@article{hahn_bharath_kim_kim_jeong_pearl_2013, title={Adsorption Site Selectivity for Thiophene on Reconstructed Si(5512)-2 x 1 Surface}, volume={117}, ISSN={["1932-7447"]}, DOI={10.1021/jp401932r}, abstractNote={The covalent binding of thiophene molecules to a Si(5 5 12)–2 × 1 surface was investigated using scanning tunneling microscopy and density functional theory calculations. The molecular attachment occurred exclusively between the bonding of the 2,5 carbon atoms and the two silicon adatoms without the involvement of the sulfur atom (over 90%). The binding structure formed a di−σ bond with a planar butterfly-like configuration. Adsorption at other sites, including at the dimer, tetramer, or honeycomb rows, occurred much less frequently. Our calculations predicted that the adsorption energies of the thiophene molecules were 1.02–1.56 eV at the adatom, dimer, and tetramer sites. The molecules adsorbed on the honeycomb rows with a low adsorption energy (below 1 eV). The binding modes of the simple aromatic molecules onto the Si(5 5 12)–2 × 1 surface are compared and discussed.}, number={21}, journal={JOURNAL OF PHYSICAL CHEMISTRY C}, author={Hahn, Jae Ryang and Bharath, Satyaveda C. and Kim, Gyu-Hyeong and Kim, Ki Wan and Jeong, Sukmin and Pearl, Thomas P.}, year={2013}, month={May}, pages={11197–11202} }
 @article{hahn_bharath_kim_jeong_pearl_2011, title={Binding Structures of Pyrrole on Si(5512)-2 x 1 Surfaces}, volume={115}, ISSN={["1932-7447"]}, DOI={10.1021/jp205553f}, abstractNote={In an effort to understand the reaction mechanisms involved in the adsorption of organic aromatic molecules on high-index Si surfaces, the reactions of pyrrole molecules adsorbed onto Si(5 5 12)–2 ...}, number={34}, journal={JOURNAL OF PHYSICAL CHEMISTRY C}, author={Hahn, Jae Ryang and Bharath, Satyaveda C. and Kim, Gyu-Hyeong and Jeong, Sukmin and Pearl, Thomas P.}, year={2011}, month={Sep}, pages={17111–17117} }
 @article{hahn_bharath_jeong_pearl_2011, title={Binding structures of propylene glycol stereoisomers on the Si(001)-2x1 surface: A combined scanning tunneling microscopy and theoretical study}, volume={134}, ISSN={["1089-7690"]}, DOI={10.1063/1.3523650}, abstractNote={The binding configuration of propylene glycol stereoisomer molecules adsorbed on the Si(001)-2×1 surface was investigated using a combination of scanning tunneling microscopy (STM) and density functional theory calculations. Propylene glycol was found to adsorb dissociatively via two hydroxyl groups exclusively as a bridge between the ends of two adjacent dimers along the dimer row. The chirality was preserved during bonding to Si atoms and was identifiable with STM imaging. The large number of propylene glycol conformers in the gas phase was reduced to a single configuration adsorbed on the surface at low molecular coverage.}, number={4}, journal={JOURNAL OF CHEMICAL PHYSICS}, author={Hahn, Jae Ryang and Bharath, Satyaveda C. and Jeong, Sukmin and Pearl, Thomas P.}, year={2011}, month={Jan} }
 @article{luo_bemelmans_pearl_2011, title={Unveiling Molecular Adsorption Geometry in Cyclohexanethiolate Self-Assembled Monolayers with Local Barrier Height Imaging}, volume={115}, ISSN={["1932-7447"]}, DOI={10.1021/jp205637f}, abstractNote={The Au–S interface of thiol-based, self-assembled monolayers grown on Au(111) surfaces is far less understood than it should be. Local barrier height imaging, which has recently resolved work function variations in the buried interface of alkanethiolate monolayers, is now used to study self-assembled monolayers on Au(111) formed by cyclohexanethiol, a molecule with a flexible aliphatic ring structure. Multiple ordered phases are observed, consistent with its conformational flexibility which makes multiple interadsorbate interactions possible. In one particular phase, the appearance of two readily distinguishable features in local barrier height images implies at least two types of adsorption sites. Correlation of simultaneously acquired topographic and local barrier height data allows for a preliminary structural model that accounts for adsorption geometry.}, number={34}, journal={JOURNAL OF PHYSICAL CHEMISTRY C}, author={Luo, Pengshun and Bemelmans, Norman L. and Pearl, Thomas P.}, year={2011}, month={Sep}, pages={17118–17122} }
