S. Alex Kandel

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

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Publications (44)235.76 Total impact

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    ABSTRACT: The preparation of 7-Fc(+) -8-Fc-7,8-nido-[C2 B9 H10 ](-) (Fc(+) FcC2 B9 (-) ) demonstrates the successful incorporation of a carborane cage as an internal counteranion bridging between ferrocene and ferrocenium units. This neutral mixed-valence Fe(II) /Fe(III) complex overcomes the proximal electronic bias imposed by external counterions, a practical limitation in the use of molecular switches. A combination of UV/Vis-NIR spectroscopic and TD-DFT computational studies indicate that electron transfer within Fc(+) FcC2 B9 (-) is achieved through a bridge-mediated mechanism. This electronic framework therefore provides the possibility of an all-neutral null state, a key requirement for the implementation of quantum-dot cellular automata (QCA) molecular computing. The adhesion, ordering, and characterization of Fc(+) FcC2 B9 (-) on Au(111) has been observed by scanning tunneling microscopy.
    No preview · Article · Oct 2015 · Angewandte Chemie International Edition
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    ABSTRACT: Monolayers of indole-2-carboxylic acid and indole-3-carboxylic acid on gold are studied using ultrahigh-vacuum scanning tunneling microscopy. Both molecules form symmetric, cyclic, hydrogen-bonded pentamers, a structure that is stabilized by the presence of a weak hydrogen-bond donor (NH or CH) adjacent to the carboxylic acid on the five-membered ring. In addition to pentamers, indole-2-carboxylic acid forms hexamers and catemer chains, while indole-3-carboxylic acid monolayers are generally disordered. Density functional theory calculations show that pentamers and hexamers have stability comparable to dimers or short catemers. The coexistence of all of these structures likely arises from the nonequilibrium conditions present in solution during pulse deposition of the monolayer.
    No preview · Article · Sep 2015 · The Journal of Physical Chemistry C
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    ABSTRACT: Low-temperature scanning tunneling microscopy is used to observe self-assembled structures of ferrocenedicarboxylic acid (Fc(COOH)2) on the Au(111) surface. The surface is prepared by pulse-deposition of Fc(COOH)2 dissolved in methanol, and the solvent is evaporated before imaging. While the rows of hydrogen-bonded dimers that are common for carboxylic acid species are observed, the majority of adsorbed Fc(COOH)2 is instead found in six-molecule clusters with a well-defined and chiral geometry. The coverage and distribution of these clusters are consistent with a random sequential adsorption model, showing that solution-phase species are determinative of adsorbate distribution for this system under these reaction conditions.
    No preview · Article · Mar 2015 · The Journal of Chemical Physics
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    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.
    No preview · Article · Jul 2014 · Chemical Communications
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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.
    No preview · Article · Mar 2014 · Nature
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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.
    No preview · Article · Mar 2014 · Journal of Vacuum Science & Technology A Vacuum Surfaces and Films
  • Rebecca C. Quardokus · Natalie A. Wasio · S. Alex Kandel
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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.
    No preview · Article · Jan 2014 · Journal of chemical education
  • 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.
    No preview · Article · Nov 2013 · Journal of Physical Chemistry Letters
  • 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.
    No preview · Article · Oct 2013 · The Journal of Chemical Physics
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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.
    No preview · Article · Oct 2013 · The Review of scientific instruments
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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.
    No preview · Article · Jul 2013 · Physical Chemistry Chemical Physics
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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.
    No preview · Article · Apr 2013 · Physical Chemistry Chemical Physics
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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).
    No preview · Article · Jan 2013 · Journal of Vacuum Science & Technology B Microelectronics and Nanometer Structures
  • David Y. Lee · S. Alex Kandel

    No preview · Article · Jan 2013 · The Journal of Chemical Physics
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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.
    No preview · Article · Nov 2012 · The Journal of Physical Chemistry C
  • 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.
    No preview · Article · Apr 2012 · The Journal of Chemical Physics
  • 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.
    No preview · Article · Apr 2012 · The Review of scientific instruments
  • Matthew M Jobbins · Annette F Raigoza · S Alex Kandel
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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.
    No preview · Article · Mar 2012 · The Review of scientific instruments
  • 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.
    No preview · Article · Feb 2012 · The Journal of Physical Chemistry C
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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.
    Preview · Article · Jan 2012 · The Journal of Physical Chemistry C

Publication Stats

592 Citations
235.76 Total Impact Points


  • 2004-2015
    • University of Notre Dame
      • Department of Chemistry and Biochemistry
      South Bend, Indiana, United States
  • 2000-2004
    • Pennsylvania State University
      • Department of Chemistry
      University Park, Maryland, United States