Secondary bonding interactions in biomimetic [2Fe-2S] clusters

A series of synthetic [2Fe-2S] complexes with terminal thiophenolate ligands and tethered ether or thioether moieties has been prepared and investigated in order to provide models for the potential interaction of additional donor atoms with the Fe atoms in biological [2Fe-2S] clusters. X-ray crystal structures have been determined for six new complexes that feature appended Et (1(C)), OMe (1(O)), or SMe (1(S)) groups, or with a methylene group (2(C) ), an ether-O (2(O)), or an thioether-S (2(S)) linking two aryl groups. The latter two systems provide a constrained chelate arrangement that induces secondary bonding interactions with the ether-O and thioether-S, which is confirmed by density functional theory (DFT) calculations that also reveal significant spin density on those fifth donor atoms. Structural consequences of the secondary bonding interactions are analyzed in detail, and effects on the spectroscopic and electronic properties are probed by UV-vis, M?ssbauer, and (1)H NMR spectroscopy, as well by SQUID measurements and cyclic voltammetry. The potential relevance of the findings for biological [2Fe-2S] sites is considered.     

Synthese und Kristallstruktur des Goldclusters [Au16(AsPh3)8Cl6]

Synthesis and Structures of the Gold Cluster [Au₁₆(AsPh₃)₈Cl₆] Reduction of Ph₃AsAuCl with NaBH₄ in ethanol yields the gold cluster [Au₁₆(AsPh₃)₈Cl₆]. It can be crystallized from dichloromethane/diisopropyl ether in form of dark red, light sensitive crystals with the space group P2₁/n and a = 1777.68(8), b = 3372.7(1), c = 2696.2(1)pm, β = 94.166(6)°, Z = 4). The inner skeleton of the 16 Au atoms consists of a centered icosahedron of which one of the corners binds to three additional Au atoms forming a tetrahedron pendent. The shortest Au–Au distances of 264.3 to 266.6 pm correspond to the bonds to the three external Au atoms. Within the icosahedron the distances between the central atom and the peripheral atoms (273.0–279.1 pm) are distinctly shorter than the distances between the peripheral atoms (283.6–299.0 pm).     

Structural Comparison of Oligoribonucleotides and Their 2′-Deoxy-2′-fluoro Analogs by heteronuclear NMR spectroscopy

1-(2′-Deoxy-2′-fluororibofuranosyl)pyrimidines were synthesized and incorporated into an RNA oligonucleotide to give 5′-r[C_fGC_f(U_fU_fC_fG)GC_fG]-3′ (C_f: short form of C = 2′-deoxy-2′-fluorocytidine; U_f: short form of U = 2′-deoxy-2′-fluorouridine). The oligomer was investigated by means of UV, CD, and NMR spectroscopy to address the question of how F-labels can substitute ¹³C-labels in the ribose ring. Through-space (NOE) and through-bond (scalar couplings) experiments were performed that make use of the ameliorated chemical-shift dispersion induced by ¹⁹F as an alternative heteronucleus. A comparison of the structures of fluorinated vs. unmodified oligomer is given. It turns out that the fluorinated oligonucleotide exists in a 14:3 equilibrium between a hairpin and a duplex conformation, in contrast to the unmodified oligonucleotide which predominantly adopts the hairpin conformation. Furthermore, the fluorinated hairpin structure adopts two distinct conformations that differ in the sugar conformation of the U and C nucleoside units, as detected by the ¹⁹F-NMR chemical shifts. The role of the 2′-OH group as stabilizing element in RNA secondary structure is discussed.     

Integration of electron density and molecular orbital techniques to reveal questionable bonds: the test case of the direct Fe-Fe bond in Fe2(CO)9

The article illustrates the advantages of partitioning the total electron density rho(rb), its Laplacian (inverted Delta)2 rho(rb), and the energy density H(rb) in terms of orbital components. By calculating the contributions of the mathematically constructed molecular orbitals to the measurable electron density, it is possible to quantify the bonding or antibonding character of each MO. This strategy is exploited to review the controversial existence of direct Fe-Fe bonding in the triply bridged Fe2(CO)9 system. Although the bond is predicted by electron counting rules, the interaction between the two pseudo-octahedral metal centers can be repulsive because of their fully occupied t(2g) sets. Moreover, previous atoms in molecules (AIM) studies failed to show a Fe-Fe bond critical point (bcp). The present electron density orbital partitioning (EDOP) analysis shows that one sigma bonding combination of the t(2g) levels is not totally overcome by the corresponding sigma* MO, which is partially delocalized over the bridging carbonyls. This suggests the existence of some, albeit weak, direct Fe-Fe bonding.     

Investigation into the formation of supramolecular compounds from mixed As/S-ligand complexes [(Cp*Mo)2As2S3] (Cp* = C5Me5) and copper halides

The coordination behavior of [(Cp*Mo)2As2S3] (3) (Cp* = C5Me5) toward Cu(I) halides was investigated. One dimensional polymers of the general formula [(Cp*Mo)2As2S3(CuHal)2]n (Hal = Cl, 4; Br, 5) and an oligomer of composition [{(Cp*Mo)2As2S3}3(CuI)7] (6) formed upon the reaction of 3 with the corresponding copper halide. All of the compounds were characterized by ESI-MS, elemental analysis, and single-crystal X-ray crystallography. The solid-state structures of 4 and 5 are isostructural and contain 1D S-shaped chains. This peculiar folding is achieved by alternating planar and folded Cu2Hal2 rings linked together by the central monosulfide bridge of the middle deck of the organometallic unit. The structure of 6 is characterized by a novel [CuI]7 aggregate, which forms a very flat Cu6I3S3 bowl along with three integrated peripheral [(Cp*Mo)2As2S3] building blocks. In contrast to earlier findings, the middle deck of the organometallic units consists in all structures of two trapezoidal AsS dumbbells and one monosulfide ligand.     

