Applications of microscopy and small angle scattering techniques for the characterisation of supramolecular gels

• Connor R. M. MacDonald and
• Emily R. Draper

Beilstein J. Org. Chem. 2024, 20, 2608–2634, doi:10.3762/bjoc.20.220

• force microscopy (AFM), electron microscopy (EM) techniques including transmission electron microscopy (TEM), scanning electron microscopy (SEM), and scanning transmission electron microscopy (STEM), and confocal laser scanning microscopy (CLSM) are the most common techniques for imaging self-assembled

• ]. The work by Alakpa et al. highlights how important it is to consider how one assesses the impact of co-assembly on a molecular system [20]. AFM suggested that the addition of the surfactant-like Fmoc-serine (Fmoc-S) to the fibrous Fmoc-diphenylalanine (Fmoc-FF) did not impact the structure of the Fmoc

• could CLSM observe the initial kinetic self-sorting of gelators, but it also showed that the homogenous mixture of NFs and CFs can undergo a higher level of self-sorting, resulting in macroscopic phase separation (Figure 4). To gather a three-dimensional surface profile of a material, AFM utilises a

Cage-like microstructures via sequential Ugi reactions in aqueous emulsions

• Rita S. Alqubelat,
• Yaroslava A. Menzorova and
• Maxim A. Mironov

Beilstein J. Org. Chem. 2024, 20, 2078–2083, doi:10.3762/bjoc.20.179

• pH value. According to atomic force microscopy (AFM) data, the resulting particles had a domain structure and were similar in appearance to raspberries [20]. An interesting feature of the resulting particles was the high efficiency as Pickering emulsifiers: even at a concentration below 0.3 g/L

• approached low-molecular-weight substances. We used AFM to identify the structural features of the original colloidal particles. For this, colloidal particles were adsorbed on the substrate surface and then analyzed without complete drying, which made it possible to reveal the initial microgel structure

• application. Single droplets of the Pickering emulsion attached to a glass surface. Cage-like microstructure obtained via sequential Ugi reactions. AFM images of A) single domains and B) cross-linked CMC/chitosan polymer particles. Variations of microstructures obtained via sequential Ugi reactions. A) Cap

Discovery of antimicrobial peptides clostrisin and cellulosin from Clostridium: insights into their structures, co-localized biosynthetic gene clusters, and antibiotic activity

• Moisés Alejandro Alejo Hernandez,
• Katia Pamela Villavicencio Sánchez,
• Rosendo Sánchez Morales,
• Karla Georgina Hernández-Magro Gil,
• David Silverio Moreno-Gutiérrez,
• Eddie Guillermo Sanchez-Rueda,
• Yanet Teresa-Cruz,
• Brian Choi,
• Armando Hernández Garcia,
• Alba Romero-Rodríguez,
• Oscar Juárez,
• Siseth Martínez-Caballero,
• Mario Figueroa and
• Corina-Diana Ceapă

Beilstein J. Org. Chem. 2024, 20, 1800–1816, doi:10.3762/bjoc.20.159

• force microscopy The study employed atomic force microscopy (AFM) in air to observe the bacterial morphological changes on the surface of S. epidermidis triggered by the impact of lanthipeptides. The concentrations of peptides were estimated based on the SDS gel band intensity, and we expect there is

• some uncertainty in these estimations. The samples were treated with an estimated 22.4 µg/mL concentration for 1 and 5 hours. The AFM images of untreated S. epidermidis MIQ43 displayed characteristic clustered cocci (see Figure 6A and 6F). The treatment with clostrisin and cellulosin samples resulted

• GraphPad (version 8.0.2). Atomic force microscopy AFM characterization was conducted using a MultiMode 8-HR (Bruker). Samples containing S. epidermis at an OD600 > 1 were incubated with the lanthipeptides at room temperature for 1 and 5 hours. Subsequently, 9 µL of the samples were combined with 1 µL of a

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

Preparing a liquid crystalline dispersion of carbon nanotubes with high aspect ratio

