Almost all CIF instrumentation automatically uploads acquired data to the Research Files data cloud, either when you log out of the instrument computer, or as a batch once per day. The remote data access page provides additional information on how to access your data from your personal computer.

• NMR TopSpin License Processing for Academia In order to provide students, researchers and teachers with unlimited access to the best tools for off-line NMR processing, Bruker is making their market leading NMR processing software TopSpin available free of charge for all academic users.
• Drag the new licenses into the same folder and then restart MestReNova. Topspin (Bruker) processing software is also free for academic users via this link. A subscription for MNova tablet is also available. This doesn’t have a license file, you have to activate it online. In order to activate the tablet version, complete the following steps.

Workstations with Agilent VNMRJ, Bruker TopSpin and Mestrelab MNOVA software are provided for data processing and user training. An unlimited user site license for Mestrelab MNOVA software allows each user to install data processing software on their personal computer. There is academic license on TopSpin. This means that students and employees at UiB can use the software on their own machine. Installation Client Hosted Windows PC. TopSpin is installed from Windows - Software Center. If you do not find the software, please report an issue via or call 555 84700 (for employees). The MestreNova License should not be shared with outside parties as the license is only available to UO students and researchers. If a data processing software is required and you are not affiliated with the University of Oregon, Bruker offers the TopSpin data processing software free to academic, government and non-profit institutions.

The CIF and ISU Chemistry undergraduate lab courses supply all NMR users and students in organic chemistry lab courses with a software license for MNova NMR data processing. This license is maintained by CIF staff. Please email Sarah Cady if you have questions or problems with MNova Software.

For new installations, go to the MNova website to download the latest version of the software. The licenses for the MNova processing software are available on this Iowa State CyBox folder. You must log into CyBox with your ISU credentials in order to access the folder. Download the license to your Desktop or another easily accessible spot. After installation, follow the prompts in the software to activate the license. You can delete the license from your desktop after installation is complete.

There are four license files in the CyBox folder. The license necessary for NMR processing is 'Iowa State University Campus NMR v1.8.lic' The other three licenses are optional. They are for quantitative NMR analysis, reaction monitoring, and IUPAC naming features. The MNova website has more information and tutorials on each of the additional features, and you can decide if the features will be useful for your research.

Your computer must be on the ISU network in order to activate the licenses. For Ames Lab users located in Spedding Hall or other Ames Lab facilities, you are technically 'off campus' and must log in to the ISU VPN in order to activate the licenses.

If you already have MNova installed, but need the most recent licenses, follow the instructions above to download the licenses. Then follow the instructions to replace the old licenses:

• Open MNova. Click 'Help' at the top menu bar, and then click 'Get/Install Licenses'
• Click 'Install' and it will allow you to open the folder where you saved the license file. Select the license file and click 'Open.'
• A box will pop up that asks: 'A license file for NMR already exists. Do you wish to replace it?' and select 'Yes'
• Restart MNova to complete installation. The license file has been copied to its permanent location and you can delete the other copy from your Desktop.

For Mac users, there is an occasional issue with the automatic replacing of licenses. To resolve this issue, try the following procedure or email Sarah Cady for further assistance.

Bruker Topspin Student License Verification

• In MNova, Go to Help -> License Manager to find the folder where the licenses are located.
• On my computer the license files are located at /Users/$MYUSERNAME/Application Support/Mestrelab Research S.L./MestReNova/
• If you cannot see the folder, you may have to type ⌘+shift+. (period) in order to make hidden folders visible.
• Go to the folder and drag the old license files to the trash. When you try to drag them to the trash it may ask you for the administrator password.
• Drag the new licenses into the same folder and then restart MestReNova.

Topspin (Bruker) processing software is also free for academic users via this link.

A subscription for MNova tablet is also available. This doesn’t have a license file, you have to activate it online. In order to activate the tablet version, complete the following steps:

• Go to the MNova Tablet License website and sign up with your ISU email address.
• Download the MNova tablet software from the app store onto your device.
• Open the software on your tablet.
• Tap on any of the icons that have a little “lock” over them. This will lead you to a registration pop-up screen.
• Type in your ISU email once again.
• Wait for a confirmation email to activate your tablet license and click the link in that email to activate.
• I did have issues with these activation emails going to my junk mail, so be advised of that.

WELCOME TO THE ISIC's NMR SERVICE WIKI

We hope you will find here answers to your questions regarding the NMR service of the Institut des Sciences et Ingénieurie Chimiques de l'EPFL. If you need some complement, do not hesitate to contact us at pascal.mieville'at'epfl.ch.

Table of Content (links):

1. Available NMR spectrometers and ideal use
2. Useful links
3. Data access and account management
4. Routine TOPSPIN commands for manual machine
5. Unlock Screen saver
6. MestreNOVA
7. Automatic structure verification
8. NMR references tables
9. Useful NMR tricks
10. Kinetic experiments

1. Available NMR spectrometers and ideal use

Table of all available probes and machines at epfl © Martial Rey
Table of Signal to Noise ratio © Martial Rey

2. Useful links and documents

Please, if you use information coming from the following sites, be careful to correctly cite them in your references.

