Highly stable preferential carbon monoxide oxidation by dinuclear heterogeneous catalysts.

Atomically dispersed catalysts have been shown highly active for preferential oxidation of carbon monoxide in the presence of excess hydrogen (PROX). However, their stability has been less than ideal. We show here that the introduction of a structural component to minimize diffusion of the active metal center can greatly improve the stability without compromising the activity. Using an Ir dinuclear heterogeneous catalyst (DHC) as a study platform, we identify two types of oxygen species, interfacial and bridge, that work in concert to enable both activity and stability. The work sheds important light on the synergistic effect between the active metal center and the supporting substrate and may find broad applications for the use of atomically dispersed catalysts.

Structure of the antenna complex expressed during far-red light photoacclimation in Synechococcus sp. PCC 7335.

Far-red light photoacclimation, or FaRLiP, is a facultative response exhibited by some cyanobacteria that allows them to absorb and utilize lower energy light (700-800 nm) than the wavelengths typically used for oxygenic photosynthesis (400-700 nm). During this process, three essential components of the photosynthetic apparatus are altered: photosystem I, photosystem II, and the phycobilisome. In all three cases, at least some of the chromophores found in these pigment-protein complexes are replaced by chromophores that have red-shifted absorbance relative to the analogous complexes produced in visible light. Recent structural and spectroscopic studies have elucidated important features of the two photosystems when altered to absorb and utilize far-red light, but much less is understood about the modified phycobiliproteins made during FaRLiP. We used single-particle, cryo-EM to determine the molecular structure of a phycobiliprotein core complex comprising allophycocyanin variants that absorb far-red light during FaRLiP in the marine cyanobacterium Synechococcus sp. PCC 7335. The structure reveals the arrangement of the numerous red-shifted allophycocyanin variants and the probable locations of the chromophores that serve as the terminal emitters in this complex. It also suggests how energy is transferred to the photosystem II complexes produced during FaRLiP. The structure additionally allows comparisons with other previously studied allophycocyanins to gain insights into how phycocyanobilin chromophores can be tuned to absorb far-red light. These studies provide new insights into how far-red light is harvested and utilized during FaRLiP, a widespread cyanobacterial photoacclimation mechanism.

Mutation-induced shift of the photosystem II active site reveals insight into conserved water channels.

Photosystem II (PSII) is the water-plastoquinone photo-oxidoreductase central to oxygenic photosynthesis. PSII has been extensively studied for its ability to catalyze light-driven water oxidation at a Mn4CaO5 cluster called the oxygen-evolving complex (OEC). Despite these efforts, the complete reaction mechanism for water oxidation by PSII is still heavily debated. Previous mutagenesis studies have investigated the roles of conserved amino acids, but these studies have lacked a direct structural basis that would allow for a more meaningful interpretation. Here, we report a 2.14-Å resolution cryo-EM structure of a PSII complex containing the substitution Asp170Glu on the D1 subunit. This mutation directly perturbs a bridging carboxylate ligand of the OEC, which alters the spectroscopic properties of the OEC without fully abolishing water oxidation. The structure reveals that the mutation shifts the position of the OEC within the active site without markedly distorting the Mn4CaO5 cluster metal-metal geometry, instead shifting the OEC as a rigid body. This shift disturbs the hydrogen-bonding network of structured waters near the OEC, causing disorder in the conserved water channels. This mutation-induced disorder appears consistent with previous FTIR spectroscopic data. We further show using quantum mechanics/molecular mechanics methods that the mutation-induced structural changes can affect the magnetic properties of the OEC by altering the axes of the Jahn-Teller distortion of the Mn(III) ion coordinated to D1-170. These results offer new perspectives on the conserved water channels, the rigid body property of the OEC, and the role of D1-Asp170 in the enzymatic water oxidation mechanism.

High-resolution cryo-electron microscopy structure of photosystem II from the mesophilic cyanobacterium, Synechocystis sp. PCC 6803.

