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

• of a neighboring ‘arm’; (ii) H-bonds between arginine terminal N–H and C=O of the peptide bond of phenylalanine of an adjacent cyclic pentapeptide (see Supporting Information File 1), yielding adjacent cyclic pentapeptides in close proximity for a large set of conformations. This separation between

• this large molecule, the conformations reported here represent relaxed geometries showing possible intermolecular contacts between the cyclic pentapeptides. The analysis and visualization of MD simulations were carried out using DS BIOVIA and Chimera [84] software. Targeted multivalent phototherapeutic

Design, synthesis and structure of novel G-2 melamine-based dendrimers incorporating 4-(n-octyloxy)aniline as a peripheral unit

• Cristina Morar,
• Pedro Lameiras,
• Attila Bende,
• Gabriel Katona,
• Emese Gál and
• Mircea Darabantu

Beilstein J. Org. Chem. 2018, 14, 1704–1722, doi:10.3762/bjoc.14.145

• (IEFPCM) and considering DMSO (ε = 46.826) as the solvent environment; the total electronic energies of the anti–anti conformations were taken as the reference value. Free energies of solvation (ΔG) of compounds 2a, 3, D-Cl and D-N

  NH were calculated at the M06-2X/def2-TZVP level of theory (solvent

Natural and redesigned wasp venom peptides with selective antitumoral activity

• Marcelo D. T. Torres,
• Gislaine P. Andrade,
• Roseli H. Sato,
• Cibele N. Pedron,
• Tania M. Manieri,
• Giselle Cerchiaro,
• Anderson O. Ribeiro,
• Cesar de la Fuente-Nunez and
• Vani X. Oliveira Jr.

Beilstein J. Org. Chem. 2018, 14, 1693–1703, doi:10.3762/bjoc.14.144

• electrostatic interactions, after which they tend to adopt helical conformations, which causes cell membrane permeabilization or even membrane disruption that may lead to necrosis [33]. These peptides may also be internalized into the cell, leading to the disruption of the mitochondrial membrane and causing

The phenyl vinyl ether–methanol complex: a model system for quantum chemistry benchmarking

• Dominic Bernhard,
• Fabian Dietrich,
• Mariyam Fatima,
• Cristóbal Pérez,
• Hannes C. Gottschalk,
• Axel Wuttke,
• Ricardo A. Mata,
• Martin A. Suhm,
• Melanie Schnell and
• Markus Gerhards

Beilstein J. Org. Chem. 2018, 14, 1642–1654, doi:10.3762/bjoc.14.140

• linearity of the technique and the comparable IR absorption cross section of all predicted dimer conformations (cf. Table 1 and Table S1, Supporting Information File 1): the global minimum structure and any other, higher lying isomers which are initially formed and impeded from relaxation to the global

A conformationally adaptive macrocycle: conformational complexity and host–guest chemistry of zorb[4]arene

• Liu-Pan Yang,
• Song-Bo Lu,
• Arto Valkonen,
• Fangfang Pan,
• Kari Rissanen and
• Wei Jiang

Beilstein J. Org. Chem. 2018, 14, 1570–1577, doi:10.3762/bjoc.14.134

• binding behavior of ZB4 and lays the basis for the construction of stimuli-responsive materials with ZB4 as a major component. Keywords: conformations; host–guest chemistry; macrocycles; supramolecular chemistry; zorb[4]arene; Introduction Macrocyclic receptors are the principal workhorses used in

• solutions and the different conformations in the solid state may result from the packing of the different lower-rim alkyl groups. For the conformers with cavities (Scheme 1b), three out of the four have been predominantly selected by three different guests. For example, guests 2+ and 3+ induced conformers

• IV and III, respectively, to achieve optimal binding [37]. This has been unambiguously confirmed by X-ray single crystallography (Figure 1b and 1c). Guest 10+ is a strong binder and its induction on the conformations of ZB4 was further analyzed. The guest exchange in solution of 10+@ZB4 is fast

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

• ; Introduction EPR spectroscopy is well established to study the structure and dynamics of nucleic acids [1][2][3][4][5][6][7][8]. Although the information attainable by EPR is less detailed when compared to NMR, it is often complementary. While local conformations are normally obtained from NMR data, EPR can

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

• respect to the central benzene ring. In such twisted conformations there is a remarkable steric hindrance between the ortho hydrogen atoms of the central benzene ring and the ortho' hydrogen atoms of the peripheral aromatic units. These conformations are not favorable for a complexation of aromatic guests

• and the host–guest interactions must be able to equilibrate the previously described ortho–ortho' hindrance and to bring the aromatic rings of the caps to coplanar conformations. In this work, we decided to investigate a new cryptand in which this steric hindrance is removed. Thus, we changed the

