•Catalytic reactions of oxygen-evolving complex during the S2→S3 transition are investigated.•Two reaction pathways, R- and L-reactions are elucidated.•Both reactions start by moving the Ca-bound ...water (W3) to the vacant Mn(III) coordination.•The L-reaction is more energetically favored than the R-reaction.•Proton transfer occurs through O5, W2(OH) and the active site water molecules (W5–W7).
Catalytic reactions of the proton and electron transfers occurring at the oxygen-evolving complex (OEC) of photosystem II during the S2–S3 transition were investigated by the quantum mechanics/molecular mechanics (QM/MM) methodology. Two favorable reaction pathways were elucidated. Both reactions start by moving the Ca-bound water (W3) to the vacant Mn(III) coordination at the left-opened (L) or right-opened (R) form. The former reaction pathway, in which W3 coordinates to the Mn4 at the S2-L form, has lower activation barriers than the latter. Thus, easier proton transfers from W3 to the Tyr161 phenol anion can be performed.
The field of protein residue network (PRN) research has brought several useful methods and techniques for structural analysis of proteins and protein complexes. Many of these are ripe and ready to be ...used by the proteomics community outside of the PRN specialists. In this paper we present software which collects an ensemble of (network) methods tailored towards the analysis of protein-protein interactions (PPI) and/or interactions of proteins with ligands of other type, e.g. nucleic acids, oligosaccharides etc. In parallel, we propose the use of the network differential analysis as a method to identify residues mediating key interactions between proteins. We use a model system, to show that in combination with other, already published methods, also included in pyProGA, it can be used to make such predictions. Such extended repertoire of methods allows to cross-check predictions with other methods as well, as we show here. In addition, the possibility to construct PRN models from various kinds of input is so far a unique asset of our code. One can use structural data as defined in PDB files and/or from data on residue pair interaction energies, either from force-field parameters or fragment molecular orbital (FMO) calculations. pyProGA is a free open-source software available from
This review article describes a historical perspective of elucidation of the nature of the chemical bonds of the high-valent transition metal oxo (M=O) and peroxo (M-O-O) compounds in chemistry and ...biology. The basic concepts and theoretical backgrounds of the broken-symmetry (BS) method are revisited to explain orbital symmetry conservation and orbital symmetry breaking for the theoretical characterization of four different mechanisms of chemical reactions. Beyond BS methods using the natural orbitals (UNO) of the BS solutions, such as UNO CI (CC), are also revisited for the elucidation of the scope and applicability of the BS methods. Several chemical indices have been derived as the conceptual bridges between the BS and beyond BS methods. The BS molecular orbital models have been employed to explain the metal oxyl-radical character of the M=O and M-O-O bonds, which respond to their radical reactivity. The isolobal and isospin analogy between carbonyl oxide R2C-O-O and metal peroxide LFe-O-O has been applied to understand and explain the chameleonic chemical reactivity of these compounds. The isolobal and isospin analogy among Fe=O, O=O, and O have also provided the triplet atomic oxygen (3O) model for non-heme Fe(IV)=O species with strong radical reactivity. The chameleonic reactivity of the compounds I (Cpd I) and II (Cpd II) is also explained by this analogy. The early proposals obtained by these theoretical models have been examined based on recent computational results by hybrid DFT (UHDFT), DLPNO CCSD(T0), CASPT2, and UNO CI (CC) methods and quantum computing (QC).
Photosynthetic water oxidation is catalyzed by a Mn4CaO5-cluster in photosystem II through an S-state cycle. Understanding the roles of heterogeneity in each S-state, as identified recently by the ...EPR spectroscopy, is very important to gain a complete description of the catalytic mechanism. We performed herein hybrid DFT calculations within the broken-symmetry formalism and associated analyses of Heisenberg spin models to study the electronic and spin structures of various isomeric structural motifs (hydroxo–oxo, oxyl–oxo, peroxo, and superoxo species) in the S3 state. Our extensive study reveals several factors that affect the spin ground state: (1) (formal) Mn oxidation state; (2) metal–ligand covalency; (3) coordination geometry; and (4) structural change of the Mn cluster induced by alternations in Mn···Mn distances. Some combination of these effects could selectively stabilize/destabilize some spin states. We found that the high spin state (S total = 6) of the oxyl–oxo species can be causative for catalytic function, which manifests through mixing of the metal–ligand character in magnetic orbitals at relatively short O5···O6 distances (<2.0 Å) and long MnA···O5 distances (>2.0 Å). These results will serve as a basis to conceptually identify and rationalize the physicochemical synergisms that can be evoked by the unique “distorted chair” topology of the cluster through cooperative Jahn–Teller effects on multimetallic centers.
