Controlled Formation of Nanoribbons and Their Heterostructures via Assembly of Mass-Selected Inorganic Ions.

Control of nanomaterial dimensions with atomic precision through synthetic methods is essential to understanding and engineering of nanomaterials. For single-layer inorganic materials, size and shape controls have been achieved by self-assembly and surface-catalyzed reactions of building blocks deposited at a surface. However, the scope of nanostructures accessible by such approach is restricted by the limited choice of building blocks that can be thermally evaporated onto surfaces, such as atoms or thermostable molecules. Herein this limitation is bypassed by using mass-selected molecular ions obtained via electrospray ionization as building blocks to synthesize nanostructures that are inaccessible by conventional evaporation methods. As the first example, micron-scale production of MoS2 and WS2 nanoribbons and their heterostructures on graphene are shown by the self-assembly of asymmetrically shaped building blocks obtained from the electrospray. It is expected that judicious use of electrospray-generated building blocks would unlock access to previously inaccessible inorganic nanostructures.

Direct observation of glycans bonded to proteins and lipids at the single-molecule level.

Proteins and lipids decorated with glycans are found throughout biological entities, playing roles in biological functions and dysfunctions. Current analytical strategies for these glycan-decorated biomolecules, termed glycoconjugates, rely on ensemble-averaged methods that do not provide a full view of positions and structures of glycans attached at individual sites in a given molecule, especially for glycoproteins. We show single-molecule analysis of glycoconjugates by direct imaging of individual glycoconjugate molecules using low-temperature scanning tunneling microscopy. Intact glycoconjugate ions from electrospray are soft-landed on a surface for their direct single-molecule imaging. The submolecular imaging resolution corroborated by quantum mechanical modeling unveils whole structures and attachment sites of glycans in glycopeptides, glycolipids, N-glycoproteins, and O-glycoproteins densely decorated with glycans.

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.

Landing Proteins on Graphene Trampoline Preserves Their Gas-Phase Folding on the Surface.

Molecule-surface collisions are known to initiate dynamics that lead to products inaccessible by thermal chemistry. These collision dynamics, however, have mostly been examined on bulk surfaces, leaving vast opportunities unexplored for molecular collisions on nanostructures, especially on those that exhibit mechanical properties radically different from those of their bulk counterparts. Probing energy-dependent dynamics on nanostructures, particularly for large molecules, has been challenging due to their fast time scales and high structural complexity. Here, by examining the dynamics of a protein impinging on a freestanding, single-atom-thick membrane, we discover molecule-on-trampoline dynamics that disperse the collision impact away from the incident protein within a few picoseconds. As a result, our experiments and ab initio calculations show that cytochrome c retains its gas-phase folded structure when it collides onto freestanding single-layer graphene at low energies (∼20 meV/atom). The molecule-on-trampoline dynamics, expected to be operative on many freestanding atomic membranes, enable reliable means to transfer gas-phase macromolecular structures onto freestanding surfaces for their single-molecule imaging, complementing many bioanalytical techniques.

Identifying the origin of local flexibility in a carbohydrate polymer.

Correlating the structures and properties of a polymer to its monomer sequence is key to understanding how its higher hierarchy structures are formed and how its macroscopic material properties emerge. Carbohydrate polymers, such as cellulose and chitin, are the most abundant materials found in nature whose structures and properties have been characterized only at the submicrometer level. Here, by imaging single-cellulose chains at the nanoscale, we determine the structure and local flexibility of cellulose as a function of its sequence (primary structure) and conformation (secondary structure). Changing the primary structure by chemical substitutions and geometrical variations in the secondary structure allow the chain flexibility to be engineered at the single-linkage level. Tuning local flexibility opens opportunities for the bottom-up design of carbohydrate materials.

Fast Molecular Compression by a Hyperthermal Collision Gives Bond-Selective Mechanochemistry.

Using electrospray ion beam deposition, we collide the complex molecule Reichardt's dye (C_{41}H_{30}NO^{+}) at low, hyperthermal translational energy (2-50 eV) with a Cu(100) surface and image the outcome at single-molecule level by scanning tunneling microscopy. We observe bond-selective reaction induced by the translational kinetic energy. The collision impulse compresses the molecule and bends specific bonds, prompting them to react selectively. This dynamics drives the system to seek thermally inaccessible reactive pathways, since the compression timescale (subpicosecond) is much shorter than the thermalization timescale (nanosecond), thereby yielding reaction products that are unobtainable thermally.

Direct observation of knock-on reaction with umbrella inversion arising from zero-impact-parameter collision at a surface.

