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PubMed2005

Density functional study of lithium-aromatic sandwich compounds and their crystals.

Using density functional theory, we have theoretically studied the formation of neutral lithium-aromatic complexes R-nLi and R-nLi-R, where R is benzene, naphthalene, or pyrene. We first find that the maximum number of lithium atoms n in the complexes increases with the size of R. In addition, pyrene favors the sandwich compound R-4Li-R over R-4Li more than three times that of the corresponding tendency for benzene, strongly suggesting the possible existence of oligomer (R-4Li)x. We have also investigated energetics and band structures of infinite one-dimensional crystals of R-nLi, finding them metallic. Detailed analysis of the electronic structure shows that all these observations are related to the strong electrostatic interaction among the species, which is originated from the charge transfer from Li atoms to the aromatic rings. In addition, it is shown that the pyrene crystal is mechanically stable with respect to deformation. This also suggests the possibility of its existence, which, in turn, holds potential application in lithium storage in respect to its large Li/C ratio.

Journal Article↗
PubMed2006

Photodissociation spectroscopy of the Mg+-acetic acid complex.

We have studied the structure and photodissociation of Mg(+)-acetic acid clusters. Ab initio calculations suggest four relatively strongly bound ground state isomers for the [MgC(2)H(4)O(2)](+) complex. These isomers include the cis and trans forms of the Mg(+)-acetic acid association complex with Mg(+) bonded to the carbonyl O atom of acetic acid, the Mg(+)-acetic acid association complex with Mg(+) bonded to the hydroxyl O atom of acetic acid, or to a Mg(+)-ethenediol association complex. Photodissociation through the Mg(+)-based 3p<--3s absorption bands in the near UV leads to direct (nonreactive) and reactive dissociation products: Mg(+), MgOH(+), Mg(H(2)O)(+), CH(3)CO(+), and MgCH(3) (+). At low energies the dominant reactive quenching pathway is through dehydration to Mg(H(2)O)(+), but additional reaction channels involving C-H and C-C bond activation are also open at higher energies.

Journal Article↗
PubMed2003

Bonding of multiple noble-gas atoms to CUO in solid neon: CUO(Ng)n (Ng=Ar, Kr, Xe; n=1, 2, 3, 4) complexes and the singlet-triplet crossover point.

Laser-ablated U atoms co-deposited with CO in excess neon produce the novel CUO molecule, which forms distinct Ng complexes (Ng=Ar, Kr, Xe) with the heavier noble gases. The CUO(Ng) complexes are identified through CO isotopic and Ng reagent substitution and comparison to results of DFT frequency calculations. The U[bond]C and U[bond]O stretching frequencies of CUO(Ng) complexes are slightly red-shifted from neon matrix (1)Sigma(+) CUO values, which indicates a (1)A' ground state for the CUO(Ng) complexes. The CUO(Ng)(2) complexes in excess neon are likewise singlet molecules. However, the CUO(Ng)(3) and CUO(Ng)(4) complexes exhibit very different stretching frequencies and isotopic behaviors that are similar to those of CUO(Ar)(n) in a pure argon matrix, which has a (3)A" ground state based on DFT vibrational frequency calculations. This work suggests a coordination sphere model in which CUO in solid neon is initially solvated by four or more Ne atoms. Up to four heavier Ng atoms successively displace the Ne atoms leading ultimately to CUO(Ng)(4) complexes. The major changes in the CUO stretching frequencies from CUO(Ng)(2) to CUO(Ng)(3) provides evidence for the crossover from a singlet ground state to a triplet ground state.

Journal Article↗
PubMed1996

Artificial peroxidase-like hemoproteins based on antibodies constructed from a specifically designed ortho-carboxy substituted tetraarylporphyrin hapten and exhibiting a high affinity for iron-porphyrins.

