Homologated amino acids with three vicinal fluorines positioned along the backbone: development of a stereoselective synthesis

• Raju Cheerlavancha,
• Ahmed Ahmed,
• Yun Cheuk Leung,
• Aggie Lawer,
• Qing-Quan Liu,
• Marina Cagnes,
• Hee-Chan Jang,
• Xiang-Guo Hu and
• Luke Hunter

Beilstein J. Org. Chem. 2017, 13, 2316–2325, doi:10.3762/bjoc.13.228

• diastereoisomers of this fluorinated δ-amino acid adopt distinct conformations in solution, suggesting that these molecules might have value as shape-controlled building blocks for future applications in peptide science. Keywords: amino acids; conformation; deoxyfluorination; fluorine; stereochemistry

• configurations that can affect the conformation. Organofluorine chemistry offers a particular attraction here, since fluorinated molecules (e.g., 3–5) tend to adopt predictable conformations due to hyperconjugative and/or dipole–dipole interactions associated with the C–F bond [11][12][13][14][15]. Such a

• spectra of 6a and 6b were simulated (see Supporting Information File 1) in order to measure the spin–spin coupling constants and thereby gain information on the solution-state conformations (Figure 2). For 6a, the observed J values about the Cα–Cβ and Cβ–Cγ bonds are intermediate in magnitude [42

Structural diversity in the host–guest complexes of the antifolate pemetrexed with native cyclodextrins: gas phase, solution and solid state studies

• Magdalena Ceborska,
• Magdalena Zimnicka,
• Aneta Aniela Kowalska,
• Kajetan Dąbrowa and
• Barbara Repeć

Beilstein J. Org. Chem. 2017, 13, 2252–2263, doi:10.3762/bjoc.13.222

• the free PTX molecule is engaged in strong H-bonds between the carboxylate donor –NH group, which are gradually broken. Overall all the data obtained from 1D and 2D NMR experiments suggests formation of exclusion-type associate of two equally probable conformations depicted in Figure 3a. Moreover

• : rotaxane-like); for α-CD/PTX two equally probable conformations are shown. 2D ROESY NMR spectrum of an equimolar mixture of β-CD and PTX in D2O at 298 K. Inset: splitting of the bridging ethylene protons after addition of β-CD. 2D ROESY NMR spectra of a mixture of γ-CD with a 16-fold molar excess of PTX

Intramolecular glycosylation

• Xiao G. Jia and
• Alexei V. Demchenko

Beilstein J. Org. Chem. 2017, 13, 2028–2048, doi:10.3762/bjoc.13.201

• conformations and energies chose the latter linker [55]. To apply the remote glycosidation methodology to the synthesis of the 4,6-branched trisaccharide, phthaloylated thioglycoside 17 was coupled with the 6-hydroxy group of the acceptor precursor 16 in the presence of DCC and DMAP (Scheme 5). The tethering

Remarkable functions of sn-3 hydroxy and phosphocholine groups in 1,2-diacyl-sn-glycerolipids to induce clockwise (+)-helicity around the 1,2-diacyl moiety: Evidence from conformation analysis by ¹H NMR spectroscopy

• Yoshihiro Nishida,
• Mengfei Yuan,
• Kazuo Fukuda,
• Kaito Fujisawa,
• Hirofumi Dohi and
• Hirotaka Uzawa

Beilstein J. Org. Chem. 2017, 13, 1999–2009, doi:10.3762/bjoc.13.196

• (+) and gg(−) conformations around the 1,2-diacyl moiety (Figure 1). From X-ray crystallography data, a common structure in which the 1,2-diacyl chains are aligned in parallel is observed, which adopts either the gt(+) or gg(−) conformer [7][10][12]. An analogous conformation has been reportedly observed

• are maintained at δ 3.69 ppm (Figure 2b). As shown in Table 2, entries 1–6, the change in the chemical shifts is related to that in the vicinal coupling constants, indicative of a change in the dynamic conformations occurring around the 1,2-diacyl moiety in 3. From the analysis of the 1H NMR data

p-tert-Butylthiacalix[4]arenes functionalized by N-(4’-nitrophenyl)acetamide and N,N-diethylacetamide fragments: synthesis and binding of anionic guests

• Alena A. Vavilova and
• Ivan I. Stoikov

Beilstein J. Org. Chem. 2017, 13, 1940–1949, doi:10.3762/bjoc.13.188

• -diethylacetamide groups in cone and partial cone conformations have been synthesized. Their complexation ability towards a number of tetrabutylammonium salts n-Bu4NX (X = F−, Cl−, Br−, I−, CH3CO2−, H2PO4−, NO3−) was studied by UV spectroscopy. The effective receptor for the anions studied as well as selective

