Cyclodextrin-based rotaxanes for polymer materials: challenge on simultaneous realization of inexpensive production and defined structures

• Yosuke Akae

Beilstein J. Org. Chem. 2024, 20, 3026–3049, doi:10.3762/bjoc.20.252

• synthetic study, the structural analysis of the obtained (poly)rotaxanes was performed to evaluate the fundamental relationship between the axle length and the number and directions of the CD wheels. The directions of the CDs on the PEG-based polyrotaxane framework were analyzed by scanning tunneling

Ligand effects, solvent cooperation, and large kinetic solvent deuterium isotope effects in gold(I)-catalyzed intramolecular alkene hydroamination

• Ruichen Lan,
• Brock Yager,
• Yoonsun Jee,
• Cynthia S. Day and
• Amanda C. Jones

Beilstein J. Org. Chem. 2024, 20, 479–496, doi:10.3762/bjoc.20.43

• hydroamination (1b) a KIE of 2.4 is estimated based on their statement of percent conversions in MeOH (61%) compared to MeOH-d4 (25%) after 20 hours at 50 °C [7]. Large isotope effects (>7) have been seen in a number of organometallic reactions [75] and tunneling need not be invoked if proton transfer involves

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

Perspectives on push–pull chromophores derived from click-type [2 + 2] cycloaddition–retroelectrocyclization reactions of electron-rich alkynes and electron-deficient alkenes

• Michio Yamada

Beilstein J. Org. Chem. 2024, 20, 125–154, doi:10.3762/bjoc.20.13

• through scanning tunneling microscopy [85]. For TCBDs bearing unsubstituted anilino (p-H2NC6H4–) groups, their conversion into the p-iodophenyl derivatives via the Sandmeyer reaction and subsequent post-functionalization via the Suzuki and Sonogashira coupling reactions are achieved [86]. In the reaction

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

Mechanochemical bottom-up synthesis of phosphorus-linked, heptazine-based carbon nitrides using sodium phosphide

• Blaine G. Fiss,
• Georgia Douglas,
• Michael Ferguson,
• Jorge Becerra,
• Jesus Valdez,
• Trong-On Do,
• Tomislav Friščić and
• Audrey Moores

Beilstein J. Org. Chem. 2022, 18, 1203–1209, doi:10.3762/bjoc.18.125

• absorption band corresponding to the heptazine breathing mode at 800 cm−1, while also retaining the characteristic P–C vibration at 950 cm−1 (Supporting Information File 1, Figure S3, green). STEM-EELS analysis The composition and particle morphology were investigated further using scanning tunneling

Experimental and theoretical studies on the synthesis of 1,4,5-trisubstituted pyrrolidine-2,3-diones

• Nguyen Tran Nguyen,
• Vo Viet Dai,
• Nguyen Ngoc Tri,
• Luc Van Meervelt,
• Nguyen Tien Trung and
• Wim Dehaen

Beilstein J. Org. Chem. 2022, 18, 1140–1153, doi:10.3762/bjoc.18.118

• ···O intramolecular hydrogen bond (distance ca. 1.7–1.8 Å) (cf. Figures 4–6). The isomerization of 4a/4a’ is extremely fast due to the high rate constant of about 1012 s−1 at 298 K, calculated by the transitional state theory method and quantum tunneling effect [47]. It is thus impossible to

• reaction coordinates (IRCs) were performed at the same level of theory to determine two local minima through transition states in each stepwise [50]. Besides, the rate constant of reaction based on the transitional state theory method and quantum tunneling effect was calculated by the following expression

• [47]: with Qtun, ΔG#, ωi are tunneling transmission coefficient, Gibbs free energy values, and imaginary frequencies of transition states, respectively. Structure of naturally occurring and synthetic 2-pyrrolidone derivatives. Structure of natural compounds containing a 1,5-dihydro-2H-pyrrol-2-one

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

Preparation of 2-phospholene oxides by the isomerization of 3-phospholene oxides

• Péter Bagi,
• Réka Herbay,
• Nikolett Péczka,
• Zoltán Mucsi,
• István Timári and
• György Keglevich