In order to get catalytic antibodies modelling peroxidases BALB/c mice have been immunized with iron(III)-alpha,alpha,alpha,beta-mesotetrakis-orthocarboxypheny l-porphyrin (Fe-(ToCPP))-KLH conjugates. Monoclonal antibodies have been produced by the hybridoma technology. Three antibodies, 2 IgG1 and 1 IgG2a, were found to bind both Fe(ToCPP) and the free base ToCPPH2 with similar binding constants. None of those antibodies was found to bind tetraphenylporphyrin. Those results suggest that the recognition of Fe(ToCPP) by the antibodies was mainly due to the binding of the carboxylate groups to some amino acid residues of the protein. True Kd values of 2.9 x 10(-9) M and 5.5 x 10(-9) M have been determined for the two IgG1-Fe(ToCPP) complexes. Those values are the best ones ever reported for iron-porphyrin-antibody complexes. UV-vis. studies have shown that the two IgG1-Fe(ToCPP) complexes were high-spin hexacoordinate iron(III) complexes, with no amino acid residue binding the iron, whereas the IgG2a-Fe(ToCPP) complex was a low-spin hexacoordinate iron(III) complex with two strong ligands binding the iron atom. Both IgG1-Fe(ToCPP) complexes were found to catalyze the oxidation of 2,2'-azinobis (3-ethylbenzothiazoline-6-sulfonic acid (ABTS) 5-fold more efficiently than Fe(ToCPP) alone whereas the binding of IgG2a to this iron-porphyrin had no effect on its catalytic activity. kcat values of 100 min(-1) and 63 min(-1) and kcat/Km values of 105 M(-1) s(-1) and 119 M(-1) s(-1) have been found respectively for the two IgG1-Fe(ToCPP) complexes.

Animals↗
PubMed2004

The effects of axial ligands on electron distribution and spin states in iron complexes of octaethyloxophlorin, intermediates in heme degradation.

The results presented here show that the nature of the axial ligand can alter the distribution of electrons between the metal and the porphyrin in complexes where there is an oxygen atom replacing one of the meso protons. The complexes (1-MeIm)(2)Fe(III)(OEPO) and (2,6-xylylNC)(2)Fe(II)(OEPO(*)) (where OEPO is the trianionic octaethyloxophlorin ligand and OEPO(*) is the dianionic octaethyloxophlorin radical) were prepared by addition of an excess of the appropriate axial ligand to a slurry of [Fe(III)(OEPO)](2) in chloroform under anaerobic conditions. The magnetic moment of (2,6-xylylNC)(2)Fe(II)(OEPO(*)) is temperature invariant and consistent with a simple S = (1)/(2) ground state. This complex with an EPR resonance at g = 2.004 may be considered as a model for the free-radical like EPR signal seen when the meso-hydroxylated heme/heme oxygenase complex is treated with carbon monoxide. In contrast, the magnetic moment of (1-MeIm)(2)Fe(III)(OEPO) drops with temperature and indicates a spin-state change from an S = (5)/(2) or an admixed S = (3)/(2),(5)/(2) state at high temperatures (near room temperature) to an S = (1)/(2) state at temperatures below 100 K. X-ray diffraction studies show that each complex crystallizes in centrosymmetric form with the expected six-coordinate geometry. The structure of (1-MeIm)(2)Fe(III)(OEPO) has been determined at 90, 129, and 296 K and shows a gradual and selective lengthening of the Fe-N(axial bond). This behavior is consistent with population of a higher spin state at elevated temperatures.

Crystallography, X-Ray↗
PubMed1997

Evaluating standardized coding and classification systems for clinical practice: a critical review of the nursing literature in the United States.

Developers of healthcare information systems are challenged by the difficulty of meeting the simultaneous goals of 1) capturing and electronically representing the broad array of data related to healthcare with sufficient expressibility to provide adequate documentation of the patient encounter, and 2) utilizing standardized coding and classification systems to facilitate linkages among computer-based systems. The evaluation studies to date have primarily focused on matching actual clinical data with terms in the recognized classification systems. These studies have provided evidence that the classification systems are relatively domain complete for categorizing patient problems and nursing interventions. Although several of the published criteria for evaluation relate to structure, it is noteworthy that this has not yet been a major focus of study in nursing. There are several areas of critical need that must be addressed. First, additional work is needed to develop and refine a standardized set of atomic-level terms relevant to nursing, including those for assessments, problems, and activities. Second, knowledge representations must be developed to support the building of complex concepts from atomic-level data.

Classification↗
PubMed2005

Mechanisms of lead biosorption on cellulose/chitin beads.

Environment-friendly cellulose/chitin beads being prepared by coagulating a blend of cellulose and chitin in 6 wt% NaOH/5 wt% thiourea aqueous solution with 5% H2SO4 possessed higher heavy metals uptake capacity than pure chitin flakes. The mechanisms of Pb2+ adsorption on cellulose/chitin beads at pH0=5 were investigated at the molecular levels by scanning electron micrographs (SEM), transmission electron micrographs (TEM), X-ray photoelectron spectroscopy (XPS), Fourier transform infrared spectroscopy (FTIR) and powder X-ray diffraction (XRD). The result revealed that mechanisms for the adsorption of Pb2+ on the cellulose/chitin beads could be described as complexation between Pb2+ and N atom in the chitin, and further adsorption of Pb2+ nearby the complexed Pb2+ and precipitation of the hydrolysis product of the Pb2+ complex on the beads as the crystalline state. Furthermore, structural factors such as larger surface area of the beads resulted from microporous-network structure, low crystallinity of cellulose/chitin beads and high hydrophilicity induced by hydrophilic skeleton of cellulose played an important role in increasing adsorption ability.

