Structure of the polyisoprenyl-phosphate glycosyltransferase GtrB and insights into the mechanism of catalysis.

The attachment of a sugar to a hydrophobic polyisoprenyl carrier is the first step for all extracellular glycosylation processes. The enzymes that perform these reactions, polyisoprenyl-glycosyltransferases (PI-GTs) include dolichol phosphate mannose synthase (DPMS), which generates the mannose donor for glycosylation in the endoplasmic reticulum. Here we report the 3.0 Å resolution crystal structure of GtrB, a glucose-specific PI-GT from Synechocystis, showing a tetramer in which each protomer contributes two helices to a membrane-spanning bundle. The active site is 15 Å from the membrane, raising the question of how water-soluble and membrane-embedded substrates are brought into apposition for catalysis. A conserved juxtamembrane domain harbours disease mutations, which compromised activity in GtrB in vitro and in human DPM1 tested in zebrafish. We hypothesize a role of this domain in shielding the polyisoprenyl-phosphate for transport to the active site. Our results reveal the basis of PI-GT function, and provide a potential molecular explanation for DPM1-related disease.

Low temperature crystal structures of two rhodanine derivatives, 3-amino rhodanine and 3-methyl rhodanine: geometry of the rhodanine ring

Rhodanines (2-thio-4-oxothiazolidines) are synthetic small molecular weight organic molecules with diverse applications in biochemistry, medicinal chemistry, photochemistry, coordination chemistry and industry. The X-ray crystal structure determination of two rhodanine derivatives, namely (I), 3-aminorhodanine [3-amino-2-thio-4-oxothiazolidine], C3H4N2OS2, and (II) 3-methylrhodanine [3-methyl-2-thio-4-oxothiazolidine], C4H5NOS2, have been conducted at 100 K. I crystallizes in the monoclinic space group P2(1)/n with unit cell parameters a = 9.662(2), b = 9.234(2), c = 13.384(2) angstrom, beta = 105.425(3)degrees, V = 1151.1(3) angstrom(3), Z = 8 (2 independent molecules per asymmetric unit), density (calculated) = 1.710 mg/m(3), absorption coefficient = 0.815 mm(-1). II crystallizes in the orthorhombic space group Iba2 with unit cell a = 20.117(4), b = 23.449(5), c = 7.852(2) angstrom, V = 3703.9(12) angstrom(3), Z = 24 (three independent molecules per asymmetric unit), density (calculated) = 1.584 mg/m(3), absorption coefficient 0.755 mm(-1). For I in the final refinement cycle the data/restraints/parameter ratios were 2639/0/161, goodness-of-fit on F-2 = 0.934, final R indices [I > 2sigma(I)] were R1 = 0.0299, wR2 = 0.0545 and R indices (all data) R1 = 0.0399, wR2 = 0.0568. The largest difference peak and hole were 0.402 and -0.259 e angstrom(-3). For II in the final refinement cycle the data/restraints/parameter ratios were 3372/1/221, goodness-of-fit on F(2) = 0.950, final R indices [I > 2sigma(I)] were R1 = 0.0407, wR2 = 0.1048 and R indices (all data) R1 = 0.0450, wR2 = 0.1088. The absolute structure parameter = 0.19(9) and largest difference peak and hole 0.934 and -0.301 e angstrom(-3). Details of the geometry of the five molecules (two for I and three for II) and the crystal structures are fully discussed. Corresponding features of the molecular geometry are highly consistent and firmly establish the geometry of the rhodanine

Structure of Ionic Liquid-Benzene Mixtures

Neutron diffraction has been used to investigate the structure of liquid mixtures of 1,3-dimethylimidazolium hexafluorophosphate with benzene. Two concentrations of benzene were investigated, namely, 33 mol % and 67 mol %, and show similar structures in each case. The presence of benzene significantly alters the ionic liquid structure, in particular, in the cation-cation interactions, in agreement with the single-crystal structure described recently (Holbrey, J. D.; Reichert, W. M.; Nieuwenhuyzen, M.; Sheppard, O.; Hardacre, C.; Rogers, R. D. Chem. Commun. 2003, 476). In each case, the data was analyzed using an empirical potential structure refinement process.

Structure of the adenylation domain of an NAD+-dependent DNA ligase

Background: DNA ligases catalyse phosphodiester bond formation between adjacent bases in nicked DNA, thereby sealing the nick. A key step in the catalytic mechanism is the formation of an adenylated DNA intermediate. The adenyl group is derived from either ATP (in eucaryotes and archaea) or NAD+4 (in bacteria). This difference in cofactor specificity suggests that DNA ligase may be a useful antibiotic target.

