Better insight into molecular interactions
This sketch demonstrates the principle of measurement which enables to address atom-specific and state-dependent emission of photons. With the help of first principles theory the spectral features can be associated with molecular orbitals. © Uni Rostock
How exactly atoms and molecules in biochemical solutions or at solid-liquid interfaces do interact, is a question of great importance. Answers will provide insights at processes in catalysts, smart functional materials and even physiological processes in the body, which are essential for health. Until now, scientists could have a look at these interactions by methods of spectroscopy, but it was hard to distinguish the many different interactions, which take place simultaneously.
“Basically we are looking at how atoms and molecules interact in biochemical materials in solution”, says Professor Dr. Emad Flear Aziz, leader of the Young Investigator Group for Functional Materials in Solution at the HZB and Professor at Freie Universität Berlin. Their now published work is based on a discovery by Aziz’ team made three years before: They then analyzed samples with x-ray spectroscopy and observed the disappearance of photons at some specific photon energy. These results have been replicated by other teams worldwide. To explain this effect, Aziz and colleagues proposed a “dark channel mechanism”, which should provide information about binding processes and interactions between atoms or molecules. This explanation stirred a big debate among scientists.
Now they have gathered arms with theoretical physicists around Professor Oliver Kühn from the University of Rostock in order to get a coherent picture: Aziz’ team sharpened the experimental methods further using a new approach to high resolution spectroscopy. In order to understand, how the spectral findings are linked to binding and structural processes inside the sample, Oliver Kühn and his postdoc Sergey Bokarev provided a theoretical tool, based on ab initio calculations of energy levels inside the molecules. “We can map all electronic states in the systems we probe, and we can distinguish those which are involved in building bonds with neighbors from those which are not involved”, Aziz explains. Metaphorically speaking: if the interacting molecules produce a sort of party chatter, the scientists are now able to listen to specific conversations. They are convinced that these new tools will bring deeper insights into the chemistry of life.
To the publication in PRL: State-Dependent Electron Delocalization Dynamics at the Solute-Solvent Interface: Soft-X-Ray Absorption Spectroscopy and Ab Initio Calculations
DOI:10.1103/PhysRevLett.111.083002
More about the "Dark Channel Mechanism" in the press release 2010
- Protein crystallography at BESSY II: faster, better and more and more automaticMany diseases are linked to malfunctions of proteins in the organism. The three-dimensional architecture of these molecules is often highly complex, but it can provide valuable insights into biological processes and the development of drugs. X-ray diffraction at the MX beamlines of BESSY II can be used to decipher the 3D structure of proteins. To date, more than 5000 structures have been solved at the three MX beamlines. Here, we present a review and an outlook with Manfred Weiss, head of the research group for macromolecular crystallography.
- 5000th protein structure at BESSY II: Starting point for a COVID drugMany proteins have a complex architecture that enables biological functions. Molecules can bind to specific sites on a protein and alter its function. A team at HZB has now investigated the Nsp1 protein, which plays a role in infection with the SARS-CoV-2 virus. They analysed protein crystals, previously mixed with molecules from a fragment library, and discovered a total of 21 candidates as starting points for drug development. At the same time, they also decoded the 5000th structure at BESSY II.
- What Zinc concentration in teeth revealsTeeth are composites of mineral and protein, with a bulk of bony dentin that is highly porous. This structure is allows teeth to be both strong and sensitive. Besides calcium and phosphate, teeth contain trace elements such as zinc. Using complementary microscopy imaging techniques, a team from Charité Berlin, TU Berlin and HZB has quantified the distribution of natural zinc along and across teeth in 3 dimensions. The team found that, as porosity in dentine increases towards the pulp, zinc concentration increases 5~10 fold. These results help to understand the influence of widely-used zinc-containing biomaterials (e.g. filling) and could inspire improvements in dental medicine.