Project DRIVE: A Compendium of Cancer Dependencies and Synthetic Lethal Relationships Uncovered by Large-Scale, Deep RNAi Screening.

Elucidation of the mutational landscape of human cancer has progressed rapidly and been accompanied by the development of therapeutics targeting mutant oncogenes. However, a comprehensive mapping of cancer dependencies has lagged behind and the discovery of therapeutic targets for counteracting tumor suppressor gene loss is needed. To identify vulnerabilities relevant to specific cancer subtypes, we conducted a large-scale RNAi screen in which viability effects of mRNA knockdown were assessed for 7,837 genes using an average of 20 shRNAs per gene in 398 cancer cell lines. We describe findings of this screen, outlining the classes of cancer dependency genes and their relationships to genetic, expression, and lineage features. In addition, we describe robust gene-interaction networks recapitulating both protein complexes and functional cooperation among complexes and pathways. This dataset along with a web portal is provided to the community to assist in the discovery and translation of new therapeutic approaches for cancer.

Molecular motor crossing the frontier of classical to quantum tunneling motion.

The reliability by which molecular motor proteins convert undirected energy input into directed motion or transport has inspired the design of innumerable artificial molecular motors. We have realized and investigated an artificial molecular motor applying scanning tunneling microscopy (STM), which consists of a single acetylene (C2H2) rotor anchored to a chiral atomic cluster provided by a PdGa(111) surface that acts as a stator. By breaking spatial inversion symmetry, the stator defines the unique sense of rotation. While thermally activated motion is nondirected, inelastic electron tunneling triggers rotations, where the degree of directionality depends on the magnitude of the STM bias voltage. Below 17 K and 30-mV bias voltage, a constant rotation frequency is observed which bears the fundamental characteristics of quantum tunneling. The concomitantly high directionality, exceeding 97%, implicates the combination of quantum and nonequilibrium processes in this regime, being the hallmark of macroscopic quantum tunneling. The acetylene on PdGa(111) motor therefore pushes molecular machines to their extreme limits, not just in terms of size, but also regarding structural precision, degree of directionality, and cross-over from classical motion to quantum tunneling. This ultrasmall motor thus opens the possibility to investigate in operando effects and origins of energy dissipation during tunneling events, and, ultimately, energy harvesting at the atomic scales.

Growth Optimization and Device Integration of Narrow-Bandgap Graphene Nanoribbons.

The electronic, optical, and magnetic properties of graphene nanoribbons (GNRs) can be engineered by controlling their edge structure and width with atomic precision through bottom-up fabrication based on molecular precursors. This approach offers a unique platform for all-carbon electronic devices but requires careful optimization of the growth conditions to match structural requirements for successful device integration, with GNR length being the most critical parameter. In this work, the growth, characterization, and device integration of 5-atom wide armchair GNRs (5-AGNRs) are studied, which are expected to have an optimal bandgap as active material in switching devices. 5-AGNRs are obtained via on-surface synthesis under ultrahigh vacuum conditions from Br- and I-substituted precursors. It is shown that the use of I-substituted precursors and the optimization of the initial precursor coverage quintupled the average 5-AGNR length. This significant length increase allowed the integration of 5-AGNRs into devices and the realization of the first field-effect transistor based on narrow bandgap AGNRs that shows switching behavior at room temperature. The study highlights that the optimized growth protocols can successfully bridge between the sub-nanometer scale, where atomic precision is needed to control the electronic properties, and the scale of tens of nanometers relevant for successful device integration of GNRs.

On-surface Synthesis: What Happens Behind the Scenes?

On-surface synthesis has become a powerful approach to produce low-dimensional carbon-based nanostructures with atomistic precision. A large variety of analytical tools and methods are available to provide efficient monitoring of on-surface reactions, among which, scanning probe microscopy (SPM) has proven to be particularly efficient to characterize reaction intermediates and products down to the atomic scale. Nevertheless, due to limited temporal resolution, difficulties to explore the full temperature range, and lack of identifying the chemical environment of all elements involved in on-surface processes, SPM is ideally complemented with temperature programmed X-ray photoelectron spectroscopy (TP-XPS). In this short review, we aim to unveil some of the capabilities of synchrotron based TP-XPS reporting on our own research on Ullmann-type on-surface coupling reactions.

