MXAN and Molecular Dynamics: A New Way to Look to the XANES (X-ray Absorption Near Edge Structure) Energy Region

  • Maurizio BenfattoEmail author
  • Elisabetta Pace
  • Nico Sanna
  • Cristiano Padrin
  • Giovanni Chillemi
Conference paper
Part of the Springer Proceedings in Physics book series (SPPHY, volume 204)


X-ray Absorption Near Edge Structure (XANES) spectroscopy is a powerful method to obtain local structural and electronic information around a well-defined absorbing site of matter in many possible different conditions. Few years ago we presented a new method, called MXAN, that allows a complete fit of the XANES energy region in terms of well-defined set of structural parameters. MXAN calculates the photo-absorption cross-section using the full multiple scattering theory and, in this way, the analysis can start from the edge without any limitations in the energy range and polarization conditions. In this paper we present with details the MXAN method and new possibilities, coming from the combination of molecular dynamic simulations and MXAN, in the analysis of structural disordered system. Applications to the solvation spheres analysis of Ni, Cu and Cl ions in water are also presented in details.



We thank Dr. P. Frank, of Stanford Chemistry Department and SSRL Laboratory, Dr. R. Sarangi and Dr. B. Hedman of SSRL Laboratory for giving us the permission of using the experimental data presented in this paper and for constructive criticism, suggestions in the use of mxan code. M.B. also thanks the financial support provided over the past few years by SLAC for the two-month visit as visiting scientist. Text in Sect. 7.6 is adapted with permission from “Equilibrium between 5- and 6- fold coordination in the first shell of Cu(II)” by G. Chillemi et al., Journal of Physical Chemistry A, 120, 3958 (2016). Copyright 2016 American Chemical Society.


