PubMed Health⌕ Search

SEARCH · PubMed Health

Results for “ATOM complex”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 613 records · Page 34Linked to original sources

Computational investigation of adsorption of molecular hydrogen on lithium-doped corannulene.

Density functional theory and classical molecular dynamics simulations are used to investigate the prospect of lithium-doped corannulene as adsorbent material for H(2) gas. Potential energy surface scans at the level of B3LYP/6-311G(d,p) show an enhanced interaction of molecular hydrogen with lithium-atom-doped corannulene complexes with respect to that found in undoped corannulene. MP2(FC)/6-31G(d,p) optimizations of 4H(2)-(Li(2)-C(20)H(10)) yield H(2) binding energies of -1.48 kcal/mol for the H(2)-Li interaction and -0.92 kcal/mol for the H(2)-C interaction, whereas values of -0.94 and -0.83 kcal/mol were reported (J. Phys. Chem. B 2006, 110, 7688-7694) for physisorption of H(2) on the concave and the convex side of corannulene using MP2(full)/6-31G(d), respectively. Classical molecular dynamics simulations predict hydrogen uptakes in Li-doped corannulene assemblies that are significantly enhanced with respect to that found in undoped molecules, and the hydrogen uptake ability is dependent on the concentration of lithium dopant. For the Li(6)-C(20)H(10) complex, a hydrogen uptake of 4.58 wt % at 300 K and 230 bar is obtained when the adsorbent molecules are arranged in stack configurations separated by 6.5 A, and with interlayer distances of 10 A, hydrogen uptake reaches 6.5 wt % at 300 K and 215 bar.

Journal Article↗

Acrylic bone cements incorporating polymeric active components derived from salicylic acid: curing parameters and properties.

A methacrylic monomer derived from salicylic acid, 5-hydroxy-2-methacrylamido benzoic acid, 5-HMA, was incorporated with 2-hydroxyethyl methacrylate, (HEMA), in different proportions to the liquid phase of classical bone cement formulations. The monomer 5-HMA shows the ability to form molecular complexes with calcium atoms in order to improve osteointegration in the application of bone cement formulations used for the fixation of joint prostheses such as knee and hip. Kinetic parameters, peak temperature and setting time of the bone cement formulations prepared were determined, obtaining lower peak temperature values when 5-HMA was incorporated, with respect to classical acrylic bone cements based on PMMA. Mechanical and thermal properties as well as surface energy values, have been determined for all cured bone cement formulations.

Journal Article↗

Solution and solid state 13C NMR and X-ray studies of genistein complexes with amines. Potential biological function of the C-7, C-5, and C4'-OH groups.

Parent genistein and its new amine complexes with morpholine and piperazine were studied comparatively in the solid and liquid states by X-ray crystallography and 13C and 15N NMR spectroscopy. Biochanine A and its complexes were used as reference. Secondary deuterium isotope effects on 13C chemical shifts in solution were studied in parent isoflavones and their morpholine and piperazine complexes to aid in evaluation of the electronic distribution in both systems. In addition, to quantify the extent of proton transfer as well as to establish strong hydrogen bonding of the 7-OH group in a morpholine complex, proton transfer from the 7-OH group to the piperazine nitrogen atom was also confirmed by 13C NMR in the solid state and by X-ray studies. The effect of 7-OH deprotonation yields a high frequency shift of 7-8 ppm on the C-7 carbon atom of the piperazine complex whereas it is as large as 12 ppm in the morpholine complex in the solid. The former trend is confirmed from solution state concentration studies which also show that the isoflavones have a strong tendency to form complexes with bases. Depending on the pKa difference between the isoflavones and the base this leads either to proton transfer and ion-pair formation or, in the case of a larger pKa difference, to a hydrogen bonded ion pair. The concentration studies show formation of a 1:1 genistein-piperazine complex in DMSO. Addition of water leads to formation of solvent separated ions. The C-5 OH group is involved in strong intramolecular hydrogen bonding leading to a pseudo aromatic ring extending the aromatic part of the drug pharmacophore. The analysis also suggests the way that both the C-7 and C-4' hydroxyl group of genistein may participate in stabilising the ternary inhibitor complexes of tyrosine-specific kinases or DNA topoisomerase II.

