Hydrothermal synthesis and structure characterization of the first organically templated metal iodates

The first organically templated molybdenum iodates (C₅H₆N)₂Mo₂O₅(IO₃)₄(H₂O)₂ (1), (C₁₀H₈N₂)[MoO₂(IO₃)₃] · H₃O (2), and uranium iodate (C₅H₅N)₂[(UO₂)(IO₃)₃](IO₃) (3), have been successfully synthesized under mild hydrothermal conditions. Compound 1 is simple zero-dimensional units consisting of [(Mo₂O₅(IO₃)₄)]²⁻ anions, which can be described as a tetranuclear unit hanged on either side by two [IO₃] groups. The [Mo₂O₅(IO₃)₄]²⁻ anions are in a close connection through the water molecules and protonated pyridine cations, via hydrogen bonds and intermolecular actions. Compound 2 is built up from [MoO₆] octahedra and [IO₃] pyramids to two-dimensional layers, in which 4,4′-bipy molecules and water cations are located, forming strong hydrogen bonds with the inorganic framework, leading to pseudo three-dimensional structure. Compound 3 is one-dimensional ribbons containing {[(UO₂)(IO₃)₃](IO₃)}²⁻ anions and charge neutrality is achieved by the protonated 4,4′-bipy cations, which reside between two ribbons, forming hydrogen bonds with the inorganic framework and resulting in pseudo two-dimensional structure. Crystal data are as follows: (C₅H₆N)₂Mo₂O₅(IO₃)₄(H₂O)₂ (1), orthorhombic, Pnma, a = 24.097(5) Å, b = 13.532(3) Å, c = 7.836(16) Å, Z = 4, V = 2555.2(9) Å³; (C₁₀H₈N₂)[MoO₂(IO₃)₃] · H₃O (2), monoclinic, C2/c, a = 24.176(5) Å, b = 10.751(2) Å, c = 7.5074(15) Å, β = 107.44(3)°, Z = 8, V = 1861.6(6) Å³; (C₅H₅N)₂[(UO₂)(IO₃)₃](IO₃) (3), monoclinic, P2₁/n, a = 14.430(3) Å, b = 7.3459(15) Å, c = 19.811(4) Å, β = 106.70(3)°, Z = 4, V = 2011.3(7) Å³.     

Hydrothermal syntheses and structures of vanadium oxyfluorides templated by organic and metal organic cations

The hydrothermal reactions of V₂O₅, HF and an organodiphosphonic acid, in the presence of appropriate templating organoammonium or metal-organic complex cations provided three new oxyfluorovanadate compounds. The V(IV) species [H₃N(CH₂)₂NH₂(CH₂)₂NH₂(CH₂)₂NH₃][V₃O₃F₂(H₂O){O₃PCH₂PO₃}₂]·2H₂O (1·2H₂O) exhibits a three-dimensional anionic framework constructed from {VO(O₃PCH₂PO₃)}_n²ⁿ⁻ chains and {VF₂O₄} octahedra. The molecular structure of [N(CH₂CH₂NH₃)₃]₂[NH₄][V₃O₂F₆(O₃PCH₂PO₃)₂]·2H₂O (2·2H₂O) is characterized by the presence of unique {V₃O₂F₆(O₃PCH₂PO₃)₂}⁷⁻ clusters. The bimetallic phase [{Cu(ophen)}VOF{HO₃P(CH₂)₅PO₃}] (3) is one-dimensional with {Cu₂V₂O₂F₂(HO₃PR)₂(O₃PR)₂} cluster building blocks.     

Solvothermal synthesis, crystal structure and luminescence of the first organic amine templated europium sulfate

The first organic amine templated europium sulfate [C₂N₂H₁₀]_1.5[Eu(SO₄)₃(H₂O)] · 2H₂O (1), has been synthesized under solvothermal conditions by using a mixture of n-butanol and water as the solvent. The colorless block crystals were characterized by IR, TGA and ICP. Crystal structure analysis shows that the corrugated layered framework of compound 1 is constructed from EuO₉ polyhedra and sulfate groups, while non-coordination water molecules and ethylenediamine molecules link the adjacent layers by hydrogen bonds. Compound 1 represents a strong luminescence upon the excitation.     

