Controlling the stereochemistry and regularity of butanethiol self-assembled monolayers on au(111)

Probing surface properties of organic molecular layers by scanning tunneling microscopy

In view of the relevance of organic thin layers in many fields, the fundamentals, growth mechanisms, and dynamics of thin organic layers, in particular thiol-based self-assembled monolayers (SAMs) on Au(111) are systematically elaborated. From both theoretical and practical perspectives, dynamical and structural features of the SAMs are of great intrigue. Scanning tunneling microscopy (STM) is a remarkably powerful technique employed in the characterization of SAMs. Numerous research examples of investigation about the structural and dynamical properties of SAMs using STM, sometimes combined with other techniques, are listed in the review. Advanced options to enhance the time resolution of STM are discussed. Additionally, we elaborate on the extremely diverse dynamics of various SAMs, such as phase transitions and structural changes at the molecular level. In brief, the current review is expected to supply a better understanding and novel insights regarding the dynamical events happening in organic SAMs and how to characterize these processes.

Silicon - single molecule - silicon circuits

In 2020, silicon - molecule - silicon junctions were fabricated and shown to be on average one third as conductive as traditional junctions made using gold electrodes, but in some instances to be even more conductive, and significantly 3 times more extendable and 5 times more mechanically stable. Herein, calculations are performed of single-molecule junction structure and conductivity pertaining to blinking and scanning-tunnelling-microscopy (STM) break junction (STMBJ) experiments performed using chemisorbed 1,6-hexanedithiol linkers. Some strikingly different characteristics are found compared to analogous junctions formed using the metals which, to date, have dominated the field of molecular electronics. In the STMBJ experiment, following retraction of the STM tip after collision with the substrate, unterminated silicon surface dangling bonds are predicted to remain after reaction of the fresh tips with the dithiol solute. These dangling bonds occupy the silicon band gap and are predicted to facilitate extraordinary single-molecule conductivity. Enhanced junction extendibility is attributed to junction flexibility and the translation of adsorbed molecules between silicon dangling bonds. The calculations investigate a range of junction atomic-structural models using density-functional-theory (DFT) calculations of structure, often explored at 300 K using molecular dynamics (MD) simulations. These are aided by DFT calculations of barriers for passivation reactions of the dangling bonds. Thermally averaged conductivities are then evaluated using non-equilibrium Green's function (NEGF) methods. Countless applications through electronics, nanotechnology, photonics, and sensing are envisaged for this technology.

Covalent Linkages of Molecules and Proteins to Si-H Surfaces Formed by Disulfide Reduction

Thiols and disulfide contacts have been, for decades, key for connecting organic molecules to surfaces and nanoclusters as they form self-assembled monolayers (SAMs) on metals such as gold (Au) under mild conditions. In contrast, they have not been similarly deployed on Si owing to the harsh conditions required for monolayer formation. Here, we show that SAMs can be simply formed by dipping Si-H surfaces into dilute solutions of organic molecules or proteins comprising disulfide bonds. We demonstrate that S-S bonds can be spontaneously reduced on Si-H, forming covalent Si-S bonds in the presence of traces of water, and that this grafting can be catalyzed by electrochemical potential. Cyclic disulfide can be spontaneously reduced to form complete monolayers in 1 h, and the reduction can be catalyzed electrochemically to form full surface coverages within 15 min. In contrast, the kinetics of SAM formation of the cyclic disulfide molecule on Au was found to be three-fold slower than that on Si. It is also demonstrated that dilute thiol solutions can form monolayers on Si-H following oxidation to disulfides under ambient conditions; the supply of too much oxygen, however, inhibits SAM formation. The electron transfer kinetics of the Si-S-enabled SAMs on Si-H is comparable to that on Au, suggesting that Si-S contacts are electrically transmissive. We further demonstrate the prospect of this spontaneous disulfide reduction by forming a monolayer of protein azurin on a Si-H surface within 1 h. The direct reduction of disulfides on Si electrodes presents new capabilities for a range of fields, including molecular electronics, for which highly conducting SAM-electrode contacts are necessary and for emerging fields such as biomolecular electronics as disulfide linkages could be exploited to wire proteins between Si electrodes, within the context of the current Si-based technologies.

