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At least 937 records · Page 52Linked to original sources
PubMed2005

Crystal structures of the wild-type, P1A mutant, and inactivated malonate semialdehyde decarboxylase: a structural basis for the decarboxylase and hydratase activities.

Malonate semialdehyde decarboxylase (MSAD) from Pseudomonas pavonaceae 170 is a tautomerase superfamily member that converts malonate semialdehyde to acetaldehyde by a mechanism utilizing Pro-1 and Arg-75. Pro-1 and Arg-75 have also been implicated in the hydratase activity of MSAD in which 2-oxo-3-pentynoate is processed to acetopyruvate. Crystal structures of MSAD (1.8 A resolution), the P1A mutant of MSAD (2.7 A resolution), and MSAD inactivated by 3-chloropropiolate (1.6 A resolution), a mechanism-based inhibitor activated by the hydratase activity of MSAD, have been determined. A comparison of the P1A-MSAD and MSAD structures reveals little geometric alteration, indicating that Pro-1 plays an important catalytic role but not a critical structural role. The structures of wild-type MSAD and MSAD covalently modified at Pro-1 by 3-oxopropanoate, the adduct resulting from the incubation of MSAD and 3-chloropropiolate, implicate Asp-37 as the residue that activates a water molecule for attack at C-3 of 3-chloropropiolate to initiate a Michael addition of water. The interactions of Arg-73 and Arg-75 with the C-1 carboxylate group of the adduct suggest these residues polarize the alpha,beta-unsaturated acid and facilitate the addition of water. On the basis of these structures, a mechanism for the inactivation of MSAD by 3-chloropropiolate can be formulated along with mechanisms for the decarboxylase and hydratase activities. The results also provide additional evidence supporting the hypothesis that MSAD and trans-3-chloroacrylic acid dehalogenase, a tautomerase superfamily member preceding MSAD in the trans-1,3-dichloropropene degradation pathway, diverged from a common ancestor but retained the key elements for the conjugate addition of water.

Arginine↗
PubMed2006

Crystal structure of mouse succinic semialdehyde reductase AKR7A5: structural basis for substrate specificity.

The aldo-keto reductases make up a superfamily of enzymes which can reduce a variety of aldehydes and ketones to their corresponding alcohols. Within each family are distinct preferences for certain substrates, presumably reflecting their role within the cell. The original member of the AKR7A subfamily was purified from liver as an aflatoxin dialdehyde reductase AKR7A1. However, recent additions to the family have revealed that even closely related enzymes have clear substrate preferences with AKR7A2, AKR7A4, and AKR7A5 showing much higher affinities for succinic semialdehyde (SSA) than does AKR7A1. To investigate the structural basis of this specificity, the crystal structure of mouse AKR7A5 has been determined to better than 2.5 A resolution. The structure is of the ternary complex of the enzyme with NADP+ and tartrate as an inhibitor. This structure has the same overall fold as the previously determined structure of AKR7A1; however, there are a number of differences in loops around the active site that contribute to observed differences in the substrate specificity between the AKR7A enzymes. Several differences are the result of bulky hydrophobic residues found in AKR7A5, namely, Met44, Trp77, and Trp224, which significantly restrict the size and modify the architecture of the substrate-binding pocket, producing a tighter or less flexible binding site for SSA than in AKR7A1. Site-directed mutagenesis was used to introduce Met44, Trp77, and Trp224 individually into AKR7A1, to test if they improved the affinity of the enzyme for SSA. Each mutation showed improved affinity for SSA, with Trp77Met having the largest effect. This confirms the role of these amino acids as substrate determinants for SSA.

Alcohol Oxidoreductases↗
PubMed1996

Structure of the autoregulatory pseudoknot within the gene 32 messenger RNA of bacteriophages T2 and T6: a model for a possible family of structurally related RNA pseudoknots.

