Methane sorption and structural characterization of the sorption sites in Zn2(bdc)2(dabco) by single crystal X-ray crystallography.

Sorption isotherms of methane in Zn(2)(bdc)(2)(dabco) are measured up to a pressure of 35 bar in the temperature range between 198-296 K. The methane sorption measurements at 296 K showed an uptake of 137 cm(3) cm(-3) at 35 bar. The enthalpy of methane adsorption for Zn(2)(bdc)(2)(dabco) estimated by the virial equation is 13.6 kJ mol(-1) at zero coverage. X-ray structure analysis of methane-adsorbed Zn(2)(bdc)(2)(dabco) by synchrotron radiation at 90 K revealed that methane molecules occupy three independent sorption sites (A, B, and C) with a stoichiometry of Zn(2)(bdc)(2)(dabco) x 6.69 CH(4), which is consistent with the results of the gas sorption measurements at 198 K. In a cavity, eight symmetry-related methane sorption sites A are located near the {Zn(2)(CO(2))(4)} paddle-wheel units, while four symmetry-related methane sorption sites B are near the center of the small windows along the a and b axes. Both A and B sites are half-occupied. Methane molecules occupying sites A are not only in van der Waals contact with the paddle-wheel units, but also interact with the phenyl rings of bdc ligands through partial pi-HC interactions. Methane molecules in B sites interact with the side of the phenyl rings through van der Waals interaction. The site C, located at the center of the cavity, is a secondary sorption site; methane molecules occupying sites C are in van der Waals contact with those in sites A and B.

A dodecanuclear metallamacrocycle having a multidentate bridging ligand in two different binding modes.

The reaction of Mn(OAc)2 x 4H2O with 2,6-dimethoxybenzoylsalicylhydrazide (H3dmbshz) leads to a dodecanuclear manganese metallamacrocycle [Mn12(dmbshz)12(EtOH)6], 1. The successive manganese centers are connected by the hydrazide N-N groups of the ligands in an alternating pentadentate binding mode, hexadentate binding mode. The alternation results in two alternating chelation modes around the metal centers, a tridentate-tridentate chelation mode and a bidentate-tridentate chelation mode. The metal ions in 1 are in a (A(A)Delta(B)C(A)Lambda(B))(A(A)Delta(B)C(A)Lambda(B)) chiral sequence, the alternation of the chiralities expanding the cyclic ring system to a 36-membered dodecanuclear manganese metallamacrocyclic ring system with S6 point group symmetry.

Novel 48-membered hexadecanuclear and 60-membered icosanuclear manganese metallamacrocycles.

Either an S 8 symmetrical 48-membered hexadecanuclear or an S 10 symmetrical 60-membered icosanuclear manganese metallamacrocycle was self-assembled using a manganese ion and a ditopic pentadentate ligand. This was either N-4-phenylbenzoylsalicylhydrazide (H 3pbshz) containing a rigid rod-shaped, bulky biphenyl residue as a terminal N-acyl group or N-3,3-diphenylpropionylsalicylhydrazide (H 3dppshz) containing a flexible beta-branched N-acyl group, but with two sterically bulky phenyl residues at the Cbeta position. The backbone of these metal-organic assemblies is a repeating unit consisting of a -[Mn-N-N-] link that extends to complete either the 48-membered cyclic structure involving 16 manganese(III) centers and 16 ditopic linker ligands or the 60-membered cyclic structure involving 20 manganese(III) centers and 20 ditopic linker ligands (depending on the ligand used). Even though the nuclearity of the metallamacrocycles was different, the successive manganese centers were in the same chiral sequence, ...(LambdaLambdaDeltaDelta)(LambdaLambdaDeltaDelta)....

Steric control of the nuclearity of metallamacrocycles: formation of a hexanuclear gallium metalladiazamacrocycle and a hexadecanuclear manganese metalladiazamacrocycle.

An S6-symmetric hexanuclear gallium metalladiazamacrocycle, [Ga(III)(6)L2(6)S6] with a -(lamda delta)(lamda delta)-chiral sequence and an S-symmetric hexadecanuclear manganese metalladiazamacrocycle, [Mn(III)(16)L2(16)S16] with a -(lamda lamda delta delta)(lamda lamda delta delta)-chiral sequence were prepared using the same N2-trans-cinnamoyl-2-hydroxy-3-naphthoylhydrazide (H3L2) as a bridging pentadentate ligand between the metal centers for the formation of a macrocyclic system.

