Conformational Engineering of Flexible Protein Fragments on the Surface of Different Nanoparticles: The Surface-Atom Mobility Rules

As a newly emerging technology, conformational engineering (CE) has been gradually displaying the power of producing protein-like nanoparticles (NPs) by tuning flexible protein fragments into their original native conformation on NPs. But apparently, not all types of NPs can serve as scaffolds for CE. To expedite the CE technology on a broader variety of NPs, the essential characteristic of NPs as scaffolds for CE needs to be identified. Herein, we investigate the potential of two distinct types of NPs as scaffolds for CE: CdSe/ZnS quantum dots (QDs), an ionic compound NP, and palladium NPs (PdNPs), a metal NP. The results demonstrate that while QDs cannot support the restoration of the native conformation and function of the complementary-determining region (CDR) fragments of antibodies, PdNPs can. The notably disparate outcomes unequivocally show that the mobility of the surface atoms/adatoms of the NPs or the mobility of the conjugating bonds to the NPs is essential for CE, which allows the conjugated peptides to undergo a conformational change from their initial random conformation to their most stable native conformation under the constraints mimicking the native long-range interactions in the original proteins. This discovery opens the door for CE on more NPs in the future.

Gold Nanoparticle-Based Artificial Antibodies as Stable Substitutes for Antibodies in the Immunoassay

Sandwich enzyme-linked immunosorbent assay (ELISA) is a widely used powerful method to detect antigens in complicated environments, due to the high sensitivity and specificity of monoclonal antibodies. Yet, the intrinsic instability of antibodies limits the applications of sandwich ELISA. To overcome the shortcomings of antibodies, we previously demonstrated that a class of gold nanoparticle (AuNP)-based artificial antibody, named goldbody, can be created by "Goldization" technology, i.e., reconstructing the fragments of antibodies on AuNPs. Goldbody has the same binding specificity as the original antibody, but has a much better stability. However, it is still a big challenge to design matched goldbody pairs to develop a sandwich ELISA entirely based on goldbodies. Herein, an anti-EGFR goldbody is designed and synthesized by reconstructing ("Goldization") the "dimerization arm" fragment of EGFR on AuNPs. As expected, this new anti-EGFR goldbody binds to EGFR at a site far away from where the previously developed one binds, allowing the two anti-EGFR goldbodies to bind the same EGFR simultaneously and qualify as a matched pair. Subsequently, a goldbody-based sandwich ELISA is developed, and the goldbodies in the ELISA kit can be used for the detection of EGFR even after preheatment at 100 °C, demonstrating the excellent stability of goldbody.

Mobility of thiolates on Au(111) surfaces

Self-assembled monolayers (SAMs), especially those based on thiol containing compounds on gold, are of both practical and fundamental interest. Thiols and thiolates can bind to gold in several ways due to the presence of holes and edges on the surfaces. The variety of binding motifs is increased by the presence of adatoms, i.e. gold atoms present on the surface, that sit between the thiolate and the surface. Although these motifs bind strongly to gold surfaces, they are sufficiently mobile to allow for self-assembly of thiols, either by movement across the surface or by desorption/re-adsorption. The motifs have been investigated primarily in the context of high surface coverage, with some attention given to the mobility of these motifs. Here we focus on the binding in the low-coverage regime, i.e. the initial stage of SAM formation, using theoretical methods. We determine the relative stability of the motifs formed with methane thiolate in the low-coverage regime, and rationalize their relative mobilities. Methane thiolate is used to minimize contributions of intermolecular interactions. Competition between the rates of adsorption, movement, and formation of the motifs can influence the formation of SAMs. In this work we expand the understanding of the early stages of monolayer formation and conclude that the type of motif formed initially depends strongly on the availability of gold adatoms and defects (edges and holes) on the surface at the point of adsorption.

Highly Robust and Self-Adhesive Soft Strain Gauge via Interface Design Engineering

Highly robust soft strain gauges are rapidly emerging as a promising candidate in the fields of vital signs and machine conditions monitoring. However, it is still a key challenge to achieve high-performance strain sensing in these sensors with mechanical/electrical robustness for long-term usage. The multilayer structural design of sensors enhances sensing performance while the interfacial connection of heterogeneous materials between different layers is weak. Herein, inspired by the efficient perception mechanism of scorpion slit sensilla with tough interface interconnections, the synergy of ultra-high electrical performance and mechanical robustness is successfully achieved via interface design engineering. The developed multilayer soft strain gauge (MSSG) exhibits a strain sensitivity beyond 105, a lower detection limit of 8.3 µm, a frequency resolution within 0.1 Hz, and cyclic stability over 63 000 strain cycles. Also, the tough interface improves the level of heterogeneous integration in the MSSG which allows to endure different stresses. Furthermore, an MSSG-based wireless strain monitoring system is developed that enables applications on different complex dynamic surfaces, including accurate identification of human throat activity and monitoring of rolling bearing conditions.

Unveiling the Properties of Sulfhydryl Groups in a Single-Molecule Junction

The metal-thiol interface is ubiquitous in nanotechnology and surface chemistry. It is not only used to construct nanocomposites but also plays a decisive role in the properties of these materials. When organothiol molecules bind to the gold surface, there is still controversy over whether sulfhydryl groups can form disulfide bonds and whether these disulfide bonds can remain stable on the gold surface. Here, we investigate the intrinsic properties of sulfhydryl groups on the gold surface at the single-molecule level using a scanning tunneling microscope break junction technique. Our findings indicate that sulfhydryl groups can react with each other to form disulfide bonds on the gold surface, and the electric field can promote the sulfhydryl coupling reaction. In addition to these findings, ultraviolet irradiation is used to effectively regulate the coupling between sulfhydryl groups, leading to the formation and cleavage of disulfide bonds. These results unveil the intrinsic properties of sulfhydryl groups on the gold surface, therefore facilitating the accurate construction of broad nanocomposites with the desired functionalities.

