Ligand-receptor docking with the Mining Minima optimizer

The optimizer developed for the Mining Minima algorithm, which uses ideas from Genetic Algorithms, the Global Underestimator Method, and Poling, has been adapted for use in ligand-receptor docking. The present study describes the resulting methodology and evaluates its accuracy and speed for 27 test systems. The performance of the new docking algorithm appears to be competitive with that of previously published methods. The energy model, an empirical force field with a distance-dependent dielectric treatment of solvation, is adequate for a number of test cases, although incorrect low-energy conformations begin to compete with the correct conformation for larger sampling volumes and for highly solvent-exposed binding sites that impose little steric constraint on the ligand.     

A new strategy for solid phase synthesis of a secondary amide library using sulfonamide linker via radical traceless cleavage

A new strategy for solid phase synthesis of a secondary amide library using sulfonamide linker via radical traceless cleavage is reported. Polystyrylsulfonyl chloride (1) reacted with primary amines to afford polystyryl-supported N-alkyl sulfonamides (2), which were acylated with acid chlorides and followed by radical cleavage with TiCl₄/Zn to afford secondary amides. It was interestingly found that the products released from acyl alkanesulfonamide resins are closely dependent on the substituents of benzene rings of alkyl or acyl groups on the resins. When the substituent on benzene ring of N-benzyl group of sulfonamides is an electron rich MeO-group, the products released from sulfonamide resins are dependent on the substitution position on benzene ring: para-MeO- to yield 1,2-bis (p-methoxylphenyl)ethane and N-p-methoxylbenzyl benzamide (30:1); ortho-MeO- to give 1,2-bis (o-methoxylphenyl)ethane and N-o-methoxylbenzyl benzamide (1:15); and meta-MeO- only to release N-m-methoxylbenzyl benzamide. Neither N-benzoyl sulfonamide resins on benzene ring with electron-drawing para-O₂N-, nor the one with electron-donating para-H₂N- could release any amide product, while the N-benzoyl sulfonamide resins on benzene ring with para-acetamido group released para-acetamidobenzamides. The conjugation effect to stabilize the radical groups in the radical cleaving process was observed.     

Closed path integrals and the quantum action

We suggest a closed form expression for the path integral of quantum transition amplitudes. We introduce a quantum action with parameters different from the classical action. We present numerical results for the harmonic oscillator with weak perturbation, the quartic potential, and the double well potential. The quantum action is relevant for quantum chaos and quantum instantons.     

Hadronic loop corrections to the muon anomalous magnetic moment

The dominant theoretical uncertainties in both the anomalous magnetic moment of the muon and the value of the electromagnetic coupling at the Z scale, M(Z), arise from their hadronic contributions. Since these will ultimately dominate the experimental errors, we study the correlation between them, as well as with other fundamental parameters. To this end we present analytical formulas for the QCD contribution from higher energies and from heavy quarks. Including these correlations affects the Higgs boson mass extracted from precision data.     

Self-induced phase matching in stimulated four-wave mixing in a nonbirefringent single-mode optical fiber

Self-induced phase matching in stimulated four-wave mixing in a nonbirefringent single-mode optical fiber has been observed. It is shown that in a nonbirefringent single-mode fiber the phase matching that is necessary for stimulated four-wave mixing can be accomplished with a combination of self-phase modulation and cross-phase modulation induced by a pump-laser pulse.     

Asymptotic approach to the truncated cosh-Gaussian beams

The propagation behavior and M ²-factor of truncated cosh-Gaussian (ChG) beams are studied by using the asymptotic approach. Detailed numerical results are given to illustrate the dependence of M ²-factor on the beam decentered parameter , truncation fraction p and power fraction f. Our results are self-consistent and reduce to those of Pare and Belanger [Opt. Commun. 123, p. 679 (1996a); Proc. SPIE 2870, p. 104 (1996b)]. The advantage of the approach is shown, and the problems introduced by the hard-aperture diffraction and the approach used are discussed.     

Characterisation of precipitate phases in magnesium alloys using electron microdiffraction

Recent results of the characterisation of the structure, morphology and orientation of fine-scale, strengthening precipitate phases in selected magnesium alloys using transmission electron microscopy and microdiffraction are reviewed. The strengthening precipitate phases in Mg–Y–Nd alloys, aged to maximum hardness at 250°C, have been found to include two metastable precipitate phases β′ and β₁, and the equilibrium precipitate β. The β′ phase has a globular form, a base-centred orthorhombic structure (potential point group of mmm), and an orientation relationship such that (100)_β′//(1 10)_α, [001]_β′//[0001]_α. The β₁ phase has an f.c.c. structure (space group and an orientation relationship that may be described by (100)_β1//[0001]_α, and forms as plates parallel to The β phase has an f.c.c. structure (space group ) and also forms as plates on with an orientation relationship with the matrix phase that is identical to that observed for β₁ phase. Precipitates in Mg–Al alloys, aged isothermally at 200°C, invariably have the b.c.c. structure of the equilibrium precipitate phase β (Mg₁₇Al₁₂). Three orientation relationships have been observed between β and the matrix phase. Most precipitates have an irrational orientation relationship that approximates to the Burger's relationship, (001)_β//(0001)_α, and a faceted lath morphology with habit plane parallel to (0001)_α. A minor fraction of precipitates posses an orientation relationship that is of the form

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and have a prismatic rod morphology. The long axes of these rods are parallel to [0001]_α, and their faceted surfaces are parallel to A few precipitates are observed to have an orientation relationship such that

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and a rod shape, with their long axes apparently inclined with respect to [0001]_α.     

Characterization of spiroiminodihydantoin as a product of one-electron oxidation of 8-Oxo-7,8-dihydroguanosine

[reaction: see text] Further oxidation of the common DNA lesion 8-oxo-7,8-dihydroguanosine by one-electron oxidants such as IrCl6(2-), Fe(CN)6(3-), or SO4-* leads to two major products, depending upon reaction conditions. In nucleosides at pH 7, 22 degrees C, the principal product is shown herein to be a spiroiminodihydantoin nucleoside, as a diastereomeric mixture, that can be characterized by NMR, ESI-MS/MS, and independent synthesis.     

Pd与CeO2(111)面的相互作用的第一性原理研究

采用基于广义梯度近似的投影缀加平面波(projector augmented wave) 赝势和具有三维周期性边界条件的超晶胞模型，用第一性原理计算方法，计算并分析了Pd在CeO₂(111)面上不同覆盖度时的吸附能，价键结构和局域电子结构. 考虑了单层Pd和1/4单层Pd两种覆盖度吸附的情况. 结果表明：1)在单层吸附时，Pd的最佳吸附位置是O的顶位偏向Ce的桥位；在1/4单层吸附时，Pd最易在O的桥位偏向次层O的顶位吸附.2) 单层覆盖度吸附时，吸附原子Pd之间的作用较强；1/4单 关键词： 三元催化剂 Pd 2')" href="#">CeO₂ 吸附 密度泛函理论