XRD FAQ

Frequently Asked Questions for X-Ray Crystallography

  1. How do I get crystals?
  2. I think I have crystals, now what?
  3. How do I fill out the form?
  4. My crystals are air/temperature/light/time-sensitive, how should I handle them?
  5. What happens to my samples when you are done with the experiment?
  6. I left my sample in the queue and haven’t heard anything.  What’s going on?
  7. How do you decide what instrument to use for my sample?
  8. Can you run my chiral sample on the Mo instrument?
  9. Where do I get my data?
  10. Is this structure publishable?
  11. What do I need in order to publish this structure?
  12. How can I tell if this structure has already been published?
  13. How do I solve my own structures?
  14. How do I run my own data collections?
  15. My samples need to go to APS, can you help?

 

 

1.   How do I get crystals?
There are many ways to grow crystals of your target materials.  They can form spontaneously in reaction vessels or NMR tubes, or they can take weeks of careful recrystallization attempts to appear.  Check with others in your lab who might have had success in growing crystals, or view the IMSERC X-Ray Crystallization Guide  for tips on recrystallization techniques.  Additional resources are available on the web.

 

 

2.  I think I have crystals, now what?
Once you suspect you have crystals, bring the vial to the X-ray lab for a visual assessment on the polarized light microscopes.  X-Ray staff members will tell you if your sample is crystalline and if it might succeed on the diffractometer.  You will need to fill out a sample submission form  and leave your crystals together with the form at the end of the queue in the lab.  See staff members if you need assistance.  Remember to leave your sample in a clearly labeled vial and to fill out the form completely.  If your crystals are sensitive to ambient conditions, see here.

 

 

3.  How do I fill out the form?
Log on to NUCore and choose the appropriate Service.  Fill out the form, add to your cart and remember to click “purchase” to complete the submission.  Return to your form and print the PDF file.  For full detailed instructions, click here.

 

 

4.  My crystals are air/temperature/light/time-sensitive, how should I handle them?
If your samples will decompose rapidly under ambient conditions, please leave them in a safe place in your lab.  Fill out a sample submission form and leave it in the queue.  You must contact an X-Ray staff member to arrange a time to bring your samples to the lab for data collection.   If your samples decay rapidly over time, see a staff member as soon as possible to arrange a day for the data collection.

 

 

5.  What happens to my samples when you are done with the experiment?
Some air- or temperature-sensitive samples may decompose while we are working with them but we do our best to preserve the bulk of the material submitted so that we can return it to you for further analysis.  If you know you will need your sample or the specific crystal used for the data collection returned, talk to a staff member and we will save what material we can.  Unused material is deposited in the sample return box on the bench by the queue and may be picked up at any time.  We empty the boxes approximately every two weeks, so be sure to retrieve your sample as soon as possible after the experiment.

 

 

6.  I left my sample in the queue and haven’t heard anything.  What’s going on?
The most likely explanation is that your sample is still waiting its turn in the queue.  You will be notified when your sample is into data collection or if your sample did not diffract well enough for data collection.  If your crystals were not of good enough quality for data collection, your sample submission form will be set aside by the queue, and a note given on the form why the sample did not work.  We will also send an email or notification through NUCore.  If you are concerned, feel free to e-mail us, or come by the lab.

 

 

7.  How do you decide what instrument to use for my sample?
We have three different diffractometers in the lab, that run two different radiations.  See our instrument descriptions  for details on each instrument.  In general, MoKα radiation is good for strong diffractors, heavy X-Ray absorbers, and/or small unit cells.  CuKα radiation is useful for weak diffractors, large unit cells and/or light-atom chiral molecules.  After years of experience, X-Ray staff members have a good feel for which materials will work best on a particular instrument.  If your sample fails on one of the less-powerful diffractometers, we will switch to a higher intensity instrument and try again.

