Heteroleptic metallosupramolecular aggregates/complexation for supramolecular catalysis

• Prodip Howlader and
• Michael Schmittel

Beilstein J. Org. Chem. 2022, 18, 597–630, doi:10.3762/bjoc.18.62

• of the cage/architecture depends on its dynamics: the catalytic activity will correlate with the rate of thermal motion. As illustrated below, there are presently two phenomena known where continuous nanomechanical motion influences the catalytic activity: a) Increasing nanomechanical speed reduces

• , thermodynamic stabilization quantitatively drives the reaction to the hetero-assembly 59, simply by mixing the components in the correct stoichiometric ratio (Figure 13). Various nanorotor assemblies are possible by this approach. The dynamics of the four-component rotor 59 = [Cu2(55)(57)(60)]2+ cannot be

Synthesis of a new water-soluble hexacarboxylated tribenzotriquinacene derivative and its competitive host–guest interaction for drug delivery

• Man-Ping Li,
• Nan Yang and
• Wen-Rong Xu

Beilstein J. Org. Chem. 2022, 18, 539–548, doi:10.3762/bjoc.18.56

• -rich cavity of TBTQ-CB6 [32]. In addition, the proton resonances became broadened caused by the complexation dynamics, indicating the successful host–guest complexation between TBTQ-CB6 and MV. Subsequently, the association stoichiometry of the complex was studied by the Job plot method using

• electron-rich cavity of TBTQ-CB6 exerts a shielding effect on DOX, i.e., DOX is located in the internal cavity of TBTQ-CB6. Furthermore, the proton signals were all significantly broadened as a result of the complexation dynamics, indicating the formation of a host–guest complex between TBTQ-CB6 and DOX

Peptide stapling by late-stage Suzuki–Miyaura cross-coupling

• Hendrik Gruß,
• Rebecca C. Feiner,
• Ridhiwan Mseya,
• David C. Schröder,
• Michał Jewgiński,
• Kristian M. Müller,
• Rafał Latajka,
• Antoine Marion and
• Norbert Sewald

Beilstein J. Org. Chem. 2022, 18, 1–12, doi:10.3762/bjoc.18.1

• its native binding partner β-catenin. An increased proteolytic stability against proteinase K has been demonstrated. Keywords: accelerated molecular dynamics; halotryptophan; intrinsically disordered peptides; late-stage diversification; macrocyclisation; molecular dynamics; stapled peptides; Suzuki

• cyclised RGD peptides. It could be proven that an isomerisation is not caused by the cross-coupling but by the presence of stable isomers/conformers. Molecular dynamics (MD) simulations verified the appearance of stable, distinct conformers or atropisomers, which were in accordance with the experimental

• . The conformational preferences of the stapled peptide P5 and of the linear peptides P6 and aAxWt were investigated via extensive accelerated molecular dynamics simulations (aMD) as implemented within the Amber18 program package [85]. The aMD methodology developed by McCammon and co-workers [86] has

GlycoBioinformatics

• Kiyoko F. Aoki-Kinoshita,
• Frédérique Lisacek,
• Niclas Karlsson,
• Daniel Kolarich and
• Nicolle H. Packer

Beilstein J. Org. Chem. 2021, 17, 2726–2728, doi:10.3762/bjoc.17.184

• article by Barnett et al. [2] uses molecular dynamics to show that O-linked glycosylation alters peptide conformation, which influences the binding of the peptides to antibodies, despite the fact that glycans are not directly involved in the binding. Another molecular modeling article by Fogarty et al. [3

• one of the authors of this article, Fadda, used glyco-adapted molecular dynamics to explain in a separate publication [4] how the COVID-19 spike protein recognition element requires N-linked glycosylation to be exposed. Another approach to understanding glyco-interactions is described in a review

(Phenylamino)pyrimidine-1,2,3-triazole derivatives as analogs of imatinib: searching for novel compounds against chronic myeloid leukemia

