Nmr

 

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

 

LOCAL SPECTROMETER TYPICAL APPLICATION CRYOPROBE
BCH 1508

Avance 500 MHz
CPTCIxyz 5 mm
TOPSPIN 2
(nmr1508.epfl.ch)

Low concentration samples
1H, 13C/15N
NMR development and routine
!! T° limit 0°C to 80°C (due to the cryoprobe) 

yes (Helium)
factor 4 in sensitivity

BCH 1510

AvanceII 800 MHz
CPTCIz 5 mm
CP/MAS 2.5 mm
TOPSPIN 2
(nmr1510.epfl.ch)

Liquid: High resolution, low concentration samples (bio) 
1H, 13C/15N, NMR development
!! T° limit 0°C to 60°C (due to the cryoprobe) 

Solid: 1H, 13C,14N, NMR development

yes (He) factor 4 in sensitivity
BCH 1512L

DRX-400 MHz
BBO 5 mm
XWINNMR
(nmr1512L.epfl.ch)

1H,13C, BB, good sensitivity on carbon and other low gamma nuclei such as 31P
15N,51V,11B are accessible on this machine

NMR development or routine
!! DO NOT USE FOR LOW CONC. 13C samples - Prefer CryoProbes in this case

no
BCH 1512R

Avance 400 MHz
BBIz 5 mm
TOPSPIN 2
ATMA, , TOPSHIM
(nmr1512r.epfl.ch)

 

1H, {BB}, very good sensitivity on proton, simple gradient, medium sensitivity on broad band.
Short to medium experiments for NMR routine
!! DO NOT USE FOR 13C SAMPLES
!! IDEAL for 1H (zg and COSY) and all reverse experiments such HSQC and HMQC. 

no
BCH 1516

AVANCE III HD 600 MHz
CPTCIz 5 mm
TOPSPIN 3
ATMA, TOPSHIM
(nmr1516.epfl.ch)

Low concentration samples
1H,13C
NMR development and routine
!! T° limit 0°C to 60°C (due to the cryoprobe)
!! IDEAL for low concentrated 13C samples

yes (He) factor 4 in sensitivity
BCH 2407L

Avance I 400MHz
BBFO-Plusz 5 mm
TOPSPIN 2
ATMA, TOPSHIM
(nmr2407l.epfl.ch)

Good routine machine for 1H, 13C, 19F and 31P no
BCH 2407R

DRX 400 MHz
BBO10 mm
XWINNMR
(nmr2407r.epfl.ch)

Special machine for high pressure measurments no
BCH 3204

DRX 400 MHz
TBO BB{1H/13C}
5 mm
XWINNMR
(nmr3204.epfl.ch)

!! GOOD for 1H (zg and COSY) and all reverse experimet
such HSQC and HMQC. 
Works with 19F, 2H and 13C.
High temperature experiments.

no
BCH
3404L

AvanceIII 400MHz
BBFO-Plusz 5 mm
TOPSPIN 3
ATMA, TOPSHIM,
AUTOSAMPLER
(nmr3404L.epfl.ch)

Good routine machine for 1H, 13C, 19F and 31P.
Can be used as an automat.

no
BCH 3404R

Avance 200MHz
QNP 5 mm
(nmr3404r.epfl.ch)

Low resolution 13C, 19F, 31P.
Good for kinetic measurements		 no

BCH
4313L

AvanceIII 400MHz
Prodigy probe 5mm
ICONNMR
ATMA, TOPSHIM, AUTOSAMPLER

(nmr4313L.epfl.ch)

AUTOMAT, high sensitivity in 1H, 19F, 13C and 31P, good for characterization.

Priority for less than 15 minutes.
Night for more than 30 minutes.

yes (prodigy, N2) factor 2 in sensitivity
BCH
4313R		 AvanceIII 400MHz
Smartprobe 5mm
ICONNMR
ATMA, TOPSHIM, AUTOSAMPLER
(nmr4313L.epfl.ch)

AUTOMAT,very good sensitivity in 1H and 19F. Good sensitivity in 13C and 31P. 
Dedicated to short terms experiments < 20 minutes 

no
BCH 5313 AvanceIII 400MHz
BBFO-Plusz 5 mm
TOPSPIN 3
ATMA, TOPSHIM,
(nmr5313.epfl.ch)