Reversible Dehalogenation in On-Surface Aryl-Aryl Coupling.

In the emerging field of on-surface synthesis, dehalogenative aryl-aryl coupling is unarguably the most prominent tool for the fabrication of covalently bonded carbon-based nanomaterials. Despite its importance, the reaction kinetics are still poorly understood. Here we present a comprehensive temperature-programmed x-ray photoelectron spectroscopy investigation of reaction kinetics and energetics in the prototypical on-surface dehalogenative polymerization of 4,4''-dibromo-p-terphenyl into poly(para-phenylene) on two coinage metal surfaces, Cu(111) and Au(111). We find clear evidence for reversible dehalogenation on Au(111), which is inhibited on Cu(111) owing to the formation of organometallic intermediates. The incorporation of reversible dehalogenation in the reaction rate equations leads to excellent agreement with experimental data and allows extracting the relevant energy barriers. Our findings deepen the mechanistic understanding and call for its reassessment for surface-confined aryl-aryl coupling on the most frequently used metal substrates.

Near-Enantiopure Trimerization of 9-Ethynylphenanthrene on a Chiral Metal Surface.

Enantioselectivity in heterogeneous catalysis strongly depends on the chirality transfer between catalyst surface and all reactants, intermediates, and the product along the reaction pathway. Herein we report the first enantioselective on-surface synthesis of molecular structures from an initial racemic mixture and without the need of enantiopure modifier molecules. The reaction consists of a trimerization via an unidentified bonding motif of prochiral 9-ethynylphenanthrene (9-EP) upon annealing to 500 K on the chiral Pd3 -terminated PdGa{111} surfaces into essentially enantiopure, homochiral 9-EP propellers. The observed behavior strongly contrasts the reaction of 9-EP on the chiral Pd1 -terminated PdGa{111} surfaces, where 9-EP monomers that are in nearly enantiopure configuration, dimerize without enantiomeric excess. Our findings demonstrate strong chiral recognition and a significant ensemble effect in the PdGa system, hence highlighting the huge potential of chiral intermetallic compounds for enantioselective synthesis and underlining the importance to control the catalytically active sites at the atomic level.

On-Surface Synthesis of Cumulene-Containing Polymers via Two-Step Dehalogenative Homocoupling of Dibromomethylene-Functionalized Tribenzoazulene.

Cumulene compounds are notoriously difficult to prepare and study because their reactivity increases dramatically with the increasing number of consecutive double bonds. In this respect, the emerging field of on-surface synthesis provides exceptional opportunities because it relies on reactions on clean metal substrates under well-controlled ultrahigh-vacuum conditions. Here we report the on-surface synthesis of a polymer linked by cumulene-like bonds on a Au(111) surface via sequential thermally activated dehalogenative C-C coupling of a tribenzoazulene precursor equipped with two dibromomethylene groups. The structure and electronic properties of the resulting polymer with cumulene-like pentagon-pentagon and heptagon-heptagon connections have been investigated by means of scanning probe microscopy and spectroscopy methods and X-ray photoelectron spectroscopy, complemented by density functional theory calculations. Our results provide perspectives for the on-surface synthesis of cumulene-containing compounds, as well as protocols relevant to the stepwise fabrication of carbon-carbon bonds on surfaces.

Heteroatom-Doped Perihexacene from a Double Helicene Precursor: On-Surface Synthesis and Properties.

We report on the surface-assisted synthesis and spectroscopic characterization of the hitherto longest periacene analogue with oxygen-boron-oxygen (OBO) segments along the zigzag edges, that is, a heteroatom-doped perihexacene 1. Surface-catalyzed cyclodehydrogenation successfully transformed the double helicene precursor 2, i.e., 12a,26a-dibora-12,13,26,27-tetraoxa-benzo[1,2,3-hi:4,5,6-h'i']dihexacene, into the planar perihexacene analogue 1, which was visualized by scanning tunneling microscopy and noncontact atomic force microscopy. X-ray photoelectron spectroscopy, Raman spectroscopy, together with theoretical modeling, on both precursor 2 and product 1, provided further insights into the cyclodehydrogenation process. Moreover, the nonplanar precursor 2 underwent a conformational change upon adsorption on surfaces, and one-dimensional self-assembled superstructures were observed for both 2 and 1 due to the presence of OBO units along the zigzag edges.