Spontaneous S-Si bonding of alkanethiols to Si(111)-H: towards Si-molecule-Si circuits

We report the synthesis of covalently linked self-assembled monolayers (SAMs) on silicon surfaces, using mild conditions, in a way that is compatible with silicon-electronics fabrication technologies. In molecular electronics, SAMs of functional molecules tethered to gold via sulfur linkages dominate, but these devices are not robust in design and not amenable to scalable manufacture. Whereas covalent bonding to silicon has long been recognized as an attractive alternative, only formation processes involving high temperature and/or pressure, strong chemicals, or irradiation are known. To make molecular devices on silicon under mild conditions with properties reminiscent of Au–S ones, we exploit the susceptibility of thiols to oxidation by dissolved O₂, initiating free-radical polymerization mechanisms without causing oxidative damage to the surface. Without thiols present, dissolved O₂ would normally oxidize the silicon and hence reaction conditions such as these have been strenuously avoided in the past. The surface coverage on Si(111)–H is measured to be very high, 75% of a full monolayer, with density-functional theory calculations used to profile spontaneous reaction mechanisms. The impact of the Si–S chemistry in single-molecule electronics is demonstrated using STM-junction approaches by forming Si–hexanedithiol–Si junctions. Si–S contacts result in single-molecule wires that are mechanically stable, with an average lifetime at room temperature of 2.7 s, which is five folds higher than that reported for conventional molecular junctions formed between gold electrodes. The enhanced “ON” lifetime of this single-molecule circuit enables previously inaccessible electrical measurements on single molecules.

Spontaneously formed Si–S bonds enable monolayer and single-molecule Si–molecule–Si circuits.

Chemistry of cysteine assembly on Au(100): electrochemistry, in situ STM and molecular modeling

Cysteine (Cys) is an essential amino acid with a carboxylic acid, an amine and a thiol group. We have studied the surface structure and adsorption dynamics of l-cysteine adlayers on Au(100) from aqueous solution using electrochemistry, high-resolution electrochemical scanning tunnelling microscopy (in situ STM), and molecular modelling. Cys adsorption on this low-index Au-surface has been much less studied than Cys adsorption on Au(111)- and Au(110)-electrode surfaces. Chronopotentiometry was employed to monitor the adsorption dynamics at sub-second resolution and showed that adsorption is completed in 30 minutes at Cys concentrations above 100 μM. Two consecutive steps could be fitted to these data. Two separate reductive desorption peaks of Cys adlayers on Au(100) with a total coverage of 2.52 (±0.15) × 10-10 mol cm-2 were observed. In situ STM showed that the adsorbed Cys is organized in stripes with "fork-like" features which co-exist in (11 × 2)-2Cys and (7 × 2)-2Cys lattices, quite differently from Cys adsorption on Au(111)-electrode surfaces. Stripe structures with bright STM contrast in the center suggest that a second Cys adlayer on top of a first adlayer is formed, supporting the dual-peak reductive desorption of Cys adlayers. In addition, monolayers of both pure l-Cys and pure d-Cys and a 1 : 1 racemic mixture of l- and d-Cys on Au(100) were studied. Virtually identical macroscopic electrochemical features were found, but in situ STM discloses many more defects for the racemic mixture than for the pure enantiomers due to structural mismatch of l- and d-Cys. Density functional theory (DFT) calculations combined with a cluster model for the Au(100) surface were carried out to investigate the adsorption energy and geometry of the adsorbed monomer and dimer Cys species in different orientations, with detailed attention to the chirality effects. Optimized DFT geometries were used to construct model STM images, and kinetic Monte Carlo simulations undertaken to illuminate the growth of adsorbate rows and the mechanism of the adlayer formation as well as the Cys adsorption patterns specific to the Au(100)-electrode surface.

Steering the Achiral into Chiral with a Self-Assembly Strategy

Chirality transfer from self-assembly of achiral titanyl phthalocyanine (TiOPc) to its top-sitting TiOPc molecule has been successfully achieved. The TiOPc molecules first assemble into a porous network on Au(111) that contains periodic chiral voids, each being fenced by four axially rotating TiOPc molecules in upward adsorption geometry where their ending O atoms exclusively point away from the substrate. The additional top-sitting TiOPc molecule turns out to be chiral upon adsorption on a chiral void with its ending O atom toward the substrate. The chirality of the top-sitting TiOPc is associated with a charge transfer between its indole rings and the ending O atoms of the underlying TiOPc molecules that form the chiral void, resulting in asymmetric electronic density of the indole rings in the top-sitting molecule and accordingly the chirality of the molecular orbitals. Such a scenario also validates other planar achiral metallophthalocyanines such as copper phthalocyanine that become chiral upon adsorption on the chiral voids in the underlying TiOPc assembly, indicating that the chirality transfer mechanism from assembly to the top-sitting molecule is not uncommon.

