Tautomerism as primary signaling mechanism in metal sensing: the case of amide group

• Vera Deneva,
• Georgi Dobrikov,
• Aurelien Crochet,
• Daniela Nedeltcheva,
• Katharina M. Fromm and
• Liudmil Antonov

Beilstein J. Org. Chem. 2019, 15, 1898–1906, doi:10.3762/bjoc.15.185

• achieved only when R’ = NMe2 (Scheme 2). Theoretical modelling of structures 4 and 5 have also shown that only one of the carbonyl groups from the ionophore unit really participates in the capturing of the metal ion upon complexation. Therefore, the aim of the current article is to estimate theoretically

Functional panchromatic BODIPY dyes with near-infrared absorption: design, synthesis, characterization and use in dye-sensitized solar cells

• Quentin Huaulmé,
• Cyril Aumaitre,
• Outi Vilhelmiina Kontkanen,
• David Beljonne,
• Alexandra Sutter,
• Gilles Ulrich,
• Renaud Demadrille and
• Nicolas Leclerc

Beilstein J. Org. Chem. 2019, 15, 1758–1768, doi:10.3762/bjoc.15.169

• were computed by density functional theory modelling (DFT) and characterized through UV–vis spectroscopy and cyclic voltammetry (CV) measurements. Finally, we report preliminary results obtained using these functional dyes as photosensitizers in dye-sensitized solar cells (DSSCs). Keywords: boron

Water inside β-cyclodextrin cavity: amount, stability and mechanism of binding

• Stiliyana Pereva,
• Valya Nikolova,
• Silvia Angelova,
• Tony Spassov and
• Todor Dudev

Beilstein J. Org. Chem. 2019, 15, 1592–1600, doi:10.3762/bjoc.15.163

• experimental) approaches are sometimes conflicting and contradictory. There is no “standard” method to investigate the complexation behavior of CDs. Thus, in our study a computational quantum mechanical modelling method, namely density functional theory (DFT) was chosen to investigate the electronic structure

Synthesis and biological evaluation of truncated derivatives of abyssomicin C as antibacterial agents

• Leticia Monjas,
• Peter Fodran,
• Johanna Kollback,
• Carlo Cassani,
• Thomas Olsson,
• Maja Genheden,
• D. G. Joakim Larsson and
• Carl-Johan Wallentin

Beilstein J. Org. Chem. 2019, 15, 1468–1474, doi:10.3762/bjoc.15.147

• Supporting Information File 102: Experimental part (modelling and docking, synthesis and biological evaluation), and copies of NMR spectra. Acknowledgements The Olle Engkvist Byggmästare foundation, the Centre for Antibiotic Resistance Research at the University of Gothenburg (CARe) and the Swedish Research

2,3-Dibutoxynaphthalene-based tetralactam macrocycles for recognizing precious metal chloride complexes

• Li-Li Wang,
• Yi-Kuan Tu,
• Huan Yao and
• Wei Jiang

Beilstein J. Org. Chem. 2019, 15, 1460–1467, doi:10.3762/bjoc.15.146

• between the amide NH protons and the pyridine nitrogen atoms in 2, which pre-organizes the cavity for molecular recognition. How would this affect the binding affinity of 2? To answer this question, molecular modelling was performed. Only conformer I of 1 was used for the molecular modelling but both

Bambusuril analogs based on alternating glycoluril and xylylene units

• Tomáš Lízal and
• Vladimír Šindelář

Beilstein J. Org. Chem. 2019, 15, 1268–1274, doi:10.3762/bjoc.15.124

• characterized in the same manner as 1a. The molecular modelling showed that 1b also exists in two forms of conformers 1b-1, 1b-2 differing by the position of the glycoluril units (Figure 2). The NMR spectra (Supporting Information File 1, Figure S9) measured at low temperature featured two sets of signals

• the orientation of one glycoluril unit were obtained. The building blocks within the macrocycles connected via methylene bridges are flexible giving rise to two preferred conformers for each diastereomer. These conformers were identified by molecular modelling and also by low-temperature NMR

Understanding the unexpected effect of frequency on the kinetics of a covalent reaction under ball-milling conditions

• Ana M. Belenguer,
• Adam A. L. Michalchuk,
• Giulio I. Lampronti and
• Jeremy K. M. Sanders

Beilstein J. Org. Chem. 2019, 15, 1226–1235, doi:10.3762/bjoc.15.120

• not occur and that the two milling balls simultaneously impact the powder directly. This has a similar effect as simply modelling a milling ball with a larger surface area [38]. Double impacts, and ball–ball collisions are certainly important considerations for future development of this simple model

