The thiolate anion as a nucleophile Part XII. Reactions of Lead(II) Benzenethiolate

The reactions of various fluoroaromatics, C₆F_6?xH_x, and C₆F₅X (X = C₆F₆, Cl, Me, NO₂, CF₃, COCl, CH₂Br, OMe, and NH₂) with lead(II) benzenethiolate in DMF have been examined. Lead thiolate acted as an excellent source of benzenethiolate anions and displacement of fluorine, chlorine or the nitro group was observed. The new products have been characterized by elemental analysis, and NMR (H?1 and F?19), infrared and mass spectroscopy.     

Thiophene and butadiene-thiolate complexes of molybdenum: observations relevant to the mechanism of hydrodesulfurization

Mo(PMe3)6 reacts with thiophene to give the eta5-thiophene complex (eta5-C4H4S)Mo(PMe3)3 and the eta5-butadiene-thiolate complex (eta5-C4H5S)Mo(PMe3)2(eta2-CH2PMe2), which are the first examples of (i) eta5-thiophene coordination and (ii) C-S cleavage and hydrogenation by a molybdenum compound. Deuterium labeling studies suggest that the hydrogenation of thiophene may involve an alkylidene intermediate, an observation that has ramifications for the mechanisms of hydrodesulfurization.     

Novel binding of beryllium to dicarboxyimidazole-based model compounds and polymers

The ligand 4,5-dicarboxyimidazole (H(2)DCI) and its methyl derivative 1-methyl-4,5-dicarboxyimidazole (H(2)MDCI) have been shown to bind to Be(II) forming a zwitterionic species that has been structurally characterized. A new dicarboxyimidazole-based polymer has been prepared and its Be-binding properties have been studied using NMR ((1)H and (9)Be) and fluorescence spectroscopy; it represents a rare example of beryllium binding to a polymer. Models of the mononuclear and polymeric Be(II)-binding sites have been studied using density functional theory (DFT), and the (9)Be NMR chemical shifts of these model materials have been calculated for the purpose of direct comparison to experimentally observed values. Differences in the binding modes of the mononuclear and polymeric species are discussed.     

Simulation of the Adhesion of Particles to Surfaces

The removal of micrometer and submicrometer particles from dielectric and metal films represents a challenge in postchemical mechanical polishing cleaning. Proper modeling of the adhesive force between contaminant particles and these films is needed to develop optimal solutions to postchemical mechanical polishing cleaning. We have previously developed and experimentally validated a model to describe the adhesion between spherical particles and thin films. This simulation expands previous models to characterize the adhesive interaction between asymmetrical particles, characteristic of a polishing slurry, and various films. Our simulation accounts for the contact area between particles and substrates, as well as the morphology of the surfaces. Previous models fail to accurately describe the contact of asymmetrical particles interacting with surfaces. By properly accounting for nonideal and geometry and morphology, the simulation predicts a more accurate adhesive force than predictions based upon an ideal van der Waals model. The simulation is compared to experimental data taken for both semi-ideal particle-substrate systems (polystyrene latex spheres in contact with silicon films) and asymmetrical systems (alumina particles in contact with various films). Copyright 2001 Academic Press.     

Optimization of a MALDI TOF-TOF mass spectrometer for intact protein analysis

A MALDI TOF-TOF instrument was optimized and evaluated for intact protein analysis by tandem mass spectrometry. Ion source voltages and delay times were adjusted to affect an up to a 10-fold improvement in fragment ion yield compared to data obtained using default settings employed in peptide analysis. For large peptides (3-4.5 kDa), up to 90% of all possible b- and y-fragment ions were observed, which provides sufficient information for de novo sequencing and unambiguous protein identification. Product ion signals associated with preferential cleavages C-terminal to aspartic acid and glutamic acid residues and N-terminal to proline residues became dominant with increased protein molecular weight. Matrix effects were also evaluated and, among the eight matrices examined, alpha-cyano-4-hydroxycinnamic acid (CHCA) was found to produce the best intact protein tandem mass spectra for proteins up to 12 kDa. Optimized performance yielded detection limits of 50-125 fmol for proteins of 4 and 12 kDa, respectively. This improved performance has yielded an instrument with potential to be a useful tool in proteomic investigations via analysis of intact proteins.     

Mild and practical method for the alpha-arylation of nitriles with heteroaryl halides

[reaction: see text] A mild and transition-metal-free method for the alpha-arylation of aliphatic nitriles with activated heteroaryl halides was developed using NaHMDS or KHMDS as base at ambient temperature. The key to the success of this method is generation of the nitrile anion in the presence of the heteroaryl halide. The method is applicable to both primary and secondary carbonitriles and a wide range of heteroaryl halides. Selective monoarylation was observed with primary carbonitriles. The operational simplicity and the mild reaction conditions add to the value of this method as a practical alternative to the preparation of alpha-heteroaryl carbonitriles.     

