Xichen Li

Water oxidation mechanism for synthetic Co-oxides with small nuclearity.

Hybrid DFT model calculations have been performed for some cobalt complexes capable of oxidizing water. Since a very plausible mechanism for the oxygen-evolving complex involving the cuboidal Mn4Ca structure in photosystem II (PSII) has recently been established, the most important part of the present study concerns a detailed comparison between cobalt and manganese as water oxidation catalysts. One similarity found is that a M(IV)-O(•) state is the key precursor for O-O bond formation in both cases. This means that simply getting a M(IV) state is not enough; a formal M(V)═O state is required, with two oxidations on one center from M(III). For cobalt, not even that is enough. A singlet coupled state is required at this oxidation level, which is not the ground state. It is shown that there are also more fundamental differences between catalysts based on these metals. The favorable low-barrier direct coupling mechanism found for PSII is not possible for the corresponding cobalt complexes. The origin of this difference is explained. For the only oxygen-evolving cubic Co4O4 complex with a defined structure, described by Dismukes et al., the calculated results are in good agreement with experiments. For the Co4 models of the amorphous cobalt-oxo catalyst found by Nocera et al., higher barriers are found than the one obtained experimentally. The reasons for this are discussed.

A comparison between artificial and natural water oxidation

Two artificial water oxidation catalysts, the blue dimer and the Llobet catalyst, have been studied using hybrid DFT methods. The results are compared to those for water oxidation in the natural photosystem II enzyme. Studies on the latter system have now reached a high level of understanding, at present much higher than the one for the artificial systems. A recent high resolution X-ray structural investigation of PSII has confirmed the main features of the structure of the oxygen evolving complex (OEC) suggested by previous DFT cluster studies. The O-O bond formation mechanism suggested is of direct coupling (DC) type between an oxygen radical and a bridging oxo ligand. A similar DC mechanism is found for the Llobet catalyst, while an acid-base (AB) mechanism is preferred for the blue dimer. All of them require at least one oxygen radical. Full energy diagrams, including both redox and chemical steps, have been constructed illustrating similarities and differences to the natural system. Unlike previous DFT studies, the results of the present study suggest that the blue dimer is rate-limited by the initial redox steps, and the Llobet catalyst by O(2) release. The results could be useful for further improvement of the artificial systems.

Theoretical study on stabilities of multiple hydrogen bonded dimers

A series of self-constituted multiple hydrogen bonded (MHB) complexes has been investigated systematically by density functional theory (PBE1PBE /6-31G**), the Morokuma energy decomposition method (HF/6-31G**) and MP2 (6-31G** and 6-311++G**) calculation. We have discovered that (i) for doubly hydrogen bonded (DHB) complexes, both the interaction energy and stability increase with the charge transfer energy; (ii) for quadruple hydrogen bonded (QHB) complexes, cooperativity is the most important factor determining stability of the complex: stronger cooperative energy correlates well with larger interaction energy and thus more stable complex and vice versa; (iii) correlation energy plays an important role in intermolecular interactions. The correlation energy, mainly consisting of dispersive energy, also exhibits cooperativity in MHB dimers: positive for M-aadd and generally negative for other complexes.

Ruthenium(II) Complexes of Aryl Triazole Foldamers as Receptors for Anions

Ruthenium(II) complexes of oligo(bipyridine-phenyl triazole)s were synthesized as receptors for anions. The receptors, which are partially preorganized through metal-ligand interactions, can fold into a helical conformation to bind chloride, bromide, iodide, or nitrate anions in their inner cavities in acetone or competitive H-bonding media such as 5% water in acetone and DMSO. The short oligomer 1 can sandwich the studied anions with high affinity in acetone. Addition of 5% water to acetone results in overall decreases in the binding strength due to the binding competition from water, but does not change the basic binding mode. The highly competitive H-bonding solvent DMSO causes the receptor-anion interactions to become even weaker. However, in DMSO, the short receptor 1 is still able to bind the halide anions with moderate affinities in a 1:1 stoichiometry, whereas the longer oligomer 2 forms double-strand helices with an anion wrapped inside for all anions investigated so far.

Water Oxidation for Simplified Models of the Oxygen-Evolving Complex in Photosystem II.

For the main parts of the mechanism for water oxidation in photosystem II there has recently been very strong experimental support for the mechanism suggested by theoretical model studies. The question addressed in the present study is to what extent this knowledge can be used for the design of artificial catalysts. A major requirement for a useful artificial catalyst is that it is small enough to be synthesized. Small catalysts also have the big advantage that they could improve the catalysis per surface area. To make the mechanism found for PSII useful in this context, it needs to be analyzed in detail. A small model system was therefore used and the ligands were replaced one by one by water-derived ligands. Only the main chemical step of O-O bond formation was investigated in this initial study. The energetics for this small model and the larger one previously used for PSII are remarkably similar, which is the most important result of the present study. This shows that small model complexes have a potential for being very good water oxidation catalysts. It was furthermore found that there is a clear correlation between the barrier height for O-O bond formation and the type of optimal structure for the S3 state. The analysis shows that a flexible central part of the complex is the key for efficient water oxidation.

