Simon Petrie

Rationalizing the 1.9 Å Crystal Structure of Photosystem II—A Remarkable Jahn–Teller Balancing Act Induced by a Single Proton Transfer

Green plants and algae oxidize water to molecular oxygen in photosystem II (PS II) within a calcium/tetramanganese site known as the water-oxidizing complex (WOC). Oxygen is generated by the WOC in a four-electron process involving a series of intermediate states (S states, labeled S0...S4) of increasingly higher mean oxidation level. Over the past decade, X-ray crystallographic (XRD) structures of PS II at progressively improved resolution have revealed much detail of the WOC. At present, only PS II from thermophilic cyanobacteria has been crystallized for XRD study and the enzyme is presumed to be in the dark stable S1 state. The first PS II structure (at 3.5 resolution) to resolve side chain positions was presented by Barber and co-workers. Consistent with subsequent studies at higher resolution, it revealed the compact Mn3Ca “cube” structure of the WOC connected more distantly to a single Mn, referred to as the “dangler”. More recent improved structures at 3.0 and 2.9 , substantially clarified the metaland proteinsupplied ligand positions within the WOC, but were still of insufficient resolution to reveal the positions of bridging oxo groups and water molecules (including the substrate water molecules). Finally, Umena et al., using a new crystallization method, produced an atomic resolution structure at 1.9 , the most resolved to date. Despite this remarkable achievement, revealing, for the first time, the positions of bridging O atoms within the Mn4Ca core of the WOC, aspects of the new structure have been met with scepticism. 4] Central concerns over this structure involve 1) the identity and unexpected placement of the O(5) moiety (Figure 1), which appears to be either a weakly bound oxo, hydroxo, or water ligand at distances of 2.4–2.7 from four of the metal atoms in the WOC, and 2) the disparity in some key metal– metal distances when compared with earlier, high-precision extended X-ray absorption fine structure (EXAFS) results and the previous lower-resolution XRD structures (see Table 1). Although the Mn EXAFS data do not unambigu-

Dodecanuclear‐Ellipse and Decanuclear‐Wheel Nickel(II) Thiolato Clusters with Efficient Femtosecond Nonlinear Absorption

Thiolate ligands have been of longstanding interest for a variety of reasons: 1) their diverse binding modes give rise to an array of bonding motifs that are of fundamental importance in coordination chemistry, 2) metal–thiolate interactions are key elements of numerous metalloproteins and play a crucial role in the broader field of bioinorganic chemistry, and 3) thiolate-mediated magnetic coupling is an essential component in novel molecular magnets. Amongst the range of metal thiolate-derived structures, the synthesis, structure, and magnetic properties of toroidal (or tiara-like) architectures have raised considerable interest. However, most of the known tiara-like [M(m-SR)]n (M = Ni, Pd) clusters to date have been constructed by single thiolate ligands and possess geometrically similar ring systems, which has restricted, to some extent, the abundance of examples and structural diversity of the tiara family. The development of high-performance molecular materials with optimized nonlinear optical (NLO) properties has also been the focus of much current research. 7] Previous studies have demonstrated that the presence of large pelectron delocalization and a symmetrical planar structure play crucial roles in determining the properties of nonlinear chromophores. 8] Curiously, though, despite the quasiaromatic nature of the bonding that has been proposed in nickel toroidal species, their optical properties are little explored; in particular, no study of the NLO properties is extant. We present here the synthesis of the largest tiara-like nickel(II)–thiolate cluster thus far by a novel route that employs two different thiolate bridges, structural studies that reveal an unprecedented elliptical structure for [Ni(m-StBu)(m-etet)]12 (etet = 2-ethylthioethanethiolate) and two new decanuclear-wheel nickel(II)–thiolato clusters [Ni(m-StBu)(m-pyet)]10 (pyet = 2-(2-mercaptoethyl)pyridine) and [Ni(mStBu)(m-atet)]10 (atet = 2-aminoethanethiol), and the first NLO studies of examples from this important class of molecules, together with time-dependent DFT studies that shed light on the optical behavior. The reaction of NiCl2·6 H2O with 1 equivalent K(etet) gave, after work-up, separable [(CH3C6H5) {Ni(m-StBu)(metet)}10] (1a) and [Ni(m-StBu)(m-etet)]12·(CH3C6H5)2 (1 b), whereas similar reactions with K(pyet) or K(atet), instead of K(etet), afforded [(CH3C6H5) {Ni(m-StBu)(m-pyet)}10]·(CH3C6H5)4 (2) and [(0.5CH3C6H5) {Ni(m-StBu)(m-atet)}10]·(CH3C6H5)2 (3), respectively. The atomic arrangements and stoichiometries of 1 a, 1b, 2, and 3 were unequivocally established from low-temperature CCD area-detector X-ray diffraction studies. The single-crystal X-ray analysis of 1b reveals a heretofore unknown dodecagonal-ellipse Ni12S24 framework, as displayed in Figure 1. The top view (Figure 1 a) of the cyclic Ni12S24 architecture shows that edge-fusion of the 12 localized planar [NiS4] subunits along opposite nonbonding S–S edges gives rise to a triple-layer elliptical geometry that approximately conforms to pseudo-D2 symmetry. The transannular Ni···Ni distances of 1 b are in the range of 11.343(6)–13.528(7) , while the dihedral angles between adjoining [NiS2] planes vary from 140.32 to 157.848 because of the unsymmetrical elliptical geometry of this unique 12membered Ni ring. The side view (Figure 1b) of the toroid 1b [*] Prof. Dr. C. Zhang, Dr. S. C. Meng, Dr. J. F. Zhang Molecular Materials Research Center, Scientific Research Academy, School of Chemistry and Chemical Engineering, Jiangsu University Zhenjiang 212013 (P.R. China) Fax: (+ 86)511-8879-7815 E-mail: chizhang@ujs.edu.cn

