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The Source of Image Contrast in STM Images of Functionalized Alkanes on Graphite: A Systematic Functional Group Approach

C.L. Claypool*, F. Faglioni, W.A. Goddard III, H.B. Gray, N.S. Lewis, and R.A. Marcus

California Institute of Technology

This is an abstract for a talk to be given at the Fifth Foresight Conference on Molecular Nanotechnology.

A series of functionalized alkanes and/or alkyl alcohols have been prepared and imaged by scanning tunneling microscopy (STM) methods on graphite surfaces. The stability of these ordered overlayers has facilitated reproducible collection of STM images at room temperature with sub-molecular resolution, in most cases allowing identification of individual hydrogen atoms in the alkane chains, but in all cases allowing identification of molecular length features and other aspects of the image that can be unequivocally related to the presence of functional groups in the various molecules of concern. Functional groups imaged in this study include halides (X=F, Cl, Br, I), amines, alcohols, nitriles, alkenes, alkynes, ethers, thioethers, and disulfides. Except for -Cl and -OH, all of the other functional groups could be distinguished from each other and from -Cl or -OH through an analysis of their STM metrics and image contrast behavior. The dominance of molecular topography in producing the STM images of alkanes and alkanols was established experimentally and also was consistent with quantum chemistry calculations. Unlike the contrast of the methylene regions of the alkyl chains, the STM contrast produced by the various functional groups was not dominated by topographic effects, indicating that variations in local electronic coupling were important in producing the observed STM images of these regions of the molecules. For molecules in which electronic effects overwhelmed topographic effects in determining the image contrast, a simple model is presented to explain the variation in the electronic coupling component that produces the contrast between the various functional groups observed in the STM images.

*Corresponding Address:
Christopher Claypool, California Institute of Technology, Dept. of Chemistry,127-72, Pasadena, CA 91125 ph: (818) 395-3964 e-mail:
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