Search

The Diels–Alder reaction is one of the most popular reactions in organic chemistry. However, its use in the field of on-surface synthesis is hampered by the spatial restrictions of this cycloaddition reaction. Herein we selected a cyclic strained triyne to demonstrate an on-surface hexadehydro-Diels–Alder reaction in a single molecule. The reaction was studied in detail by means of atomic force microscopy (AFM) with CO-functionalized tips. Our results pave the way to use this iconic pericyclic reaction for on-surface synthesis, introducing the concept of atom economy in the field We thank Rolf Allenspach and Enrique Guitián for discussions. We thank the European Union (Project SPRING, contract no. 863098), the ERC grant AMSEL (682144), the Spanish Agencia Estatal de Investigación (PID2019-107338RB-C62, PID2019-110037GB-I00 and PCI2019-111933-2), Xunta de Galicia (Centro de Investigación de Galicia accreditation 2019–2022, ED431G 2019/03) and the European Regional Development Fund-ERDF for financial support SI

We report the on-surface synthesis of a non-benzenoid triradical through dehydrogenation of truxene (C27H18) on coinage metal and insulator surfaces. Voltage pulses applied via the tip of a combined scanning tunneling microscope/atomic force microscope were used to cleave individual C-H bonds in truxene. The resultant final product truxene-5,10,15-triyl (1) was characterized at the single-molecule scale using a combination of atomic force microscopy, scanning tunneling microscopy and scanning tunneling spectroscopy. Our analyses show that 1 retains its open-shell quartet ground state, predicted by density functional theory, on a two monolayer-thick NaCl layer on a Cu(111) surface. We image the frontier orbital densities of 1 and confirm that they correspond to spin-split singly occupied molecular orbitals. Through our synthetic strategy, we also isolate two reactive intermediates toward the synthesis of 1 - derivatives of fluorenyl radical and indeno[1,2-a]fluorene, with predicted spin-doublet and spin-triplet ground states, respectively. Our results should have bearings on the synthesis of non-benzenoid high-spin polycyclic frameworks with magnetism beyond Lieb's theorem., 8 pages, 5 figures and supporting information containing additional data

Glaser‐like coupling of terminal alkynes by thermal activation is extensively used in on‐surface chemistry. Here we demonstrate an intramolecular version of this reaction performed by atom manipulation. We used voltage pulses from the tip to trigger a Glaser‐like coupling between terminal alkyne carbons within a custom‐synthesized precursor molecule adsorbed on bilayer NaCl on Cu(111). Different conformations of the precursor molecule and the product were characterized by molecular structure elucidation with atomic force microscopy and orbital density mapping with scanning tunneling microscopy, accompanied by density functional theory calculations. We revealed partially dehydrogenated intermediates, providing insight into the reaction pathway., We demonstrated a Glaser‐like coupling reaction by atom manipulation. The intramolecular reaction was performed within a single molecule, facilitated by the design of the precursor molecule. By using high‐resolution atomic force microscopy, we revealed precursors, intermediates, and products. Resolving and manipulating the positions of individual hydrogen atoms in intermediates provided information about the reaction pathway.

By employing single charge injections with an atomic force microscope, we investigated redox reactions of a molecule on a multilayer insulating film. First, we charged the molecule positively by attaching a single hole. Then we neutralized it by attaching an electron and observed three channels for the neutralization. We rationalize that the three channels correspond to transitions to the neutral ground state, to the lowest energy triplet excited states and to the lowest energy singlet excited states. By single-electron tunneling spectroscopy we measured the energy differences between the transitions obtaining triplet and singlet excited state energies. The experimental values are compared with density functional theory calculations of the excited state energies. Our results show that molecules in excited states can be prepared and that energies of optical gaps can be quantified by controlled single-charge injections. Our work demonstrates the access to, and provides insight into, ubiquitous electron-attachment processes related to excited-state transitions important in electron transfer and molecular optoelectronics phenomena on surfaces.