Antihydrophobic cosolvent effects for alkylation reactions in water solution, particularly oxygen versus carbon alkylations of phenoxide ions

Antihydrophobic cosolvents such as ethanol increase the solubility of hydrophobic molecules in water, and they also affect the rates of reactions involving hydrophobic surfaces. In simple reactions of hydrocarbons, such as the Diels-Alder dimerization of 1,3-cyclopentadiene, the rate and solubility data directly reflect the geometry of the transition state, in which some hydrophobic surface becomes hidden. In reactions involving polar groups, such as alkylations of phenoxide ions or S(N)1 ionizations of alkyl halides, cosolvents in water can have other effects as well. However, solvation of hydrophobic surfaces is still important. By the use of structure-reactivity relationships, and comparing the effects of ethanol and DMSO as solvents, it has been possible to sort out these effects. The conclusions are reinforced by an ab initio computer model for hydrophobic solvation. The result is a sensible transition state for phenoxide ion as a nucleophile, using its oxygen n electrons to avoid loss of conjugation. The geometry of alkylation of aniline is very different, involving packing (stacking) of the aniline ring onto the phenyl ring of a benzyl group in the benzylation reaction. The alkylation of phenoxide ions by benzylic chlorides can occur both at the phenoxide oxygen and on ortho and para positions of the ring. Carbon alkylation occurs in water, but not in nonpolar organic solvents, and it is observed only when the phenoxide has at least one methyl substituent ortho, meta, or para. The effects of phenol substituents and of antihydrophobic cosolvents on the rates of the competing alkylation processes indicate that in water the carbon alkylation involves a transition state with hydrophobic packing of the benzyl group onto the phenol ring. The results also support our conclusion that oxygen alkylation uses the n electrons of the phenoxide oxygen as the nucleophile and does not have hydrophobic overlap in the transition state. The mechanisms and explanations for competing oxygen and carbon alkylations differ from previous proposals by others.     

Asymmetric total synthesis of rollicosin

[structure: see text] The first total synthesis of rollicosin, a member of a rare subgroup of Annonaceous acetogenins containing two terminal gamma-lactones, is reported. The approach features a highly regio- and stereoselective tandem ring-closing/cross-metathesis reaction for construction of the east-wing lactone and incorporation of the alkyl spacer. Establishment of the C4 stereocenter and addition of the west-wing lactone were achieved by Sharpless asymmetric dihydroxylation and enolate alkylation.     

Self-assembling of helical poly(phenylacetylene) carrying L-valine pendants in solution, on mica substrate, and on water surface

In the present work, we investigated self-assembling of a poly(phenylacetylene) carrying L-valine pendants (PPA-Val) in a water/methanol solution, upon evaporation of the solution on mica, and on the water surface. With intercalation of a fluorescence probe of Ru(phen)2(dppx)2+ (phen = 1,10-phenanthroline, dppx=7,8-dimethyldipyridophenazine) into the hydrophobic cavities associated by the PPA-Val chains, their helical structures were directly detected in solution with an in situ fluorescence microscope. Helical aggregates were observed with AFM upon evaporation of the solvents, suggesting that the helical structures in the solution are the building blocks of the helical aggregates. Self-assembling structures of PPA-Val on the water surface were, however, very different from that formed upon evaporation of its THF solution on the mica surface. The polymer chains associated into a monolayer of extended fibers on the water surface, whereas superhelical fibers formed on the mica surface. Water molecules play a critical role in inducing the polymer to form diverse morphological structures in its bulk solution and on its surface. In solution, the isotropic hydrophobic effect drove the polymer chains to form superhelical aggregates, while on the water surface, the hydrophobic effect concentrated mainly on the lateral part of the polymer, thus giving a monolayer of extended fibers.     

Flexible ligand docking without parameter adjustment across four ligand–receptor complexes

Understanding molecular recognition is one of the fundamental problems in molecular biology. Computationally, molecular recognition is formulated as a docking problem. Ideally, a molecular docking algorithm should be computationally efficient, provide reasonably thorough search of conformational space, obtain solutions with reasonable consistency, and not require parameter adjustments. With these goals in mind, we developed DIVALI (Docking wIth eVolutionary AlgorIthms), a program which efficiently and reliably searches for the possible binding modes of a ligand within a fixed receptor. We use an AMBER-type potential function and search for good ligand conformations using a genetic algorithm (GA). We apply our system to study the docking of both rigid and flexible ligands in four different complexes. Our results indicate that it is possible to find diverse binding modes, including structures like the crystal structure, all with comparable potential function values. To achieve this, certain modifications to the standard GA recipe are essential. © 1995 John Wiley & Sons, Inc.