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Effect of Sample Volume – a compelling example

We generally recommend at least 600 micro Litre of solvent volume to observe un-distorted lineshapes, for small molecule NMR, where mostly we use Organic solvents that tend to show narrow lines.  The lineshape of Organic solvent peak tend to closely resemble a Lorentzian curve due to its long T2.  This means that it is much more prone to distortions close to the baseline, if the higher order shims are not properly adjusted.  There is another condition that can exactly mirror this ‘poor higher order shim’ effect.

The NMR sample coil i.e. the inductance coil that picks up the NMR response after a pulse of RF is applied,  is about 25 mm long. 

The 1H nuclei that completely fill up a cylindrical volume of this height are the only ones that provide most of the observable NMR signal.  But, limiting the sample volume that reaches only this height leads to a problem. There is an abrupt transition from the liquid volume to the air (or gas such as N2) above this column of liquid.   The magnetic susceptibility of these two materials are vastly different such that the way they ‘bend’ or distort the magnetic field lines of the static B0 field are quite different.  The shim system, actually functions on the singular assumption that the sample is, ideally, an infinitely long tubular column of liquid.  In other words,  B0 field lines are distorted by a single medium and the distortions are smoothly continuous.  Such a variation is easy to model so that the shim system can apply gradients that are of opposite signs to the inherent distortion gradients and cancel them out.  The net effect is that all the protons within this volume pretty much feels the effect of only one value of B0 i.e. a highly homogeneous magnetic field.

But, an abrupt jump or a ‘kink’ in the way the distortions occur along the vertical axis, makes the above method of cancelling out the existing gradients pretty difficult.  The shim system and the software algorithm try their best.  It is similar to fitting a very noisy raw data with as good a fitting curve as possible.   Since the higher order shims are mostly responsible for optimizing the lineshape closer to the edge of the sample coil, they are the ones that get mis-set during shimming. This mis-set value of higher order shims such as Z5 and Z6, translate into an artificial assymetric lineshape. For Organic solvents that are fully deuterated, this is the predominant distortion that we have to deal with.

When you use samples that are dissolved in H2O or H2O+D2O, the rather large solvent peak at 4.7 ppm needs to be suppressed cleanly so that all the solute resonances are clearly identifiable. Generally the concentration of the H2O molecules are 3 to 4 orders or magnitude higher than that of Solutes. For this case of ‘solvent suppression’ also, the optimal shimming is very critical and an adequate amount of minimum volume becomes important.

The overlaid spectra of two cases shown below demonstrates this nicely. I recorded the red colored spectrum on our 800 MHz spectrometer with a cryoprobe. Even though the Topshim method minimized the B0 field variation to the minimum possible, the water suppression pulse sequence led to these spurious wiggle like structure that spans almost 0.7 ppm or 560 Hz. Arrow 1 points to the position of water resonance at 4.7 ppm. Positions 2 and 3 point to the peaks that are of main interest in the spectra and these are rather weak. Although the absolute intensity of water resonance (Peak 1) is effectively reduced, the wiggles that arise out of the water suppression method drowns out the peaks of importance. The volume of this sample was close to 500 micro L.

The remedy was to just add 100 microL of solvent i.e. water and the result now is dramatically improved. The green colored spectrum is the result. All the important peaks are clearly visible. I had used the same number of scans for both these spectra and the dynamic range of the green spectra is much better than the former.


Conclusion When you have limited availability of solute, choosing the correct volume of solvent to run NMR, such that you maximize the concentration and get ‘all’ the Nuclei give useful signal, is a balancing act.

HAPPY SPINNING !

TEST DRIVING THE REBORN DRX499 – ICONNMR INTERFACE – A FIRST LOOK

HAPPY NEW YEAR !  (ALMOST)

Welcome to the completely Refurbished and Newborn DRX499 !

The following pages should give a visual feel for how the new interface looks like, when you visit the system. 

But, do not worry ! Under the hood, it is the same old Topspin NMR software that is doing all the work for you.

It is actually more intuitive, user friendly and easy to operate, with a few mouse clicks and minimal amount of typing.