• Keiko Kojima,
• Nodoka Kosugi,
• Hirokuni Jintoku,
• Kazufumi Kobashi and
• Toshiya Okazaki

Beilstein J. Org. Chem. 2024, 20, 52–58, doi:10.3762/bjoc.20.7

• microscopy (AFM) (see Supporting Information File 1, Figure S2). In both images, rod-like DWCNTs were observed, while spaghetti-like agglomerates were hardly observed. The average length (L) and diameter (D) of the DWCNT samples were ≈2.9 μm and ≈2.1 nm, respectively. The L/D of the DWCNTs was 1378, which

• examined using scanning electron microscopy (SEM) (HITACHI High-Tech, SU8200) and atomic force microscopy (AFM) (OLYMPUS, OLS-4500). Additionally, the ζ-potential of the DWCNTs was determined by measuring the ζ potential analyzer (Malvern Panalytical, ZETASIZER Pro Red label) in a disposable cell (Malvern

Facile access to pyridinium-based bent aromatic amphiphiles: nonionic surface modification of nanocarbons in water

• Lorenzo Catti,
• Shinji Aoyama and
• Michito Yoshizawa

Beilstein J. Org. Chem. 2024, 20, 32–40, doi:10.3762/bjoc.20.5

• (PA-OCH3)n·(C60)m showed only a minor change in the ZP (ΔZP = +1.0 mV) under similar conditions, confirming the importance of the noncovalent imidazole functionalities [27]. Solubilization and AFM analysis of a nitrogen-doped nanocarbon Finally, water-solubilization and aqueous processing of nitrogen

• PA-OCH3 to solubilize not only conventional nanocarbons but also heteroatom-containing ones. To obtain direct structural information of the encircled (g-C3N4)m, dry-state AFM measurements (on mica) were conducted using an aqueous solution of (PA-OCH3)n·(g-C3N4)m. The obtained AFM images showed large

• a filter. b) UV–visible spectra (H2O, rt, 1.0 mM based on PA-OCH3) of (PA-OCH3)n and (PA-OCH3)n·(g-C3N4)m. c) AFM image (dry, rt, mica) of (PA-OCH3)n·(g-C3N4)m and d) its selected size profiles. Zeta potentials (ZP) of aromatic micelles (PA-R)n and (AA)n [23]. Zeta potentials of (PA-OCH3)n·(C60 or s

Charge carrier transport in perylene-based and pyrene-based columnar liquid crystals

• Alessandro L. Alves,
• Simone V. Bernardino,
• Carlos H. Stadtlober,
• Edivandro Girotto,
• Giliandro Farias,
• Rodney M. do Nascimento,
• Sergio F. Curcio,
• Thiago Cazati,
• Marta E. R. Dotto,
• Juliana Eccher,
• Leonardo N. Furini,
• Hugo Gallardo,
• Harald Bock and
• Ivan H. Bechtold

Beilstein J. Org. Chem. 2023, 19, 1755–1765, doi:10.3762/bjoc.19.128

• positive and negative charge carrier transport of 1 and 2. The active layers of 1 or 2 were spin-coated from chloroform solutions (10 mg/mL). Scheme S1 in Supporting Information File 1 illustrates the device structure with the energy levels of the layers. Figure 5 shows atomic force microscopy (AFM) images

• the analysis procedure. AFM measurements of the organic films were performed using a Nanosurf EasyScan2 apparatus in tapping mode with a scanning rate of 1.0 Hz covering 512 × 512 lines. Hole-only devices were fabricated using indium tin oxide (ITO) coated glass plates (sheet resistance of about 15 Ω

• absorption. AFM images of spin-coated films of compound 1 (a, c) and compound 2 (b, d) on PEDOT:PSS (a, b) and Al (c, d). Log–log plot of the J–V curves of the hole-only (a,b) and electron-only (c,d) of 1 (a,c) and 2 (b,d). The open circles are the experimental data, and the red solid lines indicate the

Constrained thermoresponsive polymers – new insights into fundamentals and applications