Amines↗

New cobalt(II) and zinc(II) coordination frameworks incorporating a pyridyl-pyrazole ditopic ligand.

The metal-directed assembly of new molecular frameworks incorporating 4-(4-pyridyl)pyrazole (L), containing non-linear coordination vectors, is presented. Three metallo-arrays of types [Co(LH)2(NO3)4], [Co(LH)2(H2O)4][NO3]4.H2O and [Zn2(L-H)2Cl2].2EtOH are reported. The cobalt(II) in [Co(LH)2(NO3)4] displays distorted octahedral geometry, with the two protonated pyridyl-pyrazole ligands coordinated through their pyrazole nitrogen atoms in a trans-orientation; the remaining four coordination sites are occupied by nitrate anions. Two internal hydrogen bonds occur between each pyrazole NH and the oxygens of adjacent coordinated nitrato ligands. Short intermolecular hydrogen bonds also occur between the two pyridinium hydrogens and bound nitrate ligands on different molecules to yield a two-dimensional hydrogen-bonded array. Two of these arrays interpenetrate to form an extended two dimensional layer; such layers stack throughout the crystal structure. A second product of type [Co(LH)2(H2O)4][NO3]4.H2O exists as two crystallographically independent, but chemically similar, forms. In each form, the two protonated pyridyl-pyrazole ligands occupy trans positions about the cobalt, with the remaining four coordination sites being filled by water molecules to yield a distorted octahedral coordination geometry. Intramolecular hydrogen-bonding is observed between the two non-coordinated pyrazoyl nitrogen atoms and bound water oxygen atoms. The third complex, [Zn2(L-H)2Cl2].2EtOH, contains dimer units consisting of two zinc(II) ions bridged by two pyrazoylate groups in which the coordination geometry of each zinc approximates a tetrahedron. Each zinc is bound to two deprotonated pyridine-pyrazole ligands (L-H), one pyridyl group (from a different dimeric unit) and one chloro ligand. Each pyridyl nitrogen thus connects each of these zinc dimers to an adjacent dimer unit, forming a three-dimensional network containing small voids. The latter are occupied by ethanol molecules which form hydrogen bonds to the chloro ligands.

Journal Article↗

Mitochondrial proton conductance and H+/O ratio are independent of electron transport rate in isolated hepatocytes.

In this paper we examine the non-linearity of the relationship between the proton electrochemical gradient across the mitochondrial inner membrane (delta p) and oxygen consumption of non-phosphorylating mitochondria in situ in hepatocytes. Models proposing to explain the non-linear relationship were tested experimentally. It was shown that the mitochondrial proton conductance and the number of protons pumped to the cytosolic side of the mitochondrial inner membrane by the electron transport complexes per oxygen atom consumed (H+/O ratio) are independent of electron transport rate in mitochondria in isolated hepatocytes. The non-linearity of the plot of delta p against the non-phosphorylating oxygen consumption is due to either a potential-dependent slippage of the proton pumps of the mitochondrial inner membrane and/or a potential-dependent leakage of protons back across the mitochondrial inner membrane.

Animals↗

The effect of chloroform on mitochondrial energy transduction.

