A Comparison Between Experimental and Broken Symmetry Density Functional Theory (BS-DFT) Calculated Electron Paramagnetic Resonance (EPR) Parameters of the S 2 State of the Oxygen Evolving Complex of Photosystem II in its Native (Calcium) and Strontium Substituted Form. Nathan J. Beal, Thomas A. Corry and Patrick J. O’Malley * School of Chemistry, The University of Manchester, Manchester M13 9PL, UK. ABSTRACT A comparison between experimental and Broken Symmetry Density Functional Theory (BS-DFT) calculated hyperfine couplings for the S 2 state of the oxygen evolving complex (OEC) has been performed. The effect of Ca substitution by Sr combined with the protonation state of two terminal hydroxo or aqua ligands, W1 and W2, on the calculated hyperfine couplings of 55 Mn, 13 C, 14 N, 17 O and 1 H nuclei has been investigated. Our findings show best agreement with experiment for OEC models which contain a hydroxide group at the W2 position and a 1
Transcript
A Comparison Between Experimental and Broken Symmetry Density
Functional Theory (BS-DFT) Calculated Electron Paramagnetic
Resonance (EPR) Parameters of the S2 State of the Oxygen Evolving
Complex of Photosystem II in its Native (Calcium) and Strontium
Substituted Form.
Nathan J. Beal, Thomas A. Corry and Patrick J. O’Malley*
School of Chemistry, The University of Manchester, Manchester M13 9PL, UK.
ABSTRACT
A comparison between experimental and Broken Symmetry Density Functional Theory
(BS-DFT) calculated hyperfine couplings for the S2 state of the oxygen evolving complex
(OEC) has been performed. The effect of Ca substitution by Sr combined with the
protonation state of two terminal hydroxo or aqua ligands, W1 and W2, on the calculated
hyperfine couplings of 55Mn, 13C, 14N, 17O and 1H nuclei has been investigated. Our
findings show best agreement with experiment for OEC models which contain a hydroxide
group at the W2 position and a water molecule at W1. For this model the agreement
between calculated and experimental data for all hyperfine couplings is excellent. Models
with a hydroxide group at W1 are particularly poor models. Sr substitution has a minor
influence on calculated hyperfine couplings in agreement with experimental
determinations. The sensitivity of the hyperfine couplings to relatively minor changes in
the OEC structure demonstrates the power of this methodology in refining the details of its
steric and electronic structure which is an essential step in formulating a complete
mechanism for water oxidation by the OEC.
1
INTRODUCTION
Photosystem II (PSII) is a multi-unit pigment protein complex found in the thylakoid
membrane of organisms that perform oxygenic photosynthesis. One of its key functions is
the accumulation of visible light driven oxidising equivalents on its donor side leading to
oxidation of water to molecular oxygen in its oxygen evolving complex (OEC).1–9 Only
recently has the fundamental atomic-level detailed molecular structure of this important
biological complex been successfully revealed. The 2011 X-ray study by Umena et al. and
the subsequent X-Ray Free Electron Laser (XFEL) crystal structure helped to provide an
atomic-level high resolution structure,10,11 which provides a primary landmark for any
suggested proposals regarding the molecular structure and mechanism of the OEC.1,12–14
The structure of the dark adapted state, Figure 1, showed that the OEC was a Mn4CaO5
cluster arranged in a distorted chair form with four terminal oxygen atoms presumably
water or hydroxide, labelled W1-W4, directly coordinated to the OEC.10 Two of these can
be confidently assigned as water molecules W3 and W4 ligated to the Ca2+ ion and the
other two W1 and W2 are either water or hydroxide ligands to the MnA ion. It has been
suggested that some of these OEC coordinated water or hydroxide molecules may serve as
substrates for water splitting.15,16 Various studies have highlighted an important role for the
calcium ion in the oxygen formation reaction with removal of the calcium ion found to
block the Sn state transition beyond the S2 state resulting in a complete loss of oxygen
evolving activity.17,18 Cation substitution experiments have shown that the only other cation
to restore oxygen evolution was strontium albeit at a reduced activity (approximately half
that of the native OEC).19–22
2
Figure 1. Structure of the model used in this study for the OEC found in dark-adapted PSII generated from PDB ID: 4UB6. The protein residues are labelled along with the Mn and Ca bound aqua ligands. Colour coding: manganese (pink), oxygen (red), nitrogen (purple), carbon (yellow) and calcium (white). Hydrogen atoms are omitted for clarity.
Substituting calcium for strontium has been reported to slightly modify the EPR
parameters of the S2 state,19,23 and additionally the substitution has been found to have an
effect on several carboxylate stretching modes of the S2−S1 FTIR difference spectra.24–28
These results imply that the calcium ion performs more than simply a structural role in the
OEC and may be mechanistically involved.
The improved structural information provided by the high resolution crystal structures has
provided the key and necessary underpinning for the mechanism of oxygen formation to be
investigated in greater detail with theoretical methods or other experimental techniques.
6,7,29–36 This report focuses on the S2 state for both native (Ca) and Sr substituted systems.
3
The S2 state is the best characterised Sn state in the Kok cycle, especially in terms of EPR
spectroscopy.16,37–49 X-band EPR spectra of the S2 state exhibits a multiline signal at g ≈ 2,
originating from an S = 1/2 ground state, most likely with a MnIII(MnIV)3 distribution of
oxidation states although other assignments have been discussed at length in the
literature.29,35,50,51 Sometimes accompanying this signal at g ≈ 2 is a broad signal occurring
at g ≥ 4.1 attributed to an S = 5/2 spin state of the OEC.52 The presence of the multiline
signal indicates an antiferromagentically coupled mixed valence manganese cluster,
resembling the multiline signal of synthetic or biological dinuclear MnIIIMnIV complexes.53–
55 In addition to the metal hyperfine couplings of the S2 state, ligand hyperfine couplings,
e.g. 17O, 14N, 1H and 13C have been used to provide insight into the molecular and
electronic structure of the OEC.16,38,40,56,57 As the S2 state is the best characterised state of
the Kok cycle in terms of experimental EPR data it therefore provides a good test of
computational results on model complexes for both native and Sr substituted forms of the
OEC. A large number of computational studies are currently being applied to OEC models
but it is important to limit the suitability of such models and the conclusions drawn from
them to well determined experimental parameters, something which is not widely adhered
to. As we will show in this study, correct prediction of EPR parameters provides very
rigorous constraints on proposed models of the S2 state and such restraints are essential
before models can be used further in the S-state cycle progression. In particular, the study
focuses on the protonation states of the two MnA ligated oxygen atoms, W1 and W2 using
both native and Sr substituted models. As mentioned above, crystallographic studies
cannot distinguish hydroxide and water ligands and while protonated states for both waters
are energetically and structurally similar, we show that the protonation state can be clearly
deciphered by its effect on the EPR hyperfine couplings of the manganese ions in the
cluster and its associated ligands. Earlier reports44 on this problem for smaller Ca models
4
have indicated that W1 and W2 are aqua and hydroxo ligands respectively in the S2 state.
This was based solely on the ability of the model to reproduce the experimental 55Mn HFCs
for a small model of the open cubane form. There is however not a complete consensus on
this particular protonation pattern58 and further investigations are required using larger
models of both the open and closed cubane forms and extending the range of comparison
between calculated and experimental HFCs. In this report therefore we extend this analysis
to both open and closed cubane forms of S2 using an extensive model incorporating in
particular the crucial redox active YZ residue and extend the analysis beyond 55Mn HFCs to
the ligand 17O, 14N, 13C and 1H nuclei. In addition we include a similar analysis and
comparison for Sr substituted S2 models.
