S Alex Kandel

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

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Publications (32)132.39 Total impact

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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. · 38.60 Impact Factor
  • 01/2014; 91(2).
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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 01/2014; 32(2):023201-023201-2. · 1.43 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. · 6.59 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. · 3.16 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. · 1.52 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; · 3.83 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; · 3.83 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-.
  • David Y. Lee, S. Alex Kandel
    The Journal of Chemical Physics 01/2013; 139:161103. · 3.16 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. · 3.16 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. · 1.52 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. · 1.52 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. · 10.68 Impact Factor
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    ABSTRACT: {Cp*(dppe)Fe(C≡C-)}(2)(1,3-C(6)H(4)) is studied both as a neutral molecule, Fe(II)-Fe(II), and as a mixed-valence complex, Fe(II)-Fe(III). Scanning tunneling microscopy (STM) is used to image these species at 77 K under ultrahigh-vacuum conditions. The neutral molecule Fe(II)-Fe(II) has a symmetric, "dumbbell" appearance in STM images, while the mixed-valence complex Fe(II)-Fe(III) demonstrates an asymmetric, bright-dim double-dot structure. This asymmetry results from localization of the electron to one of the iron-ligand centers, a result which is confirmed through comparison to theoretical STM images calculated using constrained density-functional theory (CDFT). The observation of charge localization in mixed-valence complexes outside of the solution environment opens up new avenues for the control and patterning of charge on surfaces, with potential applications in smart materials and molecular electronic devices.
    Journal of the American Chemical Society 09/2010; 132(38):13519-24. · 10.68 Impact Factor
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    ABSTRACT: Scanning tunneling microscopy is used to investigate the structure of sequentially adsorbed coronene/octanethiol monolayers on Au(111). In these experiments, coronene-covered gold surfaces are exposed to octanethiol vapor. The resulting mixed monolayers are covered by close-packed octanethiol domains with clusters of coronene located within octanethiol domain boundaries. For these systems, the positions of coronene on the surface are determined by the kinetics of octanethiol monolayer formation and the local structure of the gold. The initial coverage and order of the coronene-covered surface influence the final structure of the mixed coronene/alkanethiol monolayer: deposition of coronene from the vapor phase, which creates a relatively lower coverage and higher degree of order than solution-based deposition, results in smaller coronene clusters. Statistical analysis of the locations of clusters of coronene shows that depending on the deposition parameters, coronene clusters are repelled in varying degree by upward-going and downward-going steps or are attracted to the top edges of surface step defects. In contrast to clusters, isolated coronene molecules are observed in the middle of close-packed octanethiol domains, but also appear to have an affinity for the edge of downward-going steps. We compare these results to mixed monolayers composed of C70 and octanethiol.
    Surface Science 01/2010; · 1.84 Impact Factor
  • Song Guo, S. Alex Kandel
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    ABSTRACT: Single-molecule electronic components are potential building blocks for next-generation electronic devices. One architecture for such devices is quantum dot cellular automata (QCA), in which binary information is encoded in the charge configuration of a single cell and transferred by electric coupling between neighboring cells. A single mixed-valence molecule with two oxidation−reduction centers can serve as a QCA cell, and ensemble measurements have shown that such molecules may have the desired electronic properties. Scanning tunneling microscopy (STM) is used to image dinuclear metal complexes, trans-[Cl(dppe)2Ru(C≡C)6Ru(dppe)2Cl] (Ru2) on Au(111) at 77 K. Oxidation to Ru2+[PF6]− creates an unbalanced charge that localizes on one end group of the otherwise symmetric Ru2 molecule. This electronic asymmetry appears in STM images, which also resolve the associated [PF6]− counterions. Comparison of Ru2 and Ru2+ monolayers show that Coulomb interactions create long-range ordering of Ru2+ electronic charge. This is a requirement for functionality in a QCA device.Keywords (keywords): quantum dot cellular automata (QCA); pulse deposition; ultrahigh vacuum (UHV); low-temperature scanning tunneling microscopy; molecular line