 @article{santagata_lakhani_davis_luo_nardelli_pearl_2010, title={Chiral Steering of Molecular Organization in the Limit of Weak Adsorbate-Substrate Interactions: Enantiopure and Racemic Tartaric Acid Domains on Ag(111)}, volume={114}, ISSN={["1932-7447"]}, DOI={10.1021/jp912124v}, abstractNote={The influence of intermolecular interactions involving molecular chiral centers on two-dimensional organization in the limit of a weak adsorbate−surface interaction has been studied with low-temperature scanning tunneling microscopy (STM) and density functional theory (DFT). A model system composed of a chiral organic molecule, tartaric acid, and an inert metallic surface, Ag(111), was employed. Dual component films formed from the serial deposition of (S,S)- and (R,R)-tartaric acid enantiomers onto this surface exhibit homochiral domain formation as revealed by molecularly resolved STM images. In contrast, a unique tartaric acid enantiomeric heteropair is experimentally and computationally verified as the basis unit of films formed via the deposition of both enantiomers simultaneously from a racemic (1:1) mixture. The molecular adsorption geometry relative to the Ag(111) lattice in both enantiomerically pure and racemic domains is determined primarily by the interaction of chiral centers between nearest ...}, number={19}, journal={JOURNAL OF PHYSICAL CHEMISTRY C}, author={Santagata, Nancy M. and Lakhani, Amit M. and Davis, Bryce F. and Luo, Pengshun and Nardelli, Marco Buongiorno and Pearl, Thomas P.}, year={2010}, month={May}, pages={8917–8925} }
 @article{bharath_pearl_2010, title={Growth of ultrathin layers of Au on LiNbO3(0001) measured with atomic force microscopy}, volume={604}, ISSN={["1879-2758"]}, DOI={10.1016/j.susc.2010.01.022}, abstractNote={Abstract Atomic force microscopy (AFM) has been used to characterize the growth of Au deposited via evaporation onto the positive face of single crystalline, lithium niobate, LiNbO 3 (0 0 0 1) surface. In order to study the mechanisms for the ordering and aggregation of a noble metal on this ferroelectric surface, topographic and phase contrast imaging of the fractional surface coverage of Au were performed. Atomically flat, uniformly poled LiNbO 3 surfaces were prepared via an ambient high temperature anneal and served as a support for the thin gold films. These gold atomic layers were grown using electron bombardment evaporation sources under ultra-high vacuum (UHV) conditions and subsequently characterized under both vacuum and ambient environments. Using AFM it was found that gold preferentially nucleates at the top of LiNbO 3 substrate step edges. With increased coverage, island formation proceeds due to local aggregation of adsorbed gold on each substrate terrace. Based on local imaging of the growth morphology, the data is discussed in terms of thin film growth mechanisms as well as the influence of native surface features such as defects and charge distribution. Understanding growth mechanisms for gold layers on ferroelectric surfaces allows for a fuller appreciation of how atomic deposition of metal atoms on patterned poled LiNbO 3 surfaces would occur as well as yielding greater insight on the atomic characteristics of metals on ferroelectric interfaces.}, number={7-8}, journal={SURFACE SCIENCE}, author={Bharath, Satyaveda C. and Pearl, Thomas P.}, year={2010}, month={Apr}, pages={713–717} }
 @article{andrews_pearl_2010, title={Modification of Ag(111) surface electronic structure via weak molecular adsorption of adenine measured with low temperature scanning tunneling microscopy and spectroscopy}, volume={132}, ISSN={["1089-7690"]}, DOI={10.1063/1.3427248}, abstractNote={Low temperature scanning tunneling microscopy and spectroscopy have been used to resolve modifications to the Ag(111) surface electronic structure due to the weak adsorption of the nucleobase adenine. Differential conductance spectroscopy recorded at 15 K reveals an upward energetic shift of the surface state native to Ag(111) from a band edge of -67 meV on the clean surface to +82.5 meV recorded over adenine islands. Differential conductance images show the impact of adenine domains on the density of available states as a function of energy relative to the uncovered Ag terraces as well as free-electron-like scattering in the adenine domains. Dispersion of the parallel wave vector of scattered electrons in the adenine domains is compared with the dispersion for electron scattering in bare silver and the ratio of effective masses for electrons in those bands is 1.1+/-0.2. It is hypothesized that this shift occurs due to a combination of effects brought on by the adsorption of adenine including dielectric screening of the first image potential.}, number={21}, journal={JOURNAL OF CHEMICAL PHYSICS}, author={Andrews, Katie M. and Pearl, Thomas P.}, year={2010}, month={Jun} }
