α-Photooxygenation of chiral aldehydes with singlet oxygen

• Dominika J. Walaszek,
• Magdalena Jawiczuk,
• Jakub Durka,
• Olga Drapała and
• Dorota Gryko

Beilstein J. Org. Chem. 2019, 15, 2076–2084, doi:10.3762/bjoc.15.205

• force field within 5 kcal/mol energy ranges. Further optimization was carried out at DFT level using the B3LYP functional and the Def2TZVP basis set in the Gaussian 09 [36]. Simulations of ECD spectra were carried out with TD-DFT methods for conformers found in the range of 2.5 kcal/mol. The B3LYP

• functional in conjunction with the Def2TZVP basis set was used for computing the first 80 electronic transitions. The final spectrum was obtained by Boltzmann averaging (T = 298 K) according to the population percentages of individual conformers based on the relative Gibbs energies calculated at the same

Synthesis and anion binding properties of phthalimide-containing corona[6]arenes

• Meng-Di Gu,
• Yao Lu and
• Mei-Xiang Wang

Beilstein J. Org. Chem. 2019, 15, 1976–1983, doi:10.3762/bjoc.15.193

• conveniently by means of a macrocyclic condensation reaction between N-functionalized 3,6-dihydroxyphthalimides and 3,6-dichlorotetrazine under mild conditions in a one-pot reaction manner. The novel macrocycles exist as a mixture of rapidly interconvertible conformers in solution while in the solid state they

• ]. The observation of the single set of proton and carbon resonance signals of 3 indicated the presence of the conformer with high symmetry or most likely a mixture of conformers which underwent very fast interconversion relative to the NMR time scale. In comparison to diethyl terephthalate, a

• macrocyclic condensation reaction between N-functionalized 3,6-dihydroxyphthalimides and 3,6-dichlorotetrazine. The unprecedented macrocycles exist as a mixture of rapidly inter-convertible conformers in solution relative to the NMR time scale. The novel O6-corona[3]arene[3]tetrazines self-regulated

Synthesis, enantioseparation and photophysical properties of planar-chiral pillar[5]arene derivatives bearing fluorophore fragments

• Guojuan Li,
• Chunying Fan,
• Guo Cheng,
• Wanhua Wu and
• Cheng Yang

Beilstein J. Org. Chem. 2019, 15, 1601–1611, doi:10.3762/bjoc.15.164

• that differs from the common macrocycles is the planar chirality resulting from the different orientations of the alkoxy substituents on the rims. Theoretically, eight conformers can be formed including diastereomeric ones: (Sp,Sp,Sp,Sp,Sp), (Rp,Sp,Sp,Sp,Sp), (Rp,Rp,Sp,Sp,Sp), (Rp,Sp,Rp,Sp,Sp) and

• their antipodal enantiomers: (Rp,Rp,Rp,Rp,Rp), (Sp,Rp,Rp,Rp,Rp), (Sp,Sp,Rp,Rp,Rp), (Sp,Rp,Sp,Rp,Rp). Among them, the enantiomeric per-Sp (Sp,Sp,Sp,Sp,Sp) and per-Rp (Rp,Rp,Rp,Rp,Rp) conformers (abbreviated as Sp and Rp, respectively), in which all of the alkoxy substituents at both rims are oriented in

• the same direction, are the most stable conformers due to the steric-hindrance effect of the substituents in other conformers. In general, the Sp and Rp conformers can interconvert from each other in solution through the oxygen-through-annulus rotation along the methylene bridges [18], and the

Synthesis and conformational preferences of short analogues of antifreeze glycopeptides (AFGP)

• Małgorzata Urbańczyk,
• Michał Jewgiński,
• Joanna Krzciuk-Gula,
• Jerzy Góra,
• Rafał Latajka and
• Norbert Sewald

