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| Newsletter Vol. 4, No. 1, Spring 2006 | |||||
| In this issue | ||||||
 | A word from our president |
As a graduate student I always felt that the larger and more complicated instruments must surely produce the most important research results. In those long ago days, space constraints, energy consumption, and usability weren't as important as they are now. I feel that instrument manufacturers today are obligated to address the needs of the global community and provide instrumentation that is sized for specific applications with an extra effort made to provide maximum capabilities with minimal power and water requirements. An instrument doesn't have to be large and bulky if sufficient thought goes into designing for the specific applications in mind. In this issue of the newsletter we discuss the launch of our MiniLab series which provides benchtop capabilities for powder X-ray diffraction, X-ray fluorescence, and single crystal analysis. Our new single crystal system, the SCXmini™, is particularly exciting to me, having learned crystallography on a manual GE-XRD5 single crystal instrument 30 years ago. The thought of a synthetic chemistry lab having a benchtop single crystal instrument for rapid materials characterization is really quite amazing. It actually makes me want to get back in the lab and solve some structures - but for some reason the application scientists won't give me the password! Paul N. Swepston | ||||
| | Calendar of events | |||||
| | Improving Rietveld analysis | |||||
| | Rigaku's MiniLab | |||||
| | First structure published using SCXmini | |||||
| | Environmental water studies | |||||
| | 2005-2006 Training sessions | |||||
| | Cr SAD workshop | |||||
| | ActiveSight adds targets, signs deal | |||||
| Visit us on the web at www.Rigaku.com | ||||||
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Improving Rietveld analysis: Parallel beam and para-focusing beam geometry | ||||||
Rigaku will be attending the following conferences in
the coming months:
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The Rietveld method (Whole Pattern Fitting structure refinement) is widely accepted as a valuable method for structural analysis of nearly all classes of crystalline materials not available as single crystals. It also provides effective quantitative phase analysis of simple-to-complex materials where the crystal structures are known, as well as yielding microstructural information such as crystallite size, shape and strain. Before this advance, an accurate and standardless quantitative phase analysis of complex materials using powder diffraction was almost impossible.
In our study, Rietveld refinements results are presented for X-ray powder diffraction data collected using a Rigaku Ultima III X-ray powder diffractometer with Cross Beam Optics (CBO) on four standard reference materials and two other materials, acetaminophen (C8H9NO2)—a common pharmaceutical drug—and a rock sample composed of six mineral phases; a typical geological material. The data were collected in both parallel beam and para-focusing beam geometry. The presence of both geometries, easily selectable, on one machine provides choice for best possible data for a particular type of sample. In general, for a well packed powder sample, Bragg Brentano para-focusing geometry provide both higher intensity and higher resolution. However, when samples have rough or curved surfaces and have errors associated with sample displacement, higher intensity and resolution are obtained on data collected with parallel beam geometry. Accuracy in peak position is always higher with parallel beam data irrespective of the sample type. >>> Click here to read the complete application note | |||||
| First structure published using the Rigaku SCXmini | ||||||
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Rigaku offers three benchtop X-ray products: the SCXmini™ for small molecule crystallography, the Miniflex™ for X-ray diffraction, and the ZSXmini II for X-ray fluorescence. Each represents a new paradigm in superior performance from a small package:
See all three systems together at Rigaku's new Northeast MiniLab Application Laboratory (by appointment only). Location: Rigaku Americas Corp, Wyeth Research Facilty, Cambidge, MA |
