. In the structure, cysteine SBC-CAT beamline was supported by the U.S. Department of Energy (DOE) Office 528 sits in the binding groove for the Author affiliation > of Biological and Environmental Research SNUPN leucine-rich NES, showing University of Texas Southwestern under Contract No. DE-AC02-06CH11357. clearly why Leptomycin B inhibits Medical Center at Dallas Use of the Advanced Photon Source was supported by the DOE Office of Science, nuclear export by CRM1. This is Office of Basic Energy Sciences, under important information because Correspondence > Contract No. DE-AC02-06CH11357. Leptomycin B, in addition to its uses *[email protected] as an anti-fungal and anti-bacterial agent, has shown promise as an anti-cancer agent. Knowledge of its mode of action could inform drug > 19-ID • SBC-CAT • Life science design efforts aimed at improving • Anomalous diffraction (MAD/ the efficacy of CRM1 inhibitors SAD), subatomic (<0.85 Å) resolution, ultra-low-temperature in medicine. (15K) • 3.3-cm Undulator A • Accepting general users — Sandy Field

The Advanced Photon Source Annual Science Report 2009 93 Structural Biology

RNA Finds a Groove in ERA to Act as a GAP

> Fig. 1 The functional cycle of ERA is IN SHORT > Making new proteins is one of the most composed of four states, including fundamental functions of any cell, from bacteria to humans. apo-ERA, ERA-GTP, ERA-GTP- RNA and ERA-GDP. The GTPase All living things use DNA to create messenger RNA (mRNA) domain (in yellow) and KH domain that contains the code for making the proteins of life from (in orange) of ERA and the 3′ end of their component amino acids. Ribosomes are complexes of 16S rRNA (12 nucleotides, in green) protein and RNA and are responsible for using the mRNA are shown as molecular surfaces, code to assemble proteins. Bacterial ribosomes consist of a while the GTP (in blue) and GDP complex of proteins and RNA that form two particles, the (in cyan) molecules are represented large 50S particle and the smaller 30S particle. The 30S as atomic spheres. particle contains 21 ribosomal proteins and a 1,540-nucleotide ribosomal RNA (16S rRNA). Before proteins can be made, this complex must be assembled, a process that is regulated site of ERA. The AUCA of this by about 20 protein cofactors. Some of these cofactors, RNA sequence is conserved among named GTPases, use the energy of hydrolysis of the GTP bacteria, archaea, and eukaryotes. nucleotide as a molecular switch to check that each step The CCUCC is conserved among prokaryotes and is known as the occurs in the proper order before moving on to the next. One anti-Shine-Delgarno sequence of these GTPases, ERA, is an essential protein in bacteria essential for translation start that is required for the final processing of the 16S rRNA and site recognition. assembly of the 30S ribosomal subunit. Structural studies The GDP-bound form of performed at two U.S. Department of Energy synchrotron ERA adopted the same conformation x-ray light sources, including the SER-CAT 22-BM beamline as a previously solved structure for at the APS, have now shown how the interaction of ERA with ERA with no nucleotide, called apo- ERA. The ERA-GNP-RNA complex 16S rRNA affects its GTPase activity and function as a key adopted a different conformation that regulator of protein translation. was the same as the conformation previously shown for ERA-GNP without RNA and showed that RNA binding to ERA does not affect the structure of the protein. However, GTP binding does appear to have MORE > Bacterial ERA contains the X9B beamline of the National a large effect on the structure of an N-terminal GTPase domain Synchrotron Light Source at the protein and also makes a big connected by a 17 amino acid linker Brookhaven National Laboratory, difference to the way RNA can bind. to a KH domain that binds to RNA. researchers from the National Cancer In the ERA-GNP-RNA structure, It has been shown to bind to both Institute of the National Institutes RNA lies within a positively-charged the 16S rRNA and to components of of Health solved two structures, one groove of the KH domain making the 30s ribosomal subunit. However, of ERA bound to GDP and the other contact through the first 9 nucleotides the interaction of the two domains of ERA bound to a GTP analog, of the RNA. In the ligand-free and with each other and with RNA was GNP, plus the 3′ end of the 16S GDP-bound structures, this groove unknown. In this work, carried rRNA, 1531AUCACCUCCUUA1542, is occluded by the movement of a out at the SER-CAT beamline and which is thought to be the binding negatively charged helix, effectively

94 A rgonne National Laboratory Structural Biology

See > Chao Tu, Xiaomei Zhou, Joseph E. Tropea, Brian P. Austin, David S. Waugh, Donald L. Court, and Xinhua Ji*, “Structure of ERA in complex with the 3′ end of 16S rRNA: Implications for ribosome biogenesis,” Proc. Nat. Acad. Sci. USA 106(35), 14843 (September 1, 2009). DOI:10.1073/ pnas.0904032106

Author affiliation > National Cancer Institute, National Institutes of Health

Correspondence > *[email protected]

blocking the binding of negatively activity might be affected by other > This work was supported by the charged RNA. ribosomal proteins as well. Intramural Research Program of the RNA binding does not affect Based on their discoveries, National Institutes of Health, National Cancer Institute, Center for Cancer the structure of ERA but it does these researchers propose a Research. Use of the Advanced Photon affect the function. The team showed functional cycle for ERA activity Source at Argonne National Laboratory that RNA binding affects the rate of including its GTP hydrolysis cycle was supported by the U.S. Department of Energy, Office of Science, Office of GTP hydrolysis of ERA by speeding and RNA binding (Fig. 1). Now, Basic Energy Sciences, under Contract it up, acting as a GTPase-activating to fill in the gaps, the team will No. DE-AC02-06CH11357. protein or GAP. Further investigation focus on identifying the impact showed that both the AUCA and of each nucleotide in the RNA on the CCUCC were required for this ERA binding and activity and on GAP activity. However, the effect on learning more about its function > 22-BM • SER-CAT • Life science GTPase activity was modest, only by studying the mouse and human • Macromolecular crystallography about a 6-fold increase, compared to forms of ERA. • Bending magnet • Accepting 105 in other GTPases, leaving open general users the possibility that ERA’s GTPase — Sandy Field

The Advanced Photon Source Annual Science Report 2009 95 Environmental & Geological Science

A Surprise in Old Water Pipes

vanadium can exist in several IN SHORT > Although vanadium, a moderately abundant oxidation states, spectral signatures element in the Earth’s crust, isn’t known to cause significant can arise from a confusing variety human health problems, the U.S. Environmental Protection of compounds. The XANES Agency (USEPA) lists it as a “contaminant candidate” in technique was key in confirming drinking water, meaning that regulatory action could follow if that the oxidizing environment of the drinking waters produced vanadium data emerge showing that the metal poses a health risk and is compounds in the V5+ oxidation state. sufficiently widespread in occurrence. Meanwhile, surprisingly In 14 of the 19 samples, XANES large amounts of the metal sometimes show up in scale deposits identified the presence of the lead- on the inner surfaces of old lead water pipes. Scientists from vanadium mineral vanadinite, the USEPA used several x-ray techniques at the APS to Pb5(VO4)3Cl, along with a smaller probe the chemical make-up and structure of these deposits. fraction of vanadium oxide in The results illuminate how vanadium-containing minerals some samples. could have built up inside the pipes, even though the metal’s To pin down where in the pipe concentration in water is low, and hint at ways in which changes deposits the vanadinite resided, the researchers then used the in water treatment might release the trapped vanadium into micro-focused x-ray beam at the water supply. beamline XOR/PNC 20-ID to analyze cross-sections cut through two scale samples (Fig. 2). Mapping by μ-x-ray fluorescence tests revealed vanadium mainly in the surface layers of the scales MORE > While vanadium is not by x-ray powder diffraction failed that would have had immediate routinely tracked by the USEPA, to identify specific vanadium contact with water. Subsequent in a 2008 study of scale taken from compounds, most likely because μ-XANES spectra taken of spots lead pipes that had been part of they were in an amorphous form highlighted in the fluorescence municipal drinking water systems or, if in a crystalline form, at very map again confirmed the presence for 70 years or more, the amount of low concentration. Turning to the of vanadinite. vanadium in the mineralized deposits XOR/PNC 20-BM beamline at the One of the scale samples varied enormously, from as little as APS, the team tested 19 powdered that included significant amounts 13 ppm to as much as 22,500 ppm. samples using the bulk x-ray of vanadinite came from a water Researchers from the USEPA and absorption near edge spectroscopy supply system that used chloramine the University of Cincinnati decided (XANES) technique. Because for disinfection and orthophosphate to dig deeper into the origin of these vanadium deposits and to assess the dangers they might present. The researchers collected 34 scale samples from 15 lead pipes representing 8 water systems in the northeast and midwestern U.S. (Fig 1). Analysis of these samples

< < Fig. 1 Inner surface of old lead water pipes.

96 A rgonne National Laboratory Environmental & Geological Science < Fig. 2 Scale deposits taken from a variety of locations on the inner surface the pipes in Fig. 1 turn out to have unexpectedly high concentrations of the vanadium-containing mineral vanadinite. (Photos courtesy of Michael K. DeSantis, Pegasus Technical Services [contractor for USEPA])

to control corrosion of the pipes. similar studies are needed of pipes > The XOR/PNC facilities at the Advanced Modeling these chemical conditions, made of other metals, notably iron, Photon Source, and research at these facilities, are supported by the U.S. the researchers concluded that to see if vanadium deposits can Department of Energy-Basic Energy dissolved V5+ ions in the water can build up in the same way, or if Sciences, a major facilities access react with lead(II) compounds in the the accumulation mechanism grant from NSERC, the University of surface layers of the pipe to form (and hence, mobility) differs. Washington, Simon Fraser University, and the Advanced Photon Source. Use of the vanadinite, which is highly insoluble. Advanced Photon Source is supported by In this way, the surface scale layers — David Lindley the U.S. Department of Energy, Office of can accumulate high concentrations Science, Office of Basic Energy Sciences, under Contract DE-AC02-06CH11357. of vanadium from low concentrations All ICP analyses were conducted by in the water itself. The researchers the United States Geological Survey’s also used these results to provide See > Tammie L. Gerke1, Kirk G. Mineral Resource Surveys Program an estimate of an upper limit to Scheckel 2 and Michael R. Schock2*, under Interagency Agreement DWI4999901 under the direction of the solubility of vanadinite, a very “Identification and Distribution Dr. Stephen A. Wilson. 5+ useful datum for environmental of Vanadinite (Pb5(V O4)3Cl) in and geochemists. Lead Pipe Corrosion By-Products,” These findings raise the Enviro. Sci. Tech. 43, 4412 (2009). possibility that changes in the DOI:10.1021/es900501t > 20-BM • XOR/PNC • Chemistry, chemicals used for water treatment environmental science, could reverse the reactions by which Author affiliations > 1University geoscience, materials science • vanadium is mineralized in the pipe of Cincinnati; 2U.S. Environmental Microfluorescence (hard x-ray), micro x-ray absorption fine surface, possibly leading to the Protection Agency, Cincinnati structure, x-ray absorption fine release of large amounts of the metal structure • Bending magnet into the water supply, the researchers Correspondence > • Accepting general users caution. They also suggest that *[email protected]

The Advanced Photon Source Annual Science Report 2009 97 Environmental & Geological Science

Rice’s Reliability as a Source of Selenium

high concentrations allowed detailed IN SHORT > Selenium is good for you—in tiny quantities, investigation of the chemical form anyway. We need from 55 to 200 μg of the element per day in and location of selenium in the rice, our food to avoid muscle and cartilage problems, reproductive using x-ray fluorescence (XRF) and XANES (x-ray absorption near-edge impairment, and other disorders. Insufficient dietary selenium structure) methods. affects perhaps 1 billion people worldwide; for many of these Bulk XANES analysis of people, rice provides a significant portion of their essential powdered samples of Jianshi rice minerals. As part of a program to assess the selenium content showed that selenium was about of rice from different parts of the world, an international equally distributed between organic and inorganic forms in the husk and team of researchers used XOR/PNC beamline 20-ID at the bran, but was about 95% organic in APS to distinguish between organic and inorganic selenium- the endosperm (the starchy central containing molecules, and to determine where in the rice part of the grain). To further pin grain the element is most likely to accumulate. Their findings down the location of selenium, the provide guidance on how rice supplies can be mixed and team cut individual rice grains to make transverse and longitudinal managed to ensure adequate selenium content. sections that they studied using μ-XRF and μ-XANES (Fig. 1). Fluorescence maps showed selenium mostly in the outer layers of the grain, infiltrating the endosperm through structures that carry nutrients MORE > Scientists from the that three quarters of the samples into the growing grain. Micro- Chinese Academy of Sciences, they tested could not provide even XANES analysis of a few 5-μm-wide the University of Aberdeen, the 70% of the minimum daily spots in the cross sections indicated University of Copenhagen, the requirement. that most of the selenium was in the U.S. Environmental Protection Selenium’s dietary value form of methyl-selenocysteine, an Agency, and the University of Ghana depends on whether it resides in organic molecule thought to have collected 1,092 samples of polished inorganic or organic molecules, anticarcinogenic properties. or white rice from 11 countries that the latter being more useful. But The team’s results provide collectively produce about two- it’s difficult to identify chemical a previously absent quantitative thirds of the world’s rice. Chemical species and locate their distribution perspective on the problem of analyses of total selenium content in rice grains when the concentration selenium deficiency around the revealed large variations both within of the element is so low, so the world. About two-thirds of the rice and among countries, resulting researchers obtained an additional from India, the world’s second from differences in soil chemistry sample of rice, from Jianshi biggest producer and biggest as well as agricultural management county in south-central China, exporter of the grain, already has techniques that influence water where natural conditions produce adequate selenium content, whereas quality. Egyptian rice had the least extraordinarily high selenium rice from Thailand, the second selenium, averaging less than 10 ppt concentrations—almost 10 parts biggest exporter, is much poorer by weight of selenium, while rice ppm in brown and polished rice, in the essential element. Rice like from India and the United States had and 17 ppm in rice bran. Residents that from Jianshi, with selenium the most, averaging 157 ppt and 180 of this area who subsist largely on content hundreds of times higher ppt, respectively, with some samples local rice can suffer from selenium than the global average, could be going as high as 400 ppt. Assuming toxicity, leading to hair loss, liver used as a simple food additive, the an average rice consumption of enlargement and other disorders. For researchers say. They warn, though, 300 g per day, the researchers found the research team, however, these that rice bran should probably not

98 A rgonne National Laboratory Environmental & Geological Science

< < Fig. 1 Selenium content of a grain of Chinese rice (top) shows up in a image produced by x-ray fluorescence mapping (below). XANES spectra of the numbered locations revealed the chemical form in which selenium accumulated in the grain, particularly the relative amounts of organic and inorganic species.

be used as an additive, even though it holds most of the selenium in the rice grain, because toxic elements such as arsenic and lead also tend to accumulate there.

— David Lindley

See > Paul N. Williams1,2, Enzo Lombi3,4, Gui-Xin Sun1, Kirk Scheckel5, Yong-Guan Zhu1*, Xinbin Feng1, Jianming Zhue1, Anne-Marie Carey2, Eureka Adomako2,6, Youseff > This research was supported by the 2 2 Lawgali , Claire Deacon , and Natural Science Foundation of China Andrew A. Meharg2**, “Selenium (20720102042), Chinese Academy of Characterization in the Global Rice Sciences (KZCX1-YW-06-03), the CAS Research Fellowship for International Supply Chain,” Enviro. Sci. Tech. Young Researchers, and the Royal Society 43, 6024 (2009). DOI:10.1021/ of Edinburgh’s International Exchange es900671m Programme. XOR/PNC facilities at the Advanced Photon Source and research at these facilities are supported by the U.S. Author affiliations > Department of Energy, Office of Basic 1 Energy Sciences, a major facilities access Chinese Academy of Sciences; > 20-ID • XOR/PNC • Materials grant from NSERC, the University of 2University of Aberdeen; science, environmental science, Washington, Simon Fraser University, and 3 chemistry, geoscience • University of Copenhagen; the Advanced Photon Source. Use of the Microfluorescence (hard x-ray), 4University of South Australia; Advanced Photon Source is supported by x-ray absorption fine structure, 5 the U.S. Department of Energy, Office of U.S. Environmental Protection surface diffraction, micro x-ray Science, Office of Basic Energy Sciences, absorption fine structure, x-ray Agency, Cincinnati; under Contract DEAC02-06CH11357. The Raman scattering, time-resolved 6University of Ghana U.S EPA, through its Office of Research x-ray absorption fine structure, and Development, funded and managed x-ray emission spectroscopy • a portion of the research. It has not been Correspondence > 3.3-cm Undulator A • Accepting subject to Agency review and, therefore, general users *[email protected] does not necessarily reflect the views of **[email protected] the Agency.

The Advanced Photon Source Annual Science Report 2009 99 Environmental & Geological Science

Geology's “Insect in Amber”

to a chlorine-copper bond length IN SHORT > Tiny droplets of fluid trapped for millennia of 2.11(2) Å. The XANES and inside crystals within ancient rocks can reveal important EXAFS data are consistent with a - clues about Earth’s geological history. A detailed analysis of [CuCl2] ion. This species is apparent in the spectrum at all temperatures so-called “inclusions”—samples of a geological fluid or melt from 200° C to 700° C and was that were trapped in a crystal as it grew (a little like an insect present in all 15 of the inclusions in amber)—can provide useful information about how a rock tested. The team also recorded or ore deposit formed. Over the last 15 years, researchers have XANES spectra for the copper-rich published several thousand papers reporting such analyses. inclusions, which are similar to These inclusions are unique in that they essentially “lock in” those of the low-copper samples, but shifted to higher energy. This the physical and chemical conditions present in a fluid or characteristic was seen at melt at the time the host rock crystallised. An international 350° C to 700° C from all three team used the GSECARS 13-ID beamline of the APS to study of the copper-rich inclusions studied. samples of a Russian granite. Their work revealed, for the first The subsequent EXAFS study at time, the type of copper molecules that are present in fluids 700° C seemed to show that a that may form ore deposits. This research has implications for copper-containing ion with a different bond length—2.19(1) Å—was understanding fundamental geochemistry as well as in the hunt present, suggesting that chlorine for valuable mineral ores. may not be the partner atom in this case. This is the first time that copper speciation has been determined at these temperatures and provides an example of how inclusions can MORE > Granite from the brine fluid inclusions found in the be used as sample cells for the industrial region known as the miarolitic quartz component of this spectroscopic study of fluids at Omsukchan trough in Russia is a granite. They tracked the spectra extreme conditions. particularly rich vein of geochemical up to 700° C for two different types The team now plans to information. Aqueous, or of fluids that had been trapped as investigate iron, manganese, and hydrothermal, fluids that de-gas from inclusions. One contained 0.02% zinc in the same inclusions. This a magma are particularly important in by weight of copper and the other will allow them to explore the geochemistry and forming ores. The 0.94 wt.%. In both cases the copper geochemistry of these ore metals at researchers in this study published distributed evenly throughout the much higher temperatures than have results on melt inclusions in Nature, inclusion above the salt dissolution been studied before. The ultimate aim 455, 960 (2008,), which were temperature at 350° C to 550° C. This will be to understand how different featured in the article “Heat in the indicated that the copper was present metals speciate from magmatic to Archaean Mantle” in APS Science in solution and not as a crystal. depositional temperatures and so help 2008, pg. 110. For the current study, The team studied the x-ray clarify the chemical and physical the researchers, from Imperial absorption near edge structure conditions that give rise to different College London, the University of (XANES) spectra of the solution types of ore deposits. Tasmania, and The University of phase for the inclusions containing Chicago, recorded copper K-edge the low copper concentration. These — David Bradley x-ray absorption spectra from natural displayed an intense edge feature at samples of Omsukchan granite an energy close to 8983 eV. Extended (Fig. 1). More specifically, they x-ray absorption fine structure recorded the spectra for polyphase (EXAFS) spectra at 550° C point

100 A rgonne National Laboratory Environmental & Geological Science

Cu Fe

Mn Zn < See > Andrew J. Berry1*, Anthony Fig. 1 Ka x-ray fluorescence maps of a fluid inclusion at 500° C. The copper is C. Harris2, Vadim S. Kamenetsky2, homogeneously distributed in the fluid, as is most of the manganese and zinc. Matthew Newville3, Stephen R. Iron is present as a crystal in the bottom-right corner. The inclusion is approximately Sutton3, “The speciation of copper 60 µm across. in natural fluid inclusions at temperatures up to 700° C,” Chem. Geol. 259, 2 (2009). DOI:10.1016/j. > A.C.H. visited GSECARS with support chemgeo.2008.10.018 13-ID • GSECARS • Geoscience, from the Access to Major Research environmental science • Facilities Program funded by the Microfluorescence (hard x-ray), Author affiliations > Commonwealth of Australia. GSECARS microdiffraction, x-ray absorption 1Imperial College London, is supported by the U.S. National Science fine structure, micro x-ray absorp- Foundation (EAR-0622171) and the 2 tion fine structure, high-pressure University of Tasmania, U.S. Department of Energy (DEFG02- diamond anvil cell, high-pressure 3 The University of Chicago 94ER14466). Use of the Advanced multianvil press, inelastic x-ray Photon Source was supported by the U.S. scattering • 3.3-cm Undulator A • Department of Energy, Office of Science, Accepting general users Correspondence > Office of Basic Energy Sciences, under *[email protected] Contract No. DE-AC02-06CH11357.

The Advanced Photon Source Annual Science Report 2009 101 Environmental & Geological Science

Airing the Laundry: What Happens to Silver Nanoparticles in the Wash?

