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Computational simulations for ultrafast X-ray spectroscopy and diffraction of chemical and biological systems

Applicant Tavernelli Ivano
Number 137717
Funding scheme Project funding
Research institution Laboratoire de chimie et biochimie computationnelles EPFL - SB - ISIC - LCBC
Institution of higher education EPF Lausanne - EPFL
Main discipline Physical Chemistry
Start/End 01.01.2012 - 30.06.2015
Approved amount 190'111.00
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All Disciplines (3)

Discipline
Physical Chemistry
Condensed Matter Physics
Material Sciences

Keywords (3)

ultrafast dynamics; nonadiabatic dynamics; X-ray absorption spectroscopy

Lay Summary (English)

Lead
Lay summary

SNF200021-137717

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 [1].

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 [4].

For this proposal we aim to study the excited state dynamics of two metal complexes in solution; namely [Pt2(P2O5H2)4]4-[5] and [Cu(I)(2,9-dimethyl-1,10-phenanthroline)2]+[6]. 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 [7]. 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).

References

[1] M. Chergui, “Picosecond and femtosecond X-ray absorption spectroscopy of molecular systems”, Acta Crystallographica Section A, 66:229-239, 2010.

[2] E. Tapavicza, I. Tavernelli, and U. Rothlisberger. “Trajectory surface hopping within linear response time-dependent density-functional theory”, Phys. Rev. Lett., 98:023001, 2007.

[3] 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.

[4] 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.

[5] 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.

[6] 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.

[7] 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.
Direct link to Lay Summary Last update: 21.02.2013

Responsible applicant and co-applicants

Employees

Publications

Publication
Characterising the excited state solvent effects and the role for spin orbit coupling for Cu(I)-phenanthroline complexes
Capano Gloria, Rothlisberger Ursula, Tavernelli Ivano, Penfold Thomas (2015), Characterising the excited state solvent effects and the role for spin orbit coupling for Cu(I)-phenanthroline complexes, in J. Phys. Chem. A, 119, 7026-7037.
Nonadiabatic Molecular Dynamics Simulations: Synergies between Theory and Experiments
Tavernelli Ivano (2015), Nonadiabatic Molecular Dynamics Simulations: Synergies between Theory and Experiments, in Accounts of Chemical Research, 48, 792.
A quantum dynamics study of the ultrafast relaxation in a prototypical Cu(I)-phenanthroline
Capano Gloria, Chergui Majed, Rothlisberger Ursula, Tavernelli Ivano, Penfold Thomas J. (2014), A quantum dynamics study of the ultrafast relaxation in a prototypical Cu(I)-phenanthroline, in J. Phys. Chem. A, 118, 9861.
A wavelet analysis for the X-ray absorption spectra of molecules.
Penfold T J, Tavernelli I, Milne C J, Reinhard M, Nahhas A El, Abela R, Rothlisberger U, Chergui M (2013), A wavelet analysis for the X-ray absorption spectra of molecules., in The Journal of chemical physics, 138(1), 014104-014104.
Hydrophobicity with atomic resolution: Steady state and ultrafast X-ray absorption and molecular dynamics studies
Penfold Thomas, Tavernelli Ivano, Milne Christopher, Chergui Majed (2013), Hydrophobicity with atomic resolution: Steady state and ultrafast X-ray absorption and molecular dynamics studies, in Pure and Applied Chemistry, 85, 53.
Solvent induced luminescence quenching: Static and time-resolved X-ray absorption spec- troscopy of a Copper(I) phenanthroline complex.
Penfold T.J., Karlsson S., Capano G., Lima F.A., Reinhard M., Rittmann-Frank H., Rittmann J., Braem O., Abela R., Baranoff E., Tavernelli I., Rothlisberger U., Milne C.J., Chergui M. (2013), Solvent induced luminescence quenching: Static and time-resolved X-ray absorption spec- troscopy of a Copper(I) phenanthroline complex., in J. Phys. Chem A, 117, 4591-4601.
Solvent rearrangements during the transition from hydrophilic to hydrophobic solvation
Penfold Thomas, Tavernelli Ivano, Doemer Manuel, Abela Raphael, Rothlisberger Ursula, Chergui Majed (2013), Solvent rearrangements during the transition from hydrophilic to hydrophobic solvation, in Chem. Phys., 410, 25-30.
The role of Hartree-Fock exchange in the simulation of X-ray absorption spectra: A study of photoexcited [Fe(bpy)3]2+
Capano G., Penfold T.J., Besley N.A., Milne C.J., Reinhard M., Rittmann-Frank H., Glatzer P., Abela R., Rothlisberger U., Chergui M., Tavernelli I. (2013), The role of Hartree-Fock exchange in the simulation of X-ray absorption spectra: A study of photoexcited [Fe(bpy)3]2+, in Chem. Phys. Lett., 580, 179-184.
X-ray Absorption Spectroscopy of Ground and Excited Rhenium-Carbonyl-Diimine Complexes: Evidence for a Two-Center Electron Transfer.
El Nahhas A, van der Veen R M, Penfold T J, Pham V T, Lima F A, Abela R, Blanco-Rodriguez A M, Zális S, Vlcek A, Tavernelli I, Rothlisberger U, Milne C J, Chergui M (2013), X-ray Absorption Spectroscopy of Ground and Excited Rhenium-Carbonyl-Diimine Complexes: Evidence for a Two-Center Electron Transfer., in The journal of physical chemistry. A, 117(2), 361-369.
Simulations of X-ray absorption spectra: the effect of the solvent
Penfold TJ, Curchod BFE, Tavernelli I, Abela R, Rothlisberger U, Chergui M (2012), Simulations of X-ray absorption spectra: the effect of the solvent, in PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 14(26), 9444-9450.
Ultrafast anisotropic x-ray scattering in the condensed phase
Penfold TJ, Tavernelli I, Abela R, Chergui M, Rothlisberger U (2012), Ultrafast anisotropic x-ray scattering in the condensed phase, in NEW JOURNAL OF PHYSICS, 14, 113002.
A Vibronic Coupling Hamiltonian to describe the ultrafast excited state dynamics of a Cu(I)- phenanthroline complex
Capano G., Penfold T.J., Rothlisberger U., Tavernelli I., A Vibronic Coupling Hamiltonian to describe the ultrafast excited state dynamics of a Cu(I)- phenanthroline complex, in CHIMIA.
Probing Wavepacket Dynamics using Ultrafast X-ray Spectroscopy
Capano Gloria, Milne Chris, Chergui Majed, Rothlisberger Ursula, Tavernelli Ivano, Penfold Thomas, Probing Wavepacket Dynamics using Ultrafast X-ray Spectroscopy, in J. Phys. B: At. Mol. Phys, xxx.