Protection of silver and gold LSPR biosensors in corrosive NaCl environment by short alkanethiol molecules; characterized by extinction spectrum, helium ion microscopy and SERS

We investigated the utility of localized surface plasmon resonance sensors in a biologically relevant environment containing NaCl. Our sensors are fabricated by depositing gold or silver on a monolayer of adsorbed monodisperse SiO₂ nanospheres. While silver nanostructures are rather unstable in air and water as assessed by drifts in the extinction peak, even gold nanostructures have been found to drift at elevated NaCl concentrations. In an attempt to protect these nanostructures against NaCl, we modified them with alkanethiols with different lengths in the vapor phase and found that shorter chain alkanethiols such as 1-butanethiol are particularly effective against even 250 mM NaCl, rather than longer-chain alkanethiols more suitable for robust SAM formation. A vapor phase treatment method, in contrast to widely used solution phase treatment methods, was selected with the intention of reducing the solvent effect, i.e. destruction of intricate nanostructures upon contact with a solvent when nanostructures have been prepared in a vacuum system. Moreover, the treatment with 1-butanethiol led to an enhanced sensitivity as expressed by peak shift in nm per refractive index unit, nm per RIU. We show the results of evaluating alkanethiol-protected silver and gold nanostructures by extinction spectroscopy, helium ion microscopy and surface-enhanced Raman spectroscopy. The vapor phase treatment method with short chain alkanethiols is an effective way to protect intricate gold and silver nanostructures prepared in a vacuum system.

We investigated the utility of localized surface plasmon resonance sensors in a biologically relevant environment containing NaCl.

Redox Potentials and Electronic States of Iron Porphyrin IX Adsorbed on Single Crystal Gold Electrode Surfaces

Metalloporphyrins are active sites in metalloproteins and synthetic catalysts. They have also been studied extensively by electrochemistry as well as being prominent targets in electrochemical scanning tunneling microscopy (STM). Previous studies of FePPIX adsorbed on graphite and alkylthiol modified Au electrodes showed a pair of reversible Fe(III/II)PPIX peaks at about -0.41 V (vs NHE) at high solution pH. We recently used iron protoporphyrin IX (FePPIX) as an intercalating probe for long-range electrochemical electron transfer through a G-quadruplex oligonucleotide (DNAzyme); this study disclosed two, rather than a single pair of voltammetric peaks with a new and dominating peak, shifted 200 mV positive relative to the ≈-0.4 V peak. Prompted by this unexpected observation, we report here a study of the voltammetry of FePPIX itself on single-crystal Au(111), (100), and (110) and polycrystalline Au electrode surfaces. In all cases the dominating pair of new Fe(III/II)PPIX redox peaks, shifted positively by more than 200 mV compared to those of previous studies appeared. This observation is supported by density functional theory (DFT) which shows that strong dispersion forces in the FePPIX/Au electronic interaction drive the midpoint potential toward positive values. The FePPIX spin states depend on interaction with the Au(111) interface, converting all the Fe(II)/(III)PPIX species into low-spin states. These results support electrochemical evidence for the nature of the electronic coupling between FePPIX and Au-surfaces, and the electronic states of adsorbate molecules, with a bearing also on recent reports of magnetic FePPIX/Au(111) interactions in ultrahigh vacuum (UHV).

Chiral Surface of Nanoparticles Determines the Orientation of Adsorbed Transferrin and Its Interaction with Receptors

When nanoparticles are exposed to a physiological environment, a "protein corona" is formed that greatly determines their biological fate. Adsorption of proteins could be influenced by chiral surfaces of nanoparticles; however, very few quantitative studies are available on the interaction of protein with the chiral surface of nanoparticles, and the underlying mechanism remains largely unresolved. We have developed a strategy to quantitatively analyze the adsorption and conformational features of transferrin on gold nanoparticles that are functionalized with d, l, and racemic penicillamine. We used a quartz microbalance platform to monitor the interaction of the adsorbed transferrin with transferrin receptors in HEK cell-derived liposomes. Results show that the chiral surface of nanoparticle determines the orientation and conformation of transferrin, which subsequently affects the interaction and recognition of transferrin with its receptor on the cellular membrane. Transferrin is widely used as a tumor-targeting ligand in cancer treatment and diagnosis since the transferrin receptor is overexpressed on the cell membrane of various types of cancer cells. Thus, the present results will help to expand the knowledge on biological identity of nanoparticles with chiral surfaces in a physiological environment and provide an insight into the rational design of therapeutic nanoparticles.