COMPUTATIONAL DETAILS
The geometries of all the models studied were optimised in their respective high spin states
using the BP86 functional, 59,60 utilising the zeroth-order regular approximation (ZORA)
Hamiltonian to include scalar relativistic effects.61–63 ZORA adapted segmented all-electron
relativistically contracted (SARC) basis sets were employed for all atoms,64 ZORA
versions of the def2-SVP basis sets were used for C and H atoms with ZORA versions of
the def2-TZVP basis set used for all other atoms with f functions removed.65 The
computational time of the calculations was decreased by invoking the resolution of identity
approximation (RI) along with decontracted auxillary def2-TZVP/J coulomb fitting basis
sets.66–68 The optimizations also included the third generation (D3) semi-empirical van der
waals corrections proposed by Grimme.69,70 Increased integration grids (grid 4 and grid x4
in orca convention) and tight SCF convergence criteria were used throughout the
calculations. The Heisenberg exchange coupling constants, hyperfine and nuclear
quadrupole coupling values were calculated for all atoms of interest using the broken
symmetry DFT methodology using the hybrid meta-GGA TPSSh functional with the chain
5
of spheres (RIJCOSX) approximation to exact exchange using the same decontracted
auxillary basis sets that were used in the geometry optimization steps.71,72 Initial broken
symmetry guesses were constructed using the ‘flipspin’ feature of ORCA.73 Calculation of
the hyperfine and quadrupole tensors used basis sets developed by Neese et al. based on
the SARC def2-TZVP for the Mn, N and O atoms and def2-TZVP(-f) for all other
atoms.68,74 The integration grids were increased to an integration accuracy of 11 and 9 for
Mn, N and O respectively. Picture change effects were applied for the calculation of
hyperfine and nuclear quadrupole tensors. Heisenberg exchange coupling constants were
calculated using the methodology proposed by Pantazis et al.75 The calculated 55Mn
isotropic hyperfine couplings were scaled by a factor of 1.47 to account for the known spin
polarisation deficiency in the calculation of the Fermi contact term.76,77 This factor has been
validated for 6 models of mononuclear, dinuclear and tetranuclear manganese complexes
(see Table S1 in supporting information; structures are shown in Figure S1). Convergence
to the correct BS and HS states in all calculations was confirmed by examination of the
calculated Mulliken spin populations.
Model Systems
The model systems studied were constructed using starting coordinates taken from two
crystal structures of the OEC of PSII available in the literature (PDB ID: 4UB6 (native
PSII isolated from Thermosynechococcus vulcanus) and 4IL6 (Sr-substituted PSII isolated
from Thermosynechococcus vulcanus)).11,78
6
Figure 2. Numbering scheme for the constructed cluster models of the OEC. Colour coding: manganese (pink), calcium/strontium (white), oxygen (red), nitrogen (purple), carbon (yellow). Hydrogen atoms omitted for clarity. The complete model used for the calculations is given in Figure S1 of the Supporting Information.
The labelling scheme for all the models (Figure 2) is as follows: the model designators Ca
and Sr correspond to the crystal structure that was used as a starting point for the
calculations. The native PSII 4UB6 is denoted by Ca, while the Sr-substituted PSII 4IL6 is
represented by the label Sr. A second label is used to distinguish between the various
protonation patterns of the water or hydroxide groups (W1 and W2) studied which for
clarity can be seen in Table 1 below.
Table 1. Labelling scheme to distinguish the various protonation states of W1 and W2 in the Ca and Sr models.
Protonation stateLabel W1 W2
1 OH2 OH2 OH OH3 OH OH2
4 OH2 OH2
All the OEC cluster models studied contain the seven directly coordinated amino acid
residues (all found in the D1 protein chain unless otherwise indicated): Asp-170, Glu-189,
His-332, Glu-333, Asp-342, Ala-344 and CP43-Glu-354. Additionally the two fully
protonated water molecules coordinated to the calcium/strontium ion were also included as
7
well as the W1 and W2 groups coordinated to MnA. As well as this the models include the
important second sphere residues: Asp-61, Tyr-161, Gln-165, His-190, Asn-298, His-337
and CP43-Arg-357. In addition to this twelve closely associated crystallographic water
molecules as well as partial backbone of Glu-329 was involved, having previously found to
hydrogen bond with His-332.79 Inclusion of Tyr-161(YZ) and its hydrogen bonding partner
His-190 is essential for all S2 models. This is illustrated in Figure 3 where it is shown that
the Highest Occupied Molecular Orbital (HOMO) is located on the phenoxyl head group
of this residue with the HOMO-1 (predominantly anti-bonding dZ2) located on the MnD
III
ion along the Jahn Teller axis. This is in line with the observed subsequent photooxidation
sequence leading first to YZ oxidation to YZ• followed by eventual oxidation of MnD
III to
MnDIV
forming the S3 state. To reduce computational costs all residues were truncated after
the R group, in addition all residues took their standard proton states apart from His-337
where it has been shown a fully protonated histidine is present.79 A representative model is
shown in Figure S1 and coordinates of all models are given in the Supporting Information.
Figure 3. HOMO (a) and HOMO-1 (b) electron density contours for the Ca-1 model. Only selected regions are shown without hydrogen atoms.
8
RESULTS AND DISCUSSION
A full detailed analysis of the geometric structures and the Heisenberg exchange couplings
is provided in the Supporting Information. There is little experimental data concerning the
closed form of S2 other than the characteristically broad signal in the EPR spectrum. As a
result, no hyperfine coupling data will be presented for this form.
55Mn Hyperfine Couplings
Table 2 shows the spin projected isotropic and anisotropic hyperfine coupling (HFC)
tensors calculated for the open cubane form Ca models along with several experimental
data sets. At the present time there are numerous sets of experimental hyperfine coupling
tensors obtained from various simulations of the spectra obtained from EPR and ENDOR
experiments. The differences found in the experimental datasets reflect not only variations
in the methodology of the simulations but also aspects of sample origin and preparation. It
should be noted that a change in species from spinach to Thermosynechoccus elongatus
PSII or treatment of the sample with MeOH may have a visible effect on the splitting
pattern in the spectra on the order of ca. 10 MHz for a given HFC value.80 These data sets
will therefore be regarded as a range to compare the calculated results with. All three data
sets featured in Table 2 find one isotropic HFC around 300 MHz. Two of the data sets
feature two HFC near 200 MHz with the remaining HFC being found around 250 MHz.41,81
In contrast, Charlot et al. found two HFCs near to 250 MHz and only a single HFC value
around 200 MHz.82 The additional experimental value of 312 MHz found by Teutloff et al.
from single crystal Q-band ENDOR refers specifically to the largest hyperfine coupling
found in the OEC.80 It is important to note that no experimental studies performed so far
have been able to yield sign information or to assign the HFCs to specific manganese sites
with any certainty.
9
Considering firstly the calculated isotropic HFCs for each of the Ca models shows that Ca-
2 and Ca-3 models may be instantly rejected, as both models produce Aiso values for MnA
and MnB which are significantly smaller than shown in any of the experimental datasets.
The model Ca-4 produces isotropic HFCs in better agreement with the experimental values
however MnB and to a lesser extent MnA are still significantly lower than any found
experimentally. An explanation for this behaviour can be seen in the small on-site spin
projection coefficients (see Supporting Information) calculated for these models. In
contrast the model Ca-1 produces isotropic HFC values in very good agreement with the
experimental values with one HFC close to 300 MHz, another HFC was found close to
250 MHz and two HFCs near to 200 MHz (the HFC value of 224 MHz could arguably be
associated to either the 250 MHz or 200 MHz grouping). As has been found previously,
the largest Aiso value is not found for the MnIII ion (MnD) but rather is calculated for a MnIV
ion (MnA). Initially this disagreed with experimentally derived models of the S2 state which
were constructed with knowledge gained from studying mixed valence models.83,84
However there is experimental evidence to support the finding of smaller than expected
HFC for MnIII centres.77 Additionally the results of other computational studies of the OEC
have provided an ever increasing body of computational data which show that the MnIII
centre is not necessarily required to provide the largest HFC value in highly connected
systems as seen in the OEC.29,44,85,86
Turning to consider the anisotropic HFCs produced by model Ca-1, it can be observed
from the experimental simulation data that the anisotropy is more spread out over all the
manganese centres. The computed anisotropic HFCs of MnA and MnD are considerably
larger than those calculated for MnB and MnC and all of the calculated anisotropic HFCs
are in poor agreement with those from experiment. A potential reason for this is the zero-
field splitting related anisotropy transfer which has been neglected in the current study and
10
may critically affect the calculated anisotropic HFC data. Efforts to extend the spin
projections schemes to include zero field splitting and zero-field splitting anisotropy
transfer has been presented in the literature but the investigations have only focused so far
on dinuclear MnIIIMnIV complexes.87
Table 2. Calculated spin projected isotropic (Aiso) and anisotropic (Ti) 55Mn hyperfine couplings (in MHz) for the investigated Ca models and comparison with experimental data.
