Skip to main content
SpringerLink
Log in

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

  • Conference paper
  • First Online:
Book cover Multiple Scattering Theory for Spectroscopies

Part of the book series: Springer Proceedings in Physics ((SPPHY,volume 204))

Abstract

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.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 139.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 179.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 179.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. C. Meneghini, M. Benfatto, in Synchrotron Radiation, Basics, Methods and Application, ed. by S. Mobilio, F. Boscherini, C. Meneghini (Springer, Berlin, 2015), p. 213

    Google Scholar 

  2. M. Benfatto, A. Filipponi, C.R. Natoli, Phys. Rev. B 40, 9626 (1989)

    Article  ADS  Google Scholar 

  3. T.A. Tyson, K.O. Hodgson, C.R. Natoli, M. Benfatto, Phys. Rev. B 46, 5997 (1992)

    Article  ADS  Google Scholar 

  4. J.J. Rehr, R.C. Albers, Rev. Mod. Phys. 72, 621 (2000)

    Article  ADS  Google Scholar 

  5. M. Benfatto, S. Della Longa, J. Synchrotron Radiat. 8, 1087 (2001)

    Google Scholar 

  6. S. Della Longa, A. Arcovito, M. Girasole, J.L. Hazemann, M. Benfatto, Phys. Rev. Lett. 87, 155501 (2001)

    Article  ADS  Google Scholar 

  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. C.R. Natoli, M. Benfatto, S. Doniach, Phys. Rev. A 34, 4682 (1986)

    Article  ADS  Google Scholar 

  9. K. Hatada, K. Hayakawa, M. Benfatto, C.R. Natoli, Phys. Rev. B 76, 060102 (2007)

    Article  ADS  Google Scholar 

  10. M. Benfatto, S. Della Longa, P. D’Angelo, Phys. Scr. T115, 28 (2005)

    Google Scholar 

  11. M. Benfatto, S. Della Longa, J. Phys.: Conf. Ser. 190, 012031 (2009)

    Google Scholar 

  12. L. Hedin, S. Lundqvist, Solid State Physics, vol. 23 (Academic Press, New York, 1969), p. 1

    Google Scholar 

  13. J.E. Müller, O. Jepsen, J.W. Wilkins, Solid State Commun. 42, 365 (1982)

    Article  ADS  Google Scholar 

  14. C.R. Natoli, M. Benfatto, C. Brouder, M.F. Ruiz López, D.L. Foulis, Phys. Rev. B 42, 1944 (1990)

    Article  ADS  Google Scholar 

  15. M. Benfatto, J.A. Solera, J.G. Ruiz, J. Chaboy, Chem. Phys. 282, 441 (2002)

    Article  Google Scholar 

  16. B. Holm, U. von Barth, Phys. Rev. B 57, 2108 (1998)

    Article  ADS  Google Scholar 

  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)

    Article  ADS  Google Scholar 

  18. M. Benfatto, Phys. B 208, 42 (1995)

    Article  ADS  Google Scholar 

  19. P. D’Angelo, O.M. Roscioni, G. Chillemi, S. Della Longa, M. Benfatto, JACS 128, 1853 (2006)

    Article  Google Scholar 

  20. G. Chillemi, E. Pace, M. D’Abramo, M. Benfatto, J. Phys. Chem. A 120, 3958 (2016)

    Article  Google Scholar 

  21. M.P. Allen, D.J. Tildesley, Computer Simulation of Liquids (Oxford Science Publishing, Oxford, 1989)

    Google Scholar 

  22. T. Darden, D. York, L. Pedersen, J. Chem. Phys. 98, 10089 (1993)

    Article  ADS  Google Scholar 

  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. 43

    Google Scholar 

  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)

    Article  ADS  Google Scholar 

  25. G. Bussi, D. Donadio, M. Parrinello, J. Chem. Phys. 126, 014101 (2007)

    Article  ADS  Google Scholar 

  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)

