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PubMed2006

Synthesis, crystal structure and DNA binding studies of a binuclear copper(II) complex with phenanthroline.

A new binuclear copper(II) complex, [Cu2Phen2Cl4] (Phen=1,10-phenanthroline), has been synthesized and characterized. Single crystal X-ray diffraction results suggest that this complex structure belongs to monoclinic crystal system, Cc (no. 9) with the cell dimensions: a=9.849(2)A, b=17.833(4)A, c=13.374(3)A, beta=106.61(3) degrees , V=2251.0(8)A(3), Dc=1.8569 Mgm(-3), F(000)=1256.0, Z=4. One Cu(II) central atom situated in a distorted square planar geometry is four-coordinated. The other situated in a distorted square pyramidal geometry is five-coordinated. Only one bridging Cl atom exists in the complex. Spectroscopic studies, including electronic absorption and fluorescence spectra, conductivity measurements and parallel factor analysis (PARAFAC) of fluorescence excitation-emission three-way data array, were carried out on the DNA binding behavior of the complex. All the results suggested that the breakage of DNA secondary structure took place at low molar ratio of complex to DNA (0.3 at most) and intercalation into the base pair of DNA took place at high molar ratio. Additionally, the equilibrium concentration of EB-DNA and EB (EB: ethidium bromide) could be directly obtained by PARAFAC algorithm, proved to be a convincing method for studying the interaction of complexes with DNA.

Copper↗

PubMed2005

Structural insight into the dioxygenation of nitroarene compounds: the crystal structure of nitrobenzene dioxygenase.

Nitroaromatic compounds are used extensively in many industrial processes and have been released into the environment where they are considered environmental pollutants. Nitroaromatic compounds, in general, are resistant to oxidative attack due to the electron-withdrawing nature of the nitro groups and the stability of the benzene ring. However, the bacterium Comamonas sp. strain JS765 can grow with nitrobenzene as a sole source of carbon, nitrogen and energy. Biodegradation is initiated by the nitrobenzene dioxygenase (NBDO) system. We have determined the structure of NBDO, which has a hetero-hexameric structure similar to that of several other Rieske non-heme iron dioxygenases. The catalytic subunit contains a Rieske iron-sulfur center and an active-site mononuclear iron atom. The structures of complexes with substrates nitrobenzene and 3-nitrotoluene reveal the structural basis for its activity with nitroarenes. The substrate pocket contains an asparagine residue that forms a hydrogen bond to the nitro-group of the substrate, and orients the substrate in relation to the active-site mononuclear iron atom, positioning the molecule for oxidation at the nitro-substituted carbon.

Amino Acid Sequence↗

PubMed2003

The infinite double-stranded chain polymer catena-poly[[bis(dicyanamido)zinc(II)]-di-mu-1,2-bis(1,2,4-triazol-1-yl)ethane-kappa4N4:N4'].

The coordination geometry of the Zn(II) atom in the title complex, [Zn(C(2)N(3))(2)(C(6)H(8)N(6))(2)](n) or [Zn(dca)(2)(bte)(2)](n), where bte is mu-1,2-bis(1,2,4-triazol-1-yl)ethane and dca is dicyanamide, is distorted compressed octahedral, in which the Zn(II) atom lies on an inversion center and coordinates four N atoms from the triazole rings of four symmetry-related bte ligands and two N atoms from two symmetry-related monodentate dca ligands. The structure is polymeric, with 18-membered spiro-fused rings extending in the b direction and each 18-membered ring involving two inversion-related bte molecules.

Journal Article↗

PubMed2002

Molecular views and measurements of hemostatic processes using atomic force microscopy.

Hemostasis and thrombosis are highly complex and coordinated interfacial responses to vascular injury. In recent years, atomic force microscopy (AFM) has proven to be a very useful approach for studying hemostatic processes under near physiologic conditions. In this report, we review recent progress in the use of AFM for studying hemostatic processes, including molecular level visualization of plasma proteins, protein aggregation and multimer assembly, and structural and morphological details of vascular cells under aqueous conditions. AFM offers opportunities for visualizing surface-dependent molecular and cellular interactions in three dimensions on a nanoscale and for sensitive, picoNewton level, measurements of intermolecular forces. AFM has been used to obtain molecular and sub-molecular, resolution of many biological molecules and assemblies, including coagulation proteins and cell surfaces. Surface-dependent molecular processes including protein adsorption, conformational changes, and subsequent interactions with cellular components have been described. This review outlines the basic principles and utility of AFM for imaging and force measurements, and offers objective perspectives on both the advantages and disadvantages. We focus primarily on molecular level events related to hemostasis and thrombosis, particularly coagulation proteins, and blood platelets, but also explore the use of AFM in force measurements and surface property mapping.