Beilstein J. Org. Chem. 2019, 15, 1581–1591, doi:10.3762/bjoc.15.162

• conformational preferences of the examined glycopeptides. Based on the NOESY/ROESY experiments we obtained 6, 27, 10 and 50 distance constrains for peptide 1, 2, 3, and 4, respectively (see Supporting Information File 1). For each of the investigated peptides optimization of 1 000 stable conformers have been

• conformation [36][37]. In case of pentapeptide 4 the calculation resulted in 1 000 conformers. Cluster analysis based on all backbone dihedral angles allowed to identify multiclusters, containing approximately 1% of structures each. However, the clustering based only on the part of the main chain led to higher

An azobenzene container showing a definite folding – synthesis and structural investigation

• Abdulselam Adam,
• Saber Mehrparvar and
• Gebhard Haberhauer

Beilstein J. Org. Chem. 2019, 15, 1534–1544, doi:10.3762/bjoc.15.156

• possible conformations [cis,trans-(M), cis,trans-(P), cis,cis-(M,M), cis,cis-(M,P) and cis,cis-(P,P)]. However, it turned out that the P conformers represent no minima on the potential energy surface. Furthermore, single point calculations by means of the density functionals B3LYP and B3LYP-D3 were

2,3-Dibutoxynaphthalene-based tetralactam macrocycles for recognizing precious metal chloride complexes

• Li-Li Wang,
• Yi-Kuan Tu,
• Huan Yao and
• Wei Jiang

Beilstein J. Org. Chem. 2019, 15, 1460–1467, doi:10.3762/bjoc.15.146

• suggests that the conformational interconversion is slow at this temperature and only one conformer is predominant in the solution at 298 K. However, the exact conformer cannot be assigned because the two conformers have the same number of peaks. In contrast, H3 of 2 are broadened even at room temperature

• conformers are possible. As shown in Figure 5a, AuCl4− can be well accommodated in the cavity of 1. AuCl4− is sandwiched by the two 2,3-dibutoxynaphthalene moieties, and the electron-poor gold centre of AuCl4− may interact with the electron-rich naphthalenes through electrostatic interactions. In addition

Efficient resolution of racemic crown-shaped cyclotriveratrylene derivatives and isolation and characterization of the intermediate saddle isomer

• Sven Götz,
• Andreas Schneider and
• Arne Lützen

Beilstein J. Org. Chem. 2019, 15, 1339–1346, doi:10.3762/bjoc.15.133

• stable saddle conformers. A first example of such a saddle isomer of an achiral hexamethoxy-substituted CTV could be isolated and described by Luz and co-workers in 2004 [26]. At that time, they achieved this by heating the crown form to high temperatures and subsequent rapid cooling of the mixture

• elaborated derivatives [58][59] and the ease of a recently established large-scale synthesis reported by Rousseau and co-workers [60]. Hence, we decided to revisit this compound in order to improve the separation in terms of both better resolution of the enantiomeric bowl-shaped conformers and isolation of

• six conformers. The equilibrium between these species is, in fact, so fast that the individual conformers cannot be isolated, even by cooling down to 100 K in a freon solvent as tried by Luz and co-workers for a nonamethoxy-CTV [27][28]. On the NMR time scale this results in an average C3h-symmetry of

Bambusuril analogs based on alternating glycoluril and xylylene units

• Tomáš Lízal and
• Vladimír Šindelář

Beilstein J. Org. Chem. 2019, 15, 1268–1274, doi:10.3762/bjoc.15.124

• product. Two disastereomers of the macrocycle were separated and characterized by means of NMR spectroscopy and X-ray crystallography. Conformational changes of these diastereomers were investigated using DFT models and variable-temperature NMR. Keywords: bambusurils; conformers; glycolurils; macrocycles

• macrocycle, we envisioned that the signal broadening is caused by rapid interconversion between several preferred conformers of the macrocycle. The DFT optimization performed at the CAM-B3LYP/6-31G(d) level of theory revealed that 1a can occur in form of two preferred conformers 1a-1 and 1a-2 (Figure 2). The

