The Flexibility of SIMPSON and SIMMOL for Numerical Simulations in Solid- and Liquid-State NMR Spectroscopy
Summary
Addressing the need for numerical simulations in the design and interpretation of advanced solid- and liquid-state NMR experiments, we present a number of novel features for numerical simulations based on the SIMPSON and SIMMOL open source software packages. Major attention is devoted to the flexibility of these Tcl-interfaced programs for numerical simulation of NMR experiments being complicated by demands for efficient powder averaging, large spin systems, and multiple-pulse rf irradiation. These features are exemplified by fast simulation of second-order quadrupolar powder patterns using crystallite interpolation, analysis of rotary resonance triple-quantum excitation for quadrupolar nuclei, iterative fitting of MQ-MAS spectra by combination of SIMPSON and MINUIT, simulation of multiple-dimensional PISEMA-type correlation experiments for macroscopically oriented membrane proteins, simulation of Hartman-Hahn polarization transfers in liquid-state NMR, and visualization of the spin evolution under complex composite broad-band excitation pulses.
Keywords
Solid-state NMR Numerical simulations Software Membrane proteins Inorganic materials.Preview
Unable to display preview. Download preview PDF.
References
- [1]Ernst RR, Bodenhausen G, Wokaun A (1987) Principles of Nuclear Magnetic Resonanced in One and Two Dimensions. Calendron Press, OxfordGoogle Scholar
- [2]Wütrich K (1986) NMR of Proteins and Nucleic Acids. Wiley, NYGoogle Scholar
- [3]Cavanagh J, Fairbrother WJ, Parmer III AG, Skelton NJ (1996) Protein NMR Spectroscopy. Principles and Practice. Academic Press, San DiegoGoogle Scholar
- [4]Haeberlen U, Waugh JS (1968) Phys Rev 175: 453CrossRefGoogle Scholar
- [5]Hohwy M, Nielsen NC (1998) J Chem Phys 108: 3780CrossRefGoogle Scholar
- [6]Untidt TS, Nielsen NC (2002) Phys Rev E 65: 021108-1Google Scholar
- [7]Sorensen OW, Eich GW, Levitt MH, Bodenhausen G, Ernst RR (1983) Progr Nucl Magn Reson Spectrosc 16: 163CrossRefGoogle Scholar
- [8]Wokaun A, Ernst RR (1977) J Chem Phys 67: 1752CrossRefGoogle Scholar
- [9]Vega S (1978) J Chem Phys 68: 5518CrossRefGoogle Scholar
- [10]Haeberlen U (1976) High-Resolution NMR in Solids. Selective Averaging. Academic Press, NYGoogle Scholar
- [11]Mehring M (1983) High-resolution NMR in solids. Springer, Berlin, Heidelberg, New York, TokyoGoogle Scholar
- [12]Spiess HW (1978) Rotations of Molecular and Nuclear Spin Relaxation, NMR Basic Principles and Progress. vol 15, Springer, BerlinGoogle Scholar
- [13]Gerstein BC, Dybowski CR (1985) Transient Techniques in NMR of Solids. An Introduction to Theory and Practice. Academic Press, OrlandoGoogle Scholar
- [14]Schmidt-Rohr K, Spiess HW (1996) Multidimensional Solid-State NMR and Polymers. Academic Press, LondonGoogle Scholar
- [15]Raleigh DP, Levitt MH, Griffin RG (1988) Chem Phys Lett 146: 71CrossRefGoogle Scholar
- [16]Gullion T, Schaefer J (1989) J Magn Reson 81: 196Google Scholar
- [17]Gregory DM, Mitchell DJ, Stringer JA, Kiihne S, Shiels JC, Callahan J, Mehta MA, Drobny GP (1995) Chem Phys Lett 246: 654CrossRefGoogle Scholar
- [18]Bennett AE, Ok JH, Griffin RG, Vega S (1992) J Chem Phys 96: 8624CrossRefGoogle Scholar
- [19]Nielsen NC, Bildsoe H, Jakobsen HJ, Levitt MH (1994) J Chem Phys 101: 1805CrossRefGoogle Scholar
- [20]Sommer W, Gottwald J, Demco DE, Spiess HW (1995) J Magn Reson A 113: 131CrossRefGoogle Scholar
- [21]Lee YK, Kurur ND, Helmle M, Johannessen OG, Nielsen NC, Levitt MH (1995) Chem Phys Lett 242: 304CrossRefGoogle Scholar
- [22]Bielecki A, Kolbert AC, Levitt MH (1989) Chem Phys Lett 155: 341CrossRefGoogle Scholar
