Line Fitting Primer
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No previous exposure to iNMR is required to follow this tutorial.The pictures you will see have been generated with version 2.4.2.With older incarnations of iNMR you can get the same results, but through a differentsequence of commands.
Our purpose is to measure the integrals of two multiplets on top of a hump (thewater signal). It can be argued that what we are doing is not necessary, becausethe eye of a spectroscopist can reach the sameresult in a fraction of second. This is a primer and the example had to be simple.The fact that visual inspection leads to the same results should increase your confidenceinto the method, therefore this is an ideal spectrum for a primer.Once you have mastered the tools described here, you'llbe able to solve more difficult cases.
The article includes step-by-step instructions,comments and further hints. It is easy-to-follow just because it's so long.The tutorial itself can be repeated in one or two minutes.It takes more to say it that to make it.
The pictures are conveniently small for a web site. When working at your computer,you are warmly invited to zoom all the windows up to their maximum allowed size.You can also close the iNMR palette, because we aren't going to use it, this time.iNMR is pleasure: the larger the windows, the bigger the pleasure.
Download this archive on your hard disc and decompress itwith a double click. It contains a Bruker spectrum (a folder) whose origin doesn't matter.It's a proton spectrum acquired in DMSO-d6. It's our raw material.
Open the Spectrum
Open iNMR and, through it, open any of the files of the decompressed folder.The spectrum has already been processed. A simple, first-order, baseline correctionhas been applied.The water signal is centered at 4.09 ppm.It is closely surrounded by the two multiplets we are going to integrate.All the integral regions are already defined and the integral values normalized.It's important to normalize the integrals before starting the line-fitting module, becausethe latter will automatically inherit the same normalization factorand the final results will be expressed in the sameunits. We'll be able to compare the results of best-fitting directly with theother integrals of the spectrum.When the integrals arenot normalized, the values are instead expressed as percentage of the total area.
Select the Region to Fit
Select the gray region shown below. To select a region click and drag the mouse.
OPTIONAL: If you want to reproduce the same identical results of this article, there isa more complicated alternative to click-and-dragging:
- Open the console with the combination Cmd-zero and type:
region( 3.6497, 4.5274 )- Press ; press ; close the console.
Look how two tiny spikes on the tails of the water signalare left outside the selection.While it is advantageous, in general, to fit as many experimental points as possible, there is nonecessity to sample the whole line-shape. Our model spectrum will only contain peaks ofregular shape. It's impossible to formulate a model that explains the spikes, thereforeit's better to avoid them. We are still forced to sample the biggestspike at 4.24 ppm, unfortunately! When the selection is gray, issue the menu command'Simulate/Deconvolution'. A new window appears, containing the capturedregion.
Improve the Automatic Guess
The program suggests an initial number of peaks. This initial guess is terribly cursory,with a reason. iNMR tries, at the first attempt, to include not only the peaks, but also theshoulders into the model. Unfortunately, with such a noisy spectrum and such a broad peak, almost every point corresponds toa shoulder and iNMR gets fooled.We have the option, however, to generate the initial model froma smoothed version of the spectrum. Click the icon 'smooth'. Click it again. Clickit a third time. Something happens each time. At the end your window will be exactlyas shown here:
Simulate the Water Signal
The number of peaks is now nearer to reality, but manually adjustment is still necessary. The upper part of the modulecontains a table. Select the row that begins with a '6' (click on the digit '6').The correspondingpeak will become red. Four little square handles mark the peak and let you move or resize it.Drag the bottom handle to the left, until it corresponds to the center of the water signal:
Drag down the top handle, until it coincides with the top of the water peak. Drag either of theside handles to enlarge the red peak. We can't make it as large as we need:the maximum allowed by iNMR is less than the experimental width.Don't worry: it's enough for an initial guess.
Simulate the Quartet
Click on the leftmost green peak (the wide one). It will become red:
Drag the bottom handle to the left, until the red peak corresponds to theleftmost component of the quartet.
Click the icon 'split'. This creates two peaks of half intensity.Initially they look as a single peak because they are equal and superimposed.Drag the bottom handle to the right, until the red peak corresponds to therightmost component of the quartet.
Run It!
Now we are ready for the calculations.Press the button 'Check All'. This tells the program thatall the parameters are to be recalculated (optimized for best-fitting).Click the 'same %' button.It's located at the opposite side, just below the table.You have told the program to fit the spectrum with pure Lorentzian line-shapes.This is the most common and simple strategy.Click the icon 'FIT' to run the optimization.
Check the Fit
You can see that we had overestimated all the individual heights(with the exception of the hump).To appreciate the goodnessof the fit, click the icon 'toggle'. It will show a different kind of plot.Instead of the individual peaks, their sum is shown (in green) and the differencefrom the experimental spectrum too (in red). The residual error is reported numerically, in red.
To make sure that the best fit has been reached, click again the icon 'FIT'.You can click it many times, because cycles are so fast. Even if the plot seemsthe same, some decimal digits change into the table. At the fourth additionalrun, no digits change anymore. It means that iNMR can't find anything better, givenour initial guess.
Save the Results
The Deconvolution window is not saved into the original document. How shall we save our work?Click the icon 'copy'. This copies the content of the table, as text,into the clipboard. You canpaste the text into TextEdit, for example, and preserve it as a file.From there, it can be reintroduced, with the icon'paste', into another deconvolution window, regenerating the table.
Examine the Results
On my computer, I get the following results:
The quartet (first 4 rows) has the total intensity of 1 hydrogen; the total intensity of the triplet(last 3 rows) is the double. Incidentally,the intensity pattern of the 'quartet' (?) is 1:4:4:1, not 1:3:3:1;Interpreting it would lead us outside the scope of this tutorial.
Can iNMR calculate the areas of the multiplets?Instead of summing the individual components, we can remove the water completelyand see what remains. It will be faster. Let's go!
Create an Artificial Blank
Delete, from the text above, all the lines but the water peak. It is easily recognized bythe large values of intensity and width.You can also correct the '8'in the header into a '1', if you like, to reflect the fact that there are less lines now,but it's not necessary (it takes more than a typo to make iNMR crash):
- Copy the edited text here above.
- Close the deconvolution module.
- Issue the command: 'Edit/Select All'.
- Issue the command: 'Simulate/Deconvolution'.
- Click the icon 'paste' into the new module.
- Click the icon 'export'. Choose a name for the new file. Create it.
- Close the deconvolution module.
- Open the new file.
We have created an artificial spectrum with the same spectral width of the example.There is a single lorentzian curve and it is equivalent to the water hump.The file format is identical to that of an experimental spectrum and we can applyall the operations that iNMR allows for frequency-domain spectra.
Remove the Water
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Return to the experimental spectrum (click that window). Issue the command:'Format/Overlay..'. Check the box at the top-left;it corresponds to the fake blank. Check the otherbox labeled 'Subtract'. Wow!
Dismiss the dialog, the job is done.
The Extra Trick
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You may wonder why the numerical values are so perfect. The trick was explainedinto a previous tutorial.
Viscosity 1 4 6 – graphical user interface for openvpn. The whole manual of the line-fittingmodule is shorter than this page.You can reach it by clicking the icon 'help'.
