After you define the spin system(s) 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 main things you note are the plot on the right and the list of adjustable parameters on the left. At any moment, only one of the two areas has the keyboard focus. To move the focus, click into the desired area.
The plot responds to all the usual iNMR commands and shortcuts. The difference is that now, under the spectrum, you 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 plot and into the list. When you select a coupling constant into the list, the two corresponding labels in the plot are highlighted. If you create two or three systems, the labels for each of them have a different color.
 |
 |
 |
|
|
Name |
Purpose |
||
|---|---|---|---|
 |
 |
 |
|
|
MHz |
The frequency of your virtual spectrometer. The starting value is copied from the application preferences. |
||
|
step |
When you select a parameter, like MHz above, for example, you can enter a new value with the keyboard. Alternatively, to see the effect of changing the parameter slowly, you can 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 parameter, with the notable exception of chemical shifts for which the step is measured in Hz, even if the shifts are measured in ppm. In the case of exchange rates, when their value is > 100 and the step parameter is < 100, the increment is not absolute but percentual. The fastest way to change a parameter is: when the cursor is over the numerical value you want to change, use the scroll wheel (no click needed). |
||
|
span |
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. |
||
|
cut% |
If your system has one nucleus only, two quantic states are possible and there is a single transition. 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 is 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. |
||
|
pull |
In the absence of this parameter, the total line shape fitting is almost useless. A simplified description of the fitting algorithm would be: each peak is moved by a minimal distance (= the digital resolution) until the difference between experiment and simulation is minimized. As soon as the first two peaks overlap (usually the wrong ones), the algorithm stops, because to move in either direction it must increase the difference between the two spectra. To go further you need a pulling force, given by this parameter. When iNMR begins to correlate peaks far apart, the fitting process doesn't stop at the first minimum and in many cases the global minimum is found. For a very special case see: Estimating the Concentrations into a Mixture. |
||
|
%Lor |
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. |
||
|
defW |
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 between adjacent points. |
||
|
pop, 1pop, 2pop... |
Population of a system, in arbitrary units. Directly proportional to the intensity of the peaks. 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 optional. 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 across the two 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 removed) by the command Simulate > Dynamic with an 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: |
||
|
refresh |
|
||
|
fix |
|
||
|
round button (Mac) |
It's a main switch for the check boxes below; a shortcut to check and uncheck them all with a single click. |
||
|
First Order Approximation |
This is a global option that ignores all the second orders effects.
You can find it under the menu Simulate.
When it's on, iNMR skips a few lengthy calculations,
but still allocates all the memory required by the rigorous treatment.
As a result, calculations can be significantly faster.
After you invert this option, it is also necessary that you click the Refresh button of all your documents. |
||
|
|
|
|