27 research outputs found
Prediction Of Ordered Phases Of Encapsulated C60, C 70, And C78 Inside Carbon Nanotubes
No full textWe report the first detailed fully atomistic molecular dynamics study of the encapsulation of symmetric (C60) and asymmetric fullerenes (C70 and C78) inside single-walled carbon nanotubes of different diameters. Different ordered phases have been found and shown to be tube diameter dependent. Rotational structural disorder significantly affecting the volume fraction of the packing was observed for the molecular arrangements of asymmetric fullerenes. Although these effects make more difficult the existence of ordered phases, our results showed that complex packing arrangements (very similar to the ones obtained for C60) are also possible for C70 and C78. Comparisons with results from continuum and hard-sphere models, ab initio electronic structure calculations, and simulations of the high-resolution transmission electron microscopy images of the obtained fullerene packing phases are also presented. © 2005 American Chemical Society.52349355Smith, B.W., Monthioux, M., Luzzi, D.E., (1998) Nature, 396, p. 323Berber, S., Kwon, Y.-K., Tománek, D., (2002) Phys. Rev. Lett., 88, p. 185502Zhang, Z.X., Pan, Z.Y., Wei, Q., Li, Z.J., Zang, L.K., Wang, Y.X., (2003) Int. J. Mod. Phys. B, 17, p. 4667Hirahara, K., Bandow, S., Suenaga, K., Sato, H., Okazaki, T., Shinohara, H., Iijima, S., (2001) Phys. Rev. B, 64, p. 115420Okada, S., Saito, S., Oshiyama, A., (2001) Phys. Rev. Lett., 86, p. 3835Pickett, G., Gross, M., Okuyama, H., (2000) Phys. Rev. Lett., 85, p. 3652Hodak, M., Girifalco, L.A., (2003) Phys. Rev. B, 67, p. 075419Hodak, M., Girifalco, L.A., (2003) Phys. Rev. B, 68, p. 085405Khlobystov, A., Britz, D.A., Ardavan, A., Briggs, G.A.D., (2004) Phys. Rev. Lett., 92, p. 245507Mickelson, W., Aloni, S., Han, W.-Q., Cumings, J., Zettl, A., (2003) Science, 300, p. 467Rappé, A.K., Casewit, C.J., Colwell, K.S., Goddard III, W.A., Skiff, W.M., (1992) J. Am. Chetn. Soc., 114, p. 10024Root, D., Landis, C., Cleveland, T., (1993) J. Am. Chem. Soc., 115, p. 4201www.accelrys.comLegoas, S.B., Coluci, V.R., Braga, S.F., Coura, P.Z., Dantas, S.O., Galvão, D.S., (2003) Phys. Rev. Lett., 90, p. 055504Legoas, S.B., Coluci, V.R., Braga, S.F., Coura, P.Z., Dantas, S.O., Galvão, D.S., (2004) Nanotechnology, 15, pp. S184Braga, S.F., Coluci, V.R., Legoas, S.B., Giro, R., Galvão, D.S., Baughman, R.H., (2004) Nano Lett., 4, p. 881Cioslowski, J., (1995) Electronic Structure Calculations on Fullerenes and Their Derivatives, , Oxford University Press: New YorkSoler, J., Artacho, E., Gale, J.D., Garcia, A., Junquera, J., Ordejon, P., Sanchez-Portal, D., (2002) J. Phys.: Condens. Matter, 14, p. 2745Perdew, J.P., Burke, K., Ernzerhof, M., (1996) Phys. Rev. Lett., 77, p. 3865Troullier, N., Martins, J.L., (1991) Phys. Rev. B, 43, p. 1993Kleinman, L., Bylander, D.M., (1982) Phys. Rev. Lett., 48, p. 1425noteArtacho, E., Sanchez-Portal, D., Ordejon, P., Garcia, A., Soler, J.M., (1999) Phys. Status Solidi B, 215, p. 809Otani, M., Okada, S., Oshiyama, A., (2003) Phys. Rev. B, 68, p. 125424Saito, R., Dresselhaus, G., Dresselhaus, M.S., (1999) Physical Properties of Carbon Nanotubes, , Imperial College Press: LondonBritz, D.A., Khlobystov, A.N., Wang, J., O'Neil, A.S., Poliakoff, M., Ardavan, A., Briggs, G.A.D., (2004) Chem. Commun., p. 17