In fact,  the only typing you will need to do are just the following :

  • A new Data Set Name
  • Title, if you prefer

That’s it ! All the operations are under the flow of the software from here on, until the Spectrum is processed and displayed.

Ok, let’s dive in !

There are two monitors on the desk.  The LEFT one is the familiar TOPSPIN Display interface.  Using the RIGHT one, you interact with the spectrometer for almost ALL the tasks : 

 

A PICTORIAL FLOW CHART OF EVENTS FOLLOW FROM HERE ON.  I will provide captions and comments where it is useful :


Clicking on this, opens the following User Selection Dialog Box

You can either select your UWNetid by mouse click or type it in.


This palette appears. There are three mandatory steps before actual acquisition starts.

This is a branch point. You can inject new sample, continue with the one in the magnet, or quit the session to go back to the Welcome screen.

If you choose to inject new sample, this dialog appears.

This DATASET creation dialog appears automatically ! No need to click on the FileName button above.

You might want to change either the Exp number OR the Dataset Name. Either way, it will be treated as a fresh experiment. If you want to overwrite the existing Dataset, proceed with the same name and Exp no.

Clicking this opens Solvent/Experiment selection dialog:

Lock solvent and Parameter set are next.

                       

 

You can enter a Title for the Exp. no. if you wish :


You are ready to Start Acquisition NOW !

AFTER THIS, EVERYTHING IS AUTOMATIC.  YOU SIT BACK AND RELAX UNTIL THE FID IS COLLECTED AND PROCESSED FOR  YOU !    YOU CAN WATCH THE ACTION ON THE LEFT MONITOR THROUGH THE TOPSPIN WINDOW.  ICONNMR GIVES YOU THE FOLLOWING SCREEN ON RIGHT MONITOR TO SHOW YOU THE PROGRESS.


END OF RUN :  You can either eject the sample at this point and put a new one (OR) continue with the same to perform other experiments.  Either way, the interface prompts you for the next step:

 

YOU MUST DO THIS TO ALLOW NEXT USER TO LOGIN !
INSERT THE DECOY SAMPLE NOW, CLICK OK TO RETURN TO LOGIN SCREEN

 


ALL DONE !

Testing code display with formatting

#!/bin/bash
# ENV Variables
SCRIPTDIR=$HOME/Scripts/BASH
# check if topspin closed properly. If not, identify and kill the children of cpr first                                                     
if [[ -n $(ps -C cpr -o pid=) ]]; then
   flagcpr=$(ps -C cpr -o pid=)
   cprparent=$(ps --pid $flagcpr -o ppid=)                                                                              
 	if [[ -n $(ps --ppid $flagcpr -o pid=) ]]; then
	    tmpflg=$(ps --ppid $flagcpr -o pid=)
	    kill -s SIGHUP $tmpflg
	fi			
# Now kill the parent process i.e. cpr
   kill -s SIGHUP $flagcpr
# Demise of cpr stops at an interactive prompt;
# to move beyond and enable a clean session end, kill parent of cpr
   kill -s SIGHUP $cprparent
#
# Make sure the desktop session is ended
   kill -s SIGHUP $(ps -C icewm-session -o pid=)

	date >> $SCRIPTDIR/toplog
	echo 'topspin terminated' >> $SCRIPTDIR/toplog
	$SCRIPTDIR/banner "TRMinated" 
#	$SCRIPTDIR/banner "TRMinated" > /dev/null
else
    $SCRIPTDIR/banner "NO Topspin" 
   #$SCRIPTDIR/banner "NO Topspin"  > /dev/null
fi

Testing shortcodes

#!/bin/bash

[[ ! $(mount) =~ 'iso9660' ]] && mount -t iso9660 -o ro,loop /root/ISO/Topspin_1.3PL10.iso /root/tmpdrv

TSDISK=/root/tmpdrv

#check if diskless exists. If so, clean up

if [[ -d /usr/diskless ]]; then
	$TSDISK/install --auto --remove --select diskless  --no-os-check --display :0 
fi

umount /root/tmpdrv                             
          

UDRIVE and AV301 : AFTER you collect data – Structure of NMR data in your UDRIVE tree

