Biosynthesis of oxygen and nitrogen-containing heterocycles in polyketides

• Franziska Hemmerling and
• Frank Hahn

Beilstein J. Org. Chem. 2016, 12, 1512–1550, doi:10.3762/bjoc.12.148

Beta-hydroxyphosphonate ribonucleoside analogues derived from 4-substituted-1,2,3-triazoles as IMP/GMP mimics: synthesis and biological evaluation

• Tai Nguyen Van,
• Audrey Hospital,
• Corinne Lionne,
• Lars P. Jordheim,
• Charles Dumontet,
• Christian Périgaud,
• Laurent Chaloin and
• Suzanne Peyrottes

Beilstein J. Org. Chem. 2016, 12, 1476–1486, doi:10.3762/bjoc.12.144

• (cN-II), an enzyme involved in the regulation of purine nucleotide pools. NMR and molecular modelling studies showed that a few derivatives adopted similar structural features to IMP or GMP. Five derivatives were identified as modest inhibitors with 53 to 64% of cN-II inhibition at 1 mM. Keywords

• inhibition and molecular modelling studies All derivatives were assayed for their ability to inhibit the human 5’-nucleotidase activity in comparison to previously published derivative (UA1776), using a rapid in vitro assay. Briefly, the enzyme catalyzes the hydrolysis of IMP into inosine and inorganic

• synthesis of derivatives 1a–q. Summary of the in vitro inhibition assays performed on human recombinant cN-II in the presence of the various derivatives and docking scores obtained from molecular modelling calculation. Supporting Information Supporting Information File 207: Description of the materials and

Interactions of cyclodextrins and their derivatives with toxic organophosphorus compounds

• Sophie Letort,
• Sébastien Balieu,
• William Erb,
• Géraldine Gouhier and
• François Estour

Beilstein J. Org. Chem. 2016, 12, 204–228, doi:10.3762/bjoc.12.23

• to these characterization methods, molecular modelling analysis can afford further clues to select the suitable CD derivative for one specific pesticide. This could also support the rational design of new macrocyclic compounds able to strongly interact with organophosphates. The structure of the

Structure and conformational analysis of spiroketals from 6-O-methyl-9(E)-hydroxyiminoerythronolide A

• Ana Čikoš,
• Irena Ćaleta,
• Dinko Žiher,
• Mark B. Vine,
• Ivaylo J. Elenkov,
• Marko Dukši,
• Dubravka Gembarovski,
• Marina Ilijaš,
• Snježana Dragojević,
• Ivica Malnar and
• Sulejman Alihodžić

Beilstein J. Org. Chem. 2015, 11, 1447–1457, doi:10.3762/bjoc.11.157

• spectroscopy and molecular modelling. The reaction kinetics and mechanistic aspects of this transformation are discussed. These rearrangements provide a facile synthesis of novel macrolide scaffolds. Keywords: configuration; conformation; 6-O-methyl-9(E)-hydroxyiminoerythronolide A; reaction mechanism

• antibiotic. This 14-membered macrolide contains a [4.4]spiroketal unit connecting 6-C–O–9-C–O–12-C. Stereochemistry at position 9-C of this spiroketal was determined by combination of NMR spectroscopy and molecular modelling [42]. The kinetics of its formation has also been extensively studied [43][44][45

• less stable nonanomeric form [23]. To determine the configuration at 9-C and elucidate the conformation of 2, nOe analysis was performed (Tables SI1 and SI2, in Supporting Information File 1), followed by molecular modelling. Very strong nOe correlations between 2-H, 5-H and 10-H observed in both DMSO

Inclusion of trans-resveratrol in methylated cyclodextrins: synthesis and solid-state structures

• Lee Trollope,
• Dyanne L. Cruickshank,
• Terence Noonan,
• Susan A. Bourne,
• Milena Sorrenti,
• Laura Catenacci and
• Mino R. Caira

