Two-Dimensional Folding of Polypeptides into Molecular Nanostructures at Surfaces

From Short- to Long-Range Chiral Recognition on Surfaces: Chiral Assembly and Synthesis

Research on chiral behaviors of small organic molecules at solid surfaces, including chiral assembly and synthesis, can not only help unravel the origin of the chiral phenomenon in biological/chemical systems but also provide promising strategies to build up unprecedented chiral surfaces or nanoarchitectures with advanced applications in novel nanomaterials/nanodevices. Understanding how molecular chirality is recognized is considered to be a mandatory basis for such studies. In this review, a series of recent studies in chiral assembly and synthesis at well-defined metal surfaces under ultra-high vacuum conditions are outlined. More importantly, the intrinsic mechanisms of chiral recognition are highlighted, including short/long-range chiral recognition in chiral assembly and two main strategies to steer the reaction pathways and modulate selective synthesis of specific chiral products on surfaces.

Molecular sensitised probe for amino acid recognition within peptide sequences

The combination of low-temperature scanning tunnelling microscopy with a mass-selective electro-spray ion-beam deposition established the investigation of large biomolecules at nanometer and sub-nanometer scale. Due to complex architecture and conformational freedom, however, the chemical identification of building blocks of these biopolymers often relies on the presence of markers, extensive simulations, or is not possible at all. Here, we present a molecular probe-sensitisation approach addressing the identification of a specific amino acid within different peptides. A selective intermolecular interaction between the sensitiser attached at the tip-apex and the target amino acid on the surface induces an enhanced tunnelling conductance of one specific spectral feature, which can be mapped in spectroscopic imaging. Density functional theory calculations suggest a mechanism that relies on conformational changes of the sensitiser that are accompanied by local charge redistributions in the tunnelling junction, which, in turn, lower the tunnelling barrier at that specific part of the peptide.

DNA-templated self-assembly of bradykinin into bioactive nanofibrils

Bradykinin (BK) is a peptide hormone that plays a crucial role in blood pressure control, regulates inflammation in the human body, and has recently been implicated in the pathophysiology of COVID-19. In this study, we report a strategy for fabricating highly ordered 1D nanostructures of BK using DNA fragments as a template for self-assembly. We have combined synchrotron small-angle X-ray scattering and high-resolution microscopy to provide insights into the nanoscale structure of BK-DNA complexes, unveiling the formation of ordered nanofibrils. Fluorescence assays hint that BK is more efficient at displacing minor-groove binders in comparison with base-intercalant dyes, thus, suggesting that interaction with DNA strands is mediated by electrostatic attraction between cationic groups at BK and the high negative electron density of minor-grooves. Our data also revealed an intriguing finding that BK-DNA complexes can induce a limited uptake of nucleotides by HEK-293t cells, which is a feature that has not been previously reported for BK. Moreover, we observed that the complexes retained the native bioactivity of BK, including the ability to modulate Ca²⁺ response into endothelial HUVEC cells. Overall, the findings presented here demonstrate a promising strategy for the fabrication of fibrillar structures of BK using DNA as a template, which keep bioactivity features of the native peptide and may have implications in the development of nanotherapeutics for hypertension and related disorders.

Innovations in nanosynthesis: emerging techniques for precision, scalability, and spatial control in reactions of organic molecules on solid surfaces

The surface science-based approach to synthesising new organic materials on surfaces has gained considerable attention in recent years, owing to its success in facilitating the formation of novel 0D, 1D and 2D architectures. The primary mechanism used to date has been the catalytic transformation of small organic molecules through substrate-enabled reactions. In this Topical Review, we provide an overview of alternate approaches to controlling molecular reactions on surfaces. These approaches include light, electron and ion-initiated reactions, electrospray ionisation deposition-based techniques, collisions of neutral atoms and molecules, and superhydrogenation. We focus on the opportunities afforded by these alternative approaches, in particular where they may offer advantages in terms of selectivity, spatial control or scalability.

