4,231 research outputs found
Solvation Of 5-fluorouracil In Supercritical Co2
No full textThe solvation properties of 5-fluorouracil in supercritical carbon dioxide (SC-CO2) is investigated by means of molecular dynamics computer simulations using a force field that treats all atoms explicitly. Solvation shell distribution functions and solvent density maps around the solute were computed at different supercritical temperatures in the range 308-328 K and densities varying from 0.117 to 0.94 g/cm3. At the lowest density, we detect a strongly inhomogeneous local density augmentation effect manifested as the clustering of solvent molecules above and below the solute molecular plane and around its carbonyl and N-H groups. The free-energy benefit for a CO 2 molecule to be in the first solvation shell relative to the bulk is roughly twice the thermal energy at such conditions. The distribution of the relative orientation of CO2 with respect to the solute suggests that local bond multipolar solute-solvent interactions are responsible for the solvent density enhancement in these systems. © 2008 Wiley Periodicals, Inc.1081325572563(1999) Chem Rev, 99 (2). , Noyori, R, Guest editor, Special Issue(2006) J Supercrit Fluids, 38 (2). , Erkeya, C, Kiran, E, Guest editors, Special IssueHutchinson, K.W., Foster, N.R., Innovations in Supercritical Fluids Science and Technology (1995) ACS Symposium Series, 608. , American Chemical Society: WashingtonEckert, C.A., Knutson, B.L., Debenedetti, P.G., (1996) Nature, 383, p. 313McHugh, M.A., Krokonis, V.J., (1994) Supercritical Fluids Extraction: Principles and Practice, , 2 nd ed, Butterworths: Boston, MAEckert, C.A., Liotta, C.L., Bush, D., Brown, J.S., Hallett, J.P., (2004) J Phys Chem B, 108, p. 18108Tucker, S. C.Maddox, M. W. J Phys Chem B 1998, 102, 2437Stephens, M.D., Saven, J.G., Skinner, J.L., (1997) J Chem Phys, 106, p. 2129Elles, C.G., Crim, F.F., (2006) Annu Rev Phys Chem, 57, p. 273Marcus, Y., (2005) J Phys Org Chem, 18, p. 373Patel, N., Biswas, R., Maroncelli, M., (2002) J Phys Chem B, 106, p. 7096Song, W., Biswas, R., Maroncelli, M., (2000) J Phys Chem A, 104, p. 6924Rocha, S. R. P.Johnston, K. P.Westacott, R. E.Rossky, P. J. J Phys Chem B 2001, 105, 12092Rocha, S. R. P.Johnston, K. P.Rossky, P. J. J Phys Chem B 2002, 106, 13250Fávero, F.W., Skaf, M.S., (2005) J Supercrit Fluids, 34, p. 237Guney, O., Akgerman, A., (2000) J Chem Eng Data, 45, p. 1049Suleiman, D., Estevez, L.A., Pulido, J.C., Garcia, J.E., Mojica, C., (2005) J Chem Eng Data, 50, p. 1234Harris, J.G., Yung, K.H., (1995) J Phys Chem, 99, p. 12021Vorholz, J., Harismiadis, V.I., Rumpf, B., Panagiotopoulos, A.Z., Maurer, G., (2000) Fluid Phase Equil, 170, p. 203Adams, J. F.Siavosh-Haghighi, A. J Phys Chem B, 2002, 106, 7973Frisch, M. J, Trucks, G. W, Schlegel, H. B, Scuseria, G. E, Robb, M. A, Cheeseman, J. R, Zakrzewski, V. G, Montgomery, J. A, Jr, Stratmann, R. E, Burant, J. C, Dapprich, S, Millam, J. M, Daniels, A. D, Kudin, K. N, Strain, M. C, Farkas, O, Tomasi, J, Barone, V, Cossi, M, Cammi, R, Mennucci, B, Pomelli, C, Adamo, C, Clifford, S, Ochterski, J, Petersson, G. A, Ayala, P. Y, Cui, Q, Morokuma, K, Malick, D. K, Rabuck, A. D, Raghavachari, K, Foresman, J. B, Cioslowski, J, Ortiz, J. V, Stefanov, B. B, Liu, G, Liashenko, A, Piskorz, P, Komaromi, I, Gomperts, R, Martin, R. L, Fox, D. J, Keith, T, Al-Laham, M. A, Peng, C. Y, Nanayakkara, A, Gonzalez, C, Challacombe, M, Gill, P. M. W, Johnson, B, Chen, W, Wong, M. W, Andres, J. L, Gonzalez, C, Head-Gordon, M, Replogle, F. S, Pople, J. A. Gaussian 98, Revision A. 7Gaussian, Inc: Pittsburgh, PA, 1998Kaminski, G.A., Friesner, R.A., Tirado-Rives, J., Jörgensen, W.L., (2001) J Phys Chem B, 105, p. 6474Ponder, J. W. TINKER Software Tools for Molecular Design, Version 3.9, 2000Tucker, S. C. Chem Rev 1999, 99, 391Rodriguez, J., Skaf, M.S., Laria, D., (2003) J Chem Phys, 119, p. 6044Laria, D., Skaf, M.S., (2002) J Phys Chem A, 106, p. 8066Raveendran, P., Ikushima, Y., Wallen, S.L., (2005) Acc Chem Res, 38, p. 478Fávero, F.W., (2007), PhD Thesis, Institute of Chemistry, State University of Campina
Molecular Dynamics Simulation Of Solvation Dynamics In Methanol-water Mixtures
No full textThe solvation dynamics following charge-transfer electronic excitation of diatomic solutes immersed in methanol-water mixtures is investigated through molecular dynamics simulations. The solvation response functions associated with an instantaneous reversal of the solute's dipole moment for two different solute sizes in mixtures with methanol mole fractions, xm = 0.2, 0.5, and 0.8, are calculated and compared to the corresponding ones in the pure liquids. The solvation response of the mixtures is separated into methanol and water contributions in order to elucidate the role played by each molecular species on the solvation dynamics. We find significantly different responses for the two solutes and relate them to the fact that the solute with the smaller site diameters is a much better hydrogen (H)-bond acceptor than the larger diameter solute. For the