< < Fig. 1 X-ray absorption near-edge IN SHORT > The number of commercial applications structure spectra for Ag reference of nanotechnology is burgeoning. Products containing materials, sock samples, and elemental Ag nanoparticles in nanoparticles are entering the marketplace, and the chloride and hypochlorite/detergent environment, at a rapidly increasing rate, and well before solutions. When the elemental Ag is their safety has been definitively determined. Among the exposed to chloride ion alone, there products on store shelves today are socks that contain is no evidence for the formation of silver (Ag) nanoparticles with antibacterial and fungicidal AgCl. The XANES spectra show properties. Laboratory experiments using zebrafish, the lab that the edge energy shift in the hypochlorite solution is similar rat of the aquatic environment, have demonstrated serious to that of the AgCl reference developmental defects and mortality of fish exposed to ionic material. (Copyright © 2009 by Ag nanoparticles in purified water. But the fate and toxicity of the American Society of Agronomy, Ag nanoparticles in aquatic systems outside the lab remains Crop Science Society of America, uncertain, so gaining a better understanding of the chemical and Soil Science Society of America. transformations that nanoparticles experience under a variety All rights reserved.) of real-world conditions is vital in assessing any potential health risks from this new technology. A research team from the U.S. Environmental Protection Agency (EPA) utilized the APS to explore the ways in which sock fabric impregnated with Ag nanoparticles reacts to simulations of an ordinary laundry the nanoparticles were converted to process, using bleach, detergent, and tap water, and uncovered the chloride form. The EPA scientists suggest that repeated laundering some enlightening transformations. of the sock material may convert additional Ag nanoparticles to AgCl, thus reducing or eliminating the odor-eating and antibacterial properties of the relatively expensive apparel. MORE > X-ray absorption solution was agitated for two minutes The elemental Ag nanopowder near edge structure (XANES) and left to soak for 10 minutes, and immersed in an ionic saline (NaCl) spectroscopy was carried out at the this cycle was repeated once. Using solution, however, remained in its MR-CAT beamline 10-ID to compare tap water from Argonne, they then elemental, and potentially more toxic, unwashed sock material with fabric rinsed the fabric, wrung it out three state. It appears that the hypochlorite that went through the washing times, and mounted the 10-cm2 bleach/detergent solution used to process. The team also gathered samples for XANES analysis. wash the sock fabric provides an XANES spectra from an Ag chloride The researchers found that oxidation step necessary to transform reference material and elemental ionic Ag nanoparticles react with ionic nanosilver into a stable, non- nanopowder in a chloride solution chloride present in the hypochlorite reactive compound. This is indicated (NaCl). The researchers exposed bleach/detergent mixture, resulting in by a distinct shift in the edge energy samples of fabric to a mixture using an inert and more stable compound, that is similar for the washed fabric products in common use around the Ag chloride (AgCl). In the one wash and the reference material AgCl house: bleach and detergent. The and rinse operation, about 50% of (Fig. 1). The scientists caution that

102 A rgonne National Laboratory Environmental & Geological Science

Elemental Nano Ag + HOCl and Detergent 2 a Elemental Nano Ag + 1 M NaCl

Washed Sock a 1.5 Sock

(E) See > Christopher A. Impellitteri, Thabet M. Tolaymat*, and Kirk G. AgCl Scheckel, “The Speciation of Silver

ed a Nanoparticles in Antimicrobial Elemental Nano Ag 1 Fabric Before and After Exposure to a Hypochlorite/Detergent Solution,” J. Environ. Qual. 39, 1528 Normaliz (July-August 2009). DOI:10.2134/ 0.5 jeq2008.0390

Author affiliation > U.S. Environmental Protection Agency, Cincinnati 0 25500 25550 25600 25650 Correspondence > *[email protected] Energy (eV)

> Any opinions expressed in this paper are those of the author(s) and do not, necessarily, reflect the official positions and policies of the USEPA. Any mention of products or trade names does not constitute recommendation for use by the solution used in this experiment Silver has been used since the USEPA. MR-CAT operations are supported by the Department of Energy may not be typical of an ordinary ancient times as a disinfectant. But and the MR-CAT member institutions. laundry process. Further studies only in the modern era have there Use of the Advanced Photon Source is with laundry detergent in ordinary been calls for its use to be regulated, supported by the U.S. Department of Energy, Office of Science, Office of Basic washing machines may further whether by the U.S. Food and Drug Energy Sciences, under Contract No. clarify whether Ag nanoparticles Administration or the EPA. Some DE-AC02-06CH11357. are consistently converted to an groups have petitioned the EPA to inert form. Furthermore, the team regulate ionic Ag nanoparticles as proposes that as Ag nanoparticles a pesticide. It is only by examining enter public sewer systems and the properties of Ag species in real > 10-ID • MR-CAT • Materials finally wastewater treatment plants, world conditions that regulators can science, environmental science, very little if any ionic Ag will remain ascertain whether Ag nanoparticles chemistry • Microfluorescence because chloride is so common. pose any real threat to aquatic (hard x-ray), x-ray absorption Should Ag impregnated socks wind resources or human health. fine structure, diffraction anomalous fine structure, micro up in landfills, it is also likely that x-ray absorption fine structure • repeated washing in a chloride — Elise LeQuire 3.3-cm Undulator A • Accepting solution will have converted most of general users the Ag to the less reactive form.

The Advanced Photon Source Annual Science Report 2009 103 Environmental & Geological Science

Electronic and Magnetic Structures of Hematite Post-Perovskite under Deep Planetary Conditions

geophysical observations. The weak IN SHORT > Iron compounds found on the surfaces of Earth magnetic field of Martian impact craters has been related to the and other terrestrial planets provide a paleomagnetic record demagnetization by the shocks of that yields important clues to the history of the inner planets. many impacts over time. However, Paleomagnetism was instrumental in uncovering seafloor this study reveals that, at least for spreading as the mechanism for tectonic plate movements on hematite, the high temperatures and Earth, and iron compounds afford insight into magnetism deep pressures generated by the impacts in planetary interiors. Hematite (Fe O ), for example, is proxy would trigger a sequence of changes 2 3 in magnetic ordering rather than a for iron in alloys in the core and silicates and oxides in the monotonic decrease in magnetism. mantle. Using synchrotron Mössbauer spectroscopy (SMS) and In iron silicate and oxide x-ray diffraction (XRD) at two APS beamlines, researchers phases at temperatures and pressures measured the electromagnetic properties of pure hematite found in deep planetary interiors, recent studies revealed that the Fe (Fe2O3) at high pressure. It has been known that Fe2O3 undergoes a sequence of phase transitions at high pressure: transitions from HS to LS. However, this study demonstrated that the from hematite to Rh2O3-II type (RhII), and then to post- degree of spin pairing in the mantle perovskite (PPv). For iron, magnetic ordering is destroyed and may not increase monotonically with then reconstructed, and electronic configuration changes from pressure and different environments high-spin to low-spin and then about half converting back to for Fe in perovskite (PV) and PPv high-spin. These results have implications for paleomagnetic may result in a complicated pattern of spin state. The spin state change studies at meteorite impact sites and geophysical applications is particularly important because for high-iron regions in deep planetary interiors. iron spin state affects physical properties such as density, optical properties, electrical conductivity, and element partitioning. The evidence suggests that

Fe2O3-PPv under lowermost MORE > To investigate the show that Fe2O3 undergoes mantle P-T conditions behaves properties of the hematite at a structural transition from hematite as a metal. At the D′′ layer, in high pressures, the research team to Rh2O3-II type (RhII) at 50 the lowermost 200 to 400 km of from the Massachusetts Institute GPa and 300K. At this transition, Earth’s mantle at the core-mantle of Technology, the University magnetization is erased and the boundary, the PPv has high electrical of Wisconsin, the University of electron spin state collapses from conductivity, which is important Chicago, and Argonne exposed pure high-spin (HS) to low-spin (LS). for the electromagnetic coupling Fe2O3 to experimental pressures Laser heating at 73 GPa initiated the between the mantle and core. The in a diamond-anvil cell. Analysis transition of RhII into postperovskite slight irregular motion of the planet, of the samples at the XOR 3-ID (PPv), which revived the magnetic known as nutation, may be due to beamline and the GSECARS 13-ID ordering and reversed the spin from the metal-like electrical conductivity beamline by synchrotron Mössbauer LS to HS of at least half of the of the D′′ layer. 3+ spectroscopy and x-ray diffraction Fe ions. The Fe2O3 alters from a was followed by theoretical first- semiconductor to a metal (Fig. 1). — Dana Desonie principles calculations of Fe spin The behavior of Fe2O3 at high and magnetic states. The results pressures can explain important

104 A rgonne National Laboratory Environmental & Geological Science < Fig. 1 Left: Hematite phase stable at 0-50 GPa. Middle: Rh2O3-II type phase stable at 50-70 and high temperature. Right: Post-perovskite phase stable at pressures above 70 GPa and high temperature.

See > Sang-Heon Shim1*, Amelia > This work was supported by the Bengtson2, Dane Morgan2, Wolfgang National Science Foundation (NSF) 3 1 Grants EAR0738655 (to S.H.S.) and Sturhahn , Krystle Catalli , Jiyong EAR0738886 (to D.M.), respectively. Zhao3, Michael Lerche3,4, and K.C. is supported by a Department of Vitali Prakapenka5, “Electronic Energy (DOE) National Nuclear Security and magnetic structures of the Administration Stewardship Science > 3-ID • XOR • Physics, Graduate Fellowship. GSECARS is geoscience, life science, chemistry, postperovskite-type Fe2O3 and supported by the NSF and DOE. Use materials science • Nuclear implications for planetary magnetic of XOR 3-ID was supported in part by resonant scattering, high-pressure records and deep interiors,” Proc. the Consortium for Materials Properties diamond anvil cell, inelastic x-ray Research in Earth Sciences under NSF Natl. Acad. Sci. USA 106(4), 5508 scattering • 2.7-cm undulator (US), Cooperative Agreement EAR 06-49658. 2.7-cm undulator (DS) • Accepting (April 7, 2009). DOI: 10.1073/ Use of the Advanced Photon Source was general users pnas.0808549106 supported by the U.S. Department of Energy, Office of Science, Office of Basic > 13-ID • GSECARS • Geoscience, Energy Sciences, under Contract No. Author affiliations > environmental science • DE-AC02-06CH11357. Microfluorescence (hard x-ray), 1 Massachusetts Institute of Technology, microdiffraction, x-ray absorption 2University of Wisconsin, fine structure, micro x-ray 3Argonne National Laboratory, absorption fine structure, 4 high-pressure diamond anvil cell, Carnegie Institution of Washington, high-pressure multianvil press, 5The University of Chicago inelastic x-ray scattering • 3.3-cm Undulator A • Accepting Correspondence > general users *[email protected]

The Advanced Photon Source Annual Science Report 2009 105 Environmental & Geological Science

Calcium and Heavy Metal Distribution in Fly Ash and Geopolymers

IN SHORT > Using fly ash to produce geopolymer concrete in place of limestone- derived Portland cement valorizes an abundant waste product and

releases 80% less CO2 into the atmosphere. To ensure safety when using waste materials to make concretes, and to better understand the formation of fly ash geopolymers, scientists mapped nanoscale elemental distributions in the ash by utilizing synchrotron currently produces 5% to 8% of heat. Most importantly, fly ash x-ray fluorescence at the anthropogenic greenhouse gas geopolymer cement emits around hard x-ray nanoprobe emissions worldwide, an amount 80% less greenhouse gases than instrument on CNM/ that will expand as developing Portland cement. XOR beamline 26-ID at nations improve their infrastructures. While replacing a highly used Since nearly all of the Portland commodity with a product that the APS. They found that cement-derived CO2 is due to emits less climate-altering pollution the calcium distribution the use of limestone in cement and is made from abundant waste depends markedly on the manufacture, researchers are seeking materials is obviously desirable, pH of the geopolymer- a replacement binder material that this is only true if the replacement forming system; is widely available, inexpensive, product is safe to use. To look chromium is bound to durable, and environmentally sound. for any possible hazards from the iron and is unlikely to The need for such a binder is likely use of fly ash and fly ash-derived to explode as governments adopt geopolymers, researchers from problematically enter climate change legislation. the University of Melbourne, the environment. Each year about 700 Universidad del Valle, and Argonne million tons of fly ash waste are analyzed samples using the Hard produced from coal-fired electricity X-ray Nanoprobe at 26-ID. Their generation, and fly ash disposal is research revealed the nanoscale a large problem. Fly ash reacting elemental disposition in fly ash with alkaline solutions creates a and in geopolymers activated with MORE > To slow climate change, geopolymer that can be used as the potassium silicate or hydroxide greenhouse gas emissions must be binder in concrete. The resulting solutions, as determined by x-ray reduced in many different ways. material is fire and acid resistant fluorescence mapping with nominal Portland cement manufacturing and does not have a high reaction 30-nm spatial resolution.

106 A rgonne National Laboratory Environmental & Geological Science

< Precast geopolymer concrete panels in use in residential construction in Melbourne, Australia. (Photographs courtesy of Zeobond Pty Ltd.)

See > John L. Provis1*, Volker Rose2, Susan A. Bernal1,3, and Jannie S.J. van Deventer1, “High-Resolution Nanoprobe X-ray Fluorescence Characterization of Heterogeneous Calcium and Heavy Metal Distributions in Alkali- Activated Fly Ash,” Langmuir 25(19), 11897 (2009). DOI: 10.1021/ la901560h

Author affiliations > 1University of Melbourne, 2Argonne National Laboratory, 3Universidad del Valle

Correspondence > The hydroxide-activated fly is highly mobile and toxic in its [email protected] 2- ash contained regions a few tens of hexavalent form (CrO4 ), and can nanometers in size that were highly sometimes be present in fly ash. enriched in calcium, providing However, the x-ray fluorescence > This work was funded by the Australian the first direct confirmation of the mapping shows that chromium Research Council (ARC), including partial funding from the Particulate Fluids nucleation of Ca(OH)2 precipitates in the fly ash appears to be bound Processing Centre, a Special Research in the solution. Calcium in the fly as essentially immobile Cr3+ in Centre of the ARC, and through Discovery ash-potassium silicate geopolymer ferrite spinel phases, which are Project grants. The work of S.A.B. was supported by travelling scholarships from was more dispersed and was likely relatively resistant to alkali attack Colciencias and from the Walter Mangold released in preference to iron during geopolymer synthesis. The Trust. Travel funding for J.L.P. was from fly ash particles rich in both. use of a silicate activator can also supplied by the Australian Synchrotron Research Program. Use of the Center for These results have important minimize Cr extraction from the Nanoscale Materials and the Advanced implications for understanding spinel phases. The researchers Photon Source at Argonne National the calcium chemistry within concluded that the likelihood of Laboratory was supported by the U.S. Department of Energy, Office of Science, aluminosilicate geopolymer gel Cr being released problematically Office of Basic Energy Sciences, under phases, which is key to controlling into the environment from the Contract No. DE-AC02-06CH11357. geopolymer permeability and geopolymer is low, and potentially durability. even lower than the possibility of Some fly ashes also contain it being released from the fly ash in measurable levels of heavy metals. a landfill. > 26-ID • CNM/XOR • Materials Because leaching studies show that science, physics • Microdiffraction, the most likely problems are due — Dana Desonie microfluorescence ( hard x-ray ), tomography • 3.3-cm Undulator A to species that form oxyanions, (US), 3.3-cm Undulator A (DS) the researchers were particularly • Operational interested in chromium, which

The Advanced Photon Source Annual Science Report 2009 107 Environmental & Geological Science

Pumping through the Middle Crust

bands, while towards the more IN SHORT > The movement and behavior of fluid—generally deformed areas, this microfabric water, sometimes other types—is a prime factor in geological of the rock gives way to a finer- processes including earthquake nucleation, mantle degassing, grained (>10 μm) homogenized mylonite pattern. The reduction and the formation of mineral deposits. The workings of fluid in grain size in the high-strain transfer in Earth’s middle crust have been controversial and areas of the sample shows that this not well understood, although it has been clear that they are rock was progressively softened associated with shear zones where rock deforms viscously. as it deformed, and the gradual When it comes to fluid migration, the middle crust is different disappearance of K-feldspar and from other crustal regions because it is generally thought to plagioclase indicates that they be both too hot and too viscous to allow fluid to pass through were dissolved and their chemical components redistributed through the fractures. A team of geologists and geophysicists using the rock by a fluid at the same time. XOR 2-BM and 32-ID beamlines at the APS has shed light on For the researchers, this a fluid transfer in the middle continental crust, a phenomenon realization pointed the way to that was formerly poorly understood. Their work could lead their “granular fluid pump” model. to a fuller understanding of fluid migration through rock, with Micron-scale grains in the high- possible wide application in deciphering important geological strain regions of the rock slide past each other under stress, in a process processes including earthquakes. called viscous grain-boundary sliding (VGBS). As this happens, pores open up while others close in the rock structure, to accommodate incompatibilities that arise between neighboring grains. This mechanism MORE > Researchers from the from the Redbank midcrustal shear is called creep cavitation, and has University of Western Australia, zone in Central Australia (Fig. 1). been observed in some ceramic CSIRO Exploration & Mining, Examining 55-mm-sized rock cubes and metallic materials. In the and Argonne have confirmed culled from various points of a rock middle crust, fluid moves from the that a phenomenon called “creep hand specimen, the team was able closing to the opening pores as the cavitation” is instrumental in the to visualize the structure of all pores fluid pressure changes from pore deformation of rock and the creation larger than 1.3-μm in diameter. They to pore during creep cavitation. of porosity that allows fluid to could thus obtain a detailed picture This mechanism is supported by permeate into these mid-crustal shear of the porosity architecture of the chemical reactions between the zones, ultimately leading to large- entire rock sample. fluid and the minerals forming the scale structural weaknesses that can The rock sample covered rock; as minerals get dissolved in, cause fault slippage, and even slow a strain gradient, allowing study or precipitated from the fluid, the earthquakes. The team has developed and comparison of the evolution fluid pressure changes locally. The a model for a granular fluid pump of porosity from the low- to high- resulting granular fluid pump is driven by stress gradients and strain regions. This strain gradient self-sustaining and steady as long chemical potentials on the grain scale was traced by the microstructural as grains slide past each other, that can move fluid through rocks transformation of the rock from and creep cavitation occurs. The deforming at mid-crustal conditions. a gneiss to a mylonite: low-strain experimenters speculate that aside The research team used regions are largely characterized by from affecting rock deformation synchrotron x-ray microtomography grains of K-feldspar and plagioclase on the small scale, the same at the 2-BM beamline to study a minerals (hundreds of microns in combination of processes—creep characteristic rock sample collected diameter) interlayered with quartz cavitation and the granular fluid

108 A rgonne National Laboratory Environmental & Geological Science

See > F. Fusseis1,3*, K. Regenauer- Lieb1,2,3, J. Liu2, R.M. Hough2, and F. De Carlo3, “Creep cavitation can establish a dynamic granular fluid pump in ductile shear zones,” Nature 459, 975 (18 June, 2009). DOI: 10.1038/nature08051

Author affiliations > 1The University of Western Australia, 2CSIRO Exploration & Mining, 3Argonne National Laboratory

Correspondence > *[email protected] < Fig. 1 The rock outcrop west of Alice Springs, central Australia, where the hand specimen was collected. The outcrop is characterized by a shear zone (from bottom left to upper right corner of the image) that formed in about 15-km depth in the middle continental > This work was supported by the crust. The rock specimen, which can be seen in the centre of the image still in-situ, Australian Synchrotron Research Program, which is funded by the covers the low-strain margin and high-strain centre of the shear zone. Commonwealth of Australia under the Major National Research Facilities Program; the Western Australian Premier’s Research Fellowship program and the University of Western Australia pump could—on a greater scale, fluid transfer in specific rock types through a research grant; iVEC through influence phenomena such as fault quite well, and is, as such quite the use of visualization resources slippage and slow earthquakes. significant. and expertise provided by the WASP and ARRC facilities; and the Centre The work represents the Fusseis and his team plan to for Microscopy, Characterization and first time that x-ray synchrotron expand upon the work by examining Analysis at the University of Western tomography has been used to further mid-crustal shear zone Australia for the use of its FESEM. visualize porosity in a mid-crustal samples at even finer resolutions of Use of the Advanced Photon Source at Argonne National Laboratory was shear zone rock at such small scale. approximately 35 nm at the XOR supported by the U.S. Department of The x-ray tomography allowed the 32-ID beamline. Along with the Energy, Office of Science, Office of Basic researchers to clearly follow the collection of this more detailed Energy Sciences, under contract number DE-AC02-06CH11357. evolution of the porosity of the data, and comparison and study of sample during rock deformation different samples from other parts and quantify it with great precision, of the world, the researchers hope to making synchrotron tomography the use the micro- and nanotomography > 2-BM • XOR • Physics, life perfect technique for investigating capabilities of the APS to observe science • Phase-contrast imaging, porosity in crystalline rocks. porosity formation in real-time tomography, microdiffraction, general diffraction • Bending Using this technique, the controlled experiments. This magnet • Accepting general users researchers have managed to shed multipronged approach will lead to light on a phenomenon that was a better understanding of the highly > 32-ID • XOR • Materials science, life science • Phase-contrast formerly poorly understood and to complex and sometimes mysterious imaging, ultra-small-angle x-ray develop a model with possible wide workings of the Earth’s middle scattering, radiography • 3.3-cm application. The team believes that crustal zones. Undulator A • Accepting their granular fluid pump applies to general users many tectonic settings and explains — Mark Wolverton

The Advanced Photon Source Annual Science Report 2009 109 Nanoscience

Number of Walls, not Diameter, Determines Plasmon Behavior in Carbon Nanotubes

the tubes. Therefore,the research IN SHORT > The existence of carbon nanotubes was posited team ruled out diameter as a factor affecting plasmon energy, at the as early as the 1950s, but it has taken several generations of relatively large size scale in this imaging advances to begin to understand the structure and study. These results apply only to properties of these nanomaterials, which exhibit extraordinary nanotubes of a sufficiently strength—several times that of steel—and a wide range of large diameter. conductivity from metallic to semiconducting. They show The team then measured EELS great promise for use in solar cells, fuel cells, and medical spectra at Brookhaven National delivery systems. A team of researchers has solved one Laboratory (BNL), to individual nanotubes with two, three, five, question about plasmon behavior in carbon nanotubes that and six walls, and samples of bulk may be key in controlling the electronic length scale of graphite, and compared the plasmon these materials. Using two powerful and complementary peak energies as the number of walls instruments, electron energy loss spectroscopy (EELS) varied. By observing the shift in the and inelastic x-ray scattering (IXS), the researchers teased plasmon energy with the number of out from three physical parameters—diameter, number walls, changes in the strength of the of walls, and chirality—the single factor that may allow screening (and, hence, the effective interactions at interatomic distances) tailoring the properties of carbon nanotubes for useful can be determined. optical applications. While EELS is a powerful tool to examine individual CNTs, IXS is superior in measuring the momentum dependence of an array of nanotubes, though because of its low signal rates it cannot be MORE > Single-walled carbon chirality, but ruled it out as a factor used to probe individual nanotubes. nanotubes (SWCNT) are formed because nanotubes with different To determine the momentum when a thin sheet of graphite with diameters had identical plasmon dependence of the plasmon shift, hexagonal lattice structure somewhat energies and the chiral angle, or the team turned to IXS performed like chicken wire is rolled into degree of twist of the cylinder, is at XOR/CMC beamline 9-ID at a cylinder. Multi-walled carbon extremely unlikely to be the same in the APS. The research team used nanotubes (MWCNT) consist of two different nanotubes. few-walled (FW) and multi-walled or more SWCNTs nestled one inside The researchers in this study— (MW) CNT arrays grown on a the other, and have been compared from Argonne, the University of silicon substrate and aligned in one to Russian dolls. Previous probes Illinois, Brookhaven National orientation. Because the tubes were of plasmon behavior using EELS Laboratory, and Oak Ridge National loosely packed, and therefore not seemed to suggest that shifts in the Laboratory—measured EELS prone to strong interactions, their π + σ plasmon energies occurred as spectra from individual, double- behavior can be interpreted as that of the number of walls and the diameter walled CNTs measuring 14-nm, single nanotubes (Fig. 1). of the nanotubes increased, but until 7.2-nm, and 3.6-nm in diameter. A IXS verified the EELS findings now no one has shown whether the distinct shift of the π + σ plasmon that momentum of π + σ plasmon shift is related to the diameter or energies relative to graphite occurred energies differs in nanotubes with the number of walls. This study did at around 18 eV, a shift that was just two to three walls from those not directly address the effect of identical no matter the diameter of with 5 to 14 walls, with higher

