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Search for "conformer" in Full Text gives 185 result(s) in Beilstein Journal of Organic Chemistry.

Preparation of neuroprotective condensed 1,4-benzoxazepines by regio- and diastereoselective domino Knoevenagel–[1,5]-hydride shift cyclization reaction

  • László Tóth,
  • Yan Fu,
  • Hai Yan Zhang,
  • Attila Mándi,
  • Katalin E. Kövér,
  • Tünde-Zita Illyés,
  • Attila Kiss-Szikszai,
  • Balázs Balogh,
  • Tibor Kurtán,
  • Sándor Antus and
  • Péter Mátyus

Beilstein J. Org. Chem. 2014, 10, 2594–2602, doi:10.3762/bjoc.10.272

Graphical Abstract
  • compared with the computed ECD spectra of the gas-phase optimized conformers (>1%) of model compound (2S,15aS)-7d (1 conformer, B3LYP/TZVP) and (2S,15aS)-7b (2 conformers, BH&HLYP/TZVP). Bars represent the computed rotational strength values (R/8) of the lowest-energy conformer. c) Structure of the (2S
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Published 06 Nov 2014

Pyrrolidine nucleotide analogs with a tunable conformation

  • Lenka Poštová Slavětínská,
  • Dominik Rejman and
  • Radek Pohl

Beilstein J. Org. Chem. 2014, 10, 1967–1980, doi:10.3762/bjoc.10.205

Graphical Abstract
  • interconverting conformer in solution, resulting in the observation of averaged experimental 3JHH. Nevertheless, even these averaged 3JHH can be used for conformational analysis by means of the program PSEUROT [10], which minimizes differences between experimental and calculated 3JHH, assuming a two-state
  • pyrrolidine ring on its conformation. The conformation of phosphonomethyl derivatives 7 and 9 with trans configuration on 3’ and 4’ carbon atoms tends to occupy mainly (~60%) the 1T2 or 1E conformation in an equilibrium with the less populated (~40%) 1E conformer. This equilibrium is significantly shifted in
  • hydrogen bonding between the 3’-OH group and the 4’-nucleobase substituent. A similar effect in the conformer populations was observed for phosphonoformyl derivatives. While trans derivatives 11 and 13 exist as an about 1:1 equilibrium mixture of 3T4 and 3T4 conformations, cis derivatives 12 and 14 prefer
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Published 22 Aug 2014

Isoxazolium N-ylides and 1-oxa-5-azahexa-1,3,5-trienes on the way from isoxazoles to 2H-1,3-oxazines

  • Alexander F. Khlebnikov,
  • Mikhail S. Novikov,
  • Yelizaveta G. Gorbunova,
  • Ekaterina E. Galenko,
  • Kirill I. Mikhailov,
  • Viktoriia V. Pakalnis and
  • Margarita S. Avdontceva

Beilstein J. Org. Chem. 2014, 10, 1896–1905, doi:10.3762/bjoc.10.197

Graphical Abstract
  • of compound 3a in the crystal corresponds to the most stable conformer according to calculations at DFT B3LYP/6-31G(d) level in vacuo (ΔΔG298 K (equatorial/axial = 1.2 kcal/mol). One of the possible reasons for the higher stability of conformer 3a with a pseudo-axial methoxycarbonyl group in
  • comparison to conformer 3a' with a pseudo-equatorial methoxycarbonyl group, is assumed to be the anomeric effect [24]. The lengthening of the C–CO2Me bond in conformer 3a compared to conformer 3a' (1.563/1.554 Å), corroborates this hypothesis. The pseudo-axia position of the methoxycarbonyl group is
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Published 14 Aug 2014

The chemoenzymatic synthesis of clofarabine and related 2′-deoxyfluoroarabinosyl nucleosides: the electronic and stereochemical factors determining substrate recognition by E. coli nucleoside phosphorylases

