Low-temperature mobility and structure formation of a prochiral aromatic thiol (2,5-dichlorothiophenol) on Cu(111).
TL;DR: A low-temperature scanning tunneling microscopy study of increasing coverages of 2,5-dichlorothiophenol finds the formation of adsorbate islands at low coverage, which coalesce into a well-ordered film of horizontally adsorbed molecules at increasing coverage, indicating significant mobility of the thiols on Cu(111) even at low temperatures and attractive adsorbates-adsorbate interactions.
Abstract: We present a low-temperature scanning tunneling microscopy study of increasing coverages of 2,5-dichlorothiophenol, an asymmetrically halo-substituted aromatic thiol, on Cu(111). At low coverage, deprotonation of the thiol occurs spontaneously upon adsorption at 80 K. Albeit the low deposition temperature, we find the formation of adsorbate islands at low coverage, which coalesce into a well-ordered film of horizontally adsorbed molecules at increasing coverage. This behavior indicates (i) significant mobility of the thiols on Cu(111) even at low temperatures and (ii) attractive adsorbate-adsorbate interactions. At higher coverages intermolecular interactions prevent long-range diffusion of adsorbates and thermal activation of the S-H bond becomes necessary. A close analysis of the molecular films reveals chiral recognition between neighboring molecules, which leads to the formation of enantiopure areas on the surface. Upright orientation of individual molecules starts at the boundaries between such phases and can be induced by scanning tunneling microscopy.
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TL;DR: This Review provides an overview of vacuum-deposited organic networks at metal surfaces, using intermolecular hydrogen bonding, metal-atom coordination and in situ polymerization.
Abstract: The formation of single-layer-thick molecular networks at metal surfaces is governed by the interplay between intermolecular and interfacial interactions. This Review highlights how, with films built by vacuum deposition, these interactions can be modulated to form substrates that may be useful as catalysts or templates for further deposition steps.
422 citations
TL;DR: This review presents a simple hierarchical scheme to categorize the chirality of adsorbate-surface systems and suggests that there is no clear evidence of any preference for either homochiral or heterochiral aggregation at the molecular level by chiral and prochiral adsorbates on surfaces.
Abstract: Research on surface chirality is motivated by the need to develop functional chiral surfaces for enantiospecific applications. While molecular chirality in 3D has been the subject of study for almost two centuries, many aspects of 2D chiral surface chemistry have yet to be addressed. In 3D, racemic mixtures of chiral molecules tend to aggregate into racemate (molecularly heterochiral) crystals much more frequently than conglomerate (molecularly homochiral) crystals. Whether chiral adsorbates on surfaces preferentially aggregate into heterochiral rather than homochiral domains (2D crystals or clusters) is not known. In this review, we have made the first attempt to answer the following question based on available data: in 2D racemic mixtures adsorbed on surfaces, is there a clear preference for homochiral or heterochiral aggregation? The current hypothesis is that homochiral packing is preferred on surfaces; in contrast to 3D where heterochiral packing is more common. In this review, we present a simple hierarchical scheme to categorize the chirality of adsorbate–surface systems. We then review the body of work using scanning tunneling microscopy predominantly to study aggregation of racemic adsorbates. Our analysis of the existing literature suggests that there is no clear evidence of any preference for either homochiral or heterochiral aggregation at the molecular level by chiral and prochiral adsorbates on surfaces.
83 citations
TL;DR: Initial stages of a chiral phase transition in the monolayer of a quinacridone derivative on the Au(111) surface were investigated by scanning tunneling microscopy at submolecular resolution and are significant for the understanding and control of chiralphase transitions in related molecular systems like liquid crystals.
Abstract: Initial stages of a chiral phase transition in the monolayer of a quinacridone derivative on the Au(111) surface were investigated by scanning tunneling microscopy at submolecular resolution. The prochiral molecules form a homochiral lamella phase at low coverages upon adsorption. A transition to a racemate lattice is observed with increasing coverage. Enantiomers of a homochiral lamella line become specifically substituted by opposite enantiomers such that a heterochiral structure evolves. Due to the higher density, lateral alkyl chains are bent away from the surface. Our findings are significant for the understanding and control of chiral phase transitions in related molecular systems like liquid crystals.
35 citations
TL;DR: It is demonstrated that the hard/soft rules of inorganic chemistry can be used to rationalize the observed trend of molecular interaction strengths with the soft gold surface, that is, P>Se>S.
