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.     

Mechanism of [M + H]<Superscript>+</Superscript> formation in photoionization mass spectrometry

In this paper we examine the mechanism of [M + H]+ (henceforth MH+) formation by direct photoionization. Based on comparisons of the relative abundance of M+ and MH+ ions for photoionization of a variety of compounds M as vapor in air versus in different solvents, we conclude that the mechanism is M + hnu --> M+ + e- followed by the reaction M+ + S --> MH+ + S(-H). The principal evidence for molecular radical ion formation M+ followed by hydrogen atom abstraction from protic solvent S are: (1) Nearly exclusive formation of M+ for headspace ionization of M in air, (2) significant relative abundance of MH+ in the presence of protic solvents (e.g., CH3OH, H2O, c-hexane), but not in aprotic solvents (e.g., CCl4-), (3) observation of induced equilibrium oscillations in the abundance of MH+ and M+, and (4) correlation of the ratio of MH+/M+ to reaction length in the photoionization source. Thermodynamic models are advanced that explain the qualitative dependence of the MH+/M+ equilibrium ratio on the properties of solvent S and analyte M. Though the hydrogen abstraction reaction is endothermic in most cases, it is shown that the equilibrium constant is still expected to be much greater than unity in most of the cases studied due to the very slow reverse reaction involving the very low abundant MH+ and S(-H) species.     

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.     

Adaptation of a fast Fourier transform-based docking algorithm for protein design

Designing proteins with novel protein/protein binding properties can be achieved by combining the tools that have been developed independently for protein docking and protein design. We describe here the sequence-independent generation of protein dimer orientations by protein docking for use as scaffolds in protein sequence design algorithms. To dock monomers into sequence-independent dimer conformations, we use a reduced representation in which the side chains are approximated by spheres with atomic radii derived from known C2 symmetry-related homodimers. The interfaces of C2-related homodimers are usually more hydrophobic and protein core-like than the interfaces of heterodimers; we parameterize the radii for docking against this feature to capture and recreate the spatial characteristics of a hydrophobic interface. A fast Fourier transform-based geometric recognition algorithm is used for docking the reduced representation protein models. The resulting docking algorithm successfully predicted the wild-type homodimer orientations in 65 out of 121 dimer test cases. The success rate increases to approximately 70% for the subset of molecules with large surface area burial in the interface relative to their chain length. Forty-five of the predictions exhibited less than 1 A C(alpha) RMSD compared to the native X-ray structures. The reduced protein representation therefore appears to be a reasonable approximation and can be used to position protein backbones in plausible orientations for homodimer design.     

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.