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David Fushman Department of Chemistry & Biochemistry University of Maryland, College Park PowerPoint Presentation
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David Fushman Department of Chemistry & Biochemistry University of Maryland, College Park

David Fushman Department of Chemistry & Biochemistry University of Maryland, College Park

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David Fushman Department of Chemistry & Biochemistry University of Maryland, College Park

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  1. Virtual NMR Spectrometera software package for accurate andefficient calculation of the outcome of NMR experiments and a computer tool for learning NMR David Fushman Department of Chemistry & Biochemistry University of Maryland, College Park

  2. 90o 90o t1 d1 Why do we need computer simulations in NMR? 3D CT-HN(CA)CB, Shan et al., 1996, JACS 118, 6570

  3. Why do we need computer simulations in NMR?  Modern multidimensional NMR experiments involve pulse-field gradients, shaped RF pulses, off-resonance effects, complex decoupling schemes, and much more it has become practically impossible to accurately predict the outcome of these complicated pulse sequences under real conditions  We need to be able to optimize experimental conditions with minimal cost of NMR time (especially for 3D, 4D expts)  We need efficient tools for designing new pulse sequences (especially for multidimensional expts)  Learning NMR -- Difficulties in understanding theoretical aspects of NMR – Practical aspects: insufficient access to NMR instruments

  4. We have theoretical approaches that allow us to accurately predict the outcome of many NMR experiments under ideal conditions, but… Real experimental conditions can be far from ideal conditions Pulse imperfectionsOff-resonance effectsSpin relaxationExchange phenomena Water suppression etc

  5. Introducing VNMR – The Virtual NMR Spectrometer A NMR spectrometer that you can carry in your bag

  6. VNMR – The Virtual NMR SpectrometerFlowchart of the Virtual Spectrometer Experimental or user-designed pulse sequence TRANSLATOR SIMULATOR NMR ‘Experiment’: Preparation  Evolution  Data Acquisition DATA PROCESSING 1D or nD Spectra Experimental Conditions Spin System Setup Input Output Calculation

  7. VNMR: Treatment of spin evolution Spin Density Evolution: Spin Hamiltonian in the rotating frame: Spin Relaxation, Cross-relaxation, Chem.Exchange etc:

  8. VNMR – Basic Goals Accuracy and efficiency in simulation of various pulse sequences, including PFG and shaped RF pulses The ability to execute the actual pulse sequences from the spectrometer Ease of use (intuitive GUI, no programming skills, OS/platform independence) Flexibility in selecting various spin systems and experimental conditions Tools for data processing, analysis, and visualization

  9. VNMR 3.1 (pre-beta) – Highlight of Basic Features 1D, 2D, almost finished 3D Translator (Bruker  VNMR) allows “running” actual pulse sequences Simulation of various pulse sequences, including PFG and shaped RF pulses Data processing, analysis, and visualization of the results Shaped pulse generator Tracing/visualization of spin-density components Relaxation calculator Save/load capabilities Converters to basic NMR processing packages: XWINNMR, (nmrPIPE) Experimental noise

  10. Virtual NMR Spectrometera tool for in silico NMR

  11. 90o 90o acq t1 d1 30 b b’ 20 12 a A simple example – COSY 3-spin system: Jab = 20 Hz Jab’ = 12 Hz Jb’b = 30 Hz Ha = 4.2 ppm Hb = 2.8 ppm Hb’ = 3.3 ppm

  12. 90o 90o acq t1 d1 A simple example: Homonuclear COSY ns = 1 ns = 8 Suppression of the axial noise

  13. 90o 90o 90o acq d1 t1 Another example – DQF COSY 3-spin DQF COSY

  14. DQF COSY

  15. 90o 90o acq d1 t1 1H G NMR Experiments Involving Pulsed Field Gradients Next example: Gradient-selective COSY (cosygs) How to treat gradients accurately?

  16. z 3 L 2 Lmin Bo’= Bo+G.z 1 Z Magnetic field gradient along the z-axis Orientation of magnetization vectors Representation of NMR sample as a set of layers nz=0 Lmin/2 -1 -2 -3 0 -Lmin/2 NMR Experiments Involving Pulsed Field Gradients Gradient treatment – ‘Salami’ model

  17. First PFG Initialization: Calculate Ba, Hevol, R Initialize spin density: s1= seq Set i = 1; GRAD=off Gradient treatment flowchart Calculate Hi, si+1 Increment i N GRAD=on ? Y CTP Salami Split si into NL layers For each layer nz Calculate Hi(nz), si+1(nz) Store si+1(nz) Increment i Calculate Hi ,si+1 Calculate T, then wi, ki Increment i End of pulse sequence? End of pulse sequence? N N Y Y Integrate s Average s Acquisition Increment ns and phases N ns > NS ? Y Stop

  18. 90o 90o acq d1 t1 1H G Gradient selection of P- or N- type coherences or both

  19. 90o 180o acq d1 1H t1/2 t1/2 15N dec Another example -- decoupled 1H-15N HSQC

  20.   DD +CSA   DD - CSA  Closer to reality – differential line broadening

  21. Relaxation calculator In order to reconstruct the actual experimental conditions, we need to be able to use spin-relaxation parameters as close as possible to the reality

  22. 90o 180o acq d1 1H t1/2 t1/2 15N dec Coupled 1H-15N HSQC

  23. 90o 90o 180o 180o acq acq d1 d1 1H 1H t1/2 t1/2 t1/2 t1/2 15N 15N dec dec 1H-15N HSQC coupled/decoupled Now with differential line widths

  24. Projections displayallows tracking of user-selected components of the spin density in the course of NMR experiment, for testing and educational purposes HSQC example

  25. TROSYsimulation

  26.   DD +CSA   DD - CSA  Transverse-Relaxation Optimized SpectroscopY (TROSY) Using the interference between Dipolar interaction and CSA

  27. Virtual Spectrometer Web Site:www.vsnmr.org Coming soon: Beta-testing version Demo versions for students

  28. VNMR as NMR learning tool Easiness of use and broad accessibility: It does not require programming skills Even more so -- you don’t need a spectrometer!!! Intuitive User Interface Compatibility with Bruker programming language Future plans: Web access Demo versions Set of basic NMR experiments

  29. Acknowledgements David Cowburn (Rockefeller U.) Vlad Ruchinsky (Yale U.) Peter Nicholas (UNC Medical School) Konstantin Berlin (U.Maryland) Grant Support: Camille & Henry Dreyfus Foundation National Science Foundation