Search results
Search for "conformation" in Full Text gives 771 result(s) in Beilstein Journal of Organic Chemistry. Showing first 200.
Mining raw plant transcriptomic data for new cyclopeptide alkaloids
Beilstein J. Org. Chem. 2024, 20, 1548–1559, doi:10.3762/bjoc.20.138
- the β-carbon of leucine ether linkage. Structurally related cyclopeptide alkaloids have similar J-values (Jα-β ≈ 8.0 Hz) and have been assigned as ʟ-erythro (anti) conformation [20][39]. Metabolomic analysis and GNPS networking Live samples of C. americanus and G. jasminoides were separated into
Photoswitchable glycoligands targeting Pseudomonas aeruginosa LecA
Beilstein J. Org. Chem. 2024, 20, 1486–1496, doi:10.3762/bjoc.20.132
- /off or from low to high. This strategy can be used for specific targeting or local drug activation to reduce its toxicity [14]. There is an increasing use of the photoisomerization to control the conformation as well as the activities of various biomolecules with the development of photopharmacology
- the known crystal structure. The extended E-isomer establishes contact through galactoside and the first aryl ring only, while the bent Z-isomer has proper conformation to wrap around the central His53 residue and to establish a more extended interaction with the protein surface. This would be in
- LecA binding by light. Few differences were observed for the meta- (2 and 4) and ortho-substituted azobenzenes (5). Thermodynamics contributions exhibit larger variations with stronger enthalpy of binding for the Z-isomer, probably in relation with a folded conformation generating additional contact
Selectfluor and alcohol-mediated synthesis of bicyclic oxyfluorination compounds by Wagner–Meerwein rearrangement
Beilstein J. Org. Chem. 2024, 20, 1462–1467, doi:10.3762/bjoc.20.129
- compounds by changing their metabolic stability, hydrogen bonding ability, lipophilicity, solubility, bioavailability, conformation and general structure [1][2][3][4]. About 20% of commercially available drugs contain fluorine, and this ratio is estimated to increase further [5][6]. Among organofluorines
Synthesis of cyclic β-1,6-oligosaccharides from glucosamine monomers by electrochemical polyglycosylation
Beilstein J. Org. Chem. 2024, 20, 1421–1427, doi:10.3762/bjoc.20.124
- disaccharide 16 was obtained as an exclusive product. The optimized structure of 15 calculated by DFT (B3LYP/6-31G(d)) suggested that the pyran ring preferred the boat conformation because the chair conformation of the pyran ring was controlled by the introduction of the 2,3-oxazolidinone protecting group (see
Computation-guided scaffold exploration of 2E,6E-1,10-trans/cis-eunicellanes
Beilstein J. Org. Chem. 2024, 20, 1320–1326, doi:10.3762/bjoc.20.115
- . Scaffold exploration of the eunicellane skeleton During protonation-induced cyclization of 1 and 2, the C6–C7 alkene showed higher nucleophilicity than either of the other two double bonds likely due to the unique conformation of the eunicellane skeleton. This selective reactivity was further supported
Sustainable tandem acylation/Diels–Alder reaction toward versatile tricyclic epoxyisoindole-7-carboxylic acids in renewable green solvents
Beilstein J. Org. Chem. 2024, 20, 1308–1319, doi:10.3762/bjoc.20.114
- in a much shorter time (Table 1, entry 4) when the temperature of the reaction medium was increased to 50 °C. According to X-ray and Raman spectroscopy techniques, triglyceride molecules in liquid form are arranged in a dynamic chain-like conformation [114][115][116]. As the temperature of the
- in good agreement with those reported for this compound in the literature. In all synthesized compounds, Ha and Hb protons are only in endo conformation and therefore the amide and carboxylic acid functional groups are arranged in exo conformation. The fact that the flexible 2n and 2o compounds in
- reaction medium has been previously demonstrated by 1H NMR studies [129]. The elongation of the alkyl chain attached to the N atom facilitates the formation of the epoxyisoindole product by favoring the s-cis conformation due to steric factors (Thorpe–Ingold effect) [130][131]. Briefly, in this type of
Domino reactions of chromones with activated carbonyl compounds
Beilstein J. Org. Chem. 2024, 20, 1256–1269, doi:10.3762/bjoc.20.108