Dynamics Of Graphene Nanodrums
No full textRecently, it was proposed that graphene sheets deposited on silicon oxide can act as impermeable atomic membranes to standard gases, such as helium, argon, and nitrogen. It is assumed that graphene membrane is clamped over the surface due only to van der Waals forces. The leakage mechanism can be experimentally addressed only indirectly. In this work we have carried out molecular dynamics simulations to study this problem. We have considered nano-containers composed of a chamber of silicon oxide filled with gas and sealed by single and multi-layer graphene membranes. The obtained results are in good qualitative agreement with the experimental data. We observed that the graphene membranes remain attached to the substrate for pressure values up to two times the largest value experimentally investigated. We did not observe any gas leakage through the membrane/substrate interface until the critical limit is reached and then a sudden membrane detachment occurs. © 2011 Materials Research Society.1284173178Novoselov, K.S., Geim, A.K., Morozov, S.V., Jiang, D., Zhang, Y., Dubonos, S.V., Grigorieva, I.V., Firsov, A.A., (2004) Science, 306, p. 666Frank, I.W., Tanenbaum, D.M., Van Der Zande, A.M., McEuen, P.L., (2007) J. Vac. Sci. Technol. B, 25, p. 2558Faccio, R., Denis, P.A., Pardo, H., Goyenola, C., Mombrú, A.W., (2009) J. Phys.: Condens. Matt., 21, p. 285304Geim, A.K., Novoselov, K.S., (2007) Nature Materials, 6, p. 183Cadelano, E., Palla, P.L., Giordano, S., Colombo, L., (2009) Phys. Rev. Lett., 102, p. 235502Lee, C., Wei, X., Kysar, J.W., Hone, J., (2008) Science, 321, p. 385Bunch, J.S., Verbridge, S.S., Alden, J.S., Van Der Zande, A.M., Parpia, J.M., Craighead, H.G., McEuen, P.L., (2008) Nano Lett., 8, pp. 2458-2462MacKerell, A.D., Bashford, D., Bellot, M., Dunbrack, R.L., Evanseck, J., Field, M.J., Fischer, S., Karplus, M., (1998) J. Phys. Chem. B, 102, p. 3586Phillips, J.C., Braun, R., Wang, W., Gumbart, J., Tajkhorshid, E., Villa, E., Chipot, C., Schulten, K., (2005) J. Comput. Chem., 26, p. 1781. , http://www.ks.uiuc.edu/Research/namd/, NAMDStone, J.E., Phillips, J.C., Freddolino, P.L., Hardy, D.J., Trabuco, L.G., Schulten, K., (2007) J. Comput. Chem., 28, p. 2618Brunetto, G., Legoas, S.B., Coluci, V.R., Lucena, L.S., Galvao, D.S., to be publishe
Carcinogenic Classification Of Polycyclic Aromatic Hydrocarbons Through Theoretical Descriptors
No full textPolycyclic aromatic hydrocarbons (PAHs) constitute an important family of molecules capable of inducing chemical carcinogenesis. In this work we report a comparative structure-activity relationship (SAR) study for 81 PAHs using different methodologies. The recently developed electronic indices methodology (EIM) with quantum descriptors obtained from different semiempirical methods (AM1, PM3, and PM5) was contrasted against more standard pattern recognition methods (PRMs), principal component analysis (PCA), hierarchical cluster analysis (HCA), Kth nearest neighbor (KNN), soft independent modeling of class analogies (SIMCA), and neural networks (NN). Our results show that PRMs validate the statistical value of electronic parameters derived from EIM analysis and their