- [23]Hohwy M, Nielsen NC (1997) J Chem Phys 106: 7571CrossRefGoogle Scholar
- [24]Larsen FH, Jakobsen HJ, Ellis PD, Nielsen NC (1998) Mol Phys 95: 1185CrossRefGoogle Scholar
- [25]Hohwy M, Jakobsen HJ, Edén M, Levitt MH, Nielsen NC (1998) J Chem Phys 108: 2686CrossRefGoogle Scholar
- [26]Verel R, Ernst M, Meier BH (2001) J Magn Reson 150: 81CrossRefGoogle Scholar
- [27]Vosegaard T, Florian P, Massiot D, Grandinetti PJ (2001) J Chem Phys 114: 4618CrossRefGoogle Scholar
- [28]Opella SJ (1997) Nature Struct Biol 4: 845Google Scholar
- [29]Griffin RG (1998) Nature Struct Biol 5: 508CrossRefGoogle Scholar
- [30]Bak M, Rasmussen JT, Nielsen NC (2000) J Magn Reson 147: 296. SIMPSON is open-source software freely available from the web site http://nmr.imsb.au.dk Google Scholar
- [31]Bak M, Schultz R, Vosegaard T, Nielsen NC (2002) J Magn Reson 154: 28. SIMMOL is open-source software freely available from the web site http://nmr.imsb.au.dk Google Scholar
- [32]Bak M, Schultz R, Nielsen NC (2001) In: Kiihne SR, de Groot HJM (eds) Perspectives on Solid State NMR in Biology. Kluwer Academic Publishers, Dordrecht, pp 95 - 109Google Scholar
- [33]Welch BB (1995) Practical Programming in Tcl and Tk. Prentice Hall, Englewood cliffs, NJ. The open source Tcl/Tk software can be downloaded via, eg, the Tcl Developers Xhange homepage, http://dev.scriptics.com Google Scholar
- [34]James F, Ross M (1975) Comput Phys Commun 10: 343. Manual available from the web site http://wwwinfo.cern.ch/asdoc/minuit/minmain.html Google Scholar
- [35]The SIMPSON and SIMMOL input files for all examples presented in this paper are available for download from the web site http://nmr.imsb.au.dk. SIMPSON and SIMMOL is open source software freely available from the the same web siteGoogle Scholar
- [36]Levitt MH (1989) J Magn Reson 82: 427Google Scholar
- [37]Skibsted J, Nielsen NC, Bilds¢e H, Jakobsen HJ (1991) J Magn Reson 95: 88Google Scholar
- [38]Charpentier T, Fermon C, Virlet J (1998) J Magn Reson 132: 181CrossRefGoogle Scholar
- [39]Levitt MH, Edén M (1998) Mol Phys 95: 879CrossRefGoogle Scholar
- [40]Hohwy M, Bildste H, Jakobsen HJ, Nielsen NC (1999) J Magn Reson 136: 6CrossRefGoogle Scholar
- [41]Zaremba SK (1966) Ann Mat Pura Appl 4-73: 293CrossRefGoogle Scholar
- [42]Conroy H (1967) J Chem Phys 47: 5307CrossRefGoogle Scholar
- [43]Cheng VB, Suzukawa Jr HH, Wolfsberg M (1973) J Chem Phys 59: 3992CrossRefGoogle Scholar
- [44]Wang D, Hanson GR (1995) J Magn Reson A 117: 1CrossRefGoogle Scholar
- [45]Alderman DW, Solum MS, Grant DM (1986) J Chem Phys 84: 3717CrossRefGoogle Scholar
- [46]Bak M, Nielsen NC (1997) J Magn Reson 125: 132CrossRefGoogle Scholar
- [47]Edén M, Levitt MH (1998) J Magn Reson 132: 220CrossRefGoogle Scholar
- [48]Kundla E, Samoson A, Lippmaa E (1981) Chem Phys Lett 83: 229CrossRefGoogle Scholar
- [49]Charpentier T, Fermon C, Virlet J (1998) J Chem Phys 109: 3116CrossRefGoogle Scholar
- [50]Vosegaard T, Skibsted J, Bilds0e H, Jakobsen HJ (1995) J Phys Chem 99: 10731Google Scholar
- [51]Vosegaard T, Skibsted J, Bildsoe H, Jakobsen HJ (1996) J Magn Reson A 122: 111CrossRefGoogle Scholar
- [52]Frydman L, Harwood JS (1995) J Am Chem Soc 117: 5367CrossRefGoogle Scholar
- [53]Medek A, Harwood JS, Frydman L (1995) J Am Chem Soc 117: 12779CrossRefGoogle Scholar
- [54]Marinelli L, Frydman L (1997) Chem Phys Lett 275: 188CrossRefGoogle Scholar
- [55]Marinelli L, Medek A, Frydman L (1998) J Magn Reson 132: 88Google Scholar
- [56]Ding S, McDowell CA (1998) J Magn Reson 135: 1998CrossRefGoogle Scholar
- [57]Wu G, Rovnyak D, Griffin RG (1996) J Am Chem Soc 118: 9326CrossRefGoogle Scholar
