Orthogonal photoswitching of heterobivalent azobenzene glycoclusters: the effect of glycoligand orientation in bacterial adhesion

• Leon M. Friedrich and
• Thisbe K. Lindhorst

Beilstein J. Org. Chem. 2025, 21, 736–748, doi:10.3762/bjoc.21.57

• simulation (MD) [54] over 10 ns to determine the relative stability of the complexes (Supporting Information File 1, Figure S17 and Figure S18). The most stable receptor–ligand complexes so obtained were then submitted to a MM-GBSA calculation to deliver IFD binding energies (Table 3 and Supporting

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

Computational toolbox for the analysis of protein–glycan interactions

• Ferran Nieto-Fabregat,
• Maria Pia Lenza,
• Angela Marseglia,
• Cristina Di Carluccio,
• Antonio Molinaro,
• Alba Silipo and
• Roberta Marchetti

Beilstein J. Org. Chem. 2024, 20, 2084–2107, doi:10.3762/bjoc.20.180

• –ligand complexes, and analyse MD outcomes. Moreover, selected case studies have been reported to highlight the importance of computational tools in studying protein–glycan systems, revealing the capability of these tools to provide valuable insights into the binding kinetics, energetics, and structural

• determinants that govern specific molecular interactions. Keywords: computational tools; glycan–protein interactions; MD; molecular recognition; Review Introduction Carbohydrates also referred to as saccharides, sugars, or glycans, constitute one of the main building blocks of biomolecules, alongside lipids

• glycans [42] and in the early 1990s on complex type glycans [43], great steps forward have been made in the computational analysis of complex carbohydrates. The advancement of computing power, the emergence of GPUs, and specialised processors accelerated MD simulations making it a key scientific tool to

Synthesis of cyclic β-1,6-oligosaccharides from glucosamine monomers by electrochemical polyglycosylation

• Md Azadur Rahman,
• Hirofumi Endo,
• Takashi Yamamoto,
• Shoma Okushiba,
• Norihiko Sasaki and
• Toshiki Nokami

Beilstein J. Org. Chem. 2024, 20, 1421–1427, doi:10.3762/bjoc.20.124

• Md Azadur Rahman Hirofumi Endo Takashi Yamamoto Shoma Okushiba Norihiko Sasaki Toshiki Nokami Department of Chemistry and Biotechnology, Tottori University, 4-101 Koyamacho-minami, Tottori city, 680-8552 Tottori, Japan Center for Research on Green Sustainable Chemistry, Faculty of Engineering

• of compound 6a. The contents of this paper have been published by Md Azadur Rahman as a Ph.D. thesis at Tottori University in 2023. Funding The authors acknowledge financial support by the Grant-in-Aid for Scientific Research (JP23H01961 and JP22KK0078).

A new analog of dihydroxybenzoic acid from Saccharopolyspora sp. KR21-0001

• Rattiya Janthanom,
• Yuta Kikuchi,
• Hiroki Kanto,
• Tomoyasu Hirose,
• Arisu Tahara,
• Takahiro Ishii,
• Arinthip Thamchaipenet and
• Yuki Inahashi

Beilstein J. Org. Chem. 2024, 20, 497–503, doi:10.3762/bjoc.20.44

• %, 40%, 50%, 60%, 80%, and 100%) with 0.05% FA. The 20% fraction was purified by HPLC (Shimadzu, Columbia, MD, U.S.A.) with an ODS column (Pegasil ODS SP100, 20 i.d. × 250 mm) at a flow rate of 7 mL·min−1 and eluted with 20% MeOH with 0.05% FA (Scheme 1). The fraction with a retention time of 64.5 min

Spatial arrangements of cyclodextrin host–guest complexes in solution studied by ¹³C NMR and molecular modelling

• Konstantin Lebedinskiy,
• Ivan Barvík,
• Zdeněk Tošner,
• Ivana Císařová,
• Jindřich Jindřich and
• Radim Hrdina

Beilstein J. Org. Chem. 2024, 20, 331–335, doi:10.3762/bjoc.20.33

• ten classical molecular dynamics (MD) simulations [16] (each lasting 100 ns, Figure 3). Then, we superimposed α-CD structures from different snapshots of each MD run. Further, the 3D densities, showing the spatial distribution of prochiral atoms of ligands (that rotate and wobble towards α-CD), were

• compound 4, we were thus able to select representative conformations of the guest molecule in all types of cyclodextrins (Figure 5) using the spatial densities gained from classical MD simulations. Compounds 1–8 (as hydrochloride salts or free bases), were attempted to co-crystallize with α-, β- and γ