The synthesis of a threefold symmetric nanographene with 19 cata-fused benzene rings distributed within six branches is reported. This flat dendritic starphene, which is the largest unsubstituted cata-condensed PAH that has been obtained to date, was prepared in solution by means of a palladium-catalyzed aryne cyclotrimerization reaction and it was characterized on surface by scanning probe microscopy with atomic resolution.

This study addresses the effect of sample preparation conditions on the structural integrity and composition of heavy hydrocarbon mixtures imaged by non-contact atomic force microscopy (nc-AFM). We designed and prepared a set of organic molecules mimicking well-accepted key characteristics of heavy oil asphaltenes including molecular architecture, molecular weight, boiling point, atomic H/C ratio and bond strength. We deliberately focused on multi-core molecule structures with long aliphatic linkers as this architecture was largely absent in previous nc-AFM studies of petroleum samples. The results confirm that all these molecules can be successfully imaged and remain intact under the same preparation conditions. Moreover, comparison with ultra-high resolution FT ICR-MS of a steam-cracked tar asphaltene sample suggests that the single molecules identified by nc-AFM span the entire molecule spectrum of the bulk sample. Overall, these results suggest that petroleum molecules within the scope of chosen molecules studied herein can be prepared intact and without bias and the imaged data can be representative.

Quantum devices depend on addressable elements, which can be modified separately and in their mutual interaction. Self-assembly at surfaces, for example, formation of a porous (metal-) organic network, provides an ideal way to manufacture arrays of identical quantum boxes, arising in this case from the confinement of the electronic (Shockley) surface state within the pores. We show that the electronic quantum box state as well as the interbox coupling can be modified locally to a varying extent by a selective choice of adsorbates, here C60, interacting with the barrier. In view of the wealth of differently acting adsorbates, this approach allows for engineering quantum states in on-surface network architectures.

The charge state of a molecule governs its physicochemical properties, such as conformation, reactivity, and aromaticity, with implications for on-surface synthesis, catalysis, photoconversion, and applications in molecular electronics. On insulating, multilayer sodium chloride (NaCl) films, we controlled the charge state of organic molecules and resolved their structures in neutral, cationic, anionic, and dianionic states by atomic force microscopy, obtaining atomic resolution and bond-order discrimination using carbon monoxide (CO)-functionalized tips. We detected changes in conformation, adsorption geometry, and bond-order relations for azobenzene, tetracyanoquinodimethane, and pentacene in multiple charge states. Moreover, for porphine, we investigate the charge state-dependent change of aromaticity and conjugation pathway in the macrocycle. This work opens the way to studying chemical-structural changes of individual molecules for a wide range of charge states.

By atom manipulation we performed on-surface chemical reactions of a single molecule on a multilayer insulating film using noncontact atomic force microscopy. The single-electron sensitivity of atomic force microscopy allows us to follow the addition of single electrons to the molecule and the investigation of the reaction products. By performing a novel strategy based on long-lived doubly charged states a single molecule is fragmented. The fragmentation can be reverted by again changing the charge state of the system, characterizing a reversible reaction. The experimental results in addition to density-functional theory provide insight into the charge states of the different products and reaction pathways. Similar molecular systems could be used as charge-transfer units and to induce reversible chemical reactions.

Dissolved organic carbon (DOC) is the largest pool of exchangeable organic carbon in the ocean. However, less than 10% of DOC has been molecularly characterized in the deep ocean to understand DOC's recalcitrance. Here we analyze the radiocarbon (14C) depleted, and presumably refractory, low molecular weight (LMW) DOC from the North Central Pacific using atomic force microscopy to produce the first atomic-resolution images of individual LMW DOC molecules. We evaluate surface and deep LMW DOC chemical structures in the context of their relative persistence and recalcitrance. Atomic force microscopy resolved planar structures with features similar to polycyclic aromatic compounds and carboxylic-rich alicyclic structures with less than five aromatic carbon rings. These compounds comprise 8% and 20% of the measurable molecules investigated in the surface and deep, respectively. Resolving the structures of individual DOC molecules represents a step forward in molecular characterization of DOC and in understanding its long-term stability.

