Combined Scanning Tunneling Microscopy and Infrared Spectroscopic Characterization of Mixed Surface Assemblies of Linear Conjugated Guest Molecules in Host Alkanethiolate Monolayers on Gold

Journal of Physical Chemistry B

Volumn 104, Issue 20, 2000, Pages 4880-4893

  Dunbar, T D ^a,c   Cygan, M T ^a   Bumm, L A ^a   McCarty, G S ^a   Burgin, T P ^d   Reinerth, W A ^b   Jones II, L ^b   Jackiw, J J ^a   Tour, J M ^a,e   Weiss, P S ^a   Allara, D L ^a  

^a PENNSYLVANIA STATE UNIVERSITY   (United States)

^b UNIVERSITY OF SOUTH CAROLINA   (United States)

^c SANDIA NATIONAL LABORATORIES   (United States)

^d MOTOROLA INC   (United States)

^e RICE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 0001532125     PISSN: 15206106     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp993724+     Document Type: Article

References (85)

1. (a) Metzger, R. M.; Panetta, C. A. New J. Chem. 1991, 15, 209.
2. (b) Gomez-Lopez, M.; Preece, J. A.; Stoddart, J. F. Nanotechnology 1996, 7, 183.
3. Freitas, R. A., Jr. Artif. Cells, Blood Substitutes, Immobilization Biotechnol. 1998, 26, 411.
4. (a) Aviram, A.; Ratner, M. A. Chem. Phys. Lett. 1974, 29, 277.
5. (b) Goldhaber-Gordon, D.; Montemerlo, M. S.; Love, J. C.; Opiteck, G. J.; Ellenbogen, J. C. Proc. IEEE 1997, 85, 521.
6. (c) Wada, Y. Surf. Sci. 1997, 386, 265.
7. (c) Roth, S.; Burghard, M.; Leising, G. Curr. Opin. Solid State Mater. Sci. 1998, 3, 209.
8. (d) Joachim, C.; Gimzewski, J. K. Proc. IEEE 1998, 86, 184.
9. (e) Sato, T.; Ahmed, H.; Brown, D.; Johnson, B. F. G. J. Appl. Phys. 1997, 82, 696.
10. Allara, D. L.; Dunbar, T. D.; Weiss, P. S.; Bumm, L. A.; Cygan, M. T.; Tour, J. M.; Reinerth, W. A.; Yao, Y.; Kozaki, M.; Jones, L., II, Ann. N. Y. Acad. Sci. 1998, 852, 349.
11. Cygan, M. T.; Dunbar, T. D.; Arnold, J. J.; Bumm, L. A.; Shedlock, N. F.; Burgin, T. P.; Jones, L., II; Allara, D. L.; Tour, J. M.; Weiss, P. S. J. Am. Chem. Soc. 1998, 120, 2721.
12. Bumm, L. A.; Arnold, J. J.; Cygan, M. T.; Dunbar, T. D.; Burgin, T. P.; Jones, L., II; Allara, D. L.;. Tour, J. M.; Weiss, P. S. Science 1996, 271, 1705.
13. (a) Eigler, D. M.; Weiss, P. S.; Schweizer, E. K.; Lang, N. D. Phys. Rev. Lett. 1991, 66, 1189.
14. (b) Weiss, P. S.; Eigler, D. M. Phys. Rev. Lett. 1993, 71, 3139.
15. (c) Salmeron, M.; Neubauer, G.; Folch, A.; Tomitori, M.; Ogletree, D. F.; Sautet, P. Langmuir 1993, 9, 3600.
16. (d) Weiss, P. S. Trends Anal. Chem. 1994, 13, 61.
17. Bumm, L. A.; Arnold, J. J.; Charles, L. F.; Dunbar, T. D.; Allara, D. L.; Weiss, P. S., J. Am. Chem. Soc. 1999, 121, 8017.
18. Bumm, L. A.; Arnold, J. J.; Dunbar, T. D.; Allara, D. L.; Weiss, P. S. J. Phys. Chem. B 1999, 103, 8122.
19. The chemical structure of 1 was incorrectly given in refs 5 and 6. The location of the ethyl group is correctly shown in Table 1 of this article.
