Spin System Parameters

NMR-SIM is very powerful simulation tool based on a density matrix approach and is designed to make low demands on computer resources. The spin system parameters consist of a small basic set of spin parameters chemical shift, weak/strong scalar J coupling, dipolar coupling, quadrupolar coupling, longitudinal and transverse relaxation time. Currently the calculated coherence transfer processes are limited to polarization transfer and cross polarization. 

The most important spin system parameters can often be obtained directly from a NMR spectrum by simply measuring the signal positions, the line separation in multiplets and the line widths. It must be stressed that a molecular parameter measured directly from a NMR spectrum, particularly in second order spectra, is not necessarily the same as the spin system parameter. 

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Even in the absence of relaxation, Hartmann-Hahn transfer depends on a large number of parameters pulse sequence parameters (multiple-pulse sequence, irradiation frequency, average rf power, etc.) and spin system parameters (size of the spin system, chemical shifts, /-coupling constants). For most multiple-pulse sequences, these parameters may be destilled into effective coupling tensors, which completely determine the transfer of polarization and coherence in the spin system. This provides a general classification scheme for homo- and heteronuclear Hartmann-Hahn experiments and allows one to characterize the transfer properties of related... 

Transformation of ID and 2D raw data into corresponding spectra to analyse and understand experiments and to study influences of experimental or spin system parameters... 

A multitude of spin system parameters exist and all of them influence the response of a molecule to a particular experiment to a lesser or greater extent. Conversely the pulse sequence can induce processes on the spin system such that a response can be obtained which can be attributed to a spin system parameter that is not directly available. In this section a short overview of spin system parameters is given including the parameters available for use with NMR-SIM and the spin system processes which can currently be simulated using NMR-SIM. 

In the first section of this chapter spin systems and pulse sequences are discussed. Starting with the definition of a spin system and a description of the various spin parameters used by NMR-SIM. Using suitable examples the correct definition of spin system parameters, how to reduce the number of spin system parameters and the application of variable spin system parameters is illustrated. Following on, pulse sequences are discussed in some detail and the difference between a pulse sequence and a pulse program is emphasized. The pulse program language of NMR-SIM should be familiar to users of Bruker NMR spectrometers as it uses the same syntax. However, because this is not covered in the NMR-SIM manual, pulse sequence elements such as pulses, phases and delays are explained in detail and illustrated using a variety of examples. 

The labels used in the definition of the NMR-SIM spin system parameters depend to some extent upon personal preference. As with any programming language it is important to include comments comments not only makes the spin system file more readable, they also make it easier to keep track of any modifications to the file and help other users to understand the spin system definitions. Comment lines start with a semicolon ( ) and both the semicolon and the following text are ignored by the NMR-SIM processor. 

In conclusion it should now be possible for the reader to define their own spin systems depending upon the types of problems they want to simulate by NMR-SIM. If required, the spin systems defined in this section may be used as a starting point and modified accordingly. It is very important, particularly when simulating 2D experiments, that the number of spin system parameters, where possible, be reduced to the minimum consistent with the type of analysis that is being performed. 

The use of variable spin system parameters and the visualization of magnetization vectors using the Bloch simulator module require additional commands to be implemented in the NMR-SIM pulse programs that do not appear in the standard BRUKER pulse programs. The increment or decrement of a spin system parameter is triggered by a command line in the pulse program. The Bloch simulator module uses the increment of the virtual chemical shift to generate the offset dependence of a pulse. 

If variable spin system parameters are used the increment step HS1...32, the start value HV1...32 and the loop limit L0...L31 must be assigned. The range over which a variable parameter is varied depends upon the increment step size and the loop limit. If required by the pulse program these parameters will appear the Go Check Experiment Parameters dialog box. As discussed in previous sections, loop definitions are not only restricted to spin system variable incrementation. 

Using the File I Job... command select the job file Ihexp.job. Modify the spin system (Edit I Spin system) by replacing the existing spin system parameters with those listed on the left-hand side of this Check it. In the Options I NMR-SIM settings... dialog box select the option Output File to User defined. Start the job using the Go I Start Job command. Enter appropriate output file names and process the spectra at the end of the job execution in ID WIN-NMR and respectively 2D WIN-NMR. 

