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Search for "conformers" in Full Text gives 230 result(s) in Beilstein Journal of Organic Chemistry. Showing first 200.

A novel bis-triazole scaffold accessed via two tandem [3 + 2] cycloaddition events including an uncatalyzed, room temperature azide–alkyne click reaction

  • Ksenia Malkova,
  • Andrey Bubyrev,
  • Vasilisa Krivovicheva,
  • Dmitry Dar’in,
  • Alexander Bunev and
  • Mikhail Krasavin

Beilstein J. Org. Chem. 2022, 18, 1636–1641, doi:10.3762/bjoc.18.175

Graphical Abstract
  • compound crystalized in two distinct conformers. Finally, we were curious to see if terminally substituted propargylamine 20 would react with 1 and aldehyde 3a under the same reaction conditions. To our delight, the additional phenyl substituent did not dramatically influence the course of the reaction
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Published 02 Dec 2022

Synthesis of (−)-halichonic acid and (−)-halichonic acid B

  • Keith P. Reber and
  • Emma L. Niner

Beilstein J. Org. Chem. 2022, 18, 1629–1635, doi:10.3762/bjoc.18.174

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  • coupling constant between the two methine hydrogens at the ring fusion (3J = 12.9 Hz). The rigid nature of the trans-fused 6/5 ring system results in distinct conformers for 9 and 10; fortunately, this allowed for the unambiguous assignment of the relative configurations of these diastereomers via NMR
  • acyclic conformational analysis. Three divergent mechanistic pathways can be formulated by considering the different conformers of protonated imine 7, namely iminium ions 12a–c (Scheme 3). In each case, the chair-like transition state of the intramolecular aza-Prins reaction is controlled by the C7
  • to give oxocarbenium ion 17. In comparing conformers 12b and 12c, it appears that the chair-like transition state 12c should be lower in energy since the more sterically demanding cyclohexenyl ring is located in a pseudo-equatorial position. Although we did observe a slightly higher yield of 10 as
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Published 01 Dec 2022

Comparison of crystal structure and DFT calculations of triferrocenyl trithiophosphite’s conformance

  • Ruslan P. Shekurov,
  • Mikhail N. Khrizanforov,
  • Ilya A. Bezkishko,
  • Tatiana P. Gerasimova,
  • Almaz A. Zagidullin,
  • Daut R. Islamov and
  • Vasili A. Miluykov

Beilstein J. Org. Chem. 2022, 18, 1499–1504, doi:10.3762/bjoc.18.157

Graphical Abstract
  • °, −60°, and 173°, respectively (Table 1). The lowest energy has been predicted for the gtt conformer, nevertheless the energy differences between the gtt and cgt conformers are negligible (0.23 kcal/mol). Interestingly, the cgt conformation has been found previously for tricymantrenyl trithiophosphite
  • pair dihedral angle for the ttt conformer is ≈ 150°, and for the ggg conformer it is ≈ −35°. For the gtt/cgt conformers the trans S–Fc bonds are almost antiparallel to the phosphorus lone pair (LEP): 175°, −161°/173°. The dihedral angle for the gauche S–Fc bond in the gtt conformer is −56°, and a close
  • a negative charge at the Fe ion and positive charges at hydrogen atoms (Figure 3). Thus the crystal structure of (FcS)3P is defined rather by plural intermolecular interactions than by relative energetics of conformers (Figures S1–S3 in Supporting Information File 1). Previously, for triferrocenyl
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Published 25 Oct 2022

A Streptomyces P450 enzyme dimerizes isoflavones from plants

  • Run-Zhou Liu,
  • Shanchong Chen and
  • Lihan Zhang

Beilstein J. Org. Chem. 2022, 18, 1107–1115, doi:10.3762/bjoc.18.113

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  • compound for calculation of ABTS-reducing activity (in %). Computational ECD calculation of compound 1 Merck molecular force field (MMFF) and DFT as well as TDDFT calculations were carried out with the Spartan 14 software (Wavefunction Inc.) and the Gaussian 16 program [41], respectively. Conformers within
  • conformers were chosen for ECD calculations in methanol at the B3LYP/6-311+G (d,p) level. Solvent effects were taken into consideration using the self-consistent reaction field (SCRF) method with the polarizable continuum model (PCM). The ECD spectrum was generated by the SpecDis program [42] using a
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Published 26 Aug 2022