A 36-nucleotide RNA with a sequence corresponding to the 5' end region of the gene 32 mRNA of bacteriophages T2 and T6 was analyzed by one- and two-dimensional NMR methods. NMR results provide clear evidence that the RNA is folded into a pseudoknot structure with two coaxial stems connected by two loops, in a classic pseudoknot topology. The pseudoknot is unusual in that one of the loops consists of only one nucleotide, which spans the major groove of a seven base pair helical stem. Imino proton resonances indicate the hydrogen bonding pattern within the pseudoknot, and two-dimensional NOE spectra provide information that describes many of the structural features. The temperature dependence of the UV absorption and imino proton exchange rates provides insight into the stability of the pseudoknot. A three-dimensional model of the pseudoknot that is consistent with our NMR data is presented, and features that may be important for stabilizing the pseudoknot structure are discussed. A substantial number of other putative RNA pseudoknots described in the literature have sequences and topologies that appear to be related to the T2 and T6 pseudoknots. We propose that these RNAs may be members of a family of pseudoknots related by a similar structural motif, which we refer to as "common pseudoknot motif 1" or CPK1. The bacteriophage T2/T6 pseudoknot can be considered a structural model for the CPK1 family. The common features of the CPK1 pseudoknots are a stem 2 with six or seven base pairs, a loop 1 consisting of a single adenosine, and a variable length stem 1 and loop 2. The first "dangling" nucleotide at the 3' end of the molecule probably stabilizes stem 2. The CPK1 family includes several of the retroviral pseudoknots associated with mRNA frameshifting and readthrough. The work presented here describes the first detailed NMR analysis of an RNA pseudoknot with an entirely natural nucleotide sequence.

Bacteriophages↗
PubMed1996

Investigation of the structural basis for thermodynamic stabilities of tandem GU mismatches: solution structure of (rGAGGUCUC)2 by two-dimensional NMR and simulated annealing.

The duplex (rGAGGUCUC)2 contains the motif [sequence: see text] which is unusually stable compared with other symmetric tandem GU mismatches and occurs in the P5 helix of the group I intron of Tetrahymena thermophila. The three-dimensional solution structure of (rGAGGUCUC)2 was determined using two-dimensional NMR and a simulated annealing protocol. The structure is remarkably similar to the A-DNA crystal structure of (dGGGGTCCC)2 [Kneale, G., Brown, T., & Kennard, O. (1985) J. Mol. Biol. 186, 805-814] which contains the analogous motif [sequence: see text]. Incorporation of the [sequence: see text] motif has little effect on backbone torsion angles and helical parameters compared with standard A-form. The only significant departure from A-form is a slight overtwisting 5' of the G in the GU mismatch and a displacement of the mismatches toward the minor groove. Inspection of stacking patterns of this structure and comparison with symmetric tandem GT mismatches in A-DNA oligonucleotides from crystal structure data suggest that electrostatics are important in determining motif stability.

Hydrogen Bonding↗
PubMed1997

Determination of tumor necrosis factor binding protein disulfide structure: deviation of the fourth domain structure from the TNFR/NGFR family cysteine-rich region signature.

Tumor necrosis factor binding protein is a soluble molecule derived from the extracellular domain of the 55 kDa human tumor necrosis factor receptor, which can block the biological function of tumor necrosis factor by binding to the growth factor. This cysteine-rich molecule is subdivided into four domains, each containing six conserved cysteines that form three intrachain disulfide linkages known as the tumor necrosis factor receptor/nerve growth factor receptor family cysteine-rich region signature structure. In an effort to elucidate the molecular integrity of the molecule, we performed detailed analysis and searched for strategies to elucidate the complete disulfide structure of the E. coli-derived tumor necrosis factor binding protein and to determine the disulfide arrangement in the fourth domain of Chinese hamster ovary cell-derived molecule. The methods employed included various proteolytic digestions, peptide mapping, partial reduction, and assignment of disulfides by N-terminal sequencing and matrix-assisted laser desorption ionization mass spectrometry with post-source decay. The first three domains of the molecule were confirmed to have disulfide structures identical to the cysteine-rich region signature structure found in the above-mentioned receptor superfamily. The fourth domain has a different structure from the first three domains where the last four cysteines form two disulfide bonds in opposite positions.

Amino Acid Sequence↗
PubMed1998

Two high-resolution crystal structures of the recombinant N-lobe of human transferrin reveal a structural change implicated in iron release.

The N-lobe of human serum transferrin (hTF/2N) has been expressed in baby hamster kidney cells and crystallized in both orthorhombic (P212121) and tetragonal (P41212) space groups. Both crystal forms diffract to high resolution (1.6 and 1.8 A, respectively) and have been solved by molecular replacement. Subsequent refinement resulted in final models for the structure of hTF/2N that had crystallographic R-factors of 18.1 and 19.7% for the two crystal forms, respectively; these models represent the highest-resolution transferrin structures determined to date. The hTF/2N polypeptide has a folding pattern similar to those of other transferrins, including the presence of a deep cleft that contains the metal-binding site. In contrast to other transferrins, both crystal forms of hTF/2N display disorder at the iron-binding site; model building suggests that this disorder consists of alternative conformations of the synergistically bound carbonate anion, the side chain for Arg-124, and several solvent molecules. Subsequent refinement revealed that conformation A has an occupancy of 0.63-0. 65 and corresponds to the structure of the iron-binding site found in other transferrins. The alternative conformation B has an occupancy of 0.35-0.37; in this structure, the carbonate has rotated 30 degrees relative to the iron and the side chain for Arg-124 has moved to accommodate the new carbonate position. Several water molecules appear to stabilize the carbonate anion in the two conformations. These structures are consistent with the protonation of the carbonate and resulting partial removal of the anion from the metal; these events would occur prior to cleft opening and metal release.

