Part of the Springer Theses book series (Springer Theses)


The work in this thesis is focused on molecules that are able to self-assemble on different surfaces by forming two-dimensional templates stabilised via double or triple hydrogen bonding. In particular, assemblies of molecules such as melamine, perylene tetra-carboxylic di-imide (PTCDI), perylene tetra-carboxylic di-anhydride (PTCDA), naphthalene tetracarboxylic-dianhydride (NTCDA) and naphthalene tetracarboxylic diimide (NTCDI) are studied in detail. The aim is to give a complete characterisation of the supramolecular networks, taking into account the balance between the molecule-molecule and molecule-substrate interactions. All our assembly calculations are done within the gas phase approximation, i.e. without taking into account the surface, which is a good approximation assuming that the molecules are quite mobile on the surface. Using a systematic method based on considering all possible hydrogen bond connections between the molecules we investigate planar superstructures that organic molecules can form in one and two dimensions. The structures studied are based on two or more molecules per unit cell and all structures considered, assemble in flat periodic patterns. Most of the calculations are performed using the density functional theory method. We show that the calculated lattice parameters of the structures considered compare well with those measured experimentally. To specifically check the applicability of the gas-phase approximation, we systematically investigated the adsorption of the molecules on the Au(111) metal surface with the particular attention being paid to the characterisation of the potential energy surface of our molecules on this surface. We performed these calculations using both a conventional functional (PBE) which does not include the dispersion interaction, and the newly developed vdW-DF method which does. We find that the adsorption energies of these flat molecules on the metal surface calculated with the vdW-DF method are effected significantly by the dispersion interaction and depend linearly on the size of the molecules. While the PBE method predicts very weak adsorption energies which do not depend on the sizes of the molecules, the vdW-DF method gives strong binding entirely due to the dispersion interaction. We found that both PBE and vdW-DF methods predict a very small corrugation of the total energy of the molecules on gold. These results support our main assumption of the molecule-surface interaction changing little laterally and resulting in a mobility of the molecules at room temperature on the surface, i.e. the gas-phase modelling is a good approximation for the Au(111) surface.


Scan Tunnelling Microscopy Scan Tunnelling Microscopy Image Cyanuric Acid Scan Tunneling Microscopy Experiment PTCDA Molecule 
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  1. 1.
    Binnig G, Rohrer H, Gerber C, Werbel E (1983) Phys Rev Lett 50:120CrossRefGoogle Scholar
  2. 2.
    Binnig G, Rohrer H (1987) Rev Mod Phys 59:615CrossRefGoogle Scholar
  3. 3.
    Binnig G et al (1985) Phys Rev Lett 55:991Google Scholar
  4. 4.
    De Feyter S, De Schryver FC (2003) Chem Soc Rev 32:139CrossRefGoogle Scholar
  5. 5.
    De Feyter S, Miura A, Yao A, Chen Z, Wurthner F, Jonkheijm P, Schenning APH, Meijer EW, De Schryver FC (2005) Nano Lett 5:77CrossRefGoogle Scholar
  6. 6.
    Perdigão LMA, Champness NR, Beton PH (2006) Chem Commun 5:538CrossRefGoogle Scholar
  7. 7.
    Perdigão LMA, Perkins EW, Ma J, Staniec PA, Rogers BL, Champness NR, Beton PH (2006) J Phys Chem B 110:12539CrossRefGoogle Scholar
  8. 8.
    Perdigão LMA, Fontes GN, Rogers BL, Oxtoby NS, Goretzki G, Champness NR, Beton PH (2007) Phys Rev B 76:245402CrossRefGoogle Scholar
  9. 9.
    Lingenfelder M, Tomba G, Constantini G, Colombi Ciacchi L, De vita A, Kern K (2007) Angew Chem Int Ed 46:4492Google Scholar
  10. 10.
    Tomba G, Lingenfelder M, Constantini G, Kern K, Klappernberger F, Barth JV, De Vita J (2007) Phys Chem A 111:12740CrossRefGoogle Scholar
  11. 11.