  • Ilja V. Fateev,
  • Konstantin V. Antonov,
  • Irina D. Konstantinova,
  • Tatyana I. Muravyova,
  • Frank Seela,
  • Roman S. Esipov,
  • Anatoly I. Miroshnikov and
  • Igor A. Mikhailopulo

Beilstein J. Org. Chem. 2014, 10, 1657–1669, doi:10.3762/bjoc.10.173

Graphical Abstract
  • characterized by the closely related total energy (ET) values were found for the α-anomer 12a. The slightly more stable conformation (C-3-exo conformer; ET = −732311.2 kcal/mol) is stabilized by the intramolecular C-3OH···−OP (1.68 Å) hydrogen bond and the close proximity of the C-5OH hydrogen and FC-2 fluorine
  • atoms (C-5OH···FC-2 1.98 Å). The other structure (C-3-exo conformer; ET = −732310.1 kcal/mol) does not contain the intramolecular hydrogen bonds. The torsion angles of the vicinal hydrogen atoms H-1/H-2 and H-2/H-3, the hydrogen–fluorine (H-1/F and H-3/F) and hydrogen–phosphorus (H-1/P), and the carbon
  • the less stable conformer (ET = −732297.1 kcal/mol) with a twist 3T2 spatial structure of the pentofuranose ring is in accordance with the experimental coupling constant of 5.40 Hz, whereas those of H-1/H-2 and H-2/H-3 disagree with the relevant couplings (Figure 3; for detailed information, see Table
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Published 22 Jul 2014

Synthesis of the first examples of iminosugar clusters based on cyclopeptoid cores

  • Mathieu L. Lepage,
  • Alessandra Meli,
  • Anne Bodlenner,
  • Céline Tarnus,
  • Francesco De Riccardis,
  • Irene Izzo and
  • Philippe Compain

Beilstein J. Org. Chem. 2014, 10, 1406–1412, doi:10.3762/bjoc.10.144

Graphical Abstract
  • by compound 9a (Figure 2i). This phenomenon, already observed for N-substituted cyclic α-peptoid derivatives [35][36][37][38][39], indicated the presence of more than one conformer in slow exchange on the NMR time scale. It is well known that the conformational heterogeneity is due to tertiary amide
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Published 23 Jun 2014

Substitution effect and effect of axle’s flexibility at (pseudo-)rotaxanes

  • Friedrich Malberg,
  • Jan Gerit Brandenburg,
  • Werner Reckien,
  • Oldamur Hollóczki,
  • Stefan Grimme and
  • Barbara Kirchner

Beilstein J. Org. Chem. 2014, 10, 1299–1307, doi:10.3762/bjoc.10.131

Graphical Abstract
  • for the understanding and the development of rotaxanes. Zerbetto et al. showed that the shuttling motion can be separated from the other degrees of freedom, and that the effective coordinate of the motion can be described as a double-minimum potential [18]. The co-conformer stability for rotaxane
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Published 05 Jun 2014

The Ugi four-component reaction as a concise modular synthetic tool for photo-induced electron transfer donor-anthraquinone dyads

  • Sarah Bay,
  • Gamall Makhloufi,
  • Christoph Janiak and
  • Thomas J. J. Müller

Beilstein J. Org. Chem. 2014, 10, 1006–1016, doi:10.3762/bjoc.10.100

Graphical Abstract
  • pairs resulting in four stacked (hetero)aromatic units (Figure 2), so that the anthraquinone moieties of two molecules display an average distance of ~3.8 Å. Based upon the X-ray data quantum mechanical computations on this conformer were envisioned (vide infra). Electronic properties and electronic
  • dyad 1 an electronic prerequisite for electronically favored electron-transfer processes in donor–acceptor systems is the spatial proximity of PT and AQ. This conformer is additionally stabilized by π-stacking of the donor and the acceptor, which is adopted in the solid state and results in a strong
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Published 05 May 2014