• . The 3D densities show the spatial distribution of prochiral atoms within MD simulations. Studied host–guest complexes and splitting of guests’ prochiral carbons in their 13C NMR spectra. Molecular modelling of the host–guest complexes of compound 4 with α-CD, β-CD and γ-CD. X-ray analysis of the α-CD

Electron-beam-promoted fullerene dimerization in nanotubes: insights from DFT computations

• Laura Abella,
• Gerard Novell-Leruth,
• Josep M. Ricart,
• Josep M. Poblet and
• Antonio Rodríguez-Fortea

Beilstein J. Org. Chem. 2024, 20, 92–100, doi:10.3762/bjoc.20.10

• the subsequent irreversible C–C fusions occurring in phase 2 are proposed with the help of accelerated Car–Parrinello MD simulations. Results and Discussion Nanotube-C60 interaction: stabilization of the peapod First, we estimated the size of the stabilizing interaction that holds the peapod, that is

Multi-redox indenofluorene chromophores incorporating dithiafulvene donor and ene/enediyne acceptor units

• Christina Schøttler,
• Kasper Lund-Rasmussen,
• Line Broløs,
• Philip Vinterberg,
• Ema Bazikova,
• Viktor B. R. Pedersen and
• Mogens Brøndsted Nielsen

Beilstein J. Org. Chem. 2024, 20, 59–73, doi:10.3762/bjoc.20.8

• molecular sieves, or by drying over 3 Å molecular sieves. All remaining anhydrous solvents were obtained from a solvent drying tower (IT model PS-MD-05). HPLC grade solvents were used unless otherwise specified. Purification by chromatography was performed using silica gel (flash: 40–63 μm, Sepacore® Flash

Studying specificity in protein–glycosaminoglycan recognition with umbrella sampling

• Mateusz Marcisz,
• Sebastian Anila,
• Margrethe Gaardløs,
• Martin Zacharias and
• Sergey A. Samsonov

Beilstein J. Org. Chem. 2023, 19, 1933–1946, doi:10.3762/bjoc.19.144

• explanation and prediction of GAG specificity [35]. Computational methodologies like molecular docking and molecular dynamics (MD) have proven to be successful in modelling protein–GAG interactions, particularly examining the fundamental questions related to these interactions such as their specificity, the

• multipose character of GAG binding and the polarity of the binding poses of these periodic molecules. In the present work, all-atom MD simulations are conducted to study the dynamics of the protein–GAG complexes, and are complemented by free energy analysis. The free energy analysis of the protein–GAG

• sulfate-6 was added to the reducing end of the GAG. The starting binding mode for the cathepsin K complex with chondroitin sulfate corresponded to the 3CE9 complex. Literature data for the sulfate groups [38] and GLYCAM06 [39] force field parameters were used for GAGs in the subsequent MD simulations. A

Unraveling the role of prenyl side-chain interactions in stabilizing the secondary carbocation in the biosynthesis of variexenol B

• Moe Nakano,
• Rintaro Gemma and
• Hajime Sato

Beilstein J. Org. Chem. 2023, 19, 1503–1510, doi:10.3762/bjoc.19.107

• , computational chemistry including DFT [5][6][7][8][9], QM/MM [10][11][12][13][14][15][16] and QM/MM MD [14][15][16][17] calculations have been used for the biosynthetic studies of terpene/terpenoids [18]. Terpene-forming reactions, which involve various types of carbocation species stabilized by

Phenanthridine–pyrene conjugates as fluorescent probes for DNA/RNA and an inactive mutant of dipeptidyl peptidase enzyme

• Josipa Matić,
• Tana Tandarić,
• Marijana Radić Stojković,
• Filip Šupljika,
• Zrinka Karačić,
• Ana Tomašić Paić,
• Lucija Horvat,
• Robert Vianello and
• Lidija-Marija Tumir

Beilstein J. Org. Chem. 2023, 19, 550–565, doi:10.3762/bjoc.19.40

• molecular dynamics (MD) simulations of different protonation forms of Phen-Py-1 and Phen-Py-2 placed in explicit water solvation, and analyzed structural preferences in the obtained trajectories. In setting up our simulations, we prepared the geometries of unionized Phen-Py-1 and Phen-Py-2 and their

• (MD) simulations were performed employing standard generalized AMBER force fields (ff14SB [49] and GAFF [50]) as implemented within the AMBER16 program package [51]. All structures were subsequently solvated in a truncated octahedral box of TIP3P water molecules spanning a 10 Å thick buffer of solvent