The Selective Population Transfer (SPT) experiment is usually used in spin system analysis with a FT spectrometer. Normally the experimental SPT spectra are compared with calculated SPT spectra simulated using different combinations of coupling constant signs. In common with many textbooks the AMX spin system 2,3-dibromopropionic acid will be used to introduce the concepts behind the SPT experiment. The IH spin system parameters for 2,3-dibromopropionic acid are shown below. The only difference between Spin System A and Spin System B is the sign of the coupling constant J(H(2), H(3)), the results of SPT experiments will be used to distinguish between the two possible spin systems. 

Whilst the changes between the PENDANT and PENDANT S pulse sequence are small, Check it 5.2.6.16 once again illustrates another advantage of NMR-SIM compared to experimental measurement, the comparison is based upon changes in a single spin system parameter which cannot be achieved experimentally. 

Because NMR-SIM uses simple text files for both the definition of spin system parameters and for writing pulse sequences, it offers a straightforward method for investigating and comparing filter elements. In addition, the results are presented in a graphical format in the form of NMR spectra, which are easier to interpret than the results obtained from a purely mathematical simulation. 

The practical goal of EPR is to measure a stationary or time-dependent EPR signal of the species under scrutiny and subsequently to detemiine magnetic interactions that govern the shape and dynamics of the EPR response of the spin system. The infomiation obtained from a thorough analysis of the EPR signal, however, may comprise not only the parameters enlisted in the previous chapter but also a wide range of other physical parameters, for example reaction rates or orientation order parameters. 

It should be realized that unlike the study of equilibrium thermodynamics for which a model is often mapped onto Ising system, elementary mechanism of atomic motion plays a deterministic role in the kinetic study. In an actual alloy system, diffusion of an atomic species is mainly driven by vacancy mechanism. The incorporation of the vacancy mechanism into PPM formalism, however, is not readily achieved, since the abundant freedom of microscopic path of atomic movement demands intractable number of variational parameters. The present study is, therefore, limited to a simple spin kinetics, known as Glauber dynamics [14] for which flipping events at fixed lattice points drive the phase transition. Hence, the present study for a spin system is regarded as a precursor to an alloy kinetics. The limitation of the model is critically examined and pointed out in the subsequent sections. 

It is also evident from the above that with some previous knowledge of the physical parameters of the spin systems we must rely on certain tests for quantitativeness. The distortion of the intensities of the spectral bands has been particularly noted in connection with aromatic carbons. Hays 55) has reached the following conclusions on the basis of the spectra of coal ... 

Low temperatures are required to slow down paramagnetic relaxation in order to get sharp EPR spectra. However, when a paramagnet can relax back to the ground state only slowly, then it is easy to saturate the system with microwaves, and this will lead to deformed spectra. In this chapter we consider the two key experimental parameters power (intensity of the microwaves) and temperature (of the sample) in combination with the key system parameter the spin. For a given system of spin S at a temperature T there is a single optimal value of P, which must be determined experimentally. The combined set of P, T, and S determines the complexity and the costs of EPR spectroscopy. 

The EPR spectrum is a reflection of the electronic structure of the paramagnet. The latter may be complicated (especially in low-symmetry biological systems), and the precise relation between the two may be very difficult to establish. As an intermediate level of interpretation, the concept of the spin Hamiltonian was developed, which will be dealt with later in Part 2 on theory. For the time being it suffices to know that in this approach the EPR spectrum is described by means of a small number of parameters, the spin-Hamiltonian parameters, such as g-values, A-values, and )-values. This approach has the advantage that spectral data can be easily tabulated, while a demanding interpretation of the parameters in terms of the electronic structure can be deferred to a later date, for example, by the time we have developed a sufficiently adequate theory to describe electronic structure. In the meantime we can use the spin-Hamiltonian parameters for less demanding, but not necessarily less relevant applications, for example, spin counting. We can also try to establish... 

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