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

Novel mixed self-assembled monolayers of L-cysteine and methanol on gold surfaces under ambient conditions

In this work, we carried out an experimental and theoretical study on the formation of self-assembled monolayers of L-cysteine molecules on gold surfaces in the presence of methanol as a solvent. We report for the first time L-cysteine and methanol ordered structures forming a mixed self-assembled mono-layer on Au(100) surfaces under ambient conditions. Finger-like ordered structures with a relative height of 0.10-0.20 nm, average width of 2.0 nm and variable lengths were observed using scanning tunneling microscopy under room temperature and ambient pressure conditions. Using X-ray photoemission spectroscopy, it was determined that L-cysteine molecules bind to the gold surface through the sulfur atom of their thiol group in two molecular configurations: neutral and zwitterionic. We found that the finger-like structures are the result of complex interactions of L-cysteine molecules with gold surfaces and L-cysteine molecules with methanol molecules and among all three components of the system (L-cysteine + methanol + gold surfaces). These interactions were detected through attenuated total reflectance-Fourier transform infrared spectroscopy. Furthermore, adsorbate/substrate interactions were studied by employing ab initio calculations using density functional theory, resulting in molecular arrangements formed by chains of L-cysteine pairs surrounded by physisorbed methanol molecules.

Kinetic Controlled Chirality Transfer and Induction in 2D Hydrogen-Bonding Assemblies of Glycylglycine on Au(111)

Chirality transfer is of vital importance that dominates the structure and functionality of biological systems and living matters. External physical stimulations, e.g. polarized light and mechanical forces, can trigger the chirality symmetry breaking, leading to the appearance of the enantiomeric entities created from a chiral self-assembly of achiral molecule. Here, several 2D assemblies with different chirality, synthesized on Au(111) surface by using achiral building blocks - glycylglycine (digly), the simplest polypeptide are reported. By delicately tuning the kinetic factors, i.e., one-step slow/rapid deposition, or stepwise slow deposition with mild annealing, achiral square hydrogen-bond organic frameworks (HOF), homochiral rhombic HOF and racemic rectangular assembly are achieved, respectively. Chirality induction and related symmetry broken in assemblies are introduced by the handedness (H-bond configurations in principle) of the assembled motifs and then amplified to the entire assemblies via the interaction between motifs. The results show that the chirality transfer and induction of biological assemblies can be tuned by altering the kinetic factors instead of applying external forces, which may offer an in-depth understanding and practical approach to peptide chiral assembly on the surfaces and can further facilitate the design of desired complex biomolecular superstructures.

Self-Assembly of Glutamic Acid and Serine on Au(111)

Amino acids provide novel and superior performance for two-dimensional materials and bio-based devices. The interaction and adsorption of amino acid molecules on substrates have thus attracted extensive research for exploring the driving forces involved in the formation of nanostructures. Nevertheless, the interactions within amino acid molecules on inert surfaces have not been fully understood. Herein, from the interplay of high-resolution scanning tunneling microscopy imaging and density functional theory calculations, we show the self-assembled structures of Glu and Ser molecules on Au(111), which are dominated by intermolecular hydrogen bonds, and further investigate their most stable structural models at the atomic scale. This study would be of fundamental importance in understanding the formation processes of biologically relevant nanostructures and provide possibilities for chemical modification.

Adsorption of glutamic acid on clean and hydroxylated rutile TiO2(110): an XPS and NEXAFS investigation

Due to its biocompatibility, TiO₂is a relevant material for the study of bio-interfaces. Its electronic and chemical properties are influenced by defects, which mainly consist of oxygen vacancies or adsorbed OH groups and which affect, consequently, also the interaction with biological molecules. Here we report on an x-ray photoemission spectroscopy and near edge adsorption fine structure study of glutamic acid (Glu) adsorption on the rutile TiO₂(110) surface, either clean or partially hydroxylated. We show that Glu anchors to the surface through a carboxylate group and that the final adsorption state is influenced by the presence of hydroxyl groups on the surface prior to Glu deposition. Indeed, molecules adsorb both in the anionic and in the zwitterionic form, the former species being favored on the hydroxylated substrate.

