Supramolecular assembly of strongly chemisorbed size- and shape-defined chiral clusters: S- and R-alanine on Cu(110)

Enantiopure molecules form apparently racemic monolayers of chiral cyclic pentamers

Ultra-high vacuum scanning tunneling microscopy (UHV-STM) was used to investigate two related molecules pulse-deposited onto Au(111) surfaces: indoline-2-carboxylic acid and proline (pyrrolidine-2-carboxylic acid). Indoline-2-carboxylic acid and proline form both dimers and C5-symmetric "pinwheel" pentamers. Enantiomerically pure S-(-)-indoline-2-carboxylic acid and S-proline were used, and the pentamer structures observed for both were chiral. However, the presence of apparently equal numbers of 'right-' and 'left-handed' pinwheels is contrary to the general understanding that the chirality of the molecule dictates supramolecular chirality. A variety of computational methods were used to elucidate pentamer geometry for S-proline. Straightforward geometry optimization proved difficult, as the size of the cluster and the number of possible intermolecular interactions produced an interaction potential with multiple local minima. Instead, the Amber force field was used to exhaustively search all of phase space for chemically reasonable pentamer structures, producing a limited number of candidate structures that were then optimized as gas-phase clusters using density functional theory (DFT). The binding energies of the two lowest-energy pentamers on the Au(111) surface were then calculated by plane-wave DFT using the VASP software, and STM images predicted. These calculations indicate that the right- and left-handed pentamers are instead two different polymorphs.

Covalent and Hydrogen Bonding in Adsorption of Alanine Molecules on Si(111)7×7

Molecular adsorption bonding configurations and specific interfacial chemistry of alanine on Si(111)7×7 have been determined by combining the results from scanning tunneling microscopy (STM) and X-ray photoelectron spectroscopy (XPS) with ab initio calculations based on the density functional theory (DFT). XPS spectra of the N 1s region show that alanine molecules bind to the 7×7 surface by N-Si covalent bonding, while STM imaging reveals that such N-H dissociative adsorption of alanine occurs on an adjacent Si adatom-restatom pair, with the dehydrogenated alanine moiety and dissociated H atom occupying the Si adatom and restatom sites, respectively. At a sample bias above +2 V, the dehydrogenated alanine appears as a bright round protrusion, slightly off-center from a Si adatom site and leaning toward the opposite Si adatom across the dimer wall. The off-center character can be attributed to an electrostatic attraction between the electron-rich carbonyl O of the dehydrogenated alanine and electron-deficient nearest Si adatom across the dimer wall. Our DFT calculation also shows that the monodentate O-Si bonding configuration resulting from O-H dissociative adsorption is more thermodynamically favorable than the experimentally observed N-Si bonding configuration, suggesting that the interfacial dissociative adsorption reaction is a kinetically controlled rather than a thermodynamically driven process. Alanine molecules in the second adlayer (transitional layer) are found to attach to those in the first adlayer (interfacial layer) by N···HO hydrogen bonding, as supported by the presence of the N 1s feature at 401.0 eV. An alanine molecule H-bonded to a dehydrogenated alanine in the first adlayer has also been observed in STM as a brighter and larger protrusion close to the expected location of the free OH group in the dehydrogenated first-adlayer alanine. No thick zwitterionic alanine film can be obtained at room temperature possibly due to steric constraint caused by the methyl group.

Breakdown of chiral recognition of amino acids in reduced dimensions

The homochirality of amino acids in living organisms is one of the great mysteries in the phenomena of life. To understand the chiral recognition of amino acids, we have used scanning tunnelling microscopy to investigate the self-assembly of molecules of the amino acid tryptophan (Trp) on Au(111). Earlier experiments showed only homochiral configurations in the self-assembly of amino acids, despite using a mixture of the two opposite enantiomers. In our study, we demonstrate that heterochiral configurations can be favored energetically when L- and D-Trp molecules are mixed to form self-assembly on the Au surface. Using density functional theory calculations, we show that the indole side chain strongly interacts with the Au surface, which reduces the system effectively to two-dimension, with chiral recognition disabled. Our study provides important insight into the recognition of the chirality of amino acid molecules in life.

