Resonances and Spin systems

Resonances

In NMR, a resonance is generally understood as the phenomenon that is induced when a nuclear spin absorbs energy from RF radiation, and subsequently emits the energy. In Fourier Transform NMR the emitted radiation is detected as a Free Induction Decay, which after Fourier Transformation gives rise to local extrema at the resonance frequency in a frequency domain NMR spectrum. Thus, an NMR resonance is associated with a particular atom in the molecule of which the NMR spectrum is recorded.

Resonances in CcpNmr Analysis

In CcpNmr Analysis (Analysis), the concept of resonance is different, and it should be distinguished from the resonance phenomenon in NMR. A resonance in Analysis is a rather abstract object that is central to the data model, and is used in the process of assignment and connecting information between other objects within the data model (Figure 1).

Figure 1a. The resonance is central to the CCPN data model, and connects information of the different data types and packages.

Figure 1b. The resonance and its attributes. A resonance can be seen as composed of three attributes, an Identifier (ID) e.g. 23, an  Assignment, e.g. 17GluCα, and a chemical shift e.g. 121.23 ppm. The Identifier is a constant, unchangeable number, the Assignment is set by the user and the Chemical shift is derived from peaks that are assigned to the resonance.

A resonance can, but does not necessarily have to, be associated with a particular atom in the molecule(s) that you have defined in your molecular system, although in many cases it is convenient to think about resonances as associated with particular atoms. Resonances can also be grouped into spin systems (see spin systems).

Using resonances in assignment

The concept of a resonance becomes more clear when we look at how it is used in assignment. In many NMR analyses one may want to assign a peak directly to an atom in the molecules on which the NMR experiments have been performed. In practice however, a peak often cannot be directly assigned to a particular atom in a given dimension, because not enough information is available yet to make such a full assignment.

Now, in Analysis you can assign a peak dimension to a ‘resonance’, without knowing to which atom this resonance refers. If at a later stage enough information is available to make a specific atom assignment for a peak, the resonance is used to make this assignment by assigning it to an atom or atom type (Figure 2). Or in other words: a peak is first assigned to a resonance, and the resonance is then assigned to an atom, which connects the peak with a particular atom in the molecule (see also Core Concepts - Assignment).

Figure 2. The central role of a resonance in assignment. A peak dimension is first assigned to a resonance, and the resonance is then assigned to an atom type or atom, and can be grouped into a spin system (see also spin systems and assignments).

The power of using resonances becomes visible in a number of its properties and applications:

• • A series of peaks can be assigned to the same resonance, and changing the atom assignment of that resonance automatically affects all the peaks that are assigned to this resonance. This means that a change in assignment from one to another atom only needs to be done once, and all the associated peaks are automatically updated.

  • Resonances are used to connect spin systems (see spin systems), and making a single resonance to atom assignment automatically assigns all the peaks of connected spin systems to specific residues and their atoms.

  • Resonances can deal with different experimental conditions, such temperature, pH etcetera, and thus with different chemical shifts of an atom. A resonance allows the user to assign multiple chemical shifts to a single atom in the molecule in order to deal with various experimental circumstances.

  • Resonances can be merged. In most cases it is initially not known which peaks originate from which atoms, and peaks that originate from the same atoms may be assigned to different resonances. At the point where it becomes clear that different assigned resonances actually originate from the same atom, these resonances can be merged into one and all related peak assignments are instantly updated. 

Spin systems

In general, a spin system can be any group of nuclear spins that interact with one another in a magnetic field. These can be a group of J-coupled spins, but also of spins that interact through dipolar couplings or relaxation mechanisms.

In NMR of biopolymers, e.g. proteins, nucleic acids and carbohydrates, spin systems are generally considered as the group of nuclear spins from a single residue. This limited but practically very useful definition of spin systems is used in characterizing residue types of spin systems as well as making sequential assignments in for example proteins.

Spin systems in CcpNmr Analysis

A spin system in CcpNmr Analysis is in its basic form just a collection of resonances that are grouped together, and which has a number of other attributes (Figure 3). Typically the grouping involves resonances that belong to the same residue in the sequence. However, CcpNmr Analysis allows spin systems to contain more resonances than would be needed to describe a single residue, and resonances within a spin system can be added, deleted and merged to remove duplicates.

Figure 3. A spin system in Analysis can contain a list of resonances, and be assigned to a residue type or residue.

Just like resonances in CcpNmr Analysis can be assigned to atom types or atoms, spin systems can be assigned to residue types and to specific residues in a sequence. For example, to type Alanine or to Ala34. The residue type assignment is done based on the spin system’s resonances using the nucleus or atom types and chemical shifts of the resonances. Again like resonances, multiple spin systems that refer to the same residue in a sequence can be merged into one.

Figure 4. A peak and its resonance assignments can be used to link spin systems.

Spin systems can be sequentially linked through resonance assignments to peaks that contain sequential information (see Figure 4). These sequential links are very powerful at the stage where e.g. for a series sequentially connected spin systems an assignment can be made of one spin system to a specific residue in the sequence. In such case, the assignments of the sequentially linked spin systems all are updated instantly.