QM/MM Studies of Nitrogenase

Abstract

Nitrogenase is the only enzyme that can cleave the strong triple bond in N₂, making nitrogen available for biological life. Despite extensive research, the mechanism of nitrogen fixation by nitrogenase is not fully understood, partly due to the enzyme’s complex structure, which includes the largest iron–sulfur cluster known in metalloenzymes, the FeMo cluster. Understanding this process requires the integration of various scientific disciplines, such as inorganic chemistry, biochemistry, crystallography, spectroscopy, and computational chemistry. This thesis employs combined quantum-mechanics and molecular-mechanics (QM/MM) computational methods to investigate the structure and function of nitrogenase, focusing on its reaction mechanisms, intermediates, and electronic states.
The thesis comprises eight papers that explore different parts of the nitrogenase catalytic cycle. Papers I and II focus on the early part (E₀–E₄), revealing variability in the predictions of different DFT functionals regarding H₂ formation and N₂ binding. Papers III and IV examine the latter part (E₄–E₈), emphasizing the role of the S2B ligand and proton-transfer mechanisms, which suggest that S2B should remain bound to ensure lower energy barriers for proton transfers. Papers V and VI investigate the possibility of S2B ligand dissociation, and the results indicate that the stability of various structures is highly dependent on the DFT method used. Paper VII presents redox-potential calculations that provide insights into the redox properties of nitrogenase. Paper VIII analyzes the first Fe-nitrogenase structure, focusing on protonation states and the electronic structure in the E₀ and E₁ states.
These studies highlight the complexities of nitrogenase catalysis and underscore the limitations of current experimental techniques in capturing reaction intermediates. Computational methods have proven invaluable for studying these intermediates, offering insights that are difficult to obtain experimentally. While challenges remain, particularly in determining the exact structure of the E₄ intermediate, this research advances our understanding of nitrogenase.

• author: Jiang, Hao
• supervisor: Ulf Ryde
• opponent: Professor Raugei, Simone, Pacific Northwest National Laboratory
• organization: Computational Chemistry; eSSENCE: The e-Science Collaboration
• publishing date: 2024-09-27
• type: Thesis
• publication status: published
• subject: Theoretical Chemistry (including Computational Chemistry)
• keywords: Nitrogenase, QM/MM, DFT, nitrogen fixation, reaction mechanism, H2 formation, N2 binding, proton transfer, E2 intermediate, redox potential, broken-symmetry state
• pages: 225 pages
• defense location: Chemical Centre, Lecture Hall A
• defense date: 2024-09-27 09:00:00
• ISBN: 978-91-8096-058-8
• ISBN: 978-91-8096-059-5
• language: English
• LU publication?: yes
• id: e1971d63-8682-49ef-af62-2f248e1c64e9
• date added to LUP: 2024-07-29 14:55:07
• date last changed: 2025-04-04 15:21:41