Carbon-based nanostructures as a versatile platform for tunableπ-magnetism

Emergence ofπ-magnetism in open-shell nanographenes has been theoretically predicted decades ago but their experimental characterization was elusive due to the strong chemical reactivity that makes their synthesis and stabilization difficult. In recent years, on-surface synthesis under vacuum conditions has provided unprecedented opportunities for atomically precise engineering of nanographenes, which in combination with scanning probe techniques have led to a substantial progress in our capabilities to realize localized electron spin states and to control electron spin interactions at the atomic scale. Here we review the essential concepts and the remarkable advances in the last few years, and outline the versatility of carbon-basedπ-magnetic materials as an interesting platform for applications in spintronics and quantum technologies.

Navigate Flying Molecular Elephants Safely to the Ground: Mass-Selective Soft Landing up to the Mega-Dalton Range by Electrospray Controlled Ion-Beam Deposition

The prototype of a highly versatile and efficient preparative mass spectrometry system used for the deposition of molecules in ultrahigh vacuum (UHV) is presented, along with encouraging performance data obtained using four model species that are thermolabile or not sublimable. The test panel comprises two small organic compounds, a small and very large protein, and a large DNA species covering a 4-log mass range up to 1.7 MDa as part of a broad spectrum of analyte species evaluated to date. Three designs of innovative ion guides, a novel digital mass-selective quadrupole (dQMF), and a standard electrospray ionization (ESI) source are combined to an integrated device, abbreviated electrospray controlled ion-beam deposition (ES-CIBD). Full control is achieved by (i) the square-wave-driven radiofrequency (RF) ion guides with steadily tunable frequencies, including a dQMF allowing for investigation, purification, and deposition of a virtually unlimited m/z range, (ii) the adjustable landing energy of ions down to ∼2 eV/z enabling integrity-preserving soft landing, (iii) the deposition in UHV with high ion beam intensity (up to 3 nA) limiting contaminations and deposition time, and (iv) direct coverage control via the deposited charge. The maximum resolution of R = 650 and overall efficiency up to T_total = 4.4% calculated from the solution to UHV deposition are advantageous, whereby the latter can be further enhanced by optimizing ionization performance. In the setup presented, a scanning tunneling microscope (STM) is attached for in situ UHV investigations of deposited species, demonstrating a selective, structure-preserving process and atomically clean layers.

Depositing Molecular Graphene Nanoribbons on Ag(111) by Electrospray Controlled Ion Beam Deposition: Self-Assembly and On-Surface Transformations

The chemical processing of low‐dimensional carbon nanostructures is crucial for their integration in future devices. Here we apply a new methodology in atomically precise engineering by combining multistep solution synthesis of N‐doped molecular graphene nanoribbons (GNRs) with mass‐selected ultra‐high vacuum electrospray controlled ion beam deposition on surfaces and real‐space visualisation by scanning tunnelling microscopy. We demonstrate how this method yields solely a controllable amount of single, otherwise unsublimable, GNRs of 2.9 nm length on a planar Ag(111) surface. This methodology allows for further processing by employing on‐surface synthesis protocols and exploiting the reactivity of the substrate. Following multiple chemical transformations, the GNRs provide reactive building blocks to form extended, metal–organic coordination polymers.

Low-energy electron holography imaging of conformational variability of single-antibody molecules from electrospray ion beam deposition

Molecular imaging at the single-molecule level of large and flexible proteins such as monoclonal IgG antibodies is possible by low-energy electron holography after chemically selective sample preparation by native electrospray ion beam deposition (ES-IBD) from native solution conditions. The single-molecule nature of the measurement allows the mapping of the structural variability of the molecules that originates from their intrinsic flexibility and from different adsorption geometries. Additionally, we can distinguish gas-phase–related conformations and conformations induced by the landing of the molecules on the surface. Our results underpin the relation between the gas-phase structure of protein ions created by native electrospray ionization (ESI) and the native protein structure and are of relevance for structural biology applications in the gas phase.

