Multiscale modelling of biomolecular corona formation on metallic surfaces

• Parinaz Mosaddeghi Amini,
• Ian Rouse,
• Julia Subbotina and
• Vladimir Lobaskin

Beilstein J. Nanotechnol. 2024, 15, 215–229, doi:10.3762/bjnano.15.21

• replacement of a set of adsorbates by a single molecule, but does not allow for the converse in which a set of incoming molecules can displace an adsorbate. We justify this neglect on the basis that the required event of multiple simultaneous collisions on a single target would occur so rarely that it would

Molecular nanoarchitectonics: unification of nanotechnology and molecular/materials science

• Katsuhiko Ariga

Beilstein J. Nanotechnol. 2023, 14, 434–453, doi:10.3762/bjnano.14.35

• intermolecular bond. Such an attempt is a promising approach to realize molecular nanoelectronics using molecule–polymer nanojunctions. Molecular nanoarchitectonics of single molecule heterowires of conducting polymers has also been reported. Sakaguchi et al. realized the synthesis of molecular heterowires by a

• other words, a controlled addition reaction in a single molecule adsorbed on a surface by a local probe at low temperature was demonstrated. Long-lived radicals could be obtained, and C60 molecules could be selectively added to the sites. Such direct addition reactions enable the synthesis of single

Single-step extraction of small-diameter single-walled carbon nanotubes in the presence of riboflavin

• Polina M. Kalachikova,
• Anastasia E. Goldt,
• Eldar M. Khabushev,
• Timofei V. Eremin,
• Timofei S. Zatsepin,
• Elena D. Obraztsova,
• Konstantin V. Larionov,
• Liubov Yu. Antipina,
• Pavel B. Sorokin and
• Albert G. Nasibulin

Beilstein J. Nanotechnol. 2022, 13, 1564–1571, doi:10.3762/bjnano.13.130

• . Biomedical applications apply an additional constraint on the diameter of nanotubes. Small-diameter SWCNTs display intrinsic photoluminescence in the spectral range of 900–1100 nm within the biological transparency window, making them ideal candidates for single-molecule biosensors or biomedical imaging

Revealing local structural properties of an atomically thin MoSe₂ surface using optical microscopy

• Lin Pan,
• Peng Miao,
• Anke Horneber,
• Alfred J. Meixner,
• Pierre-Michel Adam and
• Dai Zhang

Beilstein J. Nanotechnol. 2022, 13, 572–581, doi:10.3762/bjnano.13.49

• single-molecule detection level [18][19]. The Raman enhancement originates from an electromagnetic mechanism, provided by the excitation of surface plasmons, and a chemical mechanism which is related to the modification of Raman polarizability of molecules [20]. It has been reported that 2D materials

Investigation of electron-induced cross-linking of self-assembled monolayers by scanning tunneling microscopy

• Patrick Stohmann,
• Sascha Koch,
• Yang Yang,
• Christopher David Kaiser,
• Julian Ehrens,
• Jürgen Schnack,
• Niklas Biere,
• Dario Anselmetti,
• Armin Gölzhäuser and
• Xianghui Zhang

Beilstein J. Nanotechnol. 2022, 13, 462–471, doi:10.3762/bjnano.13.39

• cannot completely rule out the possibility of single-molecule desorption. The apparent depth of these dark spots is 1.4 ± 0.1 Å and the spatial distribution can be approximated by a Poisson distribution (Figure S5 in Supporting Information File 1), implying that these dark spots are random and

Topographic signatures and manipulations of Fe atoms, CO molecules and NaCl islands on superconducting Pb(111)

• Carl Drechsel,
• Philipp D’Astolfo,
• Jung-Ching Liu,
• Thilo Glatzel,
• Rémy Pawlak and
• Ernst Meyer

Beilstein J. Nanotechnol. 2022, 13, 1–9, doi:10.3762/bjnano.13.1

• enable the development of functionalized tips, obtained by picking up a single molecule from a surface. This has been an important milestone for low-temperature STM/AFM techniques since the CO tip nowadays enables systematic high-resolution measurements of surfaces, molecules and atoms [33][34][35]. It

The role of convolutional neural networks in scanning probe microscopy: a review

• Ido Azuri,
• Irit Rosenhek-Goldian,
• Neta Regev-Rudzki,
• Georg Fantner and
• Sidney R. Cohen

Beilstein J. Nanotechnol. 2021, 12, 878–901, doi:10.3762/bjnano.12.66

• , myelin, somata, and different neuronal cell types were automatically identified [109]. Li et al. developed a tool, AutoSiM, for automatic classification and segmentation of single-molecule fluorescence time traces through deep learning [110]. In this approach, a recurrent neural network (RNN, see [28