Table 3 shows the spin projected isotropic and anisotropic HFCs for the Sr models. The
strontium substituted OEC has been investigated to a lesser extent than the native form,
however recent EPR experiments have probed its electronic structure. The available
11
experimental data is also included in Table 3. Similar to the native OEC, both of the
experimental data sets feature a HFC near to 300 MHz and a smaller HFC below
200 MHz. The data set of Cox et al. shows a second HFC slightly above 200 MHz and a
final HFC near 350 MHz.23 However the data set of Lohmiller et al. shows the remaining
HFCs to be close together at ca. 220/230 MHz.86 The Sr models display the similar trends
to those observed previously for the Ca models. It can be seen that Sr-2 and Sr-3 display
calculated Aiso values substantially smaller than those observed in the experimental
datasets.
Table 3. Calculated spin projected isotropic (A iso) and anisotropic (Ti) 55Mn hyperfine couplings (in MHz) for the investigated Sr models and comparison with experimental data.
Additionally similar to the model Ca-4, the isotropic HFCs calculated for model Sr-4 are
an improvement over the Sr-2 and Sr-3 but the Aiso values for MnA and MnB are in poor
agreement with those found experimentally. The poor agreement for these models can be
attributed again to the small on-site spin projection coefficients found for these models.
Again, the only model which provides reasonable calculated HFCs is that of Sr-1 which
produces isotropic HFCs which coincide with the experimental data very well. Contrasting
the isotropic HFCs calculated for both the Ca-1 and Sr-1 model shows there is little
difference in the calculated HFCs following substitution of the Ca2+ ion. Historically
substitution of the OEC calcium with strontium was thought to change the oxidation state
distribution within the OEC cluster and therefore alter the coordination environment of the
MnIII ion.88 Instead the current thinking supported by experimental and computational
studies in the literature and found in this work is that strontium substitution produces minor
alterations to the manganese tetramer.23,43,89
No specific 55Mn HFCs have been reported for the closed cubane form, so a comparison
between theoretical and experimental values is not possible. The calculated spin projected
55Mn hyperfine couplings for the closed cubane form are presented for Ca-1, Ca-4, Sr-1
and Sr-4 models in Table S11 of the Supporting Information.
14N Hyperfine Couplings
As well as studying the 55Mn hyperfine couplings, further information and insight into the
electronic structure may be provided by the hyperfine interactions of various ligating EPR
active nuclei.90 One such nucleus is the 14N nucleus of the histidine residue (D1-His-332), a
ligand to MnD. Experimentally the HFC for this residue have been used to probe the
oxidation state assignment of the histidine bound metal.38 Additionally Pérez-Navarro et al.
found that the 14N signal observed for the native S2 state from Thermosynechococcus
13
elongatus was very similar to that seen in samples of PSII isolated from both higher plants
(spinach) as well as the cyanobacteria Synechosytstis sp. PCC6803, illustrating the high
structural homogeneity of the OEC.40,46,56
Table 4 shows calculated 14N HFC as well as nuclear quadrupole coupling constants for the
Ca models studied in this work. At the present time no information is available regarding
the potential sign of the isotropic HFC. Although computationally the sign of the
calculated 14N isotropic HFC is dependent on the sign of the projection coefficient of MnD.
As a result of the dominant spin polarisation, A iso is positive when the MnD spin is down
and negative when the MnD spin is found to be up. Comparing the calculated and
experimental 14N EPR parameters shows that all models produce an isotropic HFC that is in
good agreement with that found from experiment. This is due to the spin projection
coefficients for MnD in all the models being similar. As a result of this it is expected that all
models produce an isotropic HFC value that agrees well with the experimental HFC.
Turning to consider the anisotropic HFC, it can be seen from Table 4 that in particular
model Ca-1 produces anisotropic HFCs, which are in excellent agreement with those
determined from experiment. The other Ca model results shown in Table 4 show
anisotropic HFCs which are in poorer agreement with those determined from experiment.
Early ESEEM experiments typically simulated the EPR spectra using axially symmetric
HFC tensors;38,40 however more modern measurements have found rhombic HFC
tensors.16,56 The calculations presented here would support the finding of rhombic tensors
for these HFCs.
Table 4. Calculated spin projected isotropic (A iso) and anisotropic (Ti) 14N hyperfine couplings and nuclear quadrupole couplings for the investigated Ca models studied and comparison with experimental data. All values are given in MHz.
Exp.56* |6.95| −1.50 0.20 1.30 −1.98 0.82* Similar experimental values have been reported in references 16,91
The calculated nuclear quadrupole coupling constant e2Qq/h is found to be slightly lower
than the experimental value in all Ca models but is similar to those previously found for
superoxidised manganese catalase or other imidazole nitrogen atoms that are coordinated
to metal centres.55,92 The asymmetry parameter η is also found to be under calculated. The
experimental asymmetry parameter of 0.82 is larger than that found in the superoxidised
manganese catalase or other metal-coordinated imidazole ligands.92 It should be noted that
the uncertainties in the asymmetry parameter in the ESEEM simulations are found to be
considerably larger than those for the nuclear quadrupole coupling constant. A good
example of this is the MnIII coordinated histidine in two different manganese catalase
samples (purified from Lactobacillus plantarum and Thermus thermophilus), the measured
asymmetry values were found to disagree significantly although the nuclear quadrupole
coupling constants were found to be very close to each other.92
Table 5. Calculated spin projected isotropic (A iso) and anisotropic (Ti) 14N hyperfine couplings and nuclear quadrupole couplings (in MHz) for the investigated Sr models studied and comparison with experimental data.
Comparing the calculated and experimental 14N EPR parameters for the Sr models shown
in Table 5 allows additional insight into the electronic structure of the strontium substituted
OEC. It can be seen that in a similar fashion to the Ca models, all the Sr models produce
isotropic HFCs which are found to be close to the reported experimental HFC. The
15
anisotropic HFC tensors of model Sr-1 were found to agree very well with those
determined from experiment. However as was seen when studying the Ca models, the
remaining Sr models anisotropic HFCs were found to be in poorer agreement with the
experimental values. The calculated nuclear quadrupolar coupling constant is found to be
calculated in good agreement for all Sr models and is actually calculated in better
agreement with experimental data than the Ca models. Comparing the asymmetry
parameter with the experimental value shows an improvement over the Ca model data,
although Sr-1 and Sr-3 produce asymmetry values which are over calculated. Studying the
Ca-1 and Sr-1 models appears to support the earlier findings that substitution of the
calcium ion with strontium does not significantly perturb the electronic structure of the
MnD ion and by extension the tetranuclear manganese cluster, as there is very little
difference between the calculated isotropic and anisotropic HFCs or in the nuclear
quadrupole coupling constants.
From the analysis of the 55Mn and 14N HFCs above, we can confidently rule out the -2 and
-3 models which contain W1 as a hydroxo group and will confine our further analysis to
the -1 and -4 models.
17O Hyperfine Couplings
Rapatskiy et al. performed W-band ELDOR detected NMR on 17O labelled PSII samples
and found three classes of signal in the spectra which were termed strong, intermediate and
matrix.16 The strong signal was found to have an isotropic HFC of magnitude 9.7 MHz and
was experimentally assigned to a μ-oxo bridging oxygen on the basis of HFCs previously
measured for a MnIIIMnIV μ-oxo bridged model complex.16,93 In addition Rapatskiy et al.
used the relative orientations of the 14N and 17O experimental hyperfine tensors to assign
the exchangeable μ-oxo bridging HFC to either O4 or O5, although subsequent 14N
16
experiments by Lohmiller et al. found there to be disagreement between the 14N datasets
questioning this assignment.16,86 The intermediate signal produced an isotropic HFC value
of magnitude 4.5 MHz and was assigned to one or both of the terminal water ligands of
MnA. The matrix class of signal was found to possess an isotropic HFC value of magnitude
1.4 MHz and assigned to weakly coupled matrix waters (either manganese or calcium
coordinated).16
Bridging atoms currently highlight a problem in the spin projection techniques currently
used to calculate hyperfine couplings for BS-DFT calculations. Non-bridging ligand nuclei
are normally spin projected using the spin projection coefficients of the metal ion they are
coordinated to. For bridging nuclei a number of solutions have been proposed. The first is
to simply average the two projected hyperfine couplings,94,95 while an alternative approach
is to sum the spin projections.96 From our investigations of several μ-oxo bridged
manganese complexes (see Tables S2 and S3 in Supporting Information) and the results of
Rapatskiy et al. we conclude that the second spin projection technique produces results in
better agreement with experiment.96 A comparison of calculated and experimental 17O
HFCs obtained for the Ca-1 and Ca-4 models is shown in Table 6.