Results: The crystal structure of the adenylation domain of the NAD+-dependent DNA ligase from Bacillus stearothermophilus has been determined at 2.8 Å resolution. Despite a complete lack of detectable sequence similarity, the fold of the central core of this domain shares homology with the equivalent region of ATP-dependent DNA ligases, providing strong evidence for the location of the NAD+-binding site.

Conclusions: Comparison of the structure of the NAD+4-dependent DNA ligase with that of ATP-dependent ligases and mRNA-capping enzymes demonstrates the manifold utilisation of a conserved nucleotidyltransferase domain within this family of enzymes. Whilst this conserved core domain retains a common mode of nucleotide binding and activation, it is the additional domains at the N terminus and/or the C terminus that provide the alternative specificities and functionalities in the different members of this enzyme superfamily.

Liquid structure of the ionic liquid 1,3-dimethylimidazolium bis{(trifluoromethyl)sulfonyl}amide

Neutron diffraction has been used to determine the liquid structure of 1,3-dimethylimidazolium bis{( trifluoromethyl) sulfonyl} amide ([dmim][NTf2]). Significantly smaller charge ordering is found in this liquid compared with analogous chloride and hexafluorophosphate salts due to the diffuse charge density and size of the [NTf2](-) anion. This is manifested in a much larger cation-cation and cation-anion separation and an overlap of the cation-cation and cation-anion shells. Comparison of the liquid structure with the crystal structure reported by Holbrey et al. ( Dalton Trans. 2004, 2267) indicates little correlation, for example, the [NTf2](-) anion adopts a trans orientation predominantly in the liquid whereas a cis orientation is found in the solid phase.

[Ag(NH3)(2)]ClO4: Crystal structures, phase transition, and vibrational spectra

[Ag(NH3)(2)](ClO4) is obtained from a solution of AgClO4 in cone. ammonia as colourless single crystals (orthorhombic, Pnmn, Z = 4, a = 795.2(1) pm, b 617.7(1) pm, c = 1298.2(2) pm, R-all = 0.0494). The structure consists of linearly coordinated cations, [Ag(NH3)(2)](+), stacked in a staggered conformation and of tetrahedral (ClO4)(-) anions. A first order phase transition was observed between 210 and 200 K and the crystal structure of the low-temperature modification (monoclinic. P2/m, Z = 4, a = 789.9(5) pm, b = 604.1(5) pm, c = 1290.4(5) pm, beta = 97.436(5)degrees, at 170 K, R-all = 0.0636) has also been solved. Spectroscopic investigations (IR/Raman) have been carried out and the assignment of the spectra is discussed.

Synthesis, Structure, and Spectroscopic Properties of the New Lanthanum(III) Fluoride Oxomolybdate(VI) La3FMo4O16

La3FMo4O16 crystallizes in the triclinic crystal system with space group P (1) over bar [a = 724.86(2) pm, b = 742.26(2) pm, c = 1469.59(3) pm, a = 101.683(2)degrees, beta 102.118(2)degrees, gamma = 100.279(2)degrees] with two formula units per unit cell. The three crystallographically independent La3+ cations show a coordination number of nine each, with one F- and eight O2- anions forming distorted monocapped square antiprisms. The fluoride anion is coordinated by all three lanthanum cations to form a nearly planar triangle. Besides three crystallographically independent tetrahedral [MoO4](2-) units, a fourth one with a higher coordination number (CN = 4 +1) can be found in the crystal structure, forming a dimeric entity with a formula of [Mo2O8](4-) consisting of two edge-connected square pyramids. Several spectroscopic measurements were performed on the title compound, such as infrared, Raman, and diffuse reflectance spectroscopy. Furthermore, La3FMo4O16 was investigated for its capacity to work as host material for doping with luminescent active cations, such as Ce3+ or Pr3+. Therefore, luminescence spectroscopic as well as EPR measurements were performed with doped samples of the title compound. Both the pure and the doped compounds can be synthesized by fusing La2O3, LaF3 and MoO3 (ratio 4:1:12; ca. 1 % CeF3 and PrF3 as dopant, respectively) in evacuated silica ampoules at 850 degrees C for 7 d.

Structure-based design of selective high-affinity telomeric quadruplex-binding ligands.

A library of triazole-based telomeric quadruplex-selective ligands has been developed that mimic an established family of tri-substituted acridine-based ligands, using crystal structure data as a starting-point for computer-based design. Binding affinities, estimated by electrospray mass spectrometry, are in accord with the design concept.