On-Surface Evolution of meso-Isomerism in Two-Dimensional Supramolecular Assemblies

Chiral structures created through the adsorption of molecules onto achiral surfaces play pivotal roles in many fields of science and engineering. Here, we present a systematic study of a novel chiral phenomenon on a surface in terms of organizational chirality, that is, meso-isomerism, through coverage-driven hierarchical polymorphic transitions of supramolecular assemblies of highly symmetric π-conjugated molecules. Four coverage-dependent phases of dehydrobenzo[12]annulene were uniformly fabricated on Ag(111), exhibiting unique chiral characteristics from the single-molecule level to two-dimensional supramolecular assemblies. All coverage-driven phase transitions stem from adsorption-induced pseudo-diastereomerism, and our observation of a lemniscate-type (∞) supramolecular configuration clearly reveals a drastic chiral phase transition from an enantiomeric chiral domain to a meso-isomeric achiral domain. These findings provide new insights into controlling two-dimensional chiral architectures on surfaces.

Imaging on-surface hierarchical assembly of chiral supramolecular networks

The bottom-up assembly of chiral structures usually relies on a cascade of molecular recognition interactions. A thorough description of these complex stereochemical mechanisms requires the capability of imaging multilevel coordination in real-time. Here we report the first direct observation of hierarchical expression of supramolecular chirality at work, for 10,10'-dibromo-9,9'-bianthryl (DBBA) on Cu(111). Molecular recognition first steers the growth of chiral organometallic chains and then leads to the formation of enantiopure islands. The structure of the networks was determined by noncontact atomic force microscopy (nc-AFM), while high-speed scanning tunnelling microscopy (STM) revealed details of the assembly mechanisms at the ms time-scale. The direct observation of the chirality transfer pathways allowed us to evaluate the enantioselectivity of the interchain coupling.

Surface-Mediated Hydrogen Bonding of Proteinogenic α-Amino Acids on Silicon

Understanding the adsorption, film growth mechanisms, and hydrogen bonding interactions of biological molecules on semiconductor surfaces has attracted much recent attention because of their applications in biosensors, biocompatible materials, and biomolecule-based electronic devices. One of the most challenging questions when studying the behavior of biomolecules on a metal or semiconductor surface is "What are the driving forces and film growth mechanisms for biomolecular adsorption on these surfaces?" Despite a large volume of work on self-assembly of amino acids on single-crystal metal surfaces, semiconductor surfaces offer more direct surface-mediated interactions and processes with biomolecules. This is due to their directional surface dangling bonds that could significantly perturb hydrogen bonding arrangements. For all the proteinogenic biomolecules studied to date, our group has observed that they generally follow a "universal" three-stage growth process on Si(111)7×7 surface. This is supported by corroborating data obtained from a three-pronged approach of combining chemical-state information provided by X-ray photoelectron spectroscopy (XPS) and the site-specific local density-of-state images obtained by scanning tunneling microscopy (STM) with large-scale quantum mechanical modeling based on the density functional theory with van der Waals corrections (DFT-D2). Indeed, this three-stage growth process on the 7×7 surface has been observed for small benchmark biomolecules, including glycine (the simplest nonchiral amino acid), alanine (the simplest chiral amino acid), cysteine (the smallest amino acid with a thiol group), and glycylglycine (the smallest (di)peptide of glycine). Its universality is further validated here for the other sulfur-containing proteinogenic amino acid, methionine. We use methionine as an example of prototypical proteinogenic amino acids to illustrate this surface-mediated process. This type of growth begins with the formation of a covalent-bond driven interfacial layer (first adlayer), followed by that of a transitional layer driven by interlayer and intralayer hydrogen bonding (second adlayer), and then finally the zwitterionic multilayers (with intralayer hydrogen bonding). The important role of surface-mediated hydrogen bonding as the key for this universal three-stage growth process is demonstrated. This finding provides new insight into biomolecule-semiconductor surface interactions often found in biosensors and biomolecular electronic devices. We also establish the trends in the H-bond length among different types of the hydrogen bonding for dimolecular structures in the gas phase and on the Si(111)7×7 surface, the latter of which could be validated by their STM images. Finally, five simple rules of thumb are developed to summarize the adsorption properties of these proteinogenic biomolecules as mediated by hydrogen bonding, and they are expected to provide a helpful guide to future studies of larger biomolecules and their potential applications.