Surface science at the PEARL beamline of the Swiss Light Source.

The Photo-Emission and Atomic Resolution Laboratory (PEARL) is a new soft X-ray beamline and surface science laboratory at the Swiss Light Source. PEARL is dedicated to the structural characterization of local bonding geometry at surfaces and interfaces of novel materials, in particular of molecular adsorbates, nanostructured surfaces, and surfaces of complex materials. The main experimental techniques are soft X-ray photoelectron spectroscopy, photoelectron diffraction, and scanning tunneling microscopy (STM). Photoelectron diffraction in angle-scanned mode measures bonding angles of atoms near the emitter atom, and thus allows the orientation of small molecules on a substrate to be determined. In energy scanned mode it measures the distance between the emitter and neighboring atoms; for example, between adsorbate and substrate. STM provides complementary, real-space information, and is particularly useful for comparing the sample quality with reference measurements. In this article, the key features and measured performance data of the beamline and the experimental station are presented. As scientific examples, the adsorbate-substrate distance in hexagonal boron nitride on Ni(111), surface quantum well states in a metal-organic network of dicyano-anthracene on Cu(111), and circular dichroism in the photoelectron diffraction of Cu(111) are discussed.

Bottom-Up Synthesis of Metalated Carbyne.

Because of stability issues, carbyne, a one-dimensional chain of carbon atoms, has been much less investigated than other recent carbon allotropes such as graphene. Beyond that, metalation of such a linear carbon nanostructure with regularly distributed metal atoms is even more challenging. Here we report a successful on-surface synthesis of metalated carbyne chains by dehydrogenative coupling of ethyne molecules and copper atoms on a Cu(110) surface under ultrahigh-vacuum conditions. The length of the fabricated metalated carbyne chains was found to extend to the submicron scale (with the longest ones up to ∼120 nm). We expect that the herein-developed on-surface synthesis strategy for the efficient synthesis of organometallic carbon-based nanostructures will inspire more extensive experimental investigations of their physicochemical properties and explorations of their potential with respect to technological applications.

The (111) surface of NaAu2: structure, composition, and stability.

The (111) surface of single-crystal NaAu(2) is a model for catalytically active, powdered NaAu(2). We prepare and characterize this surface with a broad suite of techniques. Preparation in ultrahigh vacuum consists of the traditional approach of ion bombardment (to remove impurities) and thermal annealing (to restore surface order). Both of these steps, however, cause loss of sodium (Na), and repeated treatments eventually trigger conversion of the surface and near-surface regions to crystalline gold. The bulk has a limited ability to repopulate the surface Na. Under conditions where Na depletion is minimized, electron diffraction patterns are consistent with the bulk-terminated structure, and scanning tunneling microscopy reveals mesa-like features with lateral dimensions of a few tens of nanometers. The tops of the mesas do not possess fine structure characteristic of a periodic lattice, suggesting that the surface layer is disordered under the conditions of these experiments.

Highly enantioselective adsorption of small prochiral molecules on a chiral intermetallic compound.

Intrinsically chiral surfaces of intermetallic compounds are shown to be novel materials for enantioselective processes. Their advantage is the significantly higher thermal and chemical stability, and therefore their extended application range for catalyzed chiral reactions compared to surfaces templated with chiral molecular modifiers or auxiliaries. On the Pd1 -terminated PdGa(111) surface, room-temperature adsorption of a small prochiral molecule (9-ethynylphenanthrene) leads to exceptionally high enantiomeric excess ratios of up to 98 %. Our findings highlight the great potential of intrinsically chiral intermetallic compounds for the development of novel, enantioselective catalysts that can be operated at high temperatures and potentially also in harsh chemical environments.

Adsorption of small hydrocarbons on the three-fold PdGa surfaces: the road to selective hydrogenation.

