Conformations and cryo-force spectroscopy of spray-deposited single-strand DNA on gold

On-Surface Synthesis and Cryogenic Exfoliation of Sterically Frustrated Atropisomers

On-surface synthesis provides exceptional control over nanostructure and material composition, enabling the creation of molecular compounds that are difficult or impossible to obtain with other synthesis methods. In this work, we demonstrate the possibility of synthesizing atropisomeric molecules made of chains of polyaromatic hydrocarbon units via on-surface synthesis. Scanning probe microscopy reveals that molecules adsorbed on Au(111) surfaces adopt a planar structure, with adjacent monomeric units aligning either in parallel or antiparallel configurations, influencing the alignment of the molecule on the surface. Cryo-force spectroscopy peeling experiments show that metastable conformers can be mechanically stabilized during the lifting-redeposition process of the polymer from the surface. In this process, periodic drops in frequency shift are observed, corresponding to monomer detachment-readsorption. Interestingly, this periodicity is independent of the parallel/antiparallel configuration but is counterintuitively smaller than the monomer size. Molecular dynamics simulations relate this effective reduction in unit length to a tethering effect between the chain and the surface. This, in turn, allowed us to test and validate Silva's analytical phenomenological power law model for peeling. Our findings not only provide a method for studying the elusive class 1 atropisomeric molecules but also offer deeper insight into the peeling phenomenon at the nanoscale.

Selection of Plastic-Binding DNA Aptamers for Microplastics Detection

Plastics are critical materials for modern technological applications, yet environmental contamination by microplastics has become a growing concern. In this study, DNA aptamers were isolated for two of the most abundant plastic materials: polyvinylchloride (PVC) and polystyrene (PS). These aptamers contain approximately 90 % cytosine and thymine but only 10 % purine content. Among them, the PVC-1 aptamer binds to PVC with a six-fold higher capacity than a random sequenced DNA. Among the tested plastic materials, PVC and PS exhibited the highest specific binding capacity. Using fluorophore-labeled PVC-1 aptamer, PS/PVC microplastics as low as 1 mg were detected, and the aptamer was selective for microplastics over other environmentally relevant materials, such as silica. Molecular dynamics simulations indicated that the aptamer attempted to maximize contact with the plastic surface for adsorption. This plastic-binding aptamer is expected to find applications in environmental monitoring and has fundamental implications for surface-binding aptamers.

Scanning Probe Microscopy Characterization of Biomolecules enabled by Mass-Selective, Soft-landing Electrospray Ion Beam Deposition

Scanning probe microscopy (SPM), in particular at low temperature (LT) under ultra-high vacuum (UHV) conditions, offers the possibility of real-space imaging with resolution reaching the atomic level. However, its potential for the analysis of complex biological molecules has been hampered by requirements imposed by sample preparation. Transferring molecules onto surfaces in UHV is typically accomplished by thermal sublimation in vacuum. This approach however is limited by the thermal stability of the molecules, i. e. not possible for biological molecules with low vapour pressure. Bypassing this limitation, electrospray ionisation offers an alternative method to transfer molecules from solution to the gas-phase as intact molecular ions. In soft-landing electrospray ion beam deposition (ESIBD), these molecular ions are subsequently mass-selected and gently landed on surfaces which permits large and thermally fragile molecules to be analyzed by LT-UHV SPM. In this concept, we discuss how ESIBD+SPM prepares samples of complex biological molecules at a surface, offering controls of the molecular structural integrity, three-dimensional shape, and purity. These achievements unlock the analytical potential of SPM which is showcased by imaging proteins, peptides, DNA, glycans, and conjugates of these molecules, revealing details of their connectivity, conformation, and interaction that could not be accessed by any other technique.

Molecular machines working at interfaces: physics, chemistry, evolution and nanoarchitectonics

