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Search for "structure" in Full Text gives 2936 result(s) in Beilstein Journal of Organic Chemistry. Showing first 200.
Chemoenzymatic synthesis of the cardenolide rhodexin A and its aglycone sarmentogenin
Beilstein J. Org. Chem. 2025, 21, 2637–2644, doi:10.3762/bjoc.21.204
- absorption and metabolism, and specific moieties like rhamnose can enhance CG potency markedly by more than 25 times [1][7]. In addition, the -OH groups on the steroids’ structure also play an important role on their activity. However, these compounds are mainly isolated from plants or animals, which not
- -electron demand Diels–Alder (IEDDA) reaction was utilized to successfully construct the BCD tricyclic structure with the correct configuration of the four contiguous stereocenters in just one step. However, the requirement of a series of protecting group manipulations undermined the step-economy and
Thiazolidinones: novel insights from microwave synthesis, computational studies, and potentially bioactive hybrids
Beilstein J. Org. Chem. 2025, 21, 2618–2636, doi:10.3762/bjoc.21.203
- aldehyde 1, activated by protonation of the oxygen atom through structure ii, forming the intermediate aldol iii. In the presence of EDDA, water elimination occurs in intermediate iv, yielding the Knoevenagel adducts 3 or 4. Synthesis of novel imidazo[1,2-a]pyridine–thiazolidinone hybrids To further
- inconsistency made it challenging to rely on NMR as the primary method for confirming the structure of the expected products. To overcome this limitation, other analytical techniques, such as mass spectrometry and infrared (IR) spectroscopy, were employed. These methods successfully corroborated the formation
- tautomerization within the structure of the products, likely induced by the presence of the 4-diethylamino (4-NEt2) group, a strong electron-donating substituent. The canonical structure of thiazolidines, due to the presence of one or two carbonyl groups, thiol groups, and α-hydrogens, allows the formation of
Efficient solid-phase synthesis and structural characterization of segetalins A–H, J and K
Beilstein J. Org. Chem. 2025, 21, 2612–2617, doi:10.3762/bjoc.21.202
- . Secondary structure analysis by circular dichroism (CD) The secondary structures of compounds 1–10 were investigated using circular dichroism (CD) spectroscopy in aqueous buffer (0.01×PBS), deionized H₂O, and 30% TFE (2,2,2-trifluoroethanol) (Figure 2). CD spectra in the far-UV region (190–250 nm) provide
- evaluation and structure–activity relationship studies. The systematic investigation of the their key biological activities, including estrogenic activity (assessed via breast cell proliferation assays), antitumor activity (evaluated through HeLa cell inhibition assays), and antibacterial activity (evaluated
Recent advances in total synthesis of illisimonin A
Beilstein J. Org. Chem. 2025, 21, 2571–2583, doi:10.3762/bjoc.21.199
- . However, subsequent density functional theory (DFT) calculations by the Tantillo group on rearrangements of potential biosynthetic precursors revealed that structure 10 corresponds to a transition state rather than a stable intermediate of the 1,2-alkyl migration [27]. Their study further indicated that
- Suzuki and co-workers in 2021 [44]. Their work proposed that this core structure could be generated from a highly oxidized allo-cedrane moiety through a tandem retro-Claisen/aldol reaction. Beginning with compound 100, a 6-step sequence afforded ortho-quinone 101 (Scheme 10). Heating 101 promoted an
Total syntheses of highly oxidative Ryania diterpenoids facilitated by innovations in synthetic strategies
Beilstein J. Org. Chem. 2025, 21, 2553–2570, doi:10.3762/bjoc.21.198
- . This field serves not only as a vital tool for molecular structure validation and the discovery of new reaction mechanisms but also as a fundamental driving force behind advances in related disciplines such as pharmaceutical science. Throughout this endeavor, innovations in methods and strategies
- intermediate, systematically deriving multiple structurally related natural products through functional group transformations and oxidation-state adjustments [3][4]. This approach efficiently constructs compound family libraries, greatly facilitating drug screening and structure–activity relationship (SAR
