Living on Acetylene. A Primordial Energy Source - The Metal-Driven Biogeochemistry of Gaseous Compounds in the Environment - page 28

Vincent et al. [ 37 ] used a truncated model of the AH active site, consisting of
the W ion ligated by 4 dithiolene sulfur atoms, Cys141, and a water molecule and
the carboxylic acid group of Asp13 hydrogen-bonded to the water molecule, to
calculate the energy barriers between intermediates of several putative reaction
pathways. A very similar approach was followed by Liao et al. [ 35 ]. Here, a much
larger model complex of the active site of AH was used, consisting of the W ion
ligated by the two pterin cofactors, Cys141, and a water molecule. Additionally,
Asp13 and several other amino acids in close proximity (Cys12, Met140, Ile142,
Trp179, and Arg606) were included [ 35 ]. While the reaction pathways deriving
from the DFT calculation will be discussed in Section 4.8 , it is noteworthy that Liao
et al. [ 35 ] calculated a p K a of 6.3 for the Asp13 residue. Thus in this model, Asp13
will most likely be deprotonated under reaction conditions in contrast to the model
of Seiffert et al. [ 21 ] in which Asp13 is always protonated.
Using their established model for DFT calculations on the reaction mechanism
of AH [ 35 ], Liao and Himo [ 36 ] calculated the binding and activation energies for
several other compounds such as ethylene, acetonitrile, and propyne. In biochem-
ical experiments none of these compounds was turned over by AH [ 22 ]. The DFT
calculations showed that compared to acetylene, ethylene and propyne have a
about ~6 kcal/mol and ~5 kcal/mol higher binding energy for the initial displace-
ment of the water molecule at the W ion. The subsequent steps of the reaction
would have a much higher barrier than in the case of acetylene, showing why these
compounds are no substrates for AH (see Figure 7 in Section 4.8 )[ 36 ]. Acetonitrile
had a much higher binding energy than acetylene (~13 kcal/mol) but the differences
of ~3 kcal/mol more for the barriers of the subsequent steps were too low to draw a
firm conclusion whether acetonitrile is a substrate of AH or not [ 36 ].

4.8 Towards the Reaction Mechanism

When the crystal structure of AH was solved at a resolution of 1.26 , Seiffert

et al. [ 21 ] proposed two alternative reaction mechanisms on the basis of their
structural data. Depending on the nature of the oxygen ligand of the W ion (OH
or H 2 O), either a nucleophilic addition or an electrophilic Markovnikov-type
addition were proposed [ 21 ]. In both cases, acetylene, located in the pocket formed
by the hydrophobic ring, would not interact directly with the W ion but only with
the oxygen ligand activated by the W IV center and Asp13. A hydroxo ligand (OH )
would constitute a strong nucleophile that would yield a vinyl anion with acetylene.
The basicity of the vinyl anion would be sufficient to deprotonate Asp13 to form a
vinyl alcohol that would tautomerize to acetylene. A water molecule would then
bind to the W ion and get deprotonated by the now basic Asp13 to restore the active
site for the next reaction cycle [ 21 ].
A bound water molecule would gain a partially positive net charge by the
proximity of the protonated Asp13, turning it into an electrophile that could directly
attack the C

Å

C triple bond with a vinyl cation as intermediate (Figure 6 )[ 21 ].