Chiral selectivity of amino acid adsorption on chiral surfaces--the case of alanine on Pt

We study the binding pattern of the amino acid alanine on the naturally chiral Pt surfaces Pt(531), Pt(321), and Pt(643). These surfaces are all vicinal to the {111} direction but have different local environments of their kink sites and are thus a model for realistic roughened Pt surfaces. Alanine has only a single methyl group attached to its chiral center, which makes the number of possible binding conformations computationally tractable. Additionally, only the amine and carboxyl group are expected to interact strongly with the Pt substrate. On Pt(531), we study the molecule in its pristine as well as its deprotonated form and find that the deprotonated one is more stable by 0.47 eV. Therefore, we study the molecule in its deprotonated form on Pt(321) and Pt(643). As expected, the oxygen and nitrogen atoms of the deprotonated molecule provide a local binding "tripod" and the most stable adsorption configurations optimize the interaction of this "tripod" with undercoordinated surface atoms. However, the interaction of the methyl group plays an important role: it induces significant chiral selectivity of about 60 meV on all surfaces. Hereby, the L-enantiomer adsorbs preferentially to the Pt(321)(S) and Pt(643)(S) surfaces, while the D-enantiomer is more stable on Pt(531)(S). The binding energies increase with increasing surface density of kink sites, i.e., they are largest for Pt(531)(S) and smallest for Pt(643)(S).

Formation of bioinorganic complexes by the corrosive adsorption of (S)-proline on Ni/Au(111)

Nickel nanoparticles modified by the adsorption of chiral amino acids are known to be effective enantioselective heterogeneous catalysts. The leaching of nickel by amino acids has a number of potential effects including the induction of chirality in the nickel atoms left behind in the nanoparticle and the creation of catalytically active nickel complexes. The adsorption of (S)-proline onto Au(111) precovered by two-dimensional nickel nanoclusters was investigated by scanning tunneling microscopy, X-ray photoelectron spectroscopy, and high-resolution electron energy loss spectroscopy. Adsorption of (S)-proline at 300 K resulted in the corrosion of the nickel clusters, the oxidation of the leached nickel, and the on-surface formation of bioinorganic complexes, which are concluded to contain three prolinate species in an octahedral arrangement around the central Ni ion. Two distinguishable forms of nickel prolinate complexes were identified. One form self-assembles into 1-D chains, and the other form gives rise to porous 2-D islands. Octahedral complexes of the type M(AB)3 are intrinsically chiral, resulting in two pairs of enantiomers. The mirror symmetry of each pair of enantiomers is broken when, as in this study, the bidentate ligand itself possesses a chiral center. DFT calculations are used to examine the relative energies of each Ni(prolinate)3 complex as isolated gas phase species and isolated adsorbed species.

Co-adsorption of water and glycine on Cu{110}

In this study, we use density functional theory (DFT) to investigate the surface co-adsorption of glycine with water on Cu{110}. Our results show that, under UHV conditions and for a wide range of temperatures, a pure glycine monolayer is more stable than either mixed gly-water phases or pure water (ice) monolayers, but for a high water pressure half-dissociated water layers can appear on the surface at low and medium temperatures.

Assembly of a chiral amino acid on an unreactive surface: (S)-proline on Au(111)

The adsorption of (S)-proline on Au(111) at 300 K was studied by low-temperature scanning tunnelling microscopy, X-ray photoelectron spectroscopy, and high resolution electron energy loss spectroscopy. (S)-proline adsorbs to produce a 2-D gas phase at 300 K, which can be condensed to form ordered molecular assemblies on cooling to 77 K. The chemical nature of the self-assembled structures is discussed in light of the information provided by photoelectron and vibrational spectroscopies.

Surface structure of alanine on Cu(110) studied by fast atom diffraction

We demonstrate that quantum scattering of fast atoms and molecules under grazing angles of incidence can be exploited to study the structure of organic molecules on metal surfaces. Making use of keV H and He atoms as well as H2 molecules, the surface structures of the chiral amino acid alanine adsorbed on a Cu(110) surface is studied. We present a detailed investigation on the (3×2) phase of a monolayer of enantiopure and racemic alanine on Cu(110), revealing the formation of an elongated surface unit cell of c(n×2) symmetry with n=3.16±0.04 for the sticking out methyl groups of the alanine molecules.