As a post-nanotechnology concept, nanoarchitectonics combines nanotechnology with advanced materials science. Molecular machines made by assembling molecular units and their organizational bodies are also products of nanoarchitectonics. They can be regarded as the smallest functional materials. Originally, studies on molecular machines analyzed the average properties of objects dispersed in solution by spectroscopic methods. Researchers' playgrounds partially shifted to solid interfaces, because high-resolution observation of molecular machines is usually done on solid interfaces under high vacuum and cryogenic conditions. Additionally, to ensure the practical applicability of molecular machines, operation under ambient conditions is necessary. The latter conditions are met in dynamic interfacial environments such as the surface of water at room temperature. According to these backgrounds, this review summarizes the trends of molecular machines that continue to evolve under the concept of nanoarchitectonics in interfacial environments. Some recent examples of molecular machines in solution are briefly introduced first, which is followed by an overview of studies of molecular machines and similar supramolecular structures in various interfacial environments. The interfacial environments are classified into (i) solid interfaces, (ii) liquid interfaces, and (iii) various material and biological interfaces. Molecular machines are expanding their activities from the static environment of a solid interface to the more dynamic environment of a liquid interface. Molecular machines change their field of activity while maintaining their basic functions and induce the accumulation of individual molecular machines into macroscopic physical properties molecular machines through macroscopic mechanical motions can be employed to control molecular machines. Moreover, research on molecular machines is not limited to solid and liquid interfaces; interfaces with living organisms are also crucial.

Automated Structure Discovery for Scanning Tunneling Microscopy

Scanning tunneling microscopy (STM) with a functionalized tip apex reveals the geometric and electronic structures of a sample within the same experiment. However, the complex nature of the signal makes images difficult to interpret and has so far limited most research to planar samples with a known chemical composition. Here, we present automated structure discovery for STM (ASD-STM), a machine learning tool for predicting the atomic structure directly from an STM image, by building upon successful methods for structure discovery in noncontact atomic force microscopy (nc-AFM). We apply the method on various organic molecules and achieve good accuracy on structure predictions and chemical identification on a qualitative level while highlighting future development requirements for ASD-STM. This method is directly applicable to experimental STM images of organic molecules, making structure discovery available for a wider scanning probe microscopy audience outside of nc-AFM. This work also allows more advanced machine learning methods to be developed for STM structure discovery.

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.

Visualizing Chiral Interactions in Carbohydrates Adsorbed on Au(111) by High-Resolution STM Imaging

Carbohydrates are the most abundant organic material on Earth and the structural "material of choice" in many living systems. Nevertheless, design and engineering of synthetic carbohydrate materials presently lag behind that for protein and nucleic acids. Bottom-up engineering of carbohydrate materials demands an atomic-level understanding of their molecular structures and interactions in condensed phases. Here, high-resolution scanning tunneling microscopy (STM) is used to visualize at submolecular resolution the three-dimensional structure of cellulose oligomers assembled on Au(1111) and the interactions that drive their assembly. The STM imaging, supported by ab initio calculations, reveals the orientation of all glycosidic bonds and pyranose rings in the oligomers, as well as details of intermolecular interactions between the oligomers. By comparing the assembly of D- and L-oligomers, these interactions are shown to be enantioselective, capable of driving spontaneous enantioseparation of cellulose chains from its unnatural enantiomer and promoting the formation of engineered carbohydrate assemblies in the condensed phases.

Flexible Superlubricity Unveiled in Sidewinding Motion of Individual Polymeric Chains

A combination of low temperature atomic force microcopy and molecular dynamic simulations is used to demonstrate that soft designer molecules realize a sidewinding motion when dragged over a gold surface. Exploiting their longitudinal flexibility, pyrenylene chains are indeed able to lower diffusion energy barriers via on-surface directional locking and molecular strain. The resulting ultralow friction reaches values on the order of tens of pN reported so far only for rigid chains sliding on an incommensurate surface. Therefore, we demonstrate how molecular flexibility can be harnessed to realize complex nanomotion while retaining a superlubric character. This is in contrast with the paradigm guiding the design of most superlubric nanocontacts (mismatched rigid contacting surfaces).

Visualization and identification of single meteoritic organic molecules by atomic force microscopy

Using high-resolution atomic force microscopy (AFM) with CO-functionalized tips, we atomically resolved individual molecules from Murchison meteorite samples. We analyzed powdered Murchison meteorite material directly, as well as processed extracts that we prepared to facilitate characterization by AFM. From the untreated Murchison sample, we resolved very few molecules, as the sample contained mostly small molecules that could not be identified by AFM. By contrast, using a procedure based on several trituration and extraction steps with organic solvents, we isolated a fraction enriched in larger organic compounds. The treatment increased the fraction of molecules that could be resolved by AFM, allowing us to identify organic constituents and molecular moieties, such as polycyclic aromatic hydrocarbons and aliphatic chains. The AFM measurements are complemented by high-resolution mass spectrometry analysis of Murchison fractions. We provide a proof of principle that AFM can be used to image and identify individual organic molecules from meteorites and propose a method for extracting and preparing meteorite samples for their investigation by AFM. We discuss the challenges and prospects of this approach to study extraterrestrial samples based on single-molecule identification.