Hydrothermal synthesis and characterization of a zinc-substituted gallium phosphite, [H3N(CH2)2NH3]1/2 · [GaZn(HPO3)3(H2O)2]

An organically templated zinc-substituted gallium phosphite, [H₃N(CH₂)₂NH₃]_1/2 · [GaZn(HPO₃)₃(H₂O)₂] was synthesized under mild hydrothermal conditions in the presence of ethylenediamine (en) as structure-directing agent and characterized by single-crystal X-ray diffraction analysis. It crystallizes in the orthorhombic space group Pbcn with unit cell parameters: a = 18.6146(10) Å, b = 11.0454(6) Å, c = 10.9074(4) Å, V = 2242.62(19) Å³ and Z = 8. This compound has a three-dimensional framework built up from secondary building units (SBU) of Ga(III) (or Zn(II)) and HPO₃ pseudopyramid by sharing vertices. The structure displays a two-dimensional channel system running along the [0 0 1] and [0 1 0] direction with 5-, 8- and 10-membered rings. The diprotonated ethylenediamine template molecules are located in the channels. In this structure, some of the Ga(III) sites are occupied by Zn(II) atoms. The compound was also characterized by IR spectroscopy, inductively coupled plasma (ICP), X-ray photoelectron spectra (XPS), differential thermal and thermogravimetric analyses.     

Hydrothermal synthesis and crystal structure of a novel one-dimensional arsenic vanadate decorated with organonitrogen ligand: [H3V3O26(AsO4)4(phen)8(H2O)2] · 2H2O (phen=phenanthroline)

A novel organic-inorganic hybrid vanadium arsenate [H₃V₃O₂₆(AsO₄)₄(phen)₈(H₂O)₂] · 2H₂O 1 (phen=phenanthroline) was synthesized by the hydrothermal reaction of V₂O₅, VOSO₄, Na₂HAsO₄ · 7H₂O, phen and water. Its structure was determined by elemental analyses, XPS spectra, EPR spectrum, TG analysis, IR spectrum and single-crystal X-ray diffraction.     

The first vanadate oxide phase containing two types of modified metal centers: {Mn(2,2-bpy)}[{VO2(2,2-bpy)}(VO3)(V2O6)] (2,2-bpy=2,2-bipyridine)

An unprecedented hybrid vanadate, {Mn^II(2,2^′-bpy)}[{V^VO₂(2,2^′-bpy)}(V^VO₃)(V^V₂O₆)], has been hydrothermally synthesized from the reaction of V₂O₅, 2,2^′-bipyridine, and MnCl₂. It has been characterized by IR, XPS, TGA and single-crystal X-ray diffraction. The structure of the title compound is constructed from left-handed and right-handed V-O helical chains linked through modified binuclear {Mn(2,2^′-bpy)V^VO₄(2,2^′-bpy)} moieties into a double helical structure.     

Solid state coordination chemistry of molybdenum oxides with 1,2,3-triazole (Htrz): The crystal structures of [Cu(I)Cu(II)2(trz)2Mo4O13(OH)], [MoO3(Htrz)0.5] and [Cu(I)trz]

Hydrothermal chemistry was used to prepare the bimetallic organic-inorganic hybrid oxide [Cu(I)Cu(II)₂(trz)₂Mo₄O₁₃(OH)] · 6H₂O (1 · 6H₂O). The structure consists of chains linked through into a three-dimensional framework. The structures of the simple metal-triazole phases [MoO₃(Htrz)_0.5] (2) and [Cu(trz)] (3) are also reported. Compound 2 is two-dimensional, constructed from corner-sharing {MoO₅N} octahedra. Compound 3 consists of {Cu(trz)}_n chains linked through weak Cu?Cu contacts into a virtual layer.     

Synthesis and single crystal structures of first examples of tridentate ligands of (Te, N, S) type and their complexes with palladium(II), platinum(II) and ruthenium(II)

The First examples of (Te, N, S) type ligands, 2-CH₃SC₆H₄CHNCH₂CH₂TeC₆H₄-4-OCH₃ (L¹) and 2- CH₃SC₆H₄CHNHCH₂CH₂TeC₆H₄-4-OCH₃ (L²), and their metal complexes, [PdCl(L¹)]PF₆ · CHCl₃ · 0.5H₂O (4), [PtCl(L¹)]PF₆ (5), [PdCl(L²)]ClO₄.CHCl₃ (6), [PtCl(L²)]ClO₄ (7), and [Ru(p-cymene)(L²)](PF₆)₂ · CHCl₃ (8), have been synthesized and characterized. The single crystal structures of 4, 6 and 8 have revealed that both the ligands coordinate in them in a tridentate (Te, N, S) mode. The geometry around Pd in both the complexes has been found to be square planar, whereas for Ru in a half sandwich complex 8, it is found to be octahedral. Between two molecules of 4 there are intra and inter molecular weak Te?Cl [3.334(3) and 3.500(3) Å, respectively] interactions along with weak intermolecular Pd?Te [3.621(2) Å] interactions. The Pd-Te bond lengths are between 2.517(6) and 2.541(25) Å and the Ru-Te bond length is 2.630(6) Å. The crystal structure of [PdCl₂(4-MeO-C₆H₄- TeCH₂CH₂NH₂)] (9) is also determined. It is formed when KPF₆ is not added in the synthesis of 4 and Pd-complex of L¹ is recrystallized. Apart from Te?Cl secondary interactions, C-H?π interactions also exist in the crystal of 9.     