110 A rgonne National Laboratory Nanoscience

50

40

30

20 0

Energy Loss (eV) 10 1 2 3 0 1 2 3 4 Q (Å-1) < Fig. 1 Inelastic x-ray scattering spectra > Work performed at BNL was from the few-walled carbon nanotube supported by the U.S. Department of Energy, Division of Materials Science sample, as a contour plot. and Engineering, under Contract No. DE-AC02-98CH10886 and partially by DOE-CMSN. The contribution by GE and DHL was supported by the Division of Materials Sciences and Engineering, Basic Energy Sciences, U.S. Department energies for the π + σ in graphite, See > M.H. Upton1*, R.F. Klie2, of Energy, under Contract No. DE- lower energies in MWCNT, and J.P Hill3, T. Gog1, D. Casa1, W. Ku3, AC05-00OR22725. The contribution by 3 3 3 G.E. and D.H.L. was supported by the lowest energies in FWCNT; that is, Y. Zhu , M.Y. Sfeir , J. Misewich , DMSE, under Contract No. DE-AC05- 4 4 the fewer the walls, the lower the G. Eres , D. Lowndes , “Effect 00OR22725. Use of the Advanced Photon plasmon energies. of number of walls on plasmon Source at Argonne National Laboratory By chemically manipulating behavior in carbon nanotubes,” was supported by the U.S. Department of Energy, Office of Science, Office of Basic the number of walls, we may be Carbon 47, 162 (2009). DOI: Energy Sciences, under Contract No. one step closer to harnessing the 10.1016/j.carbon.2008.09.044 DE-AC02-06CH11357. energy of the sun via solar cells here on Earth. Author affiliations > 1Argonne National Laboratory, — Elise LeQuire 2University of Illinois, > 9-ID • XOR/CMC • Physics, 3Brookhaven National Laboratory, materials science • Liquid scattering, inelastic x-ray 4 Oak Ridge National Laboratory scattering, resonant inelastic x-ray scattering • 3.3-cm Undulator A • Correspondence > Accepting general users *[email protected]

The Advanced Photon Source Annual Science Report 2009 111 Nanoscience

Tailoring Catalytic Systems: Platinum Nanoparticles on a Metallic Oxide Nanocubes

to coalesce, and the center-to-center spacing between them increased, as IN SHORT > The noble metal platinum (Pt) is widely revealed by the SAXS data, resulting recognized for its utility in achieving the high catalytic in a linear dispersion ranging from performance and reduction of toxic emissions desired in fuel 3.5 to 6.3 nm apart. Following cells, environmental remediation technologies, and production 2 to 5 cycles of ALD, WAXS probes of liquid fuels. Like other noble metals, however, Pt is rare and showed that the nanoparticles grew expensive. For catalytic systems to become more efficient and larger in a linear fashion, from 1.0 to 2.7 nm. Particle size with one economically viable, the amount of Pt needs to be minimized cycle of ALD was extrapolated to and a clearer understanding of the surface morphology and be about 0.7 nm, though the size catalytic efficiencies of those systems must emerge. Using could, in fact, be smaller. a suite of tools available at the APS—scanning electron In addition, the chemical state of microscopy (SEM), small- and wide- angle x-ray scattering the Pt particles changed, as revealed by XANES data, shifting from (SAXS and WAXS), near-edge spectroscopy (XANES), and an oxidated state with one and extended x-ray absorption fine structure (EXAFS)—a team of twocycles, to a bulk metallic state researchers from Northwestern University and Argonne has with further ALD cycles as the explored the dispersion, size, shape, chemical state, and local Pt-O bond weakened and the atomic coordination of Pt nanoparticles on nanocubes of the relative numbers of Pt-Pt bonded metal oxide strontium titanate (SrTiO : STO), adding to our particles increased. The data were 3 collected at the DND-CAT 5-BM-D understanding of catalytic systems. and 5-ID beamlines, and the XOR/BESSRC 12-ID beamline. Of particular interest was the observation that Pt loading—the amount of material adhering to the STO nanocubes—was unexpectedly MORE > In the synthetic of ALD, have remained unexplored. low. An earlier study estimated manufacture of this heterogeneous This early stage of ALD is optimal that for Pt nanocatalysts used in catalytic system, organometallic for catalyst synthesis with efficient the production of direct methanol vapors of Pt are deposited over a platinum loading. fuel cells to become economically number of cycles, layer by layer, In this study, uncoated, feasible in the market place, the on metal oxide substrates through nonporous STO nanocubes with an loading must be on the order of a process called atomic layer edge length of 60 nm and a high 1 mg cm-2. Pt loading in this study deposition (ALD). After hundreds surface-area-to-volume-ratio were was 1.1 × 10-3 mg cm-2 after five of cycles of ALD, a thin, continuous subjected to 1 through 5 cycles of ALD cycles, which was consistent film coats the support structure, but ALD of Pt. SEM images following with earlier observations of efficient the initial phases, from 1 to 5 cycles three cycles of ALD revealed Pt Pt loading on high-surface-volume nanoparticles 2 to 3 nm in size carbon aerogel substrates. uniformly dispersed on all exposed Controlling the growth of surfaces of the cubes approximately noble-metal nanoparticles on oxide 4 to 8 nm apart (Fig. 1). substrates is crucial to improving the With each successive cycle efficiency, and lowering production of ALD, the Pt nanoparticles began cost, of heterogeneous catalytic

112 A rgonne National Laboratory Nanoscience

> This work was supported by the Institute for Catalysis in Energy Processes, Northwestern University (NU) (U.S. Department of Energy Grant DE-FG02-03ER15457) and by facilities support from the NU Materials Research Center (National Science Foundation MRSEC Grant DMR-0520513).DND-CAT is supported in part by: E. I. DuPont de Nemours & Co., Dow Chemical Co., and the State of Illinois. Electron microscopy was performed at ANL’s Electron Microscopy Center for Materials Research. Use of the Advanced Photon Source was supported by the U.S. Department of Energy, Office of Science, × Office of Basic Energy Sciences, under ANL-EMC 20.0kV 5.7 mm 500k SE(U) 100 nm Contract No. DE-AC02-06CH11357. < Fig. 1 The scanning electron micrograph shows 2-nm platinum clusters grown by atomic layer deposition on strontium titanate nanocubes that measure 60 nm on an edge.

> 5-BM-D • DND-CAT • Materials science, polymer science • High- energy x-ray diffraction • x-ray process with applications in energy See > Steven T. Christensen1, absorption fine structure • Bending conservation and environmental Jeffrey W. Elam2, Federico A. magnet • Accepting general users 1 1 remediation. X-ray probes at the Rabuffetti , Qing Ma , Steven J. > 5-ID • DND-CAT • Materials nanoscale bring us one step closer Weigand1, Byeongu Lee2, Soenke science, polymer science • Powder to understanding the surface Seifert2, Peter C. Stair1, Kenneth diffraction, small-angle x-ray morphology and chemical properties R. Poeppelmeier1, Mark C. scattering, surface diffraction, wide-angle x-ray scattering, x-ray 1 1 of these systems. Hersam , and Michael J. Bedzyk *, optics development/techniques, “Controlled Growth of Platinum x-ray reflectivity, x-ray standing — Elise LeQuire Nanoparticles on Strontium Titanate waves • 3.3-cm Undulator A • Nanocubes by Atomic Layer Accepting general users Deposition” Small 5(6), 750 (2009). > 12-ID • XOR/BESSRC • Chemistry, physics, materials Author affiliations > science • Small-angle x-ray 1 scattering, wide-angle x-ray Northwestern University, scattering, grazing incidence 2Argonne National Laboratory small-angle scattering, surface diffraction • 3.3-cm Undulator A • Correspondence > Accepting general users *[email protected]

The Advanced Photon Source Annual Science Report 2009 113 Nanoscience

Self-Assembling, Polymer-Grafted Nanoparticles Lead to Unique Nanocomposites

device. Taken together, the USAXS and TEM measurements determined IN SHORT > Nanocomposites typically consist of that the nanocomposite samples nanoparticles embedded within a matrix material, such as a contained one of four distinct types polymer. Nanocomposites have elicited considerable interest of self-assembled microscopic because of their potential to synergistically combine the structures: compact objects with properties of both their organic and inorganic constituents, spherical or “platelet-like” shapes; with favorable consequences for applications—for instance, sheets and interconnected objects; using polymers in the creation of biomimetic materials that short strings; and isolated particles. The various structures observed mimic those found in nature. To achieve these potential by the USAXS and TEM techniques property gains from such nanocomposites, scientists resulted from the way in which the must have the ability to control the spatial distribution of nanocomposite was prepared. In nanoparticles in a desired matrix. To date, there has been the nanocomposite samples, some little progress in this field. Researchers using the XOR 32-ID parameters were fixed, while others beamline at the APS have derived results that address this were varied. For example, in one set of experimental trials the molecular significant challenge and present a novel strategy to achieve mass of the polystyrene matrix, as control over the nanoparticle spatial distribution. well as the total annealing time (five days), were both held constant, while the numbers and molecular weights of the grafted polystyrene chains were varied. Using such techniques, researchers observed the range of MORE > The investigators chose the hydrophilic to hydrophobic nanocomposite structures described spherical silica nanoparticles with a domains. Notably, the polystyrene- above, including spherical clusters nominal diameter of 14 nm. Earlier grafted silica particles were, like of nanoparticles, nanoparticle sheets research had shown that when such the core silica particles themselves, (both thin and thick), and string-like nanoparticles are dispersed within a spherical in shape; yet the grafted structures. liquid polymer they tend to clump silica particles could spontaneously Another important finding together. It had been suggested that assemble into anisotropic (i.e., was that most of the nanocomposite such clumping could be prevented nonspherical) structures when mixed samples demonstrated time- if polystyrene chains were attached into the polymer matrix. dependent structures, meaning that to the silica nanoparticles, thus Ultra-small-angle x-ray continued exposure to annealing and shielding the hydrophilic particle scattering (USAXS) and transmission high-vacuum conditions changed core from the hydrophobic electron microscopy (TEM) were the sizes of the various nanoparticle matrix. Instead, these researchers the two principal methods employed structures. It was also determined found that the resulting hybrid for determining the resulting that mechanical stressing changed particles—consisting of molecular nanoparticle superstructures (Fig. 1). the characteristics of some of the polystyrene chains grafted onto silica The USAXS measurements, carried nanocomposite samples. nanoparticles—exhibited amphiphile- out at the 32-ID beamline of the APS, The researchers demonstrated like (or soap-like) behavior. The extended the TEM results spatially that the nanocomposite structure can grafted nanoparticles assembled since the x-ray technique has a larger be controlled by varying a number into a variety of nanostructures field of view, and hence can image of parameters, including annealing that reflected the relative ratio of larger structures than can the TEM time, mechanical processing,

114 A rgonne National Laboratory Nanoscience < Fig. 1 Left: TEM-determined morphologies See > Pinar Akcora1, Hongjun Liu1, > This work was supported by the National for several nanocomposites, where Sanat K. Kumar1*, Joseph Moll1, Science Foundation (NSF) through the Division of Materials Research, DMR- the polystyrene matrix molecular 2 2 Yu Li , Brian C. Benicewicz , Linda 0804647 (S.K.K.), a Nanoscale Science weight is fixed at 142 kg/mol. The S. Schadler3, Devrim Acehan4, and Engineering Center, NSF Award polystyrene graft chain length (Mg) Athanassios Z. Panagiotopoulos5, Number DMR-0642573 (P.A., S.K.K., Y.L., B.C.B., and L.S.S.), and a Materials and grafting density (Greek sigma) Victor Pryamitsyn6, Venkat Research Science and Engineering at 6 7 are the variables. The samples were Ganesan , Jan Ilavsky , Pappanan Princeton (A.Z.P.). D.A. is a member of cast at room temperature and then Thiyagarajan7, Ralph H. Colby8 the New York Structural Biology Center, annealed for five days at 150° C before and Jack F. Douglas9 “Anisotropic which is a STAR Center supported by the New York State Office of Science, sampling. Right: The USAXS data self-assembly of spherical polymer- Technology, and Academic Research. are for the samples represented in grafted nanoparticles,” Nat. Mater. V.G. and V.P. acknowledge partial support the top two rows of the TEM images, 8, 354 (April 2009). DOI: 10.1038/ from the Welch Foundation, the U.S. Army Research Office under Grant No. and corroborate the TEM results. nmat2404 W911NF-07-1-0268, and funds made available through the CONTACT program Author affiliations > from AFOSR. Use of the Advanced 1Columbia University, Photon Source was supported by the U.S. Department of Energy, Office of Science, 2 University of South Carolina, Office of Basic Energy Sciences, under grafting-chain density and chain 3Rensselaer Polytechnic Institute, Contract No. DE-AC02-06CH11357. molecular mass, and the molecular 4New York University School mass of the polymer matrix. Hence, of Medicine, 5Princeton University, it can be expected that a variety of 6University of Texas, 7Argonne useful properties can be fine-tuned National Laboratory, 8Pennsylvania > 32-ID • XOR • Materials science, when producing these unique and State University, 9National Institutes life science • Phase-contrast imaging, ultra-small-angle x-ray promising types of self-assembling of Standards and Technology scattering, radiography • 3.3-cm nanocomposites. Undulator A • Accepting general Correspondence > users — Philip Koth *[email protected].

The Advanced Photon Source Annual Science Report 2009 115 Nanoscience

Growing Nanowires from Supercooled Liquid Nanodroplets

scattered from the sample material, IN SHORT > The creation of nanowires constitutes a highly and subsequently attenuated via a rod-shaped beam stop. The diffuse active area of research within the field of nanotechnology. x-ray scattering from the sample was Better techniques for producing nanowires could lead to recorded using a two-dimensional improvements in a variety of devices including batteries, charge-coupled device camera. photovoltaic cells, gas sensors, and photonic crystals. By quantitatively analyzing Currently, several popular techniques used to make nanowires both horizontal and vertical cuts of the resulting GISAXS patterns, the require a catalyst in order to synthesize the nanowires onto sizes and shapes of the evolving a substrate. The researchers in this study used relatively nanostructures could be characterized simple techniques to produce nanowires without a catalyst. over time. The GISAXS data revealed Moreover, the researchers created their nanowires in a a process of nanowire formation in variety of sizes and from different metal oxides. In order which vaporized metal oxide settled upon the SiO /Si substrate, forming to obtain real-time data detailing their nanowires’ formation 2 nanodroplets of varying sizes. The under varying conditions, the researchers utilized the liquid nanodroplets were supercooled grazing incidence small-angle x-ray scattering (GISAXS) because they existed at temperatures technique at the XOR/BESSRC 12-ID beamline at the APS. below the bulk melting point for The GISAXS data (Fig. 1) revealed real-time formation of vanadium oxide. The nanowires that nanowires from supercooled liquid nanodroplets formed by formed and grew on the substrate did so largely by absorbing material from the condensation of metal oxide vapor. the supercooled liquid nanodroplets either through coalescence (merging), or through a process known as Ostwald ripening. Named for German chemist Wilhelm Ostwald who first described the phenomenon in MORE > As a first step, the silicon dioxide (SiO2) overlaying a 1896, Ostwald ripening involves researchers, from the University of substrate of silicon (Si). In all cases the accretion of material into larger California, Santa Barbara; Argonne; either a reducing gas (helium) or precipitates at the expense of and Yale University heated metal oxidizing gas (oxygen) was blown smaller ones, which shrink. Real- oxide powder in a specially-made over the heated metal oxide powder. time GISAXS imaging showed that oven. Though nanowires were A reducing environment (helium) nanostructure growth occurred more ultimately created using several within the furnace resulted in VO2 rapidly, and was much more complex, different kinds of metal oxides, crystallites (including nanowires), at a growth temperature of 600° C vanadium oxide was the sole material while oxidizing conditions lead to versus those grown at 550° C.

chosen for the GISAXS imaging. V2O5 nanowire formation. After a maximum of 30 min., The oven contained an internal heater In the GISAXS experiments the samples were quickly cooled. and a pair of ports to allow passage carried out at the 12-ID beamline, an The solidified nanostructures were of synchrotron x-rays. In a series intense 8-keV x-ray beam impinged examined using scanning electron

of experiments, vanadium oxide upon the SiO2/Si substrate at a microscopy (SEM), and in some powder was heated to between 550 shallow angle of 0.15°, which is just cases other techniques. The SEM and 650° C. The vaporized vanadium above the critical angle for total images reinforced the GISAXS oxide subsequently condensed external reflection. The incident results indicating Ostwald ripening inside the oven on a thin film of x-ray beam was both reflected and of both nanowires and nanodroplets.

116 A rgonne National Laboratory Nanoscience

The SEM micrographs also strongly of nanowires similar to those made correlation between nanowire growth linked nanostructure growth to the of vanadium oxide produced in the and the properties of its substrate. properties of their substrates. For GISAXS experiments. The researchers have confidence that instance, in a few experiments, This research demonstrated their ability to synthesize a variety of sapphire was used as a substrate; several straight-forward techniques metal oxide nanowire systems clearly post-cooling SEM images showed for producing a variety of crystalline demonstrates both the simplicity and preferential nanowire growth along metal oxide nanowires from generality of the new techniques. a line defect at the sapphire surface. supercooled liquid nanodroplets Experiments with oxides of without the need for catalysts. Real- — Philip Koth molybdenum and ruthenium were time GISAXS data, corroborated also performed by the researchers, by SEM images, revealed that the but without the real-time data phenomenon of Ostwald ripening was provided by GISAXS. Instead, post- a major factor contributing to growth See > Myung Hwa Kim1, Byeongdu cooling analysis used SEM and other of both nanodroplets and nanowires. Lee2, Sungsik Lee2, Christopher methods to confirm the existence SEM images also indicated a strong Larson1, Jeong Min Baik1, Cafer T. Yavuz1, Sönke Seifert2, Stefan Vajda2,3, Randall E. Winans2, Martin Moskovits1, Galen D. Stucky1,*, and Alec M. Wodtke1,**, “Growth of Metal Oxide Nanowires from Supercooled Liquid Nanodroplets,” Nano Lett. 9(12), 4138 (2009). DOI: 10.1021/nl902357q

Author affiliations > 1University of California, Santa Barbara; 2Argonne National Laboratory; 3Yale University

Correspondence > *[email protected] **[email protected]

> This work was supported by the Partnership for International Research and Education – for Electronic Chemistry and Catalysis at Interfaces – National Science Foundation Grant No. OISE- 0530268. The work at the APS was supported by the U.S. Department of Energy, BES-Chemical Sciences, and BES Scientific User Facilities under Contract No. DE-AC-02-06CH11357. < Fig. 1 Real-time snapshot dynamics of the VO nanowire growth at 600° C. (a) A series 2 > 12-ID • XOR/BESSRC • of GISAXS images of VO2 nanowire growth acquired at various times during in situ Chemistry, physics, materials experiments at 600° C under atmospheric pressure. Arrows represent the Bragg-rod science • Small-angle x-ray scatterings originating from nanodroplets. (b) In situ GISAXS fringe patterns of the scattering, wide-angle x-ray scattering, grazing incidence nanowire growth measured at different growth times for 600° C, showing that the small-angle scattering, surface spacing is gradually narrower with growth time. (c) The growth time dependence diffraction • 3.3-cm Undulator A of the average width and height for nanowires extracted from the analysis of fringe • Accepting general users patterns for 600° C. (Copyright © 2009 American Chemical Society)

The Advanced Photon Source Annual Science Report 2009 117 Nanoscience

Structure of Quantum Dots Revealed

was a high concentration of InAs IN SHORT > Tiny semiconductor crystals 10 to 50 atoms at the substrate–dot interface. The across called quantum dots (QDs) promise to enable quantum researchers were able to tell that computing and revolutionize photovoltaic cells, light-emitting the interfacial InAs was associated devices, and many other applications because it should with the top unit cell of the substrate and not with the dots themselves. prove possible to tune their optoelectronic properties with Similarly, the x-ray energy unprecedented precision by carefully controlling their size, dependence of the cross sections shape, composition, and strain characteristics. The day when provided a quantitative determination scientists will actually be able to accomplish all this just got of the Sb content, which the much closer, thanks to a breakthrough by researchers aided researchers associated with an outer by the XOR/UNI 33-ID beamline at the APS. The group GaSb shell. Much of this can be seen demonstrated the ability to construct three-dimensional from Fig. 1, which depicts electron (3-D) atomic-scale maps of these tiny bits of next to nothing density profiles measured normal that detail their structural and chemical compositions to the substrate surface through quantitatively. The new atomic-scale maps will let scientists lines of Group III (top) and Group measure the locations and chemical makeup of individual V (bottom) sites in the zinc-blende components of quantum dots at a resolution of 100th of a structure. The peaks to the left represent atoms in the substrate; nanometer, thereby clearing the path to more rapid progress those to the right correspond to the in the field of quantum-dot directed assembly. QD. The profiles are shown at the Ga-edge (red line) and As-edge (blue line) x-ray photon energies, in units of effective atomic number. This work provides the first atomic-scale mapping of the MORE > The researchers, from the performing Fourier transformations interface between epitaxial QDs University of Michigan, Soreq NRC, of the resulting complex scattering and a substrate, and establishes and Hebrew University, studied factors to map the full 3-D electron the usefulness of x-ray phasing QDs crystallized from indium (In) density map, from which one can techniques for this and similar droplets exposed to antimony (Sb) obtain key parameters such as systems. The ability to quantify as the QDs were deposited on a chemical composition, stacking, structural and chemical distributions gallium arsenide (GaAs) (100) strain, and dot shape. The method is in QD systems at the atomic substrate. Measurements of the QD generally applicable to any epitaxial level could resolve long-standing structures were performed in Bragg QD system. puzzles relating, for example, to the rod geometry on the 33-ID undulator The researchers found that the inverted electron–hole alignment beamline, which provides a highly QDs form coherently and extend observed in some QD systems. intense, tunable beam of x-rays. a few unit cells below the GaAs The power of COBRA for detailed The Bragg rod data were analyzed surface. Their most interesting mapping of chemical, strain, and using coherent Bragg rod analysis observation was that the GaAs structural aspects of a broad range (COBRA)—an x-ray phase retrieval content is qualitatively similar deep of epitaxial QD systems provides a method specific to epitaxial systems. in the substrate and in the dots. This new capability that should have a The method consists of measuring shows that the dots are not simply significant impact on nanotechnology diffraction intensities along the composed of In and Sb; their cores as QD systems continue to be refined substrate-defined Bragg rods, are practically pure GaAs. Also and controlled for many applications. analyzing the results to determine evident from the energy dependence the diffraction phases, and then of the x-ray scattering cross sections — Vic Comello

