Structured near-infrared Magnetic Circular Dichroism spectra of the Mn4CaO5 cluster of PSII in T. vulcanus are dominated by Mn(IV) d-d 'spin-flip' transitions.

Photosystem II passes through four metastable S-states in catalysing light-driven water oxidation. Variable temperature variable field (VTVH) Magnetic Circular Dichroism (MCD) spectra in PSII of Thermosynochococcus (T.) vulcanus for each S-state are reported. These spectra, along with assignments, provide a new window into the electronic and magnetic structure of Mn4CaO5. VTVH MCD spectra taken in the S2 state provide a clear g=2, S=1/2 paramagnetic characteristic, which is entirely consistent with that known by EPR. The three features, seen as positive (+) at 749nm, negative (-) at 773nm and (+) at 808nm are assigned as 4A→2E spin-flips within the d3 configuration of the Mn(IV) centres present. This assignment is supported by comparison(s) to spin-flips seen in a range of Mn(IV) materials. S3 exhibits a more intense (-) MCD peak at 764nm and has a stronger MCD saturation characteristic. This S3 MCD saturation behaviour can be accurately modelled using parameters taken directly from analyses of EPR spectra. We see no evidence for Mn(III) d-d absorption in the near-IR of any S-state. We suggest that Mn(IV)-based absorption may be responsible for the well-known near-IR induced changes induced in S2 EPR spectra of T. vulcanus and not Mn(III)-based, as has been commonly assumed. Through an analysis of the nephelauxetic effect, the excitation energy of S-state dependent spin-flips seen may help identify coordination characteristics and changes at each Mn(IV). A prospectus as to what more detailed S-state dependent MCD studies promise to achieve is outlined.

The lowest-energy chlorophyll of photosystem II is adjacent to the peripheral antenna: Emitting states of CP47 assigned via circularly polarized luminescence.

The identification of low-energy chlorophyll pigments in photosystem II (PSII) is critical to our understanding of the kinetics and mechanism of this important enzyme. We report parallel circular dichroism (CD) and circularly polarized luminescence (CPL) measurements at liquid helium temperatures of the proximal antenna protein CP47. This assembly hosts the lowest-energy chlorophylls in PSII, responsible for the well-known "F695" fluorescence band of thylakoids and PSII core complexes. Our new spectra enable a clear identification of the lowest-energy exciton state of CP47. This state exhibits a small but measurable excitonic delocalization, as predicated by its CD and CPL. Using structure-based simulations incorporating the new spectra, we propose a revised set of site energies for the 16 chlorophylls of CP47. The significant difference from previous analyses is that the lowest-energy pigment is assigned as Chl 612 (alternately numbered Chl 11). The new assignment is readily reconciled with the large number of experimental observations in the literature, while the most common previous assignment for the lowest energy pigment, Chl 627(29), is shown to be inconsistent with CD and CPL results. Chl 612(11) is near the peripheral light-harvesting system in higher plants, in a lumen-exposed region of the thylakoid membrane. The low-energy pigment is also near a recently proposed binding site of the PsbS protein. This result consequently has significant implications for our understanding of the kinetics and regulation of energy transfer in PSII.

Circularly polarized luminescence spectroscopy reveals low-energy excited states and dynamic localization of vibronic transitions in CP43.

Circularly polarized luminescence (CPL) spectroscopy is an established but relatively little-used technique that monitors the chirality of an emission. When applied to photosynthetic pigment assemblies, we find that CPL provides sensitive and detailed information on low-energy exciton states, reflecting the interactions, site energies and geometries of interacting pigments. CPL is the emission analog of circular dichroism (CD) and thus spectra explore the optical activity only of fluorescent states of the pigment-protein complex and consequently the nature of the lowest-energy excited states (trap states), whose study is a critical area of photosynthesis research. In this work, we develop the new approach of temperature-dependent CPL spectroscopy, over the 2-120 K temperature range, and apply it to the CP43 proximal antenna protein of photosystem II. Our results confirm strong excitonic interactions for at least one of the two well-established emitting states of CP43 named "A" and "B". Previous structure-based models of CP43 spectra are evaluated in the light of the new CPL data. Our analysis supports the assignments of Shibata et al. [Shibata et al. J. Am. Chem. Soc. 135 (2013) 6903-6914], particularly for the highly-delocalized B-state. This state dominates CPL spectra and is attributed predominantly to chlorophyll a's labeled Chl 634 and Chl 636 (alternatively labeled Chl 43 and 45 by Shibata et al.). The absence of any CPL intensity in intramolecular vibrational sidebands associated with the delocalized "B" excited state is attributed to the dynamic localization of intramolecular vibronic transitions.

