A structural study on uranyl (VI) nitrate complexes with cyclic amides: N-n-butyl-2-pyrrolidone, N-cyclohexylmethyl-2-pyrrolidone, and 1,3-dimethyl-2-imidazolidone

Structural analyses of UO₂(NO₃)₂L₂ [L = N-n-butyl-2-pyrrolidone (NBP), N-cyclohexylmethyl-2-pyrrolidone (NCMeP), and 1,3-dimethyl-2-imidazolidone (DMI)] have been carried out using X-ray diffraction method. These uranyl complexes were found to have a hexagonal bipyramidal structure. The bond distances (Å) of UO and U-O(ligand), and bond angles (°) of U-O-C(carbonyl) are determined as follows: 1.774(2), 2.374(2), and 137.6(2) for UO₂(NO₃)₂(NBP)₂; 1.770(1), 2.383(2), and 135.3(1) for UO₂(NO₃)₂(NCMeP)₂; 1.771(2), 2.361(2), and 143.3(2) for UO₂(NO₃)₂(DMI)₂. In uranyl nitrate complexes with cyclic amides such as 2-pyrrolidone, urea, and caprolactam derivatives, a linear correlation was found to hold between U-O(ligand) bond distances and U-O-C(carbonyl) bond angles. Vibrational frequencies of UO₂(NO₃)₂L₂ have also been measured by IR and Raman spectrophotometers. Using relationships between vibrational frequencies of OUO bonds and donor numbers (DNs) of ligands, it was found that donicities of N-substituted-2-pyrrolidones (Me, Et, Bu, cyclohexyl, and cyclohexylmethyl) are in the range of 26-29, and the DN of 1,3-dimethyl-2-imidazolidone was estimated as 27.8.     

Macrocyclic dinuclear gold(I) and silver(I) NHCs complexes

The ligands bis-(imidazolium) hexafluorophosphate (Himy = -C₃N₂H₃-, imidazolium; R = 1-naphthylmethylene, 1a; 9-anthracenylmethylene, 1b) with an oxoether chain were easily prepared by the reaction of substituted imidazole with the diglycol diiodide, followed by exchange of anions with . 1a and 1b reacted with Ag₂O in DMSO or CH₃CN to yield [2 + 2] dinuclear Ag(I) NHCs macrocyclic complexes 2a and 2b, which showed much different conformation in solid corresponding to the R- substituent. Carbene transmetalation reactions of 2a-b with Au(SMe₂)Cl give dinuclear Au(I) analogs 3a and 3b. The new NHCs complexes were characterized by elemental analyses, ¹H NMR, ¹³C NMR and the structures of 2a-b and 3a were confirmed by X-ray diffraction determination.     

Oxalate, squarate and croconate complexes with bis(2-pyrimidylcarbonyl)amidatecopper(II): synthesis, crystal structures and magnetic properties

The preparation and magnetic properties of three copper(II) compounds of formulae [Cu₂(bpcam)₂(H₂O)₂(C₂O₄)] (1), [Cu₂(bpcam)₂(H₂O)₄(C₄O₄)] · 10 H₂O (2) and Cu₂(bpcam)₂(C₅O₅)(H₂O)₃ (3) [bpcam = bis(2-pyrimidyl)amidate, and are reported. The structures of two of them (1 and 2) have been solved by single crystal X-ray diffraction and consists of centrosymmetric discrete copper(II) dinuclear units bridged by bis-bidentate oxalate (1) and bis-monodentate squarate (2), with the bpcam group acting as a terminal tridentate ligand. Each copper atom in 1 exhibits a distorted elongated octahedral coordination geometry. Three bpcam nitrogen atoms and one oxalate oxygen define the basal plane while the other oxalate oxygen and a water molecule take up the axial positions. Each copper atom in 2 is in an elongated octahedral surrounding with three bpcam nitrogen atoms and one squarate oxygen in the equatorial plane and two water molecules in the axial positions. The intramolecular copper-copper separations are 5.677(1) (1) and 7.819(53) Å (2). Magnetic susceptibility measurements for 1-3 in the temperature range 1.9-290 K show the occurrence of weak ferromagnetic interactions through oxalato (J = +0.75 cm⁻¹) and squarato (J = +1.26 cm⁻¹), the Hamiltonian being defined by . These values are analyzed and discussed in the light of the available magneto-structural data for analogous systems. The quasi-Curie law observed in 3 (θ = −1.15 K) contrasts with the significant antiferromagnetic interaction through bis-chelating croconate in other structurally characterized croconate-bridged copper(II) complexes and rules out the presence of bridging croconate in this compound.     