118 A rgonne National Laboratory Nanoscience

See > Divine P. Kumah1, Sergey Shusterman2, Yossi Paltiel3, Yizhak Yacoby3, and Roy Clarke1,*, “Atomic-Scale Mapping of Quantum Dots Formed by Droplet Epitaxy,” Nat. Nano. 4, 835 (27 September 2009). DOI: 10.1038/NNANO.2009.271

Author affiliations > 1University of Michigan, 2Soreq NRC, 3Hebrew University

Correspondence > *[email protected]

> The work was supported by the U.S. National Science Foundation under Grant DMR-0606048. Use of the Advanced Photon Source was supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, under < Fig. 1 (a) The almost identical Group III peak heights at two energies in the range Contract No. DE-AC02-06CH11357. –6 Å ≤ z ≤0 indicate a high concentration of InAs at the substrate surface; (b) split Group V dot peaks for 6 Å ≤ z ≤ 40 Å indicate a GaSb-like shell. The black arrow indicates the stacking sequence shift between the substrate and the dot. Top inset: schematic of the core-shell structure of the droplet QDs, illustrating > 33-ID • XOR/UNI • Chemistry, the penetration of the dot through the InAs surface layer into the GaAs substrate. materials science, physics Bottom inset: occupancy fraction of In and Sb as a function of height, z, above • Anomalous and resonant the nominal dot–substrate interface. scattering (hard x-ray), diffuse x-ray scattering, general diffraction, surface diffraction, x-ray reflectivity, x-ray standing waves • 3.3-cm Undulator A • Accepting general users

The Advanced Photon Source Annual Science Report 2009 119 Nanoscience

Seeing Strain Inside a Nanocrystal

of the x-ray beam, the researchers IN SHORT > The electronic, optical, and magnetic properties tweaked its orientation until they of nanocrystals and other nanostructures can dramatically found the first strong reflection. With depend on fine details of these materials' atomic structures, that orientation identified, they could then move the nanocrystal into other such as departures from ideal crystal geometry. Such alignments where the angle of the variations arise almost inevitably during the growth of x-ray beam with respect to the lattice nanocrystals on substrates, from the influence of neighboring also produced strong reflections. At nanocrystals, or from the presence of dopant atoms in the each of six positions, they recorded a crystal lattice. Using the XOR/UNI 34-ID beamline at the series of 2-dimensional slices of the APS, researchers for the first time measured x-ray diffraction diffraction pattern, from which they could reconstruct the full patterns from a single nanocrystal in six different orientations, 3-D pattern (Fig. 1). obtaining enough information to construct a full three- Determining the strain on the dimensional (3-D) map of the distortion of the crystal lattice nanocrystal from these measurements from its ideal form. The technique allows researchers to study required inferring the phase shifts closely how a nanocrystal's properties relate to its structure, in the x-ray reflections from the diffraction patterns, then inferring the in principle enabling those properties to be fine-tuned for a distortion of the crystal lattice from desired application. the phase shifts. The researchers did this through an iterative procedure, first modeling the lattice to predict diffraction patterns, then comparing the predictions against the experimental results in order MORE > X-ray diffraction been able to measure coherent x-ray to adjust the model. In principle, measurements can reveal the diffraction from a single orientation, diffraction data from three crystal distortion or strain in a single crystal, from which limited information orientations are enough to obtain a provided the x-rays are coherent about strain on the lattice can be 3-D map of the strain. With data from in phase throughout the crystal's deduced. six orientations, over-determining the volume. If x-rays hit an ideal crystal To get a fuller picture, problem, the researchers employed a at certain angles, reflections from the researchers from University College statistical technique to obtain a best- atoms will maintain a coherent phase London, Argonne, and the Diamond fit solution. relationship and produce a strong Light Source devised a mounting The resolution of the signal. Any of the atoms that are system that allowed them to move measurements is about 40 nm, an displaced from their ideal positions a nanocrystal through a series of order or magnitude greater than the will reflect x-rays out of phase, chosen orientations. They first typical distances between atoms. creating an interference pattern. Until grew ZnO crystals in the form of On this scale, the ZnO nanocrystal now, however, the inability to adjust hexagonal prisms measuring 2-4 µm showed a pattern of alternating precisely a nanocrystal's alignment long and 1- 2 μm across. They then compression and tension along its has meant that researchers have only selected a single nanocrystal and length, which the researchers suggest stood it end up on a small sheet of results from the absorption of oxygen silicon. Heating the assembly in pure atoms into the base of the crystal as oxygen formed a thin SiO layer that it was being secured to the silicon secured the nanocrystal in place. mounting sheet. Placing the nanocrystal on its Measurements at higher mounting sheet positioned in the path resolution, which would require

120 A rgonne National Laboratory Nanoscience < Fig. 1 (a) Two-dimensional slices showing the six independent components of the strain tensor for a ZnO nanocrystal, describing the distortion of its crystal lattice from ideal form. The orientations of the slices correspond to the three axes depicted in (b). Purple and red indicate compression of the lattice, green and blue expansion. Scanning electron micrograph (c) shows the ZnO rod secured to a silicon sheet. (Scale bar: 2 μm)

improvements to both the x-ray See > Marcus C. Newton1*§, > This work was supported by EPSRC beam quality and the instrumentation, Steven J. Leake1, Ross Harder2, Grant EP/D052939/1 and an ERC FP7 could measure the distortion and Ian K. Robinson1,3, “advanced grant.” Beamline 34-ID was built with funds from the U.S. National introduced into a lattice by the “Three-dimensional imaging Science Foundation under Grant presence of individual dopant of strain a single ZnO nanorod,” DMR-9724294 and operated by the U.S. atoms, or allow engineering of Nat.Mater., 9, 120 (2010). Department of Energy, Office of Science, semiconductors to improve their Office of Basic Energy Sciences, under electrical properties. Performed Author affiliations > Contract DE-AC02-06CH11357. with femtosecond x-ray pulses 1University College London, from free-electron lasers, the 2Argonne National Laboratory, technique could even capture 3Diamond Light Source § > 34-ID • XOR/UNI • Materials snapshots of the dynamic distortion Present address: University of science, physics • Coherent x-ray of a crystal structure. Surrey, U.K. scattering, microdiffraction • 3.3-cm Undulator A • Accepting — David Lindley Correspondence > general users *[email protected]

The Advanced Photon Source Annual Science Report 2009 121 Structural Studies

Atomic Structure of the Epitaxial BaO/Si Interface Revealed

< < Fig. 1 Comparison of measured x-ray IN SHORT > The semiconductor industry has relied on scattering and DFT structure predictions. The measured scattering silica (SiO ) as the gate dielectric in field effect transistors 2 in the graphs is taken from CCD for nearly 50 years. Over this period, chipmakers have images of diffraction with 2 × 1 continued to boost electronic performance mainly through symmetry as shown in panel c. scaling—that is, by shrinking the conductors and the spaces The open circles in the graphs are between them in electronic devices to shorten the distance the data, and the solid black line is predicted from the DFT-derived traveled by electrons. But with SiO2 thicknesses currently structure in panel b. The sensitivity in the regime below 50 Å, the scaling approach to achieving of the scattering to structural details increased performance is nearing its limit, as further is shown by the dashed red line, decreases in thickness could lead to excessive tunneling which is the predicted scattering from currents. In recent years, crystalline oxides have emerged a DFT-derived structure that differs from the best-fit model by only 1 as a promising alternative to amorphous SiO2 because they monolayer of oxygen at the interface. could fundamentally change the scaling laws for silicon- based transistor technology by virtue of their high dielectric constants, so science is intent on experimentally proving the diffraction expected from first theory in regard to these potentially important materials. principles density functional theory Researchers using an APS beamline have determined the (DFT) relaxed ground states. This structure and composition of one such crystalline oxide, approach offers advantages over structural refinement using only XRD lighting the way to closing the theory-experiment gap. data because the DFT relaxed ground state structures are sensitive to the position and composition of interface elements including those that scatter x-rays weakly, such as oxygen and Si, thus making little direct contribution MORE > Barium oxide (BaO) the interface. Transmission electron to the diffracted intensities. is the simplest crystalline oxide microscopy and x-ray diffraction Epitaxial BaO was grown on that can be grown on silicon (Si). (XRD), for example, have failed Si using molecular beam epitaxy in a Nevertheless, the structure of the to provide conclusive results on layer-by-layer approach with barium BaO/Si interface is complex because interface structure because of a lack being deposited in the presence of abrupt transitions in chemistry, of either resolution or sensitivity. of oxygen. The researchers then bonding, and crystal structure. Despite all this, researchers performed XRD measurements at the Several competing theoretical from Yale University and Argonne XOR/UNI 33-ID beamline, focusing proposals as to the structure of this were able to fully determine the on diffracted intensities related to interface have been developed, which structure and composition of the the 2 × 1 unit cell reconstruction. differ fundamentally on issues as BaO/Si interface by using the This type of scattering occurs only basic as its elemental composition. existence of an epitaxial strain- in the interface region, since bulk Si Deciding among them experimentally induced 2 × 1 reconstruction at the and BaO do not have this in-plane has proven challenging because of interface to transform XRD into periodicity. By homing in on this the inherently complex chemistry an interface-specific technique that diffraction, the researchers were involved and the nanoscale depth of permits detailed comparisons with able to address questions concerning

122 A rgonne National Laboratory Structural Studies

See > Yaron Segal1, Jim W. Reiner1, Alexie Kolpak1, Zhan Zhang2, Sohrab Ismail-Beigi1, Charles Ahn1, and Fred Walker1*, “Atomic Structure of the Epitaxial BaO/ Si(001) Interface,” Phys. Rev. Lett. 102, 116101 (20 March 2009). DOI:10.1103/PhysRevLett. 102.116101

Author affiliations > 1Yale University, 2Argonne National Laboratory

Correspondence > *[email protected]

> Support for this work was provided by the National Science Foundation, under MRSEC DMR 0520495 and DMR 0705799, and SRC. Use of the Advanced interface structure and composition XRD results with the use of only Photon Source was supported by the U.S. far more precisely than would be three adjustable parameters. The Department of Energy, Office of Science, Office of Basic Energy Sciences, under possible with diffraction data from researchers concluded that the Contract No. DE-AC02-06CH11357. the entire structure. The diffraction observed BaO/Si 2 × 1 interfacial data revealed a sub-angstrom reconstruction was driven by the rumpling of the BaO and Si layers bonding configuration of the first adjacent to the interface. monolayer of oxygen in the BaO > 33-ID • XOR/UNI • Chemistry, DFT calculations for the and that an additional monolayer of materials science, physics relaxed ground states of several oxygen was bonded to the surface • Anomalous and resonant proposed interface structures revealed Si atoms. Two BaO layers and four Si scattering (hard x-ray), diffuse x-ray scattering, general that only one was consistent with layers adjacent to the interface were diffraction, surface diffraction, the observed XRD data (Fig. 1). The found to be significantly rumpled by x-ray reflectivity, x-ray standing XRD intensities from this theoretical epi ­taxial strain. waves • 3.3-cm Undulator A • structure matched all of the features Accepting general users observed in the experimental — Vic Comello

The Advanced Photon Source Annual Science Report 2009 123 Structural Studies

High Pressure Extinguishes Chromium’s Magnetism

antiferromagnet, magnetically patterns due to charge density IN SHORT > The polarized atoms line up alternately waves that accompany the spin in opposite directions, so that density waves (Fig. 1). An intense metallic element the material as a whole has no x-ray beam was needed because the chromium possesses magnetic moment. This orderly diffraction peak from the electrons an unusual form of arrangement only exists when the was only one ten billionth as strong magnetism that comes material’s temperature is below as the diffraction signals from the about because of the critical value of the Néel crystal structure itself. cooperative behavior temperature. In chromium, however, The scientists first established among conduction antiferromagnetism arises through that the lattice constant of chromium electrons. Researchers the behavior of conduction electrons shrinks in a smooth manner from that can move freely through the ambient pressures all the way up to working at XOR metal’s atomic lattice structure— about 15 GPa at low temperature, beamline 4-ID-D at hence the label “itinerant,” as in meaning that no structural change the APS have shown itinerant ferromagnetism. Below the in the lattice occurs. However, the that when the metal is Néel temperature, these electrons characteristic length-scale of the squeezed by pressures do not move independently but spin density wave behaved quite approaching 10 maintain a fixed phase relationship Gpa—about 100,000 throughout the lattice, forming so-called spin density waves with atmospheres— antiferromagnetic alignment. chromium’s magnetism The theory of these spin density > Fig. 1 Black dots show the measured unexpectedly disappears. waves is analogous to the Bardeen- intensity, relative to diffraction The transition is driven, Cooper-Schrieffer (BCS) theory from the lattice, of the x-ray the researchers argue, of superconductivity, which diffraction line from charge density by quantum fluctuations describes how electrons pair up waves (which are harmonically that allow conduction in the superconducting state. One related to spin density waves) that implication of the theory is that characterize the antiferromagnetism electrons to hop out increasing the pressure on chromium in chromium. The Néel temperature, of their orderly state. should cause its antiferromagnetism above which the spin and charge Because pure chromium to vary in a predictable way. density waves cannot exist, can be is such a “clean” system, To test this prediction, a inferred from the diffraction intensity. it can serve as a model team of researchers from The At the highest pressures, the for understanding similar University of Chicago, Argonne, intensity falls off sharply compared transitions in more the University of Cambridge, and to theoretical expectation (blue the Massachusetts Institute of dashed line), indicating the onset chemically complex Technology made use of the fact that of quantum criticality. Cartoons materials. the wavelength of the spin density are proposed representation of waves is slightly different from the density wavefronts. At low chromium’s lattice constant, which temperature and pressure, the defines the size of the unit cube in waves are strong and well-defined the metal’s body-centered cubic (bottom left), diminishing at higher structure. Placing a tiny crystal of temperature (upper left); as the MORE > Chromium displays chromium, mounted in a diamond pressure grows to about 10 GPa, a property known as itinerant anvil cell, in the 4-ID-D beamline, the waves weaken and lose their antiferromagnetism. In a typical the team obtained diffraction coherence (bottom right).

124 A rgonne National Laboratory Structural Studies

differently. Expressed as a ratio of new states—disordered, or ordered chromium is technically demanding the lattice constant, it decreased in some novel way—the electrons to study, the researchers believe its for pressures up to a few GPa, then jump into. freedom from interfering causes reached a relative minimum at A similar transition has been makes it the ideal experimental about 6 GPa, after which it began known for decades to occur at zero example of this subtle form of to increase. Similarly, the strength pressure in alloys of chromium quantum behavior. of the diffraction signal from the and vanadium as the proportion of charge density wave exhibited vanadium steadily increases. In that — David Lindley different behavior in these two case, though, the transition involves pressure ranges. Below 6 GPa chemical changes and disorder, it decreased exponentially with making the mechanism hard to figure increasing pressure, as predicted out. The pressure-driven transition See > R. Jaramillo1,§, Yejun Feng1,2, by the BCS theory. Above in pure chromium represents what J.C. Lang2, Z. Islam2, G. Srajer2, 7 GPa, however, it began to fall the scientists call a “naked quantum P.B. Littlewood3, D.B. McWhan4, off more sharply, and disappeared singularity,” in which there are and T.F. Rosenbaum1*, “Breakdown in a continuous way at a pressure no other obscuring phenomena. of the Bardeen–Cooper–Schrieffer somewhat less than 10 GPa. In contrast, a quantum transition ground state at a quantum phase The implication of these from one kind of electronic order transition,” Nature 459, 405 (2009). findings, the researchers say, is that to another is suspected to drive DOI:10.1038/nature08008 the BCS-like spin density wave state the formation of Cooper pairs in disappears because electrons jump high-temperature superconducting Author affiliations > into other states that classically copper oxides, but the underlying 1The University of Chicago, they should not be able to reach. physics is complicated by chemical 2Argonne National Laboratory, These quantum fluctuations destroy disorder and is obscured by the 3University of Cambridge, chromium’s antiferromagnetism, superconducting phase itself. 4Massachusetts Institute of Technology although it remains unclear what Although the quantum transition in §Present address: Harvard University

Correspondence > *[email protected]

> The work at The University of Chicago was supported by the U.S. National Science Foundation (NSF) Division of Materials Research. Use of the Advanced Photon Source at Argonne National Laboratory was supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, under Contract No. DE-AC02-06CH11357.

> 4-ID-D • XOR • Physics, materials science • Anomalous and resonant scattering (hard x-ray), magnetic x-ray scattering, magnetic circular dichroism (hard x-ray) • 3.5-cm undulator • Accepting general users

The Advanced Photon Source Annual Science Report 2009 125 Structural Studies

Thin Films in the Thick of It

< < Fig. 1 Stages of evolution of GISAXS IN SHORT > Agglomeration is a phenomenon that can be from an evaporated Ni film, seen on any rainy day, as water beads on the hood of a freshly- as a function of time, held at a waxed car. On a much smaller scale, however, it is important temperature that leads to the agglomeration process. in microelectronics. The breakup of a conducting film on a microchip can lead to broken electrical connections, data loss, and device malfunctions. But if properly controlled, the process annealing process, depending on the can also be used to create conducting arrays. Experimenters initial thickness of the Ni films. The using XOR/UNI beamline 34-ID employed GISAXS (grazing first regime (under 5-nm thickness) shows the formation of small clusters incidence small-angle x-ray scattering) to characterize the of Ni on a residual Ni layer, with agglomeration process in thin metal films, showing for the first no exposure of the Si substrate film. time how it happens in real time and in situ. The work provides In films of more than 5-nm initial another interesting example of how nanometer-sized systems thickness, however, the Ni breaks can behave quite differently from bulk materials, and raises the up completely into large clusters, possibility that similar agglomeration behaviors may emerge well-separated from each other, with a clean Si substrate fully exposed with nanofilms of different compositions. between the clusters. The process seems to be more time-dependent in the thicker films (greater than 5 nm), with little or no further development after about 7000 s at 625K, while in films that are thinner than 5 nm, MORE > The researchers— for its facility in revealing fine a change in temperature results in a from the University of Genoa, the surface morphology (Fig. 1). marked change in the evolution of European Synchrotron Radiation After measuring the x-ray the regime. Facility, and University College reflectivity of the silicon substrate, To explain this behavior, the London —studied the evolution of the experimenters carefully deposited experimenters propose that in the Ni films as they were deposited onto an Ni film on each sample using an thicker films, the film roughness a SiO2 substrate. The team chose the e-beam evaporator while carefully increases with temperature until, at 34-ID beamline because it allows the monitoring and maintaining the film about 625K, grooves begin to form x-ray beam to strike the experimental thickness. Samples were prepared in the film surface. As these grooves film surface directly without an with different Ni film thicknesses grow and become deeper, the silicon intervening beryllium window at the of approximately 2 to 10 nm. The substrate is eventually exposed, and exit point. This was an important thickness and density of the Ni film then the enlarging grooves finally consideration in this case because the on each sample was confirmed, and begin to merge and the film breaks diffuse scattering from a Be window then the annealing process was begun up into large islands of Ni, separated might make it difficult to measure under GISAXS monitoring as the by fully exposed substrate. In films the extremely small scattering signal silicon dioxide substrate temperature thinner than 5 nm the overall energy generated by the nanoclusters that was raised in steps up to a maximum of the system is insufficient to would form under agglomeration. of about 700K. After the annealing allow the grooves to deepen to the The GISAXS technique was chosen procedure was completed, atomic substrate, so the film cannot break force microscopy was employed to up into large separated grains. study the surface morphology of Although previous experiments each sample filmex situ. have been done on agglomeration The researchers found that two in thin films, the present work different regimes emerged under the represents one of the few attempts

126 A rgonne National Laboratory Structural Studies

to study the process under real-time that question will welcome further in situ conditions and in such detail. investigation and study. While the researchers allow that their experimental parameters do not rule — Mark Wolverton out the possibility that agglomeration might still occur in thin films under different time and temperature See > C. Boragno1, F. Buatier conditions, they emphasize that their de Mongeot1, R. Felici2, and I.K. crucial finding is the development Robinson3*, “Critical thickness of separate thickness-dependent for the agglomeration of thin > Use of the Advanced Photon Source regimes. metal films,” Phys. Rev. B 79, was supported by the U.S. Department of Energy, Office of Science, Office of Basic The work provides another 155443 (2009). DOI: 10.1103/ Energy Sciences, under Contract No. interesting example of how PhysRevB.79.155443 DE-AC02-06CH11357. nanometer-sized systems can behave quite differently from bulk Author affiliations > materials, and raises the possibility 1Università di Genova, 2European > 34-ID • XOR/UNI • Materials that similar agglomeration behaviors Synchrotron Radiation Facility, science, physics • Coherent x-ray may emerge with nanofilms 3University College London scattering, microdiffraction of different compositions. The • 3.3-cm Undulator A • Accepting important practical and commercial Correspondence > general users microelectronic implications of *[email protected]

The Advanced Photon Source Annual Science Report 2009 127 Structural Studies

Making Things Fit in a New Ce-Al Alloy

of the hexagonal Ce3Al as pressure IN SHORT > Ever since the Bronze Age, humans have known was increased. Again, the new phase the advantages of alloys. By combining atoms of different remained even as pressure was metals, it is possible to create a new material featuring not reduced. When the sample was heated only the best qualities of both, but entirely new and highly with an Nd:YLF laser to temperatures of up to approximately 900K, useful properties. In general, alloys are formed by substituting the experimenters saw reversible the atoms of one material into the crystalline structure of transitions between the hexagonal another. But nature has imposed some strict limitations on and fcc phases in the range of which particular elements can be combined in this way. Those 5 to 6 GPa. limits, called Hume-Rothery (HR) rules, dictate that metals Using Ce L3-edge x-ray can be combined only within certain limits of atomic size and absorption spectroscopy at the XOR/ valence. As is the case with many rules, there is some wiggle PNC 20-BM beamline and ab initio calculation, the team determined that room, under the proper conditions. Working at two different delocalization of the 4f electron in Ce, APS beamlines, an international team of researchers stretched along with Kondo volume collapse, those rules a little and created a new alloy from Ce and Al, are the major factors allowing the two elements that usually can’t be put together in such a way new fcc alloy to form under the according to the HR limits. This work provides insights about HR limitations. After pressure was the ways two dissimilar materials can join together to form reduced to ambient levels, the 4f electron in Ce returned to its normal something completely new and different, with properties that state and the Kondo volume collapse could be employed in a wide range of applications. reversed, but the new fcc alloy structure remained. The work opens up some intriguing possibilities both for the creation of new and novel Ce-Al alloys and for the development of MORE > The rare-earth metal HP-CAT 16-ID-B beamline at the other Ce and f-electron alloys, all of cerium (Ce) and the common alloy APS under various hydrostatic which will provide further insight ingredient aluminum (Al) are two pressures (Fig. 1). Up to 24.4 GPa, into the ways in which two dissimilar elements that generally combine the observed x-ray diffraction materials can join together to form only in stoichiometric compounds patterns were typical of the something altogether different. or highly disordered metallic glasses disordered amorphous glass state, New alloys also hold the promise within the framework of the Hume- as expected. But at 25.0 GPa, sharp of different and valuable properties Rothery rules. The experimenters diffraction features indicative of full that can be employed in a variety sought to discover if high pressure crystallization in an fcc structure of materials to fit a wide range of might overcome the atomic size abruptly appeared. The crystallization applications. But the research team’s differences between Ce and Al persisted even as the pressure was work also serves to demonstrate that atoms and allow the creation of a reduced to the ambient level. while nature’s rules can sometimes true substitutional face-centered Next, the researchers subjected seem impossible to overcome, they cubic (fcc) structure in an alloy that a Ce3Al stoichiometric compound nevertheless allow human ingenuity could exist at room temperature and to hydrostatic pressure, again to find new ways to work within ambient pressures. using XRD to detect changes in those rules.