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.

Side-chain effects on the co-existence of emergent nanopatterns in amino acid adlayers on graphene

The spontaneous tendency of amino acid adlayers to self-assemble into ordered patterns on non-reactive surfaces is thought to be chiefly influenced by amino acid termination state. Experiments have shown that different side chains can produce different patterns, with a distinction drawn between side chains that can support hydrogen bonds or electrostatic interactions, and those that are hydrophobic. However, as is demonstrated in this work, this distinction is not clear cut, implying that there is currently no way to predict in advance what type of pattern will be formed. Here, we use molecular dynamics simulations of amino acid adlayers in neutral, zwitterion, and neutral-zwitterion states for two types of amino acids, either histidine or alanine, adsorbed at the in-vacuo graphene interface. In contrast to earlier studies on adlayers of tryptophan and methionine on graphene that reveal the presence of only a single type of pattern motif, the canonical dimer row, here we find that emergent patterns of histidine and alanine adlayers supported the co-existence of several different types of motifs, influenced by the different side-chain characteristics. For alanine, the compact side-chain does not support hydrogen bonding and engages weakly with the surface, leading to the emergence of a new dimer row configuration in addition to the canonical dimer row motif. On the contrary, for histidine, the side-chain supports hydrogen bonding, leading to the emergence of a dimer row motif different from the canonical dimer row, co-existing with several different monomer row motifs. On this basis, we propose that emergent canonical dimer row patterns are more likely for amino acids with side-chains that are non-compact and that also lack extensive hydrogen bonding capacity, and that engage strongly with the underlying substrate. These findings provide a fundamental basis to rationally guide the design of desired self-assembled nanostructures on planar surfaces.

Predictions of Pattern Formation in Amino Acid Adlayers at the In Vacuo Graphene Interface: Influence of Termination State

Controlled self-assembly of biomolecules on graphene offers a pathway for realizing its full potential in biological applications. Microscopy has revealed the self-assembly of amino acid adlayers into dimer rows on nonreactive substrates. However, neither the spontaneous formation of these patterns, nor the influence of amino acid termination state on the formation of patterns has been directly resolved to date. Molecular dynamics simulations, with the ability to reveal atomic level details and exert full control over the termination state, are used here to model initially disordered adlayers of neutral, zwitterionic, and neutral-zwitterionic mixtures for two types of amino acids, tryptophan and methionine, adsorbed on graphene in vacuo. The simulations of the zwitterion-containing adlayers exhibit the spontaneous emergence of dimer row ordering, mediated by charge-driven intermolecular interactions. In contrast, adlayers containing only neutral species do not assemble into ordered patterns. It is also found that the presence of trace amounts of water reduces the interamino acid interactions in the adlayers, but does not induce or disrupt pattern formation. Overall, the findings reveal the balance between the lateral interamino acid interactions and amino acid-graphene interactions, providing foundational insights for ultimately realizing the predictable pattern formation of biomolecules adsorbed on unreactive surfaces.

Supramolecular chiral self-assemblies of Gly–Pro dipeptides on metallic fcc(110) surfaces

Adsorption of the Glycine–Proline (Gly–Pro) dipeptide has been investigated using surface science complementary techniques on Au(110) and Ag(110), showing some interesting differences both in the chemical form and surface organization of the adsorbed peptide. On Au(110), Gly–Pro mainly adsorbs in neutral form (COOH/NH₂), at low coverage or for a short interaction time; the surface species become zwitterionic at a higher coverage or longer interaction time. These changes are accompanied by a complete reorganization of the molecules at the surface. On Ag(110), only anionic molecules (COO⁻/NH₂) were detected on the surface and only one type of arrangement was observed. These results will be compared to some previously obtained on Cu(110), thus providing a unique comparison of the adsorption of the same di-peptide on three different metal surfaces; the great influence of the substrate on both the chemical form and the arrangement of adsorbed di-peptides was made clear.