• N-(4’-nitrophenyl)acetamide and N,N-diethylacetamide groups in cone and partial cone conformations were synthesized. The calculations of the proposed model for the anion binding by the synthesized thiacalix[4]arenes were carried out using molecular modeling (the quantum mechanical method PM3). Also

The chemistry and biology of mycolactones

• Matthias Gehringer and
• Karl-Heinz Altmann

Beilstein J. Org. Chem. 2017, 13, 1596–1660, doi:10.3762/bjoc.13.159

Molecular recognition of N-acetyltryptophan enantiomers by β-cyclodextrin

• Spyros D. Chatziefthimiou,
• Mario Inclán,
• Petros Giastas,
• Athanasios Papakyriakou,
• Konstantina Yannakopoulou and
• Irene M. Mavridis

Beilstein J. Org. Chem. 2017, 13, 1572–1582, doi:10.3762/bjoc.13.157

• -Ο63Β bond in two conformations, the major (−)-gauche C-Ο63Βa (occupancy 78%) pointing outward and the minor (+)-gauche C-Ο63Βb (22%) pointing towards the interior of the cavity, the latter interacting with guests C and D of neighboring dimers (Figure 3a). The aromatic moieties of both guest

Bifunctional organocatalysts for the asymmetric synthesis of axially chiral benzamides

• Ryota Miyaji,
• Yuuki Wada,
• Akira Matsumoto,
• Keisuke Asano and
• Seijiro Matsubara

Beilstein J. Org. Chem. 2017, 13, 1518–1523, doi:10.3762/bjoc.13.151

• reactions to occur. Organocatalysts have also been employed in several asymmetric cyclization reactions via intramolecular hetero-Michael addition [7][8][9][10][11][12][13][14][15][16]. In these reactions, multipoint recognition by the catalysts favors the specific conformations of the substrates in the

Strategies toward protecting group-free glycosylation through selective activation of the anomeric center

• A. Michael Downey and
• Michal Hocek

Beilstein J. Org. Chem. 2017, 13, 1239–1279, doi:10.3762/bjoc.13.123

Glycoscience@Synchrotron: Synchrotron radiation applied to structural glycoscience

• Serge Pérez and
• Daniele de Sanctis

Beilstein J. Org. Chem. 2017, 13, 1145–1167, doi:10.3762/bjoc.13.114

• shorter than the time scale of substrate diffusion in the crystals. For example, when UDP-GalNAc was soaked for 24 minutes, experiments resulted in structures with UDP-GalNAc in several conformations that are difficult to interpret. The “freeze-trigger” route was started using a series of cage compounds

G-Protein coupled receptors: answers from simulations

• Timothy Clark

Beilstein J. Org. Chem. 2017, 13, 1071–1078, doi:10.3762/bjoc.13.106

• available structures hampered investigations, however, GPCRs can exist in active or inactive conformations and in binary complexes with ligands or intracellular binding partners (IBPs, G-proteins or β-arrestin) or in ternary complexes with a ligand and an IBP. Thus, many structures would be necessary in

• five years ago that “the calculation error is comparable to the uncertainty in the experimental comparison” [25]. The error in this case refers to the ability of the force field to reproduce peptide and protein conformations determined using calibrated Karplus equations in conjunction with NMR

• variations of metadynamics allow very effective use of massively parallel supercomputers in order to investigate ligand binding and unbinding and transitions between active and inactive receptor conformations. Indeed, the power of modern simulations is such that we must revisit the relationship between

Synthesis of tetrasubstituted pyrazoles containing pyridinyl substituents

• Josef Jansa,
• Ramona Schmidt,
• Ashenafi Damtew Mamuye,
• Laura Castoldi,
• Alexander Roller,
• Vittorio Pace and
• Wolfgang Holzer

Beilstein J. Org. Chem. 2017, 13, 895–902, doi:10.3762/bjoc.13.90

• corresponding H-5 has only 7.22 ppm). A possible explanation is the proximity to nitrogen lone-pairs of pyrazole N-2 (or adjacent pyridine-N lone-pairs in suitable conformations) which affect the mentioned protons by electrostatic field effects resulting in markedly higher chemical shifts – as shown, for

The effect of cyclodextrin complexation on the solubility and photostability of nerolidol as pure compound and as main constituent of cabreuva essential oil

• Joyce Azzi,
• Pierre-Edouard Danjou,
• David Landy,
• Steven Ruellan,
• Lizette Auezova,
• Hélène Greige-Gerges and
• Sophie Fourmentin

Beilstein J. Org. Chem. 2017, 13, 835–844, doi:10.3762/bjoc.13.84

• monomeric β-CD with C7 symmetry. trans-Ner were constructed manually. Fifty conformations of trans-Ner/CD complexes were selected (Monte Carlo conformational searches: Mixed torsional/low mode sampling, 10000 structures generated, FMNR conjugate gradient minimization, convergence fixed to 0.01 kJ Å−1 mol−1