Photosystem II (PSII) enables global-scale, light-driven water oxidation. Genetic manipulation of PSII from the mesophilic cyanobacterium Synechocystis sp. PCC 6803 has provided insights into the mechanism of water oxidation; however, the lack of a high-resolution structure of oxygen-evolving PSII from this organism has limited the interpretation of biophysical data to models based on structures of thermophilic cyanobacterial PSII. Here, we report the cryo-electron microscopy structure of PSII from Synechocystis sp. PCC 6803 at 1.93-Å resolution. A number of differences are observed relative to thermophilic PSII structures, including the following: the extrinsic subunit PsbQ is maintained, the C terminus of the D1 subunit is flexible, some waters near the active site are partially occupied, and differences in the PsbV subunit block the Large (O1) water channel. These features strongly influence the structural picture of PSII, especially as it pertains to the mechanism of water oxidation.

Structure of a dimeric photosystem II complex from a cyanobacterium acclimated to far-red light.

Photosystem II (PSII) is the water-splitting enzyme central to oxygenic photosynthesis. To drive water oxidation, light is harvested by accessory pigments, mostly chlorophyll (Chl) a molecules, which absorb visible light (400-700 nm). Some cyanobacteria facultatively acclimate to shaded environments by altering their photosynthetic machinery to additionally absorb far-red light (FRL, 700-800 nm), a process termed far-red light photoacclimation or FaRLiP. During far-red light photoacclimation, FRL-PSII is assembled with FRL-specific isoforms of the subunits PsbA, PsbB, PsbC, PsbD, and PsbH, and some Chl-binding sites contain Chls d or f instead of the usual Chl a. The structure of an apo-FRL-PSII monomer lacking the FRL-specific PsbH subunit has previously been determined, but visualization of the dimeric complex has remained elusive. Here, we report the cryo-EM structure of a dimeric FRL-PSII complex. The site assignments for Chls d and f are consistent with those assigned in the previous apo-FRL-PSII monomeric structure. All sites that bind Chl d or Chl f at high occupancy exhibit a FRL-specific interaction of the formyl moiety of the Chl d or Chl f with the protein environment, which in some cases involves a phenylalanine sidechain. The structure retains the FRL-specific PsbH2 subunit, which appears to alter the energetic landscape of FRL-PSII, redirecting energy transfer from the phycobiliprotein complex to a Chl f molecule bound by PsbB2 that acts as a bridge for energy transfer to the electron transfer chain. Collectively, these observations extend our previous understanding of the structure-function relationship that allows PSII to function using lower energy FRL.

Infrared Spectroscopic Observation of Oxo- and Superoxo-Intermediates in the Water Oxidation Cycle of a Molecular Ir Catalyst.

Molecular Ir catalysts have emerged as an important class of model catalysts for understanding structure-activity relationships in water oxidation, a reaction that is central to renewable fuel synthesis. Prior efforts have mostly focused on controlling and elucidating the emergence of active species from prepared precursors. However, the development of efficient and stable molecular Ir catalysts also necessitates probing of reaction intermediates. To date, relatively little is known about the key intermediates in the cycles of the molecular Ir catalysts. Herein, we probed the catalytic cycle of a homogeneous Ir catalyst ("blue dimer") at a Au electrode/aqueous electrolyte interface by combining surface-enhanced infrared absorption spectroscopy (SEIRAS) with phase-sensitive detection (PSD). Cyclic voltammograms (CVs) from 1.4 to 1.7 VRHE (RHE = reversible hydrogen electrode) give rise to a band at ∼818 cm-1, whereas CVs from 1.4 to ≥1.85 VRHE generate an additional band at ∼1146 cm-1. Isotope labeling experiments indicate that the bands at ∼818 and ∼1146 cm-1 are attributable to oxo (IrV═O) and superoxo (IrIV-OO•) moieties, respectively. This study establishes PSD-SEIRAS as a sensitive tool for probing water oxidation cycles at electrode/electrolyte interfaces and demonstrates that the relative abundance of two key intermediates can be tuned by the thermodynamic driving force of the reaction.