Understanding the competing pathways leading to hydropyrene and isoelisabethatriene

  • Shani Zev,
  • Marion Ringel,
  • Ronja Driller,
  • Bernhard Loll,
  • Thomas Brück and
  • Dan T. Major

Beilstein J. Org. Chem. 2022, 18, 972–978, doi:10.3762/bjoc.18.97

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  • . Rather, an equilibrium may exist between GGDP and LGDP. Experimental Dynamics and Monte Carlo simulations We generated conformers using simulated annealing (SA) molecular dynamics followed by SA Monte Carlo simulation using CHARMM [28]. Force field parameters were generated using CGenFF [29] and an in
  • -house code which modifies parameters for cations from existing parameters for neutral molecules. For each intermediate in the reaction mechanism (path HP and IE) we created 100 conformers which were subsequently clustered (a cluster width of 1.0 Å was used). For each unique conformer we performed QM
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Published 04 Aug 2022

Anti-inflammatory aromadendrane- and cadinane-type sesquiterpenoids from the South China Sea sponge Acanthella cavernosa

  • Shou-Mao Shen,
  • Qing Yang,
  • Yi Zang,
  • Jia Li,
  • Xueting Liu and
  • Yue-Wei Guo

Beilstein J. Org. Chem. 2022, 18, 916–925, doi:10.3762/bjoc.18.91

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  • torsional sampling (MCMM) method and the OPLS_2005 force field. Conformers above 1% population were reoptimized at the B3LYP/6-311G** level of theory with IEFPCM (Polarizable Continuum Model using the Integral Equation Formalism variant) solvent model for acetonitrile. For the resulting geometries, ECD
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Published 25 Jul 2022

Terpenoids from Glechoma hederacea var. longituba and their biological activities

  • Dong Hyun Kim,
  • Song Lim Ham,
  • Zahra Khan,
  • Sun Yeou Kim,
  • Sang Un Choi,
  • Chung Sub Kim and
  • Kang Ro Lee

Beilstein J. Org. Chem. 2022, 18, 555–566, doi:10.3762/bjoc.18.58

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  • , and cell viability assays. The biological activity assays were performed for all compounds isolated using methods described in Supporting Information File 1. Computational analysis. All conformers of 1–3 used in this study were found using the Macromodel (version 2019-2, Schrödinger LLC) module with
  • “Mixed torsional/Low-mode sampling” in the MMFF force field. The searches were implemented in the gas phase with a 15 kJ/mol energy window limit and 10,000 maximum number of steps to explore all potential conformers. The Polak–Ribiere conjugate gradient (PRCG) method was utilized to minimize conformers
  • with 10,000 iterations and a 0.001 kJ (mol Å)−1 convergence threshold on the root mean quare (RMS) gradient. All the conformers of 1–3 within 3 kJ/mol of each global minimum were subjected to geometry optimization using the Gaussian 16 package (Gaussian Inc.) in the gas phase at B3LYP/6-31G(d) level
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Published 17 May 2022

BINOL as a chiral element in mechanically interlocked molecules

  • Matthias Krajnc and
  • Jochen Niemeyer

Beilstein J. Org. Chem. 2022, 18, 508–523, doi:10.3762/bjoc.18.53

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  • -BINOL derivative (R)-12. In a subsequent work, Takata and co-workers showed that such chirality transfer can also be achieved by deprotonation/reprotonation of the ammonium station, leading to formation of the different co-conformers in a reversible fashion [55]. 2.2 Stereoselective catalysis As
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Published 06 May 2022