Adsorption↗

PubMed2005

Vibrational spectroscopy and structures of Ni+(C2H2)(n) (n =1-4) complexes.

Nickel cation-acetylene complexes of the form Ni(+)(C(2)H(2))(n), Ni(+)(C(2)H(2))Ne, and Ni(+)(C(2)H(2))(n)Ar(m) (n = 1-4) are produced in a molecular beam by pulsed laser vaporization. These ions are size-selected and studied in a time-of-flight mass spectrometer by infrared laser photodissociation spectroscopy in the C-H stretch region. The fragmentation patterns indicate that the coordination number is 4 for this system. The n = 1-4 complexes with and without rare gas atoms are also investigated with density functional theory. The combined IR spectra and theory show that pi-complexes are formed for the n = 1-4 species, causing the C-H stretches in the acetylene ligands to shift to lower frequencies. Theory reveals that there are low-lying excited states nearly degenerate with the ground state for all the Ni(+)(C(2)H(2))(n) complexes. Although isomeric structures are identified for rare gas atom binding at different sites, the attachment of rare gas atoms results in only minor perturbations on the structures and spectra for all complexes. Experiment and theory agree that multiple acetylene binding takes place to form low-symmetry structures, presumably due to Jahn-Teller distortion and/or ligand steric effects. The fully coordinated Ni(+)(C(2)H(2))(4) complex has a near-tetrahedral structure.

Journal Article↗

PubMed1985

Atomic absorption spectrophotometric determination of microgram quantities of copper in tea after solvent extraction.

An atomic absorption spectrophotometric method is described for determining trace amounts of copper in tea. The method is based on the solvent extraction of the metal as tetraiodocuprate (I), from 2 M HCl solutions of tea samples which contain 12% (w/v) KI, into methylisobutyl ketone. The organic extracts, containing the ion-association complex of copper are atomized into an air-acetylene flame. The limit of detection is 1.14 micrograms g-1 Cu.

Copper↗

PubMed2005

Crystal structure of an ethylene sorption complex of fully vacuum-dehydrated fully Ag+-exchanged zeolite X (FAU). Silver atoms have reduced ethylene to give CH2 2- carbanions at framework oxide vacancies.

The crystal structure of an ethylene sorption complex of fully vacuum-dehydrated fully Ag(+)-exchanged zeolite X (FAU), a = 24.865(2) A, has been determined by single-crystal X-ray diffraction techniques in the cubic space group Fd at 21 degrees C. It is very different from the ethylene complex of Ag(92)-X that had been dehydrated at 400 degrees C in flowing oxygen, as were the two dehydrated structures. The crystal was prepared by ion exchange in a flowing stream of aqueous 0.05 M AgNO(3) for 3 days, followed by dehydration at 400 degrees C and 2 x 10(-6) Torr for 2 days, followed by exposure to 300 Torr of zeolitically dry ethylene gas for 2 h at 21 degrees C. The structure was determined in this atmosphere and was refined using all data to the final error indices (based upon the 534 reflections for which F(o) > 4sigma(F(o))) R(1) = 0.062 and wR(2) = 0.135. In this structure, per unit cell, 14 Ag(+) ions were found at the octahedral site I (Ag-O = 2.611(9) A), and 32 partially reduced Ag(+) ions fill two different site I' positions deep in the sodalite cavities (Ag-O = 2.601(13) and 2.618(12) A). The sodalite cavities host two different cationic silver clusters. In about 47% of sodalite units, eight silver atoms form interpenetrating tetrahedra, Ag(8)(n+) (n = 4 is suggested), with T(d)() symmetry. The other 53% of the sodalite units host cyclo-Ag(4)(m+) (m = 2 is suggested) cations with near S(4) symmetry. These clusters are very similar to those in vacuum-dehydrated Ag(92)-X. Thirty-two Ag(+) ions fill the single 6-rings, 15 at site II' (Ag-O = 2.492(10) A), and 17 at site II (Ag-O = 2.460(9) A). The latter 17 lie in supercages where each forms a lateral pi-complex with an ethylene molecule. In turn, each C(2)H(4) molecule forms two cis electrostatic hydrogen bonds to framework oxygens. The remaining 14 Ag+ ions occupy three different II' sites. Vacuum dehydration had caused substantial decomposition: per unit cell, 30 of the 92 Ag(+) ions were reduced and 15 of the 384 framework oxide ions were oxidized to O2(g), leaving lattice vacancies. The sorption of C(2)H(4) at 21 degrees C reoxidized about 7 of the 30 Ag(0) atoms to Ag(+) and reduced 1.75 ethylene molecules to give CH(2)(2-) groups which refilled 3.5 of these 15 lattice vacancies. The remaining vacancies may have been filled with H(2)C=C(2-) ions. The unit cell formula, which originally contained 384 oxygen atoms, may be |Ag(92)(C2H4)17|[Si(100)Al(92)O(369)(CH2)3.5] or |Ag(92)H(23)(C2H4)17|[Si(100)Al(92)O(369)(CH2)3.5(C2H2)11.5].