  1. 1.
    C. Meneghini, M. Benfatto, in Synchrotron Radiation, Basics, Methods and Application, ed. by S. Mobilio, F. Boscherini, C. Meneghini (Springer, Berlin, 2015), p. 213Google Scholar
  2. 2.
    M. Benfatto, A. Filipponi, C.R. Natoli, Phys. Rev. B 40, 9626 (1989)ADSCrossRefGoogle Scholar
  3. 3.
    T.A. Tyson, K.O. Hodgson, C.R. Natoli, M. Benfatto, Phys. Rev. B 46, 5997 (1992)ADSCrossRefGoogle Scholar
  4. 4.
    J.J. Rehr, R.C. Albers, Rev. Mod. Phys. 72, 621 (2000)ADSCrossRefGoogle Scholar
  5. 5.
    M. Benfatto, S. Della Longa, J. Synchrotron Radiat. 8, 1087 (2001)Google Scholar
  6. 6.
    S. Della Longa, A. Arcovito, M. Girasole, J.L. Hazemann, M. Benfatto, Phys. Rev. Lett. 87, 155501 (2001)ADSCrossRefGoogle Scholar
  7. 7.
    A. Arcovito, M. Benfatto, M. Cianci, S.S. Hasnain, K. Nienhaus, G.U. Nienhaus, C. Savino, R.W. Strange, B. Vallone, S. Della Longa, PNAS 104, 6211 (2007)Google Scholar
  8. 8.
    C.R. Natoli, M. Benfatto, S. Doniach, Phys. Rev. A 34, 4682 (1986)ADSCrossRefGoogle Scholar
  9. 9.
    K. Hatada, K. Hayakawa, M. Benfatto, C.R. Natoli, Phys. Rev. B 76, 060102 (2007)ADSCrossRefGoogle Scholar
  10. 10.
    M. Benfatto, S. Della Longa, P. D’Angelo, Phys. Scr. T115, 28 (2005)Google Scholar
  11. 11.
    M. Benfatto, S. Della Longa, J. Phys.: Conf. Ser. 190, 012031 (2009)Google Scholar
  12. 12.
    L. Hedin, S. Lundqvist, Solid State Physics, vol. 23 (Academic Press, New York, 1969), p. 1Google Scholar
  13. 13.
    J.E. Müller, O. Jepsen, J.W. Wilkins, Solid State Commun. 42, 365 (1982)ADSCrossRefGoogle Scholar
  14. 14.
    C.R. Natoli, M. Benfatto, C. Brouder, M.F. Ruiz López, D.L. Foulis, Phys. Rev. B 42, 1944 (1990)ADSCrossRefGoogle Scholar
  15. 15.
    M. Benfatto, J.A. Solera, J.G. Ruiz, J. Chaboy, Chem. Phys. 282, 441 (2002)CrossRefGoogle Scholar
  16. 16.
    B. Holm, U. von Barth, Phys. Rev. B 57, 2108 (1998)ADSCrossRefGoogle Scholar
  17. 17.
    W. Gawelda, V.T. Pham, M. Benfatto, Y. Zaushitsyn, M. Kaiser, D. Grolimund, S.L. Johnson, R. Abela, A. Hauser, C. Bressler, M. Chergui, Phys. Rev. Lett. 98, 057401 (2007)ADSCrossRefGoogle Scholar
  18. 18.
    M. Benfatto, Phys. B 208, 42 (1995)ADSCrossRefGoogle Scholar
  19. 19.
    P. D’Angelo, O.M. Roscioni, G. Chillemi, S. Della Longa, M. Benfatto, JACS 128, 1853 (2006)CrossRefGoogle Scholar
  20. 20.
    G. Chillemi, E. Pace, M. D’Abramo, M. Benfatto, J. Phys. Chem. A 120, 3958 (2016)CrossRefGoogle Scholar
  21. 21.
    M.P. Allen, D.J. Tildesley, Computer Simulation of Liquids (Oxford Science Publishing, Oxford, 1989)Google Scholar
  22. 22.
    T. Darden, D. York, L. Pedersen, J. Chem. Phys. 98, 10089 (1993)ADSCrossRefGoogle Scholar
  23. 23.
    H.J.C. Berendsen, W.F. van Gunsteren, in Molecular-Dynamics Simulations of Statistical-Mechanical Systems Enrico Fermi Summer School (North-Holland, Amsterdam, 1986), p. 43Google Scholar
  24. 24.
    H.J.C. Berendsen, J.P.M. Postma, W.F. van Gunsteren, J.R. Haak, A. Di Nola, J. Chem. Phys. 81, 3684 (1984)ADSCrossRefGoogle Scholar
  25. 25.
    G. Bussi, D. Donadio, M. Parrinello, J. Chem. Phys. 126, 014101 (2007)ADSCrossRefGoogle Scholar
  26. 26.
    S. Pronk, S. Pall, R. Schulz, P. Larsson, P. Bjelkmar, R. Apostolov, M.R. Shirts, J.C. Smith, P.M. Kasson, D. van der Spoel, B. Hess, E. Lindahl, Bioinformatics 29, 845 (2013)CrossRefGoogle Scholar
  27. 27.
    M. Antalek, E. Pace, K.O. Hodgson, G. Chillemi, M. Benfatto, R. Sarangi, P. Frank, J. Chem. Phys 145, 044318 (2016)ADSCrossRefGoogle Scholar
  28. 28.
    H.J.C. Berendsen, J.R. Grigera, T.P. Straatsma, J. Chem. Phys. 91, 6269 (1987)CrossRefGoogle Scholar
  29. 29.
    M.M. Reif, P.H. Hünenberger, J. Chem. Phys. 134, 144104 (2011)ADSCrossRefGoogle Scholar
  30. 30.
    V. Migliorati, F. Sessa, G. Aquilanti, P. D’Angelo, J. Chem. Phys. 141, 044509 (2014)ADSCrossRefGoogle Scholar
  31. 31.
    G. Chillemi, P. D’Angelo, N.V. Pavel, N. Sanna, V. Barone, JACS 124, 1968 (2002)CrossRefGoogle Scholar
  32. 32.
    G. Chillemi, V. Barone, P. D’Angelo, G. Mancini, I. Persson, N. Sanna, J. Phys. Chem. B 109, 9186 (2005)CrossRefGoogle Scholar
  33. 33.
    G. Chillemi, G. Mancini, N. Sanna, V. Barone, S. Della Longa, M. Benfatto, N.V. Pavel, P. D’Angelo, JACS 129, 5430 (2007)CrossRefGoogle Scholar
  34. 34.
    V. Migliorati, A. Zitolo, G. Chillemi, P. D’Angelo, ChemPlusChem 77, 234 (2012)CrossRefGoogle Scholar
  35. 35.
    M. Cossi, N. Rega, G. Scalmani, V. Barone, J. Comput. Chem. 24, 669 (2003)CrossRefGoogle Scholar
  36. 36.
    H.J.C. Berendsen, D. van der Spool, R. van Drunen, Comput. Phys. Commun. 91, 43 (1995)ADSCrossRefGoogle Scholar
  37. 37.
    T. Miyanaga, H. Sakane, I. Watanabe, Bull. Chem. Soc. Jpn. 68, 819 (1995)CrossRefGoogle Scholar
  38. 38.
    A. Pasquarello, I. Petri, P.S. Salmon, O. Parisel, R. Car, E. Toth, D.H. Powell, H.E. Fischer, L. Helm, A. Merbach, Science 291, 856 (2001)ADSCrossRefGoogle Scholar
  39. 39.
    S.T. Moin, T.H. Hofer, A.K.H. Weiss, B.M. Rode, J. Chem. Phys. 139, 014503 (2013)ADSCrossRefGoogle Scholar
  40. 40.
    P. Frank, M. Benfatto, R.K. Szilagyi, P. D’Angelo, S. Della Longa, K.O. Hodgson, Inorg Chem 44, 1922 (2005)CrossRefGoogle Scholar
  41. 41.
    P. Frank, M. Benfatto, M. Qayyam, B. Hedman, K.O. Hodgson, J. Chem. Phys. 142, 084310 (2015)ADSCrossRefGoogle Scholar
  42. 42.
    M.W. Mahoney, W.L. Jorgensen, J. Chem. Phys. 112, 8910 (2000)ADSCrossRefGoogle Scholar
  43. 43.
    C.I. Bayly, P. Cieplak, W. Cornell, P.A. Kollman, J. Phys. Chem. 97, 10269 (1993)CrossRefGoogle Scholar

Copyright information

© Springer International Publishing AG, part of Springer Nature 2018

Authors and Affiliations

  • Maurizio Benfatto
    • 1
    Email author
  • Elisabetta Pace
    • 1
  • Nico Sanna
    • 2
  • Cristiano Padrin
    • 2
  • Giovanni Chillemi
    • 2
  1. 1.LNF INFNFrascatiItaly
  2. 2.CINECA, SuperComputing Applications and Innovation DepartmentRomaItaly

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