Challenges in numerical simulations of solid-state NMR experiments: Spin exchange pulse sequences

Solid State Nuclear Magnetic Resonance

Volumn 38, Issue 4, 2010, Pages 77-83

  Vosegaard, Thomas ^a  

^a AARHUS UNIVERSITY   (Denmark)

Author keywords

CHHC; Coupled Bloch equations; Exchange spectroscopy; Large spin systems; Proton mediated spin diffusion; Rate matrix model; SIMPSON; Simulations; Solid state NMR; Spin exchange

Indexed keywords

LIGHT POLARIZATION; NUMERICAL MODELS; SPIN DYNAMICS;

BLOCH EQUATION; CHHC; EXCHANGE SPECTROSCOPIES; LARGE SPIN SYSTEMS; MATRIX MODEL; SIMPSON; SIMULATIONS; SOLID STATE NMR; SPIN DIFFUSIONS; SPIN EXCHANGES;

NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY;

EID: 79954416289     PISSN: 09262040     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ssnmr.2011.01.002     Document Type: Review

References (83)

1. G.E. Pake J. Chem. Phys. 16 1948 327
2. R.V. Pound Phys. Rev. 79 1950 685
3. H.J. Jakobsen, J. Skibsted, H. Bildsøe, and N.C. Nielsen J. Magn. Reson. 85 1989 173
4. J. Skibsted, N.C. Nielsen, H. Bildsøe, and H.J. Jakobsen J. Magn. Reson. 95 1991 88
5. T. Vosegaard, J. Skibsted, H. Bildsøe, and H.J. Jakobsen J. Phys. Chem. 99 1995 10731
6. D. Massiot, F. Fayon, M. Capron, I. King, S. Le Calvé, B. Alonso, J.-O. Durand, B. Bujoli, Z. Gan, and G. Hoatson Magn. Reson. Chem. 40 2002 70
7. K. Eichele, R.E. Wasylishen. WSolids NMR Simulation Package.
8. J.P. Amoureux, C. Fernandez, L. Carpentier, and E. Cochon Phys. Status Solidi A 132 1992 461
9. J.P. Amoureux, C. Fernandez, and Y. Dumazy J. Chim. Phys. 2 1995 1939
10. M. Bak, J.T. Rasmussen, and N.C. Nielsen J. Magn. Reson. 147 2000 296 (This paper describes the SIMPSON simulation program, which was the first general-purpose solid-state NMR simulation program with possibility to simulate any pulse sequence for any spin system)
11. Z. Tosner, T. Vosegaard, C. Kehlet, N. Khaneja, S.J. Glaser, and N.C. Nielsen J. Magn. Reson. 197 2009 120 (A description of the newly developed integration of SIMPSON and optimal control theory for design of efficient pulse sequences)
12. M. Veshtort, and R.G. Griffin J. Magn. Reson. 178 2006 248 (This article presents the simulation software package SPINEVOLUTION, which is a highly optimized simulation program for solid-state NMR experiments)
13. J.S. Waugh Antiope. Available from: 〈http://www.ismar.org/software/ antiope〉.
14. S.A. Smith, T.O. Levante, B.H. Meier, and R.R. Ernst J. Magn. Reson. A 106 1994 75
15. P. Hodgkinson. pNMRsim: a general simulation program for large problems in solid-state NMR. Available from: 〈http://www.dur.ac.uk/paul.hodgkinson/ pNMRsim〉.
16. P. Hodgkinson, D. Sakellariou, and L. Emsley Chem. Phys. Lett. 326 2000 515
17. I. Kuprov, Spinach. Available from: 〈http://spindynamics.org/ Spinach.php〉.
18. I. Kuprov, N. Wagner-Rundell, and P.J. Hore J. Magn. Reson. 189 2007 241
19. I. Kuprov J. Magn. Reson. 195 2008 45
20. W.B. Blanton J. Magn. Reson. 162 2003 269
21. T. Vosegaard, and N.C. Nielsen J. Biomol. NMR 22 2002 225
22. M. Bak, R. Schultz, T. Vosegaard, and N.C. Nielsen J. Magn. Reson. 154 2002 28 (A description of the SIMMOL software package that allows easy specification of spin systems for biological molecules)
