Rdm:synthesis-lab

Publishing NMR Research Data

This process has a total of five stages. You will have already done the first two stages and here are described the final three stages.

Preparing the Data Files (stage 3)

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

1. A file describing the chemical structure of your compound, in the form of a Chemdraw .cdxml file created using the Chemdraw program
   1. 
      To start, from the Software Hub panel, firstly select a chemistry filter
   2. If you cannot see anything relating to the software hub, open a Web Browser and type https://softwarehub.imperial.ac.uk/login as the URL and proceed to log in using your Imperial Credentials
   3. 
      From the list of chemistry programs (currently 32) invoke Chemdraw.
      1. Sketch out your molecule using the Chemdraw tools provided.
      2. When drawing your molecule using Chemdraw, avoid using any abbreviations such as Me, Bu, Ph etc. If you have used them, then at the finish, select the entire structure and invoke structure/Expand labels
      3. 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.
      4. Save as a chemdraw XML file (.cdxml).
2. The NMR data file(s) themselves. For NMR spectra recorded using a Bruker spectrometer, this will be a folder of files which you will have to convert to a .zip archive ( If you are using a Jeol spectrometer, this will be a single file with a .jdf extension. ).

Retrieving your raw data files from the spectrometer (stage 4)

Retrieving an NMR data file from the Bruker Spectrometer (used for Synthesis course) and Processing using MestreNova

Retrieving an NMR data file from the Jeol Spectrometer (not currently used for Synthesis course) and Processing using MestreNova

Additional data files that can be created from the raw data files

There are two additional files you can optionally generate using save as from the MestreNova program.

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).

Finally you will publish this data (stage 5)

You can check your entry(s) have appeared by viewing the list at DOI:drbg (for 2019/2020).

Summary of what you will have achieved

You will have:

1. Registered for an ORCID (Open Researcher and Collaborator Identifier) using your Imperial College affiliation and credentials.
2. Authorised the Imperial College Data Repository to associate research data publications with your ORCID account.
3. Started to prepare a set of data files for deposition in the Data Repository, including a Chemdraw file describing an associated molecule.
4. Retrieved one (or more) NMR data files from the appropriate Spectrometer and checked the spectrum resulting using the Mestrenova program.
5. Published the data files on the Repository to be associated with your ORCID and obtained a DOI (Digital object identifier) for your publication.

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Questions, please contact Prof, Rzepa

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Return to ORCID (stages 1 and 2). This page has DOI:dg3n