• Patricia Flemming,
• Alexander S. Münch,
• Andreas Fery and
• Petra Uhlmann

Beilstein J. Org. Chem. 2021, 17, 2123–2163, doi:10.3762/bjoc.17.138

Progress and challenges in the synthesis of sequence controlled polysaccharides

• Giulio Fittolani,
• Theodore Tyrikos-Ergas,
• Denisa Vargová,
• Manishkumar A. Chaube and
• Martina Delbianco

Beilstein J. Org. Chem. 2021, 17, 1981–2025, doi:10.3762/bjoc.17.129

• ]. Mono- or multi-fluorinated compounds were obtained in good yields (30–47%) with average DPs ranging from 9 to 15. The multifluorinated compound crystallized in a new cellulose allomorph. AFM and TEM images confirmed the formation of long platelets for monofluorinated compounds, similar to those

Multiswitchable photoacid–hydroxyflavylium–polyelectrolyte nano-assemblies

• Alexander Zika and
• Franziska Gröhn

Beilstein J. Org. Chem. 2021, 17, 166–185, doi:10.3762/bjoc.17.17

• also studied by AFM. For this, assembly solutions where drop cast on mica surfaces. The results are given in Figure 6 and overall they are in agreement with the DLS results. To compare the sizes of the assemblies quantitatively, the volumes of the nanoparticles measured by AFM on the surfaces are

• calculated, converted into a hypothetical radius of a volume-equivalent spherical particle, and compared to the hydrodynamic radii from DLS. The average radii calculated from the AFM volumes are given in Table 3 and Table 4. As can be seen the relative size changes are very similar to the ones observed in

• DLS and again show the reversibility of both cycles. As reported for other systems, the structures in AFM are substantially smaller than in DLS due to the shrinking upon drying in the AFM sample preparation [40][60][83][84][85]. Further, the ζ-potential was determined to understand the changes in the

Control over size, shape, and photonics of self-assembled organic nanocrystals

• Chen Shahar,
• Yaron Tidhar,
• Yunmin Jung,
• Haim Weissman,
• Sidney R. Cohen,
• Ronit Bitton,
• Iddo Pinkas,
• Gilad Haran and
• Boris Rybtchinski

Beilstein J. Org. Chem. 2021, 17, 42–51, doi:10.3762/bjoc.17.5

• stripes correspond to the overlapping aromatic cores (1.1 nm), and the light-contrast stripes correspond to the ethylpropyl residues (0.6 nm), as observed in the cryo-TEM images (Figure 3A and Figure 3B). In order to validate the bilayer width of the nanocrystals, atomic force microscopy (AFM) and SAXS

• molecular modeling and the AFM results. The presented crystalline structures are kinetically trapped products since they do not equilibrate upon changing the assembly conditions after they are fully formed. Thus, the addition of THF to preassembled 5%→0% THF crystals up to a 5% THF content did not result in

Selected peptide-based fluorescent probes for biological applications

• Debabrata Maity

Beilstein J. Org. Chem. 2020, 16, 2971–2982, doi:10.3762/bjoc.16.247

• fluorescent intensity except bovine serum albumin (BSA), which leads to a small enhancement. The size of the spherical self-assembled liposomes increases upon LPS binding, confirmed by DLS and AFM studies. Finally, PDA liposomes are utilized for fluorescence staining of the membrane of E. coli bacteria

Dirhamnolipid ester – formation of reverse wormlike micelles in a binary (primerless) system

• David Liese,
• Hans Henning Wenk,
• Xin Lu,
• Jochen Kleinen and
• Gebhard Haberhauer

Beilstein J. Org. Chem. 2020, 16, 2820–2830, doi:10.3762/bjoc.16.232

• strongly interacts with the sample. When heating to 60 °C, the material becomes liquid and the order in the structure is lost. This leads to an optical isotropic medium, yielding only a dark background. Also, atomic force microscopy (AFM) height images were taken for the dirhamnolipid ethyl ester 2/toluene