Animals↗
PubMed2000

Structure of a NifS homologue: X-ray structure analysis of CsdB, an Escherichia coli counterpart of mammalian selenocysteine lyase.

Escherichia coli CsdB, a NifS homologue with a high specificity for L-selenocysteine, is a pyridoxal 5'-phosphate (PLP)-dependent dimeric enzyme that belongs to aminotransferases class V in fold-type I of PLP enzymes and catalyzes the decomposition of L-selenocysteine into selenium and L-alanine. The crystal structure of the enzyme has been determined by the X-ray crystallographic method of multiple isomorphous replacement and refined to an R-factor of 18.7% at 2.8 A resolution. The subunit structure consists of three parts: a large domain of an alpha/beta-fold containing a seven-stranded beta-sheet flanked by seven helices, a small domain containing a four-stranded antiparallel beta-sheet flanked by three alpha-helices, and an N-terminal segment containing two alpha-helices. The overall fold of the subunit is similar to those of the enzymes belonging to the fold-type I family represented by aspartate aminotransferase. However, CsdB has several structural features that are not observed in other families of the enzymes. A remarkable feature is that an alpha-helix in the lobe extending from the small domain to the large domain in one subunit of the dimer interacts with a beta-hairpin loop protruding from the large domain of the other subunit. The extended lobe and the protruded beta-hairpin loop form one side of a limb of each active site in the enzyme. The most striking structural feature of CsdB lies in the location of a putative catalytic residue; the side chain of Cys364 on the extended lobe of one subunit is close enough to interact with the gamma-atom of a modeled substrate in the active site of the subunit. Moreover, His55 from the other subunit is positioned so that it interacts with the gamma- or beta-atom of the substrate and may be involved in the catalytic reaction. This is the first report on three-dimensional structures of NifS homologues.

Amino Acid Sequence↗
PubMed2000

The E-state as the basis for molecular structure space definition and structure similarity

The electrotopological state (E-state) is presented as a representation of molecular structure useful for definition of a space for chemical structures. This E-state representation provides the basis for chemical database management. The E-state formalism is presented along with its extension to the atom-type E-state. An approach to database organization, using polychlorobiphenyls (PCBs) as examples, reveals the descriptive power of the E-state paradigm. A well-organized chemical database, as described here, may be searched to find structures similar to a target structure with the expectation that such structures may exhibit properties similar to the target. Searches using the atom-type E-state indices are demonstrated with two example drug molecules.

Journal Article↗
PubMed2000

Structural diversity in solvated lithium aryloxides. Syntheses, characterization, and structures of [Li(OAr)(THF)x]n and [Li(OAr)(py)x]2 complexes where OAr = OC6H5, OC6H4(2-Me), OC6H3(2,6-(Me))2, OC6H4(2-Pr(i)), OC6H3(2,6-Pr(i)))2, OC6h4(2-Bu(t)), OC6H3(2,6-Bu(t)))2.