Probing the affinity of noble metal nanoparticles to the segments of the SARS-CoV-2 spike protein

Currently, scientists have devoted great efforts to finding effective treatments to combat COVID-19 infections. Although noble metal nanoparticles are able to realize protein modifications, their interactions with the protein are still unclear from the atomic perspective. To supply a general understanding, in this work, we have carried out theoretical calculations to investigate the interaction between protein segments (RBD1, RBD2, RBD3) of SARS-Cov-2 spike protein and a series of noble metal (Au, Ag, Cu, Pd, Pt) surfaces regarding the binding strength, protein orientations, and electronic modulations. In particular, the Au surface has shown the strongest binding preferences for the protein segments, which induces electron transfer between the Au and receptor-binding domain (RBD) segments. This further leads to the polarization of segments for virus denaturation. This work has offered a direct visualization of protein interactions with noble metal surfaces from the atomic level, which will benefit anti-virus material developments in the future.

Spontaneous Intercluster Electron Transfer X2- + X0 → 2 X- (X = PtAu24(SCnH2n+1)18) in Solution: Promotion by Long Alkyl Chains

In this work, we systematically investigated the ligand effects on spontaneous electron transfer (ET) between alkanethiolate-protected metal clusters in solution. The donor and acceptor clusters used were [PtAu₂₄(SC_nH_2n+1)₁₈]^2- (8e(Cn)) and [PtAu₂₄(SC_mH_2m+1)₁₈]⁰ (6e(Cm)) (n, m = 2-16), which have icosahedral Pt@Au₁₂ cores with eight and six valence electrons, respectively. The ET rate constant (k_ET) from 8e(Cn) to 6e(Cm) in benzene exhibited a novel turnover behavior as a function of the total chain length n + m: the k_ET decreased with n + m in the range of 4-12, whereas it monotonically increased with n + m in the range of 12-32. Electrospray ionization mass spectrometry of the mixture of 8e(Cn) and 6e(Cm) detected the dimer complex 8e(Cn)·6e(Cm), the relative population of which increased with n + m. The activation energy (E_a), determined based on the Arrhenius plots for n = m, monotonically decreased with n (≥ 6). Based on these results, we proposed that the promotion of ET by longer alkanethiolates was ascribed to two effects on the key intermediate 8e(Cn)·6e(Cm): (1) elongation of the lifetime and (2) the contraction of the distance between 8e(Cn) and 6e(Cm) due to the stronger van der Waals interaction between the longer alkyl chains. Such alkyl-chain-promoted ET is specific to ultrasmall clusters in solution because a nonuniform ligand layer could be formed due to the large curvature of the cluster core.

Proving Cooperativity of a Catalytic Reaction by Means of Nanoscale Geometry: The Case of Click Reaction

Establishing whether a reaction is catalyzed by a single-metal catalytic center or cooperatively by a fleeting complex encompassing two such centers may be an arduous pursuit requiring detailed kinetic, isotopic, and other types of studies─as illustrated, for instance, by over a decade-long work on single-copper versus di-copper mechanisms of the popular "click" reaction. This paper describes a method to interrogate such cooperative mechanisms by a nanoparticle-based platform in which the probabilities of catalytic units being proximal can be varied systematically and, more importantly, independently of their volume concentration. The method relies on geometrical considerations rather than a detailed knowledge of kinetic equations, yet the scaling trends it yield can distinguish between cooperative and non-cooperative mechanisms.

Folding of Flexible Protein Fragments and Design of Nanoparticle-Based Artificial Antibody Targeting Lysozyme

It is generally believed that a protein's sequence solely determines its native structure, but how the long- and short-range interactions jointly determine the native structure/conformation of the protein or every local fragment of the protein is still not fully understood. Since most protein fragments are unstructured on their own, direct observation of the folding of flexible protein fragments is very difficult. Interestingly, we show that it is possible to graft the complementary-determining regions (CDRs) of antibodies onto the surface of a gold nanoparticle (AuNP) to create AuNP-based artificial antibodies (denoted as Goldbodies), such as an antilysozyme Goldbody. Goldbodies can specifically recognize the corresponding antigens like the original natural antibodies do, but direct structural evidence for the refolding or restoration of native conformation of the grafted CDRs on AuNPs is still missing and in high demand. Herein we design a new Goldbody that targets an epitope on the lysozyme different from that of the previous antilysozyme Goldbody, and the one circle of helix in the CDR makes it possible to distinguish the unfolded conformation of the free CDR and its folded conformation on AuNPs by circular dichroism (CD) spectroscopy. The refolding of flexible protein fragments on NPs provides unique evidence and inspiration for understanding the fundamental principles of protein folding.

Conformationally engineering flexible peptides on silver nanoparticles

Molecular conformational engineering is to engineer flexible non-functional molecules into unique conformations to create novel functions just like natural proteins fold. Obviously, it is a grand challenge with tremendous opportunities. Based on the facts that natural proteins are only marginally stable with a net stabilizing energy roughly equivalent to the energy of two hydrogen bonds, and the energy barriers for the adatom diffusion of some metals are within a similar range, we propose that metal nanoparticles can serve as a general replacement of protein scaffolds to conformationally engineer protein fragments on the surface of nanoparticles. To prove this hypothesis, herein, we successfully restore the antigen-recognizing function of the flexible peptide fragment of a natural anti-lysozyme antibody on the surface of silver nanoparticles, creating a silver nanoparticle-base artificial antibody (Silverbody). A plausible mechanism is proposed, and some general principles for conformational engineering are summarized to guide future studies in this area.