Charge and Size Dependence of Liposome Diffusion in Semidilute Biopolymer Solutions

The diffusion of liposomes and PL/DNA complexes in mucin and collagen solutions, considered to model ‘in vivo’ colloidal gene delivery vector transport, is studied with FCS. The diffusion of defined liposomes is investigated as a function of particle size, surface charge, and the deviation from the Stokes‐Einstein behavior. In all cases the self‐diffusion coefficient decreases exponentially with polymer concentration. The same surface charge dependence of diffusion is observed in mucin for PL/DNA complexes with either positive or negative excess charge. Incubation of positively‐charged PL/DNA complexes in a natural lung surfactant lipid increases the diffusion coefficients to almost the same as for the negatively‐charged PL/DNA complexes.

     

Application of the level-set method to the implicit solvation of nonpolar molecules

A level-set method is developed for numerically capturing the equilibrium solute-solvent interface that is defined by the recently proposed variational implicit solvent model [Dzubiella, Swanson, and McCammon, Phys. Rev. Lett. 104, 527 (2006); J. Chem. Phys. 124, 084905 (2006)]. In the level-set method, a possible solute-solvent interface is represented by the zero level set (i.e., the zero level surface) of a level-set function and is eventually evolved into the equilibrium solute-solvent interface. The evolution law is determined by minimization of a solvation free energy functional that couples both the interfacial energy and the van der Waals type solute-solvent interaction energy. The surface evolution is thus an energy minimizing process, and the equilibrium solute-solvent interface is an output of this process. The method is implemented and applied to the solvation of nonpolar molecules such as two xenon atoms, two parallel paraffin plates, helical alkane chains, and a single fullerence C(60). The level-set solutions show good agreement for the solvation energies when compared to available molecular dynamics simulations. In particular, the method captures solvent dewetting (nanobubble formation) and quantitatively describes the interaction in the strongly hydrophobic plate system.     

Unfavorable electrostatic and steric interactions in DNA polymerase β E295K mutant interfere with the enzyme's pathway

Mutations in DNA polymerase β (pol β) have been associated with approximately 30% of human tumors. The E295K mutation of pol β has been linked to gastric carcinoma via interference with base excision repair. To interpret the different behavior of E295K as compared to wild-type pol β in atomic and energetic detail, we resolve a binary crystal complex of E295K at 2.5 ? and apply transition path sampling (TPS) to delineate the closing pathway of the E295K pol β mutant. Conformational changes are important components in the enzymatic pathway that lead to and ready the enzyme for the chemical reaction. Our analyses show that the closing pathway of E295K mutant differs from the wild-type pol β in terms of the individual transition states along the pathway, associated energies, and the active site conformation in the final closed form of the mutant. In particular, the closed state of E295K has a more distorted active site than the active site in the wild-type pol β. In addition, the total energy barrier in the conformational closing pathway is 65 ± 11 kJ/mol, much higher than that estimated for both correct (e.g., G:C) and incorrect (e.g., G:A) wild-type pol β systems (42 ± 8 and 45 ± 7 kJ/mol, respectively). In particular, the rotation of Arg258 is the rate-limiting step in the conformational pathway of E295K due to unfavorable electrostatic and steric interactions. The distorted active site in the closed relative to open state and the high energy barrier in the conformational pathway may explain in part why the E295K mutant is observed to be inactive. Interestingly, however, following the closing of the thumb but prior to the rotation of Arg258, the E295K mutant complex has a similar energy level as compared to the wild-type pol β. This suggests that the E295K mutant may associate with DNA with similar affinity, but it may be hampered in continuing the process of chemistry. Supporting experimental data come from the observation that the catalytic activity of wild-type pol β is hampered when E295K is present: this may arise from the competition between E295K and wild-type enzyme for the DNA. These combined results suggest that the low insertion efficiency of E295K mutant as compared to wild-type pol β may be related to a closed form distorted by unfavorable electrostatic and steric interactions between Arg258 and other key residues. The active site is thus less competent for proceeding to the chemical reaction, which may also involve a higher reaction barrier than the wild-type or may not be possible in this mutant. Our analysis also suggests further experiments for other mutants to test the above hypothesis and dissect the roles of steric and electrostatic factors on enzyme behavior.     

Structural Basis and Enzymatic Mechanism of the Biosynthesis of C9‐ from C10‐Monoterpenoid Indole Alkaloids

Cutting carbons : The three‐dimensional structure of polyneuridine aldehyde esterase (PNAE) gives insight into the enzymatic mechanism of the biosynthesis of C₉‐ from C₁₀‐monoterpenoid indole alkaloids (see scheme). PNAE is a very substrate‐specific serine esterase. It harbors the catalytic triad S87‐D216‐H244, and is a new member of the α/β‐fold hydrolase superfamily. Its novel function leads to the diversification of alkaloid structures.