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

Abstract

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.

Structural and Chemical Evolution of l-Cysteine Nanofilm on Si(111)-√3×√3-Ag: From Preferential Growth at Step Edges and Antiphase Boundaries at Room Temperature to Adsorbate-Mediated Metal Cluster Formation at Elevated Temperature

“…In the study of cysteine adsorption on Si(111)­7×7, we conclude that the cysteine zwitterionic structure could exist up to 85 °C, while the transitional layer (second adlayer) consisting of interlayer hydrogen bonds are stable even after annealing to 175 °C. , In the present work, no transitional layer is observed and physisorption is found to occur at the second adlayer on the as-formed chemisorbed layer. However, after annealing, the chemical composition of the cysteine film on Si(111)-√3×√3-Ag appears to resemble that of cysteine on Si(111)­7×7, which suggests the presence of a transitional layer on the interfacial layer.…”

“…Our proposed mechanism is supported by the presence of both −COOH and −NH 2 features and the corresponding −COO − and −NH 3 + (H-bond related) features in the O 1s and N 1s regions. Formation of H-bonded groups has also been observed in the transitional layer of a cysteine film on Si(111)­7×7 …”

“…Formation of H-bonded groups has also been observed in the transitional layer of a cysteine film on Si(111)7×7. 68 Upon annealing to 285 °C, the −COOH C 1s feature (at 289.0 eV) has been reduced in intensity discernibly more than the N-and S-related C 1s peaks, indicating the decomposition of the cysteine film. However, the positions of the −NH−Si (Figure 1b) and −S−Ag peaks (Figure 1d) remain unchanged, suggesting the presence of intact chemisorbed (thiolated) cysteine or its decomposition fragments.…”

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

“…In regards to previous simulation studies that considered the presence of multiple amino acids adsorbed on a solid surface, most focused on dimers which were modeled in either the neutral or zwitterionic states. [48][49][50][56][57][58] However, very little has been reported on the modeling of amino acid adlayers on solid surfaces. Notably, a pioneering simulation study by Popa and Paci reported the modeling of methionine adlayers on Au(111).…”

Does the choice of the crystal structure influence the results of the periodic DFT calculations? A case of glycine alpha polymorph GIPAW NMR parameters computations

“…Due to its common experimental application, relatively complex chemistry in the solid state, yet it's small size which has a major impact on the time of calculations, α glycine has been used as an convenient example in the computational benchmark and new methodologies tests . Some of its application as a model structure include the molecular dynamics, surface adsorption or rotational spectra prediction via calculations. The structure of the α polymorph is also commonly used while performing the GIPAW calculations.…”