small solute in methanol and in the mixed solvents, we have also calculated H-bond response functions, which measure the rate of solute-solvent H-bond formation after the solute's excitation and find that, at longer times, the solvation and H-bond formation response functions decay at similar rates. The implications of this finding for solvation dynamics of H-bonding solutes in H-bonding solvents are discussed and related to recent experimental results for such systems. © 1996 American Chemical Society.100461825818268Heitele, H., (1993) Angew. Chem., Int. Ed. Engl., 32, p. 359Hynes, J.T., (1993) Ultrafast Dynamics of Chemical Systems, , Simon, J. D., Ed.Kluwer: Dordrecht, Chapter 13Rossky, P.J., Simon, J.D., (1994) Nature (London), 370, p. 263Refs 5-8 contain reviews of various aspects of solvation dynamicsMaroncelli, M., (1993) J. Mol. Liq., 57, p. 1Maroncelli, M., Kumar, P.V., Papazyan, A., Horng, M.L., Rosenthal, S.J., Fleming, G.R., (1994) Ultrafast Reaction Dynamics and Solvent Effects, pp. 310-333. , Gauduel, Y., Rossky, P. J., Eds.American Institute of Physics: New YorkBagchi, B., Chandra, A., (1991) Adv. Chem. Phys., 80, p. 1Bagchi, B., (1989) Annu. Rev. Phys. Chem., 40, p. 115Barbara, P.F., Jarzeba, W., (1990) Adv. Photochem., 15, p. 1Jarzeba, W., Walker, G.C., Johnson, A.E., Barbara, P.F., (1991) Chem. Phys., 152, p. 57Maroncelli, M., Fleming, G.R., (1988) J. Chem. Phys., 89, p. 5044Karim, O.A., Haymet, A.D.J., Banet, M.J., Simon, J.D., (1988) J. Phys. Chem., 92, p. 3391Bader, J.S., Chandler, D., (1989) Chem. Phys. Lett., 157, p. 501Belhadj, M., Kitchen, D.B., Blair, J.T., Krogh-Jespersen, K., Levy, R.M., (1991) J. Phys. Chem., 95, p. 1082Levy, R.M., Kitchen, D.B., Blair, J.T., Krogh-Jespersen, K., (1990) J. Phys. Chem., 94, p. 4470Rao, M., Berne, B.J., (1981) J. Phys. Chem., 85, p. 1498Bursulaya, B.D., Zichi, D.A., Kim, H.J., (1995) J. Phys. Chem., 99, p. 10069(1996) J. Phys. Chem., 100, p. 1392Muiño, P., Callis, P.R., (1994) J. Chem. Phys., 100, p. 4093Ando, K., Kato, S., (1991) J. Chem. Phys., 95, p. 5966Zhu, J., Cukier, R.I., (1993) J. Chem. Phys., 98, p. 5679Fonseca, T., Ladanyi, B.M., (1991) J. Phys. Chem., 95, p. 2116Fonseca, T., Ladanyi, B.M., (1993) J. Mol. Liq., 60, p. 1Phelps, D.K., Weaver, M.J., Ladanyi, B.M., (1993) Chem. Phys., 176, p. 575Brown, R., (1995) J. Chem. Phys., 102, p. 9069Kumar, P.V., Maroncelli, M., (1995) J. Chem. Phys., 103, p. 3038Skaf, M.S., Ladanyi, B.M., (1995) J. Mol. Struct., 335, p. 181Maroncelli, M., (1991) J. Chem. Phys., 94, p. 2084Ladanyi, B.M., Stratt, R.M., (1995) J. Phys. Chem., 99, p. 2502Carter, E.A., Hynes, J.T., (1991) J. Chem. Phys., 94, p. 5961Ladanyi, B.M., Skaf, M.S., (1993) Annu. Rev. Phys. Chem., 44, p. 335Olender, R., Nitzan, A., (1995) J. Chem. Phys., 102, p. 7180Ladanyi, B.M., Skaf, M.S., (1996) J. Phys. Chem., 100, p. 1368Ferrario, M., Haughney, M., McDonald, I.R., Klein, M.L., (1990) J. Chem. Phys., 93, p. 5156Skaf, M.S., Ladanyi, B.M., (1995) J. Chem. Phys., 102, p. 6542Tanaka, H., Gubbins, K.E., (1992) J. Chem. Phys., 97, p. 2626Koh, K.A., Tanaka, H., Walsh, J.M., Gubbins, K.E., Zollweg, J.A., (1993) Fluid Phase Equilib., 83, p. 51Pálinkás, G., Hawlicka, E., Heinzinger, K., (1991) Chem. Phys., 158, p. 65Pálinkás, G., Bakó, I., Heinzinger, K., Bopp, P., (1991) Mol. Phys., 73, p. 897Bertolini, D., Cassettari, M., Salvetti, G., (1983) J. Chem. Phys., 78, p. 365Bertolini, D., Cassettari, M., Salvetti, G., Tombari, E., Veronesi, S., (1991) J. Non-Cryst. Solids, 131-133, p. 1169Mashimo, S., Kuwabara, S., Yasihara, S., Higasi, K., (1989) J. Chem. Phys., 90, p. 3292Zhang, X., Jonah, C.D., (1996) J. Phys. Chem., 100, p. 7042Lin, Y., Jonah, C.D., (1994) Ultrafast Dynamics of Chemical Systems, pp. 137-162. , Simon, J. D., Ed.Kluwer: DordrechtLin, Y., Jonah, C.D., (1993) J. Phys. Chem., 97, p. 295Lin, Y., Jonah, C.D., (1992) J. Phys. Chem., 96, p. 10119Declémy, A., Rullière, C., Kottis, P., (1990) Laser Chem., 10, p. 413Declémy, A., Rullière, C., (1994) Ultrafast Reaction Dynamics and Solvent Effects, pp. 275-295. , Gauduel, Y.Rossky, P. J., Eds.American Institute of Physics: New YorkYu, J., Berg, M., (1993) Chem. Phys. Lett., 205, p. 315Chapman, C.F., Fee, R.S., Maroncelli, M., (1995) J. Phys. Chem., 99, p. 4811Carter, E.A., Hynes, J.T., (1989) J. Phys. Chem., 93, p. 2184Allen, M.P., Tildesley, D.J., (1987) Computer Simulation of Liquids, , Clarendon Press: OxfordRappé, A.K., Casewit, C.J., Colwell, K.S., Goddard III, W.A., Skiff, W.M., (1992) J. Am. Chem. Soc., 114, p. 10024Haughney, M., Ferrario, M., McDonald, I.R., (1987) J. Phys. Chem., 91, p. 4934Jorgensen, W.L., Chandrasekhar, J., Impey, R.W., Klein, M.L., (1983) J. Chem. Phys., 79, p. 926Fonseca, T., Ladanyi, B.M., (1990) J. Chem. Phys., 93, p. 8148Skaf, M.S., Fonseca, T., Ladanyi, B.M., (1993) J. Chem. Phys., 98, p. 8929Neumann, M., (1986) J. Chem. Phys., 55, p. 1567Luzar, A., Chandler, D., (1993) J. Chem. Phys., 95, p. 8160Hockney, R.W., (1970) Methods Comput. Phys., 9, p. 136Ciccotti, G., Ryckaert, J.-P., (1986) Comput. Phys. Rep., 4, p. 345Ciccotti, G., Ferrario, M., Ryckaert, J.-P., (1982) Mol. Phys., 47, p. 1253Chandra, A., Bagchi, B., (1991) J. Chem. Phys., 94, p. 836
