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Structural Dynamics in Chemical Systems

From different scientific perspectives, we examine the movement of molecules, their atomic motion when interacting with another molecule and their characteristics. Precisely, we study the time-dependent spatial behaviour of solids and condensed matter phenomena at highest possible molecular scale and electron density resolution "in real time" and "in situ". Within this field, our research team develops and applies time-resolved optical and X-ray methods from minutes down to femtosecond time resolution.

In particular, ultrafast time-resolved optical spectroscopy, soft X-ray spectroscopy as well as high energy X-ray scattering, diffraction and crystallography methods (> 15 keV) are developed and applied to answer actual scientific questions in the field of kinetics and dynamics of molecular systems and soft condensed matter.

Structural Dynamics Principles

In a chemical reaction, typical time scales of atomic or molecular motions start from femtoseconds, meaning the billionth of a billionth of a billionth of a second. Life relevant motions, like moving a pen during writing, can be as slow as seconds or even down to minutes’ or hours’ time scales (depending on the ideas one desires to write down). How are these time scales connected? To what extend structural motifs “freeze in” in time and dynamics information of chemical reactions? Which type of apparatus needs to be built and which kind of methods needs to be developed for investigating the created femtosecond “time stamps” in the structure of complex matter during the time course of a chemical or biochemical reaction?

Some time ago, in a proof of principle experiment, it has been postulated that high flux, pulsed x-rays – as been created with synchrotrons or Free Electron Lasers – can act as the “photons of choice” for collecting of what has been called the “molecular movie” since then [1]. Figure 1, 2 and Figure 3, middle summarizes its experimental principle: after the initiation of a reaction with an ultrashort optical pulse, the proceeding reaction’s structural changes are imaged by collecting a series of ultrafast snap shots of X-ray images as a function of time. It has been envisioned that utilizing X-ray photons will allow for the development of methods well beyond energy resolution, temporal resolution and spatial resolution of alternative methods developed so far. X-ray sources of the 3rd and 4th generation should make investigations possible, where laboratory sources reach their limit in resolution.

During the time course of FEL methods development we learned that high flux X-ray sources provide much more fascinating possibilities for the characterization of chemical and biochemical reactions as we first naively thought in the begin of 2000th. When X-ray photons are created in an undulator (which is a special arrangement of magnets where the electrons, which emit the X-ray radiation, are guided through), five very typical properties characterize them:

(i) their extremely high degree of lateral and transversal coherence,
(ii) their very high brilliance (very small nanometer focus combined to a high number of generated photons),
(iii) their time resolution down to 10 femtoseconds or even – now – attoseconds,
(iv) their tunability in energy to a very high precision and
(v) their polarization tunability. So, free electron laser sources provide
all the typical characteristics for pulsed lasers, just in the X-ray regime.

From Local to Global Dynamic Structural Analysis: Ultrafast X-ray Spectroscopy and Ultrafast X-ray Diffraction Shake their Hands

As in optical laser sciences, X-ray laser science allows to couple X-ray techniques coming from entirely complementary pools of methods. Such a merge resembles the “local to global” approach when combining ultrafast X-ray diffraction (with precisions down to electron density determination) with highest energy resolution X-ray spectroscopy. Both methods are technically demanding by their own: ultraprecise structure determination requires the use of very hard X-ray radiation (starting from 18 keV X-ray energy) and very high angular momentum collection, on one hand; on the other hand, X-ray spectroscopy with ultra-high energy resolution requires highest spectrometer grating resolution (down to 0.000001 keV resolution on a scale of 5.000000 keV X-ray energy) or the implementation of two-dimensional X-ray laser spectroscopy techniques, and all of that on the ultrafast time scale (and combined).

The resolutions are necessary in order to be element and chemical site specific and specific to the type of bond which is broken and/or formed during a reaction (we want to study chemical reactions). Figure 3 summarizes some scientific results of such technical efforts. They have been realized at the free electron lasers FLASH at DESY and LCLS in Stanford:

(i) X-ray spectroscopy: LJ-endstation/SXR-LCLS (2009), FlexRIXS/BESSY (2010), ChemRIXS/TRRIXS-endstations P04/PETRA (2014), BL2-CAMP/FLASH (2016), HeisenbergRIXS/EXFEL (2018)
(ii) High-resolution X-ray diffraction: ID09B/ESRF (1998), P11-P24/PETRA-III (2014, 2018), XPP-CXI/LCLS (2012)

