Defining a Spin System

The drawing of a molecular structure will show all the bond connectivities between neighbouring atoms and, if a stereochemistry representation is used, the configuration and the conformation of the molecule. The NMR experiment is based on the detection of spin systems and consequently the molecular structure can be defined in terms of spin systems using chemical shifts, coupling networks and, for stereochemical information, the relaxation times of the NMR active nuclei. 

In NMR-SIM, simulations are based on the definition of either a single spin system or two or more spin systems. The simultaneous simulation of several independent spin systems becomes relevant if molecules with two or more mutually isolated spin systems are investigated or if the spectrum of two or more compounds have to be described. In the latter case it is also necessary to include the concentration ratio for the correct correlation of intensities and integrals. Even for a chemically pure compound the definition of several spin systems is necessary to completely define the molecule if the structure contains NMR active isotope of low natural abundance e.g. NMR-SIM 

NMR-SIM uses the predefined command molecule and endmol to set up the individual spin systems or molecules within the spin system definition file. All statements relating to nuclei, interactions and initial spin states are defined in a block that begins with the command molecule and ends with the command endmol. All the statements that occur in this block only relate to that particular spin system. Each spin system defined in this way has to be named, the name appearing on the same line as the molecule command separated by a space. Finally the relative concentration of the individual spin systems is added, separated from the name by a space. 

Layout of the spin system definition on the left hand side is shown the general scheme and on the right hand side a typical NMR-SIM text file for comparison. 

The command molecule has the highest priority in the internal hierarchy of the spin system definition. Next comes the nucleus statement, each magnetically non-equivalent nucleus is defined, one nucleus per line followed by the coupling interaction between nuclei, one interaction per line. It is also possible to define a non-thermal equilibrium spin system state such as produced in multiple quantum coherence experiments. The required coherence may be selected using the spin state definition rather than by a pulse sequence, this not only simplifies the pulse sequence but also reduces calculation times. Fig. 4.3 illustrates the general layout of a spin system file. In the case of a single spin system, the molecule and endmol commands are redundant and may be omitted. 

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