S. Alex Kandel

University of Notre Dame, South Bend, Indiana, United States

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Publications (41)215.92 Total impact

  • [Show abstract] [Hide abstract]
    ABSTRACT: Self-assembled monolayers of ferrocenecarboxylic acid (FcCOOH) contain two fundamental units, both stabilized by intermolecular hydrogen bonding: dimers and cyclic five-membered catemers. At surface coverages below a full monolayer, however, there is a significantly more varied structure that includes double-row clusters containing two to twelve FcCOOH molecules. Statistical analysis shows a distribution of cluster sizes that is sharply peaked compared to a binomial distribution. This rules out simple nucleation-and-growth mechanisms of cluster formation, and strongly suggests that clusters are formed in solution and collapse into rows when deposited on the Au(111) surface.
    Chemical Communications 07/2014; · 6.38 Impact Factor
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    ABSTRACT: The process of molecular self-assembly on solid surfaces is essentially one of crystallization in two dimensions, and the structures that result depend on the interplay between intermolecular forces and the interaction between adsorbates and the underlying substrate. Because a single hydrogen bond typically has an energy between 15 and 35 kilojoules per mole, hydrogen bonding can be a strong driver of molecular assembly; this is apparent from the dominant role of hydrogen bonding in nucleic-acid base pairing, as well as in the secondary structure of proteins. Carboxylic acid functional groups, which provide two hydrogen bonds, are particularly promising and reliable in creating and maintaining surface order, and self-assembled monolayers of benzoic acids produce structure that depends on the number and relative placement of carboxylic acid groups. Here we use scanning tunnelling microscopy to study self-assembled monolayers of ferrocenecarboxylic acid (FcCOOH), and find that, rather than producing dimeric or linear structures typical of carboxylic acids, FcCOOH forms highly unusual cyclic hydrogen-bonded pentamers, which combine with simultaneously formed FcCOOH dimers to form two-dimensional quasicrystallites that exhibit local five-fold symmetry and maintain translational and rotational order (without periodicity) for distances of more than 400 ångströms.
    Nature 03/2014; 507(7490):86-9. · 42.35 Impact Factor
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    ABSTRACT: Three-dimensional (3D) printing has many advantages over conventional machining techniques, and it is particularly well suited for rapid production of prototypes. This Shop Note reports pump-down curves for a small ultrahigh-vacuum chamber loaded with 3D-printed silver and titanium parts. Neither material showed any measurable adverse affect on the ultimate base pressure achieved, which was approximately 5 × 10−10 Torr. 3D-printed metals can therefore be considered suitable for select ultrahigh-vacuum applications.
    Journal of Vacuum Science & Technology A Vacuum Surfaces and Films 03/2014; 32(2):023201-023201-2. · 2.14 Impact Factor
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    ABSTRACT: A model scanning probe microscope, designed using similar principles of operation to research instruments, is described. Proximity sensing is done using a capacitance probe, and a mechanical linkage is used to scan this probe across surfaces. The signal is transduced as an audio tone using a heterodyne detection circuit analogous to that used in the theremin (one of the first electronic musical instruments, invented in the early 20th century). The instrument is useful for demonstrations and hands-on activities that introduce fundamentals of scanning probe microscopy and, by extension, nanoscience and nanotechnology. The details of instrument construction are provided, along with instructions for assembly and troubleshooting.
    Journal of chemical education 01/2014; 91(2). · 1.00 Impact Factor
  • David Y. Lee, Natalie A. Kautz, S. Alex Kandel
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    ABSTRACT: In chemical reactions at the gas–surface interface, the heterogeneity in structure of reaction sites plays a critical role in determining surface reactivity. This Perspective describes reaction mechanisms in such systems and details the use of in situ scanning probe microscopy to investigate reactions of gas-phase radicals with self-assembled alkanethiolate monolayers on gold surfaces. For both atomic hydrogen and atomic chlorine reagents, the presence of defects in the alkanethiolate surface order has a substantial influence on what reactions can occur and the speed at which they do so. Data acquired from a series of images were modeled using kinetic Monte Carlo simulations, and a surface radical reaction model was developed to explain the observed evolution of surface structure as the reactions proceed.
