How do you simulate the behaviour of protons and amino acids on the computer? How do you depict experiments to study their behaviour as more or less water is introduced? These questions may seem trivial in this age of powerful computers. Yet, it turns out this task will remain almost impossible to solve until new mathematical algorithms are found. Protons simply behave too quickly and too “unpredictably”.
Snapshot from ab Initio Molecular Dynamic Simulation. © Schmidt
In the DFG Research Centre MATHEON project “Modelling and optimizing functional molecules“, Dr. Burkhard Schmidt is working on this problem under the direction of Prof. Christof Schütte. He is using computer simulations to investigate the role of water as a solvent when it is added to amino acids or peptides in tiny steps. His main objective is to research the proton transfer between two end-groups – which leads to the formation of so-called zwitterions – and the proton transfer between appropriate side chains – which leads to the formation of so-called salt bridges.
Schmidt’s work is still at the fundamental research level, but his results will be of enormous significance to many fields. Proton transfer plays a role in energy conversion within solar cells and fuel cells, for example, and applies to the energy flow in batteries. It is even relevant to the development of new drugs.
A zwitterion is a molecule that has two or more functional groups, where one group is positively charged and another negatively charged. The molecule is therefore electrically neutral overall. Amino acids are natively electrically neutral molecules. If you dissolve them in water, however, the water protons start to ‘hop’, causing one end of the amino acid to become negatively charged and the other end to become positively charged. The protons involved in this process remain constantly in motion, forever forming new bonds. If protons hop all the way along neighbouring molecules, then charges can also be transported over nanometre-scale distances in so-called water bridges or “water wires”. All this happens on extremely short time scales.
Dr. Schmidt believes his project will help understand proton transfer mechanisms on a microscopic level. He is currently focusing on amino acids and small peptide chains. The researcher describes his approach: “Although the vast majority of biological processes occur in watery solution, our studies start by looking at isolated amino acids and peptides, in order to distinguish intramolecular from intermolecular processes. Then we gradually add individual water molecules to our simulations. That way, we can study the influence of the solvent in a controlled manner.” It is an ambitious project, since such studies can only be performed in computer simulations, and would be monumentally difficult or simply impossible as real experiments.
The scientist intends to explain, for example, how many water molecules are required to make amino acids or peptides change from neutral to zwitterionic form. He also intends to study what happens to a salt bridge as water molecules are added. “Furthermore, it is interesting to simulate these processes in their time-dependency, to be able to study the timescales of the investigated processes as well. Essential questions include how fast protons can be released from or deposited onto the appropriate side chains, or on what timescale protons are transferred between protein and water, and how fast protein transport is along water bridges,” Burkhard Schmidt explains.
In his studies, Schmidt will employ methods to calculate the energies or forces from the electron structure at every time step of the simulation. This distinguishes his work from “conventional” computer simulations, in which empirical models are applied to calculate energies and forces between the atoms. “Aside from the questionable accuracy and applicability of such empirical models, their fundamental limit is that they cannot describe the breaking and forming of chemical bonds. I’m not satisfied with that,” he says. His current research builds upon a previous project in which Dr. Schmidt studied the reaction of a proton and an electron in a water cluster. (Cluster=microdroplet)
Thanks to his mathematical/physical methods, Burkhard Schmidt is already able to calculate chemical processes a number of picoseconds long (1 picosecond = 0.000 000 000 001 second) on mainframe computers. “That’s a lot already, but I would like to reach up to nanoseconds (0.000 000 001 second),” the scientist concludes.More information:
Rudolf Kellermann | idw
At last, butterflies get a bigger, better evolutionary tree
16.02.2018 | Florida Museum of Natural History
New treatment strategies for chronic kidney disease from the animal kingdom
16.02.2018 | Veterinärmedizinische Universität Wien
Breakthrough provides a new concept of the design of molecular motors, sensors and electricity generators at nanoscale
Researchers from the Institute of Organic Chemistry and Biochemistry of the CAS (IOCB Prague), Institute of Physics of the CAS (IP CAS) and Palacký University...
For photographers and scientists, lenses are lifesavers. They reflect and refract light, making possible the imaging systems that drive discovery through the microscope and preserve history through cameras.
But today's glass-based lenses are bulky and resist miniaturization. Next-generation technologies, such as ultrathin cameras or tiny microscopes, require...
Scientists from the University of Zurich have succeeded for the first time in tracking individual stem cells and their neuronal progeny over months within the intact adult brain. This study sheds light on how new neurons are produced throughout life.
The generation of new nerve cells was once thought to taper off at the end of embryonic development. However, recent research has shown that the adult brain...
Theoretical physicists propose to use negative interference to control heat flow in quantum devices. Study published in Physical Review Letters
Quantum computer parts are sensitive and need to be cooled to very low temperatures. Their tiny size makes them particularly susceptible to a temperature...
Let’s say the armrest is broken in your vintage car. As things stand, you would need a lot of luck and persistence to find the right spare part. But in the world of Industrie 4.0 and production with batch sizes of one, you can simply scan the armrest and print it out. This is made possible by the first ever 3D scanner capable of working autonomously and in real time. The autonomous scanning system will be on display at the Hannover Messe Preview on February 6 and at the Hannover Messe proper from April 23 to 27, 2018 (Hall 6, Booth A30).
Part of the charm of vintage cars is that they stopped making them long ago, so it is special when you do see one out on the roads. If something breaks or...
15.02.2018 | Event News
13.02.2018 | Event News
12.02.2018 | Event News
16.02.2018 | Information Technology
16.02.2018 | Health and Medicine
16.02.2018 | Physics and Astronomy