Abstract: Surface molecular self-assembly is a fast advancing field with broad applications in sensing, patterning, device assembly, and biochemical applications. A vast number of practical systems utilize alkane thiols supported on gold surfaces. Whereas a strong Au-S bond facilitates robust self-assembly, the interaction is so strong that the surface is reconstructed, leaving etch pits that render the monolayers susceptible to degradation. By using different head group elements to adcust the molecule-surface interaction, a vast array of new systems with novel properties may be formed. In this paper we use a carefully chosen set of molecules to make a direct comparison of the self-assembly of thioether, selenoether, and phosphine species on Au(111). Using the herringbone reconstruction of gold as a sensitive readout of molecule-surface interaction strength, we correlate head-group chemistry with monolayer (ML) properties. It is demonstrated that the hard/soft rules of inorganic chemistry can be used to rationalize the observed trend of molecular interaction strengths with the soft gold surface, that is, P>Se>S. We find that the structure of the monolayers can be explained by the geometry of the molecules in terms of dipolar, quadrupolar, or van der Waals interactions between neighboring species driving the assembly of distinct ordered arrays. As this study directly compares one element with another in simple systems, it may serve as a guide for the design of self-assembled monolayers with novel structures and properties.
29 citations
TL;DR: In this paper, a combination of theory and experiment is used to interrogate the surface bonding geometry and rotational dynamics of a simple asymmetric thioether, butyl methyl sulfide.
Abstract: A combination of theory and experiment is used to interrogate the surface bonding geometry and rotational dynamics of a simple asymmetric thioether, butyl methyl sulfide. Calculations predict that binding occurs to a Au surface through one of the lone pairs on the sulfur atom and that the alkyl tails lie almost parallel to the surface. The unbonded lone pair remains unperturbed, and the geometry around the S atom is essentially tetrahedral, and hence two surface-bound enantiomers of the prochiral molecule are formed with an R-S inversion barrier that is predicted to be large. The rapidly rotating molecules can be clearly distinguished upon atomic-scale imaging by their mirror image pinwheel appearance. The binding of asymmetric dialkyl sulfides leads to the formation of surface-bound enantiomers, which has important consequences for studies in which thioether linkers are used in conjunction with chiral moieties and indicates that diastereomeric effects may be at play in these systems.
27 citations
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TL;DR: In this paper, benzene-1,4-dithiol molecules were self-assembled onto the two facing gold electrodes of a mechanically controllable break junction to form a statically stable gold-sulfur-aryl-solfur-gold system, allowing for direct observation of charge transport through the molecules.
Abstract: Molecules of benzene-1,4-dithiol were self-assembled onto the two facing gold electrodes of a mechanically controllable break junction to form a statically stable gold-sulfur-aryl-sulfur-gold system, allowing for direct observation of charge transport through the molecules. Current-voltage measurements at room temperature demonstrated a highly reproducible apparent gap at about 0.7 volt, and the conductance-voltage curve showed two steps in both bias directions. This study provides a quantative measure of the conductance of a junction containing a single molecule, which is a fundamental step in the emerging area of molecular-scale electronics.
3,114 citations
TL;DR: Over time the conductance switching of single and bundled phenylene ethynylene oligomers isolated in matrices of alkanethiolate monolayers is tracked, concluding that the switching is a result of conformational changes in the molecules or bundles, rather than electrostatic effects of charge transfer.
Abstract: We tracked over time the conductance switching of single and bundled phenylene ethynylene oligomers isolated in matrices of alkanethiolate monolayers. The persistence times for isolated and bundled molecules in either the ON or OFF switch state range from seconds to tens of hours. When the surrounding matrix is well ordered, the rate at which the inserted molecules switch is low. Conversely, when the surrounding matrix is poorly ordered, the inserted molecules switch more often. We conclude that the switching is a result of conformational changes in the molecules or bundles, rather than electrostatic effects of charge transfer.
1,158 citations
TL;DR: In this paper, the authors used the picture of Wigner and Bardeen according to which the work function is a sum of a volume contribution and a contribution due to a double layer on the surface of the metal.