Beilstein J. Org. Chem. 2014, 10, 3136–3151, doi:10.3762/bjoc.10.331

• is worth consideration in molecular modelling studies that address CD-RSV interaction in that medium. Equally significant in the context of molecular modelling is our observation in the solid-state of the potentially more probable bridging role of water in mediating host–guest binding, this feature

Come-back of phenanthridine and phenanthridinium derivatives in the 21st century

• Lidija-Marija Tumir,
• Marijana Radić Stojković and
• Ivo Piantanida

Beilstein J. Org. Chem. 2014, 10, 2930–2954, doi:10.3762/bjoc.10.312

• instance, adenine derivative 15 (Figure 6) selectively recognized the complementary nucleotide (UMP) by specific change in the UV–vis spectrum of phenanthridine subunits and high affinity [75]. Molecular modelling studies proposed a structure of the 15–UMP complex stabilized by a set of intra- and

• analogue, dihydroimidazophenanthridinium cation characterised by cyclic structure connecting positions 5 and 6, showed promising antiproliferative activity [3][98][99]. Molecular modelling results and some preliminary experiments suggest intercalative binding mode, however up till now interactions with

Photoswitchable precision glycooligomers and their lectin binding

• Daniela Ponader,
• Sinaida Igde,
• Marko Wehle,
• Katharina Märker,
• Mark Santer,
• David Bléger and
• Laura Hartmann

Beilstein J. Org. Chem. 2014, 10, 1603–1612, doi:10.3762/bjoc.10.166

• light-induced change in the geometry of the glycooligomers. Binding studies of the galactose-functionalized glycooligomers showed specific binding to PA-IL and a controlled reduction in binding affinity upon E → Z photoisomerization. We proposed a first model to explain our findings based on molecular

• modelling for ligand binding. Ongoing studies further investigate ligand binding by additional techniques such as isothermal titration calorimetry and fluorescence spectroscopy. Overall, we have successfully developed photoswitchable glycomimetics that allow for a stimulus-induced change in binding affinity

Aza-Diels–Alder reaction between N-aryl-1-oxo-1H-isoindolium ions and tert-enamides: Steric effects on reaction outcome

• Amitabh Jha,
• Ting-Yi Chou,
• Zainab ALJaroudi,
• Bobby D. Ellis and
• T. Stanley Cameron

Beilstein J. Org. Chem. 2014, 10, 848–857, doi:10.3762/bjoc.10.81

• formation of 2-(2-substitued-aryl)-3-(2-(2-oxopyrrolidin-1-yl)vinyl)isoindolin-1-one analogues indicating steric hinderance as the cause of deviation. The probable mechanism of the reaction based on the results from X-ray crystallography and molecular modelling is discussed. Keywords: alkene addition

• -phenyl)-1-oxo-1H-isoindolium ions by molecular modelling. Like biphenyl, the N-phenyl-1-oxo-1H-isoindolium ions were expected to show extended conjugation and not to acquire a mutually perpendicular conformation with respect to the N-phenyl and the oxoisoindolium moieties. Like biphenyl [44], the

Novel supramolecular affinity materials based on (−)-isosteviol as molecular templates

• Christina Lohoelter,
• Malte Brutschy,
• Daniel Lubczyk and
• Siegfried R. Waldvogel

Beilstein J. Org. Chem. 2013, 9, 2821–2833, doi:10.3762/bjoc.9.317

• additional base and operation in a sealed tube provided a satisfactory yield of 8 (Scheme 3) [61]. By molecular modelling the structural features can be visualized (Figure 5). A relatively closed C3-symmetric cleft is formed by all-syn-8 (Figure 5a), whereas the less symmetric anti,anti,syn-8 (Figure 5b

• . Furthermore, a new set of signals (Figure 7, green) can be seen in the product spectrum which show typical shifts of 1,2-disubstituted alkenes. Since the obtained analytical data strongly indicate the existence of cage compound 19, molecular modelling calculations (Figure 8, MacroModel 9.3.5) indicate a