 @article{luo_bernelmans_woody_pearl_2009, title={Molecular Voids Formed from Effective Attraction in Submonolayer DNA Deposited on Au(111)}, volume={25}, ISSN={["0743-7463"]}, DOI={10.1021/la900470h}, abstractNote={The development of DNA-based biosensors requires a deep understanding of how DNA molecules adsorb and organize on solid state surfaces as well as the electronic properties of individual and aggregates of DNA molecules. Using scanning tunneling microscopy (STM) and atomic force microscopy (AFM), we have successfully characterized an attractive force driven molecular void formation for DNA chemically adsorbed on Au(111) as a function of strand length and deposition conditions. Here we report the observation of these void structures formed on the Au(111) surface by adsorption of both 45 and 90 base pair long, thiolated double-stranded DNA. We found that the average void diameter decreases when increasing the number of base pairs exposed to the surface. The critical determinant in the molecular void formation is the total charge delivered to the surface via the adsorption of the DNA strands and the related counterions, which can ultimately be quantified by the number of base pairs in each adsorbed DNA molecule. Complementary measurements involving STM and AFM suggest that an intact Au(111) surface area is preserved inside the void and is surrounded by a submonolayer of DNA molecules adsorbed on the surface. The discussion of the possible mechanisms for the void formation implies an effective attraction between the DNA molecules.}, number={14}, journal={LANGMUIR}, author={Luo, Pengshun and Bernelmans, Norman L. and Woody, Michael S. and Pearl, Thomas P.}, year={2009}, month={Jul}, pages={7995–8000} }
 @article{bharath_pimputkar_pronschinske_pearl_2008, title={Liquid crystal deposition on poled, single crystalline lithium niobate}, volume={254}, ISSN={["1873-5584"]}, DOI={10.1016/j.apsusc.2007.08.040}, abstractNote={For the purpose of elucidating the mechanisms for molecular organization at poled ferroelectric surfaces, single crystalline lithium niobate (LN), ‘Z-cut’ along the (0 0 0 1) plane, has been prepared and characterized and subsequently exposed to liquid crystal molecules. As a model system we chose to study the anchoring of 4-n-octyl-4′-cyanobiphenyl (8CB) to LN. Liquid crystalline films are of interest because of their useful electronic and optical properties as well as chemical sensing attributes. Low-energy electron diffraction (LEED), atomic force microscopy (AFM), surface contact angle measurements (CA), and X-ray photoelectron spectroscopy (XPS) were used to characterize the surface of lithium niobate as well as the nature of 8CB films grown on the surface. Atomically flat LN surfaces were prepared as a support for monolayer thick, 8CB molecular domains. 8CB liquid crystal molecules were deposited by an ambient vaporization technique and the films were analyzed using XPS and CA. Understanding electrostatic anchoring mechanisms and thin film organization for this molecule on uniformly poled surfaces allows for a fuller appreciation of how molecular deposition of other polarizable molecules on periodically poled and patterned poled lithium niobate surfaces would occur.}, number={7}, journal={APPLIED SURFACE SCIENCE}, author={Bharath, S. C. and Pimputkar, K. R. and Pronschinske, A. M. and Pearl, T. P.}, year={2008}, month={Jan}, pages={2048–2053} }
 @article{santagata_luo_lakhani_dewitt_day_norton_pearl_2008, title={Organizational structure and electronic decoupling of surface bound chiral domains and biomolecules}, volume={8}, ISSN={["1558-1748"]}, DOI={10.1109/JSEN.2008.923187}, abstractNote={For the development of reagentless biological and chemical species detection at the single molecule level using external fields, including terahertz radiation, it is paramount to study model systems that uncover how intermolecular and molecule-surface interactions dictate monolayer ordering and electronic properties. This paper addresses two types of molecule-surface interactions and two distinct molecular systems, both of which impact our fundamental understanding of confined molecular domains and single molecule detection. We will first discuss the ordering and electronic characteristics