    Berg JM, Tymoczko JL, Stryer L (2002) Biochemistry. Michelle Julet, New YorkGoogle Scholar
  12. 12.
    Keeling DL, Oxtoby NS, Wilson C, Humphry MJ, Champness NR, Beton PH (2003) Nano Lett 3:129CrossRefGoogle Scholar
  13. 13.
    Barth JV, Costantini G, Kern K (2005) Nature 437:671CrossRefGoogle Scholar
  14. 14.
    Theobald JA, Oxtoby NS, Phillips MA, Champness NR, Beton PH (2003) Nature 424:1029CrossRefGoogle Scholar
  15. 15.
    Ma J, Rogers BL, Humphry MJ, Ring DJ, Goretzki G, Champness NR, Beton PH (2006) J Phys Chem B 110:12539CrossRefGoogle Scholar
  16. 16.
    Swarbrick JC, Ma J, Theobald JA, Oxtoby NS, O’Shea JN, Champness NR, Beton PH (2005) J Phys Chem B 109:12167CrossRefGoogle Scholar
  17. 17.
    Swarbrick JC, Rogers BL, Champness NR, Beton PH (2006) J Phys Chem B 110:6110CrossRefGoogle Scholar
  18. 18.
    Saywell A, Magnano G, Satterley CJ, Pedigão LMA, Champness PH, Beton NR, O’Shea JN J Phys Chem CGoogle Scholar
  19. 19.
    Barth JV (2007) Annu Rev Phys Chem 58:375CrossRefGoogle Scholar
  20. 20.
    Staniec PA, Perdigão LMA, Rogers BL, Champness NR, Beton PH (2007) J Phys Chem C 111:886CrossRefGoogle Scholar
  21. 21.
    Xu REA, Kelly W, Gersen H, Lægsgaard E, Stensgaard I, Kantorovich LN, Besenbacher F (2009) Prochiral guanine adsorption on au(111): An entropy-stabilized intermixed guanine-quartet chiral structure. Small 5:1952CrossRefGoogle Scholar
  22. 22.
    Sassi M, Oison V, Debierre J (2008) Surf Sci 602:2862CrossRefGoogle Scholar
  23. 23.
    Mura M, Martsinovich N, Kantorovich LN (2008) Nanotechnology 19:465704CrossRefGoogle Scholar
  24. 24.
    Chinzhov I, Kahn A, Scoles G (2000) J Crystal Growth 208:449CrossRefGoogle Scholar
  25. 25.
    Silly F, Shaw AQ, Castell MR, Briggs GAD, Mura M, Martsinovich N, Kantorovich LN (2008) J Phys Chem C 112:11476Google Scholar
  26. 26.
    Xu W, Dong M, Gersen H, Rauls E, Vázquez-Campos S, Crego-Calama M, Reinhoudt DN, Stensgaard I, Laegsgaard E, Linderoth TR, Besenbacher F (2007) Small 3:854CrossRefGoogle Scholar
  27. 27.
    Zhang H, Xie Z, Long L, Zhong H, Zhao W, Mao B, Xu X, Zhao W (2008) J Phys Chem C 112:4209CrossRefGoogle Scholar
  28. 28.
    Silly F, Weber UK, Shaw AQ, Burlakov VM, Castell MR, Briggs GAD, Pettifor DG (2008) Phys Rev B 77:201408CrossRefGoogle Scholar
  29. 29.
    Silly F, Shaw AQ, Briggs GAD (2008) Chem Comm 16Google Scholar
  30. 30.
    Silly F, Shaw AQ, Briggs GAD, Castell MR (2008) Appl Phys Lett 92:023102CrossRefGoogle Scholar
  31. 31.
    Silly F, Shaw AQ, Pettifor DG, Briggs GAD, Castell MR (2007) Appl Phys Lett 91:253109CrossRefGoogle Scholar
  32. 32.