Table 6. Calculated spin projected isotropic (A iso) and anisotropic (Ti) 17O hyperfine couplings (in MHz) for the investigated Ca models and comparison with experimental data.
Considering first the calculated results for the μ-oxo bridging atoms (O1 through to O5) the
model Ca-1 produces isotropic HFCs in the range of 0−10 MHz. The calculated isotropic
HFC for O5, -10.3 MHz agrees very well with the experimental value of |9.7| MHz
supporting the experimental assignment made, by Rapatskiy et al.16 The calculated
anisotropic magnitude is however significantly larger than the experimental determination
reported for O5. The isotropic HFCs for the manganese bound W1 and W2 calculated for
Ca-1 are also in very good agreement with the isotropic HFC magnitudes reported for the
intermediate and matrix signals. In addition the magnitude of the anisotropic HFCs, for
both W1 and W2 in the Ca-1 model, were found to agree very well with those determined
from experiment. The calculated isotropic HFCs for the model Ca-1 also correspond well
with those reported by Rapatskiy et al. (4.7 and 1.5 MHz respectively).44 Here agreement
between theory and experiment is much better for the Ca-1 model compared with Ca-4
which again adds further support to this model of the OEC in the S2 state. The calcium
bound waters W3 and W4 are expected to display only small HFCs owing to the absence
spin on the calcium ion.
The isotropic and anisotropic HFCs for the Sr models are given in Table S12 of
Supporting Information and are similar to those calculated for the Ca models.
1H Hyperfine Couplings
Table 7 shows selected 1H HFC calculated for the Ca cluster models as well as recent
HYSCORE data for the native OEC. The spectra reported by Milikisiyants et al. for the
18
native OEC showed a number of signals HI – HV originating from interacting protons.91
Milikisiyants et al. assigned the HI and HIII group of protons to fully protonated water
molecules, W1 and W2 directly ligated to MnA of the OEC. The HII proton group was
assigned to the proximal protons of the D1-His-332 residue. The remaining detected proton
signals were attributed to non-specific matrix proton interactions.
Considering the calculated results for model Ca-1, Table 7, it can be seen that the W1
protons HA and HB produce isotropic and anisotropic HFCs in good agreement to those
observed for the HI group of protons, with particular good agreement for HB of W1.
Although the two W1 protons would be expected to be equivalent in an isolated system,
the hydrogen bonding interaction between Asp-61 and HA lowers the calculated Aiso and T
value. Similar behaviour is observed in experimental and computational studies of
ammonia inhibition of the OEC, where ammonia has been to found to replace W1 and
hydrogen bond to the Asp-61 residue.97,98 The Ca-1 model also gives isotropic and
anisotropic HFCs for the W2 HC hydroxide proton in very good agreement with the
experimental results found for the HIII proton group. This result differs with the
experimental interpretation of Milikisiyants et al. who interpreted the HIII proton signal as
arising from a fully protonated W2 water and not a hydroxide group. This interpretation
was due to the observed Aiso values showing agreement to previously published 2D 1H
HYSCORE spectra of a water ligated dimanganese model complex.48,99 It was speculated
that a hydroxo group would give rise to a much larger isotropic HFC but this is not bourne
out by our calculated values. The calculated results for Ca-4 model where W2 is a water
ligand are not in as good agreement with the experimental value, lending extra support for
the hydroxo nature of W2 in the S2 state as already found above. The assignment of the
experimentally observed HII protons to the ring protons of the proximal D1-His332 residue
19
is also supported by our calculations. Both protons have small calculated isotropic and
larger anisotropic T values close to the experimental value.
Table 7. Calculated spin projected isotropic (Aiso) and anisotropic (Ti) 1H hyperfine couplings (in MHz) for the investigated Ca-1 and Ca-4 models and comparison with experimental data. T is defined as T = (T1 + T2)/2 = −T3/2
Label Aiso T1 T2 T3 T
Ca-1
W1 HA 1.0 −3.9 −2.7 6.6 −3.3W1 HB 1.7 −5.0 −4.3 9.3 −4.6W2 HC 3.0 −2.0 −1.7 3.8 −1.9W2 HD − − − − −His HE 0.1 −5.0 −1.1 6.2 −3.1His HF −0.8 −4.2 −2.9 7.1 −3.6
Ca-4
W1 HA 0.7 −2.5 −1.6 4.1 −2.0W1 HB 1.6 −3.6 −3.2 6.8 −3.4W2 HC 1.0 −2.5 −2.1 4.6 −2.3W2 HD 1.3 −2.5 −2.1 4.6 −2.3His HE 0.1 −5.6 −1.2 6.8 −3.4His HF −0.9 −4.7 −3.3 8.0 −4.0
Table 8 shows the calculated 1H isotropic and anisotropic HFCs for the Sr models in
addition to HYSCORE data from experimental studies of the Sr substituted OEC. Unlike
the native OEC, Chatterjee et al. only found a single signal, HI, originating from direct
ligation to the OEC. 100 This signal was found to have similar isotropic and anisotropic
HFCs to that seen in the native OEC and assigned to the ring protons of the D1-His-332
residue. In contrast to the native OEC, Chatterjee et al. could find no significant HFCs
signals originating from either the W1 or W2 protons leading them to conclude that Sr
substitution results in a strongly disordered geometry for these water ligands that perturbs
these groups and causes a large modification in their HFCs. 100 The BS-DFT calculated
HFCs for the Sr models are very similar to the native form and would be expected to occur
at similar positions in the experimental spectra. No significant perturbation of W1 and W2
20
are observed in our models as was also found in the Sr OEC X-ray crystal structure. As can
be seen in Table 8, the isotropic and anisotropic HFCs calculated for both the W1 protons
(HA and HB) and the W2 hydroxo proton (HC) are similar to those calculated for the Ca-1
analogue model. These calculations in conjunction with those presented earlier would
suggest that Sr substitution has little or no effect on the calculated HFCs of the W1 and W2
groups. We suggest therefore that the lack of detection of experimental signals for the W1
and W2 protons in Sr substituted OEC is due to a detection limitation rather than a major
change in value introduced by Sr substitution.
Table 8. Calculated spin projected isotropic (Aiso) and anisotropic (Ti) 1H hyperfine couplings (in MHz) for the investigated Sr-1 and Sr-4 models and comparison with experimental data. T is defined as T = (T1 + T2)/2 = −T3/2
Label Aiso T1 T2 T3 T
Sr-1
W1 HA 1.0 −4.0 −2.7 6.7 −3.4W1 HB 1.5 −4.3 −4.0 8.3 −4.2W2 HC 3.2 −2.3 −1.5 3.7 −1.9W2 HD − − − − −His HE 0.0 −4.5 −0.8 6.2 −3.1His HF −0.7 −4.3 −3.0 7.3 −3.6
Sr-4
W1 HA 0.9 −2.4 −1.6 3.9 −2.0W1 HB 1.7 −3.8 −3.0 6.7 −3.4W2 HC 0.8 −2.3 −1.8 4.1 −2.1W2 HD 1.8 −2.7 −1.2 3.9 −2.0His HE 0.1 −5.1 −1.2 6.3 −3.2His HF −0.8 −4.1 −3.3 7.4 −3.7
Stull et al. used ENDOR spectroscopy to study the S2 state in a PSII preparation where all
alanine carboxylate carbons were 13C labelled as well as a scenario where all carbon atoms
were uniformly 13C labelled. These results were then compared to a bridging carboxylate in
a synthetic dinuclear MnIIIMnIVcomplex.57 These results, published before the 2011
21
Umena et al. crystal structure,10 led to the conclusion that the D1 polypeptide alanine C-
terminus is directly bound to a manganese ion. In the simulations of the ENDOR spectra,
Stull et al. were required to make a number of assumptions in order to interpret the
experimental spectra, namely the dipolar hyperfine couplings were estimated using the
point dipole approximation from the various X-ray structures available at the time
(provided by Loll et al., Guskov et al. and Ferreira et al.).13,101,102 Table 9 summarises the
computational results obtained for the Ca models studied, in comparison with the
experimental data. For carboxylates which bridge two manganese sites, we have utilised
the same spin projection technique used above for spin projecting bridging oxygen nuclei;
the intrinsic hyperfine coupling tensors are spin projected to both of the two manganese
sites and them summed. In the case of terminal or Mn−Ca bridging carboxylates, the 13C
nuclei were spin projected to the directly bonded manganese site.
