Abstract
The present chapter depicts various theoretical methods that have been used in the context of experimental studies at the nanoscale. With the scanning tunneling microscopy (STM), we can investigate the manipulation of individual molecules and their electronic properties through electronically induced excitations. To explore in details the surface dynamics of a molecule in a bistable or quadristable motion, the nudged elastic band method is used to describe the energy barrier of the saddle point located along the molecular reaction pathway. When the physisorbed stilbene molecule is studied on the bare Si(100), the tight binding method is associated to the density functional theory (DFT) to simulate the scanning tunneling topographies. The physisorption of a molecule such as the hexaphenyle-benzene at the step edge of the Si(100) show particular lateral movements which diffusion barrier can be described accurately by the dispersive term added to the DFT to describe van der Waals interactions (DFT-D). In order to identify the nature of bonding of a porphyrin molecule adsorbed on a boron doped silicon surface, we have analyzed the Laplacian of the charge density. Finally, we present a full DFT-D study of a bidimensional nanoporous supramolecular network on a silicon surface. We have evaluated the molecule-molecule and molecule-substrate interactions energies that are key parameters to understand the mechanism of formation of these networks. In this context, the simulations of STM images with multi-diffusion with the presence of a tungsten tip show a better agreement with the experimental observations than the Tersoff-Hamann approach.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Similar content being viewed by others
References
Binning G, Rohrer H, Gerber C, Weible E (1982) Phys Rev Lett 49:57
Oppenheimer R (1928) Proc Natl Acad Sci 14:363
Eigler DM, Schweizer EK (1990) Nature 344:524
Riedel D, Lastapis M, Martin M, Dujardin G (2004) Phys Rev Lett 69:121301
Xuea QK, Hashizumec T, Sakuraia T (1999) Appl Surf Sci 141:244
Wu XL, Zhou P, Lieber CM (1988) Nature 335:55
Loth S, von Bergmann K, Ternes M, Otte AF, Lutz CP, Heinrich AJ (2010) Nat Phys 6:340
Riedel D, Delattre R, Borisov AG, Teperik TV (2010) Nano Lett 10:3857
Lang N (1986) Phys Rev B 34:5947
Rosink JJWM, Blauw MA, Geerligs LJ, van der Drift E, Radelaar S (2000) Phys Rev B 62:10459
Riedel D (2010) J Phys Condens Matter 22:264009
Hohenberg P, Kohn W (1964) Phys Rev 136:B864
Tersoff J, Hamann DR (1983) Phys Rev Lett 50:1998
Bardeen J (1961) Phys Rev Lett 6:57
Sautet P, Joachim C (1988) Phys Rev B 38:12238
Sautet P, Joachim C (1988) Chem Phys Lett 153:511
Sautet P, Joachim C (1992) Surf Sci 271:387
Repp J, Meyer G, Stojkovic S, Gourdon A, Joachim C (2005) Phys Rev Lett 94:026803
Tiwari RK, Otalvaro DM, Joachim C, Saeys M (2009) Surf Sci 603:3286
Sautet P, Joachim C (1991) Chem Phys Lett 185:23
Dahlke R, Schollwöck U (2004) Phys Rev B 69:085324