• compounds, see Supporting Information File 1. Unique structural features of (−)-isosteviol. Triphenylene ketal based on (−)-isosteviol. Structural features of triptycene derivatives. Hexaammoniumtriptycene hexachloride 4 and 15-oxo-derivatives 5a–c of (–)-isosteviol. Molecular modelling structures (Spartan

Space filling of β-cyclodextrin and β-cyclodextrin derivatives by volatile hydrophobic guests

• Sophie Fourmentin,
• Anca Ciobanu,
• David Landy and
• Gerhard Wenz

Beilstein J. Org. Chem. 2013, 9, 1185–1191, doi:10.3762/bjoc.9.133

• Saarbrücken, Germany 10.3762/bjoc.9.133 Abstract The inclusion of volatile derivatives of benzene and cyclohexane in β-cyclodextrin (β-CD), hydroxypropyl-β-CD, and hydrophilic β-CD-thioethers was investigated by static headspace gas chromatography (HS-GC) and molecular modelling. The obtained binding

• constants strongly increase with the amount of space filling of the CD cavity and the salt concentration. β-CD thioethers show a 3–10 times higher binding potential than native β-CD. Keywords: cyclodextrins; inclusion compound; molecular modelling; space filling; static headspace gas chromatography; vapor

• for benzene derivatives and 7, 10, 12 and 15 mL for cyclohexane derivatives, respectively). Molecular modelling Simulations of inclusion compounds for each benzene derivative into the cavity of host 4 were realized by means of Macromodel [45] with MMFF force field and GB/SA simulation of water [46

Enhancement of efficiency in organic photovoltaic devices containing self-complementary hydrogen-bonding domains

• Rohan J. Kumar,
• Jegadesan Subbiah and
• Andrew B. Holmes

Beilstein J. Org. Chem. 2013, 9, 1102–1110, doi:10.3762/bjoc.9.122

• -bonding interactions and insufficient to explain the changes in chemical shift at the concentrations observed here. However, given the strongly dipolar nature of the compound, the role of dipole-based interactions cannot be ruled out. We then turned to molecular modelling to shed further light on the

The β-cyclodextrin/benzene complex and its hydrogen bonds – a theoretical study using molecular dynamics, quantum mechanics and COSMO-RS

• Jutta Erika Helga Köhler and
• Nicole Grczelschak-Mick

Beilstein J. Org. Chem. 2013, 9, 118–134, doi:10.3762/bjoc.9.15

• large industrial processes [24][25][26]. Our intention for this study was to find a “modular, robust molecular-modelling workflow” for how to analyse the formation of cyclodextrin complexes for many guest molecules in general, before extensive experimental work is carried out. Lemon grass oil [27] or

Regioselective synthesis of 7,8-dihydroimidazo[5,1-c][1,2,4]triazine-3,6(2H,4H)-dione derivatives: A new drug-like heterocyclic scaffold

• Nikolay T. Tzvetkov,
• Harald Euler and
• Christa E. Müller

Beilstein J. Org. Chem. 2012, 8, 1584–1593, doi:10.3762/bjoc.8.181

• (HSQC and HMBC) in combination with 1H and 13C NMR, and additionally by LC/ESI-MS (m/z 287 [M + H]+/285 [M − H]− for 24, 355 [M + H]+/353 [M − H]− for 25). Molecular modelling was performed to calculate the respective geometries by using the MMFF95 force field [27] assuming an N1–C5 ring fusion during

Formation of smectic phases in binary liquid crystal mixtures with a huge length ratio

• Nadia Kapernaum,
• Friederike Knecht,
• C. Scott Hartley,
• Jeffrey C. Roberts,
• Robert P. Lemieux and
• Frank Giesselmann

