Sonny C. Lee

Bio: Sonny C. Lee is an academic researcher from University of Waterloo. The author has contributed to research in topics: Reactivity (chemistry) & Cytochrome c oxidase. The author has an hindex of 24, co-authored 42 publications receiving 1941 citations. Previous affiliations of Sonny C. Lee include Harvard University & Princeton University.

Developments in the Biomimetic Chemistry of Cubane-Type and Higher Nuclearity Iron–Sulfur Clusters

Abstract: A prior thematic issue of Chemical Reviews in 20041 provides broad coverage of the field of biomimetic inorganic chemistry. One principal objective of this field, which is a component of the continually burgeoning multidisciplinary enterprise that is bioinorganic chemistry, is the synthesis of analogues of mononuclear and polynuclear sites in proteins which convey information of significance in interpreting the physical and chemical properties of such sites. This article focuses on polynuclear analogues, specifically higher nuclearity, biomimetic metal-sulfur clusters. Many synthetic and biological clusters can be designated as either strong-field or weak-field. Strong-field clusters are formed by first transition series elements with π-acceptor ligands and by second and third series elements regardless of ligation, and manifest properties arising from large splittings of the d-orbital manifold at individual metal sites. Such species are subsumed under a restrictive definition of clusters as containing two or more metal atoms where direct and substantial metal-metal bonding is present.2 A broader definition now normally employed leads to recognition of weak-field clusters. These species contain σ/π-donor ligands that induce smaller d-orbital splittings favoring individual metal sites with high-spin configurations, magnetic interactions among these individual sites, paramagnetic molecular ground states, and labile ligand binding. These clusters contain first transition series elements. Prominent examples of metals in native weak-field cluster sites include (but are not limited to) Mn3–6 (catalases, photosystem II), non-heme Fe7–10 (O2 carriers, oxygenases, reductases, hydrogenase), Fe-S11–14 (electron transfer, nitrogenase, numerous nonredox functions), Ni15,16 (urease), and Ni-Fe17–19 (hydrogenase). The only exceptions to the weak-field designation are Fe sites in [FeFe]- and [NiFe]-hydrogenases, which occur as the fragments Fe(CO)(CN)(μ2-CO) and Fe(CO)(CN)2(μ2-H), respectively. We also note that the weak-field/strong field distinction does not strictly apply to zinc and copper complexes because ZnII and CuI are necessarily diamagnetic, CuII has a spin-doublet ground state, and CuIII is uniformly diamagnetic. However, all but CuIII manifest the substitutional lability associated with the weak-field case. As examples of weak-field clusters, structures of selected protein-bound sites 1–8 containing Mn, non-heme Fe, Fe-S, Ni, and Ni-Fe (Ni site) are provided in Figure 1. Because of the restricted scope of this article, a selected bibliography of summary accounts of the biomimetic chemistry of mono- and polynuclear sites is presented in Table 1. Citations are in the period 2004–2013 and do not include the contents of the previous thematic issue.1 We note in particular a book devoted to bioinorganic synthesis,20 a treatment of biosynthetic inorganic chemistry involving manipulation of protein-bound sites,21 and biomimetic research on sulfur-ligated sites.22 Other examples of weak-field metal sites in proteins are found in this issue. Figure 1 Schematic structures of illustrative weak-field protein-bound clusters: O2-evolving center in photosystem II (1), [FeFe]-hydrogenase (2), [NiFe]-hydrogenase (3); dinuclear (4), trinuclear cuboidal (5), and tetranuclear cubane-type (6) iron-sulfur clusters; ... Table 1 Selected Bibliography of Biomimetic Inorganic Chemisty: 2004–2013 The purview of this article is the biomimetic chemistry of metal-sulfur clusters as confined to post-2004 advances of homo- and heterometallic iron-sulfur clusters of nuclearity four and higher. The emphasis is on the synthetic approaches to such clusters, some of which in their native condition are implicated directly in numerous enzymological processes.

Kinetics and mechanistic analysis of an extremely rapid carbon dioxide fixation reaction

Abstract: Carbon dioxide may react with free or metal-bound hydroxide to afford products containing bicarbonate or carbonate, often captured as ligands bridging two or three metal sites. We report the kinetics and probable mechanism of an extremely rapid fixation reaction mediated by a planar nickel complex [NiII(NNN)(OH)]1- containing a tridentate 2,6-pyridinedicarboxamidate pincer ligand and a terminal hydroxide ligand. The minimal generalized reaction is M-OH + CO2 → M-OCO2H; with variant M, previous rate constants are ≲103 M-1 s-1 in aqueous solution. For the present bimolecular reaction, the (extrapolated) rate constant is 9.5 × 105 M-1 s-1 in N,N′-dimethylformamide at 298 K, a value within the range of kcat/KM≈105–108 M-1 s-1 for carbonic anhydrase, the most efficient catalyst of CO2 fixation reactions. The enthalpy profile of the fixation reaction was calculated by density functional theory. The initial event is the formation of a weak precursor complex between the Ni-OH group and CO2, followed by insertion of a CO2 oxygen atom into the Ni-OH bond to generate a four center Ni(η2-OCO2H) transition state similar to that at the zinc site in carbonic anhydrase. Thereafter, the Ni-OH bond detaches to afford the Ni(η1-OCO2H) fragment, after which the molecule passes through a second, lower energy transition state as the bicarbonate ligand rearranges to a conformation very similar to that in the crystalline product. Theoretical values of metric parameters and activation enthalpy are in good agreement with experimental values [ΔH‡ = 3.2(5) kcal/mol].