Collaboration

Group / person Country
Types of collaboration
Dr Graham Worth/ University of Birmingham Great Britain and Northern Ireland (Europe)
- in-depth/constructive exchanges on approaches, methods or results
SwissFEL project: PSI Switzerland (Europe)
- Publication
- Research Infrastructure
Prof. U Roethlisberger/ EPFL Switzerland (Europe)
- Publication

Scientific events

Active participation

Title Type of contribution Title of article or contribution Date Place Persons involved
AMOC 2015 Talk given at a conference Intramolecular excited state relaxation at sub-vibrational time scales 10.08.2015 Madrid, Spain Chergui Majed;
TSRC Excited State Workshop Talk given at a conference Nonadiabatic dynamics with relativistic effects: theory and applications 13.07.2015 Telluride (CO), United States of America Tavernelli Ivano;
CECAM workshop on: Molecular Quantum Dynamics Methods: Benchmarks and State of the Art Talk given at a conference Recent Advances in nonadiabatic dynamics: theory and applications 15.06.2015 Lausanne, Switzerland Tavernelli Ivano;
98th National Meeting of the Canadian Society for Chemistry Talk given at a conference Probing Molecular Dynamics 01.06.2015 Ottawa, Canada Chergui Majed;
CECAM workshop on “Recent progress in adiabatic and non-adiabatic methods in quantum dynamics Talk given at a conference Electron-phonon coupling from time-dependent density functional theory 12.05.2015 Lausanne, Switzerland Tavernelli Ivano;
COST Action XLIC workshop Talk given at a conference TDDFT-based nonadiabatic molecular dynamics 27.04.2015 Fruska gora, Serbien Tavernelli Ivano;
Institute of Molecular Science Talk given at a conference Ultrafast X-ray studies of (bio)molecular systems and metal oxides 22.04.2015 Okazaki, Japan Chergui Majed;
SPring-8 Angstrom Compact Free Electron Laser Talk given at a conference Ultrafast X-ray studies of (bio)molecular systems and metal oxides 20.04.2015 Hyogo, Japan Chergui Majed;
NFFA-FERMI-ELETTRA-IOM-TREX Workshop Talk given at a conference ULTRAFAST X-RAY SPECTROSCOPY OF METAL OXIDES 08.12.2014 Trieste, Italy Chergui Majed;
C4 Seminars at ETHZ Individual talk Nonadiabatic dynamics of complex molecular systems using time-dependent density functional theory 06.11.2014 Zurich, Switzerland Tavernelli Ivano;
THEOS seminars Individual talk TDDFT-based nonadiabatic molecular dynamics with relativistic effects 16.10.2014 Lausanne, Switzerland Tavernelli Ivano;
COST Joint Working Group Meeting “CM1202 Perspect H2O Supramolecular photocatalytic water splitting” Talk given at a conference PROBING ELECTRON MIGRATION IN PHOTOCATALYTIC SYSTEMS BY UL- TRAFAST X-RAY ABSORPTION SPECTROSCOPY 13.10.2014 Lund, Sweden Chergui Majed;
COST Joint Working Group Meeting Talk given at a conference PROBING ELECTRON MIGRATION IN PHOTOCATALYTIC SYSTEMS BY UL- TRAFAST X-RAY ABSORPTION SPECTROSCOPY 13.10.2014 Lund, Sweden Chergui Majed;
European Theoretical Spectroscopy Facility (ETSF) Talk given at a conference TDDFT-based nonadiabatic molecular dynamics with relativistic effects 23.09.2014 Zaragoza, Spain Tavernelli Ivano;
The Fassberg Lecture. Talk given at a conference Ultrafast structural dynamics in solutions: Viewing it with light from the visible to the X-ray domain 22.09.2014 London, Great Britain and Northern Ireland Chergui Majed;
Workshop on Prospective Applications of Attosecond Science Talk given at a conference ULTRAFAST CHEMICAL DYNAMICS AT THE FEW-FEMTOSECONDS LIMIT 15.09.2014 London, Great Britain and Northern Ireland Chergui Majed;
50th Symposium on Theoretical Chemistry, Talk given at a conference TDDFT-based nonadiabatic molecular dynamics with relativistic effects 14.09.2014 Vienna, Austria Tavernelli Ivano;
PHOTON14 Talk given at a conference COMBINING THE ATOMIC-SCALE RESOLUTIONS OF TIME AND SPACE, 08.09.2014 London, Great Britain and Northern Ireland Chergui Majed;
XXVTH IUPAC Photochemistry Talk given at a conference ULTRAFAST RELAXATION DYNAMICS IN METAL COMPLEXES: INTERPLAY OF SPIN, ELECTRONIC AND STRUCTURAL REARRANGEMENTS 23.07.2014 Bordeaux, France Chergui Majed;