Nanometer-Scale Force Profiles of Short Single- and Double-Stranded DNA Molecules on a Gold Surface Measured Using a Surface Forces Apparatus

Using a surface forces apparatus (SFA), we have studied the nanomechanical behavior of short single-stranded and partially and fully double-stranded DNA molecules attached via one end to a self-assembled monolayer on a gold surface. Our results confirm the previously proposed "mushroom-like" polymer structure for surface-attached, single-stranded DNA at low packing density and a "brush-like" structure for the same construct at higher density. At low density we observe a transition to "rigid rod" behavior upon addition of DNA complementary to the surface-attached single strand as the fraction of molecules that are double-stranded increases, with a concomitant increase in the SFA-observed thickness of the monolayer and the characteristic length of the observed repulsive forces. At higher densities, in contrast, this transition is effectively eliminated, presumably because the single-stranded state is already extended in its "brush" state. Taken together, these studies offer insights into the structure and physics of surface-attached short DNAs, providing new guidance for the rational design of DNA-modified functional surfaces.

Predicting Finite-Bias Tunneling Current Properties from Zero-Bias Features: The Frontier Orbital Bias Dependence at an Exemplar Case of DNA Nucleotides in a Nanogap

The electrical current properties of single-molecule sensing devices based on electronic (tunneling) transport strongly depend on molecule frontier orbital energy, spatial distribution, and position with respect to the electrodes. Here, we present an analysis of the bias dependence of molecule frontier orbital properties at an exemplar case of DNA nucleotides in the gap between H-terminated (3, 3) carbon nanotube (CNT) electrodes and its relation to transversal current rectification. The electronic transport properties of this simple single-molecule device, whose characteristic is the absence of covalent bonding between electrodes and a molecule between them, were obtained using density functional theory and non-equilibrium Green's functions. As in our previous studies, we could observe two distinct bias dependences of frontier orbital energies: the so-called strong and the weak pinning regimes. We established a procedure, from zero-bias and empty-gap characteristics, to estimate finite-bias electronic tunneling transport properties, i.e., whether the molecular junction would operate in the weak or strong pinning regime. We also discuss the use of the zero-bias approximation to calculate electric current properties at finite bias. The results from this work could have an impact on the design of new single-molecule applications that use tunneling current or rectification applicable in high-sensitivity sensors, protein, or DNA sequencing.

Reconfigurable Chirality of DNA-Bridged Nanorod Dimers

Gold nanorods assembled in a side-by-side chiral configuration have potential applications in sensing due to their strong chiroptical surface plasmon resonances. Recent experiments have shown that dimers of gold nanorods bridged by double-stranded DNA exhibit variable chiral configurations depending on the chemical and ionic properties of the solvent medium. Here, we uncover the underlying physics governing this intriguing chiral behavior of such DNA-bridged nanorods by theoretically evaluating their configurational free energy landscape. Our results reveal how chiral configurations emerge from an interplay between the twist-stretch coupling of the intervening DNA and the intermolecular interactions between the nanorods, with dimers exhibiting left-handed chirality when the interparticle interactions are dominated by attractive depletion or van der Waals forces and right-handed chirality when dominated by repulsive electrostatic or steric forces. We demonstrate how changes in the depletant or ion concentration of the solvent medium lead to different classes of configurational responses by the dimers, including chirality-switching behavior, in good agreement with experimental observations. Based on extensive analyses of how material properties like nanorod aspect ratio, DNA length, and graft height modulate the free energy landscape, we propose strategies for tuning the environmentally responsive reconfigurability of the nanorod dimers. Overall, this work should help control the chirality and related optical activity of nanoparticle dimers and higher-order assemblies for various applications.

Determining the Interaction Behavior of Calf Thymus DNA with Anastrozole in the Presence of Histone H1: Spectroscopies and Cell Viability of MCF-7 Cell Line Investigations

