Cloning,Expression, and Biochemical Characterization of a Novel Acidic GH16 β-Agarase,AgaJ11, from <Emphasis Type="Italic">Gayadomonas joobiniege</Emphasis> G7

A novel β-agarase AgaJ11 belonging to the glycoside hydrolase (GH) 16 family was identified from an agar-degrading bacterium Gayadomonas joobiniege G7. AgaJ11 was composed of 317 amino acids (35 kDa), including a 26-amino acid signal peptide, and had the highest similarity (44 % identity) to a putative β-agarase from an agarolytic marine bacterium Agarivorans albus MKT 106. The agarase activity of purified AgaJ11 was confirmed by zymogram analysis. The optimum pH and temperature for AgaJ11 activity were determined to be 4.5 and 40 °C, respectively. Notably, AgaJ11 is an acidic β-agarase that was active only at a narrow pH range from 4 to 5, and less than 30 % of its enzymatic activity was retained at other pH conditions. The K _m and V _max of AgaJ11 for agarose were 21.42 mg/ml and 25 U/mg, respectively. AgaJ11 did not require metal ions for its activity, but severe inhibition by several metal ions was observed. Thin layer chromatography and agarose-liquefying analyses revealed that AgaJ11 is an endo-type β-agarase that hydrolyzes agarose into neoagarohexaose, neoagarotetraose, and neoagarobiose. Therefore, this study shows that AgaJ11 from G. joobiniege G7 is a novel GH16 β-agarase with an acidic enzymatic feature that may be useful for industrial applications.     

5-Pyridine 4-yl-3H-(1,3,4) Oxadiazole-2 Thione Hydrochloride Monohydrate, (I), and 4 [5-Ethylsulfanyl)-(1,3,4) Thiadiazole-2-yl]-Pyridinium Perchlorate, (II)

Abstract  

The title compounds C₇H₈ClN₃O₂S, (I), and C₉H₁₀ClN₃O₄S_2, (II), both crystallize in monoclinic space group P2₁ /c with unit cell parameters (I) a = 7.9402(7), b = 10.6312(9), c = 11.7626(10), ?, β = 99.271(5)°, Z = 4 and (II) a = 5.1439(2), b = 9.0636(4), c = 27.1814 (7), ?, β = 95.116(2)°, Z = 4. In (I) the molecule consists of a 5-pyridine-4-yl group bonded to the carbon atom at the 5 position of (1, 3, 4) oxadiazole-2 thione hydrochloride monohydrate. The angle between the mean planes of the oxadiazole and pyridine rings is 9.6(6)°. Crystal packing in (I) is stabilized by strong N–H···O hydrogen bonds in concert with a solvent water molecule and weak O–H···Cl, O–H···S, N–H···Cl intermolecular interactions. The crystal structure of compound (II) consists of 4 [5-ethylsulfanyl)-(1, 3, 4) thiadiazole-2-yl]-pyridinium perchlorate, (C₉H₁₀N₃S₂)⁺(ClO₄)⁻, cation–anion pairs, containing strong intermolecular N–H···O hydrogen bonds and weak C–H···O and N–H···O intermolecular interactions operating between the ionic species that form a cooperative hydrogen-bonded, infinite chain O–H···O–H···O–H network which generates a sheet motif structure in the unit cell. It is also supported by weak intermolecular Cg···Cg π–π and Cl–O···Cg π-ring interactions which gives additional support to molecular packing stability in the unit cell. Geometry optimized MOPAC AM1 computational calculations on each compound provides support to the structural features in their respective crystal structures.     

