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The twinned crystal structure of mu-2,2'-bipyrimidine-1kappa2N1,N1':2kappa2N3,N3'-bis{tris[4,4,4-trifluoro-1-(2-thienyl)butane-1,3-dionato-kappa2O,O']terbium(III)} ethyl acetate solvate.

The title compound, [Tb2(C24H12F9O6S3)2(C8H6N4)].C4H8O2, has two terbium(III) centers bridged by the polyazine ligand 2,2'-bipyrimidine (bpm), which is distorted from planarity by 7.0 (2) degrees . The terminal ligand 4,4,4-trifluoro-1-(2-thienyl)butane-1,3-dione (tta) is bidentate, coordinating through the two O atoms, while the bridging ligand is bis-bidentate, coordinating through four equivalent N atoms. Both the complex and the ethyl acetate solvent molecules are disordered. The structure was refined as a non-merohedral twin.

Crystallography, X-Ray↗

Structure of aqua[N,N'-ethylenebis(N-carbamoylmethylglycinato)]copper(II) dihydrate.

The structure consists of a copper(II) cation octahedrally coordinated to the polyaminocarboxylate ligand through five ligating atoms: one N atom of the ethylenediamine ring, two carboxylate O atoms and a molecule of water form a square plane, while one amide O and the other ethylenediamine-ring N atom are above and below the plane. The latter two atoms display tetragonal distortion. Eight intermolecular hydrogen bonds involve H, N and O atoms of the complex as well as the two water molecules of crystallization.

Antineoplastic Agents↗

Extraction of functional motion in trypsin crystal structures.

The analysis of anisotropic atomic displacement parameters for the direct extraction of functionally relevant motion from X-ray crystal structures of Fusarium oxysporum trypsin is presented. Several atomic resolution structures complexed with inhibitors or substrates and determined at different pH values and temperatures were investigated. The analysis revealed a breathing-like molecular motion conserved across trypsin structures from two organisms and three different crystal forms. Directional motion was observed suggesting a change of the width of the substrate-binding cleft and a change in the length of the specificity pocket. The differences in direction of motion across the structures are dependent on the mode of substrate or inhibitor binding and the chemical environment around the active-site residues. Together with the occurrence of multiple-residue conformers, they reflect spatial rearrangement throughout the deacylation pathway.

Anisotropy↗

Computer graphics representation of levels of organization in tobacco mosaic virus structure.

Methods for simplifying computer graphics images of atomic models of complex macromolecular assemblies have been applied to the tobacco mosaic virus structure to display different levels of its organization. By constructing sharply outlined pictures of the parts of the virus particle with the image resolution reduced or with obscuring detail eliminated, aspects of the subunit packing and chain folding are distinctly illustrated.

Computers↗

Laser flash photolysis study of the photocatalytic step of the photo-fenton reaction in saline solution.

The photo-Fenton reaction (Fe2+/Fe3+, H2O2, UV light) is strongly inhibited by high concentrations of added chloride ion. In this work, the effect of added chloride ion on the photocatalytic step that converts Fe(III) back to Fe(II) is studied by nanosecond laser flash photolysis over a wide range of pH (1.0-3.3) and concentrations of Fe(III) (0.1-1.0 mM) and chloride ion (0.05-0.75 M). An explicit mechanistic model based on the preferential formation of the less-reactive Cl2*- radical anion via two routes (competitive photolysis of the iron(III)-chloride complex to chlorine atoms instead of the desired hydroxyl radical and pH-dependent scavenging of the hydroxyl radical by chloride ion) is proposed. This model, which fits the laser flash photolysis data for the production and decay of Cl2*- over the entire range of conditions investigated, suggests that inhibition of the photocatalytic step of the photo-Fenton process in the presence of chloride ion can be circumvented by maintaining the pH of the medium at or slightly above 3.0 throughout the reaction.

