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At least 811 records · Page 45Linked to original sources
PubMed2002

Cyclitol-based metal-complexing agents. Effect of the relative orientation of oxygen atoms in the ionophoric ring on the cation-binding ability of myo-inositol-based crown ethers.

myo-Inositol-derived crown ethers having varying relative orientations (1,3-diaxial, 1,2-diequatorial, and 1,2-axial-equatorial) of the oxygen atoms in the ionophoric ring were synthesized and the extent of their binding with picrates of alkali metals, ammonia, and silver were estimated. These crown ethers bind very well with potassium and silver picrates and show good to moderate binding toward lithium, sodium, cesium, and ammonium picrates. These myo-inositol-derived crown ethers exhibit very strong binding for silver, even though they do not have sulfur or nitrogen coordinating sites in them, which are known to have high affinity for silver. The ratio of binding constants for silver to other ions tested varies from 10(2) to 10(5). The ion selectivity and the strength of binding are dependent on the relative orientation of the oxygen atoms in the ionophoric ring as well as on the size of the macrocyclic ring.

Ammonia↗
PubMed2005

HRTEM imaging of atoms at sub-Angström resolution.

John Cowley and his group at Arizona State University pioneered the use of transmission electron microscopy for high-resolution imaging. Images were achieved three decades ago showing the crystal unit cell content at better than 4 A resolution. This achievement enabled researchers to pinpoint the positions of heavy atom columns within the unit cell. Lighter atoms appear as resolution is improved to sub-Angström levels. Currently, advanced microscopes can image the columns of the light atoms (carbon, oxygen, nitrogen) that are present in many complex structures, and even the lithium atoms present in some battery materials. Sub-Angström imaging, initially achieved by focal-series reconstruction of the specimen exit surface wave, will become commonplace for next-generation electron microscopes with C(S)-corrected lenses and monochromated electron beams. Resolution can be quantified in terms of peak separation and inter-peak minimum, but the limits imposed on the attainable resolution by the properties of the microscope specimen need to be considered. At extreme resolution the 'size' of atoms can mean that they will not be resolved even when spaced farther apart than the resolution of the microscope.

Journal Article↗
PubMed1985

Interactions of Streptomyces subtilisin inhibitor with Streptomyces griseus proteases A and B. Enzyme kinetic and computer simulation studies.

Streptomyces subtilisin inhibitor (SSI), a dimeric protein that strongly inhibits subtilisins, was shown to form tight inhibitory complexes with Streptomyces griseus proteases A and B (SGPA and SGPB). The apparent dissociation constants of the SGPA-SSI and SGPB-SSI complexes were found to be orders of magnitude less than those of subtilisin-SSI complexes. Using the known atomic coordinates for SGPA and SSI, the highly complementary nature of the surface geometries of the two proteins was confirmed by a computer graphics study, which led to a proposed structure for the SGPA-SSI complex. Kinetic studies further suggested that the SSI dimer can bind two molecules of either SGPA or SGPB, and the 2:1-complexes (consisting of one inhibitor dimer and one enzyme molecule) apparently possess lower intrinsic dissociation constants than the 2:2-complexes. It was also shown that both of SGPA and SGPB are inhibited by both soybean trypsin inhibitor (Kunitz) and bovine pancreatic trypsin inhibitor (Kunitz), but far less strongly than by SSI.

Aspartic Acid Endopeptidases↗
PubMed2003

Atomic resolution imaging of the (001) surface of UHV cleaved MgO by dynamic scanning force microscopy.

The (001) surface of UHV cleaved single MgO crystals was imaged with dynamic mode scanning force microscopy. Large-scale images show various defects, like steps of mostly one atomic height, rectangular holes of nanometer size, and some complex adstructures. First time images with atomic resolution show one square ionic sublattice in its bulklike dimension with a corrugation of up to 40 pm along the <001> direction. Most images exhibit atomic point defects which appear as depressions including a few ionic lattice sites proving that point defects are stable on flat terraces.

Journal Article↗
PubMed2006

Catena-poly[[diisothiocyanatocadmium(II)]-bis[mu-1,3-bis(1,2,4-triazol-1-ylmethyl)benzene-kappa2N4:N4']]: a double-chain coordination polymer.

The coordination geometry of the CdII atom in the title complex, [Cd(NCS)2(C12H12N6)2]n or [Cd(NCS)2(mbtz)2]n, where mbtz is 1,3-bis(1,2,4-triazol-1-ylmethyl)benzene, is a distorted compressed octahedron in which the CdII atom lies on an inversion centre, coordinated by four N atoms from the triazole rings of four mbtz ligands and two N atoms from two monodentate NCS- ligands. The structure is polymeric, with 24-membered spiro-fused rings extending along [100] and with the 24-membered ring containing two inversion-related mbtz molecules.