• Luiz Claudio Ferreira Pimentel,
• Lucas Villas Boas Hoelz,
• Henayle Fernandes Canzian,
• Frederico Silva Castelo Branco,
• Andressa Paula de Oliveira,
• Vinicius Rangel Campos,
• Floriano Paes Silva Júnior,
• Rafael Ferreira Dantas,
• Jackson Antônio Lamounier Camargos Resende,
• Anna Claudia Cunha,
• Nubia Boechat and
• Mônica Macedo Bastos

Beilstein J. Org. Chem. 2021, 17, 2260–2269, doi:10.3762/bjoc.17.144

• docking results were edited using the Visual Molecular Dynamics 1.9.3 (VMD) program (available for download at http://www.ks.uiuc.edu/Research/vmd/vmd-1.9.3/). Proposed structural modifications to obtain triazole derivatives 1a, b and 2a–j. Asymmetric unit representation of the 1,2,3-triazole derivative

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

• interactions in contrast to star-shaped polymers. Thus, in a polar solvent, such as water, the hydrophobic block forms an anhydrous core. The hydrophilic chains stretch into the solvent in the shape of a swollen corona (Figure 5). The size, shape and dynamics of the micelle can be essentially tuned by the

Double-headed nucleosides: Synthesis and applications

• Vineet Verma,
• Jyotirmoy Maity,
• Vipin K. Maikhuri,
• Ritika Sharma,
• Himal K. Ganguly and
• Ashok K. Prasad

Beilstein J. Org. Chem. 2021, 17, 1392–1439, doi:10.3762/bjoc.17.98

• . The analysis of the melting temperature of the duplex and extensive molecular dynamics studies revealed that the synthesized double-headed nucleotides behave as functional dinucleotide mimics and hybridize with complementary targets neatly with their Watson–Crick faces compatible with natural DNA [39

• that resulted in the formation of two novel nucleic acid motifs. The novel nucleic acid motifs could be incorporated either single or multiple times in dsDNA duplexes without altering its stability. It was revealed by molecular dynamics (MD) simulations that the DNA sugar–phosphate backbone

• strands. Oligonucleotides with fourteen consecutive incorporations of different double-headed nucleosides were synthesized and the DNA duplexes showed increased stability owing to increased stacking interactions among the nucleobases of the opposite strands [72]. Molecular dynamics simulations

Biochemistry of fluoroprolines: the prospect of making fluorine a bioelement

• Vladimir Kubyshkin,
• Rebecca Davis and
• Nediljko Budisa

Beilstein J. Org. Chem. 2021, 17, 439–460, doi:10.3762/bjoc.17.40

¹⁹F NMR as a tool in chemical biology

• Diana Gimenez,
• Aoife Phelan,
• Cormac D. Murphy and
• Steven L. Cobb

Beilstein J. Org. Chem. 2021, 17, 293–318, doi:10.3762/bjoc.17.28

• include the tags based on fluorinated phenylacetamides, such as the 2-bromo-N-(4-(trifluoromethyl)phenyl)acetamide (BTFMA, 19) and N-(4-bromo-3-(trifluoromethyl)phenyl)acetamide (3-BTFMA, 20) developed by Manglik et al. to study the structural dynamics of the cytoplasmic domain of the β2-adrenergic

• of which were consistent with those obtained in previous work but measured in cell membrane extracts [46]. Structural analysis of macromolecules using 19F NMR The three-dimensional (3D) structure of biomacromolecules and their conformational dynamics are often the starting point for the development

• probes, inherent to the side-chain dynamics within the protein hydrophobic interior [52][53][54]. 19F NMR has also been used to characterize in more detail the topography of the CAM conformational changes by using molecular contrast agents. 19F NMR solvent-induced isotope shift experiments, resulting

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

• , crystalline arrays ≈100 nm in length and ≈10 nm in width were observed after 1 min (Figure 4B). The structural differences between the 5% THF and 10% THF systems at early assembly times reveal the distinct dynamics of the nucleation and growth process. Thus, the 10% THF system shows a faster ordering process