• ) can dominate subsequent stages of the transformation, as the probability of contact formation decreases. While further work is required to capture detailed mechanistic insight, we can suggest that kinetic modelling of covalent mechanochemical reactions likely requires a model that accounts for both

Extending mechanochemical porphyrin synthesis to bulkier aromatics: tetramesitylporphyrin

• Qiwen Su and
• Tamara D. Hamilton

Beilstein J. Org. Chem. 2019, 15, 1149–1153, doi:10.3762/bjoc.15.111

• catalysis [1], photovoltaics [2], photodynamic therapy [3][4], environmental remediation [5][6], biomimetic modelling [7] and metal-organic self-assembly [8]. Porphyrins may be substituted in the meso or β-positions (Figure 1A). Tetra-meso-substituted porphyrins are usually synthesized from simple starting

• -hindered” reagent, serving as a touchstone for the wider applicability of porphyrin reaction conditions [12]. Porphyrins with bulky groups in the meso-positions, especially aromatics with bulky substituents in the position ortho to the methine bridge, have been used for biological modelling. The large

Unexpected polymorphism during a catalyzed mechanochemical Knoevenagel condensation

• Sebastian Haferkamp,
• Andrea Paul,
• Adam A. L. Michalchuk and
• Franziska Emmerling

Beilstein J. Org. Chem. 2019, 15, 1141–1148, doi:10.3762/bjoc.15.110

• , using multivariate methods to analyze the reaction. Principal component analysis (PCA) is a bilinear modelling method [25][26] that helps to extract the main information from multi-dimensional data (here a time series of Raman spectra). The information contained within the original spectral variables is

Precious metal-free molecular machines for solar thermal energy storage

• Meglena I. Kandinska,
• Snejana M. Kitova,
• Vladimira S. Videva,
• Stanimir S. Stoyanov,
• Stanislava B. Yordanova,
• Stanislav B. Baluschev,
• Silvia E. Angelova and
• Aleksey A. Vasilev

Beilstein J. Org. Chem. 2019, 15, 1096–1106, doi:10.3762/bjoc.15.106

• density functional theory (DFT) calculations at the B3LYP/6-31+G(d,p) level. The first step in the molecular modelling investigation was the optimization of the molecular structures of the cis and trans isomers of dyes 4a–d (with the –(CH2)nSO3− (n = 3, 4) tails oriented to be in proximity to the aza-15

Stereo- and regioselective hydroboration of 1-exo-methylene pyranoses: discovery of aryltriazolylmethyl C-galactopyranosides as selective galectin-1 inhibitors

• Alexander Dahlqvist,
• Axel Furevi,
• Niklas Warlin,
• Hakon Leffler and
• Ulf J. Nilsson

Beilstein J. Org. Chem. 2019, 15, 1046–1060, doi:10.3762/bjoc.15.102

• reported to enhance affinity for galectin-1 [34] failed in our hands, why other additional substituents to combine with the 4-fluorophenyltriazolylmethyl moiety of compound 1b remain to be discovered. Molecular modelling In order to gain understanding of the affinity-enhancing effects of the aryltriazolyl

Azologization of serotonin 5-HT₃ receptor antagonists

• Karin Rustler,
• Galyna Maleeva,
• Piotr Bregestovski and
• Burkhard König

Beilstein J. Org. Chem. 2019, 15, 780–788, doi:10.3762/bjoc.15.74

• photochromic properties were synthesized but lost antagonistic activity probably due to their increased steric demand. In ongoing studies, detailed molecular modelling is used to design potential photochromic antagonists fitting the requirements of the receptor’s binding pocket. Regarding the analysis method

Dispersion-mediated steering of organic adsorbates on a precovered silicon surface

• Lisa Pecher,
• Sebastian Schmidt and
• Ralf Tonner

Beilstein J. Org. Chem. 2018, 14, 2715–2721, doi:10.3762/bjoc.14.249

• modelling that accounts for dispersion interactions plays an important role. Adsorption energy profile of a direct adsorption (black, e.g., cyclooctyne/Si(001)) in comparison with adsorption via an intermediate (grey, e.g., methanol/Ge(001)). On top, the dominant type of interaction in the different regimes

Nucleoside macrocycles formed by intramolecular click reaction: efficient cyclization of pyrimidine nucleosides decorated with 5'-azido residues and 5-octadiynyl side chains

