X-RAY CRYSTALLOGRAPHY LABORATORY · Department of Chemistry · University of Alberta
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Frequently Asked Questions

 
  Q. Any suggestions on how best to grow crystals?

Q. I've got crystals - what now?

Q. Where can I get that oil you use for air-sensitive samples?

Q. Can I get an electronic version of my structure report?

Q. Can I get the structure diagrams to paste into my manuscript/poster/talk/thesis?

Q. I need a CCDC number for a manuscript we're submitting - how do I do this?

Q. We've submitted a manuscript to an ACS journal and need to send them the CIF(s) - how do we do this?

Q. Can you send me the coordinates for my structure?

Q. How can I view structures from the coordinates you've sent me?

 

 
   

Q. Any suggestions on how best to grow crystals?

A. Try Growing Crystals That Will Make Your Crystallographer Happy (HTML version | PDF version). We also have printed versions available in our office (E3-13).

Besides the tips and hints you'll pick up from the document above, we'd like to emphasize the following:

  • DON'T grow crystals in overly-large or thick-walled vessels. This includes large Erlenmeyer flasks, or round-bottomed or pear-shaped flasks. The thick walls make it hard to see the crystals (thus difficult to judge crystal quality), and crystals growing near the bottom of larger vessels are hard for us to reach with our crystal probes. Small round-bottomed or pear-shaped flasks can cause problems if e.g. you've placed the flask on its side during crystal growth - the crystals can form in hard-to-reach places. Crystals growing on the bottom of a flask can be difficult for us to view under the microscope while trying to dislodge them with a probe.

    Instead, DO try to grow crystals in small sample vials, or NMR tubes. One-dram or three-dram vials are quite adequate, and allow easy viewing and selection of crystals. The narrow diameter of NMR tubes is an advantage for crystal growing by slow evapouration or solvent diffusion. If we see crystals we like, we can easily snap the NMR tube near where they've grown.

  • If growing crystals by slow evapouration, DON'T (or at least try not to) allow evapouration to dryness. Often the very concentrated solution can solidify, cementing any good crystals that have grown to the sides of the vessel, making it difficult if not impossible to select crystals for analysis. In some cases, solvent molecules can cocrystallize with the compound of interest, but the crystals can be prone to desolvation; leaving the crystals in the presence of some of the crystallization solvent can decrease this effect.

  • Above all, don't wait until a crystal structure is absolutely crucial to your work before you try growing crystals. You can learn a lot about the crystallization characteristics of your family of compounds by trying to grow them as you make them. Not getting a structure of a particular compound can be disappointing, but you can often learn almost as much from the structure of a closely-related precursor or derivative.

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Q. I've got crystals - what now?

A. Come see us! Bring your crystals (unless e.g. they're unstable outside of the glove box) and we'll look at them under the microscope. We'd make our sample submission form available over the web, but we'd rather have a look at what you're submitting before we accept it, since it may not be suitable for a diffraction trial.

If we do like what we see, we'll give you a submission form to fill out. Please include the proposed chemical formula, molecular structure, the reaction(s) that gave this product, and the solvent(s) from which the compound was grown. Please give us as much of this information as you can - often the final structure is not exactly as was proposed, and the additional information (and our chemical intuition) can help us determine what it might be.

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Q. Where can I get that oil you use for air-sensitive samples?

A. It's called Parabar 10312 (also known as Paratone N) and it's available from Hampton Research. As of November 2015 the price was US$63.00 per 100 mL bottle.

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Q. Can I get an electronic version of my structure report?

A. When we complete a structure, we send the Word file for the structure report plus the Crystallographic Information File (CIF) to the researcher and supervisor. If you need structure reports and/or CIFs from a few years ago, let us know the XCL Code(s) for the structure(s) of interest, and we'll send you the relevant material.

We can also convert the Word file to PDF if you need this.

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Q. Can I get the structure diagrams to paste into my manuscript/poster/talk/thesis?

A. These can be copied from the (electronic) structure report, or we can send you these individually, usually as JPEG files, or GIF files from older reports. If you need them in other formats (e.g. TIFF, BMP, PostScript), please let us know.

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Q. I need a CCDC number for a manuscript we're submitting - how do I do this?

A. Let us know the XCL Code for the structure(s) you're publishing, and we'll send the Crystallographic Information File(s) (CIF) to the Cambridge Crystallographic Data Centre. We'll also need the following information to include in the CIF:

- the journal to which the manuscript is being submitted;

- the title of your manuscript;

- the authors (and their contact addresses, if not the University of Alberta Chemistry Department);

- the compound number as it will be referred to in the manuscript.

Probably the best thing to do is to forward us a copy of the title page of the manuscript (with the journal indicated).

The Cambridge database will usually forward the CCDC number within one or two working days.

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Q. We've submitted a manuscript to an ACS journal and need to send them the CIF(s) - how do we do this?

A. Again, let us know the XCL Code(s), journal of publication, manuscript title, authors (and addresses), and compound number(s), and we can do this for you. If the journal has already given you a manuscript number, please also forward this to us so that we may include it in the CIF(s) to be sent.

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Q. Can you send me the coordinates for my structure?

A. We send a Crystallographic Information File (CIF) with every structure that we complete. You can view your structure by opening the CIF with the free program Mercury (see below).

If you need Cartesian coordinates for your structure, we can send you these, most likely in Protein Data Bank (PDB)) format. Note that Mercury can also save coordinates sets in PDB format.

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Q. How can I view structures from the coordinates you've sent me?

A. We most strongly recommend Mercury, which is available from the Cambridge Crystallographic Data Centre. Mercury runs on Windows, Mac, and Linux computers, and handles a number of popular structural file formats, including CIF, MDL, MOL, PDB, XYZ, and SHELX instructions files. Mercury is perfect for handling CIFs that are presented as journal article supporting information, especially those containing multiple structures. You can also get us to send you the coordinates from Cambridge Database searches as a large CIF, then use Mercury to open the file and view the hits individually.

A number of commercial programs (such as Wavefunction Spartan and CambridgeSoft ChemOffice) are able to read PDB files.

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      Last updated 15 August 2016