Source of image contrast in STM images of functionalized alkanes on graphite: A systematic functional group approach

Christopher L. Claypool, Francesco Faglioni, William A. Goddard, Harry B. Gray, Nathan S Lewis, R. A. Marcus

Research output: Contribution to journalArticle

260 Citations (Scopus)

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 submolecular 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. Additionally, the bias dependence of these STM images has been investigated and the contrast vs bias behavior is related to factors involving electron transfer and hole transfer that have been identified as potentially being important in dominating the electronic coupling in molecular electron transfer processes.

Original languageEnglish
Pages (from-to)5978-5995
Number of pages18
JournalJournal of Physical Chemistry B
Volume101
Issue number31
Publication statusPublished - Jul 31 1997

Fingerprint

Alkanes
Graphite
image contrast
Scanning tunneling microscopy
Paraffins
Functional groups
alkanes
scanning tunneling microscopy
graphite
electronics
Molecules
electron transfer
alcohols
Alcohols
molecules
Quantum chemistry
Nitriles
Alkynes
Ethers
Electrons

ASJC Scopus subject areas

  • Physical and Theoretical Chemistry
  • Engineering(all)

Cite this

Claypool, C. L., Faglioni, F., Goddard, W. A., Gray, H. B., Lewis, N. S., & Marcus, R. A. (1997). Source of image contrast in STM images of functionalized alkanes on graphite: A systematic functional group approach. Journal of Physical Chemistry B, 101(31), 5978-5995.

Source of image contrast in STM images of functionalized alkanes on graphite : A systematic functional group approach. / Claypool, Christopher L.; Faglioni, Francesco; Goddard, William A.; Gray, Harry B.; Lewis, Nathan S; Marcus, R. A.

In: Journal of Physical Chemistry B, Vol. 101, No. 31, 31.07.1997, p. 5978-5995.

Research output: Contribution to journalArticle

Claypool, CL, Faglioni, F, Goddard, WA, Gray, HB, Lewis, NS & Marcus, RA 1997, 'Source of image contrast in STM images of functionalized alkanes on graphite: A systematic functional group approach', Journal of Physical Chemistry B, vol. 101, no. 31, pp. 5978-5995.
Claypool, Christopher L. ; Faglioni, Francesco ; Goddard, William A. ; Gray, Harry B. ; Lewis, Nathan S ; Marcus, R. A. / Source of image contrast in STM images of functionalized alkanes on graphite : A systematic functional group approach. In: Journal of Physical Chemistry B. 1997 ; Vol. 101, No. 31. pp. 5978-5995.
@article{e33761ca34a5417d8e91a1f0537274dd,
title = "Source of image contrast in STM images of functionalized alkanes on graphite: A systematic functional group approach",
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 submolecular 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. Additionally, the bias dependence of these STM images has been investigated and the contrast vs bias behavior is related to factors involving electron transfer and hole transfer that have been identified as potentially being important in dominating the electronic coupling in molecular electron transfer processes.",
author = "Claypool, {Christopher L.} and Francesco Faglioni and Goddard, {William A.} and Gray, {Harry B.} and Lewis, {Nathan S} and Marcus, {R. A.}",
year = "1997",
month = "7",
day = "31",
language = "English",
volume = "101",
pages = "5978--5995",
journal = "Journal of Physical Chemistry B Materials",
issn = "1520-6106",
publisher = "American Chemical Society",
number = "31",

}

TY - JOUR

T1 - Source of image contrast in STM images of functionalized alkanes on graphite

T2 - A systematic functional group approach

AU - Claypool, Christopher L.

AU - Faglioni, Francesco

AU - Goddard, William A.

AU - Gray, Harry B.

AU - Lewis, Nathan S

AU - Marcus, R. A.

PY - 1997/7/31

Y1 - 1997/7/31

N2 - 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 submolecular 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. Additionally, the bias dependence of these STM images has been investigated and the contrast vs bias behavior is related to factors involving electron transfer and hole transfer that have been identified as potentially being important in dominating the electronic coupling in molecular electron transfer processes.

AB - 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 submolecular 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. Additionally, the bias dependence of these STM images has been investigated and the contrast vs bias behavior is related to factors involving electron transfer and hole transfer that have been identified as potentially being important in dominating the electronic coupling in molecular electron transfer processes.

UR - http://www.scopus.com/inward/record.url?scp=0031176371&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=0031176371&partnerID=8YFLogxK

M3 - Article

AN - SCOPUS:0031176371

VL - 101

SP - 5978

EP - 5995

JO - Journal of Physical Chemistry B Materials

JF - Journal of Physical Chemistry B Materials

SN - 1520-6106

IS - 31

ER -