Setup of 2D experiments in automation

GENERAL

In two dimensional experiments resolution in the indirect dimension is usually limited.  The default spectral width settings for many experiments are therefore more restrictive and may not include chemical shift regions towards the edge of the range. For example aldehyde carbons may not be included in the default HSQC experiments.

MANUALY SETTING WINDOW

If you are running automation, you can check and modify parameters by using the “Modify Parameters” button in the experiment setup line .

This will bring up the parameters window:

The parameters to change the spectral window (highlighted) are 2SW and O1P for the direct dimension (typically proton), 1SW and O2P for the indirect dimension (can be c13, n15 etc). For COSY, set 1SW equal 2SW, and don’t set an O2p.

To translate a given sw and o1p to spectral limits, use

  • leftlimit = o1p + sw/2
  • rightlimit = o1p sw/2

For a window from leftlimit to rightlimit one needs to set

  • sw = leftlimit – rightlimit
  • o1p = rightlimit + sw/2

For example, for a 10-190ppm window, sw=180ppm and o1p=100ppm.

INCREASE SIGNAL TO NOISE OR RESOLUTION

To adjust experiment time, increase 1td (number of individual spectra) for better resolution and signal to noise, or ns (number of scans per individual spectrum) for better signal to noise only (circled in red)

AUTOMATED DETECTION OF SPECTRAL WINDOW

Optimization of spectral window can be done automatically by the Topspin software.  If you run unknown samples in automation, that can be useful.

In IconNMR, several composite experiments are available that automatically optimize the sweep width using 1D experiments.  They are showing at the bottom of the list and are prepended with a “C”:

C h1-cosy – {H1 and sweep width optimized COSY}
C h1-hsqc – {H1,f2 Sweep width optimized HSQC}
C h1-c13-hsqc – {H1,c13, f1/f2 Sweep width optimized HSQC)
C H1-dept-hsqc (H1, C-13-DEPT135, f1/f2 sweep width optimized HSQC}
C c13-cosy-hsqc – {Proton, C13, HSQC and COSY}
C hsqc-cosy-hmbc – {Proton, C13, HSQC, COSY and HMBC spectra}

The experiments will create 1D experiments, and then run the 2D experiments with the spectral widths optimized for the region of the 1D experiments containing signals. This should usually ensure that no signals are left out in the 2D experiment, but strong solvent signals can cause weak compound signals to be missed..

Use of the DEPT for setting up the HSQC should only optimize for protonated carbon signals.

 

 

Topspin 3.6.3 available

Topspin version 3.6.3 is available. I updated the workstations in B-10 with the newer version. I have not yet updated the 500 spectrometer software.

For those only doing basic processing there is no significant difference to the previous 3.6.x versions. So if you installed Topspin on your office or home computer, there is no need to rush to update. One new feature is the Dinamic NMR simulation option under Analyse->Lineshapes->Fit Dynamic NMR models (dnmr) that allows to fit exchange broadening.

For those that have not installed Topspin on their computers, I recommend installing the latest version if you do install. I updated the links on the NMR lb website at https://sites.uwm.edu/nmr/nmr-lab-software/

to reflect the redesigned Bruker website, and also updated my installation instructions accordingly.

Bruker Webinars on No-D NMR and CMCse

Bruker is currently offering a series of webinars about various NMR techniques and Topspin features.  Two in particular may be of interest to general users:

“Running NMR without deuterated Solvents (No-D NMR)”  was today, October 13, and is available on demand.

“Using CMCse classroom edition” Mon, Dec. 7, 2020, 3pm

CMCse is an analysis tool for structure elucidation using HSQC/HMBC/COSY.

The webinars are free, but require registration.  The list of webinars can be found here:

https://nam02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.bruker.com%2Fnc%2Fabout-us%2Fworld-class-bruker-nmr-trainings-now-available-online.html&data=04%7C01%7Cholger%40uwm.edu%7C3696172e825245c5bb6d08d86ffedf15%7C0bca7ac3fcb64efd89eb6de97603cf21%7C0%7C0%7C637382487754634975%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=9e41ARPVTXDI8bGWGq6z4eDm%2B4i6j%2F6ZON4otc8iYbw%3D&reserved=0

If you scroll to the bottom of the list you can see more past webinars, some of which may be of interest to you.

Off Line Processing Options

There are  different options for offline processing and plotting/exporting NMR data  outside the spectrometer.   This is not meant to be a detailed reference manual, but just an outline.

  1. Processing workstations in B-10
  2. Install Topspin on your office/home computer
  3. Use Web based spectrum viewer
  4. Virtual desktops

1) Processing Workstations in B-10

There are two workstations along the wall in B-10, that have been moved apart for social distancing.  The larger monitor is attached to the higher memory computer and is the preferred one to be used.  Login is the same username/password as the spectrometer.  If your username is not listed, select “Other” from the bottom of the list and manually enter it.  Topspin can be started from the Favorites section of the bottom left start menu.