Beilstein J. Org. Chem. 2012, 8, 1118–1125, doi:10.3762/bjoc.8.124

• and a narrow higher-ordered smectic phase. Its molecular length was determined by molecular modelling as 50.6 Å. The component with short molecular length is the asymmetric compound 2-(4-butoxyphenyl)-5-octyloxypyrimidine (2PhP) [4]. It exhibits the typical liquid-crystalline phase sequence of nematic

• , smectic A and smectic C phases. Its molecular length is 25.6 Å, according to molecular modelling, which results in a PhP16/2PhP length ratio of almost 2. First, the phase diagram of the system PhP16/2PhP was determined (Figure 3). This phase diagram is very similar to those reported in our earlier studies

• Å obtained by molecular modelling. In conclusion, the material PhP16 shows a first-order phase transition from the tilted SmC phase to the tilted SmF phase at the transition temperature Tc. Conclusion The investigations of the phase diagram of the two phenylpyrimidines PhP16 and 2PhP with a length

Fifty years of oxacalix[3]arenes: A review

• Kevin Cottet,
• Paula M. Marcos and
• Peter J. Cragg

Beilstein J. Org. Chem. 2012, 8, 201–226, doi:10.3762/bjoc.8.22

• to bind to C60 with a Kassoc of 35.5 M−1 in toluene at 25 °C; however, when methylated on the lower rim, no binding was observed. Molecular modelling was employed to illustrate how the shallow cavity of 3a allowed for optimum interactions between the oxacalix[3]arene aromatic rings and C60. While

Laterally substituted symmetric and nonsymmetric salicylideneimine-based bent-core mesogens

• Sonja Findeisen-Tandel,
• Wolfgang Weissflog,
• Ute Baumeister,
• Gerhard Pelzl,
• H. N. Shreenivasa Murthy and
• Channabasaveshwar V. Yelamaggad

Beilstein J. Org. Chem. 2012, 8, 129–154, doi:10.3762/bjoc.8.15

• scattering in the wide-angle region indicating a simple layer structure without in-plane ordering. The layer spacing of 3.8 nm is clearly smaller than the molecular length L = 5.4 nm as estimated by commercial molecular modelling software (Cerius 2) and thus from cosθ = d/L = 3.8 nm/5.4 nm a tilt angle of

The C–F bond as a conformational tool in organic and biological chemistry

• Luke Hunter

Beilstein J. Org. Chem. 2010, 6, No. 38, doi:10.3762/bjoc.6.38

• in these systems. Hyperconjugation effects Consider the well-studied molecule 1,2-difluoroethane (11, Figure 1c). There are two possible staggered conformers, with the fluorine atoms either gauche or anti. NMR and molecular modelling studies have shown that the gauche conformer is lower in energy

(Pseudo)amide-linked oligosaccharide mimetics: molecular recognition and supramolecular properties

• José L. Jiménez Blanco,
• Fernando Ortega-Caballero,
• Carmen Ortiz Mellet and
• José M. García Fernández

Beilstein J. Org. Chem. 2010, 6, No. 20, doi:10.3762/bjoc.6.20

• ] that were found to form rigid secondary structures predetermined by the linkage position as evidenced from CD and NMR measurements. Moreover, conformational analysis by molecular modelling calculation on the β(1→2)-linked decamer 9 supported a helical arrangement, stabilised by a intramolecular

• acid. Following the same objective, Xie’s group prepared orthogonally protected cyclic homo-oligomers with two to four SAA units that can be selectively or fully deprotected to afford macrocycles that can undergo further functionalisation (Figure 11) [55]. Conformational analysis by molecular modelling

• (Figure 19). Molecular modelling predicts the existence of a flexible, relatively hydrophobic cavity suited for molecular inclusion of non-polar guests [79][88]. NMR supports this fact and confirms the high symmetry of these hosts, where all glucopyranosyl units are magnetically equivalent as in the case

Molecular length distribution and the formation of smectic phases

• Nadia Kapernaum,
• C. Scott Hartley,
• Jeffrey C. Roberts,
• Robert P. Lemieux and
• Frank Giesselmann

