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SSRL Headlines Vol. 11, No. 11  May, 2011


Contents of this Issue:

  1. From the Director of SSRL: Thinking Big-Picture
  2. Science Highlight — Controlling for X-ray Radiation Damage in Measuring a Metalloenzyme Transition State
  3. Science Highlight — Hydrogen Storage Goes Nano
  4. Keith O. Hodgson Elected to the National Academy of Sciences
  5. User Jonathan Rivnay Receives Materials Research Society Graduate Student Award
  6. User Markus Guehr Receives DOE Early Career Research Award
  7. Workshop Announcement: XDL 2011 - Science at the Hard X-ray Diffraction Limit
  8. Upcoming SSRL Events: NUFO, SRXAS, Users' Conference
  9. User Administration Update
  10. In the News: Fungi, Light Source Development, PV Modules

1.   From the Director of SSRL: Thinking Big-Picture

Chi-Chang Kao
Chi-Chang Kao
As part of our ongoing effort to develop an updated strategic plan for SSRL, we held a retreat for scientific staff earlier this month. Stepping away from our day-to-day duties, we explored new scientific opportunities, listened to the research of individual scientific staff members, heard about potential accelerator performance improvements, and discussed how to translate our ideas into specific beam lines and instruments. It was a very fruitful experience for everyone involved, allowing us to learn more about our colleagues' work and take time to think outside of the box.

In parallel, over the last few months the SPEAR3 Accelerator Physics Group, working with physicists from the Accelerator Directorate's Accelerator Research Division, have accelerated their effort to increase the brightness of SPEAR3, which is critically important for most of the new scientific opportunities discussed at the retreat. Initial results from their studies are very encouraging, demonstrating an improvement of over 50% in brightness. Substantial additional effort is still necessary before such an upgrade can be implemented for normal storage ring operation, but the work is quite promising.

With the knowledge gathered from the retreat and these recent accelerator studies, division heads are now drafting plans for how they can develop SSRL's core capabilities and technologies to address tomorrow's scientific opportunities. When these draft proposals are finished, we will launch a web forum where SSRL users can view the proposals and offer feedback before the strategic plan is finalized.

SSRL continues to produce exciting science in a wide range of areas, and it is my hope that this will only increase as we define our strategic goals and align our work with these goals.

—Chi-Chang Kao

2.  Science Highlight — Controlling for X-ray Radiation Damage in Measuring a Metalloenzyme Transition State
       (contact: Michael Soltis,

CCPI figure
The metal center active site for A) the low dose structure and B) the high dose structure overlaid with the 2fo-fc electron density maps contoured at 4.0 a.
At times, different observational tools do not give the same answer when measuring the same thing. Such was the case when looking at the metalloenzyme transition state species Fe(IV)-O, important as an oxidant in a number of iron-containing enzymes. While x-ray absorption spectroscopic experiments determined the Fe-O bond length to be short (less than 1.7 Å), some results from crystallographic studies indicated that the bond length was longer (1.8-1.9 Å). This difference would be consistent with the Fe-O bond having double bond or single bond character, respectively, which would suggest different chemistry. A possible reason for this variation in structural results could, however, also be an electronic change in the iron atom imposed by the high doses of radiation from x-ray crystallographic methods, reducing it towards a Fe(III) oxidation state.

A team led by Prof. Thomas Poulos of the University of California at Irvine in collaboration with SSRL scientists used SSRL Beam Line 9-2 to systematically address the observed discrepancies. They confirmed that the intense x-ray beam encountered in crystallographic experiments did indeed change the iron electronic state, and quantified the magnitude as a function of dose with in-situ visible spectroscopy measurements, finding the exposure level that allowed the majority of the enzyme sites to remain in their original iron oxidation state. By spreading the dose over multiple crystals, they designed a method that allowed around 90% of the iron sites to be in the non-decayed state while collecting a complete crystallography data set. Analysis of these crystallographic data showed the Fe-O bond to be about 1.72 Å, very similar to that obtained from the x-ray absorption spectroscopy data. This study illustrates the sensitivity of enzyme metal sites to x-ray dose and the importance of applying complementary in-situ methods when feasible.

The equipment and methods for combined crystallography and visible spectroscopy data collection developed and used in this study are currently being made into an automated and integrated feature of SSRL Beam Line 9-2. This work was published in Biochemistry.

To learn more about this research see the full scientific highlight

3.  Science Highlight — Science Highlight: Hydrogen Storage Goes Nano
       (contact: Srivats Rajasekaran, )

swcnts image
Schematic of the "spillover" mechanism.
To expand the use of hydrogen in mobile applications-such as hydrogen-powered buses and cars-researchers will need to design lightweight, compact means of storing it. One possible method is to store hydrogen inside carbon nanotubes. Theoretical predictions suggest that, through a mechanism that forms stable carbon-hydrogen bonds, it would be possible to store one hydrogen atom for every carbon atom inside single-walled carbon nanotubes.