Syntheses and structures of Ag(I) compounds containing btp ligands

Four new Ag(I) complexes with three different modes of structures were obtained by varying the counteranions , and their structures characterized by single-crystal X-ray diffraction analysis. Compounds 1, 2, and 3 crystalize in the C-centered monoclinic space group C2/m. Compound 4 crystalizes in the monoclinic space group P2₁/c. The crystal structures of these complexes show that the complexes 1, 2, and 3 form ligand-supported dinuclear rings, and the dinuclear units of 1 and 3 are further linked by anions to form one-dimensional polymer, while the complex 4 forms an one-dimensional zigzag chain. The structural differences between 1, 2, 3, and 4 show the influences of the counteranions on the structures of the complexes.     

Syntheses, structures and vibrational spectroscopy of some unusual silver(I) (pseudo-) halide/unidentate nitrogen base polymers

The meagre (structurally defined) array of 1:2 silver(I) (pseudo-)halide:unidentate nitrogen base adducts is augmented by the single-crystal X-ray structural characterization of the 1:2 silver(I) thiocyanate:piperidine (‘pip’) adduct. It is of the one-dimensional ‘castellated polymer’ type previously recorded for the chloride: ?Ag(pip)₂(μ-SCN)Ag(pip)₂? a single bridging atom (S) linking successive silver atoms. By contrast, in its copper(I) counterpart, also a one-dimensional polymer, the thiocyanate bridges as end-bound SN-ambidentate: ?CuSCNCuSCN? A study of the 1:1 silver(I) bromide:quinoline (‘quin’) adduct is recorded, as the 0.25 quin solvate, isomorphous with its previous reported ‘saddle polymer’ chloride counterpart.Recrystallization of 1:1 silver(I) iodide:tris(2,4,6-trimethoxyphenyl)phosphine (‘tmpp’) mixtures from py and quinoline (‘quin’)/acetonitrile solutions has yielded crystalline materials which have also been characterized by X-ray studies. In both cases the products are salts, the cation in each being the linearly coordinated silver(I) species [Ag(tmpp)₂]⁺, while the anions are, respectively, the discrete [Ag₅I₇(py)₂]²⁻ species, based on the already known but unsolvated [Cu₅I₇]²⁻ discrete, and the polymeric, arrays, and polymeric . The detailed stereochemistry of the [Ag(tmpp)₂]⁺ cation is a remarkably constant feature of all structures, as is its tendency to close-pack in sheets normal to their P-Ag-P axes.The far-IR spectra of the above species and of several related complexes have been recorded and assigned. The vibrational modes of the single stranded polymeric AgX chains in [XAg(pip)₂]_(∞|∞) (X = Cl, SCN) are discussed, and the assignments ν(AgX) = 155, 190 cm⁻¹ (X = Cl) and 208 cm⁻¹ (X = SCN) are made. The ν(AgX) and ν(AgN) modes in the cubane tetramers [XAg(pip)]₄ (X = Br, I) are assigned and discussed in relation to the assignments for the polymeric AgX:pip (1:2) complexes, and those for the polymeric [XAg(quin)]_(∞|∞) (X = Cl, Br) compounds. The far-IR spectra of [Ag(tmpp)₂]₂[Ag₅I₇(py)₂] and its corresponding 2-methylpyridine complex show a single strong band at about 420 cm⁻¹ which is assigned to the coordinated tmpp ligand in [Ag(tmpp)₂]⁺, and a partially resolved triplet at about 90, 110 and 140 cm⁻¹ which is assigned to the ν(AgI) modes of the [Ag₅I₇L₂]²⁻ anion. An analysis of this pattern is given using a model which has been used previously to account for unexpectedly simple ν(CuI) spectra for oligomeric iodocuprate(I) species.     

Synthesis and characterization of new coordination polymers generated from oxadiazole-containing ligands and IIB metal ions

