Secondary Structures of Ubiquitin Ions Soft-Landed onto Self-Assembled Monolayer Surfaces

Writing with Mass-Selected Ions Using a Dynamic Field Wien Filter

We have designed and constructed a low-cost Wien filter based on strong permanent magnets and integrated it into an ion soft-landing instrument to enable parallel deposition as well as one- and two-dimensional surface patterning of mass-selected ions using dynamic fields. We show the capabilities of this device for separating ions from a multicomponent high-flux continuous ion beam and simultaneous deposition of ions of different mass-to-charge ratios onto discrete locations on a surface. When a dynamic electric field is applied parallel to the magnetic field, ions are deposited in one-dimensional arrays, laterally separated by mass. The field's strength, frequency, and waveform type determine both the lengths of the arrays and the density of ions across the 1-D pattern. Additionally, a second dynamic field from user-defined waveforms orthogonal to the magnetic field enables two-dimensional surface patterning of ions while maintaining mass separation. These experiments demonstrate the practical utility of a Wien filter for the controlled fabrication of interfaces with arbitrary patterns of mass-selected ions.

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.

Principles of Operation of a Rotating Wall Mass Analyzer for Preparative Mass Spectrometry

In this contribution, we describe the principles of operation of a rotating wall mass analyzer (RWMA), a mass-dispersive device for preparative mass spectrometry. Ions of different m/z are spatially separated by RWMA and deposited onto ring-shaped areas of distinct radii on a surface. We use a combination of an analytical equation for predicting the radius of the deposition ring and SIMION simulations to understand how to optimize the experimental conditions for the separation of multicomponent mixtures. The results of these simulations are compared with the experimental data. We introduce a universal mass calibration procedure, based on a series of polyacrylamide ions, which is subsequently used to predict the deposition radii of unknown analytes. The calibration is independent of the polarity, kinetic energy, and charge state of the ion as demonstrated by assigning m/z values of different analytes including multiply charged ubiquitin ions. We demonstrate that mass resolution of the RWMA is affected by the width and kinetic energy distribution of the ion beam. The best mass resolution obtained in this study is m/Δm = ∼20. Preparative mass spectrometry using RWMA provides the advantages of simplicity, compactness, and low fabrication cost, which are particularly promising for the development of miniaturized instrumentation. The results presented in this work can be readily adapted to preparative separation of a variety of charged species of interest to the broad scientific community.

Direct Measurement of Water Permeation in Submerged Alkyl Thiol Self-Assembled Monolayers on Gold Surfaces Revealed by Neutron Reflectometry

Self-assembled monolayers (SAMs) of alkyl thiols are frequently used to chemically functionalize gold surfaces for applications throughout materials chemistry, electrochemistry, and biotechnology. Despite this, a detailed understanding of the structure of the SAM-water interface generated from both formation and use of the SAM in an aqueous environment is elusive, and analytical measurements of the structure and chemistry of the SAM-water interface are an ongoing experimental challenge. To address this, we used neutron reflectometry (NR) to measure water association with both hydrophobic and hydrophilic SAMs under both wet and dry conditions. SAMs used for this study were made from hydrophobic decanethiol mixed with hydrophilic 11-azido-1-undecanethiol with compositions of 0-100% of the azide-terminated thiol. All SAMs were formed by conventional solution incubation of a Au substrate immersed in ethanol. Each SAM was characterized by grazing incidence angle reflection-absorption Fourier transfer infrared spectroscopy, contact angle goniometry, and electrochemical methods to confirm it was a completely formed monolayer with evidence of extensive crystalline-like domains. NR measured significant absorption of water into each SAM, ranging from 1.6 to 5.7 water molecules per alkyl thiol, when SAMs were immersed in water. Water infiltration was independent of SAM composition and terminal group hydrophilicity. These results demonstrate that water accesses defects, fluid regions, and heterogeneous domains inherent to even well-formed SAMs.

Molecular Sponge: pH-Driven Reversible Squeezing of Stimuli-Sensitive Peptide Monolayers

The cyclic change of structure, thickness, and density, with pH switching from acidic (pH = 3) to basic (pH = 11) condition, has been revealed for chemisorbed monolayers of the peptide Lipo-Aib-Lys-Leu-Aib-Lys-Lys-Leu-Aib-Lys-Ile-Lol, a trichogin GA IV-analogue carrying Lys residues instead of Gly ones at positions 2, 5, 6, and 9, while a homologous peptide not containing Lys residues does not show any response to pH changes. Experimental and theoretical results, obtained by means of quartz crystal microbalance with dissipation monitoring, surface plasmon resonance, nanoplasmonic sensing technique, Fourier transform infrared-reflection attenuated spectroscopy and dynamic force spectroscopy, and molecular dynamics simulations provide detailed information on the overall monolayer structure changes with pH, including the analysis of the intra- and interchain peptide dynamics, the structure of the peptide layer/water/solid interface, as well as the position and role of solvation and nonsolvation water. The observed stimuli-responsive behavior of L1 peptide monolayers is accounted in terms of the occurrence of a pH-induced wetting/dewetting process, due to the pH-induced switching of the hydrophilic character of charged lysine groups to hydrophobic one of the same uncharged groups, along the peptide chain. This behavior in turn promotes the collective change of the aggregation state of the peptide chains. The present results may pave the way to critically reexamine the mechanism of stimuli-responsive systems.

Reactive Landing of Gramicidin S and Ubiquitin Ions onto Activated Self-Assembled Monolayer Surfaces

Using mass-selected ion deposition combined with in situ infrared reflection absorption spectroscopy (IRRAS), we examined the reactive landing of gramicidin S and ubiquitin ions onto activated self-assembled monolayer (SAM) surfaces terminated with N-hydroxysuccinimidyl ester (NHS-SAM) and acyl fluoride (COF-SAM) groups. Doubly protonated gramicidin S, [GS + 2H]²⁺, and two charge states of ubiquitin, [U + 5H]⁵⁺ and [U + 13H]¹³⁺, were used as model systems, allowing us to explore the effect of the number of free amino groups and the secondary structure on the efficiency of covalent bond formation between the projectile ion and the surface. For all projectile ions, ion deposition resulted in the depletion of IRRAS bands corresponding to the terminal groups on the SAM and the appearance of several new bands not associated with the deposited species. These new bands were assigned to the C=O stretching vibrations of COOH and COO^- groups formed on the surface as a result of ion deposition. The presence of these bands was attributed to an alternative reactive landing pathway that competes with covalent bond formation. This pathway with similar yields for both gramicidin S and ubiquitin ions is analogous to the hydrolysis of the NHS ester bond in solution. The covalent bond formation efficiency increased linearly with the number of free amino groups and was found to be lower for the more compact conformation of ubiquitin compared with the fully unfolded conformation. This observation was attributed to the limited availability of amino groups on the surface of the folded conformation. Our results have provided new insights on the efficiency and mechanism of reactive landing of peptides and proteins onto activated SAMs. Graphical Abstract ᅟ.