The structure of bis(2-amino-3-hydroxy-1-phenylpropanolato-κ2N,O1) (ethylenediamine-κ2N,N') cobalt(III) iodide monohydrate, [Co(C9H12NO2)2(C2H8N2)]I · H2O, appeared in Acta Crystallographica Section E, 62(4), pages m696-698. It is the first publication of an X-ray crystal structure employing the new Rigaku SCXmini benchtop single crystal diffraction system. Originally synthesized and crystallized in about 1978, the compound's structure was published in 1979 as part of a synthetic and spectroscopic project. The structure was redetermined to resolve disorder observed in the earlier determination. The Rigaku SCXmini represents a new paradigm in small molecule crystallography: affordable, reliable, easy-to-use, low cost-of-ownership access for routine automated structure determination. Specifically engineered by the world's leading analytical X-ray instrumentation vendor to provide colleges, universities, and industry with access to definitive molecular structure determination, the Rigaku SCXmini system allows single crystal diffraction to become a routine laboratory method and teaching tool in the same way that NMR and FT-IR did more than a decade ago. In addition to routine structure determination by non-crystallographers in industry, the Rigaku SCXmini was developed to address two clear-cut needs within the higher education environment. First was to offer an affordable, low maintenance, low cost-of-ownership crystallography system for teaching. The Rigaku SCXmini was designed for undergraduate labs at major universities as well as for science departments at predominantly undergraduate institutions. Second, it fulfills the need within research departments to expand X-ray structure determination capability beyond the realm of professional crystallographers. Inorganic and organometallic graduate students as well as postdocs can now obtain publication-quality definitive structures on an instrument that they can easily operate themselves. This newest member of Rigaku's small molecule line of integrated solutions was designed to offer outstanding performance, in a small package and at a fraction of the price and cost-of-ownership of a conventional single crystal XRD system. It features the combination of the new advanced Mercury 2 CCD detector with a simplified goniometer, a sealed-tube X-ray source, and automated software to makes the Rigaku SCXmini perfect for either routine structure determination by non-crystallographer researchers or as a teaching tool. | |||||
| Environmental water studies: PPB detection of low concentration elements by XRF | ||||||
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For many years now, environmental impact from designated hazardous elements such as Cd, Pb, As, Cr and Se has been a concern. A method for analyzing these and other elements in water has been developed which allows a standard laboratory WDXRF system to attain PPB levels of detection. Elements such as Cd, Pb, As, Cr and Se have been designated hazardous due to their potential environmental impact. Ecological concerns centering on these elements are due to contamination or poisoning of the flora and fauna through ground and river water. Contaminates are introduced to lake and river waters, soils or into the water table through industrial waste, chemical pesticides, urban development, spills, etc. Contaminants also find their way into food supplies such as growing or grazing fields via irrigation or from rainfall.
Monitoring of contaminate levels can be accomplished through direct plant analysis. This is basically after the fact testing. A more preventative method is through water supply analysis - detect elements of concern prior to plant contamination. The problem with this is that water testing requires many site samples to be taken. In view of this the test method needs to be fast, easy, safe and accurate. Also, working directly with sampled water needing no or little pretreatment would definitely be of benefit. XRF could be an ideal tool for this except for the low levels of determinations (LLD) required and the concerns of working with liquids in an XRF system (support membrane ruptures). Typical WDXRF LLDs for direct solution analysis are in the low ppm region at best. If a filter type paper is used for drying and concentrating the liquid then these LLDs may be reduced further to the sub ppm levels. This is still high for the required detection of these hazardous elements. A solution to these many problems and concerns has been developed through a method using a product referred to as UltraCarry. This method eliminates the liquid concern of support film breaking, achieves the required LLDs, plus no helium atmosphere is required due to dried samples being dried prior to analysis. An added benefit is that without the X-ray absorption of film support, analysis is possible for most elements from B to U. The tests
reported in the attached application report were performed using UltraCarry on a
Rigaku ZSX Primus II WDXRF using a 4 kW end window Rh tube for excitation.