Crystallography, X-Ray↗
PubMed2006

THESEUS: maximum likelihood superpositioning and analysis of macromolecular structures.

UNLABELLED: THESEUS is a command line program for performing maximum likelihood (ML) superpositions and analysis of macromolecular structures. While conventional superpositioning methods use ordinary least-squares (LS) as the optimization criterion, ML superpositions provide substantially improved accuracy by down-weighting variable structural regions and by correcting for correlations among atoms. ML superpositioning is robust and insensitive to the specific atoms included in the analysis, and thus it does not require subjective pruning of selected variable atomic coordinates. Output includes both likelihood-based and frequentist statistics for accurate evaluation of the adequacy of a superposition and for reliable analysis of structural similarities and differences. THESEUS performs principal components analysis for analyzing the complex correlations found among atoms within a structural ensemble. AVAILABILITY: ANSI C source code and selected binaries for various computing platforms are available under the GNU open source license from http://monkshood.colorado.edu/theseus/ or http://www.theseus3d.org.

Algorithms↗
PubMed2003

Double bonds in motion: bis(oxazolinylmethyl)pyrroles and their metal-induced planarization to a new class of rigid chiral C2-symmetric complexes.

The synthesis of a new class of chiral C(2)-symmetric tridentate N-donor ligands, a series of 2,5-bis(2-oxazolinylmethyl)pyrroles, was achieved in four steps starting from the known 2,5-bis(trimethylammoniomethyl)pyrrole diiodide (1). Reaction of 1 with NaCN in dimethyl sulfoxide gave 2,5-bis(cyanomethyl)pyrrole (2) cleanly, which was then cyclized with amino alcohols to give the 2,5-bis(2-oxazolinylmethyl)pyrroles 3 a-c (3 a: bis[2-(4,4'-dimethyl-5-hydrooxazolyl)methyl]pyrrole; 3 b: (S,S)-bis[2-(4-isopropyl-4,5-dihydrooxazolyl)methyl]pyrrole; 3 c: (S,S)-bis[2-(4-tertiobutyl-4,5-dihydrooxazolyl)methyl]pyrrole). Metallation of 3 a-c with one molar equivalent of tBuLi and their subsequent reaction with a stoichiometric amount of [PdCl(2)(cod)] (cod=cyclooctadiene) gave the palladium(II) complexes 4 a-c. Whereas the arrangement of the N-donor atoms in the crystallographically characterized complex 4 a is almost ideally square planar, all three heterocycles in the ligand are twisted out of the coordination plane, leading to a chiral conformation of the complex. Attempts to freeze out these two conformers in solution at 200 K (NMR) failed, and this suggests that the activation barrier for conformational racemization is significantly below 10 kcal mol(-1). The palladium-induced shift of two double bonds as well as the porphyrinogen/porphyrin-type oxidation of the complexes 4 a-c led to the planarization of the 2,5-bis(oxazolinylmethyl)pyrrolide ligands in the palladium(II) complexes 5 a-c, 6 b, and 6 c, and to the formation of rigid chiral C(2)-symmetric systems as shown by X-ray diffraction studies. The formation of the conjugated system of double bonds in this transformation is accompanied by the emergence of an intra-ligand chromophore. This is evident in the absorption spectrum of 6 c which displays an intense band with a maximum at 485 nm attributable to an intra-ligand pi*<--pi transition and a characteristic vibrational progression of nu approximately 1350 cm(-1). Complexes 4 b and 4 c were tested in the catalytic asymmetric Michael addition of ethyl 2-cyanopropionate to methyl vinylketone (catalyst loading: 1 mol %) and were found to give maximum ee values of 43 % (4 b) and 21 % (4 c) at low conversions.

Journal Article↗
PubMed2006

Matrix isolation infrared spectroscopic and theoretical study of nickel, palladium, and platinum nitrous oxide complexes.

Binary nickel, palladium, and platinum nitrous oxide complexes Ni(NNO)x, Pd(NNO)x (x = 1, 2), and PtNNO have been produced by the reactions of laser-evaporated metal atoms with nitrous oxide in solid argon. The complexes were identified on the basis of isotopically substituted infrared absorptions as well as theoretical frequency calculations. These complexes were characterized to have structures with the terminal N atom of N(2)O bound to the metal atoms. The MNNO complexes are photosensitive and rearrange to OMNN or MO + N(2) upon ultraviolet-visible irradiation.