Spectroscopic evidence for neutral and anionic adsorption of (S)-glutamic acid on Ag(111)

We report here on a combined photoemission and vibrational spectroscopy investigation of (S)-glutamic acid adsorption on Ag(111). We show that, in the temperature range 250 K ≤ T ≤ 400 K, non-zwitterionic adsorption takes place and the anionic form prevails at nonvanishing coverage. Significant conformational changes of the self-assembled layer must occur above 300 K, corresponding to a substantial reduction of the sticking probability and a modification of the vibrational spectrum. The similarity of behavior with respect to glutamic acid adsorption on the previously investigated Ag(100) and Ag(110) surfaces is also discussed.

In situ STM investigation of two-dimensional chiral assemblies through Schiff-base condensation at a liquid/solid interface

Nanoscaled two-dimensional (2D) chiral architectures are increasingly receiving scientific interest, because of their potential applications in many domains. In this paper, we present a new method for constructing 2D chiral architectures on surface. Based on in situ Schiff-base reaction of achiral dialdehyde with two types of achiral amines at the solid/liquid interface, two chiral species have been directly formed and confirmed by means of a scanning tunneling microscopy (STM) technique. This work introduces a novel strategy to construct 2D surface chirality, which might be applied in fabricating functional films and nanoelectronic devices.

Biomolecules at interfaces: chiral, naturally

Interfaces are a most important environment in natural and synthetic chemistries for a wide variety of processes, such as catalysis, recognition, separation, and so on. Naturally occurring systems have evolved to one handedness and the study of interfaces where biomolecules are located is a potentially revealing pursuit with regard to understanding the reasons and importance of stereochemistry in these environments. Equally, the spontaneous resolution of achiral and chiral compounds at interfaces could lead to explanations regarding the emergence of single handedness in proteins and sugars. Also, the attachment of biomolecules to surfaces leads to systems capable of stereoselective processes which may be useful for the applications mentioned above. The review covers systems ranging from small biomolecules studied under ultrapure conditions in vacuum to protein adsorption to surfaces in solution, and the techniques that can be used to study them.

Enantiospecific desorption of R- and S-propylene oxide from D- or L-lysine modified Cu(100) surfaces

The enantiospecific desorption kinetics of R- and S-propylene oxide (PO) from a Cu(100) surface modified by enantiomerically pure D- or L-lysine have been studied using temperature programmed desorption. These experiments have used R- or S-PO as the chiral probe for study of enantiospecific adsorption on Cu(100) surfaces modified with D- or L-lysine. This chiral probe/modifier/Cu system manifests a significant diastereomeric effect in the R- and S-PO peak desorption temperatures and, hence, true enantiospecific behavior. The enantiospecificity in the PO desorption kinetics is observed only over a narrow range of lysine modifier coverage with a maximum at a lysine coverage leaving an empty site density of θ(O) ≈ 0.25. The observation of enantiospecific behavior in the PO/lysine/Cu(100) system is in contrast with the failed results of prior attempts to observe enantiospecific desorption from chirally modified Cu surfaces. The potential for hydrogen-bonding interactions between the chiral probe and chiral modifier, which can depend on the coverage and configuration of the adsorbed modifier, may play a crucial role in enantiospecific adsorption on lysine modified Cu surfaces.

Interfacial self-assembly of amino acids and peptides: scanning tunneling microscopy investigation

Proteins play important roles in human daily life. To take advantage of the lessons learned from nature, it is essential to investigate the self-assembly of subunits of proteins, i.e., amino acids and polypeptides. Due to its high resolution and versatility of working environment, scanning tunneling microscopy (STM) has become a powerful tool for studying interfacial molecular assembly structures. This review is intended to reflect the progress in studying interfacial self-assembly of amino acids and peptides by STM. In particular, we focus on environment-induced polymorphism, chiral recognition, and coadsorption behavior with molecular templates. These studies would be highly beneficial to research endeavors exploring the mechanism and nanoscale-controlling molecular assemblies of amino acids and polypeptides on surfaces, understanding the origin of life, unravelling the essence of disease at the molecular level and deeming what is necessary for the "bottom-up" nanofabrication of molecular devices and biosensors being constructed with useful properties and desired performance.

