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PubMed2006

Molecular design of neutral intramolecular complexes bearing two silicon atoms anchored by a carbonyl oxygen atom: N,N'-bis(silylmethyl)propylene ureas.

B3LYP and MP2 computations have been performed on a variety of Si,Si'-substituted N,N'-bis(silylmethyl)propylene ureas. According to electron-density atoms-in-molecules (AIM) and electron localization function (ELF) quantum-topological analyses, a transition from the unstable non-chelate forms of these compounds to mono- and bis-chelate forms results in the successive interaction of one and two tetracoordinate silicon atoms with the carbonyl oxygen and the formation, respectively, of one and two covalent, polar Si...O bonds. This previously unknown X-Si<--O-->Si-X type of bonding in isomers possessing an anchor structure may be classified as a five-center, six-electron (5c-6e) bond. The factors that favor the existence of Si,Si'-substituted N,N'-bis(silylmethyl)propylene ureas exclusively in the form of stable, bridged complexes (the size of equatorial ligands and the electronegativity of axial substituents at the silicon atom, change in the donor capability of the carbonyl group, and effect of the polar solvent) are discussed.

Journal Article↗
PubMed2004

Hexacoordinate planar main group atoms centered in hexagonal hydrocopper complexes Cu6H6X (X = Si, P, As).

Ab initio theoretical evidence of hexacoordinate planar main group atoms centered in hexagonal hydrocopper complexes Cu(6)H(6)X (X = Si, P, As) is presented at the density functional theory level in this work. The results obtained extend the bonding capacity of silicon, phosphorus, and arsenic to planar hexacoordination in hydrocopper complexes which are important in fundamental research and may shed new insight into catalyst chemistry.

Arsenic↗
PubMed2006

Solvent effects on the redox properties of Cu complexes used as mediators in atom transfer radical polymerization.

Solvent effects on the redox properties of six Cu(I) complexes used as mediators in atom transfer radical polymerization (ATRP) have been studied using cyclic voltammetry. The six ligands used were tris[2-(dimethylamino)ethyl]amine, N-(n-propyl)-2-pyridylmethanimine, N,N,N',N',N'-pentamethyldiethylenetriamine, 1,1,4,7,10,10-hexamethyl-triethylenetetramine, 2,2'-bipyridine, and 1,4,8,11-tetraaza-1,4,8,11-tetramethylcyclotetradecan. The solvents used were DMSO, DMF, MeCN, MeOH, IP, and BuOH. Significant solvent effects were observed and quantitatively analyzed in terms of Kamlet-Taft relationships. The resulting Kamlet-Taft equations were found to successfully describe the solvent effects and could thus be used as tools for the design of ATRP in new solvents. The solvent sensitivity of the different ligands and the nature of the solvent effects are also discussed to some extent.

Journal Article↗
PubMed1998

Surface analysis of the photosystem I complex by electron and atomic force microscopy.

Two-dimensional (2D) crystals of the photosystem I (PSI) reaction center from Synechococcus sp. OD24 were analyzed by electron and atomic force microscopy. Surface relief reconstructions from electron micrographs of freeze-dried unidirectionally shadowed samples and topographs recorded with the atomic force microscope (AFM) provided a precise definition of the lumenal and stromal PSI surfaces. The lumenal surface was composed of four protrusions that surrounded an indentation. One of the protrusions, the PsaF subunit, was often missing. Removal of the extrinsic proteins with the AFM stylus exposed the stromal side of the PSI core, whose surface structure could then be imaged at a resolution better than 1.4 nm. This interfacial surface between core and extrinsic subunits, had a pseudo-2-fold symmetry and protrusions that correlated with the surface helices e and e' or were at the sites of putative alpha-helix-connecting loops estimated from the 4 A map of the complex. The molecular dissection achieved with the AFM, opens new possibilities to unveil the interfaces between subunits of supramolecular assemblies.

Amino Acid Sequence↗
PubMed2000

Heteropolynuclear phosphide complexes: phosphorus as unique atom bridging coinage metal centres.