The interaction of calf thymus DNA (ct DNA) with anastrozole, which is acknowledged as an antineoplastic drug, has been enquired into in the absence and presence of histone H1, through the means of absorbance, fluorescence, circular dichroism spectroscopy, viscosity, thermal melting, and molecular modeling techniques. In addition, the effects of anastrozole on MCF 7 cell line have been thoroughly investigated. Fluorescence spectroscopy results have indicated that quenching mechanism of ct DNA-anastrozole are known as static quenching procedures, since the Stern-Volmer quenching constant (K_SV) seems to face a decrease as the temperature is enhanced; this is a significant evidence for intercalative binding mode of anastrozole with ct DNA. Regarding the ternary system in the presence of H1, the constant of Stern-Volmer quenching was increased as the temperature was heightened. The thermodynamic parameters suggested that the binding could be characterized as exothermic by negative and positive enthalpy and entropy changes in both binary and ternary systems, respectively. It is vital to mention that hydrogen bonds and hydrophobic contributions play significant roles in anastrozole association to ct DNA in the absence and presence of H1. In accordance to the absorption spectroscopy and melting temperature curve outcomes, the binding mode of anastrozole with ct DNA in absence and presence of H1 was indicative of intercalative and nonintercalative bindings, respectively. The viscosity results as binary and ternary systems, which have been elucidated from a sensitive viscometer, have confirmed the fluorescence spectroscopy determinations. The intercalation of anastrozole to ct DNA seemed to be significantly related to an induced reduction in MCF-7 cell proliferation. The molecular modeling results have suggested that anastrozole could bind to H1 in ct DNA-H1 complex in ternary systems, which supports the conclusions that have been obtained from experimental data.

Influence of electrospray deposition on C60 molecular assemblies

Maintaining clean conditions for samples during all steps of preparation and investigation is important for scanning probe studies at the atomic or molecular level. For large or fragile organic molecules, where sublimation cannot be used, high-vacuum electrospray deposition is a good alternative. However, because this method requires the introduction into vacuum of the molecules from solution, clean conditions are more difficult to be maintained. Additionally, because the presence of solvent on the surface cannot be fully eliminated, one has to take care of its possible influence. Here, we compare the high-vacuum electrospray deposition method to thermal evaporation for the preparation of C60 on different surfaces and compare, for sub-monolayer coverages, the influence of the deposition method on the formation of molecular assemblies. Whereas the island location is the main difference for metal surfaces, we observe for alkali halide and metal oxide substrates that the high-vacuum electrospray method can yield single isolated molecules accompanied by surface modifications.

Enabling autonomous scanning probe microscopy imaging of single molecules with deep learning

Scanning probe microscopies allow investigating surfaces at the nanoscale, in real space and with unparalleled signal-to-noise ratio. However, these microscopies are not used as much as it would be expected considering their potential. The main limitations preventing a broader use are the need of experienced users, the difficulty in data analysis and the time-consuming nature of experiments that require continuous user supervision. In this work, we addressed the latter and developed an algorithm that controlled the operation of an Atomic Force Microscope (AFM) that, without the need of user intervention, allowed acquiring multiple high-resolution images of different molecules. We used DNA on mica as a model sample to test our control algorithm, which made use of two deep learning techniques that so far have not been used for real time SPM automation. One was an object detector, YOLOv3, which provided the location of molecules in the captured images. The second was a Siamese network that could identify the same molecule in different images. This allowed both performing a series of images on selected molecules while incrementing the resolution, as well as keeping track of molecules already imaged at high resolution, avoiding loops where the same molecule would be imaged an unlimited number of times. Overall, our implementation of deep learning techniques brings SPM a step closer to full autonomous operation.

Defect-Induced Double-Stranded DNA Unwinding on Graphene

Several works have shown that graphene materials can effectively regulate the double-stranded DNA (dsDNA) structures and are used to remove antibiotic resistance genes in the environment, during which the morphology of the graphene surface plays a key role. However, the mechanism of how different graphene surfaces interact with dsDNA is poorly documented. Here, the interactions of dsDNA with defective graphene (D-Gra) and pristine graphene (P-Gra) have been explored by molecular dynamics simulations. Our data clearly showed that both D-Gra and P-Gra were able to attract dsDNA to form stable bindings. However, the structure evolutions of dsDNA are distinctly different. In detail, D-Gra can initiate quick unwinding of dsDNA and cause significant structural disruption. While for P-Gra, it demonstrated a much weaker capability to disrupt the dsDNA structure. This difference is due to the strong electrostatic interaction between defects and DNA nucleotides. Nucleotides can be highly restricted by the defect while the other parts of dsDNA could move along the transverse directions of D-Gra. This effectively introduces a "pulling force" from the defect that causes the breaking of the hydrogen bonds between dsDNA base pairs. Such force finally leads to the serious unwinding of dsDNA. Our present findings could help us to better understand the molecular mechanism of how the dsDNA canonical B-form was lost upon adsorption to graphene. The findings of the key roles of defects on graphene are beneficial for the design of functional graphenic materials for biological and medical applications through nanostructure engineering.