• completed after 5 min (Figure S7, Supporting Information File 1). The observed crystallization pathways are consistent with a gradual order evolution mechanism recently observed by us [34]. Exciton dynamics In order to investigate whether the morphology affects the photonic properties, we studied the

• excited state dynamics of the nanocrystals. Femtosecond transient absorption spectra of all assemblies displayed typical PDI excited state absorption peaks in the range of 600–770 nm [50], matching PDI bleaching represented by negative features at 550–600 nm. In the disaggregated state, almost no power

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

• hydrophobic groups are oriented towards the solvent. One structure which can be formed by surfactants are so-called wormlike micelles, that are characterized by a high anisotropic structure. These micelles can, if the concentration and dynamics of the surfactant micelles is right, build viscosity since the

Synthesis of purines and adenines containing the hexafluoroisopropyl group

• Viacheslav Petrov,
• Rebecca J. Dooley,
• Alexander A. Marchione,
• Elizabeth L. Diaz,
• Brittany S. Clem and
• William Marshall

Beilstein J. Org. Chem. 2020, 16, 2739–2748, doi:10.3762/bjoc.16.224

• referenced to internal tetramethylsilane or trichlorofluoromethane. The spectra were acquired at 298 K. Dynamic NMR experiments The dynamics of rotamer interconversion were studied on a Bruker AVIIIHD spectrometer with a 9.4 T magnetic field, equipped with a 10 mm F{H} probe suitable for high- and low

Comparative ligand structural analytics illustrated on variably glycosylated MUC1 antigen–antibody binding

• Christopher B. Barnett,
• Tharindu Senapathi and
• Kevin J. Naidoo

Beilstein J. Org. Chem. 2020, 16, 2540–2550, doi:10.3762/bjoc.16.206

• approach by investigating the in-silico binding of a peptide and glycopeptide epitope of the glycoprotein Mucin 1 (MUC1) binding with the antibody AR20.5. To study the binding, we performed molecular dynamics simulations using OpenMM and then used the Galaxy platform for data analysis. The same analysis

• . and others [14][16] provides a foundation for further investigation into the binding of glycopeptide antigens to antibodies using computational modeling. Molecular dynamics (MD) simulations and analysis thereof are a well-known ingredient of the in-silico process for mechanistic screening of

• (physiological temperature). Missing amino acid residues were added. Energy minimization and MD (equilibration and production) simulations were performed using OpenMM [35] and the CHARMM36 force field [36] using the OpenCL platform with mixed precision. Equilibration and production dynamics were carried out as

Leveraging glycomics data in glycoprotein 3D structure validation with Privateer

• Haroldas Bagdonas,
• Daniel Ungar and
• Jon Agirre

Beilstein J. Org. Chem. 2020, 16, 2523–2533, doi:10.3762/bjoc.16.204

• study of these glycan-mediated interactions can provide unique insight into the molecular interplay governing these processes. In addition, it can provide structural snapshots in atomistic detail that can be used to generate molecular dynamics simulations describing a wider picture underpinning glycan

• /glycoproteomics to carbohydrate 3D model building and validation in Privateer Many fields, for example pharmaceutical design and engineering [58], molecular dynamics simulations [59] and protein interaction studies [60], rely upon structural biology to produce accurate atomistic descriptions of glycoproteins

NMR Spectroscopy of supramolecular chemistry on protein surfaces

• Peter Bayer,
• Anja Matena and
• Christine Beuck

Beilstein J. Org. Chem. 2020, 16, 2505–2522, doi:10.3762/bjoc.16.203

• as distance of targeted residues and their dynamics - must be taken into account. Supramolecular chemistry is ideally suited to address these challenges because it merges the knowledge of non-covalent molecular recognition with the possibility to combine multiple recognition units into one molecule