The growth and self-assembling properties of nickel-tetraphenyl porphyrins (NiTPP) on the Cu(111) surface are analysed via scanning tunnelling microscopy (STM), X-ray photoelectron spectroscopy (XPS) and density functional theory (DFT). For low coverage, STM results show that NiTPP molecules diffuse on the terrace until they reach the step edge of the copper surface forming a 1D system with disordered orientation along the step edges. The nucleation process into a 2D superstructure was observed to occur via the interaction of molecules attached to the already nucleated 1D structure, reorienting molecules. For monolayer range coverage a 2D nearly squared self-assembled array with the emergence of chiral domains was observed. The XPS results of the Ni 2p(3/2) core levels exhibit a 2.6 eV chemical shift between the mono- and multilayer configuration of NiTPP. DFT calculations show that the observed chemical shifts of Ni 2p(3/2) occur due to the interaction of 3d orbitals of Ni with the Cu(111) substrate.

Using scanning probe microscopy techniques, at low temperatures and in ultrahigh vacuum, individual molecules adsorbed on surfaces can be probed with ultrahigh resolution to determine their structure and details of their conformation, configuration, charge states, aromaticity, and the contributions of resonance structures. Functionalizing the tip of an atomic force microscope with a CO molecule enabled atomic-resolution imaging of single molecules, and measurement of their adsorption geometry and bond-order relations. In addition, by using scanning tunneling microscopy and Kelvin probe force microscopy, the density of the molecular frontier orbitals and the electric charge distribution within molecules can be mapped. Combining these techniques yields a high-resolution tool for the identification and characterization of individual molecules. The single-molecule sensitivity and the possibility of atom manipulation to induce chemical reactions with the tip of the microscope open up unique applications in chemistry, and differentiate scanning probe microscopy from conventional methods for molecular structure elucidation. Besides being an aid for challenging cases in natural product identification, atomic force microscopy has been shown to be a powerful tool for the investigation of on-surface reactions and the characterization of radicals and molecular mixtures. Herein we review the progress that high-resolution scanning probe microscopy with functionalized tips has made for molecular structure identification and characterization, and discuss the challenges it will face in the years to come.

Two single crystalline surfaces of Au vicinal to the (111) plane were modified with Pt and studied using scanning tunneling microscopy (STM) and X-ray photoemission spectroscopy (XPS) in ultra-high vacuum environment. The vicinal surfaces studied are Au(332) and Au(887) and different Pt coverage (θPt) were deposited on each surface. From STM images we determine that Pt deposits on both surfaces as nanoislands with heights ranging from 1 ML to 3 ML depending on θPt. On both surfaces the early growth of Pt ad-islands occurs at the lower part of the step edge, with Pt ad-atoms being incorporated into the steps in some cases. XPS results indicate that partial alloying of Pt occurs at the interface at room temperature and at all coverage, as suggested by the negative chemical shift of Pt 4f core line, indicating an upward shift of the d-band center of the alloyed Pt. Also, the existence of a segregated Pt phase especially at higher coverage is detected by XPS. Sample annealing indicates that the temperature rise promotes a further incorporation of Pt atoms into the Au substrate as supported by STM and XPS results. Additionally, the catalytic activity of different PtAu systems reported in the literature for some electrochemical reactions is discussed considering our findings.

Communication.-- et al., A 2D array of electronically coupled quantum boxes is fabricated by means of on-surface self-assembly assuring ultimate precision of each box. The quantum states embedded in the boxes are configured by adsorbates, whose occupancy is controlled with atomic precision. The electronic interbox coupling can be maintained or significantly reduced by proper arrangement of empty and filled boxes., The authors would like to acknowledge financial support from the Swiss Nanoscience Institute (SNI), Swiss National Science Foundation (Grants Nos. 200020-149713 and 206021-121461), the Spanish Ministry of Economy (Grant No. MAT2013-46593-C6-4-P), the Basque Government (Grant No. IT621-13), the São Paulo Research Foundation (Grant No. 2013/04855-0), Swiss Government Excellence Scholarship Program, Netherlands Organization for Scientific Research NWO (Chemical Sciences, VIDI-Grant No. 700.10.424), the European Research Council (ERC-2012-StG 307760-SURFPRO), University of Basel, University of Heidelberg, Linköping University, University of Groningen, Paul Scherrer Institute, and the Japan Science and Technology Agency (JST) “Precursory Research for Embryonic Science and Technology (PRESTO)” for a project of “Molecular technology and creation of new function.”