    Gabriel M, Stöhr M, Möller R (2002) Appl Phys A 74:303Google Scholar
  33. 33.
    Wanger Th, Bannani A, Bobisch C, Karacuban H, Moller R (2007) Condens Matter 19:056009CrossRefGoogle Scholar
  34. 34.
    Glockler K, Seidel C, Sokolowski M, Umbach E, Bohringer M, Berndt R, Schneider W-D (1998) Surf Sci 405:1–20CrossRefGoogle Scholar
  35. 35.
    Kilian L, Hauschild A, Temiroc R, Soubatch S, Scholl A, Reinert F, Lee T-L, Tautz FS, Sokolowski M, Ulbach E (2008) Phys Rev Lett 100:136103CrossRefGoogle Scholar
  36. 36.
    Mannsfeld S, Toerker M, Schmitz-Hubsch T, Sellam F, Fritz T, Leo K (2001) Org Electron 2:121CrossRefGoogle Scholar
  37. 37.
    Kröger J, Jensen H, Berdt R, Rurali R, Lorente N (2007) Chem Phys Lett 438:249CrossRefGoogle Scholar
  38. 38.
    Schmitz-Hübsch T, Fritz T, Sellam F, Staub R, Leo K (Mar 1997) Epitaxial growth of 3,4,9,10-perylene-tetracarboxylic-dianhydride on au(111): a stm and rheed study. Phys Rev B 55(12):7972–7976CrossRefGoogle Scholar
  39. 39.
    Fenter P, Schreiber F, Zhou L, Eisenberger P, Forrest SR (Aug 1997) In situ studies of morphology, strain, and growth modes of a molecular organic thin film. Phys Rev B 56(6):3046–3053CrossRefGoogle Scholar
  40. 40.
    Nicoara N, Romani E, Gomez-Rodriguez JM, Martin-Gago J, Mendez J (2006) Org Electr 7:287CrossRefGoogle Scholar
  41. 41.
    Kunstmann T, Schlarb A, Fendrich M, Wangner Th, Moller R, Hoffmann R (2005) Phys Rev B 71:121403CrossRefGoogle Scholar
  42. 42.
    Fendrich M, Kunstmann T, Paulkowski D, Möller R (2007) Nanotechnology 18:084004CrossRefGoogle Scholar
  43. 43.
    Burke SA, Ji W, Mativetsky JM, Topple JM, Fostner S, Gao H-J, Guo H, Grutter P (2008) Phys Rev Lett 100:186104CrossRefGoogle Scholar
  44. 44.
    Lauffer P, Emtsev KV, Graupner R, Seyller T, Ley L (2008) Phys Stat Sol 245:2064Google Scholar
  45. 45.
    N. Nicoara N, Custance O, Granados D, Garcia JM, Gomez-Rodriguez JM, Baro AM, Mendez J (2003) Phys Condens Matter 15:S2619Google Scholar
  46. 46.
    Forker R, Dienel T, Fritz T, Muller K (2006) Phys Rev B 74:165410CrossRefGoogle Scholar
  47. 47.
    Mura M, Sun X, Jonkman HT, Silly F, Briggs GAD, Castell MR, Kantorovich L (2010) Experimental and theoretical analysis of h-bonded supramolecular assemblies of ptcda molecules on the au(111) surface. Phys Rev B (in print)Google Scholar
  48. 48.
    Ludwig C, Gompf B, Petersen J, Strohmaier R, Eisenmenger W (1994) Stm investigations of ptcda and ptcdi on graphite and mos2. W Z Phys B 93:365–373Google Scholar
  49. 49.
    Ait-Mansour K, Treier M, Ruffieux P, Bieri M, Jaafar R, Groning P, Fasel R, Groning O (2009) Template-dierected molecular nanostrutures on the ag/pt(111) dislocation network. J Phys Chem C 113:8407–8411Google Scholar
  50. 50.