- steric influence of the fluorine atom and of the substituent R1 might have an influence on the conformation which facilitates the intramolecular aldol reaction at the expense of the nitrile addition. In the case of formation of biphenyls 44, these products were generally obtained in good yields (63–79
Introduction of peripheral nitrogen atoms to cyclo-meta-phenylenes
Beilstein J. Org. Chem. 2024, 20, 1207–1212, doi:10.3762/bjoc.20.103
- structural features of nitrogen-doped [n]CMPs. The crystal molecular structures of 3a and 3b are shown in Figure 3. The hexagonal macrocyclic structure of 3a showed a chair-like conformation with alternating biaryl dihedral angles showing +/– values. The octagonal structure of 3b exhibited a saddle-like
- conformation with an average dihedral angle of 45.0°, which was slightly larger than that of 3a (30.4°). The shapes of nitrogen-doped [n]CMPs did not deviate from those of hydrocarbon [n]CMPs, with similar average dihedral angles (32.4° for [6]CMP and 40.6° for [8]CMP) [15]. Likewise, the crystal packings of
Structure–property relationships in dicyanopyrazinoquinoxalines and their hydrogen-bonding-capable dihydropyrazinoquinoxalinedione derivatives
Beilstein J. Org. Chem. 2024, 20, 1037–1052, doi:10.3762/bjoc.20.92
- measures 1.531 Å, comparatively larger than that of aromatic systems and on the order of Csp3–Csp3 bonds (Figure 6a). This represents the first evidence that the keto form is largely favored. Next, the molecule does not adopt a fully planar conformation, instead exhibiting a torsional angle of 4.33° with
Monitoring carbohydrate 3D structure quality with the Privateer database
Beilstein J. Org. Chem. 2024, 20, 931–939, doi:10.3762/bjoc.20.83
- overall conformation of N-glycans comes to that of validated deposited structures [16]. The PDB-REDO [21] database is a separate resource, albeit linked to the PDB in that the entries that compound PDB-REDO are those original PDB crystallographic entries that included experimental data (i.e., reflection
- valid, the ring must be in the 4C1 chair conformation. This can be measured through the Cremer–Pople parameters θ and ψ [27]. Theta angles of 0° < θ < 360° indicate that the sugar may be in a higher-energy confirmation; therefore, caution should be placed on any conclusions drawn from the molecular
- the diagram. For example, a shape with an orange highlight indicates something is abnormal about the ring’s conformation, puckering, or monosaccharide nomenclature [30]. Similarly, a linkage with an orange highlight indicates that the torsion angles between the linkages are unexpected and require
Confirmation of the stereochemistry of spiroviolene
Beilstein J. Org. Chem. 2024, 20, 852–858, doi:10.3762/bjoc.20.77
- hand, the originally proposed cyclization mechanism (Scheme 1B) involves a 3,6-cyclization of cation IM-1 through a conformation shown as IM-1A to generate cation IM-5, which was proposed to undergo a dyotropic rearrangement, followed by a 1,2-alkyl shift of cation IM-6 to yield the spirocyclic cation
- cyclization mechanism (Scheme 1C) leading to the same spirocyclic skeleton as spiroviolene with an altered stereochemistry at C7 found in GJ1012A (3) could be proposed [11][17][18]. A 3,6- or 3,7-cyclization of cation IM-1 through a conformation shown as IM-1B with β-oriented 20-methyl group, would generate
Skeletal rearrangement of 6,8-dioxabicyclo[3.2.1]octan-4-ols promoted by thionyl chloride or Appel conditions
Beilstein J. Org. Chem. 2024, 20, 823–829, doi:10.3762/bjoc.20.74
- at C4 determined the resultant ring system, as the σ* orbital is not accessible to external nucleophiles due to steric hindrance and the rigid conformation of the bicyclic ring system. When the C4–OH was equatorial, O8 migrated as it was aligned with the σ* orbital giving a 3,8-dioxabicyclo[3.2.1
Chemoenzymatic synthesis of macrocyclic peptides and polyketides via thioesterase-catalyzed macrocyclization
Beilstein J. Org. Chem. 2024, 20, 721–733, doi:10.3762/bjoc.20.66
- increase the ratio of intramolecular nucleophilic attack, resulting in macrocyclic products via preorganization of substrate and enzyme in an active conformation [17][18]. Chemoenzymatic strategies, which merge practical enzymatic transformations with modern organic synthetic methods to increase the