20. Chen, J.; Reed, M. A.; Rawlett, A. M.; Tour, J. M. Science 1999, 286, 1550.
21. (a) Pearson, D. L.; Tour, J. T. J. Org. Chem. 1997, 62, 1376.
22. (b) Jones, L., II; Schumm, J. S.; Tour, J. M. J. Org. Chem. 1997, 62, 1388.
23. Tour, J. M.; Jones, L., II; Pearson, D. L.; Lamba, J. J. S.; Burgin, T. P.; Whitesides, G. M.; Allara, D. L.; Parikh, A. N.; Atre, S. V. J. Am. Chem. Soc. 1995, 117, 9529.
24. 2/Si films exhibited small (∼10-50 nm) Au{111} terraces with ∼20-30% of grain boundary regions which made STM measurements difficult but the excellent flatness make these samples ideally suited for 1RS (see ref 5 and Nuzzo, R. G.; Fusco, F. A.; Allara, D. L. J. Am. Chem. Soc. 1987, 109, 2358). A variety of previous work shows that despite these morphology differenc es between the two types of Au samples the character of the alkanethiolate SAMs is highly similar. For example, infrared spectral features for ambient temperature films are virtually identical for good quality polycrystalline Au (see ref 15) and {111} single-crystal surfaces (e.g., Nuzzo, R. G.; Korenic, E. M.; Dubois, L. H. J. Chem. Phys. 1990, 93, 767-7 73 ), thus showing a similar high degree of conformational order. Further, IR (ref 15) data on polycrystalline Au, X-ray scattering data on {111} single crystals (see, e.g., Fenter, P.; Eberhardt, A.; Eisenberger, P. Science 1994, 266, 1216-1218) and theoretical estimates (e.g., Gerdy, J. J.; Goddard, W. A. J. Am. Chem. Soc. 1996, 118, 3233-3236) all agree on a uniform chain tilt angle value of 28° within a ±2° range. Finally, electrochemical studies show that alkanethiolate SAMs on polycrystalline Au surfaces have low defect contents in terms of the ability to effectively block Faradaic current flow to the electrode (e.g., Porter, M. D.; Bright, T. B.; Allara, D. L.; Chidsey, C. E. D. J. Am. Chem. Soc. 1987, 109, 3359). These studies together imply that the alkanethiolate chains that form in Au grain boundary regions retain high packing densities and a high degree of conformational ordering relative to the structure on the {111} terraces. Undoubtedly there will be a decay of film translational ordering in the grain boundary regions. Unfortunately, the molecular spacings in these perturbed grain boundary regions cannot be readily characterized by scattering or scanning tip probes.
25. 2/Si films exhibited small (∼10-50 nm) Au{111} terraces with ∼20-30% of grain boundary regions which made STM measurements difficult but the excellent flatness make these samples ideally suited for 1RS (see ref 5 and Nuzzo, R. G.; Fusco, F. A.; Allara, D. L. J. Am. Chem. Soc. 1987, 109, 2358). A variety of previous work shows that despite these morphology differenc es between the two types of Au samples the character of the alkanethiolate SAMs is highly similar. For example, infrared spectral features for ambient temperature films are virtually identical for good quality polycrystalline Au (see ref 15) and {111} single-crystal surfaces (e.g., Nuzzo, R. G.; Korenic, E. M.; Dubois, L. H. J. Chem. Phys. 1990, 93, 767-7 73 ), thus showing a similar high degree of conformational order. Further, IR (ref 15) data on polycrystalline Au, X-ray scattering data on {111} single crystals (see, e.g., Fenter, P.; Eberhardt, A.; Eisenberger, P. Science 1994, 266, 1216-1218) and theoretical estimates (e.g., Gerdy, J. J.; Goddard, W. A. J. Am. Chem. Soc. 1996, 118, 3233-3236) all agree on a uniform chain tilt angle value of 28° within a ±2° range. Finally, electrochemical studies show that alkanethiolate SAMs on polycrystalline Au surfaces have low defect contents in terms of the ability to effectively block Faradaic current flow to the electrode (e.g., Porter, M. D.; Bright, T. B.; Allara, D. L.; Chidsey, C. E. D. J. Am. Chem. Soc. 1987, 109, 3359). These studies together imply that the alkanethiolate chains that form in Au grain boundary regions retain high packing densities and a high degree of conformational ordering relative to the structure on the {111} terraces. Undoubtedly there will be a decay of film translational ordering in the grain boundary regions. Unfortunately, the molecular spacings in these perturbed grain boundary regions cannot be readily characterized by scattering or scanning tip probes.