A team of Stanford and SLAC researchers recently investigated the interaction of hydrogen with such single-walled carbon nanotubes coated with platinum nanoparticles. Experiments at SSRL Beam Line 13-2 revealed that the addition of platinum as a catalyst made it possible for hydrogen to bond with the carbon nanotubes at realistic conditions (<10 atmospheric pressure at room temperature). This research shows that carbon nanotubes doped with a suitable metal catalyst, such as platinum, represent viable materials for hydrogen storage. However, much work remains before these nanotubes can achieve the Department of Energy goal of 6% weight efficiency.

This research was published in the April 2011 edition of the Journal of the American Chemical Society.

To learn more about this research see the full scientific highlight

4.   Keith O. Hodgson Elected to the National Academy of Sciences
       (May 4, 2011 SLAC Today article by Lori Ann White)

K. Hodgson
Keith Hodgson
SLAC Associate Laboratory Director for Photon Science and Chief Research Officer Keith Hodgson, who is also the Stanford University David Mulvane Ehrsam and Edward Curtis Franklin Professor of Chemistry and Professor of Photon Science at SLAC, has been elected to the National Academy of Sciences. He joins 71 other new members-including seven others from Stanford-and 18 foreign associates, the NAS announced yesterday.

"I was thrilled to hear of Keith's election to the National Academy of Sciences," said Persis Drell, director of SLAC. "He has made major contributions to our use of high-intensity synchrotron radiation for diffraction studies of proteins, as well as phasing by anomalous scattering methods," a technique used to recover vital information lost during the process of X-ray diffraction. "This is a well-deserved honor."

Hodgson has been involved with SLAC in various capacities since 1973. As one of the first users of the Stanford Synchrotron Radiation Lightsource (then called the Stanford Synchrotron Radiation Project), he and his students did pioneering work in both the use of synchrotron X-rays to determine the crystal structures of proteins and the development of X-ray absorption spectroscopy to study biological and chemical systems. Since then he has published extensively on X-ray spectroscopic and crystallographic techniques, as well as using those and other techniques to further the study of a large range of biological, bioinorganic and inorganic systems. Hodgson served as SSRL Director from 1998 until 2005, helping realize both SPEAR3, a major upgrade to the venerable synchrotron light source facility, and the genesis of the Linac Coherent Light Source, the world's first hard X-ray laser and the next generation in light source technology.

Hodgson received the E.O. Lawrence Award from the Department of Energy in 2002 and was named a Fellow of the American Association for the Advancement of Science in 2006. He is also a member of several scientific societies and has been active in national scientific policy, including chairing the DOE Biological and Environmental Research Advisory Committee from 1995 to 2005. Hodgson earned his BS from the University of Virginia in 1969 and his PhD from the University of California, Berkeley in 1972, and then joined Stanford as Assistant Professor of Chemistry in 1973.

5.   User Jonathan Rivnay Receives Materials Research Society Graduate Student Award

J. Rivnay
Jonathan Rivnay
Longtime SSRL user and Stanford graduate student Jonathan Rivnay received the Materials Research Society's Graduate Student "Gold Medal" Award at the 2011 MRS Spring Meeting. The award, intended to honor and encourage graduate students whose academic achievements and current materials research display a high level of excellence and distinction, is presented to students of exceptional ability who show promise for significant future achievement in materials research. Rivnay presented a talk entitled "The Effect of Disorder on Charge Transport in High Performance Semicrystalline Polymers" at the spring meeting.

"I guess it is possible to make fundamental studies of disorder in organic semiconductors sexy," Rivnay wrote in a note to mentor Mike Toney.

Congratulations, Jonathan!

6.   User Markus Guehr Receives DOE Early Career Research Award

M. Guehr
Markus Guehr
SSRL User Markus Guehr, a Senior Staff Scientist of the PULSE Institute for Ultrafast Energy Science, has received a five-year research grant from the Department of Energy Office of Basic Energy Science. Guehr's research aims to better understand, and possibly control, light-driven chemical reactions at the level of electrons.

Guehr and his colleagues plan to excite a sample material with a pulse of light from the Linac Coherent Light Source, then probe the sample using pulses of extreme ultraviolet or soft x-ray photons to see how the electron properties within the excited sample change over time.

Congratulations, Markus!

7.   Workshop Announcement: XDL 2011 - Science at the Hard X-ray Diffraction Limit

Please join CHESS, DESY, SSRL and the Photon Factory for "XDL 2011 - Science at the Hard X-ray Diffraction Limit". This series of workshops will be devoted to science with diffraction-limited, high repetition rate, hard x-ray sources (such as energy recovery linacs and ultimate storage ring sources).

June 6 & 7:       Diffraction Microscopy, Holography and Ptychography using Coherent
June 13 & 14:Biomolecular Structure from Nanocrystals and Diffuse Scattering
June 20 & 21:Ultra-fast Science with "Tickle and Probe"
June 23 & 24:High-pressure Science at the Edge of Feasibility
June 27 & 28:Materials Science with Coherent Nanobeams at the Edge of Feasibility
June 29 & 30:Frontier Science with X-ray Correlation Spectroscopies using Continuous Sources

All workshops will be held at the Robert Purcell Conference Center, Cornell University, Ithaca, New York. Learn more on the XDL 2011 website.

