Computational simulations for ultrafast X-ray spectroscopy and
diffraction of chemical and biological systems: Lay Report
Visualizing an evolving molecular structure during the course of a chemical reaction or biological process has been the dream of scientists for decades. For this time-resolved X-ray absorption spectroscopy and X-ray scattering are ideal, due to the wealth of electronic and geometric information that can be extracted. Recent technological and methodological improvements has lead to a significant increase in the quality of experimental data, in particular it is now possible to obtain X-ray spectroscopic and scattering data with a temporal resolution of femtoseconds .
The possibility of using structural techniques in a pump-probe type setup with femtosecond resolution will allow to follow the excited state dynamics of many systems of chemical and biological interest and unambiguously ascertain the chemical dynamics or biological function. However, the complexity of these spectra and diffraction patterns means that simulations are critical in order to obtain a complete understanding of the process understudy. To this end, there have been recent developments in the treatment of nonadiabatic excited state dynamics in on-the-fly molecular dynamics simulations within the framework time-dependent density function theory (TDDFT) [2,3]. Among others advantages, this method allows also for accurate excited state dynamics simulations that include solvent effects either explicitly or through a quantum-mechanic/molecular mechanics (QM/MM) coupling scheme .
For this proposal we aim to study the excited state dynamics of two metal complexes in solution; namely [Pt2(P2O5H2)4]4- and [Cu(I)(2,9-dimethyl-1,10-phenanthroline)2]+. In particular, it has been suggested experimentally that the solvent significantly affects the dynamics of both these complexes. This has important implications, especially for the analysis of X-ray absorption spectra, which typically neglects the contribution of the solvent. In this project, we will use first-principle molecular dynamics in the framework of QM/MM to perform a detailed characterization of the effects of the solvent for both complexes. In addition, the excited state dynamics of these species is still not fully understood, especially for what concerns intersystem crossings, which play an important role in possible applications of these complexes. To this end, we will use quantum chemistry methods to calculate the potential energy surfaces of interest and perform quantum dynamics within the framework of the multi-configuration time-dependent Hartree (MCTDH) method . As an alternative to this approach, on-the-fly trajectory surface hopping dynamics will also be applied [2, 3].
This proposal marks an exciting development in the area of time-resolved X-ray studies. By exploiting the aforementioned methods and by extending the theory of calculating X-ray scattering patterns in the condensed phase we will provide further crucial understanding in the field of time-resolved condensed matter physical chemistry. These developments will also play an important role in supporting exciting experimental opportunities made possible by the X-ray Free electron Lasers (XFEL).
 M. Chergui, “Picosecond and femtosecond X-ray absorption spectroscopy of molecular systems”, Acta Crystallographica Section A, 66:229-239, 2010.
 E. Tapavicza, I. Tavernelli, and U. Rothlisberger. “Trajectory surface hopping within linear response time-dependent density-functional theory”, Phys. Rev. Lett., 98:023001, 2007.
 I. Tavernelli, B. F. E. Curchod, A. Laktionov, and U. Rothlisberger. “Nonadiabatic coupling vectors for excited states within time-dependent density functional theory in the Tamm-Dancoff approximation and beyond”, J. Chem. Phys., 133:194104, 2010.
 B. F. E. Curchod, P. Campomanes, A. Laktionov, M. Neri, T. J. Penfold, S. Vanni, I. Tavernelli, and U. Rothlisberger. “Mechanical (QM/MM) Simulations of Adiabatic and Nonadiabatic Ultrafast Phenomena”, Chimia, 65(5):330-333, 2011.
 R.M. van der Veen, C.J. Milne, A. Nahhas, F.A. Lima, V.T. Pham, J. Best, J.A. Weinstein, C.N. Borca, R. Abela, C. Bressler, and M. Chergui, “Structural determination of a photochemically active diplatinum molecule by time-resolved EXAFS spectroscopy”, Angewandte Chemie, 48:2711-2714, 2009.
 G. Smolentsev, A.V. Soldatov, and L.X. Chen, “Three-dimensional local structure of photoexcited Cu diimine complex refined by quantitative XANES analysis”, Journal Of Physical Chemistry A, 112:5363-5367, 2008.
 M. H. Beck, A. Jäckle, G. A. Worth, and H.-D. Meyer, “The multiconfiguration time dependent Hartree method: A highly efficient algorithm for propagating wavepackets”, Phys. Rep., 324:1-105, 2000.