First-principles analysis of the metal-free H2 dissociation mechanism by semiquinone radicals in mitochondrial Complex I and III
4 affiliations
- 1Anicom Specialty Medical Institute (ASM
- 2Imabayashi Meiseikai Orthopedic Hospital
- 3Biotechnology Research Center and Department of Biotechnology
- 4Toyama Prefectural University
Abstract
Although ameliorative effects of molecular hydrogen (H₂) have been reported in a wide range of pathological conditions, it remained unresolved what molecular mechanism activates H₂ in animal cells, which lack the metal hydrogenases that dissociate the nonpolar, among-the-strongest-known H-H bond.Using first-principles calculations (geometries optimized with spin-unrestricted B3LYP-D3BJ/def2-SVP/CPCM, energies evaluated with ωB97M-V/def2-TZVPP) with active-site clusters of the Q-chamber of mitochondrial respiratory-chain Complex I (PDB 7QSK) and the Qo site of Complex III (PDB 1PP9), this study examined whether semiquinone could directly dissociate H₂ in the low-dielectric environment buried within the enzyme, and what changes when a conserved residue is added as a second hydrogen atom acceptor.At both sites, the anionic semiquinone Q• had no reaction pathway for cleaving ⁻ H-H, and only the neutral QH•, protonated by nearby residues, opened a homolytic hydrogen atom transfer (HAT) pathway with a well-defined transition state and a bound product.That the spin density on the transferring hydrogen shifts continuously from nearly 0 in the reactant to +0.99 for free H• confirmed at the electronic level that this is a true homolytic HAT, being neither proton transfer nor hydride transfer.The reaction energies (+21 to +26 kcal/mol) agree with an estimate from the difference between the bond dissociation free energies (BDFE) of the O-H bond of ubiquinol QH₂ and of the H-H bond that is broken.The same BDFE comparison also makes QH• a spin-allowed hydrogen-atom abstractor superior to superoxide by about 30 kcal/mol.For HAT with a single hydrogen atom acceptor the reaction energy of QH• + H₂ → QH₂ + H• is +28.3 kcal/mol, and the barrier cannot fall below that value.In the Q-chamber the conserved residue Tyr108 can act as a second acceptor, and for hydrogen atom transfer with H₂ held between QH• and TyrO• the barrier falls to +27.0 kcal/mol.However, this reactive QH• arises only under hyper-reductive pressure, where quinone-pool overreduction and high membrane potential coincide, upon occupation and protonation at the buried semiquinone reaction site.Therefore, H₂ dissociation itself is established only when the semiquinone reaction-site environment under hyper-reductive pressure is present as a necessary condition.Because H₂ has among the strongest σ bonds, the barrier is high and sharp, and quantum tunnelling makes a substantial contribution to crossing it at body temperature.At the onedimensional Eckart level that contribution does not exceed thermal activation, and it is obtained as a lower bound.The crossover temperatures, set by the imaginary frequency at the saddle, are 293.9K for Complex I and 264.7 K for Complex III.That the buried semiquinone reaction site makes a barrier against one of the strongest known σ bonds thin enough to bring the crossover temperature to within 16 K of body temperature is itself a quantitative result obtained here.The Marcus inverted region (bell-shaped kinetics) that we observed in solution in previous work shows that H₂ can be activated at all under metal-free conditions, but what tunnels there is the electron, along a coordinate distinct from the hydrogen nucleus analysed here.For the in-enzyme mechanism, the moderate primary isotope effect predicted at the same level (kH/kD ≈ 4) could be tested by detecting dissociated deuterium using D₂ as a tracer.Taken together, the above shifts the mechanistic account of H₂ medicine from classical antioxidant scavenging to redox regulation as a quantum-tunnelling-assisted conditional hydrogenase activity conditioned by reductive pressure, and positions it as a field of quantum biology.