Imaging of proteins at the single-molecule level can reveal conformational variability, which is essential for the understanding of biomolecules. To this end, a biologically relevant state of the sample must be retained during both sample preparation and imaging. Native electrospray ionization (ESI) can transfer even the largest protein complexes into the gas phase while preserving their stoichiometry and overall shape. High-resolution imaging of protein structures following native ESI is thus of fundamental interest for establishing the relation between gas phase and solution structure. Taking advantage of low-energy electron holography’s (LEEH) unique capability of imaging individual proteins with subnanometer resolution, we investigate the conformational flexibility of Herceptin, a monoclonal IgG antibody, deposited by native electrospray mass-selected ion beam deposition (ES-IBD) on graphene. Images reconstructed from holograms reveal a large variety of conformers. Some of these conformations can be mapped to the crystallographic structure of IgG, while others suggest that a compact, gas-phase–related conformation, adopted by the molecules during ES-IBD, is retained. We can steer the ratio of those two types of conformations by changing the landing energy of the protein on the single-layer graphene surface. Overall, we show that LEEH can elucidate the conformational heterogeneity of inherently flexible proteins, exemplified here by IgG antibodies, and thereby distinguish gas-phase collapse from rearrangement on surfaces.

Interaction of cyclosporin A molecules with alkali and transition metal atoms on Cu(111)

The structure of a cyclic peptide with important biological functionalities, cyclosporin A (CsA), is investigated at the single molecule level. Its adsorption on Cu(111) under ultra-high vacuum is characterised with scanning tunnelling microscopy (STM) and density functional theory. With STM investigations, we demonstrate element specific on-surface coordination schemes of CsA with coadsorbed K, Co and Fe atoms. Thus, clear insights emerge in the behaviour of cyclic peptides at interfaces and their interactions with different metal atoms, providing control of the adsorption structure and assembly and paving the way for the integration of cyclic peptides in functional metal-organic nanostructures on surfaces.

Two-Dimensional Coordination Networks from Cyclic Dipeptides

Peptide-based biomimetic nanostructures and metal-organic coordination networks on surfaces are two promising classes of hybrid materials which have been explored recently. However, despite the great versatility and structural variability of natural and synthetic peptides, the two directions have so far not been merged in fabrication of metal-organic coordination networks using peptides as building blocks. Here we demonstrate that cyclic peptides can be used as ligands to form highly ordered, two-dimensional, peptide-based metal-organic coordination networks. The networks are formed on a Au(111) surface through coadsorption of cyclic dialanine with Cu-adatoms under Ultra-High Vacuum (UHV) conditions. Scanning Tunneling Microscopy (STM) in combination with X-ray Photoelectron spectroscopy (XPS) has been utilized to characterize the network structures at submolecular resolution and expound the chemical changes involved in network coordination. The networks involve a motif of three cyclic dialanine molecules coordinating to a central Cu-adatom. Interestingly the networks expose pores functionalized by the side chain of the cyclic peptide, suggesting a general method to form functionalized porous metal-organic networks on surfaces.

Nonconsensus motif directed chemical synthesis of glutamine-based glycopeptides

Besides the most common sequon of amino acids found in glycopeptides, namely, N-X-S/T, where X can be any amino acid except proline, a small number of nonconsensus motifs have been found in both eukaryotic and prokaryotic organisms, for example, Q-G-T. Because of the importance of glycopeptides in biotechnology and pharmacy, an adequate synthetic approach to these structures is highly important. In this manuscript, we report the efficient chemical batch synthesis of new glutamine-based glycopeptide structures, which can be used to represent cell surface elements in further biological investigations.

Synthesis of new asparagine-based glycopeptides for future scanning tunneling microscopy investigations

For investigations on the biological functions of oligosaccharides and peptidomimetics, new asparagine-based mono- and disaccharides containing glycopeptides were prepared in solution. The applicability of two common peptide coupling reagents, using an orthogonal Fmoc/t-Bu strategy along with acetyl protecting groups for the carbohydrate moiety, was studied. Thus, the prepared libraries of glycopeptides were designed as model systems of cell surfaces for future investigations by combined preparative mass spectroscopy and scanning tunneling microscopy (STM) using soft-landing electrospray beam deposition (ES-IBD), on metal surfaces.