Journal Article↗

Dynamic micro-magnetic resonance imaging of liver micrometastasis in mice with a novel liver macromolecular magnetic resonance contrast agent DAB-Am64-(1B4M-Gd)(64).

DAB-Am64-(1B4M-Gd)(64) is a newly synthesized macromolecular liver magnetic resonance imaging (MRI) contrast agent with a polypropylenimine diaminobutane (DAB) dendrimer conjugated with a bifunctional diethylenetriaminepentaacetic acid (DTPA) derivative for complexing Gd(III) atoms. The characteristics of DAB-Am64-(1B4M-Gd)(64), which quickly accumulated in the liver, have been reported recently. In the present study, the dynamic micro-MRI with DAB-Am64-(1B4M-Gd)(64) was obtained in the mouse liver metastasis model using colon carcinoma cells to evaluate the ability to visualize the micrometastatic tumors compared with that using Gd-DTPA. The dynamic micro-MRI with DAB-Am64-(1B4M-Gd)(64) was able to homogeneously enhance the normal liver parenchyma and visualize micrometastatic tumors of 0.3-mm diameter in the liver of the mice with better contrast than that with Gd-DTPA. In conclusion, DAB-Am64-(1B4M-Gd)(64) is a new liver MRI contrast agent potentially useful for diagnosis of micrometastasis in the liver.

Animals↗

[Modeling of the mechanism of interactions of oligonucleotides with 3'-end of the yeast tRNA(Phe)].

Three dimensional atomic models of complexes between 10-, 15-mer long oligonucleotides and east tRNAPhe have been calculated. It has been found that the fast-forming primary complexes are the major groove complexes with the coaxial acceptor- and T-steams of the tRNA(Phe). Oligonucleotide forms a triplex of the recombinant R-triplex type. The long steams allow to make a "strong complexes" whith oligonucleotide, which delivers its 3'-end nucleotides to the vicinity of the T-loop, adjacent to the steam. These nucleotides destabilize the loop structure and initiate conformational rearrangement with a local destruction of the tRNA(Phe) and formation of the final tRNA(Phe)-oligonucleotide complementary complex. The primary complex formation and following destruction of the tRNA(Phe) constitutes the mechanism of the 'molecular wedge'. The effective anticense oligonucleotide should consist of the three segments: 1--complex initiator, 2--complex formative, 3--loop destructor an have to be complementary to the tRNA structure element of [(free end)/loop-steam-loop].

Base Sequence↗

VQLM: a Visual Query Language for Macromolecular structural databases.

Databases of macromolecular structures allow researchers to identify general principles of molecular behavior. They do this by providing a variety of data obtained under a number of different experimental conditions. Many new tools have been developed recently to aid in exploratory analysis of structural data. However, some queries of interest still require considerable manual filtering of data. In particular, studies attempting to make generalizations about complex arrangements of atoms or building blocks in macromolecular structures cannot be approached directly with existing tools. Such studies are frequently carried out on only a few structures or else require a labor-intensive process. To address this problem, we have developed a visual language, VQLM (Visual Query Language for Macromolecules). A query is formulated in this language by drawing an abstract picture of substructures to be searched for in the database and specifying constraints on the objects in them. To illustrate the usefulness of our language, we show how to encode a number of queries that were found scientifically interesting in the published literature in molecular biology. VQLM relies on VQL, a new database language, as its underlying engine for database retrieval and computation. We believe that VQLM will make macromolecular structural data more accessible to scientists, enabling faster and deeper data analysis.

Animals↗

Strong and weak measures of efficacy: a comparison of chiropractic with biomedicine in the management of back pain.