Organometallic complexes for nonlinear optics. 42. Syntheses, linear, and nonlinear optical properties of ligated metal-functionalized oligo(p-phenyleneethynylene)s.

A combination of UV-vis-NIR spectroscopy, femtosecond Z-scan measurements, and time-dependent density functional theory (TD-DFT) calculations have been used to comprehensively investigate the linear optical and nonlinear optical (NLO) properties of pi-delocalizable metal-functionalized oligo(phenyleneethynylene)s. A range of unsymmetrically or symmetrically end-functionalized mono-, di-, tri-, penta-, hepta-, and nona(phenyleneethynylene)s were synthesized, with larger examples bearing varying numbers of 2,5-di(hexyloxy)phenyl groups to ensure sufficient solubility of the metal complex derivatives. The effect of incorporating varying numbers of solubilizing substituents in the OPE bridge, peripheral group modification, OPE lengthening, coligand variation, and metal location in the OPE on the linear optical properties has been established, with the first three molecular modifications resulting in significant changes in the optical absorption maxima. TD-DFT calculations reveal that the most intense transition in the linear optical spectra is localized on the OPE bridge and involves excitation from acetylenic to cumulenic molecular orbitals that are not greatly spatially separated from one another. The nonlinear optical properties are dominated by two-photon absorption, which for all but 1,4-{trans-[RuCl(dppm)(2)]C[triple bond]C}(2)C(6)H(4) appears as a band around 11,400 cm(-1) and a sharp increase of nonlinear absorption at frequencies >17,000 cm(-1). Surprisingly, there is relatively little influence of the length of the OPE bridge on the magnitude of the two-photon absorption cross sections, which are in the range 300-1000 GM.

Structural, Magnetic Coupling and Oxidation State Trends in Models of the CaMn4 Cluster in Photosystem II

