How are the ready and unready states of nickel–iron hydrogenase activated by H2? A density functional theory study

Literature Information

Publication Date 2006-07-27
DOI 10.1039/B608069C
Impact Factor 3.676
Authors

Prabha Jayapal, Mahesh Sundararajan, Ian H. Hillier, Neil A. Burton


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Abstract

We have explored possible mechanisms for the formation of the catalytically active Nia–S state of the enzyme, nickel iron hydrogenase, from the Ni*r (ready) or Ni*u (unready) state, by reaction with H2, using density functional theory calculations with the BP86 functional in conjunction with a DZVP basis set. We find that for the reaction of the ready state, which is taken to have an –OH bridge, the rate determining step is the cleavage of H2 at the Ni3+ centre with a barrier of ∼15 kcal mol−1. We take the unready state to have a –OOH bridge, and find that reaction with H2 to form the Nir–S state can proceed by two possible routes. One such path has a number of steps involving electron transfer, which is consistent with experiment, as is the calculated barrier of ∼19 kcal mol−1. The alternative pathway, with a lower barrier, may not be rate determining. Overall, our predictions give barriers in line with experiment, and allow details of the mechanism to be explored which are inaccessible from experiment.

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Physical Chemistry Chemical Physics

Physical Chemistry Chemical Physics
CiteScore: 5.5
Self-citation Rate: 10.3%
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Physical Chemistry Chemical Physics (PCCP) is an international journal co-owned by 19 physical chemistry and physics societies from around the world. This journal publishes original, cutting-edge research in physical chemistry, chemical physics and biophysical chemistry. To be suitable for publication in PCCP, articles must include significant innovation and/or insight into physical chemistry; this is the most important criterion that reviewers and Editors will judge against when evaluating submissions. The journal has a broad scope and welcomes contributions spanning experiment, theory, computation and data science. Topical coverage includes spectroscopy, dynamics, kinetics, statistical mechanics, thermodynamics, electrochemistry, catalysis, surface science, quantum mechanics, quantum computing and machine learning. Interdisciplinary research areas such as polymers and soft matter, materials, nanoscience, energy, surfaces/interfaces, and biophysical chemistry are welcomed if they demonstrate significant innovation and/or insight into physical chemistry. Joined experimental/theoretical studies are particularly appreciated when complementary and based on up-to-date approaches.

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