29 research outputs found
Substrate Channel in Nitrogenase Revealed by a Molecular Dynamics Approach
Mo-dependent
nitrogenase catalyzes the biological reduction of
N<sub>2</sub> to two NH<sub>3</sub> molecules at FeMo-cofactor buried
deep inside the MoFe protein. Access of substrates, such as N<sub>2</sub>, to the active site is likely restricted by the surrounding
protein, requiring substrate channels that lead from the surface to
the active site. Earlier studies on crystallographic structures of
the MoFe protein have suggested three putative substrate channels.
Here, we have utilized submicrosecond atomistic molecular dynamics
simulations to allow the nitrogenase MoFe protein to explore its conformational
space in an aqueous solution at physiological ionic strength, revealing
a putative substrate channel. The viability of this observed channel
was tested by examining the free energy of passage of N<sub>2</sub> from the surface through the channel to FeMo-cofactor, resulting
in the discovery of a very low energy barrier. These studies point
to a viable substrate channel in nitrogenase that appears during thermal
motions of the protein in an aqueous environment and that approaches
a face of FeMo-cofactor earlier implicated in substrate binding
Manganese-Based Molecular Electrocatalysts for Oxidation of Hydrogen
Oxidation of H<sub>2</sub> (1 atm)
is catalyzed by the manganese
electrocatalysts [(P<sub>2</sub>N<sub>2</sub>)ÂMn<sup>I</sup>(CO)Â(bppm)]<sup>+</sup> and [(PNP)ÂMn<sup>I</sup>(CO)Â(bppm)]<sup>+</sup> (P<sub>2</sub>N<sub>2</sub> = 1,5-dibenzyl-3,7-diphenyl-1,5-diaza-3,7-diphosphacyclooctane;
PNP = (Ph<sub>2</sub>PCH<sub>2</sub>)<sub>2</sub>NMe); bppm = (PAr<sup>F</sup><sub>2</sub>)<sub>2</sub>CH<sub>2</sub>; Ar<sup>F</sup> =
3,5-(CF<sub>3</sub>)<sub>2</sub>C<sub>6</sub>H<sub>3</sub>). In fluorobenzene
solvent using 2,6-lutidine as the exogeneous base, the turnover frequency
for [(P<sub>2</sub>N<sub>2</sub>)ÂMn<sup>I</sup>(CO)Â(bppm)]<sup>+</sup> is 3.5 s<sup>–1</sup>, with an estimated overpotential of
700 mV. For [(PNP)ÂMn<sup>I</sup>(CO)Â(bppm)]<sup>+</sup> in fluorobenzene
solvent using <i>N</i>-methylpyrrolidine as the exogeneous
base, the turnover frequency is 1.4 s<sup>–1</sup>, with an
estimated overpotential of 880 mV. Density functional theory calculations
suggest that the slow step in the catalytic cycle is proton transfer
from the oxidized 17-electron manganese hydride [(P<sub>2</sub>N<sub>2</sub>)ÂMn<sup>II</sup>HÂ(CO)Â(bppm)]<sup>+</sup> to the pendant amine.
The computed activation barrier for intramolecular proton transfer
from the metal to the pendant amine is 20.4 kcal/mol for [(P<sub>2</sub>N<sub>2</sub>)ÂMn<sup>II</sup>HÂ(CO)Â(bppm)]<sup>+</sup> and 21.3 kcal/mol
for [(PNP)ÂMn<sup>II</sup>HÂ(CO)Â(bppm)]<sup>+</sup>. The high barrier
appears to result from both the unfavorability of the metal to nitrogen
proton transfer (thermodynamically uphill by 9 kcal/mol for [(P<sub>2</sub>N<sub>2</sub>)ÂMn<sup>II</sup>HÂ(CO)Â(bppm)]<sup>+</sup> due
to a mismatch of 6.6 p<i>K</i><sub>a</sub> units) and the
relatively long manganese–nitrogen separation in the Mn<sup>II</sup>H complexes
Evaluation of the Role of Water in the H<sub>2</sub> Bond Formation by Ni(II)-Based Electrocatalysts
We
investigate the role of water in the H–H bond formation by
a family of nickel molecular catalysts that exhibit high rates for
H<sub>2</sub> production in acetonitrile solvent. A key feature leading
to the high reactivity is the Lewis acidity of the NiÂ(II) center and
pendant amines in the diphosphine ligand that function as Lewis bases,
facilitating H–H bond formation or cleavage. Significant increases
in the rate of H<sub>2</sub> production have been reported in the
presence of added water. Our calculations show that molecular water
can displace an acetonitrile solvent molecule in the first solvation
shell of the metal. One or two water molecules can also participate
in shuttling a proton that can combine with a metal hydride to form
the H–H bond. However the participation of the water molecules
does not lower the barrier to H–H bond formation. Thus these
calculations suggest that the rate increase due to water in these
electrocatalysts is not associated with the elementary step of H–H
bond formation or cleavage but rather with the proton delivery steps.
We attribute the higher barrier in the H–H bond formation in
the presence of water to a decrease in direct interaction between
the protic and hydridic hydrogen atoms forced by the water molecules
Protonation state space exploration.
