Copenhagen Small-Molecule NMR Centre
Department of Drug Design and Pharmacology houses Copenhagen Small-Molecule NMR Centre, situated in the NMR basement of building 30 on Jagtvej 162. The facility is equipped with three instruments, of which two are operated as walk-up instruments for both internal and external users, and one is dedicated to metabolomics and hyphenated HPLC-SPE-NMR experiments.
Two of the NMR instruments are operated as open-access walk-up instruments, but with the possibility to book instruments for longer experiments or experiments not suitable for automation. Descriptions of the two instruments are given below:
For procedures and rules regarding the walk-up instruments equipped with autosamplers: see House rules.
NMR analysis request procedure
- Try to solve the problem yourself by using the walk-up instruments, manuals, other litterature and by talking to colleagues.
- Download, print and fill out the form below.
- Bring form and sample(s) to Dan Stærk (or send a mail to get instructions where to put the sample).
- After the NMR-analyses are done, the data are sent by mail and the results are presented (probably during a short meeting
- Daytime experiments longer than 30 minutes per user must manually be changed to night experiments. Press the sun-symbol to turn it into a moon.
- Daytime experiments = sun =
- Nighttime experiments = moon =
- Night experiments shorter than 30 minutes (50 min for 600a) will be analyzed during day-time if the instrument is idle.
- Day-time carbon experiments can be started even though the calculated experiment time is longer than 30 minutes, but they will be halted prematurely by IconNMR.
- Night time = 22:00 - 08:00 on 400a and 17:00 - 08:00 on 600a + whole weekends.
- Day time = 08:00 - 22:00 on 400a and 08:00-17:00 Monday - Friday on 600a.
- Positions 1-4 are reserved for short experiments (to avoid a situation where a backlog of nighttime experiments completely fills up the sample changer effectively blocking all daytime experiments).
The instruments can be reserved for shorter or longer periods for experiments not suitable for automation. All reservations must be coordinated with Louise Kjærulff or Dan Stærk.
Variable temperature experiments in automation must be planned in collaboration with Louise Kjærulff, and is only allowed on the 400 MHz instrument [NMR-400-a]. There is a risk of damaging the probe by bad combinations of temperature, solvent, spinner and NMR-tube, so ask first.
Log in and name experiments
- Login using your named account.
- Name the datasets folders (
<initials>.<yymmdd>.a400for the 400 MHz instrument
<initials>.<yymmdd>.a600for the 600 MHz instrument.
- Use one folder per day (or add a trailing code if you really need several different folders). Different samples will get a experiment number ending with a zero (10, 20, 30,...). Additional experiments on the same sample will get numbers in-between the multiples of 10
- The identity of the sample should be entered into the
- By mail: pdf + raw data
- Check spam-filter if you miss any data. The encoding of the binary files as text sometimes produces words that is stopped by the spam-filer.
- Mailing of pdf and raw-data is optional (but default) for named accounts.
- By network: Data are copied to the SUND-network (possibly you need to log in at https://vpn.sund.ku.dk on your computer to get access). Copy the data to your own computer.
- Apple: Connect to server (⌘+k),
smb://sundcifs12.sund.root.ku.dk, browse to
- Data are continuously zipped and copied into a folder named '
Zipped_NMR_Data'. Look in one of the subfolders (possibly your account name or one of the general accounts such as 'MedChem'). Note that the zip-file will be updated with new data if you are acquire more experiment into the same dataset name.
- Copy the zip-file to your own computer and unzip the contents to a suitable folder. Note the text-file containing a list of the experiments in the zip-file.
- The zipped files will be automatically deleted after 14 days.
- Data are kept in the
current_data-folder for 30 days. After this the data are moved to the folder
old_dataset, one subfolder per month. The data are kept on the workstation until they are ridiculously old.
- The data is backed up every night, but to make sure your data is safe you should take care to keep your data on your own storage place.
- Processed data are deleted after seven days. You can easily recalculate the spectra from the raw data (in Topspin:
xfbfor 2D-data or
xaupfor any type of data if the program is installed correctly).