Hydration Structures Of The Squarate Dianion C4o4 2-. A Combined Molecular Dynamics Simulation And Quantum Ab Initio Study
No full textMolecular dynamics (MD) simulations are used to determine the structure of the first solvation shell around a single monocyclic oxocarbon dianion C4O4 2- in aqueous solution. The simulations were carried out using a fixed-geometry model for the oxocarbon with excess partial charges equally distributed over the oxygen atoms and the well-known SPC/E model for water. Quantum ab initio calculations for an isolated oxocarbon at different levels of approximation indicate that the such a description of the squarate dianion should be fairly accurate for the study of solvation structures. Analysis of a complete set of solute-solvent site-site radial distribution functions and hydrogen (H)-bonding distributions obtained from the MD simulations, indicates a well-defined first solvation shell consisting of approximately 18 water molecules. About 12 of these molecules are tightly H-bonded to the oxocarbon (an average of 3 molecules per oxygen atom) forming a highly symmetric solute-solvent complex, while the remaining six water molecules are more loosely distributed above and below the oxocarbon plane. The structure of a cluster consisting of a dianion and 12 water molecules was then examined through ab initio calculations at the Hartree-Fock 6-31G(d,p) level. The optimized ab initio structure of the cluster is in excellent agreement with the MD results. © 2002 Elsevier Science B.V. All rights reserved.580137145West, R., (1980), Oxocarbons Academic Press, New YorkSeltz, G., Imming, P., (1992) Chem. Rev., 92, p. 1227Tietze, L.F., Schroder, C., Gabius, S., Brinck, U., Goerlach-Graw, A., Gabius, H.-J., (1991) Bioconjugate Chem., 2, p. 148Karle, I.L., Ranganathan, D., Haridas, V., (1996) J. Am. Chem. Soc., 118, p. 7128Pu, L.S., (1991) J. Chem. Soc., Chem. Commun., 6, p. 429Kobayashi, Y., Goto, M., Kurahashi, M., (1986) Bull. Chem. Soc. Jpn., 59, p. 311Zhao, B., Back, M.H., (1991) Can. J. Chem., 69, p. 528Merrit, V.Y., Hovel, H.J., (1978) Appl. Phys. Lett., 29, p. 414Aihara, J., (1981) J. Am. Chem. Soc., 103, p. 1633Puebla, C., Ha, T.-K., (1986) J. Mol. Struct. (Theochem), 137, p. 171Herndon, W.C., (1983) J. Mol. Struct. (Theochem), 103, p. 219Zhou, L., Zhang, Y., Wu, L., Li, J., (2000) J. Mol. Struct. (Theochem), 497, p. 137Schleyer, P.R., Najafian, K., Kiran, B., Jiao, H., (2000) J. Org. Chem., 54, p. 426Quiñonero, D., Frontera, A., Ballester, P., Deyà, P.M., (2000) Tetrahedron Lett., 41, p. 2001West, R., Niu, N.-Y., Powell, D.L., Evans, M.V., (1960) J. Am. Chem. Soc., 826, p. 204Takahasi, M., Kaya, K., Ito, M., (1978) Chem. Phys., 35, p. 293Santos, P.S., Sala, O., Noda, L.K., Gonçalves, N.S., (2000) Spectrochim. Acta A, 56, p. 1553Ito, M., West, R., (1963) J. Am. Chem. Soc., 85, p. 2580MacIntyre, W.M., Wekerma, M.S., (1964) J. Chem. Phys., 40, p. 3563Semmingsen, D., (1976) Acta Chem. Scand., 30, p. 808Ribeiro, M.C.C., De Oliveira, L.F.C., Santos, P.S., (1997) Chem. Phys., 217, p. 71Berendsen, H.J.C., Grigera, J.R., Straatsma, T.P., (1987) J. Phys. Chem., 91, p. 6269Allen, M.P., Tildesley, D.J., (1987) Computer Simulations of Liquids, , Oxford University Press, Clarendon ParkJorgensen, W.L., Severence, D.L., (1990) J. Am. Chem. Soc., 112, p. 4768Frisch, M.J., Trucks, G.W., Schlegel, H.B., Gill, P.M.W., Johnson, B.G., Robb, M.A., Cheeseman, J.R., Pople, J.A., (1995) GAUSSIAN94, Revision D.2., , Gaussian, Inc., Pittsburgh, PALadanyi, B.M., Skaf, M.S., (1993) Annu. Rev. Phys. Chem., 44, p. 335Ohtaki, H., Radnai, T., (1993) Chem. Rev., 93, p. 1157Schaftenaar, G., Noordik, J.H., (2000) J. Comp.-Aided Mol. Des., 14, p. 123Bader, R.F.W., (1990) Atoms in Molecules: A Quantum Theory, , Oxford University Press, OxfordSingh, U.C., Kollman, P.A., (1984) J. Comp. Chem., 5, p. 129Breneman, C.M., Wiberg, K.B., (1990) J. Comp. Chem., 11, p. 361Cerioni, G., Janoschek, R., Rappoport, Z., Tidwell, T.T., (1996) J. Org. Chem., 61, p. 621
On using Directional Information for Parameter Space Decomposition in Ellipse Detection
No full textIn this paper we use the parametric polar representation to extend the application of edge directional information from circle to ellipse extraction. As a result we obtain a mapping which decomposes the parameter space required for ellipse extraction into two independent sub-spaces and one final histogram accumulator. The mapping includes the tangent of the angle of the first and second directional derivatives. These tangents are computed by considering edge direction at two border points. We show that the use of gradient information for parameter space decomposition avoids the intensive point labelling imposed by geometric constraints used by other approaches
Solvatipn Of Excess Electrons In Supercritical Ammonia