of a chiral molecule, tartaric acid , weakly bound to an achiral metal surface, Ag(111), as studied with low temperature scanning tunneling microscopy (STM). This particular molecule-surface system contains many key elements, including hydrogen bonding interactions and stereochemical features, that would be common to other functional detection schemes. This paper will also treat the characterization of isolated, thiolated DNA molecules chemically bound to Au(111) terraces. Ambient STM and atomic force microscopy (AFM) measurements of both short and long DNA structures in both single and double strand configurations will be discussed with particular attention paid to imaging mechanisms involved. These results are particularly relevant to systems involving biomolecules anchored to inert metal surfaces, such as those used in external field-based assays.}, number={5-6}, journal={IEEE SENSORS JOURNAL}, author={Santagata, Nancy M. and Luo, Pengshun and Lakhani, Amit M. and DeWitt, Darryl J. and Day, B. Scott and Norton, Michael L. and Pearl, Thomas P.}, year={2008}, pages={758–766} }
 @inproceedings{santagata_lakhani_dewitt_luo_pearl_2008, title={Probing molecular-level organizational structure and electronic decoupling of tartaric acid domains supported on Ag(111)}, volume={100}, booktitle={Proceedings of the 17th international vacuum congress/13th international conference on surface science/international conference on nanoscience and technology}, author={Santagata, N. M. and Lakhani, A. M. and DeWitt, D. J. and Luo, P. and Pearl, T. P.}, year={2008} }
 @article{lakhani_dewitt_sant'agata_pearl_2007, title={Persistence of chirality for a weakly bound adsorbate: (R,R)- and (S,S)-tartaric acid/Ag(111)}, volume={111}, ISSN={["1932-7447"]}, DOI={10.1021/jp068639y}, abstractNote={The interaction of tartaric acid (C4H6O6), including both (R,R) and (S,S) enantiomers, with Ag(111) has been studied using low-energy electron diffraction (LEED) and low-temperature scanning tunneling microscopy (STM). As evidenced by both diffraction and microscopy, this molecule binds very weakly to the Ag lattice, and the interadsorbate forces strongly dictate the formation of ordered monolayers that are globally chiral. In addition to a discussion of the role that hydrogen bonding plays in the formation of monolayer domains, comparisons of this system to the growth of tartaric acid on other metallic surfaces will be made.}, number={15}, journal={JOURNAL OF PHYSICAL CHEMISTRY C}, author={Lakhani, A. M. and DeWitt, D. J. and Sant'Agata, N. M. and Pearl, T. P.}, year={2007}, month={Apr}, pages={5750–5755} }
 @article{lakhani_kelly_pearl_2006, title={Design and operation of a versatile, ultrahigh vacuum, low temperature scanning probe microscope}, volume={77}, number={4}, journal={Review of Scientific Instruments}, author={Lakhani, A. M. and Kelly, S. J. and Pearl, T. P.}, year={2006} }
 @article{smith_nanayakkara_woehrle_pearl_blake_hutchison_weiss_2006, title={Spectral diffusion in the tunneling spectra of ligand-stabilized undecagold clusters}, volume={128}, ISSN={["1520-5126"]}, DOI={10.1021/ja061040r}, abstractNote={We report diffusion in the tunneling spectra of isolated, ligand-stabilized undecagold (Au11) clusters immobilized by attachment to alpha,omega-alkanedithiolate tethers inserted into alkanethiolate self-assembled monolayers. We use scanning tunneling microscopy and spectroscopy at cryogenic (UHV, 4 K) conditions to measure these clusters' conductance with complete control of their chemical and physical environment; additionally, thermal broadening of their electronic states as well as their mobility is minimized. At low temperature, the Au11 clusters demonstrate Coulomb blockade behavior, with zero-conductance gaps resulting from quantum size effects. Surprisingly, chemically identical and even single particles produced different families of tunneling spectra, comparable to previous results for heterogeneous distributions of particles. We hypothesize that, while these particles are chemically attached to the surface of the SAM for measurement, these assemblies may still be sufficiently dynamic to affect their transport properties significantly.}, number={29}, journal={JOURNAL OF THE AMERICAN CHEMICAL SOCIETY}, author={Smith, Rachel K. and Nanayakkara, Sanjini U. and Woehrle, Gerd H. and Pearl, Thomas P. and Blake, Meaghan M. and Hutchison, James E. and Weiss, Paul S.}, year={2006}, month={Jul}, pages={9266–9267} }