Applied Magnetic Resonance

, Volume 30, Issue 3–4, pp 473–498

DeerAnalysis2006—a comprehensive software package for analyzing pulsed ELDOR data

  • G. Jeschke
  • V. Chechik
  • P. Ionita
  • A. Godt
  • H. Zimmermann
  • J. Banham
  • C. R. Timmel
  • D. Hilger
  • H. Jung
Article

Abstract

Pulsed electron-electron double resonance techniques such as the four-pulse double electron-electron resonance experiment measure a dipolar evolution function of the sample. For a sample consisting of spin-carrying nanoobjects, this function is the product of a form factor, corresponding to the internal structure of the nanoobject, and a background factor, corresponding to the distribution of nanoobjects in space. The form factor contains information on the spin-to-spin distance distribution within the nanoobject and on the average number of spins per nanoobject, while the background factor depends on constraints, such as a confinement of the nanoobjects to a two-dimensional layer. Separation of the dipolar evolution function into these two contributions and extraction of the spin-to-spin distance distribution require numerically stable mathematical algorithms that can handle data for different classes of samples, e.g., spin-labelled biomacromolecules and synthetic materials. Furthermore, experimental imperfections such as the limited excitation bandwidth of microwave pulses need to be considered. The software package DeerAnalysis2006 provides access to a comprehensive set of tools for such data analysis within a common user interface. This interface allows for several tests of the reliability and precision of the extracted information. User-supplied models for the spin-to-spin distance distribution within a certain class of nanoobjects can be added to an existing library and be fitted with a universal algorithm.