Adsorption↗

PubMed2001

Quantum/classical studies of photodissociation and reaction dynamics in clusters.

In this paper, a multiple configurational time-dependent self-consistent field (TDSCF) approach for studying photodissociation and reaction dynamics is described. This approach has been applied to studies of several benchmark systems and is found to provide an accurate description of the reactions. The focus of the present work is on investigations of processes in cluster environments. Specifically, the dynamics of the O(3P) + HCl reaction and H2O photodissociation dynamics in isolation and in Van der Waals complexes with one argon atom are compared. The nature and importance of quantum mechanical effects in these systems are investigated through an analysis of the results of the quantum/classical simulations and a comparison of these results with those obtained from previously reported experimental and classical studies on these systems. It is found that, although the effects of complexation are subtle, they are not negligible. In addition, most of them can be understood in terms of kinematic and steric factors, although electronic effects cannot be dismissed.

Journal Article↗

PubMed2005

Adsorption of lanthanoid ions on calcite.

The adsorption of 14 trivalent lanthanoid ions and yttrium ion (denoted by Ln3+) on calcite surfaces was investigated under various solution conditions of pH (pH = 6.8-7.8) and calcium ion concentration (pCa = -log[Ca2+]= 2.0 and 3.0), and different surface conditions of calcite crystals (well-developed and rough surfaces). The lanthanoid ions were equilibrated in a solution of ionic strength 0.1 mol dm-3(NaCl) saturated with calcite at 25.0 degrees C using excess (solid) calcite crystals suspended in solution. The concentrations of the lanthanoid ions on the calcite crystals (C(cry)/mol kg-1) and in solution (C(soln)/mol dm-3) were determined by means of inductively coupled plasma-mass spectrometry (ICP-MS). It is found that the distribution ratio (D=C(cry)/C(soln) decreases as the atomic number of the lanthanoid increases showing the so called Tetrad Effect. D values increase with increasing pH, whereas they are independent of the calcium ion concentration (i.e., carbonate ion concentration). These results indicate that lanthanoid ions are adsorbed on the calcite surface together with hydroxide ions, i.e., the adsorption of hydroxo-complexes. The heavy lanthanoid ions (Er3+ to Lu3+) are adsorbed as monohydroxo-complexes, (Ln(OH)2+), whereas those of the light lanthanoids are predominantly adsorbed as dihydroxo-complexes (Ln(OH)2+). Other lanthanoids show competitive adsorption reactions of mono- and dihydroxo complexes. Both successive adsorption constants of hydroxo complexes increase with decreasing atomic number of the lanthanoid. The rough surface of calcite is quite active and the distribution ratio of the lanthanoid ions on the rough surface is much higher than that on the well-developed crystalline surface. Rates of adsorption of lanthanide ions were measured and mechanisms are being discussed

Journal Article↗

PubMed2004

A re-investigation of copper coordination in the octa-repeats region of the prion protein.