Conformational analysis of 2,2-difluoroethylamine hydrochloride: double gauche effect

  • Josué M. Silla,
  • Claudimar J. Duarte,
  • Rodrigo A. Cormanich,
  • Roberto Rittner and
  • Matheus P. Freitas

Beilstein J. Org. Chem. 2014, 10, 877–882, doi:10.3762/bjoc.10.84

Graphical Abstract
  • one single fluorine gauche to the nitrogen atom (anti-gauche, ag) (Table 1). In fact, the most stable conformer of the neutral compound contains two fluorines gauche to the amino group, which presents both hydrogens directed toward fluorines, suggesting the formation of F···HN hydrogen bond. However
  • . The conformational preference dramatically changes after protonation of 1 to give the 2,2-difluoroethylammonium cation (2), i.e. the conformer containing both fluorines gauche to the ammonium group (gg) is practically the single form in the equilibrium in the gas phase and, even in water solution
  • , this conformer is calculated to amount to 90%. This preference is corroborated by NMR experiments (Supporting Information, File 1), because the measured 3JH,H and 3JH,F coupling constants (which have angular dependence according to the well known Karplus curve [12][13][14]) are consistent with the
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Published 16 Apr 2014

Use of activated enol ethers in the synthesis of pyrazoles: reactions with hydrazine and a study of pyrazole tautomerism

  • Denisa Tarabová,
  • Stanislava Šoralová,
  • Martin Breza,
  • Marek Fronc,
  • Wolfgang Holzer and
  • Viktor Milata

Beilstein J. Org. Chem. 2014, 10, 752–760, doi:10.3762/bjoc.10.70

Graphical Abstract
  • Information File 1, Tables S2–S5 and S14) but because of energy reasons the relative population of the C conformer must be vanishing in agreement with experimental data. This was confirmed by calculated NMR spectra (Supporting Information File 1, Table S15). Nevertheless, DFT data indicate a much lower
  • proportion of the B conformer than implied by the experimental data. In contrast to the A tautomer, the B and C tautomers have planar >C–C–N–N–C–C< chains. X-ray and DFT optimized structures of the A tautomer exhibit significant differences in torsional angles only (see Supporting Information File 1, Tables
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Published 01 Apr 2014

Chromatographically separable rotamers of an unhindered amide

  • Mario Geffe,
  • Lars Andernach,
  • Oliver Trapp and
  • Till Opatz

Beilstein J. Org. Chem. 2014, 10, 701–706, doi:10.3762/bjoc.10.63

Graphical Abstract
  • conformer, a potential energy surface (PES) scan for the rotation around the C–N bond in steps of 10° was done. This scan provided two local minima as well as two maxima (Figure 5). The asymmetric peak shape is caused by the inversion of the pyramidal nitrogen between = 110° and = 120° as well as = 280
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Published 21 Mar 2014

New hydrogen-bonding organocatalysts: Chiral cyclophosphazanes and phosphorus amides as catalysts for asymmetric Michael additions

  • Helge Klare,
  • Jörg M. Neudörfl and
  • Bernd Goldfuss

Beilstein J. Org. Chem. 2014, 10, 224–236, doi:10.3762/bjoc.10.18

Graphical Abstract
  • nitrogen N1, which is significantly shorter in 7a (2.194/2.110 Å respectively). The intramolecular hydrogen bond is probably also the cause for the occurrence of conformational isomers when inverting the configuration at C9. While catalyst (S)-4 solely exists as one conformer on the NMR timescale, its
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Published 21 Jan 2014

The regioselective synthesis of spirooxindolo pyrrolidines and pyrrolizidines via three-component reactions of acrylamides and aroylacrylic acids with isatins and α-amino acids

  • Tatyana L. Pavlovskaya,
  • Fedor G. Yaremenko,
  • Victoria V. Lipson,
  • Svetlana V. Shishkina,
  • Oleg V. Shishkin,
  • Vladimir I. Musatov and
  • Alexander S. Karpenko