23. T. Vosegaard, A. Malmendal, and N.C. Nielsen Monatsh. Chem. 133 2002 1555 (Description of the flexibility of the SIMPSON Tcl scripting interface and the possibilities it opens in terms of the diversity of simulation problems addressed)
24. M. Bjerring, T. Vosegaard, A. Malmendal, and N.C. Nielsen Concepts Magn. Reson. 18A 2003 111
25. N. Nielsen, A. Malmendal, and T. Vosegaard Mol. Membr. Biol. 21 2004 129
26. A.C. Sivertsen, M. Bjerring, C.T. Kehlet, T. Vosegaard, N.C. Nielsen, and G.A. Webb Annu. Rep. NMR Spectrosc. 54 2004 243
27. N.C. Nielsen, T. Vosegaard, and A. Malmendal Analytical and numerical tools for experiment design in solid-state NMR spectrocopy G.A. Webb, Handbook of Modern Magnetic Resonance 2006 679
28. V. Ladizhansky Solid State Nucl. Magn. Reson. 36 2009 119
29. M.J. Bayro, M. Huber, R. Ramachandran, T.C. Davenport, B.H. Meier, M. Ernst, and R.G. Griffin J. Chem. Phys. 130 2009 114506
30. R. Tycko Phys. Rev. Lett. 99 2007 187601
31. L.A. Straasø, M. Bjerring, N. Khaneja, and N.C. Nielsen J. Chem. Phys. 130 2009 225103
32. N. Khaneja, and N.C. Nielsen J. Chem. Phys. 128 2008 015103
33. F.M. Marassi, J.J. Gesell, A.P. Valente, Y. Kim, M. Oblatt-Montal, M. Montal, and S.J. Opella J. Biomol. NMR 14 1999 141
34. F. Castellani, B. van Rossum, A. Diehl, M. Schubert, K. Rehbein, and H. Oschkinat Nature 420 2002 98
35. B. Reif, B.J. van Rossum, F. Castellani, K. Rehbein, A. Diehl, and H. Oschkinat J. Am. Chem. Soc. 125 2003 1488
36. R. Tycko, and Y. Ishii J. Am. Chem. Soc. 125 2003 6606
37. A.T. Petkova, G. Buntkowsky, F. Dyda, R.D. Leapman, W.M. Yau, and R. Tycko J. Mol. Biol. 335 2004 247
38. T. Vosegaard, and N.C. Nielsen Magn. Reson. Chem. 42 2004 285
39. H. Heise, W. Hoyer, S. Becker, O.C. Andronesi, D. Riedel, and M. Baldus Proc. Natl. Acad. Sci. 102 2005 15871
40. M. Tang, A.J. Waring, and M. Hong J. Am. Chem. Soc. 127 2005 13919
41. C. Wasmer, A. Lange, H. Van Melckebeke, A.B. Siemer, R. Riek, and B.H. Meier Science 319 2008 1523
42. A.A. Nevzorov J. Am. Chem. Soc. 130 2008 11282
43. W.T. Franks, B.J. Wylie, H.L. Schmidt, A.J. Nieuwkoop, R.M. Mayrhofer, G.J. Shah, D.T. Graesser, and C.M. Rienstra Proc. Natl. Acad. Sci. 105 2008 4621
44. J.T. Nielsen, M. Bjerring, M.D. Jeppesen, R.O. Pedersen, J.M. Pedersen, K.L. Hein, T. Vosegaard, T. Skrydstrup, D.E. Otzen, and N.C. Nielsen Angew. Chem. Int. Ed. 48 2009 2118
45. W. Li, and A. McDermott J. Biomol. NMR 45 2009 227
46. A. Lange, S. Luca, and M. Baldus J. Am. Chem. Soc. 124 2002 9704 (First description of the CHHC and NHHC experiments for distance measurements in proteins)
47. A. Lange, K. Seidel, L. Verdier, S. Luca, and M. Baldus J. Am. Chem. Soc. 125 2003 12640 (Investigates the transfer amplitude of CHHC experiments in terms of different spin-diffusion models)
48. I. de Boer, J.R. Matysik, M. Amakawa, S. Yagai, H. Tamiaki, A.R. Holzwarth, and H.J.M. de Groot J. Am. Chem. Soc. 125 2003 13374
49. K. Riedel, C. Herbst, S. Häfner, J. Leppert, O. Ohlenschläger, M.S. Swanson, M. Görlach, and R. Ramachandran Angew. Chem. Int. Ed. 45 2006 5620
50. A. Lange, K. Giller, S. Hornig, M.F. Martin-Eauclaire, O. Pongs, S. Becker, and M. Baldus Nature 440 2006 959 (This article presents the solid-state NMR structure of the potassium channel and the KTX in free and bound form)