Synthesis of 3,4,5-trisubstituted isoxazoles in water via a [3 + 2]-cycloaddition of nitrile oxides and 1,3-diketones, β-ketoesters, or β-ketoamides

  • Md Imran Hossain,
  • Md Imdadul H. Khan,
  • Seong Jong Kim and
  • Hoang V. Le

Beilstein J. Org. Chem. 2022, 18, 446–458, doi:10.3762/bjoc.18.47

Graphical Abstract
  • distance to the nitrile oxide. Then, cyclization followed by the elimination of water (formation of the aromatic ring is the driving force), produces the 3,4,5-trisubstituted isoxazole 3a (Figure 8). Of note, II-A–II-D are conformers, not resonance structures, and the isoxazole 3a is likely the
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Published 22 Apr 2022

Menadione: a platform and a target to valuable compounds synthesis

  • Acácio S. de Souza,
  • Ruan Carlos B. Ribeiro,
  • Dora C. S. Costa,
  • Fernanda P. Pauli,
  • David R. Pinho,
  • Matheus G. de Moraes,
  • Fernando de C. da Silva,
  • Luana da S. M. Forezi and
  • Vitor F. Ferreira

Beilstein J. Org. Chem. 2022, 18, 381–419, doi:10.3762/bjoc.18.43

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  • isomers and trans-conformers. Menadione as a nucleophile Electron-rich 1,4-naphthoquinones, such as 2-hydroxy-, 2-amino-, and 2-alkylnaphtho-1,4-quinones may react as nucleophiles. Hence, menadione (10) can act as a nucleophile in, for example, bromination reactions [127] and aldol-type reactions with
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Published 11 Apr 2022

Diametric calix[6]arene-based phosphine gold(I) cavitands

  • Gabriele Giovanardi,
  • Andrea Secchi,
  • Arturo Arduini and
  • Gianpiero Cera

Beilstein J. Org. Chem. 2022, 18, 190–196, doi:10.3762/bjoc.18.21

Graphical Abstract
  • conformers, in slow exchange on the NMR timescale, was finally confirmed by variable temperature NMR analysis performed for A(AuCl)2 using tetrachloroethane-d2 as the solvent (Figure 3). Catalytic studies To probe the role of the cavity and the influence of the position of the gold(I) nuclei implanted on the
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Published 10 Feb 2022

Regioselective synthesis of methyl 5-(N-Boc-cycloaminyl)-1,2-oxazole-4-carboxylates as new amino acid-like building blocks

  • Jolita Bruzgulienė,
  • Greta Račkauskienė,
  • Aurimas Bieliauskas,
  • Vaida Milišiūnaitė,
  • Miglė Dagilienė,
  • Gita Matulevičiūtė,
  • Vytas Martynaitis,
  • Sonata Krikštolaitytė,
  • Frank A. Sløk and
  • Algirdas Šačkus

Beilstein J. Org. Chem. 2022, 18, 102–109, doi:10.3762/bjoc.18.11

Graphical Abstract
  • (Supporting Information File 1 in Figures S21–S38). In 1H NMR and 13C NMR spectra of compounds 4b and 4c, double sets of signals with different intensities were observed. It is possible that these signals are associated with the presence of equilibrating conformers arising from the rotation of the tert
  • -butoxycarbonyl (Boc) moiety around a C–N single bond (Figure 4a). It is known that some N-Boc-substituted heterocyclic compounds, including oxazolidines, consist of NMR spectra showing two sets of signals due to the dynamic equilibrium between the two conformers formed by the rotation of the Boc moiety, and
  • sets of signals with different intensities were observed due to the existence of two Boc-group rotational conformers. The X-ray structure of (2S)-2-[4-(methoxycarbonyl)-1,2-oxazol-5-yl]piperidin-1-ium trifluoroacetate (6b) finally supported this structure analysis. Examples of amino-functionalized 1,2
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Published 12 Jan 2022

Efficient and regioselective synthesis of dihydroxy-substituted 2-aminocyclooctane-1-carboxylic acid and its bicyclic derivatives