- the correct structure of ryanodol to be 3-epi-ryanodol (5), thereby revising the previously accepted configuration [15]. Since then, numerous analogs based on the ryanodol scaffold have been identified and characterized. As of now, 18 natural products from this family have been successfully isolated
Ni-promoted reductive cyclization cascade enables a total synthesis of (+)-aglacin B
Beilstein J. Org. Chem. 2025, 21, 2548–2552, doi:10.3762/bjoc.21.197
- single crystals, and a corresponding X-ray diffraction analysis (inset in Scheme 3, selected H atoms have been omitted for clarity, and Table S3, Supporting Information File 1) unambiguously confirmed its precise structure with three continuous chiral centers. Conclusion In summary, the total synthesis
Rapid access to the core of malayamycin A by intramolecular dipolar cycloaddition
Beilstein J. Org. Chem. 2025, 21, 2542–2547, doi:10.3762/bjoc.21.196
- synthesis and structural determination of malaymycin A (1) as well as the subsequent design of structural analogues for biological evaluation [16][17][18][19][20]. Preliminary structure–activity relationship (SAR) studies revealed that fungicidal activity is highly dependent on the nature and
Synthesis and characterization of a isothiouronium-calix[4]arene derivative: self-assembly and anticancer activity
Beilstein J. Org. Chem. 2025, 21, 2535–2541, doi:10.3762/bjoc.21.195
- potential to load drug molecules in the bioactive nanoassembled structure. Keywords: anticancer agent; calixarene; nanostructure; self-assembly; Introduction Cancer remains one of the leading causes of morbidity and mortality worldwide. Despite significant advancements in chemotherapy, more effective and
- ). The proton signals of the NH₂ and CH₂S groups of the isothiouronium substituents were clearly observed at 9.04 ppm and 4.23 ppm, respectively. Additionally, the carbon signal of the CH₂S group appeared at 169.3 ppm. The NMR signals, consistent with a fully symmetric structure, evidenced the exhaustive
Isoorotamide-based peptide nucleic acid nucleobases with extended linkers aimed at distal base recognition of adenosine in double helical RNA
Beilstein J. Org. Chem. 2025, 21, 2513–2523, doi:10.3762/bjoc.21.193
- efficient binding and further underscore the complexity of these systems due to conformational and energetic preferences. Taken together with previous studies, we postulate that future nucleobases should be designed to overcome the positional challenges related to entropy and geometry. (a) Structure of a
Effect of a photoswitchable rotaxane on membrane permeabilization across lipid compositions
Beilstein J. Org. Chem. 2025, 21, 2498–2512, doi:10.3762/bjoc.21.192
- ; membrane fluidity; membrane permeability; photoswitchable rotaxane; Introduction Lipid membranes play a vital role in biology by acting as protective barriers for cells and organelles while regulating the passage of substances. Additionally, their structure and dynamics influence the activity of membrane
- organelles within the same cell [2]. Therefore, there is a great need to develop molecular tools capable of modulating membrane structure in a controlled manner, either to facilitate cargo transport (such as drug delivery) [3][4], to irreversibly disrupt membranes and induce cell death (e.g., for targeting
- spatiotemporal precision [9]. Rotaxanes have emerged as promising tools for performing various functions in lipid membranes, owing to their multiple sites for derivatization, which allow fine-tuning of their structure and function in membranes. For instance, they have been used to transport ions across lipid
Assembly strategy for thieno[3,2-b]thiophenes via a disulfide intermediate derived from 3-nitrothiophene-2,5-dicarboxylate
Beilstein J. Org. Chem. 2025, 21, 2489–2497, doi:10.3762/bjoc.21.191
- isolation of compounds 2 and 3 in analytically pure form allowed their structure to be established thanks to elemental analysis and HRMS. It was found that compounds 2 and 3 are dimeric derivatives of the starting thiophene, linked by sulfur bridges located at the C-3 position instead of the nitro group
Synthesis of the tetracyclic skeleton of Aspidosperma alkaloids via PET-initiated cationic radical-derived interrupted [2 + 2]/retro-Mannich reaction
Beilstein J. Org. Chem. 2025, 21, 2470–2478, doi:10.3762/bjoc.21.189
- Education and Beijing National Laboratory for Molecular Science, and Peking-Tsinghua Centre for Life Sciences, Peking University, Beijing 100871, China Shenzhen Bay Laboratory, Shenzhen 518055, China Key Laboratory of Structure-Based Drug Design & Discovery of Ministry of Education, Shenyang Pharmaceutical