• Jiang Liu,
• Peter Leonard,
• Sebastian L. Müller,
• Constantin Daniliuc and
• Frank Seela

Beilstein J. Org. Chem. 2018, 14, 2404–2410, doi:10.3762/bjoc.14.217

• macrocyclic systems [18][19][20][21][22][23][24][25]. DNA mimics with triazole linkages were constructed [26][27]. The click reaction was used to generate a cyclic ADP-ribose second messenger mimic [28]. Modelling studies using MM+ energy minimization showed that pyrimidine nucleosides are useful synthons for

Synthesis and photophysical studies of a multivalent photoreactive Ru^II-calix[4]arene complex bearing RGD-containing cyclopentapeptides

• Sofia Kajouj,
• Lionel Marcelis,
• Alice Mattiuzzi,
• Adrien Grassin,
• Damien Dufour,
• Pierre Van Antwerpen,
• Didier Boturyn,
• Eric Defrancq,
• Mathieu Surin,
• Julien De Winter,
• Pascal Gerbaux,
• Ivan Jabin and
• Cécile Moucheron

Beilstein J. Org. Chem. 2018, 14, 1758–1768, doi:10.3762/bjoc.14.150

• autocorrelation function were employed to judge the quality of the fits. For molecular modelling simulations, the initial structure of the ruthenium complex was obtained from previous DFT calculations using a previously reported methodology [82]. The geometries of the RAFTs and calixarene were built using DS

• BIOVIA© software and geometry-optimized using the CHARMM force-field, taking into account previous molecular modelling simulations on cyclic peptides [83]. The structures were linked together yielding through several steps of energy minimizations, maintaining the ruthenium complex constrained in

Phosphoramidite building blocks with protected nitroxides for the synthesis of spin-labeled DNA and RNA

• Timo Weinrich,
• Eva A. Jaumann,
• Ute M. Scheffer,
• Thomas F. Prisner and
• Michael W. Göbel

Beilstein J. Org. Chem. 2018, 14, 1563–1569, doi:10.3762/bjoc.14.133

• distance. The results for all PELDOR measurements are shown in Figure S21 (Supporting Information File 1). The experimental distances are summarized in Table 1 and coincide well with values predicted from modelling. However, although the degree of spin labeling was very high in all cases, large variations

• , 22 h; (e) N,N-diisopropylamino(2-cyanoethyl)phosphoramidic chloride, Et3N, CH2Cl2, rt, 23 h. Spin–spin distances in oligonucleotides 22c–27c determined by PELDOR and by molecular modelling. The predicted distance is an average of N–N, N–O, O–N, and O–O distances. Supporting Information Supporting

A three-armed cryptand with triazine and pyridine units: synthesis, structure and complexation with polycyclic aromatic compounds

• Claudia Lar,
• Adrian Woiczechowski-Pop,
• Attila Bende,
• Ioana Georgeta Grosu,
• Natalia Miklášová,
• Elena Bogdan,
• Niculina Daniela Hădade,
• Anamaria Terec and
• Ion Grosu

Beilstein J. Org. Chem. 2018, 14, 1370–1377, doi:10.3762/bjoc.14.115

• , Slovakia 10.3762/bjoc.14.115 Abstract The aromatic nucleophilic substitution reaction based synthesis of a three-armed cryptand displaying 2,4,6-triphenyl-1,3,5-triazine units as caps and pyridine rings in the bridges, along with NMR, MS and molecular modelling-based structural analysis of this compound

• are reported. Appropriate NMR and molecular modelling investigations proved the formation of 1:1 host–guest assemblies between the investigated cryptand and some polynuclear aromatic hydrocarbons or their derivatives. Keywords: aromatic guests; aromatic nucleophilic substitution; cryptand; NMR

• pyrene, anthracene and 1,5-dihydroxynaphthalene as guest molecules was investigated by NMR titration experiments and molecular modelling. The spectra recorded during the NMR titrations of cryptand 2 with increasing amounts of the named guests (ratio 1:9 to 9:1), revealed only one set of signals. However

Novel unit B cryptophycin analogues as payloads for targeted therapy

• Eduard Figueras,
• Adina Borbély,
• Mohamed Ismail,
• Marcel Frese and
• Norbert Sewald

Beilstein J. Org. Chem. 2018, 14, 1281–1286, doi:10.3762/bjoc.14.109

• activity of analogue 22 could be due to its poor internalization or the modification could alter the interaction with tubulin. In order to get an extensive knowledge of the novel analogues, we embarked in docking and modelling studies, herein reported, and internalization studies are ongoing in our