• optimized structures provided us with support to understand the spatial arrangement of the conformers for further NMR studies. While broad signals of 1a were obtained at 30 °C, lowering of the temperature resulted in sharpening of the signals in the 1H NMR spectra. The spectrum of 1a measured at −40 °C in

Ugi reaction-derived prolyl peptide catalysts grafted on the renewable polymer polyfurfuryl alcohol for applications in heterogeneous enamine catalysis

• Alexander F. de la Torre,
• Gabriel S. Scatena,
• Oscar Valdés,
• Daniel G. Rivera and
• Márcio W. Paixão

Beilstein J. Org. Chem. 2019, 15, 1210–1216, doi:10.3762/bjoc.15.118

• peptide 1 as colorless oil. A mixture of conformers was observed by NMR (ratio 3:1). Assigned signals belong to the mixture of conformers. Yield: 81%; Rf 0.34 (EtOAc/hexane 1:1, v/v); [α]D20 − 19.9 (c 0.0085 g·cm−3, MeOH); 1H NMR (400 MHz, CDCl3) δ 0.99–1.19 (m, 3H), 1.29–1.39 (m, 2H), 1.43 (s, 3H), 1.45

Halogen bonding and host–guest chemistry between N-alkylammonium resorcinarene halides, diiodoperfluorobutane and neutral guests

• Fangfang Pan,
• Mohadeseh Dashti,
• Michael R. Reynolds,
• Kari Rissanen,
• John F. Trant and
• Ngong Kodiah Beyeh

Beilstein J. Org. Chem. 2019, 15, 947–954, doi:10.3762/bjoc.15.91

• the motion of the molecules in solution, and the evaporation of the solvent molecules during crystal growth. Waving of the hexyl groups also affects one of the propyl groups in the lower rim of the resorcinarene. As a result, the two conformers A and B also differentiate from each other in the lower

Strong hyperconjugative interactions limit solvent and substituent influence on conformational equilibrium: the case of cis-2-halocyclohexylamines

• Camila B. Francisco,
• Cleverton S. Fernandes,
• Ulisses Z. de Melo,
• Roberto Rittner,
• Gisele F. Gauze and
• Ernani A. Basso

Beilstein J. Org. Chem. 2019, 15, 818–829, doi:10.3762/bjoc.15.79

• group and equatorial halogen) and ea (equatorial amine group and axial halogen) conformers (Figure 1) by dynamic NMR (DNMR) and theoretical calculations. Results and Discussion Experimental conformational population Low-temperature NMR experiments allow the identification of the individual conformers

• corresponds to H1, vicinal to nitrogen, and the signal at 4.32 ppm to H2, vicinal to chlorine (Figure 2). These 1H resonances, at room temperature, correspond to the average of the conformers at equilibrium. Table 1 shows the spectral data for F, Cl and Br at 25 and −80 °C, where 3JH–H refers to the

• correspond to ae (H1ax and H2eq) and ea (H1eq and H2ax) conformers individually (Table 1). The values of 3JH–H, δ and W at −80 °C allow the assignment of the signals to the respective conformers, and by the integrals, determination the percentage of each in the equilibrium. In the case of the bromine

Homo- and hetero-difunctionalized β-cyclodextrins: Short direct synthesis in gram scale and analysis of regiochemistry

• Gábor Benkovics,
• Mihály Bálint,
• Éva Fenyvesi,
• Erzsébet Varga,
• Szabolcs Béni,
• Konstantina Yannakopoulou and
• Milo Malanga

Beilstein J. Org. Chem. 2019, 15, 710–720, doi:10.3762/bjoc.15.66

• allowed the identification of the spin system of each glucopyranose unit among which the tosylated ones can be identified using the resonance frequencies of H6,6’ as an entry point. Three staggered conformers with respect to the TsO–C(6)–C(5)–H(5) dihedral angle (see Figure 3d for numbering) are possible

Influence of per-O-sulfation upon the conformational behaviour of common furanosides

