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Book cover Self-Assembly of Flat Organic Molecules on Metal Surfaces

Part of the book series: Springer Theses ((Springer Theses))

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Abstract

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.

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References

  1. Binnig G, Rohrer H, Gerber C, Werbel E (1983) Phys Rev Lett 50:120

    Article  CAS  Google Scholar 

  2. Binnig G, Rohrer H (1987) Rev Mod Phys 59:615

    Article  CAS  Google Scholar 

  3. Binnig G et al (1985) Phys Rev Lett 55:991

    Google Scholar 

  4. De Feyter S, De Schryver FC (2003) Chem Soc Rev 32:139

    Article  Google Scholar 

  5. De Feyter S, Miura A, Yao A, Chen Z, Wurthner F, Jonkheijm P, Schenning APH, Meijer EW, De Schryver FC (2005) Nano Lett 5:77

    Article  Google Scholar 

  6. Perdigão LMA, Champness NR, Beton PH (2006) Chem Commun 5:538

    Article  Google Scholar 

  7. Perdigão LMA, Perkins EW, Ma J, Staniec PA, Rogers BL, Champness NR, Beton PH (2006) J Phys Chem B 110:12539

    Article  Google Scholar 

  8. Perdigão LMA, Fontes GN, Rogers BL, Oxtoby NS, Goretzki G, Champness NR, Beton PH (2007) Phys Rev B 76:245402

    Article  Google Scholar 

  9. Lingenfelder M, Tomba G, Constantini G, Colombi Ciacchi L, De vita A, Kern K (2007) Angew Chem Int Ed 46:4492

    Google Scholar 

  10. Tomba G, Lingenfelder M, Constantini G, Kern K, Klappernberger F, Barth JV, De Vita J (2007) Phys Chem A 111:12740

    Article  CAS  Google Scholar 

  11. Berg JM, Tymoczko JL, Stryer L (2002) Biochemistry. Michelle Julet, New York

    Google Scholar 

  12. Keeling DL, Oxtoby NS, Wilson C, Humphry MJ, Champness NR, Beton PH (2003) Nano Lett 3:129

    Article  Google Scholar 

  13. Barth JV, Costantini G, Kern K (2005) Nature 437:671

    Article  CAS  Google Scholar 

  14. Theobald JA, Oxtoby NS, Phillips MA, Champness NR, Beton PH (2003) Nature 424:1029

    Article  CAS  Google Scholar 

  15. Ma J, Rogers BL, Humphry MJ, Ring DJ, Goretzki G, Champness NR, Beton PH (2006) J Phys Chem B 110:12539

    Article  Google Scholar 

  16. Swarbrick JC, Ma J, Theobald JA, Oxtoby NS, O’Shea JN, Champness NR, Beton PH (2005) J Phys Chem B 109:12167

    Article  CAS  Google Scholar 

  17. Swarbrick JC, Rogers BL, Champness NR, Beton PH (2006) J Phys Chem B 110:6110

    Article  CAS  Google Scholar 

  18. Saywell A, Magnano G, Satterley CJ, Pedigão LMA, Champness PH, Beton NR, O’Shea JN J Phys Chem C

    Google Scholar 

  19. Barth JV (2007) Annu Rev Phys Chem 58:375

    Article  CAS  Google Scholar 

  20. Staniec PA, Perdigão LMA, Rogers BL, Champness NR, Beton PH (2007) J Phys Chem C 111:886

    Article  CAS  Google Scholar 

  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 5:1952

    Article  CAS  Google Scholar 

  22. Sassi M, Oison V, Debierre J (2008) Surf Sci 602:2862

    Article  Google Scholar 

  23. Mura M, Martsinovich N, Kantorovich LN (2008) Nanotechnology 19:465704

    Article  CAS  Google Scholar 

  24. Chinzhov I, Kahn A, Scoles G (2000) J Crystal Growth 208:449

    Article  Google Scholar 

  25. Silly F, Shaw AQ, Castell MR, Briggs GAD, Mura M, Martsinovich N, Kantorovich LN (2008) J Phys Chem C 112:11476

    Google Scholar 

  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 3:854

    Article  CAS  Google Scholar 

  27. Zhang H, Xie Z, Long L, Zhong H, Zhao W, Mao B, Xu X, Zhao W (2008) J Phys Chem C 112:4209