Journal Article↗
PubMed2005

Family of mixed-valence oxovanadium(IV/V) dinuclear entities incorporating N4O3-coordinating heptadentate ligands: synthesis, structure, and EPR spectra.

Dinuclear (V(IV)V(V)) oxophenoxovanadates of general formula [V2O3L] have been synthesized in excellent yields by reacting bis(acetylacetonato)oxovanadium(IV) with H3L in a 2:1 ratio in acetone under an N2 atmosphere. Here L3- is the deprotonated form of 2,6-bis[{{(2-hydroxybenzyl)(N',N'-(dimethylamino)ethyl)}amino}methyl]-4-methylphenol (H3L1), 2,6-bis[{{(5-methyl-2-hydroxybenzyl)(N',N'-(dimethylamino)ethyl)}amino}methyl]-4-methylphenol (H3L2), 2,6-bis[{{(5-tert-butyl-2-hydroxybenzyl)(N',N'-(dimethylamino)ethyl)}amino}methyl]-4-methylphenol (H3L3), 2,6-bis[{{(5-chloro-2-hydroxybenzyl)(N',N'-(dimethylamino)ethyl)}amino}methyl]-4-methylphenol(H3L4), 2,6-bis[{{(5-bromo-2-hydroxybenzyl)(N'N'-(dimethylamino)ethyl)}amino}methyl]-4-methylphenol (H3L5), or 2,6-bis[{{(5-methoxy-2-hydroxybenzyl)(N'N'-(dimethylamino)ethyl)}methyl]-4-methylphenol (H3L6). In [V2O3L1], both the metal atoms have distorted octahedral geometry. The relative disposition of two terminal V=O groups in the complex is essentially cis. The O=V...V=O torsion angle is 24.6(2) degrees . The V-O(oxo)-V and V-O(phenoxo)-V angles are 117.5(4) and 93.4(3) degrees , respectively. The V...V bond distance is 3.173(5) A. X-ray crystallography, IR, UV-vis, and 1H and 51V NMR measurements show that the mixed-valence complexes contain two indistinguishable vanadium atoms (type III). The thermal ellipsoids of O2, O4, C10, C14, and C15 also suggests a type III complex in the solid state. EPR spectra of solid complexes at 77 K display a single line indicating the localization of the odd electron (3d(xy)1). Valence localization at 77 K is also consistent with the 51V hyperfine structure of the axial EPR spectra (3d(xy)1 ground state) of the complexes in frozen (77 K) dichloromethane solution: S = 1/2, g(parallel) approximately 1.94, g(perpendicular) approximately 1.98, A(parallel) approximately 166 x 10(-4) cm(-1), and A(perpendicular) approximately 68 x 10(-4) cm(-1). In contrast isotropic room-temperature solution spectra of the family have 15 hyperfine lines (g(iso) approximately 1.974 and A(iso) approximately 50 x 10(-4) cm(-1)) revealing that the unpaired electron is delocalized between the metal centers. Crystal data for the [V2O3L1].CH2Cl2 complex are as follows: chemical formula, C32H43O6N4Cl2V2; crystal system, monoclinic; space group, C2/c; a = 18.461(4), b = 17.230(3), c = 13.700(3) A; beta = 117.88(3) degrees ; Z = 8.

Journal Article↗
PubMed2005

Backbone metal-cyclization: a novel approach for simultaneous peptide cyclization and radiolabeling. Application to the combinatorial synthesis of rhenium-cyclic somatostatin analogs.

A novel approach for the combinatorial synthesis of backbone-derived metal-cyclic peptide libraries is presented. In this approach the metalo-cyclic peptides are prepared from their linear precursors through complexation of a metal atom via two hemi-chelating arms located on the peptide backbone. Thus, cyclization and metal labeling of the peptides are achieved simultaneously. A library, composed of 48 rhenium-cyclic somatostatin analogs, was prepared. All rhenium somatostatin complexes exhibited high to moderate in vitro binding affinities toward cloned human somatostatin receptor subtype 2 (hsstr2). Five rhenium-cyclic peptides were found to be most potent with IC50 values between 1 and 3 nM making them promising leads for further development of tumor diagnostic and therapeutic radiolabeled agents. A 99mTc somatostatin cyclic analog was successfully prepared by the same method.

Binding Sites↗
PubMed2001

Modeling platinum group metal complexes in aqueous solution.