The effect of chloroform on mitochondrial respiration with succinate was investigated by applying the method of Brand, Chien and Diolez [(1994) Biochem. J. 297, 27-29] to examine whether chloroform causes redox slip (fewer protons pumped per electron transferred) during mitochondrial electron transport. N,N,N',N'-Tetramethyl-p-phenylenediamine (TMPD), which lowers H+/O (the number of protons pumped to the external medium by the electron transport complexes per oxygen atom consumed) by altering the electron flow pathway, was investigated for comparison. Non-phosphorylating mitochondria that had been treated with 350 microM TMPD or 30 mM chloroform were titrated with malonate in the presence of submaximal concentrations of the uncoupler carbonyl cyanide m-chlorophenylhydrazone (CCCP). Linear relations between CCCP-induced extra respiration and protonmotive force were obtained. These results showed that there was no measurable protonmotive force-dependent or rate-dependent slip in mitochondria treated with either TMPD or chloroform. However, both TMPD and chloroform seemed to decrease H+/O in a manner independent of protonmotive force and rate. The relationship between non-phosphorylating respiration and protonmotive force was simulated in mitochondria of which 25% of the total population were assumed to have been broken. The simulation showed that the apparent decrease in H+/O on the addition of TMPD or chloroform to mitochondria could be in principle accounted for by breakage. Assays of mitochondrial breakage (ATP hydrolysis in the presence of atractyloside and oxidation of exogenous NADH) showed that chloroform broke mitochondria but TMPD did not. We conclude that chloroform changes the measured H+/O as an artifact by causing mitochondrial breakage and does not cause measurable redox slip, whereas TMPD genuinely lowers H+/O.

Adenosine Triphosphatases↗

Quantum mechanical map for protein-ligand binding with application to beta-trypsin/benzamidine complex.

We report full ab initio Hartree-Fock calculation to compute quantum mechanical interaction energies for beta-trypsin/benzamidine binding complex. In this study, the full quantum mechanical ab initio energy calculation for the entire protein complex with 3238 atoms is made possible by using a recently developed MFCC (molecular fractionation with conjugate caps) approach in which the protein molecule is decomposed into amino acid-based fragments that are properly capped. The present MFCC ab initio calculation enables us to obtain an "interaction spectrum" that provides detailed quantitative information on protein-ligand binding at the amino acid levels. These detailed information on individual residue-ligand interaction gives a quantitative molecular insight into our understanding of protein-ligand binding and provides a guidance to rational design of potential inhibitors of protein targets.

Aspartic Acid↗

Temperature dependent energy transfer in Ar-O3 collisions.

The energy transfer between argon atoms and ozone complexes O3*, excited in the region of the dissociation threshold, is calculated for fixed temperatures (100 K< or =T < or =2500 K) using classical trajectories. The internal energy of ozone is resolved in terms of vibrational and rotational energies. For all temperatures, energy flows from O3* to Ar. The vibrational energy transfer, relative to k(B)T, is very small below 500 K, but gradually increases towards high temperatures. The relative rotational energy transfer, on the other hand, monotonously decreases with T; around 1100 K it falls below the relative vibrational energy transfer. Thermally averaged cross sections for vibrational and rotational energy transfers are also calculated. The implications for the stabilization of ozone complexes in the energy transfer model are discussed.

Journal Article↗

Atomic-scale dynamical structures of fatty acid bilayers observed by ultrafast electron crystallography.

The structure and dynamics of a biological model bilayer are reported with atomic-scale resolution by using ultrafast electron crystallography. The bilayer was deposited as a Langmuir-Blodgett structure of arachidic (eicosanoic) fatty acids with the two chains containing 40 carbon atoms (approximately = 50 angstroms), on a hydrophobic substrate, the hydrogen terminated silicon(111) surface. We determined the structure of the 2D assembly, establishing the orientation of the chains and the subunit cell of the CH2 distances: a0 = 4.7 angstroms, b0 = 8.0 angstroms, and c0 = 2.54 angstroms. For structural dynamics, the diffraction frames were taken every 1 picosecond after a femtosecond temperature jump. The observed motions, with sub-angstroms resolution and monolayer sensitivity, clearly indicate the coherent anisotropic expansion of the bilayer solely along the aliphatic chains, followed by nonequilibrium contraction and restructuring at longer times. This motion is indicative of a nonlinear behavior among the anharmonically coupled bonds on the ultrashort time scale and energy redistribution and diffusion on the longer time scale. The ability to observe such atomic motions of complex structures and at interfaces is a significant leap forward for the determination of macromolecular dynamical structures by using ultrafast electron crystallography.

