MATERIALS SCIENCE AND CHEMISTRY

Studying the mechanochemistry of disulfide systems upon nucleophilic attack is a very rich field where each system requires computing resources and CPU time that can only be provided by very powerful supercomputers such as provided by the Gauss Centre for Supercomputing. Simulations run on JUQUEEN of JSC in the course of this project offered a wealth of surprises and novel insights into mechanochemical reactions. While they resulted in discovering unexpected reaction mechanisms, they - amongst others - brought to light an unknown phenomenon with respect to splitting disulphide bonds in water.

Highly dispersed gold/titania catalysts are widely used for key reactions, notably including the selective oxidation of alcohols in the liquid phase using molecular oxygen. The mechanistic details of this reaction are mostly unknown. Especially the pivotal role of water in stabilizing charge transfer and its actual chemical role in the reaction mechanism is of great interest. In this project, scientists at the Ruhr-Universität Bochum use enhanced sampling ab initio molecular dynamics simulations to elucidate the mechanistic detail of thermally activated liquid-phase methanol oxidation focusing also on the activation of oxygen.

The work horse of chemical industry is heterogeneous catalysis meaning that complex solid materials (catalysts) are used to facilitate chemical reactions, thus reducing production costs. To improve such catalysts in a systematic manner, knowledge of the ongoing reactions is most desirable. One of the key reactions industry performs at large scales is methanol (“wood alcohol”, H₃COH) synthesis from syngas being a mixture of gaseous CO₂, CO, and H₂. Scientists investigated the methanol production which is catalyzed using copper nanoparticles on a zinc oxide support. Based on sophisticated molecular dynamics sampling techniques in conjunction with the large-scale parallel platform SuperMUC at LRZ, they discovered a hitherto unknown complex…

Organisms which live under extreme conditions have established adaptation mechanisms during their evolution. One such mechanism with enables life under kbar pressures in deep sea habitats is an unusually high concentration of a specific molecule in their blood, namely TMAO (trimethylamine N-oxide). Yet, the so-called piezolytic mechanism which counteracts such high pressure effects within cells is not understood. As a first step, scientists investigated the properties of aqueous TMAO solutions at very high pressure compared to ambient conditions and find significant changes in the hydrogen bonding properties.

Disulfide bonds are known to stabilize protein structures by imposing covalent cross-links. More recently they have been found to regulate protein activity as well by undergoing chemical reactions themselves. However, the chemistry of disulfide bond cleavage reactions is astonishingly rich and includes also β-elimination reactions in alkaline solution instead of the usual nucleophilic substitution at one of the sulfur atoms. Using HPC system JUQUEEN, an international team of scientists computationally studied both reaction channels as a function of increasingly large mechanical forces.

Prebiotic Chemistry is the study of those chemical reactions that could have taken place on the early Earth by which, starting from small molecules like H₂O, NH₃, CO₂, SH₂ or simple amino acids, more complex molecules were formed. This leads eventually to the formation of biomacromolecules as we know them from today's life, for instance proteins, RNA or DNA but also lipids. Advanced computer simulations in conjunction with large-scale HPC facilities and scalable codes allow one to investigate at the very molecular level not only how these reactions could have happened, but more importantly how they are affected by factors like temperature, pressure, or the presence of mineral surfaces to name but a few. 

In order to initiate chemical reactions, energy must be provided in order to overcome the so-called activation barrier, which separates the reactants from the product of the reaction. This energy can be supplied in different forms such as heat, light, electrical current or as mechanical forces that distort the molecules involved.

Mechanical stress can not only accelerate chemical reactions but also induce novel reaction pathways and possibly novel products. A team of scientists from the Lehrstuhl für Theoretische Chemie at Ruhr-Universität Bochum developed computational machinery to simulate such stressed molecules at the molecular level in the “virtual lab”.