No full textSolvation of excess electrons in supercritical ammonia along the T = 450 K isotherm was investigated. Equilibrium aspects of solvation were analyzed using combined path integral-molecular dynamics techniques. Observations showed transition from localized to quasifree states at approximately one fourth of the triple point density.1191260446052Innovations in Supercritical Fluids, Science, and Technology (1995) ACS Symposium Series, 608. , edited by K. W. Hutchenson and N. R. Foster (American Chemical Society, Washington, D.C.)Me Hugh, M.A., Krukonis, V.J., (1986) Supercritical Fluid Extraction: Principles and Practice, , Butterworths, BostonKim, S., Johnston, K.P., (1987) ACS Symposium Series, 329. , Supercritical Fluids, Chemical, and Engineering Principles and Applications, edited by T. G. Squires and M. E. Paulatis (American Chemical Society, Washington, D.C.)Kim, S., Johnston, K.P., (1987) Ind. Eng. Chem. Res., 26, p. 1206Bennet, G.E., Johnston, K.P., (1994) J. Phys. Chem., 98, p. 441Peck, D.G., Mehta, A.J., Johnston, K.P., (1989) J. Phys. Chem., 93, p. 4297Johnston, K.P., Haynes, C., (1987) AIChE J., 33, p. 2017Giraud, V., Krebs, P., (1982) Chem. Phys. Lett., 86, p. 85Krebs, P., Hientze, M., (1982) J. Chem. Phys., 76, p. 5484Jou, F.-Y., Freeman, G.R., (1981) J. Phys. Chem., 85, p. 629Olinger, R., Schinderwolf, U., Gaathon, A., Jortner, J., (1971) Ber. Bunsenges. Phys. Chem., 75, p. 690Olinger, R., Hahne, S., Schinderwolf, U., (1972) Ber. Bunsenges. Phys. Chem., 76, p. 349Migus, A., Gaudel, Y., Martin, J.L., Antonetti, A., (1987) Phys. Rev. Lett., 58, p. 1559Long, F.H., Lu, H., Shi, X., Eisenthal, K.B., (1991) Chem. Phys. Lett., 185, p. 47Alfano, J.C., Walhout, P.K., Kimura, Y., Barbara, P.F., (1993) J. Chem. Phys., 98, p. 5996Kimura, Y., Alfano, J.C., Walhout, P.K., Barbara, P.F., (1994) J. Phys. Chem., 98, p. 3450Jahnke, J.A., Meyer, L., Rice, S.A., (1971) Phys. Rev. A, 3, p. 734Huang, S.S.S., Freeman, G.R., (1978) J. Chem. Phys., 68, p. 1355Floriane, M.A., Freeman, G.R., (1986) J. Chem. Phys., 85, p. 1603Coker, D.F., Berne, B.J., Thirumalai, D., (1987) J. Chem. Phys., 86, p. 5689Laria, D., Chandler, D., (1987) J. Chem. Phys., 87, p. 4088Space, B., Coker, D.F., Liu, Z.H., Berne, B.J., Martyna, G., (1992) J. Chem. Phys., 97, p. 2002Plenkiewicz, B., Frongillo, Y., Lopez-Castillo, J.-M., Jay-Gerin, J.-P., (1996) J. Chem. Phys., 104, p. 9053Lopez-Castillo, J.-M., Frongillo, Y., Plenkiewicz, B., Jay-Gerin, J.-P., (1992) J. Chem. Phys., 96, p. 9092Krebs, P., (1980) Chem. Phys. Lett., 70, p. 465Krebs, P., Giraud, V., Wantschick, M., (1980) Phys. Rev. Lett., 44, p. 211Sprik, M., Impey, R.W., Klein, M.L., (1985) J. Chem. Phys., 83, p. 5802Sprik, M., Klein, M.L., (1987) J. Chem. Phys., 87, p. 5987Sprik, M., Klein, M.L., (1988) J. Chem. Phys., 89, p. 1592Sprik, M., Klein, M.L., (1989) J. Chem. Phys., 91, p. 5665Marchi, M., Sprik, M., Klein, M.L., (1988) J. Chem. Phys., 89, p. 4918Barnett, R.N., Landman, U., Cleveland, C.L., Kestner, N.R., Jortner, J., (1988) Chem. Phys. Lett., 148, p. 249Sprik, M., Impey, R.W., Klein, M.L., (1986) Phys. Rev. Lett., 56, p. 2326Martyna, G.J., Klein, M.L., (1992) J. Chem. Phys., 96, p. 7662Laria, D., Skaf, M.S., (2002) J. Phys. Chem. A, 106, p. 8066Gaathon, A., Czapski, G., Jortner, J., (1972) J. Chem. Phys., 58, p. 2648Jortner, J., Gaathon, A., (1977) Can. J. Chem., 55, p. 1801Bausenwein, T., Bertagnolli, H., David, A., Goller, K., Zweier, H., Todheide, K., Chieux, P., (1994) J. Chem. Phys., 101, p. 672Kiselev, M., Kerdcharoen, T., Hannongbua, S., Heizinger, K., (2000) Chem. Phys. Lett., 327, p. 425Feynmann, R.P., (1972) Statistical Mechanics, , Addison-Wesley, ReadingImpey, R.W., Klein, M.L., (1984) Chem. Phys. Lett., 104, p. 579Rudge, M.R.H., (1978) J. Phys. B, 11, p. 1503(1978) J. Phys. B, 11, p. 2221Rudge, M.R.H., (1980) J. Phys. B, 13, p. 1269Jain, A., Thompson, D.G., (1982) J. Phys. B, 15, pp. L631(1983) J. Phys. B, 16, p. 1113(1983) J. Phys. B, 16, p. 2593Gianturco, F.A., (1991) J. Phys. B, 24, p. 4627Chandler, D., Wolynes, P.G., (1981) J. Chem. Phys., 74, p. 4078Tuckerman, M.E., Berne, B.J., Martyna, G.J., Klein, M.L., (1993) J. Chem. Phys., 99, p. 2796Martyna, G.J., Tuckerman, M.E., Tobias, D.J., Klein, M.L., (1996) Mol. Phys., 87, p. 1117Tuckerman, M.E., Hughes, A., Path Integral Molecular Dynamics: A Computational Approach to Quantum Statistical Mechanics (1998) Classical and Quantum Dynamics in Condensed Phase Simulations, , edited by B. J. Berne, G. Ciccotti, and D. F. Coker (World Scientific, Singapore), Chap. 14Ryckaert, J.-P., Ciccotti, G., Berendsen, H.J.C., (1977) J. Comput. Phys., 23, p. 327Webster, F., Rossky, P.J., Friesner, R., (1991) Comput. Phys. Commun., 63, p. 494Staib, A., Borgis, D., (1995) J. Chem. Phys., 103, p. 2642Yang, C.-Y., Wong, K.F., Skaf, M.S., Rossky, P.J., (2001) J. Chem. Phys., 114, p. 3598Schnitker, J., Rossky, P.J., (1987) J. Chem. Phys., 86, p. 3471Buback, M., Harder, W.D., (1977) Ber. Bunsenges. Phys. Chem., 81, p. 603Wallqvist, A., Martyna, G.J., Berne, B.J., (1988) J. Phys. Chem., 92, p. 1721Schwanz, B.J., Rossky, P.J., (1994) J. Phys. Chem., 101, p. 6902Schwartz, B.J., Rossky, P.J., (1994) J. Phys. Chem., 101, p. 6917Rossky, P.J., Nonadiabatic Quantum Dynamics Simulation Using Classical Baths (1998) Classical and Quantum Dynamics in Condensed Phase Simulations, , edited by B. J. Berne, G. Ciccotti, and D. F. Coker (World Scientific, Singapore), Chap. 22Herzberg, G., (1945) Infrared and Roman Spectra of Polyatomic Molecules, , Van Nostrand, PrincetonSchwartz, B.J., Rossky, P.J., (1996) J. Phys. Chem., 105, p. 6997Prezhdo, O.V., Rossky, P.J., (1996) J. Phys. Chem., 100, p. 17094Maroncelli, M., (1993) J. Mol. Liq., 57, p. 1Maroncelli, M., Kumar, P.V., Papazyan, A., (1993) J. Phys. Chem., 97, p. 13noteRe, M., Laria, D., (1997) J. Phys. Chem. A, 101, p. 1049