Chiral Selectivity in Inter-reactant Recognition and Electron Transfer of the Oxidation of Horse Heart Cytochrome c by Trioxalatocobaltate(III)

Outer-sphere electron transfer (ET) between optically active transition-metal complexes and either other transition-metal complexes or metalloproteins is a prototype reaction for kinetic chirality. Chirality as the ratio between bimolecular rate constants of two enantiomers mostly amounts to 1.05-1.2 with either the Λ or Δ form the more reactive, but the origin of chirality in ET parameters such as work terms, electronic transmission coefficient, and nuclear reorganization free energy has not been addressed. We report a study of ET between the Λ-/Δ-[Co(Ox)3](3-) pair (Ox = oxalate) and horse heart cytochrome c (cyt c). This choice is prompted by strong ion-pair formation that enables separation into inter-reactant interaction (chiral "recognition") and ET within the ion pair ("stereoselectivity"). Chiral selectivity was first addressed experimentally. Λ-[Co(Ox)3](3-) was found to be both the more strongly bound and faster reacting enantiomer expressed respectively by the ion-pair formation constant KX and ET rate constant kET(X) (X = Λ and Δ), with KΛ/KΔ and kET(Λ)/kET(Δ) both ≈1.1-1.2. rac-[Co(Ox)3](3-) behavior is intermediate between those of Λ- and Δ-[Co(Ox)3](3-). Chirality was next analyzed by quantum-mechanical ET theory combined with density functional theory and statistical mechanical computations. We also modeled the ion pair K(+)·[Co(Ox)3](3-) in order to address the influence of the solution ionic strength. The complex structure of cyt c meant that this reactant was represented solely by the heme group including the chiral axial ligands L-His and L-Met. Both singlet and triplet hemes as well as hemes with partially deprotonated propionic acid side groups were addressed. The computations showed that the most favorable inter-reactant configuration involved a narrow distance and orientation space very close to the contact distance, substantiating the notion of a reaction complex and the equivalence of the binding constant to a bimolecular reaction volume. The reaction is significantly diabatic even at these short inter-reactant distances, with electronic transmission coefficients κel(X) = 10(-3)-10(-2). The computations demonstrated chirality in both KX and κel(X) but no chirality in the reorganization and reaction free energy (driving force). As a result of subtle features in both KX and κel(X) chirality, the "operational" chirality κET(Λ)KΛ/κET(Δ)KΔ emerges larger than unity (1.1-1.2) from the molecular modeling as in the experimental data.

Understanding and Designing the Gold-Bio Interface: Insights from Simulations

Gold nanoparticles (AuNPs) are an integral part of many exciting and novel biomedical applications, sparking the urgent need for a thorough understanding of the physicochemical interactions occurring between these inorganic materials, their functional layers, and the biological species they interact with. Computational approaches are instrumental in providing the necessary molecular insight into the structural and dynamic behavior of the Au-bio interface with spatial and temporal resolutions not yet achievable in the laboratory, and are able to facilitate a rational approach to AuNP design for specific applications. A perspective of the current successes and challenges associated with the multiscale computational treatment of Au-bio interfacial systems, from electronic structure calculations to force field methods, is provided to illustrate the links between different approaches and their relationship to experiment and applications.

Gold surfaces and nanoparticles are protected by Au(0)-thiyl species and are destroyed when Au(I)-thiolates form

The synthetic chemistry and spectroscopy of sulfur-protected gold surfaces and nanoparticles is analyzed, indicating that the electronic structure of the interface is Au(0)-thiyl, with Au(I)-thiolates identified as high-energy excited surface states. Density-functional theory indicates that it is the noble character of gold and nanoparticle surfaces that destabilizes Au(I)-thiolates. Bonding results from large van der Waals forces, influenced by covalent bonding induced through s-d hybridization and charge polarization effects that perturbatively mix in some Au(I)-thiolate character. A simple method for quantifying these contributions is presented, revealing that a driving force for nanoparticle growth is nobleization, minimizing Au(I)-thiolate involvement. Predictions that Brust-Schiffrin reactions involve thiolate anion intermediates are verified spectroscopically, establishing a key feature needed to understand nanoparticle growth. Mixing of preprepared Au(I) and thiolate reactants always produces Au(I)-thiolate thin films or compounds rather than monolayers. Smooth links to O, Se, Te, C, and N linker chemistry are established.

