M. A. Carrondo

Ab initio determination of the crystal structure of cytochrome c6 and comparison with plastocyanin

BACKGROUNDnElectron transfer between cytochrome f and photosystem I (PSI) can be accomplished by the heme-containing protein cytochrome c6 or by the copper-containing protein plastocyanin. Higher plants use plastocyanin as the only electron donor to PSI, whereas most green algae and cyanobacteria can use either, with similar kinetics, depending on the copper concentration in the culture medium.nnnRESULTSnWe report here the determination of the structure of cytochrome c6 from the green alga Monoraphidium braunii. Synchrotron X-ray data with an effective resolution of 1.2 A and the presence of one iron and three sulfur atoms enabled, possibly for the first time, the determination of an unknown protein structure by ab initio methods. Anisotropic refinement was accompanied by a decrease in the free R value of over 7% the anisotropic motion is concentrated at the termini and between residues 38 and 53. The heme geometry is in very good agreement with a new set of heme distances derived from the structures of small molecules. This is probably the most precise structure of a heme protein to date.nnnCONCLUSIONSnOn the basis of this cytochrome c6 structure, we have calculated potential electron transfer pathways and made comparisons with similar analyses for plastocyanin. Electron transfer between the copper redox center of plastocyanin to PSI and from cytochrome f is believed to involve two sites on the protein. In contrast, cytochrome c6 may well use just one electron transfer site, close to the heme unit, in its corresponding reactions with the same two redox partners.

Electrochemical and structural studies of nickel(II) complexes with N2O2 Schiff base ligands 2. Crystal and molecular structure of N,N′-l,2-ethane-1,2-diyl-bis(2- hydroxyacetophenonylideneiminate)nickel(II), N, N′-1,2-cis cyclohexane-1,2-diyl-bis(2-hydroxyacetophenonylideneiminate)- nickel(II) and N,N′-1,2-benzene-1,2-diyl-bis(3,5-dichlorosalicylideneiminate)nickel(II)

Reductive and oxidative chemistry of three complexes of formula [Ni(L)], where L represents a N2O2 Schiff base pseudomacrocyclic ligand based on salicylaldehyde derivatives and three different diamines, was studied in (CH3)2SO: N,N′-1,2-ethane-1,2-diyl-bis(2-hydroxyacetophenonylideneiminate)nickel(II) (1); N,N′-1,2-cis-cyclohexane-1,2-diyl-bis(2-hydroxyacetophenonylideneiminate)nickel(II) (2); N,N′-1,2-benzene-1,2-diyl-(bis(3,5-dichlorosalicylideneiminate)nickel(II) (3). Electrochemical behavior of the complexes was determined by cyclic voltametry, and EPR spectroscopy was used to characterize the one-electron reduced/oxidized species. Reduction of the complexes 1 and 2 yielded Ni(I) complexes with a dxy ground state (gz>gx, gy), but the reduction of 3 is ligand-centered as suggested from the pseudo-isotropic radicalar EPR signal of frozen electrolyzed solutions. Oxidation of all three complexes is metal-centered and the oxidized products are low spin hexacoordinate Ni(III) species with two solvent molecules coordinated axially, with a dz2 ground state (gx, gy>gz). The crystal structures of the three Ni(II) complexes were determined from single crystal X-ray diffraction data collected with the use of Mo Kα radiation. 1: space group C2/c with a = 25.963(3), b = 7.2973(4), c = 17.357(2) A, β = 107.085(5)°, Z = 8 (R = 0.061); 2: space group P21/a with a = 9.645(6), b = 19.149(16), c = 10.743(5) A, β = 94.66(2)°, Z = 4 (R = 0.085); 3: space group P21/n with a = 13.372(5), b = 8.785(2), c = 16.534(5) A, β = 101.60(3)°, Z = 4 (R = 0.054). Crystal packing of 1 and 3 involves the pairing of two centrosymmetrical related molecules in dimers, but that of 2 shows no systematic parallel orientation of any part of the molecules. X-ray structural data have provided a rationale for the E12 values obtained for the reduction and oxidation processes.