Large-scale patterns in turbulent Rayleigh-Bénard convection in very large aspect ratio cells
No full textLarge-scale patterns, which are well-known from the spiral defect chaos regime of thermal convection at Rayleigh numbers Ra 105. They are uncovered when the turbulent fields are averaged in time and turbulent fluctuations are thus removed. We apply the Boussinesq closure to calculate turbulent viscosities and diffusivities, respectively. The resulting turbulent Rayleigh number Ra_, that describes the convection of the mean patterns, is indeed in the spiral defect chaos range. Interestingly, the turbulent Prandtl numbers are smaller than one with 0:2 _ Pr_ _ 0:4 for Prandtl numbers 0:7 _ Pr _ 10. Finally, we demonstrate that these mean flow patterns are robust to an additional finite-amplitude side wall-forcing when the level of turbulent fluctuations in the flow is sufficiently high
Reynolds number effect on 3D turbulent offset jet reattaching to a free surface
No full textExperimental study was carried out to investigate the effect of Reynolds number on 3D offset jet reattaching to above free surface. Sharp edged square nozzle was used to produce the jets, and the measurements were performed at the following six different Reynolds numbers: 2300, 3700, 5100, 7900, 10300 and 11900. Detailed velocity measurements were made in the symmetry plane. From the PIV data, the mean velocity and turbulence statistics were obtained to study the effects of Reynolds number on the salient features of the jet flow. Preliminary results on streamwise mean velocity decay along the nozzle centerline, contours of streamwise mean velocity and Reynolds shear stress are presented herein
The Benefits of Being Economics Professor A (and not Z)
No full textAlphabetic name ordering on multi-authored academic papers, which is the convention in the economics discipline and various other disciplines, is to the advantage of people whose last name initials are placed early in the alphabet. As it turns out, Professor A, who has been a first author more often than Professor Z, will have published more articles and experienced afaster growth rate over the course of her career as a result of reputation and visibility. Moreover, authors know that name ordering matters and indeed take ordering seriously: Several characteristics of an author group composition determine the decision to deviate from the default alphabetic name order to a significant extent.performance measurement, incentives, economists, name ordering
<i>Entrenchment, wealth, power, and the constitution of democratic societies</i> by Paul Starr
No full textEntrenchment, Wealth, Power, and the Constitution of Democratic Societies, by Paul Starr, New Haven, CT: Yale University Press. 2019. 280 pages, hardcover.Why should we, as Management scholars and educators, care about a book on political diagnosis? The answer is twofold. First, the calibre of the author (Paul Starr), an awardee of both Bancroft and Pulitzer Prizes, a former policy advisor to the Clinton administration, and the author of The Transformation of American Medicine (1982), a book with a profound impact on American policy circles. Second, the core concept (entrenchment) of the book, and its potential to advance the process of institutional development, and the ways in which we can reform and change our institutions to better meet the current and pressing needs of the many, rather than preserve the unequal privileges of a few. In light of the geopolitical, social, and environmental pressures we see currently rising across the world (George, Howard-Grenville, Joshi & Tihanyi, 2016; Howard-Grenville, Buckle, Hoskins & George, 2014) there is no better time to examine whether and how we can address some of these grand challenges by reforming and improving our institutions
Identification Of A New Hormone-binding Site On The Surface Of Thyroid Hormone Receptor