»

Please see the blog post on how to setup access to your unique udrive space from your computer :https://sites.uw.edu/rajanp/2017/06/06/how-to-access-udrive/

In the default setup,  the dataset storage will closely resemble what you are  familiar with in Topspin Data Browser.   The following pictorial representation should clarify this.  I am using the data file tree for the user rajanp under instrument av301, as example.  I give the MS Windows example here :


Once you connect to  udrive in Windows file explorer, you see the following :

 

In your case, you will currently see only av301 branch in the udrive tree.

note : Any directories that you have created in udrive (not necessarily related to NMR) will also appear at this level of the tree.

Let us descend into the av301 branch and navigate further down and see :

 

You can now simply drag and drop the datasets to your local Topspin data directory and process it :

See the data appear after drag and drop :

You can now confirm that the transferred dataset is appearing in Topspin File Browser on your local machine :

 

 

 

 

 

 

 

 

Chemistry NMR : After UDRIVE – What changes in TOPSPIN graphical interface

Please consult my earlier blog post on how to actviate unique UDRIVE storage space in UW cloud :  https://sites.uw.edu/rajanp/2017/06/06/how-to-access-udrive/

There will be two phases as we transition to cloud storage of NMR data via UDRIVE :

Phase 1 : 

  • Inside TOPSPIN, your unique UDRIVE  directory tree will automatically appear
  • Only for the first time login, your existing datasets from the local hard drive will be automatically copied to your UDRIVE location (depending on the size of your tree, it might take a while ; please be patient.  PLEASE BLOCK AT LEAST 20 MINUTES OF TIME FOR THIS FIRST LOGIN)
  • You can collect NMR data as usual, when this file copy proceeds in the background
  • YOU MUST START WRITING YOUR DATA IN THE UDRIVE once PHASE 1 IS ANNOUNCED.
  • During this phase, the exhaustive file tree with all userids, will still be available for you to see

Phase 2 :

  • Down the road, once all user data  from local drive are moved over successfully to the UDRIVE Cloud storage, the file tree on local hard drive will no longer appear within Topspin.
  • For software legacy reasons, you will still see a stump of a tree in the form of /opt/topspin.  But this will be empty.

Let us clarify the above in pictures

PHASE 1

The base data tree :


Appearance of your UDRIVE data branch.  Your NETID will appear under its main root. 


The old style file browser tree is still there :


PHASE 2

Use edc or new and create new datasets under your OWN UDRIVE tree (ALL OLD DATA THAT WERE COPIED ALSO APPEAR AUTOMATICALLY) :


ONCE PHASE 2 IS ANNOUNCED,  THE LEGACY DATA TREE /opt/topspin WILL NO LONGER SHOW ANY UWNetid-s :

FTP DATA ACCESS 

After Phase 2,   we will still be providing FTP server link to AV301’s local data drive, for a few weeks.  But remember, this will be a STATIC data tree and contain only your old datasets.  In case you haven’t backed up Legacy Data, that will be a good time to get it over with.

 

 

 

Chemistry NMR : ACCESSING YOUR UDRIVE FOR NMR DATA – TIPS

We will start transitioning to the UW UDRIVE  Cloud Storage to directly store all NMR data that are acquired in our spectrometers, soon.  As a first step, we begin with AV301 instrument as a test case.  The following write up should give some pointers as to how you can access your UW UDRIVE.

udrive in UW


All students, faculty and staff have their UWNetid connected to a cloud storage solution called ‘udrive’. This storage is automatically activated for all accounts. 

AT THE SPECTROMETER (AV301) :

You will not notice anything different when you run your experiments in Topspin.  Instead of writing the data to a local disk, Topspin software will directly write the data to your own udrive storage

ACCESSING DATA FROM UDRIVE :

Here is a link to IT CONNECT page that explains all details of udrive access :  https://itconnect.uw.edu/wares/online-storage/u-drive-central-file-storage-for-users/

I provide below some useful highlights from this web page.

Microsoft WINDOWS USERS :

 

Mac OS X USERS :

LINUX USERS :