Crystallography↗

Functional oligomeric state of avian sarcoma virus integrase.

Retroviral integrase, one of only three enzymes encoded by the virus, catalyzes the essential step of inserting a DNA copy of the viral genome into the host during infection. Using the avian sarcoma virus integrase, we demonstrate that the enzyme functions as a tetramer. In presteady-state active site titrations, four integrase protomers were required for a single catalytic turnover. Volumetric determination of integrase-DNA complexes imaged by atomic force microscopy during the initial turnover additionally revealed substrate-induced assembly of a tetramer. These results suggest that tetramer formation may be a requisite step during catalysis with ramifications for antiviral design strategies targeting the structurally homologous human immunodeficiency virus, type 1 (HIV-1) integrase.

Antiviral Agents↗

Three-dimensional structure of the barley beta-D-glucan glucohydrolase in complex with a transition state mimic.

Glucophenylimidazole (PheGlcIm), a tetrahydroimidazopyridine-type inhibitor and 4H3 conformer mimic of a glucoside, binds very tightly to a barley beta-d-glucan glucohydrolase, with a Ki constant of 2 x 10(-9) m and a DeltaG of 51 kJ mol(-1). PheGlcIm binds to the barley beta-d-glucan glucohydrolase approximately 2 x 10(5) times tighter than laminarin, which is the best non-synthetic ground-state substrate found so far for this enzyme, 10(6) times tighter than 4-nitrophenyl beta-d-glucopyranoside, and 2 x 10(7) tighter than glucose. The three-dimensional structure of the beta-d-glucan glucohydrolase with bound PheGlcIm indicates that the complex resembles a hypothetical transition state during the hydrolytic cycle, that the enzyme derives substrate binding energy from the "aglycone" portion of the ligand, and that it also reveals an anti-protonation trajectory for hydrolysis. Continuous electron densities at the 1.6 sigma level form between the three active site residues Asp95, His207, and Asp285, and the C6OH, C7OH, C8OH, and C9OH groups of PheGlcIm. These electron densities correspond to the most favorable interactions in the three-dimensional structure of the beta-d-glucan glucohydrolase-PheGlcIm complex and indicate atomic distances equal to or less than 2.55 A. The crystallographic data were corroborated with ab initio molecular orbital calculations. The data indicate that the 4E conformation of the glucose part of PheGlcIm is critical for tight binding and provide the first evidence for probable substrate distortion during catalysis by this enzyme.

Catalytic Domain↗

Crystal structures of Mycobacterium tuberculosis RecA and its complex with ADP-AlF(4): implications for decreased ATPase activity and molecular aggregation.

Sequencing of the complete genome of Mycobacterium tuberculosis, combined with the rapidly increasing need to improve tuberculosis management through better drugs and vaccines, has initiated extensive research on several key proteins from the pathogen. RecA, a ubiquitous multifunctional protein, is a key component of the processes of homologous genetic recombination and DNA repair. Structural knowledge of MtRecA is imperative for a full understanding of both these activities and any ensuing application. The crystal structure of MtRecA, presented here, has six molecules in the unit cell forming a 6(1) helical filament with a deep groove capable of binding DNA. The observed weakening in the higher order aggregation of filaments into bundles may have implications for recombination in mycobacteria. The structure of the complex reveals the atomic interactions of ADP-AlF(4), an ATP analogue, with the P-loop-containing binding pocket. The structures explain reduced levels of interactions of MtRecA with ATP, despite sharing the same fold, topology and high sequence similarity with EcRecA. The formation of a helical filament with a deep groove appears to be an inherent property of MtRecA. The histidine in loop L1 appears to be positioned appropriately for DNA interaction.

Adenosine Diphosphate↗

Identification of lattice vacancies on the two sublattices of SiC.