Influence of electrospray deposition on C₆₀ molecular assemblies

• Antoine Hinaut,
• Sebastian Scherb,
• Sara Freund,
• Zhao Liu,
• Thilo Glatzel and
• Ernst Meyer

Beilstein J. Nanotechnol. 2021, 12, 552–558, doi:10.3762/bjnano.12.45

• method can yield single isolated molecules accompanied by surface modifications. Keywords: alkali halide; Au(111); bulk insulator; C60; electrospray; electrospray deposition; fullerene; high-vacuum electrospray deposition (HV-ESD); molecular assembly; nc-AFM; NiO; single molecule; thermal evaporation

Extended iron phthalocyanine islands self-assembled on a Ge(001):H surface

• Rafal Zuzak,
• Marek Szymonski and
• Szymon Godlewski

Beilstein J. Nanotechnol. 2021, 12, 232–241, doi:10.3762/bjnano.12.19

• ; iron phthalocyanine (FePc); scanning tunneling microscopy; self-assembly; Introduction The development of molecular circuitry requires the preparation of nanostructures isolated from the influence of the underlying substrate. This is of crucial importance for atomic and single-molecule prototypes, but

• holds also for layered materials. Single-molecule prototypes or molecular nanostructures are often prepared on metals, which usually provide a sufficiently low diffusion barrier for efficient self-assembly and simultaneously allow for in-depth analysis through atomically precise tools from the family of

• therefore we can conclude that the island extension is always associated with the appearance of two rows of lobes. Thus, it seems reasonable to assume that the two lobes originate from a single molecule, in accordance with the tentative model of imaging shown in Figure 3c. For clarity, the anticipated

TiO_x/Pt₃Ti(111) surface-directed formation of electronically responsive supramolecular assemblies of tungsten oxide clusters

• Marco Moors,
• Yun An,
• Agnieszka Kuc and
• Kirill Yu. Monakhov

Beilstein J. Nanotechnol. 2021, 12, 203–212, doi:10.3762/bjnano.12.16

• (e.g., polyoxometalates [5][6]) with many distinct and stable redox states. Recently, representatives of this interesting chemical class have also been shown to act as stable single-molecule three‐state transistors [7]. However, controlled adsorption and molecular ordering on surfaces remain

Detecting stable adsorbates of (1S)-camphor on Cu(111) with Bayesian optimization

• Jari Järvi,
• Patrick Rinke and
• Milica Todorović

Beilstein J. Nanotechnol. 2020, 11, 1577–1589, doi:10.3762/bjnano.11.140

• approximation of a single molecule on the surface, with an average lateral separation of 10 Å between the periodic images of camphor and 50 Å separation between the periodic Cu(111) slabs. The adsorption energy Eads is calculated as in which Etot is the total energy of the camphor/Cu(111) system, ECu is the

Optically and electrically driven nanoantennas

• Monika Fleischer,
• Dai Zhang and
• Alfred J. Meixner

Beilstein J. Nanotechnol. 2020, 11, 1542–1545, doi:10.3762/bjnano.11.136

• . Prominent examples are SERS and TERS, where the intrinsically small Raman scattering cross-section is enhanced by several orders of magnitude, making single-molecule spectroscopy feasible. These spectroscopic techniques have shown tremendous progress in the last two decades [29][30][31][32]. Under high

• subject. Energy-level engineering in the gap by introducing molecules into the tunnel junction provides an additional handle to modulate photon emission from an electrically controlled optical antenna. Light emission by tunneling through a single molecule opens the door to combine electronics and quantum

• to a sharp tip is refined to a two-step procedure with high throughput. A self-assembly approach to create a dumbbell antenna consisting of a 40 nm and an 80 nm Au nanoparticle at a scanning tip is shown in [48] and applied for single molecule sensitivity imaging. The advantage of applying TERS for

Self-assembly and spectroscopic fingerprints of photoactive pyrenyl tectons on hBN/Cu(111)

• Domenik M. Zimmermann,
• Knud Seufert,
• Luka Ðorđević,
• Tobias Hoh,
• Sushobhan Joshi,
• Tomas Marangoni,
• Davide Bonifazi and
• Willi Auwärter

Beilstein J. Nanotechnol. 2020, 11, 1470–1483, doi:10.3762/bjnano.11.130

• investigations and determination of the molecular gap Both the STS studies addressing the adsorbed species on the single-molecule level and the optical spectroscopy in solution confirmed the gap reduction upon increasing the number of pyridin-4-ylethynyl substituents, as predicted by DFT calculations (Figure 6

Protruding hydrogen atoms as markers for the molecular orientation of a metallocene