In this paper we describe the synthesis and reactivity of the diphenylphosphine derivatives [Au(C6F5)(PPh2H)] and trans-[Au(C6F5)2(PPh2H)2]ClO4. Reactions of the latter or the neutral [Au(C6F5)3(PPh2H)] with the appropriate Group 11 metal reagents (M = Au, Ag, Cu) in the presence of acetylacetonate afford a series of novel Au(III)-M phosphido-bridged complexes, which have been scarcely represented to date. The crystal structure of the tetranuclear [(Au(C6F5)2(mu-PPh2)2Ag)2] and the dinuclear [Au(C6F5)3(mu-PPh2)M(PPh3)] (M = Au,Ag) complexes were established by X-ray diffraction methods. The synthesis and deprotonating activity of the anionic gold(III) complex PPN[Au(C6F5)3(acac)] (PNN = [N(PPh3)2]+) was studied.

Journal Article↗
PubMed1992

Reaction of cyanide with cytochrome ba3 from Thermus thermophilus: spectroscopic characterization of the Fe(II)a3-CN.Cu(II)B-CN complex suggests four 14N atoms are coordinated to CuB.

Cytochrome ba3 from Thermus thermophilus reacts slowly with excess HCN at pH 7.4 to create a form of the enzyme in which CuA, cytochrome b, and CuB remain oxidized, while cytochrome a3 is reduced by one electron, presumably with the formation of cyanogen. We have examined this form of the enzyme by UV-visible, resonance Raman, EPR, and electron nuclear double resonance spectroscopies in conjunction with permutations of 13C- and 15N-labeled cyanide. The results support a model in which one CN- binds through the carbon atom to ferrous a3, supporting a low-spin (S = 0) configuration on the Fe; bridging by this cyanide to the CuB is weak or absent. Four 14N atoms, presumably donated by histidine residues of the protein, provide a strong equatorial ligand field about CuB; a second CN- is coordinated through the carbon atom to CuB in an axial position.

Binding Sites↗
PubMed2002

Bis(isoquinoline-1-carboxylato-kappa2O,N)(1,10-phenanthroline-kappa2N,N')zinc(II) dimethylformamide sesquisolvate.

The asymmetric unit of the title compound, [Zn(C(10)H(6)NO(2))(2)(C(12)H(8)N(2))] x 1.5C(3)H(7)NO, contains one monomeric zinc complex and 1.5 disordered dimethylformamide solvate molecules. The Zn atom is coordinated to one 1,10-phenanthroline ligand and to two isoquinolinecarboxylate anions (IQC-) via their N and O atoms. The complex exhibits a distorted octahedral geometry around the Zn(II) atom, with the apical positions occupied by the O atoms of the IQC- ligands. The Zn atom lies 0.049 (1) A out of the basal plane. The crystal packing is characterized by several hydrogen bonds.

Journal Article↗
PubMedDate not supplied

[Electronic structure of hemoglobin's heme complexes with nitric oxide and dynamics of atomic base under physiological temperature].

The comparative study of atomic and electronic structure of hem complexes of hemoglobin with molecular oxygen and nitric oxide has been performed by semiempirical quantum chemical PM3 method. It has been shown that the length of chemical bonding in oxygen molecule coordinated with hem increases by 0.046 A and the length of chemical bonding in nitrogen oxide coordinated with hem increases by 0.064 A in comparison with pure substances. This fact indicates that chemical bonding between nitric oxide and Fe atom of hem is stronger that one with oxygen molecule. Analysis of charge of the molecules indicates that NO bounded with Fe by covalent chemical bonding and oxygen molecule bounded with Fe by weak dipole interaction. Atomic orbitals of ligand atoms in oxygen complex play small part in high occupied (HOMO) and low vacant (LVMO) molecular orbitals in comparison with HOMO and LVMO of complex with NO. In the last one unpaired electron of NO molecule moves from ligand to d-orbitals of Fe atom and creates d7-configuration. Molecular dynamics simulation under physiological temperature (310 K) indicates visible difference in atomic and electronic structure of the complexes in comparison with ones under low (from 77 up to 0 K) temperatures.

