Chemistry and Biochemistry

XRD Lab

C330 BNSN


XRD Facility Manager

Dr. Stacey J. Smith
Office: C314 BNSN
Office Phone: 801-422-2090
Lab Phone: 801-422-7563
Email: ssmith@chem.byu.edu


 

X-ray Diffraction

The diffraction of X-rays by a crystalline solid helps us understand and map its 3-dimensional atomic and molecular structure. Knowing the structure of a material, we can better understand its properties, utilize its attributes, and engineer new materials with similar or better functionality.

The X-ray Diffraction (XRD) facility at BYU currently operates two XRD instruments. One instrument is optimized for analyzing polycrystalline samples (P-XRD), and the other is optimized for analyzing single crystal samples (SC-XRD). The XRD facility supports both research and teaching in the department and the university.


SC-XRD

P-XRD

Trainings

XRD lab publications


SC-XRD

Equipment

To analyze single crystal samples, the BYU XRD lab is equipped with a MACH3 four circle diffractometer coupled to a Bruker-Nonius FR591 Cu rotating anode X-ray source, a Bruker Apex II CCD detector, and a low temperature (100-300 K) Kryoflex device. The high intensity of the X-ray source combined with the sensitivity of the Apex II detector allows high-resolution data to be collected on crystals with dimensions as small as 10µm. The latest versions of the Bruker Apex2 software are employed to collect, solve, and refine the data. Access to the Cambridge Structural Database (CSD) is also available.

Services

This instrument is routinely used to solve and refine all molecule single crystal structures The high intensity of the rotating anode Cu X-ray source can be utilized to collect data on macromolecular samples such as proteins as well.

Powder samples can also be investigated at low temperatures via transmission mode capillary experiments.

Other non-traditional samples such as films and machined parts can be investigated using custom-made sample mounts.

Sample Specifications

A ‘single’ crystal is a solid in which the crystal lattice is continuous and unbroken (containing no grain boundaries) throughout the entire sample. Single crystals for SC-XRD experiments typically have dimensions between 20-500µm, though crystals with dimensions as small as 10µm have been successfully characterized, and crystals larger than a few hundred µm can be cut into more suitably sized pieces.

Good single crystals typically have well-defined faces and are transparent (not cloudy, cracked, or otherwise opaque). They also often rotate plane polarized light. If the plane of polarization is changed continuously as shown in the video, the crystals grow bright then dark or even change colors. To evaluate crystal quality, a microscope with a polarizing lense is available in C330A BNSN. There are many techniques for growing single crystals. Click here for more information on crystal growing tips and tricks.

 

Instrument Scheduling

The SC-XRD instrument is currently primarily a service facility. Use of the instrument and Dr. Smith’s expertise are free of charge for BYU groups. To submit a sample, fill out the SC-XRD sample submission form, place your sample and the completed form in the sample submission box in the southeast corner of C330 BNSN, and write your name and your PI’s initials on the SC-XRD queue board. Contact Dr. Smith for more information, for help assessing crystal quality, or for help submitting a sample for analysis.

  


 

 

P-XRD

Equipment

To analyze polycrystalline samples, the BYU XRD lab is equipped with a PANalytical X’Pert Pro MPD diffractometer with a sealed tube Cu X-ray source and an X’Celerator detector. A Ge monochromator is routinely used to provide a monochromatic source of the Cu Kα1 wavelength (1.5406 Å). Programmable divergence and anti-scatter slits enable the use of both fixed slit (for amply thick sample volumes) and automated slit (for very thin sample volumes) configurations. The standard configuration of the instrument includes a 15-position automatic sample changer coupled to a reflection/ transmission sample stage with sample spinning capabilities. A bracket sample stage is available for mounting wafers, films, and other flat solid samples (< 3.0 mm thick). For in-situ high temperature experiments with powder samples, the instrument is equipped with an Anton Paar HTK 1200 high temperature stage (300-1200°C). For air-sensitive samples, the instrument is equipped with a capillary sample mount and a focusing mirror. The PANalytical software programs X’Pert Data Collector (v ), X’Pert Data Viewer, and X’Pert HighScore Plus (v. 3.0) are employed to collect, view, and analyze P-XRD data. Access to the International Center for Diffraction Data (ICDD) database is also available.