Adsorption↗
PubMed2001

Structural correlation of catecholase-like activities of oxy-bridged dinuclear copper(II) complexes.

Eight oxy-bridged dinuclear copper(II) complexes with catecholase-like sites, [Cu(L1)X]2 (HL1 = 1-diethylaminopropan-2-ol, X=N3- 1, NCO- 2, and NO2- 3), [Cu(L2)X]2 (HL2=N-ethylsalicylaldimine, X=NO3- 4, Cl- 5, N3- 6, NCS- 7), and [Cu(L3)]2(ClO4)2, 8 (HL3=N-(salicylidene)-N'-(2-pyridylaldene)propanediamine) have been prepared and characterized. The single crystal X-ray analysis show that the structures of complexes 6 and 8 are dimeric with two adjacent copper(II) atoms bridged by pairs of micro-oxy atoms from the L2 and L3 ligands. Magnetic susceptibility measurements in the temperature range 4-300 K indicate significant antiferromagnetic coupling for 4, 5 and 7 and ferromagnetic coupling for 6 between the copper(II) atoms. The catecholase activity of complexes for the oxidation of 3,5-di-tert-butylcatechol by O2 was studied and it was found that the complexes with the bond distance of Cu(II)...Cu(II) located at 2.9-3.0 A show higher catecholase activity.

Catalytic Domain↗
PubMed2005

A knowledge-based energy function for protein-ligand, protein-protein, and protein-DNA complexes.

We developed a knowledge-based statistical energy function for protein-ligand, protein-protein, and protein-DNA complexes by using 19 atom types and a distance-scale finite ideal-gas reference (DFIRE) state. The correlation coefficients between experimentally measured protein-ligand binding affinities and those predicted by the DFIRE energy function are around 0.63 for one training set and two testing sets. The energy function also makes highly accurate predictions of binding affinities of protein-protein and protein-DNA complexes. Correlation coefficients between theoretical and experimental results are 0.73 for 82 protein-protein (peptide) complexes and 0.83 for 45 protein-DNA complexes, despite the fact that the structures of protein-protein (peptide) and protein-DNA complexes were not used in training the energy function. The results of the DFIRE energy function on protein-ligand complexes are compared to the published results of 12 other scoring functions generated from either physical-based, knowledge-based, or empirical methods. They include AutoDock, X-Score, DrugScore, four scoring functions in Cerius 2 (LigScore, PLP, PMF, and LUDI), four scoring functions in SYBYL (F-Score, G-Score, D-Score, and ChemScore), and BLEEP. While the DFIRE energy function is only moderately successful in ranking native or near native conformations, it yields the strongest correlation between theoretical and experimental binding affinities of the testing sets and between rmsd values and energy scores of docking decoys in a benchmark of 100 protein-ligand complexes. The parameters and the program of the all-atom DFIRE energy function are freely available for academic users at http://theory.med.buffalo.edu.

Algorithms↗
PubMed2005

Bonding and metal-atom dynamics in two unique Sn(I)-Sn(III) complexes.

Two recently reported tin complexes, which incorporate both Sn(I) and Sn(III) sites in their structure, have been examined by temperature-dependent 119Sn Mössbauer effect (ME) spectroscopy. The distinct hyperfine parameters of the two sites make it possible to assign relative occupancies of the two sites (at 90 K) on the basis of the recoil-free fraction data extracted from the ME spectra. The temperature dependencies of the recoil-free fractions, elucidated from the ME spectra, show that the metal-atom dynamics are very similar for the two sites in the temperature range 90<T<150 K.

Journal Article↗
PubMed2005

Coordination of ScO+ and YO+ by multiple Ar, Kr, and Xe atoms in noble gas matrixes: a matrix isolation infrared spectroscopic and theoretical study.

The combination of matrix isolation infrared spectroscopic and quantum chemical calculation results provide strong evidence that scandium and yttrium monoxide cations, ScO+ and YO+, coordinate multiple noble gas atoms in forming noble gas complexes. The results showed that ScO+ coordinates five Ar, Kr, or Xe atoms, and YO+ coordinates six Ar or Kr and five Xe atoms in solid noble gas matrixes. Hence, the ScO+ and YO+ cations trapped in solid noble gas matrixes should be regarded as the [ScO(Ng)5]+ (Ng = Ar, Kr, or Xe), [YO(Ng)6]+ (Ng = Ar or Kr) or [YO(Xe)5]+ complexes. Experiments with dilute krypton or xenon in argon or krypton in xenon produced new IR bands, which are due to the stepwise formation of the [ScO(Ar)(5-n)(Kr)n]+, [ScO(Kr)(5-n)(Xe)n]+ (n = 1-5), [YO(Ar)(6-n)(Kr)n]+ (n = 1-6), and [YO(Ar)(6-n)(Xe)n]+ (n = 1-4) complexes.