Challenges facing an understanding of the nature of low-energy excited states in photosynthesis.

While the majority of the photochemical states and pathways related to the biological capture of solar energy are now well understood and provide paradigms for artificial device design, additional low-energy states have been discovered in many systems with obscure origins and significance. However, as low-energy states are naively expected to be critical to function, these observations pose important challenges. A review of known properties of low energy states covering eight photochemical systems, and options for their interpretation, are presented. A concerted experimental and theoretical research strategy is suggested and outlined, this being aimed at providing a fully comprehensive understanding.

Optical identification of the long-wavelength (700-1700 nm) electronic excitations of the native reaction centre, Mn4CaO5 cluster and cytochromes of photosystem II in plants and cyanobacteria.

Visible/UV absorption in PS II core complexes is dominated by the chl-a absorptions, which extend to ~700 nm. A broad 700-730 nm PS II core complex absorption in spinach has been assigned to a charge transfer excitation between ChlD1 and ChlD2. Emission from this state, which peaks at 780 nm, has been seen for both plant and cyanobacterial samples. We show that Thermosynechococcus vulcanus PS II core complexes have parallel absorbance in the 700-730 nm region and similar photochemical behaviour to that seen in spinach. This establishes the low energy charge transfer state as intrinsic to the native PS II reaction centre. High-sensitivity MCD measurements made in the 700-1700 nm region reveal additional electronic excitations at ~770 nm and ~1550 nm. The temperature and field dependence of MCD spectra establish that the system peaking near 1550 nm is a heme-to-Fe(III) charge transfer excitation. These transitions have not previously been observed for cyt b559 or cyt c550. The distinctive characteristics of the MCD signals seen at 770 nm allow us to assign absorption in this region to a dz(2)→d(x2-y2) transition of Mn(III) in the Ca-Mn4O5 cluster of the oxygen evolving centre. Current measurements were performed in the S1 state. Detailed analyses of this spectral region, especially in higher S states, promise to provide a new window on models of water oxidation.

Determination of the PS I content of PS II core preparations using selective emission: a new emission of PS II at 780nm.

Routinely prepared PS II core samples are often contaminated by a significant (~1-5%) fraction of PS I, as well as related proteins. This contamination is of little importance in many experiments, but masks the optical behaviour of the deep red state in PS II, which absorbs in the same spectral range (700-730nm) as PS I (Hughes et al. 2006). When contamination levels are less than ~1%, it becomes difficult to quantify the PS I related components by gel-based, chromatographic, circular dichroism or EPR techniques. We have developed a fluorescence-based technique, taking advantage of the distinctively different low-temperature emission characteristics of PS II and PS I when excited near 700nm. The approach has the advantage of providing the relative concentration of the two photosystems in a single spectral measurement. A sensitivity limit of 0.01% PS I (or better) can be achieved. The procedure is applied to PS II core preparations from spinach and Thermosynechococcus vulcanus. Measurements made of T. vulcanus PS II preparations prepared by re-dissolving crystallised material indicate a low but measurable PS I related content. The analysis provides strong evidence for a previously unreported fluorescence of PS II cores peaking near 780nm. The excitation dependence of this emission as well as its appearance in both low PS I cyanobacterial and plant based PS II core preparations suggests its association with the deep red state of PS II.

An analytical data inversion method for Magnetic Circular Dichroism spectra dominated by the "B-term".