Abstract: Work function is experimentally known to be different for different faces of a crystal by amounts ranging from one-tenth to half a volt. For tungsten the faces can be arranged according to decreasing work function as follows: 110, 211, 100 and finally 111. The explanations so far suggested for the differences of the work function are discussed and shown to give either an incorrect sequence or a wrong order of magnitude of the observed differences. The author uses the picture of Wigner and Bardeen according to which the work function is a sum of a volume contribution and a contribution due to a double layer on the surface of the metal. The origin of the latter can be described in the following manner. With every atom one can associate a polyhedron ("$s$-polyhedron") with the atom at its center, such that it contains all points nearer to the atom under consideration than to any other atom. If the distribution of the electron density within these polyhedra of the surface atoms was the same as for the inside atoms then there would be no double layer on the surface. However, this is not the case since the total energy is lowered by a redistribution of the electron cloud on the surface. There are two effects: the first is a partial spread of the charge out of the $s$-polyhedra and the second is a tendency to smooth out the surface of the polyhedra. In consequence of the second effect the surfaces of equal charge density are more nearly plane than in the original picture. The two effects have opposite influences and since they are comparable in magnitude, it is not possible to predict the sign of the total double layer without numerical computations. Some general formulae for the double layers are derived and discussed more fully in the case of a simple cubic and a body-centered cubic lattice. The minimum problem of the surface energy is solved for four faces of a body-centered crystal and the results are applied to the case of tungsten. One obtains the differences between the work functions for different directions. The results agree satisfactorily with the experimental data: assuming a reasonable density of the free electrons, one obtains the correct sequence of faces and the correct differences of the work function. The surface energies are calculated an d found in agreement with the observed stability of certain crystal faces.
1,117 citations
University of California, Berkeley1, Alcatel-Lucent2, University of Southern California3, Georgia Institute of Technology4, University of Cambridge5, University at Buffalo6, University of Mainz7, University of Nottingham8, Northwestern University9, Rutgers University10, Plant & Food Research11, University of Arkansas System12, Tokyo Institute of Technology13
TL;DR: This article contains brief descriptive discussions of the key physical features of all new algorithms and theoretical models, together with sample calculations that illustrate their performance.
Abstract: Q-Chem 2.0 is a new release of an electronic structure programpackage, capable of performing first principles calculations on the ground andexcited states of molecules using both density functional theory and wavefunction-based methods. A review of the technical features contained withinQ-Chem 2.0 is presented. This article contains brief descriptive discussions of thekey physical features of all new algorithms and theoretical models, together withsample calculations that illustrate their performance. c 2000 John Wiley S electronic structure; density functional theory;computer program; computational chemistry Introduction A reader glancing casually at this article mightsuspect on the basis of its title that it is a thinlydisguised piece of marketing for a program pack-age. This is not the case. Rather, it is an attemptto document the key methodologies and algorithmsof our electronic structure program package, Q-Chem 2.0, in a complete and scientifically accurateway, with full references to the original literature.This is important for two principal reasons. First,while the use of electronic structure programs isburgeoning, many users of such programs do nothave much feel for the underlying algorithms thatmake large-scale calculations routine even on suchreadily available hardware as personal computers.Therefore, a link between the program package andthe original literature that is written at the level ofan introductory overview can be a useful bridge.Second, while citations of large-scale commercialprograms in published applications are tradition-ally part of the conditions of use of such codes, they
610 citations
TL;DR: Scanning tunnelling microscopy studies of cysteine adsorbed to a (110) gold surface show that molecular pairs formed from a racemic mixture of this naturally occurring amino acid are exclusively homochiral, and that their binding to the gold surface is associated with local surface restructuring.
Abstract: Stereochemistry plays a central role in controlling molecular recognition and interaction: the chemical and biological properties of molecules depend not only on the nature of their constituent atoms but also on how these atoms are positioned in space. Chiral specificity is consequently fundamental in chemical biology and pharmacology1,2 and has accordingly been widely studied. Advances in scanning probe microscopies now make it possible to probe chiral phenomena at surfaces at the molecular level. These methods have been used to determine the chirality of adsorbed molecules3,4,5, and to provide direct evidence for chiral discrimination in molecular interactions6 and the spontaneous resolution of adsorbates into extended enantiomerically pure overlayers3,7,8,9. Here we report scanning tunnelling microscopy studies of cysteine adsorbed to a (110) gold surface, which show that molecular pairs formed from a racemic mixture of this naturally occurring amino acid are exclusively homochiral, and that their binding to the gold surface is associated with local surface restructuring. Density-functional theory10 calculations indicate that the chiral specificity of the dimer formation process is driven by the optimization of three bonds on each cysteine molecule. These findings thus provide a clear molecular-level illustration of the well known three-point contact model11,12 for chiral recognition in a simple bimolecular system.
540 citations