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Prediction of scanning tunneling microscope images by computational quantum chemistry: chemical models and software design


Coley, Terry Ronald (1993) Prediction of scanning tunneling microscope images by computational quantum chemistry: chemical models and software design. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/jey5-ex12.


We have created chemical models for predicting and interpreting STM images of several specific systems. Detailed studies are made of transition metal dichalcogenides (MoS_2 and MoTe_2), Xe on Ni (110), C_3H_4 on Ni (110) and n-butyl benzene on a graphite model (C_(42)O_6H_(12). In the case of MoS_2 we study the ambiguity in the STM images regarding the assignment of peaks to the subsurface metal or the surface chalcogenide. In the Ni models we study STM imaging mechanisms for cases where the adsorbate states lie far above and below the metal Fermi level. The large n-butyl on graphite system models a system where adsorbate states can play a direct role in the imaging. Results from the cluster studies are related to various STM imaging modes, including constant current mode, constant height mode, and barrier height imaging. Two new procedures are developed to aid in computational prediction of STM images. First, we implement an algorithm for computing Bardeen-type tunneling matrix elements from ab initio wave functions in Gaussian basis sets. Second, we show how to obtain state densities as a function of energy for bulk substrate/adsorbate systems using only Fock matrix elements from cluster calculations. Initial results are presented for a linear chain of Ni atoms with a perturbing Xe atom. A software environment for computational chemistry developed in the course of performing these calculations is presented. Tools for creating computational servers to perform chemistry calculations are described. Embedded in each chemistry server is a public domain control language created by J. Ousterhout at the University of California, Berkeley. This allows the development of a variety of clients for controlling the servers using a common language. Clients can be simple text "scripts" that organize a calculation, graphical interfaces, or control streams from other programs. All software entities are designed in an object oriented fashion discussed in the text.

Item Type:Thesis (Dissertation (Ph.D.))
Subject Keywords:Chemistry
Degree Grantor:California Institute of Technology
Division:Chemistry and Chemical Engineering
Major Option:Chemistry
Thesis Availability:Public (worldwide access)
Research Advisor(s):
  • Goddard, William A., III (advisor)
  • Baldeschwieler, John D. (co-advisor)
Thesis Committee:
  • Unknown, Unknown
Defense Date:10 May 1993
Record Number:CaltechTHESIS:10192009-102157942
Persistent URL:
Default Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:5310
Deposited By: Tony Diaz
Deposited On:09 Nov 2009 20:22
Last Modified:19 Apr 2021 22:32

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