    Article  CAS  Google Scholar 

  28. Silly F, Weber UK, Shaw AQ, Burlakov VM, Castell MR, Briggs GAD, Pettifor DG (2008) Phys Rev B 77:201408

    Article  Google Scholar 

  29. Silly F, Shaw AQ, Briggs GAD (2008) Chem Comm 16

    Google Scholar 

  30. Silly F, Shaw AQ, Briggs GAD, Castell MR (2008) Appl Phys Lett 92:023102

    Article  Google Scholar 

  31. Silly F, Shaw AQ, Pettifor DG, Briggs GAD, Castell MR (2007) Appl Phys Lett 91:253109

    Article  Google Scholar 

  32. Gabriel M, Stöhr M, Möller R (2002) Appl Phys A 74:303

    Google Scholar 

  33. Wanger Th, Bannani A, Bobisch C, Karacuban H, Moller R (2007) Condens Matter 19:056009

    Article  Google Scholar 

  34. Glockler K, Seidel C, Sokolowski M, Umbach E, Bohringer M, Berndt R, Schneider W-D (1998) Surf Sci 405:1–20

    Article  CAS  Google Scholar 

  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 100:136103

    Article  CAS  Google Scholar 

  36. Mannsfeld S, Toerker M, Schmitz-Hubsch T, Sellam F, Fritz T, Leo K (2001) Org Electron 2:121

    Article  CAS  Google Scholar 

  37. Kröger J, Jensen H, Berdt R, Rurali R, Lorente N (2007) Chem Phys Lett 438:249

    Article  Google Scholar 

  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):7972–7976

    Article  Google Scholar 

  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):3046–3053

    Article  Google Scholar 

  40. Nicoara N, Romani E, Gomez-Rodriguez JM, Martin-Gago J, Mendez J (2006) Org Electr 7:287

    Article  CAS  Google Scholar 

  41. Kunstmann T, Schlarb A, Fendrich M, Wangner Th, Moller R, Hoffmann R (2005) Phys Rev B 71:121403

    Article  Google Scholar 

  42. Fendrich M, Kunstmann T, Paulkowski D, Möller R (2007) Nanotechnology 18:084004

    Article  Google Scholar 

  43. Burke SA, Ji W, Mativetsky JM, Topple JM, Fostner S, Gao H-J, Guo H, Grutter P (2008) Phys Rev Lett 100:186104

    Article  CAS  Google Scholar 

  44. Lauffer P, Emtsev KV, Graupner R, Seyller T, Ley L (2008) Phys Stat Sol 245:2064

    Google Scholar 

  45. N. Nicoara N, Custance O, Granados D, Garcia JM, Gomez-Rodriguez JM, Baro AM, Mendez J (2003) Phys Condens Matter 15:S2619

    Google Scholar 

  46. Forker R, Dienel T, Fritz T, Muller K (2006) Phys Rev B 74:165410

    Article  Google Scholar 

  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. 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 93:365–373

    Google Scholar 

  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 113:8407–8411

    Google Scholar 

  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 548:129–137

    Article  CAS  Google Scholar 

  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):205414

    Article  Google Scholar 

  52. Cañas ME, Xiao W, Wasserfallen D, Müller K, Brune H, JV Barth, Fasel R (2007) Angew Chem Int Ed 46:1814–1818

    Google Scholar 

  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 113:21840–21848

    Article  CAS  Google Scholar 

  54. Nowakoski R, Seidel C, Fuchs H (2004) Surf Sci 562:53–64

    Article  Google Scholar 

  55. Ziroff J, Gold P, Bendounan A, Forster F, Reinert F (2000) Surf Sci 603:354

    Article  Google Scholar 

  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):25573–25577

    Google Scholar 

  57. Taylor JB, Beton PH (2006) Phys Rev Lett 97:236102

    Google Scholar 

  58. Weber UK, Burlakov VM, Pedigão LMA, Fawcett RHJ, Beton PH, Champness NR, Briggs GAD, Pettifor DG (2008) Phys Rev Lett 100:156101