    Guillermet O, Glachant A, Hoarau JY, Mossoyam JC, Mossoyam M (2004) Perylene tetracarboxylic diimide ultrathin film depositon on pt(1 0 0): a leed, aes and stm study. Surf Sci 548:129–137CrossRefGoogle Scholar
  51. 51.
    Topple JM, Burke SA, Fostner S, Grütter P (2009) Thin film evolution: dewetting dynamics of a bimodal molecular system. Phys Rev B 79(20):205414CrossRefGoogle Scholar
  52. 52.
    Cañas ME, Xiao W, Wasserfallen D, Müller K, Brune H, JV Barth, Fasel R (2007) Angew Chem Int Ed 46:1814–1818Google Scholar
  53. 53.
    Mura M, Silly F, Briggs GAD, Castell MR, Kantorovich L (2009) H-bonding supramolecular assemblies of ptcdi molecules on the au(111) surface. J Phys Chem C 113:21840–21848CrossRefGoogle Scholar
  54. 54.
    Nowakoski R, Seidel C, Fuchs H (2004) Surf Sci 562:53–64CrossRefGoogle Scholar
  55. 55.
    Ziroff J, Gold P, Bendounan A, Forster F, Reinert F (2000) Surf Sci 603:354CrossRefGoogle Scholar
  56. 56.
    Silanes I, Ruiz-Oses M, Gonzalez-Lakunza N et al (2006) Self-assembly of heterogeneous supramolecular structures with uniaxial anisotropy. J Chem Phys B 110(51):25573–25577Google Scholar
  57. 57.
    Taylor JB, Beton PH (2006) Phys Rev Lett 97:236102Google Scholar
  58. 58.
    Weber UK, Burlakov VM, Pedigão LMA, Fawcett RHJ, Beton PH, Champness NR, Briggs GAD, Pettifor DG (2008) Phys Rev Lett 100:156101CrossRefGoogle Scholar
  59. 59.
    Stepanow S, Lingenfelde M, Dmitriev A, Spillmann H, Delvigne E, Lin N, Deng X, Cai C, Barth JV, Kern K (2004) Nature 3:229CrossRefGoogle Scholar
  60. 60.
    Kühnle A (2009) Curr Opin Colloid Interface Sci 14:157Google Scholar
  61. 61.
    Perdigão LMA, Staniec PA, Champness NR, Kelly REA, Kantorovich LN, Beton PH (2006) Adenine monolayers on ag-terminated si(111). Phys Rev B 73:195423CrossRefGoogle Scholar
  62. 62.
    Otero R, Lukas M, Kelly REA, Xu W, L<E6>gsgaard E, Stensgaard I, Kantorovich LN, Besenbacher F (2008) Elementary structural motifs in a random network of cytosine adsorbed on a gold(111) surface. Science 319:312–315Google Scholar
  63. 63.
    Kelly REA, Kantorovich LN (2006) Planar nucleic acid base super-structures. J Mater Chem 16:1894–1905Google Scholar
  64. 64.
    Kelly REA, Xu W, Lukas M, Otero R, Mura M, Lee YJ, Lægsgaard E, Stensgaard I, Kantorovich LN, Besenbacher F (2008) An investigation into the interactions between self-assembled adenine molecules and the au(111) surface. Small 4:1494CrossRefGoogle Scholar
  65. 65.
    Xu W, Kelly REA, Schöck M, Otero R, Laesgaard E, Stensgaard I, Kantorovich LN, Besenbacher F (2007) Probing the hierarchy of thymine-thymine interactions in self-assembled structures by manipulation with scanning tunneling microscopy. Small 3:2011–2014CrossRefGoogle Scholar
  66. 66.
    Heimel G, Romaner L, Brédas J-L, Zojer E (2006) Phys Rev Lett 96:196806Google Scholar
  67. 67.
    Picozzi S, Pecchia A, Gheorghe M, Di Carlo A, Lugli P, Delly B, Elstner E (2003) Phys Rev B 68:195309CrossRefGoogle Scholar
  68. 68.