• camera. Atomic force microscopy Atomic force microscopy (AFM) images were performed in the tapping mode using a NanoDrive Controller with an Innova Scanning Probe Microscope (Veeco) and an N-type silicon cantilever (Olympus AC 16TS). The samples were prepared by drop-coating the solution (50 µM) on a

• freshly cleaned mica surface (Plano) and waiting for 12 h. The AFM data were analyzed using the Gwyddion-2.53 software. Rheological measurements The rheological data were obtained using an Anton Paar MCR 301 rheometer equipped with a cylindrical geometry (CC27 – measuring unit). The temperature was

Naphthalene diimide bis-guanidinio-carbonyl-pyrrole as a pH-switchable threading DNA intercalator

• Poulami Jana,
• Filip Šupljika,
• Carsten Schmuck and
• Ivo Piantanida

Beilstein J. Org. Chem. 2020, 16, 2201–2211, doi:10.3762/bjoc.16.185

• the DNA/RNA conjugate NDI-GCP2 showed also aggregation along the ds-polynucleotide and AFM and DLS demonstrated that NDI-GCP2 has pronounced ds-DNA condensation ability. Keywords: AFM; circular dichroism; DNA/RNA recognition; fluorescence; guanidinio-carbonyl-pyrrole; naphthalene diimide

• , usually also cause DNA condensation, as we have shown previously for some GCP analogues [16]. Thus, we performed AFM (Figure 6) and DLS experiments (Figure S25, Supporting Information File 1) at conditions of excess of 4 over ct-DNA. The AFM images clearly showed that the elongated structure of the free

• , as was demonstrated by AFM and DLS results. Since agents that efficiently condense DNA are often employed for cell-transfection purposes, in future prospects of the here presented results we plan to pursue this application as we have shown previously for some GCP analogues [33]. Experimental General

pH- and concentration-dependent supramolecular self-assembly of a naturally occurring octapeptide

• Goutam Ghosh and
• Gustavo Fernández

Beilstein J. Org. Chem. 2020, 16, 2017–2025, doi:10.3762/bjoc.16.168

• fractal-like morphologies, as verified by circular dichroism (CD), Fourier-transform infrared (FTIR) spectroscopy, thioflavin T (ThT) fluorescence spectroscopy assay, and atomic force microscopy (AFM). Upon changing the pH value (using pH 5.5 and 13.0), PEP-1 forms different types of secondary structures

• with PEP-1 (Figure 1c), confirming the formation of a β-sheet structure and supporting the results obtained from CD and FTIR spectroscopy. Microscopic studies by AFM revealed the formation of fractal-like structures (Figure 2a and Figure 2c) of several micrometers in length along with discrete short

• acids, such as two Arg (containing free amine groups) and two Glu residues (containing free acids) prompted us to investigate the effect of the pH value on the self-assembly and secondary structures. For this, we performed CD and AFM (Figure 3 and Figure S4, Supporting Information File 1) both in acidic

Application of olefin metathesis in the synthesis of functionalized polyhedral oligomeric silsesquioxanes (POSS) and POSS-containing polymeric materials

• Patrycja Żak and
• Cezary Pietraszuk

Beilstein J. Org. Chem. 2019, 15, 310–332, doi:10.3762/bjoc.15.28

• of polymers and copolymers with 3-(trifluoromethyl)phenyl-7-oxanorbornene-5,6-dicarboximide (Scheme 25) [48]. It was found that the increase in the content of POSS units in the copolymer results in a decrease in thermal stability and Tg values. TEM and AFM microimages show spherical POSS aggregates

Functionalization of graphene: does the organic chemistry matter?