Faraday Discussion 171 Talk given at a conference EMERGING PHOTON TECHNOLOGIES FOR CHEMICAL DYNAMICS 09.07.2014 Sheffield, Great Britain and Northern Ireland Chergui Majed;
Conference on "New Frontiers in Multiscale Modelling of Advanced Materials" Talk given at a conference Nonadiabatic dynamics and material design 17.06.2014 Trento, Italy Tavernelli Ivano;
CECAM workshop on Recent progress in adiabatic and non-adiabatic methods in quantum dynamics Talk given at a conference Electron-phonon coupling from time-dependent density functional theory 12.05.2014 Lausanne, Switzerland Tavernelli Ivano;
Ultrafast X-Ray Science Laboratory Talk given at a conference TRACKING THE ELECTRON IN PROTEINS AND NANOSYSTEMS: ULTRA- FAST 2D UV AND X-RAY ABSORPTION SPECTROSCOPIES 05.05.2014 Berkeley, United States of America Chergui Majed;
COST Action MP 1006 workshop Talk given at a conference Nonadiabatic molecular dynamics with classical and quantum trajectories 05.05.2014 Frankfurt, Germany Tavernelli Ivano;
COST Meeting XLIC Talk given at a conference Chemical dynamics in solutions probed using ultrashort UV, VUV and X-ray pulses 09.02.2014 Port-en-Bessin, France Chergui Majed;
6th international TDDFT school Poster Solvent effects and non-adiabatic dynamics of [Cu(dmp)2]+ 10.01.2014 Benasque, Spain Capano Gloria;
Workshop on Five pieces and a do in computational physics, chemistry, biology, mathematics and engineering Talk given at a conference The Bohmian way to nonadibatic dynamics 18.12.2013 Rome, Italy Tavernelli Ivano;
COST meeting ”Spin-effects on the ultrafast dynamics of photoactive transition metal com- plexes” Talk given at a conference Factors determining the ultrafast spin dynamics in metal complexes 18.11.2013 Vienna, Austria Chergui Majed;
Colloquium of the Steacie Institute for Molecular Sciences Individual talk Chemical dynamics in solutions with ultrashort X-ray and optical pulses 10.11.2013 Ottawa, Canada Chergui Majed;
Paul Scherrer Institute Individual talk TDDFT-based nonadiabatic molecular dynamics of complex molecular systems 04.11.2013 Villigen, Switzerland Tavernelli Ivano;
IBM Research Laboratories Individual talk TDDFT-based nonadiabatic molecular dynamics of complex molecular systems 31.10.2013 Rueschlikon, Switzerland Tavernelli Ivano;
BESSY VSR-Workshop ”TheVariablepulselengthSynchrotronRadiationSource” Talk given at a conference Ultrafast X-ray absorption spectroscopy of solutions. New avenues 14.10.2013 Berlin, Germany Chergui Majed;
ESCE-2013 Talk given at a conference Nonadiabatic molecular dynamics with quantum and classical trajectories 08.10.2013 Muenster, Germany Tavernelli Ivano;
Dynamic Pathways in Multidimensional Landscapes Talk given at a conference Ultrafast X-ray and UV studies of solvation dynamics 16.09.2013 Berlin, Germany Chergui Majed;
DFT 2013: 15th International Conference on Density Functional Theory and its Applications. Poster Solvent effects and non-adiabatic dynamics of [Cu(dmp)2]+ 10.09.2013 Dhuram, Great Britain and Northern Ireland Capano Gloria;
FisMat 2013 Talk given at a conference TDDFT-based nonadiabatic dynamics and the electron-phonon coupling 09.09.2013 Milano, Italy Tavernelli Ivano;
ACS Meeting Talk given at a conference Ultrafast structural dynamics with photons and electrons 08.09.2013 Indianapolis, United States of America Chergui Majed;
Gordon Research Conference on: Time-Dependent Density-Functional Theory Talk given at a conference Nonadiabatic molecular dynamics with quantum and classical trajectories 11.08.2013 New England, Biddeford, ME , United States of America Tavernelli Ivano;
The Copenhagen Conference on Femtochemistry Talk given at a conference Ultrafast X-ray and 2-dimensional UV studies of molecular and nanosystems in solu- tion 07.07.2013 Copenhagen, Denmark Chergui Majed;