They first created a Ce3Al the compound’s normal hexagonal metallic glass by rapid cooling crystalline structure. Beginning — Mark Wolverton of melt, examining the structure at 15 GPa, an fcc phase began to with XRD (x-ray diffraction) at the appear, replacing more and more

128 A rgonne National Laboratory Structural Studies

< Fig. 1 In situ high-pressure synchrotron

x-ray diffraction patterns of Ce3Al at 298K using x-ray wavelength l = 0.3681(1) Å and atomic

structures of Ce3Al phases. (a) Starting with a metallic glass, the transition occurs at 25 GPa. Intensity mismatch to the fcc structure is due to the growth of large crystals in the sample. (b) Starting with hexagonal

a-Ce3Al, the transition occurs at 15 GPa. (c) Crystal structures of the

two ordered compounds α-Ce3Al

and β-Ce3Al, and the new disordered

fcc-Ce3Al alloy.

W. M. Keck Foundation. XOR/PNC facilities at the Advanced Photon Source, and research at these facilities, are supported by the U.S. Department of Energy, Office of Basic Energy Sciences, a major facilities access grant from Natural Sciences and Engineering Research Council of Canada, the University of Washington, Simon Fraser University, and the Advanced Photon See > Qiao-Shi Zeng1,2, Yang > This work was supported by the Balzan Source. Ding2, Wendy L. Mao3,4, Wei Luo5,6, Foundation; National Natural Science 5 5,6 Foundation of China Grants 50425102, Andreas Blomqvist , Rajeev Ahuja , 50601021, 50701038, 60776014, Use of the Advanced Photon Source was 2 2 Wenge Yang , Jinfu Shu , 60876002, and 10804096; the Zhejiang supported by the U.S. Department of Stas V. Sinogeikin2, Yue Meng2, University–Helmholtz Cooperation Energy, Office of Science, Office of Basic Energy Sciences, under Contract No. Dale L. Brewe7, Jian-Zhong Jiang1*, Fund;the Ministry of Education of China (Program for Changjiang Scholars, DE-AC02-06CH11357. 1,2 and Ho-kwang Mao **, the Research Fund for the Doctoral “Substitutional alloy of Ce and Al,” Program of Higher Education from China Proc. Natl. Acad. Sci. USA 106(8), Scholarship Council); the Department 2515 (February 24, 2009). of Science and Technology of Zhejiang Province; and Zhejiang University. DOI: 10.1073_pnas.0813328106 > 16-ID-B • HP-CAT • Materials W.L., A.B., and R.A. are grateful to the science, geoscience • Swedish Research Council for providing Microdiffraction, powder diffraction, Author affiliations > 1Zhejiang financial support, the Swedish National single-crystal diffraction • 3.3-cm 2 Infrastructure for Computing, and the Undulator A • Accepting University, Carnegie Institution of Uppsala Multidisciplinary Center for 3 general users Washington, Stanford University, Advanced Computational Science for 4SLAC National Accelerator providing computational resources. > 20-BM • XOR/PNC • Chemistry, Laboratory, 5Uppsala University, Use of the High Pressure Collaborative environmental science, Access Team facility was supported by 6Royal Institute of Technology, geoscience, materials science the Department of Energy, Office of Basic • Microfluorescence (hard x-ray), 7 Argonne National Laboratory Energy Sciences; Department of Energy, micro x-ray absorption fine National Nuclear Security Administration structure, x-ray absorption fine Correspondence > (Carnegie/Department of Energy Alliance structure • Bending magnet Center); the National Science Foundation; • Accepting general users *[email protected] Department of Defense, Tank-Automotive **[email protected] and Armaments Command; and the

The Advanced Photon Source Annual Science Report 2009 129 Structural Studies

Seeing Microstates through the Speckles

(1 × 1) surface. Although the general IN SHORT > It is easy to miss the forest for the trees, kinetics of the process has been but sometimes it is necessary to pay attention to both at observed in previous studies, the the same time, as in the study of surfaces where interesting use of coherent scattering in the structural changes can occur. Using different techniques, current work allowed the dynamics of the reconstructions to be directly scientists can look with high resolution at small areas of atoms observed in real time. (the trees) or at the average properties of the larger surface Speckle patterns obtained from (the forest) during an experiment. It can also be important the coherent x-ray scattering show to observe changes on the atomic scale and over a very large that at room temperature, the surface area at the same time, such as when the average surface dynamics of the Au(001) monolayer properties of a sample appear constant but the surface itself are fairly quiescent, but begin to change quickly as the temperature is dynamically evolving through different configurations. is increased. This is due to the These microstates are important to catalytic processes movement of the boundaries of the and other interactions, but often difficult to study. Many hex domains and the rearrangement techniques, such as standard x-ray scattering, average out of a uniaxial corrugation within information about the entire structure so that data on the very each domain. The increasingly rapid evolution of the microdomains is limited and transient microstates is lost. Working at the XOR demonstrated by fluctuations in 8-ID-E beamline at the APS, researchers used a new coherent the speckle patterns at different x-ray scattering technique to capture microstate surface temperatures. Speckle patterns were dynamics in a monolayer of gold atoms with unprecedented shown to be relatively stable at clarity in real time. Their work points to new possibilities for 1105K with only very slow changes a greater and more detailed understanding of surface phase in intensity and configuration. However, at higher temperatures transitions and how various crystalline solids interact with such as 1120K and 1130K, the other solids, liquids, and gases. speckle evolved rapidly, indicating that the surface microstates were undergoing significant changes, even when the temperature was held constant and the overall intensity and width of the peak did MORE > The researchers from the system—observing changes not change. Argonne, Safarik University, and in those patterns allowed the By measuring how fast the HASYLAB collected speckled experimenters to see the temperature- speckle changed, the research team scattering patterns from the surface dependent dynamics of this surface was able to obtain quantitative data reconstruction of Au(001) for the first time, even when the on the surface dynamics, which (Fig. 1). Because each speckle average properties of the system revealed two definite temperature pattern acts like a detailed picture appeared static. regimes separated by a transition of the microstate—a fingerprint of The surface reconstruction of point at ∼1070K. Below this Au(001) is a quasihexagonal (hex) transition temperature, speckle arrangement of atoms, known to patterns changed at a slow rate, but occur in two different orientations. the rate of change sharply increased The properties of the surface are above the transition point. Above also dependent on temperature, with the transition temperature, the fast the reconstruction vanishing at high surface dynamics were governed temperature, leaving a disordered mainly by hex domains changing to

130 A rgonne National Laboratory Structural Studies

See > M.S. Pierce1*, K.C. Chang1, D. Hennessy1, V. Komanicky1,2, M. Sprung1,3, A. Sandy1, and H. You1, “Surface X-Ray Speckles: < Fig. 1 Highly coherent x-rays scatter from the gold surface at a position that maximizes Coherent Surface Diffraction from the available signal from the surface atoms. The main view shows the inside of the Au(001),” Phys. Rev. Lett. 103, sample chamber during the experiment. Because of the large degree of coherence 165501 (16 October 2009). DOI: of the x-rays, the scattering patterns are highly speckled and contain information 10.1103/PhysRevLett.103.165501 about the configuration and profile of the surface. The sample is being held at a constant temperature of 1200K and the glow from the sample illuminates the inside Author affiliations > of the chamber. Top Left Inset: An example of a speckle pattern collected. If the 1Argonne National Laboratory, surface is unchanging then the speckle will stay in the same configuration. If the 2Safarik University, surface is changing, the speckle with change too. Bottom Right Inset: A cartoon 3Deutsches Elektronen-Synchrotron picture of the two orientations of the quasi-hexagonal surface atom reconstruction over the (1 x 1) bulk. The height variation is exaggerated. Correspondence > *[email protected]

(1 × 1) areas and by (1 × 1) thick surface layer as a viable > This work and use of the Advanced areas reconstructing back to hex technique and used it to observe the Photon Source were supported by the U.S. Department of Energy, Office of domains. The experimenters microstate dynamics of the Au(001) Science, Office of Basic Energy Sciences, conclude that this is due to the surface layer phases with enhanced under Contract No. DE-AC02-06CH11357. increasing activation of the (1 × 1) clarity in real time. The work opens domains, resulting from a steadily new experimental possibilities decreasing difference in free energy for achieving a greater and more between the hex and (1 × 1) regions. detailed understanding of surface > 8-ID-E • XSD • Materials science, Below the transition temperature, phase transitions and how various physics, polymer science • Grazing however, the slow dynamics crystalline solids interact with other incidence small-angle scattering, intensity fluctuation spectroscopy, consisted mostly of changes between solids, liquids, and gases. x-ray reflectivity, x-ray photon the two hex phases. correlation spectroscopy • 3.3-cm Through this work, — Mark Wolverton Undulator A • Accepting general the experimenters have both users demonstrated coherent x-ray surface scattering from a mono-atomic

The Advanced Photon Source Annual Science Report 2009 131 Novel X-ray Techniques & Instrumentation

A Synchrotron as a Lens to Observe Condensed Matter under Extreme Shockwave Compression

broadening in the diffraction IN SHORT > The behavior of materials under extreme patterns was observed, as shown in Fig. 1. The broadening indicates conditions is of great scientific interest. The effects of planar that these LiF(100) crystals shock waves—such as those generated by laser drivers, developed substructures with lattice flyer plate impacts, or high explosives—can lead to large rotations of order 1 degree and a compressions and uniaxial strain in the material, but studies characteristic size for coherently of these phenomena have been largely restricted to continuum diffracting domains (CDD) ranging measurements and analysis. The ability to perform real-time from 0.1 to 10 µm. Experiments were also carried out for contrast on measurements of the changes taking place in the crystal LiF crystals elastically compressed structure and the lattice deformation at pico- to nanosecond along [111]. In this case, the time scales is crucial in order to better understand the physical diffraction pattern indicated lattice and chemical properties of condensed matter under extreme compression, but did not change in conditions. Experiments carried out at the HP-CAT 16-ID-D size, indicating the lack of crystal beamline at the APS have yielded for the first time real-time, substructure. In addition, the research group microstructural data on the lattice compression that occurs also succeeded in demonstrating as a lithium fluoride crystal (LiF) plate is subjected to shock that the amount of lattice disorder wave compression. More importantly, this research effort for shocked LiF along [100] successfully demonstrated that a synchrotron, in tandem with depends on the loading history. an appropriate impact or shock wave facility, is a feasible Indeed, when magnesium-doped and ultrapure LiF crystals were approach to permit high resolution, real-time x-ray diffraction shocked to the same peak stress, it measurements in shock wave or plate impact experiments. was found that the broadening was larger for the magnesium-doped LiF crystals than for ultrapure LiF [100]; this can be understood by noting that the magnesium- doped LiF has a large elastic MORE > Previous work has during the transition from elastic precursor. The ability to resolve shown that shocked single crystals to plastic deformation under shock microstructural details in shocked are unable to sustain the large stress compression remained unknown. crystals is important and was made deviators associated with elastic The experiments in this possible by the synchrotron x-rays. compression, and this gives rise to study, by researchers from All of the data was compared plastic deformations at nanosecond Washington State University with results from simulations using or perhaps even shorter time scales. with support from the Carnegie a model consisting of coherently However, the lack of high resolution, Institution of Washington, made diffracting domains where the real-time microstructural data use of subnanosecond x-ray pulses lattice orientation and lattice strain meant that the micromechanisms to record diffraction data from are assumed constant within each responsible for the lattice changes pure and magnesium-doped LiF domain, but vary from domain single crystals shocked along the to domain following a Gaussian [100] and [111] orientations. For distribution. In every instance, shock compression of LiF along the experimental results were in the [100] direction,elastic-plastic excellent agreement with simulated deformation occurs and significant diffraction patterns.

132 A rgonne National Laboratory Novel X-ray Techniques & Instrumentation

See > Stefan J. Turneaure1*, Y.M. Gupta1, K. Zimmerman1, K. Perkins1, C.S. Yoo1, and G. Shen2, “Real-time microstructure of shocked LiF crystals: Use of synchrotron x-rays,” J. Appl. Phys. 105, 053520 (2009). DOI:10.1063/1.3080176

Author affiliations > 1Washington State University, 2Carnegie Institution of Washington

Correspondence > *[email protected]

> This work was supported primarily by DOE Grant No. DE-FG03-97SF21388. HP-CAT is supported by DOE-BES, DOE-NNSA, NSF, and the W.M. Keck Foundation. Use of the Advanced Photon < Fig. 1 Diffraction patterns for ambient (white/green disks) and shocked (black disks) Source at Argonne National Laboratory was supported by the U.S. Department of LiF samples. The simulation results for coherently diffracting domains of 4 and 10 Energy, Office of Science, Office of Basic micrometer size are denoted by dashed and solid lines, respectively. (Copyright © Energy Sciences, under Contract No. 2009 American Institute of Physics) DE-AC02-06CH11357.

The high-resolution, real-time changes. This research represents > 16-ID-D • HP-CAT • Materials x-ray diffraction experimental a new paradigm, paving the way science, geoscience, physics • Nuclear resonant scattering, set-up employed at the HP-CAT for future work in the field of shock inelastic x-ray scattering, x-ray beamline allowed the researchers compression in crystals. Raman scattering, x-ray emission to examine how the load history spectroscopy • 3.3-cm Undulator A for pure and Mg-doped LiF(100) — Luis Nasser • Accepting general users influence the microstructural

The Advanced Photon Source Annual Science Report 2009 133 Novel X-ray Techniques & Instrumentation

Timing it Right

electric fields do not affect it. It IN SHORT > The pulsed nature of the x-rays from the APS is also highly selective to krypton enables a variety of time-resolved research—often involving ions because neutral krypton atoms ultrafast lasers. To perform meaningful time-resolved absorb ~40 times fewer x-rays at the resonant x-ray energy measurements with the combined system of laser and x-rays (Fig. 1 insert). The combination it is important to accurately determine their relative timing. of the two processes is called a Reducing intrinsic response times from several picoseconds “laser pump/x-ray probe” technique to a few femtoseconds, researchers from Argonne National because of the synchronized nature Laboratory used a gas phase technique at XOR beamline 7-ID of the pump and probe beams. The to temporally reference the two types of ultrafast pulses—hard scanning of the relative delay time of the two processes is called a x-ray and optical—with the use of fluorescence emission. The “cross correlation” measurement results produced here provide a way to monitor and diagnose because it reveals whether, and how, the time-based overlap of infrared laser and hard x-ray pulses. they correlate. Specifically, as advances occur the technique should also be The laser pump/x-ray probe able to characterize the implementation of picosecond x-ray measurements used two APS operating modes: 24-bunch and pulses proposed for the APS Upgrade. hybrid fill, with different x-ray pulse lengths. XOR beamline 7-ID produces a monochromatized hard x-ray beam (the probe)—which focuses to about 10 × 10 µm2. An infrared light titanium-sapphire MORE > Understanding the samples, because of its ability to laser, also located at this beamline, interaction of electromagnetic produce quick responses of a few was used to produce the pump radiation with matter on an atomic femtoseconds. They combined two beam—focused to approximately scale is essential for much of the ultrafast atomic physics processes. 100 × 100 µm2. The infrared research carried out at the APS. First, optical-field tunnel ionization laser pulses (~50 fs) are about For this reason, these researchers was applied to a neutral, closed- 1,000 times shorter than the x-ray performed a simple cross correlation shell krypton (Kr) atom. The tunnel pulses in either operating mode. between hard x-ray and infrared ionization process—the pump The two beams met at a small pulses (Fig. 1). Specifically, phase—allows electrons from Kr crossing angle of 1.5°, with the the researchers concentrated on atoms to escape, leaving behind focus inside a vacuum chamber preparing, or pumping, atoms with a krypton ion (Kr+), because their containing neutral krypton gas. Two ultrafast infrared pulses and probing binding barrier is distorted after x-ray fluorescence detectors were them with hard x-rays, focusing being subjected to the intense positioned perpendicular to the on core excitations and subsequent electric field of the laser pulse. x-ray beam, with 1-mm slits limiting fluorescence emissions. The hard Secondly, the researchers their viewing length to the region of x-ray pulses were produced from a applied x-ray resonant absorption to spatial overlap. synchrotron radiation source, while distinguish unambiguously between As shown in Fig. 1, negative the infrared pulses were created the pumped Kr+ ions and the delays mean that the x-ray pulses from a tabletop laser. unpumped Kr atoms. The resonant from the beamline arrived before the The Argonne researchers x-ray fluorescence—resulting from Ti: sapphire laser pulses generated used the gas phase technique, Kr+—acts as an excellent probe Kr+ ions and, thus, resonant rather than the traditional x-ray because it is not reabsorbed by the fluorescence was not detected. At diffraction methods using solid surrounding sample, and external positive delays, however, the x-ray

134 A rgonne National Laboratory Novel X-ray Techniques & Instrumentation

See > Bertold Krässig*, Robert W. Dunford, Elliot P. Kanter, Eric C. Landahl§, Steve H. Southworth, and Linda Young, “A simple cross-correlation technique between infrared and hard x-ray pulses,” Appl. Phys. Lett. 94, 171113 (2009). DOI: 10.1063/1.3125256 < Fig. 1 The cross-correlation data of resonant fluorescence from laser-produced krypton ions as a function of the relative delay between the x-ray and laser pulses for two APS Author affiliations > operating modes with different x-ray pulse lengths. Note that the data accumulation Argonne National Laboratory time in 24-bunch mode was twice as long as in hybrid fill mode. Insert: Fluorescence §Present address: De Paul University signal as a function of incident x-ray energy for neutral Kr atoms (gray line and shading) and for Kr+ ions (purple line). The arrow indicates the x-ray energy at which Correspondence > the cross correlation measurements were conducted. *[email protected]

> This work was supported by the Argonne Chemical Sciences, pulses arrived after the laser pulses, of a temporal resolution down to a Geosciences, and Biosciences divisions, leading to maximum resonant x-ray few femtoseconds, but is currently and also in the case of the Advanced absorption with rapid emissions of Photon Source, the U.S. Department of limited by the temporal jitter in the Energy Office of Science, Office of Basic fluorescence photons. The resonant synchronization between laser and Energy Sciences, under Contract No. fluorescence is perceivable for some x-ray source. DE-AC02-06CH11357. time after the laser pulse because the This simple cross-correlation ions diffuse out of the interaction technique may aid future research region on a time scale much longer employing both infrared and than the hard x-ray and infrared laser hard x-ray pulses because it is > 7-ID • XOR • Atomic physics, pulses. The interesting region is nondestructive to the beams and chemistry, materials science • Phase contrast imaging, the transition from no to maximum has the ability to drastically reduce time-resolved x-ray absorption fluorescence near zero delay because response times. fine structure, time-resolved x-ray it provides a diagnostic of the scattering • 33-cm Undulator A • Accepting general users temporal integral of the x-ray pulse. — William Arthur Atkins Intrinsically, the technique is capable

The Advanced Photon Source Annual Science Report 2009 135 Novel X-ray Techniques & Instrumentation

Superconducting Undulators: The Best Route to Bright X-ray Sources above 20 keV

MORE > The emerging development project, many short IN SHORT > Increasingly, superconducting undulator (SCU) prototype magnetic structures many experiments with technology potentially outperforms have been built at the APS. After all other technologies in terms of detailed magnetic modeling analysis, high-energy (>20 keV) peak magnetic field at small periods refining of the winding geometry, x-rays are on systems (near 1.5 cm), thereby resulting in and development of winding undergoing dynamic higher photon brilliances at higher techniques, a magnetic structure processes. Examples energies. The expected brilliance design was chosen. The core must include measuring the of superconducting devices is be potted in epoxy resin to hold the strain rate response of shown and compared with the APS windings firmly; a technique for this composite materials under Undulator A (UA) in Fig. 1 [1]. epoxy vacuum impregnation was tension or compression, As part of the APS developed in a collaboration with determination of superconducting undulator the Technical Division of Fermilab metastable phases that briefly appear during amorphous to crystalline phase transformations, and response of materials to dynamic loading (e.g., shock waves). Such experiments are inherently “flux hungry” and are often limited by beam intensity. More photons equate to the ability to probe faster time scales and to explore wider parameter spaces, increasing our full understanding of the dynamic processes, both from a basic science point of view, but also toward practical ends that can be used to produce better materials for applications. < Users engaged in these Fig. 1 Tuning curves for Undulator A and some shorter-period SCUs. Note that the shorter types of experimental periods give higher brightness, especially at higher photon energies. The advantage programs are requesting of SCUs and their stronger field is that the tuning range extends to a lower photon energy for each harmonic, giving the user more flexibility in choice of photon energy. higher photon fluxes The limited achievable field strength results in gaps in the tuning range like that seen at higher energies. for the 1.6-cm-period SCU. With permanent-magnet undulators, such gaps are wider and persist for period lengths as long as 2.7 cm. The SCU 1.6 cm is five times brighter than the Undulator A at 20 keV.