Density functional theory calculations are reported on a set of isomeric structures I, II and III that share the structural formula [CaMn4C9H10N2O16]q+.(H2O)3 (q= -1, 0, 1, 2, 3). Species I has a skeletal structure, which has been previously identified as a close match to the ligated CaMn4 cluster in Photosystem II, as characterized in the most recent 3.0 angstroms crystal structure. Structures II and III are rearrangements of I, which largely retain that models bridging ligand framework, but feature metal atom positions broadly consistent with, respectively, the earlier 3.5 and 3.2 angstroms crystal structures for the Photosystem II water-oxidising complex (WOC). Our study explores the influence of the cluster charge state (and hence S state) on several important properties of the model structures; including the relative energies of the three models, their interconversion, trends in the individual Mn oxidation states, preferred hydration sites and favoured modes of magnetic coupling between the manganese atoms. We find that, for several of the explored cluster charge states, modest differences in the bridging-ligand geometry exert a powerful influence over the individual manganese oxidation states, but throughout these states the robustness of the tetrahedron formed by the Ca and three of the Mn atoms remains a significant feature and contrasts with the positional flexibility of the fourth Mn atom. Although structure I is lowest in energy for most S states, the energy differences between structures for a given S state are not large. Overall, structure II provides a better match for the EXAFS derived metal-metal distance parameters for the earlier S states (S0 to S2), but not for S3 in which a significant structural change is observed experimentally. In this S state structure III provides a closer fit. The implications of these results, for the possible action of the WOC, are discussed.

Laboratory Studies of Ion/Molecule Reactions of Fullerenes: Chemical Derivatization of Fullerenes within Dense Interstellar Clouds and Circumstellar Shells

We discuss recent experimental results for ion/molecule reactions of ionized and multiply-ionized fullerenes, and of derivatized fullerene ions, with molecules relevant to the chemistry of interstellar clouds and circumstellar envelopes These reactions were studied using a selected-ion flow tube (SIFT) at 294 ± 2 K in helium at a pressure of 0.35 ± 0.01 torr. The present study supplements an earlier discussion on aspects of interstellar fullerene ion chemistry explored by the same technique. Several implications are apparent for the chemical processing of fullerenes in various astrophysical environments. Triply charged fullerene ions, such as C603+, may be formed under conditions prevailing within dense IS clouds, but their abundance will be very low owing to the large number of loss processes identified for such species. Derivatization of fullerene ions under interstellar or circumstellar conditions is less probable for larger fullerenes than for fullerenes smaller than C60. Hydrogenation may severely impede the efficiency of fullerene ion association with polar molecules and small unsaturated molecules, but should not substantially affect the efficiency of addition of radicals or PAHs under these conditions. We discuss prospects for neutralization of ionized fullerene adducts. Four classes of adduct ions are described, differing in their structure and expected neutralization tendencies. Adducts of fullerene ions with interstellar isonitriles, with radicals, and with linear polycyclic aromatic hydrocarbons (PAHs; class 1) are most likely to form derivatized fullerenes on neutralization, while fullerene ion adducts of nitriles, most hydrocarbons (class 3), and nonlinear PAHs (class 4) are most likely to yield the bare fullerene cage upon neutralization. Adducts of ammonia (class 2) appear to have an intermediate probability of surviving neutralization with the functionalizing group(s) intact.

Magnesium- and calcium- containing molecular dications: a high level theoretical study

Abstract High-level ab initio quantum chemical calculations, using the GAUSSIAN-2 (G2), G2(MP2), and G2(QCI) procedures, are reported for the species MX2+ (M = Mg and Ca; X = NH3, H2O, HF, PH3, H2S, HCl, CO, and N2). In most instances, these molecular dications are predicted to be thermodynamically stable with respect to the lowest energy dissociation products. For M(CO)2+, the two linear geometries MCO2+ and MOC2+ are both found to represent strongly bound equilibrium structures, with the MCO2+ isomer lying lower in energy. It is hoped that the present thermochemical data may aid in future experimental investigations of metal-containing dications.

Hydration preferences for Mn4Ca cluster models of photosystem II: location of potential substrate-water binding sites.