- The essential lists of solvent traces and chemical shift references :
J. Org. Chem. 1997, 62, 7512-7515 (contains also chemical shift HDO vs T°)
Organometallics 2010, 29, 2176–2179
Magn. Reson. Chem. 2006; 44: 606–616 (contains 2H values and TMS)

- Our estimated colleague Dr. Luc Patiny's tools for NMR prediction and simulation :
http://www.nmrdb.org/predictor
http://www.nmrdb.org/simulator

- An excellent reference about NMR nuclear properties of many elements from Roy Hoffman at Hebrew
University of Jerusalem : http://chem.ch.huji.ac.il/nmr/techniques/1d/multi.html

- A famous and very useful spectral database from Japan :
http://sdbs.riodb.aist.go.jp/sdbs/cgi-bin/cre_index.cgi

Topspin Academic License

- Bruker software (and updates) - good prices for student licenses on TOPSPIN and CMC-assist
http://www.bruker.com/service/support-upgrades/software-downloads/nmr.html.

- A useful Solid State NMR link :
http://www.solidstatenmr.org.uk/lectures.html

- A good reference for structure elucidation : Richards, S. A., Hollerton, J. C. Essential Practical NMR for Organic Chemistry; John Wiley and Sons: United Kingdom, 2011; 157-159. ISBN: 978-0-470-71092-0

- A NMR blog maintained by Dr. Glenn Facey from Ottawa University that contains a lot of very useful and smart tricks and good explanations about common NMR experiments :http://www.u-of-o-nmr-facility.blogspot.ch/

3. Data access and account management

3.1 For EPFL registered users (possessing a GASPAR account)

3.1.1. To access data directly from your own computer:

On any machine type (windows, mac & Linux) it is possible to use a SFTP software like FileZilla to connect.
Here is the link to download FileZilla (it is free and easy to use) : https://filezilla-project.org
Once installed on your machine, apply first a small correction into the preferences :
- In the Menu Bar, go to FileZilla, then choose Preferences.
- In the Setting window, choose the Tranfers -> FileTypes options.
- In the upper window (Default Transfer Type) choose the 'Binary' option. This will avoid any modification of the files during the file transfer.

Then connect with the following information:

Host : nmr.epfl.ch
Username : your GASPAR username
Password : your GASPAR password
Port : 22 (new for more security)
Finally press : Quickconnect

In the right window (red one, server) choose the spectro link, then choose the correct spectrometer. You should have all your data available. You can therefore drag them in your computer (left window, blue).

It is also possible to connect directly to the server using the drive mapping process, see below.

For confidentiality reasons, we do not store nor backup any external user data. We therefore ask GUESTS users to directly retrieve their data after acquisition and to erase them from the spectrometer (see 2.2.2).

Dedicated folders are specifically not backed-up.

NMR service can not be considered as responsible in case of loss or diffusion of data that have not been correctly removed from the spectrometer by external/guests users.

The two dedicated machines for external users are nmr1512l and nmr1512r.

3.2.1 Data generation

In TOPSPIN or XWINNMR, type 'EDC' or 'NEW', in the popup window fill the following information :

NAME = EXPERIMENT_NAME
EXPNO = 1
PROCNO = 1
DIR type : /opt/data/guests (this folder is in mode 770, root : 500000)

This will generate data into the following folder : /opt/data/guests/data/USER/nmr/...

3.2.2 Data recovery using FileZilla

A dedicated MAC machine is available in the BCH 1512 room. This machine is equipped with FileZilla

Connect yourself to the server using FileZilla, connexion information are host = nmr.epfl.ch , user = USER (e.g. G13000, G has to be capital) and you password (port 21 = FTP mode).

The right window in FileZilla is the remote machine (server) and the left window is the local machine. Your USB key should be visible in the left window under 'Volume' folder.

Data are available on the right window under path : /spectro/MACHINE/guests/data/USER/nmr

Copy all data simply by drag and drop from server to your key, then suppress all data on the server. This will also suppress them on the spectrometer.

Finally, in FileZilla, erase your connexion data using the small arrow on right of 'connexion rapide' and clicking on 'effacer historique'.

4. Routine TOPSPIN commands for manual machine

5. Unlock Screen Saver

Under the new LDAP configuration (GASPAR login), the screen saver has to be set individually. In order to avoid to block the machine in case of absence, please configure the screen saver to not request password to unlock.This has to be done in the linux configuration as described hereafter:

5.1 On CentOS

a. Go to the 'CENTOS' menu, then select 'Control Center' -> 'Appearance & Themes' -> 'Screen Saver'

b. In the 'Screen Saver' window, uncheck the checkbox 'Request Password to stop'

5.2 On RedHat

a. Go to the ' REDHAT Application' menu (upper left corner), then select 'Preferences' -> 'Screen Saver'

b. In the 'Screen Saver' window, change 'mode' to 'Disable screen saver'.