136 A rgonne National Laboratory Novel X-ray Techniques & Instrumentation < Fig. 2 Left: A single SCU core, after winding. The superconductor is wound in the grooves between poles. The current travels in opposite directions in adjacent coil packs. Right: A pair of cores, assembled as for an undulator magnetic structure with a gap between for the beam tube. Here they are ready to go into a vertical dewar for cold testing.

in Illinois. A 42-pole prototype is coil winding is such that, without installation and testing in the shown in Fig. 2, where the left photo magnetic field corrections in the storage ring in two years. After is of a single core after winding with body of the undulator, the magnetic that, the length of the magnetic superconducting wire. There are field phase error requirement of structure will be increased grooves between the poles where 8 deg is met, with a 7.1-deg phase from the initial 42-pole length the wire is placed, and the winding error at the current needed for (at 1.6-cm period) to about 1.1 m, is arranged so the current goes in 20-keV photons, and a 3.3-deg phase to achieve a corresponding increase opposite directions in adjacent error at the current for 25 keV. For in brilliance. Eventually, after winding packs. In order to provide a comparison, today’s permanent additional R&D on manufacturing smooth trajectory entrance into and magnet undulators routinely achieve and field correction techniques, exit from the undulator, there are 4-degrees phase error after tuning. and construction of a larger test fewer windings of the main current Lower phase errors have their facility, the magnetic length will coil in the last two grooves at each strongest impact on the higher increase to something closer to end. The extra space allows separate harmonics in the photon spectrum, the APS-standard 2.4 m. windings—which will be connected so for users who want to work to separate power supplies—in at higher energies and higher those end grooves. Those coils will harmonics, reducing the phase Contact > Yury Ivanyushenkov allow for trajectory correction at the error would be desirable. ([email protected]), ends. The right photo in Fig. 2 is of Now that a magnetic structure Liz Moog ([email protected]), a pair of cores assembled together, has been successfully tested, the and Dean Haeffner ready for testing in a vertical dewar. work is focusing on the design of a ([email protected]) The beam will travel through a cryostat that will complete the SCU beam chamber that will fit in the and result in a device that could be Reference > [1] R. Dejus, M. Jaski, gap between the two cores. For the installed on the APS storage ring. and S.H. Kim, “On-Axis Brilliance vertical dewar tests, a guide tube for A collaboration with the Budker and Power of In-Vacuum Undulators a Hall probe is inserted instead. The Institute in Novosibirsk is under for the Advanced Photon Source,” test measurements of the field are way. The plan is to complete the ANL/APS/LS-314, formerly very encouraging. The quality of the undulator and have it ready for Technical Note MD-TN-2009-004.

The Advanced Photon Source Annual Science Report 2009 137 Novel X-ray Techniques & Instrumentation

An Intermediate-Energy X-ray Beamline at the APS

beamline. The beamline, shown schematically in Fig. 1, will use IN SHORT > A new beamline is under construction at mirrors to select low-energy x-rays APS Sector 29. The IEX collaborative development team from the undulator. The grating (IEX-CDT) beamline will cover the energy range from monochromator and the focusing 0.2 to 2.5 keV, with resolving powers in the range of 5000 mirrors provide the end stations to 20,000 in the high-energy end of the spectrum and a with high resolving power and spot size of order σ = 2.2 μm. The beamline will serve small focus. two experimental techniques: high-energy, angle-resolved The x-ray source for this beamline is a 4.8-m-long, photoemission spectroscopy (ARPES), which is a bulk probe 12.5-cm-period, electromagnetic, of the low-energy excited states in condensed matter; and elliptically polarizing undulator. resonant soft x-ray scattering (RSXS), which is a direct probe The device is capable of operating of electronic ordering. ARPES and RSXS complement one in one of three polarization modes: another scientifically, are of interest to the same scientific circular, horizontal linear, and vertical linear. Additionally, the community, and in particular have highly compatible source device is capable of operating in and beamline technical requirements. quasi-period fashion if needed to enhance harmonic suppression for the beamline optics. The device

MORE > The application of advantage of providing radiation < Fig. 1 Isometric view of key beamline electron and x-ray spectroscopy in with variable linear polarization elements for the IEX beamline. the 0.2- to 2.5-keV energy range has and circular polarization. In the M0, M1, and M2 are white-beam significant potential for advancing circularly polarized mode, studies of mirrors, while M3x and M4x are our knowledge of condensed magnetic structures and excitations monochromatic mirrors. matter science by elucidating the can be facilitated, and in addition, low-energy electronic excitations the source does not produce in both materials and artificial significant harmonics—an important structures, which govern most consideration for the experiments of their physical properties. to be carried out on the IEX-CDT The source for this beamline will be an elliptically polarized undulator. This source has the

138 A rgonne National Laboratory Novel X-ray Techniques & Instrumentation

< Fig. 2 Design engineer Mark Jaski (ANL-ASD) working on the prototype 4-period, electromagnetic, elliptically polarizing undulator.

necessary for people engaged in this type of research. This will help to maintain a forefront materials research program in the U.S., particularly in complex materials, which hold much promise for future technologies. To make the IEX-CDT beamline still more accessible, it is already slated to participate in the the National School on Neutron and X-ray Scattering, which is a collaborative effort of the APS at Argonne and the Spallation Neutron Source (SNS) at Oak Ridge National Laboratory. The school is funded by the DOE and is intended to introduce beginning graduate students to the utilization of national research facilities. The school meets for two weeks every summer and typically includes 30 hours of lectures followed by a series of experiments at both the APS and the SNS. Each year, the school invites is being designed and built at available to researchers from across approximately 60 students from a the APS; a 4-period prototype the nation and abroad through the wide geographic and demographic (Fig. 2) has been fabricated and APS General User Program. It will, distribution. Many past students is undergoing testing at the time therefore, contribute critically to are now current users of national of this writing. this nation’s scientific infrastructure. facilities across the U.S. Through The IEX beamline is being Currently, facilities such as this participation in this program, the designed and constructed by the beamline are only available at the IEX-CDT beamline will be an active IEX-CDT group, which consists SPring-8 synchrotron in Japan component in training an ethnically of principal investigators from the and at the European Synchrotron and demographically diverse body University of Illinois at Chicago, Radiation Facility in France. A of students to become the next the University of Illinois at Urbana- significant advantage of having such generation of U.S. scientists. Champaign, and the University of a facility at the APS for carrying Michigan together with personnel out cutting-edge experiments is that from the APS. The project is jointly it will become a valuable resource funded by the National Science in training future generations of Contact > Juan Carlos Campuzano Foundation and the U.S. Department researchers and educators, who will ([email protected]), George of Energy (DOE). The beamline will not be required to use light sources Srajer ([email protected]), Mohan be a national user facility openly in other countries, as is currently Ramanathan ([email protected])

The Advanced Photon Source Annual Science Report 2009 139 Reports from the X-ray Science Division

A Dedicated Fuel-Spray Beamline at APS 7-BM

< < Jin Wang (ANL-XSD) in the 7-BM IN SHORT > “The evolution of fuel sprays plays a defining beamline enclosure. role…in determining both combustion efficiency and the formation of…pollutants. This level of understanding may permit extraordinary new technologies, such as smart fuel as better spray definition, better use injectors…” of air charge, and minimized needle Basic Research Needs for Clean and Efficient Combustion of 21st bouncing. Century Transportation Fuels. Report from the U.S. Department The time has now arrived of Energy Office of Basic Energy Sciences Workshop on Clean for the creation of a dedicated, ultrafast-imaging facility on the and Efficient Combustion of 21st Century Transportation Fuels, Sector 7 bend magnet beamline October 29-November 1, 2006. at the APS. This facility will provide a centralized resource for transportation engine technologies, offering high-throughput measurement capabilities for a large user community. The MORE > High-pressure, high- ultrafast x-radiography carried U.S. Department of Energy’s speed fuel sprays are a critical out mainly at XOR Sector 1 at Office of Energy Efficiency and technology for many applications, the APS and at the Cornell High Renewable Energy, Office of including engine fuel-injection Energy Synchrotron Source, with Vehicle Technologies program systems where the structure and microsecond x-ray tomography also made a significant investment in dynamics of the fuel sprays are key being employed. Results, which rebuilding the beamline, where two to increasing fuel efficiency and have seen wide circulation in several research stations and associated reducing pollutants. But because peer-reviewed journals articles, have beam transport components were liquid sprays are difficult to yielded information on quantitative already in place. image with conventional (optical) fuel mass distribution and high- The beamline makes available techniques, particularly in the region speed spray and combustion ultrafast (µs) x-radiography, close to the nozzle, quantitative models. Perhaps the most (to date) ultrafast (µs) x-tomography, high information the structure of these intriguing result has been capturing beam intensity, wide-bandpass sprays has been elusive. Research the propagation of spray-induced mono (1013-1014 ph/s, tunable from on this critical subject has been shock waves in a gaseous medium 6 to 12 keV), and flexible beam ongoing at the APS for several (MacPhee et al., Science 295[5558], size. Instrumentation includes a years. The primary technique 1261 [2002] and Powell et al., sagittal focusing double-multilayer for these investigations has been J. Synchrotron Rad. 7, 356, [2000], monochromator, a harmonics Im et al, Phys. Rev. Lett., in press). rejection mirror for use with area The researchers have engaged detectors, a secondary Kirkpatrick- with an ever-expanding roster of Baez focusing mirror for use with academic, industrial, and federal- point detectors, modular sample lab partners in order to improve stations, pressurized chambers, injector system design in areas such unpressurized chambers, and

140 A rgonne National Laboratory Reports from the X-ray Science Division

rapid compression machines. optics components were installed Major emphasis is placed on safe in January 2009. At the time of operation under high-pressure, high- this writing, the beamline was temperature conditions. Ultrafast in its commissioning period and area detectors are the coming from scheduled to be available to general Cornell and the APS. users during user the third user The beamline control system run in 2010. Contact Jin Wang was completed and major x-ray ([email protected])

The Advanced Photon Source Annual Science Report 2009 141 Reports from the X-ray Science Division

Two Independent Beamlines for SAXS at 12-ID

as an important complement to the IN SHORT > The APS Strategic Plan calls for XOR/ infrastructure for the Center for BESSRC beamline 12-ID to become a dedicated small- Nanoscale Materials at Argonne angle x-ray scattering (SAXS) facility. For the last seven and further increase the demand for this beamline. This will enable years, the demand for SAXS beam time by users of 12-ID XSD to pursue options such as has consistently exceeded the available time by a factor high-throughput SAXS, which of two. The current SAXS facility (originally funded could be used for combinatorial from the FY1996 DOE Scientific Facilities Initiative) has materials studies. steadily grown to now represent 50% of the usage of the The vacuum chamber for the 12-ID beamline. With the current instrument configuration canted undulators was installed in FY2006 and the canted undulator oversubscribed, the only way in which the present SAXS front end (Fig. 1) has now also community can continue to grow, and new users can take been installed. Currently, two advantage of these new capabilities, is to provide simultaneous undulators are installed inline: a operation of two 12-ID experimental stations by adding canted U30S and U33S; in May 2010 they undulators and new beamline optics. This enhancement would will be canted. In the future the provide the APS with a dedicated SAXS beamline to better U33S will be replaced with a U27 serve the general user community in a number of areas in undulator, which is optimized for materials science, chemistry, and biology. At least half of current 12-ID users are doing bioSAXS.

MORE > The increasing universities, 9 national laboratories demand for SAXS beam time and government institutions, 6 has been driven by research into industrial research laboratories, the structure and dynamics of and researchers from 11 foreign nanoscale materials (for which universities and laboratories. SAXS is an extremely valuable Increasing interest in time- probe), an increased interest in dependent SAXS experiments led soft matter, and increased usage of the CMS Group to add a pink- the 12-ID SAXS facility for time- light mirror system to the 12-ID dependent structural investigations. beamline. Installed in late FY 2005, General-user experiments have this addition has enhanced the flux included these areas, as well as the on sample by over three orders of extensive use of the 12-ID SAXS magnitude, providing new time- instrumentation for biological resolved experimental opportunities research. The more than 350 users for small-angle scattering who have done experiments on experiments. With the development the X-ray Science Division (XSD) of dedicated instrumentation for Chemical and Materials Science anomalous grazing-incidence (CMS) Group’s SAXS instrument small-angle x-ray scattering at < represent more than 42 U.S. 12-ID, the beamline will also serve Fig. 1 Canted undulator front end.

142 A rgonne National Laboratory Reports from the X-ray Science Division < Fig. 2 Conceptual drawing for the large-offset side-bounce monochromator to be used for the 12-ID-B branch beamline.

the energy range on the 12-ID-B a large offset monochromator range and no dark current. These beamline. One of the resulting (870 mm). This monochromator detectors will make 12-ID-B a undulator beamlines will use a (Fig. 2) will use a cryo-cooled very versatile SAXS beamline. more stable version of the current silicon [220] first crystal to provide Monthly meetings are held monochromator with an energy an energy range of 7.4 – 13.9 keV. with the user community to update range of 4.5 to 35 keV and a mirror A Pilatus large-area detector will them on progress as the upgrade system that includes the existing be used in conjunction with a of 12-ID moves forward, and give pink-beam mirror. This beam will large vacuum-scattering chamber them the opportunity for input. feed 12-ID-C/D and be used for where the position of the detector The final installation of beamline anomalous, time resolved, grazing can be changed automatically to components and commissioning incidence SAXS in the C hutch, and access different Q ranges, and is scheduled for the May 2010 surface scattering and metal organic a wide-angle detector will be shutdown through the 2010-2 chemical vapor deposition studies attached permanently to the front run cycle. Randall Winans in the D hutch. The experiments in of the chamber. A two-dimensional ([email protected]) the C hutch will use a new mosaic detector with high linearity, large-area charge-coupled device dynamic range, stability, and low detector built by XSD. or no dark current is crucial for After canting, the second SAXS. The Pilatus detector has undulator will feed 12-ID-B as overwhelming capability in these a dedicated SAXS station using respects, with a 20-bit dynamic

The Advanced Photon Source Annual Science Report 2009 143 Reports from the X-ray Science Division

The APS User Community

IN SHORT > During 2009, the APS user community continued its relatively steady growth, with the number of unique users by fiscal year demonstrating a sharp increase from FY2008 to FY 2009. Figure 1 shows the number of unique users by fiscal year since the APS began operations, as well as the number of operating beamlines. Figure 2, which shows the < number of experiments Fig. 1 Number of APS unique users and operating beamlines, by fiscal year. by fiscal year, also demonstrates steady user community growth, with a sharp increase from FY2008 to 2009.

MORE > The character of the user community, however, is begining to change. Although the number of on-site unique users is continuing to increase, this increase may be moderated in the future by the number of users choosing to either operate beamlines remotely or mail < Fig. 2 Number of experiments at the APS, by fiscal year.

14 4 A rgonne National Laboratory Reports from the X-ray Science Division

in samples for beamline staff to handle. Figure 3 demonstrates this change over the past three years. During FY2009, users affiliated with universities continued to constitute our largest community, which has been the case since the APS began user operations. Figure 4 shows the institutional distribution of FY2009 users. Figure 5 shows the distribution < by research field, with biology/life Fig. 3 Number of remote and mail-in users at the APS during the years sciences once again constituting 2007 through 2009. the majority community. Demand for general user beam time also increased slightly in 2009, with 3095 beam-time requests (BTRs) submitted (vs. 2900 BTRs in 2008), with an average oversubscription rate across all beamlines during 2009 of 1.7. Beginning in 2010, all beam time, not just general user time, will be requested through a central beam-time request system. This new system will provide better tracking of beam-time use and permit the APS to respond more quickly to changing user needs < and demographics. Fig. 4 FY09 APS user distribution by institution. < Fig. 5 FY09 APS user distribution by research field.

The Advanced Photon Source Annual Science Report 2009 145 Reports from the X-ray Science Division

User Week 2009

(in addition to research funding at the APS. Janet Smith, (University IN SHORT > Although already designated in facility budgets) of Michigan) discussed “Finding Argonne’s 2009 User will also be available for accelerator Gems in Low-quality Crystalline Week focused primarily and detector research. Montano Proteins with an X-ray Mini-Beam,” on the APS Upgrade, it confirmed that the APS Upgrade is a and Brian Stephenson (Argonne) first priority in new construction for spoke on “Chemical Switching of also included talks on a the Office of Science, but cautioned Polarization in Ultrathin Ferroelectric wide range of research- that the project must be designed PbTiO3 Films.” related topics, and reports so that it does not impact ongoing A special session on the APS from two other Argonne science. He noted that, in terms Upgrade included a perspective user facilities: the Center of the APS Upgrade, the goal is from the APS Scientific Advisory for Nanoscale materials to achieve another 10 to 12 years Committee, a detailed review of (CNM) and the Electron at top performance, and because the science drivers (the result of beamlines become obsolete earlier extensive discussion by 10 science Microscopy Center (EMC) than machines do, beamlines must teams), a report on proposed for Materials Research. be refreshed during this process. accelerator upgrades, and a summary In FY 2008, BES facilities served of the overall vision for how the 10,995 users. The light sources were Upgrade will be structured. the highest volume facilities, serving The 2009 Compton Award was 8,492 users (39% of those at APS). presented jointly to Gerhard Grübel, According to Montano, the five BES Simon Mochrie, and Mark Sutton MORE > Monday featured nanoscience centers are also doing (Fig. 1) for their pioneering efforts in scientific highlights and a session very well; all of them have hit the x-ray photon correlation spectroscopy on the APS Upgrade proposal. In ground running. (XPCS), which exploits the coherent his opening APS update, Argonne In reports from the CNM and properties of synchrotron x-rays Associate Laboratory Director for EMC, Stephen Streiffer and Dean to study the slow dynamics of Photon Sciences and APS Director Miller (respectively) highlighted condensed matter at short length Murray Gibson reviewed a current and upcoming capabilities. scales. Each winner spoke briefly on broad range of topics, including Streiffer noted that the CNM is his perspective on the development better-burning fuels, natural solar discussing the merits of targeting a and applications of XPCS. cells, metal oxide frameworks for 5-nm beam size. Miller noted that Recognition was also provided hydrogen storage, better batteries, the Sub-Angstrom Microscopy for student users Naji Sami Husseini climate change, human health, and Microanalysis Facility is now (University of Michigan), who gave infrastructure concerns, ancient complete and operational. The the student invited talk, and for cultures, high-pressure science, and EMC has been closely involved poster award winners Jonathan D. of course, basic science. Gibson also in the TEAM project, a multi- Emery (Northwestern University), addressed possible changes to the laboratory collaboration to develop David Kissick (Purdue University), General User Program to address a transmission electron aberration- and D.K. Schreiber (Northwestern the expertise of judges on the review corrected microscope. Portions University). panels and to better accommodate of the new technology are already Tuesday morning was devoted industrial proposals. in use, and the exciting results being to talks that explored the pressing Pedro Montano of the U.S. obtained with aberration correction research questions in the areas of Department of Energy (DOE) Office were the subject of a Monday the dynamics of life (Keith Moffat, of Science, Office of Basic Energy afternoon presentation by Bernd University of Chicago), materials for Sciences (BES) painted a promising Kabius (EMC). energy applications (George Crabtree, picture of upcoming funding for Two other afternoon Argonne, presenting on behalf of facility operations. New funding presentations highlighted recent work Michelle Buchanan, Oak Ridge

146 A rgonne National Laboratory Reports from the X-ray Science Division

National Laboratory), materials “user visions” sessions, eight users topics supporting the Upgrade under pressure (Russell Hemley, presented their cases for scientific proposal: detectors, optics, Carnegie Institution of Washington), directions for the APS Upgrade. nanopositioning, high-speed imaging, and characterization of real-world On Wednesday, users selected imaging of biological systems, and materials systems (Roger Leach, from three half-day and three chemical science. Susan Strasser DuPont). On Tuesday afternoon, the full-day workshops focusing on ([email protected]) focus turned to new techniques, with overviews of coherent diffraction and x-ray imaging (Keith Nugent, University of Melbourne), x-ray

microscopy (Chris Jacobsen, Stony < Fig. 1 The 2009 Compton Award was presented by (left) APSUO Chair Laurence Lurio Brook University), metrology and (Northern Illinois University) and Argonne Associate Laboratory Director Murray optics (Lahsen Assoufid, Argonne), Gibson to (center) Mark Sutton (McGill University), Simon Mochrie (Yale University), and ultrafast x-ray spectroscopy and Gerhard Grübel (European Synchrotron Radiation Facility) for their pioneering (Robert Schoenlein, Lawrence efforts in x-ray photon correlation spectroscopy, which exploits the coherent properties Berkeley National Laboratory). of synchrotron x-rays to study the slow dynamics of condensed matter at short During the morning and afternoon length scales.

The Advanced Photon Source Annual Science Report 2009 147 Reports from the Accelerator Systems Division

Beam Stabilization Developments

> Fig. 1 Diagram showing the geometry for IN SHORT > As reported in last year’s annual report, the high-power grazing-incidence upgrade work is underway to improve the data acquisition for hard x-ray beam position monitor the broadband (monopulse) rf beam position monitor (bpm) for insertion device beamlines. system. By the end of 2009, a total of 5 sectors have been (Courtesy S.H. Lee, AES-MED) installed in the ring, specifically in sectors 33 through 36 and 38. With parts on hand for three additional sectors, eight assemblies (not shown) make use of sectors will be instrumented by the summer of 2010, with a diode array coupled with pinhole production of components for additional sectors in process. camera apertures to sense motions Operationally, these units have already shown their value, of the x-ray fluorescence footprint allowing rapid diagnosis of unscheduled beam loss events along the inclined glidcop surfaces. An in-air scale model of this design using turn-by-turn data waveforms encompassing a quarter has been installed in beamline million turns (approx. one second) for each of the 7 channels 35-ID and has been used to validate per sector so instrumented. From an accelerator physics the geometry (Fig. 2). standpoint, this capability provides the potential for some Coupled with improvements very extensive investigations of beam dynamics sup­porting and upgrades to beam position new machine optics for the APS upgrade. From a beam monitoring systems will be an upgrade to the real-time feedback stabilization standpoint, this new data acquisition system has system, including a new high- an extremely low noise floor (< 100 nm rms) over a relatively speed data link transmitting bpm wide frequency bandwidth (1-200 Hz), and will allow the and steering corrector information long term goal of 0.42 microns rms AC beam stability to be around the ring. The existing real- realized. Presently, rms beam motion in this band is about time feedback system was designed in the early 1990’s and some of the 5 microns horizontally, and 1.6 microns vertically, at insertion hardware is as much as 15 years old. device source points. It operates at a rate of 1534 correction steps per second, but is restricted to use at most 160 bpms and only 38 steering correctors in each plane. In order to achieve 200 Hz closed loop bandwidth taking into account MORE > In other developments, and predictable. This work has been computational and data distribution a prototype high-power hard x-ray ongoing for the past few years, and latencies, a sample rate of between beam position monitor is being tested will make use of pin diodes sensing 10 and 20 kHz will be required. In in the sector 35 beam diagnostic the x-ray flourescence emitted from addition, the use of modern network insertion device beamline. This a cooled Glidcop surface oriented hardware should allow access to all of device holds the promise of pro­ at grazing incidence (Fig. 1). One the more than 500 channels of beam viding long term pointing stability interesting design feature of the final position monitoring (narrowband rf, at the level of 500 nanoradians design will be that all sensors will be broadband rf, and bend­ing magnet peak-to-peak or better over a one outside of vacuum, obviating the need and insertion device photon bpms). week period. Planned to be located for electrical vacuum feedthroughs One other goal will be to relocate in insertion device beamline front while simplifying maintenance and a significant number (dozens) of ends as part of the APS upgrade, repair; the x-ray fluorescence will “slow” steering correctors to vacuum this device should improve orbit be viewed through a large beryl­lium spool pieces, converting them to reproducibility and make beamline window located off-axis transversely “fast” correctors by eliminating the steering adjustments more precise as shown in the figure. The detector retarding effects of eddy currents

148 A rgonne National Laboratory Reports from the Accelerator Systems Division

associated with the thick alumi­num vacuum chambers. This will provide the ability to compensate noise sources with a finer spatial density, providing more local correction of these sources. The end result of these developments will be a world-class orbit stabilization system providing AC stability better than half a micron and 200 nanoradians rms in the 1-200 Hz bandwidth, and long term stability at the level of one micron and 500 nanoradians p-p over one- week time peri­ods.