Heme↗
PubMed1998

Stepwise Cluster Assembly Using VO(2)(acac) as a Precursor: cis-[VO(OCH(CH(3))(2))(acac)(2)], [V(2)O(2)(&mgr;-OCH(3))(2)(acac)(2)(OCH(3))(2)], [V(3)O(3){&mgr;,&mgr;-(OCH(2))(3)CCH(3)}(2)(acac)(2)(OC(2)H(5))], and [V(4)O(4)(&mgr;-O)(2)(&mgr;-OCH(3))(2)(&mgr;(3)-OCH(3))(2)(acac)(2)(OCH(3))(2)].2CH(3)CN(1).

The studies of an underexplored synthetic reagent, VO(2)(acac) (Hacac = acetylacetone) and semirational strategies for the formation of a complete series of simple vanadium(V) alkoxide clusters in alcohol-containing solvents. The neutral mono-, di-, tri-, and tetranuclear oxovanadium(V) complexes [V(2)O(2)(&mgr;-OCH(3))(2)(acac)(2)(OCH(3))(2)] (1), [V(4)O(4)(&mgr;-O)(2)(&mgr;-OCH(3))(2)(&mgr;(3)-OCH(3))(2)(acac)(2)(OCH(3))(2)].2CH(3)CN (2), [V(4)O(4)(&mgr;-O)(2)(&mgr;-OCH(3))(2)(&mgr;(3)-OCH(3))(2)(acac)(2)(OCH(3))(2)] (3), [V(3)O(3){&mgr;,&mgr;-(OCH(2))(3)CCH(3)}(2)(acac)(2)(OR)] (R = CH(3) (4), C(2)H(5) (5)), and cis-[VO(OCH(CH(3))(2))(acac)(2)] (6) with alkoxide and acac(-) ligands were obtained by reaction of VO(2)(acac) with a monoalcohol and/or a tridentate alcohol. The structures of complexes 1-3, 5, and 6 were determined by X-ray diffraction methods. Complex 1 crystallized in the monoclinic system, P2(1)/n, with a = 7.8668(5) Å, b = 15.1037(9) Å, c = 8.5879(5) Å, beta = 106.150(1) degrees, V = 980.1(1) Å(3), Z = 2, and R (wR2) = 0.040 (0.121). Complex 2 crystallized in the monoclinic system, P2(1)/n, with a = 8.531(2) Å, b = 14.703(3) Å, c = 12.574(2) Å, beta = 95.95(2) degrees, V = 1568.7(5) Å(3), Z = 2, and R (wR2) = 0.052 (0.127). Complex 3 crystallized in the triclinic system, P&onemacr;, with a = 8.5100(8) Å, b = 8.9714(8) Å, c = 10.3708(10) Å, alpha = 110.761(1) degrees, beta = 103.104(1) degrees, gamma = 100.155(1) degrees, V = 691.85(11) Å(3), Z = 1, and R (wR2) = 0.040 (0.105). Complex 5 crystallized in the monoclinic system, P2(1)/n, with a = 14.019(2) Å, b = 11.171(2) Å, c = 19.447(3) Å, beta = 109.18(1) degrees, V = 2876.5(8) Å(3), Z = 4, and R (wR2) = 0.062 (0.157). Complex 6 crystallized in the monoclinic system, P2(1)/n, with a = 15.0023(8) Å, b = 8.1368(1) Å, c = 26.5598(2) Å, beta = 95.744(1) degrees, V = 3225.89(8) Å(3), Z = 8, and R (wR2) = 0.060 (0.154). Complex 1 is a discrete, centrosymmetric dimer in which two vanadium atoms are bridged by two methoxide ligands. Compound 2 contains a V(4)O(4) eight-membered ring with both &mgr;-oxo and &mgr;-alkoxo bridging ligands; the ring is capped above and below by two triply bridging methoxo ligands. Compound 3 has the same structure as 2. The three vanadium atoms in complex 5 are linked by four bridging oxygen atoms from two tridentate thme(3)(-) ligands to form a V(3)O(4) chain in which V-O bonds alternate in length. The V-O(isopropoxo) bond in 6 is cis to V=O, and the V-O(acac) bond trans to the oxo group is relatively long. The V(2)O(2) rings of complex 1 and the mononuclear 1:2 complex can be considered to be the basic building block of the trinuclear complexes 4 and 5 and the tetranuclear complex 2, acting to extend the vanadium-oxide framework. (51)V and (1)H NMR spectroscopic studies of the solution state of complexes 1-6 revealed dramatic differences in structural and hydrolytic stability of these complexes. Compounds 1 and 3 only remained intact at low temperature in CDCl(3) solution, whereas the mononuclear compound 6 could remain at ambient temperature for approximately 10 h. Compound 4 only maintained its solid-state structure at low temperature in CDCl(3) solution, whereas compound 5 was significantly more stable. The structural integrity of oligomeric vanadium-oxygen frameworks increased significantly when the coordinating alkoxide group showed more resistance to exchange reactions than the methoxide group. The solid state and solution properties of this new group of complexes not only testify to the versatility of VO(2)(acac) as a vanadium(V) precursor but also raise questions relating to solution structure and properties of related vanadium complexes with insulin-mimetic properties and catalytic properties.