A series of sterically varied aryl alcohols H-OAr [OAr = OC6H5 (OPh), OC6H4(2-Me) (oMP), OC6H3(2,6-(Me))2 (DMP), OC6H4(2-Pr(i)) (oPP), OC6H3(2,6-(Pr(i)))2 (DIP), OC6H4(2-Bu(t)) (oBP), OC6H3(2,6-(Bu(t)))2 (DBP); Me = CH3, Pr(i) = CHMe2, and Bu(t) = CMe3] were reacted with LiN(SiMe3)2 in a Lewis basic solvent [tetrahydrofuran (THF) or pyridine (py)] to generate the appropriate "Li(OAr)(solv)x". In the presence of THF, the OPh derivative was previously identified as the hexagonal prismatic complex [Li(OPh)(THF)]6; however, the structure isolated from the above route proved to be the tetranuclear species [Li(OPh)(THF)]4 (1). The other "Li(OAr)(THF)x" products isolated were characterized by single-crystal X-ray diffraction as [Li(OAr)(THF)]4 [OAr = oMP (2), DMP (3), oPP (4)], [Li(DIP)(THF)]3 (5), [Li(oBP)(THF)2]2, (6), and [Li(DBP)(THF)]2, (7). The tetranuclear species (1-4) consist of symmetric cubes of alternating tetrahedral Li and pyramidal O atoms, with terminal THF solvent molecules bound to each metal center. The trinuclear species 5 consists of a six-membered ring of alternating trigonal planar Li and bridging O atoms, with one THF solvent molecule bound to each metal center. Compound 6 possesses two Li atoms that adopt tetrahedral geometries involving two bridging oBP and two terminal THF ligands. The structure of 7 was identical to the previously reported [Li(DBP)(THF)]2 species, but different unit cell parameters were observed. Compound 7 varies from 6 in that only one solvent molecule is bound to each Li metal center of 7 because of the steric bulk of the DBP ligand. In contrast to the structurally diverse THF adducts, when py was used as the solvent, the appropriate "Li(OAr)(py)x" complexes were isolated as [Li(OAr)(py)2]2 (OAr = OPh (8), oMP (9), DMP (10), oPP (11), DIP (12), oBP (13)) and [Li(DBP)(py)]2 (14). Compounds 8-13 adopt a dinuclear, edge-shared tetrahedral complex. For 14, because of the steric crowding of the DBP ligand, only one py is coordinated, yielding a dinuclear fused trigonal planar arrangement. Two additional structure types were also characterized for the DIP ligand: [Li(DIP)(H-DIP)(py)]2 (12b) and [Li2(DIP)2(py)3] (12c). Multinuclear (6,7Li and 13C) solid-state MAS NMR spectroscopic studies indicate that the bulk powder possesses several Li environments for "transitional ligands" of the THF complexes; however, the py adducts possess only one Li environment, which is consistent with the solid-state structures. Solution NMR studies indicate that "transitional" compounds of the THF precursors display multiple species in solution whereas the py adducts display only one lithium environment.

Journal Article↗
PubMed2001

Solid-state coordination chemistry: structural influences of copper-phenanthroline subunits on oxovanadium organophosphonate phases. hydrothermal synthesis and structural characterization of the two-dimensional materials [Cu(phen)(VO)(O3PCH2PO3)(H2O)], [[Cu(phen)]2(V2O5)(O3PCH2CH2PO3)], and [[Cu(phen)]2(V3O5)(O3PCH2CH2CH2PO3)2(H2O)] and the three-dimensional phase [[Cu(phen)]2(V3O5)(O3PCH2PO3)2(H2O)].

The hydrothermal reactions of CuCl2*2H2O, Na3VO4, 1,10-phenanthroline, and the appropriate organodiphosphonate ligand yield [Cu(phen)(VO)(O3PCH2PO3)(H2O)] (1), [[Cu(phen)]2(V2O5)(O3PCH2CH2PO3)] (2), [[Cu(phen)]2(V3O5)(O3PCH2CH2CH2PO3)2 (H2O)] (3), and [[Cu(phen)]2(V3O5)(O3PCH2PO3)2(H2O)] (4). Compounds 1-3 exhibit two-dimensional structures. The structures exhibit distinct vanadium building blocks: square pyramidal, mononuclear V(IV) sites in 1, a binuclear unit of corner-sharing V(V) tetrahedra in 2, and a trinuclear unit of corner-sharing V(V) square pyramids and a V(IV) octahedron in 3. The network structures of 1 and 2 are constructed from one-dimensional oxovanadium-diphosphonate chains linked by Cu(II) square pyramids into two-dimensional layers. In contrast, compound 3 exhibits a two-dimensional oxovanadium-organodiphosphonate network, with Cu(II) sites decorating the surfaces. Compound 4 is unique in exhibiting a framework structure, which may be described as a three-dimensional oxovanadium-organodiphosphonate substructure with [Cu(phen)]2+ subunits covalently attached to the surface of channels running parallel to the a-axis. The magnetic properties of 1-4 are also correlated to the structural characteristics. The magnetic behavior of 2 is thus dominated by antiferromagnetic interactions. The magnetic behavior of 1 and 4 is consistent with the presence of two distinct paramagnetic metal ions, Cu(II) and V(IV). In contrast, 3 does not exhibit ferrimagnetic behavior, but rather weak antiferromagnetic coupling. Crystal data: 1, C13H10N2CuP2VO8, monoclinic P2(1)/c, a = 9.0656(5) A, b = 8.6584(5) A, c = 20.934(1) A, beta = 97.306(1) degrees, Z = 4; 2, C26H20N4Cu2P2V2O11, triclinic P1, a = 10.6096(5) A, b = 11.6951(5) A, c = 13.1796(6) A, alpha = 71.369(1) degrees, beta = 70.790(1) degrees, gamma = 80.738(1) degrees, Z = 2; 3, C30H28N4Cu2P4V3O18, triclinic P1, a = 9.4356(6) A, b = 10.6556(6) A, c = 11.0354(7) A, alpha = 118.187(1) degrees, beta = 91.416(1) degrees, gamma = 107.821(1) degrees, Z = 1; 4, C26H20N4Cu2P4V3O18, monoclinic, P2(1)/c a = 8.3947(3) A, b = 16.8401(7) A, c = 11.9144(5) A, beta = 93.903(1) degrees, Z = 2.