In both the Loll et al. and Guskov et al. X-ray crystallographic structures, the alanine C-
terminus of the D1 polypeptide chain was bonded to one manganese centre,101,102 unlike the
Ferreira et al. crystal structure, which proposed the alanine C-terminus to be bonded only
to the calcium atom of the OEC.13 The high resolution 2011 Umena et al. structure and
2014 XFEL structure of Suga et al. found the D1-Ala-344 residue to be bonded to both
MnC and the Ca2+ ion of the OEC.10,11
Inspection of the data in Table 9 of the Ca-1 model shows that the Ala-344 residue
provides an isotropic and anisotropic hyperfine coupling which is in good agreement with
the experimental data. Additionally Stull et al. found that in the uniformly labelled sample
there were multiple 13C containing moieties which produced hyperfine couplings similar to
that observed for the Ala-344 labelled example.57 This observation is supported by the
results shown in Table 9, as multiple residues in model Ca-1 provide similar isotropic and
anisotropic hyperfine couplings (Asp-170 and Asp-342) within the joint uncertainties of
22
computation and simulation. Schinzel et al 82 also previously compared BS-DFT calculated
13C HFCs with the experimental values. This study was performed before the high
resolution crystal structure of the OEC was available which limited accurate assignment
possibilities.
Table 9. Calculated spin projected isotropic (Aiso) and anisotropic (Ti) 13C hyperfine couplings (in MHz) for the investigated Ca models and comparison with experimental data.
Exp.57 -1.0 −2.4 −0.8 3.2a Residue from the CP43 protein chain, all other residues from the D1 protein chain
13C data for the Sr models are similar to the Ca models and are given in the Supporting
Information.
CONCLUSIONS
In this study a thorough BS-DFT analysis of the OEC S2 state 55Mn and ligand hyperfine
couplings was performed investigating the effects of altering the protonation states of the
W1 and W2 ligands. In addition the effect of Sr substitution for Ca was investigated.
Using large geometry optimised cluster models of high resolution dark adapted crystal
structures, we show that slight changes in the structure as a result of altering the
protonation state of the W1 and W2 oxygens had a profound effect on the calculated 55Mn
23
HFCs. Such variations arise due to small changes in the Heisenberg exchange coupling
constants which affect the spin projection coefficients. Comparison between experimental
and calculated HFCs for both the native Ca OEC and Sr substituted form clearly show that
W1 is present in the S2 state as a water molecule and W2 is present as a hydroxo.
Substitution of the Ca for Sr has a minor effect on the calculated HFCs showing that the S2
electronic structure of the OEC is not significantly altered by this substitution. The ability
to be able to distinguish between small structural differences such as protonation patterns
using this combination of experimental and BS-DFT calculated EPR parameters
demonstrates the unique ability of this combination of theory and spectroscopy to probe
the OEC electronic structure. Such an analysis can now be confidently applied to the S3
state where it has been found that Ca/Sr substitution gives rise to large differences in its
EPR properties. Probing the electronic origin of such differences can provide a key and
unique insight into the final stages of the water oxidation cycle.
ACKNOWLEDGEMENTS
NJB and TAC acknowledge support from the UK BBSRC Doctoral Training Partnership
(DTP) program.
ASSOCIATED CONTENT
Supporting Information
Additional analysis and discussion of calculated exchange coupling constants, spin
projection coefficients and hyperfine couplings mentioned in manuscript. Available free of
charge at http://pubs.acs.org
REFERENCES
(1) Yachandra, V. K.; Sauer, K.; Klein, M. P. Manganese Cluster in Photosynthesis:
24
Where Plants Oxidize Water to Dioxygen. Chem. Rev. 1996, 96, 2927–2950.
(2) Renger, G. Photosynthetic Water Oxidation to Molecular Oxygen: Apparatus and Mechanism. Biochim. Biophys. Acta - Bioenerg. 2001, 1503, 210–228.
(3) McEvoy, J. P.; Brudvig, G. W. Water-Splitting Chemistry of Photosystem II. Chem. Rev. 2006, 106, 4455–4483.
(4) Dau, H.; Zaharieva, I. Principles, Efficiency, and Blueprint Character of Solar-Energy Conversion in Photosynthetic Water Oxidation. Acc. Chem. Res. 2009, 42, 1861–1870.
(5) Renger, G. Light Induced Oxidative Water Splitting in Photosynthesis: Energetics, Kinetics and Mechanism. J. Photochem. Photobiol. B Biol. 2011, 104, 35–43.
(6) Cox, N.; Pantazis, D. A.; Neese, F.; Lubitz, W. Biological Water Oxidation. Acc. Chem. Res. 2013, 46, 1588–1596.
(7) Cox, N.; Messinger, J. Reflections on Substrate Water and Dioxygen Formation. Biochim. Biophys. Acta - Bioenerg. 2013, 1827, 1020–1030.
(8) Pérez-Navarro, M.; Neese, F.; Lubitz, W.; Pantazis, D. A.; Cox, N. Recent Developments in Biological Water Oxidation. Curr. Opin. Chem. Biol. 2016, 31, 113–119.
(9) Barber, J. Mn4Ca Cluster of Photosynthetic Oxygen-Evolving Center: Structure, Function and Evolution. Biochemistry 2016, 55, 5901–5906.
(10) Umena, Y.; Kawakami, K.; Shen, J.-R.; Kamiya, N. Crystal Structure of Oxygen-Evolving Photosystem II at a Resolution of 1.9 Å. Nature 2011, 473, 55–60.
(11) Suga, M.; Akita, F.; Hirata, K.; Ueno, G.; Murakami, H.; Nakajima, Y.; Shimizu, T.; Yamashita, K.; Yamamoto, M.; Ago, H.; et al. Native Structure of Photosystem II at 1.95 Å Resolution Viewed by Femtosecond X-Ray Pulses. Nature 2014, 517, 99–103.
(12) Carrell, T. G.; Tyryshkin, A. M.; Dismukes, G. C. An Evaluation of Structural Models for the Photosynthetic Water-Oxidizing Complex Derived from Spectroscopic and X-Ray Diffraction Signatures. J. Biol. Inorg. Chem. 2002, 7, 2–22.
(13) Ferreira, K. N.; Iverson, T. M.; Maghlaoui, K.; Barber, J.; Iwata, S. Architecture of the Photosynthetic Oxygen-Evolving Center. Science 2004, 303, 1831–1838.
(14) Dau, H.; Grundmeier, A.; Loja, P.; Haumann, M. On the Structure of the Manganese Complex of Photosystem II: Extended-Range EXAFS Data and Specific Atomic-Resolution Models for Four S-States. Philos. Trans. R. Soc. B Biol. Sci. 2008, 363, 1237–1244.
(15) Kawakami, K.; Umena, Y.; Kamiya, N.; Shen, J.-R. Structure of the Catalytic, Inorganic Core of Oxygen-Evolving Photosystem II at 1.9 Å Resolution. J. Photochem. Photobiol. B Biol. 2011, 104, 9–18.
(16) Rapatskiy, L.; Cox, N.; Savitsky, A.; Ames, W. M.; Sander, J.; Nowaczyk, M. M.;
25
Rögner, M.; Boussac, A.; Neese, F.; Messinger, J.; et al. Detection of the Water-Binding Sites of the Oxygen-Evolving Complex of Photosystem II Using W-Band 17O Electron–Electron Double Resonance-Detected NMR Spectroscopy. J. Am. Chem. Soc. 2012, 134, 16619–16634.
(17) Ono, T.; Inoue, Y. Discrete Extraction of the Ca Atom Functional for O2 Evolution in Higher Plant Photosystem II by a Simple Low pH Treatment. FEBS Lett. 1988, 227, 147–152.
(18) Vrettos, J. S.; Stone, D. A.; Brudvig, G. W. Quantifying the Ion Selectivity of the Ca2+ Site in Photosystem II: Evidence for Direct Involvement of Ca2+ in O2
Formation. Biochemistry 2001, 40, 7937–7945.
(19) Boussac, A.; Rutherford, A. W. Nature of the Inhibition of the Oxygen-Evolving Enzyme of Photosystem II Induced by NaCl Washing and Reversed by the Addition of Ca2+ or Sr2+. Biochemistry 1988, 27, 3476–3483.
(20) Ono, T.; Rompel, A.; Mino, H.; Chiba, N. Ca2+ Function in Photosynthetic Oxygen Evolution Studied by Alkali Metal Cations Substitution. Biophys. J. 2001, 81, 1831–1840.