Journal Article↗
PubMed2002

N-Myristoylethanolamine-cholesterol (1:1) complex: first evidence from differential scanning calorimetry, fast-atom-bombardment mass spectrometry and computational modelling.

The interaction of N-myristoylethanolamine (NMEA) with cholesterol is investigated by differential scanning calorimetry (DSC), fast-atom-bombardment mass spectrometry (FAB-MS) and computational modelling. Addition of cholesterol to NMEA leads to a new phase transition at 55 degrees C besides the chain-melting transition of NMEA at 72.5 degrees C. The enthalpy of the new transition increases with cholesterol content up to 50 mol%, but decreases thereafter, vanishing at 80 mol%. The enthalpy of the chain-melting transition of NMEA decreases with an increase in cholesterol; the transition disappears at 50 mol%. FAB-MS spectra of mixtures of NMEA and cholesterol provide clear signatures of the formation of ([NMEA+cholesterol]+) ([NMEA+cholesterol+Na]+). These results are consistent with the formation of a 1:1 complex between NMEA and cholesterol. Molecular modelling studies support this experimental finding and provide a plausible structural model for the complex, which highlights multiple H-bond interactions between the hydroxy group of cholesterol and the hydroxy and carbonyl groups of NMEA besides appreciable dispersion interaction between the hydrocarbon domains of the two molecules.

Calorimetry, Differential Scanning↗
PubMed1989

Substrate specificity and affinity of a protein modulated by bound water molecules.

Water molecules influence molecular interactions in all biological systems, yet it is extremely difficult to understand their effects in precise atomic detail. Here we present evidence, based on highly refined atomic structures of the complexes of the L-arabinose-binding protein with L-arabinose, D-fucose and D-galactose, that bound water molecules, coupled with localized conformational changes, can govern substrate specificity and affinity. The atoms common to the three sugars are identically positioned in the binding site and the same nine strong hydrogen bonds are formed in all three complexes. Two hydrogen-bonded water molecules in the site contribute further to tight binding of L-arabinose but create an unfavourable interaction with the methyl group of D-fucose. Equally tight binding of D-galactose is attained by the replacement of one of the hydrogen-bonded water molecules by its--CH2OH group, coordinated with localized structural changes which include a shift and redirection of the hydrogen-bonding interactions of the other water molecule. These observations illustrate how ordered water molecules can contribute directly to the properties of proteins by influencing their interaction with ligands.

Arabinose↗
PubMed2001

Application of the Marcus cross relation to hydrogen atom transfer reactions.

The transfer of a hydrogen atom-a proton and an electron-is a fundamental process in chemistry and biology. A variety of hydrogen atom transfer reactions, involving iron complexes, phenols, hydroxylamines, tBuOOH, toluene, and related radicals, are shown to follow the Marcus cross relation. Thus, the Marcus theory formalism based on ground-state energetics and self-exchange rates, originally developed for electron transfer processes, is also valuable for hydrogen atom transfer. Compounds that undergo slow proton transfer (C-H bonds) or slow electron transfer (cobalt complexes) also undergo slow hydrogen atom transfer. Limitations of this approach are also discussed.

Chemical Phenomena↗
PubMed1997

X-ray Crystallographic Studies of the Products of Oxidative Additions of Iodine to Cyclic Trinuclear Gold(I) Complexes: Directional Effects for Au-I.I-Au Interactions.