26. 2/Si films exhibited small (∼10-50 nm) Au{111} terraces with ∼20-30% of grain boundary regions which made STM measurements difficult but the excellent flatness make these samples ideally suited for 1RS (see ref 5 and Nuzzo, R. G.; Fusco, F. A.; Allara, D. L. J. Am. Chem. Soc. 1987, 109, 2358). A variety of previous work shows that despite these morphology differenc es between the two types of Au samples the character of the alkanethiolate SAMs is highly similar. For example, infrared spectral features for ambient temperature films are virtually identical for good quality polycrystalline Au (see ref 15) and {111} single-crystal surfaces (e.g., Nuzzo, R. G.; Korenic, E. M.; Dubois, L. H. J. Chem. Phys. 1990, 93, 767-7 73 ), thus showing a similar high degree of conformational order. Further, IR (ref 15) data on polycrystalline Au, X-ray scattering data on {111} single crystals (see, e.g., Fenter, P.; Eberhardt, A.; Eisenberger, P. Science 1994, 266, 1216-1218) and theoretical estimates (e.g., Gerdy, J. J.; Goddard, W. A. J. Am. Chem. Soc. 1996, 118, 3233-3236) all agree on a uniform chain tilt angle value of 28° within a ±2° range. Finally, electrochemical studies show that alkanethiolate SAMs on polycrystalline Au surfaces have low defect contents in terms of the ability to effectively block Faradaic current flow to the electrode (e.g., Porter, M. D.; Bright, T. B.; Allara, D. L.; Chidsey, C. E. D. J. Am. Chem. Soc. 1987, 109, 3359). These studies together imply that the alkanethiolate chains that form in Au grain boundary regions retain high packing densities and a high degree of conformational ordering relative to the structure on the {111} terraces. Undoubtedly there will be a decay of film translational ordering in the grain boundary regions. Unfortunately, the molecular spacings in these perturbed grain boundary regions cannot be readily characterized by scattering or scanning tip probes.
27. 2/Si films exhibited small (∼10-50 nm) Au{111} terraces with ∼20-30% of grain boundary regions which made STM measurements difficult but the excellent flatness make these samples ideally suited for 1RS (see ref 5 and Nuzzo, R. G.; Fusco, F. A.; Allara, D. L. J. Am. Chem. Soc. 1987, 109, 2358). A variety of previous work shows that despite these morphology differenc es between the two types of Au samples the character of the alkanethiolate SAMs is highly similar. For example, infrared spectral features for ambient temperature films are virtually identical for good quality polycrystalline Au (see ref 15) and {111} single-crystal surfaces (e.g., Nuzzo, R. G.; Korenic, E. M.; Dubois, L. H. J. Chem. Phys. 1990, 93, 767-7 73 ), thus showing a similar high degree of conformational order. Further, IR (ref 15) data on polycrystalline Au, X-ray scattering data on {111} single crystals (see, e.g., Fenter, P.; Eberhardt, A.; Eisenberger, P. Science 1994, 266, 1216-1218) and theoretical estimates (e.g., Gerdy, J. J.; Goddard, W. A. J. Am. Chem. Soc. 1996, 118, 3233-3236) all agree on a uniform chain tilt angle value of 28° within a ±2° range. Finally, electrochemical studies show that alkanethiolate SAMs on polycrystalline Au surfaces have low defect contents in terms of the ability to effectively block Faradaic current flow to the electrode (e.g., Porter, M. D.; Bright, T. B.; Allara, D. L.; Chidsey, C. E. D. J. Am. Chem. Soc. 1987, 109, 3359). These studies together imply that the alkanethiolate chains that form in Au grain boundary regions retain high packing densities and a high degree of conformational ordering relative to the structure on the {111} terraces. Undoubtedly there will be a decay of film translational ordering in the grain boundary regions. Unfortunately, the molecular spacings in these perturbed grain boundary regions cannot be readily characterized by scattering or scanning tip probes.