• Linda Laflör,
• Michael Reichling and
• Philipp Rahe

Beilstein J. Nanotechnol. 2020, 11, 1432–1438, doi:10.3762/bjnano.11.127

• , respectively. Molecules of both geometries oriented along one of the possible angles are present in the experimental images, two examples for each geometry are marked. The experimental contrast is similar to the pattern of a single molecule within the calculated images in Figure 2h and Figure 2m for geo 1 and

• as for the CO image calculations. (o, p) Structure of the simulation cell with each molecule in the single-molecule DFT-optimised geometry geo 1 [22]. NC-AFM image calculation for a row of FDCA molecules in geo 2. (a–c) Constant-height frequency-shift Δf data (inverted colour scale used) simulated

Growth of a self-assembled monolayer decoupled from the substrate: nucleation on-command using buffer layers

• Robby Reynaerts,
• Kunal S. Mali and
• Steven De Feyter

Beilstein J. Nanotechnol. 2020, 11, 1291–1302, doi:10.3762/bjnano.11.113

• (lower) on the buffer layer compared to that on the solid substrate. These factors may lead to different adsorption conformation for initial single molecule adsorption coupled with higher orientational freedom and significantly different (often reduced) lateral corrugation barriers for molecular

Role of redox-active axial ligands of metal porphyrins adsorbed at solid–liquid interfaces in a liquid-STM setup

• Thomas Habets,
• Sylvia Speller and
• Johannes A. A. W. Elemans

Beilstein J. Nanotechnol. 2020, 11, 1264–1271, doi:10.3762/bjnano.11.110

• single-molecule level, employing scanning tunneling microscopy (STM) [7][8][9]. Since our aim was to stay as close as possible to the laboratory conditions at which catalysis takes place (typically in an organic solvent under ambient conditions), we carried out our STM studies at a solid–liquid interface

• insights into reactivity at the single-molecule scale, some mechanistic aspects still remained unclear. For instance, the reduction of the Mn(III) porphyrin to a Mn(II) porphyrin also involves the dissociation of the axially coordinating Cl ligand from the metal center, and it is as yet unclear what the

Scanning tunneling microscopy and spectroscopy of rubrene on clean and graphene-covered metal surfaces

• Karl Rothe,
• Alexander Mehler,
• Nicolas Néel and
• Jörg Kröger

Beilstein J. Nanotechnol. 2020, 11, 1157–1167, doi:10.3762/bjnano.11.100

• ] and hexagonal boron nitride (h-BN) [3] have been studied in detail. In contrast, vibrational spectroscopy at the single-molecule level is scarce. Scanning tunneling spectroscopy (STS) of vibronic levels of 1,3,5-tris(2,2-dicyanovinyl)benzene on graphene-covered h-BN on SiO2 [4], of cobalt

• both frontier orbitals, induced by different molecular vibrational quanta and with different Huang–Rhys factors. Consequently, graphene represents an appropriate buffer layer for exploring electronic and vibronic properties at the single-molecule level. (a) Skeletal formula of C42H28 including

Thermophoretic tweezers for single nanoparticle manipulation

• Jošt Stergar and
• Natan Osterman

Beilstein J. Nanotechnol. 2020, 11, 1126–1133, doi:10.3762/bjnano.11.97

• dynamically created in parallel and relocated to an arbitrary position. The use of multiple thermo-optical traps enables a host of exciting applications, most prominently single-molecule chemistry. We demonstrate the thermophoretic tweezers by the trapping and parallel manipulation of individual particles

• with a 10–15 μm diameter. In contrast, our system enables the independent steering of particles/molecules on arbitrary paths and could be thus used as a tool for single-molecule chemistry. For example, one could imagine an experimental chamber with a few randomly diffusing labeled (bio)molecules that

• would never react due to the low contact probability. However, using thermophoretic tweezers, they could be easily trapped and brought close to each other to increase the reaction probability by confining them to a smaller volume. For such single-molecule chemistry reactions, tight confinement of

Monolayers of MoS₂ on Ag(111) as decoupling layers for organic molecules: resolution of electronic and vibronic states of TCNQ

• Asieh Yousofnejad,
• Gaël Reecht,
• Nils Krane,
• Christian Lotze and
• Katharina J. Franke

Beilstein J. Nanotechnol. 2020, 11, 1062–1071, doi:10.3762/bjnano.11.91

• hybridization, charge transfer and screening [1][2][3][4]. These effects lead to a broadening and shift of the molecular resonances [5]. Often the molecular functionality is also lost due to these interactions [6]. However, addressing individual molecules in devices or by single-molecule spectroscopy as offered

Hexagonal boron nitride: a review of the emerging material platform for single-photon sources and the spin–photon interface