- ). Further geometrical adjustment and conformational restriction of the transient structure enable the N9 nonbonding p orbital to align parallel to the σ(C19–C3)* orbital (Figure 2f, TS2 → F-10 → F-40 → IN3), which reinforces the hyperconjugative interaction. Facilitated by the bond stretching and bond-angle
- bending of the transient structure with a pseudo bicyclo[2.2.0]hexane unit, the favorable hyperconjugative interaction ultimately leads to cleavage of the C19–C3 bond (TS2 → IN3) and release of the ring strain. DFT analysis hereby explains that the orbital symmetry involved in this process does not
The intramolecular stabilizing effects of O-benzoyl substituents as a driving force of the acid-promoted pyranoside-into-furanoside rearrangement
Beilstein J. Org. Chem. 2025, 21, 2456–2464, doi:10.3762/bjoc.21.187
- energies of starting methyl β-galactopyranoside structure 1 were computed. The initial orientation of the methyl aglycon was chosen so that the torsional angle H1–C1–O1–C(Me) had the value of +40° for the β-structures and −40° for the α-isomers. The benzoate substituents at positions O-2 and O-3 were
- furanoside structure 2. Thus, when this angle had the starting values of 180° or −60°, all the calculations led to a conclusion that no transformation to a furanoside should occur (the resulting energies are given in Supporting Information File 1, Table S2). Only when optimizations started at the value of
Transformation of the cyclohexane ring to the cyclopentane fragment of biologically active compounds
Beilstein J. Org. Chem. 2025, 21, 2416–2446, doi:10.3762/bjoc.21.185
- information. Keywords: biological activity; cyclopentane/enone; rearrangements; ring/cycle contractions; total synthesis; Introduction The functionalized cyclopentane/enone fragment is part of the structure of a large number of natural and synthetic biologically active compounds, including prostaglandins
- with two attached side chains – of seven (α-chain) and eight (β- or ω-chain) carbon atoms. Their main physiological role is to maintain the homeostatic harmony of the organism [1][2]. Among the terpenoids containing cyclopentane in their structure, we should mention jatrophane or latirane diterpenoids
- octahydrophenanthrene, is a natural follicular hormone essential for normal development of the female body [6]. An example of an alkaloid whose structure includes cyclopentane is lappaconitine, which is noteworthy because its hydrobromide is the active ingredient in the highly effective antiarrhythmic drug allapinine
The high potential of methyl laurate as a recyclable competitor to conventional toxic solvents in [3 + 2] cycloaddition reactions
Beilstein J. Org. Chem. 2025, 21, 2389–2415, doi:10.3762/bjoc.21.184
- structure, results in elevated cis or trans diastereoselectivity [85][111]. Furthermore, the [3 + 2] cycloaddition reactions of nitrones with electron-poor dipolarophiles, such as N-phenylmaleimide, is controlled by the HOMO FMO of the nitrone. Consequently, it can be deduced that HOMOnitrone–LUMON
Synthetic study toward vibralactone
Beilstein J. Org. Chem. 2025, 21, 2376–2382, doi:10.3762/bjoc.21.182
- ][21]. Additionally, a series of vibralactone homodimers and oxime esters 10–12 were reported by the groups of Liu and Zhang, respectively [22][23]. Through modification of the primary hydroxy group, a structure-based optimization of vibralactone (6) was carried out by Liu and co-workers and yielded
- several potent pancreatic lipase inhibitors with nanomolar IC50 values [24], further supporting vibralactone as a promising lead compound warranting further investigation. Although vibralactone (6) is a relatively small natural product, its molecular structure features a unique 4/5-fused bicyclic β
- and ClpP2 and it could be utilized as a probe to study the activity and structure of the ClpP1P2 complex from Listeria monocytogenes [25]. Previously, Snider and co-worker reported the first total synthesis of vibralactone (6) employing Birch reductive alkylation, intramolecular aldol reaction and
Conformational effects on iodide binding: a comparative study of flexible and rigid carbazole macrocyclic analogs
Beilstein J. Org. Chem. 2025, 21, 2369–2375, doi:10.3762/bjoc.21.181