  • İlknur Polat,
  • Selçuk Eşsiz,
  • Uğur Bozkaya and
  • Emine Salamci

Beilstein J. Org. Chem. 2022, 18, 77–85, doi:10.3762/bjoc.18.7

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  • profile at 298.15 K for the reaction mechanism of 14 shown in Scheme 5. Solvent-corrected relative free energy profile at 298.15 K for the reaction mechanism of 17 shown in Scheme 5. The optimized geometries of the conformers 7a and 7b with selected interatomic distances at the B3LYP/6-311++G(d,p) level
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Published 06 Jan 2022

Peptide stapling by late-stage Suzuki–Miyaura cross-coupling

  • Hendrik Gruß,
  • Rebecca C. Feiner,
  • Ridhiwan Mseya,
  • David C. Schröder,
  • Michał Jewgiński,
  • Kristian M. Müller,
  • Rafał Latajka,
  • Antoine Marion and
  • Norbert Sewald

Beilstein J. Org. Chem. 2022, 18, 1–12, doi:10.3762/bjoc.18.1

Graphical Abstract
  • diastereomers, i.e. cis/trans isomers or conformers with a high interconversion barrier. For complestatin-based macrocyclic peptides, the existence of biaryl atropisomers caused by the indole of tryptophan has been reported [82]. Recently, the occurrence of isomers was also observed in our group for SMC
  • cyclised RGD peptides. It could be proven that an isomerisation is not caused by the cross-coupling but by the presence of stable isomers/conformers. Molecular dynamics (MD) simulations verified the appearance of stable, distinct conformers or atropisomers, which were in accordance with the experimental
  • macrocycle and of the Lys–His bond, which is part of the cross-link, is prevented by the stapling (Figure 3 and Supporting Information File 1, Figures S8 to S10). Conformational analysis The identification of two isomers of P5 by LC–MS led us investigate the possibility of diastereomers and conformers in the
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Published 03 Jan 2022

Biological properties and conformational studies of amphiphilic Pd(II) and Ni(II) complexes bearing functionalized aroylaminocarbo-N-thioylpyrrolinate units

  • Samet Poyraz,
  • Samet Belveren,
  • Sabriye Aydınoğlu,
  • Mahmut Ulger,
  • Abel de Cózar,
  • Maria de Gracia Retamosa,
  • Jose M. Sansano and
  • H. Ali Döndaş

Beilstein J. Org. Chem. 2021, 17, 2812–2821, doi:10.3762/bjoc.17.192

Graphical Abstract
  • rotation of the thioketone carbon–N-pyrrolidine bond, are energetically accessible, in agreement with the two set of signals observed by 1H NMR spectroscopy (energy differences between conformers lower than 1 kcal·mol–1 in both cases). However, this equilibrium is strongly affected by the coordination to
  • the metal atom considered, only one of the ligand conformations were energetically accessible (energetic difference of +14.6 and +5.7 kcal·mol−1, for nickel and palladium conformers, respectively, Figure 2). In these cases, the energetic difference between conformers A and B lies in the existence of
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Published 02 Dec 2021

N-Sulfinylpyrrolidine-containing ureas and thioureas as bifunctional organocatalysts

  • Viera Poláčková,
  • Dominika Krištofíková,
  • Boglárka Némethová,
  • Renata Górová,
  • Mária Mečiarová and
  • Radovan Šebesta

Beilstein J. Org. Chem. 2021, 17, 2629–2641, doi:10.3762/bjoc.17.176

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  • -range London dispersion interactions. Geometrical optimizations were performed with the Karlsruhe split-valence def2-SV(P) basis set [41]. Energies were refined using the Minnesota M06-2X functional [42] and valence triple-zeta def2-TZVP basis set [43]. The lowest energy conformers of both catalyst (S,R
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Published 25 Oct 2021

Nomimicins B–D, new tetronate-class polyketides from a marine-derived actinomycete of the genus Actinomadura