> Fig. 2 Beamline scientist Bingxin Yang (ANL-ASD) with scale model of the grazing incidence insertion device pho­ton bpm at diagnostic beamline 35-ID.

The Advanced Photon Source Annual Science Report 2009 149 Reports from the Accelerator Systems Division

R&D for an X-ray Free-Electron Laser Oscillator

100 A, the round-trip reflectivity of higher than 89%. The cavity could IN SHORT > Research 50% is sufficient even with a larger be shorter, 50 m rather than 100 m, and development on emittance (0.3-mm-mrad) and a leading to a relaxed angular stability. the x-ray free-electron smaller number of undulator periods Thus, the shorter bunch operation laser oscillator (XFELO) (Nu = 1000) [1]. The requirement offers improved time resolution with on the reflectivity of each element relaxed tolerances. The XFELO has now progressed becomes significantly relaxed, such parameters with two-pulse-length significantly further than that the reflectivity of each should be operation are compared in Table 1. reported in APS Science 2008 (“R&D Progress on

an X-ray Free-Electron < Table 1 Comparison of XFELO parameters with 1-ps and 0.1-ps electron bunches. Laser Oscillator,” p. 134). The main progress is

summarized here. Electron Bunch

Energy (GeV) 7.0

Energy spread (MeV) 1.4

Repetition rate (MHz) 1 MORE > 100-fs- Pulse Operation with Relaxed Tolerances Length (rms) (ps) 1.0 0.1

The previous study used an Charge (pC) 50 25 electron beam with 20 A of current Current (A) 20 100 in a 1-ps, 0.2-mm-mrad emittance bunch at 7 GeV, which interacted Emittance (mm mrad) 0.2 0.3 with an undulator of about 3000 periods in an x-ray cavity whose Undulator total round-trip reflectivity was 81%. Since the tunable x-ray Period length (cm) 1.8 cavity scheme requires six optical Undulator length (m) 57 25 elements (four diamond crystals and two grazing incident mirrors), the X-ray Cavity reflectivity per each element should be higher than 96.5%. We have Roundtrip reflectivity (%) 81 50 studied another parameter regime with relaxed requirements. Reflectivity per element (%) 96.5 89

We found that when X-ray Output compressing the bunch to 0.1 ps, thereby increasing the current to Peak power (MW) 3.9 3.8

# Photons/pulse 4 ´ 109 0.5 ´ 109

Pulse length (95% rms) (ps) 0.69 0.084

Dw/w (95% rms) 1 × 10-7 6 × 10-7

150 A rgonne National Laboratory Reports from the Accelerator Systems Division

conductivity at low temperatures, this discovery helps pave the way to solving the heat load problem of the x-ray cavity.

A pilot experiment to stabilize crystal angles via a feedback loop based on the null-detection Generation of 1-fs Pulses APS have provided the first evidence preliminary selection of near-perfect without Fluctuation? principlethat diamonds was discussed perform in in the practice previous APScrystal Science regions report. was Stabilization done using x-raywithin 15 nrad in 1-Hz noiseclose bandwidth to the theoretical was achieved predictions, [6]. Further whiteprogress beam for topography. tighter angular These stability data (10 nm), broader While the narrow bandwidth bandwidthin terms of(1 reflectivitykHz), and multi-axes and energy system arewill shown be required. in Fig.1. Note the close of the Bragg mirrors precludes the bandwidth [4]. We have shown that correlation of diamond qualities possibility of directly producing A testsmall x-ray areas cavity (about 1 × 1 mm2) of seen in the topograms to the spectral femtosecond x-ray pulses using an Forcommercially an integrated available, test, we willsynthetic construct thewidth prototype and reflectivity x-ray cavity measurement. shown schematically in Fig. 3 XFELO, it may be advantageous [6].type This IIa prototype diamond shouldcrystals be can built in an available The space temperature at an APS variation insertion of device beamline so to use this concept to seed a very thatexhibit high-brightness a high degree x-ray of perfection,beams can be injecteda lattice into parameter the cavity. of aThe synthetic length of the prototype will short electron beam; an electron be with23-24 the m, measured about one-fourth spectral width of the actual x-raydiamond cavity crystal for (typean XFELO, IIa) was which will be convenient beam so prepared could then be becauseand reflectivity in this case, approaching the mirror their is smaller thanmeasured that required using high-energy- for the 100-m cavity. The round-trip extracted from the oscillator region paththeoretical length will values, be chosen DE = 2.9to bemeV either the sameresolution as the x-ray APS Bragg bunch diffraction spacing (46 m) for studying and passed through a short (a couple theand evolution R = 89%, of respectively.the single high-intensity These mode,in backscattering or longer by [5]. about By 1improving m to allow for time of gain lengths) undulator section to measurementswere measured of x-rayin Bragg pulses diffraction circulating inthe the measurement cavity. The crystalaccuracy and by mirrors two will be aligned produce fully coherent, femtosecond withat normalnanoradian-precision incidence to the angular reflecting and submicron-precisionorders of magnitude high-stiffness from previous linear stages. The atomic planes, using hard x-rays with x-ray pulses. The femtosecond pulse stages will be driven by piezo actuators coupledexperiments, to the feedbac we werek system.able to directly Room-temperature, as produced in this scheme will be a photon energy of E = 23.7 keV. The probe the linear thermal expansion well as cryogenically cooled, optical elements will be tested. stable, in contrast to the ultrafast self-amplified spontaneous emission pulses proposed recently [2], which have inherent fluctuations. Extracting and transporting a high-energy beam from the oscillator while maintaining the Å-scale microbunching is challenging and will require careful beam optics design [3].

Diamond Crystal

With the cavity scheme using four crystals, the photon energy can be tuned continuously in a finite spectral region and all spectral regions of interest can be covered by one crystal material working at different Bragg planes. The choice of material is diamond, a crystal with Fig. 1. X-ray images of the sample diamond crystal. (a) White-beam x-ray topogram of the the highest reflectivity and excellent diamond crystal plate in transmission. (b) and (c) Color maps for the relative spectral width, mechanical and chemical properties. ΔE=ΔEmin (b), and the relative peak reflectivity for the (995) Bragg reflection, R=Rmax (c), at < The reflectivity of a perfect diamond different Fig. 1 pointsX-ray images on the of diamondthe sample crystal,diamond measuredcrystal. (a) White-beam with a 23.765-keV x-ray topogram x-ray of photonthe beam of 0.7 × crystal is predicted to be 98-99% in 0.7mm2diamond cross section. crystal plate The in beam transmission. footprint (b) andis larger (c) Color than maps the for pixels the relative on the spectral color maps, and has the hard x-ray region of 5 to 25 keV. been reducedwidth, D E=in DsizeEmin (b)to ,allow and the direct relative comparison peak reflectivity with for the the underl(995) Braggying reflection, white-beam topogram. The required volume is not large, R=Rmax (c), at different points on the diamond crystal, measured with a 23.765-keV about 1 × 1 × 0.1 mm3. x-ray photon beam of 0.7 × 0.7mm2 cross section. The beam footprint is larger than the

Experiments performed at pixels on the color maps, and has been reduced in size to allow direct comparison with XOR/IXS beamline 30-ID at the the underlying white-beam topogram.

The Advanced Photon Source Annual Science Report 2009 151 Reports from the Accelerator Systems Division

> Fig. 2 Linear thermal expansion coefficient of diamond, obtained by point-by-point determination from experiment 1 (circles) and from experiment 2 (squares), calculated from the polynomial approximation (solid line) and the Debye model approximation ~T3 (dashed line). The shaded area represents the region that was inaccessible to previous experiments due to their limited measurement accuracy.

Fig. 2. Linear thermal expansion coefficient of diamond, obtained by point-by-point determination from experiment 1 (circles) and from experiment 2 (squares), calculated from the polynomial approximation (solid line) and the Debye model approximation ~T3 (dashed line). The shaded area represents the region that was inaccessible to previous experiments due to their coefficient at temperatures below A Test X-ray Cavity limitedcavity. measurement The crystal accuracy. and mirrors will 100K, as shown in Fig. 2. The lowest be aligned with nanoradian-precision value measured was 2 × 10−9K−1 near For an integrated test, we angular and submicron-precision 30K. It was found that the coefficient will construct the prototype x-ray high-stiffness linear stages. The deviates from the expected Debye cavity shown schematically in stages will be driven by piezo law (T3) below ~50K, while no Fig. 3 [6]. This prototype should actuators coupled to the feedback negative thermal expansion was be built in an available space at an system. Room-temperature, as well observed. When used in conjunction APS insertion device beamline so as cryogenically cooled, optical with the known value of the thermal that high-brightness x-ray beams elements will be tested. conductivity at low temperatures, can be injected into the cavity. The Fig. 3. A concept for a test x-ray cavity. length of the prototype will be 23- this discovery helps pave the way to References solving the heat load problem of the 24 m, about one-fourth of the actual x-ray cavity. x-ray cavity for an XFELO, which [1] R. Lindberg and K.-J. Kim, to be published A pilot experiment to stabilize will be convenient because in this [2] J. Rosenzweig et al., Nucl. Instrum. Methods A 593, 39 (2008). crystal angles via a feedback loop case, the mirror is smaller than that [3]References M. Borland, private > communication based on the null-detection principle required for the 100-m cavity. The [1] R. Lindberg and K.-J. Kim, was discussed in the previous APS round-trip path length will be chosen to be published Science report. Stabilization within to be either the same as the APS [2] J. Rosenzweig et al., Nucl. Instrum 15 nrad in 1-Hz noise bandwidth bunch spacing (46 m) for studying Methods A 593, 39 (2008). was achieved [6]. Further progress the evolution of the single high- [3] M. Borland, private communication for tighter angular stability (10 nm), intensity mode, or longer by about [4] Yuri V. Shvyd’ko, Stanislav broader bandwidth (1 kHz), and 1 m to allow for time measurements Stoupin, Alessandro Cunsolo, Fig. 2. Linear thermal expansion coefficient of diamond, obtained by point-by-point multi-axesdetermination system from experiment will be 1required. (circles) and fromof experiment x-ray pulses 2 (squares), circulating calculated in thefrom the Ayman H. Said, and Xianrong polynomial approximation (solid line) and the Debye model approximation ~T3 (dashed line). Huang, Nat. Phys. 6(3). The shaded area represents the region that was inaccessible to previous experiments due to their Published online 17 January 2010.

< limited Fig. 3 measurement A concept for accuracy. a test x-ray cavity. DOI:10.1038/nphys1506 [5] Stanislav Stoupin and Yuri V. Shvyd’ko, Phys. Rev. Lett. 104 (2010) [6] Stanislav Stoupin, F. Lenkszus, R. Laird, K. Goetze, Yuri V. Shvyd’ko, and K.-J. Kim, submitted to Rev. Sci. Instrum. Methods A. [7] Yuri V. Shvyd’ko and K.-J. Kim, unpublished Fig. 3. A concept for a test x-ray cavity.

References 152 A rgonne National Laboratory [1] R. Lindberg and K.-J. Kim, to be published

[2] J. Rosenzweig et al., Nucl. Instrum. Methods A 593, 39 (2008).

[3] M. Borland, private communication Reports from the Accelerator Systems Division

Development of a 352-MHz Solid-State Rf Amplifier

and utilizing single-package transistor IN SHORT > The Radio Frequency Group of the Accelerator power amplifier devices operating at Systems Division has initiated a long-term program to 1-kW CW is feasible. A total of four 352-MHz/1-kW ultimately design and built a solid-state, 200-kW, 352-MHz amplifiers have been built, two with radio-frequency (rf) amplifier to replace the existing APS one-piece copper cold plates and two klystron-based rf systems. This initiative is being undertaken with carrier/cold-plate construction. by the group in order to address the potential long-term The carrier-version amplifiers unavailability of this product by developing an alternative were constructed with copper and aluminum cold plates to determine any approach to deal with the issue. The RF Group is progressing differences in thermal performance. toward construction and testing of a 352-MHz/4-kW, CW, Two 352-MHz four-port solid-state rf amplifier demonstration system to be used combiners, a standard 1/4λ combiner to evaluate the practicality of solid-state rf systems for the (Fig. 2) requiring external circulators APS accelerators. for isolation, and one Gysel with inherent isolation have been designed to combine the output from four 1-kW amplifiers to produce the 4-kW

MORE > The group has built and cold plate designed to maximize tested several 352-MHz/1-kW CW cooling of the transistor die (Fig. 1). amplifiers utilizing the Freescale Preliminary tests indicate that the MRF6VP41KHR6 LDMOS rf power design of a 200-kW, solid-state rf transistor, and a high-efficiency power system operating at 352-MHz < Fig. 2 Cut-away view of a four-way rf combiner.

demonstration system. The 4-kW system will be tested to understand how to improve overall system efficiency, reduce cooling water requirements, and estimate reliability. A 1/4λ combiner was designed in advance of fabrication. Initial tests of the 4-kW system are tentatively scheduled for April 2010. Ali Nassiri ([email protected]), and Doug < Fig. 1 A 1-kW, 352-MHz test amplifier. Horan ([email protected])

The Advanced Photon Source Annual Science Report 2009 153 Reports from the Accelerator Systems Division

Progress on the P0 Feedback Project

diagram of the system. The system An initial system was installed IN SHORT > The samples the transverse beam position in 2008 and beam tests were Advanced Photon Source of each target bunche at a stripline performed. Several system upgrades storage ring has several monitor, filters the sampled data to of the design followed: improvement bunch fill patterns for user generate the correct drive signal, and of the front-end electronics, moving sends the drive signal to high-power a horizontal stripline to a new high-βx operation. The hybrid fill radio frequency amplifiers that drive region, installation of two 500-watt pattern consists of a single the target bunch through a drive amplifiers, addition of a remote bunch with a charge of 16 stripline. Closed-loop operation of mA and a bunch train of the system generates damping on lower-charge bunches. Due all target bunches and achieves to its high single-bunch beam stabilization. < Fig. 1 Main rack of the P0 feedback system. charge, beam instabilities exist and are currently compensated for with high chromaticity correction. High chromaticity reduces dynamic aperture, reduces beam lifetime, and generally increases non-linear effects on the storage ring beam. The P0 feedback project was initiated as part of an effort to control beam instability and reduce the chromatic correction for the APS storage ring. An initial system was installed and tested. It has achieved the goal of stabilizing beam and storing beam with high single-bunch charge and balanced chromaticity.

MORE > Figure 1 shows a picture of the main part of the system installed at the Sector 2 storage ring mezzanine, and Figure 2 is a block

15 4 A rgonne National Laboratory Reports from the Accelerator Systems Division

< Fig. 2 Block diagram of the P0 feedback system.

The plot shows: (1) Around target charge of 17-mA per bunch a reduction of 2.5 to 3 of chromaticity is achievable. (2) Areas B and C, which were previously not available for operations, are now included by operating with closed feedback loops. Work is under way to review and implement operation readiness of the system so that a test run period can be conducted during user operations to further optimization and evaluation of the system. Contact: C.Y. Yao (e-mail: [email protected])

FPGA slave for horizontal drive, x and y chromaticities with the < Fig. 3 Stability and accumulation limits and design of a new two-blade loop open and closed. Region A is versus chromaticity with and without horizontal stripline. the area where we can operate the closing the feedback system loops. Commissioning of the system storage ring with the loops open. The black curve is the accumulation continued after the system upgrade. Generally, we attempt to operate limit when the feedback system is Significant progress was achieved near the limiting curve for reduced turned on. The green curve is the during closed-loop beam tests. lattice non-linearity. Regions B and accumulation limit when the feedback We achieved the first goal of C are areas where either vertical or system is turned off. Beam is always stabilizing standard 24-singlet-pattern horizontal instabilities are observed stable in region A and has instability beam with reduced chromaticity with feedback loops open. in both regions B. on November 3, 2009. A 10-mA 24-singlet fill pattern beam was injected and kept in top-up mode with feedback loops closed at reduced chromaticity of 0.5 in the horizontal plane and 2.5 in the vertical plane. Normal operation chromaticity for  this fill pattern is around 6 for both  planes. We ran in top-up for 2 h and observed an increase of beam life from 8.5 h to 15 h. We did not  observe any obvious side effects  on either beam emittance or rms beam motion. On December 19 we  !  achieved our second goal of storing beam with high single-bunch charge with reduced chromaticity. Figure 3 shows the results of a scan experiment, in which beam  current stability and accumulation   limit were measured while varying

The Advanced Photon Source Annual Science Report 2009 155 Reports from the APS Engineering Support Division

Collaboration with the NSLS-II at Brookhaven National Laboratory

conductivity, impedance issues, and ease of in situ bake out. IN SHORT > Vacuum Chambers for the NSLS-II Brookhaven engineers adopted The National Synchrotron Light Source-II (NSLS-II) at the designs for their aluminum U.S. Department of Energy’s (DOE’s) Brookhaven National chambers from existing APS Laboratory will be a new, 3-GeV, 500-mA storage ring chamber designs, with the assistance designed to deliver x-rays 10,000 brighter than those available of engineers at the APS. from the current NSLS. Construction of NSLS-II began in 2009; early operations are expected in 2014. The lattice of the

< Fig. 1 The first prototype NSLS-II dipole NSLS-II storage ring calls for 60 dipole vacuum chambers, vacuum chamber was welded at the 90 multipole vacuum chambers, and 45 straight-section APS and sent to Brookhaven for vacuum chambers to contain the electron beam that will orbit testing and evaluation. around the 792-m ring and the x-ray beams that will be delivered down the facility’s 58 beamlines. These vacuum chambers are the subject of a two-year collaboration among Brookhaven and Argonne scientists and engineers that has brought the extensive APS expertise in aluminum vacuum chamber design, fabrication, and commissioning to the service of a sister DOE light source.

MORE > The NSLS-II storage ring vacuum chambers (Fig.1) will be made of extruded aluminum 6063-T5, similar to the chambers used at the APS and based on good experience at the APS with extrusions, the cost of fabrication compared to other methods, the ability to obtain a smooth interior cross section, good thermal

156 A rgonne National Laboratory Reports from the APS Engineering Support Division

Accommodating the NSLS-II chamber design required extensive IN SHORT > Nanopositioning welding development work. The cross sections of the NSLS-II Based on the experiences gained from the nanopositioning chambers have a different profile system designed at Argonne for the Center for Nanoscale than that of the APS chambers, and Materials (CNM)/APS multilayer Laue lens (MLL)-based the NSLS-II multipole and dipole hard x-ray nanoprobe project, a new nanopositioning system chambers have two completely is being designed for the NSLS-II Hard X-ray Nanoprobe different cross sections. The new (HXN) prototype through a Brookhaven/Argonne joint work chamber extrusion geometry required new tooling for the project. The joint work project was started in September 6-in. × 4.63-in. and 6-in × 6-in. 2009 and is expected to last for three years. Scientists and flanges to multipole and dipole end engineers at the Argonne APS Engineering Support and adapters. Because most NSLS-II X-ray Science divisions and the CNM, and their counterparts chambers are shorter in length than at the NSLS-II are collaborating on the following important those used at the APS, a tooling nanopositioning tasks: adapter was fabricated so as to not require repositioning of the • Identifying and solving engineering and technical tasks tail stock tooling on the automated welding machines at the APS. New with the HXN prototype. headstock tooling and tailstock • Developing a laser encoding scheme to ensure stability tooling was installed on both between the sample and the MLL optics. welding machines to accommodate the two different cross sections. In • Developing a sample holder allowing easy fiducialization addition, new tooling was needed of the sample with ancillary pre-alignment microscopes. for chamber components, including pumping ports, absorber ports, • Developing an HXN with adequate vibration properties. instrumentation ports, and x-ray exit ports. Because of the number • Solving various engineering challenges that will be of welding-part computer programs encountered during prototype development. needed, the automated welding machines at the APS were upgraded, quadrupling the amount of part- program storage. Where possible, welding joint profiles and material selection were duplicated from the MORE > The design and proto- APS chambers and implemented typing activities for the NSLS-II into the NSLS-II chambers. nanopositioning system will also Additional APS engineering benefit further development of the assistance has been applied to the CNM/APS MLL-based hard x-ray NSLS-II process water system nanoprobe. Contact Deming Shu designs and to R&D for thermal ([email protected]) stability of the vacuum system support girders. Contact George Goeppner ([email protected])

The Advanced Photon Source Annual Science Report 2009 157 Reports from the APS Engineering Support Division

Novel Nanopositioning Stages with a Sub-Centimeter Travel Range

link stage, T8-32. It is designed to perform a 2-D sub-nanometer IN SHORT > Recent developments in hard x-ray focusing resolution scanning function in a at the nanometer scale with linear multilayer Laue lenses 3-mm × 3-mm range for a nanoprobe (MLLs) have demonstrated promising new x-ray optics for sample holder with a maximum focusing to a spot of a few nanometers. In order to use x-ray weight of 5 kg for the MLL test optics with a nanometer-scale resolution limit, scanning setup. Figure 1 shows a three- x-ray nanoprobes with corresponding mechanical positioning dimensional (3-D) model of the APS capabilities must be designed. In particular, positioning T8-31/T8-32 2-D weak-link stage. stages with both sub-nanometer resolution and a positioning/ There are four fishbone-shaped laminar weak-link modules for scanning range of several millimeters are a necessity. The the T8-31 vertical stage guiding precision ball-bearing or roller-bearing-based stage systems structure. A commercial PZT-based provide large travel range. However, they present difficulties nanopositioning motor, such as the in meeting the required sub-nanometer resolution, high tilting N-214 NEXLINETM motor made stiffness, and high straightness of trajectory within a single by PI GmbH and Co., provides the guiding system. It has always been a dream to have a compact, driving force for the T8-31. With the N-214 NEXLINETM motor, the single-flexure stage to cover a large travel range with very T8-31 weak-link stage has a 10-kg high positioning resolution. load capacity, 3-mm travel range with 10-nm closed-loop resolution, and sub-nanometer resolution within a 3-µm step. For applications that need a long scanning range with sub-nanometer resolution, a MORE > A two-dimensional able to construct a strain-limited, laser encoder with sub-nanometer (2-D) linear flexure stage system over-constrained mechanism on resolution will be equipped for designed at the APS features high thin metal sheets by stacking the the stage positioning closed-loop structure stiffness through the use thin metal weak-link sheets with feedback system. A customized of a laminar overconstrained weak- alignment-pins, resulting in a stepping-motor-driven linear driver, link mechanism. This represents a solid, complex, laminar weak-link combined with a PZT actuator, new development in the application structure with ultrahigh positioning can provide the driving force for of redundantly constrained sensitivity and stability. The novelty sub-nanometer-level, closed-loop laminar structures as weak-link of this new 2-D linear flexure stages resolution in the entire 3-mm mechanisms. Using a photochemical system lies in its fishbone-shaped travel range. machining process together with multiple-parallelogram guiding The horizontal-stage T8-32 lithography techniques, we were structure, which performs the consists of three laminar weak- function of a high-stiffness, high- link modules with an inverse precision linear motion guider with “U” configuration for a 5-kg load sub-centimeter travel range and sub- capacity. As for the vertical stage, nanometer positioning resolution. there are two options for the stage’s The 2-D linear flexure stages driver. With a PI N111 NEXLINETM system comprises two weak-link motor, the T8-32 stage has 5-nm stages: a vertical weak-link stage, closed-loop resolution for a 3-mm APS T8-31, and a horizontal weak- travel range and sub-nanometer

