High-nuclearity iridium carbonyl clusters containing phenylgermyl ligands: synthesis, structures, and reactivity

The reaction of Ir4(CO)12 with Ph3GeH at 97 degrees C has yielded the new tetrairidium cluster complexes Ir4(CO)7(GePh3)(mu-GePh2)2[mu3-eta3-GePh(C6H4)](mu-H)2 (10) and Ir4(CO)8(GePh3)2(mu-GePh2)4 (11). The structure of 10 consists of a tetrahedral Ir4 cluster with seven terminal CO groups, two bridging GePh2) ligands, an ortho-metallated bridging mu3-eta3-GePh(C6H4) group, a terminal GePh3 ligand, and two bridging hydrido ligands. Compound 11 consists of a planar butterfly arrangement of four iridium atoms with four bridging GePh2 and two terminal GePh3 ligands. The same reaction at 125 degrees C yielded the two new triiridium clusters Ir3(CO)5(GePh3)(mu-GePh2)3(mu3-GePh)(mu-H) (12) and Ir3(CO)6(GePh3)3(mu-GePh2)3 (13). Compound 12 contains a triangular Ir3 cluster with three bridging GePh2), one triply bridging GePh, and one terminal GePh3 ligand. The compound also contains a hydrido ligand that bridges one of the Ir-Ge bonds. Compound 13 contains a triangular Ir3 cluster with three bridging GePh2 and three terminal GePh3 ligands. At 151 degrees C, an additional complex, Ir4H4(CO)4(mu-GePh2)4(mu4-GePh)2 (14), was isolated. Compound 14 consists of an Ir4 square with four bridging GePh2, two quadruply bridging GePh groups, and four terminal hydrido ligands. Compound 12 reacts with CO at 125 degrees C to give the compound Ir3(CO)6(mu-GePh2)3(mu3-GePh) (15). Compound 15 is formed via the loss of the hydrido ligand and the terminal GePh3 ligand and the addition of one carbonyl ligand to 12. All compounds were fully characterized by IR, NMR, single-crystal X-ray diffraction analysis, and elemental analysis.     

Calculated electronic spectra of model ferric cytochrome P450 complexes

Restricted open-shell ground state properties and electronic spectra of two closely related low-spin, ferric, 6-coordinate, model cytochrome P450 complexes, one with a methyl mercaptide and the other a mercaptan as the second axial ligands, have been calculated with a newly modified, semiempirical INDO-SCF-CI method. The sensitivity of the calculated spectra to protonation of the sixth axial ligand, and the ability of the method to predict characteristic spectral features for the complexes investigated, are determined. Assignment of transitions, including xy- and z-polarized transitions, are made and compared with experimental observations where available. In particular, the origin of the anomalous split Soret spectrum observed in low-spin ferric complexes with mercaptide but not a mercaptan is investigated. Finally, a two part hypothesis is presented which provides a general explanation for the origin of both the observed split Soret and the red-shifted normal Soret in various ferrous and ferric P450 complexes in terms of the ground state orbital characters and simple symmetry considerations.     

Oxidation of coordinated olefins: the reactions of Cl2 with trichloro(ehtylene)platinate(II)

The oxidation of [PtCl₃(C₂H₄)]- by Cl₂ in aqueous solution, to yield CH₂ClCH₂OH and [PtCl₄]^2-, has been shown to proceed through the following sequence of steps: [PtCl₃(C₂H₄)] Cl₂Cl [PtCl₅(CH₂CH₂Cl)]^2-$\text{H}{}_2\text{O}\text{(HCl)}$ [PtCl₅(CH₂CH₂OH)]^2- → [PtCl₄^2- + CH₂ClCH₂OHEach of the steps and intermediates in this mechanistic sequence has been identified and characterized.     

DNA polymerase-mediated DNA synthesis on a TNA template

TNA, or threose nucleic acid, is capable of Watson-Crick base pairing with DNA, RNA, and TNA; coupled with its chemical simplicity, this suggests that TNA is a possible progenitor of RNA. As an initial step toward developing the molecular tools necessary to investigate the functional capabilities of TNA by in vitro selection, we have screened a variety of DNA polymerases for activity on a TNA template. We report that despite having a repeating unit that is one atom shorter than that of DNA, several polymerases showed surprisingly good ability to copy limited stretches of TNA.     

Ammonium cyanate shows N-H...N hydrogen bonding, not N-H...O

The transformation of ammonium cyanate into urea, first studied over 170 years ago by W?hler and Liebig, has an important place in the history of chemistry. To understand the nature of this solid state reaction, knowledge of the crystal structure of ammonium cyanate is a prerequisite. Employing neutron powder diffraction, we demonstrate conclusively that, in the structure of ammonium cyanate, the NH(4)(+) cation forms N-H...N hydrogen bonds to four cyanate N atoms at alternate corners of a distorted cube, rather than our previously proposed alternative arrangement with N-H...O hydrogen bonds to cyanate O atoms at the other four corners.     

