Molecular Dynamics Simulations Combined to X-Ray Spectroscopies XANES and EXAFS

In my Tesi di Laurea (equivalent to M.Sc. Diploma Thesis) in 1992, I have for the first time investigated and attempted the combination MD simulations and theoretical spectra calculation for the interpretation of experimental XANES (X-ray Absorption Near-Edge Spectroscopy) [4]. The method was used to study the crystal structure of the aquatrisimidazole copper (II) sulfate complex, but the results not yet published. The thesis is in Italian, and it is available on request to the interested reader.

Figure 2: Crystal structure of the aquatrisimidazole copper (II) sulfate complex.

We have also proposed and applied a novel approach to combine MD simulations to the refinement of experimental data from Extended X-ray Absorption Fine Structure (EXAFS) spectroscopy on the analysis of different molecular systems [1,2,3]. In this approach (see schema below) MD simulations are used to obtain a model of pair distribution functions between the central photo-absorber and the surrounding scattering atoms. The distributions functions were used as a starting model to refine the experimental. The same procedure was used to validate intermolecular potential models used in the MD [3]. The method was applied to the study of an aqueous solution of ions and small molecules and can be extended to more complex systems like metalloproteins, inorganic complexes, and organometallic [4] compounds. These studies were the first example of the use of MD simulations to the interpretation and refinement of EXAFS experimental data.



  1. D’Angelo, A. Di Nola, A. Filipponi, N. V. Pavel, D. Roccatano. An extended X-ray absorption fine structure study of aqueous solutions. J. Chem. Phys., 100, 985-994 (1994).
  2. D’Angelo, N. V. Pavel, H. F. Nolting, D. Roccatano. Multielectron excitations at the L-edges of barium in aqueous solution. Phys. Rev. B, 54, 12129-12138 (1996).
  3. Roccatano, H. J. C. Berendsen, P. D’Angelo. Assessment of the validity of intermolecular potential models used in molecular dynamics simulations by extended X-ray absorption fine structure spectroscopy: A case study of Sr in methanol solution. J. Chem. Phys., 108, 9487-9497 (1998).
  4. Roccatano. Determinazione della struttura dello Cu(II) aquatrisimidazolo solfato mediante dinamica molecolare e spettroscopia XANES. Tesi di Laurea, equivalent to a Master Thesis (in Italian). Advisors: Prof’s A. Di Nola and M. Barteri, Rome 1992.

About Danilo Roccatano

I have a Doctorate in chemistry at the University of Roma “La Sapienza”. I led educational and research activities at different universities in Italy, The Netherlands, Germany and now in the UK. I am fascinated by the study of nature with theoretical models and computational. For years, my scientific research is focused on the study of molecular systems of biological interest using the technique of Molecular Dynamics simulation. I have developed a server (the link is in one of my post) for statistical analysis at the amino acid level of the effect of random mutations induced by random mutagenesis methods. I am also very active in the didactic activity in physical chemistry, computational chemistry, and molecular modeling. I have several other interests and hobbies as video/photography, robotics, computer vision, electronics, programming, microscopy, entomology, recreational mathematics and computational linguistics.
This entry was posted in Research. Bookmark the permalink.

Leave a Reply

Fill in your details below or click an icon to log in: Logo

You are commenting using your account. Log Out /  Change )

Google photo

You are commenting using your Google account. Log Out /  Change )

Twitter picture

You are commenting using your Twitter account. Log Out /  Change )

Facebook photo

You are commenting using your Facebook account. Log Out /  Change )

Connecting to %s

This site uses Akismet to reduce spam. Learn how your comment data is processed.