In Surface-Aligned-Reactions (SAR), the degrees of freedom of chemical reactions are restricted and therefore the reaction outcome is selected. Using the inherent corrugation of a Cu(110) substrate the adsorbate molecules can be positioned and aligned and the impact parameter, the collision miss-distance, can be chosen. Here, substitution reaction for a zero impact parameter collision gives an outcome which resembles the classic Newton's cradle in which an incident mass 'knocks-on' the same mass in the collision partner, here F + CF3 → (CF3)' + (F)' at a copper surface. The mechanism of knock-on was shown by Scanning Tunnelling Microscopy to involve reversal of the CF3 umbrella as in Walden inversion, with ejection of (F)' product along the continuation of the F-reagent direction of motion, in collinear reaction.

Exploring the Molecular Conformation Space by Soft Molecule-Surface Collision.

Biomolecules function by adopting multiple conformations. Such dynamics are governed by the conformation landscape whose study requires characterization of the ground and excited conformation states. Here, the conformational landscape of a molecule is sampled by exciting an initial gas-phase molecular conformer into diverse conformation states, using soft molecule-surface collision (0.5-5.0 eV). The resulting ground and excited molecular conformations, adsorbed on the surface, are imaged at the single-molecule level. This technique permits the exploration of oligosaccharide conformations, until now, limited by the high flexibility of oligosaccharides and ensemble-averaged analytical methods. As a model for cellulose, cellohexaose chains are observed in two conformational extremes, the typical "extended" chain and the atypical "coiled" chain-the latter identified as the gas-phase conformer preserved on the surface. Observing conformations between these two extremes reveals the physical properties of cellohexaose, behaving as a rigid ribbon that becomes flexible when twisted. The conformation space of any molecule that can be electrosprayed can now be explored.

Contrasting Efficiency of Electron-Induced Reaction at Cu(110) in Aliphatic and Aromatic Bromides.

We report a comparative study of the electron-induced reaction of pentyl bromide (PeBr) and phenyl bromide (PhBr) on Cu(110) at 4.6 K, observed by scanning tunneling microscopy (STM). The induced dissociation of the intact adsorbed molecule for both reagents occurred at an energy of 2.0 eV, producing a hydrocarbon radical and a Br atom. Electron-induced C-Br bond dissociation was found to be a single-electron process for both reagents. The impulsive two-state (I2S) model was used to describe the Br atom recoil as due to molecular excitation to a repulsive anti-bonding state, in which recoil of the dissociation products occurred due to C·Br repulsion along the prior C-Br bond direction. The measured reaction yield was 3 orders of magnitude greater for PeBr, 2.0 × 10-7 reactive events per electron, than for PhBr with a yield of 1.7 × 10-10. The low yield of dissociation products from the aromatic PhBr was attributed to the presence of two additional anionic states below the 2.0 eV energy limit, absent for the aliphatic PeBr; these additional anionic states for PhBr could provide a pathway for electron transfer to the surface in the case of the aromatic, but not the aliphatic, anion. The consequent shorter lifetime of the repulsive aromatic anion of PhBr is consistent with the observation of shorter mean recoil distance (3.2 Å) of its Br dissociation product, as compared with the markedly longer recoil (8.7 Å) of Br observed from the anion of PeBr.

Electron-induced molecular dissociation at a surface leads to reactive collisions at selected impact parameters.

Crossed molecular beams of gases have provided definitive information concerning the dynamics of chemical reactions. The results have, however, of necessity been averaged over collisions with impact parameters ranging from zero to infinity, thus obscuring the effect of this important variable. Here we employ a method through which impact parameter averaging is suppressed in a surface reaction. We aim a highly collimated reactive 'projectile' molecule along a surface at a stationary adsorbed 'target' molecule, with both the projectile and target being observed by Scanning Tunnelling Microscopy (STM). The projectile was CF2 recoiling from electron-induced bond-breaking in chemisorbed CF3 on Cu(110) at 4.6 K. The collimation of the resulting CF2 'surface-molecular-beam' restricted it to a lateral spread of ±1° as a consequence of its interaction with the Cu rows below. This collimation was modelled by molecular dynamics simulations. In the experiments the recoiling CF2 projectile was aimed, successively, at impact parameters of b = 0 and +3.6 Å at a chemisorbed second CF2, b = +1.8 Å at a chemisorbed I-atom, or b = -4.0, b = -0.4 and b = +3.2 Å at a chemisorbed vinyl radical. The pattern of reactive and non-reactive scattering was determined by STM. These collimated surface-molecular-beams have the potential to aim molecular projectiles with selected impact parameters at the many target species identifiable at a surface by STM.

Approaching the forbidden fruit of reaction dynamics: Aiming reagent at selected impact parameters.

Collision geometry is central to reaction dynamics. An important variable in collision geometry is the miss-distance between molecules, known as the "impact parameter." This is averaged in gas-phase molecular beam studies. By aligning molecules on a surface prior to electron-induced dissociation, we select impact parameters in subsequent inelastic collisions. Surface-collimated "projectile" molecules, difluorocarbene (CF2), were aimed at stationary "target" molecules characterized by scanning tunneling microscopy (STM), with the observed scattering interpreted by computational molecular dynamics. Selection of impact parameters showed that head-on collisions favored bimolecular reaction, whereas glancing collisions led only to momentum transfer. These collimated projectiles could be aimed at the wide variety of adsorbed targets identifiable by STM, with the selected impact parameter assisting in the identification of the collision geometry required for reaction.