Combination of Thin-Layer Chromatography and Mass Spectrometry Using Cluster-Induced Desorption/Ionization

Desorption/ionization induced by neutral clusters (DINeC) was employed for mass spectrometry (MS) of oligopeptides and lipids after separation by means of thin-layer chromatography (TLC). Clear and fragmentation-free spectra were obtained from the TLC plates without any further sample treatment. Mass-resolved chromatograms were deduced when scanning the TLC plates with the cluster beam along the direction of solvent movement. Using vancomycin and noncovalently bound complexes, the soft nature of DINeC was demonstrated also when used in combination with TLC. As a test application, TLC and DINeC-MS were employed to separate and detect different phospholipids obtained from egg yolk.

Cluster-induced desorption investigated by means of molecular dynamics simulations-Microsolvation in clusters of polar and non-polar constituents

The desorption of surface-adsorbed molecules induced by cluster-surface collisions of neutral molecular clusters, in particular, SO₂ clusters, was investigated by means of molecular dynamics simulations. The desorption efficiency was found to be in general much higher for clusters of polar molecules when compared to nonpolar cluster constituents, for both nonpolar and polar adsorbates. In all cases, desorption is shown to proceed via dissolvation of the analyte in the cluster. In systems with nonpolar cluster constituents, the process is mainly driven by the increase in the entropy of the dissolved analyte in a larger cluster fragment. The latter process is enhanced by polar cluster constituents since the respective clusters show lower fragmentation at comparable kinetic energy and thus provide in average larger cluster fragments for the analytes to be dissolved in. In systems with clusters of polar constituents and polar adsorbates, the process is most efficient due to the additional energetic stabilization of the desorbed molecule in the solvation shell formed in the cluster fragment.

Polymorphism in carbohydrate self-assembly at surfaces: STM imaging and theoretical modelling of trehalose on Cu(100)

Saccharides, also commonly known as carbohydrates, are ubiquitous biomolecules, but little is known about their interaction with surfaces. Soft-landing electrospray ion beam deposition in conjunction with high-resolution imaging by scanning tunneling microscopy now provides access to the molecular details of the surface assembly of this important class of bio-molecules. Among carbohydrates, the disaccharide trehalose is outstanding as it enables strong anhydrobiotic effects in biosystems. This ability is closely related to the observed polymorphism. In this work, we explore the self-assembly of trehalose on the Cu(100) surface. Molecular imaging reveals the details of the assembly properties in this reduced symmetry environment. Already at room temperature, we observe a variety of self-assembled motifs, in contrast to other disaccharides like e.g. sucrose. Using a multistage modeling approach, we rationalize the conformation of trehalose on the copper surface as well as the intermolecular interactions and the self-assembly behavior.

We rationalize the experimentally observed variety of trehalose assemblies on Cu(100) by modeling based on STM images and global optimization.

Aspartic and Glutamic Acid Templated Peptides Conjugation on Plasma Modified Nanofibers for Osteogenic Differentiation of Human Mesenchymal Stem Cells: A Comparative Study

Optimization of nanofiber (NF) surface properties is critical to achieve an adequate cellular response. Here, the impact of conjugation of biomimetic aspartic acid (ASP) and glutamic acid (GLU) templated peptides with poly(lactic-co-glycolic acid) (PLGA) electrospun NF on osteogenic differentiation of human bone marrow-derived mesenchymal stem cells (hMSCs) was evaluated. Cold atmospheric plasma (CAP) was used to functionalize the NF surface and thus to mediate the conjugation. The influence of the CAP treatment following with peptide conjugation to the NF surface was assessed using water contact angle measurements, Fourier-Transform Infrared Spectroscopy (FTIR) and X-ray Photoelectron Spectroscopy (XPS). The effect of CAP treatment on morphology of NF was also checked using Scanning Electron Microscopy (SEM). Both the hydrophilicity of NF and the number of the carboxyl (-COOH) groups on the surface increased with respect to CAP treatment. Results demonstrated that CAP treatment significantly enhanced peptide conjugation on the surface of NF. Osteogenic differentiation results indicated that conjugating of biomimetic ASP templated peptides sharply increased alkaline phosphatase (ALP) activity, calcium content, and expression of key osteogenic markers of collagen type I (Col-I), osteocalcin (OC), and osteopontin (OP) compared to GLU conjugated (GLU-pNF) and CAP treated NF (pNF). It was further depicted that ASP sequences are the major fragments that influence the mineralization and osteogenic differentiation in non-collagenous proteins of bone extracellular matrix.