• [122][123], extend the possibility to monitor binding events to very large protein assemblies by NMR. It has mostly been used to investigate protein–protein interactions within large multi-protein assemblies [120][121] and the effect of small natural ligands like ATP or ADP on the dynamics of

Dawn of a new era in industrial photochemistry: the scale-up of micro- and mesostructured photoreactors

• Emine Kayahan,
• Mathias Jacobs,
• Leen Braeken,
• Leen C.J. Thomassen,
• Simon Kuhn,
• Tom van Gerven and
• M. Enis Leblebici

Beilstein J. Org. Chem. 2020, 16, 2484–2504, doi:10.3762/bjoc.16.202

• in the next section. Scaling up and energy efficiency Photoreactors cannot be scaled up by the conventional strategy of enlarging the dimensions due to the light attenuation effect. The heterogeneous flow dynamics and the light field complicate the design further. As a result, photochemical processes

Computational tools for drawing, building and displaying carbohydrates: a visual guide

• Kanhaya Lal,
• Rafael Bermeo and
• Serge Perez

Beilstein J. Org. Chem. 2020, 16, 2448–2468, doi:10.3762/bjoc.16.199

• , 3D representation of structures is provided by tools such as Visual Molecular Dynamics (VMD) [21] , and LiteMol [22], which allow for quick analysis of structural features in 3D space. All the tools mentioned were evaluated against a set of pre-selected criteria relating to ease of use, scientific

• models. These tools generally use 3D molecular templates of monosaccharides to reconstruct a 3D model. Energy minimisation methods can further refine the models. These models are essential for structure-based studies and complex calculations like Molecular Dynamics simulations. Therefore, the accurate

• various force fields dedicated for carbohydrates. The accurately predicted oligosaccharide conformations are good starting points for further investigations. Of particular interest are the evaluations of the dynamics of glycans and their interactions with proteins which is a most significant concern in

Design and synthesis of a bis-macrocyclic host and guests as building blocks for small molecular knots

• Elizabeth A. Margolis,
• Rebecca J. Keyes,
• Stephen D. Lockey IV and
• Edward E. Fenlon

Beilstein J. Org. Chem. 2020, 16, 2314–2321, doi:10.3762/bjoc.16.192

• spectrum at elevated temperature (e.g., 45, 90, 105 °C) had sharper peaks. This effect of temperature on the spectrum is consistent with restricted dynamics of the backbone such as reputation [30] or slow exchange between different conformers; however, both the trefoil knot and the macrocyclic unknot could

Isolation and structure determination of a tetrameric sulfonyl dilithio methandiide in solution based on crystal structure analysis and ⁶Li/¹³C NMR spectroscopic data

• Jürgen Vollhardt,
• Hans Jörg Lindner and
• Hans-Joachim Gais

Beilstein J. Org. Chem. 2020, 16, 2057–2063, doi:10.3762/bjoc.16.172

• and dynamics in solution [1][2][16][17][18][19][20][21][22][23][24][25][26][27][28][29][30][31][32][33][34][35][36][37][38][39][40][41][42][43]. The main obstacles at characterizing dilithio methandiides in terms of aggregate size, C–Li connectivity, Li coordination of the dianionic C atoms, and

• dynamics were poor solubility and problems to locate the 13C signals of the dianionic C atoms or the detection of only broad ones. Knowledge of the solution structure of dilithio methandiides would be, however, highly desirable in order to obtain a more complete understanding of the reactivity and

How and why plants and human N-glycans are different: Insight from molecular dynamics into the “glycoblocks” architecture of complex carbohydrates

• Carl A. Fogarty,
• Aoife M. Harbison,
• Amy R. Dugdale and
• Elisa Fadda

Beilstein J. Org. Chem. 2020, 16, 2046–2056, doi:10.3762/bjoc.16.171

• diversity generates a rich collection of structures, all diversely able to trigger molecular cascades and to activate pathways, which also include adverse immunogenic responses. These events are inherently linked to the N-glycans’ 3D architecture and dynamics, which remain for the large part unresolved and