Stereoselective Synthesis and X-Ray Structure Determination of Labeled [1, 2, 3-<Superscript>13</Superscript>C<Subscript>3</Subscript>]-1-(Phenylsulfinyl)-3-Benzyloxyacetone

[1,2,3-¹³C₃]-1-(Phenylsulfinyl)-3-benzyloxyacetone, C₁₆H₁₆O₃S, (3) has been synthesized and its crystal structure has been determined by a single-crystal X-ray diffraction analysis. The X-ray diffraction study revealed that compound 3 crystallizes in the monoclinic crystal system in the acentric space group Pc, with cell constants at T = 100 K: a = 16.073(5), b = 5.5079(16), c = 7.949(2) Å, β = 100.221(4)^°, V = 692.6(3) ų, Z = 2, d _calc = 1.383 g/cm³. Compound 3 contains the chiral tetravalent three-coordinated sulfur atom, which has a distorted tetrahedral configuration with a lone electron pair occupying one of the tetrahedron vertices. In the crystal, the molecules are packed in stacks along the b axis; the stacks consist of the molecules of the same chirality. Furthermore, the stacks of the molecules of the opposite chirality alternate along the c axis. The molecules in neighboring stacks are arranged by head-to-tail orientations. There are no short intermolecular contacts in the crystal of 3.     

Synthesis and Crystal Structure of 2,13-Bis(acetamido)-3,14-dimethyl-2,6,13,17-tetraazatricyclo[14,4,0<Superscript>1.18</Superscript>,0<Superscript>7.12</Superscript>]docosane Tetrachlorocobalt(II)dihydrate

Abstract The novel ionic compound [H₂bdtd][CoCl₄] · 2H₂O (1) was prepared by the reaction between CoCl₂ and 2,13-bis(acetamido)-3,14-dimethyl-2,6,13,17-tetraazatricyclo[14,4,0^1.18,0^7.12]docosane (bdtd) in adjusted to pH 3.0 by 1.0 M HCl and structurally characterized. The crystals are monoclinic C2/c with a = 18.7777(9), b = 9.7356(4), c = 20.0884(9) ?, β = 109.6340(10)°, V = 3458.9(3) ?³, Z = 4. The dication H₂bdtd occupies a special position about an inversion center. The cobalt(II) atom in the anion is in a distorted tetrahedral environment with four chloride ligands. The crystal structure is stabilized by a variety of hydrogen-bonding contacts involving the dication, chloride anions and solvent water molecules. Cyclic voltammetry of [CoCl₄]²⁻ anion in 1 undergoes irreversible one-electron reduction to the Co^II/Co^I. Graphical abstract The crystal structure of the ionic compound [H₂bdtd][CoCl₄] · 2H₂O (1) consists of [H₂bdtd]²⁺ cation, [CoCl₄]²⁻ anion and water molecules joined together by ionic interaction and hydrogen bonds. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Synthesis and Crystal Structure of [Na(H<Subscript>2</Subscript>O)<Subscript>1.5</Subscript>][Na(H<Subscript>2</Subscript>O)<Subscript>3.5</Subscript>] X<Subscript>2</Subscript>·2H<Subscript>2</Subscript>O (X = 4′-Methoxy-7-Hydroxyisoflavone-3′-Sulfonate)

Abstract  

Water-soluble derivative of formononetin, [Na(H₂O)_1.5][Na(H₂O)_3.5] X₂·2H₂O(X = 4′-methoxy-7-hydroxyisoflavone-3′-sulfonate) was synthesized by sulfonation reaction. It was characterized by IR, ¹H NMR and single-crystal X-ray diffraction analysis. Single-crystal X-ray diffraction analysis showed that the title compound crystallized in a triclinic space group P-1 with cell parameters a = 6.9642(15) ?, b = 13.343(3) ?, c = 20.634(5) ?, α = 107.115(3)˚, β = 93.121(4)˚, γ = 91.911(3)˚, V = 1827.3(7) ?⁻³, D _c  = 1.575 Mg m ⁻³, Z = 2. There are two conformers of 4′-methoxy-7-hydroxyisoflavone-3′-sulfonate anions, two kinds of sodium cations, five coordinated water molecules and two lattice water molecules in the crystal structure. The sodium atoms coordinated with the oxygen atoms from water molecules, hydroxyl groups and sulfo-groups to form a Na–O coordinated network. Aromatic π···π stacking interactions and hydrogen bonding existed in the crystal structure of title compound, which together with coordinated interactions and electrostatic interactions between sodium cations and anions sulfonates C₁₆H₁₀O₄SO₃ ⁻ lead to the moieties into a three-dimensional network.     