ability to identify active compounds. EIM outperformed more standard SAR methodologies and does not appear to be significantly Hamiltonian-dependent. © 2005 Wiley Periodicals, Inc.1035718730Jeringa, D.M., Sayer, J.M., Thakker, D.R., Yagi, H., Levin, W., Wood, A.W., Conney, A.H., (1980) Carcinogenesis: Fundamental Mechanisms and Environmental Effects, , Pullman, B.Ts'o, P. O. P.Gelboin, H., Eds.D. Reidel Publishing: Dordrecht, The NetherlandsGoves, H.A.J., (1990) Practical Applications of Quantitative Structure-activity Relationships (QSAR) in Environmental Chemistry and Toxicology, p. 411. , Karcher, W.Devilers, J., Eds.Kluwer Academic Publishers: Dordrecht, The NetherlandsHarvey, R.G., Geacintov, N.E., (1988) Ace Chem Res, 21, p. 66Pullman, A., Pullman, B., (1955) Adv Cancer Res, 3, p. 117Gayoso, J., Kimri, S., (1990) Int J Quantum Chem, 38, p. 461Gayoso, J., Kimri, S., (1990) Int J Quantum Chem, 38, p. 487Nordén, U.E., Svante, W., (1978) Acta Chem Scand, B32, p. 602Villemin, D., Cherqaoui, D., Mesbah, A., (1994) J Chem Inf Comput Sci, 34, p. 1288Song, X.H., Xiao, M., Yu, R.Q., (1994) Comput Chem, 18, p. 391Barone, P.M.V.B., Camilo Jr., A., Galvão, D.S., (1996) Phys Rev Lett, 77, p. 1186Braga, R.S., Barone, P.M.V.B., Galvão, D.S., (1999) J Mol Struct (Theochem), 464, p. 257Vendrame, R., Braga, R.S., Takahata, Y., Galvão, D.S., (1999) J Chem Inf Comput Sci, 39, p. 1094Vendrame, R., Braga, R.S., Takahata, Y., Galvão, D.S., (2001) J Mol Struct (Theochem), 539, p. 253Coluci, V.R., Vendrame, R., Braga, R.S., Galvão, D.S., (2002) J Chem Inf Comput Sci, 42, p. 1479Santo, L.L.E., Galvão, D.S., (1999) J Mol Struct (Theochem), 464, p. 273Vendrame, R., Coluci, V.R., Braga, R.S., Galvão, D.S., (2002) J Mol Struct (Theochem), 619, p. 195Braga, R.S., Vendrame, R., Galvão, D.S., (2000) J Chem Inf Comput Sci, 40, p. 1377Cyrillo, M., Galvão, D.S., (1999) J Mol Struct (Theochem), 464, p. 267Braga, S.F., Galvão, D.S., (2003) J Chem Inf Comput Sci, 43, p. 699Cavalieri, E.L., Rogan, E.G., Roth, R.W., Saugier, R.K., Hakan, A., (1983) Chem Biol Interact, 47, p. 87Dewar, M.J.S., Zoebisch, E.G., Healy, E.F., Stewart, J.J.P., (1985) J Am Chem Soc, 107, p. 3902Stewart, J.J.P., (1989) J Comput Chem, 10, p. 209Stewart, J.J.P., (1989) J Comput Chem, 10, p. 221MOPAC Program, Version 6.0, , http://qcpe.chem.indiana.edu, Quantum Chemistry Program Exchange No. 455Cyrillo, M., Galvão, D.S., (1999) EPA Newslett, 67 (31), p. 34. , http://www.ifi.unicamp.br/gsonm/chem2pachttp:www.CACheSoftware.com, CAChe 5.0, 2000-2001 Fujitsu: JapanBraga, S.F., Galvão, D.S., Barone, P.M.V.B., Dantas, S.O., (2001) J Phys Chem B, 105, p. 8334Braga, S.F., Galvão, D.S., (2002) J Mol Graph Model, 21, p. 57Da'Vila, L.Y.A., Caldas, M.J., (2002) J Comput Chem, 23, p. 1135Hihara, T., Okada, Y., Morita, Z., (2003) Dyes Pigments, 59, p. 25Przybylski, P., Schroeder, G., Brzezinski, B., Bartl, F., (2003) J Phys Org Chem, 16, p. 289Levine, I.N., Quantum Chemistry, 4th Ed., p. 1991. , Prentice-Hall: Englewood Cliffs, NJBarone, P.M.V.B., Braga, R.S., Camilo, A., Galvão, D.S., (2000) J Mol Struct (Theochem), 505, p. 55Naes, T., Baardseth, P., Helgesen, H., Isakson, T., (1996) Meat Sci, 43, pp. s135Hagan, M.T., Demuth, H.B., Beale, M., (1996) Neural Network Design, , PWS Publishing: BostonIchikawa, H., PSDD: Perceptron-type Neural Network Simulator, QCPE, 614. , Indiana University Press: Bloomington, INAoyama, T., Suzuki, Y., Ichikawa, H., (1990) J Med Chem, 33, p. 2583Beebe, K.R., Pell, R.J., Seasholtz, M.B., (1998) Chemometrics a Practical Guide, , John Wiley & Sons: New York;Ferreira, M.M.C., (2002) J Braz Chem Soc, 13, p. 742. , and references thereinMassart, D.L., Vandeginste, B.G.M., Deming, S.N., Michotte, Y., Kaufman, L., Chemometrics: A Textbook, 2, p. 369. , Elsevier: AmsterdamPirouette, (1996) Multivariate Data Analysis for IBM-PC System, Version 2.0, , Infometrix: Seattle, WACoulson, C.A., (1953) Adv Cancer Res, , 1 and references therei
Structural And Electronic Properties Of A Buckycatcher
No full textIn the present work we report preliminary molecular mechanics and molecular dynamics results for the structural and dynamical properties of a recently synthesized new buckycatcher (BCKY). Our results show the existence of three stable conformers with small relative difference energy among them but presenting a high barrier to thermal interconversion. When the C60 is encapsulated the difference energy among the different complexed conformers is increased but a thermal barrier interconversion is now possible. The nature of the electronic interaction between C60 and BCKY is also addressed. © 2009 Materials Research Society.11301318Sygula, A., Fronczek, F.R., Sygula, R., Rabideau, P.W., Olmstead, M.M., (2007) J. Am. Chem. Soc., 129, p. 3842Klärner, F.G., Kahlert, B., Nellesen, A., Zienau, J., Ochsenfeld, C., Schrader, T., (2006) J. Am. Chem. Soc., 128, p. 4831Xiao, W., Passerone, D., Ruffieux, P., Aït-Mansour, K., Gröning, O., Tosatti, E., Siegel, J.S., Fasel, R., (2008) J. Am. Chem. Soc., 130, p. 4767Nielsen, K.A., Cho, W.-S., Sarova, G.H., Petersen, B.M., Bond, A.D., Becher, J., Jensen, F., Jeppesen, J.O., (2006) Angew. Chem. Int. Ed., 45, p. 6848Klärner, F.G., Kahlert, B., (2003) Acc. Chem. Res., 36CERIUS2 and Materials Studio are Suites of Simulation Packages Available from Accelrys, , http://ww.accelrys.comRappé, A.K., Casewitt, C.J., Colwell, K.S., Goddard III, W.A., Skiff, W.M., (1992) J. Am. Chem. Soc., 114, p. 10024Root, D., Landis, C., Cleveland, T., (1993) J. Am. Chem. Soc., 114, p. 4201Legoas, S.B., Coluci, V.R., Braga, S.F., Coura, P.Z., Dantas, S.O., Galvão, D.S., (2003) Phys. Rev. Lett., 90, p. 055504Otero, R., Hümmelink, F., Sato, F., Legoas, S.B., Thostrup, P., Lágsgaard, E., Stensgaard, I., Besenbacher, F., (2004) Nat. Mat., 3, p. 779Troche, K.S., Coluci, V.R., Braga, S.F., Chinellato, D.D., Sato, F., Legoas, S.B., Rurali, R., Galvão, D.S., (2005) Nano Letters, 5, p. 349Braga, S.F., Coluci, V.R., Legoas, S.B., Giro, R., Galvão, D.S., Baughman, R.H., (2004) Nano Letters, 4, p. 881Voityuk, A.A., Duran, M., (2008) J. Phys. Chem., 112, p. 1672Zhao, Y., G Truhlar, D., (2008) Phys. Chem. Chem. Phys., 10, p. 2813Pérez, E.M., Capodilupo, A.L., Fernández, G., Sánchez, L., Viruela, P.M., Viruela, R., Ortí, E., Martín, N., (2008) Chem. Commun., p. 4567Koch, W., Holthausen, M.C., (2001) A Chemist's Guide to Density Functional Theory, Second Edition, , Wiley-VCH, New YorkFlores, M.Z.S., Sato, F., Galvão, D.S., unpublishe
A Molecular Dynamics Study Of The Rotational Dynamics And Polymerization Of C60 In C60-cubane Crystals