158 A rgonne National Laboratory Reports from the APS Engineering Support Division < Fig. 1 A 3-D model of the APS T8-31/T8-32 2-D weak-link stage with 3-mm × 3-mm travel range and sub-nanometer positioning resolution.

resolution within a 0.8-µm step. weak-link stage has a vertical See > D. Shu and J. Maser, With a laser encoder system and a stiffness comparable to a worm- “Study of precision weak-link stage customized motor/PZT combined gear-driven precision screw stage in systems with large travel range and linear driver, the T8-32 stage has a similarly sized guiding structure sub-nanometer-scale resolution,” sub-nanometer level resolution for using crossed-roller bearings. to be published in Nucl. Instrum. the entire 3-mm travel range. The straightness of our trajectory and Methods A, the AIP Conference Using a commercial dual- test results show that the T8-31 Proceedings of the 10th International beam laser interferometer system vertical weak-link stage has motion Conference on Synchrotron with 0.9-µrad resolution, we tested trajectory accuracy better than many Radiation Instrumentation, the vertical stage system’s stiffness commercial motor-driven, linear SRI-2009 (27 September-2 October, for all six degrees of freedom. The bearing-guiding vertical stages with 2009, Melbourne, Australia). test results show that, driven by a a similar structure size. Contact PI N-214 driver, the T8-31 vertical Deming Shu ([email protected])

The Advanced Photon Source Annual Science Report 2009 159 Reports from the APS Engineering Support Division

Beamline Scheduling System

> Fig. 1 An example of the application IN SHORT > When the APS began operations, all beamlines “view-all” screen. had been designed, funded, built, and were being operated by independent collaborative access teams (CATs). Each CAT was responsible for managing the operations of its own allowing for reversible tentative beamlines, including soliciting, reviewing, and scheduling scheduling followed by a formal requests for beam time. In early 2002, the Department of commitment to the experimenters. Energy, Office of Basic Energy Sciences, which funded The beamline staff supporting several CATs, began to transition this funding to the APS, the incoming experimenters may also be independently scheduled. directing the APS to assume operational responsibilities for Fine-grained authorization allows these CAT beamlines. As the operation of more and more each beamline to control the level beamlines was transitioned to the APS, it became clear of detail visible to the different that centralization of many processes would provide strong customers of the application. A benefits to users, as well as to the scientists operating the variety of guidance, warning, and statistics are provided during the beamlines. A centralized General User Program (for the graphical scheduling process. submission, review, and allocation of general user beam time) Another popular feature is the was established in 2003, but individual beamlines continued automated emails, which provide to manage their own scheduling. As more and more beamlines beamlines the ability to create were commissioned and began operations, the collection of custom email templates that drive automated email notifications during uniform data for various types of reporting and planning scheduling. became increasingly more difficult. The project was a unique challenge for three reasons. Foremost was that many of the processes for scheduling developed over the prior 15 years were largely undocumented. The domain MORE > During the next few scientists. The committee reviewed knowledge was distributed among years, the APS began to consider progress and provided regular many people, and had to be collected methods for centralized beamline feedback to the developers. The and represented formally. Secondly, scheduling, eventually appointing software was successfully launched supporting the scheduling process a project team to build an entirely for use in late 2009 for a pilot graphically proved to be a challenge. new database-based scheduling program involving approximately Much of what seems simple and application. Requirements were half of all APS beamlines. The intuitive about the act of scheduling gathered in 2008, and a technical overall schedule for each run is actually quite difficult to support review committee was formed cycle can now be viewed in single, with a simple user interface. This comprising several senior beamline zoomable, scrollable chart (Fig. 1). necessitated a more sophisticated The application allows each application platform, and so the beamline to schedule all types of third challenge was evaluating APS-defined beam time: general and selecting the technology. The user, collaborative access team, application user interface was built beamline staff, and partner user. using Adobe Flex, and all business These beam-time requests may logic is provided as web services be scheduled in two phases, built using Java, Spring, Hibernate

160 A rgonne National Laboratory Reports from the APS Engineering Support Division

object-relational modeling, and the requirements. The future holds the Oracle database. possibility of integrating scheduling Feedback from users has with other systems such as the been very positive, with several detector pool, and further integration citing significant expected time into a comprehensive scientific savings and the ease-of-use of the workflow management architecture. user interface. Work still remains, Contact Claude Saunders particularly in regard to reporting ([email protected])

The Advanced Photon Source Annual Science Report 2009 161 Reports from the APS Engineering Support Division

A Synthesis of Sustainability and Science

All of this energy is converted to This work was a joint effort of the IN SHORT > Sustainable low-grade waste heat in the range Argonne APS Engineering Support building design is of 20 to 35º C, removal of which (AES) and Facilities Management challenging engineers has relied on a typical combination and Services divisions, leveraging of mechanical refrigeration and the resources and expertise of both. to push the envelope in evaporative cooling. Needless APS has been the beneficiary of a innovation and adaptation to say, the APS has an enormous substantial reduction in operating of the latest breakthroughs carbon footprint. costs, which to date is on the order in scientific research. The Long before the current of $600,000 per year. Department of Energy DOE sustainability requirements, The APS has long recognized (DOE) now requires the APS strove to reduce energy the need to reclaim the vast consumption and increase facility amount of waste heat it generates that a minimum of 15% sustainability. These efforts included in the production of x-rays. of all existing DOE lighting upgrades, improvement Taking advantage of our cold buildings meet stringent in temperature control, increases winter weather, engineers at the high-performance in system operational efficiencies, AES Division have developed and sustainability and novel techniques in the recovery a process of segregating air requirements by 2015. and reuse of low-grade waste heat. streams in ventilation systems In the article “Saving Energy to isolate and directly heat cold Further, all new buildings for Science” (APS Science 2008, outdoor ventilation air. This is a with a construction cost pg. 139), we documented a novel approach that achieves the in excess of $5 M must number of the energy efficiency segregation without additional meet achieve a “Gold” enhancements at the APS that had dedicated air conditioning systems sustainability rating from been completed or were in the and their associated capital and planning and construction phase. maintenance costs. Isolating the the United States Green As of the beginning of 2010 all the cold outdoor air stream increases Building Council. energy efficiency improvements the heat exchange temperature outlined in that article will have differentials and substantially been completed and become improves heat transfer with the operational. The projected energy low-grade waste-heat source, savings and improvement in our making this a practical and efficient carbon footprint resulting from process. Since laboratories require MORE > Commercial buildings, the newly completed facility the continuous introduction of which include most laboratories, enhancements are projected to large quantities of outdoor air, account for 17% of all energy used provide an annual savings of cold weather conditions provide in the United States and are fertile 33,296 x 106 Btu (10 million an opportunity to recycle a portion ground for making a significant kW h) with a resulting yearly of our waste heat. impact on the nation’s energy use reduction of 12,269,768 pounds Another feature of laboratories and carbon footprint. Research of carbon dioxide (CO2) 16,576 and research facilities is the need facilities like the APS can use pounds of nitrogen oxides (NOx), to continuously heat space supply more than 10 times the energy and 35,450 pounds of sulfur air to achieve temperature and per square foot than a typical dioxide (SO2). All of this work humidity conditions required for commercial office building. The was completed under Energy scientific programs. In order to keep APS itself has an average power Savings and Performance Contracts heat transfer surfaces as efficient demand of nearly 20 MW, at a cost (ESPC’s) requiring no up-front as possible, and minimize air in excess of $11 million per year. capital expenditure by Argonne. pressure drops, these reheat coils

162 A rgonne National Laboratory Reports from the APS Engineering Support Division

require heating-water temperatures the installation of a heat-recovery with state-of-the-art LED lamps. well above those of our low-grade chiller at the APS central cooling This would not only reduce lighting waste heat. Past attempts to tap the plant in building 450. Advances in power usage by nearly 65%, but low-grade heat has resulted in heat centrifugal chiller technology, along with the longer life span of light- transfer coils either dimensionally with the expanded capability of the emitting diode (LED) lamps, the too large to fit in the available space APS temperature control network labor for re-lamping the fixtures or with excessive air pressure drops have allowed us to push the limit on would be reduced by at least 50%. resulting in a substantial increase the hot water temperature generated A mock-up of the new experiment in fan energy consumption. In by the chiller. This chiller would hall LED lighting will be installed response, we have investigated operate as a large heat pump capable in spring 2010 along with LED two other approaches to waste-heat of providing the simultaneous lighting for one laboratory/office recovery; using fuel cell technology cooling and heating required by module office for on-site electrical generation the APS in the spring, summer, The preliminary estimated with simultaneous heating, and the and autumn seasons. Approximately cost savings for the three new application of heat pumps that push 1.8 MW of accelerator and beamline projects is on the order of $300,000 the envelope of state-of-the-art waste heat would be extracted from per year and will be submitted technology. the deionized process water cooling for inclusion in the next Argonne In a cooperative effort with loop to produce heating water in Energy Savings Performance the Argonne Chemical Sciences the range of 65 to 70º C. This water contract scheduled for release at and Engineering Division, AES would be used to provide a preheat the end of 2010. Implementation is participating in the preparation stage in the APS heating plant. of these projects relies on close of a proposal for the purchase and Monitoring heating water demand cooperation among the various installation of a 400-kW stationary against outdoor air conditions Argonne divisions and a continuing fuel cell for the Argonne Center would allow the APS to adjust the commitment to energy efficiency for Nanoscale Materials (CNM) heating system temperatures to and sustainability. This, coupled building. This fuel cell will provide take maximum advantage of heat with the willingness to push the electrical power at a lower cost reclaimed from the new chiller. envelope on emerging technologies than our utility provider and make At the same time, a significant part should insure the successful available two new sources of usable of the DI process water cooling completion of these projects and waste heat; a low-grade source load would be shifted to the our ability to exceed the current at 60° C and a high-grade source heat-recovery chiller, freeing up DOE building sustainability at 120° C. The addition of these valuable chiller capacity needed goals. Marvin Kirshenbaum two sources to the existing during the summer. ([email protected]) waste-heat recovery system at Another large source of the CNM would shift all building energy consumption is the APS heating needs strictly to waste heat. lighting system. The existing The combination of lower electrical experiment hall high-intensity generation cost and elimination of discharge (HID) lamps consume the need for heat from the Argonne approximately 2 million kW h per site steam system would provide year with a yearly operating cost of sufficient energy cost savings to $160,000. Due to the long warm-up make the purchase and installation time of the lamps, the use of timers of a stationary fuel cell affordable. or other on/off control devices To expand our ability for is not practical. AES is currently low-grade heat extraction, AES has investigating the replacement of all prepared a preliminary design for HID and other inefficient lighting

The Advanced Photon Source Annual Science Report 2009 163 Reports from the APS Engineering Support Division

Sector Safety Reviews

and general experimental work, IN SHORT > The APS has established a comprehensive user unique hazards encountered during safety program to ensure the safe operation of the facility and the past year and their mitigation, a safe environment for its users. A portion of this program reports on safety incidents, follow- is the periodic review of each sector, its associated facilities up on action items (if any) from the previous review, and lessons learned (office areas, control areas, labs, experiment equipment with and good safety practices. engineered safety controls, etc.), and experimental safety The review committee verifies program. The review program was started in 1997 as the that the APS has safe operations Independent CAT Safety Assessments. In this peer review sector records for the sector on file program the individual sectors operated by collaborative and that they are consistent with access teams (CATs) were divided into groups that reviewed the beamline as-built conditions. Typically, these records include the each other. The reviews were organized and directed by the beamline sector layout, synchrotron APS, with the CATs being part of the review team. and bremsstrahlung ray-traces, shielding component designs (e.g., assembly drawings that show component functionality for shutters, stops, and critical dimensions), personnel safety system operations, MORE > In 2004 the program status report of the beamline and shielding designs, the safe- was modified to verify that all APS experiment safety programs, and operations envelope for the beamline beamline facilities were safe and met demonstrating how Integrated Safety (e.g., maximum beam current or APS/Argonne safety standards. In Management (ISM) is incorporated minimum gap limits), and reports addition, the scope was broadened into the program. They note any of outstanding items from previous to include verification of beamline changes in the sector since the last safety inspections. The committee documentation records that are design review. Suggested topics also conducts an inspection of maintained by the APS. The APS that are covered in the summary the beamlines, experiment stations, took on primary responsibility include sector safety organization/ and associated. for organizing and executing the changes, overview of the sector The findings of the review sector reviews. Each APS sector is safety plan and (in subsequent are reported to Sector management reviewed through this program on reviews) changes to the plan, for correction, comment, or prompt a three-year cycle. changes in management, examples mitigation of identified problems. The APS User Safety Officer of communication of safety The report may include notable chairs the review and appoints a information to sector members and safety practices found on the review committee that includes the users, standard procedures followed beamline, opportunities for safety Radiation Safety System Manager, at the beamlines and in the LOM enhancements, and findings of the User Technical Interface, Labs, new procedures, as applicable, deficiencies where the beamline Area Emergency Supervisor, the experimental program safety, operations have not met APS/ X-ray Science Division ES&H significant shop activity and shop Argonne standards. The report coordinators, and others as operational problems and solutions, is entered in the APS Integrated appropriate to the sector’s programs waste handling complications and Content Management System and facilities. The APS provides resolutions, safety reviews of new and tracked for completion. suggested topics to be covered in instrumentation, management The number of currently the review. of critical shielding and issues operating beamlines requires The sector staff submits an related to PSS and EPS operation, that approximately one review updated safety plan, providing experience with safety planning for is completed every month. Bruce a 20-30 minute summary and beamline commissioning/operations Glagola ([email protected])

16 4 A rgonne National Laboratory Other Reports from the APS

GeoSoilEnviroCARS (Sector 13) Receives Federal Grants for Canted Undulator Upgrade

U.S. Department of Energy– IN SHORT > GeoSoilEnviroCARS (GSECARS) at APS Midscale Instrumentation, U.S. Sector 13, which is dedicated to Earth, environmental, and National Science Foundation– planetary science, has received funding to implement a canted Division of Earth Sciences– Instrumentation and Facilities, and undulator upgrade (Fig. 1). This upgrade will double the the National Aeronautics and Space available undulator beam time on this highly oversubscribed Administration– Sample Return beamline, and provide new sector capabilities, thereby Laboratory Instruments and Data enhancing the science conducted at the sector. Analysis. The combined total of these grants is $2.3 M. In addition, a portion of the $5.6 M awarded to the APS under the American Reinvestment and Recovery Act is being used to support the installation of the two new, optimized undulators and MORE > The upgrade involves a horizontal compound-focusing required front-end components. the installation of two undulators, geometry to produce focal spots The scientific impact of the optimized for different energy ranges, down to 250 nm for the microprobe. GSECARS upgrade will be in in the Sector 13 straight section. With this single instrument, detailed high-pressure mineral physics and The two insertion devices (IDs) speciation and compositional research chemistry, non-crystalline and nano- are arranged in a canted geometry will be conducted on both light crystalline materials at high pressure, to provide two independent x-ray elements (as low as sulfur) and heavy chemistry of hydrothermal fluids, sources. The upstream undulator, elements in systems of geochemical, reactions at mineral-water interfaces, optimized for lower x-ray energies environmental, and cosmochemical biogeochemistry, flow dynamics of (2.3-23 keV), will be the source for a significance. The second undulator fluids and solids, oxidation states sub-micron-resolution, Kirkpatrick- will be optimized for higher x-ray of magmas, and cosmochemistry of Baez mirror-based, x-ray microprobe energies (5.6-80 keV) to significantly extraterrestrial materials. In particular, in a dedicated enclosure (13-ID-E). enhance the high-pressure (laser- the ability to access S, Cl, K, and This new enclosure will be produced heated diamond anvil cell and Ca K-edges, as well as K- and by isolating the upstream one-third of multi-anvil press) and surface and L-edges of heavy elements with the the existing 13-ID-C enclosure with interface scattering (general purpose sub-micron-resolution micro­probe an interior wall installed perpendicular diffractometer) research programs. will offer tremendous new scientific to the beams. A 300-mm horizontal Modifications to existing beamline opportunities. separation between the two undulator components will be made to allow An aggressive design, beams in the 13-ID-E enclosure will independent, full-time utilization of fabrication, and installation timeline be achieved using dual deflecting the two undulator beams. is being pursued which will allow this mirrors (located in the first optics Support of the beamline upgrade to be achieved with minimal enclosure, 13-ID-A) on the outboard component modifications and impact and interruption to the existing (13-ID-E) beam. The second of these additions is being shared equally user program. Commissioning of the mirrors will be bendable to allow by three separate federal programs: upgraded sector is planned for 2012. < Fig. 1 A schematic of the planned canted-undulator upgrade of GSECARS Sector 13.

The Advanced Photon Source Annual Science Report 2009 165 Other Reports from the APS

Mitigating Obsolescence

MORE > The electronics that are and assigned a risk to each, based on IN SHORT > The APS is relied upon in today’s world have an the likelihood of system to failure now entering its fifteenth increasingly short lifespan, and the if no action is taken to address year of providing beam APS is now confronted with the fact problems, and the impact on the APS to users. During this that many of the operating systems if such a failure was to occur. This that were designed nearly 20 years list of projects is regularly reviewed first decade- and-a-half ago (and parts acquired soon by APS management and updated of operations, the APS thereafter) are no longer available. as needed. Some of the projects has arguably become This is particularly true for the most on this list involve straightforward known for (among complex (and therefore most fault procurements and installation of new other achievements) prone) systems. Budgets during hardware; other projects require more operating the most reliable the last few years have allowed for complex integration into the APS facility, because the new components accelerator serving a repairs of known problems, but not for development of new systems to are not identical to the obsolete broad user community. replace those that are aging. components. In other cases, the APS scientists have The APS has planned to deal replacements do not exist in industry enjoyed beam availability with this through an aggressive and the overall project will require greater than 97% since program of systems upgrades an extensive R&D program prior to 2002. The mean time utilizing capital expenditures, development and implementation. between unplanned beam known as Accelerator Improvement An example of this latter category is Projects. Technical experts have the klystrons used in the APS booster dumps exceeded 50 h (the assessed the state of their systems and storage ring (Fig 2). original goal) in 2004 and has remained well over that number ever since. The rewards of this success contribute to the way in which science is done at our beamlines, which can now accommodate more users in shorter time slots. Thus, even a short accelerator downtime may mean that some very good science simply does not get done. The APS accelerator staff is continually looking for ways to ramp-up their efforts in order to ! maintain the optimum < level of operation. Fig. 1 Evidence based on APS systems maintenance records indicates that some critical systems within the facility are nearing the end of the “Constant Failure Rate” period. Without replacments, the APS will soon enter a period of “Increasing Failure Rate.”

166 A rgonne National Laboratory Other Reports from the APS < Examples of other systems Fig. 2 Chief technician Dave Mayer (ANL-ASD) inspects one of the APS storage ring needing major obsolescence upgrades klystrons. The APS is dependent on three or four of these for operation. At present are low-level radio-frequency there is only one vendor, and new units cost $800 K. The APS is undertaking an systems, beam monitoring systems, R&D program to develop a solid-state amplifier, which will eliminate our dependence vacuum systems, water systems, on these klystrons. computing systems, and storage ring power supply controllers. We plan to allocate roughly $25M in obsolescence upgrades, spread out over a five-year period. Contact Rod Gerig ([email protected])

The Advanced Photon Source Annual Science Report 2009 167 Data

APS Organization Chart

APS Staffing and Funding

500 Senior Mgmt. 125 Technical Mgmt. Supplemental/ARRA 450 ESH/QA 120 GPP/Special Secretarial/Clerical 115 AIP 400 Admin. Mgmt./Staff Capital equipment Technical Staff 110 Operating 350 Designers/Drafters Technicians 105 300 100 250 95 200 90 150 85

100 80

50 75

0 70 FY93 FY95 FY99 FY02 FY03 FY04 FY05 FY06 FY07 FY08 FY09 FY99 FY00 FY01 FY02 FY03 FY04 FY05 FY06 FY07 FY08 FY09

APS Staffing Levels FY93 – FY09 APS Funding Levels FY99 – FY09

168 A rgonne National Laboratory Acknowledgments

APS Science Editorial Board: Cele Abad-Zapatero (University of Illinois at Chicago), Mark A. Beno (ANL-XSD), Paul Fuoss (ANL-MSD), Rodney E. Gerig (ANL-PSC), J. Murray Gibson (ANL-PSC), Efim Gluskin (ANL-ASD), Denis Keane (Northwestern University), Dennis M. Mills, (ANL-PSC), William G. Ruzicka (ANL-AES), George Srajer (ANL-XSD)

The Research Highlights in this report were written by: William Arthur Atkins ([email protected]) David Bradley ([email protected]) Yvonne Carts-Powell ([email protected]) Vic Comello (ANL-TSD, [email protected]) Sandy Field ([email protected]) Carol Hart ([email protected]) Emma Hitt ([email protected]) Philip Koth ([email protected]) Elise LeQuire ([email protected]) David Lindley ([email protected]) JR Minkel ([email protected]) Mona A. Mort ([email protected]) Luis Nasser ([email protected]) Patricia E. Panatier ([email protected]) Mark Wolverton ([email protected])

Art Direction: MeachamHowellDesign ([email protected]) Design: Daniel F. Sarro (ANL-TSD) Printing Coordination: Gary Weidner (ANL-TSD) Photography: Wes P. Agresta and George J. Joch (both ANL-TSD), Richard B. Fenner (ANL-PSC) Aerial Photograph of the APS: Tigerhill Studio (www.tigerhillstudio.com/) Contracts, rights and permissions: Jessie L. Skwarek (ANL-PSC) Project Coordination: APS Scientific Information Services

Our thanks to the corresponding authors who assisted in the preparation of the research highlights, to the users and APS personnel who wrote articles for the report, and our apologies to anyone inadvertently left off this list. To all: your contributions are appreciated.

The Advanced Photon Source Annual Science Report 2009 169 APS Science 2009

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