Home About us Contact
|
Home About us Contact | ||
|
|
||
Form Hydrogen Bonds (form + hydrogen_bond)
Selected AbstractsVariability in the Structures of Luminescent [2-(Aminomethyl)pyridine]silver(I) Complexes: Effect of Ligand Ratio, Anion, Hydrogen Bonding, and ,-StackingEUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 16 2005Rodney P. Feazell Abstract The reaction of 2-(aminomethyl)pyridine (2-amp) with silver(I) salts of triflate (OTf,), trifluoroacetate (tfa,), and tetrafluoroborate (BF4,) produce monomeric, dimeric, bridged, and polymeric structural motifs. The structural characteristics are dependent upon the ratio of ligand/metal in the structure as well as the ability of the anion to coordinate to the metal centers and form hydrogen bonds to the bound ligands. The silver coordination environment takes on several geometries including near linear (6), trigonal (4), tetrahedral (1), and both trigonal-bipyramidal and square-based pyramidal in a single structure (2). Structures 2, 3, and 5 also display short Ag,Ag contacts ranging from 2.8958(3) to 3.0305(4) Å. The species with metal,metal interactions, which are connectively very similar to their metal-isolated counterparts of 1, 4, and 6, are held together only by weak ,-stacking interactions or hydrogen bonds to their respective anions. Low-temperature luminescence spectra were collected for all compounds and are compared. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2005) [source] NMR Quantification of Tautomeric Populations in Biogenic Purine BasesEUROPEAN JOURNAL OF ORGANIC CHEMISTRY, Issue 9 2009Bartl Abstract Purine bases such as purine, adenine, hypoxanthine, and mercaptopurine are known to exist in several tautomeric forms. Characterization of their tautomeric equilibria is important not only for predicting the regioselectivity of their N -alkylation reactions, but also for gaining knowledge of the patterns with which these compounds of significant biological activity form hydrogen bonds with their biological targets. The tautomeric equilibria of purine and some purine derivatives in methanol and N,N -dimethylformamide solutions were investigated by low-temperature 1H and 13C NMR spectroscopy. The N(7)H and N(9)H tautomeric forms were quantified by integrating the individual 1H NMR signals at low temperatures. The Gibbs free energy differences were calculated and the effects of substitution on the N(7)H/N(9)H ratio discussed. A previously published theoretically predicted mechanism of the tautomeric exchange is compared with our measurements in deuteriated solvents. The influence of concentration on the temperature of coalescence indicates that supramolecular clusters play a significant role in this proton transfer process. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2009) [source] The role of residues R97 and Y331 in modulating the pH optimum of an insect ,-glycosidase of family 1FEBS JOURNAL, Issue 24 2003Sandro R. Marana The activity of the digestive ,-glycosidase from Spodoptera frugiperda (Sf,gly50, pH optimum 6.2) depends on E399 (pKa = 4.9; catalytic nucleophile) and E187 (pKa = 7.5; catalytic proton donor). Homology modelling of the Sf,gly50 active site confirms that R97 and Y331 form hydrogen bonds with E399. Site-directed mutagenesis showed that the substitution of R97 by methionine or lysine increased the E399 pKa by 0.6 or 0.8 units, respectively, shifting the pH optima of these mutants to 6.5. The substitution of Y331 by phenylalanine increased the pKa of E399 and E187 by 0.7 and 1.6 units, respectively, and displaced the pH optimum to 7.0. From the observed ,pKa it was calculated that R97 and Y331 contribute 3.4 and 4.0 kJ·mol,1, respectively, to stabilization of the charged E399, thus enabling it to be the catalytic nucleophile. The substitution of E187 by D decreased the pKa of residue 187 by 0.5 units and shifted the pH optimum to 5.8, suggesting that an electrostatic repulsion between the deprotonated E399 and E187 may increase the pKa of E187, which then becomes the catalytic proton donor. In short the data showed that a network of noncovalent interactions among R97, Y331, E399 and E187 controls the Sf,gly50 pH optimum. As those residues are conserved among the family 1 ,-glycosidases, it is proposed here that similar interactions modulate the pH optimum of all family 1 ,-glycosidases. [source] Smart Hydrogels Co-switched by Hydrogen Bonds and ,,, Stacking for Continuously Regulated Controlled-Release SystemADVANCED FUNCTIONAL MATERIALS, Issue 4 2010Fang Li Abstract A series of hydrogels with continuously regulatable release behavior can be achieved by incorporating hydrogen bonding and ,,, stacking co-switches in polymers. A