    Journal of Physical Chemistry Letters 11/2013; 4:4103. · 6.69 Impact Factor
  • David Y Lee, S Alex Kandel
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    ABSTRACT: The chemical reaction of atomic chlorine with mixed monolayers of alkanethiolates having different chain lengths was investigated. In situ scanning tunneling microscopy was used to acquire time-lapsed series of images, allowing the measurement of the effect of monolayer structure and composition on reactivity. The rate of chemical reaction is strongly site-dependent. In particular, the boundary between two different-length alkanethiolates greatly promotes the reactivity of nearby molecules, much more so than any other native defect typical of single-component alkanethiolate monolayers.
    The Journal of Chemical Physics 10/2013; 139(16):161103. · 3.12 Impact Factor
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    ABSTRACT: We have designed and built a scanning tunneling microscope with a compact inertial-approach mechanism that fits inside the piezoelectric scanner tube. Rigid construction allows the microscope to be operated without the use of external vibration isolators or acoustic enclosures. Thermoelectric cooling and a water-ice bath are used to increase temperature stability when scanning under ambient conditions.
    The Review of scientific instruments 10/2013; 84(10):103708. · 1.58 Impact Factor
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    ABSTRACT: Scanning tunneling microscopy (STM) in ultra-high-vacuum is used to investigate the reaction of gas-phase atomic chlorine with octanethiolate self-assembled-monolayers on Au(111). Exposure to Cl atoms results in the formation of a variety of surface defects, and eventually leads to a complete loss of order within the alkanethiolate monolayer. X-ray photoelectron spectroscopy and thermal desorption mass spectrometry show that these morphological changes are accompanied by significant chlorination of the monolayer as well as a ∼30% decrease in the amount of adsorbed sulfur. The rate of reaction is measured through the analysis of sequences of STM images, and coverage-vs.-exposure data shows that the average reactivity of any given molecule within the monolayer decreases as the reaction progresses. Working with the assumption that monolayer defects created by Cl-atom reaction will affect the reactivity of neighboring molecules, a kinetic Monte Carlo simulation shows the data are consistent with defect sites inhibiting reaction rate by a factor of 5 or more. This behavior is opposite to that found for hydrogen-atom reactions, where edge and defect sites were far more reactive. The dynamics of chlorine-atom reactivity are described primarily in terms of the formation and subsequent reaction of surface-adsorbed radicals, with surface defects providing sites where these radicals can be quenched.
    Physical Chemistry Chemical Physics 07/2013; · 4.20 Impact Factor
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    ABSTRACT: Scanning tunneling microscopy images of diferrocenylacetylene (DFA) coadsorbed with benzene on Au(111) show individual and close-packed DFA molecules, either adsorbed alongside benzene or on top of a benzene monolayer. Images acquired over a range of positive and negative tip-sample bias voltages show a shift in contrast, with the acetylene linker appearing brighter than the ferrocenes at positive sample bias (where unoccupied states primarily contribute) and the reverse contrast at negative bias. Density functional theory was used to calculate the electronic structure of the gas-phase DFA molecule, and simulated images produced through two-dimensional projections of these calculations approximate the experimental images. The symmetry of both experimental and calculated molecular features for DFA rules out a cis adsorption geometry, and comparison of experiment to simulation indicates torsion around the inter-ferrocene axis between 90° and 180° (trans); the cyclopentadienyl rings are thus angled with respect to the surface.
    Physical Chemistry Chemical Physics 04/2013; · 4.20 Impact Factor
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    ABSTRACT: The authors have developed a method of performing scanning tunneling microscopy experiments with a sample that can be controllably heated and quickly cooled. Temperatures in excess of 100 °C are achievable, and the same scanning area can be imaged multiple times before and after repeated heating cycles. This opens up for study any physical process or chemical reaction where the reactants, products, and/or intermediates can be kinetically trapped on a conductive surface at room temperature. As a demonstration of this approach, the authors have investigated desorption from 1-octanethiolate self-assembled monolayers on Au(111).