Water Ligands Regulate the Redox Leveling Mechanism of the Oxygen-Evolving Complex of the Photosystem II.

Understanding how water ligands regulate the conformational changes and functionality of the oxygen-evolving complex (OEC) in photosystem II (PSII) throughout the catalytic cycle of oxygen evolution remains a highly intriguing and unresolved challenge. In this study, we investigate the effect of water insertion (WI) on the redox state of the OEC by using the molecular dynamics (MD) and quantum mechanics/molecular mechanics (QM/MM) hybrid methods. We find that water binding significantly reduces the free energy change for proton-coupled electron transfer (PCET) from Mn to YZ•, underscoring the important regulatory role of water binding, which is essential for enabling the OEC redox-leveling mechanism along the catalytic cycle. We propose a water binding mechanism in which WI is thermodynamically favored by the closed-cubane form of the OEC, with water delivery mediated by Ca2+ ligand exchange. Isomerization from the closed- to open-cubane conformation at three post-WI states highlights the importance of the location of the MnIII center in the OEC and the orientation of its Jahn-Teller axis to conformational changes of the OEC, which might be critical for the formation of the O-O bond. These findings reveal a complex interplay between conformational changes in the OEC and the ligand environment during the activation of the OEC by YZ•. Analogous regulatory effects due to water ligand binding are expected to be important for a wide range of catalysts activated by redox state transitions in aqueous environments.

Electron Transfer Dynamics at Dye-Sensitized SnO2/TiO2 Core/Shell Electrodes in Aqueous/Nonaqueous Electrolyte Mixtures.

The dynamics of photoinduced electron transfer were measured at dye-sensitized photoanodes in aqueous (acetate buffer), nonaqueous (acetonitrile), and mixed solvent electrolytes by nanosecond transient absorption spectroscopy (TAS) and ultrafast optical-pump terahertz-probe spectroscopy (OPTP). Higher injection efficiencies were found in mixed solvent electrolytes for dye-sensitized SnO2/TiO2 core/shell electrodes, whereas the injection efficiency of dye-sensitized TiO2 electrodes decreased with the increasing acetonitrile concentration. The trend in injection efficiency for the TiO2 electrodes was consistent with the solvent-dependent trend in the semiconductor flat band potential. Photoinduced electron injection in core/shell electrodes has been understood as a two-step process involving ultrafast electron trapping in the TiO2 shell followed by slower electron transfer to the SnO2 core. The driving force for shell-to-core electron transfer increases as the flat band potential of TiO2 shifts negatively with increasing concentrations of acetonitrile. In acetonitrile-rich electrolytes, electron injection is suppressed due to the very negative flat band potential of the TiO2 shell. Interestingly, a net negative photoconductivity in the SnO2 core is observed in mixed solvent electrolytes by OPTP. We hypothesize that an electric field is formed across the TiO2 shell from the oxidized dye molecules after injection. Conduction band electrons in SnO2 are trapped at the core/shell interface by the electric field, resulting in a negative photoconductivity transient. The overall electron injection efficiency of the dye-sensitized SnO2/TiO2 core/shell photoanodes is optimized in mixed solvents. The ultrafast transient conductivity data illustrate the crucial role of the electrolyte in regulating the driving forces for electron injection and charge separation at dye-sensitized semiconductor interfaces.

Bridging the Coordination Chemistry of Small Compounds and Metalloproteins Using Machine Learning.