No full textThyroid hormone receptors (TRs) are members of the nuclear receptor superfamily of ligand-activated transcription factors involved in cell differentiation, growth, and homeostasis. Although X-ray structures of many nuclear receptor ligand-binding domains (LBDs) reveal that the ligand binds within the hydrophobic core of the ligand-binding pocket, a few studies suggest the possibility of ligands binding to other sites. Here, we report a new x-ray crystallographic structure of TR-LBD that shows a second binding site for T3 and T4 located between H9, H10, and H11 of the TRα LBD surface. Statistical multiple sequence analysis, site-directed mutagenesis, and cell transactivation assays indicate that residues of the second binding site could be important for the TR function. We also conducted molecular dynamics simulations to investigate ligand mobility and ligand-protein interaction for T3 and T4 bound to this new TR surface-binding site. Extensive molecular dynamics simulations designed to compute ligand-protein dissociation constant indicate that the binding affinities to this surface site are of the order of the plasma and intracellular concentrations of the thyroid hormones, suggesting that ligands may bind to this new binding site under physiological conditions. Therefore, the second binding site could be useful as a new target site for drug design and could modulate selectively TR functions. © 2014 by the Endocrine Society.284534545Yen, P., Physiological and molecular basis of thyroid hormone action (2001) Physiol Rev, 81, pp. 1097-10142Ribeiro, R.C., Kushner, P.J., Baxter, J.D., The nuclear hormone receptor gene superfamily (1995) Annu Rev Med, 46, pp. 443-453Lazar, M.A., Chin, W.W., Nuclear thyroid hormone receptors (1990) J Clin Invest, 86, pp. 1777-1782Wagner, R., Huber, B., Shiau, A., Hormone selectivity in thyroid hormone receptors (2001) Mol Endocrinol, 15, pp. 398-410Sandler, B., Webb, P., Apriletti, J., Thyroxine-thyroid hormone receptor interactions (2004) J Biol Chem, 279, pp. 55801-55808Blange, I., Drvota, V., Yen, P.M., Sylven, C., Species differences in cardiac thyroid hormone receptor isoforms protein abundance (1997) Biol Pharm Bull, 20, pp. 1123-1126Schwartz, H.L., Strait, K.A., Ling, N.C., Oppenheimer, J.H., Quantitation of rat tissue thyroid hormone binding receptor isoforms by immunoprecipitation of nuclear triiodothyronine binding capacity (1992) J Biol Chem, 267, pp. 11794-11799Martínez, L., Nascimento, A.S., Nunes, F.M., Gaining ligand selectivity in thyroid hormone receptors via entropy (2009) Proc Natl Acad Sci USA, 106, pp. 20717-20722Bleicher, L., Aparicio, R., Nunes, F., Structural basis of GC-1 selectivity for thyroid hormone receptor isoforms (2008) BMCStruct Biol, 8, p. 8Gauthier, K., Chassande, O., Plateroti, M., Different functions for the thyroid hormone receptors TRα and TRα in the control of thyroid hormone production and post-natal development (1999) EMBO J, 18, pp. 623-631Johansson, C., Vennström, B., Thorén, P., Evidence that decreased heart rate in thyroid hormone receptor-α1-deficient mice is an intrinsic defect (1998) Am J Physiol, 275, pp. R640-R646Weatherman, R.V., Fletterick, R.J., Scanlan, T.S., Nuclear-receptor ligands and ligand-binding domains (1999) Annu Rev Biochem, 68, pp. 559-5581Webb, P., Nguyen, N.H., Chiellini, G., Design of thyroid hormone receptor antagonists from first principles (2002) J Steroid Biochem Mol Biol, 83, pp. 59-73Cunha Lima, S.T., Nguyen, N.H., Togashi, M., Differential effects of TR ligands on hormone dissociation rates: Evidence for multiple ligand entry/exit pathways (2009) J Steroid Biochem Mol Biol, 117, pp. 125-131Perakyla, M., Ligand unbinding pathways from the vitamin D receptor studied by molecular dynamics simulations (2009) Eur Biophys J, 38, pp. 185-198Sonoda, M.T., Martínez, L., Webb, P., Skaf, M.S., Polikarpov, I., Ligand dissociation from estrogen receptor is mediated by receptor dimerization: Evidence from molecular dynamics simulations (2008) Mol Endocrinol, 22, pp. 1565-1578Martínez, L., Polikarpov, I., Skaf, M.S., Only subtle protein conformational adaptations are required for ligand binding to thyroid hormone receptors: Simulations using a novel multipoint steered mo lecular dynamics approach (2008) J Phys Chem B, 112, pp. 10741-10751Genest, D., Garnier, N., Arrault, A., Marot, C., Morin-Allory, L., Genest, M., Ligand-escape pathways from the ligand-binding domain of PPARγ receptor as probed by molecular dynamics simulations (2008) Eur Biophys J, 37, pp. 369-379Carlsson, P., Burendahl, S., Nilsson, L., Unbinding of retinoic acid from the retinoic acid receptor by random expulsion molecular dynamics (2006) Biophys J, 91, pp. 3151-3161Martínez, L., Webb, P., Polikarpov, I., Skaf, M.S., Molecular dynamics simulations of ligand dissociation from thyroid hormone receptors: Evidence of the likeliest escape pathway and its implications for the design of novel ligands (2006) J Med Chem, 49, pp. 23-26Martínez, L., Sonoda, M.T., Webb, P., Baxter, J.D., Skaf, M.S., Polikarpov, I., Molecular dynamics simulations reveal multiple pathways of ligand dissociation from thyroid hormone receptors (2005) Biophys J, 89, pp. 2011-2023Moras, D., Gronemeyer, H., The nuclear receptor ligand-binding domain: Structure and function (1998) Curr Opin Cell Biol, 10, pp. 384-391Glass, C.K., Rosenfeld, M.G., The coregulator exchange in transcriptional functions of nuclear receptors (2000) Genes Dev, 14, pp. 121-141Nichols, M., Rientjes, J.M., Stewart, A.F., Different positioning of the ligand-binding domain helix 12 and the F domain of