    Journal of Vacuum Science & Technology B Microelectronics and Nanometer Structures 01/2013; 31(1):3201-. · 1.36 Impact Factor
  • David Y. Lee, S. Alex Kandel
    The Journal of Chemical Physics 01/2013; 139:161103. · 3.12 Impact Factor
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    ABSTRACT: The molecule {Cp*(dppe)Fe(C≡C−)}3(1,3,5-C6H3) (Fe3) was adsorbed on a single-crystal gold surface and studied using ultrahigh-vacuum scanning tunneling microscopy (STM). Both the singly oxidized Fe3+ and doubly oxidized Fe32+ are mixed-valence ions, and localization of the charge at specific metal centers was observed as the appearance of pronounced asymmetry in STM images. Switching the tip–sample bias voltage demonstrates that this asymmetry is electronic in nature. The nature of intramolecular structure and the degree of asymmetry produced in STM images varies according to the state of the scanning tip. Constrained density functional theory was used to simulate STM images for the neutral molecule and for both mixed-valence species, and simulated images agreed closely with observed results. In particular, changing the number of molecular electronic states contributing to contrast in the STM image produced a good match to the variation in structures measured experimentally.
    The Journal of Physical Chemistry C 11/2012; 116(48):25486–25492. · 4.84 Impact Factor
  • Matthew M Jobbins, David Y Lee, S Alex Kandel
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    ABSTRACT: Scanning tunneling microscopy was used to investigate the reaction of octanethiolate self-assembled monolayers (SAMs) with atomic chlorine. We have found that exposing a SAM to low fluxes of radical Cl results primarily in the formation of new defects in areas with close-packed alkanethiolates, but has little to no effect on the domain boundaries of the SAM. Dosing high quantities of atomic chlorine results in the near-complete loss of surface order at room temperature, but not the complete removal of the thiolate monolayer. These observations are in stark contrast to the results of previous measurements of the reaction of atomic hydrogen with alkanethiolate SAMs.
    The Journal of Chemical Physics 04/2012; 136(14):141102. · 3.12 Impact Factor
  • David Y Lee, Matthew M Jobbins, S Alex Kandel
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    ABSTRACT: We describe a thermal gas cracker designed to produce low fluxes of gas-phase radicals for use in radical-surface reaction studies. A resistively heated thin piece of highly oriented pyrolytic graphite is used as the pyrolysis filament, with the major advantage that this material remains inert at high temperatures. The instrument is built within an existing titanium sublimation pump, which simplifies construction and allows for self-pumping of the radical source. Thermal generation of Cl atoms from Cl(2) was chosen to test the effectiveness of the instrument. (35)Cl and (37)Cl were generated with a concomitant decrease in parent (70)Cl(2) and (72)Cl(2) species, as monitored by a residual gas analyzer. The cracking fraction of Cl(2) as a function of cell temperature is reported, with nearly full conversion achieved at high temperature.
    The Review of scientific instruments 04/2012; 83(4):044101. · 1.58 Impact Factor
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    ABSTRACT: We present control circuits designed for electrochemically etching, reproducibly sharp STM probes. The design uses an Arduino UNO microcontroller to allow for both ac and dc operation, as well as a comparator driven shut-off that allows for etching to be stopped in 0.5-1 μs. The Arduino allows the instrument to be customized to suit a wide variety of potential applications without significant changes to hardware. Data is presented for coarse chemical etching of 80:20 platinum-iridium, tungsten, and nickel tips.
    The Review of scientific instruments 03/2012; 83(3):036105. · 1.58 Impact Factor
  • Natalie A. Kautz, S. Alex Kandel
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    ABSTRACT: We use scanning tunneling microscopy (STM) to study octanethiol self-assembled monolayers (SAMs) on Au(111) exposed to atomic hydrogen. While the overall net reaction is to remove octanethiol molecules from the underlying gold surface, the monolayer structure heavily influences the rate of this reaction and molecules located along surface defects are preferentially removed before those located in close-packed areas. Octanethiol molecules remaining on the gold surface can go through significant rearrangement: domain boundaries can change both size and structure, annealing into surrounding close-packed domains; film defects diffuse to the edge of close-packed areas; and molecules located along the edge of close-packed domains shift position, changing the size and shape of the remaining close-packed features. Monolayer reactivity increases with increasing hydrogen-atom exposure, and we compare the experimental results with kinetic Monte Carlo simulations. We find that the edges of defect sites are potentially over 500 times more reactive than close-packed monolayer areas.
