Macdonald Research Group
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X-ray Crystallography (59-553)
Classes are finished: please complete
your projects and prepare for the final exam.
Class will be on Tuesdays and Thursdays from 9 to 10:30 in Essex Hall room 254 (we may alter the times).
Course information and outline. If you have any questions regarding this course, please feel free to contact me.
Due dates and answers will be posted on this site as the assignments are assigned.
Here is a link to an example of an Acta Cryst. E paper.
Model Data SetS:
Here is a cif file with which you may practice some of the cif-checking software.
Here is a cif file with some serious problems: use some of the cif-checking software (such as Platon) to identify the most serious problem. Here is the ins and hkl data for that solution if you would like to attempt to fix the problems (you may want to use WinGX to generate res and list files too).
Friday Apr. 21, 12-3 (Exam slot 38) in Erie Hall 1115.
Exam questions: Most of the questions on the final exam are things like definitions or explanations that require descriptions and diagrams (e.g. What is Friedel's Law? Provide a mathematical expression that defines the law and an Argand diagram that illustrates why the law holds true.) I don't want to post all of the similar questions because then I won't have anything to ask you. Other questions are more practical (such as solving a simple Patterson function or determining unit cell contents on the basis of density or symmetry arguments, etc.). These are questions like the ones from the assignments and I have posted the answers to all of the assignments for your perusal.
Crystals, Crystal Growth, Crystal Properties and Basic Instrumentation
Lattices, Crystal Systems and Space Groups
Planes, Reciprocal Lattices and X-ray diffraction (Bragg's Law)
The Ewald sphere and Systematic Absences
Freidel's Law and Data Collection
Fourier Transforms, Electron Density and The Phase Problem
Patterson Methods, Direct Methods and Dual Space Methods
Structure Solution and Refinement
SHELX and WinGX
CIF files, Metrical Parameters and Databases
Preparation of Plots, Tables etc.
Disorder and Twinning
Anomalous Scattering and Absolute Configuration
Powder X-ray Diffraction (XRD)
Project and Final Exam - current topic
W. Massa, Crystal Structure Determination, 2nd Ed., Springer (less detailed than the books below but it covers almost every aspect that will be treated in the course and it is a modern, reasonable starting point that is suitable for most people in the course - this seems to be the most suggested introductory book by the crystallographers in the Bruker newsgroup)
Please note: There will be some copies of this book for sale at the bookstore soon.
P. Muller, R. Herbst-Irmer, A. L. Spek, T. R. Schneider and M. R. Sawaya, Crystal Structure Refinement: A Crystallographer;s Guide to SHELXL, Oxford University Press / IUCr (as the title suggests, this book concentrates on the refinement of single-crystal X-ray structures using the SHELX family of software that we will use in this course and that all of the researchers use here at the University of Windsor)
M. F. C. Ladd and R. A. Palmer, Structure Determination by X-ray Crystallography, Plenum Press (much more detailed than Massa; a good value for the money if you want a more complete text with more in-depth treatment of the topics)
G. H. Stout and L. H. Jensen, X-ray Structure Determination, MacMillan (again, much more detailed than Massa with significantly more in-depth treatment of many topics - some topics will seem a bit dated for most of the students in the class but they can help you to better understand certain aspects of crystallography)
Donald E. Sands, Introduction to Crystallography, Dover books
W. Clegg, Crystal Structure Determination, Oxford University Press
Again, there are a variety of books available in the library (around QD900 - QD999). You may want to go take a look.
SOFTWARE AND DATABASE SITES:
WinGX is an excellent (and free) package of software for the solution, refinement and presentation of crystal structures - the site also has links to many other crystallography programs
Olex2 is an excellent (and free) package of software for the solution, refinement and presentation of crystal structures - the site also has links to many other crystallography programs
Diamond is an excellent program for the building and viewing crystal structures (the demo version is free)
The Cambridge Crystallographic Data Centre (CCDC) is the home of the Cambridge Structural Database (the repository of crystallographic data for organic and organometallic). This is also where you can download a copy of enCIFer.
The Inorganic Crystal Structure Database contains the data for purely inorganic compounds (there is a demo version containing some mineral structures and a WWW version) - this has just been changed from what I showed you in class (and the new version works really nicely but you will have to register to use the demo version)
A very useful program for the prediction of powder diffraction patterns and much more: PowderCell
A online version of the SHELXL instructions.
A online version of the SHELXL-97 manual.
Here is a link to the IUCr checkCIF web application.
Here is a link to the IUCr printCIF web application.
Here is a link to the IUCr publCIF download site.
USEFUL LINKS (more will follow):
University of Windsor Radiation Safety Site - this has videos and other information about safe practices for the use of X-ray equipment.
IUCr Crystallography International Tables Online
IUCr Crystallography Pamphlets
IUCr Crystallography Educational Material
IUCr Crystallography Journals
Doug Powell's site from the University of Oklahoma Crystallography Notes
Texas A&M University Crystallography Links
Texas A&M University Crystallography Tutorials
Texas A&M University Crystallography Practical Examples (these are very useful!)
Michigan State University Crystallography Information - this contains a variety of good information and links. Please take a look at the Crystal Structure Determination sections.
A site from NC State University about growing nice crystals.
Crystallography 101 by Bernhard Rupp from LLNL - this site has many useful applets that you should try.
Online crystallography course from Lausanne - this site has many resources.
Crystallography course by S. Swinnea from TMI - this site has many useful resources.
Crystallography tutorials from UCLA.
A French site with an applet showing the Bravais Lattices and crystal systems.
A site from Otterbein University about Symmetry.
An interactive site discussing Bragg's Law from Stonybrook.
A course on diffraction found in the Crystallography 101 site.
- A nice site that lets you explore 2-D lattices and plane groups (2-D analogues of space groups).
- An interactive reciprocal lattice calculator.
A nice site that lets you see the construction and application of a Ewald sphere.
Download site for XrayView (Ewald sphere, reciprocal lattice and diffraction simulations)
A copy of the SADABS manual (for those of you who will be doing absorption corrections)
Kevin Cowtan's Structure Factor Tutorial - play around with this and you will understand much about phases, Miller Indices, Patterson Methods and Direct Methods, etc.)
Kevin Cowtan's Book of Fourier - a description of Fourier transforms and illustrations.
A compilation of other crystallography web sites from the crystallographic group at Michigan State University.
IUCr links for online crystallography resources.
CCP14 (Collaborative Computational Project 14) TUTORIAL links for crystallographic software - the tutorials include: WinGX and other single crystal software, various powder software and other programs that I have mentioned in class.
A great site from France that explains the different kinds of twinning.
An introduction to powder XRD from Ohio State University.
Symmetry and Group Theory Sites (for those of you who forgot about point groups - if you need to, you can look at the class notes from my 59-651 course):
Point Group Practice Page (if you want some models to practice figuring out point groups, come see me).
A web site that lets you practice using character tables (it will calculate the irreducible representation for the reducible representations that you have determined and it usually works):
A web site with more examples using group theory and another tool for determining reducible representations:
CLASS NOTES (in PDF):