Scientists from Neese-Group involved in the construction of a "computational microscope" to observe atomic structures
Atomic and subatomic forces determine molecular interactions that cannot be watched with conventional analytical methods but must be quantum-chemically calculated. For the first time, researchers have developed a "computational microscope" using a combination of calculation approaches that simulates the forces and gives an insight into interactions that drive molecules.
The method used here, called "QM/MM", combines concepts from quantum mechanics and classical physics. This method, which was significantly elaborated at the Max-Planck-Institut für Kohlenforschung in Mülheim in the department of the recently emeritus director Walter Thiel. With their new tool, the team of researchers in Illinois and Mülheim hope to better understand the chemistry of life and model large molecular systems in order to develop new pharmaceutical and industrial active ingredients. The recently deceased world-famous researcher Klaus Schulten, his wife Zaida Luthey-Schulten (both from the University of Illinois) and Frank Neese's group from the Max-Planck-Institut für Kohlenforschung were involved in the collaboration. The scientists from the Max-Planck-Institut used the ORCA program developed in Mülheim to provide the quantum mechanical expertise that was combined with the world's leading molecular dynamics program NAMD.
The combination of the methods enables the simulation of hundreds of millions of individual atoms and zooms to the subatomic range, where it shows electronic interactions. As an example, the researchers simulated the chemical behavior of transfer RNAs, ribonucleic acid molecules that play a key role in the conversion of genetic information into proteins. The functionality of the new "Computer Microscope" is described in the journal „Nature Methods“ in the article „NAMD goes quantum: an integrative suite for hybrid simulations“.
More information on the project can be found on the website of the University of Illinois.
Illustration: Source: Rafael Bernardi, Zan Luthey-Schulten and Marcelo Melo, University of Illinois. Visualization of the process by which the amino acid glutamate (Glu) is attached to a specific region of its transfer RNA (tRNA).