- (Figure S3) in Supporting Information File 1. WDG exhibited poor solubility, which hindered the direct acquisition of its single crystal structure for characterization. However, after Boc (tert-butyloxycarbonyl) protection, a single crystal structure (CCDC Number: 2339028) of the modified compound was
- successfully obtained. This indirectly confirmed the molecular structure of WDG [22]. The NH protons of the carbazole moiety in PBG and WDG were observed as singlets at δ 7.9706 and δ 7.8624, respectively, in their 1H NMR spectra (Figure 1a and 1b). In order to study the role and mechanism of anion recognition
Rotaxanes with integrated photoswitches: design principles, functional behavior, and emerging applications
Beilstein J. Org. Chem. 2025, 21, 2345–2366, doi:10.3762/bjoc.21.179
- ][10][11][12]. Depending on their structure, rotaxanes can be classified by the number of components involved. In [1]rotaxanes, the macrocycle is covalently attached to one end of the axle while remaining mechanically interlocked with another part of the axle (Figure 1) [13][14][15]. In contrast, [2
- based on the location of the photoswitch within the rotaxane structure – either integrated into the axle or situated in the macrocycle. Within these categories, we highlight widely used photoswitches, including acridane, anthracene, azobenzene, cycloheptatriene, dithienylethene, fumaramide, hydrazone
- systems, the azobenzene functions also as a recognition site for macrocycles such as cyclodextrins [18][33][34][35][36][37][38][39], or CBPQT4+ [40][41][42], while in others, it serves merely as part of the axle structure without directly participating in macrocycle recognition. Examples of the latter
Comparative analysis of complanadine A total syntheses
Beilstein J. Org. Chem. 2025, 21, 2334–2344, doi:10.3762/bjoc.21.178
- enantiomers of 51 allowed Tsukano and co-workers to prepare both enantiomers of complanadine A. Their further biological evaluation of the complanadines and several synthetic intermediates revealed that the pseudo-dimeric structure, absolute configuration, and oxidation level are important for the observed
- catalysis, C–H activation methods, biomimetic synthesis, classic rearrangements, skeletal editing logic, and others. In addition, these efforts enabled the identification of the potential cellular target of complanadine A, validation of its neurotrophic activity, establishment of preliminary structure
Recent advances in Norrish–Yang cyclization and dicarbonyl photoredox reactions for natural product synthesis
Beilstein J. Org. Chem. 2025, 21, 2315–2333, doi:10.3762/bjoc.21.177
- structure of septosone B (37) [31] (Scheme 6). All these compounds were first isolated from South China Sea sponges of the genus Dysidea by Lin's group. Dysiherbol A (33) exhibits NF-κB inhibitory activity (IC50 = 0.49 μM) and cytotoxicity against the human myeloma cell line NCI H-929 (IC50 = 0.58 μM
- -diketones, the rigid lattice structure locks molecules into a specific conformation, limiting access to certain γ-hydrogens for abstraction and thus enhancing regioselectivity [42]. Enantiopure 87 was obtained by preparative chiral supercritical fluid chromatography (SFC) resolution of the racemate, while
- -diketones, α-keto esters, α-keto amides, 1,4-quinones, and 1,2-quinones, emphasizing their unique roles in constructing diverse substructures. However, the reaction faces challenges in terms of regioselectivity and stereoselectivity, which are mainly attributed to the influence of substrate structure
Insoluble methylene-bridged glycoluril dimers as sequestrants for dyes
Beilstein J. Org. Chem. 2025, 21, 2302–2314, doi:10.3762/bjoc.21.176
- methyl substituents (H2). Fortunately, the X-ray crystal structures of G2W1 and G2W3 reported below shed further light on their poor performance as solid state sequestrants. X-ray crystal structure of G2W1 and G2W3 Eventually, we were able to grow single crystals of G2W3 (CCDC 2466611) and solve their
- H2O and TFA are also seen in the crystal structure. At one C=O portal, an H2O molecule engages in H-bonding interactions with one C=O group (O···O: 2.948 Å, H···O: 2.149 Å, O–H···O angle: 163.603˚) and one OMe (O···O: 2.963 Å, H···O: 2.169 Å, O–H···O angle: 159.887°) group. The other C=O portal
- substituents – provides a compelling explanation for the superior performance of H2 over G2W3 and G2W4. We were also fortunate to obtain single crystals of G2W1 (CCDC 2466610) and solve the structure by X-ray diffraction measurements. Crystals of G2W1 are triclinic with the P−1 space group (a/Å = 15.414(4); b