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References

  1. 1.
    Milov A.D., Salikhov K.M., Shirov M.D.: Fiz. Tverd. Tela (Leningrad)23, 975 (1981)Google Scholar
  2. 2.
    Milov A.D., Ponomarev A.B., Tsvetkov Yu.D.: Chem. Phys. Lett.110, 67 (1984)CrossRefADSGoogle Scholar
  3. 3.
    Pannier M., Schädler V., Schöps M., Wiesner U., Jeschke G., Spiess H.W.: Macromolecules33, 7812 (2000)CrossRefADSGoogle Scholar
  4. 4.
    Pannier M., Schöps M., Schädler V., Wiesner U., Jeschke G., Spiess H.W.: Macromolecules34, 5555 (2001)CrossRefADSGoogle Scholar
  5. 5.
    Jeschke G.: Macromol. Rapid Commun.23, 227 (2002)CrossRefGoogle Scholar
  6. 6.
    Jeschke G., Godt A.: Chem. Phys. Chem4, 1328 (2003)Google Scholar
  7. 7.
    Hinderberger D., Spiess H.W., Jeschke G.: J. Phys. Chem. B108, 3698 (2004)CrossRefGoogle Scholar
  8. 8.
    Hinderberger D., Schmelz O., Rehahn M., Jeschke G.: Angew. Chem. Int. Ed.43, 4616 (2004)CrossRefGoogle Scholar
  9. 9.
    Persson M., Harbridge J.R., Hammarstrom P., Mitri R., Martensson L.-G., Carlsson U., Eaton G.R., Eaton S.S.: Biophys. J.80, 2886 (2001)CrossRefGoogle Scholar
  10. 10.
    Elsässer C., Brecht M., Bittl R.: J. Am. Chem. Soc.124, 12606 (2002)CrossRefGoogle Scholar
  11. 11.
    van Amsterdam I.M.C., Ubbink M., Canters G.W., Huber M.: Angew. Chem. Int. Ed.42, 62 (2003)CrossRefGoogle Scholar
  12. 12.
    Zhou Z., DeSensi S.C., Stein R.A., Brandon S., Dixit M., McArdle E.J., Warren E.M., Kroh H.K., Song L., Cobb C.E., Hustedt E.J., Beth A.H.: Biochemistry44, 15115 (2005)CrossRefGoogle Scholar
  13. 13.
    Nakamura M., Ueki S., Hara H., Arata T.: J. Mol. Biol.348, 127 (2005)CrossRefGoogle Scholar
  14. 14.
    Fajer P.G.: J. Phys. Condens. Matter17, S1459 (2005)CrossRefADSGoogle Scholar
  15. 15.
    Bennati M., Robblee J.H., Mugnaini V., Stubbe J., Freed J.H., Borbat P.: J. Am. Chem. Soc.127, 15014 (2005)CrossRefGoogle Scholar
  16. 16.
    Kay C.W.M., Elsässer C., Bittl R., Farrell S.R., Thorpe C.: J. Am. Chem. Soc.128, 76 (2006)CrossRefGoogle Scholar
  17. 17.
    Banham J.E., Timmel C.R., Abbott R.J.M., Lea S.M., Jeschke G.: Angew. Chem. Int. Ed.118, 1058 (2006)CrossRefGoogle Scholar
  18. 18.
    Jeschke G., Wegener C., Nietschke M., Jung H., Steinhoff H.-J.: Biophys. J.86, 2551 (2004)CrossRefADSGoogle Scholar
  19. 19.
    Jeschke G., Bender A., Schweikardt T., Panek G., Decker H., Paulsen H.: J. Biol. Chem.280, 18623 (2005)CrossRefGoogle Scholar
  20. 20.
    Hilger D., Jung H., Padan E., Wegener C., Vogel K.-P., Steinhoff H.-J., Jeschke G.: Biophys. J.89, 1328 (2005)CrossRefGoogle Scholar
  21. 21.
    Borovykh I.V., Ceola S., Gajula P., Gast P., Steinhoff H.-J., Huber M.: J. Magn. Reson.180, 178 (2006)CrossRefADSGoogle Scholar
  22. 22.
    Schiemann O., Piton N., Mu Y.G., Stock G., Engels J.W., Prisner T.F.: J. Am. Chem. Soc.126, 5722 (2004)CrossRefGoogle Scholar
  23. 23.
    Milov A.D., Tsvetkov Y.D., Formaggio F., Crisma M., Toniolo C., Raap J.: J. Am. Chem. Soc.122, 3843 (2000)CrossRefGoogle Scholar
  24. 24.
    Sale K., Song L., Liu Y.-S., Perozo E., Fajer P.: J. Am. Chem. Soc.127, 9334 (2005)CrossRefGoogle Scholar
  25. 25.
    Jeschke G., Koch A., Jonas U., Godt A.: J. Magn. Reson.155, 72 (2002)CrossRefADSGoogle Scholar
  26. 26.
    Milov A.D., Tsvetkov Y.D., Formaggio F., Oancea S., Toniolo C., Raap J.: Phys. Chem. Chem. Phys.6, 3596 (2004)CrossRefGoogle Scholar
  27. 27.
    Bowman M.K., Maryasov A.G., Kim N., DeRose V.J.: Appl. Magn. Reson.26, 23 (2004)Google Scholar
  28. 28.