Journal Article↗
PubMed2004

Structural effects of the lone pair on lead(II), and parallels with the coordination geometry of mercury(II). Does the lone pair on lead(II) form H-bonds? Structures of the lead(II) and mercury(II) complexes of the pendant-donor macrocycle DOTAM (1,4,7,10-tetrakis(carbamoylmethyl)-1,4,7,10-tetraazacyclododecane).

The synthesis and structures of [Pb(DOTAM)](ClO4)2.4.5H2O (1) and [Hg(DOTAM)](ClO4)2.0.5CH3OH.1.5H2O (2) are reported, where DOTAM is 1,4,7,10-tetrakis(carbamoylmethyl)-1,4,7,10-tetraazacyclododecane. Compound 1 is triclinic, space group P, a = 12.767(3) A, b = 13.528(2) A, c = 18.385(3) A, alpha = 101.45(2) degrees, beta = 93.32(2) degrees, gamma = 90.53(2) degrees, Z = 4, R = 0.0500. Compound 2 is monoclinic, space group Cc, a = 12.767(3) A, b = 13.528(2) A, c = 18.385(3) A, beta = 101.91(2) degrees, Z = 4, R = 0.0381. The Pb(II) ion in 1 has an average Pb-N = 2.63 A to four N-donors from the macrocyclic ring, and four O-donors (average Pb-O = 2.77 A) from the amide pendant donors of the macrocycle, with a water molecule placed with Pb-O = 3.52 A above the proposed site of the lone pair (Lp) on Pb. The Hg(II) in 2 appears to be only six-coordinate, with four Hg-N bond lengths averaging 2.44 A, and two Hg-O from pendant amide donors at 2.41 A. The other two amide donors appear to be noncoordinating, with Hg-O distances of 2.74 and 2.82 A. A water situated 3.52 A above the proposed site of the lone pair on Pb(II) in 1 is oriented in such a way that it might be thought to be forming a Pb-Lp.H-O-H hydrogen bond. It is concluded that that this is not an H-bond, but that the presence of the lone pair allows a closer approach of the hydrogens to Pb than would be true otherwise. The structural analogy in the VSEPR sense between Pb(II), which has the 5d(10)6s(2) outer electron structure, and the Hg(II) ion, which has the 5d10 structure, is examined. The tendency of Hg(II) toward linear coordination, with two short Hg-L bonds (L = ligand) at 180 degrees to each other, and other donor groups at roughly 90 degrees to this and at much longer bond distances, is paralleled by Pb(II). One of the short Hg-L bonds is replaced in the Pb(II) structures by the lone pair (Lp), which is opposite the short Pb-L bond, or in some cases 2-4 shorter Pb-L bonds.

Journal Article↗
PubMed2005

Effect of the semirigid capping ligand on the structure formation of cyano-bridged bimetallic assemblies: syntheses, crystal structures, and magnetic properties.

The syntheses, crystal structures, and magnetic properties of three novel cyano-bridged bimetallic assemblies, [Ni(bpm)(2)](3)[Co(CN)(6)](2)x3.5H(2)O (1), [Co(bpm)(2)][Fe(CN)(5)NO]x2H(2)O (2), and [Co(bpm)(2)][Ni(CN)(4)] (3) (bpm = bis(1-pyrazolyl)methane), are reported. Complex 1 crystallizes in the tetragonal space group P4(3)2(1)2 with a = 12.800(5) A, b = 12.800(5) A, c = 42.80(3) A, V = 7012(6) A(3), and Z = 8. Complex 2 crystallizes in the chiral trigonal space group P3(2)21 with a = 11.9961(19) A, b = 11.9961(19) A, c = 16.062(5) A, gamma = 120 degrees , V = 2001.7(8) A(3), and Z = 3. Complex 1 is a trigonal bipyramidal complex in which three [Ni(bpm)(2)](2+) units are situated in the equatorial plane and are connected to the two apical [Co(CN)(6)](3)(-) units via three N ends of the cyanide groups. Complex 2 possesses a triangular left-handed helical chain structure composed of [Co(bpm)(2)](2+) linked by [Fe(CN)(5)NO](2)(-); the shortest intramolecular Co...Fe distance is 5.162 A. To the best of our knowledge, this is the first observation of a heteronuclear helical chain structure based on pentacyanonitrosylferrate(II). The structure of complex 3 is roughly determined by X-ray crystallograhy analysis to be a 1D zigzag chain. These structure variations, from a discrete cluster to a 1D helical chain and a 1D zigzag chain, rely on the semirigidity of the capping ligand bpm. Magnetic susceptibility measurements indicate that complex 1 has an intramolecular ferromagnetic interaction (J = 4.06 cm(-)(1)) between the nickel(II) ions; this is further confirmed by the magnetization measurements. In complexes 2 and 3, the cobalt(II) ions are located in a moderately strong field.