Unique Kinase Catalytic Mechanism of AceK with a Single Magnesium Ion

Isocitrate dehydrogenase kinase/phosphatase (AceK) is the founding member of the protein phosphorylation system in prokaryotes. Based on the novel and unique structural characteristics of AceK recently uncovered, we sought to understand its kinase reaction mechanism, along with other features involved in the phosphotransfer process. Herein we report density functional theory QM calculations of the mechanism of the phosphotransfer reaction catalysed by AceK. The transition states located by the QM calculations indicate that the phosphorylation reaction, catalysed by AceK, follows a dissociative mechanism with Asp457 serving as the catalytic base to accept the proton delivered by the substrate. Our results also revealed that AceK prefers a single Mg2+-containing active site in the phosphotransfer reaction. The catalytic roles of conserved residues in the active site are discussed.

Molecular Dynamics Simulation Studies of dTTP Binding and Catalysis Mediated by YhdE Dimerization

YhdE is a Maf-like (multicopy associated filamentation) protein that primarily acts as dTTPase to hydrolyze dTTP into dTMP and two phosphate molecules in cell metabolism pathway. Two crystal structures of YhdE have been previously determined, representing the open and closed active site conformations, respectively. Based on the structures, we have carried out molecular dynamics simulations and free energy calculations to investigate dTTP binding to and hydrolysis by YhdE. Our results suggest that YhdE closed state is structurally more compact than its open state at room temperature. YhdE open state is a favorable conformation for dTTP binding and closed state is a structurally favorable conformation for catalytic reaction. This observation is supported by the structure of YhdE homolog in complex with a nucleotide analog. Free energy calculations reveal that YhdE dimerization occurs preferentially in dTTP binding and is favorable for successive cooperative reaction. The key residues R11, R12 and K80, are found to contribute to the substrate stabilization. Further, YhdE dimerization and binding of dTTP induce the cooperative effect through a direct allosteric communication network in YhdE from the dTTP binding sites in the catalytic center to the intermolecular β-strand in YhdE dimer.

Function Coupling Mechanism of PhuS and HemO in Heme Degradation

Most bacteria possess only one heme-degrading enzyme for obtaining iron, however few bacteria such as Pseudomonas aeruginosa express two, namely PhuS and HemO. While HemO is a well-known heme oxygenase, previously we discovered that PhuS also possesses heme degradation activity and generates verdoheme, an intermediate of heme breakdown. To understand the coexistence of these two enzymes, using the DFT calculation we reveal that PhuS effectively enhances heme degradation through its participation in heme hydroxylation, the rate limiting reaction. Heme is converted to verdoheme in this reaction and the energy barrier for PhuS is substantially lower than for HemO. Thus, HemO is mainly involved in the ring opening reaction which converts verdoheme to biliverdin and free iron. Our kinetics experiments show that, in the presence of both PhuS and HemO, complete degradation of heme to biliverdin is enhanced. We further show that PhuS is more active than HemO using heme as a substrate and generates more CO. Combined experimental and theoretical results directly identify function coupling of this two-enzyme system, resulting in more efficient heme breakdown and utilization.

Distal Proton Shuttle Mechanism of Ribosome Catalysed Peptide Bond Formation-A Theoretical Study

In this work, we have investigated a novel distal proton shuttle mechanism of ribosome catalyzed peptide bond formation reaction. The reaction was found to follow a two-step mechanism. A distal water molecule located about 6.1 Å away from the attacking amine plays as a proton acceptor and results in a charge-separated intermediate that is stabilized by the N terminus of L27 and the A-site A76 5′-phosphate. The ribose A2451 bridges the proton shuttle pathway, thus plays critical role in the reaction. The calculated 27.64 kcal·mol−1 free energy barrier of the distal proton shuttle mechanism is lower than that of eight-membered ring transition state. The distal proton shuttle mechanism studied in this work can provide new insights into the important biological peptide synthesis process.

Cluster size convergence for the energetics of the oxygen evolving complex in PSII

Density functional theory calculations have been made to investigate the stability of the energetics for the oxygen evolving complex of photosystem II. Results published elsewhere have given excellent agreement with experiments for both energetics and structures, where many of the experimental results were obtained several years after the calculations were done. The computational results were obtained after a careful extension from small models to a size of about 200 atoms, where stability of the results was demonstrated. However, recently results were published by Isobe et al., suggesting that very different results could be obtained if the model was extended from 200 to 340 atoms. The present study aims at understanding where this difference comes from.