Beilstein J. Org. Chem. 2020, 16, 818–832, doi:10.3762/bjoc.16.75

• atom can be easily protonated via a high enthalpy transition state [TS(17→18)], which is the rate determining step of this reaction sequence. We suppose that this rather high enthalpy is much lower due to the tunneling effect of the proton, whose energy gap is estimated to be reduced to about 130 kJ

• ), which is more favorable than the same process at position C(5) (by ca. 3–4 kJ mol−1). An anionic intermediate 21 is formed in this manner, and the related transition state represents a low enthalpy barrier (ca. 55 kJ mol−1), which is lowered by the tunneling effect of the proton. In the final step, the

p-Pyridinyl oxime carbamates: synthesis, DNA binding, DNA photocleaving activity and theoretical photodegradation studies

• Panagiotis S. Gritzapis,
• Panayiotis C. Varras,
• Nikolaos-Panagiotis Andreou,
• Katerina R. Katsani,
• Konstantinos Dafnopoulos,
• George Psomas,
• Zisis V. Peitsinis,
• Alexandros E. Koumbis and
• Konstantina C. Fylaktakidou

Beilstein J. Org. Chem. 2020, 16, 337–350, doi:10.3762/bjoc.16.33

• calculate the quantum mechanical tunneling coefficient by employing the Skodje–Truhlar potential for parabolic potential barriers [91]. In Equation 5 the parameters α = 2π/h∙Im(ν≠) = 5.74672∙1020 J−1 and β = 1/kB∙T = 2.42928∙1020 J−1 are defined through the fundamental constants, ν≠ is the imaginary

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

• , Uniwersytet Wrocławski, ul. F. Joliot-Curie 14, 50-383 Wrocław, Poland 10.3762/bjoc.15.180 Abstract Supramolecular nanopatterns of arylene–alkynylene squares with side chains of different lengths are investigated by scanning tunneling microscopy at the solid/liquid interface of highly oriented pyrolytic

• and non-planar coronoid polycyclic aromatic hydrocarbons (i.e., butyloxy-substituted kekulene and octulene derivatives) are found to be able to intercalate into the intramolecular nanopores. Keywords: macrocycles; scanning tunneling microscopy; self-assembled monolayers; self-sorting; solid/liquid

• 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

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

Tetrathiafulvalene – a redox-switchable building block to control motion in mechanically interlocked molecules

• Hendrik V. Schröder and
• Christoph A. Schalley

Beilstein J. Org. Chem. 2018, 14, 2163–2185, doi:10.3762/bjoc.14.190

• ][89]. An ordered array of molecules enables the possibility of concerted switching. The fixed orientation on a surface allows studying molecules with sophisticated techniques such as scanning tunneling microscopy. Furthermore, redox-switchable AMMs, containing for example TTF moieties, can be

Correlation effects and many-body interactions in water clusters

• Andreas Heßelmann

Beilstein J. Org. Chem. 2018, 14, 979–991, doi:10.3762/bjoc.14.83

• exchange interaction energy terms in Equation 5 are short-range contributions to the interaction energy and stem from a tunneling of the electrons between the two monomers. They quickly decay exponentially with the distance of the interacting systems. The superscripts (1) and (2) denote the order of the

New electroactive asymmetrical chalcones and therefrom derived 2-amino- / 2-(1H-pyrrol-1-yl)pyrimidines, containing an N-[ω-(4-methoxyphenoxy)alkyl]carbazole fragment: synthesis, optical and electrochemical properties

• Daria G. Selivanova,
• Alexei A. Gorbunov,
• Olga A. Mayorova,
• Alexander N. Vasyanin,
• Igor V. Lunegov,
• Elena V. Shklyaeva and
• Georgii G. Abashev

Beilstein J. Org. Chem. 2017, 13, 1583–1595, doi:10.3762/bjoc.13.158

• scanning tunneling microscopy. Results and Discussion Synthetic toolbox The objective of the presented work involves the design and further synthesis of 4,6-diaryl-substituted 2-(pyrrol-1-yl)pyrimidines, embedding 9-[ω-(4-methoxyphenoxy)alkyl]carbazole moieties as substituents, one of which is directly

Creating molecular macrocycles for anion recognition

• Amar H. Flood

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

• geometrically appealing to work with. In our stables we have triangles, squares and pentagons represented by triacarb, triazolophane and cyanostar macrocycles. The analogy to donut shapes is obvious and the hole in their middles can be both filled with anions and observed using real-space scanning tunneling