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A silver NP-based artificial antibody is created by conformational engineering

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Function emerges on NPs from non-functional peptide by mimicking the protein folding

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A general mechanism is proposed for the conformational engineering on metal NPs

ReaxFF Molecular Dynamics Simulations of Large Gold Nanocrystals

A systematic study of gold nanocrystals is carried out using molecular dynamics simulations with reactive force fields. The nanocrystal size is varied between 2 and 10 nm with methane and butane thiolate as ligands. The reactive force fields allow investigation of the formation of staples. The simulations explain several experimental observations such as the number of staples per thiolate of about 40% and the occupation of the top adsorption sites on the facets. They also show that the frequency of staples is increased on the edges, which leads to a desorption of gold atoms from the nanocrystal edges. In contrast to previous nonreactive simulations, no difference between the distances of the ligands on the nanocrystal edges and facets is observed. Except for the 2 nm particles, the nanocrystal size and the alkane chain length of the ligands have only a small influence on the nanocrystal properties. The occupation of adsorption sites and staple frequencies are very slowly converging properties, taking more than ns.

A potential inhibitor of MDM2 by restoring the native conformation of the p53 α-helical peptide on gold nanoparticles

Many efforts have been made to develop inhibitors of MDM2 as potential drugs for cancer therapy. In this work, we use our previous developed conformational engineering technique to stabilize the binding conformation of the p53 transcription activation domain (TAD) peptide on gold NPs (AuNPs), and create an AuNP-based anti-MDM2 artificial antibody, denoted as Goldbody, that specifically binds MDM2. Though the free TAD peptide is unstructured, circular dichroism spectra confirm that its α-helical conformation in the original p53 protein is restored on the anti-MDM2 Goldbody, and surface plasmon resonance (SPR) experiments confirm that there is strong specific interaction between the anti-MDM2 Goldbody and MDM2, demonstrating the anti-MDM2 Goldbody as a potential inhibitor of MDM2. This work demonstrates that the conformational engineering technique is not limited to the antigen-antibody systems, but can also be applied more widely in other protein-protein interfaces to create more and more artificial proteins for various biomedical applications.

Adatom mediated adsorption of N-heterocyclic carbenes on Cu(111) and Au(111)

The adsorption of N-heterocyclic carbenes (NHCs) on Cu(111) and Au(111) surfaces is studied with density-functional theory. The role of the molecular side groups as well as the surface morphology in determining the adsorption geometry are explored in detail. Flat-laying NHCs, as observed experimentally for NHC with relatively small side groups, result from the adsorption at adatoms and give rise to the so-called ballbot configurations, which are more stable than adsorption on flat surfaces and provide an efficient precursor for the formation of bis(NHC) dimers. On Au(111), the resulting (NHC)₂ Au complexes are purely physisorbed and thus mobile. On the more reactive Cu(111), in contrast, the central Cu atom in the (NHC)₂ Cu dimer is still covalently bound to the surface, resulting in a mobility, which has to be thermally activated.

Hydrophobicity of Self-Assembled Monolayers of Alkanes: Fluorination, Density, Roughness, and Lennard-Jones Cutoffs

The interplay of fluorination and structure of alkane self-assembled monolayers and how these affect hydrophobicity are explored via molecular dynamics simulations, contact angle goniometry, and surface-enhanced infrared absorption spectroscopy. Wetting coefficients are found to grow linearly in the monolayer density for both alkane and perfluoroalkane monolayers. The larger contact angles of monolayers of perfluorinated alkanes are shown to be primarily caused by their larger molecular volume, which leads to a larger nearest-neighbor grafting distance and smaller tilt angle. Increasing the Lennard-Jones force cutoff in simulations is found to increase hydrophilicity. Specifically, wetting coefficients scale like the inverse square of the cutoff, and when extrapolated to the infinite cutoff limit, they yield contact angles that compare favorably to experimental values. Nanoscale roughness is also found to reliably increase monolayer hydrophobicity, mostly via the reduction of the entropic part of the work of adhesion. Analysis of depletion lengths shows that droplets on nanorough surfaces partially penetrate the surface, intermediate between Wenzel and Cassie-Baxter states.

The ligand effect on the interface structures and electrocatalytic applications of atomically precise metal nanoclusters

Metal nanoclusters, also known as ultra-small metal nanoparticles, occupy the gap between discrete atoms and plasmonic nanomaterials, and are an emerging class of atomically precise nanomaterials. Metal nanoclusters protected by different types of ligands, such as thiolates, alkynyls, hydrides, and N-heterocyclic carbenes, have been synthesized in recent years. Moreover, recent experiment and theoretical studies also indicated that the metal nanoclusters show great promise in many electrocatalytic reactions, such as hydrogen evolution, oxygen reduction, and CO₂reduction. The atomically precise nature of their structures enables the elucidation of structure-property relationships and the reaction mechanisms, which is essential if nanoclusters with enhanced performances are to be rationally designed. Particularly, the ligands play an important role in affecting the interface bonding, stability and electrocatalytic activity/selectivity. In this review, we mainly focus on the ligand effect on the interface structure of metal nanoclusters and then discuss the recent advances in electrocatalytic applications. Furthermore, we point out our perspectives on future efforts in this field.

Computational design of single-stranded DNA hairpin aptamers immobilized on a biosensor substrate

Aptamer interactions with a surface of attachment are central to the design and performance of aptamer-based biosensors. We have developed a computational modeling approach to study different system designs-including different aptamer-attachment ends, aptamer surface densities, aptamer orientations, and solvent solutions-and applied it to an anti MUC1 aptamer tethered to a silica biosensor substrate. Amongst all the system designs explored, we found that attaching the anti MUC1 aptamer through the 5' terminal end, in a high surface density configuration, and solvated in a 0.8 M NaCl solution provided the best exposure of the aptamer MUC1 binding regions and resulted in the least amount of aptamer backbone fluctuations. Many of the other designs led to non-functional systems, with the aptamer collapsing onto the surface. The computational approach we have developed and the resulting analysis techniques can be employed for the rational design of aptamer-based biosensors and provide a valuable tool for improving biosensor performance and repeatability.