>>> Click here for More information
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Rigaku is pleased to announce the
following training sessions for 2006:
All Classes are held at the Rigaku Applications Laboratory in The Woodlands, TX. |
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| First Annual SAD Workshop | ||||||
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ActiveSight, the contract crystallography arm of Rigaku Americas Corporation, has expanded their Protein Portfolio to include three new targets:
These new Portfolio targets expand a collection which includes the oncology targets FAK, Hsp90 and Aurora-A kinase; nuclear hormone receptor targets PPAR-delta and FXR, implicated in metabolic disorders; PDE-4 for asthma and inflammation; the hypertension target Renin; the type-II diabetes target FBPase; and the anti-infective target bacterial DNA gyrase. ActiveSight also announced it has signed an agreement with Novo Nordisk A/S to provide protein crystallography services. ActiveSight will co-crystallize Novo Nordisk proprietary molecules with proteins expressed by ActiveSight. "We are very pleased to add a company of Novo Nordisk's stature to our growing customer base. We look forward to supplying their scientists with structural information to accelerate their discovery efforts," stated Ronald V. Swanson, Ph.D., Chief Scientific Officer for ActiveSight. This is the first announced agreement of 2006 for the protein crystallography services provider, which was founded in 2003. For information contact Joy Silen at (858) 455-6870 x105, or e-mail info@rigaku.com. |
The First Annual Rigaku SAD Workshop was hosted by the University of Texas, M. D. Anderson Cancer Center April 3 and 4. This event was sponsored by Rigaku Americas Corporation to help users make the jump from MAD to SAD in a routine fashion. On the first day we heard opening remarks by Joe Ferrara (RAC) and Dick Brennan (UTMDACC). Bi-Cheng Wang (University of Georgia) gave a presentation on the "Theoretical Aspects of Sulfur SAD Phasing and Direct Crystallography". B.C. gave a brief history of single wavelength anomalous scattering experiment and then described methods for eliminating phase ambiguity. He also explained the effects of signal, noise and handedness on the structure solution pathway. Finally, B.C. gave us a number of examples of successful SAD structures. Zbigniew (Zbyszek) Dauter (Argonne National Laboratory) presented "SAD Phasing" which described the physics of resonance (anomalous) scattering, how it effects diffraction data in MIR, MAD and SAD cases and how that information is extracted. Zbyszek paid his respects to David Blow, perhaps the first person to use Cr radiation in macromolecular crystallography (in 1958!) and left us with the adage "SAD is not sad, SAD is jolly." Aiping Dong, (SGC-Toronto) presented "Phasing at Home: Sulfur SAD" and reviewed a number of data sets collected with Cr radiation and offered some insight into the successes and failures. Six of eleven data sets were phased successfully. The unsuccessful data sets likely failed as a result of poor data quality or the majority of sulfur atoms were located in highly mobile regions of the protein. Aiping also gave us his strategies for solving more difficult cases. After lunch we took a tour of the new X-ray facility at UTMDACC, which includes an FR-E DW SuperBright™ rotating anode X-ray generator with both Cr and Cu optics and an R-AXIS HTC imaging plate detector. After the tour Jim Pflugrath (RAC) described the finer points of collecting data in "How to Obtain Accurate Data." Aiping brought several processed diffraction data sets for the workshop attendees to try various software packages. Everyone solved a Cr SAD structure. On the second day, James Liu (Institute of Biophysics, Chinese Academy of Sciences and University of Georgia) presented "Practical Aspects of Sulfur SAD Phasing" and started a lively discussion on the merits of collecting multiple data sets. James then described the University of Georgia scale-to-structure pipeline and gave a real-time demonstration over the network. Cheng Yang (RAC) discussed "In-house S and Se Phasing with Cr Kα Radiation" and described the instrumentation required by the SAD experiment at home. Cheng also gave a number of very interesting success stories and finished by reminding us we should "know before you go."
John Badger (ActiveSight) described "Automated Scripts for SAD Phasing" with a lecture detailing the methods and demonstrated automated Python scripts he has written for SAD phasing. The second afternoon was filled with more SAD phasing hands-on training by Aiping Dong, James Liu and Cheng Yang. We closed the workshop with a mixer on the 7th floor of the UTMDACC Mitchell Basic Sciences Building overlooking the massive Texas Medical Center, the largest medical complex in the world. We would like to thank our hosts Dick Brennan and Maria Schumacher for their support and use of facilities, tutors Aiping Dong and James Liu for the added effort required to prepare phasing examples in addition to their lectures, Judy Bryan and Deborah Watkins for organizing the rooms, meals, and travel. Finally, special thanks to Cheng Yang and Angela Criswell for putting together a very successful workshop on very short notice. | |||||
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| 9009 New Trails Drive The Woodlands Texas USA 77381-5209 e-mail: info@Rigaku.com Tel: (281) 362-2300 FAX: (281) 364-3628 | Unit B6, Chaucer Business Park Watery Lane, Kemsing Sevenoaks, Kent TN15 6QY, England e-mail: info@Rigaku.com Tel: [44] 1732 763 367 FAX: [44] 1732 763 757 | |||||
In conventional unit cell parameter determination
using data collected in Bragg Brentano para-focusing
geometry, the systematic errors in peak positions—such as those
resulting from zero point shift, sample displacement and sample
transparency—are usually compensated for, at least in part, by using an
internal standard. However, a major drawback to this approach is the
contamination of sample by the internal standard. This is not
desirable particularly if one is working with a small
quantity of a rare mineral or a reactive material. For complex
powder patterns, it can be challenging to identify an internal
standard that yields sufficiently well-resolved peaks with no overlaps
to permit an accurate correction.