DRILL Interface Makes Ion Soft Landing Broadly Accessible for Energy Science and Applications

Polyoxometalates (POM) have been deposited onto carbon nanotube (CNT) electrodes using benchtop ion soft landing (SL) enabled by a vortex-confined electrohydrodynamic desolvation process. The device is based on the dry ion localization and locomotion (DRILL) mass spectrometry interface of Fedorov and co-workers. By adding electrospray emitters, heating the desolvation gas, and operating at high gas flow rates, it is possible to obtain stable ion currents up to -15 nA that are ideal for deposition. Coupled with ambient ion optics, this interface enables desolvated ions to be delivered to surfaces while excluding solvent and counterions. Electron microscopy of surfaces prepared using the device reveal discrete POM and no aggregation that degrades electrode performance. Characterization of POM-coated CNT electrodes in a supercapacitor showed an energy storage capacity similar to that achieved with SL in vacuum. For solutions that produce primarily a single ion by electrospray ionization, benchtop SL offers a simpler and less costly approach for surface modification with applications in catalysis, energy storage, and beyond.

Supramolecular Assemblies on Surfaces: Nanopatterning, Functionality, and Reactivity

Understanding how molecules interact to form large-scale hierarchical structures on surfaces holds promise for building designer nanoscale constructs with defined chemical and physical properties. Here, we describe early advances in this field and highlight upcoming opportunities and challenges. Both direct intermolecular interactions and those that are mediated by coordinated metal centers or substrates are discussed. These interactions can be additive, but they can also interfere with each other, leading to new assemblies in which electrical potentials vary at distances much larger than those of typical chemical interactions. Earlier spectroscopic and surface measurements have provided partial information on such interfacial effects. In the interim, scanning probe microscopies have assumed defining roles in the field of molecular organization on surfaces, delivering deeper understanding of interactions, structures, and local potentials. Self-assembly is a key strategy to form extended structures on surfaces, advancing nanolithography into the chemical dimension and providing simultaneous control at multiple scales. In parallel, the emergence of graphene and the resulting impetus to explore 2D materials have broadened the field, as surface-confined reactions of molecular building blocks provide access to such materials as 2D polymers and graphene nanoribbons. In this Review, we describe recent advances and point out promising directions that will lead to even greater and more robust capabilities to exploit designer surfaces.

Chemical Analysis of Complex Surface-Adsorbed Molecules and Their Reactions by Means of Cluster-Induced Desorption/Ionization Mass Spectrometry

Desorption/ionization induced by neutral SO₂ clusters (DINeC) is used for mass spectrometry (MS) of surface-adsorbed molecules. The method is shown to be a surface-sensitive analysis tool capable of detecting molecular adsorbates in a wide range of molecular weights as well as their reactions on surfaces, which are otherwise difficult to access. Two different surface/adsorbate systems prepared by means of electrospray ion beam deposition (ES-IBD) were investigated: For the peptide angiotensin II on gold, intact molecules were desorbed from the surface when deposited by soft landing ES-IBD. By comparison to the well-controlled amount of substance deposited by ES-IBD, the sensitivity of DINeC-MS was shown to be on the order of 0.1% of a monolayer coverage, corresponding to femtomoles of analyte. Depending on deposition and sample conditions, the original state of charge of the molecules could be retrieved. Reaction of the adsorbed molecules both with surface atoms as well as with coadsorbed D₂O was monitored. Rhodamine 6G was also desorbed as an intact molecule when deposited with kinetic energies below 50 eV. For higher deposition energy, fragmentation of the dye molecules was observed by means of DINeC-MS.