Self-Assembly and Rearrangement of a Polyproline II Helix Peptide on Gold

Polyproline peptide sequences have gained popularity as anchors for peptide-based self-assembled monolayers (SAMs) due to their attractive properties. In this work, peptides containing the polyproline II helix (PPII) conformation were designed and assembled on gold (Au). A quartz crystal microbalance with dissipation was used to characterize SAM formation kinetics and related properties. Peptides were designed with the sequence (GPPPPPG)₂C. It was discovered that a biexponential adsorption and rearrangement model describes the binding kinetics of the PPII-containing peptide on Au. In this model, an initial reversible binding step is followed by an irreversible rearrangement step, given by parameter k_t. This study found k_t to be approximately 0.00064 s^-1 for the PPII-containing peptides. Similarly, we found that the adsorption of the PPII-containing peptide on Au, given by ΔG_ads, was thermodynamically favorable (-7.8 kcal mol^-1) and comparable to other common thiol terminated SAMs on Au. Furthermore, we characterized SAM properties via QCM-D, Fourier-transform infrared (FTIR) spectroscopy, and electrochemical techniques to reveal high molecular density SAMs consisting of PPII helices. In addition, these SAMs were found to have high antifouling properties. Overall, this study characterizes the fundamental assembly mechanisms, particularly, rearrangement of PPII-containing peptides for the first time, which will be useful in the designing of future peptide-based SAMs with high surface coverage and antifouling properties.

Theoretical inspection of the spin-crossover [Fe(tzpy)2(NCS)2] complex on Au(100) surface

We explore the deposition of the spin-crossover [Fe(tzpy)₂(NCS)₂] complex on the Au(100) surface by means of density functional theory (DFT) based calculations. Two different routes have been employed: low-cost finite cluster-based calculations, where both the Fe complex and the surface are maintained fixed while the molecule approaches the surface; and periodic DFT plane-wave calculations, where the surface is represented by a four-layer slab and both the molecule and surface are relaxed. Our results show that the bridge adsorption site is preferred over the on-top and fourfold hollow ones for both spin states, although they are energetically close. The LS molecule is stabilized by the surface, and the HS-LS energy difference is enhanced by about 15%-25% once deposited. The different Fe ligand field for LS and HS molecules manifests on the composition and energy of the low-lying bands. Our simulated STM images indicate that it is possible to distinguish the spin state of the deposited molecules by tuning the bias voltage of the STM tip. Finally, it should be noted that the use of a reduced size cluster to simulate the Au(100) surface proves to be a low-cost and reliable strategy, providing results in good agreement with those resulting from state-of-the-art periodic calculations for this system.

Gold Chain Formation via Local Lifting of Surface Reconstruction by Hot Electron Injection on H2(D2)/Au(111)

The hexagonal close packed surface of gold shows a 22 × 3 "herringbone" surface reconstruction which makes it unique among the (111) surfaces of all metals. This long-range energetically favored dislocation pattern appears in response to the strong tensile stress that would be present on the unreconstructed surface. Adsorption of molecular and atomic species can be used to tune this surface stress and lift the herringbone reconstruction. Here we show that herringbone reconstruction can be controllably lifted in ultrahigh vacuum at cryogenic temperatures by precise hot electron injection in the presence of hydrogen molecules. We use the sharp tip of a scanning tunneling microscope (STM) for charge carrier injection and characterization of the resulting chain nanostructures. By comparing STM images, rotational spectromicroscopy and ab initio calculations, we show that formation of gold atomic chains is associated with release of gold atoms from the surface, lifting of the reconstruction, dissociation of H₂ molecules, and formation of surface hydrides. Gold hydrides grow in a zipper-like mechanism forming chains along the [11̅0] directions of the Au(111) surface and can be manipulated by further electron injection. Finally, we demonstrate that Au(111) terraces can be transformed with nearly perfect terrace selectivity over distances of hundreds of nanometers.

The Last Secret of Protein Folding: The Real Relationship Between Long-Range Interactions and Local Structures

The protein folding problem has been extensively studied for decades, and hundreds of thousands of protein structures have been solved. Yet, how proteins fold from a linear peptide chain to their unique 3D structures is not fully understood. With key clues having emerged unexpectedly from the field of nanoscience, a "Confined Lowest Energy Fragment" (CLEF) hypothesis was proposed. The CLEF hypothesis states that a protein chain can be divided into CLEFs, the semi-independent folding units, by a small number of key residues that form key long-range interactions. The native structure of a CLEF is the lowest energy state under the constraints of the key long-range interactions, but the native structure of the whole protein is not necessary the lowest energy state as Anfinsen's thermodynamic hypothesis suggested. The CLEF hypothesis proposes a unified CLEF mechanism for protein folding, basically a two-step process. In the first step, the favorable enthalpy of CLEFs for native structures quickly brings those residues for the key long-range interactions together, forming intermediates corresponding to the so-called hydrophobic collapse. In the second step, those collapsed key residues shuffle for the right combination to form the native key long-range interactions. The CLEF hypothesis provides a simple solution to all protein folding paradoxes, and proposes a "CLEF Age" or "Stone Age" for the prebiotic evolution of proteins.

A Robust Au-C≡C Functionalized Surface: Toward Real-Time Mapping and Accurate Quantification of Fe2+ in the Brains of Live AD Mouse Models

Described here is that Au-C≡C bonds showed the highest stability under biological conditions, with abundant thiols, and the best electrochemical performance compared to Au-S and Au-Se bonds. The new finding was also confirmed by theorical calculations. Based on this finding, a specific molecule for recognition of Fe²⁺ was designed and synthesized, and used to create a selective and accurate electrochemical sensor for the quantification of Fe²⁺ . The present ratiometric strategy demonstrates high spatial resolution for real-time tracking of Fe²⁺ in a dynamic range of 0.2-120 μM. Finally, a microelectrode array with good biocompatibility was applied in imaging and biosensing of Fe²⁺ in the different regions of live mouse brains. Using this tool, it was discovered that the uptake of extracellular Fe²⁺ into the cortex and striatum was largely mediated by cyclic adenosine monophosphate (cAMP) through the CREB-related pathway in the brain of a mouse with Alzheimer's disease.

