ClcR-based biosensing system in the detection of cis-dihydroxylated (chloro-)biphenyls

Polychlorinated biphenyls (PCBs) are a group of organic pollutants that are persistent when released into the environment. Among the metabolites of PCBs, dihydroxylated PCBs are also considered as toxic compounds. Various studies have shown that dihydroxylated PCBs affect the reproductive, immune, nervous, and endocrine systems. Detection of these chemicals in environmental and biological samples could provide first-hand information about their levels and lead to a better understanding of their role in toxicity. To that end, we developed a sensing system for the detection of dihydroxylated PCBs based on the clc operon. The Pseudomonas putida clc operon encodes a catabolic pathway for degradation of chlorocatechols, which are major metabolites of a large number of chlorinated compounds. In P. putida, the expression of these genes is regulated by a protein encoded by the gene clcR located upstream from the clcABD genes. We demonstrate here for the first time that dihydroxy PCBs can also induce the clc operon. Our sensing system employs P. putida bacteria harboring a plasmid in which the reporter gene, lacZ, is under the control of the regulatory protein ClcR. Consequently, when exposed to dihydroxy PCBs, the bacteria express β-galactosidase in an amount related to the concentration of the corresponding dihydroxy PCB. Various dihydroxylated PCBs, differing in the number and position of chlorines and in the position of hydroxyls, were tested for their ability to induce expression of β-galactosidase. Detection limits as low as 1×10⁻⁶ mol L⁻¹ were obtained for various dihydroxylated PCBs. Electronic Supplementary Material Supplementary material is available for this article at and is accessible for authorized users.     

Internally contracted multiconfiguration-reference configuration interaction calculations for excited states

Summary The calculation of electronically excited states with the internally contracted multiconfiguration-reference configuration interaction (CMRCI) method is discussed. A straightforward method, in which contracted functions for all states are included in the basis, is shown to be very accurate and stable even in cases of narrow avoided crossings. However, the expense strongly increases with the number of states. A new method is proposed, which employs different contracted basis sets for each state, and in which eigensolutions of the Hamiltonian are found using an approximate projection operator technique. The computational effort for this method scales only linearly with the number of states. The two methods are compared for various applications.Dedicated in honor of Prof. Klaus Ruedenberg     

The computer program LUDI: A new method for the de novo design of enzyme inhibitors

Summary A new computer program is described, which positions small molecules into clefts of protein structures (e.g. an active site of an enzyme) in such a way that hydrogen bonds can be formed with the enzyme and hydrophobic pockets are filled with hydrophobic groups. The program works in three steps. First it calculates interaction sites, which are discrete positions in space suitable to form hydrogen bonds or to fill a hydrophobic pocket. The interaction sites are derived from distributions of nonbonded contacts generated by a search through the Cambridge Structural Database. An alternative route to generate the interaction sites is the use of rules. The second step is the fit of molecular fragments onto the interaction sites. Currently we use a library of 600 fragments for the fitting. The final step in the present program is the connection of some or all of the fitted fragments to a single molecule. This is done by bridge fragments. Applications are presented for the crystal packing of benzoic acid and the enzymes dihydrofolate reductase and trypsin.     

Oxidation of Au by surface OH: nucleation and electronic structure of gold on hydroxylated MgO(001)

The nucleation and electronic structure of vapor-deposited Au on hydroxylated MgO(001) surfaces has been investigated under ultrahigh vacuum conditions. Hydroxylated MgO(001) surfaces with two different hydroxyl coverages, 0.4 and 1 monolayer, respectively, were prepared by exposure to water (D(2)O) at room temperature. Scanning tunneling microscopy experiments show significantly higher gold particle densities and smaller particle sizes on the hydroxylated MgO surface as compared to gold deposited on clean MgO(001). Infrared spectroscopy and X-ray photoelectron spectroscopy experiments were performed to reveal details about the initial nucleation of gold. Gold atoms are found to chemically interact with a specific type of hydroxyl groups on the MgO surface, leading to the formation of oxidized gold particles. The enhanced adhesion of Au particles, which is due to the formation of strong Au-O interfacial bonds, is responsible for the observed higher stability of small Au clusters toward thermal sintering on hydroxylated MgO surfaces. The results are compared to similar studies on Au/TiO(2)(110) model systems and powder samples prepared by the deposition-precipitation route.     