Structure of the Plasmodium falciparum M17 aminopeptidase and significance for the design of drugs targeting the neutral exopeptidases

Current therapeutics and prophylactics for malaria are under severe challenge as a result of the rapid emergence of drug-resistant parasites. The human malaria parasite Plasmodium falciparum expresses two neutral aminopeptidases, PfA-M1 and PfA-M17, which function in regulating the intracellular pool of amino acids required for growth and development inside the red blood cell. These enzymes are essential for parasite viability and are validated therapeutic targets. We previously reported the x-ray crystal structure of the monomeric PfA-M1 and proposed a mechanism for substrate entry and free amino acid release from the active site. Here, we present the x-ray crystal structure of the hexameric leucine aminopeptidase, PfA-M17, alone and in complex with two inhibitors with antimalarial activity. The six active sites of the PfA-M17 hexamer are arranged in a disc-like fashion so that they are orientated inwards to form a central catalytic cavity; flexible loops that sit at each of the six entrances to the catalytic cavern function to regulate substrate access. In stark contrast to PfA-M1, PfA-M17 has a narrow and hydrophobic primary specificity pocket which accounts for its highly restricted substrate specificity. We also explicate the essential roles for the metal-binding centers in these enzymes (two in PfA-M17 and one in PfA-M1) in both substrate and drug binding. Our detailed understanding of the PfA-M1 and PfA- M17 active sites now permits a rational approach in the development of a unique class of two-target and/or combination antimalarial therapy.

Structure of molten 1,3-dimethylimidazolium chloride using neutron diffraction

The model room temperature ionic liquid, 1,3-dimethylimidazolium chloride, has been studied by neutron diffraction for the first time. The diffraction data are used to derive a structural model of this liquid using Empirical Potential Structure Refinement. The model obtained indicates that significant charge ordering is present in the liquid salt and that the local order in this liquid closely resembles that found in the solid state. As in the crystal structure, hydrogen-bonding interactions between the ring hydrogens and the chloride dominate the structure. The model is compared with the data reported previously for both simple alkyl substituted imidazolium halides and binary mixtures with AlCl3. (C) 2003 American Institute of Physics.

Polymères de coordination et éponge cristalline : de nouveaux matériaux pour la conversion de l’énergie solaire et la résolution de la structure cristalline de composés huileux.

Le premier volet de ce travail portera sur l’expérience acquise lors d’un stage d’étude à Tokyo, au Japon, dans le groupe de recherche du Pr. Makoto Fujita, une sommité d’envergure internationale dans le domaine de l’auto-assemblage. En continuité avec les plus récents travaux du Pr. Fujita, des systèmes poreux auto-assemblés présentant des cavités fonctionnalisées ont été développés dans le but d’encapsuler des acides gras afin d’en déterminer la structure cristalline. Ces éponges ont été caractérisées par des techniques courantes telles que la spectroscopie à résonance magnétique nucléaire 1H, 13C{1H} et Cosy, la spectrométrie de masse, l’analyse élémentaire, la microscopie optique infrarouge ainsi que la diffraction des rayons X. Une autre approche employée pour obtenir de meilleures propriétés spectroscopiques fut la synthèse de dendrimères métalliques de génération 0. Un nouveau ligand de type 1,3,5-triazine a été synthétisé par une réaction typique de cyclisation de nitrile en présence catalytique d’hydrure de sodium. Des espèces mono-, bis- et trinucléaire de Ru(II) furent synthétisés ainsi que deux espèces hétérométalliques de Ru(II)/Pt(II) et de Ru(II)/Os(II). Tous les complexes obtenus furent caractérisés par spectroscopie à résonance magnétique nucléaire (1H, 13C{1H} et Cosy) à l’état liquide, par spectroscopie de masse à haute résolution et par analyse élémentaire. La génération de dihydrogène à partir de l’espèce hétérométallique a été étudiée. Les propriétés optiques et électroniques ont été analysées par spectroscopie UV-Vis, par analyse de la luminescence, du temps de vie de luminescence, par des analyses de rendement quantique ainsi que par des analyses de voltampérométrie cyclique à balayage. Finalement, dans le but d’améliorer les propriétés spectroscopiques d’absorption de complexes métalliques, nous avons synthétisé une série de polymères homo- et hétérométalliques, intégrant des ligands de type bis(2,2’:6,2’’-terpyridine). Les complexes générés furent caractérisés par diverses techniques tel que la spectroscopie à résonance magnétique nucléaire (1H, 13C{1H} et Cosy) à l’état liquide, par spectroscopie de masse à haute résolution ainsi que par analyse élémentaire. Les propriétés optiques et électroniques ont été analysées par spectroscopie UV-Vis, par analyse de la luminescence, du temps de vie de luminescence, par des analyses de rendement quantique ainsi que par des analyses de voltampérométrie cyclique à balayage.