(21) Yocum, C. F. The Calcium and Chloride Requirements of the O2 Evolving Complex. Coord. Chem. Rev. 2008, 252, 296–305.
(22) Yachandra, V. K.; Yano, J. Calcium in the Oxygen-Evolving Complex: Structural and Mechanistic Role Determined by X-Ray Spectroscopy. J. Photochem. Photobiol. B Biol. 2011, 104, 51–59.
(23) Cox, N.; Rapatskiy, L.; Su, J.-H.; Pantazis, D. A.; Sugiura, M.; Kulik, L.; Dorlet, P.; Rutherford, A. W.; Neese, F.; Boussac, A.; et al. Effect of Ca2+ /Sr2+ Substitution on the Electronic Structure of the Oxygen-Evolving Complex of Photosystem II: A Combined Multifrequency EPR, 55Mn-ENDOR, and DFT Study of the S2 State. J. Am. Chem. Soc. 2011, 133, 3635–3648.
(24) Kimura, Y.; Hasegawa, K.; Ono, T. Characteristic Changes of the S2/S1 Difference FTIR Spectrum Induced by Ca2+ Depletion and Metal Cation Substitution in the Photosynthetic Oxygen-Evolving Complex. Biochemistry 2002, 41, 5844–5853.
(25) Strickler, M. A.; Walker, L. M.; Hillier, W.; Debus, R. J. Evidence from Biosynthetically Incorporated Strontium and FTIR Difference Spectroscopy That the C-Terminus of the D1 Polypeptide of Photosystem II Does Not Ligate Calcium. Biochemistry 2005, 44, 8571–8577.
(26) Suzuki, H.; Taguchi, Y.; Sugiura, M.; Boussac, A.; Noguchi, T. Structural Perturbation of the Carboxylate Ligands to the Manganese Cluster upon Ca2+/Sr2+
Exchange in the S-State Cycle of Photosynthetic Oxygen Evolution as Studied by Flash-Induced FTIR Difference Spectroscopy. Biochemistry 2006, 45, 13454–13464.
(27) Taguchi, Y.; Noguchi, T. Drastic Changes in the Ligand Structure of the Oxygen-Evolving Mn Cluster upon Ca2+ Depletion as Revealed by FTIR Difference Spectroscopy. Biochim. Biophys. Acta - Bioenerg. 2007, 1767, 535–540.
26
(28) Noguchi, T. Fourier Transform Infrared Analysis of the Photosynthetic Oxygen-Evolving Center. Coord. Chem. Rev. 2008, 252, 336–346.
(29) Krewald, V.; Retegan, M.; Cox, N.; Messinger, J.; Lubitz, W.; DeBeer, S.; Neese, F.; Pantazis, D. A. Metal Oxidation States in Biological Water Splitting. Chem. Sci. 2015, 6, 1676–1695.
(30) Siegbahn, P. E. M. Water Oxidation Mechanism in Photosystem II, Including Oxidations, Proton Release Pathways, O-O Bond Formation and O2 Release. Biochim. Biophys. Acta - Bioenerg. 2013, 1827, 1003–1019.
(31) Siegbahn, P. E. M. Substrate Water Exchange for the Oxygen Evolving Complex in PSII in the S1, S2, and S3 States. J. Am. Chem. Soc. 2013, 135, 9442–9449.
(32) Siegbahn, P. E. M. Mechanisms for Proton Release during Water Oxidation in the S2
to S3 and S3 to S4 Transitions in Photosystem II. Phys. Chem. Chem. Phys. 2012, 14, 4849–4856.
(33) Klauss, A.; Haumann, M.; Dau, H. Alternating Electron and Proton Transfer Steps in Photosynthetic Water Oxidation. Proc. Natl. Acad. Sci. U. S. A. 2012, 109, 16035–16040.
(34) Pokhrel, R.; Brudvig, G. W. Oxygen-Evolving Complex of Photosystem II: Correlating Structure with Spectroscopy. Phys. Chem. Chem. Phys. 2014, 16, 11812–11821.
(35) Terrett, R.; Petrie, S.; Stranger, R.; Pace, R. J. What Computational Chemistry and Magnetic Resonance Reveal Concerning the Oxygen Evolving Centre in Photosystem II. J. Inorg. Biochem. 2016, 162, 178–189.
(36) Zahariou, G.; Chrysina, M.; Petrouleas, V.; Ioannidis, N. Can We Trap the S3YZ•
Metalloradical Metalloradical Intermediate during the S-State Transitions of Photosystem II? An EPR Investigation. FEBS Lett. 2014, 588, 1827–1831.
(37) Oyala, P. H.; Stich, T. A.; Stull, J. A.; Yu, F.; Pecoraro, V. L.; Britt, R. D. Pulse Electron Paramagnetic Resonance Studies of the Interaction of Methanol with the S2
State of the Mn4O5Ca Cluster of Photosystem II. Biochemistry 2014, 53, 7914–7928.
(38) Yeagle, G. J.; Gilchrist, M. L.; McCarrick, R. M.; Britt, R. D. Multifrequency Pulsed Electron Paramagnetic Resonance Study of the S2 State of the Photosystem II Manganese Cluster. Inorg. Chem. 2008, 47, 1803–1814.
(39) Britt, R. D.; Campbell, K. A.; Peloquin, J. M.; Gilchrist, M. L.; Aznar, C. P.; Dicus, M. M.; Robblee, J.; Messinger, J. Recent Pulsed EPR Studies of the Photosystem II Oxygen-Evolving Complex: Implications as to Water Oxidation Mechanisms. Biochim. Biophys. Acta - Bioenerg. 2004, 1655, 158–171.
(40) Yeagle, G. J.; Gilchrist, M. L.; Walker, L. M.; Debus, R. J.; Britt, R. D. Multifrequency Electron Spin-Echo Envelope Modulation Studies of Nitrogen Ligation to the Manganese Cluster of Photosystem II. Philos. Trans. R. Soc. B Biol. Sci. 2008, 363, 1157–1166.
(41) Peloquin, J. M.; Campbell, K. A.; Randall, D. W.; Evanchik, M. A.; Pecoraro, V. L.; Armstrong, W. H.; Britt, R. D. 55Mn ENDOR of the S2-State Multiline EPR Signal
27
of Photosystem II: Implications on the Structure of the Tetranuclear Mn Cluster. J. Am. Chem. Soc. 2000, 122, 10926–10942.
(42) Kulik, L. V.; Epel, B.; Lubitz, W.; Messinger, J. 55Mn Pulse ENDOR at 34 GHz of the S0 and S2 States of the Oxygen-Evolving Complex in Photosystem II. J. Am. Chem. Soc. 2005, 127, 2392–2393.
(43) Su, J.-H.; Cox, N.; Ames, W.; Pantazis, D. A.; Rapatskiy, L.; Lohmiller, T.; Kulik, L. V.; Dorlet, P.; Rutherford, A. W.; Neese, F.; et al. The Electronic Structures of the S2 States of the Oxygen-Evolving Complexes of Photosystem II in Plants and Cyanobacteria in the Presence and Absence of Methanol. Biochim. Biophys. Acta - Bioenerg. 2011, 1807, 829–840.
(44) Ames, W.; Pantazis, D. A.; Krewald, V.; Cox, N.; Messinger, J.; Lubitz, W.; Neese, F. Theoretical Evaluation of Structural Models of the S2 State in the Oxygen Evolving Complex of Photosystem II: Protonation States and Magnetic Interactions. J. Am. Chem. Soc. 2011, 133, 19743–19757.
(45) Pantazis, D. A.; Ames, W.; Cox, N.; Lubitz, W.; Neese, F. Two Interconvertible Structures That Explain the Spectroscopic Properties of the Oxygen-Evolving Complex of Photosystem II in the S2 State. Angew. Chemie Int. Ed. 2012, 51, 9935–9940.
(46) Perez Navarro, M.; Ames, W. M.; Nilsson, H.; Lohmiller, T.; Pantazis, D. A.; Rapatskiy, L.; Nowaczyk, M. M.; Neese, F.; Boussac, A.; Messinger, J.; et al. Ammonia Binding to the Oxygen-Evolving Complex of Photosystem II Identifies the Solvent-Exchangeable Oxygen Bridge (μ-Oxo) of the Manganese Tetramer. Proc. Natl. Acad. Sci. 2013, 110, 15561–15566.
