J. Appl. Cryst.の発刊に際して

Recent advances in the field of electron cryo-microscopy (cryo-EM) have resulted in a rapidly increasing number of atomic models of bio-macromolecules solved using this technique and deposited in the Protein Data Bank and the Electron Microscopy Data Bank. Similar to macromolecular crystallography, validation tools for these models and maps are required. While some of these validation tools may be borrowed from crystallography, new methods specifically for cryo-EM validation are required. We discuss new computational methods and tools implemented in Phenix, including d99 to estimate resolution, phenix.auto_sharpen to improve maps, and phenix.mtriage to analyze cryo-EM maps. We suggest that cryo-EM half-maps and masks are deposited to facilitate evaluation and validation of cryo-EM derived atomic models and maps. We also present the application of these tools to deposited cryo-EM atomic models and maps.

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New tools for the analysis and validation of Cryo-EM maps and atomic models

To address the serious threat of bacterial infection to public health, great efforts have been devoted to the development of antimicrobial agents for inhibiting bacterial growth, preventing biofilm formation, and sterilization. Very recently, metal-organic frameworks (MOFs) have emerged as promising materials for various antimicrobial applications owing to their different functions including the controlled/stimulated decomposition of components with bactericidal activity, strong interactions with bacterial membranes, and formation of photogenerated reactive oxygen species (ROS) as well as high loading and sustained releasing capacities for other antimicrobial materials. This review focuses on recent advances in the design, synthesis, and antimicrobial applications of MOF-based materials, which are classified by their roles as component-releasing (metal ions, ligands, or both), photocatalytic, and chelation antimicrobial agents as well as carriers or/and synergistic antimicrobial agents of other functional materials (antibiotics, enzymes, metals/metal oxides, carbon materials, etc.). The constituents, fundamental antimicrobial mechanisms, and evaluation of antimicrobial activities of these materials are highlighted to present the design principles of efficient MOF-based antimicrobial materials. The prospects and challenges in this research field are proposed.

Metal-Organic-Framework-Based Materials for Antimicrobial Applications.

Four novel complexes, {[Ni4(HEIDC)4(H2O)8]·2H2O} (1), {[Mn(HEIDC)(4,4′-bipy)0.5(H2O)]·H2O}n (2), [Mn6(EIDC)4(py)(H2O)4]n (3), and {[Cd2(EIDC)(H2EIDC)(4,4′-bipy)1.5]·H2O}n (4) (H3EIDC = 2-ethyl-1H-imidazole-4,5-dicarboxylic acid, 4,4′-bipy = 4,4′-bipyridine, and py = pyridine) have been hydro(solvo)thermally synthesized by fine control over synthetic conditions, such as solvent and pH value, and structurally characterized. It is shown through single-crystal X-ray diffractions that the ligands H3EIDC can be either singly, doubly, or triply deprotonated and can coordinate to Ni(II), Mn(II) or Cd(II) ions in μ2 or μ3 modes. Compound 1 is a zero-dimensional (0D) symmetrical tetranuclear molecular square. Compound 2 exhibits a two-dimensional (2D) sheet, in which alternate left- and right-handed helical chains are bridged by 4,4′-bipy linkages. Compound 3 assumes a 2D honeycomb-like sheet built up from μ3-EIDC3− and Mn(II) atoms. Compound 4 possesses a novel three-dimensional (3D) structure constructed from 2D ...

Four novel frameworks built by imidazole-based dicarboxylate ligands: hydro(solvo)thermal synthesis, crystal structures, and properties.

Two new metal–organic frameworks [Cd3(H2O)2(C5N2O4H)2·H2O] 1 and [KCd(C7N2O4H5)] 2 have been hydrothermally synthesized employing 4,5-imidazoledicarboxylic acid (IMDC) and 2-ethyl-4,5-imidazoledicarboxylic acid (2-EtIMDC) as organic ligands. The single-crystal structure analysis reveals that compound 1 exhibits a 3-D framework, which is generated from 2-D layers pillared by 1-D chains along the c-axis. Compound 2 presents a 3-D structure with 1-D channels, which are connected in a cross-like fashion by [CdN2O3] trigonal bipyramid units and 2-EtIMDC ligands.