Hofer WA (2003) Prog Surf Sci 71:147
Palotas K, Hofer WA (2005) J Phys Condens Matter 17:2705
Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR et al (2004) Gaussian 03, Revision C.02. Gaussian, Inc., Wallingford
Kudernac T, Ruangsupapichat N, Parschau M, Macià B, Katsonis N, Harutyunyan SR, Ernst KH, Feringa B (2011) Nature 479:208
Sugimoto Y, Abe M, Hirayama S, Oyabu N, Custance Ó, Morita S (2005) Nat Mater 4:156
Liljeroth P, Swart I, Paavilainen S, Repp J, Meyer G (2010) Nano Lett 10:2475
Swart I, Sonnleitner T, Niedenführ J, Repp J (2012) Nano Lett 12:1070
Liljeroth P, Repp J, Meyer G (2007) Science 317:1203
Comtet G, Dujardin G, Hellner H, Lastapis M, Martin M, Mayne AJ, Riedel D (2002) Phil Trans R Soc A 362:1217
Ruda HE, Polanyi JC, Yang J, Wu Z, Philipose U, Xu T, Yang S, Kavanagh KL, Liu JQ, Yang L, Wang Y, Robbie K, Yang J, Kaminska K, Cooke DG, Hegmann FA, Budz AJ, Haugen HK (2006) Nanoscale Res Lett 1:99
Yang J, Deng J, Chandrasekhar N, Joachim C (2007) J Vac Sci Technol B 25:1694
Khajetoorians AA, Wiebe J, Chilian B, Lounis S, Blügel S, Wiesendanger R (2012) Nat Phys 8:497
Riedel D, Cranney M, Martin M, Guillory R, Dujardin G, Dubois M, Sonnet P (2009) J Am Chem Soc 131:5414
Watkins M, Trevethan T, Sushko ML, Shluger A (2008) J Phys Chem C 112:4226
Cheng Z, Chu ES, Sun D, Kim D, Zhu Y, Luo M, Pawin G, Wong KL, Kwon KY, Carp R, Marsella M, Bartels L (2010) J Am Chem Soc 132:13578
He Y, Ye T, Borguet E (2002) J Am Chem Soc 124:1964
Stroscio JA, Eigler DM (1991) Science 254:1320
Custance O, Perez R, Morita S (2009) Nat Nanotechnol 4:803
Ueba H, Persson BNJ (2004) Surf Sci 566:1
Ueba H, Mii T, Lorente N, Persson BNJ (2005) J Chem Phys 123:084707
Komeda T, Kim Y, Kawai M, Persson BNJ, Ueba H (2002) Science 295:2055
Meyer G, Bartels L, Zöphel S, Henze E, Rieder KH (1997) Phys Rev Lett 78:1512
Huang Y, Rettner CT, Auerbach DJ, Wodtke AM (2000) Science 290:111
Sainoo Y, Kim Y, Okawa T, Komeda T, Shigekawa H, Kawai M (2005) Phys Rev Lett 95:246102
Ohara M, Kim Y, Kawai M (2008) Phys Rev B 78:201405(R)
Lastapis M, Martin M, Riedel D, Hellner L, Comtet G, Dujardin G (2005) Science 308:1000
Kohn W, Sham LJ (1965) Phys Rev 140:A1133
Kresse G, Furthmüller J (1996) Phys Rev B 54:11169. http://cms.mpi.univie.ac.at/vasp/
Dubois M, Delerue C, Rubio A (2007) Phys Rev B 75:041302R
Mamatkulov M, Stauffer L, Minot C, Sonnet P (2006) Phys Rev B 73:035321
McKee ML, Page M (1993) In: Lipkowitz KB, Boyd DB (eds) Reviews in computational chemistry, vol IV. VCH Publishers Inc, New York
Rasmussen T, Jacobsen KW, Leffers T, Pedersen OB, Srinivasan SG, Jónsson H (1997) Phys Rev Lett 79:3676
Jónsson H, Mills G, Jacobsen KW (1998) In: Berne BJ, Ciccotti G, Coker DF (eds) Classical and quantum dynamics in condensed phase simulations. World Scientific, Singapore
Henkelman G, Jónsson H (2000) J Chem Phys 113:9978
Henkelman G, Uberuaga BP, Jónsson H (2000) J Chem Phys 113:9901
Riedel D, Bocquet M-L, Lesnard H, Lastapis M, Lorente N, Sonnet P, Dujardin G (2009) J Am Chem Soc 131:7344
