What contributes to an effective mannose recognition domain?

• Christoph P. Sager,
• Deniz Eriş,
• Martin Smieško,
• Rachel Hevey and
• Beat Ernst

Beilstein J. Org. Chem. 2017, 13, 2584–2595, doi:10.3762/bjoc.13.255

• an identical H-bond network with the conformationally rigid FimHLD (I) was established, the higher flexibility of the seven-membered ring septanose led to a 10-fold loss in affinity. In fact, the number of possible solution conformations was considerably higher for the septanose ligand as compared to

• known as a catch-bond and in the case of UPECs enables them to evade clearance during micturition. When shear force ceases, FimH reverts back to the equilibrium between low-affinity and medium-affinity conformations [72]. In general, flexible receptors are associated with higher entropic costs resulting

¹⁵N-Labelling and structure determination of adamantylated azolo-azines in solution

• Sergey L. Deev,
• Alexander S. Paramonov,
• Tatyana S. Shestakova,
• Igor A. Khalymbadzha,
• Oleg N. Chupakhin,
• Julia O. Subbotina,
• Oleg S. Eltsov,
• Pavel A. Slepukhin,
• Vladimir L. Rusinov,
• Alexander S. Arseniev and
• Zakhar O. Shenkarev

Beilstein J. Org. Chem. 2017, 13, 2535–2548, doi:10.3762/bjoc.13.250

• expectations, the adamantane groups in the crystals of 15a and 15b were found disordered between two conformations with different rotameric configurations around the N–C1' bond (Figure 5 and Supporting Information Files 2 and 3). These forms differ by the rotation around the N–C1' bond by 40–60°; thus, in each

Syntheses, structures, and stabilities of aliphatic and aromatic fluorous iodine(I) and iodine(III) compounds: the role of iodine Lewis basicity

• Tathagata Mukherjee,
• Soumik Biswas,
• Andreas Ehnbom,
• Subrata K. Ghosh,
• Ibrahim El-Zoghbi,
• Nattamai Bhuvanesh,
• Hassan S. Bazzi and
• John A. Gladysz

Beilstein J. Org. Chem. 2017, 13, 2486–2501, doi:10.3762/bjoc.13.246

• polar nature of the crystal. Also, the C–C–C–C and F–C–C–F segments in the perfluorohexyl groups do not exhibit the idealized antiperiplanar and gauche conformations associated with saturated alkanes. Rather, the torsion angles for the roughly anti linkages average 164.4(1.6)° and 166.0(3.6

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

• measurements can be used to study ligand–protein [12] and protein–protein interactions [13]; membrane proteins [14][15][16] and membrane-associated peptides [17][18]; equilibria among conformations of RNA [19], DNA [20], and peptide nucleic acids (PNA) [21]; and many others. Particularly recent is the

• ]. Side chain conformation The side-chain conformations of proline are restricted by the pyrrolidine ring structure. The two main envelope conformations are exo- and endo- (alternatively designated as up-/down-, respectively), in which by the C4-ring atom is oriented toward or away from the carboxyl group

• contribution from the two conformations. This result indicates that the C-terminal partially fluorinated ester has a negligible influence on the side chain conformation of the prolyl moiety. Conformation of short oligopeptides We then examined how the properties observed this far impact the conformational

Structure–property relationships and third-order nonlinearities in diketopyrrolopyrrole based D–π–A–π–D molecules

• Jan Podlesný,
• Lenka Dokládalová,
• Oldřich Pytela,
• Adam Urbanec,
• Milan Klikar,
• Numan Almonasy,
• Tomáš Mikysek,
• Jaroslav Jedryka,
• Iwan V. Kityk and
• Filip Bureš

Beilstein J. Org. Chem. 2017, 13, 2374–2384, doi:10.3762/bjoc.13.235

• optical gap was extended from 1.96 to 1.99 eV. Despite its extending effect, the acetylene π-linker also shows a low rotational barrier (≈0.025 eV) and various dynamic conformations may exist in series b, which lowers the D–A interaction and results in hypsochromically shifted spectra [37][38]. This also

Solvent-free copper-catalyzed click chemistry for the synthesis of N-heterocyclic hybrids based on quinoline and 1,2,3-triazole

• Martina Tireli,
• Silvija Maračić,
• Stipe Lukin,
• Marina Juribašić Kulcsár,
• Dijana Žilić,
• Mario Cetina,
• Ivan Halasz,
• Silvana Raić-Malić and
• Krunoslav Užarević

Beilstein J. Org. Chem. 2017, 13, 2352–2363, doi:10.3762/bjoc.13.232

• Information File 1, Figure S22). Thus, the molecular structures differ in the substituent bonded to the C24 atom of the C21–C26 phenyl ring, which is chlorine in 5, bromine in 6, iodine in 7, and hydrogen in 8. The corresponding bond lengths in these structures are similar, as well as the conformations of the

• click reaction to provide the target 6-phenyl-2-(trifluoromethyl)quinolines containing p-halogen-substituted and non-substituted phenyl-1,2,3-triazole unit attached at the O-4 position of the quinoline fragment. All triazole products have almost identical conformations in the solid state, with no

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