Metalloproteins require metal ions as cofactors to catalyze specific reactions with remarkable efficiency and specificity. In various electron transfer reactions, metals in the active sites change their oxidation states to facilitate the biochemical reactions. Cryogenic electron microscopy, X-ray, and X-ray free electron laser (XFEL) crystallography are used to image metalloproteins to understand the reaction mechanisms. However, radiation damage in cryoEM and X-ray crystallography, and the challenge of generating homogeneous crystals and keeping the appropriate experimental conditions for all the crystals in XFEL crystallography, may alter the oxidation states. Here, we build machine learning models trained on a large data set from the Cambridge Crystallographic Data Center to evaluate the metal oxidation states. The models yield high accuracy scores (from 82% to 94%) for all metals in the small molecules. Then, they were used to predict the oxidation states of more than 30 000 metal clusters in metalloproteins with Fe, Mn, Co, and Cu in their active sites. We found that most of the metals exist in the lower oxidation states (Fe2+ 77%, Mn2+ 85%, Co2+ 65%, and Cu+ 64%), and these populations correlate with the standard reduction potentials of the metal ions. Furthermore, we found no clear correlation between these populations and the resolution of the structures, which suggests no significant dependence of these predictions on the resolution. Our models represent a valuable tool for evaluating the oxidation states of the metals in metalloproteins imaged with different techniques. The data files and the machine learning code are available in a public GitHub repository: https://github.com/mamin03/OxitationStatesMetalloprotein.git.

Active Sites of Cobalt Phthalocyanine in Electrocatalytic CO2 Reduction to Methanol.

Many metal coordination compounds catalyze CO2 electroreduction to CO, but cobalt phthalocyanine hybridized with conductive carbon such as carbon nanotubes is currently the only one that can generate methanol. The underlying structure-reactivity correlation and reaction mechanism desperately demand elucidation. Here we report the first in situ X-ray absorption spectroscopy characterization, combined with ex situ spectroscopic and electrocatalytic measurements, to study CoPc-catalyzed CO2 reduction to methanol. Molecular dispersion of CoPc on CNT surfaces, as evidenced by the observed electronic interaction between the two, is crucial to fast electron transfer to the active sites and multi-electron CO2 reduction. CO, the key intermediate in the CO2 -to-methanol pathway, is found to be labile on the active site, which necessitates a high local concentration in the microenvironment to compete with CO2 for active sites and promote methanol production. A comparison of the electrocatalytic performance of structurally related porphyrins indicates that the bridging aza-N atoms of the Pc macrocycle are critical components of the CoPc active site that produces methanol. In situ X-ray absorption spectroscopy identifies the active site as Co(I) and supports an increasingly non-centrosymmetric Co coordination environment at negative applied potential, likely due to the formation of a Co-CO adduct during the catalysis.

Structure of a photosystem I-ferredoxin complex from a marine cyanobacterium provides insights into far-red light photoacclimation.

Far-red light photoacclimation exhibited by some cyanobacteria allows these organisms to use the far-red region of the solar spectrum (700-800 nm) for photosynthesis. Part of this process includes the replacement of six photosystem I (PSI) subunits with isoforms that confer the binding of chlorophyll (Chl) f molecules that absorb far-red light (FRL). However, the exact sites at which Chl f molecules are bound are still challenging to determine. To aid in the identification of Chl f-binding sites, we solved the cryo-EM structure of PSI from far-red light-acclimated cells of the cyanobacterium Synechococcus sp. PCC 7335. We identified six sites that bind Chl f with high specificity and three additional sites that are likely to bind Chl f at lower specificity. All of these binding sites are in the core-antenna regions of PSI, and Chl f was not observed among the electron transfer cofactors. This structural analysis also reveals both conserved and nonconserved Chl f-binding sites, the latter of which exemplify the diversity in FRL-PSI among species. We found that the FRL-PSI structure also contains a bound soluble ferredoxin, PetF1, at low occupancy, which suggests that ferredoxin binds less transiently than expected according to the canonical view of ferredoxin-binding to facilitate electron transfer. We suggest that this may result from structural changes in FRL-PSI that occur specifically during FRL photoacclimation.