Journal Article↗
PubMed1998

Atomic structure of progesterone complexed with its receptor.

The physiological effects of progestins are mediated by the progesterone receptor, a member of the steroid/nuclear receptor superfamily. As progesterone is required for maintenance of pregnancy, its receptor has been a target for pharmaceuticals. Here we report the 1.8 A crystal structure of a progesterone-bound ligand-binding domain of the human progesterone receptor. The nature of this structure explains the receptor's selective affinity for progestins and establishes a common mode of recognition of 3-oxy steroids by the cognate receptors. Although the overall fold of the progesterone receptor is similar to that found in related receptors, the progesterone receptor has a quite different mode of dimerization. A hormone-induced stabilization of the carboxy-terminal secondary structure of the ligand-binding domain of the progesterone receptor accounts for the stereochemistry of this distinctive dimer, explains the receptor's characteristic pattern of ligand-dependent protease resistance and its loss of repression, and indicates how the anti-progestin RU486 might work in birth control. The structure also indicates that the analogous 3-keto-steroid receptors may have a similar mechanism of action.

Amino Acid Sequence↗
PubMed1978

Crystallization, crystal structure analysis and atomic model of the complex formed by a human Fc fragment and fragment B of protein A from Staphylococcus aureus.

Crystals of the complex formed by human Fc fragment and fragment B (FB) of protein A from Staphylococcus aureus were prepared and the crystal structure determined at high resolution by multiple isomorphous replacement. Phase were improved considerably by combining these phases with calculated phases from the Fc component. FB is a small globular protein built of three parallel helices arranged in a triangular array. It binds by the first two helices of Fc and is attached to segments of CH2 and CH3. The CH3 module is unchanged between complex and Fc fragment crystals, but CH2 changes its position slightly relative to CH3. In addition, the upper third of CH2 is disordered in the complex crystals. Possible sources of this disorder are discussed.

Antigen-Antibody Complex↗
PubMed2001

Design of functionalized lipids and evidence for their binding to photosystem II core complex by oxygen evolution measurements, atomic force microscopy, and scanning near-field optical microscopy.