Crystal structure of Escherichia coli MazG, the regulator of nutritional stress response.

MazG is a nucleoside triphosphate pyrophosphohydrolase that hydrolyzes all canonical nucleoside triphosphates. The mazG gene located downstream from the chromosomal mazEF "addiction module," that mediated programmed cell death in Escherichia coli. MazG activity is inhibited by the MazEF complex both in vivo and in vitro. Enzymatic activity of MazG in vivo affects the cellular level of guanosine 3',5'-bispyrophosphate (ppGpp), synthesized by RelA under amino acid starvation. The reduction of ppGpp, caused by MazG, may extend the period of cell survival under nutritional stress. Here we describe the first crystal structure of active MazG from E. coli, which is composed of two similarly folded globular domains in tandem. Among the two putative catalytic domains, only the C-terminal domain has well ordered active sites and exhibits an NTPase activity. The MazG-ATP complex structure and subsequent mutagenesis studies explain the peculiar active site environment accommodating all eight canonical NTPs as substrates. In vivo nutrient starvation experiments show that the C terminus NTPase activity is responsible for the regulation of bacterial cell survival under nutritional stress.

Preparation and X-ray structures of 3-[Bis(trifluoroacetoxy)iodo]benzoic acid and 3-[hydroxy(tosyloxy)iodo]benzoic acid: new recyclable hypervalent iodine reagents.

Preparation, structural characterization, and reactivity of 3-[bis(trifluoroacetoxy)iodo]benzoic acid and 3-[hydroxy(tosyloxy)iodo]benzoic acid, new recyclable iodine(III) reagents derived from 3-iodosylbenzoic acid, are described. The reduced form of these reagents, 3-iodobenzoic acid, can be easily recovered from the reaction mixtures using ion-exchange resin or basic aqueous workup followed by acidification with HCl.

Porous metal-organic frameworks based on metal-organic polyhedra with nanosized cavities as supramolecular building blocks: two-fold interpenetrating primitive cubic networks of [Cu6L8]12+ nanocages.

Discrete metal-organic polyhedra (MOP) with nanosized cavities and/or clusters of MOP could be prepared when C3-symmetric facial ligands and a potential hexatopic Cu(II) ion are combined in the presence of perchlorate as a weak linker, while similar reaction conditions in the presence of a nitrate linker led to extended metal-organic frameworks made of MOP as supramolecular building blocks.

Expression, purification, crystallization and initial crystallographic characterization of the p-hydroxybenzoate hydroxylase from Corynebacterium glutamicum.

p-Hydroxybenzoate hydroxylase (PHBH) is an FAD-dependent monooxygenase that catalyzes the hydroxylation of p-hydroxybenzoate (pOHB) to 3,4-dihydroxybenzoate in an NADPH-dependent reaction and plays an important role in the biodegradation of aromatic compounds. PHBH from Corynebacterium glutamicum was crystallized using the hanging-drop vapour-diffusion method in the presence of NaH(2)PO(4) and K(2)HPO(4) as precipitants. X-ray diffraction data were collected to a maximum resolution of 2.5 A on a synchrotron beamline. The crystal belongs to the hexagonal space group P6(3)22, with unit-cell parameters a = b = 94.72, c = 359.68 A, gamma = 120 degrees . The asymmetric unit contains two molecules, corresponding to a packing density of 2.65 A(3) Da(-1). The structure was solved by molecular replacement. Structure refinement is in progress.

Two octanuclear gallium metallamacrocycles of topologically different connectivities.

Two topologically different metallamacrocycles--S8 symmetric octanuclear gallium(III) metalladiazamacrocycle and pseudo-D4 symmetric octanuclear gallium(III) metalladiazamacrocycle--could be prepared using two similar heteroditopic bridging ligands having asymmetrical tridentate-bidentate binding residues.

Microporous magnesium and manganese formates for acetylene storage and separation.