  • Zhiwei Zhang,
  • Tao Zhou,
  • Taehui Yang,
  • Keisuke Fukaya,
  • Enjuro Harunari,
  • Shun Saito,
  • Katsuhisa Yamada,
  • Chiaki Imada,
  • Daisuke Urabe and
  • Yasuhiro Igarashi

Beilstein J. Org. Chem. 2021, 17, 2194–2202, doi:10.3762/bjoc.17.141

Graphical Abstract
  • Minimum (MCMM) method with PRCG energy minimization by the OPLS3e force field to obtain 56 conformational isomers within 10.0 kcal/mol from the minimum energy conformer. Geometries of the conformers were then optimized at the M06-2X/6-31G(d) level of theory with the SMD solvation model. Frequency
  • of theory, affording 24 conformers within 3.0 kcal/mol from the minimum Gibbs free energy. The ECD spectrum of each conformer was simulated by the TDDFT calculation of 25 excited states at the ωB97X-D/def2-TZVP-PCM level of theory. The spectrum of structure 4a was created by the weighted average of
  • 26, 22, and 31 DFT-optimized structures, respectively. The spectrum of 4 was created using the weighted average of the spectra of all low-lying conformers of 4a–d according to the respective Boltzmann distribution. The Cartesian coordinates and the energies of the most stable conformers for each
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Published 27 Aug 2021

Menthyl esterification allows chiral resolution for the synthesis of artificial glutamate analogs

  • Kenji Morokuma,
  • Shuntaro Tsukamoto,
  • Kyosuke Mori,
  • Kei Miyako,
  • Ryuichi Sakai,
  • Raku Irie and
  • Masato Oikawa

Beilstein J. Org. Chem. 2021, 17, 540–550, doi:10.3762/bjoc.17.48

Graphical Abstract
  • give rise to 10. The stereochemical configuration of 10 was determined to be 2R, in consideration of the fact that a NOESY crosspeak at CO2Me/Hx observed for 10 was consistent with the top three conformers (total population: 76.5%) for the (2R)-isomer generated by CONFLEX (Version 5, MMFF94S, Figure 3
  • in the top five conformers (total population: 94.4%, data not shown, see below for detailed discussions). Although the characteristic NOESY crosspeak shown in Scheme 4 seemed to be attributable to the second conformer of the (2S)-isomer (29.4% population, data not shown), the other conformers were
  • CONFLEX, as follows. Thus, as for 21* (see Figure 7), three characteristic NOESY crosspeaks observed between isopropyl protons and methyl ester protons (MeA/MeB, MeA/MeC, MeA/HD) were found to be reasonably accounted for by the top 5 stable conformers (89.9% total population) calculated for the (2S
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Published 24 Feb 2021

Biochemistry of fluoroprolines: the prospect of making fluorine a bioelement

  • Vladimir Kubyshkin,
  • Rebecca Davis and
  • Nediljko Budisa

Beilstein J. Org. Chem. 2021, 17, 439–460, doi:10.3762/bjoc.17.40

Graphical Abstract
  • featured in proline residues as well as the high conformational stability of the trans- and cis-amide conformers assign proline another important structural role: the structure freezer. The incorporation of proline residues in connecting loops has been described as a general strategy towards the
  • heterogeneity can markedly complicate folding. In addition, the stability of the amide bonds translates into the thermodynamic stability of the protein structures by altering the free energy of folding. Fluoroprolines alter the relative thermodynamic stability of the amide conformers. Compared to proline, R-Flp
  • preferences should be considered when judging the stability of the folded structures containing fluoroprolines. 2.6 Kinetics of the amide rotation The kinetic stability of the amide conformers generates another important aspect of protein folding. Generally, the amide rotation is considered very slow in
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Published 15 Feb 2021