Journal Article↗
PubMed2007

Atomic distributions in the gamma-brass structure of the Cu-Zn system: a structural and theoretical study.

The crystal structures, atomic distributions, and theoretical electronic structures of five different Cu5-xZn8+x gamma-brass compounds (x = -0.59(3), -0.31(3), 0.00(3), 0.44(3), and 0.79(3)) are reported with the goal of identifying chemical influences on the observed phase width. These structures have been refined by both neutron and X-ray powder diffraction to obtain accurate crystal chemical parameters. All compounds crystallize in the space group Iz3m (No. 217) (Z = 4), and the unit cell parameters are a = 8.8565(4), 8.8612(5), 8.8664(3), 8.8745(4), and 8.8829(7) A, respectively, for Cu5.59Zn7.41, Cu5.31Zn7.69, Cu5.00Zn8.00, Cu4.56Zn8.44, and Cu4.21Zn8.79. The results indicate specific site substitutions on both sides of the ideal composition "Cu5Zn8". In all cases, the 26-atom cluster building up the -brass structure shows a constant inner [Cu4Zn4] tetrahedral star with compositional variation occurring at the outer octahedron and cuboctahedron. First principles and semiempirical electronic structure calculations using both a COHP and Mulliken population analysis were performed to understand the observed compositional range and to address the "coloring problem" for the site preferences of Cu and Zn atoms for this series of compounds.

Journal Article↗
PubMed1996

Syntheses and Crystal Structures of Ruthenium Complexes of 1,4,8,11-Tetraazacyclotetradecane, Tris(2-aminoethyl)amine (tren), and Bis(2-aminoethyl)(iminomethyl)amine. A Microporous Layered Structure Consisting of {[K(tren)](2)[RuCl(6)]}(n)()(n)()(-) and {(H(5)O(2))(4)[RuCl(6)]}(n)()(n)()(+).

The second method for the synthesis of cis-[Ru(III)Cl(2)(cyclam)]Cl (1) (cyclam = 1,4,8,11-tetraazacyclotetradecane), with use of cis-Ru(II)Cl(2)(DMSO)(4) (DMSO = dimethyl sulfoxide) as a starting complex, is reported together with the synthesis of [Ru(II)(cyclam)(bpy)](BF(4))(2).H(2)O (2) (bpy = 2,2'-bipyridine) from 1. The syntheses of Ru complexes of tris(2-aminoethyl)amine (tren) are also reported. A reaction between K(3)[Ru(III)(ox)(3)] (ox = oxalate) and tren affords fac-[Ru(III)Cl(3)(trenH)]Cl.(1)/(2)H(2)O (3) (trenH = bis(2-aminoethyl)(2-ammonioethyl)amine = monoprotonated tren) and (H(5)O(2))(2)[K(tren)][Ru(III)Cl(6)] (4) as major products and gives fac-[Ru(III)Cl(ox)(trenH)]Cl.(3)/(2)H(2)O (5) in very low reproducibility. A reaction between 3 and bpy affords [Ru(II)(baia)(bpy)](BF(4))(2) (6) (baia = bis(2-aminoethyl)(iminomethyl)amine), in which tren undergoes a selective dehydrogenation into baia. The crystal structures of 2-6 have been determined by X-ray diffraction, and their structural features are discussed in detail. Crystallographic data are as follows: 2, RuF(8)ON(6)C(20)B(2)H(34), monoclinic, space group P2(1)/c with a = 12.448(3) Å, b = 13.200(7) Å, c = 17.973(4) Å, beta = 104.28(2) degrees, V = 2862(2) Å(3), and Z = 4; 3, RuCl(4)O(0.5)N(4)C(6)H(20), monoclinic, space group P2(1)/a with a = 13.731(2) Å, b = 14.319(4) Å, c = 13.949(2) Å, beta = 90.77(1) degrees, V = 2742(1) Å(3), and Z = 8; 4, RuKCl(6)O(4)N(4)C(6)H(28), trigonal, space group R&thremacr; with a = 10.254(4), c = 35.03(1) Å, V = 3190(2) Å(3), and Z = 6; 5, RuCl(2)O(5.5)N(4)C(8)H(22), triclinic, space group P&onemacr; with a = 10.336(2) Å, b = 14.835(2) Å, c = 10.234(1) Å, alpha = 90.28(1) degrees, beta = 90.99(1) degrees, gamma = 92.07(1) degrees, V = 1567.9(4) Å(3), and Z = 4; 6, RuF(8)N(6)C(16)B(2)H(24), monoclinic, space group P2(1)/c, a = 10.779(2) Å, b = 14.416(3) Å, c = 14.190(2) Å, beta = 93.75(2) degrees, V = 2200.3(7) Å(3), and Z = 4. Compound 4 possesses a very unique layered structure made up of both anionic and cationic slabs, {[K(tren)](2)[Ru(III)Cl(6)]}(n)()(n)()(-) and {(H(5)O(2))(4)[Ru(III)Cl(6)]}(n)()(n)()(+) (n = infinity), in which both sheets {[K(tren)](2)}(n)()(2)(n)()(+) and {(H(5)O(2))(4)}(n)()(4)(n)()(+) offer cylindrical pores that are occupied with the [Ru(III)Cl(6)](3)(-) anions. The presence of a C=N double bond of baia in 6 is judged from the C-N distance of 1.28(2) Å. It is suggested that the structural restraint enhanced by the attachment of alkylene chelates at the nitrogen donors of amines results in either the mislocation or misdirection of the donors, leading to the elongation of the Ru-N(amine) distances and to the weakening of their trans influence. Such structural strain is also discussed as related to the spectroscopic and electrochemical properties of the cis-[Ru(II)L(4)(bpy)](2+) complexes (L(4) = (NH(3))(4), (ethylenediamine)(2), and cyclam).

