Monday, March 26, 2012

Getting nervous at the biomolecular dance

Enzymes are amazing.
Today I went to an interesting chemistry seminar today by Ian Dance,
Nitrogenase reduces N2 to NH3 and CO to hydrocarbons. What chemistry is used?
It was also a David Craig lecture and was a model seminar for a general audience.

A major industrial process is the fixation of nitrogen to from ammonia.
N2 + 3H2 -> 2 NH3.
This is done via the Haber-Bosch process and requires pressures of 1000 atm and high temperatures of 450 degrees C with iron or ruthenium as catalysts.

However, nature does this at room temperature and pressure via nitrogenase enzymes. A surprising recent discovery was that vanadium nitrogenase can also reduce carbon monoxide to small hydrocarbons.

Dance used an interesting dance (!) metaphor during the talk. You need a stage [key part of the enzyme], centre stage [the active sites], dancers [the intermediate states], and a choreography [reaction mechanisms].

The stage for nitrogenase is shown below. the FeMo-co, which can be viewed as two  cubes [one is Fe4S3 and one Fe3MoS3] that have been fused together at a N vertex. Only very recently was the N atom seen in the enzyme structure.

Previously it was thought that the Mo atom on the bottom was the active site but now it is believed to be a pair of the Fe ions in the upper cube.

Something I thought were particularly interesting:
To obtain a good supply of protons to the active site one possible mean is a chain of hydrogen bonded water molecules [see the orange circles below].

A few things in the talk made me nervous.
All the calculations are based on some version of DFT. There was no mention of what functional was used, basis sets, convergence tests, or benchmarking.
Dance is using his own personal method for finding transition states.
It is not clear that he has a ground state with the correct spin, S=3/2.
There are tens of "molecular orbitals" [presumably actually Kohn-Sham orbitals] within about 1 eV of the so-called "HOMO" and "LUMO".
All the calculations are done in gas phase without implicit or explicit solvent (water + protein).
Many of the calculated activation energies are in the range 2-20 kcal/mol [0.1-1 eV for the physicists]. Is DFT really very reliable on this scale for such large molecules, particularly including 8 transition metal atoms?
Because the calculation gives too large an activation energy compared to experiment it was suggested that proton tunneling may occur below the barrier. [Apparently, it is not possible to test this hypothesis experimentally with isotope substitution.] [My experience with proton tunneling in enzymes is that this is subtle and murky issue].

Much of the material in the talk is in a summary paper

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