Production of non-natural 5-methylorsellinate-derived meroterpenoids in Aspergillus oryzae
Beilstein J. Org. Chem. 2024, 20, 638–644, doi:10.3762/bjoc.20.56
- the structures of 1 and 2 were deduced based on their HRMS spectra and the predicted biosynthetic pathway. Biosynthetic mechanisms of the 5-MOA-derived meroterpenoids obtained in this study. In the reaction by InsA7, the cyclization should proceed via a pre-boat-chair conformation, and the
- conformational change after cyclization would afford the chair-chair conformation of 7 [19]. Supporting Information Supporting Information File 46: Experimental details, analytical data, tables of primer sequences, constructed plasmids, and A. oryzae transformants and figures showing the X-ray crystal
Recent developments in the engineered biosynthesis of fungal meroterpenoids
Beilstein J. Org. Chem. 2024, 20, 578–588, doi:10.3762/bjoc.20.50
- led to the production of preterretonin A (7) (Figure 2) [9]. These data indicated that Trt1 protonates the epoxide of (10'R)-epoxyfarnesyl-DMOA-3,5-methyl ester (6), leading to the cyclization of the terpenoid moiety in the chair–chair conformation, and catalyzes the deprotonation of H-9' of the
- meroterpenoids: insuetusin A1 (12) and insuetusin B1 (10), respectively (Figure 2) [9]. Like other Trt1-type enzymes, InsB2 catalyzes the protonation of the epoxide, the formation of two six-membered rings in a chair–chair conformation, but the reaction finishes with the deprotonation of the hydroxy group at C-3
- to produce compound 10. In contrast, InsA7 commonly initiates and terminates the reaction with the protonation of the epoxide and the deprotonation of OH-3, respectively, but it produces product 12 via a boat–chair conformation. Since all of the other Trt1-like cyclases catalyze the reaction with
Possible bi-stable structures of pyrenebutanoic acid-linked protein molecules adsorbed on graphene: theoretical study
Beilstein J. Org. Chem. 2024, 20, 570–577, doi:10.3762/bjoc.20.49
- stable configuration (conformation 1) in a straight form on graphene. There is at least one metastable bent configuration (conformation 2) on the potential energy surface. Besides, the reaction barrier of the conformational change of the PASE was determined. In this paper, we further examine a reaction
- structures on graphene [1]. Therefore, the pyrene moiety is bound to graphene, and at the same time, the protein is supplemented by a dehydration-condensed linker with the protein. As introduced, on graphene, PASE is found to be straight as the most stable conformation (conformation1 in Figure 1c) [9]. On
- the potential energy surface, a curved conformation (conformation 2 in Figure 1d) exists. Our previous results suggested that conformation 2 is a metastable state. The relative stability of these conformations is known to vary depending on the surrounding environment, e.g., solvents and solutes [9
Synthesis of photo- and ionochromic N-acylated 2-(aminomethylene)benzo[b]thiophene-3(2Н)-ones with a terminal phenanthroline group
Beilstein J. Org. Chem. 2024, 20, 552–560, doi:10.3762/bjoc.20.47
- lists of bond lengths and bond angles are given in Tables S1–S4, Supporting Information File 3. Compound 3b had the structure of an O-acylated isomer and possessed an E-s-cis(S,N) conformation relative to the C(l)–C(9) bond (Figure 3). The benzo[b]thiophene fragment was planar, whereas the propionyl
Switchable molecular tweezers: design and applications
Beilstein J. Org. Chem. 2024, 20, 504–539, doi:10.3762/bjoc.20.45
- macroscopic analogs, exhibit mechanical motion between an open and closed conformation in response to stimuli. Such systems constitute an essential component of artificial molecular machines. This review will present selected examples of switchable molecular tweezers and their potential applications. The
- mainly driven by intramolecular hydrogen bonds. The methoxyphenyl-pyridine-methoxyphenyl moiety, developed by Petitjean et al. [19], demonstrates conformational switching upon the addition of acid in aqueous media (Figure 2). The neutral tweezers adopt a "U"-shaped conformation with both arms pointing in
