Ruthenium bipyridyl compounds with two terminal alkynyl ligands

Compounds of the form Ru(X2bipy)(PPh3)2(-C triple bond CC6H4NO2-p)2(X2bipy = 4,4'-X(2)-2,2'-bipyridine, X = Me 3a, Br 3b, I 3c) have been synthesised from the mono-alkynyl precursors Ru(X2bipy)(PPh3)2(-C triple bond CC6H4NO2-p)Cl (X = Me 2a, Br 2b, I 2c); the former are the first ruthenium bis-alkynyl compounds that also contain a bipyridyl ligand. Spectroelectrochemical investigation of 3a shows that the metal is readily oxidised to form the ruthenium(III) compound 3a+, and will also undergo a single-electron reduction at each nitro group to form 3a2-. ESR and UV/visible spectra of these redox congeners are presented. We also report the synthesis of [Ru(Me2bipy)(PPh3)2(-C triple bond CBut)(N triple bond N)][PF6] during the attempted synthesis of Ru(Me2bipy)(PPh3)2(-C triple bond CBut)2, and report its X-ray crystal structure and IR spectrum. X-Ray crystal structures of 3b and 3c(as two different solvates) are presented, and the nature of the intermolecular interactions seen therein is discussed. Z-Scan measurements on Ru(Me2bipy)(PPh3)2(-C triple bond CR)Cl (R = C6H4NO2-p2a, But, Ph, C6H4Me) are also reported, and show that Ru(Me2bipy)(PPh3)2(-C triple bond CR)Cl (R = C6H4NO2-p2a, Ph) exhibit moderate third-order non-linearities.     

Electron capture dissociation distinguishes a single D-amino acid in a protein and probes the tertiary structure

First results are reported on the application of ECD in analysis of 2+ and 3+ ions of stereoisomers of Trp-cage (NLYIQWLKDGGPSSGRPPPS), the smallest and fastest-folding protein, which exhibits a tightly folded tertiary structure in solution. The chiral recognition based on the ratios of the abundances of z(18) and z(19) fragments in ECD of 2+ ions was excellent even for a single amino acid (Tyr) D-substitution (R(chiral) = 8.6). The chiral effect decreased with an increase of temperature at the electrospray ion source, as well as at a higher degree of ionization, 3+ ions (R(chiral) = 1.5). A general approach is suggested for charge localization in n+ ions by analysis of ECD mass spectra of (n + 1)+ ions. Application of this approach to 3+ Trp-cage ions revealed the protonation probability order in 2+ ions: Arg(16) > Gln(5) > approximately N-terminus. The ECD results for native form of the 2+ ions favor the preservation of the solution-phase tertiary structure, and chiral recognition through the interaction between the charges and the neutral bond network. Conversely, ECD of 3+ ions supports the dominance of ionic hydrogen bonding which determines a different gas-phase structure than found in solution. Vibrational activation of 2+ ions indicated greater stability of the native form, but the fragmentation patterns did not provide stereoisomer differentiation, thus underlying the special position of ECD among other MS/MS fragmentation techniques. Further ECD studies should yield more structural information as well as quantitative single-amino acid D/L content measurements in proteins.     

Phosphorylation reaction in cAPK protein kinase-free energy quantum mechanical/molecular mechanics simulations

We present results of a theoretical analysis of the phosphorylation reaction in cAMP-dependent protein kinase using a combined quantum mechanical and molecular mechanics (QM/MM) approach. Detailed analysis of the reaction pathway is provided using a novel QM/MM implementation of the nudged elastic band method, finite temperature fluctuations of the protein environment are taken into account using free energy calculations, and an analysis of hydrogen bond interactions is performed on the basis of calculated frequency shifts. The late transfer of the substrate proton to the conserved aspartate (D166), the activation free energy of 15 kcal/mol, and the slight exothermic (-3 kcal/mol) character of the reaction are all consistent with the experimental data. The near attack conformation of D166 in the reactant state is maintained by interactions with threonine-201, asparagine-177, and most notably by a conserved water molecule serving as a strong structural link between the primary metal ion and the D166. The secondary Mg ion acts as a Lewis acid, attacking the beta-gamma bridging oxygen of ATP. This interaction, along with a strong hydrogen bond between the D166 and the substrate, contributes to the stabilization of the transition state. Lys-168 maintains a hydrogen bond to a transferring phosphoryl group throughout a reaction process. This interaction increases in the product state and contributes to its stabilization.     