An aqueous solution spectroscopic (Vis and EPR) study of the copper(II) complexes with the Ac-HGGG-NH2 and Ac-PHGGGWGQ-NH2 polypeptides (generically designated as L) suggests square base pyramids ascribable to [Cu(L)H(-2)] complex species, which contain three nitrogen donor atoms, arising from imidazole and peptide groups, in the equatorial plane and for a pseudo-octahedral geometry in the case of [CuLH-3]- and [Cu(L)H-4]2- which have four nitrogen donor atoms in their equatorial plane. The coordination sphere of the copper complex in the [Cu(L)H(-2)] species, which is present at neutral pH values, is completed by two oxygen donor atoms. ESI-MS spectra ascertained that water molecules are not present in the coordination equatorial plane of this latter species, in comparison with other copper(II) complexes with ligands bearing nitrogen and oxygen donor atoms and surely having equatorial water molecules. This indicates the coordination of a carbonyl oxygen atom in the equatorial plane has to be invoked. However, no direct proof about the involvement of a carbonyl group oxygen donor atom apically linked to copper was obtained, due to the flexibility of these structures at room temperature. Additionally, the low A(ll) value leads one to consider another oxygen atom of a carbonyl group being involved in the apical bond to copper in a fast exchange fashion. This apical interaction, which may also involve a water molecule, is more pronounced in the Cu-Ac-HGGG-NH2 than in the analogous Cu-Ac-PHGGGWGQ-NH2 system, probably because of the presence of tryptophan and proline in the polypeptide sequence.

Copper↗

PubMed2004

Synthesis, crystal structure and DNA cleavage activities of copper(II) complexes with asymmetric tridentate ligands.

Two asymmetric tridentate copper(II) complexes, [Cu(dppt)Cl(2)].0.25H(2)O (1) (dppt=3-(1,10-phenanthrolin-2-yl)-5,6-diphenyl-as-triazine) and [Cu(pta)Cl(2)] (2) (pta=3-(1,10-phenanthrolin-2-yl)-as-triazino[5,6-f]acenaphthylene), have been prepared and characterized by elemental analysis, IR and Fast atomic bombardment mass spectra. Complex 1 has also been structurally characterized. The complexes exist as distorted square pyramid with five co-ordination sites occupied by the tridentate ligand and the two chlorine anions. DNA interaction studies suggest that the ligand planarity of the complex has a significant effect on DNA binding affinity increasing in the order [Cu(dppt)Cl(2)]< [Cu(pta)Cl(2)]. In the presence of ascorbate or glutathione, the two complexes are found to cause significant cleavage of double-strand pBR 322 DNA and [Cu(pta)Cl(2)] exhibited the higher cleaving efficiency.

Animals↗

PubMed1983

Human factor VIII: a calcium-linked protein complex.

The possible role of Ca2+ as an essential constituent part of the human factor VIII complex has been investigated by stability studies, metal determinations, and gel filtration experiments. In citrated plasma, the factor VIII coagulant activity (VIII:C) deteriorated during storage in a biphasic manner. Collection of blood in heparin, instead of chelating anticoagulants, or neutralization of citrate by addition of CaCl2 to heparinized citrate phosphate dextrose (CPD) plasma rendered VIII:C noticeably stable. At physiologic levels of ionized calcium, VIII:C was almost completely stable during incubation of plasma for 6 hr at 37 degrees C. The influence of other divalent ions was also studied. Highly purified factor VIII complex was subjected to atomic absorption spectrophotometric analysis and found to contain about 1.0 mole calcium per 220,000 daltons. This intrinsic calcium could be readily removed by EDTA. When heparin plasma and CPD plasma were chromatographed on Sepharose CL-6B at 37 degrees C, all the factor-VIII-related activities eluted together as large protein complexes. In contrast, factor VIII coagulant antigen (VIII:CAg) and factor-VIII-related antigen (VIIIR:Ag) were completely dissociated upon exposure to EDTA. From these observations it is concluded that human factor VIII circulates in normal plasma as a calcium-linked protein complex.

Anticoagulants↗

PubMed1999

Monoprotic Tetradentate N(3)O-Donor Ligands and Their Cu(II) and Ni(II) Complexes.