Photosystem II core complex (PSII CC) absorbs light energy and triggers a series of electron transfer reactions by oxidizing water while producing molecular oxygen. Synthetic lipids with different alkyl chains and spacer lengths bearing functionalized headgroups were specifically designed to bind the Q(B) site and to anchor this large photosynthetic complex (240 kDa) in order to attempt two-dimensional crystallization. Among the series of different compounds that have been tested, oxygen evolution measurements have shown that dichlorophenyl urea (DCPU) binds very efficiently to the Q(B) site of PSII CC, and therefore, that moiety has been linked covalently to the headgroup of synthetic lipids. The analysis of the monolayer behavior of these DCPU-lipids has allowed us to select ones bearing long spacers for the anchoring of PSII CC. Oxygen evolution measurements demonstrated that these long-spacer DCPU-lipids specifically bind to PSII CC and inhibit electron transfer. With the use of atomic force microscopy (AFM) and scanning near-field optical microscopy (SNOM), it was possible to visualize domains of PSII CC bound to DCPU-lipid monolayers. SNOM imaging has enabled us to confirm that domains observed by AFM were composed of PSII CC. Indeed, the SNOM topography images presented similar domains as those observed by AFM, but in addition, it allowed us to determine that these domains are fluorescent. Electron microscopy of these domains, however, has shown that the bound PSII CC was not crystalline.

Diuron↗
PubMed2003

Structural analysis of the reaction center light-harvesting complex I photosynthetic core complex of Rhodospirillum rubrum using atomic force microscopy.

The bacterium Rhodospirillum rubrum contains a simple photosynthetic system, in which the reaction center (RC) receives energy from the light-harvesting (LH1) complex. We have used high-resolution atomic force microscopy (AFM) to image two-dimensional crystals of the RC-LH1 complex of R. rubrum. The AFM topographs show that the RC-LH1 complex is approximately 94 A in height, the RC-H subunit protrudes from the cytoplasmic face of the membrane by 40 A, and it sits 21 A above the highest point of the surrounding LH1 ring. In contrast, the RC on the periplasmic side is at a lower level than LH1, which protrudes from the membrane by 12 A. The RC-LH1 complex can adopt an irregular shape in regions of uneven packing forces in the crystal; this reflects a likely flexibility in the natural membrane, which might be functionally important by allowing the export of quinol formed as a result of RC photochemistry. Nanodissection of the RC by the AFM tip removes the RC-H subunit and reveals the underlying RC-L and -M subunits. LH1 complexes completely lacking the RC were also found, providing ideal conditions for imaging both rings of LH1 polypeptides for the first time by AFM. In addition, we demonstrate the ellipticity of the LH1 ring at the cytoplasmic and periplasmic sides of the membrane, in both the presence and absence of the RC. These AFM measurements have been reconciled with previous electron microscopy and NMR data to produce a model of the RC-LH1 complex.

Bacterial Proteins↗
PubMed1990

Direct visualization of phosphorylase-phosphorylase kinase complexes by scanning tunneling and atomic force microscopy.

In skeletal muscle the activation of phosphorylase b is catalyzed by phosphorylase kinase. Both enzymes occur in vivo as part of a multienzyme complex. The two enzymes have been imaged by atomic force microscopy and the results compared to those previously found by scanning tunneling microscopy. Scanning tunneling microscopy and atomic force microscopy have been used to view complexes between the activating enzyme phosphorylase kinase and its substrate phosphorylase b. Changes in the size and shape of phosphorylase kinase were observed when it bound phosphorylase b.

Animals↗
PubMed2003

Bis[1-(p-chlorophenyl)-5-isopropylbiguanide-kappa2N2,N4]nickel(II) dichloride dimethylformamide solvate.

The asymmetric unit of the title compound, [Ni(C(11)H(16)ClN(5))(2)]Cl(2).C(3)H(7)NO, contains one monomeric nickel(II) complex cation, two Cl(-) anions and one dimethylformamide solvent molecule. The Ni atom is coordinated to each of two 1-(p-chlorophenyl)-5-isopropylbiguanide (proguanil) ligands via two N atoms. The complex exhibits a square-planar coordination, with the Ni atom lying 0.021 (2) A out of the basal plane. The crystal packing is characterized by several hydrogen bonds.

Journal Article↗