Crystal Structure,Thermal Analysis and IR Spectroscopic Investigation of Bis Benzyl Ammonium Monohydrogentetraoxoarsenate(V) Monohydrate

Abstract  

The salt bis benzyl ammonium monohydrogentetraoxoarsenate(V) monohydrate [C₆H₅CH₂NH₃ ⁺]₂HAsO₄ ²⁻·H₂O, M = 373.92, Triclinic, P−1. a = 6.514(1), b = 8.910(2), c = 15.061(3) ?, α = 99.26(2), β = 93.93(1), γ = 97.64(1)°, V = 851.5(3), Z = 2, D _x  = 1.460, λ (MoKα) = 0.71073 ?, μ = 0.99 mm⁻¹, F(000) = 126, T = 20(2)  °C, final R = 0.673 for 5488 unique reflections. Planes of HAsO₄ ²⁻ alternate with planes of C₆H₅CH₂NH₃ ⁺ groups. The structure consists of infinite parallel two-dimensional planes built of mutually connected ions and water molecules by strong O–H···O and N–H···O hydrogen bonding. There are no contacts other than van der Waals interactions between the layers. Differential scanning calorimetry study on bis benzyl ammonium monohydrogentetraoxoarsenate(V) monohydrate was carried out. The infrared of polycrystalline samples of this compound have been recorded at room temperature.     

Synthesis and Crystal Structure of 1,3-Bis[2-(pyrrol-2-carbonyloxy)ethoxy]Benzene

Abstract  

A new compound, 1,3-bis[2-(pyrrol-2-carbonyloxy)ethoxy]benzene (1), was synthesized and characterized by X-ray diffraction. The crystal is monoclinic, space group P2₁/c with a = 6.3571(7), b = 11.0416(11), c = 28.156(3) ?, b = 92.821(2), V = 1974.0(4) ?³, Z = 4, Dc = 1.293 g/cm³, F(000) = 808, μ = 0.097 mm⁻¹. The final R = 0.0395 and wR = 0.0927 for 3478 observed reflections with I > 2 σ(I), and R = 0.0660 and wR = 0.1058 for all reflections. The title compound assembles into 2-D structure through a catemer type N–H⋯O hydrogen bonding motif and further forms 3-D structure through C–H···O hydrogen bonds.     

Crystallographic and Computational Studies of Non-Covalent Interactions of Molecular Clips with a Series of Small Solvent Molecules

Molecular clips hold the potential of self-association and the ability to form host–guest complexes. Here we describe the synthesis of a 1,2-dimethoxyphenyl terminated glycoluril molecular clip (2) that binds with smaller solvent molecules by π?H–C and C=O?H–O non-covalent interactions. We obtained single crystals of 2 and 2 + CH₂Cl₂, CH₃OH, CH₃CN, and DMF solvents complexed within the clip. These solvents always form two π?H–C interactions between the aromatic rings in the clip, and CH₃OH formed an additional C=O?H–O hydrogen bond with the glycoluril carbonyl group. Based on single crystal data we found that π?H–C interactions of 2 + CH₂Cl₂ are stronger than 2 + CH₃CN and 2?+?DMF, due to the presence of stronger electron withdrawing groups in CH₂Cl₂, which lead to a decrease in dihedral angle of two glycoluril aromatic planes. We also investigated the non-covalent interaction energies of these solvent molecules with 2 using computational methods.

Graphical Abstract

Several solvent adducts of a glycoluril derivative have been isolated and characterized by single crystal X-ray diffraction, revealing two common pi?H–C non-covalent bonds within the molecular clip.

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