28. 2/Si films exhibited small (∼10-50 nm) Au{111} terraces with ∼20-30% of grain boundary regions which made STM measurements difficult but the excellent flatness make these samples ideally suited for 1RS (see ref 5 and Nuzzo, R. G.; Fusco, F. A.; Allara, D. L. J. Am. Chem. Soc. 1987, 109, 2358). A variety of previous work shows that despite these morphology differenc es between the two types of Au samples the character of the alkanethiolate SAMs is highly similar. For example, infrared spectral features for ambient temperature films are virtually identical for good quality polycrystalline Au (see ref 15) and {111} single-crystal surfaces (e.g., Nuzzo, R. G.; Korenic, E. M.; Dubois, L. H. J. Chem. Phys. 1990, 93, 767-7 73 ), thus showing a similar high degree of conformational order. Further, IR (ref 15) data on polycrystalline Au, X-ray scattering data on {111} single crystals (see, e.g., Fenter, P.; Eberhardt, A.; Eisenberger, P. Science 1994, 266, 1216-1218) and theoretical estimates (e.g., Gerdy, J. J.; Goddard, W. A. J. Am. Chem. Soc. 1996, 118, 3233-3236) all agree on a uniform chain tilt angle value of 28° within a ±2° range. Finally, electrochemical studies show that alkanethiolate SAMs on polycrystalline Au surfaces have low defect contents in terms of the ability to effectively block Faradaic current flow to the electrode (e.g., Porter, M. D.; Bright, T. B.; Allara, D. L.; Chidsey, C. E. D. J. Am. Chem. Soc. 1987, 109, 3359). These studies together imply that the alkanethiolate chains that form in Au grain boundary regions retain high packing densities and a high degree of conformational ordering relative to the structure on the {111} terraces. Undoubtedly there will be a decay of film translational ordering in the grain boundary regions. Unfortunately, the molecular spacings in these perturbed grain boundary regions cannot be readily characterized by scattering or scanning tip probes.
29. Laibinis, P. E.; Whitesides, G. M., Allara, D. L.; Tao, Y.-T.; Parikh, A. N.; Nuzzo, R. G. J. Am. Chem. Soc. 1991, 113, 7152.
30. Collins, R. W.; Allara, D. L.; Kim, Y.-T.; Lu, Y.; Shi, J. In Characterization of Organic Thin Films; Ulman, A., Ed.; Manning: Greenwich, CT, 1995; pp 35-55.
31. Shi, J.; Hong, B.; Parikh, A. N.; Collins, R. W.; Allara, D. L. Chem. Phys. Lett. 1995, 246, 90.
32. Parikh, A. N.; Allara, D. L. In Physics of Thin Films Series; Vedam, K., Ed.; Academic Press; New York, 1994; Vol. 19 (Optical Characterization of Real Surfaces Films), pp 279-314.
33. Ghose, A. K.; Crippen, G. M. J. Chem. Inf. Comput. Sci. 1987, 27, 21.
34. Immirzi, A.; Perini, B. Acta Crystallogr. 1971, A 33, 216. Because of possible errors due to the small sizes of crystals used in the float method of density determination, the above-referenced density estimation method was used as a check. Calculated densities were within 5% of those measured.
35. a.
36. a.
37. Parikh, A. N.; Allara, D. L. J. Chem. Phys. 1992, 96, 927.
38. For recent examples involving aromatic ring molecules, see: (a) Liedberg, B.; Yang, Z.; Engquist, I.; Wirde, M.; Gelius, U.; Götz, G.; Bäuerle, P.; Rummel, R.-M.; Ziegler, Ch.; Göpel, W. J. Phys. Chem. B 1997, 101, 5951.
39. (b) Young, J. T.; Boerio, F. J.; Zhang, Z.; Beck, T. L. Langmuir 1996, 12, 1219.
40. -1 (S-CO stretch).
41. The humidity of the chamber during imaging was found to be critical in obtaining quality images. At relative humidities above 10%, the monolayers often appeared featureless and streaky. At lower humidities, molecular resolution images were routinely obtained.