• Stefania Castelletto,
• Faraz A. Inam,
• Shin-ichiro Sato and
• Alberto Boretti

Beilstein J. Nanotechnol. 2020, 11, 740–769, doi:10.3762/bjnano.11.61

• single atom, a single molecule, a single solid-state color center or a single quantum dot. The spontaneous emission from these isolated systems has the characteristics of either a 2-level [67] or a 3-level atomic model [68]. A 2-level system representation is shown in Figure 1a. It comprises a ground

Mobility of charge carriers in self-assembled monolayers

• Zhihua Fu,
• Tatjana Ladnorg,
• Hartmut Gliemann,
• Alexander Welle,
• Asif Bashir,
• Michael Rohwerder,
• Qiang Zhang,
• Björn Schüpbach,
• Andreas Terfort and
• Christof Wöll

Beilstein J. Nanotechnol. 2019, 10, 2449–2458, doi:10.3762/bjnano.10.235

• by tip size effects. The schematics presented in Figure 3 rationalize the observation that the conductivity increases with island size. In the hypothetical case that the AFM tip contacts only a single PAT molecule, i.e., an island consisting of a single molecule only, we would obtain the resistance

• of a single molecule. Such values have been reported in the literature, e.g., for TP1 this value amounts to 55.5 MΩ [41]. For larger islands, in addition to the vertical current through one single molecule, additional current (lateral) pathways through adjacent molecules are available. While for HDT

• (conductivity only in one direction) is too simple for the present PAT SAM. In any case, the value obtained from the fit is consistent with previous studies. For the resistance Rmol of a PAT molecule (governing the vertical current through a single molecule) we yield a value of 142.1 MΩ. This value is somewhat

Self-assembly of a terbium(III) 1D coordination polymer on mica

• Quentin Evrard,
• Giuseppe Cucinotta,
• Felix Houard,
• Guillaume Calvez,
• Yan Suffren,
• Carole Daiguebonne,
• Olivier Guillou,
• Andrea Caneschi,
• Matteo Mannini and
• Kevin Bernot

Beilstein J. Nanotechnol. 2019, 10, 2440–2448, doi:10.3762/bjnano.10.234

• embedded in a suitable electrostatic environment. Indeed, mononuclear single-molecule magnets (SMMs), which are objects showing magnetic hysteresis at the molecular level comprising only one metallic ion (instead of a collective assembly of ions), have been initially observed for a Tb-based molecule [13

Nitrogen-vacancy centers in diamond for nanoscale magnetic resonance imaging applications

• Alberto Boretti,
• Lorenzo Rosa,
• Jonathan Blackledge and
• Stefania Castelletto

Beilstein J. Nanotechnol. 2019, 10, 2128–2151, doi:10.3762/bjnano.10.207

• allow for single-molecule resolution and extend the imaging techniques to molecular biology. Magnetic imaging is fundamental for exploring chemical–physical magnetic processes and expanding the capacity of magnetic data storage units, enabling high-resolution, real-time imaging beyond the limitations of

Molecular attachment to a microscope tip: inelastic tunneling, Kondo screening, and thermopower

• Rouzhaji Tuerhong,
• Mauro Boero and
• Jean-Pierre Bucher

Beilstein J. Nanotechnol. 2019, 10, 1243–1250, doi:10.3762/bjnano.10.124

• thermopower measured across the single-molecule junction. Keywords: inelastic electron tunneling; molecular quantum dot; Kondo physics; single molecule; thermopower; tunnel junction; Introduction Scanning tunneling microscopy (STM) has the capability to detect the electron transport through a molecule not

• only adsorbed on a surface, but also when it is attached to the probe tip itself [1][2][3][4]. The sharp tip of the STM is then used to lift a single molecule from the surface in order to efficiently minimize the influence of the substrate on the molecule. In this way, the intrinsic physical properties

• to study, with atomic resolution, the coupling of the tunneling electrons to other elementary excitations such as vibrations, plasmons and spins [5][6][7][8]. Furthermore, a molecular junction in STM can serve as a reliable and controllable model system for the study of a single molecule in a way

Scavenging of reactive oxygen species by phenolic compound-modified maghemite nanoparticles

• Małgorzata Świętek,
• Yi-Chin Lu,
• Rafał Konefał,
• Liliana P. Ferreira,
• M. Margarida Cruz,
• Yunn-Hwa Ma and
• Daniel Horák

Beilstein J. Nanotechnol. 2019, 10, 1073–1088, doi:10.3762/bjnano.10.108

• flavonoids and lignins have many functional groups attached to the multiple benzene rings within a single molecule. The simplest phenolic compounds consist of only one aromatic ring and a type, number, and arrangement of functional groups that strongly determine the antioxidant activity [5]. Generally