Beilstein J. Org. Chem. 2014, 10, 117–126, doi:10.3762/bjoc.10.8

Graphical Abstract
  • verified by calculations of vibrational frequencies within the harmonic approximation, using analytical second derivatives at the same level of theory. All stationary points possess zero imaginary frequencies. It was found that the acrylamide conformer I was more stable than conformer II by 1.24 kcal/mol
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Published 09 Jan 2014

Stereoselectively fluorinated N-heterocycles: a brief survey

  • Xiang-Guo Hu and
  • Luke Hunter

Beilstein J. Org. Chem. 2013, 9, 2696–2708, doi:10.3762/bjoc.9.306

Graphical Abstract
  • contrast however, introduction of a (6R)-fluorine atom (compound 23) greatly rigidified the ring system, to the extent that a single conformer of 23 dominated in solution. This work highlights the subtleties that can arise when fluorine atoms are incorporated into highly flexible molecules with pre
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Published 29 Nov 2013

Dipolar addition to cyclic vinyl sulfones leading to dual conformation tricycles

  • Steven S. Y. Wong,
  • Michael G. Brant,
  • Christopher Barr,
  • Allen G. Oliver and
  • Jeremy E. Wulff

Beilstein J. Org. Chem. 2013, 9, 1419–1425, doi:10.3762/bjoc.9.159

Graphical Abstract
  • (HSQC, HMBC, ROESY, TOCSY and EXSY). The most significant difference between the NMR data for the two conformations was the substantial upfield shift for the two protons adjacent to the carbonyl (‘d’ in Figure 2) in the major conformer. This was consistent with this methylene group being substantially
  • shielded by the electron-rich aromatic ring, as would be expected for the conformation observed in the X-ray structure (Figure 1). This upfield shift was not present in the minor conformer, suggesting that the pyrazolidinone ring had moved away from the aromatic ring’s magnetic influence. Analysis of
  • the two lowest-energy structures shown in Figure 2A. Compellingly, the difference in ΔHf between these two structures (0.93 kcal/mol in favor of the exo conformer) agrees very well with the experimental difference in energy calculated from NMR integration of the two conformations at 213 K (0.8 kcal
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Published 15 Jul 2013

Conformational analysis and intramolecular interactions in monosubstituted phenylboranes and phenylboronic acids

  • Josué M. Silla,
  • Rodrigo A. Cormanich,
  • Roberto Rittner and
  • Matheus P. Freitas

Beilstein J. Org. Chem. 2013, 9, 1127–1134, doi:10.3762/bjoc.9.125

Graphical Abstract
  • to evaluate the difference in affinity of boron towards oxygen and nitrogen electron pairs in 2-aminocarbonylphenylboronic acid (2-AC-PBA) and its corresponding ester, ethanediol(2-aminocarbonyl)phenylboronate (ED-2-AC-PB), that has been identified for some conformer interactions of type B–N and B–O
  • 1a and 1b relative to 2a. Conformer 1c was found to be stabilized by a nonbonding F∙∙∙O interaction, which contributes to the formation of pseudo five-membered rings. This would be possible because of an nF→π*CC interaction (Figure 3), which contributes to a resonance structure with positive fluorine
  • capable of interacting attractively with oxygen. Table 1 shows that the nF→π*CC interaction in 1c is ca. 3 kcal mol−1 stronger than in 1a and 1b, but not strong enough to make this conformer appreciably populated. Overall, 1a was calculated to be practically the only existing conformer, because of its
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Published 11 Jun 2013

