Manipulating a simulated spectrum
After you define the spin system(s) to simulate and create their parameters into the specific dialog, you can manipulate the resulting spectrum in many ways. This page of the manual describes how. The first thing you note is that you have got a main window, containing the plot, and a drawer at its side, containing the list of adjustable parameters (another list, containing non-adjustable parameters too, can be accessed through the command “Simulate/Listing...”). At any moment, only one of the two windows has the keyboard focus. To move the focus, click into the desired window.
Here you will find a brief description for each parameter. Paragraphs beginning with [advanced] can be skipped at first reading.
The main window responds to all the usual iNMR commands and shortcuts. The difference is that now, under the spectrum you. will see displayed alphabetical labels. They indicate the current position of the chemical shifts. One way to modify a shift is simply to drag the corresponding label. In this case you also select the parameter, which remains highlighted both into the main window and into the drawer. When you select a coupling constant into the drawer, the two corresponding labels in the main window are highlighted. If you create two or three systems, the labels for each of them are colored differently.
Quite simply, the frequency of your virtual spectrometer. You can change the default value inside the application preferences.
When you select a parameter, like MHz above, for example, you can change its value by typing with the keyboard. Alternatively, to see the effect of changing the parameter slowly, you can also press the little arrows on top (a few parameters, however, can only be adjusted by the keyboard). The minimal increment/decrement is specified by the parameter “step”. Normally it's in the same unit of the selected parameters, with the notable exception of chemical shifts for which the step is measured in Hz, even if the shifts are measured in ppm.
In theory a peak curve goes from minus infinite to plus infinite. To draw faster, iNMR only draws the central region, whose width is given by the parameter “span” times the line width. Lorentzian lines have large tails. When span=50, the integral is only the 99% of the theoretical value. When span=150, the integral is the 99.9%. To approximate the 100%, it is required a value of span=200. This parameter is ignored in dynamic NMR, where a full treatment is always employed.
IF YOU WANT TO ENLARGE THE SPECTRAL WIDTH, SET span = 5000. defW also affects the spectral width.
[advanced] If your system has one nucleus only, two quantic states are possible and the single transition connecting them. When the nuclei are 2, the states are 4 which, like the corners of a square, can be connected by 4 sides and two diagonals. The number of transitions is not 6, however, because quantum mechanics predicts that 4 transitions are allowed (the sides) and 2 forbidden (the diagonals). The intensity of the former ones is 100%, and that of the latter ones 0. With more nuclei there are more transitions and more complications, because the intensity of allowed transitions is slightly less than 100 and the intensity of forbidden transitions is slightly more than zero. The less the difference in chemical shifts, the more intense the forbidden transitions. To ignore transitions whose intensity is less than x%, set the cutoff (“cut%”) equal to x. This parameter is ignored in dynamic NMR
[advanced] In the absence of this parameter, the total line shape fitting is almost useless. A simplified description of the fitting algorithm can be: each peak is moved by a minimal distance (= the digital resolution). Normally the fit improves so little that the algorithm gives up. In other cases, as soon as the first two peaks overlap (usually the wrong ones), the algorithm also stops. To go further you need a pulling force, given by this parameter. When iNMR begins to correlate peaks far apart, the fitting process continues and in many cases the global minimum is found.
If you want Lorentzian line shapes, set this parameter = 100. If you prefer Gaussian line shapes, set it = 0. For mixed line shapes, use any intermediate value. This parameter is ignored in dynamic NMR, where all lines are either Lorentzian or distorted Lorentzian, but never Gaussian.
This is the default linewidth AND also governs the digital resolution. In normal situations (never during fitting!) the digital resolution is 10 times less than the “defW” value. The digital resolution measures, along the frequency axis, the distance from a point to the next one.
pop, 1pop, 2pop...
Population of a system, in arbitrary units. Directly proportional to the intensity of the peaks, intended both as peak eight and integrated area. The index indicates the system.
A, B, C, D...
Chemical shifts, in ppm units.
W A, W B, W C, W D...
Full line widths, in Hz. They are optionally created by the user. The line width W is correlated to the transversal relaxation time T2 through the formula: T2 π W = 1.
JAB, JCD... DBA, DDC... JAa, JBa...
Coupling constants, in Hz. J = scalar coupling. D = dipolar coupling. The lowercase letter appears for long range couplings between different halves of a symmetric system.
k12, k13, k23...
Kinetic constants for chemical exchange. The unit is sec-1 (they are all first-order or pseudo-first constants). They are created (or cancelled) with the command “Simulate / Dynamic” and set to the initial value of zero. All the systems must have the same number of nuclei and the same labels (e.g: all AB2C systems). The reverse constants are implicitly defined through the populations at equilibrium:
Pop1 k1->2 = Pop2 k2->1 .
the button Refresh:
- Recalculates the spectrum from start, eliminating possible rounding errors that may have accumulated.
- Brings the document into its natural state, where the spectral width is elastic.
- Enlarges the spectral width in order to enclose all existing peaks.
- Includes the “View/Full” command.
the button Assimilate:
- Fixes the spectral width to the region currently displayed.
- Switches from the normal state, in which the spectral width is flexible, to the one in which it is fixed.
- If there is an overlay, copies from it such information like: spectrometer frequency, digital resolution, name of the nucleus under observation... and sets to 1 the relative amplification of the overlay.
- If there is also one of the “pop” parameters selected, the total areas of the spectrum and of the overlay are equalized.
- Includes the “View/Full” command.
Everything Written, Copiable & Printable
What you normally see is the graphic interface of iNMR. Hidden behind the command “Simulate/Listing...”, there are the lists of both the input parameters and the primary output, e. g. the positions and the intensities of the lines. This table is useful to save the parameters or to count the lines (just the first examples that come to mind). Before printing or saving, or even scrolling, you need to copy the text and paste it into another application. There is also a description of the resulting multiplets, one by one. To copy a single list there is the menu command “Edit/Select All”.
First Order Approximation
This is a global option that ignores all the second orders effects. When it's activated, iNMR skips a few lengthy calculations, but still allocates all the memory required by the rigorous treatment. As a result, calculations are a little bit faster. After you invert this option, it is also necessary that you click the "Refresh" button of all your documents.
When any of your systems contains more than 7-8 spins, you can use this approximation for setting up the simulation and adjust the chemical shifts; remove it before performing the final adjustments. It's better if all other applications are closed because iNMR does not optimize the memory usage.