6. MestreNOVA

This licenses are only destinated to ISIC (Chemistry) users. All other will be banned when detected on the license server.

All ISIC collaborators have access to a license site for MestreNOVA NMR, Mestre NOVA predict and two add-ons : qNMR (for quantitation) and Reaction Monitor.

The link to download the main software is http://mestrelab.com/software/mnova-suite/download/

6.1 Install Mnova

Go to the 'Mestre License Download' tab on http://isic.epfl.ch/NMR

qNMR add-on can be downloaded here: qNMR add-on

Reaction Monitor add-on can be downloaded here: Reac_Monitor_add-on

To install the add-ons, download them on your desktop, unzip them and drag the .xml file into the MestreNova open window.

7. Automatic structure verification

ISIC has bought two softwares/licenses dedicated to help users to evaluate the consistency of their spectra. A first soft is included in ICONNMR on the automatic NMR machines (see 7.1) and does not requires installation on the user machine. A second soft is MestreNova Verify and is an add-on to Mestre (see 7.2).

These tools are not intended to replace the chemist but only to support him. It is always the chemist at the end that has to decide if the spectra is good or not.

A good reference for structure elucidation : Richards, S. A., Hollerton, J. C. Essential Practical NMR for Organic Chemistry; John Wiley and Sons: United Kingdom, 2011; 157-159. ISBN: 978-0-470-71092-0

7.1 CMC-assit Fast Lane on Bruker automatic machines (nmr3404l, nmr4313l & r and nmrf492l)

go to the following page : Bruker Fast-Lane, to have a complete description to work with CMC-assist
Fast Lane

here is a reference manual for CMC-assist (pdf) - not really required to read it.

7.2 MestreNova Verify

On specific request, ISIC users only can obtain a license for Mnova Verify. To do this request please click on the following link : https://isic-nmr.epfl.ch/licenses-request/verify

More information about this software :http://mestrelab.com/software/mnova-verify/

A MestRe site treating of Automatic Structure Verification/Elucidation

A Mestre blog concerning their scoring procedure

8. NMR references tables

8.1 Shigemi & Wilmad matched insert color code

8.2 Reference compounds for chemical shift

- a more complete list is available at this page : http://www.nmrnotes.org/NMRPages/refcomps.html

- a good list of 19F reference compounds : http://chemnmr.colorado.edu/manuals/19F_NMR_Reference_Standards.pdf

- an interesting article about standardization of chemical shift in NMR.

9. Useful NMR tricks

9.1 Aromatic solvents to easily increase the spectral resolution

Changing your deuterated solvent from CDCl3 or any other non aromatic solvent by an aromatic deuterated solvent such as Toluene-d8 or Benzene-d6 helps greatly to spread the peaks in the spectrum.

source : http://www.u-of-o-nmr-facility.blogspot.ch/ © Dr. Glenn Facey cited with kind authorization of author.

9.2 some drops of concentrated TFA to simplify spectra

adding some drops of concentrated TFA in NMR samples allows suppressing signals of exchangeable protons inside molecules and generates a broad global peak located halfway between the original peaks and the one of TFA (ca. 15 ppm) - it is therefore generally out of interesting signals.

source : http://www.u-of-o-nmr-facility.blogspot.ch/ © Dr. Glenn Facey cited with kind authorization of author.

10. Kinetic experiments

We have set an automatic kinetic experiment on the nmr1512r machine

Procedure:

1. Acquire a 1D spectrum using the standard refe_1Hzg experiment. This acquisition should be performed on a sample as similar as possible to your kinetic sample

• same compounds and solvent (except a minor component such a catalyser or minor reactant)
• same solvent height
• same tube

2. Check carefully your NS & RGA
3. Once done, type in the TOPSPIN bar command : makekinetic2D.
4. Answer the delays questions (the mentioned delays are the one placed between each loop of acquisition).
5. Type the command 'i' to go to the next experiment which is the pseudo 2D kinetic experiment correctly parametrised.
6. Eject your sample and add the missing compound, shake your sample and inject it. Rapidly check manually the shimming (Z1 & Z2) and start the acquisition with 'zg'
7. Once the acquisition is finished, you can treat the data with xf2, phase your spectra, correct the baseline and integrate the interesting peaks.

Some tips :

• try to minimise the duration of each acquisition with respect to the global experiment time. It would not be very significant to have each point taking 3 minutes to acquire on a 15 minute experiment. The error on t would be very big. So try to conserve NS as small as possible.
• Since generally kinetic profiles are exponential, it is interesting to acquire more point at the beginning in order to have a good fit. This is possible by defining different delays duration within the experiment.