4-Pyridylnitrene and 2-pyrazinylcarbene

  • Curt Wentrup,
  • Ales Reisinger and
  • David Kvaskoff

Beilstein J. Org. Chem. 2013, 9, 754–760, doi:10.3762/bjoc.9.85

Graphical Abstract
  • liquid N2 at −196 °C, or at 2092 cm−1 upon isolation in an Ar matrix at 10 K. The diazo compound is also formed on matrix photolysis of the triazole (Figure 1). Compound 22 can exist as s-Z and s-E conformers. One conformer dominates, absorbing strongly at 2092 cm−1; the other, minor absorption is at
  • 2092 cm−1 (major conformer) and 2076 cm−1 (minor conformer) (Figure 1): IR (Ar, 7 K) 795, 835, 918, 1009, 1056, 1150, 1299, 1434, 1476, 1574, 2076, 2092 cm−1. A small amount of the photoproduct 20 also appeared (1872 cm−1; Figure 1). Further photolysis afforded the product spectrum shown in Figure 2
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Published 17 Apr 2013

Chemoenzymatic synthesis and biological evaluation of enantiomerically enriched 1-(β-hydroxypropyl)imidazolium- and triazolium-based ionic liquids

  • Paweł Borowiecki,
  • Małgorzata Milner-Krawczyk and
  • Jan Plenkiewicz

Beilstein J. Org. Chem. 2013, 9, 516–525, doi:10.3762/bjoc.9.56

Graphical Abstract
  • previously [58]. The absolute configuration of the substrate is deduced by interpretation of the signs of the ΔδRS values, by using an empirical model that assumes that in MPA esters of secondary alcohols, the most representative conformer has the methoxy group of MPA, the carbonyl group, and a proton bonded
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Published 12 Mar 2013

Thermotropic and lyotropic behaviour of new liquid-crystalline materials with different hydrophilic groups: synthesis and mesomorphic properties

  • Alexej Bubnov,
  • Miroslav Kašpar,
  • Věra Hamplová,
  • Ute Dawin and
  • Frank Giesselmann

Beilstein J. Org. Chem. 2013, 9, 425–436, doi:10.3762/bjoc.9.45

Graphical Abstract
  • scattering. As an example, the temperature dependence of the smectic layer spacing d, for TL1 is shown in Figure 4. The MOPAC/AM1 model has been used to calculate the length of TL1 in the energy-optimized conformation, which gives 41 Å for the most extended conformer. In X-ray data taken at small scattering
  • conformer. This fact gives evidence for the bent-like conformation of the molecule, i.e., the molecule core is rigid but the flexible chains are bent and not extended at all. The increase of scattered X-ray signal intensity on cooling also confirms the increase of the order with temperature decrease (Figure
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Published 25 Feb 2013

Caryolene-forming carbocation rearrangements

  • Quynh Nhu N. Nguyen and
  • Dean J. Tantillo

Beilstein J. Org. Chem. 2013, 9, 323–331, doi:10.3762/bjoc.9.37

Graphical Abstract
  • -energy conformer found); see Experimental for details. Computed minima and transition-state structure involved in the single-step conversion of A to C. Relative energies shown (kcal/mol) were calculated at the mPW1PW91/6-31+G(d,p)//B3LYP/6-31+G(d,p) level. IRC from TS-AC toward C. Relative energies were
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Published 13 Feb 2013

Synthesis of 5-(ethylsulfonyl)-2-methoxyaniline: An important pharmacological fragment of VEGFR2 and other inhibitors

  • Miroslav Murár,
  • Gabriela Addová and
  • Andrej Boháč

Beilstein J. Org. Chem. 2013, 9, 173–179, doi:10.3762/bjoc.9.20

Graphical Abstract
  • ; S, 14.77%. The AAZ ligand conformer from PDB complex 1Y6A and its VEGFR2 intermolecular interaction map depicting three hydrogen bonds and two stacked (π,π) interactions. No lipophilic interactions are shown here. The part of the skeleton AAZ in bold represents the fragment originating from the
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Published 25 Jan 2013

The diketopiperazine-fused tetrahydro-β-carboline scaffold as a model peptidomimetic with an unusual α-turn secondary structure