In order to reach the desired chemically meaningful temporal resolution (Figure 3, middle), the optical laser pump initiates the reaction and the X-ray laser pulse probes the ultrafast proceeding chemical reaction by collecting the X-ray spectroscopic signal and/or the X-ray diffraction signal in common photon in / photon out type of approach. In the first time of experiment the photographic camera is a detector which collects the X-ray diffraction signal, in the 2nd type of experiment a second camera is attached which collect the energy resolved X-ray spectroscopic signal in emission. An example of a two-dimensional X-ray spectroscopy study of simple water following such an experimental approach [3,4] is shown on the top of Figure 3. On the bottom left of Figure 3, the migration of electrons through a wire type of organic molecule, as been determined by ultrafast x-ray diffraction and after ultrafast optical excitation is shown. The methods can be utilized for reaction in all thermodynamic phases (gaseous, liquid and solid).
Applied methods include photo electron diffraction or Coulomb explosion schemes [5], ultrafast two-dimensional X-ray spectroscopy [6], ultrafast X-ray emission spectroscopy and X-ray scattering schemes [7,8] or ultrafast diffraction [9]. Proceeding laboratory based methods, free electron laser radiation makes it possible not only to study unimolecular reactions, which is the classical theme of ultrafast chemical research, but also to investigate bimolecular reaction in the liquid phase which are the more common type of reactions in nature (Figure 3, bottom right – in the “movie”).

From Structural to Functional Dynamics: Optimizing Optoelectronical Devices

In order to optimize the efficiency of next generation solar cells made of plastics, the FS-SCS group’s aim is to apply the fundamental understanding about the electron redistribution and structural reorganization in chemical systems.
As a consequence of the technical developments summarized, and based on the chemical time laws derived during the various method development steps, as a side result it has become possible to optimize functional performances i.e. of organic materials or devices with solar cell activities (Figure 4). By moving the fundamental methods developments into the application regime (again as a proof for the methods’ developments), the circle of promises closes that 3rd and 4th generation X-ray sources may help to optimize strategies for modern material performances. Figure 4 presents such efforts. Since the time-resolved X-ray spectroscopy and X-ray diffraction experiments allow for detangling local to and local from global structural responses, desired functional actions of a device like energy storage can be distinguished from “energy-eating” processes based on non-desired heating and energy quenching processes. In Figure 2, the performance of an optimized all-over organic solar cell is presented. Small atomic (even not molecular) changes on the light-absorbing chromophore unit lead to a complete switch of its functional dynamics – from light absorbing solar cell devices [11-13] to a light emitting organic diode [14]. In another example the understanding of the crystallization processes of organic material out of TRXRD studies has been influenced by the optimization of the recycling process of molten PET bottles to ultra-hard polyethylene [15]. Such ultra-hard plastic material is currently built in every 2nd wind craft machine produced. Other applications may include the study of complex energy transforming steps in complex macromolecules [16].

From Structural to Topological Dynamics: Proteins Dynamics

One example of a various techniques merge is the combination of high flux and high energy resolution X-ray spectroscopy with electro spray ionization and mass spectrometry.

Since the absorption of X-ray photons is element specific (Figure 5, top), and selective towards its chemical environment, tuning the X-ray excitations with defined photon properties [17] allows to collect ionization and chemical fragmentation pattern generated in an initial step of “electron time clocking” on this internal femtosecond X-ray clock. Consequently, the chemical fragments are defined through the characteristics of the X-ray excitation [18]. The combination of X-ray spectroscopy (Figure 5 bottom, left) with mass spectrometric tools (Figure 5 bottom, right) [19] allows for the precise determination of the experimental energies of occupied and low lying non-occupied molecular orbitals of complex molecules (polyaromatic systems, nucleotides,amino acids, peptides, proteins [20,21]). In comparison, optical spectroscopy in the VIS und UV regime delivers relative transition energies. Therefore it is possible to determine with extremely high precision experimentally binding energies and characterize ionization processes during ion and radical formation or hydrogen bonding processes. The recorded, corresponding decomposition pattern include – again – chemical analytical information typical for mass spectrometry – simply precisely connected to the initial orbitals of biomolecules from which the journey of chemical decomposition starts. Such correlations deliver additional puzzle pieces in determining time stamps of biochemical reactions in structural features of the relevant

Figure 5 summarizes other method compositions of synchrotron and free electron laser X-ray scattering and structure determination methods with reaction initiating or thermodynamically and kinetically modulating techniques which can be distinguished as physical modulation techniques or chemical modulation techniques [22]. As in Figure 5, the presented examples are various types of macromolecules. Depending on the time scale to be studied in real time it is possible to merge X-ray scattering techniques like diffuse X-ray scattering with pressure jump, electric field modulations, temperature jump – or – on the chemical modulation site with structural freezing methods, rapid mixing or photo switching methods [22].


Filming chemical reactions in real time and the “local to global” approach utilizing ultrafast high flux X-ray sources
[1] S. Techert, F. Schotte, M. Wulff, Picosecond x-ray diffraction probed transient structural changes in organic solids, Phys. Rev. Lett. 86, 2030-2034 (2001).

[2] S. Bari, R. Boll, S. E. Canton, L. Glaser, K. Idzik, K. Kubicek, D. Raiser, S. Thekku Veedu, Z. Yin, S. Techert, High flux X-ray sources and Free Electron Lasers for studying ultrafast time structure imprints in complex chemical and biochemical reactions, in: X-ray Free Electron Lasers, eds. U. Bergmann, P. Pellegrini, Oxford University Press, in press (2016) and references therein.