Acetylene sorption of microporous metal formates M(HCOO)2 (M = Mg and Mn) was investigated. Measurements of acetylene sorption at 196, 275, and 298 K showed a Type I isotherm with quick saturation at low pressures, and 50-75 cm3 g(-1) uptake at 1.0 atm. The single-crystal X-ray structure analysis of the acetylene-adsorbed metal formates revealed that acetylene molecules occupy two independent positions in the zigzag channels of the frameworks with a stoichiometry of M(HCOO)2 x 1/3C2H2, which is consistent with the gas sorption experiments. No specific interaction except van der Waals interactions between the adsorbed acetylene molecules and the walls of the frameworks was found. Sorption properties of other gases, including CO2, CH4, N2, O2, and H2, were also investigated. When the temperature was increased to 298 K, the amount of adsorbed acetylene was still above 60 cm3 g(-1) for Mg(HCOO)2 and 50 cm3 g(-1) for Mn(HCOO)2, whereas the uptake of other gases decreased substantially. The microporous metal formates may thus be useful not only for the storage of acetylene but also its separation from other gases at room or slightly higher temperatures.

Preparation, crystal structure, and thermal stability of the cadmium sulfide nanoclusters Cd6S44+ and Cd2Na2S4+in the sodalite cavities of zeolite A (LTA).

The crystal structure and thermal stability of two cadmium sulfide nanoclusters prepared in zeolite A (LTA) have been studied by XPS, TGA, and single-crystal and powder XRD. The crystal structures of Cd2.4Na3.2(Cd6S4)0.4(Cd2Na2S)0.6(H2O)> or =5.8[Si12Al12O48]-LTA (a = 12.2919(7) A, crystal 1 (hydrated)) and /Cd4Na2(Cd2O)(Na2O)/[Si12Al12O48]-LTA (a = 12.2617(4) A, crystal 2 (dehydrated)) were determined by single-crystal methods in the cubic space group Pm3m at 294(1) K. Crystal 1 was prepared by ion exchange of Na12-LTA in an aqueous stream 0.05 M in Cd2+, followed by washing in a stream of water, followed by reaction in an aqueous stream 0.05 M in Na2S. Crystal 2 was made by dehydrating crystal 1 at 623 K and 1 x 10(-6) Torr for 3 days. In crystal 1, Cd6S4(4+) nanoclusters were found in and extending out of about 40% of the sodalite cavities. Central to each Cd6S4(4+) cluster is a Cd4S4 unit (interpenetrating Cd2+ and S2- tetrahedra with near Td symmetry, Cd-S = 2.997(24) A, Cd-S-Cd = 113.8(12) degrees, and S-Cd-S = 58.1(24) degrees). Each of the two remaining Cd2+ ions bonds radially through a 6-ring of the zeolite framework to a sulfide ion of this Cd4S4 unit (Cd-S = 2.90(8) A). In each of the remaining 60% of the sodalite cavities of crystal 1, a planar Cd2Na2S4+ cluster was found (Cd-S/Na-S = 2.35(5)/2.56(14) A and Cd-S-Cd/Na-S-Na = 122(5)/92(7) degrees). Cd6S4(4+) and Cd2Na2S4+ are stable within the zeolite up to about 700 K in air. Upon vacuum dehydration at 623 K, all sulfur was lost (crystal 2). Instead as anions, only two oxide ions remain per sodalite unit. One bridges between two Cd2+ ions (Cd2O2+, Cd-O = 2.28(3) A) and the other between two Na+ ions (Na2O, Na-O = 2.21(10) A).

Vapor phase inclusion of ferrocene and its derivative in a microporous metal-organic porous material and its structural characterization by single crystal X-ray diffraction.

The inclusion of ferrocene and its derivative in metal-organic porous material MOF-5 is achieved by vapor diffusion; single-crystal X-ray diffraction studies using synchrotron radiation of ferrocene-loaded MOF-5 reveal well-ordered guest molecules packed into the pores.

Steric control of a bridging ligand for high-nuclearity metallamacrocycle formation: a highly puckered 60-membered icosanuclear metalladiazamacrocycle.

A novel S4-symmetric icosanuclear manganese metalladiazamacrocycle was synthesized using a pentadentate ligand, N-3-phenyl-trans-2-propenoylsalicylhydrazide (H3L), that has a rigid and bulky terminal N-acyl group. A 20 cyclic repeat of an--(Mn-N-N)--linkage resulted in a highly puckered diaza-bridged 60-membered icosanuclear metallamacrocycle. The steric interaction between the ligands in the cyclic system leads to five consecutive Mn(III) centers in a chemically different--(Mn(A)Mn(B)Mn(C)Mn(D)Mn(E))--environment, with the chiralities of the metal centers being in a rather complicated--(LambdaLambdaDeltaLambdaLambda)(DeltaDeltaLambdaDeltaDelta)--sequence.