Assembly of two 3-D metal–organic frameworks from Cd(II) and 4,5-imidazoledicarboxylic acid or 2-ethyl-4,5-imidazoledicarboxylic acid

Eight new metal complexes with two kinds of phenyl substituted pyrazole carboxylic acid, [Ni(HL1)2(H2O)2] (1), [Cu(HL1)2(H2O)2] (2), [Zn(HL1)2] (3), [Ni(HL2)2(H2O)2] (4), [Ni(HL2)2(HL3)2] (5), [Cu(HL2)2]·2H2O (6), [Zn(HL2)2] (7), [Zn2(HL2)2(L2)] (8) [H2L1 = 5-phenyl-1H-pyrazole-3-carboxylic acid; H2L2 = 3-phenyl-1H-pyrazole-4-carboxylic acid; HL3 = 3-phenyl-1H-pyrazole] were prepared by hydro/solvothermal reactions and structurally characterized. Complexes 1 and 2 have monomeric structures; 3 and 4 exhibit 1-D zig-zag chains; 5 and 6 possess 2D layer structures consisting of rhomboid grids; 7 features a 2-fold interpenetrated 3-D diamondoid framework; while complex 8 holds a 3-D NaCl-like framework. Hydrogen bonding and aromatic π–π stacking interactions link the eight complexes into 2-D (1–3) or 3-D (4–8) supramolecular networks, of which 5, 6 and 8 contain single, single and double-stranded helical chains, respectively. The thermal stabilities of complexes 1–8 and photophysical properties of complexes 3 and 7 were investigated.

Structural diversity and properties of M(II) phenyl substituted pyrazole carboxylate complexes with 0D-, 1D-, 2D- and 3D frameworks

In the title compound, [Cd(C6H7N2O5)2], the Cd atom lies on an inversion center and has a slightly distorted octa­hedral geometry. The equatorial plane contains two bidentate 5-carb­oxy-2-methyl-1H-imidazole-4-carboxyl­ate monoanionic ligands. Two coordinated water mol­ecules occupy the axial sites. Inter­molecular N—H⋯O hydrogen bonds link the mol­ecules into chains, which are further connected by inter­molecular O—H⋯O hydrogen bonds, resulting in a three-dimensional supra­molecular framework.

Diaqua­bis(5-carb­oxy-2-methyl-1H-imid­azole-4-carboxyl­ato-κ2N3,O4)cadmium(II)

Effects of anthocyanins from purple sweet potato (APSP) against the fungal growth of Geotrichum candidum and Candida albicans were assessed. Response surface methodology was applied for optimization of proportions of sodium benzoate, potassium sorbate, and APSP. Optimum concentrations against G. candidum were 0.300 mg/mL of sodium benzoate, 0.290mg/mL of potassium sorbate, and 13.9mg/mL of APSP. Optimum concentrations against C. albicans were 0.380 mg/mL of sodium benzoate, 0.240 mg/mL of potassium sorbate, and 3.56 mg/mL of APSP. APSP exhibited enhanced antifungal properties in the presence of food preservatives.

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Antifungal activities of anthocyanins from purple sweet potato in the presence of food preservatives.

Syntheses, crystal structures and antibacterial activities of six cobalt(II) pyrazole carboxylate complexes with helical character

Rational assembly of Pb(II)/Cd(II)/Mn(II) coordination polymers based on flexible V-shaped dicarboxylate ligand: Syntheses, helical structures and properties

Hui-Liang Wen

Papers

Structural diversity and properties of M(II) phenyl substituted pyrazole carboxylate complexes with 0D-, 1D-, 2D- and 3D frameworks

Diaquabis(5-carboxy-2-methyl-1H-imidazole-4-carboxylato-κ2N3,O4)cadmium(II)

Antifungal activities of anthocyanins from purple sweet potato in the presence of food preservatives.

Syntheses, crystal structures and antibacterial activities of six cobalt(II) pyrazole carboxylate complexes with helical character

Rational assembly of Pb(II)/Cd(II)/Mn(II) coordination polymers based on flexible V-shaped dicarboxylate ligand: Syntheses, helical structures and properties

Hui-Liang Wen

Papers

Structural diversity and properties of M(II) phenyl substituted pyrazole carboxylate complexes with 0D-, 1D-, 2D- and 3D frameworks

Diaqua­bis(5-carb­oxy-2-methyl-1H-imid­azole-4-carboxyl­ato-κ2N3,O4)cadmium(II)

Antifungal activities of anthocyanins from purple sweet potato in the presence of food preservatives.

Syntheses, crystal structures and antibacterial activities of six cobalt(II) pyrazole carboxylate complexes with helical character

Rational assembly of Pb(II)/Cd(II)/Mn(II) coordination polymers based on flexible V-shaped dicarboxylate ligand: Syntheses, helical structures and properties

Diaquabis(5-carboxy-2-methyl-1H-imidazole-4-carboxylato-κ2N3,O4)cadmium(II)