A simple procedure is developed enabling the analytical inversion of an (unpolarized) absorption spectrum combined with a Magnetic Circular Dichroism (MCD) spectrum to resolve two overlapping bands of orthogonal polarization. This method is appropriate when (i) the overlapping transitions are well isolated from other bands, and (ii) when their electronic spacing is large enough so that the "A-term" and "C-term" contributions to the MCD spectrum can be ignored and hence only the "B-term" contribution need be considered. We apply this procedure to assign the Q-band system of chlorophylls, though similar challenges also commonly arise throughout both conventional and X-ray MCD (XMCD) spectroscopy. Analytical data inversion has not previously been possible as the inversion process is two-fold underdetermined. We show that the assumptions of isolated spectra and "B-term" dominance yields one generally valid constraint, leaving only one quantity unspecified by the experimental data. For some systems, an approximation leading to equal but opposite sign B-term magnitudes of the two components may be reasonable, but for chlorophyllides we find this constraint to be inappropriate. Instead, we constrain a bounded variable controlling the relative absorption strengths. Derived spectral bandshapes of the individual components are shown to be insensitive to its particular value, allowing weak spectral components of one polarization overlapped by intense components of the other to be immediately exposed. This is demonstrated for the chlorophylls, molecules for which the failure to detect such weak features historically led to incorrect proposals for the Q-band assignments.

Formation of water-chlorophyll clusters in dilute samples of chlorophyll-a in ether at low temperature.

Simultaneously measured absorption (ABS) and magnetic circular dichroism (MCD) spectra of the Q-bands of chlorophyll-a (Chl-a) in ether over 150-186 K reveal that the species that forms at low temperature is a chlorophyll hydrate rather than a diether complex. We have recently proposed a new assignment paradigm for the spectra of chlorophillides which, for the first time, quantitatively accounts for a wide range of observed data. Observations performed at low temperature in ether have historically been very important for the interpretation of the spectra of Chl-a. While our assignment for this system initially anticipated only small spectral changes as the temperature is lowered, significant changes are known to occur. Extensive CAM-B3LYP time-dependent density-functional theory (TD-DFT) calculations verify that the observed spectra of the hydrated species conforms to expectations based on our new assignment, as well as supporting the feasibility of the proposed hydration reactions.

Selective and differential optical spectroscopies in photosynthesis.

Photosynthetic pigments are inherently intense optical absorbers and have strong polarisation characteristics. They can also luminesce strongly. These properties have led optical spectroscopies to be, quite naturally, key techniques in photosynthesis. However, there are typically many pigments in a photosynthetic assembly, which when combined with the very significant inhomogeneous and homogeneous linewidths characteristic of optical transitions, leads to spectral congestion. This in turn has made it difficult to provide a definitive and detailed electronic structure for many photosynthetic assemblies. An electronic structure is, however, necessary to provide a foundation for any complete description of fundamental processes in photosynthesis, particularly those in reaction centres. A wide range of selective and differential spectral techniques have been developed to help overcome the problems of spectral complexity and congestion. The techniques can serve to either reduce spectral linewidths and/or extract chromophore specific information from unresolved spectral features. Complementary spectral datasets, generated by a number of techniques, may then be combined in a 'multi-dimensional' theoretical analysis so as to constrain and define effective models of photosynthetic assemblies and their fundamental processes. A key example is the work of Renger and his group (Raszewski, Biophys J 88(2):986-998, 2005) on PS II reaction centre assemblies. This article looks to provide an overview of some of these techniques and indicate where their strengths and weaknesses may lie. It highlights some of our own contributions and indicates areas where progress may be possible.

Spin-forbidden near-infrared luminescence from a F3+ colour centre generated upon annealing in mechanochemically prepared nanocrystalline BaLiF3.

We report the properties of a unique colour centre in mechanochemically synthesized inverse perovskite BaLiF3 submicron crystals that are luminescent at ∼765 nm. The spin-forbidden luminescence with a lifetime of 5 ms is attributed to a F3+ (F-centre aggregate) in the fluoride octahedra, with three fluoride anion vacancies (3F+) filled with two electrons (2e-). The Zeeman splitting of the electronic origin and its temperature dependence indicate that the transition is from a singlet excited state to a triplet ground state. The F3+ emission occurred after annealing (≥500 °C) the mechanochemically prepared pure BaLiF3 nanocrystals and is characterized by a structured emission with a relatively narrow zero-phonon line. A reduction of photoluminescence intensity of the F3+ band upon increasing X-ray dose was observed. Importantly, it is observed that the F3+ luminescence is stable in the dark but bleaches upon exposure to natural sunlight. Our results point to the potential for a new colour centre-based nano-laser in the near-infrared region. Additionally, our experiments also indicate that BaLiF3 : F3+ has some potential for data storage, and X-ray imaging and dosimetry.

