Synthesis of π-conjugated polycyclic compounds by late-stage extrusion of chalcogen fragments

• Aissam Okba,
• Pablo Simón Marqués,
• Kyohei Matsuo,
• Naoki Aratani,
• Hiroko Yamada,
• Gwénaël Rapenne and
• Claire Kammerer

Beilstein J. Org. Chem. 2024, 20, 287–305, doi:10.3762/bjoc.20.30

• tip of a scanning tunneling microscope (STM) [11][34][35][36]. Owing to the subatomic resolution now available with scanning probe microscopy techniques (STM and non-contact atomic force microscopy, nc-AFM), the “precursor approach” has opened the way for in-depth structural and electronic

• adsorbed on the metallic surface were characterized by combined STM and nc-AFM at low temperature (5 K), thus evidencing the presence of the two bridging oxygens. Next, the STM tip-induced extrusion of oxygen was investigated: application of a bias voltage of ≈2.2 V on top of one 1,4-epoxide bridge led to

• a planarization of the carbon-based scaffold along with the elimination of one oxygen atom to give a monoepoxide species. When the latter was submitted to a second voltage pulse, a fully planar and aromatic backbone made of four linearly-fused benzene rings was observed on STM and AFM images, thus

Biphenylene-containing polycyclic conjugated compounds

• Cagatay Dengiz

Beilstein J. Org. Chem. 2023, 19, 1895–1911, doi:10.3762/bjoc.19.141

• ]. In their study, they effectively synthesized POA 87 utilizing 2,3-dibromotetracene (85) as substrate at a temperature of 430 K, employing ultra high vacuum conditions on Ag(111). Subsequent scanning tunneling microscopy (STM) analyses unveiled not only the linear POA 87 resulting from surface

Synthesis of new asparagine-based glycopeptides for future scanning tunneling microscopy investigations

• Laura Sršan and
• Thomas Ziegler

Beilstein J. Org. Chem. 2020, 16, 888–894, doi:10.3762/bjoc.16.80

• cell surfaces for future investigations by combined preparative mass spectroscopy and scanning tunneling microscopy (STM) using soft-landing electrospray beam deposition (ES-IBD), on metal surfaces. Keywords: amino acids; asparagine; carbohydrates; glycopeptides; peptidomimetics; Introduction

• comparison with naturally occurring amino acids [14]. Thus, there is still a great effort in finding new potential drugs derived from glycopeptides [4][15]. By using preparative mass spectrometry (pMS) combined with STM on submolecular-resolution peptides and carbohydrates can be investigated regarding their

• the frequently used onium salts HBTU and HATU as coupling reagents [20]. The canonical amino acids ʟ-phenylalanine, ʟ-tryptophane, and ʟ-alanine were chosen in order to allow for different side chain motifs that, in turn, would increase the suitability for the following investigation via STM. Due to

Nanopatterns of arylene–alkynylene squares on graphite: self-sorting and intercalation

• Tristan J. Keller,
• Joshua Bahr,
• Kristin Gratzfeld,
• Nina Schönfelder,
• Marcin A. Majewski,
• Marcin Stępień,
• Sigurd Höger and
• Stefan-S. Jester

Beilstein J. Org. Chem. 2019, 15, 1848–1855, doi:10.3762/bjoc.15.180

• tunneling microscopy (STM). Throughout all STM images, surface regions covered by arylene–alkynylene backbones and (intermolecularly interdigitating) alkoxy side chains appear in bright and dark colors, which indicate high and low tunneling currents, respectively [31]. In most of our STM images, we achieve

• chains, that are attached to the corner building blocks to increase the compound’s solubility, do not contribute to the intermolecular packing and remain unresolved by STM. However, dark image regions are observed in the extraannular regions near the dithiophene corner units (e.g., arrow 2 in Figure 2a

• hexadecyloxy and decyloxy substituents of the quadrangle sides with γ(d1,d2) = 60° leads to a deviation of the (nominally) quadratic backbones towards rhombic-shaped objects with an interior angle of α◊= (80 ± 4)°. In addition, some of the high-resolution STM images of 1a on HOPG (e.g., Figure 2a) show a

Norbornadiene-functionalized triazatriangulenium and trioxatriangulenium platforms

• Roland Löw,
• Talina Rusch,
• Tobias Moje,
• Fynn Röhricht,
• Olaf M. Magnussen and
• Rainer Herges

Beilstein J. Org. Chem. 2019, 15, 1815–1821, doi:10.3762/bjoc.15.175

• decomposition, which is a necessary precondition for ultra-high vacuum STM investigations. The 3-bromo-2-cyano-substituted norbornadiene 4 was synthesized as described in the literature (Scheme 1) [10][11][12]. 4 was converted to 5 with trimethylsilylacetylene (72%) in a Sonogashira cross-coupling reaction. The