• molecules around each system, and submitted to periodic simulations where the excess positive charge was neutralized with an equivalent number of chloride anions in monoprotonated systems corresponding to pH 5. Upon gradual heating from 0 K, MD simulations were performed at 300 K for a period of 300 ns

Discrimination of β-cyclodextrin/hazelnut (Corylus avellana L.) oil/flavonoid glycoside and flavonolignan ternary complexes by Fourier-transform infrared spectroscopy coupled with principal component analysis

• Nicoleta G. Hădărugă,
• Gabriela Popescu,
• Dina Gligor (Pane),
• Cristina L. Mitroi,
• Sorin M. Stanciu and
• Daniel Ioan Hădărugă

Beilstein J. Org. Chem. 2023, 19, 380–398, doi:10.3762/bjoc.19.30

• MS identification was performed with the NIST Mass Spectral Search Program for the NIST/EPA/NIH Mass Spectral Library 2.0 (Gaithersburg, MD, USA). Determinations were performed in duplicate and the main findings reveal a high oleic acid relative content (as methyl ester) of 69.91(± 4.14) % at a RI of

Synthesis of (−)-halichonic acid and (−)-halichonic acid B

• Keith P. Reber and
• Emma L. Niner

Beilstein J. Org. Chem. 2022, 18, 1629–1635, doi:10.3762/bjoc.18.174

• Keith P. Reber Emma L. Niner Department of Chemistry, Towson University, 8000 York Road, Towson, MD, 21252, USA 10.3762/bjoc.18.174 Abstract The first syntheses of the amino acids (–)-halichonic acid and (–)-halichonic acid B have been achieved in ten steps starting from commercially available

Computational model predicts protein binding sites of a luminescent ligand equipped with guanidiniocarbonyl-pyrrole groups

• Neda Rafieiolhosseini,
• Matthias Killa,
• Thorben Neumann,
• Niklas Tötsch,
• Jean-Noël Grad,
• Alexander Höing,
• Thies Dirksmeyer,
• Jochen Niemeyer,
• Christian Ottmann,
• Shirley K. Knauer,
• Michael Giese,
• Jens Voskuhl and
• Daniel Hoffmann

Beilstein J. Org. Chem. 2022, 18, 1322–1331, doi:10.3762/bjoc.18.137

• functional protein–protein binding. One theoretical option to identify putative binding sites of compound 1 on 14-3-3ζ would be by all-atom molecular dynamics (MD) simulations. However, as numerous studies have shown [21][22][23], the resources needed for a suitable sampling of such flexible systems by MD

Synthesis of protected precursors of chitin oligosaccharides by electrochemical polyglycosylation of thioglycosides

• Md Azadur Rahman,
• Kana Kuroda,
• Hirofumi Endo,
• Norihiko Sasaki,
• Tomoaki Hamada,
• Hiraku Sakai and
• Toshiki Nokami

Beilstein J. Org. Chem. 2022, 18, 1133–1139, doi:10.3762/bjoc.18.117

• Md Azadur Rahman Kana Kuroda Hirofumi Endo Norihiko Sasaki Tomoaki Hamada Hiraku Sakai Toshiki Nokami Department of Chemistry and Biotechnology, Tottori University, 4-101 Koyamacho-minami, Tottori City, 680-8552 Tottori, Japan Center for Research on Green Sustainable Chemistry, Faculty of

Terpenoids from Glechoma hederacea var. longituba and their biological activities

• Dong Hyun Kim,
• Song Lim Ham,
• Zahra Khan,
• Sun Yeou Kim,
• Sang Un Choi,
• Chung Sub Kim and
• Kang Ro Lee

Beilstein J. Org. Chem. 2022, 18, 555–566, doi:10.3762/bjoc.18.58

• a Jasco P-2000 polarimeter using methanol as solvent. High-resolution ESI mass spectrometer data were recorded on a Waters SYNAPT G2 mass spectrometer. ECD spectra were garnered with a JASCO J-1500 CD spectrometer (JASCO, Easton, MD, USA). The NMR spectra were recorded on a Bruker AVANCE III 700 NMR

Synthesis of 3,4,5-trisubstituted isoxazoles in water via a [3 + 2]-cycloaddition of nitrile oxides and 1,3-diketones, β-ketoesters, or β-ketoamides

• Md Imran Hossain,
• Md Imdadul H. Khan,
• Seong Jong Kim and
• Hoang V. Le

Beilstein J. Org. Chem. 2022, 18, 446–458, doi:10.3762/bjoc.18.47

• Md Imran Hossain Md Imdadul H. Khan Seong Jong Kim Hoang V. Le Department of BioMolecular Sciences and Research Institute of Pharmaceutical Sciences, School of Pharmacy, University of Mississippi, Mississippi 38677, USA Natural Products Utilization Research Unit, United States Department of

