The Catalytic Mechanism of Biological Nitrogen Fixation

The enzyme nitrogenase was the target of my Ph.D. work with Peter Blöchl. Atmospheric N₂ is the main natural source of nitrogen, which makes up about 10 % of the dry mass of biological matter. Nitrogenase, a bacterial enzyme, is able to convert atmospheric nitrogen into ammonia and thus to break the strongest chemical bond in nature. The reaction it catalyzes is

N₂ + 8 e^– + 8 H⁺ + 16 ATP → 16 ADP + 16 P_i + 2 NH₃ + H₂

Although the structure of the protein had been resolved almost ten years ago, the reaction mechanism is still in the dark. The active center of the enzyme (FeMo-cofactor) is a cluster containing one molybdenum atom and seven iron atoms connected by sulfur bridges. A central ligand in the cage, most probably nitrogen, has only been discovered in 2002 (Science 197, 1696 (2002)). Thus although there are a lot of experimental data available on this system, they alone are not sufficient for unraveling the reaction mechanism. Theory is required.

The system is a real challenge for a theoretician as the complicated spin structure of the FeMo-cofactor (shown on the right) is difficult – if not impossible – to describe with standard methods. Therefore we used the PAW method with a noncollinear description of the spin density. This avoids metastable minima and thus increases the reliability of the calculations.

We investigated the resting state of the FeMo-cofactor, reductions and protonations, and nitrogen binding. We found two stable binding modes, shown on the right [2]. The FeMo-cofactor was found to be flexible: a sulfur bridge opens during N₂ binding.

We worked out a model for the complete reaction mechanism of biological nitrogen reduction [3,9]. An overview, similar to the one in Ref. [3], is shown above. The energetically most difficult step is the first protonation of N₂ bound to FeMo-cofactor [1]. As it can already be seen from the nitrogen binding modes, the central ligand plays an important role as it can offer a variable number of bonds to its iron neighbors. Therfore it allows efficient binding of differently-sized intermediates.

The mechanism we found explains many experimental facts. In order to verify it, we also investigated the experimentally observed hydrogen production. Additionally, investigations on acetylene (C₂H₂) interacting with the FeMo-cofactor explain how C₂H₂ and N₂ inhibit each other [4].