Dynamic behaviors of interfacial water on the self-assembly monolayer (SAM) heterogeneous surface

Dynamic behaviors of water molecules near the surface with mixed hydrophobic and hydrophilic areas are studied by molecular dynamics simulation. More specifically, the diffusion coefficient and hydrogen bond lifetime of interfacial water on the self-assembly monolayer composed of hydrophobic and hydrophilic groups and their dependence on the mixing ratio are studied. The diffusion dramatically slows down, and the hydrogen bond lifetime considerably increases when a few hydrophilic groups are added to the hydrophobic surface. When the percentage of hydrophilic groups increases to 25%, the behavior of interfacial water is similar to the case of the pure hydrophilic surface. The sensitivity to the hydrophilic group can be attributed to the fact that the grafted hydrophilic groups can not only retard the directly bound water molecules but also affect indirectly bound water by stabilizing hydrogen bonds among interfacial water molecules.

A Comprehensive Study of the Bridge Site and Substrate Relaxation Asymmetry for Methanethiol Adsorption on Au(111) at Low Coverage

We use dispersion-corrected density functional theory to explore the bridge-site asymmetry for methanethiol adsorbed on Au(111) with two different S-C bond orientations. We attribute the asymmetry to the intrinsic character of the Au(111) surface rather than the adsorbate. The preference for bridge-fcc versus bridge-hcp SCH3 adsorption sites is controlled by the S-C bond orientation. The system energy difference favors the bridge-fcc site by 8.1 meV on the unrelaxed Au(111) surface. Relaxing the Au substrate increased this energy difference to 26.1 meV. This asymmetry is also reflected in the atomic displacement of the relaxed Au surface. Although in both cases, the bridge-site Au atoms shift away from the fcc 3-fold hollow site, the motion is greater for the bridge-fcc allowing a more favorable geometry for the sulfur atom to bond to the bridging atoms. We confirm that the adsorption energy is strongly dependent on the S-C bond orientation and position, which can be understood in terms of a simple coordination geometry model. This work has important implications for alkanethiol surface diffusion and the structure of their self-assembled monolayers.

Interaction of the (2√3 × 3)rect. Adsorption-Site Basis and Alkyl-Chain Close Packing in Alkanethiol Self-Assembled Monolayers on Au(111): A Molecular Dynamics Study of Alkyl-Chain Conformation

We show that the adsorption site basis of the (2√3 × 3)rect. phase of n-alkanethiol self-assembled monolayers plays a key role in determining the molecular conformation of the close-packed alkyl chains. Ten proposed reconstructed Au-S interfaces are used to explore the minimized energy alkyl-chain packing of n-decanethiol molecules using molecular dynamics with the all-atom description. In this comparative study, all models have the same alkyl-chain surface density of four molecules per unit cell; thus, differences are due to the headgroup spacing within the 4-molecule basis as opposed to the average surface density. We demonstrate for the first time the 4-molecule-basis twist structure driven by the packing of alkanethiol molecules in a large simulation box (100 molecules, 25 unit cells) using molecular dynamics. Our results validate the prediction put forward by Mar and Klein that to achieve the 4-molecule-basis twist symmetry observed by the experiment, the headgroups must deviate from the high-symmetry (√3 × √3)R30° sites. The key structural parameters: tilt, twist, and end-group height, as well as their spatial order, are compared with experimental results, which we show is a highly sensitive approach that can be used to vet proposed Au-S interfacial models.

Force Field Parameter Development for the Thiolate/Defective Au(111) Interface

A molecular-level understanding of the interplay between self-assembled monolayers (SAMs) of thiolates and gold surface is of great importance to a wide range of applications in surface science and nanotechnology. Despite theoretical research progress of the past decade, an atomistic model, capable of describing key features of SAMs at reconstructed gold surfaces, is still missing. In this work, periodic ab initio density functional theory (DFT) calculations were utilized to develop a new atomistic force field model for alkanethiolate (AT) SAMs on a reconstructed Au(111) surface. The new force field parameters were carefully trained to reproduce the key features, including vibrational spectra and torsion energy profiles of ethylthiolate (C₂S) in the bridge or staple motif model on the Au(111) surface, wherein, the force constants of the bond and angle terms were trained by matching the vibrational spectra, while the torsion parameters of the dihedral angles were trained via fitting the torsion energy profiles from DFT calculations. To validate the developed force field parameters, we performed classical molecular dynamics (MD) simulations for both pristine and reconstructed Au-S interface models with a (2√3 × 3) unit cell, which includes four dodecanethiolate (C₁₀S) molecules on the Au(111) surface. The simulation results showed that the geometrical features of the investigated Au-S interface models and structural properties of the C₁₀S SAMs are in good agreement with the ab initio MD studies. The newly developed atomistic force field model provides new fundamental insights into AT SAMs on the reconstructed Au(111) surface and adds advancement to the existing interface research knowledge.

Manipulating chemistry through nanoparticle morphology

We demonstrate that the protonation chemistry of molecules adsorbed at nanometer distances from the surface of anisotropic gold nanoparticles can be manipulated through the effect of surface morphology on the local proton density of an organic coating. Direct evidence of this remarkable effect was obtained by monitoring surface-enhanced Raman scattering (SERS) from mercaptobenzoic acid and 4-aminobenzenethiol molecules adsorbed on gold nanostars. By smoothing the initially sharp nanostar tips through a mild thermal treatment, changes were induced on protonation of the molecules, which can be observed through changes in the measured SERS spectra. These results shed light on the local chemical environment near anisotropic colloidal nanoparticles and open an alternative avenue to actively control chemistry through surface morphology.