Elongated silica nanoparticles with a mesh phase mesopore structure by fluorosurfactant templating

Mesoporous silica materials with pore structures such as 2D hexagonal close packed, bicontinuous cubic, lamellar, sponge, wormhole-like, and rectangular have been made by using surfactant templating sol-gel processes. However, there are still some "intermediate" phases, in particular mesh phases, that are formed by surfactants but which have not been made into analogous silica pore structures. Here, we describe the one-step synthesis of mesoporous silica with a mesh phase pore structure. The cationic fluorinated surfactant 1,1,2,2-tetrahydroperfluorodecylpyridinium chloride (HFDePC) is used as the template. Like many fluorinated surfactants, HFDePC forms intermediate phases in water (including a mesh phase) over a wider range of compositions than do hydrocarbon surfactants. The materials produced by this technique are novel elongated particles in which the layers of the mesh phase are oriented orthogonal to the main axis of the particles.     

Trinuclear rhodium hydride complexes

Three novel trinuclear rhodium hydride complexes of the type {[Rh(PP*)H](3)(μ(2)-H)(3)(μ(3)-H)}[BF(4)](2) containing diphosphines Tangphos, t-Bu-BisP* and Me-DuPHOS have been synthesised. The new compounds are very stable. Their structures have been characterized by X-ray analysis in the solid state and by NMR-spectroscopic investigations in solution.     

Highly selective palladium catalyzed kinetic resolution and enantioselective substitution of racemic allylic carbonates with sulfur nucleophiles: asymmetric synthesis of allylic sulfides,allylic sulfones,and allylic alcohols

We describe the highly selective palladium catalyzed kinetic resolutions of the racemic cyclic allylic carbonates rac-1 a-c and racemic acyclic allylic carbonates rac-3 aa and rac-3 ba through reaction with tert-butylsulfinate, tolylsulfinate, phenylsulfinate anions and 2-pyrimidinethiol by using N,N'-(1R,2R)-1,2-cyclohexanediylbis[2-(diphenylphosphino)-benzamide] (BPA) as ligand. Selectivities are expressed in yields and ee values of recovered substrate and product and in selectivity factors S. The reaction of the cyclohexenyl carbonate 1 a (>/=99 % ee) with 2-pyrimidinethiol in the presence of BPA was shown to exhibit, under the conditions used, an overall pseudo-zero order kinetics in regard to the allylic substrate. Also described are the highly selective palladium catalyzed asymmetric syntheses of the cyclic and acyclic allylic tert-butylsulfones 2 aa, 2 b, 2 c, 2 d and 4 a-c, respectively, and of the cyclic and acyclic allylic 2-pyrimidyl-, 2-pyridyl-, and 4-chlorophenylsulfides 5 aa, 5 b, 5 ab, 6 aa-ac, 6 ba and 6 bb, respectively, from the corresponding racemic carbonates and sulfinate anions and thiols, respectively, in the presence of BPA. Synthesis of the E-configured allylic sulfides 6 aa, 6 ab, 6 ac and 6 bb was accompanied by the formation of minor amounts of the corresponding Z isomers. The analogous synthesis of allylic tert-butylsulfides from allylic carbonates and tert-butylthiol by using BPA could not be achieved. Reaction of the cyclopentenyl esters rac-1 da and rac-1 db with 2-pyrimidinethiol gave the allylic sulfide 5 c having only a low ee value. Similar results were obtained in the case of the reaction of the cyclohexenyl carbonate rac-1 a and of the acyclic carbonates rac-3 aa and rac-3 ba with 2-pyridinethiol and lead to the formation of the sulfides 5 ab, 6 ab, and 6 bb, respectively. The low ee values may be ascribed to the operating of a "memory effect", that is, both enantiomers of the substrate give the substitution product with different enantioselectivities. However, in the reaction of the racemic carbonate rac-1 a as well as of the highly enriched enantiomers 1 a (>/=99 % ee) and ent-1 a (>/=99 % ee) with 2-pyrimidinethiol the ee values of the substrates and the substitution product remained constant until complete conversion. Similar results were obtained in the reaction of the cyclic carbonates rac-1 a, ent-1 a (>/=99 % ee) and ent-1 c (>/=99 % ee) with lithium tert-butylsulfinate. Thus, in the case of rac-1 a and 2-pyrimidinthiol and tert-butylsulfinate anion as nucleophiles the enantioselectivity of the substitution step is, under the conditions used, independent of the chirality of the substrate; this shows that no "memory effect" is operating in this case. Hydrolysis of the carbonates ent-1 a-c, ent-3 aa and ent-3 ba, which were obtained through kinetic resolution, afforded the enantiomerically highly enriched cyclic allylic alcohols 9 a-c (>/=99 % ee) and acyclic allylic alcohols 10 a (>/=99 % ee) and 10 b (99 % ee), respectively.