Intermetallic compounds are a promising class of materials as stable and selective heterogeneous catalysts. Here, the (111) and (-1-1-1) single crystal surfaces of the PdGa intermetallic compound were studied as model catalysts with regard to the selective hydrogenation of acetylene (C2H2) to ethylene (C2H4). The distinct atomic surface structures exhibit isolated active centers of single atomic and three atomic Pd ensembles, respectively. For the two prototypal model catalyst surfaces, the adsorption sites and configurations for hydrogen (H2), acetylene, and ethylene were investigated by combining scanning tunneling microscopy, temperature-programmed desorption, and ab initio modeling. The topmost Pd surface atoms provide the preferred adsorption sites for all studied molecules. The structural difference of the Pd ensembles has a significant influence on the adsorption energy and configuration of C2H2, while the influence of the ensemble structure is weak for C2H4 and H2 adsorption. To approach the question of catalytic performance, we simulated the reaction pathways for the heterogeneous catalytic hydrogenation of acetylene on the two surfaces by means of density functional theory. Due to the geometrical separation of the Pd sites on the surfaces, the steric approach of the reactants (H and C2Hx) was found to be of importance to the energetics of the reaction. The presented study gives a direct comparison of binding properties of catalytic Pd on-top sites vs three-fold Pd hollow sites and is therefore of major relevance to the knowledge-based design of highly selective hydrogenation catalysts.

Site-selective adsorption of phthalocyanine on h-BN/Rh(111) nanomesh.

Experiment and computer simulations were conducted in order to study the adsorption of the phthalocyanine molecules H2Pc and CuPc on the h-BN/Rh(111) nanomesh. We combine STM investigations with the exploration of the potential energy surface as resulting from density functional theory calculations. Both approaches indicate a pronounced adsorption selectivity in the so called pore regions of the h-BN nanomesh, whereas the adsorption energy landscape in the pore turns out to be very shallow. This is seen by the inability to image the molecule stably at 77 K by scanning tunneling microscopy. Understanding the nature of the binding by rationalizing the site-selectivity and the mobility of the molecules is quite a challenge for both experiment and theory. In particular, we observe that the choice of the functional in the DFT description is crucial to be able to discriminate among adsorption sites that are very close in energy and to resolve low energy barriers. Our study reveals how the shape of the corrugated h-BN layer is the dominant factor that determines the subtle features of the potential energy surface for the adsorption of phthalocyanine.

Asymmetric Molecular Adsorption and Regioselective Bond Cleavage on Chiral PdGa Crystals.

Homogenous enantioselective catalysis is nowadays the cornerstone in the manufacturing of enantiopure substances, but its technological implementation suffers from well-known impediments like the lack of endurable catalysts exhibiting long-term stability. The catalytically active intermetallic compound Palladium-Gallium (PdGa), conserving innate bulk chirality on its surfaces, represent a promising system to study asymmetric chemical reactions by heterogeneous catalysis, with prospective relevance for industrial processes. Here, this work investigates the adsorption of 10,10'-dibromo-9,9'-bianthracene (DBBA) on the PdGa:A( 1 ¯ 1 ¯ 1 ¯ $\bar{1}\bar{1}\bar{1}$ ) Pd3-terminated surface by means of scanning tunneling microscopy (STM) and spectroscopy (STS). A highly enantioselective adsorption of the molecule evolving into a near 100% enantiomeric excess below room temperature is observed. This exceptionally high enantiomeric excess is attributed to temperature activated conversion of the S to the R chiral conformer. Tip-induced bond cleavage of the R conformer shows a very high regioselectivity of the DBBA debromination. The experimental results are interpreted by density functional theory atomistic simulations. This work extends the knowledge of chirality transfer onto the enantioselective adsorption of non-planar molecules and manifests the ensemble effect of PdGa surfaces resulting in robust regioselective debromination.

Sterically Selective [3 + 3] Cycloaromatization in the On-Surface Synthesis of Nanographenes.

Surface-catalyzed reactions have been used to synthesize carbon nanomaterials with atomically predefined structures. The recent discovery of a gold surface-catalyzed [3 + 3] cycloaromatization of isopropyl substituted arenes has enabled the on-surface synthesis of arylene-phenylene copolymers, where the surface activates the isopropyl substituents to form phenylene rings by intermolecular coupling. However, the resulting polymers suffered from undesired cross-linking when more than two molecules reacted at a single site. Here we show that such cross-links can be prevented through steric protection by attaching the isopropyl groups to larger arene cores. Upon thermal activation of isopropyl-substituted 8,9-dioxa-8a-borabenzo[fg]tetracene on Au(111), cycloaromatization is observed to occur exclusively between the two molecules. The cycloaromatization intermediate formed by the covalent linking of two molecules is prevented from reacting with further molecules by the wide benzotetracene core, resulting in highly selective one-to-one coupling. Our findings extend the versatility of the [3 + 3] cycloaromatization of isopropyl substituents and point toward steric protection as a powerful concept for suppressing competing reaction pathways in on-surface synthesis.