• Alexey G. Gerbst,
• Vadim B. Krylov,
• Dmitry A. Argunov,
• Maksim I. Petruk,
• Arsenii S. Solovev,
• Andrey S. Dmitrenok and
• Nikolay E. Nifantiev

Beilstein J. Org. Chem. 2019, 15, 685–694, doi:10.3762/bjoc.15.63

• and β-galactose. Full exploration of the furanoside ring by means of ab initio calculations was performed and coupling constants were calculated for each of the low-energy conformers. The results demonstrated preferred trans-orientation of H4–H5 protons in the non-sulfated molecules which changed to

• -energy conformers which differed from each other by less than 2 kcal/mol. The other conformations found had considerably higher energies. For non-sulfated structures 1–3 sometimes high-energy conformations were obtained with the same puckering state of the furanoside ring (see Tables in Supporting

• descriptions of all the low-energy conformations obtained. The whole list of the resulting conformers can be found in Supporting Information File 1. All the obtained conformers are plotted on the pseudo-rotation wheel diagrams, where low-energy conformers are shown in red dots (Figure 1). Schematic views of

Conformational signature of Ishikawa´s reagent using NMR information from diastereotopic fluorines

• Laize A. F. Andrade,
• Lucas A. Zeoly,
• Rodrigo A. Cormanich and
• Matheus P. Freitas

Beilstein J. Org. Chem. 2019, 15, 506–512, doi:10.3762/bjoc.15.44

• parameter is sensitive to this dihedral angle according to a Karplus-like shape [27], while its sign is subjected to other effects [28]. Also, the observed 3JH,F(pro-S/R) values (Table 1) are expected to be dependent on the medium, because the conformers of 1 are anticipated to have different molecular

• solvent dependence of 3JH,F(pro-S/R), indicating that the conformational equilibrium of 1 changes on going from cyclohexane (nonpolar) to pyridine (polar) solution. According to the calculated molecular dipole moments for the possible conformers of 1 (Table 2), a significant interplay of conformers 1B and

• 3JH,F(pro-S/R) with the solvent is due to a shift from 1A towards 1B or 1C. According to the Karplus curve, conformers 1A are not anticipated to have significantly different 3JH,F(1) SSCCs, since both diastereotopic fluorines are gauche to H-2. However, SSCC calculations (Supporting Information File 1

Synthesis and fluorescent properties of N(9)-alkylated 2-amino-6-triazolylpurines and 7-deazapurines

• Andrejs Šišuļins,
• Jonas Bucevičius,
• Yu-Ting Tseng,
• Irina Novosjolova,
• Kaspars Traskovskis,
• Ērika Bizdēna,
• Huan-Tsung Chang,
• Sigitas Tumkevičius and
• Māris Turks

Beilstein J. Org. Chem. 2019, 15, 474–489, doi:10.3762/bjoc.15.41

• , steepest descent algorithm) and systematic conformational analysis as implemented in Avogadro 1.1.1 software. The minimum energy conformers found by molecular mechanics were further optimized with the Gaussian 09 program package [57] by the means of DFT using B3LYP exchange–correlation hybrid functional

Sigmatropic rearrangements of cyclopropenylcarbinol derivatives. Access to diversely substituted alkylidenecyclopropanes

• Guillaume Ernouf,
• Jean-Louis Brayer,
• Christophe Meyer and
• Janine Cossy

Beilstein J. Org. Chem. 2019, 15, 333–350, doi:10.3762/bjoc.15.29

• , which is opposite at C2, was assigned by comparison of their computed and experimentally observed CD spectra [33][34]. To tentatively explain the observed stereochemical outcome in the absence of additional knowledge on the transition state of the rearrangement [36], two reactive conformers G and G

A simple and effective preparation of quercetin pentamethyl ether from quercetin

• Jin Tatsuzaki,
• Tomohiko Ohwada,
• Yuko Otani,
• Reiko Inagi and
• Tsutomu Ishikawa