No full textRecently, heteromolecular crystals of fullerene C60 and cubane (C8H8) have been synthesized. For some temperatures the C60 molecules are free to rotate whereas cubanes behave like a static bearing in a so-called rotor-stator phases. In this work we report classical and tight-binding molecular dynamics simulations in order to investigate the rotor-stator dynamics and polymerization processes. Our results show that, for 200 K and 400 K, cubane molecules remain basically fixed, presenting only thermal vibrations within the timescale of our simulations, while C60 fullerenes show rotational motions. Fullerenes perform "free" rotational motions at short times (<s), small amplitude hindered rotational motions (librations) at intermediate times, and rotational diffusive dynamics at long times (>ps). Random copolymerization among cubanes and fullerenes were observed when temperature is increased, leading to the formation of a disordered structure. © 2009 Materials Research Society.11307479Eaton, P.E., (1992) Angew. Chem. Int. Ed. Engl., 31, p. 421Pekker, S., Kováts, É., Oszlányi, G., Bényei, Gy., Klupp, G., Bortel, G., Jalsovszky, I., Faigel, G., (2005) Nature Materials, 4, p. 764Kováts, E., Klupp, G., Jakab, E., Pekker, Á., Kamarás, K., Jalsovszky, I., Pekker, S., (2006) Phys. Stat. Sol. (b), 243, p. 2985Pekker, S., Kováts, É., Oszlányi, G., Gy. Bényei, Klupp, G., Bortel, G., Jalsovszky, I., Faigel, G., (2006) Phys. Stat. Sol. (b), 243, p. 3032Iwasiewicz-Wabnig, A., Sundqvist, B., Kováts, É., Jalsovszky, I., Pekker, S., (2007) Phys. Rev. B, 75, p. 024114MacKerell Jr., A.D., Bashford, D., Bellott, M., Dunbrack Jr., R.L., Evanseck, J.D., Field, M.J., Fischer, S., Karplus, M., (1998) J. Phys. Chem. B, 102, p. 3586Phillips, J.C., Braun, R., Wang, W., Gumbart, J., Tajkhorshid, E., Villa, E., Chipot, C., Schulten, K., (2005) J. Comput. Chem., 26, p. 1781Brünger, A., Brooks, C.B., Karplus, M., (1984) Chem. Phys. Lett., 105, p. 495Frenkel, D., Smit, B., (2002) Understanding Molecular Simulation: From Algorithms to Applications, , Academic Press, San Diego, CAPorezag, D., Frauenheim, T., Kohler, T., Seifert, G., Kaschner, R., (1995) Phys. Rev. B, 51, p. 12947Rurali, R., Hernandez, E., (2003) Comput. Mat. Sci., 28, p. 85Sanz-Serna, J.M., Calvo, M.P., (1995) Numerical Hamiltonian Problems, , Chapman and Hall, New YorkBond, S.D., Leimkuhler, B.J., Laird, B.B., (1999) J. Comput. Phys., 151, p. 114Berne, B.J., Pecora, R., (2000) Dynamic Light Scattering: With Applications to Chemistry, Biology, and Physics, , Dover Publications, Inc. Mineola, New YorkColuci, V.R., Sato, F., Braga, S.F., Skaf, M.S., Galvão, D.S., (2008) J. Chem. Phys., 129, p. 064506Williams, G., (1978) Chem. Soc. Rev., 7, p. 89Li, Z., Anderson, S.L., (2003) J. Phys. Chem. A, 107, p. 1162. , references thereinMartin, H.D., Urbanek, T., Pfohler, P., Walsh, R., (1985) J. Chem. Soc. Chem. Commun., 964Martin, H.D., Urbanek, T., Walsh, R., (1985) J. Am. Chem. Soc., 107, p. 5532Martin, H.D., Pfohler, P., Urbanek, T., Walsh, R., (1983) Chem. Ber., 116, p. 1415Han, S., Yoon, M., Berber, S., Park, N., Osawa, E., Ihm, J., Tománek, D., (2004) Phys. Rev. B, 70, p. 11340
Rotational Dynamics And Polymerization Of C60 In C60 -cubane Crystals: A Molecular Dynamics Study