The first holocomplex structure of ribonucleotide reductase gives new insight into its mechanism of action

Ribonucleotide reductase is an indispensable enzyme for all cells, since it catalyses the biosynthesis of the precursors necessary for both building and repairing DNA. The ribonucleotide reductase class I enzymes, present in all mammals as well as in many prokaryotes and DNA viruses, are composed mostly of two homodimeric proteins, R1 and R2. The reaction involves long-range radical transfer between the two proteins. Here, we present the first crystal structure of a ribonucleotide reductase R1/R2 holocomplex. The biological relevance of this complex is based on the binding of the R2 C terminus in the hydrophobic cleft of R1, an interaction proven to be crucial for enzyme activity, and by the fact that all conserved amino acid residues in R2 are facing the R1 active sites. We suggest that the asymmetric R1/R2 complex observed in the 4A crystal structure of Salmonella typhimurium ribonucleotide reductase represents an intermediate stage in the reaction cycle, and at the moment of reaction the homodimers transiently form a tight symmetric complex.     

Catalytic center of an archaeal type 2 ribonuclease H as revealed by X-ray crystallographic and mutational analyses

The catalytic center of an archaeal Type 2 RNase H has been identified by a combination of X-ray crystallographic and mutational analyses. The crystal structure of the Type 2 RNase H from Thermococcus kodakaraensis KOD1 has revealed that the N-terminal major domain adopts the RNase H fold, despite the poor sequence similarity to the Type 1 RNase H. Mutational analyses showed that the catalytic reaction requires four acidic residues, which are well conserved in the Type 1 RNase H and the members of the polynucleotidyl transferase family. Thus, the Type 1 and Type 2 RNases H seem to share a common catalytic mechanism, except for the requirement of histidine as a general base in the former enzyme. Combined with the results from deletion mutant analyses, the structure suggests that the C-terminal domain of the Type 2 RNase H is involved in the interaction with the DNA/RNA hybrid.     

Reaction of carbon monoxide with tri-tert-butylgallium: The first example of CO insertion into a gallium-carbon bond

Reactions of ^tBu₃M (M = Al, Ga) with CO have been studied by density functional theory employing the B3PW91 functional. Calculations suggest that CO insertion into a M-C bond of ^tBu₃M is thermodynamically favorable at room temperature, whereas CO coordination to ^tBu₃M to form ^tBu₃M·CO is unfavorable due to an unfavorable entropy change. These results are in agreement with experimental observations. Reaction of carbon monoxide with ^tBu₃Ga at 50 °C and atmospheric pressure yields the dimeric tert-butylacyl complex [^tBu₂GaC(O)^tBu]₂ (1). Compound 1 has been characterized by X-ray crystallography and NMR and IR spectroscopy. Isotopic labeling with ¹³CO confirmed that the acyl carbon of 1 results from the CO starting material. CO insertion into a Ga-C bond does not occur for Me₃Ga or ⁿBu₃Ga under a range of reaction conditions.     

The use of polyoxometalates in charge transfer salts

Several Organo/mineral charge transfer salts based on the polyoxometalates anions with the Keggin and Lindquist structures have been prepared with organic radical cations derived from TTF (Tetrathiafulvaalene) by the electrocrystallization technique. Electron transfer from the organic units to the anionic part has been evidenced in the [(TTF)₆(HPM₁₂O₄₀)(Et₄N), M=Mo, W] salts leading to the first radical cation salt with delocalized paramagnetic centers on the polyoxmetalate. Additionally, a metallic state has been observed in (BEDT-TFF)₅VW₅O₁₉, 5H₂O (BEDT=Bisethyleneditithio) containing substituted Lindquist anion.TMTTF Tetramethyltetrathiafulvalene - TMTSF Tetramethyl-tetraselena Fulvalene - BEDT-TTF or ET Bis (Ethylenedithiotetrathiafulvalene) - TPTTF Tetraphenyltetrathiafulvalene - DMDPTTF Dimethyldiphenyl-TTF - Et⁴N=(C²H⁵)N Tetraethylammonium - MDT-TTF Methylenedithiotetrathiafulvalene - DMET-TTF Dimethyl Ethylene Dithio Tetrathiafulvalene - M(dmit)² Bis-[bis(dimercapto-dithiol-thione)metal(II)]     

