Simulation: an Introduction
Quantum mechanics can predict an NMR spectrum with accuracy. iNMR includes this treatment, limited to nuclei with spin 1/2, like hydrogen, phosphorus, etc... either in liquid phase or in liquid crystals solvents. The following situations can be handled, even simultaneously:
- chemical shifts, scalar and dipolar coupling;
- magnetic equivalence and symmetry;
- chemical exchange, including mutual exchange;
- Lorentzian, Gaussian and mixed line shapes;
- individual line widths for each nucleus, if required;
- multiple spin systems;
- X approximation (with nuclei of any spin number);
- manual or automatic fitting to an experimental spectrum;
- variable magnetic field (the same document simulates spectra at any magnetic field).
NOTE: The following situations are NOT handled:
- solid state;
- 2D spectra and other complex experiments;
- spectra of deuterium and other non 1/2 spins;
This vast matter has been unified under a simple, highly interactive and intuitive interface, tightly integrated with the rest of the program. You have a menu dedicated to this topic (Simulate). The first item (New Spectrum) creates a group of three windows:
- A standard iNMR window, enriched with chemical shift labels under the spectrum;
- A drawer at its side, containing the parameters specific to simulation;
- A dialog (sheet) where the user specifies the number and kind of systems, nuclei and parameters.
The dialog can be opened at any time (to create new parameters or delete old ones), but it's necessary to close it before interacting with the spectrum. The drawer contains the controls and the main window provides the visual feedback.
Other commands in the Simulate menu:
- open the dialog;
- introduce chemical exchange (dynamic NMR);
- fit an experimental spectrum that must already be visible as overlay.
The obvious usefulness of this section of iNMR is to derive the parameters (like chemical shifts and coupling constants) of an experimental spectrum through simulation and fitting. The mathematical part of the problem was explained in the literature during the 60s. iNMR has added many mechanisms for MANUAL fitting, which was obviously impossible before the advent of graphical user interfaces. Manual and automatic fitting complement each other quite well. The former is intuitive and, at the high fields in use today, often the faster one. The latter methods solve the most intricate problems, but must be learned and are not as automatic as their name says. The most ancient method, that only fits a selected number of lines, and only their frequency, requires the assignment of each experimental line to a line into a theoretical spectrum, used as starting point. The alternative approach fits the total line shape of the spectrum. It eliminates the need of assignments but suffers when the experimental spectrum is not perfect. Not only it's necessary to correct the phase and baseline with accuracy, but it's desirable to have an homogeneous magnetic field, no impurities and a decent signal/noise ratio. Both automatic methods require starting values for the parameters to be adjusted. This is where manual fit comes into play: it brings the simulated spectrum near to the perfect fit, which is eventually obtained using the automated methods. Manual fitting is so intuitive that it will not be described further. Read, however, the page on automatic fitting, because it contains essential information for manual operations as well.
Quantum mechanics and the theory of liquid NMR are not described into this manual. For simple applications, however, it is enough to understand the concepts of chemical shift and J-coupling. Fitting an experimental spectrum requires a specific experience that can be, however, acquired on the field, using common sense and spirit of observation, as always. The toughest topic is dynamic NMR, but mainly on the experimental side. Below are summarized all the pages of the manual on the subject.