- attached functional arms. The formation of new hydrogen bonds between -OMe groups and protonated pyridine stabilizes a "W"-shaped open conformation. The conformation switch can be easily followed by NMR spectroscopy in solution. Remarkably, the water-soluble tweezers 1, when functionalized with hydrophobic
Ligand effects, solvent cooperation, and large kinetic solvent deuterium isotope effects in gold(I)-catalyzed intramolecular alkene hydroamination
Beilstein J. Org. Chem. 2024, 20, 479–496, doi:10.3762/bjoc.20.43
- of complex 7a. Our preliminary hypothesis is that two conformations exist in solution, one of which is symmetrical (presenting as a singlet), one of which is not. A lack of symmetry in one conformation would mean that each phosphorous is magnetically inequivalent, and thus shows splitting to the
Synthesis of 2,2-difluoro-1,3-diketone and 2,2-difluoro-1,3-ketoester derivatives using fluorine gas
Beilstein J. Org. Chem. 2024, 20, 460–469, doi:10.3762/bjoc.20.41
- intermolecular interactions with an aryl ring in an adjacent molecule. The two aryl rings within the molecule are near-perpendicular to each other and this conformation leads to enhanced, orthogonal π-stacking interactions. We next turned our attention to difluorination of related 2-ketoester substrates
Mechanisms for radical reactions initiating from N-hydroxyphthalimide esters
Beilstein J. Org. Chem. 2024, 20, 346–378, doi:10.3762/bjoc.20.35
- photosensitizer in an energy-transfer (EnT) mechanism. This proposal was supported by fluorescence quenching measurements, as well as the direct excitation of 44 by UV irradiation, resulting in the formation of 45 in a 45% yield. According to this hypothesis, NHPI ester 44 would adopt a favorable conformation (46
Spatial arrangements of cyclodextrin host–guest complexes in solution studied by 13C NMR and molecular modelling
Beilstein J. Org. Chem. 2024, 20, 331–335, doi:10.3762/bjoc.20.33
- , we reveal the conformation (spatial arrangement) of the host–guest complex in solution spectroscopically by measuring the 13C NMR spectra of a suitable guest molecule. We decided to take Cs symmetric guest molecules, CD as a host and measure the 13C NMR spectra of these complexes. We expect that the
- carbons (Figure 1). The degree of the signal split correlates with the distance of prochiral atoms (carbons) to the host cavity and thus gives information about the conformation of the guest molecule in the host cavity. First, we measured simple 1D 13C NMR spectra and indeed observed the split of the
Elucidating the glycan-binding specificity and structure of Cucumis melo agglutinin, a new R-type lectin
Beilstein J. Org. Chem. 2024, 20, 306–320, doi:10.3762/bjoc.20.31
- nitrogen. CH−π stacking and hydrophobic interactions occur between the aromatic ring of Trp36 and the alpha face of the ring as well as the hydroxymethyl moiety of the galactose residue, additionally ensuring specificity for galactoside over glucoside as an equatorial conformation of the O4 hydroxy group
Synthesis of π-conjugated polycyclic compounds by late-stage extrusion of chalcogen fragments
Beilstein J. Org. Chem. 2024, 20, 287–305, doi:10.3762/bjoc.20.30
- conformation of the thiepine ring, thus weakening the π–π stacking intermolecular interactions. Finally, solid-state S-extrusion could be triggered in a controlled way upon thermal activation of 21, as observed in thermogravimetric analysis, with the loss of sulfur detected at 223 °C to yield the planar S
- ) and side view (b) of the X-ray crystal structure of thiepine 3b showing its bent conformation. Thermal ellipsoids are shown at the 50% probability level, and all hydrogen atoms as well as propyl groups on imide substituents have been omitted for clarity. Reprinted with permission from [57]. Copyright
Photochromic derivatives of indigo: historical overview of development, challenges and applications
Beilstein J. Org. Chem. 2024, 20, 228–242, doi:10.3762/bjoc.20.23
- melting point of indigo is bifurcated intra- and intermolecular hydrogen bonding [11], and face-to-face π–π stacking of parallel aromatic rings (Figure 2) [12]. Single crystal X-ray diffraction analysis showed that the indigo molecule is almost planar and exists in the E-conformation. The central C=C bond
Other Beilstein-Institut Open Science Activities