    The Journal of Physical Chemistry C 02/2012; 116(7):4725–4731. · 4.84 Impact Factor
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    ABSTRACT: Au(111) surfaces are exposed to solutions containing both octanethiol and dithiocarbamate (DTC) molecules, and the resulting surface composition and structure are studied using scanning tunneling microscopy (STM). DTC adsorption and monolayer formation are favored when present at the same concentration as octanethiol in solution. Higher octanethiol concentration in solution results in the incorporation of thiol into the resulting monolayer, with a strong dependence on the chain length of the DTC molecules. For diethyldithiocarbamate, thiol adsorption is limited and close-packed thiolate monolayers are not formed even at 100:1 excesses of the thiol in solution. For didecyldithiocarbamate, higher thiol concentrations lead to the formation of full thiolate mononlayers and the complete displacement of DTC.
    The Journal of Physical Chemistry C 01/2012; 116(2):1930–1934. · 4.84 Impact Factor
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    ABSTRACT: Scanning tunneling microscopy (STM) is used to study two dinuclear organometallic molecules, meta-Fe2 and para-Fe2, which have identical molecular formulas but differ in the geometry in which the metal centers are linked through a central phenyl ring. Both molecules show symmetric electron density when imaged with STM under ultrahigh-vacuum conditions at 77 K. Chemical oxidation of these molecules results in mixed-valence species, and STM images of mixed-valence meta-Fe2 show pronounced asymmetry in electronic state density, despite the structural symmetry of the molecule. In contrast, images of mixed-valence para-Fe2 show that the electronic state density remains symmetric. Images are compared to constrained density functional (CDFT) calculations and are consistent with full localization of charge for meta-Fe2 on to a single metal center, as compared with charge delocalization over both metal centers for para-Fe2. The conclusion is that electronic coupling between the two metal centers occurs through the bonds of the organic linker, and through-space coupling is less important. In addition, the observation that mixed-valence para-Fe2 is delocalized shows that electron localization in meta-Fe2 is not determined by interactions with the Au(111) substrate or the position of neighboring solvent molecules or counterion species.
    Journal of the American Chemical Society 12/2011; 134(3):1710-4. · 11.44 Impact Factor
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    ABSTRACT: Scanning tunneling microscopy is used to study monolayers of 1-adamantanethiolate as they are exposed to gas-phase atomic hydrogen. H-atom reaction results in complete removal of the organic monolayer. The relaxation of the reconstruction present at the gold–sulfur interface results in the formation of gold-atom islands, as well as the addition of gold atoms to extant surface defects such as steps and pits. Characterization of these changes shows that for 1-adamantanethiolate monolayers, 0.18 ± 0.033 monolayers of gold adatoms participate in bonding with thiolate sulfur atoms. This results in a 1:1 Au:S ratio, in contrast to the 1:2 Au:S ratio reported for n-alkanethiolate monolayers. The difference in adatom density implies a qualitative difference in binding between n-alkanethiols and 1-adamantanethiols.
    The Journal of Physical Chemistry C 12/2011; 115(51):25437–25441. · 4.84 Impact Factor
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    ABSTRACT: Two-component octanethiolate-dialkyldithiocarbamate (DTC) monolayers were formed on Au(111) surfaces and studied using scanning tunneling microscopy (STM). Octanethiolate monolayers exposed to DTC in solution results in the erosion of octanethiolate domain boundaries and areas along terrace step edges and the insertion of DTC into these areas; this is consistent with the broad literature of substitution in alkanethiolate monolayers. Conversely, a DTC monolayer exposed to octanethiol results in displacement of DTC and the eventual formation of ordered octanethiolate domains. The effects of temperature, solution concentration, and deposition time are investigated.
    The Journal of Physical Chemistry C 09/2011; 115(41):20274–20281. · 4.84 Impact Factor

Publication Stats

401 Citations
215.92 Total Impact Points


  • 2004–2014
    • University of Notre Dame
      • • Department of Chemistry and Biochemistry
      • • Department of Electrical Engineering
      South Bend, Indiana, United States
  • 2008
    • Notre Dame de Sion
      Kansas City, Missouri, United States
  • 2000–2004
    • Pennsylvania State University
      • Department of Chemistry
      University Park, Maryland, United States