A holistic, biocultural model for identifying efficacy in the management of back pain by chiropractic and medical doctors is proposed based on adopting the concepts of vertical reasoning and dual-level control. Using this approach, four different ways in which efficacy can be measured are identified: (a) anatomical-physiological (curing of disease), (b) body/mind (healing of illness), (c) sociocultural (termination of sickness) and (d) political-economic (ending no access to care). These four are conceptualized as relating to levels in a hierarchy of structures of increasing size and complexity ranging from atoms and molecules to societies and nations. In measuring efficacy at each level, it is important to distinguish weak from strong measures. Strong measures conform to a Guttman scale model; each higher measure of efficacy also demonstrates efficacy at all levels lower than itself. Weak measures fail to conform to a Guttman-like scale, and are therefore of questionable value when used to support decisions relating to health care policy.

Ambulatory Care↗

Axial Bonding Capabilities of Square Planar d(8)-ML(4) Complexes. Theoretical Study and Structural Correlations.

A qualitative molecular orbital study and a structural analysis of the bonding capabilities of the metal atoms in square planar ML(4) complexes of d(8) ions are presented. In addition to analyzing the donor-acceptor properties of the metal atom in such complexes, the following aspects are also studied: (a) the effect of axial groups (bases or acids) on the donor-acceptor properties of the metal atom; (b) the effect of the axial groups on the deviation of the ML(4) ensemble from planarity; (c) the effect of an axial group on the bond between the metal atom and another group in trans; and (d) the implications on chemical reactivity.

Journal Article↗

Atomic force microscopy imaging of DNA-cationic liposome complexes optimised for gene transfection into neuronal cells.

BACKGROUND: Cationic liposomes represent an important gene delivery system due to their low immunogenicity, but are relatively inefficient, with optimisation of DNA-liposome complexes (lipoplexes) for transfection necessary for each cell type of interest. There have been few studies examining optimisation in neuronal cell types or determining how the structure of lipoplexes affects transfection efficiency. METHODS: Four commercially available cationic liposome formulations were used to optimise transfection efficiency in neuronal cells. The DNA to liposome ratio and the amount of DNA used in transfections were varied. Transfection efficiency was determined by the percentage of cells positive for the micro-galactosidase reporter gene product. The structure of lipoplexes was studied using atomic force microscopy. Lipoplexes were characterised further using dynamic light scattering to determine size and fluorescence techniques to show DNA compaction. RESULTS: Optimal transfection conditions were found to differ between immortalised cell lines and primary cells. High transfection efficiencies in immortalised cell lines were achieved predominantly with multivalent cationic liposomes while primary neuronal cells showed optimal transfection efficiency with monovalent cationic liposomes. The structure of lipoplexes was observed with atomic force microscopy and showed globular complexes for multivalent cationic liposomes, while monovalent liposomes gave less compact structures. In support of this finding, high levels of DNA compaction with multivalent liposomes were observed using fluorescence quenching measurements for all DNA to liposome ratios tested. One monovalent liposome showed increasing levels of compaction with increasing liposome amount. Dynamic light scattering showed little change in complex size when the different lipoplexes were studied. CONCLUSIONS: Optimisation of transfection efficiency was different for cell lines and primary neurons. Immortalised cells showed optimal transfection with multivalent liposomes while primary neurons showed optimal transfection with monovalent liposomes. The charge ratio of the monovalent liposome was below one, suggesting a different mechanism of lipoplex binding and uptake in primary neurons. The structure of lipoplexes, as

Animals↗

Time-dependent complex formation of dendritic poly(L-lysine) with plasmid DNA and correlation with in vitro transfection efficiencies.

Dendritic poly(L-lysine) of the 6th generation shows high transfection efficiency into several cultivated cells with low cytotoxicity. In order to understand the mechanism of complex formation with plasmid DNA, the complex was observed using atomic force microscopy. After mixing for 15 min, 1-2 microns assemblies of complexes composed of several small particles (50-200 nm) were observed. At the same time, individual small complexes of 50 to 500 nm were observed on a mica surface. After incubation for 2 h, only the large complexes were found on the mica surface. As a result of further dynamic light scattering analysis and measurement of the transfection efficiency at different time points, the transfection efficiency of KG6 was found to increase with increasing size of the DNA-complexes. This result indicates that large complexes of more than 1 micron are major species that contribute to transfection in vitro.

