Cursuri: Computational methods for exploring biomolecule reactivity and structure și Computational studies of nitrogenase

Cursuri susținute de Prof. Dr. Ulf Ryde (International Advanced Fellow – Star UBB), găzduite de Facultatea de Chimie și Inginerie Chimică.

• Computational methods for exploring biomolecule reactivity and structure – Joi, 7 Octombrie, ora 14.00–15.00 EEST

During the latest decades, computational methods have been established as an important alternative and complement to experiments to study structures and reactivities of biomolecules. In this lecture, I will present various useful computational methods. I will concentrate on methods employing a combination of quantum mechanics (QM) and molecular mechanics (MM), which provide a proper balance between accuracy and computational speed. In these, accurate QM calculations are performed for a rather small (some hundred atoms), but interesting part of the biomolecule, where reactions of interest take place. For the remainder of the biomolecule, as well for the surrounding solvent, cheaper MM methods are employed. I will discuss how such calculations are constructed, how the systems are set up, discuss the performance, show some applications and how a detailed understanding can be obtained. Finally, I will discuss how the method may be combined with experimental data to obtain accurate structures and to interpret crystal structures.

Venue: Zoom https://lu-se.zoom.us/j/63765179965.

• Computational studies of nitrogenase – Joi, 14 Octombrie, ora 14.00–15.00 EEST

Nitrogenase is the only enzyme in nature that can cleave the triple bond in N₂ to form ammonia and make nitrogen available for living creatures. The MoFe protein of nitrogenase contains two unusual metal clusters, the P cluster, which is a Fe₈S₇ cluster that transfers electrons and the catalytic FeMo cluster, a MoFe₇S₉C (homocitrate) complex, bound to the protein by a cysteine and a histidine residue. It performs the reaction: N₂ + 8 e^– + 8 H⁺ + 16 ATP -> 2 NH₃ + H₂ + 16 ADP + 16 P_i. The mechanism is normally described as sequence of eight E₀–E₇ states, differing in the number of delivered electrons and protons. It is believed that N₂ binds to the E₄ state, concomitant with the release of H₂. Many groups have employed density-functional theory calculations to understand the mechanism, but this has not led to any consensus. Instead, different groups have suggested totally different mechanisms and even diverging models for the E₄ state. We have performed systematic studies of nitrogenase with the combined quantum mechanics and molecular mechanics (QM/MM) approach. In this talk, I will describe some of these results.

Venue: Zoom https://lu-se.zoom.us/j/66636465571.