REFINEMENT OF THE THREE-DIMENSIONAL STRUCTURES OF CYTOCHROME C3 FROM DESULFOVIBRIO VULGARIS HILDENBOROUGH AT 1.67 A RESOLUTION AND FROM DESULFOVIBRIO DESULFURICANS ATCC 27774 AT 1.6 A RESOLUTION

Abstract The three-dimensional X-ray structures of cytochrome c 3 from Desulfovibrio vulgaris Hildenborough and from Desulfovibrio desulfuricans ATCC 27774 were previously determined at 1.9 and 1.75 A resolution, respectively. More recently, higher resolution data were collected (at 1.67 and 1.6 A respectively) using synchrotron radiation. The refinement of the previously determined three-dimensional structures using the new data resulted in more accurate structural models, with no significant changes of the initial structures. In cytochrome c 3 from D. vulgaris Hildenborough, the R -factor was lowered from 19.6 to 15.3% using SHELXL-93, complemented with inspection and correction of the model relative to the electron density. This cytochrome crystallises in space group P 6 1 with a =77.3, b =77.3, c =77.1 A, Z =12. Cytochrome c 3 from D. desulfuricans ATCC 27774 crystallises in space group P 6 1 22 with a =62.71, b =62.71, c =111.09 A, Z =12. The R -factor was lowered from 17.8 to 16.6% using the same refinement procedure. In this cytochrome the 71–74 loop region was rearranged with no evidence of the previously found disorder, and disorder models were introduced in the terminal regions of residues serine 84 and lysine 90. The resulting higher-resolution structural models for both cytochromes are analyzed and compared with those previously obtained.

Cationic benzyl nickel complexes as homogeneous catalysts for styrene oligomerization. X-ray crystal structure of [Ni(η3-CH2C6H5)(PPh3)2]PF6 · CH2CI2 *

Abstract New cationic complexes [Ni(η3-CH2C6H5)(PPh3)2]PF6 (3) and [Ni(η3-CH2C6H5)((+)-DIOP)]PF6 (4) were synthesized from the corresponding neutral compounds [Ni(η3-CH2C6H5)X(PR3)2] (X = Cl, Br), by metathetical halide abstraction with TIPF6. Complex 3 was characterized by X-ray crystallography and shown to have a distorted square-planar geometry with the benzylic group coordinated in a quasi-allylic fashion. Crystals are monoclinic, space group P21/n, a = 11.798(5), b = 19.251(2), c = 18.561(3) A, β = 93.03°, V = 4208.6 A3. Solution NMR studies showed benzyl fluxionality and phosphine lability in compound 3, but not in 4. The latter one is catalytically inactive towards styrene oligomerization, whereas 3 produces styrene oligomers ( M ¯ n ≈ 1000 ) with 67% isotactic content. Although [Ni(η3-CH2C6H5)CI(PCy3)] and trans[Ni(Cl)(H)(PCy3)2] are inactive, addition of TlPF6 induced catalytic activity with formation of highly isotactic (90%) styrene oligomers with similar M ¯ n and a different terminal group.

Bis-(N-hydroxy-iminodiacetate)vanadate(IV), a synthetic model of ‘amavadin’

The vanadium(IV) octaco-ordinated complex (NH4+)[N(CH3)4+][V(HIDA)2](HIDA =N-hydroxy-iminodiacetate), whose anion is a likely model for the natural compound ‘amavadin,’ has been prepared and its crystal and molecular structures have been determined by X-ray crystallography; this is the first example of an octaco-ordinated vanadium(IV) complex with just N and O donor atoms.

Molecular structure of trans-bis[1,2-bis(diphenylphosphino)ethane]chloro(t-butylisocyanide)rhenium(I)-tetrahydrofuran solvate, trans-{ReCl[CN(t-C4H9)]-(Ph2PCH2CH2PPh2)2}•C4H8O

Abstract Crystals of trans -{ReCl[CN(t-C 4 H 9 )](Ph 2 PCH 2 CH 2 PPh 2 ) 2 } · C 4 H 8 O solvate are monoclinic, space group P 2 1 / n , a 24.098(7), b 16.558(5), c 13.402(4) A, β 90.97(3)°, V 5346.82 A 3 at 25°C. F (000)= 2392, Z = 4, λ(Cu-K α 1.5418 A, μ(Cu-K α ) 57.99 cm −1 D c 1.46 g cm −3 . The structure was solved by Patterson and difference Fourier electron density syntheses and refined to R ( F )= 0.048 and R w ( F )= 0.067 for 4763 observed reflections. The Re atom is in a distorted octahedral coordination with the chloride and the isocyanide as axial ligands and the two dppe groups as equatorial ligands. The Reue5f8C bond length is 1.926(9) A and the Clue5f8Reue5f8C bond angle is 175.5(2)°. The CNBu t ligand is nearly linear with a 174.0(9)° angle at the N and a Cue5fcN bond length of 1.154(10) A. The t-Bu group and the solvate molecules are disordered.

