Bioinorganic Chemistry. Rosette M. Roat-Malone

      1 Chapter 1TABLE 1.1 Percentage Composition of Selected Elements in the Human BodyTABLE 1.2 Hard–soft Acid–base Classification of Metal Ions and Ligands...TABLE 1.3 Metals in Biological Systems: Charge CarriersTABLE 1.4 Metals in Biological Systems: Structural and TriggersTABLE 1.5 Metals in Biological Systems: Electron TransferTABLE 1.6 Metals in Biological Systems: Dioxygen TransportTABLE 1.7 Metals in Biological Systems: Enzyme CatalysisTABLE 1.8 Ligand Contributions to the 16‐ or 18‐electron RuleTABLE 1.9 Nitrogenous Bases, Nucleosides, Nucleotides, and Sugars Found in DNA an...TABLE 1.10 Some Properties of A DNA, B DNA, and Z DNA

      2 Chapter 2TABLE 2.1 Computing Units

      3 Chapter 3TABLE 3.1 Cytochrome c Oxidase (CcO) Bond Distances: X‐ray Crystallographic, ...

      4 Chapter 5TABLE 5.1 Metric Prefixes

      5 Chapter 6TABLE 6.1 Comparison of IC₅₀ Values for Pt, Ir, and Ru Antitumor Complexes

      List of Illustrations

      1 Chapter 1Figure 1.1 Dose‐response curve for elements.Figure 1.2 Common transition metal coordination geometries.Figure 1.3 Ligand field splitting for d electrons in various ligand fields....Figure 1.4 High‐spin and low‐spin electron configurations in an octahedral f...Figure 1.5 Electron configurations for high‐spin Cr(II) and Cu(II).Figure 1.6 Complexes obeying the 16‐e and 18‐e rule.Figure 1.7 (a) Rubredoxin. (b) [2Fe2S] cluster in ferredoxins. (c) [4Fe4S] c...Figure 1.8 Possible amino acid‐metal complexation structures found in metall...Figure 1.9 (a) Primary structure of a peptide chain. (b) Possible rotation a...Figure 1.10 Hydrogen bonding to form protein α‐helical and β‐pleated sheet s...Figure 1.11 Graphical representation of the Michaelis–Menten equation for no...Figure 1.12 Lineweaver–Burk plot for no inhibitor, competitive and noncompet...Figure 1.13 Watson–Crick base‐pairing in DNA.Figure 1.14 Complimentary antiparallel double‐stranded (ds) DNA (dsDNA).Figure 1.15 Orientations found in DNA helices.Figure 1.16 Schematic representation of replication, transcription, and tran...Figure 1.17 (a) Cas9 (green); crRNA (orange); tracrRNA (purple); PAM sequenc...Figure 1.18 Visualization of Cas9 ribonucleoprotein (RNP) from PDB 4UNS [24]...Figure 1.19 A ruthenium complex that can detect a DNA mismatch. PDB 4E1U dat...Figure 1.20 Cyclic voltammetry of wild‐type and mutant EndoIII from figure 6...Figure 1.21 Structures for counting electrons using 16‐ and 18‐electron rule.

      2 Chapter 2Figure 2.1 Example of a People's Split Valence Basis Set.Figure 2.2 Structure of the binuclear center (BNC) of protein data bank (PDB...