    Jeschke G., Panek G., Godt A., Bender A., Paulsen H.: Appl. Magn. Reson.26, 223 (2004)Google Scholar
  29. 29.
    Jeschke G., Bender A., Paulsen H., Zimmermann H., Godt A.: J. Magn. Reson.169, 1 (2004)CrossRefADSGoogle Scholar
  30. 30.
    Chiang W.-Y., Borbat P.P., Freed J.H.: J. Magn. Reson.172, 279 (2005)CrossRefADSGoogle Scholar
  31. 31.
    Maryasov A.G., Tsvetkov Y.D.: Appl. Magn. Reson.18, 583 (2000)CrossRefGoogle Scholar
  32. 32.
    Milov A.D., Naumov B.D., Tsvetkov Y.D.: Appl. Magn. Reson.26, 587 (2004)CrossRefGoogle Scholar
  33. 33.
    Jeschke G.: ChemPhysChem3, 927 (2002)CrossRefGoogle Scholar
  34. 34.
    Godt A., Franzen C., Veit S., Enkelmann V., Pannier M., Jeschke G.: J. Org. Chem.65, 7575 (2000)CrossRefGoogle Scholar
  35. 35.
    Chechik V., Wellsted H.J., Korte A., Gilbert B.C., Caldararu H., Ionita P., Caragheorgheopol A.: Faraday Discuss.125, 279 (2004)CrossRefGoogle Scholar
  36. 36.
    Pannier M., Veit S., Godt A., Jeschke G., Spiess H.W.: J. Magn. Reson.142, 331 (2000)CrossRefADSGoogle Scholar
  37. 37.
    Stoll S., Schweiger A.: J. Magn. Reson.178, 42 (2006)CrossRefADSGoogle Scholar
  38. 38.
    Lindner P., Zemb T. (eds.): Neutrons, X-rays and Light: Scattering Methods Applied to Soft Condensed Matter, chapt. 13. Amsterdam: Elsevier 2002.Google Scholar
  39. 39.
    Milov A.D., Tsvetkov Yu.D.: Appl. Magn. Reson.12, 495 (1997)CrossRefGoogle Scholar
  40. 40.
    Hubbell W.L., Altenbach C.: Curr. Opin. Struct. Biol.4, 556 (1994)CrossRefGoogle Scholar
  41. 41.
    Tikhonov A.N., Goncharsky A., Stepanov V.V., Yagola A.G.: Numerical Methods for the Solution of Ill-posed Problems. Dordrecht: Kluwer Academic 1995.MATHGoogle Scholar
  42. 42.
    Jeschke G., Zimmermann H., Godt A.: J. Magn. Reson.179, 412 (2006)Google Scholar
  43. 43.
    Martin R.E., Pannier M., Diederich F., Gramlich V., Hubrich M., Spiess H.W.: Angew. Chem. Int. Ed.37, 2834 (1998)Google Scholar
  44. 44.
    Jeschke G., Pannier M., Godt A., Spiess H.W.: Chem. Phys. Lett.331, 243 (2000)CrossRefADSGoogle Scholar
  45. 45.
    Hansen P.C.: SIAM Rev.34, 561 (1992)MATHCrossRefMathSciNetGoogle Scholar
  46. 46.
    Honerkamp J., Weese J.: Continuum Mech. Thermodyn.2, 17 (1990)MATHCrossRefADSMathSciNetGoogle Scholar
  47. 47.
    Weese J.: Comput. Phys. Commun.69, 99 (1992)CrossRefADSGoogle Scholar
  48. 48.
    Larsen R.G., Singel D.J.: J. Chem. Phys.98, 5134 (1993)CrossRefADSGoogle Scholar
  49. 49.
    Schweiger A., Jeschke G.: Principles of Pulse Electron Paramagnetic Resonance. Oxford: Oxford University Press 2001.Google Scholar
  50. 50.
    Wilhelm J., Frey E.: Phys. Rev. Lett.77, 2581 (1996)CrossRefADSGoogle Scholar
  51. 51.
    Ionita P., Caragheorgheopol A., Gilbert B.C., Chechik V.: J. Phys. Chem. B109, 3734 (2005)CrossRefGoogle Scholar

Copyright information

© Springer 2006

Authors and Affiliations

  • G. Jeschke
    • 1
  • V. Chechik
    • 2
  • P. Ionita
    • 2
  • A. Godt
    • 3
  • H. Zimmermann
    • 4
  • J. Banham
    • 5
    • 6
  • C. R. Timmel
    • 6
  • D. Hilger
    • 7
  • H. Jung
    • 7
  1. 1.Max Planck Institute for Polymer ResearchMainzGermany
  2. 2.Department of ChemistryUniversity of YorkHeslingtonUK
  3. 3.Department for ChemistryUniversity BielefeldBielefeldGermany
  4. 4.Max Planck Institute for Medical ResearchHeidelbergGermany
  5. 5.Physical and Theoretical Chemistry LaboratoryUniversity of OxfordOxfordUK
  6. 6.Inorganic Chemistry LaboratoryUniversity of OxfordOxfordUK
  7. 7.Department Biology ILudwig-Maximilians-Universität MünchenMünchenGermany

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