Good routine machine for 1H, 13C, 19F and 31P.
Reserved for manual short term (< 20 minutes) routine experiments.

no
CH F0492L AvanceIII 400MHz
BBFO-Plusz 5 mm
TOPSPIN 3
ATMA, TOPSHIM,
(nmrCHF0492L.epfl.ch)

Good routine machine for 1H, 13C, 19F and 31P
Can be used as an automat.

no
CH F0492R

Avance 400 MHz
BBOz 5 mm
TOPSPIN 2
(nmrCHF0492r.epfl.ch)

Good routine machine for 1H, 13C, 19F and 31P no

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

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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

- 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/

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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.

3.1.1.a. Windows: 
1. First, click on the Computer shortcut from your desktop or from the Start Menu. In the toolbar you will find several buttons,
    including one called Map network drive.
2. Click on it and the Map Network Drive window will open. Firstly, leave the automatically assigned  drive letter and then type the
    folder you want to connect to. In our case \\nmr.epfl.ch\isic 
3. Click on Finish then double click on the new icon. 
4. If necessary, in the login window, type the user "intranet\GASPAR_USER" and your gaspar password (replace GASPAR_USER by your specific one). For STI, Master students and ENAC people, replace "intranet\" by sti\, students\ and enac\ respectively.
 
The new NMR data are accessible under the  following path : /your_group/user_name/machine_name (replace machine_name by the name of the NMR where you did the acquisition and the user_name by your specific name).
The old NMR data are accessible under the following path : /your_group/user_name/nmrws# (replace # by the number of your level, e.g. /level_3 -> nmrsw3 and the user_name by your specific name).
 
3.1.1.b. MAC:
1. First, click on a free zone of your Desktop then press "CMD + K"
2. In the opened window, type the following address : smb://nmr.epfl.ch/isic. (You can press on the small "+" to add this address
    to your list).
3. Click on Connect.
4. In the login window, type the gaspar user and your gaspar password
The new NMR data are accessible under the  following path : /your_group/user_name/machine_name (replace machine_name by the name of the NMR where you did the acquisition and the user_name by your specific name).
The old NMR data are accessible under the following path : /your_group/user_name/nmrws# (replace # by the number of your level, e.g. /level_3 -> nmrsw3 and the user_name by your specific name)
 
3.1.2 To retrieve "old" data directly on the NMR computer:
When you log on for the first time using the new LDAP protocol (with your gaspar account), the TOPSPIN version is reseted. 
Therefore you have to validate the license (click "Agree"), then in the left vertical bar, click the left mouse button, then select "Add new directory" and type "level_#" (replace # by your specific level number). 
3.1.3 To store create new data on the NMR machines:
3.1.3.a  To copy an old experiment - first recover the desired experiment using point 2, type "EDC" in the command bar and type "/opt" in the DIR line. All the other lines are similar to the former procedure. If your folder does not exist already, it will be generated automatically at this step.
 
3.1.3.b  To start an totally new experiment -  type "NEW" or "EDC" in the command bar and type "/opt" in the DIR line. All the other lines
are similar to the former procedure. If your folder does not exist already, it will be generated automatically at this step.
 
3.2 For GUEST users (external users)

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". 

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4. Routine TOPSPIN commands for manual machine

download routine TOPSPIN commands for manual machine

 

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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". 

 

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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.

 

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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

http://mestrelab.com/blog/related/book-asv/

A Mestre blog concerning their scoring procedure

http://mestrelab.com/blog/article/score-significance-and-quality-in-the-context-of-an-automatic-verification-system/

 

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8. NMR references tables

8.1 Shigemi & Wilmad matched insert color code

Solvent Code Glass Color
Chloroform CMS clear
D2O BMS clear
DMSO DMS green
Methanol  MMS blue

8.2 Reference compounds for chemical shift

 

Nuclei Substance

Chemical Shift

1H TMS or DSS (aquous solution) 0 ppm (definition)
13C TMS 0 ppm (definition)
19F

CFCl3
TFA
HF (aq.)

0 ppm (definition)
-76.55 ppm (w.r.t CFCl3)
-204.0 ppm (w.r.t CFCl3)

31P H3PO4
(CH3O)3PO		 0 ppm (definition)
0 ppm

- 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.

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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.

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