Kinetics

kinetics1d follows the intensity of one or more regions of a spectrum against time. It is the general-purpose routine for a reaction, an exchange process, or anything else recorded as a series of 1D spectra: rather than fitting a particular model, it gives you the intensity trace for each region you mark, which you can then fit or plot yourself.

Running the analysis

kinetics1d needs the times, because there is no acquisition parameter that reliably holds them:

using NMRAnalysis

times = 0:120:7200                      # seconds, one per spectrum
results = kinetics1d("21", times)

The analysis window opens with one region on the tallest peak. Add a region for each signal you want to follow by pressing A, name it with R, and press Save.

<!– TODO screenshot (6): docs/src/assets/kinetics1d-window.png kinetics1d with three named regions over separate signals, their intensity traces plotted below in their own colours. There is no existing screenshot to replace. –>

Several runs

Where a series contains repeats, tag each spectrum with run and each run is treated as its own series and plotted in its own colour:

kinetics1d("21", times; run=[1, 1, 1, 2, 2, 2])

Fitting a model

By default nothing is fitted: the deliverable is the intensity against time. Pass a SeriesModel to fit one, for instance a single exponential decay:

kinetics1d("21", times; model=ExponentialModel())

Reading the traces

Save writes series.csv, which for a kinetics run is the whole result: one row per region per time point.

source,label,time (s),I,I_err,I_fit
21/pdata/1,reactant,0.0,9421.3,12.4,NA
21/pdata/1,reactant,60.0,7724.5,12.4,NA
21/pdata/1,product,0.0,0.0,12.4,NA
21/pdata/1,product,60.0,1702.1,12.4,NA

Each region also gets its own copy in regions/<name>.csv, beside its plot. Where a series has several runs, run appears as a further column, so runs need not share the same times. I_fit is NA because nothing was fitted.

The returned results carry the same traces:

results = kinetics1d("21", times)
results[1].x        # times
results[1].y        # integrated intensities, with uncertainties