    Article  Google Scholar 

  27. M. Antalek, E. Pace, K.O. Hodgson, G. Chillemi, M. Benfatto, R. Sarangi, P. Frank, J. Chem. Phys 145, 044318 (2016)

    Article  ADS  Google Scholar 

  28. H.J.C. Berendsen, J.R. Grigera, T.P. Straatsma, J. Chem. Phys. 91, 6269 (1987)

    Article  Google Scholar 

  29. M.M. Reif, P.H. Hünenberger, J. Chem. Phys. 134, 144104 (2011)

    Article  ADS  Google Scholar 

  30. V. Migliorati, F. Sessa, G. Aquilanti, P. D’Angelo, J. Chem. Phys. 141, 044509 (2014)

    Article  ADS  Google Scholar 

  31. G. Chillemi, P. D’Angelo, N.V. Pavel, N. Sanna, V. Barone, JACS 124, 1968 (2002)

    Article  Google Scholar 

  32. G. Chillemi, V. Barone, P. D’Angelo, G. Mancini, I. Persson, N. Sanna, J. Phys. Chem. B 109, 9186 (2005)

    Article  Google Scholar 

  33. G. Chillemi, G. Mancini, N. Sanna, V. Barone, S. Della Longa, M. Benfatto, N.V. Pavel, P. D’Angelo, JACS 129, 5430 (2007)

    Article  Google Scholar 

  34. V. Migliorati, A. Zitolo, G. Chillemi, P. D’Angelo, ChemPlusChem 77, 234 (2012)

    Article  Google Scholar 

  35. M. Cossi, N. Rega, G. Scalmani, V. Barone, J. Comput. Chem. 24, 669 (2003)

    Article  Google Scholar 

  36. H.J.C. Berendsen, D. van der Spool, R. van Drunen, Comput. Phys. Commun. 91, 43 (1995)

    Article  ADS  Google Scholar 

  37. T. Miyanaga, H. Sakane, I. Watanabe, Bull. Chem. Soc. Jpn. 68, 819 (1995)

    Article  Google Scholar 

  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)

    Article  ADS  Google Scholar 

  39. S.T. Moin, T.H. Hofer, A.K.H. Weiss, B.M. Rode, J. Chem. Phys. 139, 014503 (2013)

    Article  ADS  Google Scholar 

  40. P. Frank, M. Benfatto, R.K. Szilagyi, P. D’Angelo, S. Della Longa, K.O. Hodgson, Inorg Chem 44, 1922 (2005)

    Article  Google Scholar 

  41. P. Frank, M. Benfatto, M. Qayyam, B. Hedman, K.O. Hodgson, J. Chem. Phys. 142, 084310 (2015)

    Article  ADS  Google Scholar 

  42. M.W. Mahoney, W.L. Jorgensen, J. Chem. Phys. 112, 8910 (2000)

    Article  ADS  Google Scholar 

  43. C.I. Bayly, P. Cieplak, W. Cornell, P.A. Kollman, J. Phys. Chem. 97, 10269 (1993)

    Article  Google Scholar 

Download references

Acknowledgements

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.

Author information

Authors and Affiliations

  1. LNF INFN, Via Enrico Fermi 44, Frascati, Italy

    Maurizio Benfatto & Elisabetta Pace

  2. CINECA, SuperComputing Applications and Innovation Department, Via dei Tizii, 6, Roma, Italy

    Nico Sanna, Cristiano Padrin & Giovanni Chillemi

Authors
  1. Maurizio Benfatto
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Elisabetta Pace
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Nico Sanna
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Cristiano Padrin
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Giovanni Chillemi
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Maurizio Benfatto .

Editor information

Editors and Affiliations

  1. Institut de Physique de Rennes (IPR), Univ Rennes, CNRS, UMR 6251, Rennes, France

    Didier Sébilleau

  2. Department Chemie, Ludwig-Maximilians-Universität München, Munich, Bavaria, Germany

    Keisuke Hatada

  3. Department Chemie, Ludwig-Maximilians-Universität München, Munich, Bavaria, Germany

    Hubert Ebert

Rights and permissions

Reprints and permissions

Copyright information

© 2018 Springer International Publishing AG, part of Springer Nature

About this paper

Check for updates. Verify currency and authenticity via CrossMark

Cite this paper

Benfatto, M., Pace, E., Sanna, N., Padrin, C., Chillemi, G. (2018). MXAN and Molecular Dynamics: A New Way to Look to the XANES (X-ray Absorption Near Edge Structure) Energy Region. In: Sébilleau, D., Hatada, K., Ebert, H. (eds) Multiple Scattering Theory for Spectroscopies. Springer Proceedings in Physics, vol 204. Springer, Cham. https://doi.org/10.1007/978-3-319-73811-6_7

Download citation

Publish with us

Policies and ethics

Search

Navigation