Rotational Dynamics And Polymerization Of C60 In C60 -cubane Crystals: A Molecular Dynamics Study

We 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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Designing Conducting Polymers Using Bioinspired Ant Algorithms

Ant algorithms are inspired in real ants and the main idea is to create virtual ants that travel into the space of possible solution depositing virtual pheromone proportional to how good a specific solution is. This creates a autocatalytic (positive feedback) process that can be used to generate automatic solutions to very difficult problems. In the present work we show that these algorithms can be used coupled to tight-binding hamiltonians to design conducting polymers with pre-specified properties. The methodology is completely general and can be used for a large number of optimization problems in materials science

Carcinogenic Classification Of Polycyclic Aromatic Hydrocarbons Through Theoretical Descriptors

Polycyclic 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

Dynamics Of Graphene Nanodrums

Recently, 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

How Similar Are Branching Networks In Nature? A View From The Ocean: Caribbean Gorgonian Corals

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Graphyne Nanotubes: New Families Of Carbon Nanotubes

Fundamentally 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

On The Existence Of Ordered Phases Of Encapsulated Diamondoids Into Carbon Nanotubes

We have investigated some diamondoids encapsulation into single walled carbon nanotubes (with diameters ranging from1.0 up to 2.2 nm) using fully atomistic molecular dynamics simulations. Diamondoids are the smallest hydrogen-terminated nanosized diamond-like molecules. Diamondois have been investigated for a large class of applications, ranging from oil industry to pharmaceuticals. Molecular ordered phases were observed for the encapsulation of adamantane, diamantane, and dihydroxy diamantanes. Chiral ordered phases, such as; double, triple, 4- and 5-stranded helices were also observed for those diamondoids. Our results also indicate that the modification of diamondoids through chemical functionalization with hydroxyl groups can lead to an enhancement of the molecular packing inside the carbon nanotubes in comparison to non-functionalized molecules. For larger diamondoids (such as, adamantane tetramers), we have not observed long-range ordering, but only a tendency of incomplete helical structural formation. © 2012 Materials Research Society.14075560The Multi-Scale Technologies Institute (MuSTI),Technological University,Int. Cent. Young Sci. (ICYS) Natl. Inst. Mater. Sci.,Angstrom Engineering Inc.Dahl, J.E., Liu, S.G., Carlson, R.M.K., (2003) Science, 299, p. 96Mansoori, G.A., (2005) Principles of Nanotechnology. Molecular-Based Study of Condensed Matter in Small Systems, , World Scientific, SingaporeMarchand, A.P., (1995) Aldrichimica Acta, 28, p. 95Marsusi, F., Mirabbaszadeh, K., Mansoori, G.A., (2009) Physica e, 41, p. 1151Xue, Y., Mansoori, G.A., (2010) Int. J. Mol Sci., 11, p. 288De Araujo, E.S., Mansoori, G.A., Xue, Y., De Araujo, P.L.B., (2011) Phys. Exp., 1, p. 67Fort, R.C., (1976) Adamantane: The Chemistry of Diamond Molecules, , Dekker, New YorkMerkle, R.C., (2000) Nanotechnology, 11, p. 89Tkachenko, B.A., (2006) Org. Lett., 8, p. 1767McIntosh, G.C., (2004) Phys. Rev. B, 70, p. 045401Rappé, A.K., (1992) J. Am. Chem. Soc., 114, p. 10024http://www.accelrys.comLegoas, S.B., (2003) Phys. Rev. Lett., 90, p. 055504Troche, K.S., (2005) Nano Lett., 5, p. 349Schreiner, P.R., (2006) J. Org. Chem., 71, p. 6709Ishizone, T., (2001) Tetrahedron Lett., 42, p. 8645Nosé, S., (1991) Prog. Theor. Phys., Suppl., 103, p. 1Hodak, M., Girifalco, L.A., (2003) Phys. Rev. B, 67, p. 075419Pickett, G.T., Gross, M., Okuyama, H., (2000) Phys. Rev. Lett., 85, p. 3652Legoas, S.B., (2011) Nanotechnology, 22, p. 31570