poly(nitrophenyl methacrylate- co -methacrylic acid) hydrogel (NPMAAHG) for control over drug release is fabricated by copolymerizing 4-nitrophenyl methacrylate and methacrylic acid using ethylene glycol dimethacrylate as a crosslinker. The carboxylic acid groups and nitrylphenyl groups form hydrogen bonds and ,,, stacking interactions, respectively, which act as switches to control the release of guest molecules from the polymers. As revealed by the simulated gastrointestinal tract drug release experiments, the as-synthesized NPMAAHG hydrogels can be regulated to release only 4.7% of drugs after 3,h in a simulated stomach and nearly 92.6% within 43,h in the whole digestive tract. The relation between the release kinetics and structures and the mechanism of the smart release control are analyzed in terms of diffusion exponent, swelling interface number, drug diffusion coefficient, and velocity of the swelling interface in detail. The results reveal that the release of guest molecules from the hydrogels can be continuously regulated for systemic administration by controlling the ratio of the hydrophilic hydrogen bonds and the hydrophobic ,,, stacking switches. [source] Proton transfer versus nontransfer in compounds of the diazo-dye precursor 4-(phenyldiazenyl)aniline (aniline yellow) with strong organic acids: the 5-sulfosalicylate and the dichroic benzenesulfonate salts, and the 1:2 adduct with 3,5-dinitrobenzoic acidACTA CRYSTALLOGRAPHICA SECTION C, Issue 10 2009Graham Smith The structures of two 1:1 proton-transfer red,black dye compounds formed by reaction of aniline yellow [4-(phenyldiazenyl)aniline] with 5-sulfosalicylic acid and benzenesulfonic acid, and a 1:2 nontransfer adduct compound with 3,5-dinitrobenzoic acid have been determined at either 130 or 200,K. The compounds are 2-(4-aminophenyl)-1-phenylhydrazin-1-ium 3-carboxy-4-hydroxybenzenesulfonate methanol solvate, C12H12N3+·C7H5O6S,·CH3OH, (I), 2-(4-aminophenyl)-1-phenylhydrazin-1-ium 4-(phenyldiazenyl)anilinium bis(benzenesulfonate), 2C12H12N3+·2C6H5O3S,, (II), and 4-(phenyldiazenyl)aniline,3,5-dinitrobenzoic acid (1/2), C12H11N3·2C7H4N2O6, (III). In compound (I), the diazenyl rather than the aniline group of aniline yellow is protonated, and this group subsequently takes part in a primary hydrogen-bonding interaction with a sulfonate O-atom acceptor, producing overall a three-dimensional framework structure. A feature of the hydrogen bonding in (I) is a peripheral edge-on cation,anion association also involving aromatic C,H...O hydrogen bonds, giving a conjoint R12(6)R12(7)R21(4) motif. In the dichroic crystals of (II), one of the two aniline yellow species in the asymmetric unit is diazenyl-group protonated, while in the other the aniline group is protonated. Both of these groups form hydrogen bonds with sulfonate O-atom acceptors and these, together with other associations, give a one-dimensional chain structure. In compound (III), rather than proton transfer, there is preferential formation of a classic R22(8) cyclic head-to-head hydrogen-bonded carboxylic acid homodimer between the two 3,5-dinitrobenzoic acid molecules, which, in association with the aniline yellow molecule that is disordered across a crystallographic inversion centre, results in an overall two-dimensional ribbon structure. This work has shown the correlation between structure and observed colour in crystalline aniline yellow compounds, illustrated graphically in the dichroic benzenesulfonate compound. [source] The Predicted 3D Structures of the Human M1 Muscarinic Acetylcholine Receptor with Agonist or Antagonist BoundCHEMMEDCHEM, Issue 8 2006Joyce Yao-chun Peng Abstract The muscarinic acetylcholine G-protein-coupled receptors are implicated in diseases ranging from cognitive dysfunctions to smooth-muscle disorders. To provide a structural basis for drug design, we used the MembStruk computational method to predict the 3D structure of the human M1 muscarinic receptor. We validated this structure by using the HierDock method to predict the binding sites for three agonists and four antagonists. The intermolecular ligand,receptor contacts at the predicted binding sites agree well with deductions from available mutagenesis experiments, and the calculated relative binding energies correlate with measured binding affinities. The predicted binding site of all four antagonists is located between transmembrane (TM) helices,3, 4, 5, 6, and 7, whereas the three agonists prefer a site involving residues from TM3, TM6, and TM7. We find that Trp,157(4) contributes directly to antagonist binding, whereas Pro,159(4) provides an indirect conformational switch to position Trp,157(4) in the binding site (the number in parentheses indicates the TM helix). This explains the large decrease in ligand binding affinity and signaling efficacy by mutations of Trp,157(4) and Pro,159(4) not previously explained by homology models. We also found that Asp,105(3) and aromatic residues Tyr,381(6), Tyr,404(7), and Tyr,408(7) are critical for binding the quaternary ammonium head group of the ligand through cation,, interactions. For ligands with a charged tertiary amine head group, we suggest that proton transfer from the ligand to Asp,105(3) occurs upon binding. Furthermore, we found that an extensive aromatic network involving Tyr,106(3), Trp,157(4), Phe,197(5), Trp,378(6), and Tyr,381(6) is important in stabilizing antagonist binding. For antagonists with two terminal phenyl rings, this aromatic network extends to Trp,164(4), Tyr,179(extracellular loop,2), and Phe,390(6) located at the extracellular end of the TMs. We find that Asn,382(6) forms hydrogen bonds with selected antagonists. Tyr381(6) and Ser,109(3) form hydrogen bonds with the ester moiety of acetylcholine, which binds in the gauche conformation. [source] Two transition metal coordination polymers of the 7,7,8,8-tetracyanoquinodimethane dianion (TCNQ2,)ACTA CRYSTALLOGRAPHICA SECTION C, Issue 1 2009Guangbin Wang Each of the two novel title transition metal coordination polymers, namely catena -poly[[bis{[tris(2-pyridylmethyl)amine]cobalt(II)}-,4 -7,7,8,8-tetracyanoquinodimethanide(2,)] bis[7,7,8,8-tetracyanoquinodimethanide(1,)] methanol disolvate], {[Co2(C12H4N4)(C18H18N4)2](C12H4N4)2·2CH3OH}n, (I), and catena -poly[[[[tris(2-pyridylmethyl)amine]iron(II)]-,2 -7,7,8,8-tetracyanoquinodimethanide(2,)] methanol solvate], {[Fe(C12H4N4)(C18H18N4)]·CH3OH}n, (II), contains ,4 -TPA and cis -bridging TCNQ2, ligands [TPA is tris(2-pyridylmethyl)amine and TCNQ is 7,7,8,8-tetracyanoquinodimethane], but the two compounds adopt entirely different structural motifs. Compound (I) consists of a ribbon coordination polymer featuring ,4 -TCNQ2, radical anion ligands bridging four different octahedral CoII centers. Each formula unit of the polymer is flanked by two uncoordinated TCNQ, anions and two methanol solvent molecules. All three TCNQ anions have crystallographic inversion symmetry. In (II), the 21 symmetry operator generates a one-dimensional zigzag chain of octahedral FeII centers with ,2 -TCNQ2, bridges. A methanol solvent molecule forms hydrogen bonds to one of the terminal N atoms of the bridging TCNQ2, dianion. To the best of our knowledge, these are the first examples of one-dimensional coordination polymers forming from cis coordination of two TCNQ ligands to octahedral metal centers. [source] Structural basis of the histidine-mediated vitamin D receptor agonistic and antagonistic mechanisms of (23S)-25-dehydro-1,-hydroxyvitamin D3 -26,23-lactoneACTA CRYSTALLOGRAPHICA SECTION D, Issue 8 2010Shinji Kakuda TEI-9647 antagonizes vitamin D receptor (VDR) mediated genomic actions of 1,,25(OH)2D3 in human cells but is agonistic in rodent cells. The presence of Cys403, Cys410 or of both residues in the C-terminal region of human VDR (hVDR) results in antagonistic action of this compound. In the complexes of TEI-9647 with wild-type hVDR (hVDRwt) and H397F hVDR, TEI-9647 functions as an antagonist and forms a covalent adduct with hVDR according to MALDI,TOF MS. The crystal structures of complexes of TEI-9647 with rat VDR (rVDR), H305F hVDR and H305F/H397F hVDR showed that the agonistic activity of TEI-9647 is caused by a hydrogen-bond interaction with His397 or Phe397 located in helix 11. Both biological activity assays and the crystal structure of H305F hVDR complexed with TEI-9647 showed that the interaction between His305 and TEI-9647 is crucial for antagonist activity. This study indicates the following stepwise mechanism for TEI-9647 antagonism. Firstly, TEI-9647 forms hydrogen bonds to His305, which promote conformational changes in hVDR and draw Cys403 or Cys410 towards the ligand. This is followed by the formation of a 1,4-Michael addition adduct between the thiol (,SH) group of Cys403 or Cys410 and the exo -methylene group of TEI-9647. [source] Phase transition of triclinic hen egg-white lysozyme crystal associated with sodium bindingACTA CRYSTALLOGRAPHICA SECTION D, Issue 4 2004Kazuaki Harata A triclinic crystal of hen egg-white lysozyme obtained from a D2O solution at 313,K was transformed into a new triclinic crystal by slow release of solvent under a temperature-regulated nitrogen-gas stream. The progress of the transition was monitored by X-ray diffraction. The transition started with the appearance of strong diffuse streaks. The diffraction spots gradually fused and faded with