Single-Molecule Measurement of Adsorption Free Energy at the Solid-Liquid Interface

Adsorption plays a critical role in surface and interface processes. Fractional surface coverage and adsorption free energy are two essential parameters of molecular adsorption. However, although adsorption at the solid-gas interface has been well-studied, and some adsorption models were proposed more than a century ago, challenges remain for the experimental investigation of molecular adsorption at the solid-liquid interface. Herein, we report the statistical and quantitative single-molecule measurement of adsorption at the solid-liquid interface by using the single-molecule break junction technique. The fractional surface coverage was extracted from the analysis of junction formation probability so that the adsorption free energy could be calculated by referring to the Langmuir isotherm. In the case of three prototypical molecules with terminal methylthio, pyridyl, and amino groups, the adsorption free energies were found to be 32.5, 33.9, and 28.3 kJ mol^-1 , respectively, which are consistent with DFT calculations.

Non-chemisorbed gold-sulfur binding prevails in self-assembled monolayers

Gold-thiol contacts are ubiquitous across the physical and biological sciences in connecting organic molecules to surfaces. When thiols bind to gold in self-assembled monolayers (SAMs) the fate of the hydrogen remains a subject of profound debate-with implications for our understanding of their physical properties, spectroscopic features and formation mechanism(s). Exploiting measurements of the transmission through a molecular junction, which is highly sensitive to the nature of the molecule-electrode contact, we demonstrate here that the nature of the gold-sulfur bond in SAMs can be probed via single-molecule conductance measurements. Critically, we find that SAM measurements of dithiol-terminated molecular junctions yield a significantly lower conductance than solution measurements of the same molecule. Through numerous control experiments, conductance noise analysis and transport calculations based on density functional theory, we show that the gold-sulfur bond in SAMs prepared from the solution deposition of dithiols does not have chemisorbed character, which strongly suggests that under these widely used preparation conditions the hydrogen is retained.

Determination of the structure and geometry of N-heterocyclic carbenes on Au(111) using high-resolution spectroscopy

N-heterocyclic carbenes (NHCs) bind very strongly to transition metals due to their unique electronic structure featuring a divalent carbon atom with a lone pair in a highly directional sp2-hybridized orbital. As such, they can be assembled into monolayers on metal surfaces that have enhanced stability compared to their thiol-based counterparts. The utility of NHCs to form such robust self-assembled monolayers (SAMs) was only recently recognized and many fundamental questions remain. Here we investigate the structure and geometry of a series of NHCs on Au(111) using high-resolution X-ray photoelectron spectroscopy and density functional theory calculations. We find that the N-substituents on the NHC ring strongly affect the molecule-metal interaction and steer the orientation of molecules in the surface layer. In contrast to previous reports, our experimental and theoretical results provide unequivocal evidence that NHCs with N-methyl substituents bind to undercoordinated adatoms to form flat-lying complexes. In these SAMs, the donor-acceptor interaction between the NHC lone pair and the undercoordinated Au adatom is primarily responsible for the strong bonding of the molecules to the surface. NHCs with bulkier N-substituents prevent the formation of such complexes by forcing the molecules into an upright orientation. Our work provides unique insights into the bonding and geometry of NHC monolayers; more generally, it charts a clear path to manipulating the interaction between NHCs and metal surfaces using traditional coordination chemistry synthetic strategies.

Computational and experimental approach to understanding the structural interplay of self-assembled end-terminated alkanethiolates on gold surfaces

Molecular organization dictates phases, stability and subsequent electronic structure of self-assembled monolayers. With appropriate density functionals, ab initio molecular dynamics (AIMD) simulations predicted and elucidated experimental orientations.

Self-assembled monolayers in organic electronics

Self-assembly is possibly the most effective and versatile strategy for surface functionalization. Self-assembled monolayers (SAMs) can be formed on (semi-)conductor and dielectric surfaces, and have been used in a variety of technological applications. This work aims to review the strategy behind the design and use of self-assembled monolayers in organic electronics, discuss the mechanism of interaction of SAMs in a microscopic device, and highlight the applications emerging from the integration of SAMs in an organic device. The possibility of performing surface chemistry tailoring with SAMs constitutes a versatile approach towards the tuning of the electronic and morphological properties of the interfaces relevant to the response of an organic electronic device. Functionalisation with SAMs is important not only for imparting stability to the device or enhancing its performance, as sought at the early stages of development of this field. SAM-functionalised organic devices give rise to completely new types of behavior that open unprecedented applications, such as ultra-sensitive label-free biosensors and SAM/organic transistors that can be used as robust experimental gauges for studying charge tunneling across SAMs.

Spontaneous protein desorption from self-assembled monolayer (SAM)-coated gold nanoparticles

Interfacial water molecules and lateral diffusion of protein reduce the adsorption affinity of protein and promote protein desorption.

Dumbbell gold nanoparticle dimer antennas with advanced optical properties

Plasmonic nanoantennas have found broad applications in the fields of photovoltaics, electroluminescence, non-linear optics and for plasmon enhanced spectroscopy and microscopy. Of particular interest are fundamental limitations beyond the dipolar approximation limit. We introduce asymmetric gold nanoparticle antennas (AuNPs) with improved optical near-field properties based on the formation of sub-nanometer size gaps, which are suitable for studying matter with high-resolution and single molecule sensitivity. These dumbbell antennas are characterized in regard to their far-field and near-field properties and are compared to similar dimer and trimer antennas with larger gap sizes. The tailoring of the gap size down to sub-nanometer length scales is based on the integration of rigid macrocyclic cucurbituril molecules. Stable dimer antennas are formed with an improved ratio of the electromagnetic field enhancement and confinement. This ratio, taken as a measure of the performance of an antenna, can even exceed that exhibited by trimer AuNP antennas composed of comparable building blocks with larger gap sizes. Fluctuations in the far-field and near-field properties are observed, which are likely caused by distinct deviations of the gap geometry arising from the faceted structure of the applied colloidal AuNPs.