Structure of a monomeric photosystem II core complex from a cyanobacterium acclimated to far-red light reveals the functions of chlorophylls d and f.

Far-red light (FRL) photoacclimation in cyanobacteria provides a selective growth advantage for some terrestrial cyanobacteria by expanding the range of photosynthetically active radiation to include far-red/near-infrared light (700-800 nm). During this photoacclimation process, photosystem II (PSII), the water:plastoquinone photooxidoreductase involved in oxygenic photosynthesis, is modified. The resulting FRL-PSII is comprised of FRL-specific core subunits and binds chlorophyll (Chl) d and Chl f molecules in place of several of the Chl a molecules found when cells are grown in visible light. These new Chls effectively lower the energy canonically thought to define the "red limit" for light required to drive photochemical catalysis of water oxidation. Changes to the architecture of FRL-PSII were previously unknown, and the positions of Chl d and Chl f molecules had only been proposed from indirect evidence. Here, we describe the 2.25 Å resolution cryo-EM structure of a monomeric FRL-PSII core complex from Synechococcus sp. PCC 7335 cells that were acclimated to FRL. We identify one Chl d molecule in the ChlD1 position of the electron transfer chain and four Chl f molecules in the core antenna. We also make observations that enhance our understanding of PSII biogenesis, especially on the acceptor side of the complex where a bicarbonate molecule is replaced by a glutamate side chain in the absence of the assembly factor Psb28. In conclusion, these results provide a structural basis for the lower energy limit required to drive water oxidation, which is the gateway for most solar energy utilization on earth.

Selective Methane Oxidation by Heterogenized Iridium Catalysts.

Oxidative methane (CH4) carbonylation promises a direct route to the synthesis of value-added oxygenates such as acetic acid (CH3COOH). Here, we report a strategy to realize oxidative CH4 carbonylation through immobilized Ir complexes on an oxide support. Our immobilization approach not only enables direct CH4 activation but also allows for easy separation and reutilization of the catalyst. Furthermore, we show that a key step, methyl migration, that forms a C-C bond, is sensitive to the electrophilicity of carbonyl, which can be tuned by a gentle reduction to the Ir centers. While the as-prepared catalyst that mainly featured Ir(IV) preferred CH3COOH production, a reduced catalyst featuring predominantly Ir(III) led to a significant increase of CH3OH production at the expense of the reduced yield of CH3COOH.

Structural comparison of allophycocyanin variants reveals the molecular basis for their spectral differences.

Allophycocyanins are phycobiliproteins that absorb red light and transfer the energy to the reaction centers of oxygenic photosynthesis in cyanobacteria and red algae. Recently, it was shown that some allophycocyanins absorb far-red light and that one subset of these allophycocyanins, comprising subunits from the ApcD4 and ApcB3 subfamilies (FRL-AP), form helical nanotubes. The lowest energy absorbance maximum of the oligomeric ApcD4-ApcB3 complexes occurs at 709 nm, which is unlike allophycocyanin (AP; ApcA-ApcB) and allophycocyanin B (AP-B; ApcD-ApcB) trimers that absorb maximally at ~ 650 nm and ~ 670 nm, respectively. The molecular bases of the different spectra of AP variants are presently unclear. To address this, we structurally compared FRL-AP with AP and AP-B, performed spectroscopic analyses on FRL-AP, and leveraged computational approaches. We show that among AP variants, the α-subunit constrains pyrrole ring A of its phycocyanobilin chromophore to different extents, and the coplanarity of ring A with rings B and C sets a baseline for the absorbance maximum of the chromophore. Upon oligomerization, the α-chromophores of all AP variants exhibit a red shift of the absorbance maximum of ~ 25 to 30 nm and band narrowing. We exclude excitonic coupling in FRL-AP as the basis for this red shift and extend the results to discuss AP and AP-B. Instead, we attribute these spectral changes to a conformational alteration of pyrrole ring D, which becomes more coplanar with rings B and C upon oligomerization. This study expands the molecular understanding of light-harvesting attributes of phycobiliproteins and will aid in designing phycobiliproteins for biotechnological applications.