Pathway economy in cyclization of 1,n-enynes
Beilstein J. Org. Chem. 2025, 21, 2260–2282, doi:10.3762/bjoc.21.173
- Hezhen Han Wenjie Mao Bin Lin Maosheng Cheng Lu Yang Yongxiang Liu Key Laboratory of Structure-Based Drug Design and Discovery (Shenyang Pharmaceutical University), Ministry of Education, Shenyang 110016, P. R. China Wuya College of Innovation, Shenyang Pharmaceutical University, Shenyang 110016
- assembled the pentacyclic spiroindole framework 61 (Scheme 13, path b). The controllability of this cyclization process arose from the steric and electronic effects of the aryl group, where the π–π interactions and rigid structure of the aryl group facilitated the stabilization of the five-membered spiro
- allene intermediate 141, which subsequently underwent 5-exo-trig cyclization to construct polysubstituted furan compounds 142. Liu et al. discovered that the regioselectivity of cyclization could be completely altered by introducing a cyclic structure to modify the bond angle of the enol ether
Research towards selective inhibition of the CLK3 kinase
Beilstein J. Org. Chem. 2025, 21, 2250–2259, doi:10.3762/bjoc.21.172
- , examination of the structure of CLK3 shows that this key lysine 241 is very close to the entry of the ATP binding site (Figure 1B). Lysine 241 could be considered as an opportunity to design new molecules with an improved affinity to CLK3, by adding specific interactions with this amino acid bearing a primary
- ). Second, molecular docking using DYRK1A crystal structure was used to understand the unexpected binding on the DYRK kinases (Figure 6). Surprisingly, another lysine (K175) is also located near the acidic group of VS-77 (at 3.2 Å between the carbonyl carbon atom and nitrogen from amine). This residue is
- ) Structure of CLK3 highlighting the lysine in position 241 (PDB ID: 2WU6 [25]). A) Docking of our previous inhibitor (DB18) in CLK3 and B) our working hypothesis. Design of our target molecules. Primary evaluation of the inhibition of the new quinazolines against a short panel of mammalian kinases. Residual
Thiadiazino-indole, thiadiazino-carbazole and benzothiadiazino-carbazole dioxides: synthesis, physicochemical and early ADME characterization of representatives of new tri-, tetra- and pentacyclic ring systems and their intermediates
Beilstein J. Org. Chem. 2025, 21, 2220–2233, doi:10.3762/bjoc.21.169
- closed vial in which the reaction is carried out does not contain the necessary amount of oxygen. Structure determination of the products was also supported by single-crystal X-ray diffraction in the case of several representatives: 3b, 3d, 3e, 3g, 3h, (E)-7a, 7b, 7d, 7e, (E)-7f, (Z)-7h, 7i, and (E)-9a
- permeability values, meanwhile, most of the gray datapoints with insufficient solubility scattered in the right side of the plot, indicating their high lipophilicity. As part of the discussion on structure–property relationships, most of the compounds with low kinetic solubility showed similarities in their
- structure. It can be clearly seen that the majority of these compounds have at least 4 rings (Table 2). Moreover, all derivatives with a phenyl moiety in position 4 fell into this category (3f–j, 7f–j, (E)-9b, 10b) obviously making the 4-phenyl substituent undesirable. The solubility of compounds is also
A m-quaterphenyl probe for absolute configurational assignments of primary and secondary amines
Beilstein J. Org. Chem. 2025, 21, 2211–2219, doi:10.3762/bjoc.21.168
- twist of the two chromophores of quaternary ammonium salts (S)-2f,g and (R)-2h can be determined from the sign of the Cotton effect in CD. However, it is more difficult to predict the direction of twist from the structure of the quaternary ammonium salts than in the case of the 1–primary amine
- structure analysis was performed on a Bruker SMART diffractometer equipped with a CCD area detector at 120 K. Silica gel 60 F254 precoated plates on glass from Merck Ltd. were used for thin-layer chromatography (TLC). General procedure for the synthesis of conjugates 2a–h (S)-2-[2,10-Bis(4-methoxyphenyl
- based on B3LYP/6-31G* level. Four major conformers of (S)-3f based on B3LYP/6-31G* level. The distribution of conformers of (S)-3a–h against dihedral angles ϕ (C6–C1–C1'–C6') calculated by B3LYP/6-31G*. Crystal structure of (S)-2b. Four conformers exist in the unit cell. Hydrogen atoms are omitted for
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