Services

The P-XRD is routinely used to identify crystalline materials, calculate the crystallite size of nanomaterials, quantify mixtures of crystalline solids, refine crystal structures via Rietveld refinement, perform in-situ high temperature experiments, and perform capillary experiments for air-sensitive samples.

Sample specifications

Materials or particles consisting of more than one crystal or distinct crystal lattice are ‘polycrystalline’ materials. Polycrystalline samples can range from powders and nanoparticles to thin films and machined parts. In essence, if it is solid, crystalline, and can be made to have or form a relatively flat surface, the P-XRD can be used to investigate its atomic structure.

A variety of sample holders are available for the P-XRD to accommodate different sample volumes and forms:

The specifications of these holders are listed below.

P-XRD Sample Holders

 

 

Composition

Holding Area Dimensions

Sample Volume Required

Sample Form

1

Standard holder

Steel

2mm depth, 27mm diameter

1145 mm3

Powder

2

Standard + 1.0mm insert

Steel + Al

1mm depth, 25mm diameter

491 mm3

Powder

3

Standard + 0.5mm insert

Steel + Al

0.5mm depth, 25mm diameter

245 mm3

Powder

4

Zero Background holder

Si

0.1mm depth, 15mm diameter

18 mm3

Powder, Solids

5

Adjustable height holder

Al

0-4mm height, 41mm diameter

Variable

Solids

6

Tension holder

Al

0-7mm height, 41mm diameter

Variable

Solids

7

Flat slide

Glass

20mm x 20mm x 0.2mm depth

80 mm3

Powder

 

Instrument Scheduling

The P-XRD instrument is both a user facility and a service facility. Use of the instrument is free of charge for BYU groups. To run experiments autonomously, you must complete the requisite trainings (see below for more information). Once you are trained, you may schedule time on the instrument using the Chemistry Department Resource Scheduling Page. To submit a sample to Dr. Smith for analysis, fill out the P-XRD sample submission form, place your sample and the completed form in the sample submission box in the center of the south wall of C330 BNSN, and write your name and your PI’s initials on the P-XRD queue board. Contact Dr. Smith for more information, for trainings, for assistance in running an experiment, or for help submitting a sample for analysis.


Data Processing Computers

The two computers along the south wall of room C330 in the XRD facility are available for off-line processing of your XRD data. The software packages for analyzing data from both the P-XRD and SC-XRD are installed on both computers.   


Trainings

The XRD lab is both a user facility and a service facility.  You must complete the appropriate XRD trainings in order to use the XRD facility independently. Please contact Dr. Smith if you need training. The following training modules are available:

X-ray safety

This training is required to obtain access to the facility and the instruments. Complete the online training module and answer all questions of the follow-up quiz correctly to gain access. 

Basic P-XRD

This training is required to obtain access to the facility and the P-XRD instrument. Topics include sample preparation, instrument setup, running the Data Collector software, writing data collection programs for the 15-position sample changer, and performing basic data processing with the HighScore Plus software and ICDD database. Basic P-XRD handout.

Crystallite Size Analysis

Topics include a discussion of the theory/equations involved, data collection requirements, basic profile fitting techniques using Highscore Plus, determining instrumental broadening parameters, making/using a template, using a Williamson-Hall plot.

Rietveld refinement & quantitative analysis of mixtures

Topics include a discussion of the theory/equations involved, data collection requirements, determining instrumental broadening parameters, using .cif files, crystal structure nomenclature, basic fitting techniques using HighScore Plus.

P-XRD temperature variable experiments

This training is required to independently use the high temperature stage for the P-XRD instrument. Topics covered include mounting the stage, sample preparation/mounting, operating the stage, writing data collection programs, and processing the data using HighScore Plus.

P-XRD capillary experiments

This training is required to independently use the capillary stage for the P-XRD. Topics covered include mounting the stage, sample preparation/mounting, operating the stage, writing data collection programs, and processing the data using HighScore Plus.