<p>(A) GB corrected energy (E<sub>corr</sub>) as a function of MC step for the MC/MD sampling on hIns<sub>2</sub> at the main charge state (q = 6+). (B) Prediction of the main charge state of hIns<sub>2</sub>. GB<sub>app</sub> values (in kJ/mol) were calculated for the lowest energy protonation states of hIns<sub>2</sub> (black line and cycle symbols). Standard deviation from the average is given as error bars. When not visible, the standard deviation is smaller than the symbol size. The red horizontal line indicates the GB of water (660.3 kJ/mol taken from ref. <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003838#pcbi.1003838-Hunter1" target="_blank">[101]</a>). The experimental main charge state <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003838#pcbi.1003838-Salbo1" target="_blank">[52]</a> is shown by red solid diamond.</p
Photoinduced Reductive Elimination of H<sub>2</sub> from the Nitrogenase Dihydride (Janus) State Involves a FeMo-cofactor‑H<sub>2</sub> Intermediate
N<sub>2</sub> reduction
by nitrogenase involves the accumulation of four reducing equivalents
at the active site FeMo-cofactor to form a state with two [Fe–H–Fe]
bridging hydrides (denoted E<sub>4</sub>(4H), the Janus intermediate),
and we recently demonstrated that the enzyme is activated to cleave
the Nî—ĽN triple bond by the reductive elimination (<i>re</i>) of H<sub>2</sub> from this state. We are exploring a photochemical
approach to obtaining atomic-level details of the <i>re</i> activation process. We have shown that, when E<sub>4</sub>(4H) at
cryogenic temperatures is subjected to 450 nm irradiation in an EPR
cavity, it cleanly undergoes photoinduced <i>re</i> of H<sub>2</sub> to give a reactive doubly reduced intermediate, denoted E<sub>4</sub>(2H)*, which corresponds to the intermediate that would form
if thermal dissociative <i>re</i> loss of H<sub>2</sub> preceded
N<sub>2</sub> binding. Experiments reported here establish that photoinduced <i>re</i> primarily occurs in two steps. Photolysis of E<sub>4</sub>(4H) generates an intermediate state that undergoes subsequent photoinduced
conversion to [E<sub>4</sub>(2H)* + H<sub>2</sub>]. The experiments,
supported by DFT calculations, indicate that the trapped intermediate
is an H<sub>2</sub> complex on the ground adiabatic potential energy
suface that connects E<sub>4</sub>(4H) with [E<sub>4</sub>(2H)* +
H<sub>2</sub>]. We suggest that this complex, denoted E<sub>4</sub>(H<sub>2</sub>; 2H), is a thermally populated intermediate in the
catalytically central <i>re</i> of H<sub>2</sub> by E<sub>4</sub>(4H) and that N<sub>2</sub> reacts with this complex to complete
the activated conversion of [E<sub>4</sub>(4H) + N<sub>2</sub>] into
[E<sub>4</sub>(2N2H) + H<sub>2</sub>]
Comparison of a local inter- and intra-molecular hydrogen bond network in water (A) and in the gas phase (B).
<p>The final snapshots obtained from the MD simulations in water and in the gas phase at the main charge were selected. The monomer I and II are indicated in cyan and green, respectively. The water oxygen atoms are indicated by yellow balls. Nitrogen, dark blue; oxygen, red; hydrogen, white. Hydrogen bonds are shown as dashed lines.</p
Correlation plots of the differences in energy for 60 protonation states of the hIns<sub>2</sub> relative to the lowest-energy protonation state.
<p>(A) Energy differences calculated with the OPLS/AA force field (ΔE<sub>FF</sub>) <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003838#pcbi.1003838-Jorgensen2" target="_blank">[63]</a> versus differences calculated with DFT (ΔE<sub>QM</sub>) <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003838#pcbi.1003838-Marchese2" target="_blank">[38]</a>. (B) Energy differences calculated with the OPLS/AA force field along with the GB correction (ΔE<sub>corr</sub>) versus differences calculated with DFT (ΔE<sub>QM</sub>). The correlation is much better with GB correction than with OPLS/AA (<i>R</i><sup>2</sup> = 0.81 and 0.03, respectively), confirming the crucial role of GB for estimating the energies of the protonation states.</p
MD simulations in the gas phase of the [hIns<sub>2</sub>]<sup>6+</sup>.
