Distributed automated docking of flexible ligands to proteins: Parallel applications of AutoDock 2.4

Summary AutoDock 2.4 predicts the bound conformations of a small, flexible ligand to a nonflexible macromolecular target of known structure. The technique combines simulated annealing for conformation searching with a rapid grid-based method of energy evaluation based on the AMBER force field. AutoDock has been optimized in performance without sacrificing accuracy; it incorporates many enhancements and additions, including an intuitive interface. We have developed a set of tools for launching and analyzing many independent docking jobs in parallel on a heterogeneous network of UNIX-based workstations. This paper describes the current release, and the results of a suite of diverse test systems. We also present the results of a systematic investigation into the effects of varying simulated-annealing parameters on molecular docking. We show that even for ligands with a large number of degrees of freedom, root-mean-square deviations of less than 1 Å from the crystallographic conformation are obtained for the lowest-energy dockings, although fewer dockings find the crystallographic conformation when there are more degrees of freedom.The AutoDock 2.4 suite is written in ANSI C, and is supplied with Makefiles for the following platforms: Convex, DEC Alpha OSF/1, Hewlett-Packard Precision Architecture, Silicon Graphics, and Sun. The AutoDock suite of programs is freely available to the noncommercial scientific community and to educational establishments. Further information, including additional figures and MPEG animations showing all docked conformations for each test system, can be found at the following URL: http://www.scripps.edu/pub/olson-web/doc/autodock.     

Efficient terahertz coupling lens based on planar photonic crystals on silicon on insulator

We present a promising coupling device, namely, a terahertz (THz) planar photonic crystal (PhC) lens based on the effective refractive-index contrast between the PhC and the surrounding unpatterned area. Three-dimensional finite-difference time-domain calculations show a 90% power transfer from a 100-microm silicon waveguide to a 10-microm waveguide, and 45% coupling efficiency is confirmed experimentally. These results demonstrate the utility of the PhC lens as an effective approach to coupling into PhC THz circuits.     

Evidence for nontermination of rotational bands in 74Kr

Three rotational bands in 74Kr were studied up to (in one case one transition short of) the maximum spin I(max) of their respective single-particle configurations. Their lifetimes have been determined using the Doppler-shift attenuation method. The deduced transition quadrupole moments reveal a modest decrease, but far from a complete loss of collectivity at the maximum spin I(max). This feature, together with the results of mean field calculations, indicates that the observed bands do not terminate at I = I(max).     

Three-dimensional subwavelength imaging by a photonic-crystal flat lens using negative refraction at microwave frequencies

We experimentally demonstrate subwavelength resolution imaging at microwave frequencies by a three-dimensional (3D) photonic-crystal flat lens using full 3D negative refraction. The photonic crystal was fabricated in a layer-by-layer process. A subwavelength pinhole source and a dipole detector were employed for the measurement. By point-by-point scanning, we obtained the image of the pinhole source shown in both amplitude and phase, which demonstrated the imaging mechanism and subwavelength feature size in all three dimensions. An image of two pinhole sources with subwavelength spacing showed two resolved spots, which further verified subwavelength resolution.     

Highly selective asymmetric hydrogenation using a three hindered quadrant bisphosphine rhodium catalyst

A concise synthesis of both enantiomers of ligand 2 and rhodium complex 5 is presented. The crux of the synthesis is a chiral HPLC separation of the enantiomers of 4. Rhodium complex 5 possesses three hindered quadrants in the steric environment within which a substrate binds. Evidence is presented that this configuration leads to high enantioselectivity (>99% ee) for rhodium-catalyzed asymmetric hydrogenation of alpha-acetamido dehydroamino acids, 6a-e. High enantioselectivities are also reported for the hydrogenation of a substrate precursor, 8, of pharmaceutical candidate, pregabalin. Advantages for large-scale hydrogenation of 8 using catalyst 5a vs Rh-Me-DuPhos are discussed.     

Nature of the pygmy resonance in continuous <Emphasis Type="Italic">γ</Emphasis> spectra

Two-step-cascade spectra of the ¹⁷¹Yb(n, γγ)¹⁷²Yb reaction have been measured using thermal neutrons. They are compared to calculations based on experimental values of the level density and radiative strength function obtained from the ¹⁷³Yb(³He, aγ)¹⁷²Yb reaction. The multipolarity of a 6.5(15) μ _N ² resonance at 3.3(1) MeV in the strength function is determined to be M1 by this comparison.