SC-XRD temperature variable experiments

This training is required to independently use the SC-XRD to perform low temperature experiments. Topics covered include sample preparation/mounting, operating the instrument, writing data collection programs, and processing the data using the Bruker Apex II software.

Miscellaneous Topics 

Other specialized topics and questions can be addressed via one-on-one training.


XRD lab publications

 

Email Dr. Smith to report any publications or presentations that involved or benefitted from the use of the XRD facility.1-27

 

SC-XRD

1. Walker, W. K.; Stokes, R. J.; Smith, S. J.; Michaelis, D. J., Allylic Aminations with Hindered Secondary Amine Nucleophiles Catalyzed by Heterobimetallic Ti–Pd Complexes. J. Am. Chem. Soc. 2014, Submitted for publication.

2. Walker, W. K.; Michaelis, S. A.; Anderson, D. L.; Smith, S. J.; Ess, D. H.; Michaelis, D. J., Origin of Enhanced Pd Electrophilicity in Pd-Ti Heterobimetallic Catalysts for Allylic Amination. J. Am. Chem. Soc. 2014, Submitted for publication.

P-XRD

3. Wang, H.; Madaan, N.; Bagley, J.; Diwan, A.; Liu, Y.; Davis, R. C.; Lunt, B. M.; Smith, S. J.; Linford, M. R., Spectroscopic ellipsometric modeling of a Bi-Te-Se write layer of an optical data storage device as guided by atomic force microscopy, scanning electron microscopy, and X-ray diffraction. Thin Solid Films 2014, 569, 124-130.

4. Smith, S. J.; Huang, B.; Liu, S.; Liu, Q.; Olsen, R. E.; Boerio-Goates, J.; Woodfield, B. F., Synthesis of metal oxide nanoparticles via a robust "solvent-deficient" method. Nanoscale 2014, 7 (1), 144-156.

5. Olsen, R. E.; Bartholomew, C. H.; Huang, B.; Simmons, C. L.; Woodfield, B. F., Synthesis and characterization of pure and stabilized mesoporous anatase titanias. Micropor. Mesopor. Mater. 2014, 184, 7-14.

6. Huang, B.; Schliesser, J.; Olsen, R. E.; Smith, S. J.; Woodfield, B. F., Synthesis and Thermodynamics of Porous Metal Oxide Nanomaterials. Curr. Inorg. Chem. 2014, 4 (1), 40-53.

7. Huang, B.; Bartholomew, C. H.; Woodfield, B. F., Improved calculations of pore size distribution for relatively large, irregular slit-shaped mesopore structure. Micropor. Mesopor. Mater. 2014, 184, 112-121.

8. Huang, B.; Bartholomew, C. H.; Woodfield, B. F., Facile structure-controlled synthesis of mesoporous g-alumina: effects of water to aluminum molar ratio. Micropor. Mesopor. Mater. 2014, 183, 37-47.

9. Woodfield, B. F.; Smith, S.; Selck, D.; Bartholomew, C. H.; Ma, X.; Xu, F.; Olsen, R. E.; Astle, L. Single reaction synthesis of texturized catalysts. US20130267411A1, 2013.

10. Woodfield, B. F.; Bartholomew, C. H.; Brunner, K.; Hecker, W.; Ma, X.; Xu, F.; Astle, L. Iron and cobalt based Fischer-Tropsch pre-catalysts and catalysts. US20130274093A1, 2013.

11. Spencer, E. C.; Huang, B.; Parker, S. F.; Kolesnikov, A. I.; Ross, N.; Woodfield, B. F., The Thermodynamic Properties of Hydrated γ-Al2O3 Nanoparticles. Journal of Physical Chemistry C 2013.

12. Spencer, E.; Huang, B.; Parker, S.; Kolesnikov, A.; Ross, N.; Woodfield, B. F., The Thermodynamic Properties of Hydrated γ-Al2O3 Nanoparticles. J. Chem. Phys. 2013.

13. Smith, S. J.; Amin, S.; Woodfield, B. F.; Boerio-Goates, J.; Campbell, B. J., Phase Progression of gamma-Al2O3 Nanoparticles Synthesized in a Solvent-Deficient Environment. Inorg. Chem. 2013, 52 (8), 4411-4423.