Artificial antibody created by conformational reconstruction of the complementary-determining region on gold nanoparticles

Mimicking protein-like specific interactions and functions has been a long-pursued goal in nanotechnology. The key challenge is to precisely organize nonfunctional surface groups on nanoparticles into specific 3D conformations to function in a concerted and orchestrated manner. Here, we develop a method to graft the complementary-determining regions of natural antibodies onto nanoparticles and reconstruct their “active” conformation to create nanoparticle-based artificial antibodies that recognize the corresponding antigens. Our work demonstrates that it is possible to create functions on nanoparticles by conformational engineering, namely tuning flexible surface groups into specific conformations. Our straightforward strategy could be used further to create other artificial antibodies for various applications and provides a new tool to understand the structure and folding of natural proteins.

To impart biomedical functions to nanoparticles (NPs), the common approach is to conjugate functional groups onto NPs by dint of the functions of those groups per se. It is still beyond current reach to create protein-like specific interactions and functions on NPs by conformational engineering of nonfunctional groups on NPs. Here, we develop a conformational engineering method to create an NP-based artificial antibody, denoted “Goldbody,” through conformational reconstruction of the complementary-determining regions (CDRs) of natural antibodies on gold NPs (AuNPs). The seemingly insurmountable task of controlling the conformation of the CDR loops, which are flexible and nonfunctional in the free form, was accomplished unexpectedly in a simple way. Upon anchoring both terminals of the free CDR loops on AuNPs, we managed to reconstruct the “active” conformation of the CDR loops by tuning the span between the two terminals and, as a result, the original specificity was successfully reconstructed on the AuNPs. Two Goldbodies have been created by this strategy to specifically bind with hen egg white lysozyme and epidermal growth factor receptor, with apparent affinities several orders of magnitude stronger than that of the original natural antibodies. Our work demonstrates that it is possible to create protein-like functions on NPs in a protein-like way, namely by tuning flexible surface groups to the correct conformation. Given the apparent merits, including good stability, of Goldbodies, we anticipate that a category of Goldbodies could be created to target different antigens and thus used as substitutes for natural antibodies in various applications.

Comparative Study of the Adsorption of Thiols and Selenols on Au(111) and Au(100)

The effect of the Au crystalline plane on the adsorption of different thiols and selenols is studied via reductive desorption (RD) and X-ray photoelectron spectroscopy (XPS) measurements. Self-assembled monolayers (SAMs) using aliphatic (ATs) and aromatic thiols (ArTs) on both Au(111) and Au(100) were prepared. The electrochemical stability of these SAMs on both surfaces is evaluated by comparing the position of the RD peaks. The longer the AT chain the more stable the SAM on Au(100) when compared to Au(111). By means of XPS measurements, we determine that the binding energy (BE) of the S 2p signal corresponding to the S atoms at the thiol/Au interface, commonly assigned at 162.0 eV, shifts 0.2 eV from Au(111) to Au(100) for SAMs prepared using thiols with the C* (C atom bonded to S) in sp³ hybridization, such as ATs. However, when the thiol presents the C* with an sp² hybridization, such as in the case of ArTs, the BE remains at 162.0 eV regardless of the surface plane. Selenol-based SAMs were characterized comparatively on both Au(100) and Au(111). Our results show that selenol SAMs become even more electrochemically stable on Au(100) with respect to Au(111) than the analogue sulfur-based SAM. According to our results, we suggest that the electronic distribution around the Au-S/Se bond could be responsible for the different structural arrangements reported in the literature (gold adatoms, etc.), which should be dependent on the crystalline face (Au(hkl)-S) and the chemical nature of the environment of the adsorbates (sp³-C* vs sp²-C* and Au-SR vs Au-SeR).

N-Heterocyclic carbenes on close-packed coinage metal surfaces: bis-carbene metal adatom bonding scheme of monolayer films on Au, Ag and Cu

By means of scanning tunnelling microscopy (STM), complementary density functional theory (DFT) and X-ray photoelectron spectroscopy (XPS) we investigate the binding and self-assembly of a saturated molecular layer of model N-heterocyclic carbene (NHC) on Cu(111), Ag(111) and Au(111) surfaces under ultra-high vacuum (UHV) conditions. XPS reveals that at room temperature, coverages up to a monolayer exist, with the molecules engaged in metal carbene bonds. On all three surfaces, we resolve similar arrangements, which can be interpreted only in terms of mononuclear M(NHC)2 (M = Cu, Ag, Au) complexes, reminiscent of the paired bonding of thiols to surface gold adatoms. Theoretical investigations for the case of Au unravel the charge distribution of a Au(111) surface covered by Au(NHC)2 and reveal that this is the energetically preferential adsorption configuration.

Gold nanoparticles with patterned surface monolayers for nanomedicine: current perspectives

Molecular self-assembly is a topic attracting intense scientific interest. Various strategies have been developed for construction of molecular aggregates with rationally designed properties, geometries, and dimensions that promise to provide solutions to both theoretical and practical problems in areas such as drug delivery, medical diagnostics, and biosensors, to name but a few. In this respect, gold nanoparticles covered with self-assembled monolayers presenting nanoscale surface patterns-typically patched, striped or Janus-like domains-represent an emerging field. These systems are particularly intriguing for use in bio-nanotechnology applications, as presence of such monolayers with three-dimensional (3D) morphology provides nanoparticles with surface-dependent properties that, in turn, affect their biological behavior. Comprehensive understanding of the physicochemical interactions occurring at the interface between these versatile nanomaterials and biological systems is therefore crucial to fully exploit their potential. This review aims to explore the current state of development of such patterned, self-assembled monolayer-protected gold nanoparticles, through step-by-step analysis of their conceptual design, synthetic procedures, predicted and determined surface characteristics, interactions with and performance in biological environments, and experimental and computational methods currently employed for their investigation.