Practical Guide to Single-Protein AFM Nanomechanical Spectroscopy Mapping: Insights and Pitfalls As Unraveled by All-Atom MD Simulations on Immunoglobulin G

Atomic force microscopy is an invaluable characterization tool in almost every biophysics laboratory. However, obtaining atomic/sub-nanometer resolution on single proteins has thus far remained elusive-a feat long achieved on hard substrates. In this regard, nanomechanical spectroscopy mapping may provide a viable approach to overcome this limitation. By complementing topography with mechanical properties measured locally, one may thus enhance spatial resolution at the single-protein level. In this work, we perform all-atom molecular dynamics simulations of the indentation process on a single immunoglobulin G (IgG) adsorbed on a graphene slab. Our simulations reveal three different stages as a function of strain: a noncontact regime-where the mechanical response is linked to the presence of the water environment- followed by an elastic response and a final plastic deformation regime. In the noncontact regime, we are able to identify hydrophobic/hydrophilic patches over the protein. This regime provides the most local mechanical information that allows one to discern different regions with similar height/topography and leads to the best spatial resolution. In the elastic regime, we conclude that the Young modulus is a well-defined property only within mechanically decoupled domains. This is caused by the fact that the elastic deformation is associated with a global reorganization of the domain. Differences in the mechanical response are large enough to clearly resolve domains within a single protein, such as the three subunits forming the IgG. Two events, unfolding or protein slipping, are observed in the plastic regime. Our simulations allow us to characterize these two processes and to provide a strategy to identify them in the force curves. Finally, we elaborate on possible challenges that could hamper the interpretation of such experiments/simulations and how to overcome them. All in all, our simulations provide a detailed picture of nanomechanical spectroscopy mapping on single proteins, showing its potential and the challenges that need to be overcome to unlock its full potential.

Atomic Scale Three-Dimensional Au Nanocluster on a Rutile TiO2 (110) Surface Resolved by Atomic Force Microscopy

The atomic structure of a three-dimensional Au nanocluster on a TiO₂ surface is important for various studies such as photocatalysis and chemical reactions on metal oxide surfaces. However, accessing the atomic structure of a metal nanocluster supported on a metal oxide surface is still challenging possibly because of its small size, complexity, and flexible structure. Here, we report a detuning imaging mode combined with an atomically sharp tip to address these challenges. Using this method, for the first time, we resolve a three-dimensional Au nanocluster on a rutile TiO₂ (110) surface. We found that the Au nanocluster was continuously adsorbed at the upper and lower terraces. Our results open up a new methodology for studying subnanometer clusters at various surfaces at an atomic scale.

Structure-mechanics statistical learning unravels the linkage between local rigidity and global flexibility in nucleic acids

The mechanical properties of nucleic acids underlie biological processes ranging from genome packaging to gene expression, but tracing their molecular origin has been difficult due to the structural and chemical complexity. We posit that concepts from machine learning can help to tackle this long-standing challenge. Here, we demonstrate the feasibility and advantage of this strategy through developing a structure-mechanics statistical learning scheme to elucidate how local rigidity in double-stranded (ds)DNA and dsRNA may lead to their global flexibility in bend, stretch, and twist. Specifically, the mechanical parameters in a heavy-atom elastic network model are computed from the trajectory data of all-atom molecular dynamics simulation. The results show that the inter-atomic springs for backbone and ribose puckering in dsRNA are stronger than those in dsDNA, but are similar in strengths for base-stacking and base-pairing. Our analysis shows that the experimental observation of dsDNA being easier to bend but harder to stretch than dsRNA comes mostly from the respective B- and A-form topologies. The computationally resolved composition of local rigidity indicates that the flexibility of both nucleic acids is mostly due to base-stacking. But for properties like twist-stretch coupling, backbone springs are shown to play a major role instead. The quantitative connection between local rigidity and global flexibility sets foundation for understanding how local binding and chemical modification of genetic materials effectuate longer-ranged regulatory signals.

The mechanical properties of nucleic acids underlie biological processes ranging from genome packaging to gene expression. We devise structural mechanics statistical learning method to reveal their molecular origin in terms of chemical interactions.