Dynamic behavior of rearranging carbocations – implications for terpene biosynthesis

• Stephanie R. Hare and
• Dean J. Tantillo

Beilstein J. Org. Chem. 2016, 12, 377–390, doi:10.3762/bjoc.12.41

• classical mechanics (i.e., solving either Newton’s or Hamilton’s classical equations of motion to propagate nuclear positions), but there have been cases reported where quantum dynamic effects have been found to be important, particularly when tunneling effects contribute significantly to the reaction rate

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

• -molecule electrical transport properties of a molecular wire containing a π-extended tetrathiafulvalene (exTTF) group and its charge-transfer complex with F4TCNQ. We form single-molecule junctions using the in situ break junction technique using a homebuilt scanning tunneling microscope with a range of

• 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

• tunneling-only traces from those with plateaus. One can see that the colored region of the 2D histogram of OPE3-dithiol extends significantly to larger inter-electrode distances than the unmodified gold substrate. Also, it does so within a narrow band of conductance values (roughly between log(G/G0) = −3

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

• the second layer. Keywords: molecular spoked wheels; scanning tunneling microscopy; self-assembled monolayers; solid/liquid interface; template; Introduction Molecular spoked wheels (MSWs) have gained increasing interest as two-dimensional (2D) carbon-based objects of adjustable sizes [1][2][3][4][5

• , related to high and low tunneling currents, respectively [13]. At the OA/HOPG interface 1 forms a 2D-crystalline monolayer (Figure 2a and b) for which a hexagonal unit cell of a = b = 6.7 ± 0.2 nm, γ(a,b) = 60 ± 2° can be indexed. The unit cell vector a is oriented with γ(a,d1) = 9 ± 2° relative to one of

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

• -dimensional (2D) crystalline monolayer patterns are obtained by in situ scanning tunneling microscopy. A concentration-dependent conformational polymorphism is found, and open and more dense packing motifs are observed. For all three compounds alike lattice parameters are found, therefore the intermolecular

•  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

• macrocycle sizes are induced by the intraannular strands and vary by less than 2 Å. (b) and (c) are adapted with permission from [22]. Copyright 2012 The Royal Society of Chemistry. Scanning tunneling microscopy images and supramolecular models of (a)–(c) porous (= polymorph A) and (d)–(f) dense patterns

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

• Department, Quynhon University, 170 An Duong Vuong; Quynhon, Vietnam Institute of Experimental Physics, University of Wroclaw, MaxaBorna 9, 50-204, Wroclaw, Poland 10.3762/bjoc.10.233 Abstract A combination of cyclic voltammetry and in situ scanning tunneling microscopy was employed to examine the

• effects, in the structure formation process of DBV cations on these modified Cu electrode surfaces. Keywords: cyclic voltammogram; scanning tunneling microscopy; self-assembly; template effect; viologen; Introduction The precise control of the self-organization of molecular layers on either conducting

• could also be obtained by carefully varying the tunneling conditions [5][7][26]. Under “soft tunneling conditions”, i.e., with high bias voltage and low tunneling current, the characteristic features of the DBV2+ adlayer are observed (Figure 5a). Conversely, the chloride lattice underneath becomes

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

• 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

• PTCDA on bare Cu(100). We note that contrary to the situation on bare Cu(100) we get a more pronounced submolecular contrast of the PTCDA for similar tunneling parameters (see Figure 4(c) in comparison with Figure 3(a)) which we interpret as an indication for the electronic decoupling from the substrate

Substitution effect and effect of axle’s flexibility at (pseudo-)rotaxanes

• Friedrich Malberg,
• Jan Gerit Brandenburg,
• Werner Reckien,
• Oldamur Hollóczki,
• Stefan Grimme and
• Barbara Kirchner

Beilstein J. Org. Chem. 2014, 10, 1299–1307, doi:10.3762/bjoc.10.131

• –Sham frontier orbitals of wheel and axle upon conductivity and electron tunneling along the rotaxane [21]. A quantum chemical shuttling motion study of rotaxane-based molecular switching devices has revealed how the modification of the redox states of both entities results in changes of the