Bond selectivity in electron-induced reaction due to directed recoil on an anisotropic substrate.

Bond-selective reaction is central to heterogeneous catalysis. In heterogeneous catalysis, selectivity is found to depend on the chemical nature and morphology of the substrate. Here, however, we show a high degree of bond selectivity dependent only on adsorbate bond alignment. The system studied is the electron-induced reaction of meta-diiodobenzene physisorbed on Cu(110). Of the adsorbate's C-I bonds, C-I aligned 'Along' the copper row dissociates in 99.3% of the cases giving surface reaction, whereas C-I bond aligned 'Across' the rows dissociates in only 0.7% of the cases. A two-electronic-state molecular dynamics model attributes reaction to an initial transition to a repulsive state of an Along C-I, followed by directed recoil of C towards a Cu atom of the same row, forming C-Cu. A similar impulse on an Across C-I gives directed C that, moving across rows, does not encounter a Cu atom and hence exhibits markedly less reaction.

Clocking Surface Reaction by In-Plane Product Rotation.

Electron-induced reaction of physisorbed meta-diiodobenzene (mDIB) on Cu(110) at 4.6 K was studied by Scanning Tunneling Microscopy and molecular dynamics theory. Single-electron dissociation of the first C-I bond led to in-plane rotation of an iodophenyl (IPh) intermediate, whose motion could be treated as a "clock" of the reaction dynamics. Alternative reaction mechanisms, successive and concerted, were observed giving different product distributions. In the successive mechanism, two electrons successively broke single C-I bonds; the first C-I bond breaking yielded IPh that rotated directionally by three different angles, with the second C-I bond breaking giving chemisorbed I atoms (#2) at three preferred locations corresponding to the C-I bond alignments in the prior rotated IPh configurations. In the concerted mechanism a single electron broke two C-I bonds, giving two chemisorbed I atoms; significantly these were found at angles corresponding to the C-I bond direction for unrotated mDIB. Molecular dynamics accounted for the difference in reaction outcomes between the successive and the concerted mechanisms in terms of the time required for the IPh to rotate in-plane; in successive reaction the time delay between first and second C-I bond-breaking events allowed the IPh to rotate, whereas in concerted reaction the computed delay between excitation and reaction (∼1 ps) was too short for molecular rotation before the second C-I bond broke. The dependence of the extent of motion at a surface on the delay between first and second bond breaking suggested a novel means to "clock" sub-picosecond dynamics by imaging the products arising from varying time delays between impacting pairs of electrons.

Formation of hollow iron oxide tetrapods via a shape-preserving nanoscale Kirkendall effect.

Hollow iron oxide tetrapods are synthesized by exposing iron precursors to hollow ultrathin PtS tetrapods. Surprisingly, the heterogeneous nucleation and growth of iron takes place exclusively within the PtS interior. Oxidation of the resulting iron tetrapod produces a hollow iron oxide shell via a shape-preserving Kirkendall effect which preserves the morphology of the original tetrapod with remarkably high precision, offering a robust synthetic route to hollow iron oxide nanostructures of unprecedented geometry.

On the influence of water on the electronic structure of firefly oxyluciferin anions from absorption spectroscopy of bare and monohydrated ions in vacuo.

A complete understanding of the physics underlying the varied colors of firefly bioluminescence remains elusive because it is difficult to disentangle different enzyme-lumophore interactions. Experiments on isolated ions are useful to establish a proper reference when there are no microenvironmental perturbations. Here, we use action spectroscopy to compare the absorption by the firefly oxyluciferin lumophore isolated in vacuo and complexed with a single water molecule. While the process relevant to bioluminescence within the luciferase cavity is light emission, the absorption data presented here provide a unique insight into how the electronic states of oxyluciferin are altered by microenvironmental perturbations. For the bare ion we observe broad absorption with a maximum at 548 ± 10 nm, and addition of a water molecule is found to blue-shift the absorption by approximately 50 nm (0.23 eV). Test calculations at various levels of theory uniformly predict a blue-shift in absorption caused by a single water molecule, but are only qualitatively in agreement with experiment highlighting limitations in what can be expected from methods commonly used in studies on oxyluciferin. Combined molecular dynamics simulations and time-dependent density functional theory calculations closely reproduce the broad experimental peaks and also indicate that the preferred binding site for the water molecule is the phenolate oxygen of the anion. Predicting the effects of microenvironmental interactions on the electronic structure of the oxyluciferin anion with high accuracy is a nontrivial task for theory, and our experimental results therefore serve as important benchmarks for future calculations.