the estrogen receptor accounts for functional differences between agonists and antagonists (1998) EMBO J, 17, pp. 765-773Brzozowski, A.M., Pike, A.C., Dauter, Z., Molecular basis of agonism and antagonism in the oestrogen receptor (1997) Nature, 389, pp. 753-758Figueira, A.C., Saidemberg, D.M., Souza, P.C., Analysis of agonist and antagonist effects on thyroid hormone receptor conformation by hydrogen/deuterium exchange (2011) Mol Endocrinol, 25, pp. 15-31Wang, Y., Chirgadze, N.Y., Briggs, S.L., Khan, S., Jensen, E.V., Burris, T.P., A second binding site for hydroxytamoxifen within the coactivatorbinding groove of estrogen receptor beta (2006) Proc Natl Acad Sci U S A, 103, pp. 9908-9911Hedden, A., Müller, V., Jensen, E., A new interpretation of antiestrogen action (1995) Ann NY Acad Sci, 761, pp. 109-120Jensen, E.V., Khan, S.A., A two-site model for antiestrogen action (2004) Mech Ageing Dev, 125, pp. 679-682Estébanez-Perpiñá, E., Arnold, L.A., Nguyen, P., A surface on the androgen receptor that allosterically regulates coactivator binding (2007) Proc Natl Acad Sci USA, 104, pp. 16074-16079Lack, N.A., Axerio-Cilies, P., Tavassoli, P., Targeting the binding function 3 (BF3) site of the human androgen receptor through virtual screening (2011) J Med Chem, 54, pp. 8563-8573Munuganti, R.S., Leblanc, E., Axerio-Cilies, P., Targeting the binding function 3 (BF3) site of the androgen receptor through virtual screening. 2. Development of 2-(2-phenoxyethyl) thio)-1Hbenzimidazole derivatives (2013) J Med Chem, 56, pp. 1136-1148Mizwicki, M.T., Keidel, D., Bula, C.M., Identification of an alternative ligand-binding pocket in the nuclear vitamin D receptor and its functional importance in 1alpha, 25(OH)2-vitamin D3 signaling (2004) Proc Natl Acad Sci U S A, 101, pp. 12876-12881Bernardes, A., Souza, P.C., Muniz, J.R., Molecular mechanism of peroxisome proliferator-activated receptor α activation by WY14643: A new mode of ligand recognition and receptor stabilization (2013) J Mol Biol, 425, pp. 2878-2893Puhl, A.C., Bernardes, A., Silveira, R.L., Mode of peroxisome proliferator-activated receptor γ activation by luteolin (2012) Mol Pharmacol, 81, pp. 788-799Liberato, M.V., Nascimento, A.S., Ayers, S.D., Medium chain fatty acids are selective peroxisome proliferator activated receptor (PPAR) activators and Pan-PPAR partial agonists (2012) Plos One, 7, pp. e36297Itoh, T., Fairall, L., Amin, K., Structural basis for the activation of PPAR by oxidized fatty acids (2008) Nat Struct Mol Biol, 15, pp. 924-931Ambrosio, A.L., Dias, S.M., Polikarpov, I., Zurier, R.B., Burstein, S.H., Garratt, R.C., Ajulemic acid, a synthetic nonpsychoactive cannabinoid acid, bound to the ligand binding domain of the human peroxisome proliferator-activated receptor γ (2007) J Biol Chem, 282, pp. 18625-18633Estébanez-Perpiñá, E., Arnold, L.A., Jouravel, N., Structural insight into the mode of action of a direct inhibitor of coregulator binding to the thyroid hormone receptor (2007) Mol Endocrinol, 21, pp. 2919-2928Hwang, J.Y., Arnold, L.A., Zhu, F., Improvement of pharmacological properties of irreversible thyroid receptor coactivator binding inhibitors (2009) J Med Chem, 52, pp. 3892-3901Hwang, J.Y., Attia, R.R., Carrillo, A.K., Connelly, M.C., Guy, R.K., Synthesis and evaluation of methylsulfonylnitrobenzamides (MSNBAs) as inhibitors of the thyroid hormone receptor-coactivator interaction (2013) Bioorg Med Chem Lett, 23, pp. 1891-1895Nunes, F.M., Aparício, R., Santos, M.A., Crystallization and preliminary X-ray diffraction studies of isoform α1 of the human thyroid hormone receptor ligand-binding domain (2004) Acta Crystallogr D Biol Crystallogr, 60, pp. 1867-1870Otwinowski, Z., Minor, W., Processing of x-ray diffraction data collected in oscillation mode (1997) Methods Enzymol, 276, pp. 307-326Navaza, J., Implementation of molecular replacement in AMoRe (2001) Acta Crystallogr D Biol Crystallogr, 57, pp. 1367-1372Adams, P.D., Afonine, P.V., Bunkóczi, G., PHENIX: A comprehensive Python-based system for macromolecular structure solution (2010) Acta Crystallogr D, 66, pp. 213-221Murshudov, G., Vagin, A., Dodson, E., Refinement of macromolecular structures by the maximum-likelihood method (1997) Acta Crystallogr D Biol. Crystallogr, 53, pp. 240-255Emsley, P., Cowtan, K., Coot: Model-building tools for molecular graphics (2004) Acta Crystallogr D Biol Crystallogr, 60, pp. 2126-2132Waterhouse, A.M., Procter, J.B., Martin, D.M., Clamp, M., Barton, G.J., Jalview Version 2-a multiple sequence alignment editor and analysis workbench (2009) Bioinformatics, 25, pp. 1189-1191Lockless, S.W., Ranganathan, R., Evolutionarily conserved pathways of energetic connectivity in protein families (1999) Science, 286, pp. 295-299Süel, G.M., Lockless, S.W., Wall, M.A., Ranganathan, R., Evolutionarily conserved networks of residues mediate allosteric communication in proteins (2003) Nature Struct Biol, 10, pp. 59-69Feng, W., Ribeiro, R.C., Wagner, R.L., Hormone-dependent coactivator binding to a hydrophobic cleft on nuclear receptors (1998) Science, 