Electrospray deposition of structurally complex molecules revealed by atomic force microscopy

Advances in organic chemistry allow the synthesis of large, complex and highly functionalized organic molecules having potential applications in optoelectronics, molecular electronics and organic solar cells. Their integration into devices as individual components or highly ordered thin-films is of paramount importance to address these future prospects. However, conventional sublimation techniques in vacuum are usually not applicable since large organic compounds are often non-volatile and decompose upon heating. Here, we prove by atomic force microscopy and scanning tunneling microscopy, the structural integrity of complex organic molecules deposited onto an Au(111) surface using electrospray ionisation deposition. High resolution AFM measurements with CO-terminated tips unambiguously reveal their successful transfer from solution to the gold surface in ultra-high vacuum without degradation of their chemical structures. Furthermore, the formation of molecular structures from small islands to large and highly-ordered self-assemblies of those fragile molecules is demonstrated, confirming the use of electrospray ionisation to promote also on-surface polymerization reactions of highly functionalized organic compounds, biological molecules or molecular magnets.

Real-Time Investigation of the H/D Exchange Kinetics of Porphyrins and Oligopeptides by Means of Neutral Cluster-Induced Desorption/Ionization Mass Spectrometry

The kinetics of the H/D exchange reaction in angiotensin II, hexaglycine (Gly₆), Co(II)tetra(3-carboxyphenyl)porphyrin, and tetra(4-carboxyphenyl)porphyrin were followed in real time by mass spectrometry employing desorption/ionization induced by neutral SO₂ clusters. The change of the isotope patterns with increasing degree of deuteration was recorded as a function of D₂O exposure and the underlying H/D exchange kinetics, i.e., the dependence of the different degrees of deuteration on time, were deduced. The results were modeled by means of Monte Carlo simulations taking into account different reaction constants for the H/D exchange reaction at different functional groups. In the case of the investigated porphyrins, the rate constants were directly assigned to the functional groups involved; in the case of the peptides, reaction at the explicit functional groups and the backbone chain of the molecules could be discriminated.

On-Surface Synthesis of Porous Carbon Nanoribbons from Polymer Chains

We demonstrate the on-surface synthesis of porous carbon nanoribbons on Ag(111) via a preprogrammed isomerization of conformationally flexible polymer chains followed by dehydrogenation reactions using thermal annealing. The carbon chains are fabricated by polymerization of prochiral 1,3,5-tris(3-bromophenyl)benzene (mTBPB) directly on the surface using an Ullmann-type reaction. At room temperature, mTBPB partially self-assembles in halogen-bonded 2D networks, which transform into organometallic chains and rings after debromination. The chain and ring formation is facilitated by conformational switching from a C_3h to C_s symmetry of mTBPB via rotation of m-phenylene units. The high conformational selectivity toward C_s-conformers is templated by the twofold coordination to Ag adatoms. After thermally induced covalent-linking through aryl-aryl coupling, well-ordered nanoporous chains are created. Finally, the rotation of single phenylene units in combination with dehydrogenation cross-linking reactions within the polymer chains leads to the unexpected formation of porous carbon nanoribbons. We unveil the reaction mechanism in a low-temperature scanning tunneling microscopy study and demonstrate that the rotation of m-phenylene units is a powerful design tool to promote structural control in the synthesis of cyclic covalent organic nanostructures on metal surfaces.

Influence of the cluster constituents' reactivity on the desorption/ionization process induced by neutral SO2 clusters

The influence of the chemical nature of the cluster constituents on the desorption/ionization process was investigated for desorption/ionization induced by neutral SO₂ clusters (DINeC). The polar clusters act as a transient matrix in which the desorbed analyte molecules are dissolved during the desorption process. For drop-cast samples, the desorption/ionization efficiency was found to be largely independent of the pH value of the initial solution the samples were prepared from; positive ions were almost always dominant and no multiply charged negative ions were observed. The results were traced back to the interaction of SO₂ with water present in the samples. Both H/D exchange experiments and surface charge measurements showed that SO₂ from the cluster beam interacts with water on and in the sample forming sulfurous acid. The latter then acts as an efficient proton supply leading to an enhanced ionization efficiency. The results demonstrate the possibility to control the ionization efficiency when using reactive cluster constituents in desorption-based ionization methods such as DINeC and cluster-based secondary ion mass spectrometry.

The STM bias voltage-dependent polymorphism of a binary supramolecular network

We control complex multicomponent switches by tuning the local electric field at the liquid/solid interface.