The coordination chemistry of the oxadiazole-containing rigid bidentate ligands 2,5-bis(4-pyridyl)-1,3,4-oxadiazole (L1) and 2,5-bis(3-pyridyl)-1,3,4-oxadiazole (L2) with inorganic IIB metal salts have been investigated. Five new coordination polymers (1-5) were prepared by solution reactions and fully characterized by infrared spectroscopy, elemental analysis, and single-crystal X-ray diffraction. Cd(L1)₂(CH₃CN)₂](ClO₄)₂ · (CH₃CN)₂ (1) crystallized in the monoclinic space group P2₁/c, a = 8.4028(5) Å, b = 21.3726(13) Å, c = 10.5617(7) Å, β = 95.1200(10)°, and Z = 2. In the solid state, it adopts an infinite two-dimensional polymeric structural motif with effective cross section of ca. 14.31 × 14.31 Å. Cd(L2)(H₂O)(NO₃)₂ (2) crystallized in the monoclinic space group Ia, a = 7.1203(5) Å, b = 22.2475(15) Å, c = 20.2652(16) Å, β = 90.6080(10)°, and Z = 8. In the solid state, the two Cd(II) centers are connected to each other by L2 ligands and bridging nitrates into a two-dimensional network. [ZnCl₂(L1)] (3) and [HgI₂(L1)] · CH₃CN (4) crystallized in the monoclinic crystal system (3: P2₁/c, a = 5.3702(3) Å, b = 20.4800(11) Å, c = 12.4093(7) Å, β = 94.7930(10)°, and Z = 4; 4: P2/n, a = 17.2733(11) Å, b = 5.2173(3) Å, c = 20.4069(13) Å, β = 102.8690(10)°, and Z = 4). In the solid state, Zn(II) and Hg(II) metal centers are connected to each other by L1 ligands into a zigzag chain motif. Compound 5 (HgBr₂(L2) is different from 3 and 4, monoclinic, P2(1)/n, a = 5.470(4) Å, b = 16.271(13) Å, c = 16.486(12) Å, β = 93.197(15)°, and Z = 4) adopts a novel one-dimensional helical chain motif which resulted from the relative different coordinated orientation of the two N-donors on L2 ligand.     

Reactions of hybrid organotellurium ligands 1-(4-methoxyphenyl telluro)-2-[3-(6-methyl-2-pyridyl)propoxy]ethane (L) and 1-ethylthio-2-[2-thienyltelluro]ethane (L) with mercury (II) bromide: formation of complexes and their decomposition

Two tellurium ligands 1-(4-methoxyphenyltelluro)-2-[3-(6-methyl-2-pyridyl)propoxy]ethane (L¹) and 1-ethylthio-2-[2-thienyltelluro]ethane (L²) have been synthesized by reacting nucleophiles [4-MeO-C₆H₄Te⁻] and [C₄H₃S-2-Te⁻] with 2-[3-(6-methyl-2-pyridyl)propoxy]ethylchloride and chloroethyl ethyl sulfide, respectively. Both the ligands react with HgBr₂ resulting in complexes of stoichiometry [HgBr₂ · L¹/L²] (1/4), which show characteristic NMR (¹H and ¹³C{¹H}). On crystallization of 1 from acetone-hexane (2:1) mixture, the cleavage of L¹ occurs resulting in 4-MeOC₆H₄HgBr (2) and [RTe⁺→HgBr₂]Br⁻ (3) (where R = -CH₂CH₂OCH₂CH₂CH₂-(2-(6-CH₃-C₅H₃N))). The 2 is characterized by X-ray diffraction on its single crystal. It is a linear molecule and is the first such system which is fully characterized structurally. The Hg-C and Hg-Br bond lengths are 2.085(6) and2.4700(7) Å. The distance of four bromine atoms (3.4041(7)-3.546(7) Å) around Hg (cis to C) is greater than the sum of van der Waal’s radii 3.30 Å. This mercury promoted cleavage is observed for an acyclic ligand of RArTe type for the first time and is unique, as there appears to be no strong intramolecular interaction to stabilize the cleavage products. The 4 on crystallization shows the cleavage of organotellurium ligand L² and formation of a unique complex [(EtS(CH₂)₂SEt)HgBr(μ-Br)Hg(Br)(μ-Br)₂Hg(Br)(μ-Br)BrHg(EtS(CH₂)₂SEt)] · 2HgBr₂ (5), which has been characterized by single crystal structure determination and ¹H and ¹³C{¹H} NMR spectra. The elemental tellurium and [C₄H₃SCH₂]₂ are the other products of dissociation as identified by NMR (proton and carbon-13). The cleavage appears to be without any transmetalation and probably first of its kind. The centrosymmetric structure of 5 is unique as it has [HgBr₃]⁻ unit, one Hg in distorted tetrahedral geometry and one in pseudo-trigonal bipyramidal one. The molecule of 5 may also be described as having [(EtSCH₂CH₂SEt)HgBr]⁺ [HgBr₃]⁻ units, which dimerize and co-crystallize with two HgBr₂ moieties. There are very weak Hg?Br interactions between co-crystallized HgBr₂ units and rest of the molecule. [Hg(3)-Br(1)/Hg(3)-Br(4) = 3.148(1)/3.216(1) Å]. The bridging Hg?Br distances, Hg(2)-Br(4)′, Hg(2)′-Br(4) and Hg(1)-Br(2), are from 2.914(1) to 3.008(1) Å.     