8.   Upcoming SSRL Events

NUFO Annual Meeting at SLAC, June 27-29 - The 2011 National User Facility Organization (NUFO) Annual Meeting will be hosted by SSRL, the Linac Coherent Light Source, and SLAC Particle Physics and Astrophysics. The theme of this year's meeting is "NUFO Encourages Access and Awareness." Throughout the meeting, invited speakers and participants will be asked to consider issues related to facility access and awareness, which will be discussed in depth during breakout sessions. The meeting will include several sessions that focus on resources to help promote science, educating future scientists, encouraging diversity, how interaction with user facilities helps universities and small business, technology transfer, working with industry, and how NUFO can help to facilitate these discussions. An additional breakout session will offer practical tips for communicating science to the general public. All are welcome to attend the full program or to pick and choose the sessions that are most applicable to them. Please register in advance on the NUFO Annual Meeting website.

Synchrotron X-Ray Absorption Spectroscopy Summer School, June 28-July 1 - The SSRL Summer School on Synchrotron X-Ray Absorption Spectroscopy on June 28- July 1 seeks to provide training in theory, experimental design, data acquisition strategies, and data analysis to both beginners and advanced students. Transition metal K-edge XANES analysis for electronic structure determination and EXAFS analysis for geometric structure determination applicable to relevant systems in the fields of biology, environmental science, catalysis and material science will be covered. In addition to invited lectures presented by experts in the field, the summer school will also include practical training sessions that focus on teaching detailed experimental procedures at SSRL Beam Lines 11-2, 7-3, 4-1 and 2-3 and data analysis techniques. Learn more and register at the SRXAS website.

Annual Users' Conference, October 24-26 - Plan to participate in the Annual SSRL/LCLS Users' Meeting and Workshops, October 24-26, 2011 to learn about new developments and share exciting user research at both LCLS and SSRL. The draft program and registration details will be posted shortly. In the meantime, please take a few moments to consider nominating your colleagues or students for the William E. and Diane M. Spicer Young Investigator Award, the Melvin P. Klein Professional Development Award, and the Farrel W. Lytle Award. Submit your nominations to Cathy Knotts ( These awards will be presented at the Users' Meeting. You can also reserve lodging for the meeting by contacting the Stanford Guest House. Specify SSRL/LCLS/SLAC to take advantage of discounted rates.

9.   User Administration Update
       (contacts: Cathy Knotts,; Lisa Dunn,

REMINDER: New proposals can be submitted three times each year: Submit new X-ray/VUV proposals by June 1, September 1, December 1; submit new Macromolecular Crystallography proposals by July 1, December 1, April 1. Proposals submitted in June for X-ray/VUV or July for Crystallography will be peer reviewed over the summer and eligible to request beam time beginning when the 2012 run starts in November 2011.

10.   In the News

TEM Image
Left: TEM cross section of Mn oxide on a hypha of the fungus, Plectosphaerella cucumerina. Right: HR-TEM image showing Mn oxide with a rumpled, sheet-like morphology.
Beyond Bacteria: Fungus Study Offers Insights about Biogeochemical Cycling, Bioremediation
Collaborators from the Environmental Molecular Sciences Laboratory, Harvard University and SSRL characterized the manganese oxides produced by four different species of fungi isolated from coal mine drainage treatment systems, revealing that the species, growth conditions, and cellular structures of fungi influence the size, morphology, and structure-and, therefore, reactivity-of the manganese oxides.

Illuminating the Material and Biological World
An article highlighting the development and applications of light source technology features SLAC's Stanford Synchrotron Radiation Lightsource and Linac Coherent Light Source. The piece also quotes Director Emeritus Burton Richter.

In the same issue of Symmetry magazine, another article describes the first successful use of synchrotron radiation for protein crystallography - including a diffraction pattern of the protein rubredoxin - by Keith Hodgson and his graduate student James Phillips and postdocs Marguerite Bernheim and Alexander Wlodawer. It was performed at SSRL (then SSRP) in 1977, and the revolution of synchrotron-based structural biology research began.

Shooting for $0.50-per-Watt PV Modules
The Bay Area Photovoltaics Consortium, or BAPVC, seeks to reduce the cost of manufacturing solar cell modules to about 50 cents a watt. Portions of the work will be conducted at SSRL, Lawrence Berkeley National Laboratory and the National Renewable Energy Laboratory.
Green Tech Media


SSRL Headlines is published electronically monthly to inform SSRL users, sponsors and other interested people about happenings at SSRL. SSRL is a national synchrotron user facility operated by Stanford University for the U.S. Department of Energy Office of Basic Energy Sciences. Additional support for the structural biology program is provided by the DOE Office of Biological and Environmental Research, the NIH National Center for Research Resources and the NIH National Institute of General Medical Sciences. Additional information about SSRL and its operation and schedules is available from the SSRL WWW site.


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Last Updated: 31 May 2011
Headlines Editor: K. Tuttle