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Ion Coordination (ion + coordination)
Selected AbstractsA Study on the Effect of Lanthanide Ion Coordination on the Stereoselective Synthesis of ,-Mannopyranosides.CHEMINFORM, Issue 24 2003Young-Hoon Ahn Abstract For Abstract see ChemInform Abstract in Full Text. [source] Metal Ion Coordination to Azole NucleosidesCHEMISTRY - A EUROPEAN JOURNAL, Issue 21 2005Jens Müller Dr. Abstract To evaluate the possibility of introducing azole nucleosides as building blocks for metal-mediated base pairs in artificial oligonucleotides, imidazole nucleoside, 1,2,4-triazole nucleoside and tetrazole nucleoside have been synthesized and characterized. The X-ray crystal structures of p -toluoyl-protected 1,2,4-triazole and tetrazole nucleosides are reported. Contrary to the situation primarily found for deoxyribonucleosides, the sugar moieties adopt C3,- endo conformations. The acidity of the , nucleosides increases with increasing number of nitrogen ring atoms, giving pKa values of 6.01±0.05, 1.32±0.05 and <,3, respectively. This decrease in basicity results in a decreasing ability to form 2:1 complexes with linearly coordinating metal ions such as Ag+ and Hg2+. In all cases, the Ag+ complexes are of higher stability than the corresponding Hg2+ complexes. Whereas imidazole nucleoside forms highly stable 2:1 complexes with both metal ions (estimated log ,2 values of >10), only Ag+ is able to reach this coordination pattern in the case of triazole nucleoside (log ,2 = 4.3±0.1). Tetrazole nucleoside does not form 2:1 complexes at all under the experimental conditions used. These data suggest that imidazole nucleoside, and to a lesser extent 1,2,4-triazole nucleoside, are likely candidates for successful incorporation as ligands in oligonucleotides based on metal-mediated base pairs. DFT calculations further corroborate this idea, providing model complexes for such base pairs with glycosidic bond distances (10.8,11.0 Å) resembling those in idealized B-DNA (10.85 Å). [source] Multiple ligand simultaneous docking: Orchestrated dancing of ligands in binding sites of proteinJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 10 2010Huameng Li Abstract Present docking methodologies simulate only one single ligand at a time during docking process. In reality, the molecular recognition process always involves multiple molecular species. Typical protein,ligand interactions are, for example, substrate and cofactor in catalytic cycle; metal ion coordination together with ligand(s); and ligand binding with water molecules. To simulate the real molecular binding processes, we propose a novel multiple ligand simultaneous docking (MLSD) strategy, which can deal with all the above processes, vastly improving docking sampling and binding free energy scoring. The work also compares two search strategies: Lamarckian genetic algorithm and particle swarm optimization, which have respective advantages depending on the specific systems. The methodology proves robust through systematic testing against several diverse model systems: E. coli purine nucleoside phosphorylase (PNP) complex with two substrates, SHP2NSH2 complex with two peptides and Bcl-xL complex with ABT-737 fragments. In all cases, the final correct docking poses and relative binding free energies were obtained. In PNP case, the simulations also capture the binding intermediates and reveal the binding dynamics during the recognition processes, which are consistent with the proposed enzymatic mechanism. In the other two cases, conventional single-ligand docking fails due to energetic and dynamic coupling among ligands, whereas MLSD results in the correct binding modes. These three cases also represent potential applications in the areas of exploring enzymatic mechanism, interpreting noisy X-ray crystallographic maps, and aiding fragment-based drug design, respectively. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010 [source] Molecular structure of the outer bacterial membrane of Pseudomonas aeruginosa via classical simulationBIOPOLYMERS, Issue 6 2002Robert M. Shroll Abstract A detailed structural analysis has been performed of the outer bacterial membrane of Pseudomonas aeruginosa using a parameterized classical simulation model (R. D. Lins and T. P. Straatsma, Biophysical Journal, 2001, Vol. 81, pp. 1037,1046) with modest modifications. The structural analysis of the membrane is presented and newly discovered characteristics of the membrane are discussed. Simulations indicate that the relative contribution of different ligands to calcium ion coordination varies across the membrane, while maintaining a constant average coordination number of 6.1. Water penetrates the surface of the membrane to a depth of about 30 Å. The hydration of ions and phosphate groups is shown to depend on location within the membrane. A measure of saccharide residue orientation is defined and average orientations are presented. Saccharide residues possess varying degrees of motion with a trend of greater mobility at the membrane surface. However, their motion is limited and even in the membrane outer core region the average structure appears fairly rigid over a period of 1 ns. © 2002 Wiley Periodicals, Inc. Biopolymers 65: 395,407, 2002 [source] Dendrimers as Ligands: An Investigation into the Stability and Kinetics of Zn2+ Complexation by Dendrimers with 1,4,8,11-Tetraazacyclotetradecane (Cyclam) CoresCHEMISTRY - A EUROPEAN JOURNAL, Issue 4 2004Christophe Saudan Dr. Abstract We have investigated the complexation of Zn2+ with 1,4,8,11-tetrakis(naphthylmethyl) cyclam (1; cyclam=1,4,8,11-tetraazacyclotetradecane) and with two dendrimers consisting of a cyclam core with four dimethoxybenzene and eight naphthyl appendages (2), and twelve dimethoxybenzene and sixteen naphthyl appendages (3). An important, common feature of model compound 1 and dendrimers 2 and 3 is that their potentially fluorescent naphthyl units are quenched by exciplex formation with the cyclam nitrogen atoms. Complexation with Zn2+, however, prevents exciplex formation and results in the appearance of an intense naphthyl fluorescence signal that can be used for monitoring the complexation process. Luminescence titration, together with competition experiments and 1H NMR titration, have shown that 1:1 and 1:2 (metal/ligand) complexes are formed in the cases of 2 and 3, whereas model compound 1 gives only a 1:1 complex. We have also investigated the 1:1 complexation kinetics by the stopped-flow technique. In the case of 1, a second-order process (k1=44×105,M,1,s,1) is followed by two consecutive first-order steps (k2=0.53 s,1 and k3=0.10 s,1). For 2, a slower second-order process (k1=4.9×105,M,1,s,1) is followed by a slow first-order step (k2=0.40 s,1). In the case of 3, only a very slow second-order process was observed (k1=1.2×105,M,1,s,1). The different metal,ion incorporation rates for model compound 1 and dendrimers 2 and 3 have been discussed in terms of conformational changes of the dendron subunits affecting the chelating properties of the cyclam core. This work reports the first kinetic study on metal,ion coordination by dendrimers with a well-defined coordination site. [source] | ||||||||||