(47) Bovi, D.; Narzi, D.; Guidoni, L. The S2 State of the Oxygen-Evolving Complex of Photosystem-II Explored by QM/MM Dynamics: Spin Surfaces and Metastable States Suggest a Reaction Path towards the S3 State. Angew. Chemie - Int. Ed. 2013, 52, 11744–11749.
(48) Milikisiyants, S.; Chatterjee, R.; Coates, C. S.; Koua, F. H. M.; Shen, J.-R.; Lakshmi, K. V. The Structure and Activation of Substrate Water Molecules in the S2
State of Photosystem II Studied by Hyperfine Sublevel Correlation Spectroscopy. Energy Environ. Sci. 2012, 5, 7747–7756.
(49) Jin, L.; Smith, P.; Noble, C. J.; Stranger, R.; Hanson, G. R.; Pace, R. J. Electronic Structure of the Oxygen Evolving Complex in Photosystem II, as Revealed by 55Mn Davies ENDOR Studies at 2.5 K. Phys. Chem. Chem. Phys. 2014, 16, 7799–7812.
(50) Pace, R. J.; Jin, L.; Stranger, R. What Spectroscopy Reveals Concerning the Mn Oxidation Levels in the Oxygen Evolving Complex of Photosystem II: X-Ray to near Infra-Red. Dalt. Trans. 2012, 41, 11145–11160.
(51) Gatt, P.; Stranger, R.; Pace, R. J. Application of Computational Chemistry to Understanding the Structure and Mechanism of the Mn Catalytic Site in Photosystem II - A Review. J. Photochem. Photobiol. B Biol. 2011, 104, 80–93.
(52) Vinyard, D. J.; Khan, S.; Askerka, M.; Batista, V. S.; Brudvig, G. W. Energetics of the S2 State Spin Isomers of the Oxygen-Evolving Complex of Photosystem II. J.
28
Phys. Chem. B 2017, 121, 1020–1025.
(53) Teutloff, C.; Schäfer, K. O.; Sinnecker, S.; Barynin, V.; Bittl, R.; Wieghardt, K.; Lendzian, F.; Lubitz, W. High-Field EPR Investigations of MnIIIMnIV and MnIIMnIII
States of Dimanganese Catalase and Related Model Systems. Magn. Reson. Chem. 2005, 43, 51–64.
(54) Schäfer, K. O.; Bittl, R.; Zweygart, W.; Lendzian, F.; Haselhorst, G.; Weyhermüller, T.; Wieghardt, K.; Lubitz, W. Electronic Structure of Antiferromagnetically Coupled Dinuclear Manganese (MnIIIMnIV) Complexes Studied by Magnetic Resonance Techniques. J. Am. Chem. Soc. 1998, 120, 13104–13120.
(55) Schäfer, K.-O.; Bittl, R.; Lendzian, F.; Barynin, V.; Weyhermüller, T.; Wieghardt, K.; Lubitz, W. Multifrequency EPR Investigation of Dimanganese Catalase and Related Mn(III)Mn(IV) Complexes. J. Phys. Chem. B 2003, 107, 1242–1250.
(56) Stich, T. A.; Yeagle, G. J.; Service, R. J.; Debus, R. J.; Britt, R. D. Ligation of D1-His332 and D1-Asp170 to the Manganese Cluster of Photosystem II from Synechocystis Assessed by Multifrequency Pulse EPR Spectroscopy. Biochemistry 2011, 50, 7390–7404.
(57) Stull, J. A.; Stich, T. A.; Service, R. J.; Debus, R. J.; Mandal, S. K.; Armstrong, W. H.; Britt, R. D. 13C ENDOR Reveals That the D1 Polypeptide C-Terminus Is Directly Bound to Mn in the Photosystem II Oxygen Evolving Complex. J. Am. Chem. Soc. 2010, 132, 446–447.
(58) Askerka, M.; Brudvig, G. W.; Batista, V. S. The O2 -Evolving Complex of Photosystem II: Recent Insights from Quantum Mechanics/Molecular Mechanics (QM/MM), Extended X-Ray Absorption Fine Structure (EXAFS), and Femtosecond X-Ray Crystallography Data. Acc. Chem. Res. 2017, 50, 41–48.
(59) Becke, A. D. Density-Functional Exchange-Energy Approximation with Correct Asymptotic Behavior. Phys. Rev. A 1988, 38, 3098–3100.
(60) Perdew, J. P. Density-Functional Approximation for the Correlation Energy of the Inhomogeneous Electron Gas. Phys. Rev. B 1986, 33, 8822–8824.
(61) van Lenthe, E.; Baerends, E. J.; Snijders, J. G. Relativistic Regular Two-Component Hamiltonians. J. Chem. Phys. 1993, 99, 4597–4610.
(62) van Lenthe, E.; Baerends, E. J.; Snijders, J. G. Relativistic Total Energy Using Regular Approximations. J. Chem. Phys. 1994, 101, 9783–9792.
(63) van Wüllen, C. Molecular Density Functional Calculations in the Regular Relativistic Approximation: Method, Application to Coinage Metal Diatomics, Hydrides, Fluorides and Chlorides, and Comparison with First-Order Relativistic Calculations. J. Chem. Phys. 1998, 109, 392–399.
(64) Pantazis, D. A.; Chen, X.-Y.; Landis, C. R.; Neese, F. All-Electron Scalar Relativistic Basis Sets for Third-Row Transition Metal Atoms. J. Chem. Theory Comput. 2008, 4, 908–919.
(65) Weigend, F.; Ahlrichs, R. Balanced Basis Sets of Split Valence, Triple Zeta Valence and Quadruple Zeta Valence Quality for H to Rn: Design and Assessment of
(66) Eichkorn, K.; Treutler, O.; Öhm, H.; Häser, M.; Ahlrichs, R. Auxiliary Basis Sets to Approximate Coulomb Potentials. Chem. Phys. Lett. 1995, 240, 283–289.
(67) Eichkorn, K.; Weigend, F.; Treutler, O.; Ahlrichs, R. Auxiliary Basis Sets for Main Row Atoms and Transition Metals and Their Use to Approximate Coulomb Potentials. Theor. Chem. Accounts Theory, Comput. Model. (Theoretica Chim. Acta) 1997, 97, 119–124.
(68) Weigend, F. Accurate Coulomb-Fitting Basis Sets for H to Rn. Phys. Chem. Chem. Phys. 2006, 8, 1057–1065.
(69) Grimme, S.; Antony, J.; Ehrlich, S.; Krieg, H. A Consistent and Accurate Ab Initio Parametrization of Density Functional Dispersion Correction (DFT-D) for the 94 Elements H-Pu. J. Chem. Phys. 2010, 132, 154104.
(70) Grimme, S.; Ehrlich, S.; Goerigk, L. Effect of the Damping Function in Dispersion Corrected Density Functional Theory. J. Comput. Chem. 2011, 32, 1456–1465.
(71) Staroverov, V. N.; Scuseria, G. E.; Tao, J.; Perdew, J. P. Comparative Assessment of a New Nonempirical Density Functional: Molecules and Hydrogen-Bonded Complexes. J. Chem. Phys. 2003, 119, 12129–12137.
(72) Neese, F.; Wennmohs, F.; Hansen, A.; Becker, U. Efficient, Approximate and Parallel Hartree-Fock and Hybrid DFT Calculations. A “Chain-of-Spheres” Algorithm for the Hartree-Fock Exchange. Chem. Phys. 2009, 356, 98–109.
(73) Neese, F. The ORCA Program System. Wiley Interdiscip. Rev. Comput. Mol. Sci. 2012, 2, 73–78.
(74) Cox, N.; Ames, W.; Epel, B.; Kulik, L. V.; Rapatskiy, L.; Neese, F.; Messinger, J.; Wieghardt, K.; Lubitz, W. Electronic Structure of a Weakly Antiferromagnetically Coupled MnIIMnIII Model Relevant to Manganese Proteins: A Combined EPR, 55Mn-ENDOR, and DFT Study. Inorg. Chem. 2011, 50, 8238–8251.
(75) Pantazis, D. A.; Orio, M.; Petrenko, T.; Zein, S.; Bill, E.; Lubitz, W.; Messinger, J.; Neese, F. A New Quantum Chemical Approach to the Magnetic Properties of Oligonuclear Transition-Metal Complexes: Application to a Model for the Tetranuclear Manganese Cluster of Photosystem II. Chem. - A Eur. J. 2009, 15, 5108–5123.