Structural and functional analysis of PucM, a hydrolase in the ureide pathway and a member of the transthyretin-related protein family.

The ureide pathway, which produces ureides from uric acid, is an essential purine catabolic process for storing and transporting the nitrogen fixed in leguminous plants and some bacteria. PucM from Bacillus subtilis was recently characterized and found to catalyze the second reaction of the pathway, hydrolyzing 5-hydroxyisourate (HIU), a product of uricase in the first step. PucM has 121 amino acid residues and shows high sequence similarity to the functionally unrelated protein transthyretin (TTR), a thyroid hormone-binding protein. Therefore, PucM belongs to the TTR-related proteins (TRP) family. The crystal structures of PucM at 2.0 A and its complexes with the substrate analogs 8-azaxanthine and 5,6-diaminouracil reveal that even with their overall structure similarity, homotetrameric PucM and TTR are completely different, both in their electrostatic potential and in the size of the active sites located at the dimeric interface. Nevertheless, the absolutely conserved residues across the TRP family, including His-14, Arg-49, His-105, and the C-terminal Tyr-118-Arg-119-Gly-120-Ser-121, indeed form the active site of PucM. Based on the results of site-directed mutagenesis of these residues, we propose a possible mechanism for HIU hydrolysis. The PucM structure determined for the TRP family leads to the conclusion that diverse members of the TRP family would function similarly to PucM as HIU hydrolase.

Face-driven corner-linked octahedral nanocages: M6L8 cages formed by C3-symmetric triangular facial ligands linked via C4-symmetric square tetratopic Pd(II) ions at truncated octahedron corners.

The face-driven corner-linked truncated octahedral nanocages, [Pd6L8]12+ (1, L1 = N,N',N' '-tris(3-pyridinyl)-1,3,5-benzenetricarboxamide; 2, L2 = N,N',N' '-tris(4-pyridinylmethyl)-1,3,5-benzenetricarboxamide), were prepared with eight C3-symmetric tridentate ligands and six square planar tetratopic palladium(II) ions. The combination of the nitrogen donor atom at a approximately 120 degrees kink position of the carboxamido pyridinyl group and the tilted pyridyl versus the facial plane of the ligands can provide the needed curvature for the formation of octahedral cages. The nitrogen atoms can coordinate to the square planar palladium(II) ions to form kinks with approximately 120 degrees angles at the C4-symmetric square planar corners of the truncated octahedron. Depending on the conformation of the ligand, L1, two different truncated octahedral cages of around 2.4 nm in diameters were formed. The major form of 1 with syn-conformational ligands has a cavity volume of approximately 1600 A3. The cage has 12 ports (3.4 x 3.5 A2) at all edges of the octahedron. The minor form of cage 1 with anti-conformational ligands has a slightly increased cavity volume ( approximately 1900 A3) and port size (3.3 x 8.0 A2). The insertion of a methylene group in L2 has not only increased the cavity volume of 2 to approximately 2200 A3 but also enlarged the port size to 4.1 x 8.0 A2. However, an atomic force microscopy (AFM) study of cage 2 showed that the cages had a height of 1.8 +/- 0.1 nm. This value is about 30% smaller than the calculated size of 2.6 nm from the crystal structure. This tip-induced decrease in height in cage 2 suggests the nonrigidity of cage 2.

The inverted cucurbit[n]uril family.

We report the isolation, characterization, and recognition behavior of iCB[6] and iCB[7], which are diastereomers of CB[6] and CB[7], respectively, containing a single inverted glycoluril unit. Product resubmission experiments establish that these inverted CB[n] are intermediates in the mechanism of CB[n] formation. As a consequence of the inverted glycoluril ring, these inverted cucurbiturils possess a permanent dipole moment, are slightly smaller than their diastereomers, show distinctive selectivity in their recognition behavior, and report directly on the contents of their hydrophobic cavity.

Crystallization and preliminary X-ray crystallographic analysis of a yedU gene product from Escherichia coli.

A yedU gene product with a molecular mass of 31 kDa is a hypothetical protein with no known function. The protein was purified and crystallized at 296 K. X-ray diffraction data have been collected to 2.3 A using synchrotron radiation. The crystals belong to the primitive orthorhombic system, with unit-cell parameters a = 50.56, b = 63.45, c = 168.02 A. The asymmetric unit contains two monomers of the protein, with a corresponding V(M) of 2.25 A(3) Da(-1) and a solvent content of 44.84%.