Synthesis, characterization, and structure of a new cobalt(II) Schiff-base complex with quinoxaline- 2-carboxalidine-2-amino-5-methylphenol

The mononuclear cobalt(II) complex [CoL2] H2O (where HL is quinoxaline-2-carboxalidine- 2-amino-5-methylphenol) has been prepared and characterized by elemental analysis, conductivity measurement, IR, UV-Vis spectroscopy, TG-DTA, and X-ray structure determination. The crystallographic study shows that cobalt(II) is distorted octahedral with each tridentate NNO Schiff base in a cis arrangement. The crystal exhibits a 2-D polymeric structure parallel to [010] plane, formed by O-H...N and O-H... O intermolecular hydrogen bonds and pye stacking interactions, as a racemic mixture of optical enantiomers. The ligand is a Schiff base derived from quinoxaline-2-carboxaldehyde

Transition metal complexes of some N4-phenylsemicarbazones: crystal structures and spectral studies

The unusual coordination modes of semicarbazones when bound to metals, the wide applications and structural diversity of metal complexes of semicarbazones provoked us to synthesize and characterize the tridentate ONO and NNO-donor semicarbazones and their transition metal complexes. This work is focused on the studies on complexes of three N4-phenylsemicarbazones synthesized by changing the carbonyl compounds. This work is concerned with the studies of two new semicarbazones, 2- formylpyridine-N4-phenylsemicarbazone (HL1) and 3-ethoxysalicylaldehyde- N4-phenylsemicarbazone (H2L2) and a reported semicarbazone 2-benzoylpyridine-N4-phenylsemicarbazone (HL3) [29]. The compositions of these semicarbazones were determined by the CHN analyses and IR, UV and NMR spectral studies were used for the characterization of these compounds. The molecular structure of 3-ethoxysalicylaldehyde-N4-phenylsemicarbazone (H2L2) was obtained by single crystal X-ray diffraction studies. Also, we have synthesized Cu(II), Cd(II), Zn(II) and Ni(II) complexes of these three semicarbazones. The complexes were characterized by various spectroscopic techniques, magnetic and conductivity studies. We could isolate single crystals of some complexes of all metals suitable for X-ray diffraction studies. This thesis is divided into six chapters.

Transition metal complexes derived from ketone based N(4)-substituted thiosemicarbazones: Crystal structures and spectral studies

Thiosemicarbazones have recently attracted considerable attention due to their ability to form tridentate chelates with transition metal ions through either two nitrogen and sulfur atoms, N–N–S or oxygen, nitrogen and sulfur atoms, O–N–S. Considerable interest in thiosemicarbazones and their transition metal complexes has also grown in the areas of biology and chemistry due to biological activities such as antitumoral, fungicidal, bactericidal, antiviral and nonlinear optical properties. They have been used for metal analyses, for device applications related to telecommunications, optical computing, storage and information processing.The versatile applications of metal complexes of thiosemicarbazones in various fields prompted us to synthesize the tridentate NNS-donor thiosemicarbazones and their metal complexes. As a part of our studies on transition metal complexes with these ligands, the researcher undertook the current work with the following objectives. 1. To synthesize and physico-chemically characterize the following thiosemicarbazone ligands: a. Di-2-pyridyl ketone-N(4)-methyl thiosemicarbazone (HDpyMeTsc) b. Di-2-pyridyl ketone-N(4)-ethyl thiosemicarbazone (HDpyETsc) 2. To synthesize oxovanadium(IV), manganese(II), nickel(II), copper(II), zinc(II) and cadmium(II) complexes using the synthesized thiosemicarbazones as principal ligands and some anionic coligands. 3. To study the coordination modes of the ligands in metal complexes by using different physicochemical methods like partial elemental analysis, thermogravimetry and by different spectroscopic techniques. 4. To establish the structure of compounds by single crystal XRD studies

Syntheses, EPR spectral studies and crystal structures of manganese(II) complexes of neutral N,N donor bidentate Schiff bases and azide/thiocyanate as coligand

Four manganese(II) complexes Mn2(paa)2(N3)4 (1), [Mn(paa)2(NCS)2] 3/2H2O (2), Mn(papea)2(NCS)2 (3), [Mn(dpka)2(NCS)2] 1/2H2O(4) of three neutral N,N donor bidentate Schiff bases were synthesized and physico- chemically characterized by means of partial elemental analyses, electronic, infrared and EPR spectral studies. Compounds 3 and 4 were obtained as single crystals suitable for X-ray diffraction. Compound 4 recrystallized as Mn(dpka)2(NCS)2. Both the compounds crystallized in the monoclinic space groups P21 for 3 and C2/c for 4. Manganese(II) is found to be in a distorted octahedral geometry in both the monomeric complexes with thiocyanate anion as a terminal ligand coordinating through the nitrogen atom. EPR spectra in DMF solutions at 77 K show hyperfine sextets with low intensity forbidden lines lying between each of the two main hyperfine lines and the zero field splitting parameters (D and E) were calculated.