DNA↗

Nature of metal binding sites in Cu(II) complexes with histidine and related N-coordinating ligands, as studied by EXAFS.

Knowledge of the complexes formed by N-coordinating ligands and Cu(II) ions is of relevance in understanding the interactions of this ion with biomolecules. Within this framework, we investigated Cu(II) complexation with mono- and polydentate ligands, such as ammonia, ethylenediamine (en), and phthalocyanine (Pc). The obtained Cu-N coordination distances were 2.02 A for [Cu(NH(3))(4)](2+), 2.01 A for [Cu(en)(2)](2+), and 1.95 A for CuPc. The shorter bond distance found for CuPc is attributed to the macrocyclic effect. In addition to the structure of the first shell, information on higher coordination shells of the chelate ligands could be extracted by EXAFS, thus allowing discrimination among the different coordination modes. This was possible due to the geometry of the complexes, where the absorbing Cu atoms are coplanar with the four N atoms forming the first coordination shell of the complex. For this reason multiple scattering contributions become relevant, thus allowing determination of higher shells. This knowledge has been used to gain information about the structure of the 1:2 complexes formed by Cu(II) ions with the amino acids histidine and glycine, both showing a high affinity for Cu(II) ions. The in-solution structure of these complexes, particularly that with histidine, is not clear yet, probably due to the various possible coordination modes. In this case the square-planar arrangements glycine-histamine and histamine-histamine as well as tetrahedral coordination modes have been considered. The obtained first-shell Cu-N coordination distance for this complex is 1.99 A. The results of the higher shells EXAFS analysis point to the fact that the predominant coordination mode is the so-called histamine-histamine one in which both histidine molecules coordinate Cu(II) cations through N atoms from the amino group and from the imidazole ring.

Absorptiometry, Photon↗

Competition between nonclassical hydrogen-bonded acceptor sites in complexes of neutral AH2 Radicals (A = B, Al, and Ga): A theoretical investigation.

An ab initio computational study of the properties of the neutral AH2 radicals (A = B, Al, Ga) as hydrogen-bond (HB) acceptors, with H-X (X = F, Cl, Br, CN, and CCH) as HB donors, is carried out at the UMP2/6-311++G(2d,2p) level. Two different minima have been found for each of the 15 possible dimers. One structure corresponds to a single-electron hydrogen-bonded complex (SEHB), with the A atom acting as an HB acceptor. The second corresponds to a dihydrogen bond complex between one of the hydrogen atoms of AH2 and the H-X molecule. Thus, all the atoms of the neutral AH2 molecule can act as HB acceptors and none as donors. The stability of the SEHB complexes decreases as BH2 > AlH2 > GaH2, while for the dihydrogen-bonded complexes the order is AlH2 > GaH2 > BH2. For the BH2 radical the SEHB complexes are stronger than the dihydrogen bonded ones, while the opposite is found for the AlH2 and GaH2 systems. Regarding the HB donors, the order found for the binding energy in the two types of complexes is H2A...HF > H2A...HCl > H2A...HBr > H2A...HCN > H2A...HCCH.

Aluminum↗

Theoretical study of the external heavy atom effect on phosphorescence of free-base porphin molecule.