- [58]Madhu PK, Goldbourt A, Frydman L, Vega S (1999) Chem Phys Lett 307: 41CrossRefGoogle Scholar
- [59]Madhu PK, Goldbourt A, Frydman L, Vega S (2000) J Chem Phys 112: 2377CrossRefGoogle Scholar
- [60]Madhu PK, Levitt MH (2002) J Magn Reson 155: 150CrossRefGoogle Scholar
- [61]Kentgens APM, Verhagen R (1999) Chem Phys Lett 300: 435CrossRefGoogle Scholar
- [62]Vosegaard T, Larsen FH, Jakobsen HJ, Ellis PD, Nielsen NC (1997) J Am Chem Soc 119: 9055CrossRefGoogle Scholar
- [63]Larsen FH, Nielsen NC (1999) J Phys Chem A 103: 10825CrossRefGoogle Scholar
- [64]Massiot D (1996) J Magn Reson A 122: 240CrossRefGoogle Scholar
- [65]Amoureux JP, Pruski M, Lang DP, Fernandez C (1998) J Magn Reson 131: 170CrossRefGoogle Scholar
- [66]Goldbourt A, Madhu PK, Kababya S, Vega S (2000) Solid State Nucl Magn Reson 18: 1CrossRefGoogle Scholar
- [67]Vega S, Naor Y (1981) J Chem Phys 75: 75CrossRefGoogle Scholar
- [68]Nielsen NC, Bildsoe H, Jakobsen HJ (1992) Chem Phys Lett 191: 205CrossRefGoogle Scholar
- [69]Dirken PJ, Nachtegaal GH, Kentgens APM (1995) Solid State Nucl Magn Reson 5: 189CrossRefGoogle Scholar
- [70]Amoureux J-P, Fernandez C (1998) Solid State Nucl Magn Reson 10: 211CrossRefGoogle Scholar
- [71]Oas TG, Griffin RG, Levitt MH (1988) J Chem Phys 89: 692Google Scholar
- [72]Levitt MH, Oas TG, Griffin RG (1988) Isr J Chem 28: 271Google Scholar
- [73]Gan Z, Grandinetti P (2002) Chem Phys Lett 352: 252Google Scholar
- [74]Walls JD, Lim KH, Pines A (2002) J Chem Phys 116: 79CrossRefGoogle Scholar
- [75]Nielsen NC, Vosegaard T, Lipton AS, Ellis PD, unpublished resultsGoogle Scholar
- [76]Vosegaard T, Massiot D, Grandinetti PJ (2000) Chem Phys Lett 326: 454CrossRefGoogle Scholar
- [77]Kunath G, Losso P, Steuernagel S, Schneider H, Jäger C (1992) Solid-State Nucl Magn Reson 1: 261CrossRefGoogle Scholar
- [78]Opella SJ, Stewart PL, Valentine KG (1987) Quart Rev Biophys 19: 7CrossRefGoogle Scholar
- [79]Cross TA, Quine JR (2000) Concepts Magn Reson 12: 55CrossRefGoogle Scholar
- [80]Marassi FM, Opella SJ (2000) J Magn Reson 144: 150CrossRefGoogle Scholar
- [81]Wang J, Denny J, Tian C, Kim S, Mo Y, Kovacs F, Song Z, Nishimura K, Gan Z, Fu R, Quine JR, Cross TA (2000) J Magn Reson 144: 162CrossRefGoogle Scholar
- [82]Wu CH, Ramamoorthy A, Opella SJ (1994) J Magn Reson A 109: 270CrossRefGoogle Scholar
- [83]Marassi FM (2001) Biophys J 80: 994CrossRefGoogle Scholar
- [84]Vosegaard T, Nielsen NC (2002) J Biomol NMR 22: 225CrossRefGoogle Scholar
- [85]Berstein FC, Koetzle TF, Williams GJB, Meier Jr EF, Brice MD, Rodgers JR, Kennard O, Shimanouchi T, Tasumi M (1977) J Mol Biol 112: 535 Internet address: http://www.rcsb.org/pdb Google Scholar
- [86]Vriend G (1990) J Mol Graph 8: 52CrossRefGoogle Scholar
- [87]Shaka AJ, Lee CN, Pines A (1988) J Magn Reson 77: 274Google Scholar
- [88]Sattler M, Schleucher J, Griesinger C (1999) Progr NMR Spectrosc 34: 93CrossRefGoogle Scholar
- [89]Schwarzinger S, Kroon GJA, Foss TR, Wright PE, Dyson HJ (2000) J Biomol NMR 18: 43CrossRefGoogle Scholar
- [90]Baum J, Tycko R, Pines A (1983) J Chem Phys 79: 4643CrossRefGoogle Scholar
- [91]Baum J, Tycko R, Pines A (1985) Phys Rev A 32: 3435CrossRefGoogle Scholar
- [92]Benda11 MR (1995) J Magn Reson A 112: 126CrossRefGoogle Scholar
- [93]Kupche E, Freeman R (1996) J Magn Reson A 118: 299Google Scholar
- [94]Tannûs A, Garwood M (1996) J Magn Reson A 120: 133CrossRefGoogle Scholar
- [95]Cano KE, Smith MA, Shaka AJ (2002) J Magn Reson 155: 131CrossRefGoogle Scholar
- [96]Levy S, Munzner T, Philips M et al (1996) Geomview 1.6.1, University of Minesota, Minneapolis. Geomview is open source software freely available from the web site http://www.geomview.org