The crystal structures of cyclic trinuclear organogold compounds, Au(3)I(n)()(CH(3)N=COCH(3))(3) (n = 2, 4, 6) reveal that pairs of iodine atoms are added successively to each of the gold atoms in the triangular complexes. Deep red needles of Au(3)I(6)(CH(3)N=COCH(3))(3).CH(2)Cl(2) crystallize in the monoclinic space group P2(1)/c, with a = 14.762(4) Å, b = 8.723(3) Å, c = 22.278(6) Å, and beta = 91.58(2) degrees at 123 K with Z = 4. Refinement of 6591 reflections and 164 parameters yielded R = 0.055. The structure consists of columns of the molecular units united by weak iodine.iodine interactions which range in length from 3.636(2) to 3.716(2) Å. Within the molecular unit, all iodine.iodine distances are well beyond the sum of their van der Waals radii and fall in the range from 3.965(2) to 4.211(2) Å. The gold coordination is significantly distorted from planarity with I-Au-I angles of ca. 163 degrees. In Au(3)I(6)(CH(3)N=COCH(3))(3) the intermolecular I.I interactions are significantly shorter than the intramolecular I.I contacts. Red parallelepipeds of the tetraiodo complex, Au(2)I(4)Au(CH(3)N=COCH(3))(3), crystallize in the triclinic space group P&onemacr;, with a = 7.404(2) Å, b = 9.278(2) Å, c = 16.331(3) Å, alpha = 80.77(3) degrees, beta = 78.68(3) degrees, and gamma = 81.85(3) degrees at 123 K with Z = 2. Refinement of 4963 reflections and 124 parameters yielded R = 0.048. No noteworthy intermolecular contacts are present in this compound. Orange-red hexagonal plates of the diiodo complex, AuI(2)Au(2)(CH(3)N=COCH(3))(3), crystallize in the monoclinic space group P2(1)/c, with a = 9.309(4) Å, b = 13.597(4) Å, c = 14.899(5) Å, and beta = 101.26(3) degrees at 123 K with Z = 4. Refinement of 4133 reflections and 121 parameters yielded R = 0.064. This structure consists of discrete molecular units displaying no noteworthy inter- or intramolecular contacts.

Journal Article↗
PubMed2001

Monodithiolene molybdenum(V, VI) complexes: a structural analogue of the oxidized active site of the sulfite oxidase enzyme family.

The active sites of the xanthine oxidase and sulfite oxidase enzyme families contain one pterin-dithiolene cofactor ligand bound to a molybdenum atom. Consequently, monodithiolene molybdenum complexes have been sought by exploratory synthesis for structural and reactivity studies. Reaction of [MoO(S(2)C(2)Me(2))(2)](1-) or [MoO(bdt)(2)](1-) with PhSeCl results in removal of one dithiolate ligand and formation of [MoOCl(2)(S(2)C(2)Me(2))](1-) (1) or [MoOCl(2)(bdt)](1-) (2), which undergoes ligand substitution reactions to form other monodithiolene complexes [MoO(2-AdS)(2)(S(2)C(2)Me(2))](1-) (3), [MoO(SR)(2)(bdt)](1-) (R = 2-Ad (4), 2,4,6-Pr(i)(3)C(6)H(2) (5)), and [MoOCl(SC(6)H(2)-2,4,6-Pr(i)(3))(bdt)](1-) (6) (Ad = 2-adamantyl, bdt = benzene-1,2-dithiolate). These complexes have square pyramidal structures with apical oxo ligands, exhibit rhombic EPR spectra, and 3-5 are electrochemically reducible to Mo(IV)O species. Complexes 1-6 constitute the first examples of five-coordinate monodithiolene Mo(V)O complexes; 6 approaches the proposed structure of the high-pH form of sulfite oxidase. Treatment of [MoO(2)(OSiPh(3))(2)] with Li(2)(bdt) in THF affords [MoO(2)(OSiPh(3))(bdt)](1-) (8). Reaction of 8 with 2,4,6-Pr(i)(3)C(6)H(2)SH in acetonitrile gives [MoO(2)(SC(6)H(2)-2,4,6-Pr(i)(3))(bdt)](1-) (9, 55%). Complexes 8 and 9 are square pyramidal with apical and basal oxo ligands. With one dithiolene and one thiolate ligand of a square pyramidal Mo(VI)O(2)S(3) coordination unit, 9 closely resembles the oxidized sites in sulfite oxidase and assimilatory nitrate reductase as deduced from crystallography (sulfite oxidase) and Mo EXAFS. The complex is the first structural analogue of the active sites in fully oxidized members of the sulfite oxidase family. This work provides a starting point for the development of both structural and reactivity analogues of members of this family.

Animals↗
PubMed2006

Aqua(di-2-pyridylamine)oxalatocopper(II) monohydrate.

In the structure of the title complex, [Cu(C2O4)(C10H9N3)(H2O)].H2O, the Cu(II) atom displays a square-pyramidal geometry, being coordinated by two N atoms from the di-2-pyridylamine ligand, two O atoms from the oxalate group and one O atom of a water molecule. The complex molecules are linked to form a three-dimensional supramolecular array by hydrogen-bonding interactions between coordinated/uncoordinated water molecules and the uncoordinated oxalate O atoms of neighboring molecules.

Journal Article↗