Data can be accessed from the NMR data browser, using /nmr500 for data on the Avance-500, and /nmr300 for data from the DPX-300 spectrometer.

2) Install Topspin on your office/home computer

Topspin is available with a free Academic license and can be installed on Windows, Linux and Mac computers.  Links for downloading Topspin can be found on the NMR lab website at

https://sites.uwm.edu/nmr/nmr-lab-software/

Downloading and obtaining a license for Topspin from the Bruker website requires setting up a free account with Bruker using your UWM e-mail.  You can also download Topspin from the NMR lab website.  For on campus computers,  you can also choose to obtain the license through the NMR lab license server (five simultaneous licenses).  A quick  installation guide that is available  from above link.

To process data on your computer, you can either download them through the NMR lab website, or access them through the NMR lab uFiles file share (\\ufiles.ad.uwm.edu\uwm\LS\ResearchGroups\NMR\data)

You need to be logged into the UWM VPN with Global Protect to access uFiles from an off campus computer.

3) Use Web based spectrum viewer

The App available on the NMR lab Website can be used for searching of spectra and basic processing and printing of 1D data.  Select [Search/View] on the NMR lab  main status page or follow direct link.

https://hal.chem.uwm.edu/cgi-bin/webplot/webplot.pl

The app supports horizontal and vertical  zooming,  toggeling Hz/ppm and integral labels/trails, adding/deleting integrals, and limited peak picking and reprocessing of 1D spectra

Handling of 2D datasets is limited,in particular the incorporation of 1D projections, because of changes in Topspin that have not been fully been incorporated into the app.   Printing creates a pdf file that can be saved or printed locally.

4) Virtual desktops

Those that need full processing capabilities, but don’t want or can install Topspin on their computer, can access a virtual desktop on the NMR lab server using the VNC protocol.  These virtual desktops give the same access to Topspin and your data like  the workstations in B-10.

Webstart files for different resolutions are available at the bottom of the NMR lab status page.  Java is required on the users computer.  Off campus users also need to be logged into the UWM VPN for access.  The program will ask username and password, which are your Panther ID and -password. It will  then connect to the NMR lab server and give you a login screen .  Like with the workstations in B-10, you either select your name from the list or select “other” and enter it manually.  That will give you a desktop identical to the one when using the external workstations in B-10. Depending how close the virtual desktop size matches your screen resolution, you may need to used the scroll bars at the right and bottom of the window to move to parts of the virtual desktop.

Printing can be done by exporting as pdf and saving unter the PDF directory, or using the Cup-Pdf printer.  If you checked the “Monitor PDF directory” option on the website, a window prompting you to download the pdf file will pop up.  Otherwise, you can download the PDF files with the Download App on the NMR lab website.

If there is trouble starting the webstart file from the website (for example some Macbooks seem to block it) you can access the files from the NMR lab  uFiles file share, i.e.

U:\ResearchGroups\NMR\Programs\JavaVNC

5) Other Software

Other third party software is available that can be used for processing of Bruker NMR data, for example MNova.

NMR operations during COVID-19 outbreak

UWM Department of Chemistry and Biochemistry Nuclear Magnetic Resonance Facility COVID-19 Operational Safety Plan

Adhere to the following protocol when using the NMR equipment:

    • Do not enter the lab if you have tested positive for COVID-19 or show any of the symptoms.
    • Face mask are required inside public spaces by UWM policy, City of Milwaukee ordinance and State of Wisconsin Emergency order.
    • Reservation required.  You need to reserve time and come only down to the lab when it is your time. Wait in B-10 if the previous person is not finished
    • Wash your hands before entering.  Bathrooms are just across the stairway/elevator doors.
    • Keep your distance: Only one user at a time on each instrument.
    • One additional person can watch by logging into the computer in the opposite wall and use Remote Desktop to supervise/observe the spectrometer computer
    • Wash your hands before entering
    • If users are waiting in B-10, leave through the back door (one-way traffic)
    • Wash your hand before returning to your lab

Additional precautionary measures

    • Use disposable gloves (available next to door inside of B-10) OR
    • Use the hand sanitizer provided before touching keyboards/ sample holders
    • Use the 70% ethanol in the plastic squeeze bottle and Kimwipes to sanitize Keyboards/mouse, sample holder, sample gauge, and the part of the Sample Case carousel you are using.
    • Refill of 70% ethanol is in glass bottles on the counter next to the sink.
    • Table surfaces can be wiped with Chlorox wipes.