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.

Simple rules and the emergence of complexity in surface chirality

Surface chirality arising from self-organized molecular monolayers may manifest both a handedness and footedness, leading to a dual level of chiral expression.

L-Asparagine crystals with wide gap semiconductor features: optical absorption measurements and density functional theory computations

Results of optical absorption measurements are presented together with calculated structural, electronic, and optical properties for the anhydrous monoclinic L-asparagine crystal. Density functional theory (DFT) within the generalized gradient approximation (GGA) including dispersion effects (TS, Grimme) was employed to perform the calculations. The optical absorption measurements revealed that the anhydrous monoclinic L-asparagine crystal is a wide band gap material with 4.95 eV main gap energy. DFT-GGA+TS simulations, on the other hand, produced structural parameters in very good agreement with X-ray data. The lattice parameter differences Δa, Δb, Δc between theory and experiment were as small as 0.020, 0.051, and 0.022 Å, respectively. The calculated band gap energy is smaller than the experimental data by about 15%, with a 4.23 eV indirect band gap corresponding to Z → Γ and Z → β transitions. Three other indirect band gaps of 4.30 eV, 4.32 eV, and 4.36 eV are assigned to α3 → Γ, α1 → Γ, and α2 → Γ transitions, respectively. Δ-sol computations, on the other hand, predict a main band gap of 5.00 eV, just 50 meV above the experimental value. Electronic wavefunctions mainly originating from O 2p-carboxyl, C 2p-side chain, and C 2p-carboxyl orbitals contribute most significantly to the highest valence and lowest conduction energy bands, respectively. By varying the lattice parameters from their converged equilibrium values, we show that the unit cell is less stiff along the b direction than for the a and c directions. Effective mass calculations suggest that hole transport behavior is more anisotropic than electron transport, but the mass values allow for some charge mobility except along a direction perpendicular to the molecular layers of L-asparagine which form the crystal, so anhydrous monoclinic L-asparagine crystals could behave as wide gap semiconductors. Finally, the calculations point to a high degree of optical anisotropy for the absorption and complex dielectric function, with more structured curves for incident light polarized along the 100 and 101 directions.

Unraveling the self-assembly of the (S)-glutamic acid "flower" structure on Ag(100)

(S)-Glutamic acid adsorbed on Ag(100) organizes in different self-assembled structures depending on surface temperature [Smerieri, M.; Vattuone, L.; Kravchuk, T.; Costa, D.; Savio, L. (S)-Glutamic Acid on Ag(100): Self-Assembly in the Nonzwitterionic Form. Langmuir2011, 27, 2393-2404]. In particular, two of these structures, referred to as "square" and "flower" geometries, are found to coexist on the surface upon deposition at T = 350 K. The former assembly was fully resolved at the atomic level in the work of Smerieri et al. [Smerieri, M.; Vattuone, L.; Costa, D.; Tielens, F.; Savio, L. Self-Assembly of (S)-Glutamic Acid on Ag(100): A Combined LT-STM and Ab Initio Investigation. Langmuir2010, 26, 7208-7215], in which we proved that the driving force for adsorption is the van der Waals interactions between the molecules and the Ag surface, that is, that molecules are in a physisorbed state. In this paper, we complete our work by presenting the characterization of the "flower" structure. In contrast to the case of the "square" assembly, a strong chemical bond between glutamic acid radicals and the surface is at the basis of the "flowers" geometry. Whereas the chemisorbed central GLU tetramer interacts strongly with the surface, the physisorbed surrounding GLU molecules conserve some degree of freedom in the layer which counterbalances the weak adsorption energy. The "flower" and the "square" assemblies have similar dispersion energy and H-bond interaction energy; as a consequence of the different chemical state of the GLU molecules, however, such contributions have a very different relative weight in the stabilization of the two structures.

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.

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.