The first crystal structure of hyperthermostable NAD-dependent glutamate dehydrogenase from Pyrobaculum islandicum

The extremely thermostable NAD-dependent glutamate dehydrogenase (NAD-GluDH) from Pyrobaculum islandicum, a member of the Crenarchaeota, was crystallized, and its 3D structure has been determined by X-ray diffraction methods. The homohexameric structure of Pb. islandicum glutamate dehydrogenase (Pis-GluDH) was solved and refined at a resolution of 2.9A with a crystallographic R-factor of 19.9% (Rfree 26.0%). The structure indicates that each subunit consists of two domains separated by a deep cleft containing an active site. The secondary structural elements and catalytically important residues of the enzyme were highly conserved among the NAD(P)-dependent GluDHs from other sources. A structural comparison of Pis-GluDH with other NAD(P)-dependent GluDHs suggests that a significant difference in the alpha8-loop-alpha9 region of this enzyme is associated with its coenzyme specificity. From the analysis of the 3D structure, hydrophobic interactions between intersubunits were found to be important features for the enzyme oligomerization. It has been reported that Pis-GluDH is highly thermostable, like the GluDH of the hyperthermophilic archaeum Pyrococcus furiosus, and the increase in the intersubunit ion pair networks is responsible for the extreme thermostability of the Pc. furiosus enzyme. However, the number of intersubunit ion pairs in the Pis-GluDH molecules is much smaller than those of the Pc. furiosus GluDH. The number of hydrophobic interactions at the intersubunit interfaces were increased and responsible for the extremely high thermostability. This indicates that the major molecular strategy for high thermostability of the GluDHs may be different for each hyperthermophile.     

The first structure of a bacterial class B Acid phosphatase reveals further structural heterogeneity among phosphatases of the haloacid dehalogenase fold

AphA is a periplasmic acid phosphatase of Escherichia coli belonging to class B bacterial phosphatases, which is part of the DDDD superfamily of phosphohydrolases. The crystal structure of AphA has been determined at 2.2A and its resolution extended to 1.7A on an AuCl(3) derivative. This represents the first crystal structure of a class B bacterial phosphatase. Despite the lack of sequence homology, the AphA structure reveals a haloacid dehalogenase-like fold. This finding suggests that this fold could be conserved among members of the DDDD superfamily of phosphohydrolases. The active enzyme is a homotetramer built by using an extended N-terminal arm intertwining the four monomers. The active site of the native enzyme, as prepared, hosts a magnesium ion, which can be replaced by other metal ions. The structure explains the non-specific behaviour of AphA towards substrates, while a structure-based alignment with other phosphatases provides clues about the catalytic mechanism.     

The first crystal structure of a Mimosoideae lectin reveals a novel quaternary arrangement of a widespread domain

The crystal structures of the apo and mannose-bound Parkia platycephala seed lectin represent the first structure of a Mimosoideae lectin and a novel circular arrangement of beta-prism domains, and highlight the adaptability of the beta-prism fold as a building block in the evolution of plant lectins. The P.platycephala lectin is a dimer both in solution and in the crystals. Mannose binding to each of the three homologous carbohydrate-recognition domains of the lectin occurs through different modes, and restrains the flexibility of surface-exposed loops and residues involved in carbohydrate recognition. The planar array of carbohydrate-binding sites on the rim of the toroid-shaped structure of the P.platycephala lectin dimer immediately suggests a mechanism to promote multivalent interactions leading to cross-linking of carbohydrate ligands as part of the host strategy against phytopredators and pathogens. The cyclic structure of the P.platycephala lectin points to the convergent evolution of a structural principle for the construction of lectins involved in host defense or in attacking other organisms.     