280, pp. 1747-1749Martínez, L., Andrade, R., Birgin, E.G., Martínez, J.M., PACKMOL: A package for building initial configurations for molecular dynamics simulations (2009) J Comput Chem, 30, pp. 2157-2164Martínez, J.M., Martínez, L., Packing optimization for automated generation of complex system's initial configurations for molecular dynamics and docking (2003) J Comput Chem, 24, pp. 819-825Verlet, L., Computer experiments on classical fluids. I Thermodinamical properties of Lennard-Jones molecules (1967) Phys Rev, 159, pp. 98-103Darden, T., York, D., Pedersen, L., Particle Mesh Ewald: An Nlog(N) method for Ewald sums in large systems (1993) J Chem Phys, 98, pp. 10089-10092Phillips, J.C., Braun, R., Wang, W., Scalable molecular dynamics with NAMD (2005) J Comput Chem, 26, pp. 1781-1802McKerell Jr., A.D., Bashford, D., Bellott, M., All-atom empirical potential for molecular modeling and dynamics studies of proteins (1998) J Phys Chem B, 102, pp. 3586-3616Jorgensen, W.L., Chandrasekhar, J., Madura, J.D., Impey, R.W., Klein, M.L., Comparison of simple potential functions for simulating liquid water (1983) J Chem Phys, 79, pp. 926-935Duggan, B.M., Craik, D.J., Conformational dynamics of thyroid hormones by variable temperature nuclear magnetic resonance: The role of side chain rotations and cisoid/transoid interconversions (1997) J Med Chem, 40, pp. 2259-2265Duggan, B.M., Craik, D.J., 1H and 13C NMR relaxation studies of molecular dynamics of the thyroid hormones thyroxine, 3, 5, 3-triiodothyronine, and 3, 5-diiodothyronine (1996) J Med Chem, 39, pp. 4007-4016Hansson, A.O., Souza, P.C.T., Silveira, R.L., Martínez, L., Skaf, M.S., CHARMM force field parameterization of rosiglitazone (2011) Int J Quantum Chem, 111, pp. 1346-1354Prates, E.T., Souza, P.C.T., Pickholz, M., Skaf, M.S., CHARMM based parameterization of neutral articaine-a widely used local anesthesic (2011) Intern J Quantum Chem, 111, pp. 1339-1345Hénin, J., Fiorin, J., Chipot, C., Klein, M.L., Exploring multidimensional free energy landscapes using time-dependent biases on collective variables (2010) J Chem Theory Comput, 6, pp. 35-47Hénin, J., Chipot, C., Overcoming free energy barriers using unconstrained molecular dynamics simulations (2004) J Chem Phys, 121, pp. 2904-2914Chipot, C., Hénin, J., Exploring the free-energy landscape of a short peptide using an average force (2005) J Chem Phys, 123, p. 244906Nascimento, A.S., Dias, S.M., Nunes, F.M., Structural rearrangements in the thyroid hormone receptor hinge domain and their putative role in the receptor function (2006) J Mol Biol, 360, pp. 586-598Wagner, R.L., Apriletti, J.W., McGrath, M.E., West, B.L., Baxter, J.D., Fletterick, R.J., A structural role for hormone in the thyroid hormone receptor (1995) Nature, 378, pp. 690-697Borngraeber, S., Budny, M.J., Chiellini, G., Ligand selectivity by seeking hydrophobicity in thyroid hormone receptor (2003) Proc Natl Acad Sci USA, 100, pp. 15358-15363Escobar-Morreale, H.F., Obregón, M.J., Escobar del Rey, F., Morreale de Escobar, G., Replacement therapy for hypothyroidism with thyroxine alone does not ensure euthyroidism in all tissues, as studied in thyroidectomized rats (1995) J Clin Invest, 96, pp. 2828-2838Trost, S.U., Swanson, E., Gloss, B., The thyroid hormone receptor-β-selective agonist GC-1 differentially affects plasma lipids and cardiac activity (2000) Endocrinology, 141, pp. 3057-3064Oppenheimer, J.H., Schwartz, H.L., Stereospecific transport of triiodothyronine from plasma to cytosol and from cytosol to nucleus in rat liver, kidney, brain, and heart (1985) J Clin Invest, 75, pp. 147-154Shahrara, S., Drvota, V., Sylvén, C., Organ specific expression of thyroid hormone receptor mRNA and protein in different human tissues (1999) Biol Pharm Bull, 22, pp. 1027-1033Souza, P.C., Barra, G.B., Velasco, L.F., Helix 12 dynamics and thyroid hormone receptor activity: Experimental and molecular dynamics studies of Ile280 mutants (2011) J Mol Biol, 412, pp. 882-893Marimuthu, A., Feng, W., Tagami, T., TR surfaces and conformations required to bind nuclear receptor corepressor (2002) Mol Endocrinol, 16, pp. 271-286Togashi, M., Nguyen, P., Fletterick, R., Baxter, J.D., Webb, P., Rearrangements in thyroid hormone receptor charge clusters that stabilize bound 3, 5, 5-triiodo-L-thyronine and inhibit homodimer formation (2005) J Biol Chem, 280, pp. 25665-25673Ribeiro, R.C., Feng, W., Wagner, R.L., Definition of the surface in the thyroid hormone receptor ligand binding domain for association as homodimers and heterodimers with retinoid X receptor (2001) J Biol Chem, 276, pp. 14987-14995de Araujo, A.S., Martínez, L., de Paula Nicoluci, R., Skaf, M.S., Polikarpov, I., Structural modeling of high-affinity thyroid receptor-ligand complexes (2010) Eur Biophys J, 39, pp. 1523-1536Takayama, S., Hostick, U., Haendel, M., Eisen, J., Darimont, B., An F-domain introduced by alternative splicing regulates activity of the zebrafish thyroid hormone receptor α (2008) Gen Comp Endocrinol, 155, pp. 176-18
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