    Journal of Physical Chemistry Letters - J PHYS CHEM LETT. 12/2009; 1(1).
  • Natalie A. Kautz, S. Alex Kandel
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    ABSTRACT: The nature of the sulfur−gold bond in alkanethiol films self-assembled on Au(111) surfaces is widely contested, despite significant interest in these systems over the last 25 years. Recent theoretical and experimental studies have suggested gold adatoms are incorporated into the alkanethiol−gold interface. We have exposed alkanethiol self-assembled monolayers (SAMs) to gas-phase hydrogen atoms to remove the monolayer; the gold adatoms remain on the surface and form features that we observe using scanning tunneling microscopy (STM). The features include the formation of single-atom-thick gold islands, decreasing size of surface vacancy pits, and faceting of terrace step edges; compared to the alkanethiol-terminated surface, these features indicate a net increase in the amount of gold present on the surface, compared to the alkanethiol-terminated bulk structure. Varying the length of the alkane chain does not affect the total adatom coverage, as the adatom coverages for ethanethiol (0.172 ± 0.039), octanethiol (0.143 ± 0.033), and dodecanethiol (0.154 ± 0.024) SAMs are within experimental error of one another. This corresponds to one gold adatom for every six atoms in the bulk-terminated surface, and thus one gold adatom for every two alkanethiol molecules.
    Journal of Physical Chemistry C - J PHYS CHEM C. 10/2009; 113(44).
  • Natalie A Kautz, S Alex Kandel
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    ABSTRACT: Alkanethiol self-assembled monolayers on Au(111) are widely studied, yet the exact nature of the sulfur-gold bond is still debated. Recent studies suggest that Au(111) is significantly reconstructed, with alkanethiol molecules binding to gold adatoms on the surface. These adatoms are observed using scanning tunneling microscopy before and after removing the organic monolayer with an atomic hydrogen beam. Upon monolayer removal, changes in the gold substrate are seen in the formation of bright, triangularly shaped islands, decreasing size of surface vacancy islands, and faceting of terrace edges. A 0.143 +/- 0.033 increase in gold coverage after monolayer removal shows that there is one additional gold adatom for every two octanethiol molecules on the surface.
    Journal of the American Chemical Society 07/2008; 130(22):6908-9. · 10.68 Impact Factor
  • Song Guo, S Alex Kandel
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    ABSTRACT: Ultrahigh-vacuum scanning tunneling microscopy (STM) was used to study trans-[Cl(dppe)2Ru(C Triple Bond C)6Ru(dppe)2Cl] [abbreviated as Ru2, diphenylphosphinoethane (dppe)] on Au(111). This large organometallic molecule was pulse deposited onto the Au(111) surface under ultrahigh-vacuum (UHV) conditions. UHV STM studies on the prepared sample were carried out at room temperature and 77 K in order to probe molecular adsorption and to characterize the surface produced by the pulse deposition process. Isolated Ru2 molecules were successfully imaged by STM at room temperature; however, STM images were degraded by mobile toluene solvent molecules that remain on the surface after the deposition. Cooling the sample to 77 K allows the solvent molecules to be observed directly using STM, and under these conditions, toluene forms organized striped domains with regular domain boundaries and a lattice characterized by 5.3 and 2.7 A intermolecular distances. When methylene chloride is used as the solvent, it forms analogous domains on the surface at 77 K. Mild annealing under vacuum causes most toluene molecules to desorb from the surface; however, this annealing process may lead to thermal degradation of Ru2 molecules. Although pulse deposition is an effective way to deposit molecules on surfaces, the presence of solvent on the surface after pulse deposition is unavoidable without thermal annealing, and this annealing may cause undesired chemical changes in the adsorbates under study. Preparation of samples using pulse deposition must take into account the characteristics of sample molecules, solvent, and surfaces.
    The Journal of Chemical Physics 02/2008; 128(1):014702. · 3.16 Impact Factor