Journal Article↗
PubMed1996

Structural Variability of the Vanadium-Organodiphosphonate System: Hydrothermal Syntheses and Structural Characterizations of One-Dimensional, Two-Dimensional, and Three-Dimensional Phases.

The hydrothermal chemistry of the CsVO(3)/methylenediphosphonate system was investigated. Variations in reaction temperatures, heating times, and stoichiometries of reactants resulted in the isolation of mononuclear, one-, two-, and three-dimensional species: Cs[VO(HO(3)PCH(2)PO(3)H)(2)(H(2)O)] (1), Cs[VO(HO(3)PCH(2)PO(3))] (2), Cs[(VO)(2)V (O(3)PCH(2)PO(3))(2)(H(2)O)(2)] (3), and [V(HO(3)PCH(2)PO(3))(H(2)O)] (4), respectively. The structure of the anion of 1 consists of isolated V(IV) octahedra. Phase 2 adopts a chain structure constructed from corner-sharing V(IV) octahedra, forming infinite {-V=OV=O-} linkages. The layer structure of 3 contains trinuclear units of corner-sharing {VO(6)} octahedra with the central V site in the III oxidation state and V(IV) centers at the extremities of the cluster. The diphosphonate ligands serve to link neighboring trinuclear motifs into a layer structure three octahedra in depth. The Cs(+) cations occupy cavities within the layers, rather than the more common interlamellar positions. The structure of 4 consists of isolated {V(III)O(6)} octahedra linked by diphosphonate groups into a three-dimensional framework. Crystal data: for 1, CH(6)O(7)P(2)V(0.5)Cs, monoclinic C2, a = 10.991(2) Å, b = 10.161(2) Å, c = 7.445(1) Å, beta = 92.97(3) degrees, Z = 4; for 2, CH(3)O(7)P(2)VCs, monoclinic C2, a = 10.212(2) Å, b = 10.556(2) Å, c = 14.699(3) Å, beta = 94.57(2) degrees, Z = 8; for 3, C(2)H(8)O(16)P(4)V(3)Cs, monoclinic C2/m, a = 9.724(2) Å, b = 8.136(2) Å, c = 10.268(2) Å, beta = 103.75(3) degrees, Z = 2; for 4, CH(5)O(7)P(2)V, monoclinic P2(1)()/n, a = 5.341(1) Å, b = 11.516(2) Å, c = 10.558(2) Å, beta = 99.89(1) degrees, Z = 4.

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PubMed1998

Extension of the Fenske-Hall Molecular Orbital Approach to Tight-Binding Band Structure Calculations: Bulk and Surface Electronic Structure of MoS(2).

