Process and fit NMR data to obtain translational self-diffusion constants

Data collection:

1. d8 - diffusion delay (usually 80 ms)
2. p15 - gradient pulse length (usually 5 ms)
3. gradient strength increment - the diff2_h2o.bv sequence is hardcoded to collect a series of 1D spectra with the strength of the p15 gradient pulses increasing from 5% in 1% increments to a total of ~80%, depending on td1.

Processing in nmrPipe

1. Convert data using the bruker utility to generate a script. It should look something like this fid.com file.
2. Process the time-domain data with nmrPipe using the diffusion.pip script (available on Volkman lab linux workstations in ~volkman/nmrpipe). Only the phasing parameters should require adjustment.
3. Execution of the processing script should also start the dsView interface for nonlinear fitting of the diffusion data.

Fitting diffusion curves with dsView and dsFit

1. The program for fitting diffusion data can be invoked manually by typing dsView.tcl. The default input filename is test.ft1. The DOSY Viewer 2D window should display a contour plot of the processed data, where the horizontal axis is 1H chemical shift and the vertical axis corresponds to increasing gradient strength.
2. Left-click and drag the vertical cursor in the 2D window to select an appropriate column for fitting. A plot of column intensity vs gradient strength is shown in the DOSY Viewer 1D window.
3. Click the export button to perform an automated nonlinear fit to the curve using the standard parameters (delay=80 ms; pulse=5 ms; 5-80% gradient strength in 1% increments). Results of the iterative fitting process and Monte Carlo simulations are displayed in one window:
   and a second window plots the experimental data and simulated values obained from the optimal fit, along with a value for Ds, the self-diffusion constant. If desired, the fitted data may be saved to a text file for plotting or further analysis in another program.
   NOTE: if non-standard parameters were used in the acquisition, copy the dsFit1D.tcl program to your own directory and modify the values contained at the top of the script (type echo $TCLPATH to find out where this file is located on your computer).
4. Record the fitted values for Ds from a series of columns in different regions of the spectrum to gauge the precision of the resulting values. Ideally, the experiment should be recorded multiple times so that experimental uncertainties can be derived from the standard deviation of Ds values from separate datasets.