• as realized in compound 1. Consequently, future surface chemistry investigations will be performed with compound 1 including the TATA platform and an ethynyl spacer. STM Measurements The adsorption behaviour of the NBD 1a on Au(111) surfaces was studied by scanning tunnelling microscopy (STM) at room

• ][20][21]. Two types of molecules with a distinct difference in apparent height of ≈1 Å were observed in the STM images (Figure 5b). Both types of molecules are located at identical positions of the (√19 × √19) R23.4° lattice and seem to be distributed rather randomly on the surface. Two explanations

Diazocine-functionalized TATA platforms

• Roland Löw,
• Talina Rusch,
• Fynn Röhricht,
• Olaf Magnussen and
• Rainer Herges

Beilstein J. Org. Chem. 2019, 15, 1485–1490, doi:10.3762/bjoc.15.150

• . The half-lives (298 K) are similar for both systems (2.12 h for 1 and 2.32 h for 2). The lack of conjugation between the azo function and the ethynyl spacer of 2 yields in a slightly higher half-life, which is in agreement with earlier results [11]. STM Measurements The adsorption behavior of the

• diazocine-TATA molecules on Au(111) surfaces was studied by STM at room temperature (Figure 3). Adlayers of both compounds show a hexagonally ordered superstructure with lattice constants of 1 and 2 being (12.2 ± 0.6) Å and (12.1 ± 0.5) Å, respectively. Additionally, two rotational domains with an angle of

• (15 ± 4)° are observed. Altogether these parameters are in good agreement with a (√19 × √19) R23.4° superstructure which has been also observed in previous STM investigations of TATA and azobenzene-TATA molecules with octyl ligands [18][20][30]. Conclusion In summary, we present the syntheses of two

Efficiency Eff_syn of complex syntheses as multicomponent reactions, its algorithm and calculations based on concrete criteria

• Heiner Eckert

Beilstein J. Org. Chem. 2019, 15, 1425–1433, doi:10.3762/bjoc.15.142

• only show the synthesis path with the most spectacular molecules, such as the target molecule (TM), the total synthesis with all reactions is essential for production. The quantity of potential start molecule (STM) sets also rises strongly in complex syntheses. The example shows 5 STM sets (consisting

• set-1, operation Π[Σ(Πyn)j]k This synthesis consists of n = 8 synthesis steps, so the synthesis efficiency is Modification of the calculation execution Most chemists look exclusively at the interesting target molecule (TM) of a synthesis and only follow that path from STM to TM, while blanking out

The LANCA three-component reaction to highly substituted β-ketoenamides – versatile intermediates for the synthesis of functionalized pyridine, pyrimidine, oxazole and quinoxaline derivatives

• Tilman Lechel,
• Roopender Kumar,
• Mrinal K. Bera,
• Reinhold Zimmer and
• Hans-Ulrich Reissig

Beilstein J. Org. Chem. 2019, 15, 655–678, doi:10.3762/bjoc.15.61

• this experiment was the double-coupling product OX27 and the mono-coupling product (not shown) was isolated in 5% yield [45]. A solution of the C3-symmetric compound OX28 in 1-phenyloctane was investigated by scanning tunneling microscopy (STM) to reveal its ability to form self-assembled monolayers at

• the interface with highly oriented pyrolytic graphite (HOPG). The STM current image inserted in Scheme 28 shows bright areas that indicate the positions of the π-systems, whereas the dark areas indicate the cyclopropyl groups. Synthesis of quinoxalines The acylamido-substituted 1,2-diketones DK

• vinyl and ethynyl-substituted oxazole derivatives OX21 and OX23 and their palladium-catalyzed reactions to OX22 and OX24–26 (Schwesinger P2 base). Synthesis of C3-symmetric oxazole derivative OX28 and the STM current image of its 1-phenyloctane solution on highly oriented pyrolytic graphite (HOPG

Synthesis of highly functionalized 2,2'-bipyridines by cyclocondensation of β-ketoenamides – scope and limitations

• Paul Hommes and
• Hans-Ulrich Reissig

Beilstein J. Org. Chem. 2016, 12, 1170–1177, doi:10.3762/bjoc.12.112

• acetyl group. This type of aldol condensation that generates a new benzene ring from three acetyl groups was successfully applied in our group in other cases delivering compounds whose 2D self-assembly at highly ordered pyrolytic graphite was studied by STM methods [58][59]. However, in the case of

Creating molecular macrocycles for anion recognition

• Amar H. Flood

Beilstein J. Org. Chem. 2016, 12, 611–627, doi:10.3762/bjoc.12.60

• microscopy (STM) imaging. Their shape persistence makes them ideal for the study of structure–property relationships to enable deep understanding of anion recognition phenomena. The identification of 1,2,3-triazoles as linkers, ligands and building blocks. The synthetic creation of macrocycles sets the scene