Cyanide-bridged linkage isomers with catecholateruthenium(II) centres bound to Mn(I) or M(alkyne) units

Two series of stable cyanide-bridged linkage isomers, namely [(o-O2C6Cl4)(Ph3P)(OC)2Ru(mu-XY)MnL(NO)(eta-C5Me5)] (XY = CN or NC, L = CNBu(t) or CNXyl) and [(o-O2C6Cl4)L(OC)2Ru(mu-XY)M(CO)(PhC-CPh)Tp'] {M = Mo or W, L = PPh3 or P(OPh)3, Tp' = hydrotris(3,5-dimethylpyrazolyl)borate} have been synthesised; pairs of isomers are distinguishable by IR spectroscopy and cyclic voltammetry. The molecular structure of [(o-O2C6Cl4)(Ph3P)(OC)2Ru(mu-NC)Mo(CO)(PhC-CPh)Tp'] has the catecholate-bound ruthenium atom cyanide-bridged to a Mo(CO)(PhC[triple band]CPh)Tp' unit in which the alkyne acts as a four-electron donor; the alignment of the alkyne relative to the Mo-CO vector suggests the fragment (CN)Ru(CO)2(PPh3)(o-O2C6Cl4) acts as a pi-acceptor ligand. The complexes [(o-O2C6Cl4)(Ph3P)(OC)2Ru(mu-XY)Mn(NO)L(eta-C5Me5)] undergo three sequential one-electron oxidation processes with the first and third assigned to oxidation of the ruthenium-bound o-O2C6Cl4 ligand; the second corresponds to oxidation of Mn(I) to Mn(n). The complexes [(o-O2C6Cl4)L(OC)2Ru(mu-XY)M(CO)(PhC[triple band]CPh)Tp'] are also first oxidised at the catecholate ligand; the second oxidation, and one-electron reduction, are based on the M(CO)(PhC[triple band]CPh)Tp' fragment. Chemical oxidation of [(o-O,C6Cl4)(Ph3P)(OC)2Ru(mu-XY)MnL(NO)(eta-C5Me5)] with [Fe(eta-C5H4COMe)(eta-C5H5)][BF4], or of [(o-O2C6Cl4)L(OC)2Ru(mu-XY)M(CO)(PhC[triple band]CPh)Tp'] with AgBF4, gave the paramagnetic monocations [(o-O2C6Cl4)(Ph3P)(OC)2Ru(mu-XY)MnL(NO)(eta-C5Me5)]+ and [(o-O2C6Cl4)L(OC)2Ru(mu-XY)M(CO)(PhC[triple band]CPh)Tp']+, the ESR spectra of which are consistent with ruthenium-bound semiquinone ligands. Linkage isomers are distinguishable by the magnitude of the 31P hyperfine coupling constant; complexes with N-bound Ru(o-O2C6Cl4) units also show small hyperfine coupling to the nitrogen atom of the cyanide bridge.     

Mono- and dinuclear five-coordinate cyclometalated palladium(II) compounds

Reaction of cyclometalated halide-bridged Pd(II) complexes 1-4 with the tertiary triphosphine ligand (Ph2PCH2CH2)2PPh (triphos) yielded complexes [((Ph2PCH2CH2)2PPh-P,P,P)Pd(N(Cy)=(H)C)C6H2(C(H)=N(Cy))Pd((Ph2PCH2CH2)2PPh-P,P,P)][ClO4]2 5, [Pd(C6H4-N=NC6H5)((Ph2PCH2CH2)2PPh-P,P,P)][ClO4] 6, and [Pd(R-C6H3C(H)=NCy)((Ph2PCH2CH2)2PPh-P,P,P)][ClO4] (7; R = 4-CHO, 8; 3-CHO). Spectroscopic and analytic data suggest five-coordination on the palladium atom, which, for complexes 5, 6, and 7, was confirmed by X-ray crystallography. The geometry around palladium may be view as a distorted trigonal bipyramid, with the palladium, nitrogen, and terminal phosphorus atoms in the equatorial plane. Compound 5 is the first doubly cyclometalated palladium(II) compound with two pentacoordinated metal centers. The structure of 6 comprises two discrete cations with slightly different geometries, showing the importance of crystal packing forces in order to determine the coordination arrangement.     