- Clean your tubes before putting them into the spinner and once more before putting them into the NMR.
- Do not handle the spinners with your bare hands — use the tube as a handle and touch the spinner with a tissue if you must.
- Do not use any kind of sticker labels or parafilm. Please write on the upper 3 cm of the tube or on the cap.
- Adjust the sample position with the depth gauge (solvent should be centered around horizontal line on depth gauge).
- Remove your samples when they are analyzed.
- Samples are moved from the autosampler each morning. Samples not collected will eventually (after two weeks) be put in the trash.
Dos and Don'ts
- Obey all house rules. Discuss them with Louise Kjærulff or Dan Staerk if you want to change anything.
- Never let anyone else use your NMR account, and never use anyone else's.
- Learn more about NMR to use the instruments and techniques as efficiently as possible.
- Don’t reconfigure anything on the computer!
- Don’t fiddle with things if you do not know what you are doing…
- Do ask questions if you are in doubt. It is much more fun to help someone than to fix the problems created by someone who did not know what they were doing. Asking before doing also causes less instrument downtime.
- If you notice that the cryo system of 600a stops chirping, it is crucial that NMR Manager Louise Kjærulff is notified ASAP - it may be possible to prevent a couple of days down-time IF the warm-up process is interrupted within 30-45 min.
- In most cases, e-mails are however sent automatically from the instrument in case of serious problems (red blinking lamps, repeated errors, consecutive failed experiments). Recipients to these mails are:
- Telephone number to the phone by the 600-A: +45 35 33 60 12.
The daily management of the facility is carried out by Louise Kjærulff, and tasks include monitoring system usage and performance, introducing routine operation and experiments to users, and assisting specialist users in setting up non-routine experiments. Additional tasks of the NMR manager include preparation of standard operational procedures and user guides, managing data storage and retrieval solutions, assisting with users' installation of data processing software, and organizing workshops and training courses.
For processing and handling of NMR data, we recommend the three following programs (in no specific order):
- MNova: We share a site license on a server hosted by Department of Chemistry. To gain access you need to be on the network with IP-adresses 220.127.116.11/24 (the new SUND-network, old Pharma faculty).
Download and install the program Mnova. Subsequently you can download and install the Mnova license-file (new file from 2019-11-18) by right-clicking the link and saving it on your pc, then install the license from MNova. Additionally we have licenses for the Mnova qNMR module and the Mnova IUPAC module if you need them.
Christian Tortzen <email@example.com> is in charge of the license server and might help you if things doesn't work. Please, check with colleagues first so that we do not swamp him with questions.
- Topspin: A free single-user license can be downloaded for employees and students at universities. Available for Windows, Linux, and iOS (Mac, Apple). Download the latest Bruker Topspin software package. You can obtain a free academia license code here: https://www.bruker.com/service/support-upgrades/software-downloads/nmr.html
- After installation
- Start the program.
- Install the free license ticket obtained above, via the CodeMeter License website: Paste the license number and press '
Next', then '
Activate licenses'. Choose if you prefer the license to be installed on the computer you are currently working on or locked to a USB key. The rest of the license install process is straightforward.
- Perform the '
Expinstall'-routine. This will prepare the system to make it aware of installed pulse sequences and automation programs. The administrator password is not set (empty, press return). Accept all suggested settings.
- You probably do not need the suggested automatic backup of Topspin-related very important files. Mark '
Do not show this message again' and press '
- Right click in the data browser panel (to the left) and '
Add New Data Dir...'. Best practice is to choose a folder (maybe named '
MyNMR' on your
P-drive) containing a sub folder with the name '
data' (all small letters). Save all your NMR-data in this data-folder and make sure that the data uses the following structure:
<data>/<any name>/<nmr>/<experiment number>.
Alternatively, choose a folder below which you have your dataset folders (e.g. jd.180101.a400) in which the individual experiments are sorted in folders named 10, 11, etc. E.g.
<NMR>/<jd.180101.a400>/<10>. This will also work.
- After installation
- ACD/Spectrus platform with a series of processing and verification tools. License must be bought. Set up an account and download the software via acdlabs.com.