Electronic Decoupling and Hole-Doping of Graphene Nanoribbons on Metal Substrates by Chloride Intercalation.

Atomically precise graphene nanoribbons (GNRs) have a wide range of electronic properties that depend sensitively on their chemical structure. Several types of GNRs have been synthesized on metal surfaces through selective surface-catalyzed reactions. The resulting GNRs are adsorbed on the metal surface, which may lead to hybridization between the GNR orbitals and those of the substrate. This makes investigation of the intrinsic electronic properties of GNRs more difficult and also rules out capacitive gating. Here, we demonstrate the formation of a dielectric gold chloride adlayer that can intercalate underneath GNRs on the Au(111) surface. The intercalated gold chloride adlayer electronically decouples the GNRs from the metal and leads to a substantial hole-doping of the GNRs. Our results introduce an easily accessible tool in the in situ characterization of GNRs grown on Au(111) that allows for exploration of their electronic properties in a heavily hole-doped regime.

Surface investigation of intermetallic PdGa(111).

The intermetallic PdGa is a highly selective and potent catalyst in the semihydrogenation of acetylene, which is attributed to the surface stability and isolated Pd atom ensembles. In this context PdGa single crystals of form B with (111) orientation were investigated by means of X-ray photoelectron spectroscopy (XPS), ultraviolet photoelectron spectroscopy (UPS), scanning tunneling microscopy (STM), X-ray photoelectron diffraction (XPD), and low-energy electron diffraction (LEED) to study the electronic and geometric properties of this surface. UPS and thermal desorption spectroscopy (TDS) were used to probe the chemisorption behavior of CO. The PdGa(111) surface exhibits a (1 × 1) LEED and a pronounced XPD pattern indicating an unreconstructed bulk-truncated surface. Low-temperature STM reveals a smooth surface with a (1 × 1) unit cell. No segregation occurs, and no impurities are detected by XPS. The electronic structure and the CO adsorption properties reveal PdGa(111) to be a bulk-truncated intermetallic compound with Pd-Ga partial covalent bonding.

Electrodeposition of gold thin films with controlled morphologies and their applications in electrocatalysis and SERS.

Here, an easy and effective electrochemical route towards the synthesis of gold thin films with well-controlled roughness, morphology and crystallographic orientation is reported. To control these different factors, the applied potential during deposition played a major role. A tentative nucleation and growth mechanism is demonstrated by means of electrochemical characterizations and a formation mechanism is proposed. Interestingly, the differences in geometry and orientation of the different gold deposits have shown a clear correlation with the electrocatalytical activity in the case of oxygen sensing. In addition, not only the electrocatalytical activity but also the surface-enhanced Raman scattering of the gold deposits have been found to depend both on the roughness and on the size of the surface nanostructures, allowing a fine tuning by controlling these two parameters during deposition.

Asymmetric Elimination Reaction on Chiral Metal Surfaces.

The production of enantiopure materials and molecules is of uttermost relevance in research and industry in numerous contexts, ranging from nonlinear optics to asymmetric synthesis. In the context of the latter, dehalogenation, which is an essential reaction step for a broad class of chemical reactions, is investigated; specifically, dehalogenation of prochiral 5-bromo-7-methylbenz(a)anthracene (BMA) on prototypical, chiral, intermetallic PdGa{111} surfaces under ultrahigh vacuum conditions. Asymmetric halogen elimination is demonstrated by combining temperature-programmed X-ray photoelectron spectroscopy, scanning probe microscopy, and density functional theory. On the PdGa{111} surfaces, the difference in debromination temperatures for the two BMA surface enantiomers amounts up to an unprecedented 46 K. The significant dependence of the dehalogenation temperature of the BMA surface enantiomers on the atomic termination of the PdGa{111} surfaces implies that the ensemble effect is pronounced in this reaction step. These findings evidence enantiospecific control and hence promote intrinsically chiral crystals for asymmetric on-surface synthesis.