D1 protein variants in Photosystem II from Thermosynechococcus elongatus studied by low temperature optical spectroscopy.

In Photosystem II (PSII) from Thermosynechococcus elongatus, high-light intensity growth conditions induce the preferential expression of the psbA(3) gene over the psbA(1) gene. These genes encode for the D1 protein variants labeled D1:3 and D1:1, respectively. We have compared steady state absorption and photo-induced difference spectra at <10 K of PSII containing either D1:1 or D1:3. The following differences were observed. (i) The pheophytin Q(x) band was red-shifted in D1:3 (547.3 nm) compared to D1:1 (544.3 nm). (ii) The electrochromism on the Pheo(D1) Q(x) band induced by Q(A)(-) (the C550 shift) was more asymmetric in D1:3. (iii) The two variants differed in their responses to excitation with far red (704 nm) light. When green light was used there was little difference between the two variants. With far red light the stable (t(1/2)>50 ms) Q(A)(-) yield was approximately 95% in D1:3, and approximately 60% in D1:1, relative to green light excitation. (iv) For the D1:1 variant, the quantum efficiency of photo-induced oxidation of side-pathway donors was lower. These effects can be correlated with amino acid changes between the two D1 variants. The effects on the pheophytin Q(x) band can be attributed to the hydrogen bond from Glu130 in D1:3 to the 13(1)-keto of Pheo(D1), which is absent for Gln130 in D1:1. The reduced yield with red light in the D1:1 variant could be associated with either the Glu130Gln change, and/or the four changes near the binding site of P(D1), in particular Ser153Ala. Photo-induced Q(A)(-) formation with far red light is assigned to the direct optical excitation of a weakly absorbing charge transfer state of the reaction centre. We suggest that this state is blue-shifted in the D1:1 variant. A reduced efficiency for the oxidation of side-pathway donors in the D1:1 variant could be explained by a variation in the location and/or redox potential of P+.

The S(1) split signal of photosystem II; a tyrosine-manganese coupled interaction.

Detailed optical and EPR analyses of states induced in dark-adapted PS II membranes by cryogenic illumination permit characterization and quantification of all pigment derived donors and acceptors, as well as optically silent (in the visible, near infrared) species which are EPR active. Near complete turnover formation of Q(A)((-)) is seen in all centers, but with variable efficiency, depending on the donor species. In minimally detergent-exposed PS II membranes, negligible (<5%) oxidation of chlorophyll or carotenoid centers occurs for illumination temperatures 5-20 K. An optically silent electron donor to P680(+) is observed with the same decay kinetics as the S(1) split signal. Cryogenic donors to P680(+) seen are: (i) transient (t(1/2) approximately 150 s) tyrosine related species, including 'split signals' ( approximately 15% total centers), (ii) reduced cytochrome b(559) ( approximately 30-50% centers), and (iii) an organic donor, possibly an amino acid side chain, ( approximately 30% centers).

The primary donor of far-red photosystem II: ChlD1 or PD2?

Far-red light (FRL) Photosystem II (PSII) isolated from Chroococcidiopsis thermalis is studied using parallel analyses of low-temperature absorption, circular dichroism (CD) and magnetic circular dichroism (MCD) spectroscopies in conjunction with fluorescence measurements. This extends earlier studies (Nurnberg et al 2018 Science 360 (2018) 1210-1213). We confirm that the chlorophyll absorbing at 726 nm is the primary electron donor. At 1.8 K efficient photochemistry occurs when exciting at 726 nm and shorter wavelengths; but not at wavelengths longer than 726 nm. The 726 nm absorption peak exhibits a 21 ±â€¯4 cm-1 electrochromic shift due to formation of the semiquinone anion, QA-. Modelling indicates that no other FRL pigment is located among the 6 central reaction center chlorins: PD1, PD2 ChlD1, ChlD2, PheoD1 and PheoD2. Two of these chlorins, ChlD1 and PD2, are located at a distance and orientation relative to QA- so as to account for the observed electrochromic shift. Previously, ChlD1 was taken as the most likely candidate for the primary donor based on spectroscopy, sequence analysis and mechanistic arguments. Here, a more detailed comparison of the spectroscopic data with exciton modelling of the electrochromic pattern indicates that PD2 is at least as likely as ChlD1 to be responsible for the 726 nm absorption. The correspondence in sign and magnitude of the CD observed at 726 nm with that predicted from modelling favors PD2 as the primary donor. The pros and cons of PD2 vs ChlD1 as the location of the FRL-primary donor are discussed.