14. Olsen, R. E.; Bartholomew, C. H.; Enfield, D. B.; Lawson, J. S.; Rohbock, N.; Scott, B. S.; Woodfield, B. F., Optimizing the synthesis and properties of Al-modified anatase catalyst supports by statistical experimental design. Chem. Eng. Sci. 2013.

15. Olsen, R. E.; Barthalemew, C. H.; Enfield, D. B.; Woodfield, B. F., One-pot synthesis of Pt catalysts supported on Al-modified TiO2. Appl. Catal. A 2013.

16. M., M. K.; Woodfield, B. F.; Bartholomew, C. H. Synthesis of high surface area and thermally stable gamma alumina. 2013.

17. M., M. K.; Woodfield, B.; Burt, S.; Andrus, M., Generalized preparation method and characterization of aluminum isopropoxide, aluminum phenoxide, and aluminum n-hexyloxide. Polyhedron 2013, 62, 18-25.

18. K. Chesnel, M. T., Y. Cai, J. M. Hancock, S. J. Smith and R. G. Harrison, Particle size effects on the magnetic behaviour of 5 to 11 nm Fe3O4 nanoparticles coated with oleic acid. Journal of Physics, via the conference on Fine Particles Magnetism 2013.

19. Huang, B.; Bartholomew, C. H.; Woodfield, B. F., Facile structure-controlled synthesis of mesoporous g-alumina: effects of alcohols in precursor formation and calcination. Micropor. Mesopor. Mater. 2013, 177, 37-46.

20. Huang, B.; Bartholomew, C. H.; Smith, S. J.; Woodfield, B. F., Facile solvent-deficient synthesis of mesoporous g-alumina with controlled pore structures. Micropor. Mesopor. Mater. 2013, 165, 70-78.

21. Hancock, J. M.; Rankin, W. M.; Hammad, T. M.; Salam, J. K.; Chesnel, K.; Harrison, R. G., Optical and magnetic properties of ZnO nanoparticles doped with Co, Ni, and Mn and synthesized at low temperature. J. Nanosci. Nanotech. 2013.

22. Brunner, K. M.; Harper, G. E.; Keyvanloo, K.; Woodfield, B. F.; Barthalemew, C. H.; Hecker, W. C., Synthesis and Performance of Novel Iron Fischer-Tropsch Catalyst Prepared by Solvent Deficient Precipitation (SDP). Chem. Cat. 2013.

23. Boerio-Goates, J.; Smith, S. J.; Liu, S.; Lang, B. E.; Li, G.; Woodfield, B. F.; Navrotsky, A., Characterization of Surface Defect Sites on Bulk and Nanophase Anatase and Rutile TiO2 by Low-Temperature Specific Heat. J. Phys. Chem. C 2013, 117 (9), 4544-4550.

24. Smith, S. J.; Page, K.; Kim, H.; Campbell, B. J.; Boerio-Goates, J.; Woodfield, B. F., Novel synthesis and structural analysis of ferrihydrite. Inorg. Chem. 2012, 51 (11), 6421-6424.

25. Shi, Q.; Boerio-Goates, J.; Woodfield, K.; Rytting, M.; Pulispher, K.; Spencer, E. C.; Ross, N.; Navrotsky, A.; Woodfield, B. F., Heat Capacity Studies of Surface Water Confined on Cassiterite (SnO2) Nanoparticles. J. Phys. Chem. C 2012, 116, 3910-3917.

26. Snow, C. L.; Martineau, L. N.; Hilton, R. J.; Brown, S.; Farrer, J.; Boerio-Goates, J.; Woodfield, B. F.; Watt, R. K., Ferritin iron mineralization proceeds by different mechanisms in MOPS and imidazole buffers. J. Inorg. Biochem. 2011, 105 (7), 972-977.

27. Bartholomew, C. H.; Woodfield, B. F.; Huang, B.; Olsen, R. E.; Astle, L. Method for making highly porous, stable metal oxide with a controlled pore structure. WO2011119638A2, 2011.