The preparation and crystal structure analysis of bis(L-Arginine)Cu(II)(acetate)2trihydrate

Abstract The crystal structure of bis(L-arginine)Cu(II)(acetate)2trihydrate has been determined by X-ray analysis. The complex crystallizes in the monoclinic space group P21, with cell dimensions a = 15.948(2), b = 16.878(2), c = 10.378(2) A, β = 108.47(1)°, Z = 4. There are two independent formula units in the asymmetric unit. The Cu atoms were located from a Patterson synthesis and the remaining atoms from difference Fourier syntheses. The structure was refined by least-squares to R = 0.079 and R = 0.11. Each copper atom has an essentially square planar coordination with the two arginine molecules chelated via the carboxy oxygens and the α-amino nitrogens, but with distorted six-fold coordinations completed by weak Cu…O (acetate) interactions. Electrostatic interactions between the acetates and the protonated ends of the amino acid residues link the two independent [Cu(L-arginine)2(acetate)2] units into dimers, which are then connected via hydrogen bonds, also involving the water molecules, into an infinite network.

The preparation and crystal structure analysis of a 2:1 complex between L-lysine and copper(II) chloride

Abstract The crystal structure of bis(L-lysine)Cu(II) chloride dihydrate has been determined by X-ray analysis. The complex crystallizes in the monoclinic space group P 2 1 , with cell dimensions a = 5.189(1), b = 16.988(3), c = 11.482(2) A, β = 93.57(1)°. The position of the Cu atom was found from a Patterson synthesis, the remaining atoms were located with DIRDIF. The structure was refined by least-squares to R = 0.060 and R w = 0.065 for 2637 observed reflections. The copper(II) atom has an essentially square planar coordination with the two lysine molecules chelated via the carboxy oxygen and the α-amino nitrogen. However the two chlorine atoms form weak interactions with the metal to complete a strongly tetragonally elongated six-fold coordination. The two aliphatic chains have rather different geometries and are extended in a zig-zag mode. Extensive hydrogen bonding links the complex and the water molecules together.

Synthesis, electrochemical behaviour and structural characterization of the mercury complex [Hg([18]aneN6)]·(HgCl4)

Abstract Reaction of HgCl2, in slight excess of 1 molar equivalent of the ligand ([18]aneN6) in water, produces a colourless solution containing [Hg([18]aneN6)](HgCl4). The X-ray structure of this complex shows that the six nitrogen donor atoms of the macrocycle surround the mercury(II) atom in a distorted trigonal prismatic coordination. Cyclic voltammetry of [Hg([18]ane)]2+ shows a chemically reversible reduction at a HDM electrode, with E 1 2 = −0.293 V vs S.C.E. at pH 9.37 and a scan rate of 200 mV s−1. The global oxidation-reduction process involves two electrons and two protons.

Synthesis, characterization and bonding of fulvalene dimolybdenum(III) and ditungsten(III) cations with one thiolate bridging ligand. Crystal structure of [Mo2(μ-η5: η5-C10H8)(μ-SC6H5)(μ5-C5H5) 2][Re2(μ-SC6H5)3(CO)6]

Abstract New bridged fulvalene (Fv = μ-η 5 : η 5 -C 10 )H 8 ) binuclear molybdenum(III) and tungsten(III) compounds were obtained from the reaction of [M(η 5 -C 5 H 5 ) 2 (SC 6 H 5 ) 2 ] (M = Mo or W) with dirhenium decacarbonyl. The complex [Mo 2 Fv(μ-SC 6 H 5 )Cp 2 ][Re 2 (μ-SPh) 3 (CP) 6 ] was characterized by single crystal X-ray diffraction. The cation [Mo 2 Fv(μ-SC 6 H 5 )Cp 2 ] + showed a relatively rigid [Mo 2 FvCp 2 ] unit with an Mo-S-Mo angle of 83.88(7)°, M-S distances 2.442(2) and 2.450(2) A and a Mo⋯Mo distance of 3.256(1) A. In the [Re 2 (μ-SPh) 3 (CO) 6 ] − anion, each metal atom has an octahedral environment (three carbonyl and three thiolate groups) with the two octahedra sharing the face containing the sulphur donor atoms (Re-S-Re angles from 86.63(8) to 86.83(8)°). The Re⋯Re distance of 3.457(1) A is long. Extended Huckel molecular orbital calculations were done in order to understand the nature of the metal-metal interaction in the cation and some related complexes. Although the Mo⋯Mo distance is relatively long, there is a strong interaction between the two d 3 metal atoms, assigned to a μ bond, which leads to diamagnetic behaviour (the anion with two d 6 Re I centres is also diamagnetic).