Two dimensional NMR data processing

Recently, MD simulation has been applied as a tool in the refinement of three-dimensional biomolecular structures from X-ray diffraction and two-dimensional NMR data. In the refinement process, MD trajectories are run at elevated temperatures (perhaps several thousand degrees Kelvin) to enhance conformational sampling. The molecular systems are cooled periodically to permit the trajectories to settle into local minimum energy conformations. Constraint terms based on X-ray structure factors or NMR NOE distances are added to the standard potential energy functions, so that the MD trajectories relax to conformations that satisfy the experimental data as the systems are cooled. Thus, the complete potential function in a refinement simulation has the form... 

Another technique that supplements the results of X-ray diffraction has come into wide use in recent years. It is a form of nuclear magnetic resonance (NMR) spectroscopy. In this particular application of NMR, called 2-D (two dimensional) NMR, lai e collections of data points are subjected to computer analysis (Figure 4.14b). Like X-ray diffraction, this method uses a Fourier series to analyze results. It is similar to X-ray diffraction in other ways It is a long process, and it requires considerable amounts of computing power and milligram quantities of protein. One way in which 2-D NMR differs from X-ray diffraction... 

Friebolin H (1998) Basic One- and Two-Dimensional NMR Spectroscopy, 3rd edn. Weinheim Wiley-VCH. Lindon JC and Ferrige AG (1980) Digitisation and data processing in Fourier transform NMR. Progress in NMR Spectroscopy 14 27-66. 

Computers play a central part in modern NMR spectroscopy. Their use for the real-time control of pulsed NMR experiments has enabled the development of multiple pulse techniques such as two-dimensional NMR this article deals with the part played by computers in the acquisition, processing and presentation of experimental NMR data. 

See also Diffusion Studied Using NMR Spectroscopy Fourier Transformation and Sampling Theory Magnetic Field Gradients in High Resolution NMR MRI Theory NMR Data Processing NMR Principles NMR Pulse Sequences NMR Relaxation Rates Solid State NMR, Methods Solvent Suppression Methods in NMR Spectroscopy Two-Dimensional NMR, Methods. 

Jeener first described a two-dimensional NMR experiment in 1971, but it was not until 1975 that the first two-dimensional spectra were published by Ernst (1975). The pioneering efforts of Ernst and co-woricers in developing the technique should be appreciated by those who glean information from two-dimensional experiments. The NMR community also owes a debt of gratitude to the laboratory of Ray Freeman. His contributions and those of his associates to two-dimensional NMR have expanded the technique and promoted its growth. The NMR spectrometer manufacturers have also been instrumental in the development and application of two-dimensional NMR. By 1980 all of the commercially available Fourier-transform spectrometer systems provided two-dimensional data processing as part of then-standard software package. 

Computer control of NMR instruments has led to great advances in both data acquisition and processing and has given rise to advanced NMR structural elucidation techniques. One of the the first of these was two-dimensional... 

LC-NMR can be operated in two different modes on-flow and stopped-flow. In the onflow mode, LC-NMR spectra are acquired continuously during the separation. The data are processed as a two-dimensional (2D) NMR experiment. The main drawback is the inherent low sensitivity. The detection limit with a 60 p.1 cell in a 500 MHz instrument for a compound with a molecular weight around 400 amu is 20 pig. Thus, on-flow LC-NMR runs are mainly restricted to the direct measurement of the main constituents of a crude extract and this is often under overloaded HPLC conditions. Typically, 1 to 5 mg of crude plant extract will have to be injected on-column.In the stopped-flow mode, the flow of solvent after HPLC separation is stopped for a certain length of time when the required peak reaches the NMR flow cell. This makes it possible to acquire a large number of transients for a given LC peak and improves the detection limit. In this mode, various 2D correlation experiments (COSY, NOESY, HSQC, HMBC) are possible. 

Prior to Fourier transformation the time domain data may be modified by multiplication by a function q(t), a process commonly called digital filtering. By suitable choice of q(t), digital filtering may be used in NMR spectroscopy to enhance sensitivity, to improve spectral resolution, or to avoid truncation effects. Conceptually, there is very little difference between filtering of ID and 2D NMR spectra, so the treatment here may later be extended readily to the two-dimensional case. 

NMR samples contained 0.6 ml receptor (0.5-2.0 mM) dissolved in refolding buffer (vide supra) with 10% DjO. One-dimensional F NMR spectra were obtained at 470 mHz on a General Electric GN 500 spectrometer fitted with a 5 mm F probe. Parameters included 16K data points, 3.0 second relaxation delay and 25 Hz linebroadening for processing spectra. T, relaxation times were measured by the inversion recovery method. The two-dimensional F NOESY NMR spectrum was obtained on a Varian Unity Plus 500 using the standard Varian pulse sequence. A total of 128 experiments with a mixing time of 0.3 seconds were performed with collection of 1024 data points. Quadrature detection in the second dimension was obtained through the method of States and Haberkom. C ( H NMR spectra were obtained on a Varian 500 Unity Plus fitted with a 10 mm broadband probe. 

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