The field of molecular electronics aims at using single molecules as functional building blocks for electronics components, such as switches, rectifiers or transistors. A key challenge is to perform measurements with atomistic control over the alignment of the molecule and its contacting electrodes. Here we use atomic force microscopy to examine charge transfer between weakly coupled pentacene molecules on insulating films with single-electron sensitivity and control over the atomistic details. We show that, in addition to the imaging capability, the probe tip can be used to control the charge state of individual molecules and to detect charge transfers to/from the tip, as well as between individual molecules. Our approach represents a novel route for molecular charge transfer studies with a host of opportunities, especially in combination with single atom/molecule manipulation and nanopatterning techniques., Detection and manipulation of single charges in molecules are fundamental cornerstones in molecular electronics. Here, Steurer et al. demonstrate a technique with the use of an atomic force microscope that is able to resolve charge states and single electron charge transfer between molecules.

The Bergman cyclization is one of the most fascinating rearrangements in chemistry, with important implications in organic synthesis and pharmacology. Here we demonstrate a reversible Bergman cyclization for the first time. We induced the on-surface transformation of an individual aromatic diradical into a highly strained ten-membered diyne using atomic manipulation and verified the products by non-contact atomic force microscopy with atomic resolution. The diyne and diradical were stabilized by using an ultrathin NaCl film as the substrate, and the diyne could be transformed back into the diradical. Importantly, the diradical and the diyne exhibit different reactivity, electronic, magnetic and optical properties associated with the changes in the bond topology, and spin multiplicity. With this reversible, triggered Bergman cyclization we demonstrated switching on demand between the two reactive intermediates by means of selective C-C bond formation or cleavage, which opens up the field of radical chemistry for on-surface reactions by atomic manipulation.

The use of divergent, V-shaped, 4,2':6',4''-terpyridine building blocks that self-assemble into hydrogen-bonded domains and upon addition of copper atoms undergo metallation with concomitant transformation into a coordination network is described; multiple energetically similar structural motifs are observed in both hydrogen-bonded and adatom-coordinated networks.

Condensation processes are of key importance in nature and play a fundamental role in chemistry and physics. Owing to size effects at the nanoscale, it is conceptually desired to experimentally probe the dependence of condensate structure on the number of constituents one by one. Here we present an approach to study a condensation process atom-by-atom with the scanning tunnelling microscope, which provides a direct real-space access with atomic precision to the aggregates formed in atomically defined ‘quantum boxes’. Our analysis reveals the subtle interplay of competing directional and nondirectional interactions in the emergence of structure and provides unprecedented input for the structural comparison with quantum mechanical models. This approach focuses on—but is not limited to—the model case of xenon condensation and goes significantly beyond the well-established statistical size analysis of clusters in atomic or molecular beams by mass spectrometry., Condensation in the regime of weakly interactions is of fundamental importance. Here, the authors study the condensation process one atom at a time, showing the forces driving the behaviour of xenon atoms as they condense into aggregate structures in nanoscale pores.

Intermolecular single-electron transfer on electrically insulating films is a key process in molecular electronics1–4 and an important example of a redox reaction5,6. Electron-transfer rates in molecular systems depend on a few fundamental parameters, such as interadsorbate distance, temperature and, in particular, the Marcus reorganization energy 7 . This crucial parameter is the energy gain that results from the distortion of the equilibrium nuclear geometry in the molecule and its environment on charging8,9. The substrate, especially ionic films 10 , can have an important influence on the reorganization energy11,12. Reorganization energies are measured in electrochemistry 13 as well as with optical14,15 and photoemission spectroscopies16,17, but not at the single-molecule limit and nor on insulating surfaces. Atomic force microscopy (AFM), with single-charge sensitivity18–22, atomic-scale spatial resolution 20 and operable on insulating films, overcomes these challenges. Here, we investigate redox reactions of single naphthalocyanine (NPc) molecules on multilayered NaCl films. Employing the atomic force microscope as an ultralow current meter allows us to measure the differential conductance related to transitions between two charge states in both directions. Thereby, the reorganization energy of NPc on NaCl is determined as (0.8 ± 0.2) eV, and density functional theory (DFT) calculations provide the atomistic picture of the nuclear relaxations on charging. Our approach presents a route to perform tunnelling spectroscopy of single adsorbates on insulating substrates and provides insight into single-electron intermolecular transport. An atomic force microscope is used as an ultralow current sensor to measure the reorganization energy of a single naphthalocyanine molecule during a redox reaction on a NaCl film.