[3] Z. Yin et al., Probing the Hofmeister effect with ultra-fast core-hole spectroscopy, J. Phys. Chem. B 118 (31), 9398-9403 (2014).

[4] S. Schreck et al. Reabsorption of soft x-ray emission at high x-ray free-electron laser fluences, Phys. Rev. Lett. 113 (15), 153002 (2014).

[5] R. Boll et al., Imaging molecular structure through femtosecond photoelectron diffraction on spatially aligned and oriented gas-phase molecules, Faraday Discuss. 171, 1–24 (2014).

[6] P. Wernet et al., Orbital-specific mapping of the ligand exchange dynamics of Fe(CO)5 in solution, Nature 520 (7545), 78-81 (2015).

[7] W. Zhang et al., K. Kubicek et al., Tracking excited state charge and spin dynamics in iron coordination complexes, Nature 509 (7500), 345-8 (2014).

[8] S. E. Canton et al., Visualizing the non-equilibrium dynamics of photoinduced intramolecular electron transfer with femtosecond X-ray pulses, Nat. Comm. 6 (3), 6359-6362 (2015).

[9] I. Rajkovic et al., Diffraction properties of periodic lattices under free electron laser radiation, Phys. Rev. Lett. 104, 125503-6 (2010).

From Structural to Functional Dynamics.
[10] S. Thekku Veedu et al., Ultrafast dynamical study of pyrene-N,N-dimethylaniline as an organic molecular diode in solid state, J. Phys. Chem. B 118 (12), 3291 - 3297 (2014).

[11] S. Mildner et al., Temperature and doping dependent optical absorption in the small polaron system Pr1-xCaxMnO3, Phys. Rev. B 92 (3), 35145-35148 (2015).

[12] D. Raiser et al., Evolution of hot polaron states with ns lifetime in a manganite, submitted (2016).

[13] K. R. Idzik et al., The optical properties and quantum chemical calculations of thienyl and furyl derivatives of pyrene, Phys. Chem. Chem. Phys., 17 (35), 22758-22769 (2015).

[14] M. Petri, private communication (2016) and http://www.armacell-core foams.com/www/armacell/INETArmacell.nsf/standard/ DC2C5D13EA92BD46802576E200526C26.

[15] C. Kupitz et al., S. Bari et al., Serial time-resolved crystallography of photosystem II using a femtosecond X-ray laser, Nature 513 (7417), 261-265 (2014).

From Structural to Topological Dynamics.
[16] E. Ferrari et al., L. Glaser et al., Single shot polarization characterization of XUV FEL pulses from crossed polarized undulators, Nat. Sci Rep. 5, 13531-4 (2015).

[17] Z. Yin et al., Experimental setup for high resolution X-ray spectroscopy of solids and liquid samples, Proc. SPIE 8849, X-Ray Lasers and Coherent X-Ray Sources: Development and Applications X, 88490I (2013).

[18] J. Schulz, S. Bari et al., Sample refreshment schemes for high repetition rate FEL experiments, Proc. SPIE 8778, Advances in X-Ray Free Electron Lasers II: Instrumentation, 87780T (2013).

[19] O. González-Magaña et al., S. Bari et al., Fragmentation of protonated oligonucleotides by energetic photons and Cq+ ions, Phys. Rev. A 87 (3), 032702-12 (2013).

[20] S. MacLot et al., S. Bari et al., Ion-induced fragmentation of amino acids: effect of the environment, Chem. Phys. Chem. 12 (5), 930-936 (2011).

[21] R. Jain, S. Techert, Time-resolved and in-situ X-ray scattering methods beyond photoactivation: utilizing high-flux X-ray sources for the study of ubiquitious non-photon active proteins, Special Issue: “Synchrotron Applications in Life Sciences”, Prot. Pept. Lett. 23 (999), 01-08 (2016) and references therein.

Our Group: Scíentifically Diverse

Considering the group’s name, one may believe that the FS-SCS group consists of chemists only. But this is not the case. Our group members are not only chemists, but also physicists and biologists. Therefore, our group’s name shouldrather be Structural Dynamics in Biophysical Chemistry. Currently, we even have more physicists than any other scientists. Personally, we really like this fact because due to these different scientific fields within our group, we never stay focused on one particular research area. This fact makes an inspiring, stimulating and creative exchange of ideas possible, often leading to great new scientific findings.

How does this scientific diversity work?

Within the field of physics, we develop instrumentation for high flux X-ray sources which are necessary for further research, precisely for the investigation of structural dynamics of complex chemical systems which then, eventually, may lead to an optimization of functional dynamics in not only chemical but also biological systems. So for example, the X-ray spectroscopy of molecular switches makes it possible to measure the molecules’ change of structure as a function of time, leading to an optimization of their structure for fast time response = 0 and therefore, generating new possibilities in the field of optical switches.