Inclusion complexes of β-cyclodextrin with tricyclic drugs: an X-ray diffraction, NMR and molecular dynamics study

• Franca Castiglione,
• Fabio Ganazzoli,
• Luciana Malpezzi,
• Andrea Mele,
• Walter Panzeri and
• Giuseppina Raffaini

Beilstein J. Org. Chem. 2017, 13, 714–719, doi:10.3762/bjoc.13.70

• comparison of the X-ray structure and the MD simulations in water of 2/β-CD complex showed that 2 is present as single conformer in the crystal and in two conformations in the solution state. Materials and Methods X-ray diffraction Single crystals of 1/β-CD and 2/β-CD were obtained after many attempts by

• the distance between the centers of mass of the host and of the guest molecule [17]. Final optimizations (up to an energy gradient lower than 4 × 10−3 kJ mol−1 Å−1) of many conformations generated during the MD runs yielded the most stable host–guest geometries discussed in the main text. Molecular

Dimerization reactions of aryl selenophen-2-yl-substituted thiocarbonyl S-methanides as diradical processes: a computational study

• Michael L. McKee,
• Grzegorz Mlostoń,
• Katarzyna Urbaniak and
• Heinz Heimgartner

Beilstein J. Org. Chem. 2017, 13, 410–416, doi:10.3762/bjoc.13.44

• a 1.2 kcal/mol activation barrier (TS2) forming a C–C bond to give the intermediate, delocalized diradical 12 in a spontaneous reaction (∆G = −50.5 kcal/mol, Figure 3). This diradical can adopt a number of conformations. While the conformer surface was not fully explored, five conformers were

Synthesis and optical properties of new 5'-aryl-substituted 2,5-bis(3-decyl-2,2'-bithiophen-5-yl)-1,3,4-oxadiazoles

• Anastasia S. Kostyuchenko,
• Tatyana Yu. Zheleznova,
• Anton J. Stasyuk,
• Aleksandra Kurowska,
• Wojciech Domagala,
• Adam Pron and
• Alexander S. Fisyuk

Beilstein J. Org. Chem. 2017, 13, 313–322, doi:10.3762/bjoc.13.34

• exist only as a single conformer of planar structure. An increasing conformational variety has been observed for derivatives with substituents of increasing size. Thus, 15e can exist in two conformations with different orientation of the terminal substituents with respect to the central core. At the

Computational methods in drug discovery

• Sumudu P. Leelananda and
• Steffen Lindert

Beilstein J. Org. Chem. 2016, 12, 2694–2718, doi:10.3762/bjoc.12.267

• various docking algorithms has been evaluated and they are able to generate docked ligand conformations that are similar to experimental complexes [146]. Compared to co-crystallized X-ray structures of target–ligand complexes docking results can sometimes even predict poses with RMSDs of less than 1 Å

• . These methods include molecular dynamics simulations [186], Monte Carlo simulations [187], enhanced sampling [177] or just simply experimental ensembles from NMR or multiple crystal structures, to generate an ensemble of conformations based on the starting target structure. By doing so, conformations of

• the target structure that are relevant to the biological function which are not accessible by experimental structure determination, can be obtained. The trajectories can be clustered to obtain a set of representative conformations. The difference here is that instead of using one structure, an

Thiazol-4-one derivatives from the reaction of monosubstituted thioureas with maleimides: structures and factors determining the selectivity and tautomeric equilibrium in solution

• Alena S. Pankova,
• Pavel R. Golubev,
• Alexander F. Khlebnikov,
• Alexander Yu. Ivanov and
• Mikhail A. Kuznetsov

Beilstein J. Org. Chem. 2016, 12, 2563–2569, doi:10.3762/bjoc.12.251

• monosubstituted thioureas 1a–f with maleimides 2a–e. Reaction of monoalkylthioureas 1d–f with N-phenylmaleimide (2a) at room temperature. Relative Gibbs free energies of the optimized conformations of model thiazolidines, ΔG (kcal/mol) [DFT B3LYP/6-31+G(d,p)), 298 K, DMSO (PCM)]. Supporting Information

Inhibition of peptide aggregation by means of enzymatic phosphorylation

• Kristin Folmert,
• Malgorzata Broncel,
• Hans v. Berlepsch,
• Christopher H. Ullrich,
• Mary-Ann Siegert and
• Beate Koksch

Beilstein J. Org. Chem. 2016, 12, 2462–2470, doi:10.3762/bjoc.12.240

• functional templates like conductive nanowires [7], water-filled nanotubes [8] or biocompatible hydrogels [9]. Likewise, nature uses amyloid-like cross-β-sheet-rich conformations to store peptide hormones in secretory granules of the endocrine system [10]. As another example it was found that mammalian