    Hauschild A, Karki K, Cowie BCC, Rohlfing M, Tautz FS, Sokolowski M (2005) Phys Rev Lett 94:036106CrossRefGoogle Scholar
  69. 69.
    Hauschild A, Karki K, Cowie BCC, Rohlfing M, Tautz FS, Sokolowski M (2005) Phys Rev Lett 95:209602CrossRefGoogle Scholar
  70. 70.
    Rurali R, Lorente L, Ordejon P (2005) Phys Rev Lett 95:208601CrossRefGoogle Scholar
  71. 71.
    Seitsonen AP, Lingenfelder M, Spillmann H, Dmitriev A, Stepanow S, Lin N, Kern K, Barth JV (2006) J Am Chem Soc 128:5634CrossRefGoogle Scholar
  72. 72.
    Kelly REA, Kantorovich LN (2005) Hexagonal adenine networks constructed from their homo-pairings. Surf Sci 589:139–152CrossRefGoogle Scholar
  73. 73.
    Bilic A, Reimers JR, Hush NS, Hoft RC, Ford MJ (2006) J Chem Theory Comput 2:1093CrossRefGoogle Scholar
  74. 74.
    Riben M, Payer D, Landa A, Comisso A, Gattinoni C, Lin N, Collin J-P, Sauvage A, De Vita J-P, Kern K (2006) J Am Chem Soc 128:15644CrossRefGoogle Scholar
  75. 75.
    Kelly REA, Lukas M, Kantorovich LN, Otero R, Xu W, Mura M, Laesgaard E, Stensgaard I, Besenbacher F (2008) Understanding disorder of the dna base cytosine on the au(111) surface. J Chem Phys 129:184707CrossRefGoogle Scholar
  76. 76.
    Kelly REA, Kantorovich LN (2006) J Mater Chem 16:1894CrossRefGoogle Scholar
  77. 77.
    Kelly REA, Lee YJ, Kantorovich LN (2005) J Phys Chem B 109:11933CrossRefGoogle Scholar
  78. 78.
    Kelly REA, Lee YJ, Kantorovich LN (2006) J Phys Chem B 110:2249CrossRefGoogle Scholar
  79. 79.
    Kelly REA, Lee YJ, Kantorovich LN (2005) J Phys Chem B 109:22045CrossRefGoogle Scholar
  80. 80.
    Sponer J, Leszczynski J, Hobza PJ, Phys ChemGoogle Scholar
  81. 81.
    Sponer J, Leszczynski J, Hobza PJ, Mol Str (Theochem)Google Scholar
  82. 82.
    Sponer J, Leszczynski J, Hobza P, BiopolymersGoogle Scholar
  83. 83.
    Jurecka P, Sponer J, Cemý J, Hobza P (2009) Phys Rev B 79:201105CrossRefGoogle Scholar
  84. 84.
    Otero R, Xu W, Lukas M, Kelly REA, Laegsgaard E, Stensgaard I, Kjems J, Kantorovich L, Besenbacher F (2008) Specificity of watson-crick base pairing on a solid surface studied at the atomic scale. Angew Chem Int Ed 47:9673–9676CrossRefGoogle Scholar
  85. 85.
    Lukas M, Kelly R, Kantorovich L, Otero R, Laesgaard E, Stensgaard I, Besenbacher F (2009) Adenine monolayers on the au(111) surface: structure identification by stm experiment and ab initio calculations. J Chem Phys 130:024705CrossRefGoogle Scholar
  86. 86.
    Romaner L, Nabok D, Puschnig P, Zojer C, Ambrosch-Draxl E (2009) N J Phys 11:053010CrossRefGoogle Scholar
  87. 87.
    Perdew JP, Burke K, Ernzerhof M (1998) Phys Rev Lett 80:891CrossRefGoogle Scholar
  88. 88.
    Perdew JP, Burke K, Ernzerhof M (1996) Phys Rev Lett 77:3865CrossRefGoogle Scholar
  89. 89.
