Mechanistic investigations of the nitrogenase enzyme

Abstract

The nitrogenase reaction mechanism has been examined using several variations of QM/MM
(Quantum Mechanical/Molecular Mechanical) methods. All calculations were based on a
1.0Å X-ray crystal structure and were performed with the software ComQum and Turbomole.
The investigation consists of three distinct projects.
First, redox potentials between different states of the P-cluster and the FeMo cluster were
calculated in order to examine which charge state that could be used for the nitrogen fixation
reaction. This project is based on a recently calibrated methodology to calculate redox
potential for iron-sulfur clusters. We found that a charge assignment of FeIIFe6
III for the seven
Fe ions in the FeMo cluster in the resting E0 state gives redox potentials that are closest to
experiments and to those obtained for the standard Fe8
III/Fe7
IIFeIII redox couple of the Pcluster, in contrast to current consensus that the E0 state is in the Fe3
IIFe4
III configuration.
In the second project, proton movements are studied for the E4 to E5 transition with a
dissociated S2B sulfide ligand. This work is based on a previous study, which indicated that
protonation of S5A might constitute a thermodynamic sink. Therefore, an additional proton
was placed on S5A to see if the problem can be reduced. The results showed slight lowering
of the activation energies of certain key proton transfers compared to the previous study.
However, this energy lowering was not enough for the protonation mechanism to be
considered completely realistic.
In the third project, we studied the structure of the FeMo cluster in the doubly protonated and
reduced E2 state. A previous study by Bjornsson and Thorhallsson had indicated that
structures with the S2B ligand dissociated from one Fe ion are most stable for this
intermediate. Our results show that several different types of structure (with S2B ligand
bound to one or two Fe ions) are close in energy and that the most stable structure depends on
what DFT functional is used and what broken-symmetry state is employed.

Popular Abstract

Nitrogen is essential for all life because it is a fundamental building block of DNA and
proteins. DNA is important for reasons I am sure most people know, but proteins might
require a slight explanation.
When one hears the word “protein”, the first thing that might come to mind is muscles. This
is logical since muscles are built from proteins, but it is only scratching the surface of their
functionality. The vast majority of chemical processes in your body involve proteins. A few
examples are signalling, metabolism and, as stated structural proteins like muscle tissue.
Every single type of protein contains nitrogen which illustrates the importance of this
element.
The air we breathe is mostly gaseous nitrogen (N2), but most organisms (including humans)
cannot intake nitrogen for the air. This seems strange. Why do we not intake nitrogen through
our lungs if it is so important?
Well, N2 consists of two nitrogen atoms connected through a triple bond. These bonds are
very strong and human beings do not have the tool needed to break up the nitrogen atoms. In
fact, every single animal you have seen (with your unaided eyes) is incapable of splitting up
N2. This logically leads to a new question. How does nitrogen end up in our food if none of
the animals and plants we eat can split N2?
To split up N2, you need a tool. This tool is a protein called nitrogenase and it exists only
within certain microorganisms such as cyanobacteria. In these microorganisms, nitrogenase
takes N2 and turns it in to ammonia (NH3). NH3 can then be taken up by plants and continues
to make its way through the food chain and ends up in our bodies ready to be used.
Nitrogenase is the only known way to biologically perform this reaction and it is the origin of
the majority of the non-synthetic nitrogen we intake from our food. This makes nitrogenase
one of the most important proteins for all life.
This work focuses on the study of precise atom and electron movements that occur during the
conversion of N2 to NH3 within nitrogenase. The detailed order of atom and electron
movements during a reaction is called a reaction mechanism. The examination consists of
undertaking computational calculations of energy levels for different atom and electron
positionings. Comparing energy changes between different electron or atom positions can
give an insight in how the reaction actually occurs in nature.
Today, a large amount of the nitrogen we intake comes from synthetic sources. Synthesised
NH3 used in fertiliser has directly led to millions of people being able to live. However, the
method which is mainly used to create NH3 is extremely energy demanding. The reaction
mechanism of nitrogenase is largely unknown and unlocking its secret could lead to a low
energy alternative to our current synthetic methods. This could help in keeping humanity fed
while consuming less from the environment.

• author: Svensson, Oskar
• supervisor: Ulf Ryde
• organization: Department of Chemistry
• course: KEML10 20221
• year: 2022
• type: M2 - Bachelor Degree
• subject: Chemistry
• keywords: Theoretical Chemistry, Nitrogenase, Reaction Mechanism
• language: English
• id: 9085555
• date added to LUP: 2022-08-08 09:44:39
• date last changed: 2022-08-08 09:44:39