• undetected because of their intrinsic structural disorder. In this work we use molecular dynamics (MD) simulations to provide insight into N-glycans’ 3D structure by analysing the effects of a set of very specific modifications found in plants and invertebrate N-glycans, which are immunogenic in humans. We

• relationships in complex carbohydrates, with important implications in glycoengineering design. Keywords: complex carbohydrates; fucose; glycoblocks; molecular dynamics; molecular recognition; N-glycans; xylose; Introduction Complex carbohydrates (or glycans) are an essential class of biomolecules, directly

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

• (Glu−) amino acids [73][74]. Mechanistic insights into the observed conformational transformation via molecular dynamics simulations are underway in our laboratory. Conclusion In summary, we synthesized a naturally occurring amphiphilic peptide fragment, PEP-1, from a β-sheet lectin protein, galectin-1

Synthesis, docking study and biological evaluation of ᴅ-fructofuranosyl and ᴅ-tagatofuranosyl sulfones as potential inhibitors of the mycobacterial galactan synthesis targeting the galactofuranosyltransferase GlfT2

• Marek Baráth,
• Jana Jakubčinová,
• Zuzana Konyariková,
• Stanislav Kozmon,
• Katarína Mikušová and
• Maroš Bella

Beilstein J. Org. Chem. 2020, 16, 1853–1862, doi:10.3762/bjoc.16.152

• mechanism studies using computational chemistry methods. The probable reaction mechanisms were studied by hybrid DFT QM/MM molecular dynamics simulations [11] where the possible transition state (TS) structures were localized. The observation of the possible TS structure opens the opportunities for the in

• structures. All fructofuranose and tagatofuranose derivatives were docked into the GlfT2 structure obtained by QM/MM molecular dynamics simulations, which representes the structure close to the transition state structure of the GlfT2 catalytic reaction. The best ten docking poses of each docked molecule were

Models of necessity

• Timothy Clark and
• Martin G. Hicks

Beilstein J. Org. Chem. 2020, 16, 1649–1661, doi:10.3762/bjoc.16.137

• today, high-level combinations of an accurate Hamiltonian to describe the structure and energy and adequate sampling of the dynamics of the system are extremely rare. Atoms, bonds and molecules Although there are no atoms or bonds in molecules, there have been many attempts to construct Lewis-like

• become apparent [40]. This is because non-equilibrium structures such as transition states that cannot be described by the conventional Lewis model are passed through during reactions. Quantum chemical methods, often in combination with molecular dynamics, can predict the course of a specific reaction

Heterogeneous photocatalysis in flow chemical reactors

• Christopher G. Thomson,
• Ai-Lan Lee and
• Filipe Vilela

Beilstein J. Org. Chem. 2020, 16, 1495–1549, doi:10.3762/bjoc.16.125

• (HER). The FSO-FS polymer displayed the highest rates of hydrogen evolution (170 μmol⋅h−1), significantly higher than its structural isomer FSO-FSz. The authors studied the charge transfer dynamics of the different polymers through temperature-dependent photoluminescence, photoelectrochemical

• complimentary functional group. As the immobilised photocatalyst is generally non-conjugated to the support, its photophysical properties are generally unaltered from the homogeneous equivalent, and the complex semiconductor charge dynamics are avoided. Alternatively, semiconductor supports can be used that can

Disposable cartridge concept for the on-demand synthesis of turbo Grignards, Knochel–Hauser amides, and magnesium alkoxides

• Mateo Berton,
• Kevin Sheehan,
• Andrea Adamo and
• D. Tyler McQuade

Beilstein J. Org. Chem. 2020, 16, 1343–1356, doi:10.3762/bjoc.16.115

• flow rate produced by propane released during the reaction, and thus affecting the fluid dynamics and the back-pressure control. The product purities, a quantitative iPrCl conversion, and the yields were confirmed by NMR (Section 5, Supporting Information File 1), demonstrating the ODR prototype