    Priya S, Puschnig P, Nabok D, Ambrosch-Drax C (2007) Phys Rev Lett 99:176401CrossRefGoogle Scholar
  90. 90.
    Wu X, Vargas S, Nayak MC, Lotrich V, Scoles G (2001) J Chem Phys 115:8748CrossRefGoogle Scholar
  91. 91.
    Langreth DC, Lundqvist BI, Chakarova-Draxl SD, Cooper VR, Dion M, Hyldgaard P, Kelkkanen A, Kleis J, Kong LZ, Li S, Moses PG, Murray E, Puzder A, Rydberg H, Schroder E, Rydberg T, Thonhauser H (2009) Cond Matter 21:084203CrossRefGoogle Scholar
  92. 92.
    Piana S, Bilic A (2006) J Phys Chem B 110:23467CrossRefGoogle Scholar
  93. 93.
    Grimme S (2004) J Comput Chem 25:1463CrossRefGoogle Scholar
  94. 94.
    Grimme S (2006) J Comput Chem 27:1787CrossRefGoogle Scholar
  95. 95.
    Langreth DC, Dion M, Rydberg H, Schroder E, Hyldgaard P, Lundqvist BI (2005) J Quantum Chem 101:599CrossRefGoogle Scholar
  96. 96.
    Thonhauser T, Puzder A, Langreth DC (2006) J Chem Phys 124:164106CrossRefGoogle Scholar
  97. 97.
    Jurecka P, Sponer J, Cemý J, Hobza P (2006) Phys Chem Chem Phys 8:1985CrossRefGoogle Scholar
  98. 98.
    Piacenza M, Grimme S (2005) J Am Chem Soc 127:14841CrossRefGoogle Scholar
  99. 99.
    Morgado C, Vincent MA, Hillier IH, Shan X (2007) Phys Chem Chem Phys 9:448CrossRefGoogle Scholar
  100. 100.
    Foster ME, Shohlberg K (2010) Phys Chem Chem Phys 12:307CrossRefGoogle Scholar
  101. 101.
    Nguten M-T, Pignedoli CA, Treier M, Fasel R, Paserone D (2010) Phys Chem Chem Phys 12:992CrossRefGoogle Scholar
  102. 102.
    Cooper VR, Thonhauser T, Puzder A, Schroeder E, Lundqvist BI, Langreth DC (2008) J Am Chem Soc 130:1304CrossRefGoogle Scholar
  103. 103.
    Thonhauser T, Cooper VR, Li S, Puzder A, Hyldgaard P, Langreth DC (2007) Phys Rev B 76:125112CrossRefGoogle Scholar
  104. 104.
    Dion M, Rydberg H, Schroeder E, Langreth DC, Lundqvist BI (2004) Phys Rev Lett 92:246401CrossRefGoogle Scholar
  105. 105.
  106. 106.
    Bardeen J (1961) Phys Rev Lett 6:57CrossRefGoogle Scholar
  107. 107.
    Tersoff J, Hamann DR (1985) Stm theory. Phys Rev B 31:805CrossRefGoogle Scholar
  108. 108.
  109. 109.
    Mura M, Gulans A, Thonhauser T, Kantorovich L (2009). Role of van der waals interaction in forming molecule-metal junctions: flat organic molecules on the au(111) surface. Phys Chem Chem Phys (submitted)Google Scholar
  110. 110.
    Xu W, Wang J, Jacobsen MF, Mura M, Yu M, Kelly REA, Meng Q, Laegsgaard E, Kjems J, Linderoth TR, Kantorovich L, Gothelf KV, Besenbacher F. Supramolecular porous network formed by molecular recognition between chemical modified nucleobases g ans c. Angew Chem Int EdGoogle Scholar

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© Springer-Verlag Berlin Heidelberg 2012

Authors and Affiliations

  1. 1.University of Central Lancashire PrestonLancashireUK

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