A convenient four-step procedure was developed to prepare the novel monoprotic tetradentate ligands N-(2-hydroxy)benzyl-N-methyl-N'-(2-pyridyl)methyl-1,3-propanediamine (Hpamap) and N-(2-hydroxy)benzyl-N'-methyl-N'-(2-pyridyl)methyl-1,3-propanediamine (Hpmaap), which provide an N(3)O metal coordination sphere. A mononuclear copper(II) complex, [Cu(pamap)Cl] (A), was obtained by reaction of Hpamap with CuCl(2).2H(2)O. The binuclear copper(II) complexes [Cu(pamap)](2)(BF(4))(2) (B) and [Cu(pmaap)](2)(BF(4))(2) (C) were obtained when these ligands were reacted with Cu(II) in the presence of the noncoordinating BF(4)(-) anion. Reaction of nickel(II) with the Hpamap ligand generated the binuclear Ni(II) complex [Ni(2)(pamap)(2)(NO(3))]NO(3) (D). The crystal of A (C(17)H(22)ClCuN(3)O) is orthorhombic Pbca (No. 61), a = 11.837(4) Å, b = 15.648(5) Å, c = 11.002(11) Å, Z = 8; that of B (C(34)H(44)B(2)Cu(2)F(8)N(6)O(2)) is triclinic P&onemacr; (No. 2), a = 9.147(0) Å, b = 10.375(0) Å, c = 10.535(1) Å, alpha = 107.20(0) degrees, beta = 91.19(0) degrees, gamma = 105.05(0) degrees, Z = 1; that of C (C(34)H(44)B(2)Cu(2)F(8)N(6)O(2)) is monoclinic P2(1)/c (No. 14), a = 9.158(2) Å, b = 10.714(2) Å, c = 19.085(4) Å, beta = 90.58(2) degrees, Z = 4; and that of D (C(34)H(44)N(8)NiO(8)) is monoclinic C2/c (No. 15), a = 13.849(0) Å, b = 13.609(0) Å, c = 19.558(1) Å, beta = 92.34 (0) degrees, Z = 4. The copper atoms of all three complexes are five-coordinate in the solid state, assuming the geometry of a distorted square pyramid with the deprotonated tetradentate ligand in the basal plane. The mononuclear complex A has a chloride ligand in the axial position, while each copper center in the binuclear complexes B and C has, in the axial position, a bridging phenolate O donor from the other unit of the dimer. Each nickel center in the binuclear complex D is six-coordinate, with the pseudo-octahedron formed by a deprotonated tetradentate ligand, a bridging nitrato oxygen atom, and a bridging phenoxy donor from the tetradentate ligand bound to the second nickel center.

Journal Article↗

PubMed1999

Approximate solvent-accessible surface areas from tetrahedrally directed neighbor densities.

A fast analytical formula (TDND) has been derived for the calculation of approximate atomic and molecular solvent-accessible surface areas (SASA), as well as the first and second derivatives of these quantities with respect to atomic coordinates. Extending the work of Stouten et al. (Molecular Simulation, 1993, Vol. 10, pp. 97-120), as well as our own (Journal of Computational Chemistry, 1999, Vol. 20, pp. 586-596), the method makes use of a Gaussian function to calculate the neighbor density in four tetrahedral directions in three-dimensional space, sometimes twice with different orientations. SASA and first derivatives of the 2366 heavy atoms of penicillopepsin are computed in 0.13 s on an SGI R10000/194 MHz processor. When second derivatives are computed as well, the total time is 0.23 s. This is considerably faster than timings reported previously for other algorithms. Based on a parameterization set of nineteen compounds of different size (11-4346 atoms) and class (organics, proteins, DNA, and various complexes) consisting of a total 23,197 atoms, the method exhibits relative errors in the range 0.2-12.6% for total molecular surface areas and average absolute atomic surface area deviations in the range 1.7 to 3.6 A(2).

Molecular Structure↗

PubMed2005

Dual room-temperature fluorescent and phosphorescent emission in 8-quinolinolate osmium(II) carbonyl complexes: rationalization and generalization of intersystem crossing dynamics.