A new tight-binding band structure calculation method is described. This method, which is based on the Fenske-Hall molecular orbital technique, should be extremely useful in the study of the bulk and surface electronic structure of inorganic materials. The approximations used in the Fenske-Hall method are reviewed, and the extension of this approach to periodic band structure calculations is outlined. Results of calculations for bulk MoS(2) are in good agreement with previous experimental and theoretical results. Results of calculations for two-dimensional MoS(2) slabs exposing (100) edge planes provide a description of coordinatively unsaturated Mo and S atoms on these edges. Coordinative unsaturation at the Mo atoms introduces new surface states near the Fermi level. Coordinative unsaturation at the S atoms leads to high-energy occupied bands that can be attributed to S lone pair electrons. Surface bonds between Mo atoms and terminal S atoms are stronger than bulk Mo-S bonds, suggesting that terminal S atoms may be more difficult to remove from the edges of MoS(2) than bridging S atoms. Bonding in a single two-dimensional layer of MoS(2) is found to be more ionic than the bonding in the full three-dimensional structure. This effect is also observed in one-dimensional MoS(2) ribbons that expose (100) edge planes. The simplified one-dimensional ribbons will be used for further studies of the electronic structure of the edge planes of MoS(2).

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PubMed1999

Synthesis and Crystal Structure of Zr(2)Te. Distinctions in Bonding to Isotypic Sc(2)Te and the Relationship to the Structures of Congeneric Hf(2)Te and Zr(2)Se.

Zr(2)Te is accessible by high-temperature synthesis. The structure of the zirconium-rich telluride was determined by means of powder X-ray diffraction to be orthorhombic, Pnma (No. 62), Z = 12, Pearson symbol oP36, a = 1995.0(2) pm, b = 382.36(2) pm, c = 1065.63(9) pm. Pairwise interpenetrating columns of trans-face-shared, centered Zr(9) cuboids, reminiscent of the bcc high-temperature form of zirconium can be recognized as the topologically characteristic structural feature. Tellurium atoms capping the remaining square faces complete the motif of a [Zr(8)Te(4)] double string running parallel [010]. The tellurium atoms are 7-, 8- and 9-fold coordinated by zirconium. The coordination figures represent mono-, bi- and tricapped distorted trigonal prisms, with zirconium atoms capping the square faces of the prisms. Extended Hückel calculations revealed distinctions in bonding in Zr(2)Te and the isotypic Sc(2)Te. According to Mulliken overlap populations, the heteronuclear interactions are similar in both tellurides. However, the lower valence electron concentration available for M-M bonding in Sc(2)Te is reflected in a considerable restriction of the attractive homonuclear interactions to one-dimensional metal cores, whereas in Zr(2)Te M-M bonding regions extend in space. The structure of Zr(2)Te is contrasted with two other types of bcc fragment structures adopted by the congeneric Hf(2)Te and Zr(2)Se. We show that the structural diversity observed for various dimetal chalcogenides is controlled by an intimate interplay of electronic and geometric factors.

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PubMed2000

Synthesis, crystal structure, EXAFS, and magnetic properties of catena [mu-tris(1,2-bis(tetrazol-1-yl)propane-N1,N1')iron(II)] bis(perchlorate). First crystal structure of an iron(II) spin-crossover chain compound.

[Fe(btzp)3](ClO4)2 (btzp = 1,2-bis(tetrazol-1-yl)propane) represents the first structurally characterized Fe(II) linear chain compound exhibiting thermal spin crossover. It shows a very gradual spin transition (T1/2 = 130 K) which has been followed by magnetic susceptibility measurements and 57Fe Mössbauer spectroscopy. The structure has been solved at 200 and 100 K by single-crystal X-ray analysis. It crystallizes in the trigonal space group P3c1 with Z = 2 Fe(II) units at both temperatures. The molecular structure consists of chains running along the c axis in which the Fe(II) ions are linked by three N4,N4' coordinating bis(tetrazole) ligands. The main difference between the two forms appears to be in the Fe-N bond lengths, which are 2.164(4) A at 200 K and 2.038(4) A at 100 K. The Fe-Fe separations are 7.422(1) A at 200 K and 7.273(1) A at 100 K. The EXAFS results are consistent with the crystal structure. In both spin states, the FeN6 octahedron is almost regular within the EXAFS resolution. The Fe-N distance is found as 2.16(2) A at 300 K and 2.00(2) A at 40 K. The absence of the "7 A peak" in the EXAFS spectra of [Fe(btzp)3](ClO4)2, in contrast with what has been observed for the [Fe(4-R-1,2,4-triazole)3]-(anion)2 chain compounds, confirms that this peak can be used as the signature of a metal alignment only when it involves a strongly enhanced multiple scattering M-M-M path, with M-M spacing less than 4 A. Irradiation with green light at 5 K has led to the population of the metastable high-spin state for the iron(II) ion. The nature of the spin-crossover behavior has been discussed on the basis of the structural features.

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