• research group. Docking and modelling of cryptophycin derivatives There is no X-ray analysis of cryptophycin–tubulin complexes available to provide information on the binding site. Based on biochemical evidence, binding close to the vinca-alkaloid binding site of β-tubulin, the so called “peptide-site

Are dispersion corrections accurate outside equilibrium? A case study on benzene

• Tim Gould,
• Erin R. Johnson and
• Sherif Abdulkader Tawfik

Beilstein J. Org. Chem. 2018, 14, 1181–1191, doi:10.3762/bjoc.14.99

• Technology Sydney, Ultimo, New South Wales 2007, Australia Institute for Biomedical Materials and Devices (IBMD), Faculty of Science, University of Technology Sydney, Sydney, NSW, Australia 10.3762/bjoc.14.99 Abstract Modern approaches to modelling dispersion forces are becoming increasingly accurate, and

Mechanochemistry of nucleosides, nucleotides and related materials

• Olga Eguaogie,
• Joseph S. Vyle,
• Patrick F. Conlon,
• Manuela A. Gîlea and
• Yipei Liang

Beilstein J. Org. Chem. 2018, 14, 955–970, doi:10.3762/bjoc.14.81

• mechanochemical bond activation are mainly based upon examination and/or modelling the behaviour of single molecules under tension in an atomic force microscope [24][25][26] and have included relating traditional Arrhenius reaction parameters to applied forces [27][28]. However, early models of macroscopic scale

Synthesis and in vitro biochemical evaluation of oxime bond-linked daunorubicin–GnRH-III conjugates developed for targeted drug delivery

• Sabine Schuster,
• Beáta Biri-Kovács,
• Bálint Szeder,
• Viktor Farkas,
• László Buday,
• Zsuzsanna Szabó,
• Gábor Halmos and
• Gábor Mező

Beilstein J. Org. Chem. 2018, 14, 756–771, doi:10.3762/bjoc.14.64

• , Hungary Research Centre for Natural Sciences, Institute of Enzymology, Hungarian Academy of Sciences, 1117 Budapest, Hungary MTA-ELTE Protein Modelling Research Group, Hungarian Academy of Sciences, Eötvös L. University, 1117 Budapest, Hungary Department of Biopharmacy, Faculty of Pharmacy, University of

Synthetic mRNA capping

• Fabian Muttach,
• Nils Muthmann and
• Andrea Rentmeister

Beilstein J. Org. Chem. 2017, 13, 2819–2832, doi:10.3762/bjoc.13.274

• compared to the standard cap. The cap analogue is exclusively incorporated in the correct (forward) orientation and molecular modelling studies pointed to a stronger binding of the propargyl-modified cap to eIF4E compared to the standard cap [65]. With regard to translational activity, several dinucleotide

Binding abilities of polyaminocyclodextrins: polarimetric investigations and biological assays

• Marco Russo,
• Daniele La Corte,
• Annalisa Pisciotta,
• Serena Riela,
• Rosa Alduina and
• Paolo Lo Meo

Beilstein J. Org. Chem. 2017, 13, 2751–2763, doi:10.3762/bjoc.13.271

• significantly affected. The latter consideration may also justify the possible formation of higher order host–guest aggregates with anionic guests mentioned previously. In fact, due to molecular size, modelling considerations rule out the accommodation of more than one guest unit into the host cavity. Thus, we

Hydrolysis, polarity, and conformational impact of C-terminal partially fluorinated ethyl esters in peptide models

• Vladimir Kubyshkin and
• Nediljko Budisa

Beilstein J. Org. Chem. 2017, 13, 2442–2457, doi:10.3762/bjoc.13.241

• solvent is known to be marginal [73][74]. To explain the elevated trans/cis ratio observed with partially fluorinated esters 3–5, we simulated the dipolar moment of compound 5 by DFT modelling. The dipolar moment for the lowest energy structure predicted a strong preference in favor of the less polar s

Enzymatic synthesis of glycosides: from natural O- and N-glycosides to rare C- and S-glycosides

• Jihen Ati,
• Pierre Lafite and
• Richard Daniellou

Beilstein J. Org. Chem. 2017, 13, 1857–1865, doi:10.3762/bjoc.13.180

• the fast screening of their activities, as well as powerful molecular modelling and crystallization of proteins. No doubt then that such biocatalysts will represent a competitive tool for glycosylation so to obtain complex O-, S- or C-glycoconjugates of biological interests. Mechanisms of O-GTs