Biomimetic Hydrogen Evolution: MoS2 Nanoparticles as Catalyst for Hydrogen Evolution

Abstract: The electrochemical hydrogen evolution reaction is catalyzed most effectively by the Pt group metals. As H2 is considered as a future energy carrier, the need for these catalysts will increase and alternatives to the scarce and expensive Pt group catalysts will be needed. We analyze the ability of different metal surfaces and of the enzymes nitrogenase and hydrogenase to catalyze the hydrogen evolution reaction and find a necessary criterion for high catalytic activity. The necessary criterion is that the binding free energy of atomic hydrogen to the catalyst is close to zero. The criterion enables us to search for new catalysts, and inspired by the nitrogenase active site, we find that MoS2 nanoparticles supported on graphite are a promising catalyst. They catalyze electrochemical hydrogen evolution at a moderate overpotential of 0.1−0.2 V.

Multicopper Oxidases and Oxygenases

Abstract: Copper is an essential trace element in living systems, present in the parts per million concentration range. It is a key cofactor in a diverse array of biological oxidation-reduction reactions. These involve either outer-sphere electron transfer, as in the blue copper proteins and the Cu{sub A} site of cytochrome oxidase and nitrous oxide redutase, or inner-sphere electron transfer in the binding, activation, and reduction of dioxygen, superoxide, nitrite, and nitrous oxide. Copper sites have historically been divided into three classes based on their spectroscopic features, which reflect the geometric and electronic structure of the active site: type 1 (T1) or blue copper, type 2 (T2) or normal copper, and type 3 (T3) or coupled binuclear copper centers. 428 refs.

Structural and Functional Aspects of Metal Sites in Biology

Abstract: For present purposes, a protein-bound metal site consists of one or more metal ions and all protein side chain and exogenous bridging and terminal ligands that define the first coordination sphere of each metal ion. Such sites can be classified into five basic types with the indicated functions: (1) structural -- configuration (in part) of protein tertiary and/or quaternary structure; (2) storage -- uptake, binding, and release of metals in soluble form: (3) electron transfer -- uptake, release, and storage of electrons; (4) dioxygen binding -- metal-O{sub 2} coordination and decoordination; and (5) catalytic -- substrate binding, activation, and turnover. The authors present here a classification and structure/function analysis of native metal sites based on these functions, where 5 is an extensive class subdivided by the type of reaction catalyzed. Within this purview, coverage of the various site types is extensive, but not exhaustive. The purpose of this exposition is to present examples of all types of sites and to relate, insofar as is currently feasible, the structure and function of selected types. The authors largely confine their considerations to the sites themselves, with due recognition that these site features are coupled to protein structure at all levels. In themore » next section, the coordination chemistry of metalloprotein sites and the unique properties of a protein as a ligand are briefly summarized. Structure/function relationships are systematically explored and tabulations of structurally defined sites presented. Finally, future directions in bioinorganic research in the context of metal site chemistry are considered. 620 refs.« less

Efficient Visible Light Nitrogen Fixation with BiOBr Nanosheets of Oxygen Vacancies on the Exposed {001} Facets

Abstract: Even though the well-established Haber–Bosch process has been the major artificial way to “fertilize” the earth, its energy-intensive nature has been motivating people to learn from nitrogenase, which can fix atmospheric N2 to NH3 in vivo under mild conditions with its precisely arranged proteins Here we demonstrate that efficient fixation of N2 to NH3 can proceed under room temperature and atmospheric pressure in water using visible light illuminated BiOBr nanosheets of oxygen vacancies in the absence of any organic scavengers and precious-metal cocatalysts The designed catalytic oxygen vacancies of BiOBr nanosheets on the exposed {001} facets, with the availability of localized electrons for π-back-donation, have the ability to activate the adsorbed N2, which can thus be efficiently reduced to NH3 by the interfacial electrons transferred from the excited BiOBr nanosheets This study might open up a new vista to fix atmospheric N2 to NH3 through the less energy-demanding photochemical process

Structures of metal sites of oxidized bovine heart cytochrome c oxidase at 2.8 A

Abstract: The high resolution three-dimensional x-ray structure of the metal sites of bovine heart cytochrome c oxidase is reported. Cytochrome c oxidase is the largest membrane protein yet crystallized and analyzed at atomic resolution. Electron density distribution of the oxidized bovine cytochrome c oxidase at 2.8 A resolution indicates a dinuclear copper center with an unexpected structure similar to a [2Fe-2S]-type iron-sulfur center. Previously predicted zinc and magnesium sites have been located, the former bound by a nuclear encoded subunit on the matrix side of the membrane, and the latter situated between heme a3 and CuA, at the interface of subunits I and II. The O2 binding site contains heme a3 iron and copper atoms (CuB) with an interatomic distance of 4.5 A; there is no detectable bridging ligand between iron and copper atoms in spite of a strong antiferromagnetic coupling between them. A hydrogen bond is present between a hydroxyl group of the hydroxyfarnesylethyl side chain of heme a3 and an OH of a tyrosine. The tyrosine phenol plane is immediately adjacent and perpendicular to an imidazole group bonded to CuB, suggesting a possible role in intramolecular electron transfer or conformational control, the latter of which could induce the redox-coupled proton pumping. A phenyl group located halfway between a pyrrole plane of the heme a3 and an imidazole plane liganded to the other heme (heme a) could also influence electron transfer or conformational control.