London dispersion as important factor for the stabilization of (Z)-azobenzenes in the presence of hydrogen bonding

• Andreas H. Heindl,
• Raffael C. Wende and
• Hermann A. Wegner

Beilstein J. Org. Chem. 2018, 14, 1238–1243, doi:10.3762/bjoc.14.106

• can be reversed by the incorporation of azobenzene units in macrocyclic arrangements [15]. For example, the groups of Tamaoki [16] and Herges [17] reported azobenzophanes that isomerize thermally to their energetically lower Z-conformations from their corresponding higher energy E-isomers. Moreover

• are possible for the stabilization of Z-azobenzenes 4–7. To estimate the influences of those effects, a conformer distribution analysis was performed to identify low-lying conformations of the corresponding (Z)-azobenzenes. The energetically favored conformers found (within 1.5 kcal mol−1 for 4 and 5

• kcal mol−1 for 5–7, respectively, relative to the lowest energy conformer) were then re-optimized at the B3LYP/6-31G** [26][27][28][29] level of theory with and without D3(BJ) [30][31] dispersion correction (gas phase) (conformations of one enantiomer of each diastereomer of 4 were analyzed. The

Stereoselective nucleophilic addition reactions to cyclic N-acyliminium ions using the indirect cation pool method: Elucidation of stereoselectivity by spectroscopic conformational analysis and DFT calculations

• Koichi Mitsudo,
• Junya Yamamoto,
• Tomoya Akagi,
• Atsuhiro Yamashita,
• Masahiro Haisa,
• Kazuki Yoshioka,
• Hiroki Mandai,
• Koji Ueoka,
• Christian Hempel,
• Jun-ichi Yoshida and
• Seiji Suga

Beilstein J. Org. Chem. 2018, 14, 1192–1202, doi:10.3762/bjoc.14.100

• reacted with several nucleophiles. These reactions afforded disubstituted piperidine derivatives with high diastereoselectivities and good to excellent yields. The conformations of the obtained N-acyliminium ions were studied by low temperature NMR analyses and DFT calculations and were found to be

• , and C6 were also performed. The conformations of C2 and C6 were similar to those of C1 and C5, respectively (C2: pseudo-equatorial, C6: pseudo-axial). Although the conformation of C4 could not be determined by the NMR analysis, the conformation is assumed to be similar to that of C3 (pseudo-equatorial

• ). First, ΔG of pseudo-equatorial and pseudo-axial conformations of C1 was calculated at the B3LYP/6-31G(d) level of theory. The pseudo-equatorial conformation of C1 was more stable than the pseudo-axial conformation by 1.27 kcal/mol. Similarly, DFT calculations of C3 and C5 were performed, and the results

An overview of recent advances in duplex DNA recognition by small molecules

• Sayantan Bhaduri,
• Nihar Ranjan and
• Dev P. Arya

Beilstein J. Org. Chem. 2018, 14, 1051–1086, doi:10.3762/bjoc.14.93

Fluorocyclisation via I(I)/I(III) catalysis: a concise route to fluorinated oxazolines

• Felix Scheidt,
• Christian Thiehoff,
• Gülay Yilmaz,
• Stephanie Meyer,
• Constantin G. Daniliuc,
• Gerald Kehr and
• Ryan Gilmour

Beilstein J. Org. Chem. 2018, 14, 1021–1027, doi:10.3762/bjoc.14.88

• conformations around the two respective torsion angles [37][38]. In this case, it is also highly probable that hydrogen bonding will reinforce these conformational preferences. Whilst it was not possible to isolate crystals of 3 that were suitable for X-ray analysis, it was possible to unambiguously establish

Correlation effects and many-body interactions in water clusters

• Andreas Heßelmann

Beilstein J. Org. Chem. 2018, 14, 979–991, doi:10.3762/bjoc.14.83

• essential to describe the structures of (H2O)2 and (H2O)3 in many different conformations [15]. A rather good correlation between the coupled-cluster energies and the force-field energies is found for the polarisable AMOEBA2003 [9][16] and TTM4-F [17] potentials both for the dimer and for the trimer. Both

• accounted for by the HF method, see also below. The dependence of the electrostatic and dispersion energy on the structure is highlighted in Figure 5 for three different conformations of the water dimer. These three structures have in common the distance of the oxygen atoms (2.98 Å in this example), but

• interaction strongly reduces by +6 kcal/mol, yet remains attractive having a magnitude of about −6 kcal/mol for the structures 2 and 3. The blue horizontal bars in Figure 6 show the energy levels of the corresponding three-body dispersion energy for the three conformations. As can be seen, it possesses just

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