A quantitative assessment of (bacterio)chlorophyll assignments in the cryo-EM structure of the Chloracidobacterium thermophilum reaction center.

Chlorophylls and bacteriochlorophylls are the primary pigments used by photosynthetic organisms for light harvesting, energy transfer, and electron transfer. Many molecular structures of (bacterio)chlorophyll-containing protein complexes are available, some of which contain mixtures of different (bacterio)chlorophyll types. Differentiating these, which sometimes are structurally similar, is challenging but is required for leveraging structural data to gain functional insight. The reaction center complex from Chloroacidobacterium thermophilum has a hybrid (bacterio)chlorophyll antenna system containing both chlorophyll a and bacteriochlorophyll a molecules. The recent availability of its cryogenic electron microscopy (cryo-EM) structure provides an opportunity for a quantitative analysis of their identities and chemical environments. Here, we describe a theoretical basis for differentiating chlorophyll a and bacteriochlorophyll a in a cryo-EM map, and apply the approach to the experimental cryo-EM maps of the (bacterio)chlorophyll sites of the chloroacidobacterial reaction center. The comparison reveals that at ~ 2.2-Å resolution, chlorophyll a and bacteriochlorophyll a are easily distinguishable, but the orientation of the bacteriochlorophyll a acetyl moiety is not; however, the latter can confidently be assigned by identifying a hydrogen bond donor from the protein environment. This study reveals the opportunities and challenges in assigning (bacterio)chlorophyll types in structural biology, the accuracy of which is vital for downstream investigations.

Dominant Role of Hole Transport Pathway in Achieving Record High Photoconductivity in Two-Dimensional Metal-Organic Frameworks.

Metal-organic frameworks (MOFs) with mobile charges have attracted significant attention due to their potential applications in photoelectric devices, chemical resistance sensors, and catalysis. However, fundamental understanding of the charge transport pathway within the framework and the key properties that determine the performance of conductive MOFs in photoelectric devices remain underexplored. Herein, we report the mechanisms of photoinduced charge transport and electron dynamics in the conductive 2D M-HHTP (M=Cu, Zn or Cu/Zn mixed; HHTP=2,3,6,7,10,11-hexahydroxytriphenylene) MOFs and their correlation with photoconductivity using the combination of time-resolved terahertz spectroscopy, optical transient absorption spectroscopy, X-ray transient absorption spectroscopy, and density functional theory (DFT) calculations. We identify the through-space hole transport mechanism through the interlayer sheet π-π interaction, where photoinduced hole state resides in HHTP ligand and electronic state is localized at the metal center. Moreover, the photoconductivity of the Cu-HHTP MOF is found to be 65.5 S m-1 , which represents the record high photoconductivity for porous MOF materials based on catecholate ligands.

How to correct relative voxel scale factors for calculations of vector-difference Fourier maps in cryo-EM.

The atomic coordinates derived from cryo-electron microscopy (cryo-EM) maps can be inaccurate when the voxel scaling factors are not properly calibrated. Here, we describe a method for correcting relative voxel scaling factors between pairs of cryo-EM maps for the same or similar structures that are expanded or contracted relative to each other. We find that the correction of scaling factors reduces the amplitude differences of Fourier-inverted structure factors from voxel-rescaled maps by up to 20-30%, as shown by two cryo-EM maps of the SARS-CoV-2 spike protein measured at pH 4.0 and pH 8.0. This allows for the calculation of the difference map after properly scaling, revealing differences between the two structures for individual amino acid residues. Unexpectedly, the analysis uncovers two previously overlooked differences of amino acid residues in structures and their local structural changes. Furthermore, we demonstrate the method as applied to two cryo-EM maps of monomeric apo-photosystem II from the cyanobacteria Synechocystis sp. PCC 6803 and Thermosynechococcus elongatus. The resulting difference maps reveal many changes in the peripheral transmembrane PsbX subunit between the two species.