(76) Sinnecker, S.; Neese, F.; Noodleman, L.; Lubitz, W. Calculating the Electron Paramagnetic Resonance Parameters of Exchange Coupled Transition Metal Complexes Using Broken Symmetry Density Functional Theory: Application to a MnIII/MnIV Model Compound. J. Am. Chem. Soc. 2004, 126, 2613–2622.
(77) Schinzel, S.; Kaupp, M. Validation of Broken-Symmetry Density Functional Methods for the Calculation of Electron Paramagnetic Resonance Parameters of Dinuclear Mixed-Valence MnIVMnIII Complexes. Can. J. Chem. 2009, 87, 1521–1539.
(78) Koua, F. H. M.; Umena, Y.; Kawakami, K.; Shen, J.-R. Structure of Sr-Substituted Photosystem II at 2.1 Å Resolution and Its Implications in the Mechanism of Water
30
Oxidation. Proc Natl Acad Sci U S A 2013, 110, 3889–3894.
(79) Retegan, M.; Neese, F.; Pantazis, D. A. Convergence of QM/MM and Cluster Models for the Spectroscopic Properties of the Oxygen-Evolving Complex in Photosystem II. J. Chem. Theory Comput. 2013, 9, 3832–3842.
(80) Teutloff, C.; Pudollek, S.; Keßen, S.; Broser, M.; Zouni, A.; Bittl, R. Electronic Structure of the Tyrosine D Radical and the Water-Splitting Complex from Pulsed ENDOR Spectroscopy on Photosystem II Single Crystals. Phys. Chem. Chem. Phys. 2009, 11, 6715–6726.
(81) Kulik, L. V.; Epel, B.; Lubitz, W.; Messinger, J. Electronic Structure of the Mn4OxCa Cluster in the S0 and S2 States of the Oxygen-Evolving Complex of Photosystem II Based on Pulse 55Mn-ENDOR and EPR Spectroscopy. J. Am. Chem. Soc. 2007, 129, 13421–13435.
(82) Charlot, M.-F.; Boussac, A.; Blondln, G. Towards a Spin Coupling Model for the Mn4 Cluster in Photosystem II. Biochim. Biophys. Acta - Bioenerg. 2005, 1708, 120–132.
(83) Siegbahn, P. E. M. Structures and Energetics for O2 Formation in Photosystem II. Acc. Chem. Res. 2009, 42 , 1871–1880.
(84) Pantazis, D. A.; Orio, M.; Petrenko, T.; Zein, S.; Lubitz, W.; Messinger, J.; Neese, F. Structure of the Oxygen-Evolving Complex of Photosystem II: Information on the S2 State through Quantum Chemical Calculation of Its Magnetic Properties. Phys. Chem. Chem. Phys. 2009, 11, 6788–6798.
(85) Krewald, V.; Retegan, M.; Pantazis, D. A. Principles of Natural Photosynthesis. In Solar Energy for Fuels. Topics in Current Chemistry; Springer, Cham, 2015; Vol. 371, pp 23–48.
(86) Lohmiller, T.; Krewald, V.; Navarro, M. P.; Retegan, M.; Rapatskiy, L.; Nowaczyk, M. M.; Boussac, A.; Neese, F.; Lubitz, W.; Pantazis, D. A.; et al. Structure, Ligands and Substrate Coordination of the Oxygen-Evolving Complex of Photosystem II in the S2 State: A Combined EPR and DFT Study. Phys. Chem. Chem. Phys. 2014, 16, 11877–11892.
(87) Schraut, J.; Arbuznikov, A. V.; Schinzel, S.; Kaupp, M. Computation of Hyperfine Tensors for Dinuclear MnIIIMnIV Complexes by Broken-Symmetry Approaches: Anisotropy Transfer Induced by Local Zero-Field Splitting. ChemPhysChem 2011, 12, 3170–3179.
(88) Zheng, M.; Dismukes, G. C. Orbital Configuration of the Valence Electrons, Ligand Field Symmetry, and Manganese Oxidation States of the Photosynthetic Water Oxidizing Complex: Analysis of the S2 State Multiline EPR Signals. Inorg. Chem. 1996, 35, 3307–3319.
(89) Lohmiller, T.; Cox, N.; Su, J.-H.; Messinger, J.; Lubitz, W. The Basic Properties of the Electronic Structure of the Oxygen-Evolving Complex of Photosystem II Are Not Perturbed by Ca2+ Removal. J. Biol. Chem. 2012, 287, 24721–24733.
(90) Oyala, P. H.; Stich, T. A.; Britt, R. D. Metal Ion Oxidation State Assignment Based
31
on Coordinating Ligand Hyperfine Interaction. Photosynth. Res. 2015, 124, 7–18.
(91) Milikisiyants, S.; Chatterjee, R.; Weyers, A.; Meenaghan, A.; Coates, C.; Lakshmi, K. V. Ligand Environment of the S2 State of Photosystem II: A Study of the Hyperfine Interactions of the Tetranuclear Manganese Cluster by 2D 14N HYSCORE Spectroscopy. J. Phys. Chem. B 2010, 114, 10905–10911.
(92) Stich, T. A.; Whittaker, J. W.; Britt, R. D. Multifrequency EPR Studies of Manganese Catalases Provide a Complete Description of Proteinaceous Nitrogen Coordination. J. Phys. Chem. B 2010, 114, 14178–14188.
(93) McConnell, I. L.; Grigoryants, V. M.; Scholes, C. P.; Myers, W. K.; Chen, P.-Y.; Whittaker, J. W.; Brudvig, G. W. EPR–ENDOR Characterization of (17O, 1H, 2H) Water in Manganese Catalase and Its Relevance to the Oxygen-Evolving Complex of Photosystem II. J. Am. Chem. Soc. 2012, 134, 1504–1512.
(94) Han, W.-G.; Liu, T.; Lovell, T.; Noodleman, L. Active Site Structure of Class I Ribonucleotide Reductase Intermediate X: A Density Functional Theory Analysis of Structure, Energetics, and Spectroscopy. J. Am. Chem. Soc. 2005, 127, 15778–15790.
(95) Han, W.-G.; Noodleman, L. DFT Calculations of Comparative Energetics and ENDOR/Mössbauer Properties for Two Protonation States of the Iron Dimer Cluster of Ribonucleotide Reductase Intermediate X. Dalt. Trans. 2009, 6045–6057.
(96) Rapatskiy, L.; Ames, W. M.; Pérez-Navarro, M.; Savitsky, A.; Griese, J. J.; Weyhermüller, T.; Shafaat, H. S.; Högbom, M.; Neese, F.; Pantazis, D. A.; et al. Characterization of Oxygen Bridged Manganese Model Complexes Using Multifrequency 17O-Hyperfine EPR Spectroscopies and Density Functional Theory. J. Phys. Chem. B 2015, 119, 13904–13921.
(97) Oyala, P. H.; Stich, T. A.; Debus, R. J.; Britt, R. D. Ammonia Binds to the Dangler Manganese of the Photosystem II Oxygen-Evolving Complex. J. Am. Chem. Soc. 2015, 137, 8829–8837.
(98) Askerka, M.; Vinyard, D. J.; Brudvig, G. W.; Batista, V. S. NH3 Binding to the S2
State of the O2 -Evolving Complex of Photosystem II: Analogue to H2O Binding during the S2 → S3 Transition. Biochemistry 2015, 54, 5783–5786.
(99) Milikisiyants, S.; Chatterjee, R.; Lakshmi, K. V. Two-Dimensional 1H HYSCORE Spectroscopy of Dimanganese Di-μ-Oxo Mimics of the Oxygen-Evolving Complex of Photosystem II. J. Phys. Chem. B 2011, 115, 12220–12229.
(100) Chatterjee, R.; Milikisiyants, S.; Coates, C. S.; Koua, F. H. M.; Shen, J.-R.; Lakshmi, K. V. The Structure and Activation of Substrate Water Molecules in Sr2+-Substituted Photosystem II. Phys. Chem. Chem. Phys. 2014, 16, 20834–20843.
(101) Loll, B.; Kern, J.; Saenger, W.; Zouni, A.; Biesiadka, J. Towards Complete Cofactor Arrangement in the 3.0 Å Resolution Structure of Photosystem II. Nature 2005, 438, 1040–1044.
(102) Guskov, A.; Kern, J.; Gabdulkhakov, A.; Broser, M.; Zouni, A.; Saenger, W. Cyanobacterial Photosystem II at 2.9-Å Resolution and the Role of Quinones,