(S)-glutamic acid on Ag(100): self-assembly in the nonzwitterionic form

The fundamental understanding of adsorption and self-organization of biological molecules at surfaces is of greatest importance for a huge variety of possible applications, ranging from molecular electronics to the study of biocompatible materials, hygiene, and biofouling. In spite of that, the characterization of the interactions of organic molecules of biological interest with surfaces is far from being complete. In the present paper we report on a combined microscopic (scanning tunneling microscopy (STM)) and spectroscopic (X-ray photoemission spectroscopy and high-resolution electron energy loss spectroscopy) study of glutamic acid (Glu) adsorption and self-assembly on Ag(100) at different temperature. STM allows one to determine the structures of the Glu layers, for which empirical models are proposed, while photoemission spectra exclude adsorption in the zwitterionic form, which is the most common especially for weakly interacting substrates.

Probing enantioselectivity on chirally modified Cu(110), Cu(100), and Cu(111) surfaces

Temperature programmed desorption methods have been used to probe the enantioselectivity of achiral Cu(100), Cu(110), and Cu(111) single crystal surfaces modified by chiral organic molecules including amino acids, alcohols, alkoxides, and amino-alcohols. The following combinations of chiral probes and chiral modifiers on Cu surfaces were included in this study: propylene oxide (PO) on L-alanine modified Cu(110), PO on L-alaninol modified Cu(111), PO on 2-butanol modified Cu(111), PO on 2-butoxide modified Cu(100), PO on 2-butoxide modified Cu(111), R-3-methylcyclohexanone (R-3-MCHO) on 2-butoxide modified Cu(100), and R-3-MCHO on 2-butoxide modified Cu(111). In contrast with the fact that these and other chiral probe/modifier systems have exhibited enantioselectivity on Pd(111) and Pt(111) surfaces, none of these probe/modifier/Cu systems exhibit enantioselectivity at either low or high modifier coverages. The nature of the underlying substrate plays a significant role in the mechanism of hydrogen-bonding interactions and could be critical to observing enantioselectivity. While hydrogen-bonding interactions between modifier and probe molecule are believed to induce enantioselectivity on Pd surfaces (Gao, F.; Wang, Y.; Burkholder, L.; Tysoe, W. T. J. Am. Chem. Soc. 2007, 129, 15240-15249), such critical interactions may be missing on Cu surfaces where hydrogen-bonding interactions are believed to occur between adjacent modifier molecules, enabling them to form clusters or islands.

Hierarchic self-assembly of nanoporous chiral networks with conformationally flexible porphyrins

We report the hierarchic design of homochiral 2D nanoporous networks under ultrahigh vacuum conditions on the Ag(111) surface by using a flexible porphyrin derivative as a primary unit. The conformational adaptation of the molecular module gives rise to two enantiomers upon 2D confinement, which self-assemble in enantiopure clusters made of three molecules reflecting chiral recognition, which constitute the secondary supramolecular building block mediating the formation of the tertiary complex open networks. Our results show that the creation of homochiral superstructures based on the hierarchical assembly of conformationally flexible molecular components constitutes a unique pathway toward the design of novel and functional chiral structures.

Ion strength and pH sensitive phase transition of N-isobutyryl-L-(D)-cysteine monolayers on Au(111) surfaces

Self-assembled monolayers (SAMs) of N-isobutyryl-L-(D)-cysteine (NIBC) on Au(111) surfaces were successfully prepared by immersing the Au(111) surfaces in the preheated pure NIBC aqueous solutions for a certain time and characterized by means of scanning tunneling microscopy. Close-packed lamellar structures with a rectangular (4 x radical3) lattice were found both in the SAMs of L-NIBC and D-NIBC. The pH value of the aqueous solutions was found to be sensitive to adjust the SAM structures during the assembly. Changing the pH value from 5 to 7 may completely shift the SAM structures from close-packed lamellar phase to loose-packed perpendicular phase. Combined with density functional theory calculations, such kind of phase transition was explained by the breaking of hydrogen bonds between carboxylic groups and the formation of extra interactions between COO(-) and Au.

Self-assembly of (S)-glutamic acid on Ag(100): a combined LT-STM and ab initio investigation

Self-assembly of organic molecules at metal surfaces is of greatest importance in nanoscience; in fact, it opens new perspectives in the field of molecular electronics and in the study of biocompatible materials. Combining an experimental low-temperature scanning tunneling microscopy investigation with ab initio calculations, we succeeded to describe in detail (S)-glutamic acid adsorption on Ag(100) at T = 350 K. We find that (S)-glutamic acid organizes in a squared structure and, at variance with the majority of cases reported in literature, it adsorbs in the neutral form, 4.6 A above the surface plane. The interaction with the poorly reactive Ag substrate is only due to weak van der Waals forces, while H-bonds between carboxyl groups and the formation of a OCOH-OCOH-OCOH-OCOH cycle at the vertex of the squares are the main responsible for the self-assembly.