<p>(A) Models of [hIns<sub>2</sub>]<sup>6+</sup> obtained from MD simulations in the gas phase (from left to right, at 0 µs, 5.7 µs, 8.1 µs, 27.6 µs, 36.3 µs, 42.6 µs, 54.9 µs, and 75.0 µs). The monomer I and II are indicated in cyan (lower structure) and green (upper structure), respectively. The α-helices and β-sheets are highlighted in blue and red, respectively. Schematic representations of the complex models are shown below the complex structures, at corresponding positions on the simulation time axis. The backbone RMSD values of the models in respect to the one at 0 µs are 0.25 nm (5.7 µs), 0.54 nm (8.1 µs), 0.55 nm (27.6 µs), 0.49 nm (36.3 µs), 0.45 nm (42.6 µs), and 0.49 nm (54.9 µs), and 0.50 (75.0 µs). (B) Secondary structure analysis for [hIns<sub>2</sub>]<sup>6+</sup>. (C) The angle between the center of mass (COM) of monomer I – β-sheet region – monomer II. (D) CCS values. The experimental value of 12.9 nm<sup>2</sup>, as reported <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003838#pcbi.1003838-Salbo1" target="_blank">[52]</a>, at the main charge state is indicated by a red solid line and its 5% variations are indicated by the dashed lines. The average value from our MD simulation in the gas phase is 12.8±0.2 nm<sup>2</sup>. (E) Number of contact pairs between the carbon atoms of the monomers within 0.60 nm.</p
CO<sub>2</sub> Reduction Catalyzed by Nitrogenase: Pathways to Formate, Carbon Monoxide, and Methane
The
reduction of N<sub>2</sub> to NH<sub>3</sub> by Mo-dependent nitrogenase
at its active-site metal cluster FeMo-cofactor utilizes reductive
elimination of Fe-bound hydrides with obligatory loss of H<sub>2</sub> to activate the enzyme for binding/reduction of N<sub>2</sub>. Earlier
work showed that wild-type nitrogenase and a nitrogenase with amino
acid substitutions in the MoFe protein near FeMo-cofactor can catalytically
reduce CO<sub>2</sub> by two or eight electrons/protons to carbon
monoxide (CO) and methane (CH<sub>4</sub>) at low rates. Here, it
is demonstrated that nitrogenase preferentially reduces CO<sub>2</sub> by two electrons/protons to formate (HCOO<sup>–</sup>) at
rates >10 times higher than rates of CO<sub>2</sub> reduction to
CO and CH<sub>4</sub>. Quantum mechanical calculations on the doubly
reduced FeMo-cofactor with a Fe-bound hydride and S-bound proton (E<sub>2</sub>(2H) state) favor a direct reaction of CO<sub>2</sub> with
the hydride (“direct hydride transfer” reaction pathway),
with facile hydride transfer to CO<sub>2</sub> yielding formate. In
contrast, a significant barrier is observed for reaction of Fe-bound
CO<sub>2</sub> with the hydride (“associative” reaction
pathway), which leads to CO and CH<sub>4</sub>. Remarkably, in the
direct hydride transfer pathway, the Fe-H behaves as a hydridic hydrogen,
whereas in the associative pathway it acts as a protic hydrogen. MoFe
proteins with amino acid substitutions near FeMo-cofactor (α-70<sup>Val→Ala</sup>, α-195<sup>His→Gln</sup>) are found
to significantly alter the distribution of products between formate
and CO/CH<sub>4</sub>
Achieving Reversible H<sub>2</sub>/H<sup>+</sup> Interconversion at Room Temperature with Enzyme-Inspired Molecular Complexes: A Mechanistic Study
Inspired
by the contribution of the protein scaffold to the efficiency
with which enzymes function, we used outer coordination sphere features
to develop a molecular electrocatalyst for the reversible production/oxidation
of H<sub>2</sub> at 25 °C: [NiÂ(P<sup>Cy</sup><sub>2</sub>N<sup>Phe</sup><sub>2</sub>)<sub>2</sub>]<sup>2+</sup> (<b>CyPhe</b>; P<sup>R</sup><sub>2</sub>N<sup>R<sup>′</sup></sup><sub>2</sub> = 1,5-diaza-3,7-diphosphacyclooctane, Cy = cyclohexyl, Phe = phenylalanine).
Electrocatalytic reversibility is observed in aqueous, acidic methanol.
The aromatic rings in the peripheral phenylalanine groups appear to
be essential to achieving reversibility based on the observation that
reversibility for arginine (<b>CyArg</b>) or glycine (<b>CyGly</b>) complexes is only achieved with elevated temperature
(>50 °C) in 100% water. A complex with a hydroxyl group in
the <i>para</i>-position of the aromatic ring, R′
= tyrosine
(<b>CyTyr</b>), shows similar reversible behavior. NMR spectroscopy
and molecular dynamics studies suggest that interactions between the
aromatic groups as well as between the carboxylic acid groups limit
conformational flexibility, contributing to reversibility. NMR spectroscopy
studies also show extremely fast proton exchange along a pathway from
the Ni–H through the pendant amine to the carboxyl group. Further,
a complex containing a side chain similar to tyrosine but without
the carboxyl group (<b>CyTym</b>; Tym = tyramine) does not display
reversible catalysis and has limited proton exchange from the pendant
amine, demonstrating an essential role for the carboxylic acid and
the proton pathway in achieving catalytic reversibility. This minimal
pathway mimics proton pathways found in hydrogenases. The influence
of multiple factors on lowering barriers and optimizing relative energies
to achieve reversibility for this synthetic catalyst is a clear indication
of the intricate interplay between the first, second, and outer coordination
spheres that begins to mimic the complexity observed in metalloenzymes