42. Takami, T.; Delamarche, E.; Michel, B.; Gerber, Ch.; Wolf, H.; Ringsdorf, H. Langmuir 1995, 11, 3876.
43. (a) Camillone, N., III; Eisenberger, P.; Leung, T. Y. B.; Scoles, G.; Poirier, G. E.; Tarlov, M. J. J. Chem. Phys. 1994, 101, 11031.
44. (b) Delamarche, E.; Michel, B.; Gerber, Ch.; Anselmetti, D.; Guntherodt, H.-J.; Wolf, H.; Ringsdorf, H. Langmuir 1994, 10, 2869.
45. (a) Wong, M. W.; Frisch, M. J.; Wiberg, K. B. J. Am. Chem. Soc. 1991, 113, 4776.
46. (b) Wong, M. W.; Wiberg, K. B. J. Chem. Phys. 1991, 95, 8991.
47. (c) Wong, M. W.; Wiberg, K. B.; Frisch, M. J. J. Am. Chem. Soc. 1992, 114, 523.
48. (d) Wong, M. W.; Wiberg, K. B.; Frisch, M. J. J. Am. Chem. Soc. 1992, 114, 1645.
49. Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Gill, P. M. W.; Johnson, B. G.; Robb, M. A.; Cheeseman, J. R.; Keith, T.; Petersson, G. A.; Montgomery, J. A.; Raghavachari, K.; Al-Laham, M. A.; Zakrzewski, V. G.; Ortiz, J. V.; Foresman, J. B.; Cioslowski, J.; Stefanov, B. B.; Nanayakkara, A.; Challacombe, M.; Peng, C. Y.; Ayala, P. Y.; Chen, W.; Wong, M. W.; Andres, J. L.; Replogle, E. S.; Gomperts, R.; Martin, R. L.; Fox, D. J.; Binkley, J. S.; Defrees, D. J.; Baker, J.; Stewart, J. P.; Head-Gordon, M.; Gonzalez, C.; Pople, J. A. Gaussian 94, Revision E.2; Gaussian, Inc.: Pittsburgh, 1994.
50. (a) Rauhut, G.; Pulay, P. J. Phys. Chem. 1995, 99, 3093.
51. (b) DegliEsposti, A.; Zerbetto, F. J. Phys. Chem. A 1997, 101, 7283.
52. Ramondo, R. Can. J. Chem. 1992, 70, 314.
53. Laposa, J. D. Spectrochim. Acta 1979, 35 A, 65.
54. Lide, D. R., Ed. CRC Handbook of Chemistry and Physics, CRC Press: Boca Raton, FL, 1990.
55. The presence of negative frequencies reveals that the structure is at a saddle point on the geometric potential energy surface.
56. Varsyanyi, G. Assignments for Vibrational Spectra of Seven Hundred Benzene Derivatives; Wiley: New York, 1974; Vol. I.
57. yy = 0) yields d ∼14.6 Å. This leaves a discrepancy of 14.6-13.5 = 1.6. Further changes in any of these parameters to give thickness values approaching the limit of the molecular length (13.5 Å) become physically unrealistic.
58. yy = 0) yields d ∼14.6 Å. This leaves a discrepancy of 14.6-13.5 = 1.6. Further changes in any of these parameters to give thickness values approaching the limit of the molecular length (13.5 Å) become physically unrealistic.
59. These shifts arise from intrinsic perturbations of the bonding potentials in the two molecular environments. Accompanying perturbations of the charge flow dynamics, and thus the intrinsic mode intensities, also can be expected.
60. (a) Collard, D. M.; Fox, M. A. Langmuir 1991, 7, 1192.
61. (b) Schlenoff, J. B.; Li, M.; Ly, H. J. Am. Chem. Soc. 1995, 117, 12528.
62. (c) Biebuyck, H. A.; Whitesides, G. M. Langmuir 1993, 9, 1766.