Homochiral recognition among organic molecules on copper(110)

The adsorption of a prochiral quinacridone derivative (QA16C) with two alkyl chains of 16 carbon atoms on a Cu(110) surface was investigated with variable-temperature scanning tunneling microscopy. QA16C molecules prefer to assemble at 150 K into short homochiral molecular lines with two enantiomorphous orientations in which the lateral alkyl chains exhibit partial disorder. With increasing sample temperatures, the QA16C lines form larger well-ordered homochiral domains. As a reason for the homochiral recognition, we identify a rigid alignment of the molecule due to the interaction with the substrate. In addition, lateral intermolecular interactions in the form of hydrogen bonding and van der Waals interactions are identified.

Molecular orientation and intermolecular interaction in alanine on Cu(001)

Molecular orientation of L-alanine and structure model of racemic alanine on Cu(001) have been studied by RAIRS, LEED, and STM. The appearance of characteristic frequencies of the NH(2) wagging, the symmetric stretch of carboxylate group (COO(-)), the symmetric CH(3) stretch, and the C*-H (C* denotes a chiral carbon) bending modes in RAIRS is consistent with an adsorption configuration in which alanine molecule is bonded to three Cu atoms through the two oxygen atoms of carboxylate group and the nitrogen atom of amino group in its anionic form with the methyl group standing up over near bridge sites. In the adlayer, hydrogen bonds between the hydrogen atoms of the amino group and the oxygen atom of the carboxylate group contribute to assemble D(L)-alanine molecules along [130] ([310]) as well as [110] directions with a c(2 x 4) periodicity. In the adsorption of racemic mixtures, DL-alanine, D- and L-alanine molecules segregate to form their own c(2 x 4) domains, thus creating the boundary lines along the [110] direction. A submolecular resolution STM image of these domains exhibits distinction between some functional groups and the surrounding intermolecular hydrogen bonds along the [130] or [310] direction. In the submolecular resolution STM, it is most reasonably interpreted that intermolecular network between adsorption alanines is connected by N-H(1)...O(2) and N-H(2)...O(2) hydrogen bonds to form each homochiral domain and the bond at the domain boundary is enhanced by scanning tip which is most probably modified.

Effect of Interaction Energies on the Adsorption of Glycine onto a Cu(110) Surface: A Monte Carlo Simulation

The purpose of the present work was to study the effect of the adsorbate–adsorbate interaction energy for the glycine/Cu(110) system using a Monte Carlo simulation in the grand canonical ensemble. The dependence of the surface pattern structures upon the temperature and diffusion rate was studied. For either reversible or irreversible adsorption, the results showed that it is possible to obtain condensed phases with a large degree of correlation for high diffusion rates and temperatures. Depending on the set of interaction energies for nearest- and next-nearest-neighbour molecules, these patterns form either hetero- or homo-chiral footprint domains.

The results obtained are qualitatively consistent with the experimental pattern observed by other authors and allow an interpretation of the different proposed theoretical models used to explain experimental data.

Submolecular electronic mapping of single cysteine molecules by in situ scanning tunneling imaging

We have used L-cysteine (Cys) as a model system to study the surface electronic structures of single molecules at the submolecular level in aqueous buffer solution by a combination of electrochemical scanning tunneling microscopy (in situ STM), electrochemistry including voltammetry and chronocoulometry, and density functional theory (DFT) computations. Cys molecules were assembled on single-crystal Au(110) surfaces to form a highly ordered monolayer with a periodic lattice structure of c(2x2) in which each unit contains two molecules; this conclusion is confirmed by the results of calculations based on a slab model for the metal surface. The ordered monolayer offers a platform for submolecular scale electronic mapping that is an issue of fundamental interest but remains a challenge in STM imaging science and surface chemistry. Single Cys molecules were mapped as three electronic subunits contributed mainly from three chemical moieties: thiol (-SH), carboxylic (-COOH), and amine (-NH2) groups. The contrasts of the three subunits depend on the environment (e.g., pH), which affects the electronic structure of adsorbed species. From the DFT computations focused on single molecules, rational analysis of the electronic structures is achieved to delineate the main factors that determine electronic contrasts in the STM images. These factors include the molecular orientation, the chemical nature of the elements or groups in the molecule, and the interaction of the elements with the substrate and tip. The computational images recast as constant-current-height profiles show that the most favorable molecular orientation is the adsorption of cysteine as a radical in zwitterionic form located on the bridge between the Au(110) atomic rows and with the amine and carboxyl group toward the solution bulk. The correlation between physical location and electronic contrast of the adsorbed molecules was also revealed by the computational data. The present study shows that cysteine packing in the adlayer on Au(110) from the liquid environment is in contrast to that from the ultrahigh-vacuum environment, suggesting solvent plays a role during molecular assembly.