the emergence of diffraction from the new lattice; the scattering power of the crystal fell to a resolution of 1.5,Å from the initial 0.9,Å resolution. At the end of the transition, the diffuse streaks disappeared and the scattering power recovered to 1.1,Å resolution. The transformed crystal contained two independent molecules and the solvent content had decreased to 18% from the 32% solvent content of the native crystal. The structure was determined at 1.1,Å resolution and compared with the native structure refined at the same resolution. The backbone structures of the two molecules in the transformed crystal were superimposed on the native structure with root-mean-square deviations of 0.71 and 0.96,Å. A prominent structural difference was observed in the loop region of residues Ser60,Leu75. In the native crystal, a water molecule located at the centre of this helical loop forms hydrogen bonds to main-chain peptide groups. In the transformed crystal, this water molecule is replaced by a sodium ion with octahedral coordination that involves water molecules and a nitrate ion. The peptide group connecting Arg73 and Asn74 is rotated by 180° so that the CO group of Arg73 can coordinate to the sodium ion. The change in the X-ray diffraction pattern during the phase transition suggests that the transition proceeds at the microcrystal level. A mechanism is proposed for the crystal transformation. [source] Preliminary investigation of the three-dimensional structure of Salmonella typhimurium uridine phosphorylase in the crystalline stateACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 4 2005Olga K. Molchan Uridine phosphorylase (UPh) catalyzes the phosphorolytic cleavage of the C,N glycosidic bond of uridine to ribose 1-phosphate and uracil in the pyrimidine-salvage pathway. The crystal structure of the Salmonella typhimurium uridine phosphorylase (StUPh) has been determined at 2.5,Å resolution and refined to an R factor of 22.1% and an Rfree of 27.9%. The hexameric StUPh displays 32 point-group symmetry and utilizes both twofold and threefold non-crystallographic axes. A phosphate is bound at the active site and forms hydrogen bonds to Arg91, Arg30, Thr94 and Gly26 of one monomer and Arg48 of an adjacent monomer. The hexameric StUPh model reveals a close structural relationship to Escherichia coli uridine phosphorylase (EcUPh). [source] The Predicted 3D Structures of the Human M1 Muscarinic Acetylcholine Receptor with Agonist or Antagonist BoundCHEMMEDCHEM, Issue 8 2006Joyce Yao-chun Peng Abstract The muscarinic acetylcholine G-protein-coupled receptors are implicated in diseases ranging from cognitive dysfunctions to smooth-muscle disorders. To provide a structural basis for drug design, we used the MembStruk computational method to predict the 3D structure of the human M1 muscarinic receptor. We validated this structure by using the HierDock method to predict the binding sites for three agonists and four antagonists. The intermolecular ligand,receptor contacts at the predicted binding sites agree well with deductions from available mutagenesis experiments, and the calculated relative binding energies correlate with measured binding affinities. The predicted binding site of all four antagonists is located between transmembrane (TM) helices,3, 4, 5, 6, and 7, whereas the three agonists prefer a site involving residues from TM3, TM6, and TM7. We find that Trp,157(4) contributes directly to antagonist binding, whereas Pro,159(4) provides an indirect conformational switch to position Trp,157(4) in the binding site (the number in parentheses indicates the TM helix). This explains the large decrease in ligand binding affinity and signaling efficacy by mutations of Trp,157(4) and Pro,159(4) not previously explained by homology models. We also found that Asp,105(3) and aromatic residues Tyr,381(6), Tyr,404(7), and Tyr,408(7) are critical for binding the quaternary ammonium head group of the ligand through cation,, interactions. For ligands with a charged tertiary amine head group, we suggest that proton transfer from the ligand to Asp,105(3) occurs upon binding. Furthermore, we found that an extensive aromatic network involving Tyr,106(3), Trp,157(4), Phe,197(5), Trp,378(6), and Tyr,381(6) is important in stabilizing antagonist binding. For antagonists with two terminal phenyl rings, this aromatic network extends to Trp,164(4), Tyr,179(extracellular loop,2), and Phe,390(6) located at the extracellular end of the TMs. We find that Asn,382(6) forms hydrogen bonds with selected antagonists. Tyr381(6) and Ser,109(3) form hydrogen bonds with the ester moiety of acetylcholine, which binds in the gauche conformation. [source] | ||||||||||