Electrocatalytic, Homogeneous Ammonia Oxidation in Water to Nitrate and Nitrite with a Copper Complex.

Electrocatalytic ammonia oxidation at room temperature and pressure allows energy-economical and environmentally friendly production of nitrites and nitrates. Few molecular catalysts, however, have been developed for this six- or eight-electron oxidation process. We now report [Cu(bipyalk)]+, a homogeneous electrocatalyst that realizes the title reaction in water at 94% Faradaic efficiency. The catalyst exhibits high selectivity against water oxidation in aqueous media, as [Cu(bipyalk)]+ is not competent for water oxidation.

Spectroelectrochemistry of Water Oxidation Kinetics in Molecular versus Heterogeneous Oxide Iridium Electrocatalysts.

Water oxidation is the step limiting the efficiency of electrocatalytic hydrogen production from water. Spectroelectrochemical analyses are employed to make a direct comparison of water oxidation reaction kinetics between a molecular catalyst, the dimeric iridium catalyst [Ir2(pyalc)2(H2O)4-(µ-O)]2+ (IrMolecular, pyalc = 2-(2'pyridinyl)-2-propanolate) immobilized on a mesoporous indium tin oxide (ITO) substrate, with that of an heterogeneous electrocatalyst, an amorphous hydrous iridium (IrOx) film. For both systems, four analogous redox states were detected, with the formation of Ir(4+)-Ir(5+) being the potential-determining step in both cases. However, the two systems exhibit distinct water oxidation reaction kinetics, with potential-independent first-order kinetics for IrMolecular contrasting with potential-dependent kinetics for IrOx. This is attributed to water oxidation on the heterogeneous catalyst requiring co-operative effects between neighboring oxidized Ir centers. The ability of IrMolecular to drive water oxidation without such co-operative effects is explained by the specific coordination environment around its Ir centers. These distinctions between molecular and heterogeneous reaction kinetics are shown to explain the differences observed in their water oxidation electrocatalytic performance under different potential conditions.

Comparison of PsbQ and Psb27 in photosystem II provides insight into their roles.

Photosystem II (PSII) catalyzes the oxidation of water at its active site that harbors a high-valent inorganic Mn4CaOx cluster called the oxygen-evolving complex (OEC). Extrinsic subunits generally serve to protect the OEC from reductants and stabilize the structure, but diversity in the extrinsic subunits exists between phototrophs. Recent cryo-electron microscopy experiments have provided new molecular structures of PSII with varied extrinsic subunits. We focus on the extrinsic subunit PsbQ, that binds to the mature PSII complex, and on Psb27, an extrinsic subunit involved in PSII biogenesis. PsbQ and Psb27 share a similar binding site and have a four-helix bundle tertiary structure, suggesting they are related. Here, we use sequence alignments, structural analyses, and binding simulations to compare PsbQ and Psb27 from different organisms. We find no evidence that PsbQ and Psb27 are related despite their similar structures and binding sites. Evolutionary divergence within PsbQ homologs from different lineages is high, probably due to their interactions with other extrinsic subunits that themselves exhibit vast diversity between lineages. This may result in functional variation as exemplified by large differences in their calculated binding energies. Psb27 homologs generally exhibit less divergence, which may be due to stronger evolutionary selection for certain residues that maintain its function during PSII biogenesis and this is consistent with their more similar calculated binding energies between organisms. Previous experimental inconsistencies, low confidence binding simulations, and recent structural data suggest that Psb27 is likely to exhibit flexibility that may be an important characteristic of its activity. The analysis provides insight into the functions and evolution of PsbQ and Psb27, and an unusual example of proteins with similar tertiary structures and binding sites that probably serve different roles.