Martin M, Lastapis M, Riedel D, Dujardin G, Mamatkulov M, Stauffer L, Sonnet P (2006) Phys Rev Lett 97:216103
Waldeck DH (1991) Chem Rev 91:415
Choi BY, Kahng SJ, Kim S, Kim H, Kim HW, Song YJ, Ihm J, Kuk Y (2006) Phys Rev Lett 96:156106
Su C, Lee L-X, Chen C-F (2003) Synth Met 137:865
Alemani M, Peters MV, Hecht S, Rieder K-H, Moresco F, Grill L (2006) J Am Chem Soc 128:14446
Comstock MJ, Levy N, Kirakosian A, Cho J, Lauterwasser F, Harvey JH, Strubbe DA, Fréchet JM, Trauner D, Louie SG, Crommie MF (2007) Phys Rev Lett 99:038301
Henzl J, Bredow T, Morgenstern K (2007) Chem Phys Lett 435:278
Clemen L, Wallace RM, Taylor PA, Dresser MJ, Choyke WJ, Weinberg WH, Yates JT (1992) Surf Sci 268:205
Schmidt PM, Horn K, Dil JH, Kampen TU (2007) Surf Sci 601:1775
Rydberg H, Lundqvist BI, Langreth DC, Dion M (2000) Phys Rev B 62:6997
Hooper J, Cooper VR, Thonhauser T, Romero NA, Zerilli F, Langreth DC (2008) ChemPhysChem 9:891
Dubois M, Delerue C, Allan G (2005) Phys Rev B 71:165435
Porezag D, Frauenheim T, Köhler T, Seifert G, Kaschner R (1995) Phys Rev B 51:12947
Elstner M, Porezag D, Jungnickel G, Elsner J, Haugk M, Frauenheim T, Suhai S, Seifert G (1998) Phys Rev B 58:7260
Eschrig H (1988) The optimized LCAO method and electronic structure of extended systems. Akademieverlag, Berlin
Krüger T, Elstner M, Schiffels P, Frauenhein T (2005) J Chem Phys 122:114110
Lefebvre I, Lannoo M, Allan G, Martinage L (1988) Phys Rev B 88:8593
Labidi H, Sonnet P, Riedel D (2013) J Phys Chem C 117:13663
Gagnon E, Maris T, Arseneault PM, Maly KE, West JD (2010) Cryst Growth Des 10:648
Wang J, Cooper G, Tulumello D, Hitchcock AP (2005) J Phys Chem A 109:10886
Gagnon E, Halperin S, Métivaud V, Maly KE, Wuest JD (2010) J Org Chem 75:399
Gross L, Moresco F, Ruffieux P, Gourdon A, Joachim C, Rieder KH (2005) Phys Rev B 71:165428
Chiaravalloti F, Gross L, Rieder K-H, Stojkovic SM, Gourdon A, Joachim C, Moresco F (2007) Nat Mater 6:30
Perdew P, Burke K, Ernzerhof M (1996) Phys Rev Lett 77:3865
Blöchl E (1994) Phys Rev B 50:17953
Kresse G, Hafner J (1993) Phys Rev B 47:558
Kresse G, Furthmüller J (1996) Phys Rev B 54:11169
Kresse G, Furthmüller J (1996) Comput Mater Sci 6:15
Tersoff J, Hamann DR (1985) Phys Rev B 31:805
Grimme S (2004) J Comput Chem 25:1463
Grimme S (2006) J Comput Chem 27:1787
Grimme S, Antony J, Schwabe T, Mück-Lichtenfeld C (2007) Org Biomol Chem 5:741
Nguyen MT, Pignedoli CA, Treier M, Fasel R, Passerone D (2010) Phys Chem Chem Phys 12:992
Bellec A, Ample F, Riedel D, Dujardin G, Joachim C (2009) Nano Lett 9:144
Mingo N, Flores F (1998) Surf Sci 395:342
Devel M, Girard C, Joachim C, Martin OJF (1995) Appl Surf Sci 87:390
Roland C, Gilmer GH (1991) Phys Rev Lett 67:3188
Devel M, Girard C, Joachim C (1996) Phys Rev B 53:13159
Rogge S, Timmerman RH, Scholte PMLO, Geerligs LJ, Salemink HWM (2001) J Vac Sci Technol B 19:659
Teichmann K, Wenderoth M, Loth S, Ulbrich RG, Garleff JK, Wijnheijmer AP, Koenraad PM (2008) Phys Rev Lett 101:076103