  • Francesco Airaghi,
  • Andrea Fiorati,
  • Giordano Lesma,
  • Manuele Musolino,
  • Alessandro Sacchetti and
  • Alessandra Silvani

Beilstein J. Org. Chem. 2013, 9, 147–154, doi:10.3762/bjoc.9.17

Graphical Abstract
  • molecular modeling and these experimental results, for 1a we can presume the presence in solution of conformers bearing a 13-membered intramolecular hydrogen bond involving the NHMe proton and the Cbz carbonyl group, as visualized in the perspective view of the low energy conformer of 1a. Conclusion In
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Published 22 Jan 2013

The β-cyclodextrin/benzene complex and its hydrogen bonds – a theoretical study using molecular dynamics, quantum mechanics and COSMO-RS

  • Jutta Erika Helga Köhler and
  • Nicole Grczelschak-Mick

Beilstein J. Org. Chem. 2013, 9, 118–134, doi:10.3762/bjoc.9.15

Graphical Abstract
  • , 290, 280, and 273 K for 500 ps each, and their release of the guest was analysed from these trajectories. Results and Discussion AM1 Calculations The four conformers of empty β-CD The BCDO23rO6l structure turned out to be the lowest energy conformer, also having the lowest dipole moment of only 0.5618
  • about 6 kcal mol−1 above, was conformer BCDO23rO6r. This oval structure has the highest dipole moment of 2.5639 D (x = +0.0268; y = +0.0236; z = −2.5637) and its O6 atomic charges display a range from −0.340 to −0.349 (average −0.344), but all O2 atoms still have the same charge of 0.325, and O3 and O4
  • oxygen charges vary very little (−0.337 to −0.338 and −0.300 to −0.301, respectively). The third conformer BCDO23lO6l, lying about 7 kcal mol−1 above, was again total symmetric as shown by its dipole moment components of x = 0.0; y = 0.0; z = −1.0687 and also with respect to all its oxygen charge values
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Published 18 Jan 2013

The chemistry of bisallenes

  • Henning Hopf and
  • Georgios Markopoulos

Beilstein J. Org. Chem. 2012, 8, 1936–1998, doi:10.3762/bjoc.8.225

Graphical Abstract
  • analysis of the transformation, including its study in the solid state [105], revealed that it begins with a rotation around the central single bond, thus converting the transoid structure into the cisoid conformer 140. Conrotatory ring closure subsequently leads to the bismethylenecyclobutene 141. The
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Published 15 Nov 2012

Determination of the relative configuration of tropinone and granatanone aldols by using TBDMS ethers

  • Ryszard Lazny,
  • Aneta Nodzewska,
  • Katarzyna Sidorowicz and
  • Przemyslaw Kalicki

Beilstein J. Org. Chem. 2012, 8, 1877–1883, doi:10.3762/bjoc.8.216

Graphical Abstract
  • preliminary synthetic report the major isomeric products accessible under these conditions were assigned the exo,syn configuration. DFT calculations suggest that selectivity in the solventless reaction results from equilibration and the higher stability of the O–H…N-hydrogen-bond-stabilized conformer of the
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Published 02 Nov 2012

Asymmetric desymmetrization of meso-diols by C2-symmetric chiral 4-pyrrolidinopyridines

  • Hartmut Schedel,
  • Keizo Kan,
  • Yoshihiro Ueda,
  • Kenji Mishiro,
  • Keisuke Yoshida,
  • Takumi Furuta and
  • Takeo Kawabata

Beilstein J. Org. Chem. 2012, 8, 1778–1787, doi:10.3762/bjoc.8.203

Graphical Abstract
  • responsible for the asymmetric acylation. The most stable conformer A of the acylpyridinium ion was generated by a molecular modeling search (AMBER* force field with the GB/SA solvation model for chloroform using MacroModel V 9.0 (50,000 steps MCMM)) and shown in Figure 2a and Figure 2b. Since the amide
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Published 17 Oct 2012
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