Unraveling the mechanism of biomimetic hydrogen fuel production – a first principles molecular dynamics study

Puthenkalathil, Rakesh; Etinski, Mihajlo; Ensing, Bernd

doi:10.1039/c9cp06770a

Cited by 6 publications

(5 citation statements)

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“…The PBE functional is a GGA-type functional that provides a very good compromise between accuracy and efficiency, which is essential for carrying out our DFT-based MD simulations within a QM/MM framework. PBE has been extensively benchmarked by us for our previous studies on hydrogenase catalysis , and by others, showing for example the good performance on hydrogen-bonded systems. − For the MM region, the same CHARMM force field is employed as for the Gromacs simulations. The QM/MM simulations , are carried out in the NVT ensemble with a QM box size of 15 × 15 × 25 Å 3 .…”

Section: Methodsmentioning

confidence: 99%

“…Much of the material in the paper was previously published in the Ph.D. thesis of the first author. 44 …”

Section: Acknowledgmentsmentioning

confidence: 99%

“…Authors also acknowledge the SURF Cooperative for the computer resources provided for the calculations. Much of the material in the paper was previously published in the Ph.D. thesis of the first author …”

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confidence: 99%

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Fast Proton Transport in FeFe Hydrogenase via a Flexible Channel and a Proton Hole Mechanism

Puthenkalathil

Ensing

2022

J. Phys. Chem. B

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Di-iron hydrogenases are a class of enzymes that are capable of reducing protons to form molecular hydrogen with high efficiency. In addition to the catalytic site, these enzymes have evolved dedicated pathways to transport protons and electrons to the reaction center. Here, we present a detailed study of the most likely proton transfer pathway in such an enzyme using QM/MM molecular dynamics simulations. The protons are transported through a channel lined out from the protein exterior to the di-iron active site, by a series of hydrogen-bonded, weakly acidic or basic, amino acids and two incorporated water molecules. The channel shows remarkable flexibility, which is an essential feature to quickly reset the hydrogen-bond direction in the channel after each proton passing. Proton transport takes place via a “hole” mechanism, rather than an excess proton mechanism, the free energy landscape of which is remarkably flat, with a highest transition state barrier of only 5 kcal/mol. These results confirm our previous assumptions that proton transport is not rate limiting in the H 2 formation activity and that cysteine C299 may be considered protonated at physiological pH conditions. Detailed understanding of this proton transport may aid in the ongoing attempts to design artificial biomimetic hydrogenases for hydrogen fuel production.

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Section: Methodsmentioning

confidence: 99%

“…Much of the material in the paper was previously published in the Ph.D. thesis of the first author. 44 …”

Section: Acknowledgmentsmentioning

confidence: 99%

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Fast Proton Transport in FeFe Hydrogenase via a Flexible Channel and a Proton Hole Mechanism

Puthenkalathil

Ensing

2022

J. Phys. Chem. B

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“…Figure shows the active site of the [FeFe] hydrogenase enzyme and a prototypical catalyst complex synthesized to mimic this structure. , We have recently characterized the structure and the electrochemical properties of such di-iron–hydrogenase models using density functional theory (DFT) calculations and DFT-based molecular dynamics simulations. , The properties of such synthetic catalysts can be tuned by changing the bridgehead ligand, one or more terminal ligands, the chalcogen atoms, and even by changing the metal ions. The catalytic center of the natural enzyme contains an azadithiolate ligand in the bridgehead position and CO and CN – groups as terminal ligands .…”

Section: Introductionmentioning

confidence: 99%

Linear Scaling Relationships to Predict pK_a’s and Reduction Potentials for Bioinspired Hydrogenase Catalysis

Puthenkalathil

Ensing

2021

Inorg. Chem.

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Biomimetic catalysts inspired by the active site of the [FeFe] hydrogenase enzyme can convert protons into molecular hydrogen. Minimizing the overpotential of the electrocatalytic process remains a major challenge for practical application of the catalyst. The catalytic cycle of the hydrogen production follows an ECEC mechanism (E represents an electron transfer step, and C refers to a chemical step), in which the electron and proton transfer steps can be either sequential or coupled (PCET). In this study, we have calculated the p K a ’s and the reduction potentials for a series of commonly used ligands (80 different complexes) using density functional theory. We establish that the required acid strength for protonation at the Fe–Fe site correlates with the standard reduction potential of the di-iron complexes with a linear energy relationship. These linear relationships allow for fast screening of ligands and tuning of the properties of the catalyst. Our study also suggests that bridgehead ligand properties, such as bulkiness and aromaticity, can be exploited to alter or even break the linear scaling relationships.

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“…It has been pointed out that better understanding of tunnelling in proton or hydrogen transfer reactions may create a chance for innovations such as an efficient control of the reactions' course 15 , artificial (more efficient) enzymes 16 or fast charging lithium-ion batteries 17 . Therefore, a constant effort is put into development of more accurate models that can be used to describe proton and hydrogen transfer reactions 7,[18][19][20][21][22][23][24][25][26][27][28][29][30][31][32][33] . Consequently, the experimental data that can be used to verify new models can be invaluable.…”

Section: Introductionmentioning

confidence: 99%

Influence of local microenvironment on the double hydrogen transfer in porphycene

Kasprzycki

Kopycki

Listkowski

et al. 2020

Phys. Chem. Chem. Phys.

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Unraveling the mechanism of biomimetic hydrogen fuel production – a first principles molecular dynamics study

Abstract: The Fe2(bdt)(CO)6 [bdt = benzenedithiolato] complex, a synthetic mimic of the [FeFe] hydrogenase enzyme can electrochemically convert protons into molecular hydrogen. The free energy landscape reveals a different mechanism for the biomimetic cycle.

Cited by 6 publications

References 57 publications

Fast Proton Transport in FeFe Hydrogenase via a Flexible Channel and a Proton Hole Mechanism

Fast Proton Transport in FeFe Hydrogenase via a Flexible Channel and a Proton Hole Mechanism

Linear Scaling Relationships to Predict pK_a’s and Reduction Potentials for Bioinspired Hydrogenase Catalysis

Influence of local microenvironment on the double hydrogen transfer in porphycene

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Unraveling the mechanism of biomimetic hydrogen fuel production – a first principles molecular dynamics study

Abstract: The Fe2(bdt)(CO)6 [bdt = benzenedithiolato] complex, a synthetic mimic of the [FeFe] hydrogenase enzyme can electrochemically convert protons into molecular hydrogen. The free energy landscape reveals a different mechanism for the biomimetic cycle.

Cited by 6 publications

References 57 publications

Fast Proton Transport in FeFe Hydrogenase via a Flexible Channel and a Proton Hole Mechanism

Fast Proton Transport in FeFe Hydrogenase via a Flexible Channel and a Proton Hole Mechanism

Linear Scaling Relationships to Predict pKa’s and Reduction Potentials for Bioinspired Hydrogenase Catalysis

Influence of local microenvironment on the double hydrogen transfer in porphycene

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Linear Scaling Relationships to Predict pK_a’s and Reduction Potentials for Bioinspired Hydrogenase Catalysis