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.