• Artur Kasprzak,
• Agnieszka Zuchowska and
• Magdalena Poplawska

Beilstein J. Org. Chem. 2018, 14, 2018–2026, doi:10.3762/bjoc.14.177

• for functionalized GO: 1639 cm−1). This unexpected statement was supported, not by further spectroscopic analyses, but by morphological studies (transmission electron microscopy (TEM) and atomic force microscopy (AFM)) only. Once again, the possible electrostatic adsorption or hydrogen bonding

Natural and redesigned wasp venom peptides with selective antitumoral activity

• Marcelo D. T. Torres,
• Gislaine P. Andrade,
• Roseli H. Sato,
• Cibele N. Pedron,
• Tania M. Manieri,
• Giselle Cerchiaro,
• Anderson O. Ribeiro,
• Cesar de la Fuente-Nunez and
• Vani X. Oliveira Jr.

Beilstein J. Org. Chem. 2018, 14, 1693–1703, doi:10.3762/bjoc.14.144

• low as 12.5 μmol L−1 for the selective targeting of MCF-7 breast cancer cells. Flow cytometry assays further revealed that treatment with wild-type (WT) peptide Dec-NH2 led to necrosis of MCF-7 cells. Additional atomic force microscopy (AFM) measurements indicated that the roughness of cancer cell

• was increased to 50 μmol L−1. This is consistent with the MTT assay results obtained with the same peptide (Figure 2), indicating that Dec-NH2 triggers membrane disruption thus leading to cell death and necrosis of cancer cells. AFM measurements AFM was used to quantify the cellular structure (i.e

• ,E). Our data indicates that peptide treatment leading to membrane disruption and subsequent cell death is associated with changes in the membrane of cancer cells, specifically, greater roughness. The AFM results are in line with the activity of the peptides obtained in MTT assays, which highlights

Polarization spectroscopy methods in the determination of interactions of small molecules with nucleic acids – tutorial

• Tamara Šmidlehner,
• Ivo Piantanida and
• Gennaro Pescitelli

Beilstein J. Org. Chem. 2018, 14, 84–105, doi:10.3762/bjoc.14.5

• chiroptical properties and will not be discussed here, but if a similar signal is obtained, it is advisable to refer to a set of methods dealing with DNA condensation (AFM, DLS). 4. Linear dichroism, LD Circular and linear dichroism spectroscopy (ECD and LD) are often used as complementary tools for the

BODIPY-based fluorescent liposomes with sesquiterpene lactone trilobolide

• Ludmila Škorpilová,
• Silvie Rimpelová,
• Michal Jurášek,
• Miloš Buděšínský,
• Jana Lokajová,
• Roman Effenberg,
• Petr Slepička,
• Tomáš Ruml,
• Eva Kmoníčková,
• Pavel B. Drašar and
• Zdeněk Wimmer

Beilstein J. Org. Chem. 2017, 13, 1316–1324, doi:10.3762/bjoc.13.128

• the prepared liposomes with incorporated construct 6 was performed by atomic force microscopy (AFM) analysis in a tapping mode in 2D and 3D arrangement, see Figure 4 (Supporting Information File 1, section 3). We confirmed the successful preparation of liposomes, the average size of which was 150 nm

• in width and 30 nm in height. The larger dimension of the liposomes in width, than expected, was probably caused by their adhesion to the glass surface, which was on the other hand necessary in order to perform the AFM analysis. The values of average roughness described in the Figure 4 for both (2

Aggregation behaviour of a single-chain, phenylene-modified bolalipid and its miscibility with classical phospholipids

• Simon Drescher,
• Vasil M. Garamus,
• Christopher J. Garvey,
• Annette Meister and
• Alfred Blume

Beilstein J. Org. Chem. 2017, 13, 995–1007, doi:10.3762/bjoc.13.99

• side by side within the fibrous aggregate but slightly twisted relative to each other leading to a helical super structure of the fibres. This helicity was previously confirmed by cryo-transmission electron microscopy (cryo-TEM), high resolution atomic force microscopy (AFM) [26], and Monte Carlo

Interactions between shape-persistent macromolecules as probed by AFM

• Johanna Blass,
• Jessica Brunke,
• Franziska Emmerich,
• Cédric Przybylski,
• Vasil M. Garamus,
• Artem Feoktystov,
• Roland Bennewitz,
• Gerhard Wenz and
• Marcel Albrecht

