Oxygen-evolving_complex

# Oxygen-evolving complex  ## Microsims — three.js ### Oxygen-evolving complex (three.js) <div class="microsim-player"> <iframe src="https://wikitube-3d-microsims.netlify.app/Oxygen-evolving_complex.html" width="100%" height="620" frameborder="0" loading="lazy" sandbox="allow-scripts allow-same-origin" title="Oxygen-evolving complex — three.js microsim"></iframe> </div> **Open it full-screen:** [Oxygen-evolving_complex.html](https://wikitube-3d-microsims.netlify.app/Oxygen-evolving_complex.html) · library `threejs` · route `microsim/threejs/` ### Related microsims Live sims on neighbouring articles: - [[Allotropes_of_oxygen]] - [[Chlorophyll]] - [[Molecular_orbital]] - [[Ozone_layer]] - [[Photosynthesis]] - [[Thylakoid]] *Sim hosted off-article; the article owns the reference, not the runtime (WIKI_RULES §10.4).*  ## Overview The oxygen-evolving complex is the catalytic cluster at the heart of photosystem II, and it is the source of essentially all the free oxygen in Earth's atmosphere. It is a small inorganic assembly, four manganese atoms and one calcium bridged by five oxygens, embedded in a protein scaffold on the lumenal side of the thylakoid membrane. Its job is to strip electrons from water and release dioxygen as the waste product. What makes it remarkable is a counting problem. Splitting two water molecules into O2 requires removing four electrons, but the photochemistry that powers the reaction delivers only one electron per photon. The cluster solves this by acting as a charge accumulator: it stores oxidising equivalents one at a time, holds them without falling apart, and discharges only when the fourth arrives. Nothing in industrial chemistry matches it for durability at ambient conditions, which is why it remains the reference target for artificial photosynthesis. ## The physics The cluster is a Mn4CaO5 assembly whose geometry was resolved to 1.9 angstroms by Umena and colleagues in 2011. Three manganese and the calcium sit at the corners of a distorted cubane; the fourth manganese, Mn4, hangs off the cube outside it, linked through a bridging oxygen. The distortion is not incidental. A perfectly symmetric cube would delocalise charge evenly, whereas the dangling manganese gives the cluster a distinguished site where substrate water can bind and where the O-O bond is thought to form. Turnover follows the Kok cycle, a five-state clock labelled S0 through S4. Each absorbed photon oxidises the reaction-centre chlorophyll P680, which pulls an electron through the redox-active tyrosine Yz from the manganese cluster, advancing it one S-state and depositing a proton in the lumen. S4 is never observed directly: it forms and immediately collapses back to S0, releasing one O2. | S-state | Photons absorbed | Net change | Observable | |---|---|---|---| | S0 | 0 | most reduced stable state | dark-stable minority | | S1 | 1 | dark-adapted resting state | the state a rested leaf sits in | | S2 | 2 | first strongly oxidised state | multiline EPR signal | | S3 | 3 | second substrate water bound | poised for O-O coupling | | S4 | 4 | transient | collapses, releasing O2 | The signature evidence for this scheme is the flash experiment of Kok, Forbush and McGloin: illuminate dark-adapted chloroplasts with a train of short saturating flashes and the oxygen yield oscillates with a period of four, peaking on flashes 3, 7, 11 and so on. The peak on flash 3 rather than 4 is what establishes S1 as the dark-adapted resting state. The oscillation damps out over successive flashes because individual centres fall out of step, through "misses" where a flash fails to advance a centre and "double hits" where one flash advances it twice. The net reaction is 2 H2O -> O2 + 4 H+ + 4 e- How the O-O bond actually forms is still contested, and this article does not pick a winner. The two leading proposals are nucleophilic attack, in which a calcium-bound hydroxide attacks an electrophilic Mn(V)=O oxo, and oxo-oxyl radical coupling, in which an Mn(IV)-O radical couples with a bridging oxide. Both are consistent with much of the spectroscopy; distinguishing them is an active research problem. ## Controls -> what each maps to | Control | Maps to | Range / values | Physical meaning | |---|---|---|---| | Fire 1 photon | single turnover of P680 | one advance | Advances the cluster one S-state and deposits one proton in the lumen | | Auto-cycle | continuous flash train | on / off | Runs the clock freely; disabled under prefers-reduced-motion | | Flash rate | flash frequency | 0.2 - 5.0 Hz | How fast the photon train arrives; the cluster's own turnover sets the ceiling | | Kok miss probability | alpha, per-flash failure rate | 0 - 30 % | Fraction of flashes that fail to advance a centre; raising it damps the period-four oscillation, as in real chloroplasts | | Atom and residue labels | -- | on / off | Names the four manganese, the calcium, the bridging oxygens and the coordinating residues | | Reset | return to dark-adapted state | -- | Restores S1, the state a rested leaf occupies | ## Learning objective After playing, a learner can explain why photosynthetic oxygen evolution requires four photons per O2, describe what each S-state transition does, and account for the period-four oscillation in flash-yield experiments including why the first peak falls on flash 3 and why the oscillation damps. ## Limits and connections The sim treats the S-state advance as a clean counter with an adjustable miss probability. Real centres also show double hits, and the proton release pattern across the cycle is not a uniform one-per-state. The cluster geometry is idealised from the 1.9 angstrom structure, and the radiation damage that afflicts X-ray structures of this centre is an active caveat in the literature. The O-O bond-forming step is animated as a single event rather than committing to either mechanism, because the mechanism is unsettled. The light reactions that feed the cluster are the subject of [[Photosynthesis]]; the pigment that does the absorbing is [[Chlorophyll]]; the membrane compartment that the protons accumulate in is [[Thylakoid]]. The product of all this work, and what it did to the planet, is [[Great_Oxidation_Event]]. ## References - Umena, Y., Kawakami, K., Shen, J.-R. and Kamiya, N. (2011). Crystal structure of oxygen-evolving photosystem II at a resolution of 1.9 A. *Nature* 473, 55-60. - Kok, B., Forbush, B. and McGloin, M. (1970). Cooperation of charges in photosynthetic O2 evolution. *Photochemistry and Photobiology* 11, 457-475. - Joliot, P., Barbieri, G. and Chabaud, R. (1969). Un nouveau modele des centres photochimiques du systeme II. *Photochemistry and Photobiology* 10, 309-329. - Cox, N., Pantazis, D. A. and Lubitz, W. (2020). Current understanding of the mechanism of water oxidation in photosystem II and its relation to XFEL data. *Annual Review of Biochemistry* 89, 795-820. - Yano, J. and Yachandra, V. (2014). Mn4Ca cluster in photosynthesis: where and how water is oxidized to dioxygen. *Chemical Reviews* 114, 4175-4205. - Blankenship, R. E. *Molecular Mechanisms of Photosynthesis*, 2nd edition. Wiley-Blackwell, 2014. ## Wikipedia : Wikitube **Strict pair:** [Wikipedia](https://en.wikipedia.org/wiki/Oxygen-evolving_complex) : [Wikitube](https://en.wikitube.io/wiki/Oxygen-evolving_complex) ## Previous hub tags Tree parent: [[Oxygen]]. Legacy hubs: `REACTION`. --- *Created 2026-08-05 - append-only - hand-authored to WIKI_REPOPULATION_PROTOCOL v1.0 section 5 - 0 deletions*