Racemic versus enantiopure alanine on Cu(110): an experimental study

The adsorption of racemic alanine on the Cu(110) surface has been compared to that of enantiopure alanine using low-energy electron diffraction (LEED), reflection absorption infrared spectroscopy (RAIRS), and scanning tunneling microscopy (STM). No evidence of chiral resolution at the surface was observed for the racemic system, indicating that the formation of separate enantiopure areas is not preferred. Also, in contrast to the enantiopure system, no chirally organized phase was observed for the racemic system. LEED shows that both systems display a common (3 x 2) phase at high coverage. However, the pathway and kinetic barriers to this phase differ markedly for the racemic and the enantiopure systems, with the racemic (3 x 2) appearing at a temperature that is more than 100 K below that required for the enantiopure system. In addition, we report intriguing complexities for the (3 x 2) LEED structure that is ubiquitous in amino acid/Cu(110) systems. First, a common (3 x 2) pattern with a zigzag distortion can be associated with both the racemic and enantiopure systems. For the racemic system, the coverage can be increased further to give a "true" (3 x 2) LEED pattern, which is a transformation that is impossible to enact for the enantiopure system. Most importantly, STM images of the "distorted" and "true" (3 x 2) structures created in the racemic system show subtle differences with neither arrangement being fully periodic over distances greater than a few molecules. Thus, the (3 x 2) phase appears to be more complicated than at first indicated and will require more complex models for a full interpretation.

Structure and Bonding of the Multifunctional Amino Acid l-DOPA on Au(110)

In investigations of the proteins which are responsible for the surface adhesion of the blue mussel Mytilus edulis, an unusually frequent appearance of the otherwise rare amino acid 3-(3,4-dihydroxyphenyl)-L-alanine (L-DOPA) has been observed. This amino acid is thought to play a major role in the mechanism of mussel adhesion. Here we report a detailed structural and spectroscopic investigation of the interface between L-DOPA and a single-crystalline Au(110) model surface, with the aim of understanding fundamentals about the surface bonding of this amino acid and its role in mussel adhesion. Molecular layers are deposited by organic molecular beam deposition (OMBD) in an ultrahigh-vacuum environment. The following experimental techniques have been applied: ex situ Fourier transform infrared spectroscopy (FTIR), X-ray photoelectron spectroscopy (XPS), low-energy electron diffraction (LEED), high-resolution electron energy loss spectroscopy (HREELS), and scanning tunneling microscopy (STM). Vibrational spectra of isolated L-DOPA molecules and the zwitterionic bulk have been calculated using density functional theory (DFT). The predicted modes are assigned to observed spectra, allowing conclusions regarding the molecule-substrate and molecule-molecule interactions at the L-DOPA/Au(110) interface. We find that zwitterionic L-DOPA forms a monochiral, one-domain commensurate monolayer on Au(110), with the catechol rings on top of [110] gold rows, oriented parallel to the surface. The (2 x 1)-Au(110) surface reconstruction is not lifted. The carboxylate group is found in a bidentate or bridging configuration, the amino group is tilted out of the surface plane, and the hydroxyl groups do not dehydrogenate on Au(110). Similar to the case for the bulk, molecules form dimers on Au(110). However, the number of hydrogen bridge bonds between L-DOPA molecules is reduced as compared to the bulk. Thicker layers which are deposited onto the commensurate interface do not order in the bulk structure. In conclusion, our study shows that the aromatic ring system of L-DOPA functions as a surface anchor. Since it is also known that the hydroxyl groups support cross-link reactions between L-DOPA residues in the mussel glue protein, we can conclude that the catechol ring supports surface adhesion of mussel proteins via two independent functions.