The structure of the C-C bond hydrolase MhpC provides insights into its catalytic mechanism

2-Hydroxy-6-ketonona-2,4-diene-1,9-dioic acid 5,6-hydrolase (MhpC) is a 62 kDa homodimeric enzyme of the phenylpropionate degradation pathway of Escherichia coli. The 2.1 A resolution X-ray structure of the native enzyme determined from orthorhombic crystals confirms that it is a member of the alpha/beta hydrolase fold family, comprising eight beta-strands interconnected by loops and helices. The 2.8 A resolution structure of the enzyme co-crystallised with the non-hydrolysable substrate analogue 2,6-diketo-nona-1,9-dioic acid (DKNDA) confirms the location of the active site in a buried channel including Ser110, His263 and Asp235, postulated contributors to a serine protease-like catalytic triad in homologous enzymes. It appears that the ligand binds in two separate orientations. In the first, the C6 keto group of the inhibitor forms a hemi-ketal adduct with the Ser110 side-chain, the C9 carboxylate group interacts, via the intermediacy of a water molecule, with Arg188 at one end of the active site, while the C1 carboxylate group of the inhibitor comes close to His114 at the other end. In the second orientation, the C1 carboxylate group binds at the Arg188 end of the active site and the C9 carboxylate group at the His114 end. These arrangements implicated His114 or His263 as plausible contributors to catalysis of the initial enol/keto tautomerisation of the substrate but lack of conservation of His114 amongst related enzymes and mutagenesis results suggest that His263 is the residue involved. Variability in the quality of the electron density for the inhibitor amongst the eight molecules of the crystal asymmetric unit appears to correlate with alternative positions for the side-chain of His114. This might arise from half-site occupation of the dimeric enzyme and reflect the apparent dissociation of approximately 50% of the keto intermediate from the enzyme during the catalytic cycle.     

非典型腺苷酸激酶AK6/hCINAP的结构和功能

腺苷酸激酶广泛存在于各种生物中,在维持细胞中核苷酸的正常含量以及能量代谢活动中发挥重要作用。腺苷酸激酶6 (AK6,又称人coilin相互作用核ATP酶蛋白hCINAP)是一种非典型的腺苷酸激酶,既具有腺苷酸激酶的活性,又具有ATP酶的活性。本课题组对AK6/hCINAP的结构、酶学特征和生物学功能开展了长期的研究,证明其在调控基因转录、核糖体质量、早期胚胎发育、细胞衰老、细胞代谢、细胞增殖和凋亡、DNA损伤反应、炎症反应、肿瘤发展等诸多生物学过程中均发挥关键作用。本文对AK6/hCINAP的结构特征、生物学功能及上游调控因子进行了总结,阐明该酶生物学作用和分子机制具有重要的生物学意义,有助于开发AK6/hCINAP选择性抑制剂并应用于临床治疗。     

The Characterization of Intracellular and Extracellular Biomineralization Induced by Synechocystis sp. PCC6803 Cultured under Low Mg/Ca Ratios Conditions

In order to simulate the precipitation process of microbial limestone at the offshore of the ancient ocean, different calcites induced by Synechocystis sp. PCC6803 in culture media with low Mg/Ca ratios (0.01 M Ca²⁺, Mg/Ca = 0, 0.2, 0.4, 0.6) were investigated, and the characteristics of intracellular and extracellular biomineralization were described. Carbonic anhydrase activity of Synechocystis sp. PCC6803 in different culture medium was further detected. The ultrathin slices of Synechocystis sp. PCC6803 cells were analyzed by transmission electron microscope (TEM) and selected area electron diffraction (SAED). Then the precipitates were analyzed by polarizing microscope, scanning electron microscope (SEM), X-ray diffraction (XRD) and energy dispersive spectrometer (EDS). The results showed that the biomineralization precipitates of Synechocystis sp. PCC6803 under low Mg/Ca ratios were mainly calcites with different morphologies. The CA accelerated the pivotal rate limiting step of the calcite precipitation. It was also found that the morphology, microstructure, particle size, preferred orientation, crystallinity and cell volume of calcites changed gradually with the increasing Mg²⁺ concentrations. What is more important, it was found that Synechocystis sp. PCC6803 had the ability of intracellular biomineralization without crystal structure. The intracellular biomineralization product could be divided into two types. This study can provide some useful information for further understanding the characteristics and mechanisms of biomineralization and even the diagenetic environment research of microbial limestone.     

The preparation and crystal structure of acetatobis(l-arginine)zinc(II) acetate trihydrate, the first reported X-ray structure of a zinc(II)-arginine complex

The synthesis and X-ray crystal structure of acetatobis(l-arginine)zinc(II) acetate trihydrate, [Zn(OAc)(l-Arg)₂]OAc·3H₂O is reported. In this structure, the first of a zinc(II)-arginine complex to be reported, the geometry around zinc(II) is distorted square-pyramidal containing two trans-N,O chelated l-Arg ligands in the basal plane and the acetato ligand in an axial position. The structure contains a second acetate which is salt-bridged to the δ and ω NH groups of the guanidinium side chain of an arginine ligand and also contains three hydrogen bonded water molecules.