Theoretical study on the hydrogen migration reactions in ground state vinyl fluoride: Basis set and correlation energy effects

We performed ab initio molecular orbital (MO) calculations using Hartree—Fock SCF, and second- and fourth-order Møller—Plesset perturbation theory for hydrogen migration reactions on the singlet vinyl fluoride potential energy surface. We used different basis sets and polarization functions to obtain the stationary point geometries and activation barriers. Basis set and the polarization function extension have small effects, while the correlation energy evaluation leads to new conclusions for one of the studied reactions: the product singlet CHCH₂F is not a true local minimum on the potential energy surface.     

1,3-Cycloaddition of nitrones in ionic liquids catalyzed by Er(III): an easy access to isoxazolidines

1,3-Dipolar cycloadditions of nitrones with alkenes afforded the corresponding isoxazolidines in ionic liquids in the presence of Er(OTf)₃. The ionic liquid and the catalyst are recycled up to five times without any specific treatment or loss of activity. Extension of the procedure to the synthesis of isoxazolidinyl nucleosides has been investigated.     

Structure‐based ligand design by a build‐up approach and genetic algorithm search in conformational space

Program to engineer peptides (PEP) is a build‐up approach for ligand docking and design with implicit solvation. It requires the knowledge of a seed from which it iteratively grows polymeric ligands consisting of any type of amino acid, i.e., natural and/or nonnatural from a user‐defined library. At every growing step, a genetic algorithm is used for conformational optimization of the last added monomer in the rigid binding site. Pruning is performed at every growing step by selecting sequences according to binding energy with electrostatic solvation. PEP is applied to three members of the caspase family of cysteine proteases using Asp at P₁ as seed. The optimal P₄–P₂ peptide recognition motifs and variants thereof are docked correctly in the active site (backbone root‐mean‐square deviation < 0.9 Å). Moreover, for each caspase, the P₄–P₂ sequences of potent aldehyde inhibitors are ranked among the 15 hits with the most favorable PEP energy. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1956–1970, 2001     

Computational combinatorial ligand design: Application to human α-thrombin

Summary A new method is presented for computer-aided ligand design by combinatorial selection of fragments that bind favorably to a macromolecular target of known three-dimensional structure. Firstly, the multiple-copy simultaneous-search procedure (MCSS) is used to exhaustively search for optimal positions and orientations of functional groups on the surface of the macromolecule (enzyme or receptor fragment). The MCSS minima are then sorted according to an approximated binding free energy, whose solvation component is expressed as a sum of separate electrostatic and nonpolar contributions. The electrostatic solvation energy is calculated by the numerical solution of the linearized Poisson-Boltzmann equation, while the nonpolar contribution to the binding free energy is assumed to be proportional to the loss in solvent-accessible surface area. The program developed for computational combinatorial ligand design (CCLD) allows the fast and automatic generation of a multitude of highly diverse compounds, by connecting in a combinatorial fashion the functional groups in their minimized positions. The fragments are linked as two atoms may be either fused, or connected by a covalent bond or a small linker unit. To avoid the combinatorial explosion problem, pruning of the growing ligand is performed according to the average value of the approximated binding free energy of its fragments. The method is illustrated here by constructing candidate ligands for the active site of human -thrombin. The MCSS minima with favorable binding free energy reproduce the interaction patterns of known inhibitors. Starting from these fragments, CCLD generates a set of compounds that are closely related to high-affinity thrombin inhibitors. In addition, putative ligands with novel binding motifs are suggested. Probable implications of the MCSS-CCLD approach for the evolving scenario of drug discovery are discussed.     

Synthetic entries to 6-fluoro-7-substituted indole derivatives

Three practical synthetic entries of functionalized 6-fluoro-7-substituted indole derivatives were developed in connection with the preparation of 7-fluoro-8-substituted-1,3,4,9-tetrahydropyrano[3,4-b]indole-1-acetic acid derivatives 11 . The first route, which permits group modification about position 8 of the pyranoindole skeleton, employs 2-bromo-3-fluoroaniline ( 18 ) as a key intermediate, the preparation of which was achieved by either a novel ortho metalation of 15 or via the intermediacy of 22 . The second route utilizes 32 to append a terminally functionalized three carbon side chain onto the indole template and in addition leads to 43 from 40 . The third route to the 7-fluoro-8-substituted-pyranoindole skeleton complements route two in that the synthetic pathway exploits 32 in a nucleophilic fashion to construct a terminally functionalized two carbon appendage onto the indole nucleus.     

Effect of metal ions in organic synthesis. Part XXXI. Synthesis of new 3-carbonyl- and 3-carboxy-1-heterocyclaminopyrroles by copper(II) chloride-catalyzed reaction of heterocyclic azoalkenes

The direct synthesis of a new class of unknown 1-heterocyclamino-3-carbonylpyrroles and 1-heterocyclamino-3-carboxypyrroles by copper(II) chloride-catalyzed reaction of heterocyclic conjugated azoalkene derivatives with β-diketones and β-ketoesters is reported.     

Refractive-index and density matching in concentrated particle suspensions: a review

Optical measurement techniques such as particle image velocimetry (PIV) and laser Doppler velocimetry (LDV) are now routinely used in experimental fluid mechanics to investigate pure fluids or dilute suspensions. For highly concentrated particle suspensions, material turbidity has long been a substantial impediment to these techniques, which explains why they have been scarcely used so far. A renewed interest has emerged with the development of specific methods combining the use of iso-index suspensions and imaging techniques. This review paper gives a broad overview of recent advances in visualization techniques suited to concentrated particle suspensions. In particular, we show how classic methods such as PIV, LDV, particle tracking velocimetry, and laser induced fluorescence can be adapted to deal with concentrated particle suspensions.