19F NMR as a tool in chemical biology

  • Diana Gimenez,
  • Aoife Phelan,
  • Cormac D. Murphy and
  • Steven L. Cobb

Beilstein J. Org. Chem. 2021, 17, 293–318, doi:10.3762/bjoc.17.28

Graphical Abstract
  • and represent a distinct class of proteins that exhibit no stable 3D structure [72]. It is broadly understood that, unlike folded proteins, IDPs exist as an average combination of interconverting conformers. However, when bound to a substrate, IDPs may acquire a defined secondary structure [73]. The
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Published 28 Jan 2021

Direct synthesis of anomeric tetrazolyl iminosugars from sugar-derived lactams

  • Michał M. Więcław and
  • Bartłomiej Furman

Beilstein J. Org. Chem. 2021, 17, 115–123, doi:10.3762/bjoc.17.12

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  • oxocarbenium ion is substituted, two diastereomeric half-chair conformers are possible: 3H4 and 4H3 (shown for a 4-substituted pyranose cation in Scheme 5). Both may undergo attack by a nucleophile in two ways: on the axial trajectory from the top or the bottom face. Such an event would result in the formation
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Published 13 Jan 2021

Naphthalonitriles featuring efficient emission in solution and in the solid state

  • Sidharth Thulaseedharan Nair Sailaja,
  • Iván Maisuls,
  • Jutta Kösters,
  • Alexander Hepp,
  • Andreas Faust,
  • Jens Voskuhl and
  • Cristian A. Strassert

Beilstein J. Org. Chem. 2020, 16, 2960–2970, doi:10.3762/bjoc.16.246

Graphical Abstract
  • NMe2, we observe additional red-shifted vibrational progressions, which we assign to the existence of delocalized conformers in the frozen glassy matrix at 77 K with predominant π–π* character. Nevertheless, τ was equivalent in all bands. In the case of NMe2, no vibrational progression in the emission
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Published 02 Dec 2020

Changed reactivity of secondary hydroxy groups in C8-modified adenosine – lessons learned from silylation

  • Jennifer Frommer and
  • Sabine Müller

Beilstein J. Org. Chem. 2020, 16, 2854–2861, doi:10.3762/bjoc.16.234

Graphical Abstract
  • (or type N-conformers) [32], and the normally observed higher reactivity of the 2’-OH group in silylation reactions can be correlated with it. A closer examination of the coupling constants of the sugar protons revealed a shift from 6.3 Hz to 4.5 Hz for J1’-2’ and a minor shift from 4.9 Hz to 5.5 Hz
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Published 23 Nov 2020

Vicinal difluorination as a C=C surrogate: an analog of piperine with enhanced solubility, photostability, and acetylcholinesterase inhibitory activity

  • Yuvixza Lizarme-Salas,
  • Alexandra Daryl Ariawan,
  • Ranjala Ratnayake,
  • Hendrik Luesch,
  • Angela Finch and
  • Luke Hunter

Beilstein J. Org. Chem. 2020, 16, 2663–2670, doi:10.3762/bjoc.16.216

Graphical Abstract
  • (Figure 2), which was among the higher-energy calculated conformers of 2 (see Supporting Information File 1), bears a close resemblance to the solid-state conformation of piperine (1, Figure 1). The structure 2f has a F–C–C–F dihedral angle of 57° and a F–C–C=O dihedral angle of –133°. These angles
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Published 28 Oct 2020

Synthesis of novel fluorinated building blocks via halofluorination and related reactions

  • Attila Márió Remete,
  • Tamás T. Novák,
  • Melinda Nonn,
  • Matti Haukka,
  • Ferenc Fülöp and
  • Loránd Kiss

Beilstein J. Org. Chem. 2020, 16, 2562–2575, doi:10.3762/bjoc.16.208

Graphical Abstract
  • halofluorination of (rac)-1. Only the main conformers of (rac)-1 and (rac)-T1a,b are shown. (rac)-2a: X = Br; (rac)-2b: X = I. Halofluorination reactions of the trans-diester (rac)-1. Probable outcomes of the halofluorination of 4. Both conformers of the compounds 4, (rac)-T2a,b, and (rac)-T3a,b, respectively
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Published 16 Oct 2020
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