Polynuclear lanthanide complexes of a series of bridging ligands containing two tridentate N,N',O-donor units: structures and luminescence properties

A set of three potentially bridging ligands containing two tridentate chelating N,N',O-donor (pyrazole-pyridine-amide) donors separated by an o, m, or p-phenylene spacer has been prepared and their coordination chemistry with lanthanide(III) ions investigated. Ligand L(1) (p-phenylene spacer) forms complexes with a 2:3 M:L ratio according to the proportions used in the reaction mixture; the Ln(2)(L(1))(3) complexes contain two 9-coordinate Ln(III) centres with all three bridging ligands spanning both metal ions, and have a cylindrical (non-helical) 'mesocate' architecture. The 1:1 complexes display a range of structural types depending on the conditions used, including a cyclic Ln(4)(L(1))(4) tetranuclear helicate, a Ln(2)(L(1))(2) dinuclear mesocate, and an infinite one-dimensional coordination polymer in which metal ions and bridging ligands alternate along the sequence. ESMS studies indicate that the 1:1 complexes form a mixture of oligonuclear species {Ln(L(1))}(n) in solution (n up to 5) which are likely to be cyclic helicates. In contrast, ligands L(2) and L(3) (with o- and m-phenylene spacers, respectively) generally form dinuclear Ln(2)L(2) Ln(III) complexes in which the two ligands may be arranged in a helical or non-helical architecture about the two metal ions. These complexes also contain an additional exogenous bidentate bridging ligand, either acetate or formate, which has arisen from hydrolysis of solvent molecules promoted by the Lewis-acidity of the Ln(III) ions. Luminescence studies on some of the Nd(III) complexes showed that excitation into ligand-centred pi-pi* transitions result in the characteristic near-infrared luminescence from Nd(III) at 1060 nm.     

Cluster Chemsitry. 96. Penta- and hexa-nuclear ruthenium cluster complexes derived from reactions of cyclopentadienes with Ru5(μ5-C2PPh2)(μ-PPh2)(CO)13

The reactions between Ru₅( ₅-C₂PPh₂)(gm-PPh₂(CO)₁₃ (1) and cyclopentadienes afforded the hexanuclear clusters Ru₆( ₆-C)( ₃-PPh₂)₂(CO)₁₀(-C₅ R ₅) [R ₅ = H₅ (2), H₄Me (3), Me₅ (4)] which contain an encapsulated carbide and a face-capping ₃-CH group, formed by cleavage of CC and CP bonds of the C₂PPh₂ moiety in1. In the reaction with cyclopentadiene, the unusual ligand C₁₃H₁₂O, formed by combination of C₂, CO and two molecules of C₅H₆ (or one molecule of dicyclopentadien), was characterized in the complex Ru₅( ₄-PPh) ( ₄-C₁₃H₁₂O)(-PPh₂(CO)₁₁(-C₅H₅) (5). In the reaction with pentamethylcyclopentadiene, the vinylidene complex Ru₅( ₃-CCHPh)( ₄-PPh)( ₄-PPh) (-PPh₂)(CO)₉(-C₅Me₅) (6) was also formed.     

Cluster synthesis. 42. The synthesis and crystal and molecular structures of the sulfur-bridged platinum-ruthenium carbonyl cluster compounds PtRu3(CO)9 L(PPh3)(μ3-S)2 (L=CO,PPh3) and PtRu4(CO)12(PPh3)(μ4-S)2

Two new mixed metal cluster complexes PtRu₃(CO)₁₀(PPh₃)(₃-S)₂,3 14% yield and PtRu₃(CO)₉(PPh₃)₂(₃-S)₂,4 23% yield were obtained from the reaction of Ru₃(CO)₉(₃-S)₂,1 with Pt(PPh₃)₂(C₂H₄) at 0°C. The cluster of4 consists of a spiked triangle of four metal atoms with two triply bridging sulfido ligands. The reaction of Ru₄(CO)₁₁(₄-S)₂,2 with Pt(PPh₃)₂(C₂H₄) yielded the expanded mixed-metal cluster complex PtRu₄(CO)₁₂(PPh₃)(₄-S)₂,5 in 12% yield. The structure of the cluster5 can be described as a pentagonal bipyramid of five metal atoms and two sulfido ligands with one metal-metal bond missing. Compounds4 and5 were characterized by a single-crystal X-ray diffraction analyses.     

Controlled Annealing in Adaptive Multicomponent Gels

We use a pH-driven annealing process to convert between co-assembled and self-sorted networks in multicomponent gels. The initially formed gels at low pH are co-assembled, with the two components coexisting within the same self-assembled structures. We use an enzymatic approach to increase the pH, resulting in a gel-to-sol transition, followed by a hydrolysis to lower the pH once again. As the pH decreases, a self-sorted network is formed by a two-stage gelation process determined by the pK_a of each component. This approach can be expanded to layered systems to generate many varied systems by changing composition and rates of pH change, adapting their microstructure and so allowing access to a far greater range of morphologies and complexity than can be achieved in single component systems.