Beilstein J. Org. Chem. 2018, 14, 3112–3121, doi:10.3762/bjoc.14.291

• -consistent reaction field, SCRF) were simulated by using the CPCM method in DMSO as a solvent. The zero-point vibrational energy corrections were done without scaling. Three typical conformers of quercetin (2) were considered (Figure 3). These are the regioisomers with respect to the direction of the OH

• , 149.0, 151.2, 152.6, 159.0, 161.3, 164.1, 174.1. Structures of quercetin pentamethyl ether (QPE, 1) and quercetin (2). Selected HMBC correlations of 6-methyl-3,5,7,3',4'-penta-O-methylquercetin (5). Three representative conformers of neutral quercetin (2). Top and side views are shown. The relative

6’-Fluoro[4.3.0]bicyclo nucleic acid: synthesis, biophysical properties and molecular dynamics simulations

• Sibylle Frei,
• Andrei Istrate and
• Christian J. Leumann

Beilstein J. Org. Chem. 2018, 14, 3088–3097, doi:10.3762/bjoc.14.288

• conformers a pseudoaxial position. Consequently, the torsion angle γ was aligned in a +sc arrangement (C2’-endo conformer: 64°; C3’-exo conformer: 83°). The distance between the fluorine atom and the C(5’) oxygen was 3.3 Å in the C2’-endo conformer and 2.9 Å in the C3’-exo conformer. These two conformers

• analogs. Proposed mechanism for the formation of the 5’-phosphorylated fragments during the oxidation step in the synthesis of ON1 and ON2. a) Potential energy profile versus pseudorotation phase angle of nucleoside 8 and its two minimal energy conformers: b) C2’-endo and c) C3’-exo. Average structures of

Calixazulenes: azulene-based calixarene analogues – an overview and recent supramolecular complexation studies

• Paris E. Georghiou,
• Shofiur Rahman,
• Abdullah Alodhayb,
• Hidetaka Nishimura,
• Jaehyun Lee,
• Atsushi Wakamiya and
• Lawrence T. Scott

Beilstein J. Org. Chem. 2018, 14, 2488–2494, doi:10.3762/bjoc.14.225

• possibilities are ongoing. Examples of calix[n]arenes 1 and calix[4]azulenes 2–5. Three major computed conformers of OPC4A; a: 1,2-alternate; b: cone and c: saddle. Geometry-optimized (ωB97xD/6-31G(d)) and (ωB97xD/GenECP) structures, respectively, computed for left: (a) 5TBACl; (b) 5TBABr; and (c) 5TBAI; right

Synthesis of eunicellane-type bicycles embedding a 1,3-cyclohexadiene moiety

• Alex Frichert,
• Peter G. Jones and
• Thomas Lindel

Beilstein J. Org. Chem. 2018, 14, 2461–2467, doi:10.3762/bjoc.14.222

• conversion to the diastereomer by oxidation and reduction. Conformational analysis of some of the resulting diols obtained under McMurry conditions was complicated by the presence of several conformers of similar energy. The pinacol coupling appears to start at the ketone, as indicated by the selective

• two conformers in CDCl3. Thus, it was to be explored how open-ring cyclohexadiene precursors would be synthesized and behave under McMurry conditions, and how stable the resulting [8.4.0]bicycles would be. Normally, McMurry conditions lead to the formation of alkenes, but medium-sized ring 1,2-diols

• ). For diastereomer 19, 2-H did not show a NOESY correlation to 5-Hβ, but instead a correlation to 14-H, to the isopropyl methine hydrogen, and to 3-CH3. In addition, 3-CH3 correlates with both methylene hydrogens at C4. We found only two conformers of the (2S,3S,14R) diastereomer that meet those

Nucleoside macrocycles formed by intramolecular click reaction: efficient cyclization of pyrimidine nucleosides decorated with 5'-azido residues and 5-octadiynyl side chains

• Jiang Liu,
• Peter Leonard,
• Sebastian L. Müller,
• Constantin Daniliuc and
• Frank Seela