Versions
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BibTeX
@misc{ishibashi2026firstprinciples,
title = {{First-principles analysis of the metal-free H2 dissociation mechanism by semiquinone radicals in mitochondrial Complex I and III}},
author = {Toru Ishibashi and Enjuro Harunari},
howpublished = {ChemRxiv},
year = {2026},
month = oct,
doi = {10.26434/chemrxiv.15006405/v2},
url = {https://chemrxiv.org/doi/full/10.26434/chemrxiv.15006405/v2},
note = {CC BY},
}
RIS
TY - UNPB
TI - First-principles analysis of the metal-free H2 dissociation mechanism by semiquinone radicals in mitochondrial Complex I and III
AU - Toru Ishibashi
AU - Enjuro Harunari
PY - 2026
DA - 2026/10/09
PB - ChemRxiv
DO - 10.26434/chemrxiv.15006405/v2
UR - https://chemrxiv.org/doi/full/10.26434/chemrxiv.15006405/v2
AB - Although ameliorative effects of molecular hydrogen (H₂) have been reported in a wide range of pathological conditions, it remained unresolved what molecular mechanism activates H₂ in animal cells, which lack the metal hydrogenases that dissociate the nonpolar, among-the-strongest-known H-H bond.Using first-principles calculations (geometries optimized with spin-unrestricted B3LYP-D3BJ/def2-SVP/CPCM, energies evaluated with ωB97M-V/def2-TZVPP) with active-site clusters of the Q-chamber of mitochondrial respiratory-chain Complex I (PDB 7QSK) and the Qo site of Complex III (PDB 1PP9), this study examined whether semiquinone could directly dissociate H₂ in the low-dielectric environment buried within the enzyme, and what changes when a conserved residue is added as a second hydrogen atom acceptor.At both sites, the anionic semiquinone Q• had no reaction pathway for cleaving ⁻ H-H, and only the neutral QH•, protonated by nearby residues, opened a homolytic hydrogen atom transfer (HAT) pathway with a well-defined transition state and a bound product.That the spin density on the transferring hydrogen shifts continuously from nearly 0 in the reactant to +0.99 for free H• confirmed at the electronic level that this is a true homolytic HAT, being neither proton transfer nor hydride transfer.The reaction energies (+21 to +26 kcal/mol) agree with an estimate from the difference between the bond dissociation free energies (BDFE) of the O-H bond of ubiquinol QH₂ and of the H-H bond that is broken.The same BDFE comparison also makes QH• a spin-allowed hydrogen-atom abstractor superior to superoxide by about 30 kcal/mol.For HAT with a single hydrogen atom acceptor the reaction energy of QH• + H₂ → QH₂ + H• is +28.3 kcal/mol, and the barrier cannot fall below that value.In the Q-chamber the conserved residue Tyr108 can act as a second acceptor, and for hydrogen atom transfer with H₂ held between QH• and TyrO• the barrier falls to +27.0 kcal/mol.However, this reactive QH• arises only under hyper-reductive pressure, where quinone-pool overreduction and high membrane potential coincide, upon occupation and protonation at the buried semiquinone reaction site.Therefore, H₂ dissociation itself is established only when the semiquinone reaction-site environment under hyper-reductive pressure is present as a necessary condition.Because H₂ has among the strongest σ bonds, the barrier is high and sharp, and quantum tunnelling makes a substantial contribution to crossing it at body temperature.At the onedimensional Eckart level that contribution does not exceed thermal activation, and it is obtained as a lower bound.The crossover temperatures, set by the imaginary frequency at the saddle, are 293.9K for Complex I and 264.7 K for Complex III.That the buried semiquinone reaction site makes a barrier against one of the strongest known σ bonds thin enough to bring the crossover temperature to within 16 K of body temperature is itself a quantitative result obtained here.The Marcus inverted region (bell-shaped kinetics) that we observed in solution in previous work shows that H₂ can be activated at all under metal-free conditions, but what tunnels there is the electron, along a coordinate distinct from the hydrogen nucleus analysed here.For the in-enzyme mechanism, the moderate primary isotope effect predicted at the same level (kH/kD ≈ 4) could be tested by detecting dissociated deuterium using D₂ as a tracer.Taken together, the above shifts the mechanistic account of H₂ medicine from classical antioxidant scavenging to redox regulation as a quantum-tunnelling-assisted conditional hydrogenase activity conditioned by reductive pressure, and positions it as a field of quantum biology.
ER -