Rdm:synthesis-lab

Publishing NMR Research Data: DOI:dg3n

To publish research data such as an NMR spectrum, you will need to prepare and have ready the following files on the computer you are using

The files required for publication

1. A file describing the chemical structure of your compound, in the form of a Chemdraw .cdxml file.
   1. When drawing your molecule using Chemdraw, avoid using any abbreviations such as Me etc. If you have used them, then at the finish, select the entire structure and invoke structure/Expand labels
   2. You can also use the Structure/Convert structure to name menu option to generate a name. You might want to use this name as the title of your data deposition.
2. The NMR data file(s) themselves. If you are using a Jeol spectrometer, this will be a single file with a .jdf extension. If you are using a Bruker spectrometer, this will be a folder of files. There are two additional files you can generate.
   1. The first is the output from reading the Jeol or Bruker file using a program called MestreNova, taking the extension .mnova
   2. The second is the result of opening the Jeol or Bruker file using MestreNova and saving it as a JCAMP-DX file (extension .jdx).

Retrieving an NMR data file from the Jeol Spectrometer

1. On Windows 10, type run into the search box at the bottom
2. 
   In the run box, type \\ce-nas01.ce.ic.ac.uk\CFNMR\Jeol400Export and navigate down through chemteaching\nmr\2020 and find your own file as per issued instructions.
3. 
   Now, from the Software Hub panel, firstly select a chemistry filter
4. 
   and from the list of chemistry programs, invoke MestreNova. Drag-n-drop the Jeol data .jdf data file into the MestreNova empty window
5. 
   A spectrum will appear.
6. 
   When you have finished inspecting the spectrum, save the data file using Save as as a .mnova file and optionally repeat for .jdx format. Take care to note where you are saving the files (on the desktop in this example).

You will now have all the files you need to make your data deposition.

Publishing the NMR research data

1. 
   If you have not already done so, see instructions for registering an ORCID and connecting it to the Imperial College Data Repository.
2. You will need to complete the fields indicated with red arrows, Make sure you know the location of the files shown below, as acquired in the previous section.
3. 
   of which an example is shown here. With the item Member of collection / collaboration you should have the authority to make your deposition a member of the 1st Year undergraduate synthesis laboratory (which already has DOI:10.14469/hpc/6215 assigned).
4. 
   Press the submit button when you should get the response shown. Your publication DOI is shown with the red arrow. Record this in your notebook.
5. 
   Click on the DOI link to show the full record of your data.
   1. Item 1 is the Spectrometer data. It contains all the information collected by the instrument such as the FID.
   2. Item 2 is a licence file specific to the spectrometer data that allows you to use (un)licensed MestreNova to generate and view the spectrum. On college computers you are already using a licensed copy of MestreNova so this file is not actually needed. It allows others without a previously licensed version of MestreNova to view the spectrum.
   3. Item 3 is the MestreNova transformation of the spectrometer data, which can contain much additional information about the molecule if added.
   4. Item 4 is the license file for the Mestrenova transformation, corresponding to the spectrometer data in 2. Again, with an already licensed version of Mestrenova you do not need to use this file.
   5. Item 5 is the JCAMP-DX version of the spectrum. It contains only the spectrum and no actual spectrometer data. It is included because JCAMP-DX is a widely used format for expressing NMR spectra. It can be viewed by Mestrenova, but if you have 1 or 3 its use is not necessary.
   6. Item 6 is the InChI molecular descriptor for the compound corresponding to the data (as generated from your ChemDraw file). InChI is an international standard for identifying molecules.
   7. Item 7 is the InChI Key molecular descriptor for the compound corresponding to the data (as generated from your ChemDraw file) and is a shortened version of the InChI identifier. It can be used for searches of any molecule with the same key on the Web and in most chemical search engines.