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

• 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

Phenolic constituents from twigs of Aleurites fordii and their biological activities

• Kyoung Jin Park,
• Won Se Suh,
• Da Hye Yoon,
• Chung Sub Kim,
• Sun Yeou Kim and
• Kang Ro Lee

Beilstein J. Org. Chem. 2021, 17, 2329–2339, doi:10.3762/bjoc.17.151

• were expressed as a percentage of the control group (untreated cells). Cytotoxicity assessment. The SRB assay was performed to evaluate cytotoxicity of all the isolated compounds against four cultured human cancer cell lines. The cell lines (National Cancer Institute, Bethesda, MD, USA) were used A549

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

• ]. The replacement of a single Glc unit with a Man unit was sufficient to disrupt this secondary structure and significantly increased the isolated yield of the final compounds. Molecular dynamic (MD) simulations predicted a compact helical conformation for the fully deprotected compound, confirmed by

• ][260]. The automated solid-phase approach required only two BBs with the amino group protected either with the N-TCA 79 or with the N-Cbz group 80 (Scheme 12). Compounds 81–85 served as standards to explore the conformational space of COS with different PA. NMR analysis and MD simulations revealed 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

• 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

Enhanced target cell specificity and uptake of lipid nanoparticles using RNA aptamers and peptides

• Roslyn M. Ray,
• Anders Højgaard Hansen,
• Maria Taskova,
• Bernhard Jandl,
• Jonas Hansen,
• Citra Soemardy,
• Kevin V. Morris and
• Kira Astakhova

Beilstein J. Org. Chem. 2021, 17, 891–907, doi:10.3762/bjoc.17.75

• changed to a low-supplement endothelial cell growth medium-2 (EGM-2) basal medium (Lonza Walkerville, MD) supplemented with 2.5% FBS, 0.55 µM hydrocortisone (Stemcell Technologies, Canada), 1% penicillin/streptomycin (Millipore Sigma, MA), and 10 mM 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid

Identification of volatiles from six marine Celeribacter strains

• Anuj Kumar Chhalodia,
• Jan Rinkel,
• Dorota Konvalinkova,
• Jörn Petersen and
• Jeroen S. Dickschat

Beilstein J. Org. Chem. 2021, 17, 420–430, doi:10.3762/bjoc.17.38

• CH2Cl2 (50 μL) and the extract was analyzed by GC–MS. GC–MS GC–MS analyses were carried out through a 7890B GC – 5977A MD system (Agilent, Santa Clara, CA, USA). The GC was equipped with a HP5-MS fused silica capillary column (30 m, 0.25 mm i.d., 0.50 μm film) and operated with the settings 1) inlet

Chemical constituents of Chaenomeles sinensis twigs and their biological activity

• Joon Min Cha,
• Dong Hyun Kim,
• Lalita Subedi,
• Zahra Khan,
• Sang Un Choi,
• Sun Yeou Kim and
• Chung Sub Kim

Beilstein J. Org. Chem. 2020, 16, 3078–3085, doi:10.3762/bjoc.16.257

• a JASCO P-1020 polarimeter (JASCO, Easton, MD, USA). The NMR studies were accomplished employing a Bruker AVANCE III 700 NMR spectrometer (Bruker, Karlsruhe, Germany) and the resultant spectra were processed using MestReNova (Mnova, version 14.1.2-25024) with default weighting functions. HRFABMS

Nocarimidazoles C and D, antimicrobial alkanoylimidazoles from a coral-derived actinomycete Kocuria sp.: application of ¹J_C,H coupling constants for the unequivocal determination of substituted imidazoles and stereochemical diversity of anteisoalkyl chains in microbial metabolites

• Md. Rokon Ul Karim,
• Enjuro Harunari,
• Amit Raj Sharma,
• Naoya Oku,
• Kazuaki Akasaka,
• Daisuke Urabe,
• Mada Triandala Sibero and
• Yasuhiro Igarashi

Beilstein J. Org. Chem. 2020, 16, 2719–2727, doi:10.3762/bjoc.16.222

• Md. Rokon Ul Karim Enjuro Harunari Amit Raj Sharma Naoya Oku Kazuaki Akasaka Daisuke Urabe Mada Triandala Sibero Yasuhiro Igarashi Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama 939-0398, Japan Shokei Gakuin University, 4