• extending the cyanostar’s extremities (Figure 15a) in a bid to program the molecule’s self-assembly into a 2D array on graphite [36]. This work was undertaken in collaboration with Steve Tait who is able to resolve molecules using STM. It was gratifying to see the molecules assemble and even more so to

• self-assembly and anion binding (Figure 17a) using STM and were surprised by what we saw. Clear in the imaging (Figure 17b) were their shapes, looking like lumpy donuts; a shape similar to the one offered by Japan’s Mister Donut. Interestingly, these macrocycles displayed a reliable propensity for

Star-shaped tetrathiafulvalene oligomers towards the construction of conducting supramolecular assembly

• Masahiko Iyoda and
• Masashi Hasegawa

Beilstein J. Org. Chem. 2015, 11, 1596–1613, doi:10.3762/bjoc.11.175

• hand, the conductivities of the corresponding neutral nanoobjects are determined by pulse-radiolysis or flash-photolysis time-resolved microwave conductivity techniques [48][49]. Current-sensing atomic force microscopy (CS-AFM) and combination of scanning tunneling microscopy and spectroscopy (STM/STS

Selected synthetic strategies to cyclophanes

• Sambasivarao Kotha,
• Mukesh E. Shirbhate and
• Gopalkrushna T. Waghule

Beilstein J. Org. Chem. 2015, 11, 1274–1331, doi:10.3762/bjoc.11.142

• synthesized hexa-peri-hexabenzocoronene cyclophane 201a–c. They studied their properties by carrying out differential scanning calorimetry (DSC), optical microscopy, wide-angle X-ray scattering (WAXD), and scanning tunneling microscopy (STM). Tunneling spectroscopy reveals a diode-like behavior which

Single-molecule conductance of a chemically modified, π-extended tetrathiafulvalene and its charge-transfer complex with F₄TCNQ

• Raúl García,
• M. Ángeles Herranz,
• Edmund Leary,
• M. Teresa González,
• Gabino Rubio Bollinger,
• Marius Bürkle,
• Linda A. Zotti,
• Yoshihiro Asai,
• Fabian Pauly,
• Juan Carlos Cuevas,
• Nicolás Agraït and
• Nazario Martín

Beilstein J. Org. Chem. 2015, 11, 1068–1078, doi:10.3762/bjoc.11.120

• a clean gold substrate to the solution for a period of approximately 30 min. The sample was then dried under a flow of argon and mounted inside the scanning tunneling microscope (STM). All experiments were then performed under solvent-free, ambient conditions. In order to form molecular junctions of

• compound 5, we followed the break junction technique [28]. During the experiment, the variation in conductance (G) is recorded while an STM tip is moved vertically (z) in and out of contact with a gold substrate, forming and breaking gold nanocontacts (G vs z trace). When the two gold electrodes (the STM

Mono- and multilayers of molecular spoked carbazole wheels on graphite

• Stefan-S. Jester,
• A. Vikas Aggarwal,
• Daniel Kalle and
• Sigurd Höger

Beilstein J. Org. Chem. 2014, 10, 2783–2788, doi:10.3762/bjoc.10.295

• -persistent macrocycle with an intraannular spoke/hub system) and its synthetic precursor are investigated by scanning tunneling microscopy (STM) at the liquid/solid interface of 1-octanoic acid and highly oriented pyrolytic graphite. The submolecularly resolved STM images reveal that the molecules indeed

• polymer light emitting diodes [12]. The chemical structures of both compounds are shown in Figure 1. Their synthesis and characterization has been reported before [11]. Here, we present scanning tunnelling microscopy (STM) investigations of both compounds, aiming at an extended description of the observed

• molecular geometries and their supramolecular monolayer and multilayer formation on HOPG. Results and Discussion We started our STM investigations on the MSW 2 using TCB as a standard solvent for STM, but did not observe molecules, most probably because they do not adsorb to form two-dimensional (2D

Self-assembled monolayers of shape-persistent macrocycles on graphite: interior design and conformational polymorphism

• Joscha Vollmeyer,
• Friederike Eberhagen,
• Sigurd Höger and
• Stefan-S. Jester

Beilstein J. Org. Chem. 2014, 10, 2774–2782, doi:10.3762/bjoc.10.294

•  4a–c) and dense (“high concentration”, Figure 4d–f) adsorbate patterns, depend on the compound concentrations, as observed by scanning tunneling microscopy (STM). Bright and dark parts in the STM images correspond to regions covered by aromatic backbones and alkoxy side chains, respectively [23