    Article  CAS  Google Scholar 

  59. Stepanow S, Lingenfelde M, Dmitriev A, Spillmann H, Delvigne E, Lin N, Deng X, Cai C, Barth JV, Kern K (2004) Nature 3:229

    Article  CAS  Google Scholar 

  60. Kühnle A (2009) Curr Opin Colloid Interface Sci 14:157

    Google Scholar 

  61. Perdigão LMA, Staniec PA, Champness NR, Kelly REA, Kantorovich LN, Beton PH (2006) Adenine monolayers on ag-terminated si(111). Phys Rev B 73:195423

    Article  Google Scholar 

  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 319:312–315

    Google Scholar 

  63. Kelly REA, Kantorovich LN (2006) Planar nucleic acid base super-structures. J Mater Chem 16:1894–1905

    Google Scholar 

  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 4:1494

    Article  CAS  Google Scholar 

  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 3:2011–2014

    Article  CAS  Google Scholar 

  66. Heimel G, Romaner L, Brédas J-L, Zojer E (2006) Phys Rev Lett 96:196806

    Google Scholar 

  67. Picozzi S, Pecchia A, Gheorghe M, Di Carlo A, Lugli P, Delly B, Elstner E (2003) Phys Rev B 68:195309

    Article  Google Scholar 

  68. Hauschild A, Karki K, Cowie BCC, Rohlfing M, Tautz FS, Sokolowski M (2005) Phys Rev Lett 94:036106

    Article  CAS  Google Scholar 

  69. Hauschild A, Karki K, Cowie BCC, Rohlfing M, Tautz FS, Sokolowski M (2005) Phys Rev Lett 95:209602

    Article  Google Scholar 

  70. Rurali R, Lorente L, Ordejon P (2005) Phys Rev Lett 95:208601

    Article  Google Scholar 

  71. Seitsonen AP, Lingenfelder M, Spillmann H, Dmitriev A, Stepanow S, Lin N, Kern K, Barth JV (2006) J Am Chem Soc 128:5634

    Article  CAS  Google Scholar 

  72. Kelly REA, Kantorovich LN (2005) Hexagonal adenine networks constructed from their homo-pairings. Surf Sci 589:139–152