Putting David Craig’s Legacy to Work in Nanotechnology and Biotechnology

David Craig (1919–2015) left us with a lasting legacy concerning basic understanding of chemical spectroscopy and bonding. This is expressed in terms of some of the recent achievements of my own research career, with a focus on integration of Craig’s theories with those of Noel Hush to solve fundamental problems in photosynthesis, molecular electronics (particularly in regard to the molecules synthesized by Maxwell Crossley), and self-assembled monolayer structure and function. Reviewed in particular is the relation of Craig’s legacy to: the 50-year struggle to assign the visible absorption spectrum of arguably the world’s most significant chromophore, chlorophyll; general theories for chemical bonding and structure extending Hush’s adiabatic theory of electron-transfer processes; inelastic electron-tunnelling spectroscopy (IETS); chemical quantum entanglement and the Penrose–Hameroff model for quantum consciousness; synthetic design strategies for NMR quantum computing; Gibbs free-energy measurements and calculations for formation and polymorphism of organic self-assembled monolayers on graphite surfaces from organic solution; and understanding the basic chemical processes involved in the formation of gold surfaces and nanoparticles protected by sulfur-bound ligands, ligands whose form is that of Au0-thiyl rather than its commonly believed AuI-thiolate tautomer.

A priori calculations of the free energy of formation from solution of polymorphic self-assembled monolayers

Modern quantum chemical electronic structure methods typically applied to localized chemical bonding are developed to predict atomic structures and free energies for meso-tetraalkylporphyrin self-assembled monolayer (SAM) polymorph formation from organic solution on highly ordered pyrolytic graphite surfaces. Large polymorph-dependent dispersion-induced substrate-molecule interactions (e.g., -100 kcal mol(-1) to -150 kcal mol(-1) for tetratrisdecylporphyrin) are found to drive SAM formation, opposed nearly completely by large polymorph-dependent dispersion-induced solvent interactions (70-110 kcal mol(-1)) and entropy effects (25-40 kcal mol(-1) at 298 K) favoring dissolution. Dielectric continuum models of the solvent are used, facilitating consideration of many possible SAM polymorphs, along with quantum mechanical/molecular mechanical and dispersion-corrected density functional theory calculations. These predict and interpret newly measured and existing high-resolution scanning tunnelling microscopy images of SAM structure, rationalizing polymorph formation conditions. A wide range of molecular condensed matter properties at room temperature now appear suitable for prediction and analysis using electronic structure calculations.

Two-dimensional chiral molecular assembly on solid surfaces: formation and regulation

The expression of chirality in 2D molecular assemblies on solid surfaces has unique features compared to the analogous process in 1D and 3D supramolecular assemblies. Understanding the formation of chiral molecular assemblies on surfaces not only provides insight into the origin and transfer of chirality in many enantioselective processes, but also aids rational design and construction of chiral architectures and materials. This present contribution reviews recent studies on how chirality is induced and expressed on the surface at different levels, both from intrinsically chiral and achiral molecules. Furthermore, we discuss the regulation effect of some pivotal factors, for example, the chemical structure, the chiral auxiliary molecules, and the assembled environments, on the expression of chirality in molecular assembly.

Intermixed adatom and surface-bound adsorbates in regular self-assembled monolayers of racemic 2-butanethiol on Au(111)

In situ scanning tunneling microscopy combined with density functional theory molecular dynamics simulations reveal a complex structure for the self-assembled monolayer (SAM) of racemic 2-butanethiol on Au(111) in aqueous solution. Six adsorbate molecules occupy a (10×√3)R30° cell organized as two RSAuSR adatom-bound motifs plus two RS species bound directly to face-centered-cubic and hexagonally close-packed sites. This is the first time that these competing head-group arrangements have been observed in the same ordered SAM. Such unusual packing is favored as it facilitates SAMs with anomalously high coverage (30%), much larger than that for enantiomerically resolved 2-butanethiol or secondary-branched butanethiol (25%) and near that for linear-chain 1-butanethiol (33%).