• octadecyloxy side chains at positions 3 and 6 of which one points along d1 in the porous pattern (cf. Figure 5a). They form an ABAB packing motif (along d1, cf. Figure 5b) and are (mostly) resolved by STM (Figure 4a–c). The other four alkoxy side chains of the four naphthylene corners point towards each of the

• four directions along d2 and d3 (cf. Figure 5a), with γ(d1,d2) = γ(d2,d3) = 60°/120° as defined by the HOPG substrate, and form AB alignment motifs (Figure 5c). Although the latter remain unresolvable by STM, the observed packing can only be explained by the alkoxy side chains oriented in this fashion

Molecular ordering at electrified interfaces: Template and potential effects

• Thanh Hai Phan and
• Klaus Wandelt

Beilstein J. Org. Chem. 2014, 10, 2243–2254, doi:10.3762/bjoc.10.233

• reduction of “solution species”. The further reduction of the monocation radicals to the fully uncharged viologen molecule DBV0 (peak P3 in Figure 1) n DBV+•+ n e− n DBV0 occurs already within the regime of massive hydrogen evolution. Since under these conditions reliable in situ STM measurements are not

• possible, the influence of this second reduction step on the structure of the deposit is not considered further here. In the following sections we will now present and discuss in situ STM images as obtained for the electrode surface in different potential regimes. We start at potentials where the molecules

• the potential regime above the first reduction peak P1 in Figure 1, results in the instantaneous formation of a highly ordered DBV2+ film. Figure 4 shows representative STM images describing the surface morphology and molecular structure of the DBV2+adlayer. First, the straight step-edges in Figure 4a

Lateral ordering of PTCDA on the clean and the oxygen pre-covered Cu(100) surface investigated by scanning tunneling microscopy and low energy electron diffraction

• Stefan Gärtner,
• Benjamin Fiedler,
• Oliver Bauer,
• Antonela Marele and
• Moritz M. Sokolowski

Beilstein J. Org. Chem. 2014, 10, 2055–2064, doi:10.3762/bjoc.10.213

• ) surface [referred to as (√2 × 2√2)R45° – 2O/Cu(100)] by scanning tunneling microscopy (STM) and low energy electron diffraction (LEED). Our results confirm the (4√2 × 5√2)R45° superstructure of PTCDA/Cu(100) reported by A. Schmidt et al. [J. Phys. Chem. 1995, 99,11770–11779]. However, contrary to Schmidt

• to that of PTCDA bulk lattice planes. Keywords: Cu(100); LEED; PTCDA; STM; template; thin organic films; Introduction Interfaces between organic semiconductors and metals have gained large interest because they are present in many applications, e.g., organic field-effect transistors [1] or organic

• energy electron diffraction (LEED) measurements. Scanning tunneling microscopy (STM) data has not been reported yet. Therefore, the aim of our combined LEED and STM investigation was twofold: on the one hand to clarify the superstructure of PTCDA on Cu(100), and on the other hand to gain new information

Control over molecular motion using the cis–trans photoisomerization of the azo group

• Estíbaliz Merino and
• María Ribagorda

Beilstein J. Org. Chem. 2012, 8, 1071–1090, doi:10.3762/bjoc.8.119

• ) between both isomers is approximately 7 Å. By scanning tunnelling microscopy (STM), the authors determined the surface density of SAMazo, and the force exerted in the photoisomerization molecular motion of all the azobenzenes in the SAMazo was calculated. The individual photomovement of each azobenzene

Syntheses and properties of thienyl-substituted dithienophenazines

• Annemarie Meyer,
• Eva Sigmund,
• Friedhelm Luppertz,
• Gregor Schnakenburg,
• Immanuel Gadaczek,
• Thomas Bredow,
• Stefan-S. Jester and
• Sigurd Höger

Beilstein J. Org. Chem. 2010, 6, 1180–1187, doi:10.3762/bjoc.6.135

• scanning tunneling microscopy (STM). Synthesis The synthesis of 4 is shown in Scheme 1. It is obtained in three steps from commercially available starting materials. The synthesis of 3 has previously been reported by benzoin condensation of the corresponding bithiophene derivative [18]. Alternatively, we

• and HOMO-1 in 17a are nearly the same (ΔEHOMO,HOMO-1 =0.02 eV), while in 13 the energy difference between HOMO and HOMO-1 is larger than 0.6 eV [35]. STM study All synthesized thiophene oligomers 12–18 were investigated concerning their ability to form self-assembled monolayers (SAMs) at the HOPG/TCB

• interface (highly oriented pyrolytic graphite/1,2,4-trichlorobenzene). In situ STM was applied under typical conditions with typical tunneling parameters normally allowing the visualization of SAMs – if formed [36]. However, among all the substances only 12b (10−5 M in TCB) assembles into crystalline