Beilstein J. Org. Chem. 2009, 5, No. 65, doi:10.3762/bjoc.5.65

• extrapolated value of 46.4 Å corresponds quite well to the value of 45.5 Å we obtained for the extended length of the PhP14 molecule from molecular modelling studies (see Figure 2). For 2PhP the experimental d-value from SAXS (25.9 Å) also agrees very well with the extended length of the molecule (25.6 Å

• PhP14, 6PhPz and 2PhP differing in molecular lengths by a factor of approximately two. The molecular lengths were determined from the most extended conformers, after optimizing their energy using molecular modelling with MOPAC/AM1. Phase diagram of the system 2PhP/PhP14. Over a broad temperature and

• concentration range only the SmA phase is stable. The layer spacing in the SmA phase at T = Tc vs mole fraction for the system 2PhP/PhP14 (filled triangles) and calculated value of the molecular length for pure PhP14 from molecular modelling (open square). Reduced layer spacing for the mixtures which exhibit

Influence of spacer chain lengths and polar terminal groups on the mesomorphic properties of tethered 5-phenylpyrimidines

• Gundula F. Starkulla,
• Elisabeth Kapatsina,
• Angelika Baro,
• Frank Giesselmann,
• Stefan Tussetschläger,
• Martin Kaller and
• Sabine Laschat

Beilstein J. Org. Chem. 2009, 5, No. 63, doi:10.3762/bjoc.5.63

• values obtained from the X-ray experiments fit with the molecular lengths derived from simple molecular modelling (Chem3D) [13]. For example, the XRD pattern of the azide derivative 6c results in a layer distance of 25.5 Å, whereas the calculated length of the molecule for the most elongated conformation

Saddle-shaped tetraphenylenes with peripheral gallic esters displaying columnar mesophases

• Eugen Wuckert,
• Constanze Hägele,
• Frank Giesselmann,
• Angelika Baro and
• Sabine Laschat

Beilstein J. Org. Chem. 2009, 5, No. 57, doi:10.3762/bjoc.5.57

• mesophases with increasing chain lengths has been also observed in other columnar systems [32][33] and has been attributed to the enhanced core–core interaction necessary for the formation of the Colr phases [34]. According to molecular modelling [35] and comparison with the XRD data each disk within the

• /cooling rate 5 K/min). Texture of 2h under the POM at 25 °C upon cooling from the isotropic liquid (heating/cooling rate 5 K/min; magnification 100×). Molecular modelling of the saddle-shaped tetraphenylene (octakis)acyl core unit of 2 [35]. Clearing temperatures Tcl [°C] of tetraphenylenes 2e–l as a

A stable enol from a 6-substituted benzanthrone and its unexpected behaviour under acidic conditions

• Marc Debeaux,
• Kai Brandhorst,
• Peter G. Jones,
• Henning Hopf,
• Jörg Grunenberg,
• Wolfgang Kowalsky and
• Hans-Hermann Johannes

Beilstein J. Org. Chem. 2009, 5, No. 31, doi:10.3762/bjoc.5.31

• the reaction products is proposed and supported by DFT calculations. Keywords: consecutive reactions; intramolecular cyclization; molecular modelling; spiro compounds; X-ray structural analysis; Introduction Compounds for optoelectronic applications with electroluminescent (e.g. organic light

Methods for the synthesis of polyhydroxylated piperidines by diastereoselective dihydroxylation: Exploitation in the two-directional synthesis of aza-C-linked disaccharide derivatives

• Andrew Kennedy,
• Adam Nelson and
• Alexis Perry

Beilstein J. Org. Chem. 2005, 1, No. 2, doi:10.1186/1860-5397-1-2

• conformations of the piperidines 20-22 were determined using a combination of three approaches: (a) analysis of the magnitude of vicinal coupling constants (see Table 2); (b) the observation of through-space nOe correlations; and (c) molecular modelling using the MMFF force field. The determination of the