Density functional theory calculations are reported on a set of three model structures of the Mn(4)Ca cluster in the water-oxidizing complex of Photosystem II (PSII), which share the structural formula [CaMn(4)C(9)H(10)N(2)O(16)](q+)·(H(2)O)(n) (q=-1, 0, 1, 2, 3; n=0-7). In these calculations we have explored the preferred hydration sites of the Mn(4)Ca cluster across five overall oxidation states (S(0) to S(4)) and all feasible magnetic-coupling arrangements to identify the most likely substrate-water binding sites. We have also explored charge-compensated structures in which the overall charge on the cluster is maintained at q=0 or +1, which is consistent with the experimental data on sequential proton loss in the real system. The three model structures have skeletal arrangements that are strongly reminiscent, in their relative metal-atom positions, of the 2.9-, 3.7-, and 3.5 Å-resolution crystal structures, respectively, whereas the charge states encompassed in our study correspond to an assignment of (Mn(III))(3)Mn(II) for S(0) and up to (Mn(IV))(3)Mn(III) for S(4). The three models differ principally in terms of the spatial relationship between one Mn (Mn(4)) and a generally robust Mn(3)Ca tetrahedron that contains Mn(1), Mn(2), and Mn(3). Oxidation-state distributions across the four manganese atoms, in most of the explored charge states, are dependent on details of the cluster geometry, on the extent of assumed hydration of the clusters, and in some instances on the imposed magnetic-coupling between adjacent Mn atoms. The strongest water-binding sites are generally those on Mn(4) and Ca. However, one structure type displays a high-affinity binding site between Ca and Mn(3), the S-state-dependent binding-energy pattern of which is most consistent with the substrate water-exchange kinetics observed in functional PSII. This structure type also permits another water molecule to access the cluster in a manner consistent with the substrate-water interaction with the Mn cluster, seen in electron spin-echo envelope modulation (ESEEM) studies of the functional enzyme in the S(0) and S(2) states. It also rationalizes the significant differences in hydrogen-bonding interactions of the substrate water observed in the FTIR measurements of the S(1) and S(2) states. We suggest that these two water-binding sites, which are molecularly close, model the actual substrate-binding sites in the enzyme.

Proton-transport catalysis and proton-abstraction reactions: An ab initio dynamical study of X+HOC + and XH + + CO (X=Ne, Ar, and Kr)

Ab initio potential energy surfaces have been constructed and used to carry out classical simulations of the reactions of X with HOC+ and of XH+ with CO (X=Ne, Ar, and Kr). The competition between rearrangement, X+HOC+→OCH++X, and abstraction, X+HOC+→XH++CO, has been examined, and found to favor abstraction in the cases where both processes are energetically allowed. The reaction of XH+ with CO is found to produce highly vibrationally excited [CHO]+ products.

Locally Aromatic Polycyclic Hydrocarbons as Potential Carriers of Infrared Emission Features

We report B-LYP/6-31G* and B3-LYP/6-31G* density functional theory calculations on a set of polycyclic hydrocarbons, ranging in size from C19H22 to C36H32, combining aromatic (unsaturated) and aliphatic (saturated, sp3-hybridized carbon) ring systems. These locally aromatic polycyclic hydrocarbons (LAPHs), generally exhibiting large deviations from planarity, may be considered as intermediate structures between polycyclic aromatic hydrocarbons (PAHs) and nanodiamonds. Calculated infrared vibrational frequencies are found to be similar to those observed experimentally in spectra of hydrogenated amorphous carbon (HAC) and other carbonaceous solids. In the C-H stretching region (~3.1-3.6 μm) these species are characterized by strong absorption/emission within both the aliphatic and aromatic C-H bands. They also show spectral features associated with tertiary C-H. Similar features are evident in calculated spectra of the corresponding ions, which we have characterized in some cases. Ionization results in the particular enhancement of a spectral feature typically seen at ~6.4 μm, in the aromatic C-C stretching region. In keeping with previous experimental and theoretical studies on the spectra of neutral and cationic PAHs, we find that the influence of ionization on the relative intensities of C-C and C-H stretching features is much greater than the influence of molecular structure. We suggest that LAPHs may be significant contributors to emission in Type B unidentified infrared emission sources.

What does the Sr-substituted 2.1 Å resolution crystal structure of photosystem II reveal about the water oxidation mechanism?

A density functional study of the Sr-substituted photosystem II water oxidising complex demonstrates that its recent X-ray crystal structure is consistent with a (Mn(III))4 oxidation state pattern, and with a Sr-bound hydroxide ion. The Sr-water-hydroxide interactions rationalize differences in the exchange rates of substrate water and kinetics of dioxygen bond formation relative to the Ca-containing structure.