University of Ottawa NMR Facility Web Site

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Friday, February 28, 2014

Dirty NMR Probes

In a previous post I emphasized the importance of cleaning the outside of your NMR tube before putting samples in the NMR magnet.  The "stuff" from your fingers (on the outside of your NMR tube) accumulates on the inside of the NMR probe coil inserts and can cause spinning problems, shimming problems and problems with inserting or ejecting samples.  Furthermore, the accumulation of "stuff" causes a significant background signal.  The figure below shows the top of an NMR probe before and after cleaning.


The probe was in use for several months before cleaning.  Notice the sticky black "stuff" present in the photo on the left.  Please take care in cleaning your NMR tubes before putting them in the spectrometer.

Monday, February 24, 2014

Deternining 90° and 180° Soft Pulses

Many modern NMR pulse sequences (e.g. the 1D gradient selective NOESY experiment) depend on shaped pulses for selective excitation or inversion of specific resonances.  Since the width of the excitation profile of a shaped pulse is determined by its duration, the pulse duration is chosen by the user for the selectivity needed.  The longer the pulse, the higher the degree of selectivity.   Some spectrometer software will calculate the pulse duration based on a selected region in a spectrum containing the desired resonance for excitation.  The calculation depends on an initial pulse calibration.  The standard calibration method for hard pulses involves incrementing the pulse duration at a fixed power level.  The 90° pulse is at the first maximum and the 180° pulse is at the first null.  Since the duration of a the selective pulse is fixed by the desired selectivity, the 90° and 180° pulses must be found by varying the pulse power rather than the pulse duration.  The figure below shows the calibration for three different 50 msec shaped pulses on a Bruker AVANCE spectrometer.


An on-resonance water signal was observed as a function of pulse power using a selective one-pulse sequence.  The scale is in units of decibels of attenuation.  Maximum power is at -6 dB so the scale goes from low power on the left to higher power on the right.  The 90° and 180° pulses are indicated with arrows.  The intensity profiles are not sinusoidal due to the logarithmic dB scale.  The 90° and 180° pulses are separated by 6 dB of attenuation as expected.

Friday, February 21, 2014

Measurement of 13C 90° Pulses in Solids via Cross Polarization

The direct measurement of 13C 90° pulses in solids under MAS conditions by the conventional method suffers from the very low inherent sensitivity of 13C and is very time consuming due to the typically long 13C T1's.  These problems can be at least partially overcome by using 1H - 13C cross polarization which has a potential four-fold sensitivity gain and also a time advantage as the repetition rate depends on the 1H T1 rather than the 13C T1, the former typically being less than the latter by a factor of ten.  The 90° pulses are measured by carrying out the usual cross polarization contact which leaves the 13C magnetization along the -y axis.  The contact is followed by a 13C -x phased pulse (φ-x) which rotates the magnetization towards the z axis in the -yz plane.  The acquisition follows with high power 1H decoupling.  The sequence is illustrated in the figure below.


When φ-x = 0°, one observes the usual positively phased CP spectrum.  As φ-x is increased the signal decreases until φ-x = 90° at which point the 13C magnetization is on the z axis and a null signal is observed.  As φ-x is increased further, +y magnetization is created and a negative signal is observed until φ-x = 180° at which point the magnetization is on the y axis and a maximum negative signal is observed, etc..... The 90° pulse can be read directly from the first null or 1/3 of the second null at 270°.  The vector diagrams and a typical measurement (where φ-x was increased from 0.5 µsec to 20 µsec in 0.5 µsec steps) are illustrated in the figure below.

Thursday, February 20, 2014

Getting (x,y) ASCII Data from TOPSPIN

TOPSPIN is able to export graphical data in a number of formats for import into word processing, presentation or graphics programs.  It is also able to export a spectrum into the ASCII JCAMP format for those programs able to import such data. Often, however, one would like to have simple ASCII data as (x,y) coordinates representing an NMR spectrum for use in other computer programs.  There are two ways to do this.  The simplest way is to process the raw data as usual, producing the real NMR spectrum in the "1r" file then run the au program "convbin2asc" by simply entering "convbin2asc" on the TOPSPIN command line.  An ASCII text file like the one shown below will be created in the same directory as the "1r" file with the name "ascii-spec.txt".


This file contains a one-line header followed by four columns of comma delimited text.  The first through fourth columns contain the point number, the intensity (y values), the frequency in Hz (x values) and the chemical shift in ppm (x values), respectively. These data are very easily imported into other programs.

As described in a previous post, another way to obtain a simple ASCII file is to process the raw data as usual and display the region of the spectrum for which you would like ASCII data.  Right-click within the spectrum window and select "Save Display Region To..." from the pop-up window.  Another window will open from which you should select "text file for use with other programs" and then click "OK".  A third window will open where you can input the name of the file you wish to create, the directory in which you would like to have it stored and whether or not you would like the imaginary data stored as well (usually only the real data are desired).  You must then click "OK".


A shorter way to accomplish this is to simply enter the command "totxt" in the TOPSPIN command line.  This will take you directly to the bottom window of the figure above.  After clicking "OK" a text file like the one shown below is created with the name you have chosen in the directory you have chosen.


The file contains a header with information including the number of data points, the chemical shift of the left-most point and the chemical shift of the right-most point.  The main body of the file consists of a single column of intensities (y values) which are easily imported into other programs.  The x values must be generated separately using the information in the header.


Tuesday, February 18, 2014

Educational NMR App for the iPad

Tim Burrow from the NMR Facility of the University of Toronto has released a free iPad app called "Learn NMR FID" highlighting the key concepts for processing NMR data.  The app presents the user with the FID and NMR spectrum of a two peak spectrum.  The controls of the app allow the user to interactively change the frequencies of and coupling between the resonances, the apodization function, phase, zero filling, noise, number of scans etc... while observing changes in the real and imaginary FIDs and Fourier transformed spectrum.

This is a great tool for new NMR users to investigate how changing parameters affects the time and frequency domain NMR data.  Tim has also released an iPad/iPhone app for power conversions for NMR pulses called "Attenuator".

This too is very useful.  Both apps are available at the Apple App Store.  Great job Tim!