1,764 research outputs found

    Development of Force Field Parameters for Oxyluciferin on its Electronic Ground and Excited States

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    Construction of force field parameters of the oxyluciferin molecule on its electronic ground and excited states is presented. Several new approaches are introduced for more reliable parameterization: argon-scanning, Hessian matching, and constrained-group parameterization. The Ar-scanning approach is for fitting Lennard-Jones parameters so that the constructed force field can mimic the changes in ab initio energy of oxyluciferin-argon pair at various argon positions. The Hessian matching procedure is to closely reproduce the second derivative matrix of the bonded interaction terms of the force field functions, in comparison with the quantum chemically obtained results. The constrained-group algorithm is applied for both of these approaches to enable an automated atom-type-based parameterization. For complete description of the force field of the oxyluciferin molecule, we have also adopted the second order perturbatively corrected one-particle density matrices to obtain the atomic partial charges within the conventional framework of the restrained electrostatic potential fit. With the availability of the full force field parameter sets, the differences in condensed-phase dynamics on the two states can be investigated. As a simple demonstration, molecular dynamics simulations of aqueous oxyluciferin solution have been performed. The surrounding water structures for the two cases are analyzed by inspecting both the static solvent distribution functions as well as time variation of solvent-solute interaction. The contributions of charge-charge and dispersive interactions toward the solvation dynamics are also discussed. (C) 2010 Wiley Periodicals, Inc. Int J Quantum Chem 111: 4091-4105, 2011X112524sciescopu

    Understanding sedimentation in the Song Hong–Yinggehai Basin, South China Sea

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    The Cenozoic Song Hong–Yinggehai Basin in the South China Sea contains a large volume of sediment that has been used in previous studies, together with regional geomorphology, to argue for the existence of a large palaeodrainage system that connected eastern Tibet with the South China Sea. To test this and to understand the significance of sediment volumes deposited in the Song Hong–Yinggehai Basin, this study compared erosion histories of source regions with sediment volumes deposited during the two main stages in basin evolution spanning active rifting and subsidence (30–15.5 Ma) and postrift sedimentation (15.5 Ma to present). The study of basin provenance by detrital zircon U-Pb dating revealed Hainan was an important and continuous source of sediment, and a bedrock thermochronological study quantified its overall contribution to basin sedimentation. Comparison between the accumulated mass of basin sediment and volumes of eroded bedrock, calculated from apatite thermochronometry across the modern Red River drainage in northern Vietnam as well as Hainan Island, accounted for the bulk of sediment deposited since 30 Ma. Consequently, if an expanded paleodrainage ever existed it must have predated the Oligocene

    Dynamics on the Electronically Excited State Surface of the Bioluminescent Firefly Luciferase-Oxyluciferin System

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    Dynamics of the firefly luciferase-oxyluciferin complex in its electronic ground and excited states are studied using various theoretical approaches. By mimicking the physiological conditions with realistic models of the chromophore oxyluciferin, the enzyme luciferase, and solvating water molecules and by performing real time simulations with a molecular dynamics technique on the model surfaces, we reveal that the local chromophore-surrounding interaction patterns differ rather severely in the two states. Because of the presence of protein, the solvation dynamics of water around the chromophore is also peculiar and shows widely different time scales on the two terminal oxygen atoms. In addition, simulations of the emission with the quantum-mechanics/molecular-mechanics approach show a close relationship between the emission color variation and the environmental dynamics, mostly through electrostatic effects from the chromophore-surrounding interaction. We also discuss the importance of considering the time scales of the luminescence and the dynamics of the interaction.X114138sciescopu

    Drassyllus shaanxiensis Platnick & Song 1986

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    Drassyllus shaanxiensis Platnick & Song, 1986 ** Platnick & Song, 1986: f. 69-70; Chikuni, 1989: 121, f. 15; Kamura, 1990: f. 3-6; Song et al., 1999: f. 290 f-g,l. Material examined: 1 ♀, [08] env. of Barabash-Levada Vill, 44º45.5'N 131º27'E, 18- 19.07.1998, YM. COMMENTS. The first record in Russia, earlier known from China, from Xinjiang to Henan and Shanxi [Song et al., 1999) and Japan (Hokkaido and Honshu, Tsurusaki, personal communication).Published as part of Marusik, Yuri M. & Koponen, Seppo, 2000, New data on spiders (Aranei) from the Maritime Province, Russian Far East, pp. 55-68 in Arthropoda Selecta 9 (1) on page 59, DOI: 10.5281/zenodo.82271
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