Beilstein J. Org. Chem. 2018, 14, 2404–2410, doi:10.3762/bjoc.14.217

• conformations of the 5’-azido compounds 7 and 2 as well as dC macrocycle 4 were investigated in solution. To this end, high resolution spectra (600 MHz NMR) were measured in DMSO-d6 and the population of S vs N conformers (Supporting Information File 1, Table S2) were calculated using the program PSEUROT

D-Fructose-based spiro-fused PHOX ligands: synthesis and application in enantioselective allylic alkylation

• Michael R. Imrich,
• Jochen Kraft,
• Cäcilia Maichle-Mössmer and
• Thomas Ziegler

Beilstein J. Org. Chem. 2018, 14, 2082–2089, doi:10.3762/bjoc.14.182

• be further forced towards 9a. Since in both conformers one R2 is axial and the other is equatorial the bulkiness of R2 should have no influence on the equilibrium. Both conformers can be attacked by 8 from two different sides, where each one leads to an addition product in chair conformation or to a

• conformers 9a and 9b. Neighboring group participation of ester protective groups. For better clarity C-2 is not shown in conformers 9a and 9c. Pd catalyzed Tsuji–Trost reation. BSA: N,O-bis(trimethylsilyl)acetamide, DMM: dimethyl malonate. Synthesis of spiro-fused oxazolines 10 and 11 via Ritter reaction

Synthesis of new p-tert-butylcalix[4]arene-based polyammonium triazolyl amphiphiles and their binding with nucleoside phosphates

• Vladimir A. Burilov,
• Guzaliya A. Fatikhova,
• Mariya N. Dokuchaeva,
• Ramil I. Nugmanov,
• Diana A. Mironova,
• Pavel V. Dorovatovskii,
• Victor N. Khrustalev,
• Svetlana E. Solovieva and
• Igor S. Antipin

Beilstein J. Org. Chem. 2018, 14, 1980–1993, doi:10.3762/bjoc.14.173

• chemical calculations were done in several steps: selection of optimal conformers; organization of initial complex geometry; complex optimization procedure. The conformers search procedure has been done only for calix[4]arene’s triazolyl substituents due to complexity of the whole molecule. Conformers of

• MOPAC 2016 program [61] with discard of repeated duplicates. Then unique conformers were combined with calix[4]arene core, and corresponding cations and complexes with ATP/ADP were optimized by DFT calculations. For DFT calculations Priroda 16 program [62] with build-in PBE functional on L2 basis level

Diazirine-functionalized mannosides for photoaffinity labeling: trouble with FimH

• Femke Beiroth,
• Tomas Koudelka,
• Thorsten Overath,
• Stefan D. Knight,
• Andreas Tholey and
• Thisbe K. Lindhorst

Beilstein J. Org. Chem. 2018, 14, 1890–1900, doi:10.3762/bjoc.14.163

• force field and 30 different conformers of each ligand were docked into two different X-ray structures of FimH (for details see Supporting Information File 1). These two crystal structures differ in the conformation of the tyrosine gate, formed by Y48 and Y137 positioned at the entrance of the

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

• auxiliary Coulomb fitting basis set (cbas) for the resolution-of-identity approximation (RI) for which def2-TZVP-cbas was chosen [60]. All obtained geometries were confirmed as minima by harmonic frequency calculations. In order to evaluate the relative stability of the different conformers found on the

• confirmed the subtle difference between the six conformers, with an energy span of approximately 4–5 kJ/mol (≈1 kcal/mol, the commonly accepted definition of chemical accuracy) among all structures. Also featured in Table 1 are the computed O–H stretch fundamentals together with the IR intensity at the two

• significantly. The moiety with the largest potential as dispersion energy donor (DED) is the phenyl ring. This results in the strongest stabilization for the two conformers whereby the methanol is closest to the ring (OH–P and OH–P’). The other conformers have much more spread out contributions. What is