Automated structure discovery in atomic force microscopy

Atomic force microscopy (AFM) with molecule-functionalized tips has emerged as the primary experimental technique for probing the atomic structure of organic molecules on surfaces. Most experiments have been limited to nearly planar aromatic molecules due to difficulties with interpretation of highly distorted AFM images originating from nonplanar molecules. Here, we develop a deep learning infrastructure that matches a set of AFM images with a unique descriptor characterizing the molecular configuration, allowing us to predict the molecular structure directly. We apply this methodology to resolve several distinct adsorption configurations of 1S-camphor on Cu(111) based on low-temperature AFM measurements. This approach will open the door to applying high-resolution AFM to a large variety of systems, for which routine atomic and chemical structural resolution on the level of individual objects/molecules would be a major breakthrough.

Sequential Bending and Twisting around C-C Single Bonds by Mechanical Lifting of a Pre-Adsorbed Polymer

Bending and twisting around carbon-carbon single bonds are ubiquitous in natural and synthetic polymers. Force-induced changes were so far not measured at the single-monomer level, owing to limited ways to apply local forces. We quantified down to the submolecular level the mechanical response within individual poly-pyrenylene chains upon their detachment from a gold surface with an atomic force microscope at 5 K. Computer simulations based on a dedicated force field reproduce the experimental traces and reveal symmetry-broken bent and rotated conformations of the sliding physisorbed segment besides steric hindrance of the just lifted monomer. Our study also shows that the tip-molecule bond remains intact but remarkably soft and links force variations to complex but well-defined conformational changes.

Giant thermal expansion of a two-dimensional supramolecular network triggered by alkyl chain motion

Thermal expansion, the response in shape, area or volume of a solid with heat, is usually large in molecular materials compared to their inorganic counterparts. Resulting from the intrinsic molecule flexibility, conformational changes or variable intermolecular interactions, the exact interplay between these mechanisms is however poorly understood down to the molecular level. Here, we investigate the structural variations of a two-dimensional supramolecular network on Au(111) consisting of shape persistent polyphenylene molecules equipped with peripheral dodecyl chains. By comparing high-resolution scanning probe microscopy and molecular dynamics simulations obtained at 5 and 300 K, we determine the thermal expansion coefficient of the assembly of 980 ± 110 × 10^-6 K^-1, twice larger than other molecular systems hitherto reported in the literature, and two orders of magnitude larger than conventional materials. This giant positive expansion originates from the increased mobility of the dodecyl chains with temperature that determine the intermolecular interactions and the network spacing.

Tuning Structure and Dynamics of Blue Copper Azurin Junctions via Single Amino-Acid Mutations

In the growing field of biomolecular electronics, blue-copper Azurin stands out as one of the most widely studied protein in single-molecule contacts. Interestingly, despite the paramount importance of the structure/dynamics of molecular contacts in their transport properties, these factors remain largely unexplored from the theoretical point of view in the context of single Azurin junctions. Here we address this issue using all-atom Molecular Dynamics (MD) of Pseudomonas Aeruginosa Azurin adsorbed to a Au(111) substrate. In particular, we focus on the structure and dynamics of the free/adsorbed protein and how these properties are altered upon single-point mutations. The results revealed that wild-type Azurin adsorbs on Au(111) along two well defined configurations: one tethered via cysteine groups and the other via the hydrophobic pocket surrounding the Cu 2 + . Surprisingly, our simulations revealed that single amino-acid mutations gave rise to a quenching of protein vibrations ultimately resulting in its overall stiffening. Given the role of amino-acid vibrations and reorientation in the dehydration process at the protein-water-substrate interface, we suggest that this might have an effect on the adsorption process of the mutant, giving rise to new adsorption configurations.

Modeling nanoribbon peeling

The lifting, peeling and exfoliation of physisorbed ribbons (or flakes) of 2D material such as graphene off a solid surface are common and important manoeuvres in nanoscience. The feature that makes this case peculiar is the structural lubricity generally realized by stiff 2D material contacts. We model theoretically the mechanical peeling of a nanoribbon of graphene as realized by the tip-forced lifting of one of its extremes off a flat crystal surface. The evolution of shape, energy, local curvature and body advancement are ideally expected to follow a succession of regimes: (A) initial prying, (B) peeling with stretching but without sliding (stripping), (C) peeling with sliding, (D) liftoff. In the case where in addition the substrate surface corrugation is small or negligible, then (B) disappears, and we find that the (A)-(C) transition becomes universal, analytical and sharp, determined by the interplay between bending rigidity and adsorption energy. This general two-stage peeling transition is identified as a sharp crossover in published data of graphene nanoribbons pulled off an atomic-scale Au(111) substrate.