The semiquinone-iron complex of photosystem II: structural insights from ESR and theoretical simulation; evidence that the native ligand to the non-heme iron is carbonate.

The semiquinone-iron complex of photosystem II was studied using electron spin resonance (ESR) spectroscopy and density functional theory calculations. Two forms of the signal were investigated: 1), the native g approximately 1.9 form; and 2), the g approximately 1.84 form, which is well known in purple bacterial reaction centers and occurs in photosystem II when treated with formate. The g approximately 1.9 form shows low- and high-field edges at g approximately 3.5 and g < 0.8, respectively, and resembles the g approximately 1.84 form in terms of shape and width. Both types of ESR signal were simulated using the theoretical approach used previously for the BRC complex, a spin Hamiltonian formalism in which the semiquinone radical magnetically interacts (J approximately 1 cm(-1)) with the nearby high-spin Fe(2+). The two forms of ESR signal differ mainly by an axis rotation of the exchange coupling tensor (J) relative to the zero-field tensor (D) and a small increase in the zero-field parameter D ( approximately 6 cm(-1)). Density functional theory calculations were conducted on model semiquinone-iron systems to identify the physical nature of these changes. The replacement of formate (or glutamate in the bacterial reaction centers) by bicarbonate did not result in changes in the coupling environment. However, when carbonate (CO(3)(2-)) was used instead of bicarbonate, the exchange and zero-field tensors did show changes that matched those obtained from the spectral simulations. This indicates that 1), the doubly charged carbonate ion is responsible for the g approximately 1.9 form of the semiquinone-iron signal; and 2), carbonate, rather than bicarbonate, is the ligand to the iron.

Identification of the QY excitation of the primary electron acceptor of photosystem II: CD determination of its coupling environment.

Low-temperature absorption and CD spectra, measured simultaneously, are reported from Photosystem II (PS II) reduced with sodium dithionite. Spectra were obtained using PS II core complexes before and after photoaccumulation of Pheo(D1)(-), the anion of the primary acceptor. For plant PS II, Pheo(D1)(-) was generated under conditions in which the primary plastoquinone was present as an anion (Q(A)(-)) and as a modified species taken to be the neutral doubly reduced hydroquinone (Q(A)H(2)). The bleaches observed upon Pheo(D1)(-) formation in the presence of Q(A)(-) are shifted to the blue compared those in the presence of Q(A)H(2). This is attributed to the influence of the charge on Q(A)(-), and this effect mirrors the well-known electrochromic effect of Q(A)(-) on the neutral pigments. The absorption bleaches induced by Pheo(D1) reduction are species dependent. Structured changes of the CD in the 680-690 nm spectral region are seen upon photoaccumulation of Pheo(D1)(-) in PS II from plant, Synechocystis and Thermosynechococcus vulcanus. These CD changes are shown to be consistent with the overall electronic assignments of Raszewski et al. [Raszewski et al. Biophys. J. 2008, 95, 105], which place the dominant Pheo(D1) excitation near 672 nm. CD changes associated with Pheo(D1) reduction are modeled to arise from the shift and intensity changes of two CD features: one predominately of Chl(D1) character, the other predominately Pheo(D2) in character. The assignments are also shown to account for the Q(Y) absorption changes in samples where the quinone is its charged (Q(A)(-)) and neutral (Q(A)H(2)) states.

The highly resolved electronic spectrum of the square planar CuCl(4) (2-) ion.

