CHAPTER 3: EXPERIMENTAL TECHNIQUES
3.3 Single crystal X-ray diffraction
The background and theory of single crystal X-ray diffraction can be found inCrystal Structure Determination by Clegg and Crystal Structure Analysis: A Primer by Glusker and Trueblood.15,16
3.3.1 Synchrotron radiation
A synchrotron X-ray source produces a highly intense X-ray beam that can be used to study smaller crystals than is possible using a laboratory-based source. High resolution data can be collected, enabling time-resolved, high pressure or microcrystal studies to be undertaken.
Electrons are generated in an electron gun and accelerated through a linear accelerator and a booster synchrotron before injection into the storage ring (Figure 3.4). The storage ring consists of both straight and curved sections, and both regions can produce synchrotron radiation. In the curved sections the electron beam is bent by a strong magnetic field produced by a bending magnet. Insertion devices such as undulators and wigglers are installed in the straight sections of the storage ring, and consist of an array of magnets which ‘wiggle’ the electron beam, producing synchrotron radiation. When the electrons travelling at velocities close to the speed of light are bent with one of these magnets, synchrotron radiation is emitted tangentially to the direction of the electron beam at radiations ranging from microwaves to X-rays.
Figure 3.4: Diagram of a typical synchrotron (adapted from reference 17). Linear accelerator Electron gun Booster ring Storage ring Beamlines Endstation Optics hutch
Experimental stations, or beamlines, use the synchrotron radiation produced by its bending magnet or insertion device. The beamline’s optics adjust the radiation so that the beam received at the endstation is suitable for use in experiments.
3.3.2 Beamline 11.3.1
Single crystal X-ray diffraction was carried out on beamline 11.3.1(Figure 3.5) at the Advanced Light Source at the Lawrence Berkeley National Laboratory in Berkeley, California.
The bending magnet produces radiation with wavelengths from 0.73 to 2.07 Å. A channel-cut Si(111) monochromator positioned 6 m from the radiation source is used to selectively remove the majority of the “white” radiation to give a monochromatic beam with a wavelength of 0.77490 Å. The beam is then focussed using a toroidal mirror located 14 m from the X-ray source. A Bruker CCD shutter controls the exposure time, and a collimator narrows the beam to 100 μm. The endstation uses an Apex II 3-circle diffractometer with a CCD detector, and is equipped with an Oxford Cryostreams 700 Plus device operating in the temperature
range of 100 – 500 K.
Figure 3.5: Diagram of beamline 11.3.1 (adapted from reference 18).
3.3.3 Structure solution and refinement
Absorption corrections were performed using SADABS.19 Structure solution
was carried out using SIR-9720 in all cases, and refined on F2 using SHELXL-9821
within the WinGX22 suite. Non-hydrogen framework atoms were refined
anisotropically, and the hydrogen atom on the organic linker was positioned geometrically.
CCD detector
detector
The residual electron density within the pores was calculated using PLATON SQUEEZE.23,24 A solvent accessible void is a region of a crystal structure in which a
sphere of 1.2 Å radius can fit without intersecting the van der Waals radii of any atoms. The electron density within any such regions is estimated, and its contribution is removed from the structure to produce a new reflection file which can be refined against the original model, improving the R-factor. In this case SQUEEZE was used to estimate the excess electron density in the framework pores, which can be attributed to disordered water molecules, but the new reflection file was not used in refinements.
3.4 References
1. P. Webb and C. Orr,Analytical methods in fine particle technology, Micromeritics Instrument Corp., Norcross, Ga., 1997.
2. D. M. Young and A. D. Crowell,Physical Adsorption of Gases, Butterworths, London, 1962.
3. I. Langmuir,J. Am. Chem. Soc., 1916, 38, 2221–2295.
4. S. Brunauer, P. H. Emmett, and E. Teller,J. Am. Chem. Soc., 1938, 60, 309– 319.
5. S. Brunauer,The Adsorption of Gases and Vapours. Volume I: Physical Adsorption, Oxford University Press, Oxford, 1944.
6. D. R. Lide,CRC handbook of chemistry and physics : 2008-2009, CRC Press, Boca Raton; London; New York, 89th edn., 2008.
7. Chemistry3: introducing inorganic, organic and physical chemistry, Oxford University Press, Oxford ; New York, 2009.
8. J. H. Cole, D. H. Everett, C. T. Marshall, A. R. Paniego, J. C. Powl, and F. Rodriguez-Reinoso,J. Chem. Soc., Faraday Trans., 1974, 70, 2154.
9. M. P. Suh, H. J. Park, T. K. Prasad, and D.-W. Lim,Chem. Rev., 2012, 112, 782–835.
10. L. Czepirski and J. JagieŁŁo, Chem. Eng. Sci., 1989, 44, 797–801.
11. B. Chen, X. Zhao, A. Putkham, K. Hong, E. B. Lobkovsky, E. J. Hurtado, A. J. Fletcher, and K. M. Thomas,J. Am. Chem. Soc., 2008, 130, 6411–6423. 12. B. Xiao, P. S. Wheatley, X. Zhao, A. J. Fletcher, S. Fox, A. G. Rossi, I. L.
Megson, S. Bordiga, L. Regli, K. M. Thomas, and R. E. Morris,J. Am. Chem. Soc., 2007, 129, 1203–1209.
13. N. D. Spencer, B. Elsener, and M. Heuberger, 2011.
15. W. Clegg,Crystal structure determination, Oxford University Press, Oxford; New York, 1998.
16. J. P. Glusker,Crystal structure analysis: a primer, Oxford University Press, Oxford ; New York, 3rd ed., 2010.
17. Diamond Light Source - Technology - Components of the machine - Booster synchrotron.
http://www.diamond.ac.uk/Home/Technology/Components/booster.html (accessed 03/05/2013).
18. ALS Beamline 11.3.1: X-ray Diffraction Facility.
http://xraysweb.lbl.gov/BL1131/1131website/index.htm (accessed 02/05/2013). 19. SADABS: Area-Detector Absorption Correction, Bruker AXS Inc., Madison,
Wisconsin, USA, 2001.
20. A. Altomare, M. C. Burla, M. Camalli, G. L. Cascarano, C. Giacovazzo, A. Guagliardi, A. G. Moliterni, G. Polidori, and R. Spagna,J. Appl. Crystallogr., 1999, 32, 115–119.
21. G. M. Sheldrick,Acta Crystallogr., Sect. A: Found. Crystallogr., 2007, 64, 112– 122.
22. L. J. Farrugia,J. Appl. Crystallogr., 1999, 32, 837–838. 23. A. L. Spek,J. Appl. Crystallogr., 2003, 36, 7–13.