Guoa H, Saalfrank P, Seidemanc T (1999) Prog Surf Sci 62:239
Tran Thoai DB, Zimmermann R, Grundmann M, Bimberg D (1990) Phys Rev B 42:5906
Wu SW, Ogawa N, Ho W (2006) Science 312:1362
Nguyen TH, Mahieu G, Berthe M, Grandidier B, Delerue C, Stiévenard D, Ebert P (2010) Phys Rev Lett 105:226404
Lachaud F, Jeandon C, Beley M, Ruppert R, Gros PC, Monari A, Assfeld X (2012) J Phys Chem A 116:10736
Tsuda A, Osuka A (2001) Science 293:79
Kadish KM, Smith KM, Guilard R (2000) The porphyrin handbook, vol 1–10. Academic Press, San Diego
Heimel G, Romaner L, Zojer E, Bredas J-L (2008) Acc Chem Res 41:721
Wan LJ (2006) Acc Chem Res 39:334
Weiss PS (2008) Acc Chem Res 41:1772
Yang Z-Y, Zhang H-M, Pan G-B, Wan L-J (2008) ACS Nano 2:743
Calmettes B, Nagarajan S, Gourdon A, Abel M, Porte L, Coratger R (2008) Angew Chem Int Ed 47:6994
Yang Z-Y, Zhang H-M, Yan C-J, Li S-S, Yan H-J, Song W-G, Wan L-J (2008) Proc Natl Acad Sci U S A 104:3707
Song XZ, Jaquinod L, Jentzen W, Nurco DJ, Jia SL, Khoury RG, Ma JG, Medforth CJ, Smith KM, Shelnutt JA (1998) Inorg Chem 37:2009
Huang Q, Medforth CJ, Schweitzer-Stenner R (2005) J Phys Chem A 109:10493
Song X, Jentzen W, Jaquinod L, Khoury RG, Medforth CJ, Jia CJ, Ma JG, Smith KM, Shelnutt JA (1998) Inorg Chem 37:2117
Jentzen W, Song XZ, Shelnutt JA (1997) J Phys Chem B 101:1684
Jentzen W, Simpson MC, Hobbs JD, Song X, Ema T, Nelson NY, Medforth CJ, Smith KM, Veyrat M, Mazzanti M, Ramasseul R, Marchon JC, Takeuchi T, Goddard WA III, Shelnutt JA (1995) J Am Chem Soc 117:11085
Barth JV, Constantini G, Kern K (2005) Nature 437:671
Giva PG, DiLabio GA, Pitters JL, Zikovski J, Rezeq M, Dogel S, Hofer WA, Wolkow RA (2005) Nature 435:658
Weber-Bargioni A, Auwärter W, Klappenberger F, Reichert J, Lefrançois S, Strunskus T, Wöll C, Schiffrin A, Pennec Y, Barth JV (2008) ChemPhysChem 9:89
Hamers RJ, Coulter SK, Ellison MD, Hovis JS, Padowitz DF, Schartz MP, Greenlief CM, Russel JN (2000) Acc Chem Res 33:617
Sloan PA, Palmer RE (2005) Nature 434:367
Bedrossian P, Meade RD, Mortensen K, Chen DM, Golovchenko JA, Vanderbilt D (1989) Phys Rev Lett 63:1257
Avouris P, Lyo I-W, Bozso F, Kaxiras E (1990) J Vac Sci Technol A 8:3405
Kaxiras E, Pandey KC, Himpsel FJ, Tromp RM (1990) Phys Rev B 41:1262
Shi HQ, Radny MW, Smith PV (2002) Phys Rev B 66:85329
El Garah M, Makoudi Y, Palmino F, Duverger E, Sonnet P, Chaput L, Gourdon A, Cherioux F (2009) ChemPhysChem 10:3190
Boukari K, Sonnet P, Duverger E (2012) ChemPhysChem 13:3945
Bader RFW (1991) Chem Rev 91:893
Henkelman G, Arnaldsson A, Jónsson H (2006) Comput Mater Sci 36:354
Savin A, Flad HJ, Flad J, Preuss H, von Schnering HG (1992) Angew Chem Int Ed Engl 31:185
Kohout M, Pernal K, Wagner FR, Grin Y (2004) Theor Chem Accounts 112:453
Becke AD, Edgecombe KE (1990) J Chem Phys 92:5397–5403
Savin A, Jepsen O, Flad J, Andersen OK, Preuss H, von Schnering HG (1992) Angew Chem Int Ed Engl 31:187
Savin A, Silvi B (1994) Nature 371:683