The low temperature magnetic circular dichroism (MCD) and electron paramagnetic resonance (EPR) spectra of Cu(II) doped Cs(2)ZrCl(6) are reported. The Cu(II) ion is incorporated as the square planar copper tetrachloride ion, CuCl(4) (2-), which substitutes at the Zr(IV) site in the Cs(2)ZrCl(6) lattice, with a complete absence of axial coordination. Both the EPR and MCD show highly resolved spectra from which it is possible to determine the superhyperfine coupling constants and excited state geometries respectively. The Franck-Condon intensity patterns suggest that there is a substantial relaxation of the host lattice about the impurity ion. For the lowest energy (2)B(1g)(x(2)-y(2))-->(2)B(2g)(xy) transition, both the magnetic dipole allowed electronic origin as well as vibronic false origins are observed. The high resolution of the spectra allowed the accurate determination of the odd parity vibrations that are active in the spectra. The opposite sign of the MCD of the two components of the (2)E(g)(xz,yz) excited state allows this splitting to be determined for the first time. Accurate and unambiguous spectral parameters for the CuCl(4) (2-) ion are important as it has become a benchmark transition metal complex for theoretical electronic structure calculations.

Photochemistry beyond the red limit in chlorophyll f-containing photosystems.

Photosystems I and II convert solar energy into the chemical energy that powers life. Chlorophyll a photochemistry, using red light (680 to 700 nm), is near universal and is considered to define the energy "red limit" of oxygenic photosynthesis. We present biophysical studies on the photosystems from a cyanobacterium grown in far-red light (750 nm). The few long-wavelength chlorophylls present are well resolved from each other and from the majority pigment, chlorophyll a. Charge separation in photosystem I and II uses chlorophyll f at 745 nm and chlorophyll f (or d) at 727 nm, respectively. Each photosystem has a few even longer-wavelength chlorophylls f that collect light and pass excitation energy uphill to the photochemically active pigments. These photosystems function beyond the red limit using far-red pigments in only a few key positions.

A new fundamental type of conformational isomerism.

Isomerism is a fundamental chemical concept, reflecting the fact that the arrangement of atoms in a molecular entity has a profound influence on its chemical and physical properties. Here we describe a previously unclassified fundamental form of conformational isomerism through four resolved stereoisomers of a transoid (BF)O(BF)-quinoxalinoporphyrin. These comprise two pairs of enantiomers that manifest structural relationships not describable within existing IUPAC nomenclature and terminology. They undergo thermal diastereomeric interconversion over a barrier of 104 ± 2 kJ mol-1, which we term 'akamptisomerization'. Feasible interconversion processes between conceivable synthesis products and reaction intermediates were mapped out by density functional theory calculations, identifying bond-angle inversion (BAI) at a singly bonded atom as the reaction mechanism. We also introduce the necessary BAI stereodescriptors parvo and amplo. Based on an extended polytope formalism of molecular structure and stereoisomerization, BAI-driven akamptisomerization is shown to be the final fundamental type of conformational isomerization.

Publisher Correction: A new fundamental type of conformational isomerism.

In the version of this Article originally published, the word 'stereoisomerism' was erroneously included in the label of the upper-right box of Fig. 1. The label within the box has been corrected and it now reads: "Constitutional isomerism (same formula, different connectivity)". This has been corrected in the online version of the Article.

Charge separation in photosystem II core complexes induced by 690-730 nm excitation at 1.7 K.

The illumination of oxygen-evolving PSII core complexes at very low temperatures in spectral regions not expected to excite P680 leads to charge separation in a majority of centers. The fraction of centers photoconverted as a function of the number of absorbed photons per PSII core is determined by quantification of electrochromic shifts on Pheo(D1). These shifts arise from the formation of metastable plastoquinone anion (Q(A)(-)) configurations. Spectra of concentrated samples identify absorption in the 700-730 nm range. This is well beyond absorption attributable to CP47. Spectra in the 690-730 nm region can be described by the 'trap' CP47 absorption at 689 nm, with dipole strength of approximately 1 chlorophyll a (chl a), partially overlapping a broader feature near 705 nm with a dipole strength of approximately 0.15 chl a. This absorption strength in the 700-730 nm region falls by 40% in the photoconverted configuration. Quantum efficiencies of photoconversion following illumination in the 690-700 nm region are similar to those obtained with green illumination but fall significantly in the 700-730 nm range. Two possible assignments of the long-wavelength absorption are considered. Firstly, as a low intensity component of strongly exciton-coupled reaction center chlorin excitations and secondly as a nominally 'dark' charge-transfer excitation of the 'special pair' P(D1)-P(D2). The opportunities offered by these observations towards the understanding of the nature of P680 and PSII fluorescence are discussed.