Systems-based design of bi-ligand inhibitors of oxidoreductases: filling the chemical proteomic toolbox

Genomics-driven growth in the number of enzymes of unknown function has created a need for better strategies to characterize them. Since enzyme inhibitors have traditionally served this purpose, we present here an efficient systems-based inhibitor design strategy, enabled by bioinformatic and NMR structural developments. First, we parse the oxidoreductase gene family into structural subfamilies termed pharmacofamilies, which share pharmacophore features in their cofactor binding sites. Then we identify a ligand for this site and use NMR-based binding site mapping (NMR SOLVE) to determine where to extend a combinatorial library, such that diversity elements are directed into the adjacent substrate site. The cofactor mimic is reused in the library in a manner that parallels the reuse of cofactor domains in the oxidoreductase gene family. A library designed in this manner yielded specific inhibitors for multiple oxidoreductases.     

Conformational landscape surfing induced by off-on pi-pi stacking in a porphyrin-quinone dyad

A covalently linked porphyrin-quinone dyad crystallizes with two orientations of the quinone, extended away from (off) and cofacial with the porphyrin macrocycle (on), which induce different conformations of the macrocycle and model the recently proposed structural effect of a nearby residue on the heme prosthetic group of a nitric oxide synthase.     

Catalyzed double Michael addition of anilines to vinyl sulfone

Substituted anilines and vinyl sulfone undergo a facile double Michael addition to form substituted phenylthiomorpholine dioxide, catalyzed with AlCl₃ or H₃PO₄. Scope and conditions were explored.     

Theoretical studies on the hydrolysis of mono-phosphate and tri-phosphate in gas phase and aqueous solution

Phosphate hydrolysis by GTPases plays an important role as a molecular switch in signal transduction and as an initiator of many other biological processes. Despite the centrality of this ubiquitous reaction, the mechanism is still poorly understood. As a first step to understand the mechanisms of this process, the nonenzymatic hydrolysis of mono-phosphate and tri-phosphate esters were systematically studied in gas phase and aqueous solution using hybrid density functional methods. The dielectric effect of the environment on the energetics of these processes was also explored. Theoretical results show that for mono-phosphate ester, the dissociative pathway is much more favorable than the associative pathway. However, the reaction barriers for the dissociative and associative pathways of tri-phosphate hydrolysis are very close in aqueous solution, though the dissociative pathway is more favorable in the gas phase. High dielectric solvents, such as water, significantly lower the activation barrier of the associative pathway due to the greater solvation energy of the associative transition states than that of the reactant complex. By contrast, the barrier of the dissociative pathway, with respect to the gas phase, is less sensitive to the surrounding dielectric. In the associative hydrolysis pathway of the tri-phosphate ester, negative charge is transferred from the gamma-phosphate to beta-phosphate through the bridging ester oxygen and results in Pgamma-O bond dissociation. No analogous charge transfer was observed in the dissociative pathway, where Pgamma-O bond dissociation resulted from proton transfer from the gamma-phosphate to the bridge oxygen. Finally, the active participation of local water molecules can significantly lower the activation energy of the dissociative pathway for both mono-phosphate and tri-phosphate.     

The synthesis and reactivity of the heptanuclear dianion [Os7(CO)20]2− including the synthesis and structural characterizations of the compounds [Os7(CO)20(AuPEt)3 2] and [Os8(CO)20(η6-C6H6]

Reduction of the heptaosmium cluster [Os₇(CO)₂₁] With [Et₄N][NH₄) gives the cluster dianion [Os₇(CO)₂₀]^2–,1, in high yield. The reaction of the dianion with [AuPR ₃Cl] (R=Et or Ph) in the presence of TlPF₆ forms [Os₇((CO)₂₀(AuPR ₃)₂] [R=Et (2a);R = Ph(2b)] in 80% yield, while the corresponding reaction with (Os(C₆H₆)(CH₃CN)₃]²⁺ gives [Os₈(CO)₂₀ ( ⁶-C₆H₆)] (3) in reasonable yield (ca. 30%). The dianion,1, and the clusters2 and3 have been fully characterized by bout spectroscopic and crystallographic methods. The crystal structure of the [Ph₄P]⁺ salt of1 shows that the metals in the anion adopt a capped octahedral geometry, with all twenty carbonyl ligands in terminal sites. The metal core geometry in2a is best described as a tricapped octahedron, and is based on the structure of the dianion1 with two adjacent octahedral faces capped by the Au atoms of the two AuPEt₃ groups. In a similar fashion, the geometry of3 is related to that of1 with the addition of an Os(C₆H₆) unit capped to a triangular face, to give a bicapped octahedral framework.