We construct force fields suited for the study of three platinum group metals (PGM) as chloranions in aqueous solution from quantum chemical computations and report experimental data. Density functional theory (DFT) using the local density approximation (LDA), as well as extended basis sets that incorporate relativistic corrections for the transition metal atoms, has been used to obtain equilibrium geometries, harmonic vibrational frequencies, and atomic charges for the complexes. We found that DFT calculations of [PtCl(6)](2-).3H(2)O, [PdCl(4)](2-).2H(2)O, and [RhCl(6)](3-).3H(2)O water clusters compared well with molecular mechanics (MM) calculations using the specific force field developed here. The force field performed equally well in condensed phase simulations. A 500 ps molecular dynamics (MD) simulation of [PtCl(6)](2-) in water was used to study the structure of the solvation shell around the anion. The resulting data were compared to an experimental radial distribution function derived from X-ray diffraction experiments. We found the calculated pair correlation functions (PCF) for hexachloroplatinate to be in good agreement with experiment and were able to use the simulation results to identify and resolve two water-anion peaks in the experimental spectrum.

Journal Article↗
PubMed2003

Development of a novel gene delivery scaffold utilizing colloidal gold-polyethylenimine conjugates for DNA condensation.

We have developed a novel gene delivery scaffold based on DNA plasmid condensation with colloidal gold/polyethylenimine conjugates. This scaffold system was designed to enable systematic study of the relationships between DNA complex physical properties and transfection efficiency. Using an enhanced green fluorescent protein-coding reporter plasmid and a Chinese hamster ovary cell line, we have measured the transfection efficiencies of our complexes using flow cytometry and their cytotoxicities using the trypan blue assay. We have also assayed complex particle morphologies using atomic force microscopy, photon correlation spectroscopy, and a novel plasmon absorbance peak position analysis. We achieved comparable rates of transfection relative to the commonly used polycationic condensation agents calcium phosphate and LipofectAMINE, with comparably low cytotoxicities. In addition, by manipulating colloidal gold concentration, we could partially decouple complex physical properties including charge ratio, size, DNA loading, and polyethylenimine concentration. Our morphological analyses showed that complexes with a diameter of a few hundred nanometers and a charge ratio of approximately 8 perform best in our transfection efficiency assays. The use of colloidal gold as a component in our delivery system provides a versatile system for manipulating complex properties and morphology as well as a convenient scaffold for planned ligand conjugation studies.

Animals↗
PubMed2006

De novo design of synthetic di-iron(I) complexes as structural models of the reduced form of iron-iron hydrogenase.

Simple synthetic di-iron dithiolate complexes provide good models of the composition of the active site of the iron-iron hydrogenase enzymes. However, the formally Fe(I)Fe(I) complexes synthesized to date fail to reproduce the precise orientation of the diatomic ligands about the iron centers that is observed in the molecular structure of the reduced form of the enzyme active site. This structural difference is often used to explain the fact that the synthetic di-iron complexes are generally poor catalysts when compared to the enzyme. Herein, density functional theory computations are used for the rational design of synthetic complexes as structural models of the reduced form of the enzyme active site. These computations suggest several possible synthetic targets. The synthesis of complexes containing five-atom S-to-S linkers of the form S(CH2)2X(CH2)2S (X = CH2, NH, or O) or pendant functionalities attached to the three-carbon framework is one method. Another approach is the synthesis of asymmetrically substituted complexes, in which one iron center has strongly electron donating ligands and the adjacent iron center has strongly electron accepting ligands. The combination of a sterically demanding S-to-S linker and asymmetric substitution of the CO ligands is predicted to be a particularly effective synthetic target.

Hydrogenase↗
PubMed1999

Dynamic character of the complex of human blood coagulation factor VIIa with the extracellular domain of human tissue factor: a normal mode analysis.

As an attempt to investigate the dynamic interactions between plasma serine protease, coagulation factor VIIa (VIIa) and its cofactor, tissue factor (TF), we performed normal mode analysis (NMA) of the complex of VIIa with soluble TF (the extracellular part of TF; sTF). We compared fluctuations of Calpha atoms of VIIa or sTF derived from NMA in the VIIa-sTF complex with those of VIIa or sTF in an uncomplexed condition. The atomic fluctuations of the Calpha atoms of sTF complexed with VIIa did not significantly differ from those of sTF without VIIa. In contrast, the atomic fluctuations of VIIa complexed with sTF were much smaller than those of VIIa without sTF. These results suggest that domain motions of VIIa molecule alone are markedly dampened in the VIIa-sTF complex and that the sTF molecule is relatively more rigid than the VIIa molecule. This may indicate functions of TF as a cofactor.

Amino Acids↗