No full textWe report classical and tight-binding molecular dynamics simulations of the C60 fullerene and cubane molecular crystal in order to investigate the intermolecular dynamics and polymerization processes. Our results show that, for 200 and 400 K, cubane molecules remain basically fixed, presenting only thermal vibrations, while C60 fullerenes show rotational motions. Fullerenes perform "free" rotational motions at short times (1 ps), small amplitude hindered rotational motions (librations) at intermediate times, and rotational diffusive dynamics at long times (10 ps). The mechanisms underlying these dynamics are presented. Random copolymerizations among cubanes and fullerenes were observed when temperature is increased, leading to the formation of a disordered structure. Changes in the radial distribution function and electronic density of states indicate the coexistence of amorphous and crystalline phases. 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Graphyne Nanotubes: New Families Of Carbon Nanotubes
No full textFundamentally new families of carbon single walled nanotubes are proposed. These nanotubes, called graphynes, result from the elongation of covalent interconnections of graphite-based nanotubes by the introduction of yne groups. Similarly to ordinary nanotubes, armchair, zig-zag, and chiral graphyne nanotubes are possible. We present here results for the electronic properties of graphyne based tubes obtained from tight-binding and ab initio density functional methods.739175180Iijima, S., (1991) Nature (London), 354, p. 56Sinnott, S.B., Andrews, R., (2001) Crit. Rev. Sol. St. Mat. Sci., 26, p. 145. , and references thereinRinzler, A.G., (1995) Science, 269, p. 1550Tans, S.J., (1997) Nature, 386, p. 474Kociak, M., (2001) Phys. Rev. Lett., 86, p. 2416Kim, P., Shi, L., Majumdar, A., McEuen, P.L., (2001) Phys. Rev. Lett., 87, p. 215502Baughman, R.H., Eckhardt, H., Kertesz, M., (1987) J. Chem. Phys., 87, p. 6687Narita, N., Nagai, S., Suzuki, S., Nakao, K., (1998) Phys. Rev. B, 58, p. 11009Narita, N., Nagai, S., Suzuki, S., Nakao, K., (2000) Phys. Rev. B, 62, p. 11146Kroto, H.W., Walton, D.R.M., (1993) The Fullerenes, New Horizons for the Chemistry, Physics and Astrophysics of Carbon, pp. 103-112. , ed. H. W. Kroto and D. R. M. Walton (Cambridge University Press)Hamada, N., Sawada, S.-I., Oshiyama, A., (1992) Phys. Rev. Lett., 68, p. 1579Ordejón, P., Artacho, E., Soler, J.M., (1996) Phys. Rev. B, 53, pp. R10441. , http://www.uam.es/siesta, For more information about the Siesta packagePerdew, J.P., Burke, K., Ernzerhof, M., (1996) Phys. Rev. Lett., 77, p. 3865Delley, B., (1990) J. Chem. Phys., 92, p. 508(2000) J. Chem. Phys., 113, p. 7756. , http://www.accelrys.com, DMol3 is available from Accelrys, Inc. as part of the Cerius2 program suiteSaito, R., Fujita, M., Dresselhaus, G., Dresselhaus, M.S., (1992) Phys. Rev. B, 46, p. 1804Wallace, P.R., (1947) Phys. Rev., 71, p. 622Hoffman, R., (1963) J. Chem. Phys., 39, p. 1397Clementi, E., Raimondi, D.L., (1963) J. Chem. Phys., 38, p. 2686Sonoda, M., (2001) Org. Lett., 3, p. 2419Srinivasan, M., (2000) Org. Lett., 2, p. 3849Wan, W.B., Haley, M.M., (2001) J. Org. Chem., 66, p. 3893Zhou, Y., Feng, S., (2002) Sol. St. Commun., 122, p. 307Rana, D., Gangopadhyay, G., (2001) Chem. Phy. Lett., 334, p. 31