CECAM workshop on Many-dimensional quantum dynamics with (non)classical trajectories, Lausanne, Switzerland Talk given at a conference TDDFT-based nonadiabatic molecular dynamics of complex molecular systems 17.06.2013 Lausanne, Switzerland Tavernelli Ivano;
Ludwig-Maximilians-Universit Muenich Individual talk TDDFT-based nonadiabatic molecular dynamics of complex molecular systems 24.04.2013 Muenich, Germany Tavernelli Ivano;
ACS Meeting Talk given at a conference The Interplay between intra- and intermolecular dynamics of metal complexes in solu- tion 07.04.2013 New Orleans, United States of America Chergui Majed;
245th ACS meeting Talk given at a conference TDDFT-based nonadiabatic molecular dynamics of complex molecular systems 07.04.2013 New Orleans, United States of America Tavernelli Ivano;
Rutherford Appleton Laboratory (Didcot, England, February 2013) Individual talk Structural Dynamics: From the Atom to the Scaffold 10.02.2013 Didcot, Great Britain and Northern Ireland Chergui Majed;
CECAM workshop: Many-dimensional quantum dynamics with (non)classical trajectories. Poster Solvent effects and non-adiabatic dynamics of [Cu(dmp)2]+ 03.02.2013 Lausanne, Switzerland Capano Gloria;
CUSCO School: Simulating actives processes in physics and chemistry Poster The role of Hartree-Fock exchange in the simulation of X-ray absorption spectra: A study of photoexcited [Fe(bpy)3]2+ 31.01.2013 Villars, Switzerland, Switzerland Capano Gloria;
16th International Workshop on Computational Physics and Material Science: Total Energy and Force Methods Talk given at a conference Nonadiabatic dynamics coupled to time dependent external potentials 10.01.2013 Trieste, Italy Tavernelli Ivano;
ACS Topical Meeting Talk given at a conference Novel approaches to protein dynamics: Ultrafast X-ray and multidimensional spectroscopies 29.11.2012 University of Puerto Rico, Puerto Rico., Puerto Rico Chergui Majed;
Lecture at the "European XFEL Science Lecture Series" DESY Talk given at a conference Nonadiabatic dynamics of complex molecular systems in external laser fields 29.11.2012 Hamburg, Germany, Germany Tavernelli Ivano;
Dalton discussion 13: "Inorganic Photophysics and Photochemistry - Fundamentals and Applications" Talk given at a conference On the interplay between the charge, the spin and the structural dynamics of transition metal complexes 10.09.2012 She, Great Britain and Northern Ireland Chergui Majed;
Theory and Applications of Computational Chemistry (TACC conference) Talk given at a conference Nonadiabatic dynamics with trajectories 02.09.2012 Pavia, Italy, Italy Tavernelli Ivano;
Second SFB-Conference: Molecular Switches: Elementary Processes and Applications Talk given at a conference Ultrafast switching of spin and structure 20.08.2012 Plon, Germany, Germany Chergui Majed;
Advances in Quantum Chemistry: Interfacing Electronic Structure with Dynamics Talk given at a conference Trajectory-based nonadiabatic dynamics with TDDFT 22.06.2012 Univ. of Minnesota, Minneapolis, USA, United States of America Tavernelli Ivano;
Annual meeting of the Swiss Physical Society Talk given at a conference Charge, spin and structural dynamics of molecular systems: Ultrafast optical and X-ray studies 21.06.2012 Zurich, Switzerland, Switzerland Chergui Majed;
TYC Energy Materials Workshop Talk given at a conference On-th-fly trajectory-based nonadiabatic dynamics with TDDFT 06.06.2012 Kings College, London, UK, Great Britain and Northern Ireland Tavernelli Ivano;
Black Forest Focus meeting of the Freiburg Institute of Advanced Studies. Talk given at a conference Structural dynamics: from the atom to the scaffold 14.03.2012 Freiburg, Germany, Germany Chergui Majed;
5th TDDFT conference Talk given at a conference Nonadiabatic molecular dynamics coupled to time-dependent external potentials: towards TDDFT-based local control 07.01.2012 Benasque, Spain, Spain Tavernelli Ivano;
APS March meeting Talk given at a conference trajectory-based nonadiabatic molecular dynamics with TDDFT 04.01.2012 Boston, USA, United States of America Tavernelli Ivano;