The identification of atomic defects in solids is of pivotal interest for understanding atomistic processes and solid state properties. Here we report on the exemplary identification of vacancies on each of the two sublattices of SiC by making use of (i) electron irradiation, (ii) measurements of the positron lifetimes, (iii) coincident Doppler broadening studies of the positron-electron annihilation radiation, and (iv) a comparison of the experimental data with theoretical studies. After 0.3 MeV electron irradiation, carbon vacancies V(C) are identified, where, after 0.5 MeV electron irradiation, predomi-nantly silicon vacancies V(Si) are observed. After 2.5 MeV irradiation, divacancies V(Si)-V(Si) are detected. The present results are expected to be of general importance for reliable identification of defects and atomic processes in complex solids.

Journal Article↗

Direct versus sequential double ionization of Mg with extreme-ultraviolet radiation.

We present an ab initio calculation of multiphoton double ionization in atomic magnesium, the first of its type in an atom with a complex core, showing that direct correlated double electron ejection can be studied through analysis of the photoelectron energy spectrum, using currently or upcoming extreme-ultraviolet radiation sources.

Journal Article↗

1,2,4-Triazolo[2,3-h]-7,9-thiaza-11-crown-4.

The title compound, 4,7-dioxa-10-thia-1,12,13-triazabicyclo[9.3.0]tetradeca-11,13-diene, C(8)H(13)N(3)O(2)S, contains an 11-membered ring, which appears in a chair conformation and has approximate mirror symmetry. It may be used for the complexation of metal atoms.

Journal Article↗

(Bis(N,N-dimethylformamide)[mu-N,N'-bis(salicylidene)-1,3-propanediaminato]nickel(II))dibromozinc(II).

The title compound, [NiZnBr2(C3H7NO)2(C17H16N2O2)], is a heterodinuclear nickel complex. The Ni atom has an irregular octahedral environment involving two O and two N atoms from the bis(salicylidene)-1,3-propanediaminate ligand in the equatorial plane, and two O atoms from the dimethylformamide groups. The Zn-O-Ni, O-Zn-O, Ni-O-Zn and O-Ni-O angles in the bridged plane are 100.1 (2), 79.9 (2), 100.4 (2) and 78.89 (17) degrees, respectively. The Ni...Zn distance is 3.0738 (19) A

Journal Article↗

Hexaaquacobalt(II) bis(hypophosphite) and hexaaquacobalt(II)/nickel(II) bis(hypophosphite).

The title compounds, hexaaquacobalt(II) bis(hypophosphite), [Co(H(2)O)(6)](H(2)PO(2))(2), and hexaaquacobalt(II)/nickel(II) bis(hypophosphite), [Co(0.5)Ni(0.5)(H(2)O)(6)](H(2)PO(2))(2), are shown to adopt the same structure as hexaaquamagnesium(II) bis(hypophosphite). The packing of the Co(Ni) and P atoms is the same as in the structure of CaF(2). The Co(II)(Ni(II)) atoms have a pseudo-face-centred cubic cell, with a = b approximately 10.3 A, and the P atoms occupy the tetrahedral cavities. The central metal cation has a slightly distorted octahedral coordination sphere. The geometry of the hypophosphite anion in the structure is very close to ideal, with point symmetry mm2. Each O atom of the hypophosphite anion is hydrogen bonded to three water molecules from different cation complexes, and each H atom of the hypophosphite anion is surrounded by three water molecules from further different cation complexes.

Journal Article↗

Bis(5-hydroxy-2-hydroxymethyl-4-pyrone-kappa 2O4,O5)bis(2-hydroxymethyl-5-oxido-4-pyrone-kappa 2O4,O5)calcium(II) tetrahydrate.

In the title compound, [Ca(C(6)H(5)O(4))(2)(C(6)H(6)O(4))(2)].4H(2)O, which is a kojic acid-Ca(2+) complex, the Ca atom is on a twofold axis and is octacoordinated by O atoms from four pyrone ligand molecules. The hydroxyl and ketone O atoms of each ligand form a five-membered chelate ring with the Ca atom. The crystal structure is stabilized by partial stacking and O-H.O hydrogen bonds.

Journal Article↗