63. Porter, M. D.; Bright, T. B.; Allara, D. L.; Chidsey, C. E. D. J. Am. Chem. Soc. 1987, 109, 3359.
64. Schönenberger, C.; Jorritsma, J.; Sondag-Huethorst, J. A. M.; Fokkink, L. G. J. J. Phys. Chem. 1995, 99, 3259.
65. Poirier, G. E.; Tarlov, M. J. Langmuir 1994, 10, 2853.
66. Given the dense packing of the chains on the terraces, the exchange mechanism at the terraces could involve a preliminary desorption of an adsorbate chain followed by backfilling of the transient hole. The latter could occur by transport of a solute molecule or by migration of the hole via adsorbate hopping to a SAM defect region where solute insertion could occur (see: Stranick, S. J.; Parikh, A. N.; Tao, Y.-T.; Allara, D. L.; Weiss, P. S. J. Phys. Chem. 1994, 98, 7636). Studies to determine this mechanism are underway in our laboratories.
67. 3 hydrogen of an all-trans alkanethiolate and S to terminal O of 2a, and were determined from molecular mechanics modeling (Hyperchem). Each length was then multiplied by cos 30° to account for the tilt.
68. Herzberg, G. Infrared and Raman Spectra of Polyatomic Molecules; Van Nostrand Reinhold: New York, 1945; pp 534-537.
69. Pouchert, C. J., Ed. The Aldrich Library of FT-IR Spectra; Aldrich Chemical Co.: Milwaukee, WI, 1985 (Vol. 1), 1989 (Vol. 3).
70. Pouchert, C. J., Ed. The Aldrich Library of FT-IR Spectra; Aldrich Chemical Co.: Milwaukee, WI, 1985 (Vol. 1), 1989 (Vol. 3).
71. Weiss, P. S.; Bumm, L. A.; Dunbar, T. D.; Burgin, T. P.; Tour, J. M.; Allara, D. L. Ann. N. Y. Acad. Sci. 1998, 852, 145.
72. The errors in θ and ψ come from fitting simulations to films of 21 and 25 Å (the two limits of thickness given an uncertainty of ±2 Å). This uncertainty in thickness also roughly covers errors arising from neglecting refractive index anisotropy in the ellipsometric thickness calculation. Repeating simulations for the high and low limits on thickness led to high and low tilt angles and low and high twist angles.
73. (a) Snyder, R. G.; Strauss, H. L.; Elliger, C. A. J. Phys. Chem. 1982, 86, 5145.
74. (b) MacPhail, R. A.; Strauss, H. L.; Snyder, R. G.; Elliger, C. A. J. Phys. Chem. 1984, 88, 334.
75. Snyder, R. G.; Maroncelli, M.; Strauss, H. L.; Hallmark, V. M. J. Phys. Chem. 1986, 90, 5623
76. The most accurate model would consist of a distribution of isolated 3 molecules and bundles of 3 molecules, inserted at various defect sites in the A8 SAM, as observed by STM imaging (see section 3.3.2). Application of this model would require accurate knowledge of the optical response (optical or dielectric functions) of (1) isolated 3 molecules partially immersed in a vacuum (or a gas-phase) and partially in a hydrocarbon medium and (2) the pure solid phase of 3. Since data for the two states of case 1 would be extremely difficult to obtain, more approximate models were chosen based on case 2 in which the polycrystalline form of 3b was used as a reference state for the inserted molecules.
77. We estimate that errors in using the isotropic approximation are less than the experimental SWE measurement errors. While one expects some degree of anisotropy for the long conjugated aromatic portion of molecule 3, the alkyl chain portion, which comprises over 50% of the atoms in the molecule, is highly disordered (see discussion of the high frequency IRS data) and thus essentially isotropic. The net result is that the entire molecule exhibits only weak optical anisotropy.
78. 3 was determined for input into a new IRS simulation.
79. 3).
80. -1.
81. Poirier, G. E.; Pylant, E. D. Science 1996, 272, 1145.
82. Weck, M.; Jackiw, J. J.; Rossi, R. R.; Weiss, P. S.; Grubbs, R. H. J. Am. Chem. Soc. 1999, 121, 4088.
83. -βl, where j = tunneling current, l = tip to substrate distance through the medium, and β = the decay constant associated with the medium.
84. (a) Charles, L. F. M.S. Thesis, The Pennsylvania State University, University Park, PA.
85. (b) Charles, L. F.; Weiss, P. S. In preparation.