Structures and mechanisms of Nudix hydrolases

Nudix hydrolases catalyze the hydrolysis of nucleoside diphosphates linked to other moieties, X, and contain the sequence motif or Nudix box, GX(5)EX(7)REUXEEXGU. The mechanisms of Nudix hydrolases are highly diverse in the position on the substrate at which nucleophilic substitution occurs, and in the number of required divalent cations. While most proceed by associative nucleophilic substitutions by water at specific internal phosphorus atoms of a diphosphate or polyphosphate chain, members of the GDP-mannose hydrolase sub-family catalyze dissociative nucleophilic substitutions, by water, at carbon. The site of substitution is likely determined by the positions of the general base and the entering water. The rate accelerations or catalytic powers of Nudix hydrolases range from 10(9)- to 10(12)-fold. The reactions are accelerated 10(3)-10(5)-fold by general base catalysis by a glutamate residue within, or beyond the Nudix box, or by a histidine beyond the Nudix box. Lewis acid catalysis, which contributes 10(3)-10(5)-fold to the rate acceleration, is provided by one, two, or three divalent cations. One divalent cation is coordinated by two or three conserved residues of the Nudix box, the initial glycine and one or two glutamate residues, together with a remote glutamate or glutamine ligand from beyond the Nudix box. Some Nudix enzymes require one (MutT) or two additional divalent cations (Ap(4)AP), to neutralize the charge of the polyphosphate chain, to help orient the attacking hydroxide or oxide nucleophile, and/or to facilitate the departure of the anionic leaving group. Additional catalysis (10-10(3)-fold) is provided by the cationic side chains of lysine and arginine residues and by H-bond donation by tyrosine residues, to orient the general base, or to promote the departure of the leaving group. The overall rate accelerations can be explained by both independent and cooperative effects of these catalytic components.     

3(10)-Helix adjoining alpha-helix and beta-strand: sequence and structural features and their conservation

Does the amino acid use at the terminal positions of an α‐helix become altered depending on the context—more specifically, when there is an adjoining 3₁₀‐helix, and can a single helical cylinder encompass the resultant composite helix? An analysis of 138 and 107 cases of 3₁₀–α and α–3₁₀ composite helices, respectively, found in known protein structures indicate that the secondary structural element occurring first imposes its characteristics on the sequence of the structural element coming next. Thus, when preceded by a 3₁₀‐helix, the preference of proline to occur at the N1 position of an α‐helix is shifted to the N2 position, a typical characteristic of the C‐terminal capping of the 3₁₀‐helix. When an α‐ or a 3₁₀‐helix leads into a helix of the other type, there is a bend at the junction, especially for the 3₁₀–α composite, with the two junction residues facing inward and buried within the structure. Thus a single helical cylinder may not properly represent a composite helix, the bend providing a means for the tertiary structure to assume a globular shape, very much akin to what a proline‐induced kink does to an α‐helix. The tertiary structural context in which β–3₁₀ and 3₁₀–β composites occurs can be different, causing the angle between the secondary structural elements in the two cases to be different. Composites of 3₁₀‐helices and β‐strands are much more conserved among members in families of homologous structures than those between two types of helices; in many of the former instances, the 3₁₀‐helix constitutes the loops in β‐hairpin or β–β‐corner motifs. The overall fold of the chain may be more conserved than the actual identify of the secondary structure elements in a composite. © 2005 Wiley Periodicals, Inc. Biopolymers 78: 147–162, 2005 This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com     

Structures of wild-type and P28L/Y173F tryptophan synthase alpha-subunits from Escherichia coli

The alpha-subunit of tryptophan synthase (alphaTS) catalyzes the cleavage of indole-3-glycerol phosphate to glyceraldehyde-3-phosphate and indole, which is used to yield the amino acid tryptophan in tryptophan biosynthesis. Here, we report the first crystal structures of wild-type and double-mutant P28L/Y173F alpha-subunit of tryptophan synthase from Escherichia coli at 2.8 and 1.8A resolution, respectively. The structure of wild-type alphaTS from E. coli was similar to that of the alpha(2)beta(2) complex structure from Salmonella typhimurium. As compared with both structures, the conformational changes are mostly in the interface of alpha- and beta-subunits, and the substrate binding region. Two sulfate ions and two glycerol molecules per asymmetric unit bind with the residues in the active sites of the wild-type structure. Contrarily, double-mutant P28L/Y173F structure is highly closed at the window for the substrate binding by the conformational changes. The P28L substitution induces the exposure of hydrophobic amino acids and decreases the secondary structure that causes the aggregation. The Y173F suppresses to transfer a signal from the alpha-subunit core to the alpha-subunit surface involved in interactions with the beta-subunit and increases structural stability.