Ooi N, Rairkar A, Lindsley L, Adams JB (2006) J Phys Condens Matter 18:97
Felhösi I, Kálmán E, Póczik P (2002) Russ J Electrochem 38:230
Bain CD, Whitesides GM (1989) Angew Chem Int Ed Engl 28:506
Laibinis PE, Whitesides GM (1992) J Am Chem Soc 114:9022
Jortner J, Ratner M (eds) (1997) Molecular electronics: a chemistry of 21st century. Blackwell Science Inc., Oxford
Bosshard C, Sutter K, Prêtre P, Hulliger J, Flörsheimer M, Kaats P, Günter P (1995) Organic nonlinear optical materials, vol 1. Gordon and Breach, Amsterdam
Yokoyama T, Yokoyama S, Kamikado T, Okuno Y, Mashiko S (2001) Nature 413:619
Barth JV, Weckesser J, Cai C, Günter P, Bürgi L, Jeandupeux O, Kern K (2000) Angew Chem Int Ed 39:1230
Böhringer M, Morgenstern K, Schneider W-D, Berndt R, Mauri F, De Vita A, Car R (1999) Phys Rev Lett 83:324
Briggs GAD, Fisher AJ (1999) Surf Sci Rep 33:1
Pinto HP, Enevoldsen GH, Besenbacher F, Lauritsen JV, Foster AS (2009) Nanotechnology 20:264020
Wang YL, Cheng ZH, Deng ZT, Guo HM, Du SX, Gao HJ (2012) Chimia 66:31
Baris B, Luzet V, Duverger E, Sonnet P, Palmino F, Chérioux F (2011) Angew Chem Int Ed 50:4094
Boukari K, Duverger E, Sonnet P (2013) J Chem Phys 138:84704
Cuadrado R, Cerdá JI, Wang Y, Xin G, Berndt R, Tang H (2010) J Chem Phys 133:154701
Tkatchenko A, Romaner L, Hofmann OT, Zojer E, Ambrosch-Draxl C, Scheffler M (2010) MRS Bull 35:435
Mercurio G, McNellis ER, Martin I, Hagen S, Leyssner F, Soubatch S, Meyer J, Wolf M, Tegeder P, Tautz FS, Reuter K (2010) Phys Rev Lett 104:036102
Ruben M, Payer D, Landa A, Comisso A, Gattinoni C, Lin N, Collin J-P, Sauvage J-P, De Vita A, Kern K (2006) J Am Chem Soc 128:15644
Chen Q, Frankel DJ, Richardson NV (2002) Langmuir 18:3219
Miyake Y, Nagata T, Tanaka H, Yamazaki M, Ohta M, Kokawa R, Ogawa T (2012) ACS Nano 6:3876
Perdigão LMA, Staniec PA, Champness NR, Kelly REA, Kantorovich LN, Beton PH (2006) Phys Rev B 73:195423
Xu W, Kelly REA, Schöck M, Otero R, Lægsgaard E, Stensgaard I, Kantorovich LN, Besenbacher F (2007) Small 3:2011
Acknowledgements
This work was performed using HPC resources from GENCI-IDRIS and the supercomputer facilities of the Mésocentre de calcul de Franche-Comté. This work has been partly supported by the Agence National de la Recherche (ANR).
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2014 Springer Science+Business Media New York
About this chapter
Cite this chapter
Sonnet, P., Riedel, D. (2014). The Scanning Tunneling Microscopy of Adsorbed Molecules on Semiconductors: Some Theoretical Answers to the Experimental Observations. In: Leszczynski, J., Shukla, M. (eds) Practical Aspects of Computational Chemistry III. Springer, Boston, MA. https://doi.org/10.1007/978-1-4899-7445-7_1
Download citation
DOI: https://doi.org/10.1007/978-1-4899-7445-7_1
Published:
Publisher Name: Springer, Boston, MA
Print ISBN: 978-1-4899-7444-0
Online ISBN: 978-1-4899-7445-7
eBook Packages: Chemistry and Materials ScienceChemistry and Material Science (R0)