The radiative lifetime of phosphorescence of free-base porphin (H2P) molecule and its complexes with noble-gas atoms are calculated by time-dependent density functions theory (TD DFT) with quadratic response functions for account of spin-orbit coupling and electric dipole activity. The complexes with Ne, Ar, Kr, and Xe are used to simulate the external heavy atom (EHA) effect on phosphorescence of the H2P molecule in the corresponding noble gas matrices. The B3LYP functional and small basis set (3-21G) are used throughout the study and comparison of all complexes but other basis sets are also utilized to support the chosen approach. A slow radiative rate constant of free-base porphin phosphorescence (about 10(-3) s(-1)) is obtained with all basis sets being in the order of magnitude agreement with experimental estimations. A strong enhancement of the H2P phosphorescence rate (by 360 times) is calculated for Xe complex; while for Ne, Ar, and Kr complexes, the enhancement is equal to 1.1, 1.3, and 10.3 times, respectively. In these complexes, the noble gas atom is disposed at 3.6 A above the center of the porphin ring. In spite of shortcomings of the chosen simple model, the TD DFT calculations explain the most important features of the EHA effect on phosphorescence of free-base porphin. Calculations of the hyperfine coupling tensors for all magnetic nuclei in the lowest triplet state of H2P molecule and its complexes with noble-gas atoms indicate an appreciable penetration of the spin density to the EHA region. This can be connected with the enhancement of spin-orbit coupling in the H2P molecule.

Electrons↗

Mechanism of the palladium-catalyzed homocoupling of arylboronic acids: key involvement of a palladium peroxo complex.

The mechanism of the palladium-catalyzed homocoupling of arylboronic acids ArB(OH)(2) (Ar = 4-Z-C(6)H(4) with Z = MeO, H, CN) in the presence of dioxygen, leading to symmetrical biaryls, has been fully elucidated. The peroxo complex (eta(2)-O(2))PdL(2) (L = PPh(3)), generated in the reaction of dioxygen with the Pd(0) catalyst, was found to play a crucial role. Indeed, it reacts with the arylboronic acid to generate an adduct (coordination of one oxygen atom of the peroxo complex to the oxophilic boron atom of the arylboronic acid) characterized by (31)P NMR spectroscopy and ab initio calculations. This adduct reacts with a second molecule of arylboronic acid to generate trans-ArPd(OH)L(2) complexes. A transmetalation by the arylboronic acid gives trans-ArPdArL(2) complexes. The biaryl is then released in a reductive elimination. This reaction is at the origin of the formation of biaryls as byproducts in palladium-catalyzed Suzuki-Miyaura reactions when they are not conducted under oxygen-free atmosphere.

Journal Article↗

A bifurcated pathway of oxygen atom transfer reactions from a monooxo molybdenum(VI) complex under electrospray ionisation mass spectrometric conditions.

A stable molybdenum(V) complex, LMoOCl2(where L is hydrotris(3,5-dimethylpyrazolyl)borate), has been oxidized under mass spectrometric conditions. The oxidized species reacts with tertiary phosphines and the products have been detected by mass spectrometry. The product distribution has been followed by isotope labeling experiments, and energy dependent electrospray mass spectrometry. These experiments reveal not only oxygen atom transfer but also loss of a chlorine atom from the resulting species.

Molecular Conformation↗

Toward the understanding of the structure and dynamics of protein-carbohydrate interactions: molecular dynamics studies of the complexes between hevein and oligosaccharidic ligands.

Herein we study, through all atom molecular dynamics simulations, the complex between hevein and two N-acetylated chitin oligomers, namely N,N(')-diacetylchitobiose and N,N('),N(")-triacetylchitotriose. The results of the simulations for two disaccharide complexes and one trisaccharide complex show that a carbohydrate oligomer is able to move on the surface of the relatively flat binding pocket of hevein, therefore occupying different binding subpockets. Statistical analysis methods were also applied in order to define the principal overall motions in the complexes, showing how the different ligands in the simulations modulate the protein motions. The oligosaccharide binding can be considered as defined by a subtle balance between enthalpic (formation of intermolecular interactions between the ligand and the receptor) and entropic (due mainly to the possibility for the sugar to move on the surface of the protein domain) effects, determining multiple binding conformations. This structural and dynamical view could parallel the results obtained by regularly used restrained MD simulations based on NOE NMR data that provide a well defined structure for both the disaccharide and trisaccharide complexes, and agrees with the observations for longer oligosaccharide chains.

Antimicrobial Cationic Peptides↗