High enantiomeric excesses (ee’s) of l-amino acids, including non-proteinogenic amino acid isovaline (Iva), were discovered in the Murchison meteorite, but the detailed molecular mechanism ...responsible for the observed ee of amino acids remains elusive and inconsistent, because Iva has an inverted circular dichroism (CD) spectrum with respect to α-H amino acids, e.g., alanine. To address this issue, we resort to accurate ab initio calculations for amino acids and their precursors in the Strecker synthesis. We evaluated their photolysis-induced ee in the range 5–11 eV including the Lyman alpha emission line (Lyα), the typical intensive 10.2 eV radiation ascribed to the early phase of galactic evolution. We show that only the aminonitrile precursors are characterized by positive ee in the Lyα region, explaining why right-handed circularly polarized Lyα (R-CP-Lyα) induces homologous l-amino acids. This study shows that the homochirality of amino acids is produced at the aminonitrile precursors stage.
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•New O–O bond formation mechanism of photosystem II oxygen-evolving complex is proposed.•At least five reaction steps were required in the S4 to S0 transition.•Initial proton transfer ...requires a highest activation barrier among the five reaction steps.•O–O single bond is formed by a nonadiabatic one-electron transfer from the Mn cluster to Yz.•Proton transfer occurs to neutralize the Yz anion.
The reaction mechanism of the O2 formation in the S4 state of the oxygen-evolving complex of photosystem II was clarified at the quantum mechanics/molecular mechanics (QM/MM) level. After the Yz (Y161) oxidation and the following proton transfer in the S3 state, five reaction steps are required to produce the molecular dioxygen. The highest barrier step is the first proton transfer reaction (0 → 1). The following reactions involving electron transfers were precisely analyzed in terms of their energies, structures and spin densities. We found that the one-electron transfer from the Mn4Ca cluster to Y161 triggers the O–O sigma bond formation.
The O2 release of the oxygen-evolving complex of the photosystem II (PSII) is one of the essential processes responsible for the highly efficient O2 production. Despite its importance, the detailed ...molecular mechanism is still unsolved. In the present study, we show that the O2 release is directly coupled with water insertion into the Mn cluster based on the quantum mechanics/molecular mechanics (QM/MM) calculations. In this mechanism, the O2 molecule first dissociates from the Mn sites in order, that is, the O atom coordinating to the Mn3 (O5a) first dissociates, then the other O atom coordinating to the Mn1 (O5d) dissociates in the next step in the late S4 state (1 → 2). Next, the O2 migrates to a space surrounded by the Val185 and His332 side chains as one water molecule coordinating to the Ca2+ ion (W3) comes into the O2 bonded site (2 → 3). Finally, a pre-S0 state (4) is formed after a proton transfer from the inserted water to the other proton acceptor site (W2) (3 → 4). The highest activation barrier during these reactions was found at the O2 release step (2 → 3) that only requires E ⧧ = 12.7 kcal mol–1 (G ⧧ = 10.4 kcal mol–1). A series of the reactions (2 → 3) look like a chain crash of billiard balls because the W3 is inserted into the catalytic center from the water-abundant side (Ca2+ ion side), and then the O2 moiety is pushed out to the opposite side (Val185 side). The hydrophobic residue of Val185 covers the active O5 site and forms an O2-specific permeation tunnel. The present sequential reactions clearly demonstrate the efficient removal of the toxic O2 from the catalytic center and implications of the essential roles of Val185, Ca2+ ions and water molecules, which are all present in the active site of PSII as the indispensable constituents.
The photoinduced ligand exchange reaction of Ru(II) complexes in aqueous solution was studied using density functional theory (DFT). The optimized structures of the lowest triplet state of ...cis-Ru(bpy)2(CH3CN)22+ (bpy = bipyridine), cis-Ru(bpy)2(NH3)22+, and their monoaqua complexes were analyzed. The metal-centered (3MC) structure was lower than the metal-to-ligand charge transfer (3MLCT) structure for cis-Ru(bpy)2(CH3CN)22+, whereas the 3MLCT structure was lower than the 3MC structure for cis-Ru(bpy)2(NH3)22+. Such a difference would correlate with the higher quantum yield of the former complex. For the monoaqua complexes, the most stable local minimum structure was the 3MC structure, in which the Ru–OH2O and Ru–Nbpy (trans to the oxygen) bonds were elongated. Therefore, the dissociation of the H2O ligand would be preferred to that of the CH3CN (or NH3) ligand from the monoaqua intermediate, which might result in the reformation of the monoaqua intermediate, and thus, the formation of the bis-aqua product would take a longer time than that of the monoaqua intermediate.
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