Experimental and theoretical investigations into the stability of cyclic aminals

• Edgar Sawatzky,
• Antonios Drakopoulos,
• Martin Rölz,
• Christoph Sotriffer,
• Bernd Engels and
• Michael Decker

Beilstein J. Org. Chem. 2016, 12, 2280–2292, doi:10.3762/bjoc.12.221

• minimal energy where the residues are in equatorial position (exemplarily shown for compound 9b in Figure 7b). Both conformations of minimum energy found in this study are in agreement with crystal structures reported in the literature [46][49][50][51][52] (CCDC reference numbers for anti-axial motif

A chiral analog of the bicyclic guanidine TBD: synthesis, structure and Brønsted base catalysis

• Mariano Goldberg,
• Denis Sartakov,
• Jan W. Bats,
• Michael Bolte and
• Michael W. Göbel

Beilstein J. Org. Chem. 2016, 12, 1870–1876, doi:10.3762/bjoc.12.176

• of the guanidinium benzoate salt the six membered rings of 10 adopt conformations close to an envelope with the phenyl substituents in pseudo-axial positions. The unprotonated guanidine 10 catalyzes Diels–Alder reactions of anthrones and maleimides (25–30% ee). It also promotes as a strong Brønsted

Synthesis of the C8’-epimeric thymine pyranosyl amino acid core of amipurimycin

• Pramod R. Markad,
• Navanath Kumbhar and
• Dilip D. Dhavale

Beilstein J. Org. Chem. 2016, 12, 1765–1771, doi:10.3762/bjoc.12.165

• results on conformational preferences of 12 and 13 were corroborated using geometry-optimized density functional theory (DFT). The geometrically optimized preferred conformations of 12 and 13 are depicted in Figure 3, and geometrical parameters for torsion angles and intramolecular hydrogen bonding

Experimental and theoretical insights in the alkene–arene intramolecular π-stacking interaction

• Valeria Corne,
• Ariel M. Sarotti,
• Carmen Ramirez de Arellano,
• Rolando A. Spanevello and
• Alejandra G. Suárez

Beilstein J. Org. Chem. 2016, 12, 1616–1623, doi:10.3762/bjoc.12.158

• of equilibriums of at least four different conformations: π-stacked and face-to-edge, each of them in an s-cis/s-trans conformation. The results show that the stabilization produced by the π–π interaction makes the π-stacked conformation predominant in solution and this stabilization is slightly

• alkene groups prevents any stabilizing interaction between them. For the gauche conformations, NBO analysis [25][26] (at the M06-2X/6-31+G(d) level) revealed a two-electron stabilizing donation from the π orbital of the phenoxy ring to the π* anti-bonding orbital of the acrylate moiety, supporting the

• through-space interaction between these fragments. The associated second order perturbation energies (ΔE(2)) are in the range of −0.90 to −0.73 kcal/mol for 6-gauche_s-cis and −0.84 to −0.69 kcal/mol for 6-gauche_s-trans. The energy (ZPE) difference between gauche and anti conformations (ΔEag = Eanti

Discovery of an inhibitor of the production of the Pseudomonas aeruginosa virulence factor pyocyanin in wild-type cells

• Bernardas Morkunas,
• Balint Gal,
• Warren R. J. D. Galloway,
• James T. Hodgkinson,
• Brett M. Ibbeson,
• Yaw Sing Tan,
• Martin Welch and
• David R. Spring

Beilstein J. Org. Chem. 2016, 12, 1428–1433, doi:10.3762/bjoc.12.137

• with a bridging water molecule, which is known to be involved in a hydrogen bonding between OdDHL and Arg61 (Figure 3a) [32], and one without. In addition, both rigid and flexible conformations of LasR LBD were used in the docking runs. Tyr47 and Arg61 exhibit considerable variation in their side-chain

• conformations in various crystal structures of LasR LBD complexes and hence, they were made flexible in the flexible receptor docking runs. The best score for OdDHL (−9.1 kcal/mol) was obtained from the rigid receptor docking run with water. The docked and crystallographic conformations of OdDHL agree closely

• with each other (root mean square deviation [RMSD] = 0.54 Å) in the presence of the crystallographic water molecule. The RMSD between the docked and crystallographic conformations of OdDHL increases to 1.1 Å in the absence of water. This demonstrates the importance of the bridging water molecule in the

Conjugate addition–enantioselective protonation reactions

• James P. Phelan and
• Jonathan A. Ellman

Beilstein J. Org. Chem. 2016, 12, 1203–1228, doi:10.3762/bjoc.12.116

• using enamine catalysis [60]. Two challenges to using enamine catalysis for enantioselective protonation are the many conformations the reactive iminium intermediates can adopt and the potential for racemization of the enantioenriched product by the basic catalyst. Using the triflate salt of diamine 119