Stretching-Induced Conductance Variations as Fingerprints of Contact Configurations in Single-Molecule Junctions

Molecule-electrode contact atomic structures are a critical factor that characterizes molecular devices, but their precise understanding and control still remain elusive. Based on combined first-principles calculations and single-molecule break junction experiments, we herein establish that the conductance of alkanedithiolate junctions can both increase and decrease with mechanical stretching, and the specific trend is determined by the S-Au linkage coordination number (CN) or the molecule-electrode contact atomic structure. Specifically, we find that the mechanical pulling results in the conductance increase for the junctions based on S-Au CN two and CN three contacts, while the conductance is minimally affected by stretching for junctions with the CN one contact and decreases upon the formation of Au monatomic chains. Detailed analysis unravels the mechanisms involving the competition between the stretching-induced upshift of the highest occupied molecular orbital-related states toward the Fermi level of electrodes and the deterioration of molecule-electrode electronic couplings in different contact CN cases. Moreover, we experimentally find a higher chance to observe the conductance enhancement mode under a faster elongation speed, which is explained by ab initio molecular dynamics simulations that reveal an important role of thermal fluctuations in aiding deformations of contacts into low-coordination configurations that include monatomic Au chains. Pointing out the insufficiency in previous notions of associating peak values in conductance histograms with specific contact atomic structures, this work resolves the controversy on the origins of ubiquitous multiple conductance peaks in S-Au-based single-molecule junctions.

A van der Waals DFT study of chain length dependence of alkanethiol adsorption on Au(111): physisorption vs. chemisorption

Coverage and size dependent chain–chain electronic interactions counteract with the alkyl chain–gold surface interactions and the surface relaxation of the metal in the formation of standing up monolayer structures.

Beyond the staple motif: a new order at the thiolate-gold interface

Staple motifs in the form of -RS(AuSR)_x- (x = 1, 2, 3, etc.) are the most common structural feature at the interface of the thiolate-protected gold nanoclusters, Au_n(SR)_m. However, the recently solved structure of Au₉₂(SR)₄₄, in which the facets of the Au₈₄ core are protected mainly by the bridging thiolates, challenges the staple hypothesis. Herein, we explore the surface sensitivity of the thiolate-gold interface from first principles density functional theory. We find that the interfacial structures of thiolates on gold are surface sensitive: while a staple motif (such as -RS-Au-SR-) is preferred on Au(111), a bridging motif (-RS-) is preferred on Au(100) and Au(110). We show that this surface sensitivity is closely related to the coordination number of the surface Au atom on the different surfaces. We further confirm the preference of the bridging motif for self-assembled monolayers of two different ligands (methylthiolate and 4-tert-butylbenzenethiolate) on Au(100). With this surface sensitivity, we categorize the structure-known Au_n(SR)_m clusters into three groups: (1) no bridging; (2) ambiguous bridging; (3) distinct bridging. We further employ the surface sensitivity of the thiolate-Au interface to predict the protecting motifs of face-centered cubic (fcc) gold nanoparticles of different shapes. Our study provides a unifying view of the Au_n(SR)_m structures with guidelines for structure predictions for larger Au_n(SR)_m clusters of a fcc core.

Even the Odd Numbers Help: Failure Modes of SAM-Based Tunnel Junctions Probed via Odd-Even Effects Revealed in Synchrotrons and Supercomputers

This Account describes a body of research in atomic level design, synthesis, physicochemical characterization, and macroscopic electrical testing of molecular devices made from ferrocene-functionalized alkanethiol molecules, which are molecular diodes, with the aim to identify, and resolve, the failure modes that cause leakage currents. The mismatch in size between the ferrocene headgroup and alkane rod makes waxlike highly dynamic self-assembled monolayers (SAMs) on coinage metals that show remarkable atomic-scale sensitivity in their electrical properties. Our results make clear that molecular tunnel junction devices provide an excellent testbed to probe the electronic and supramolecular structures of SAMs on inorganic substrates. Contacting these SAMs to a eutectic "EGaIn" alloy top-electrode, we designed highly stable long-lived molecular switches of the form electrode-SAM-electrode with robust rectification ratios of up to 3 orders of magnitude. The graphic that accompanies this conspectus displays a computed SAM packing structure, illustrating the lollipop shape of the molecules that gives dynamic SAM supramolecular structures and also the molecule-electrode van der Waals (vdW) contacts that must be controlled to form good SAM-based devices. In this Account, we first trace the evolution of SAM-based electronic devices and rationalize their operation using energy level diagrams. We describe the measurement of device properties using near edge X-ray absorption fine structure spectroscopy, cyclic voltammetry, and X-ray photoelectron spectroscopy complemented by molecular dynamics and electronic structure calculations together with large numbers of electrical measurements. We discuss how data obtained from these combined experimental/simulation codesign studies demonstrate control over the supramolecular and electronic structure of the devices, tuning odd-even effects to optimize inherent packing tendencies of the molecules in order to minimize leakage currents in the junctions. It is now possible, but still very costly to create atomically smooth electrodes and we discuss progress toward masking electrode imperfections using cooperative molecule-electrode contacts that are only accessible by dynamic SAM structures. Finally, the unique ability of SAM devices to achieve simultaneously high and atom-sensitive electrical switching is summarized and discussed. While putting these structures to work as real world electronic devices remains very challenging, we speculate on the scientific and technological advances that are required to further improve electronic and supramolecular structure, toward the creation of high yields of long-lived molecular devices with (very) large, reproducible rectification ratios.