Knowledge transfer events



Self-organised

Title Date Place
CECAM workshop 16.10.2014 Lausanne, Switzerland

Awards

Title Year
Swiss Chemical Society award for the best oral presentation 2013

Abstract

It is now possible to obtain X-ray spectroscopic and scattering data with a temporal resolution of femtoseconds. Such experiments are able to give detailed insight into the structural changes at the atomic length scales and therefore provide invaluable information about the dynamics of chemical reactions. This is especially useful for chemical processes in the condensed phase, in which the interaction between the solvent and the solute can have a large effect on the outcome of the reaction. Such is the detail of state of the art experimental studies that theoretical simulations are critical to providing a complete understanding to the obtained data. This level of detail means that an accurate description of the electronic part of the molecular Hamiltonian is essential in order to accurately simulate experimental results. Recent developments in the treatment of non-adiabatic effcts, such as calculating the non-adiabatic coupling vectors on-the- y during molecular dynamics simulations within the framework time-dependent density function theory (TDDFT) allows for accurate excited state dynamics simulations that include solvent effects either explicitly or through a QM/MM coupling scheme. In addition the recent development of the direct dynamics variational multi-conigurational gaussian (DD-vMCG) method within the multi-conigurational time-dependent Hartree (MCTDH) method makes on-the-fl y quantum dynamics of such systems a possibility. This proposal marks an exciting development in the area of time-resolved X-ray studies. By exploiting the aforementioned improvements within the TDDFT and MCTDH approaches and by extending the theory of calculating X-ray scattering patterns in the condensed phase we will provide further understanding 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).
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