A new series of quinolinolate osmium carbonyl complexes were synthesized and characterized by spectroscopic methods. Single-crystal X-ray diffraction studies indicate that these complexes consist of an octahedral ligand arrangement with one chelating quinolinolate, one tfa or halide ligand, and three mutually orthogonal terminal CO ligands. Variation of the substituents on quinolinolate ligands imposes obvious electronic or structural effects, while changing the tfa ligand to an electron-donating iodide slightly increases the charge density on the central osmium atom. These Os(II) complexes show salient dual emissions consisting of fluorescence and phosphorescence, the spectral properties and relaxation dynamics of which have been studied comprehensively. The results, in combination with the theoretical approaches, lead us to propose that the emission mainly originates from the quinolinolate pi pi* state. Both experimental and theoretical approaches generalize various types of intersystem crossing versus those of the tris(quinolinolate) iridium Ir(Q)3, and their relative efficiencies were accessed on the basis of the associated frontier orbital configurations. Our results suggest that [1d(pi)pi* absolute value(H(so))3 pi pi*] (or [3d(pi)pi* absolute value(H(so))1 pi pi*]) in combination with a smaller deltaE(S1-T1) gap (i.e., increasing the MLCT (d(pi)pi*) character) is the main driving force to induce the ultrafast S1 --> T1 intersystem crossing in the third-row transition metal complexes, giving the strong phosphorescent emission.

Journal Article↗

PubMed2002

Excitons in a photosynthetic light-harvesting system: a combined molecular dynamics, quantum chemistry, and polaron model study.

The dynamics of pigment-pigment and pigment-protein interactions in light-harvesting complexes is studied with an approach that combines molecular dynamics simulations with quantum chemistry calculations and a polaron model analysis. The molecular dynamics simulation of light-harvesting (LH) complexes was performed on an 87 055 atom system comprised of a LH-II complex of Rhodospirillum molischianum embedded in a lipid bilayer and surrounded with appropriate water layers. For each of the 16 B850 bacteriochlorophylls (BChls), we performed 400 ab initio quantum chemistry calculations on geometries that emerged from the molecular dynamical simulations, determining the fluctuations of pigment excitation energies as a function of time. From the results of these calculations we construct a time-dependent Hamiltonian of the B850 exciton system from which we determine within linear response theory the absorption spectrum. Finally, a polaron model is introduced to describe both the excitonic and coupled phonon degrees of freedom by quantum mechanics. The exciton-phonon coupling that enters into the polaron model, and the corresponding phonon spectral function, are derived from the molecular dynamics and quantum chemistry simulations. The model predicts that excitons in the B850 BChl ring are delocalized over five pigments at room temperature. Also, the polaron model permits the calculation of the absorption and circular dichroism spectra of the B850 excitons from the sole knowledge of the autocorrelation function of the excitation energies of individual BChls, which is readily available from the combined molecular dynamics and quantum chemistry simulations. The obtained results are found to be in good agreement with the experimentally measured absorption and circular dichroism spectra.

Circular Dichroism↗

PubMed2000

Bis-triiodide von 1,2-ethandiaminkomplexen am beispiel des metalls kupfer

In bis(1,2-ethanediamine-N,N')bis[triiodo(1-)-I]copper, [Cu(I(3))(2)(C(2)H(8)N(2))(2)], the triiodide anions form chains parallel to [001]. The central metal ion (site symmetry 2/m) of the complex cation is coordinated to four N atoms and to two I atoms. The geometry of the square-bipyramidal complex is as expected, with d(Cu-N) = 2.006 (5) and d(Cu-I) = 3.3600 (9) A.

Journal Article↗

PubMed2006

Bis(1-methyl-1H-tetrazol-5-yl)diazene and two its copper(I) chloride complexes poly[[[mu-1,2-bis(1-methyl-1H-tetrazol-5-yl)diazene-kappa4N',N4:N,N4']dicopper(I)]-di-mu-chloro] and catena-poly[[chlorocopper(I)]-mu-1,2-bis(1-methyl-1H-tetrazol-5-yl)diazene-kappa4N',N4:N,N4'].

While bis(1-methyl-1H-tetrazol-5-yl)diazene, C4H6N10, (I), has no crystallographically imposed symmetry, in the two title chlorocopper(I) complexes, [Cu2Cl2(C4H6N10)]n, (II), and [CuCl(C4H6N10)]n, (III), the organic ligands lie across centres of inversion; in (III), the Cu and Cl atoms additionally lie about a twofold rotation axis in the space group P2/c. Complex (II) forms a two-dimensional coordination polymer containing tetrahedrally coordinated Cu(I) atoms, and complex (III) forms a one-dimensional coordination polymer containing five-coordinate square-pyramidal Cu(I) atoms.

Journal Article↗