51. A. Loquet, B. Bardiaux, C. Gardiennet, C. Blanchet, M. Baldus, M. Nilges, T. Malliavin, and A. Bockmann J. Am. Chem. Soc. 130 2008 3579
52. D. Suter, and R.R. Ernst Phys. Rev. B 25 1982 6038
53. D. Suter, and R.R. Ernst Phys. Rev. B 32 1985 5608
54. P.M. Henrichs, M. Linder, and J.M. Hewitt J. Chem. Phys. 85 1986 7077
55. A. Kubo, and C.A. McDowell J. Chem. Phys. 89 1988 63
56. A. Kubo, and C.A. McDowell J. Chem. Soc. Faraday Trans. 1 84 1988 3713
57. M. Wilhelm, H. Feng, U. Tracht, and H.W. Spiess J. Magn. Reson. 134 1998 255
58. F.M. Mulder, W. Heinen, M. van Duin, J. Lugtenburg, and H.J.M. de Groot J. Am. Chem. Soc. 120 1998 12891
59. 1H spin-exchange experiments to determine interatomic distances for structure refinement)
60. M. Aluas, C. Tripon, J.M. Griffin, X. Filip, V. Ladizhansky, R.G. Griffin, S.P. Brown, and C. Filip J. Magn. Reson. 199 2009 173
61. J.-N. Dumez, M.C. Butler, E. Salager, B. Elena-Herrmann, and L. Emsley Phys. Chem. Chem. Phys. 12 2010 9172 (This paper analyses the cross peak intensities in terms of ab initio simulations using a reduced Liouville space)
62. M.C. Butler, J.-N. Dumez, and L. Emsley Chem. Phys. Lett. 477 2009 377
63. R.R. Ernst, G. Bodenhausen, and A. Wokaun Principles of Nuclear Magnetic Resonance in One and Two Dimensions 1987 Calendron Press Oxford
64. J. Jeener, B.H. Meier, P. Bachmann, and R.R. Ernst J. Chem. Phys. 71 1979 4546
65. A.D. Bain Progr. Nucl. Magn. Reson. 43 2003 63
66. B.H. Meier, and R.R. Ernst J. Am. Chem. Soc. 101 1979 6441
67. 2H correlation experiment addressed in this article. It furthermore discusses the creation of Zeeman and quadrupolar order in the two phase sensitive variants)
68. M.R. Hansen, T. Vosegaard, H.J. Jakobsen, and J. Skibsted J. Phys. Chem. A 108 2004 586
69. M. Kamihira, T. Vosegaard, A.J. Mason, S.K. Straus, N.C. Nielsen, and A. Watts J. Struct. Biol. 149 2005 7
70. K. Bertelsen, J.M. Pedersen, B.S. Rasmussen, T. Skrydstrup, N.C. Nielsen, and T. Vosegaard J. Am. Chem. Soc. 129 2007 14717
71. T. Vosegaard, M. Kamihira-Ishijima, A. Watts, and N.C. Nielsen Biophys. J. 94 2008 241
72. K. Bertelsen, B. Paaske, L. Thøgersen, E. Tajkhorshid, B. Schiøtt, T. Skrydstrup, N.C. Nielsen, and T. Vosegaard J. Am. Chem. Soc. 131 2009 18335
73. J.J. Lopez, A.J. Mason, C. Kaiser, and C. Glaubitz J. Biomol. NMR 37 2007 97
74. T. Vosegaard, K. Bertelsen, J.M. Pedersen, L. Thøgersen, B. Schiøtt, E. Tajkhorshid, T. Skrydstrup, and N.C. Nielsen J. Am. Chem. Soc. 130 2008 5028
75. L. Thøgersen, B. Schiøtt, T. Vosegaard, N.C. Nielsen, and E. Tajkhorshid Biophys. J. 95 2008 4337
76. K. Bertelsen, J.M. Pedersen, N.C. Nielsen, and T. Vosegaard J. Magn. Reson. 184 2007 273
77. T. Vosegaard, and D. Massiot Chem. Phys. Lett. 437 2007 120
78. J.C. Hoch, and A.S. Stern NMR Data Processing 1996 John Wiley & Sons Hoboken, New Jersey
79. D. Rovnyak, D.P. Frueh, M. Sastry, Z.Y. Sun, A.S. Stern, J.C. Hoch, and G. Wagner J. Magn. Reson. 170 2004 15
80. S. Hyberts, D. Frueh, H. Arthanari, and G. Wagner J. Biomol. NMR 45 2009 283
81. S.G. Hyberts, K. Takeuchi, and G. Wagner J. Am. Chem. Soc. 132 2010 2145
82. Y. Matsuki, M.T. Eddy, and J. Herzfeld J. Am. Chem. Soc. 131 2009 4648
83. J.P. Bradley, C. Tripon, C. Filip, and S.P. Brown Phys. Chem. Chem. Phys. 11 2009 6941