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NMR Processing and Simulation
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  1. NMR Processing and Simulation

  2. Processing 1D spectra • Data processing involves application of a window function (e.g. Exponential Multiplication) followed by FT (Fourier transformation). • Resolution enhancement may be applied by setting the LB parameter to a negative value. For example, if the spectrum has peaks with a natural linewidth of 1 Hz., and the FID is gone 1/3 of the way into the acquisition time, then set LB to –.1 and GF to 0.33. Set the Window function to Lorentz to Gauss • TRAF function provides resolution enhancement. This function uses the LB parameter to calculate T2. For routine organic samples in CDCl3, a value of 0.04 to .06 Hz seems to work well. A larger value will provide more enhancement, but a poorer signal to noise ratio. • TRAFS function is a modification of the function which optimizes both the resolution and signal to noise ratio

  3. Simulation of complex spectra SpinWorks • Spin System  Edit Chemical Shifts… • a single nucleus would be entered as 1 and a methyl group would be 3. A symmetric pair (AA´) would be entered as 2*1 • symbolic label (like CH3, Para, ...) • species identifier • The spin of the nucleus. Spin ½ is default • chemical shift in Hz • Edit Scalar (J) Couplings... • Edit Dipolar (D) Couplings… SpinWorks uses the NUMARIT algorithm as described in: J. S. Martin and A. R. Quirt, J. Magn. Reson. 5, 318 (1971)

  4. Example ABX • Edit Chemical Shifts… • Group 1: 1 (number of spins), A (label), H (species), 1000 (chemical shift). • Group 2: 1 (number of spins), B (label), H (species), 1010 (chemical shift). • Group 3: 1 (number of spins), X (label), H (species), 3000 (chemical shift). • Spin values at ½. • Edit Scalar (J) Couplings… :–12 for J(A,B), 2 for J(A,X) and 10 for J(B,X)

  5. Example ABX • Simulation menu select Run NUMMRIT Simulation • In X region, coupling do not quite match input J (second order spectra can only be calculate) • In coupling menu, set J(AX) = 0, Simulate again : X is still a dd. Note combination lines that indicate second order spectra • In shift menu, set B = A (1000 Hz). Simulate: X looks like a triplet (with 2 other combination lines) • Set the shift of B to 1030 Hz. Simulate. • No more combination lines

  6. Simulate AA’XX’ • Read the ODCB spectrum (File: Open…) odcbs.001 • Read Spin System File…: odcb_ni • Edit Simulation Parameters… : Set the Display Linewidth (Hz) to 0.06 • Run NUMMRIT Simulation • left and right keyboard arrow keys will move a transition cursor across the simulated spectrum. To assign a transition, Right click on corresponding experimental peak • Edit Chemical Shifts… and Edit Scalar (J) Couplings… and check the iterate boxes for both chemical shifts and all four couplings; • NUMMRIT Simulation: experimental and calculate spectra must be similar • Spin System: Load Optimized Parameters

  7. Analysis of the Fluorobenzene Spectrum • File: Open…: \ UXNMR_XwinNMR\fluorobenzene\1 • Fourier transform (.1 Hz linebroadening) • Read in the spin system file fbenz.ss

  8. Dynamic NMR Simulation • SpinWorks can interface to two external programs for the simulation of exchanged broadened NMR spectra. • The first is DNMR3 program of G. Binch and D. Kleier • the second is the much newer MEXICO of Alex Bain

  9. DNMR3 • Can handle 5 individual spins, or more if you have equivalence • can handle both mutual(e.g. AB↔BA) exchange • And non-mutual (e.g. AB↔CD) type exchanges) • Up to three chemical configurations can be included. For example, AB↔CD↔EF • occasionally suffer from numerical instability

  10. Mexico • Handles very large spin systems • Handle both mutual and non-mutual exchange • Currently limited to two chemical configurations • faster and considerably more stable than DNMR3 • treatment of relaxation is more accurate than that in DNMR3

  11. DNMR simulation • Edit Simulation Options and DNMR Parameters… (Spin System menu) dialog is used to specify many of the dynamic NMR parameters