Heavy oil molecular mixtures were investigated on the basis of single molecules resolved by atomic force microscopy. The eight different samples analyzed include asphaltenes and other heavy oil fractions of different geographic/geologic origin and processing steps applied. The collected AFM data of individual molecules provide information about the molecular geometry, aromaticity, the content of nonhexagonal rings, typical types and locations of heterocycles, occurrence, length and connectivity of alkyl side chains, and ratio of archipelago- vs island-type architectures. Common and distinguishing structural motifs for the different samples could be identified. The measured size distributions and the degree of unsaturation by scanning probe microscopy is consistent with mass spectrometry data presented herein. The results obtained reveal the complexity, properties and specifics of heavy oil fractions with implications for upstream oil production and downstream oil processing. Moreover, the identified molec...

Here we present a new method that integrates atomic force microscopy (AFM) with analytical tools such as high-performance liquid chromatography (HPLC) with diode-array ultraviolet-visible (UV) absorbance, and mass spectrometry (MS) along with synthetic chemistry. This allows the detection, identification, and quantification of novel polycyclic aromatic hydrocarbons (PAH) in complex molecular mixtures. This multidisciplinary methodology is employed to characterize the supercritical pyrolysis products of n-decane, a model fuel. The pyrolysis experiments result in a complex mixture of both unsubstituted as well as highly methylated PAH. We demonstrate the AFM-driven discovery of a novel compound, benz[ l]indeno[1,2,3- cd]pyrene, with the chemical structure assignment serving as input for the chemical synthesis of such molecule. The synthesis is verified by AFM, and the synthesized compound is used as a reference standard in analytical measurements, establishing the first-ever unequivocal identification and quantification of this PAH as a fuel product. Moreover, the high-resolution AFM analysis detected several five- to eight-ring PAH, which represents novel fuel pyrolysis and/or combustion products. This work provides a route to develop new analytical standards by symbiotically using AFM, chemical synthesis, and modern analytical tools.

Controlling selectivity of reactions is an ongoing quest in chemistry. In this work, we demonstrate reversible and selective bond formation and dissociation promoted by tip-induced reduction-oxidation reactions on a surface. Molecular rearrangements leading to different constitutional isomers are selected by the polarity and magnitude of applied voltage pulses from the tip of a combined scanning tunneling and atomic force microscope. Characterization of voltage dependence of the reactions and determination of reaction rates demonstrate selectivity in constitutional isomerization reactions and provide insight into the underlying mechanisms. With support of density functional theory calculations, we find that the energy landscape of the isomers in different charge states is important to rationalize the selectivity. Tip-induced selective single-molecule reactions increase our understanding of redox chemistry and could lead to novel molecular machines.

We present the design of a variable temperature setup that uses a pulse tube cryocooler to perform break-junction experiments at variable temperatures ranging from 12 K to room temperature. The use of pulse tube coolers is advantageous because they are easy to use, can be highly automatized, and used to avoid wastage of cryogenic fluids. This is the reason why dry cryostats are conquering more and more fields in cryogenic physics. However, the main drawback is the level of vibration that can be up to several micrometers at the cold-head. The vibrations make the operation of scanning probe-based microscopes challenging. We implemented vibration-damping techniques that allow obtaining a vibration level of 12 pm between the tip and sample. With these adaptations, we show the possibility to perform break junction measurements in a cryogenic environment and keep in place atomic chains of a few nanometers between the two electrodes.