    Article  CAS  Google Scholar 

  73. Bilic A, Reimers JR, Hush NS, Hoft RC, Ford MJ (2006) J Chem Theory Comput 2:1093

    Article  CAS  Google Scholar 

  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 128:15644

    Article  Google Scholar 

  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 129:184707

    Article  Google Scholar 

  76. Kelly REA, Kantorovich LN (2006) J Mater Chem 16:1894

    Article  CAS  Google Scholar 

  77. Kelly REA, Lee YJ, Kantorovich LN (2005) J Phys Chem B 109:11933

    Article  CAS  Google Scholar 

  78. Kelly REA, Lee YJ, Kantorovich LN (2006) J Phys Chem B 110:2249

    Article  CAS  Google Scholar 

  79. Kelly REA, Lee YJ, Kantorovich LN (2005) J Phys Chem B 109:22045

    Article  CAS  Google Scholar 

  80. Sponer J, Leszczynski J, Hobza PJ, Phys Chem

    Google Scholar 

  81. Sponer J, Leszczynski J, Hobza PJ, Mol Str (Theochem)

    Google Scholar 

  82. Sponer J, Leszczynski J, Hobza P, Biopolymers

    Google Scholar 

  83. Jurecka P, Sponer J, Cemý J, Hobza P (2009) Phys Rev B 79:201105

    Article  Google Scholar 

  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 47:9673–9676

    Article  CAS  Google Scholar 

  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 130:024705

    Article  Google Scholar 

  86. Romaner L, Nabok D, Puschnig P, Zojer C, Ambrosch-Draxl E (2009) N J Phys 11:053010

    Article  Google Scholar 

  87. Perdew JP, Burke K, Ernzerhof M (1998) Phys Rev Lett 80:891

    Article  CAS  Google Scholar 

  88. Perdew JP, Burke K, Ernzerhof M (1996) Phys Rev Lett 77:3865

    Article  CAS  Google Scholar 

  89. Priya S, Puschnig P, Nabok D, Ambrosch-Drax C (2007) Phys Rev Lett 99:176401

    Article  Google Scholar 

  90. Wu X, Vargas S, Nayak MC, Lotrich V, Scoles G (2001) J Chem Phys 115:8748

    Article  CAS  Google Scholar 

  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 21:084203

    Article  CAS  Google Scholar 

  92. Piana S, Bilic A (2006) J Phys Chem B 110:23467

    Article  CAS  Google Scholar 

  93. Grimme S (2004) J Comput Chem 25:1463

    Article  CAS  Google Scholar 

  94. Grimme S (2006) J Comput Chem 27:1787

    Article  CAS  Google Scholar 

  95. Langreth DC, Dion M, Rydberg H, Schroder E, Hyldgaard P, Lundqvist BI (2005) J Quantum Chem 101:599

    Article  CAS  Google Scholar 

  96. Thonhauser T, Puzder A, Langreth DC (2006) J Chem Phys 124:164106

    Article  CAS  Google Scholar 

  97. Jurecka P, Sponer J, Cemý J, Hobza P (2006) Phys Chem Chem Phys 8:1985

    Article  CAS  Google Scholar 

  98. Piacenza M, Grimme S (2005) J Am Chem Soc 127:14841

    Article  CAS  Google Scholar 

  99. Morgado C, Vincent MA, Hillier IH, Shan X (2007) Phys Chem Chem Phys 9:448

    Article  CAS  Google Scholar 

  100. Foster ME, Shohlberg K (2010) Phys Chem Chem Phys 12:307

    Article  CAS  Google Scholar 

  101. Nguten M-T, Pignedoli CA, Treier M, Fasel R, Paserone D (2010) Phys Chem Chem Phys 12:992

    Article  Google Scholar 

  102. Cooper VR, Thonhauser T, Puzder A, Schroeder E, Lundqvist BI, Langreth DC (2008) J Am Chem Soc 130:1304

    Article  CAS  Google Scholar 

  103. Thonhauser T, Cooper VR, Li S, Puzder A, Hyldgaard P, Langreth DC (2007) Phys Rev B 76:125112

    Article  Google Scholar 

  104. Dion M, Rydberg H, Schroeder E, Langreth DC, Lundqvist BI (2004) Phys Rev Lett 92:246401

    Article  CAS  Google Scholar 

  105. http://en.wikipedia.org/wiki/File:ScanningTunnelingMicroscope_schematic.png

  106. Bardeen J (1961) Phys Rev Lett 6:57

    Article  CAS  Google Scholar 

  107. Tersoff J, Hamann DR (1985) Stm theory. Phys Rev B 31:805

    Article  CAS  Google Scholar 

  108. http://upload.wikimedia.org/wikipedia/commons/thumb/7/7c/Atomic_force_microscope_block_diagram.svg

  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. 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 Ed

    Google Scholar 

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  1. University of Central Lancashire Preston, Lancashire, UK

    Manuela Mura

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Mura, M. (2012). Introduction. In: Self-Assembly of Flat Organic Molecules on Metal Surfaces. Springer Theses. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-30325-8_1

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