Why molecules look the way they do in STM : a systematic functional group approach

Citation

Claypool, Christopher L. (1999) Why molecules look the way they do in STM : a systematic functional group approach. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/AAWF-HM84. https://resolver.caltech.edu/CaltechTHESIS:10192009-081325550

Abstract

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, allenes, and disulfides. 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. 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. Additionally, a theoretical model based on perturbation theory has been developed to predict the scanning tunneling microscopy (STM) images of molecules adsorbed on graphite. The model is applicable to a variety of different molecules with reasonable computational effort and provides images that are in qualitative agreement with experimental results. The computations correlate well with the STM data of functionalized alkanes and allow assessment of the structure and orientation of most of the functionalized alkanes that have been studied experimentally. In addition, the computations suggest that the highly diffuse virtual orbitals of the adsorbed molecules, despite being much farther in energy from the Fermi level of the graphite than the occupied orbitals, may play an important role in determining e STM image contrast of such systems.

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