      3 Chapter 3Figure 3.1 Dioxygen bound to myoglobin heme. Visualization from reference [1...Figure 3.2 Heme protoporphyrin IX (heme b) as found in Hb, Mb, and some cyto...Figure 3.3 Quaternary structure protein data bank (PDB) 4HHB.Figure 3.4 T and R states for iron hemes in Hb.Figure 3.5 Heme group from PDBe 5M3L as determined by cryo‐electron microsco...Figure 3.6 Possible O₂‐binding modes in hemoglobin.Figure 3.7 Heme a in Cytochrome c Oxidase (CcO).Figure 3.8 CcO CuA, Heme a, and the binuclear center (BNC) as visualized wit...Figure 3.9 Cytochrome c oxidase catalytic cycle.Figure 3.10 Proposed O–O cleavage mechanism in heme‐copper oxidases (HCOs) w...Figure 3.11 Cytochrome c oxidase (CcO) catalytic center intermediates.Figure 3.12 H K and D channels in cytochrome c oxidase using PDB 1V54 data a...Figure 3.13 Cytochrome c oxidase (CcO) Model Compounds.Figure 3.14 Reaction of a CcO model compound illustrating homolytic dioxygen...Figure 3.15 Reaction of LS‐AN, a CcO model compound, with a phenol (PhOH)....Figure 3.16 Water molecules and the H‐bonding amino acid residue side chains...Figure 3.17 FeMo cofactor (M‐cluster) in the MoFe protein of nitrogenase as ...Figure 3.18 PDB 4WN9 FeMo cofactor used in QM/QM’ calculations by Rao et al....Figure 3.19 Lowe‐Thorneley cycle proposed by Rao et al. [71].Figure 3.20 Relative Gibbs free energies for the E4 state reaction path [71]...Figure 3.21 Distal, alternating, hybrid hydrogenation of N₂ to form NH_3.Figure 3.22 Pathways from the protein surface to nitrogenase's active site. ...Figure 3.23 Molybdenum complex producing NH₃ from N₂ [79]^.Figure 3.24 Reactions producing NH₃ from N_2.Figure 3.25 Reduction system for N₂ to NH_3.Figure 3.26 Fe–dinitrogen complex with Tp^Ph,Me ligands.Figure 3.27 Model complex with adamantane (Ad) substituents [91].Figure 3.28 Model complex with boron central atom.Figure 3.29 Hydrogen evolution from a nitrogenase functional model [93].Figure 3.30 P‐Cluster Model Compound.Figure 3.31 Starting materials for FeMo‐cofactor structural model from refer...Figure 3.32 FeMoco‐factor Model Compound.Figure 3.33 Active Site of copper–zinc superoxide dismutase (CuZnSOD).Figure 3.34 (a) CuZn SOD1 dimer PDB 1E9P. (b) CuZn SOD1 dimer PDB 1L3N.Figure 3.35 Proposed SOD3 Mechanism.Figure 3.36 Superoxide dismutase (SOD) Model Compound Ligands.Figure 3.37 (a) PDB 1MTY [110] active site in α subunit of MMOH (H₂O/OH⁻...Figure 3.38 (a) Possible Q (a diiron species) structures in the mechanism fo...Figure 3.39 Metal centers and visualization of pmoB, pmoA, and pmoC for PDB ...

      4 Chapter 4Figure 4.1 Active Site of [NiFe] hydrogenase as visualized from PDB 5XLH [1]...Figure 4.2 Comparison [FeFe] hydrogenase with gamma oxygen versus gamma carb...Figure 4.3 [Fe]‐hydrogenase active site from the X‐ray crystallographic entr...Figure 4.4 PDB 4U9H [NiFe]‐hydrogenase active site.Figure 4.5 Catalytic cycle for [NiFe]‐hydrogenase.Figure 4.6 PDB 4UD6 Ni‐C form in the [NiFe]‐hydrogenase catalytic cycle illu...Figure 4.7 [NiFe]‐hydrogenase model compound.Figure 4.8 [NiFe]‐hydrogenase model compounds. (a) dppe = 1,2‐bis(diphenylph...Figure 4.9 Model compounds representing [NiFe]‐hydrogenase Ni‐L state (react...Figure 4.10 [NiFe]‐hydrogenase model compound illustrating H₂ cleavage at th...Figure 4.11 Possible proton pathways to the H‐cluster involving amino‐acid r...Figure 4.12 Amino‐acid network surrounding the 2Fe_H subcluster for the CpI^AD...Figure 4.13 [FeFe]‐hydrogenase model complexes that produce H_2.Figure 4.14 Proposed [Fe]‐hydrogenase catalytic cycle.Figure 4.15 [Fe]‐hydrogenase model compounds: (a) short‐lived model compound...Figure 4.16 Human carbonic anhydrase II (hCAII), PDB 1CA2.Figure 4.17 Hydrophilic