Crystal structure of the inclusion complex of cholesterol in β-cyclodextrin and molecular dynamics studies

• Elias Christoforides,
• Andreas Papaioannou and
• Kostas Bethanis

Beilstein J. Org. Chem. 2018, 14, 838–848, doi:10.3762/bjoc.14.69

• cavity. One disordered hydroxy group in host A and two in host B illustrate both gauche–gauche and gauche–trans conformations pointing inwards and outwards the cavity. The β-CD dimers stack along c-axis, the angle between their approximate seven-fold axis and c-axis being 7.86°, and form layers along the

Recent advances on organic blue thermally activated delayed fluorescence (TADF) emitters for organic light-emitting diodes (OLEDs)

• Thanh-Tuân Bui,
• Fabrice Goubard,
• Malika Ibrahim-Ouali,
• Didier Gigmes and
• Frédéric Dumur

Beilstein J. Org. Chem. 2018, 14, 282–308, doi:10.3762/bjoc.14.18

• twisted phenyl–pyrimidine/phenyl–pyridine conformation (i.e., a larger dihedral angle) in CN-P3/CN-P2. All the DFT-optimized data were in perfect accordance with single crystal X-ray diffraction analyses. The results showed that the molecular conformations (twist angles in D-spacer-A diads) could be

Fluorescent nucleobase analogues for base–base FRET in nucleic acids: synthesis, photophysics and applications

• Mattias Bood,
• Sangamesh Sarangamath,
• Moa S. Wranne,
• Morten Grøtli and
• L. Marcus Wilhelmsson

Beilstein J. Org. Chem. 2018, 14, 114–129, doi:10.3762/bjoc.14.7

• conformations depending on conditions. Z-DNA, a GC-repeat rich, thermodynamically less preferred, left-handed helical conformation that is favored by cytosine methylation is known to form in vivo under negative supercoiling or high salt concentrations [64][65][66][67][68]. Circular dichroism is traditionally

• breathing. Moreover, the data demonstrated that the structural changes upon binding of TFAM near the transcription initiation site are the result of sequence-independent binding to DNA. The investigation establishes the potential of using base–base FRET for studying nucleic acid conformations in vital

Microfluidic radiosynthesis of [¹⁸F]FEMPT, a high affinity PET radiotracer for imaging serotonin receptors

• Thomas Lee Collier,
• Steven H. Liang,
• J. John Mann,
• Neil Vasdev and
• J. S. Dileep Kumar

Beilstein J. Org. Chem. 2017, 13, 2922–2927, doi:10.3762/bjoc.13.285

• the low affinity (LA) and high affinity (HA) conformations of 5-HT1AR. However, agonist ligands prefer binding to the HA state of the receptor. This is coupled to G-protein and thus agonist binding gives a more meaningful functional measure of the 5-HT1AR that can reflect desensitization and

Conformational preferences of α-fluoroketones may influence their reactivity

• Graham Pattison

Beilstein J. Org. Chem. 2017, 13, 2915–2921, doi:10.3762/bjoc.13.284

• , supported by computation, that this effect is due to reactive conformations in which the C–X bond is orthogonal to the carbonyl group for good orbital overlap being disfavoured in the case of fluoro ketones. Keywords: α-halogenated ketones; conformational analysis; reactivity; stereoelectronic effects

• variants. The energy minimum for α-fluoroacetophenone was displayed at an O=C–C–X dihedral angle of around 140° in the gas phase, whilst the chloro- and bromoacetophenones both showed minima around 110°. Highly polar conformations which place the C–X bond in the same plane as the carbonyl group were

• smaller dihedral angle preferred by the chlorinated derivative in the gas phase. Figure 3 compares the lowest energy conformations of α-fluoroacetophenone and α-chloroacetophenone in the polar solvent ethanol. Experimental work by Olivato amongst others supports these conformational preferences [11][12

The use of 4,4,4-trifluorothreonine to stabilize extended peptide structures and mimic β-strands

• Yaochun Xu,
• Isabelle Correia,
• Tap Ha-Duong,
• Nadjib Kihal,
• Jean-Louis Soulier,
• Julia Kaffy,
• Benoît Crousse,
• Olivier Lequin and
• Sandrine Ongeri

Beilstein J. Org. Chem. 2017, 13, 2842–2853, doi:10.3762/bjoc.13.276

• a fluorinated substituent incorporated in the side-chain of amino acids on peptide conformations has recently raised attention [9]. While the effect of fluorinated analogs of hydrophobic aliphatic and aromatic amino acids has been prominently studied, the influence of fluorinated polar amino acids

• fluorinated Thr residues because of the absence of known random coil values. The analysis of 1Hα and 13Cα CSDs for residues Val2 and Val4 in all of the eight pentapeptides (Table 1 and Table 2) supports the predominance of extended conformations, as shown by downfield shifted Hα protons (positive CSD values

• between 0.09 and 0.22 ppm, Table 1) and upfield shifted Cα carbons (negative CSD values in the range of −2.5 to −1.6 ppm, Table 2). The high propensity for exploring extended backbone conformations was further confirmed for these pentapeptides by the analysis of Hα–HN ROE correlations, showing that

Metal-mediated base pairs in parallel-stranded DNA

• Jens Müller

Beilstein J. Org. Chem. 2017, 13, 2671–2681, doi:10.3762/bjoc.13.265

• adopted for cisoid Hoogsteen base pairing (Scheme 2b) when both nucleotides involved in the base pair adopt an identical glycosidic bond conformation, i.e., when both are oriented anti or both are oriented syn [44][45][46]. If they adopt opposing glycosidic bond conformations, an antiparallel strand

• glycosidic bond conformations [46]. It needs to be noted that these correlations are derived from base pairs and triples comprising canonical purine and pyrimidine nucleobases only. In particular, it is assumed that both Hoogsteen and reversed Hoogsteen pairing involve the Hoogsteen edge of one purine

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