 

 

8.  Will you run my chiral sample with Mo radiation?
It depends…  Absolute stereochemistry of light-atom materials cannot be determined with Molybdenum radiation.  Molecules with no atoms heavier than Na and with no known chiral centers must be run on one of the Cu instruments.   Relative stereochemistry can always be determined, so samples that diffract well enough and have at least one known chiral center can be run on the Mo instrument.  Likewise, the anomalous signal used to determine chirality is large enough with MoKα radiation for molecules containing atoms heavier than Na, so samples containing a heavy atom can be run on one of the Mo instruments.

 

 

9.  Where do I get my data?
When a structure refinement is complete, IMSERC staff send a notification through NUCore and upload the necessary files for structure viewing, analysis, and publication to Reciprocal Net.  Typical files include a report document (MS Word format), a Crystallographic Information File (CIF file), and a .RES file (refinement results).  These three files contain all the information you need to view your structure, create figures, and publish the data.  See the file information page for more details.

 

 

10.  Is this structure publishable?
We always strive to collect publishable data every time we put a crystal on the diffractometer; however, not every structure will be suitable for publication.   If you have received a structure report from us (MS Word document), then we believe your data can be published on some level.   Specific journals have certain requirements for accepting crystal structures, so not every journal will accept every structure we produce.  X-Ray staff will work with you during the publication process to ensure your data will pass the review.   Please keep in mind that a “perfect” CheckCIF report is very rare – especially for the complex structures produced by researchers at Northwestern.  If your CheckCIF report has errors – even A-level alerts – this does not mean the structure cannot be published.  It does, however, indicate the need for comments in the text or supporting information to explain the warnings.  X-Ray staff typically provide such comments in the CIF file and in the report document that you can use in your publications.  If you have any doubts or concerns, please speak with a staff member.

 

 

11.  What do I need to publish this structure?
Again, different journals have different requirements for reporting crystallographic data.  And of course, much depends on how you wish to report your structures.  Typically, CIF files are required for submission as supporting information.  Some journals may require you to submit the CIF file to the Cambridge Structural Database prior to publication.  The best course of action is to check the journal’s requirements early in the writing process and speak with a staff member if you need assistance in preparing files for publication.   See here for information on how to deposit a structure with the CSD.  The first issue of the year for most journals contains notes for authors on how to publish results, and these typically include information for crystal structure reports.  Check through your group’s old publications to see how they reported results.  But remember that our equipment changed in 2010, so data collected prior to that may be reported differently.

 

 

12.  How can I tell if this structure is already published?
The Cambridge Structural Database contains information on published crystal structures of compounds containing at least one carbon atom.  The chemistry department maintains a site license to the CSD and a copy of the database can be obtained from X-Ray staff.  We will provide a copy of the CD and license information for you to install on your local machine.  Additionally, a copy can be found on the IMSERC terminal server for remote login use.  For information on how to use the CSD, see here.  Information for inorganic structures that have been published can be found in the ICSD.

 

 

13.  How do I solve my own structures?
If you have experience solving and refining your own crystal structures, X-Ray staff members are happy to provide you with the raw data necessary for you to do this.  If you are interested in learning how to solve and refine your own structures, you can attend the Chemistry 435 class in X-Ray Crystallography offered in the Winter Quarter.  Enrollment is limited to approximately 20 students.  Speak with IMSERC staff  if you are interested in attending the class.

 

 

14.  How do I run my own data collections?
If you have successfully completed the Chem435 course, or have prior experience in running your own data collections, speak with Charlotte to schedule training.  Diffractometers are available for student use during select weekdays and all weekend.  Once you have been checked-out on an instrument, you may reserve time through NUCore.

 

 

15.  My samples need to go to APS.  Can you help?
If your crystals are deemed unsuitable for IMSERC facility diffractometers, your first step should be to attempt to recrystallize them.  If after repeated attempts, your samples are still too small for data collection at Northwestern, X-Ray staff will make arrangements to have data collected at the APS or by our collaborators at ALS.  Due to the nature of scheduling at APS beamlines, rush data collections cannot be performed.  Please budget your time accordingly.  Additionally, please remember that crystals exhibiting twinning and diffuse scattering pathologies will not be made better by exposure to synchrotron radiation.