Beilstein J. Org. Chem. 2017, 13, 938–951, doi:10.3762/bjoc.13.95

• measurements. Small-angle neutron and X-ray (SANS/SAXS) scattering experiments confirm the stiffness of the polymer chains with an apparent contour length of about 130 Å. Surface modification of planar silicon wafers as well as AFM tips was realized by covalent bound formation between the terminal amino groups

• configuration of the CD moieties. Depending on the geometrical configuration of attachment anisotropic adhesion characteristics of the polymer system can be distinguished between a peeling and a shearing mechanism. Keywords: AFM; cyclodextrin; inclusion complexes; molecular recognition; polyconjugated polymers

• spectroscopy, quartz crystal microbalance (QCM), surface plasmon resonance (SPR) and atomic force microscopy (AFM) have been employed to quantify the strength of the multivalent interactions [8]. Because binding affinities can be very high for multivalent supramolecular systems, the constituents are commonly

Molecular-level architectural design using benzothiadiazole-based polymers for photovoltaic applications

• Vinila N. Viswanathan,
• Arun D. Rao,
• Upendra K. Pandey,
• Arul Varman Kesavan and
• Praveen C. Ramamurthy

Beilstein J. Org. Chem. 2017, 13, 863–873, doi:10.3762/bjoc.13.87

• planarity of the molecules. To understand the photovoltaic results, we have also investigated the morphology of the active layers of the devices by tapping mode AFM. With this method, information about the topography as well as phase images as shown in Figure S2 (Supporting Information File 1) can be

Fluorescent carbon dots from mono- and polysaccharides: synthesis, properties and applications

• Stephen Hill and
• M. Carmen Galan

Beilstein J. Org. Chem. 2017, 13, 675–693, doi:10.3762/bjoc.13.67

• reaction, a foam was produced which resulted in green-emissive N,P-doped CDs that were hollow and had a diameter of 10 nm as determined by HRTEM and AFM. Despite the hollowness of the CDs, the nanoparticles exhibit an excitation-dependent emission profile akin to other glucose-derived, bottom-up

• conditions (90 °C) for 2 h (Scheme 24) [61]. It was demonstrated that the presence of phosphoric acid was crucial for the formation of fluorescent CDs, as the control reaction, in the absence of acid, did not produce emissive CDs. AFM and TEM indicated quasi-spherical CDs of 2–4 nm, while FTIR and XPS

• negatively-charged polysaccharide, and shown by AFM, DLS and TEM, to have formed nano-aggregates of up to 250 nm. Interestingly, the emissive properties of the CDs were unchanged upon complexation to HA. The resultant nano-aggregates were then loaded with doxorubicin (DOX) and a strong correlation between

Fast and efficient synthesis of microporous polymer nanomembranes via light-induced click reaction

• Qi An,
• Youssef Hassan,
• Xiaotong Yan,
• Peter Krolla-Sidenstein,
• Tawheed Mohammed,
• Mathias Lang,
• Stefan Bräse and
• Manuel Tsotsalas

Beilstein J. Org. Chem. 2017, 13, 558–563, doi:10.3762/bjoc.13.54

• (methyl methacrylate) (PMMA). Upon substrate dissolution, we transferred the PMMA stabilized CMP thin film to a fresh gold substrate. After drying, we dissolved the PMMA layer in acetone, leaving only the CMP thin film. We then investigated the thickness of the film by an atomic force microscope (AFM

• ) line scan along the edge of the film. Figure 3 shows the AFM image and the line-scan across the edge of the CMP thin film. The AFM investigation also suggests a homogeneous thickness of the CMP thin film and the line-scan across the edge confirms a thickness of roughly 20 nm after 20 reaction cycles

• CMP nanomembrane. Conclusion We described a new synthesis of CMP thin films and nanomembranes using a thiol–yne coupling (TYC) reaction. The TYC reaction allows a rapid synthesis of homogeneous thin films with a thickness of about 1 nm per reaction cycle as confirmed by ellipsometry and AFM